Longer Ver_Chapter 5_High-Performance Computing and AI-Assisted Scientific Discovery

MIDTERM (LESSON 1) SPECIALIZED CRIME INVESTIGATION 2 WITH INTERVIEW AND INTERROGATION INTRODUCTION Special crime investigation deals with the study of major crimes based on the application of special investigative technique. The study concentrates more on physical evidence, its collection, handling, identification and preservation in coordination with the crime laboratory. Special crime investigation involves a close relationship between the prober in the field and the crime laboratory technician. They work together as a team, reacting to and extending one another’s theories and findings both working patiently and thoroughly to solve a crime from their investigative discoveries. The present criminal justice system in our country, the court relies more on physical evidence rather than extra-judicial confession. WHAT IS INTERROGATION? Interrogation is a process of questioning by which police obtain evidence. The purpose of an interrogation is to elicit from the suspect or from his or her relatives or associate's information that they may be suppressing in order to protect the suspect from being subjected to criminal prosecution (Galero-Muftuoglu, 2017, p. 187). Interrogation process is largely outside the governance of law except for rules concerning the admissibility at trial of confessions obtained through interrogation and limitations on the power of police to detain the suspected persons against their will. THREE OBJECTIVES OF INTERROGATION Aside from obtaining information detrimental to a suspect’s case, the following are the three objectives of interrogation: 1. Establish the innocence of a suspect by clearing up facts that seem to point to guilt; 2. Obtain from the suspect or relatives and friends of the suspect: A. The names of accomplices; B. The facts and circumstances surrounding the crime; C. Follow-up leads provided unwittingly, or with ulterior motive, such as faking an alibi; D. The location of stolen goods; E. The location of physical evidence, such as documents, a weapon, or a burglar’s tool. 3. Obtain from the suspect alone: A. Admission – it refers to the express or implied statement tending to support the suspect’s involvement in the crime, but insufficient by itself to prove guilt; B. Confession – it pertains to an oral or written statement acknowledging it. WHAT IS AN INTERVIEW? Interview is defined as a structured conversation where one person or “interviewer” seeks to gather information from one another or the “interviewee” as part of any investigation or intelligence operation. The objective is to obtain accurate and reliable information while respecting human rights; eliciting facts is the aim, not confession. In the process of interviewing the suspects there is the added potential goal of obtaining an admission of guilt or a confession. However, this must not be the primary or sole purpose of interview as even a confession must be substantiated by information and evidence. This will reduce the likelihood of a false accusation and will also enable officers to present stronger case against the suspect, should a confession later be retracted. WHAT IS AN INVESTIGATIVE INTERVIEW? Investigative Interviewing, is a technique developed by practitioners to respond to the large body of scientific evidence that abusive and coercive techniques elicit unreliable information. It uses building rapport with the interviewee, which prevent abusive practices, and also improves the collection and reliability of information. It is a non-coercive approach using open questions to improve the flow of communication and information (Norwegian Center for Human Rights, 2017). GOALS OF INVESTIGATIVE INTERVIEW 1. Eliciting more accurate and reliable information during interviews. 2. Strengthening the capacity, efficiency, and professionalism of interviews. 3. Eliminating reliance on unlawful, ineffective, and counterproductive coercive questioning techniques. 4. Providing successful, affordable, and accessible methods and practices with minimal resources. 5. Delivering more effective information-gathering operations. 6. Fostering greater public trust in and cooperation with criminal justice institutions. 7. Ensuring that no person is subjected to coercion, torture or other forms of ill treatment. 8. Protecting the physical and mental integrity of all persons who interact with public authorities. REID METHOD Reid Method is also known as The Reid Technique of Interviewing and Interrogation, is the interrogation technique widely used by police departments. The Reid Technique involves three components namely: 1. Factual Analysis 2. Behavioral Analysis Interview 3. Interrogation (Nine Steps) FACTUAL ANALYSIS It is an inductive approach where each individual suspect is evaluated with respect to specific observations relating to the crime. It relies not only on crime scene analysis, but also on information learned about each suspect. Its goal is establishing an estimate of a particular suspect’s probable guilt or innocence based on such things as the suspect’s biosocial status like: gender, race, occupation, marital status, etc., opportunity and access to commit the crime, and evaluation of physical and circumstantial evidence. It is also intended to identify characteristics about the suspect and the crime which will be helpful during an interrogation of the suspect believed to be guilty such as motive or the suspect’s personality type. BEHAVIORAL ANALYSIS INTERVIEW It is a non-accusatory question and answer session, involving both standard investigative questions and structured “behavior provoking” questions to elicit behavior symptoms of truth or deception from the person being interviewed. The investigator first asks background questions, to establish personal information about the suspect and allow the investigator to evaluate the suspect’s normal verbal and nonverbal behavior. The investigator then asks behavior-provoking questions intended to elicit different verbal and nonverbal responses from truthful and deceptive suspects (Inbau, F., Reid, J.E., Buckley, J. et.al., 2013, p.63). The investigator will also ask some investigative questions during this stage. It provides objective criteria to render an opinion about the suspect’s truthfulness through evaluating responses to the behavior-provoking and investigative questions. INTERROGATION (NINE STEPS) An interrogation only occurs when the investigator is reasonably certain of the suspect’s involvement in the issue under investigation (Inbau, F., Reid, J.E., Buckley, J. et.al., 2013, p.99). This is composed of Nine steps, they are: 1. Direct, Positive Confrontation 2. Theme Development 3. Handling Denials 4. Overcoming Objections 5. Procurement and Retention of Suspect’s Attention 6. Handling the Suspect’s Passive Mood 7. Presenting an Alternative Question 8. Having the Suspect Relate Details of the Offense 9. Converting an Oral Confession to a Written Confession NINE STEPS 1. Direct, Positive Confrontation. This is where the investigator tells the suspect that the evidence demonstrates the person’s guilt. If the persons guilt seems clear to the investigator, the statement should be unequivocal. 2. Theme Development. This is where the investigator presents a moral justification(theme) for the offense, such as placing the moral blame on someone else or outside circumstances. The investigator presents the theme in a monologue and in a sympathetic manner. 3. Handling Denials. When the suspect asks for permission to speak at this stage, likely to deny accusations, the investigator should discourage allowing the suspect to do so. The innocent suspect are less likely to ask for permission and more likely to promptly and unequivocally deny the accusation. 4. Overcoming Objections. When attempts at denial do not succeed, a guilty suspect often makes objections to support a claim of innocence, phrases such as I would never do that because I love my job are commonly used. The investigator should generally accept these objections as if they where truthful, rather than arguing with the suspect, and use the objections to further develop the theme. 5. Procurement and Retention of Suspect’s Attention. The investigator must procure the suspect’s attention so that the suspect focuses on the investigator’s theme rather than on punishment. One way the investigator can do this is to close the physical distance between himself or herself and the suspect. The investigator should also channel the theme down to the probable alternative components. 6. Handling the Suspect’s Passive Mood. The investigator needs to intensify the theme presentation and concentrate on the central reasons he or she is offering as psychological justification and continue to display an understanding and sympathetic demeanor in urging the suspect to tell the truth. 7. Presenting an Alternative Question. The investigator should present two choices, assuming the suspect’s guilt and develop as a logical extension from the theme, with one alternative offering a better justification for the crime e.g., “Did you plan this thing out or did it just happen on the spur of the moment?” The investigator may follow the question with a supporting statement which encourages the suspect to choose the more understandable side of the alternative. 8. Having the Suspect Relate Details of the Offense. After the suspect accepts one side of the alternative thus admitting guilt, the investigator should immediately respond with a statement of reinforcement acknowledging that admission. The investigator then seeks to obtain a brief oral review of the basic events, before asking more detailed questions. 9. Converting an Oral Confession to a Written Confession. The investigator must convert the oral confession into a written or recorded confession. The website provides some guidelines, such as repeating Miranda Warnings, avoiding leading questions, and using the suspect’s own language. PEACE METHOD PEACE Model (Planning and Preparation, Engage and Explain, Account, Closure, Evaluation), developed in the United Kingdom in response to a number of documented forced confessions and wrongful convictions in the 1980s and 90s (Norwegian Center for Human Rights, 2017). STEP ONE: PLANNING AND PREPARATION It is one of the most important steps in investigative interviewing; without it, interviews may fall before they even begin. Planning – refers to the process of getting ready to interview, both mentally and strategically. Preparation – covers what needs to be ready prior to the interview such as the location of the interview, the environment, as well as technical and administrative matters. Essential Elements of Good Planning • Obtain as much background information as possible on the incident under investigation, including all relevant information on the person to be interviewed. • Assess what additional information is needed and how can it be best obtained. • Follow the legislation and associated guidelines and rules. • Understand the purpose of interview based on an investigation plan recognizing all the relevant and competing hypotheses to be explored, including the possibility that the suspect is innocent. • Prepare the technicalities of the interview (attending to exhibits, logistics, venue, equipment functioning, seating, lawyer, interpreter, and so on) (Norwegian Center for Human Rights, 2017). STEP TWO: ENGAGE AND EXPLAIN Engaging the interviewee and building rapport is the first step to encouraging a conversation. It is the most influential factor in ensuring productive interviews (Norwegian Center of Human Rights, 2017). At the outset the interviewee must be informed why they have been brought in for questioning and the formalities that apply. Officers must be aware that being interviewed can make people nervous and conversation that calms the interviewee may be needed. However, interviewers shall not work towards a pretend “friendship” with interviewees. The aim is to engage the interviewee so that a cooperative and relaxed relationship (one that stimulates memory and communication) is sustained throughout the interview (Boyle, and Vullierme, 2015, p. 23). In engaging with the interviewee, the officer should seek the following (Norwegian Center for Human Rights, 2017): 1. Create an empathetic and respectful relationship from the outset. 2. Explain the reasons, background, rights, formalities and procedure for the interview, including information about audio/video recording. 3. Establish certain ground rules by telling interviewees: • That what they have to say is important so they need to report everything they can and try their hardest no to leave anything out. • Not to edit as they go even if they believe some information has no relevance to the matter being investigated • That they need to concentrate because striving to retrieve memories can be hard work • That they should feel free to speak up if the officer: asks a question they do not understand; asks a question they do not know the answer to; misunderstand what the interviewee has said; asks a leading or inappropriate question. STEP THREE: ACCOUNT Interviewers should allow the interviewee to present their uninterrupted free account of the case or event under investigation; this is after establishing the ground rules for the interview. It is important that the interviewee is provided with the opportunity to present their side of the story, before more detailed questions are asked (Norwegian Center for Human Rights, 2017). Three main steps in getting the free account from the interviewee: 1. Introduce and explain the form and purpose of the free and uninterrupted account 2. Hand over the initiative (“give the floor”) to the victim, witness or suspect (as applicable) 3. Employ active listening while the interviewee presents the free and uninterrupted account Active listening assists the interviewer to establish rapport and help elicit a full and accurate account. Use TED’S PIE: Tell me, Explain, Describe Show Me-Precisely, In detail, Exactly. Using this approach helps build rapport and prevents the interviewer contaminating the account being given. The TED’S PIE approach makes use of encouragements/invitations to obtain an account (Norwegian Center for Human Rights, 2017). TYPES OF QUESTIONING OPEN-ENDED QUESTIONS Refers to the questions that allow the suspect to reply with longer, more detailed responses and lack direction from the interviewer. These can be questions such as; “What happened?” or questions that begin by asking the suspect to “tell”, “explain” or “describe” some event or situation (Boyle, and Vullierme, 2015, p.26) CLOSED QUESTIONS Refers to the questions that require more definite and distinct answers. Examples include, “What time was that?”, “Who else was present?”, “What is his address?” such questions allow more control over what the suspect says and are useful where the suspect has left out information that you need. However, they can limit the account given (Boyle, and Vullierme, 2015, p. 26) FORCED-CHOICE QUESTIONS Refers to the questions that greatly restrict the possible answers to those that you have determined. The question may be “Was it a rifle or a handgun?” when the weapon may have been a shotgun. The suspect may simply pick one of the choices offered in order to please the interviewer or just move the questioning on. You should avoid these as they don’t suggest an open mind, and because answers may lie outside those conceived of by the interviewer. Do not limit the interview in this way (Boyle, and Vullierme, 2015, p. 26) MULTIPLE QUESTIONS Refers to the questioning where the interviewer asks more than one question at the same time. This can easily confuse an interviewee and make the answers given equally confusing to the interviewer. An example would be to ask, “When did he say that and what did he do and who else was present?” (Boyle, and Vullierme, 2015, p. 26). LEADING QUESTIONS Refers to the questions that induce a particular reply and may be judged to have manipulated the interviewee. An example would be to ask, “You wanted to injure him, didn’t you?” They can lead the suspect to the point where they agree with what was being said even where they are uncertain or have no clear memory (Boyle, and Vullierme, 2015, p. 26). STEP FOUR: CLOSURE As the interview comes to an end, the interviewing officer should explain what will happen next by giving the interviewee appropriate information about the next stages of the process: for example, inform suspects of potential pre-trial detention, tell witnesses whether or not they should expect to attend court, etc. (Norwegian Center for Human Rights, 2017). Finally, the interviewee should be asked if they have any questions for the interviewing officer at this stage. This has little or no real effect if the communication has been coercive. However, if the interview has been conducted as outlined above, this question may add to the interviewee’s perception of having been treated fairly (Boyle, and Vullierme, 2015, p. 26). The goal of the closure are the following (Norwegian Center for Human Rights, 2017): 1. Ensure there is a mutual understanding of the interviewee’s accunt by reviewing and summarizing it 2. Verify that all aspects have been sufficiently covered by checking that interviewees have given all the information they are able and willing to provide 3. Secure the integrity and dignity of the interview, the legitimacy of any subsequent criminal proceedings, and keep channels open for future communication. STEP FIVE: EVALUATION This is the phase wherein the interviewee evaluates the entire process of the interview and determines if his objectives were met. He also evaluates the method he used in acquiring useful statements from the witness, victim, or suspect and the effectiveness of said method. (Galero-Muftuoglu, 2017, p. 186) If the interview is evaluated by a supervisor, senior officer or colleague, make sure that the interviewing officers are given the opportunity to comment on their own performance, before the evaluator gives their points, starting with what was positive, moving on to what could be improved next time (Norwegian Center for Human Rights, 2017) LESSON 2 SPECIALIZED CRIME INVESTIGATION 2 WITH INTERVIEW AND INTERROGATION MENDEZ METHOD The Mendez Principles, also known as the new Principles on Effective Interviewing for Investigations and Information Gathering. It was named after Juan Mendez, the Argentine lawyer, torture survivor and former UN Special Rapporteur. It is a concrete alternative to interrogation methods that rely on coercion to extract confessions. They provide guidance on obtaining accurate and reliable information in full respect of the human rights and dignity of all, including through the implementation of legal and procedural safeguards in the first hours of police custody (IRCT, 2021). The Mendez Method has three parts; Before, During, and After the interview. BEFORE THE INTERVIEW – ENSURING A NON-COERCIVE ENVIRONMENT Creating a non-coercive environment involves the respect and fulfillment of human rights from the first moment of contact between the interviewee and authorities. This allows law enforcement, intelligence, security or military officials to create conditions conductive to gathering accurate and reliable information during the interview, to fulfill State obligations under international law and to protect the lights of the interviewee. Unlawful and unprofessional behavior, and a lack of accountability, at the early stages of contact may taint the overall judicial process irreversibly (Mendez, 2016, p. 14-15). KEEPING THE INTERVIEW INFORMED Showing concern for the interviewee from the initial contact is the first opportunity for creating trust and rapport. This is more likely when an interviewee is given early, explicit explanations of why they have brought in for questioning., which formalities apply, and how the interview will proceed. Explaining procedures and likely activities is an early opportunity to display sincerity, provide predictability, to be respectful and attentive, and promote trust. The right to be informed by the detaining authority about the reasons of arrest applies regardless of manner, or the formality or informality with which an arrest is conducted, and regardless of the reasons for the deprivation of liberty (Mendez, 2016, p.15). Information regarding an interviewee’s rights and how to exercise them should be conveyed verbally, in clear, non-technical, and precise language upon arrest; and it should also be provided in writing by the detaining authority upon arrival at the place of detention in a language and format they understand. NOTIFICATION OR FAMILY OR THIRD PARTY A key safeguard for detainees is their right to promptly notify a family member, friend, or other person of their choice about the fact, place and circumstances of their detention. The detaining authority is responsible for enabling the communication with the third party and recording who has been notified and when the notification took place (Mendez, 2016, p. 16). Foreign nationals who are arrested or detained must be informed immediately of their right to communicate with a consular and diplomatic representative of their country or origin. Asylum seekers should be informed of their right to contact relevant international agencies. Contact is to be facilitated by the detaining authority (Mendez, 2016, p.17). ACCESS TO LAWYER All detained persons being interviewed have a right to a lawyer, including through legal aid, before any questioning by authorities – independent of their status or formal designation. Access to a lawyer is inextricably linked to the protection of rights, prevention of torture and other ill-treatment, and helps to protect against compelled self-incrimination. The interviewee is entitled to a lawyer of their own choosing, or to have one provided for them free of charge when the interests of justice so require. The presence of the lawyer is compulsory for detained children interviewed as suspects (Mendez, 206, p.17). PREPARATION FOR THE INTERVIEWER Once an individual has been identified as a person the authorities wish to interview, the appointed interviewer should start thorough preparations. Being fully prepared increases an interviewer’s ability to effectively communicate with the interviewees, and hence, the likelihood of obtaining reliable information. Before commencing an interview, it is crucial to maximize the investigative and evidentiary value of the information already gathered. When preparing for an interview - and throughout the process – interviewers should exercise caution to avoid ‘confirmation bias’. Interviewers should continually monitor their own emotions about the subject matter and their feelings towards the interviewee, to be able to project calm and self-control throughout the interview (Mendez, 2016, p.19). DURING THE INTERVIEW – ESTABLISHING AND MAINTAINING RAPPORT Effective interviewers are adaptable, listen carefully, communicate empathy, and adopt the ethos that non-coercive, humans, ethical, lawful and appropriate questioning serves the interest of all involved: the interviewer, the interviewee and the information-gathering authorities. They recognize that the interviewer’s role is to acquire the best possible information for decisions to be made. Only courts determine guilt or innocence. The development of rapport is essential in supporting effective information-gathering. During the interview, rapport entails establishing and maintaining a relationship characterized by: respect and trust; a non-judgmental mindset; non-aggressive body language; attentiveness; and patience (Mendez, 2016, p.20). INFORMATION GATHERING TECHNIQUES Active listening helps the interviewer process the information provided by the interviewee. By listening actively, the interviewer shows that they are following what the interviewee is saying and making efforts to understand. The interviewer takes care not to lead the interviewee inadvertently by using verbal or visual cues, including sounds, gestures or questions, which may be interpreted as agreeing or disagreeing with what the person is saying. Accurate summaries of what the interviewee has said may facilitate the positive progression of the interview and assist the interviewer and interviewee in recalling important details (Mendez, 2016, p.21). ENCOUNTERING RELUCTANCE Interviewers may encounter interviewees who are reluctant to talk and therefore should anticipate how they will handle such situations. Not wanting or agreeing to answer questions may be a deliberate choice. This decision must always be respected and has no bearing on the interviewer’s right to the presumption of innocence. Reasons why an interviewee might be reluctant to talk can include general anxiety or uncertainty about the process, especially if the person has never been involved in such a situation before. It is also possible that an interviewee maybe willing to provide information but is unable to do so. This can be because they did not have the relevant information to begin with, or they failed to register the details. Interviewers should not draw negative inferences from the interviewee’s failure or refusal to answer questions and should remain non-judgmental when an interviewee may make admission to crimes or convey embarrassing information (Mendez, 2016, p.21). SUSPENDING THE INTERVIEW It is appropriate and permissible for interviewers to suspend the interview in order to follow-up on information received or conduct additional enquiries. Other reasons to suspend an interview are (Mendez, 2016, p.22): 1. If the interviewee requires medical attention, 2. If a person originally interviewed as a witness becomes a suspect in the course of an interview; and 3. If the lawyer or the interviewee may request a break, for instance in order to rest or to consult in private. A refusal to accept such a request by the interviewer may affect the reliability of information gathered from the interview. AFTER THE INTERVIEW – ASSESSMENT AND ANALYSIS An effective interviewer should always end the interview respectfully and on a professional note. This increases the likelihood of keeping channels open for future communication, avoids possible misunderstandings and can improve trust in public institutions. The interviewer should review the information obtained with the interviewee and the lawyer, if involved; and, where a written record (as opposed to an audio/video recording) has been made, invite them to sign as a confirmation of the record’s accuracy. An amendments should be recorded, and if relevant, any refusal of the interviewee to sign the interview record. Once the interview has been completed, the interviewer ensures that the information provided during the process is subject to the appropriate level of privacy and of data protection. The interviewer should assess and analyze the following (Mendez, 2016, p.23): 1. The value and reliability of the information obtained and how it fits with known evidence, information gaps and other intelligence gathered. 2. What further enquiries are necessary in order to advance the investigation or operation; and 3. Whether all relevant safeguards were applied effectively. KINESIC INTERVIEW METHOD Kinesic Interview Method involves analyzing a person’s behavior to assess deception (Orlando, 2014). The study of kinesics focused on observable outward physical behavior of the body in order to ascertain the person’s current emotional state and the role the body plays in communicating the information. It states that, by understanding the vocabulary of the body language, along with the diagnosis of a person’s verbal output, an interviewer could more easily assess a person’s truthfulness or deception regarding current issues under discussion (Walters, 2002, p.2). It has two phases: the Practical Kinesic Analysis Phase; and the Practical Kinesic Interrogation Phase. PRACTICAL KINESIC ANALYSIS PHASE During the analysis phase, the interviewer uses several techniques to observe and analyze the subject’s behavior in order to determine the subject’s truthful and deceptive behaviors or at least to determine those areas most sensitive to the subject and, therefore, in need of further attention through verbal inquiry. It recognizes the cues of truthful and deceptive behavior generated by the subject through: 1. Verbal Cues – this involves the identification of symptoms of speech quality and content which give the interviewer the most productive body of data necessary to determine truth and deception. 2. Practical Kinesic Statement Analysis – assessment of truth and deception through the use of verbal cues coupled with methods of human recall and symptoms made self-evident in the statement taking process. 3. Body Language Cues – it refers to the observable body language cues of deception that are unbalanced or inconsistent in relation to the speech cues or emotional symptoms generated by the suspect at the same time. 4. Kinesic Subject Control – it refers to the various techniques available to the interviewer to take control and command of the interview environment. From proxemics to mirroring or the use of enhanced information gathering skills. 5. Confession Behaviors – it is the verbal and nonverbal acceptance cues generated by a subject who is prepared to give an admission of confession. PRACTICAL KINESIC INTERROGATION PHASE Practical Kinesis Interrogation Phase involves the interviewer determining the subject’s frame of mind in response to the interview stress. It also helps the interviewer in determining if the subject is suffering from personality disorder or psychosis. It also helps the interviewer determine the subject’s personality type which enables him to understand how the subject thinks and to determine the subjects’ strengths to be avoided and the weaknesses that can be exploited. Lastly it will help the investigator in determining the defense mechanism of the subject which keeps the subject from having to face the reality of his actions; and by identifying and disarming these mechanisms, the interrogator can obtain admission or confession (Walters, 2002, p.3). GUIDELINES OF CUSTODIAL INVESTIGATION According to the PNP Operational Procedures Manual (2011), the duties of the Police during custodial investigation are as follows: 1. The arresting officer, or the investigator, as the case may be, shall ensure that a person arrested, detained or under custodial investigation shall, at all times, be assisted by counsel, preferably of his own choice (PNP, 2011, p.33). 2. The arresting officer, or the investigator, as the case may be, must inform the person arrested, detained or under custodial investigation of the following rights under the Miranda Doctrine in a language or dialect known to and understood by him (PNP, 2011, p.33). a. That he has the right to remain silent; b. That if he waives his right to remain silent, anything he says can be used against him in court; c. That he has the right to counsel of his own; d. That, if he cannot afford one, he shall be provided with an independent and competent counsel; and e. That he has the right to be informed of such rights. 3. If the person arrested, detained, or under custodial investigation opted to give a sworn statement, the arresting officer, or the investigator, as the case may be, must reduce it in writing (PNP, 2011, p.34). 4. The arresting officer must ensure that, before the sworn statement is signed, or thumb marked, if there is inability to read and to write, the document shall be read and adequately explained to the person arrested, detained or under custodial investigation by his counsel of choice, or by the assesting counsel provided to him, in the language or dialect known to him (PNP, 2011, p.34). 5. The arresting officer, or the investigator, as the case may be, must ensure that any extrajudicial confession made by a person arrested, detained or under custodial investigation shall be (PNP, 2011, p.34): a. In writing; b. Signed by such person in the presence of his counsel; or c. In the latter’s absence, upon a valid waiver, and in the presence of any of the parents, elder brothers and sisters, his spouse, the municipal mayor, the municipal judge, district school supervisor, priest, imam or religious minister chosen by him. It is important to note that failure of the arresting officer, or the investigator, to observe the above mention procedures shall render the extrajudicial confession inadmissible as evidence in any proceeding (PNP, 2011, p.34) 6. The arresting officer, or the investigator, as the case may be, must, under established regulations, allow the person arrested, detained, or under custodial investigation visits by or conferences with the following: a. any member of his immediate family, b. any medical doctor, c. priest, imam or religious minister chosen by him or by any member of his immediate family or by his counsel, or by any Non-Governmental Organization (NGO) duly accredited by the Commission on Human Rights (CHR) or by any international NGO duly accredited by the Office of the President. 7. After interrogation, a person under custodial investigation shall have the right to be informed of his right to demand physical examination by an independent and competent doctor of his own choice. If he cannot afford the services of a doctor of his own choice, he shall be provided by the State with a competent and independent doctor to conduct physical examination. If the person arrested is female, she shall be attended to preferably by a female doctor (PNP, 2011, p.34-35). The physical examination of the person under custodial investigation shall be contained in a medical report, which shall be attached to the custodial investigation report. LESSON 3 LEGAL REQUIREMENTS FOR ADMISSION AND CONFESSION Admissions and confessions are only legally valid if made voluntarily, knowingly, and intelligently, with judicial or extrajudicial distinctions affecting their admissibility. DEFINITIONS AND DISTINCTIONS ●ADMISSION – A voluntary acknowledgment of a fact relevant to a case, which does not necessarily imply guilt. It can be judicial (made in court or pleadings) or extrajudicial (made outside court) and may be used as evidence against the declarant, though extrajudicial admissions are not conclusive and require proof of credibility and relevance. ●CONFESSION – A direct acknowledgment of guilt for the offense charged or any offense necessarily included therein. Confessions are always statements of criminal liability and can be judicial or extrajudicial. CORE LEGAL REQUIREMENTS 1. Voluntariness – the statement must be given freely, without coercion, force, intimidation, or inducement. Any confession obtained through threats, violence, or improper influence is inadmissible. 2. Knowledge and Intelligence – the accused must understand the nature and consequences of the statement. This ensures that the confession or admission is made knowingly and intelligently. 3. Assistance of Counsel – during custodial investigation or after arrest, the accused is entitled to competent and independent legal counsel. Extrajudicial confessions made without counsel may be inadmissible as they violate constitutional rights. 4. Judicial vs. Extrajudicial Confessions: Judicial Confession – Made in open court or in pleadings; sufficient for conviction without additional evidence. Extrajudicial Confession – Made outside court; requires corroboration by independent evidence to be admissible. 5. Relevance and Evidentiary Value – the admission or confession must relate to facts in issue and not be excluded by privilege or other legal rules. Judicial admissions are conclusive, while extrajudicial admissions are evaluated for credibility and weight by the court. 6. Corpus Delicti Rule – a confession alone is insufficient for conviction; the prosecution must establish that a crime has actually been committed. LEGAL REQUIREMENTS FOR ADMISSION Admissions can be classified as judicial (made in the course of judicial proceedings) or extrajudicial (made outside of court). For Judicial Admissions: ●Can be made in pleadings, during trial via stipulations/manifestations, or at other stages such as pre-trial. ●Requirements: They do not require formal proof and are conclusive upon the party making them. They can only be contradicted by showing that they were made through a palpable mistake or that no such admission was made. For Extrajudicial Admissions: ●Must be relevant to the issue at hand. ●May be given in evidence against the maker (as an admission against interest), but are generally subject to regular rules of relevance and hearsay exceptions. LEGAL REQUIREMENTS FOR CONFESSION Because confessions directly admit criminal liability and carry heavy penal consequences, they face strict constitutional and statutory safeguards—particularly when made outside of court (extrajudicial confessions). To be admissible as evidence in court, an extrajudicial confession must meet the following mandatory requirements: Voluntariness: ●The confession must be given freely and knowingly. It must not be the product of torture, force, violence, threat, intimidation, or any other influence that vitiates the individual's free will. Observance of Miranda Rights (Custodial Safeguards): ●If a person is under custodial investigation, they must be proactively informed in a clear, understandable manner of their rights: to remain silent, that any statement can be used against them, to have competent and independent counsel preferably of their choice, and to be provided free legal counsel if they cannot afford one. Assistance of Competent and Independent Counsel: ●The confession must be made with the active presence and genuine representation of independent counsel. ●Any waiver of the right to counsel must be made in writing and executed in the presence of the counsel. Form and Language: ● Extrajudicial confessions must ideally be in writing and signed (or thumb marked) by the confessant. ● They must be expressed clearly and interpreted/read to the accused in a language or dialect that they fully understand. The Exclusionary Rule: ● Under constitutional law, any confession obtained in violation of the right to counsel, Miranda rights, or through coercion is inadmissible as evidence in any proceeding (the "fruit of the poisonous tree" doctrine). Corroboration (Corpus Delicti Rule): ● An extrajudicial confession alone is insufficient to sustain a criminal conviction. It must be corroborated by independent evidence of the corpus delicti (proof that the crime actually happened and someone is criminally responsible). CORE REQUIREMENTS FOR ADMISSIBILITY Consciousness of Impending Death: At the time the statement was made, the declarant must have been under the fixed belief that death was near and inevitable. Complete despair of recovery must be apparent, though the exact moment of death does not need to be immediate. Subject Matter: The statement must concern the cause and surrounding circumstances of the declarant's impending death. Statements about unrelated past grudges or matters are inadmissible. Case Type Limitation: Traditionally and under most statutory rules (such as the Philippine Rules of Evidence), dying declarations are admissible primarily in criminal prosecution for homicide, murder, or parricide where the death of the declarant is the subject of the charge. Competency of the Declarant: The declarant must have been a competent witness at the time the statement was made (i.e., possessing the capacity to perceive and communicate the event). Declarant Must Be Deceased: The declarant must have actually died, and their death must be the subject of the inquiry. CONSTITUTIONAL SAFEGUARDS ●The accused has the right to remain silent and cannot be compelled to confess. ●Any admission or confession must respect due process and fundamental rights under the Philippine Constitution DYING DECLARATION VS. INDEPENDENT RELEVANT STATEMENT Dying declaration and independent relevant statement are both types of statements made by individuals that are considered to be reliable evidence in court. However, the key difference between the two lies in the circumstances under which they are made. A dying declaration is made by a person who believes they are about to die, and their statement is considered to be particularly trustworthy due to the belief that they have no reason to lie. On the other hand, an independent relevant statement is made by a person who is not in imminent danger of death, but their statement is still considered to be reliable because it is made independently of any external influence or coercion. Both types of statements play a crucial role in the legal system in determining the truth of a matter. PRINCIPLES OF A DYING DECLARATION ●A dying declaration is an out-of-court statement made by a victim regarding the cause and surrounding circumstances of their impending death. Under the rules of evidence, it serves as an exception to the hearsay rule and is admissible because of the principle of necessity (since the declarant is dead and cannot testify) and the trustworthiness presumption (that a person at the point of death has no motive to fabricate the truth). INDEPENDENT RELEVANT STATEMENTS ●An independent relevant statement (sometimes referred to as verbal acts or statements relevant independent of the truth of the facts stated) is an out-of-court statement offered in court not to prove the truth of the matter asserted, but simply to prove that the statement was made, heard, or that it had a legal effect. ●These statements are admissible in court if they meet the requirements of relevance and reliability. The declarant must have personal knowledge of the facts stated in the statement, and the statement must be relevant to the issues in the case. ●Because the truth of the utterance does not matter, these statements are not hearsay at all and are freely admissible. CATEGORIES AND EXAMPLES Statements as Verbal Acts / Constitutive Facts: Words that legally constitute a crime, contract, or civil wrong. ●Example: Words of defamation in a libel case, or words offering a bribe in a corruption case. The statement is proven just to show it was uttered. Statements Showing State of Mind / Knowledge / Notice: Words used to establish what someone knew, their belief, or their mental state. ●Example: Telling a defendant that a specific machine is dangerous. This is admissible not to prove the machine is dangerous, but to prove the defendant had notice or knowledge of the danger. Statements Showing Effect on the Hearer: Words that explain why a listener acted the way they did. ●Example: Threats made to a victim to explain why the victim acted in self-defense or fled in fear. Identifications: Out-of-court statements identifying a person (e.g., a witness pointing out a suspect in a lineup), which are relevant to establish identification independent of the factual narrative. COMPARISON Dying Declarations are considered highly reliable due to the belief that a person facing imminent death would not lie. On the other hand, Independent Relevant Statements do not carry the same level of reliability, as they are not made under the same circumstances. Dying Declarations are admissible as exceptions to the hearsay rule, while Independent Relevant Statements must meet the requirements of relevance and reliability to be admissible. Dying Declarations are made by individuals who believe they are about to die, and the statements pertain to the cause or circumstances of their impending death. In contrast, Independent Relevant Statements are made by individuals who have personal knowledge of the facts stated in the statement, and the statements are relevant to the issues in the case. Dying Declarations are often used in cases where the declarant's impending death is a central issue, such as murder trials. Independent Relevant Statements, on the other hand, are used to provide additional context or evidence to support a party's case. In some cases, both types of statements may be used in conjunction to strengthen a party's argument.

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Topic 1: Research Designs in Development Front: Human Development (Definition) Back: The scientific study of the changes that occur in people as they age from conception until death. Front: Why is age a problem in psychological research designs? Back: In an experiment, participants should be randomly assigned to independent variable conditions. However, people cannot be randomly assigned to different age groups. Front: Longitudinal Design (Definition) Back: A research design in which the same participant or group of participants is studied over a long period of time. Front: Longitudinal Design: Advantage Back: Looks at real, age-related changes as those changes occur in the same individuals. Front: Longitudinal Design: Disadvantages (2 main points) Back: 1. The huge amount of time, money, and effort involved in following participants over the years. 2. The loss of participants when they move away, lose interest, or die. Front: Cross-Sectional Design (Definition) Back: A research design in which several different age groups of participants are studied at one particular point in time. Front: Cross-Sectional Design: Advantages Back: Relatively inexpensive and easier to accomplish than the longitudinal design. Front: Cross-Sectional Design: Disadvantage Back: One is no longer comparing changes in the same individuals as they age; instead, individuals of different ages are being compared to one another. Front: Cohort Effect (Definition) Back: An effect on development when a group of people share a common time period or life experience. (Example: COVID) Front: Cross-Sequential Design (Definition) Back: A research design in which participants are first studied by means of a cross-sectional design but are followed and assessed for a period of time more than X years. Topic 2: Areas of Development & Big Questions Front: Continuity vs. Discontinuity Back: Does development happen in a continuous progression, or in a series of clear-cut stages? Front: Stability vs. Change Back: What remains stable over the course of human development, and what changes? Front: Physical Development Back: The development of the body; is fairly discontinuous, occurring in clearly defined stages that are distinct from each other. Front: Cognitive Development Back: Development of thinking and reasoning skills; is fairly continuous, and it changes over time. Front: Psychosocial Development Back: Encompasses our social and emotional lives. Front: Temperament (Definition) Back: A child's innate (born) behavioral and emotional characteristics. Front: Attachment (Definition) Back: The first emotional bond a child forms with its primary caretaker; the psychological characteristics and social relationships a person has throughout childhood, adolescence, and adulthood. Topic 3: Nature vs. Nurture & Genetics Front: Nature (Definition) Back: The influence of our inherited genes on our personality, physical growth, intellectual growth, and social interactions. Front: Nurture (Definition) Back: The influence of the environment on personality, physical growth, intellectual growth, and social interactions. Front: Behavioral Genetics Back: Tries to figure out how much of behavior is influenced by genetic inheritance and how much is due to a person's experiences. Front: Gene (Definition) Back: A section of DNA having a certain pattern of chemical elements. Front: DNA Molecules Back: Contain the instructions for all an organism's traits; these "instructions" are known as genes. Front: Environmental Influences on Development Back: Environmental influences that surround us before birth and during our lives significantly affect our development. (Examples: Parents/caretakers in early childhood; Friends/teachers in mid-to-late teens; Culture) Topic 4: Practice Questions & Scenarios Front: Practice Q1: Psychologists survey 2nd, 6th, 11th graders, and college students on their favorite genre of book at the same time. What type of study is this and why? Back: Cross-sectional. Because it studies different age groups at one single point in time. Front: Practice Q2: Explain why age can sometimes present a problem in psychology studies? Back: Age cannot be manipulated as an independent variable because researchers cannot randomly assign participants to different age groups. Front: Practice Q1: A psychologist does a longitudinal study examining how Patricia's emotions change throughout her school years. What type of development are they examining and why? Back: Psychosocial development. Because it involves studying her emotional changes and social experiences over time. Front: Practice Q2: A therapist asks Bill about his childhood experiences to understand why he has trouble trusting people. Why is that? Back: The therapist asks about Bill's childhood because early childhood experiences and attachment styles with primary caretakers heavily influence our adult psychological characteristics and relationships (Psychosocial development). Front: Practice Q1: Geraldo states: "My personality is completely determined by my genetics. I know this because I am just like my dad." Do you agree or disagree? Why? Back: Disagree. While genetics (nature) play a role, personality is not completely determined by them. Environmental factors (nurture) such as upbringing, culture, and life experiences also play a massive role (as studied in behavioral genetics).

BTEC Level 3 Applied Science – COMPLETE Biology Revision Pack This is your main revision guide based on all the B1, B2 and B3 notes you shared and everything we’ve been practising. It includes: * All the main topics you need to revise. * Definitions and key scientific terms. * Cell structures and their functions. * Specialised cells and immunity. * Tissues, lungs and circulation. * Muscles and the nervous system. * ECGs. * 6-mark practice questions. * Mnemonics with every letter explained. * Exam-ready answers. Important: Nobody can guarantee the exact questions that will come up. This covers the topics in your notes, including likely extended-answer areas. Use your official unit specification and teacher’s guidance alongside it. PART 1 – B1: CELL STRUCTURE 1. Levels of organisation Learn these definitions: Term Definition Cell Basic structural and functional unit of life. Tissue Group of similar specialised cells working together. Organ Different tissues working together to perform a function. Organ system Different organs working together. Organelle Specialised structure inside a cell. Mnemonic: Cats Take Over Sofas * Cats = Cells * Take = Tissues * Over = Organs * Sofas = Systems Order: Cell → Tissue → Organ → Organ system. 2. Differentiation Definition: Differentiation is when an unspecialised cell develops into a specialised cell to perform a particular function. Examples: * A stem cell can become a red blood cell. * A stem cell can become a neurone. * A stem cell can become a muscle cell. 3. Prokaryotic cells Prokaryotes are cells without a nucleus. Learn these structures: Structure Function Nucleoid Contains circular DNA. Plasmids Small extra rings of DNA. 70S ribosomes Protein synthesis. Capsule Protection and attachment. Cell wall Made of peptidoglycan; provides support. Cell membrane Controls substances entering and leaving. Cytoplasm Where chemical reactions occur. Mnemonic: Naughty Pigs Rarely Chase Wolves * N = Nucleoid * P = Plasmids * R = Ribosomes * C = Capsule * W = Wall Remember: Prokaryotes do not have a nucleus or membrane-bound organelles. 4. Eukaryotic cells Eukaryotic cells have: * A nucleus. * 80S ribosomes in the cytoplasm. * Membrane-bound organelles. Plant cells Structure Function Cellulose cell wall Support and protection. Chloroplasts Photosynthesis. Permanent vacuole Contains cell sap and helps maintain turgor. Tonoplast Membrane surrounding the vacuole. Amyloplasts Store starch. Plasmodesmata Connections between neighbouring plant cells. Pits Areas where the cell wall is thinner. Animal cells Animal cells can contain: * Nucleus. * Mitochondria. * Ribosomes. * Cell membrane. * Cytoplasm. * Centrioles. * Glycogen stores. Animal cells do not have cellulose cell walls or chloroplasts. 5. Organelles and their functions Organelle Function Cell membrane Controls movement of substances. Cytoplasm Site of many chemical reactions. Nucleus Contains DNA and controls cell activities. Nucleolus Produces ribosomal components. Ribosomes Protein synthesis. Rough ER Transports and processes proteins. Smooth ER Lipid and steroid synthesis. Golgi apparatus Modifies, sorts and packages proteins. Vesicles Transport substances. Lysosomes Contain digestive enzymes. Mitochondria Aerobic respiration and ATP production. Centrioles Help organise spindle fibres during cell division. Chloroplasts Photosynthesis. Identifying organelles in micrographs * Mitochondria: oval shape with folded inner membranes called cristae. * Nucleus: large structure with a double membrane and pores. * Rough ER: flattened membranes with ribosomes attached. * Chloroplast: contains stacks of membranes called grana. * Golgi: curved, flattened membrane sacs. * Bacteria: no nucleus; DNA lies free in the cytoplasm. 6. Light and electron microscopes Light microscope Electron microscope Uses light. Uses an electron beam. Lower resolution. Higher resolution. Lower magnification. Higher magnification. Can view living cells. Specimens must be dead. Can show natural colours. Original images are monochrome. Generally cheaper. Generally more expensive. Mnemonic: M R C L * M = Magnification * R = Resolution * C = Colour * L = Living specimens 7. Magnification calculations Learn these three formulas: M=\frac{I}{A}I=M\times AA=\frac{I}{M} Where: * M = Magnification * I = Image size * A = Actual size Conversions: * 1 mm = 1000 µm * 1 µm = 1000 nm Always make sure your measurements use the same units. Stage micrometer and eyepiece graticule A graticule is calibrated against a stage micrometer. Mnemonic: Lazy Chefs Dice Meat * L = Line up the scales. * C = Count the divisions. * D = Divide the known measurement by the number of divisions. * M = Measure the specimen. Recalibrate when changing magnification. PART 2 – GRAM STAINING AND ANTIBIOTICS 8. Gram-positive and Gram-negative bacteria Gram-positive Gram-negative Thick peptidoglycan wall. Thin peptidoglycan wall. No outer membrane. Has an outer membrane. Stains purple. Stains pink/red. Generally more susceptible to penicillin. Outer membrane provides additional protection. 9. Gram staining Mnemonic: Hot Cats In Autumn Spring * Hot = Heat-fix: Fix bacteria onto a microscope slide. * Cats = Crystal violet: Add purple dye. * In = Iodine: Helps retain the crystal violet. * Autumn = Alcohol: Removes the dye from Gram-negative bacteria. * Spring = Safranin: Counterstains Gram-negative bacteria pink. * Result: Gram-positive purple, Gram-negative pink/red. 10. Penicillin Penicillin prevents the formation of cross-links in bacterial peptidoglycan. This: * Weakens the bacterial cell wall. * Allows water to enter by osmosis. * Causes the bacterial cell to burst (lysis). Gram-positive bacteria are generally more susceptible because their peptidoglycan is more accessible. Gram-negative bacteria have an outer membrane that can prevent or reduce penicillin entry. PART 3 – B2: SPECIALISED CELLS 11. Palisade cells Adaptations: * Contain many chloroplasts for photosynthesis. * Tall, thin shape allows cells to be closely packed. * Found near the upper surface of leaves to receive light. * Large vacuole pushes chloroplasts towards the cell edge. * Thin cell wall helps carbon dioxide diffuse into the cell. 12. Sperm cells Mnemonic: A Happy Mouse Tails * A = Acrosome: Contains enzymes to digest the egg’s outer layers. * H = Haploid nucleus: Contains half the normal chromosome number. * M = Mitochondria: Produce ATP for movement. * T = Tail: Flagellum propels the sperm. * S = Streamlined: Helps movement through fluid. 13. Egg cells Adaptations: * Large cytoplasm containing nutrient reserves. * Haploid nucleus. * Zona pellucida surrounds the egg. * Cortical granules help prevent polyspermy after fertilisation. Polyspermy: When more than one sperm fertilises an egg. 14. Root hair cells Adaptations: * Long extension gives a large surface area. * Thin cell wall gives a short diffusion distance. * Cell sap helps water enter by osmosis. * Mitochondria supply ATP for active transport of mineral ions. 15. Red blood cells Adaptations: * Biconcave shape gives a large surface area. * No nucleus, leaving more room for haemoglobin. * Haemoglobin binds oxygen. * Flexible shape allows movement through narrow capillaries. * Thin centre gives a short diffusion distance. Oxygen + haemoglobin ⇌ oxyhaemoglobin. 16. White blood cells Two important types: Neutrophils * Have a lobed nucleus. * Engulf pathogens by phagocytosis. * Use lysosomes containing digestive enzymes. * Form part of the innate immune response. * Respond rapidly to infection. Lymphocytes * Have a large, round nucleus. * B lymphocytes can develop into plasma cells. * Plasma cells produce specific antibodies. * Some become memory cells. * T lymphocytes can destroy infected cells. 17. Neutrophils and lymphocytes: similarities and differences Similarities mnemonic: Both Need Protection * Both = Both are white blood cells. * Need = Both contain a nucleus. * Protection = Both protect against pathogens. Differences: Neutrophils Lymphocytes Phagocytosis. Specific immune response. Lobed nucleus. Large, round nucleus. Digest pathogens using lysosomes. B cells produce antibodies. Part of innate immunity. Part of adaptive immunity. Respond rapidly. Can form long-lasting memory cells. 18. Antibodies and immunity Learn: * An antigen is a molecule recognised by the immune system. * Antibodies have binding sites complementary to specific antigens. * Antibodies bind to antigens. * This can neutralise pathogens or help other immune cells destroy them. * B lymphocytes can form memory cells. * Memory cells help produce a faster secondary response. 19. Allergies Mnemonic: A M H * A = Allergen enters the body. * M = Mast cells become involved. * H = Histamine is released. Histamine causes: * Blood vessels to widen. * Capillaries to become more permeable. * Fluid to move into tissues. * Swelling, itching and other allergic symptoms. 20. Transplant rejection Learn this sequence: * Donor cells have antigens. * The recipient recognises these antigens as foreign. * T lymphocytes recognise the foreign cells. * T cells attack the transplanted tissue. * Tissue matching reduces the chance of rejection. * Immunosuppressants reduce immune activity. PART 4 – B3: TISSUES AND THE RESPIRATORY SYSTEM 21. Epithelial tissues Squamous epithelium * Thin, flat cells. * Usually one cell thick in diffusion surfaces. * Short diffusion distance. * Found in alveoli and capillary walls. Columnar epithelium * Tall cells. * Can contain goblet cells. * Ciliated columnar cells move mucus. * Microvilli in the gut increase surface area for absorption. Endothelium * Lines the inside of blood vessels. * Smooth surface reduces friction. * Thin capillary endothelium allows diffusion. 22. COPD COPD stands for chronic obstructive pulmonary disease. Two important conditions: Emphysema Mnemonic: Smoking Makes Every Alveolus Lose Elasticity * Smoking causes inflammation. * White blood cells release elastase. * Elastase destroys alveolar walls. * Alveoli merge into larger air spaces. * Surface area decreases. * Elastic recoil decreases, causing difficulty breathing out. Chronic bronchitis Mnemonic: Irritated Goblets Make Coughing Increase * I = Inflammation of the bronchi. * G = Goblet cells enlarge. * M = More mucus is produced. * C = Cilia become damaged. * I = Infections become more common. * B = Bronchi narrow, causing coughing and breathing difficulties. 23. Alveoli adaptations Mnemonic: Silly Tigers Carry Very Massive Eggs * S = Surface area: Millions of alveoli create a large surface area. * T = Thin walls: One cell thick, short diffusion distance. * C = Capillaries: Dense network maintains the concentration gradient. * V = Ventilation: Refreshes alveolar air. * M = Moisture: Gases dissolve in the lining. * E = Elasticity: Allows stretching and recoil. 24. Gas exchange Oxygen moves: Alveolar air → Alveolar epithelium → Basement membrane → Capillary endothelium → Plasma → Red blood cell → Haemoglobin. Carbon dioxide moves in the opposite direction. Fick’s law Diffusion is faster when: * Surface area is larger. * Diffusion distance is shorter. * Concentration gradient is steeper. 25. Breathing and inhalation Mnemonic: Dancing Rabbits Visit Pretty Amazing Places * D = Diaphragm contracts and flattens. * R = Ribs move upwards and outwards. * V = Thoracic volume increases. * P = Pressure inside lungs decreases. * A = Air moves into the lungs. * P = Pressure equalises as air enters. Exhalation * Diaphragm relaxes and becomes dome-shaped. * External intercostal muscles relax. * Ribs move downwards and inwards. * Thoracic volume decreases. * Pressure inside the lungs increases. * Air moves out. 26. Smoking effects Mnemonic: Cigarettes Make Every Lung Suffer * C = Cilia damaged. * M = More mucus produced. * E = Excess infections. * L = Loss of alveolar walls. * S = Surface area reduced. * S = Smoking reduces lung elasticity. Smoking also damages blood vessel endothelium and increases atherosclerosis risk. PART 5 – ATHEROSCLEROSIS AND CIRCULATION 27. Atherosclerosis High-priority 6-marker Mnemonic: Dirty Money’s Find Pipes Narrowing Today * Dirty = Damage: The endothelium lining the artery becomes damaged. * Money’s = Macrophages: Macrophages enter the artery wall and engulf LDL cholesterol. * Find = Foam cells: Macrophages become foam cells, forming fatty streaks. * Pipes = Plaque: Fatty material builds up and forms a plaque. * Narrowing = Narrowing: The plaque narrows the artery and reduces blood flow. * Today = Thrombus: A blood clot can form and block the artery, potentially causing a heart attack or stroke. Risk factors * Smoking. * High blood pressure. * High LDL cholesterol. * Diabetes. * Age. * Poor diet. PART 6 – MUSCLES 28. Skeletal muscle structure Learn these terms: Structure Function Sarcolemma Muscle fibre cell membrane. Sarcoplasm Muscle fibre cytoplasm. Myofibrils Contain actin and myosin. Sarcomere Contractile unit between Z lines. Actin Thin filament. Myosin Thick filament. Sarcoplasmic reticulum Stores and releases calcium ions. Mitochondria Produce ATP. Skeletal muscle fibres are: * Long and cylindrical. * Multinucleate. * Striated. * Packed with myofibrils. 29. Sarcomere changes Structure During contraction A band Stays the same length. I band Shortens. H zone Shortens. Z lines Move closer together. Sarcomere Shortens. Mnemonic: A stays Always the same; I and H get Hit. 30. Sliding filament theory High-priority 6-marker Mnemonic: Clever Tigers Make Powerful Animals Run * Clever = Calcium: Calcium is released from the sarcoplasmic reticulum. * Tigers = Troponin: Calcium binds to troponin, moving tropomyosin. * Make = Myosin: Myosin binds to actin, forming cross-bridges. * Powerful = Power stroke: Myosin pulls actin towards the centre of the sarcomere. * Animals = ATP: ATP binds to myosin, causing detachment. * Run = Reset: ATP is broken down, re-cocking the myosin head. Remember: Actin and myosin do not shorten; they slide past one another. 31. Slow-twitch and fast-twitch fibres Mnemonic: Slow Red Runners Have Endurance Slow-twitch Type I * Red. * Lots of myoglobin. * Many mitochondria. * Dense capillary supply. * Mainly aerobic respiration. * Resist fatigue. * Used for endurance activities such as marathons. Fast-twitch Type II * Paler. * Less myoglobin. * Fewer mitochondria. * Lower capillary density. * More reliance on anaerobic energy pathways. * Contract quickly and powerfully. * Fatigue more quickly. * Used for sprinting and weightlifting. Remember: Slow = Stamina. Fast = Force. PART 7 – NERVOUS SYSTEM 32. Motor neurone structure Mnemonic: Dogs Can Always Nip Toes * D = Dendrites receive signals. * C = Cell body contains nucleus. * A = Axon carries the impulse. * N = Nodes of Ranvier are gaps in myelin. * T = Terminals release neurotransmitters. Myelin sheath * Insulates the axon. * Increases conduction speed. * Schwann cells produce myelin in the peripheral nervous system. * Nodes of Ranvier allow saltatory conduction. 33. Resting potential Mnemonic: Three Naughty Cats Keep Purring Inside * Three = 3 sodium ions pumped out. * Naughty = 2 potassium ions pumped in. * Cats = Pump uses ATP. * Keep = Potassium ions leak out. * Purring = Negative proteins remain inside. * Inside = Inside becomes approximately −70 mV. 34. Action potential Mnemonic: Silly Dogs Run Happily Past Houses * S = Stimulus reaches threshold (−55 mV). * D = Depolarisation begins as sodium channels open. * R = Rising potential as sodium enters. * H = High positive potential, around +40 mV. * P = Potassium channels open and potassium leaves. * H = Hyperpolarisation before returning to resting potential. Important extra facts * Action potentials are all-or-nothing. * A stronger stimulus increases frequency, not the size of the action potential. * The refractory period prevents immediate re-firing. * It helps ensure impulses travel in one direction. 35. Myelinated and non-myelinated neurones Mnemonic: Myelin Jumps Fast * Myelinated neurones have a myelin sheath. * They have nodes of Ranvier. * Impulses jump from node to node. * This is called saltatory conduction. * Non-myelinated neurones conduct continuously. * Myelinated neurones are faster and generally use less energy for impulse transmission. 36. Synaptic transmission High-priority 6-marker Mnemonic: All Clever Vikings Drink Really Slowly * All = Action potential: Arrives at the presynaptic knob. * Clever = Calcium: Calcium channels open and calcium enters. * Vikings = Vesicles: Vesicles release neurotransmitter by exocytosis. * Drink = Diffusion: Neurotransmitter diffuses across the synaptic cleft. * Really = Receptors: Neurotransmitter binds to postsynaptic receptors. * Slowly = Sodium: Sodium channels open and sodium enters, causing depolarisation. Extra: * Neurotransmitter is removed by enzymes or reuptake. * Synapses are one-way because receptors are on the postsynaptic membrane. 37. Acetylcholine Mnemonic: Release, Bind, Sodium, Enzyme, Recycle * Release: Acetylcholine is released from vesicles. * Bind: It binds to postsynaptic receptors. * Sodium: Sodium channels open. * Depolarisation: The membrane becomes less negative. * Enzyme: Acetylcholinesterase breaks down acetylcholine. * Recycle: Choline is taken back into the presynaptic neurone. 38. Agonists and antagonists Mnemonic: Agonist Activates; Antagonist Blocks. * Agonist binds to a receptor and activates it. * It can mimic a natural neurotransmitter. * Antagonist binds without activating the receptor. * It blocks the natural neurotransmitter from binding. Examples: * Nicotine: agonist at certain acetylcholine receptors. * Curare: antagonist at acetylcholine receptors. Other examples to know: * L-dopa is converted into dopamine. * SSRIs block serotonin reuptake. * Botulinum toxin prevents acetylcholine release. * Organophosphates inhibit acetylcholinesterase. 39. Neurotransmitters Neurotransmitter Main role Acetylcholine Muscle contraction and signalling. Glutamate Main excitatory neurotransmitter in the brain. GABA Main inhibitory neurotransmitter in the brain. Dopamine Movement and reward. Serotonin Mood, sleep and appetite. Noradrenaline Alertness and attention. 40. Parkinson’s disease Mnemonic: Dying Dopamine Makes Movement Slow * Dopamine-producing neurones in the substantia nigra degenerate. * Less dopamine is released. * Movement control is disrupted. * Symptoms include tremors, rigidity and slow movement. * L-dopa can be converted into dopamine in the brain. * Dopamine agonists can also help manage symptoms. 41. Depression and SSRIs Mnemonic: Serotonin Reuptake is Controlled, Levels Last * Serotonin is involved in mood regulation. * Serotonin is released into the synaptic cleft. * Normally, some serotonin is taken back into the presynaptic neurone. * SSRIs block serotonin reuptake transporters. * Serotonin remains in the synaptic cleft longer. * It can continue binding to postsynaptic receptors. PART 8 – ECGs 42. ECG waves Mnemonic: Please Quit Rushing, Stay Tranquil * P wave: Atrial depolarisation. * QRS complex: Ventricular depolarisation. * T wave: Ventricular repolarisation. Remember: * Atrial depolarisation is followed by atrial contraction. * Ventricular depolarisation is followed by ventricular contraction. * Ventricular repolarisation is followed by ventricular relaxation. 43. Heart rate calculations \text{Heart rate}=\frac{60}{\text{R-R interval in seconds}} Example: If the R-R interval is 0.8 seconds: 60\div0.8=75\text{ bpm} Know: * Tachycardia: over 100 beats per minute. * Bradycardia: under 60 beats per minute. * Regular R-R intervals indicate a regular rhythm. PART 9 – ALL THE 6-MARK QUESTIONS TO PRACTISE These are the extended-answer questions I would use to test your knowledge. They are based on your notes, not guaranteed predictions. Your 30-question exam checklist Tick each question once you can answer it without notes. 0/30 All 1. B1 – CellsCompare prokaryotic and eukaryotic cells. (6 marks) 2. B1 – CellsCompare light and electron microscopes. (6 marks) 3. B1 – MicroscopyExplain how to calculate magnification and actual size. (6 marks) 4. B1 – Gram stainingDescribe how Gram staining is carried out and how it identifies bacteria. (6 marks) 5. B1 – AntibioticsExplain why penicillin is generally more effective against Gram-positive bacteria. (6 marks) 6. B2 – Specialised cellsExplain how a sperm cell is adapted for fertilisation. (6 marks) 7. B2 – Specialised cellsExplain how a red blood cell is adapted to transport oxygen. (6 marks) 8. B2 – ImmunityExplain how phagocytes destroy pathogens. (6 marks) 9. B2 – ImmunityExplain how lymphocytes defend the body against pathogens. (6 marks) 10. B2 – ImmunityCompare the similarities and differences between neutrophils and lymphocytes. (6 marks) 11. B2 – ImmunityExplain how allergies occur. (6 marks) 12. B2 – ImmunityExplain how organ transplants can be rejected. (6 marks) 13. B3 – TissuesExplain how atherosclerosis develops. (6 marks) 14. B3 – LungsExplain how emphysema affects gas exchange. (6 marks) 15. B3 – LungsExplain how chronic bronchitis develops. (6 marks) 16. B3 – LungsExplain how alveoli are adapted for gas exchange. (6 marks) 17. B3 – LungsExplain the mechanism of inhalation. (6 marks) 18. B3 – LungsExplain how smoking damages the respiratory system. (6 marks) 19. MusclesExplain the sliding filament mechanism of muscle contraction. (6 marks) 20. MusclesCompare slow-twitch and fast-twitch muscle fibres. (6 marks) 21. NervesExplain how resting potential is maintained. (6 marks) 22. NervesExplain how an action potential is generated. (6 marks) 23. NervesCompare myelinated and non-myelinated neurones. (6 marks) 24. NervesExplain how an impulse travels along a myelinated neurone. (6 marks) 25. NervesExplain how a synapse transmits a nerve impulse. (6 marks) 26. NervesExplain how acetylcholine works at a synapse. (6 marks) 27. NervesExplain the difference between agonists and antagonists. (6 marks) 28. NervesExplain how Parkinson’s disease affects the nervous system. (6 marks) 29. NervesExplain how SSRIs affect synaptic transmission. (6 marks) 30. ECGsExplain what the P wave, QRS complex and T wave represent. (6 marks) Reset checklist PART 10 – IMPORTANT DEFINITIONS TO MEMORISE Term Meaning Diffusion Net movement of particles from high to low concentration. Osmosis Net movement of water across a partially permeable membrane from higher to lower water potential. Active transport Movement against a concentration gradient using energy. Phagocytosis Engulfing and digesting pathogens. Antigen Molecule recognised by the immune system. Antibody Protein that binds to a specific antigen. Depolarisation Membrane potential becomes less negative. Repolarisation Membrane potential returns towards its resting value. Hyperpolarisation Membrane potential becomes more negative than resting potential. Synapse Junction between neurones where signals are transmitted. Neurotransmitter Chemical messenger released at a synapse. Exocytosis Release of substances when vesicles fuse with a cell membrane. Atheroma Fatty plaque in an artery wall. Thrombus Blood clot formed within a blood vessel. Sarcomere Contractile unit of a myofibril. Oxyhaemoglobin Haemoglobin bound to oxygen. COPD Chronic obstructive pulmonary disease. Differentiation Process by which cells become specialised. PART 11 – THE MOST IMPORTANT MNEMONICS TO KNOW Here is your quick podcast-style recap. Read these aloud every day. Topic Mnemonic Cell organisation Cats Take Over Sofas Prokaryotic structures Naughty Pigs Rarely Chase Wolves Graticule calibration Lazy Chefs Dice Meat Gram staining Hot Cats In Autumn Spring Sperm cell A Happy Mouse Tails Atherosclerosis Dirty Money’s Find Pipes Narrowing Today Neutrophil and lymphocyte similarities Both Need Protection Alveoli Silly Tigers Carry Very Massive Eggs Inhalation Dancing Rabbits Visit Pretty Amazing Places Chronic bronchitis Irritated Goblets Make Coughing Increase Emphysema Smoking Makes Every Alveolus Lose Elasticity Sliding filament Clever Tigers Make Powerful Animals Run Slow-twitch fibres Slow Red Runners Have Endurance Motor neurone Dogs Can Always Nip Toes Action potential Silly Dogs Run Happily Past Houses Resting potential Three Naughty Cats Keep Purring Inside Synapse All Clever Vikings Drink Really Slowly Parkinson’s Dying Dopamine Makes Movement Slow ECG Please Quit Rushing, Stay Tranquil PART 12 – HOW TO REVISE THIS FOR YOUR EXAM I would revise in this order: Your 7-day revision plan * Day 1 – Cells Cell structures, prokaryotes, eukaryotes, microscopes and magnification. * Day 2 – Specialised cells Sperm, egg, root hair, palisade and red blood cells. * Day 3 – Immunity Neutrophils, lymphocytes, antibodies, allergies and transplant rejection. * Day 4 – Lungs and circulation Alveoli, inhalation, COPD, smoking and atherosclerosis. * Day 5 – Muscles Sarcomeres, sliding filament theory and muscle fibre comparisons. * Day 6 – Nervous system Resting potential, action potentials, synapses, neurotransmitters and Parkinson’s. * Day 7 – Exam practice Attempt the 6-mark questions without notes, then check your answers. My final advice For every 6-marker, learn: * The mnemonic. * What every letter stands for. * The scientific explanation. * The correct order of events. You have already shown that you can remember the atherosclerosis sequence and explain it in your own words. That’s exactly how you should practise the rest. Don’t just memorise the mnemonics. Make sure you understand what each biological process actually means. That’s what will help you answer the question even if the examiner words it differently.

B1.2.2 - Condensation reactions forming dipeptides and longer chains of amino acids

29. An introduction to A Level organic chemistry Formulas, Fn groups, Naming Functional groups and formulae Functional group: atom/group of atoms in an organic molecule that determines its characteristic chemical and physical properties Arenes: aromatic compounds that contain a benzene ring chemical properties Compound can undergo Electrophilic attack: is e- rich due to π system of delocalised e- Resistant to addition reactions: delocalised e- ring system makes benzene stable physical properties b.p 80 C: Benzene has id-id forces of attraction between the molecules Insoluble in water: non-polar hydrocarbons in arene (not energetically favourable for benzene to break many H bonds between water molecules to be soluble) Halogenoarenes: aromatic compounds containing halogen bonded to benzene ring chemical properties Prone to Electrophilic attack can take part in substitution reactions physical properties Chloro, broom, iodo benzene liquid at r.t with oily texture b.p. Increases down group: larger halogen = more e- = stronger id-id forces = more energy to separate insoluble in water: non-polar hydrocarbon ring Phenols: aromatic compounds containing a hydroxide bonded to benzene ring chemical properties acidic: O in -OH donates a lone pair into ring (more acidic than alcohols) = increased e- density in ring = more reactive = easier for H to be donated react with reactive metals (e.g. Na) to form phenoloxide ions and H gas physical properties White, crystallline solid disinfectant-like smell soluble in water: can form H bonds with water due to -OH group Acyl chlorides: carboxylic acid derivatives containing a chlorine atom, and an acyl group attached to C=O chemical properties colourless extremely reactive and readily takes part in substitution (Cl substituted ) fuming liquids with strong smell: react with water vapor in air Physical properties react violently with water (cannot determine its solubility with water ) Amines: compounds with -NH2 (primary), -NH (2 °) , or -N (3 ° ) amine group chemical properties basic compounds: due to lone pair of e- on nitrogen physical properties lone pair on N can form H bonds soluble in water: form H bond with water solubility ↓ as nonpolar hydrocarbon chain gets longer / molecule gets bigger fishy smell Amides: compounds containing amine group (-NH2) carbonyl group (C=O) amide group -CONH2 chemical properties less basic than amides: lone pair of e- on N is delocalised physical properties soluble in water: form H bonds with water solubility ↓ as nonpolar hydrocarbon chain gets longer / molecule gets bigger Amino Acids: building blocks of proteins, consisting amine group (-NH2) and carboxylic group (-COOH) chemical properties react with bases to form salts react with alcohols to form esters react with amines to form amides physical properties most are soluble in water but insoluble in organic solvents most have chiral centres, exhibit optical isomers Formulae of Organic Compounds Nomenclature of Compounds Naming organic compounds Identify longest C chain containing the functional group Identify fn group on the chain to determine the suffix or prefix on the compound Count along the carbon chain such that the functional group has the lowest number Add any side chains or lower priority functional groups as prefixes to the beginning of the name in alphabetic order Use the prefixes di-, tri- and tetra- if there are two or more identical functional groups or side chains Characteristic organic reactions Electrophilic substitution Electrophile: e- loving species they are e- deficient and acts as e- pair acceptor Substitution reactions: reactions replacing 1 atom / group by another Electrophilic substitution: group / atom replaced by an electrophile e.g. bromine electrophile attacks e- - rich benzene ring Addition-elimination (nucleophilic) nucleophilic addition of small molecule followed by elimination of small molecule includes hydrolysis reaction of alcohols to form esters reaction with ammonia and 1° amines to form amides e.g. Hydrolysis of acyl chlorides Hydrolysis - acyl chloride to carboxylic acid water molecule adds across C=O bond HCL eliminated Ester formation - acyl chlorides + alcohol Alcohol adds across the C=O bond HCl molecule is eliminated Amide formation - acyl chloride + 1° amines + conc ammonia amine or ammonia adds across C=O bond (lone pair on N attacks carbonyl C atom in acyl chloride) HCl eliminated Shapes of aromatic organic molecules Aromatic molecules consist of one or more rings with conjugated π systems Conjugated π systems arise from alternating double and single bonds in which the electrons are delocalised Shape of benzene and aromatic compounds - why are they more stable? Benzene and other aromatic compounds are planar and regular because each carbon atom is sp² hybridised. Each C forms three σ bonds in a trigonal planar arrangement with bond angles of 120°. The remaining unhybridised p orbital on each carbon overlaps sideways with neighbouring p orbitals to form a continuous, delocalised π system above and below the ring. Because the π electrons are delocalised over the whole ring, all the C–C bonds are identical and have intermediate character between a single and double bond. This is why benzene is unusually stable. Why are benzene more stable? delocalised π electrons above and below the ring Optical isomerism, Chirality and drug production Stereoisomers: same structural formula, diff arrangement in space (geometrical, optical) Optical 4 diff groups of / atoms central chiral carbon chiral molecules exist as 2 optical isomers / enantiomers non-superimposable mirror images same physical / chemical properties rotate in opposite directions in plane polarised light (1 clockwise 1 anticlockwise ) Similarities of enantiomers differences in enantiomers same physical and chemical properties differ from ability to rotate plane polarised light and biological activity nonsuperimposable mirror images Biological activity of enzymes enzymes are chiral proteins, bond to specific active site for biological response mirror image of enantiomer will not bind to same active site as it is not the same shape, no biological response Optical activity and Racemic mixtures reaction mixture is optically active if there is an uneven mixture of each enantiomer (e.g. 20% rotates clockwise, 80% rotates anticlockwise, net effect is plane of polarised light rotates anticlockwise) racemic mixture: equal amounts of enantiomers present in soln optically inactive as enantiomers cancel out each others effect, plane polarised light not changed the rotation of plane polarised light can be used to determine the identity of an optical isomer e.g. pass plane polarised light through a sample containing one of the two optical isomers of a single substance Depending on which isomer sample contains, the plane polarised light will be rotated clockwise / anti-clockwise clockwise rotation: R enantiomer anticlockwise rotation: S enantiomer No effect will be observed when the sample is a racemic mixture Chirality and Drug production most drugs to treat disease have 1+ chiral centres and can ∴exist as enantiomers diff in biological activity in enantiomers means difference in effectiveness as medicine drugs should be prepared so that only 1 optical isomer produced, to ↑ effectiveness Potential different biological activity of enantiomers e.g. drug naproxen treats pain from arthritis 1 enantiomer eases pain 1 enantiomer causes liver damage separate racemic mixture into 2 pure enantiomers due to difference in biological activities reduce side effects ↓ dosage by half, reduces production cost chiral catalysts to produce 1 pure optical isomer only small amount chiral catalysis needed + reused e.g. enzyme 30. Hydrocarbons - Arenes Reactions of arenes substitution halogenation nitration Friedel-Craft's alkylation Friedel-Craft's acylation other reaction Complete Oxidation Hydrogenation Electrophilic substitution electrophile: e- pair acceptor, attracted to delocalised e- substitution: 1+ H replaced by a fn group generating electrophile+ using catalyst Electrophilic attack on benzene ring (electrophile accepts 2 π e- , +ve charge remains) regenerating aromaticity by heterolytically cleavage of C-H bond (bonding pair foes into benzene π system) Addition reactions of arenes arenes undergo substitution due to delocalisation of e-, aromaticity restored by heterolytic cleavage of C-H bond in addition, aromaticity / stability not restored (e.g. hydrogenation), Hydrogenation of benzene is less exothermic than expected for three isolated C=C bonds, because the aromatic stabilisation of benzene is lost Halogenation (in the aromatic ring) reactants: Cl2 / Br2 (Cl+ / Br+ electrophile) , arene conditions: rt and pressure catalyst: anhydrous AlCl3 / AlBr3 (catalyst needed due to stability of benzene structure) formation: AlCl3 + Cl2 ⇒ AlCl4- + Cl+ reformation: H+ + AlCl4- ⇒ AlCl4 + HCl product: halogenoarenes / aryl halide In halogenation of Alkylarenes, e- donating alkyl group activates positions 2, 4 (as well as OH-, NH2). forms 2 products multiple substitutions when excess halogen used Halogenation (of alkylarenes) in side chain free radical substitution reaction reactants: halogen, boiling alkyl arene conditions: UV light if excess halogen: all H on alkyl side chain will be substitution by X atoms Nitration reactants: conc HNO3 (NO2+ electrophile), arene conditions: 20-60 ° C (higher = more NO2+ substituted) catalyst: conc H2SO4 formation: HNO3 + H2SO4 ⇒ NO2+ + 2HSO4- + H3O+ reformation: H+ + HSO4- ⇒ H2SO4 In nitration of Alkylarenes, e- donating alkyl group activates positions 2, 4 Friedel-Crafts alkylation substitution of alkyl chain reactant: chloroalkane (CH3CH2+ electrophile), arene condition: heat under reflux catalyst: anhydrous AlCl3 formation: AlCl3 + CH3CH2Cl ⇒ CH3CH2+ + AlCl4- reformation: AlCl4- + H+ ⇒ AlCl3 + HCl Friedel-Crafts acylation substitution of an acyl group (group containing carbonyl, C=O ) reactant: acyl chloride (CH3CH2CO+ electrophile) conditions: heat under reflux catalyst: anhydrous AlCl3 formation: AlCl3 + CH3CH2COCl ⇒ CH3CH2C=O+ + AlCl4- reformation: AlCl4- + H+ ⇒ AlCl3 + HCl Complete oxidation of side chains alkyl side-chains in alkyl arenes are oxidised to carboxylic acids when refluxed with alkaline KMnO4 and then acidified with dilute H2SO4 reactants: hot alkaline KMnO4, dilute H2SO4, alkyl arenes conditions: heat under reflux Hydrogenation addition reaction to form cyclohexane reactants: H2 gas conditions: heat (200 ° C at 30 atm ) catalyst: Pt/Ni Directing effects of substituents on arenes substituents: already on arene that direct substitution reactions to diff. ring positions E- withdrawing groups / substituents e- donating groups / substituents remove e- density from π system in benzene ring deactivating groups (slow attack by e+) directs e+ to positions 3, 5 e.g. COOH, X, NO2 donate e- density into π system of benzene ring activating groups (allow e+ to react faster) directs e+ to positions 2, 4, 6 e.g R, NH2, OH 31. Halogen compounds Halogenoarenes: arenes bonded to X atoms Producing halogenoarenes substitution reactions of arenes with chlorine or bromine in presence of anhydrous AlCl3 catalyst reactants: Cl2 / Br2 (Cl+ / Br+ electrophile) , arene conditions: rt and pressure catalyst: anhydrous AlCl3 / AlBr3 (catalyst needed due to stability of benzene structure) formation: AlCl3 + Cl2 ⇒ AlCl4- + Cl+ reformation: H+ + AlCl4- ⇒ AlCl4 + HCl product: halogenoarenes / aryl halide Substitution of benzene Substitution of methylbenzene substitution of 6 position only occurs in excess chlorine Reactivity of halogenoarenes Why are aryl halides less reactive than haloalkanes? C-H bond in aryl halides is stronger due to the partial overlap of lone pairs on halogen atom with the π system in the benzene ring C-H bond ∴ has a partial double bond character 32. Hydroxy compounds Reactions of alcohols Formation of esters reaction: addition-elimination (esterification) reactants: alcohols/phenols, acyl chlorides nucleophile: OH- (attacks e- deficient carbonyl (COCl) C ) COCl bond breaks, Cl is substituted, HCl fumes formed Why are esters formed from acyl chlorides rather than from C. acids? more effective to form esters from acyl chlorides acyl chlorides are more reactive (produce esters faster) acyl chloride reactions go to completion (more ester formed) Esterification using phenols additional reactants: base (e.g. NaOH) base: deprotonate phenol to form phenoxide ion phenoxide better nucleophile than phenol, attack on carbonyl C occurs more readily Phenol phenol: benzene ring with -OH group attached Production of Phenol From reaction of phenylamine with nitrous acid (HNO3) reactants: NaNO2, dilute acid (to form HNO2), phenylamine conditions: ice (under 10 ° C) step 1 and 2, heat step 3 forming nitrous acid NaNO2 + HCl ⇒ (ice) HNO2 + NaCl forming unstable diazonium salt forming phenol via thermal decomposition (due to instability) reactions of phenol Many reactions due to e- rich benzene ring and polar -OH group with bases with reactive metals with diazonium salts nitration bromination Acid-base reactions Acid-base reaction of phenols with base -OH: slightly acidic (weak acids), act as acid in acid-base reaction dissolve in alkaline soln forming phenoxide salt and water Acid-base reaction of molten phenols with reactive metals forms soluble phenoxide salt and H2 gas Reaction with diazonium ions diazonium ions very reactive due to -N2+ group acid-base reaction conditions: ice for cold diazonium ion added to phenoxide ion Reactions of the aromatic ring phenols react more readily with e+ than benzene due to one lone pair of e- on O in -OH overlaps with π bonding system, ↑ e- density of phenol’s benzene ring and making it more susceptible to electrophilic attack -OH activates ring, directs e+ to 2, 4, 6 positions Nitration of phenols electrophilic substitution reaction reactant: dilute HNO3, phenol when conc HNO3 used, product is 2, 4, 6- trinitrophenol conditions: rt milder conditions as phenol is more reactive Bromination of phenols electrophilic substitution reaction reactants: bromine water, phenol conditions: rt phenol decocolourises orange bromine soln to form 2, 4, 6 - tribromophenol (white ppt) as phenol is more reactive, no need for anhydrous AlBr3 catalyst, can react with bromine water Reactions of other phenolic compounds (contain phenol functional group, e,g, 1-naphthol) -OH group is also e- donating, activates benzene ring to electrophilic substitution reactions, e+ directed to 2, 4 positions (on phenol) C in position 6 shared by both rings, no H atom = no substitution can react in similar way as phenol Acidity of phenols Phenols are weak acids phenols react more readily with e+ than benzene due to one lone pair of e- on O in -OH overlaps with π bonding system, ↑ e- density of phenol’s benzene ring and making it more susceptible to electrophilic attack Phenol’s conjugate base is the phenoxide ion. -ve charge is delocalised over the entire ion as a lone pair on O overlaps with the ring’s delocalised π system, which reduces charge density on oxygen H⁺ ions are ∴ less strongly attracted to phenoxide ion, so phenol is less likely to reform Therefore, phenol is more likely to lose H⁺ and act as an acid Stability of conjugate base phenoxide more stable as -ve charge spread out, so phenol more likely undergo ionisation eqm shifts right, more phenol donate H+ (act as acid) Relative acidities of water, phenol, ethanol smaller pKa = stronger acid order of acidity explained by conjugate bases Delocalisation of charge density phenoxide (conjugate base of phenol): charge density of O is spread out over ion, O less available for bond formation with H+ ethoxide (conjugate base of ethanol): ethyl group is e- donating, donates e- density to O atom, O more available for bond formation with H+ hydroxide (conjugate base of water): charge density of O cannot become delocalised over a ring, OH- more readily accepts H+ than phenoxide no e- donating alkyl groups to O, less -ve O, O less readily accepts H+ compared to ethoxide Overall conjugate base more readily accepts H+ = stronger conjugate base = weaker acid strong acid eqm shifts right favouring dissociated ions and H+ 33. Carboxylic acids and derivatives Benzoic acid: C6H5COOH can be used to synthesize esters Carboxylic acids Production of benzoic acid formation of benzoic acid from Oxidation of alkylbenzenes alkylbenzene heated under reflux with hot alkaline KMnO4, then acidified with dilute acid to protonate carboxylate salt and form benzoic acid reactants: hot alkaline KMnO4 (oxidising agent), dilute acid (e.g. HCl), alkylbenzene purple Mn2+ turns colourless as reduced to Mn4+ brown ppt MnO2 formed conditions: heat under reflux Reactions of Carboxylic acids Reactions of C, acids to form acyl chlorides reactants PCl5 (s) PCl3 (l) + heat SOCl2 (l) Forming carboxylic acids from oxidation of 1 ° alcohols alcohol ⇒ aldehyde ⇒ c. acid Further oxidation of c. acids such as methanoic and ethanedioic acid methanoic acid (strong reducing agent) gets further oxidised to CO2 by warming with mild oxidising agents like Fehling’s or Tollen’s reagent Fehlings: Cu2+ reduced to Cu+, form red ppt Cu2O Tollens: Ag+ reduced to Ag using stronger oxidising agents like acidified KMnO4 or acidified K2Cr2O7 KMnO4: purple soln turns colourless as Mn7+ reduced to Mn2+ K2Cr2O7: orange soln turns green as the Cr6+ reduced to Cr3+ ions Ethanedioic acid gets further oxidised to CO2 Conditions: Strong oxidised agent - warm acidified KMnO4 needed Relative acidities of C. acids, Phenols, and alcohols C acids can lose H+ in aq soln to form carboxylate salts and water Acidities of C. acids longer C chain = weaker acid inductive effect ↑ -ve charge on COO- group More substituted Cl atoms = stronger acid Cl atoms withdraw e- density from the –COOH group, weakening the O–H bond and stabilise carboxylate ion (reducing the -ve charge density on it) The more stable the carboxylate ion, the less likely it is to attract H⁺ and reform the O–H bond Acidities of c. acids, phenols, alcohols acidities explained by strength of O-H bond and stability of conjugate bases of acids Strength of O-H bond carboxylic acids e- in O-H bond drawn towards C-O bond, e- in C-O bond drawn to C=O bond O-H bond weakened due to C=O withdrawing e- density from it for itself easier to act as acid and lose H+ from OH alcohols lack e- withdrawing C=O group, O-H bond not weakened harder to act as acid and lose H+ Stability of conjugate bases carboxylate ion (c base of carboxylic acid) charge density on O spread over ion because charge is delocalised on an electronegative carbonyl O atom O less available for bond formation with H+ to reform -COOH eqm shifts right, C base more stable than carboxylic acid alkoxide ion (c base of alcohol) alkyl is e- donating group, donates e- density to O atom O more available for bond formation with H+ ion to reform OH lack ability to delocalised charge density on ion, c bases less stable than alcohols, weaker acids than c. acid and phenols eqm lies left phenoxide ion (c base of phenol) charge density of O spread out over ion due to delocalisation of e- (stabilises ion) O less available for bond formation with H+ Phenoxide more stable than phenol Phenoxide less stable than carboxylate since delocalisation of charge density is on C atoms, not electrogenative O atoms eqm lies more right than alcohols, more left than c. acids ethanol is weakest e- donating methyl group strengthens O-H bond methyl donates -ve charge to -COO-, more likely to accept H+ Esters - Production Esters: organic compounds with -COO- functions group nice smelling Naming esters alcohol acyl chloride / carboxylic acid e.g. Producing esters from alcohols and carboxylic acids condensation / esterification reaction Producing esters from alcohols and acyl chlorides more effective: acyl chlorides more reactive(faster), and reactions go to completion (no eqm, max yield) Acyl Chlorides Acyl chlorides: compounds with COCl fn group Production of acyl chlorides Carboxylic acid with solid PCl5 liquid PCl3 + heat liquid SOCl2 Reactions of acyl chlorides addition-elimination: addition of small molecule across C=O, followed by elimination of small molecule acyl chlorides under addition-elimination reactions such as hydrolysis to form carboxylic acid Reaction with alcohols and phenols to form esters Reaction with ammonia and amines to form amides General mechanism for addition-elimination reactions addition of nucleophile across C=O bond elimination of a small molecule such as HCl or H20 lone pair on nucleophile carries out initial attack on carbonyl carbon this is followed by the elimination of an HCl molecule Hydrolysis of acyl chlorides forms carboxylic acid and HCl water (nucleophile) adds across C=O bond HCl eliminated Formation of esters from acyl chlorides esterification reaction reactants: alcohol/phenol, acyl chloride conditions: rt reaction with phenol is slower than alcohol, base such as NaOH used to speed up reaction (deprotonates phenol to form phenoxide, better nucleophile to carry out attack) alcohol /phenol (nucleophile) adds across C=O bond, HCl / NaCl eliminated Formation of amides from acyl chlorides condensation reaction: nucleophile adds to C=O, Cl- eliminated, HCl formed reactants: ammonia or 1°/2 ° amines, acyl chloride nucleophile: Nitrogen (has lone pair of e- ) HCl formed is immediately neutralised by a 2nd molecule of ammonia / amine in excess, forming ammonium salt (e.g. NH4Cl, CH3NH3Cl) Relative ease of hydrolysis of aryl chlorides from most readily broken / easily hydrolysed acyl chloride > alkyl chloride > aryl chloride trend explained by strength of C-Cl bond acyl chlorides - hydrolysed at rt R-COCl C bonded to Cl is also bonded to O both Cl and O are very electronegative, pulling e- away from C, leaving it very δ+ C-Cl bond is weakened nucleophilic attack is more rapid alkyl chloride - hydrolysed by refluxing with strong alkali nucleophile R-C-Cl C bonded to Cl attached to 1 electronegative atom (Cl), pulls e- away from C C is not very δ+ (e- deficient) C-Cl bond is stronger than in acyl chlorides aryl chlorides - hydrolysis will not occur C bonded to Cl is part of delocalised π bonding system of benzene ring one lone pair of e- on Cl overlaps with delocalised system C-Cl bond has some double bond character, becoming stronger 34. Nitrogen compounds Primary and secondary amines 1 ° amines: organic compounds with NH2 fn group attached to an alkyl / aryl group 2 ° amines: organic compounds with group attached to a alkyl /aryl groups Naming -amine: after alkyl prefix (e.g. methyl amine) amino- : if another suffix present or branched/complex amines (e.g. amino methane) Production of Amines 1 ° and 2 ° amines prepared form diff reactions 1 ° amines: reaction of haloalkanes with ammonia reduction of nitriles reduction of amides 2 ° amines: reaction of haloalkanes with 1 ° amine Forming 1 ° amines from haloalkanes with ammonia nucleophilic substitution reaction reactants: excess, hot ethanolic ammonia nucleophile: N in ammonia (replaces X) conditions: heat under pressure Forming 1 ° amine from reduction of nitrile reactants: nitrile vapour, H2 gas conditions: LiAlH4 in dry ether (reducing agent), or Ni catalyst Forming 1 ° / 2 ° amines from reduction of amides reactants: LiAlH4 in dry ether (reducing agent) type of amine depends on nature of amide Forming 2 ° amines from haloalkanes with 1 ° amine nucleophilic substitution reaction reactants: 1 ° amine in ethanol nucleophile: N in 1 ° amine (replaces X) conditions: heat under pressure, sealed tube Reactions of Amines Condensation reaction between Acyl chloride and ammonia or amine produces Amides Cl in acyl chlorides is electronegative, draws e- density from carbonyl C C is e- deficient, attacked by nucleophile like N in ammonia and amines C-Cl bond broken, amide formed reaction with amines ⇒ substituted amide reaction with ammonia ⇒ nonsubstituted amide Why is acyl chloride a more effective reactant than carboxylic acids in formation of amides? c acids less reactive than acyl chloride reaction with c acids dosent fo to completion Basicity of aq soln of Amines and ammonia N in ammonia and amines can accept proton H+, can ∴ act as bases in aq soln (when donating lone pair to form dative bonds) Strength of bases strength of amine depends on availability of lone pair of e- on N to form a dative covalent bond with H+ lone pair more readily available to form dative bond = stronger base positive inductive effect ↑ basicity: alkyl groups donate e- density to N, causing lone pair to become more available delocalisation ↓ basicity: aromatic rings cause lone pair to be delocalised into benzene ring, causing lone pair to be less available Phenylamine and Azo compounds Phenylamine: organic compound with benzene ring and amine fn group Production of phenylamine 3 step synthesis, followed by separation / purification Nitration (forming nitrobenzene) reactants: benzene, conc HNO3 catalyst: conc H2SO4 conditions: 25-60 ° C Reduction (forming phenylamine ion) conditions: hot tin (Sn) and conc HCl under reflux Deprotonation (forming phenylamine) reactants: NaOH, phenylamine ion separation/purification phenylamine separated from reaction mixture by steam distillation Reactions of Phenylamine Both benzene ring and NH2 can take part in chemical reactions bromination of phenylamine formation of diazonium salt Bromination of phenylamine to form 2, 4, 6- tribromophenylamine electrophilic substitution reaction electrophile: N, donate e- density into benzene ring, ↑ e- density in benzene ring activates it, more readily attacked by electrophiles reactants: aqueous bromine, phenylamine conditions: rt Formation of diazonium salt (salt containing N2+ group) reactants: nitrous acid/HNO2, HCl, phenylamine HNO2 formed in test tube with NaNO2 and dilute HCl conditions: below 10 ° C diazonium salt forms phenol upon warming with water Azo compounds Azo compounds: organic compounds with R-N=N=R / azo group often used as dyes Diazonium compounds: contain N2+ group Formation of Azo compounds from coupling reaction of benzene diazonium chloride salt with phenol multi-step process forming nitrous acid reactants: NaNO2, HCl conditions: test tube, under 10 °C / ice NaNO2 + HCl ⇒(ice) HNO2 + NaCl Diazotisation reactants: phenylamine, HNO2, dilute HCl conditions: below 10 ° C / ice (prevent thermal decomposition of diazonium ion to phenol, N and HCl) coupling reaction reactants: phenol, diazonium ion (acts as electrophile, sub into benzene ring of phenol) conditions: alkaline conditions (NaOH deprotonates phenol to phenoxide, more reactive to e+) Why are azo compounds very stable? The delocalised e- in π bonding systems extend across both benzene rings and the –N=N– bridge Other days formed from similar route e.g. formation of yellow dye from coupling reaction between benzene diazonium chloride and C6H5N(CH3)2 Amides Amide: organic compounds with CONR2 amide group non-substituted / 1 ° amide: N bonded to 2H atoms substituted / 2 ° amide: 1 or both H replaced by a hydrocarbon group Production of Amides Formation of Amides from acyl chlorides / c. acid with ammonia / amine condensation reaction: nucleophile adds to C=O, Cl- eliminated, HCl formed nucleophile: Nitrogen (has lone pair of e- ) conditions: rt HCl formed is immediately neutralised by a 2nd molecule of ammonia / amine in excess, forming ammonium salt (e.g. NH4Cl, CH3NH3Cl) Reactions of Amides Amide group can undergo reactions Hydrolysis with aqueous alkali or aqueous acid Reduction with LiAlH4 Hydrolysis of amides to form c. acid and ammonia/ 1 ° amine conditions: reflux with aq acid / alkali products differ depending with amide is substituted nonsubstituted ⇒ c. acid + ammonia substituted ⇒ c. acid + 1 ° amine when refluxed in excess acid⇒ ammonium salt formed base⇒ carboxylate ion formed (deprotonation) Reduction of amides to form amine conditions: LiAlH4 reducing agent nonsubstituted amide ⇒ 1 ° amine + H2O substituted amide ⇒ 2 ° amine + H2O Relative basicity of Amides and Amines lone pair of e- more readily available for dative bonding = stronger base more e- =stronger base amides - weaker base e- withdrawing O in C=O causes lone pair on N to delocalise into C=O group, removed e- density from N lone pair on N less readily available for bonding amine - stronger base e- donating alkyl groups ↑ e- density on N lone pair on N more readily available for bonding Amino Acids Amino acids: organic compounds with 2 fn groups basic amino -NH2 group acidic carboxylic acid -COOH group due to presence of basic and acidic group, they are amphoteric (act as acid and base) R group can be acidic, basic, or neutral Acid-base properties of amino acids + formation of Zwitterion amino acids can undergo most reactions of amines and c. acids, including acid-base reactions (amine + acid, C. acid + base) Amino acids can interact intramolecularly to form zwitterion Zwitterion: ion with both +ve (NH3+) and -ve (COO-) charge formed from amino acids in water due to charges, there are strong intermolecular forces of attraction between amino acids this makes amino acids soluble crystalline solids Zwitterions act as buffer soln acid added: pH ↓ COO- accepts H+ to reform COOH, zwitterion becomes +vely charged base added: pH ↑ NH3+ donates H+ to reform NH2, zwitterion becomes -vely charged Isoelectric point: point at which charge = 0 / zwitterion is neutral a pH level unique to each amino acid due to R group Formation of Peptide bonds NH2 group of one amino acid can react with COOH group of another amino acid to form dipeptide condensation reaction: H2O eliminated peptide bond / link formed dipeptides can undergo condensation reaction again to form tripeptide ( 3 amino acids) polypeptide: many amino acids join to form long chain of molecules proteins are polypeptides Electrophoresis Analytical separation technique, separates ions by placing them in an electric field Sample of amino acids placed between 2 oppositely charged electrodes +ve ions move to -ve electrode -ve ions move to +ve electrode Rate of ion movement depends on size of ions (larger = slower) charge of ions (highly charged = quicker) Electropherogram: bands on gel after electrophoresis each band = particular species Amino acids can be separated according to charge and mass they are colourless, sprayed with ninhydrin (brown/purple stain) to show where they have gone to Changes in charge of amino acid due to pH of solution isoelectric point: no overall charge, no movement of zwitterions pH > isoelectric point: -ve charge, move to +ve electrode pH < isoelectric point: +ve charge, move to -ve electrode -ve charged amino acid: NH3+ donated H+, NH2 and COO- left +ve charged amino acid: COO- accepted H+, NH3+ and COOH left 35. Polymerisation Condensation Polymerisation - Forming polymers Forming polymers such as polyesters, polyamides, proteins Formation of polyesters addition polymerisation: monomers with C=C bonds join to form polymers condensation polymerisation: Small molecule is lost when monomers join together to form polyester polyesters have ester links Monomers for polyesters OH on dicarboxylic acid and H of diol expelled as H2O to form polyester diol (2 -OH) + dicarboxylic acid (2 -COOH) 2 hydroxy carboxylic acids (OH and COOH fn group) Formation of polyamides condensation polymerisation polyamides have peptide links Monomers for polyamides H on diamide and OH on dicarboxylic acid / Cl on dichloride expelled as H2O / HCl as polyamide forms diamide (2 -NH2) + dicarboxylic acid diamide + dichloride (2 -COCl) 2 aminocarboxylic acids (OH and COOH fn group) Making proteins/polypeptides from amino acid monomers (aminocarboxylic acid) amine group (-NH2) and carboxyl group (-COOH) of an amino acid polymerise with another amino acid forms peptide links proteins can be broken into its constituent amino acids through hydrolysis You can deduce the repeat units of a condensation polymer by identifying the linking between monomers chain of C: addition polymer ester link: polyester peptide link: polyamide You can identify monomers from small molecule expelled H2O: c acid H: amine Cl: dioyl chloride Predicting type of polymerisation Identifying type of polymerisation by looking at functional groups Addition polymerisation monomer contains C=C bond double bond opens up to add monomers to either side of starting polymer forms polyalkenes co-polymer: 2+ monomers used to make 1 repeating unit Condensation polymerisation makes polyamides and polyesters summary: Identifying type of polymerisation by considering structure of polymer backbone Addition polymerisation no fn groups on polymer backbone, usually chain of C atoms sidechains might branch off from backbone (e.g. benzene rings, nitrile groups (CN), halogens Condensation polymerisation backbone of polyesters contain ester links (-COO-) backbone of polyamides contain peptide links (-CONH-) Degradability of Polymers Polyalkenes and biodegradability polyalkenes are nonpolar and saturated, making them nonbiodegradable and chemically inert instead, they can be melted and recycled for new uses The energy released from burning can be used to generate electricity Burning plastics in oxygen releases carbon dioxide and water (complete combustion) which can contribute to global warming Photodegradation of polymers some polymers are biodegradable due to their ability to breakdown using light C=O groups along polymer chains absorb UV light this weakens C=O areas of polymers and breaks them down into smaller molecules e.g for polyesters and polyamides Disadvantages of photodegradability weaker polymers UV light not available (e.g. in landfills) Biodegrading polyesters and polyamides via hydrolysis polyesters and polyamides can be broken down by hydrolysis (advantage) hydrolysis: breakdown of molecules using water acid hydrolysis: acid catalyst used alkaline hydrolysis: alkaline catalyst used heating with catalyst breaks polymer Hydrolysis of polyamides acid hydrolysis: breaks polymer into di carboxylic acid and ammonium ions alkali hydrolysis breaks polymer into its sodium salts (e.g. dicarboxylic acid salt and diamines) Hydrolysis of polyesters acid hydrolysis: diol + dicarboxylic acid alkali hydro lists: diol + dicarboxylic acid salt 36. Organic synthesis Elucidating organic molecules - fn groups, properties, reactions Fn groups in AS required as well as: Production of fn groups benzoic acids acyl chlorides amides Producing benzoic acid reactants: methylbenzene oxidation: reflux with hot alkaline KMnO4 to form potassium benzoate protonation with dilute HCl to form benzoic acid Producing acyl chlorides reactants: c. acid substitution reaction: -OH replaced by Cl Producing amides condensation reaction reactants: acyl chloride, NH3 (nonsubstituted amide) / methyl amine (substituted amide) conditions: rt Reactions of functional groups Electrophilic substitution reactions of benzene reaction electrophile halogenation X+ nitration NO2+ alkylation R+ acylation RCO+ Hydrogenation of benzene addition reaction Esterification of phenol more efficient with acyl chloride than carboxylic acid Acid-base reactions of phenol phenol + base ⇒ soluble salt + water Nitration of phenol Bromination of phenol Multi-step synthetic routes Aliphatic reactions Aromatic reactions Analysis 37. Analytical techniques Thin- Layer Chromatography (TLC) Separate small samples 2 phases: stationary and mobile phase Stationary phase thin metal sheet coated in Al2O3, or SiO2 solutes adsorb onto surface and travel thru plate Mobile phase flows over stationary phase polar (water or alcohol) or nonpolar (alkanes), any liquid solvent or gas solvent carries components investigated in coloured components: investigated under UV light using ninhydrin Conducting a TLC analysis prep beaker with small amount of solvent on TLC plate, draw baseline in pencil place spot of reference compound on the left, then a spot of sample on right of baseline and air dry reserve allows identification of compounds in sample put TLC plate inside beaker with solvent - make sure pencil line above solvent, place lid to cover beaker as solvent reaches top, remove plate and draw another pencil line where solvent reached (solvent front) to use to calculate Rf Rf values The extent to which components are separated depends on solubility of each component in the mobile phase and interaction between each component and the stationary phase less polar components travel further up ⇒ larger Rf ⇒ more soluble in mobile phase more polar components do not travel far up ⇒ more attracted to polar stationary phase Gas / Liquid chromatography Analysing bases, volatile liquids, solids in vapour form Stationary phase nonpolar, non-volatile liquid applied to the inner walls of a capillary column mobile phase unreactive carrier gas noble, or inert diatomic e.g. He, N2, Ar Retention time: time taken for sample molecule to travel through the column from time inserted to time detected often recorded on chromatogram each peak = a volatile compound in the analysis sample. each peak has its own rt rt compared with data book values to identify unknown molecules longer rt: nonpolar components, attractiveness to nonpolar liquid in stationary phase shorter rt: polar components, interact with carrier gas Relative concentration of each component = area under each peak Area under peak = ½ base x height peaks roughly take shape of Δ % composition of a particular molecule in a mixture Carbon-13 NMR spectroscopy carbon-13 NMR : analytical tool used to analyse samples and determine the structure of substances Each Carbon environment gives a peak solvent used to dissolve samples for 13C-NMR : CDCl3 (solvent peak around 70 ppm) all 13C-NMR spectra measured relative to TMS / tetramethylsilane ( 0 ppm) predict the number of carbon environments refers to a specific c atom and the combination of atoms, bonds, fn groups attached each unique c environment produces a peak in 13C - NMR if there is a line of symmetry through the molecule, they belong to same environment and product a single peak e.g. predict no. peaks in 13C-NMR spectrum of 1,3-dihydroxybenzene 4 environments = 4 peaks predict each carbon’s chemical shift this is the frequency of an atomic nucleus relative to TMS reference compound measured in ppm example- 13C-NMR spectrum for propanone both CH3 groups are in same environment 2 environments = 2 peaks C=O peak over 200 C-H peaks 0-50 Proton (1H) NMR spectroscopy Technique used to determine structure of molecules paired with other techniques like Mass spec Magnetic field strengths of protons in organic compounds measured and recorded on H NMR spectrum all samples measured against reference compound TMS / Tetramethylsilane single sharp peak at 0 ppm Sample peaks plotted as a ‘shift’ away from this reference peak gives rise to ‘chemical shift’ values for protons on the sample compound (measured in ppm) Features of NMR spectrum intensity of peak against chemical shift area under peak: no. protons in particular environment height: intensity / absorption from protons Molecular / chemical environments diff. arrangements of H atoms have diff environments (identical / symmetry = same environment) no. environments = no. diff chemical shifts / peaks e.g. How many different 1H chemical environments occur in 2-methylpropane? 2 1H chemical environments 2 peaks on 1H NMR spectrum Chemical shift values for H molecular environments symmetrical H = same environment 1 ppm → Alkane 2 ppm → Next to C=O 7 ppm → Benzene ring 9–10 ppm → Aldehyde 10–12 ppm → Carboxylic acid Low resolution 1H NMR peaks on a low resolution NMR spectrum refer to the molecular environments of an organic compound High resolution 1H NMR number of peaks a signal splits into = n + 1 n = number of H on adjacent C atom n+1 splitting patterns Common pairs of splitting patterns TMS and deuterated solvents TMS gives sharp peak at 0 on NMR spectrum why is TMS an ideal reference chemical? it is inert and volatile it reduces undesirable chemical reactions with compound analyses it mixes well with most organic compounds Deuterated solvents in 1H NMR CDCl3 used as a solvent, no peak why is a solvent needed for samples in 1H NMR? dissolving samples in solvent help separate molecules and prevent them from interacting what must the solvent do? be a good solvent for organic molecules not contain any H atoms, does not interfere with NMR signals examples of non-deuterated solvents Carbon tetrachloride, CCl4: This solvent does not contain hydrogen, so it does not produce 1H NMR signals. It is suitable for 1H NMR but does not dissolve all molecules well. examples of deuterated solvents Deuterated solvents are often used in 1H NMR because deuterium (²H) is an isotope of H whose nuclei absorb in a different region from protons, so it gives no signal in a ¹H NMR spectrum Deuterochloroform / Chloroform-d, CDCl3: preferred, contains deuterium (2H) instead of H, does not interfere with the H NMR Deuterium oxide / Heavy water, D2O: deuterium atoms exchange reversibly with the H in the -OH and -NH, signals identified in NMR Identifying -OH and -NH signals Protons in -OH (hydroxyl) and -NH (amine) groups give singlet peaks in ¹H NMR but these signals can be tricky: peaks are broad or sometimes fall outside normal chemical shift ranges H in these groups exchanges quickly with protons from water or acids, so only one peak appears Their chemical shift ranges may overlap with other types of protons To identify these groups more clearly, proton exchange with deuterium oxide (D2O) is used: The deuterium atoms in D2O exchange reversibly with the protons in the -OH or -NH groups -OH + D2O ⇌ -OD + HOD -NH-CO- + D2O ⇌ -ND-CO- + HOD Since deuterium does not absorb in the same region as protons in the NMR spectrum, the signal for -OH or -NH disappears after D2O is added This confirms the presence of -OH or -NH groups in the molecule If peak disappears after D2O, it is due to the exchange of a proton from an -OH or -NH group

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Chapter 3. Ethics and Social Responsibility iStock.com/Shaun Learning Outcomes After studying this chapter, you will be able to . . . 3-1 Explain the determinants of a civil society 3-2 Explain the concept of ethical behavior 3-3 Describe ethical behavior in business 3-4 Discuss corporate social responsibility 3-5 Describe the arguments for and against social responsibility 3-6 Explain cause-related marketing 3-1. Determinants of a Civil Society 3-1 Explain the determinants of a civil society Have you ever stopped to think about the social glue that binds society together? That is, what factors keep people and organizations from running amok and doing harm, and what factors create order in a society like ours? The answer lies in social control, defined as any means used to maintain behavioral norms and regulate conflict. Behavioral norms are standards of proper or acceptable behavior. Social control is part of your life at every level, from your family to your local community, to the nation, to the global civilization. Several modes of social control are important to marketing: Ethics: Ethics are the moral principles or values that generally govern the conduct of an individual or a group. Ethical rules and guidelines, along with customs and traditions, provide principles of right action. Laws: Often, ethical rules and guidelines are codified into law. Laws governments create are then enforced by governmental authority. This process is how the dictum “Thou shall not steal” has become part of formal law throughout the land. Law, however, is not a perfect mechanism for ensuring good corporate and employee behavior. Laws often address only the lowest common denominator of socially acceptable behavior. In other words, just because something is legal does not mean that it is ethical. For example, Texas Pete is a hot sauce sold in grocery stores across the country. The packaging for Texas Pete features a lone star, just as the Texas state flag does, and a cowboy holding a lasso. The packaging, along with the name of the product, seems to indicate that the product is made in the state of Texas, or that it is at least made from ingredients sourced in Texas. Texas Pete, however, is produced by TW Garner Foods Company, a company headquartered in North Carolina, more than 800 miles from Texas. A class action lawsuit was filed against the company for false advertising. The lawsuit claimed that consumers were paying a premium price based on their belief that the product originated in Texas, which has a reputation for spicy food. Texas Pete does not explicitly state that the product is manufactured in Texas and actually lists TW Garner Foods’ North Carolina address on the bottle, but the name of the product and the packaging certainly suggest that it is a genuine Texas-based product and could be misleading to consumers. While this presentation is technically legal, is this ethical? What’s your opinion? Here’s another example: In every state, littering is a problem—and has been for many years. Threats of fines and even jail time are shrugged off as people toss food wrappers, plastic straws and cups, and everything else imaginable out the car window. Many companies are implementing new policies to try and curtail the negative effects of littering. For example, Starbucks in California no longer automatically gives straws and plastic cutlery to customers, but, rather, will only provide these items when customers specifically request them. Nicole Glass Photography/Shutterstock.com Formal and Informal Groups: Businesses, professional organizations (such as the American Marketing Association and the American Medical Association), and clubs (such as Shriners and Ducks Unlimited) all have codes of conduct. These codes prescribe acceptable and desired behaviors for their members. Self-Regulation: Self-regulation involves the voluntary acceptance of standards established by nongovernmental entities, such as the American Association of Advertising Agencies (AAAA) or the National Association of Manufacturers. The AAAA has a self-regulation arm that deals with deceptive advertising. Other associations have regulations relating to child labor, environmental issues, conservation, and a host of other issues. The Media: In an open, democratic society, the media play a key role in informing the public about the actions of individuals and organizations—both good and bad. Laundress, a luxury laundry detergent brand that claims to be better for you and better for the environment, came under fire after issuing a safety notice for almost all of its products. The company released the notice on its social media accounts but provided very little information about the reason for the notice. It was later revealed that the majority of the products the brand manufactured between January 2021 and September 2022 contained heightened levels of bacteria that were causing severe skin rashes and other physical ailments. Many major media outlets, including The New York Times and USA Today, published articles to inform the public of this safety notice and the product recall that eventually followed. An Active Civil Society: An informed and engaged society can help mold individual and corporate ethics, as well as socially responsible behavior. Research reveals that 56 percent of U.S. consumers stop buying from companies they believe are unethical. In the United Kingdom, 53 percent of consumers reported that they would completely stop buying from a brand accused of sourcing from unethical suppliers. manufactured between January 2021 and September 2022 contained heightened levels of bacteria that were causing severe skin rashes and other physical ailments. Many major media outlets, including The New York Times and USA Today, published articles to inform the public of this safety notice and the product recall that eventually followed. An Active Civil Society: An informed and engaged society can help mold individual and corporate ethics, as well as socially responsible behavior. Research reveals that 56 percent of U.S. consumers stop buying from companies they believe are unethical. In the United Kingdom, 53 percent of consumers reported that they would completely stop buying from a brand accused of sourcing from unethical suppliers. 3-2a. Ethical Theories People usually base their individual choice of ethical theory on their life experiences. The following are some of the ethical theories that apply to marketing. Deontology The deontological theory states that people should adhere to their obligations and duties when analyzing an ethical dilemma. This theory means that a person will follow their obligations to another individual or society because upholding one’s duty is considered ethically correct. For instance, a deontologist will always keep their promises to a friend and follow the law. A person who follows this theory will produce very consistent decisions because those decisions will be based on the individual’s set duties. Deontological theory is not necessarily concerned with the welfare of others. For example, suppose a salesperson has decided that it is their ethical duty (and very practical) to always be on time for meetings with clients. Today they are running late. How are they supposed to drive? Is the deontologist supposed to speed, breaking the law to uphold their duty to society, or is the deontologist supposed to arrive at their meeting late, breaking their duty to be on time? This scenario of conflicting obligations does not lead us to a clear, ethically correct resolution, nor does it protect the welfare of others from the deontologist’s decision. Utilitarianism The utilitarian ethical theory is founded on the ability to predict the consequences of an action. To a utilitarian, the choice that yields the greatest benefit to the most people is the ethically correct choice. One benefit of this ethical theory is that the utilitarian can compare similar predicted solutions and use a point system to determine which choice is more beneficial for more people. This point system provides a logical and rational argument for each decision and allows a person to use it on a case-by-case basis. There are two types of utilitarianism: act utilitarianism and rule utilitarianism. Act utilitarianism adheres exactly to the definition of utilitarianism as just described. In act utilitarianism, a person performs the acts that benefit the most people, regardless of personal feelings or societal constraints like laws. Rule utilitarianism, however, considers the law and is concerned with fairness. A rule utilitarian seeks to benefit the most people but through the fairest and most just means available. Therefore, added benefits of rule utilitarianism are that it values justice and doing good at the same time. As is true of all ethical theories, however, both act and rule utilitarianism contain numerous flaws. Inherent in both are the flaws associated with predicting the future. Although people can use their life experiences to attempt to predict outcomes, no human being can be certain that their predictions will come true. This uncertainty can lead to unexpected results, making the utilitarian look unethical as time passes because their choice did not benefit the most people, as they had predicted. Another assumption a utilitarian must make is that they can compare the various types of consequences against each other on a similar scale. However, comparing material gains such as money against intangible gains such as happiness is impossible because their qualities differ so greatly. Casuist The casuist ethical theory compares a current ethical dilemma with examples of similar ethical dilemmas and their outcomes. This theory allows one to determine the severity of the situation and to create the best possible solution according to others’ experiences. Usually, one will find examples that represent the extremes of the situation so that a compromise can be reached to include the wisdom gained from the previous situations. One drawback to this ethical theory is that there may not be a set of similar examples for a given ethical dilemma. Perhaps that which is controversial and ethically questionable is new and unexpected. Along the same line of thinking, this theory assumes that the results of the current ethical dilemma will be similar to the results in the examples. This assumption may not be true and would greatly hinder the effectiveness of applying this ethical theory. Moral Relativism Moral relativism is a belief in time-and-place ethics, that is, the truth of a moral judgment is relative to the judging person or group. According to a moral relativist, for example, stealing is not always wrong—if you are a parent and your child is starving, stealing a loaf of bread is ethically correct. The proper resolution to ethical dilemmas is based on weighing the competing factors at the moment and then deciding to take the lesser of the evils as the resolution. Moral relativists do not believe in absolute rules. Their beliefs center on the pressure of the moment and whether the pressure justifies the action taken. Virtue Ethics Aristotle and Plato taught that solving ethical dilemmas requires training—that individuals solve ethical dilemmas when they develop and nurture a set of virtues. A virtue is a character trait valued as being good. Aristotle taught the importance of cultivating virtue in his students and then having them solve ethical dilemmas using those virtues once they had become an integral part of his students’ being through their virtue training. Some modern philosophers have embraced this notion of virtue and have developed lists of what constitutes a virtuous businessperson. Some common virtues for businesspeople are self-discipline, friendliness, caring, courage, compassion, trust, responsibility, honesty, determination, enthusiasm, and humility. You may see other lists of virtues that are longer or shorter, but here is a good start for core business virtues. 3-3. Ethical Behavior in Business 3-3 Describe ethical behavior in business Depending on which, if any, ethical theory a businessperson has accepted and uses in their daily conduct, the action they take may vary. For example, faced with bribing a foreign official to get a critically needed contract or shutting down a factory and laying off a thousand workers, a person following a deontology strategy would not pay the bribe. Why? A deontologist always follows the law. However, a moral relativist would probably pay the bribe. While the boundaries of what is legal and what is not are often fairly clear (e.g., do not run a red light, do not steal money from a bank, and do not kill anyone), the boundaries of ethical decision making are predicated on which ethical theory one is following. The law typically relies on juries to determine if an act is legal or illegal. Society determines whether an action is ethical or unethical. In 2022, Oracle, an information technology company, was forced to pay $23 million to settle charges of violating the Foreign Corrupt Practices Act (FCPA). The U.S. Department of Justice and the Securities and Exchange Commission (SEC) allege that subsidiaries of the company in India, Turkey, and the United Arab Emirates used discount schemes and sham marketing reimbursements to finance funds that were then used to bribe foreign officials. Michael Egbert, corporate communications VP for Oracle, stated that “The conduct outlined by the SEC is contrary to our core values and clear policies, and if we identify such behavior, we will take appropriate action.” Morals are the rules people develop as a result of cultural values and norms. Culture is a socializing force that dictates what is right and wrong. Moral standards may also reflect the laws and regulations that affect social and economic behavior. Thus, morals can be considered a foundation of ethical behavior. Morals are usually characterized as good or bad. “Good” and “bad” have many different connotations. One such connotation is “effective” and “ineffective.” A good salesperson makes or exceeds the assigned quota. If the salesperson sells a new computer system or an OLED TV to a disadvantaged consumer—knowing full well that the person cannot keep up the monthly payments—is that still a good salesperson? What if the sale enables the salesperson to exceed their quota? “Good” and “bad” can also refer to “conforming” and “deviant” behaviors. A doctor who runs large ads offering discounts on open-heart surgery would be considered bad, or unprofessional, because they are not conforming to the norms of the medical profession. “Good” and “bad” also express the distinction between law-abiding and criminal behavior. And, finally, different religions define “good” and “bad” in markedly different ways. A Muslim who eats pork are considered bad by other Muslims, for example. Religion is just one of the many factors that affect a businessperson’s ethics. Academic researchers have examined how consumers react to the trade-offs between highly competent but less moral service providers and less competent but highly moral service providers. Their study found that consumers valued competence more than morality. In other words, purchasers of services want someone who can do the job right . . . even if that person might be a bit shady. For example, a house-painting company that does excellent work but has had some legal problems in the past would be preferred over a mediocre painting company that has never had complaints or legal problems. 3-3a. Morality and Business Ethics Today’s business ethics consist of a subset of major life values learned since birth. The values businesspeople use to make decisions have been acquired through family, educational, and religious institutions. Ethical values are situation specific and time oriented. Everyone must have an ethical base that applies to conduct in the business world and personal life. One approach to developing a personal set of ethics is to examine the consequences of a particular act. Who is helped or hurt? How long do the consequences last? What actions produce the greatest good for the greatest number of people? A second approach stresses the importance of rules. Rules come in the form of customs, laws, professional standards, and common sense. “Always treat others as you would like to be treated” is an example of a rule. 3-3a. Morality and Business Ethics Today’s business ethics consist of a subset of major life values learned since birth. The values businesspeople use to make decisions have been acquired through family, educational, and religious institutions. Ethical values are situation specific and time oriented. Everyone must have an ethical base that applies to conduct in the business world and personal life. One approach to developing a personal set of ethics is to examine the consequences of a particular act. Who is helped or hurt? How long do the consequences last? What actions produce the greatest good for the greatest number of people? A second approach stresses the importance of rules. Rules come in the form of customs, laws, professional standards, and common sense. “Always treat others as you would like to be treated” is an example of a rule. 3-3c. Ethical Guidelines and Training In recent years, many organizations have become more interested in ethical issues. Yet interest and action are not always the same thing. Although some companies are now appointing a Chief Ethics Officer (sometimes called a Chief Compliance Officer), this role is still not present at many companies. It is very common, however, for companies of various sizes to develop a code of ethics as a guideline to help marketing managers and other employees make better decisions. Creating ethics guidelines has several advantages as follows: A code of ethics helps employees identify what their firm recognizes as acceptable business practices. A code of ethics can be an effective internal control of behavior, which is more desirable than external controls, such as government regulation. A written code helps employees avoid confusion when determining whether their decisions are ethical. The process of formulating the code of ethics facilitates discussion among employees about what is right and wrong and ultimately leads to better decisions. Ethics training is an effective way to help employees put good ethics into practice. The Ethics & Compliance Initiative’s State of Ethics and Compliance in the Workplace Report found that 84 percent of employees who work for a company with a strong ethics and compliance program perceived their organization as having a strong ethical culture. Comparatively, only 13 percent of employees working for an organization classified as having an underdeveloped ethics and compliance program felt that their organization had a strong ethical culture. Strong ethical cultures give employees the appropriate guidance to handle situations involving potential wrongdoing and lead to lower rates of misconduct. Still, simply giving employees a long list of dos and don’ts does not really help employees navigate the gray areas or adapt to a changing world market. In Carson City, Nevada, all governmental lobbyists are required to attend a course on ethics and policy before they can meet with lawmakers. The training outlines exactly how and when lobbyists are allowed to interact with lawmakers and how to report any money they spend. A clear understanding of ethical expectations is essential to an industry like lobbying, where illicit—often illegal—actions are taken to promote individual causes. Because artificial intelligence (AI) is becoming so pervasive in marketing interactions with consumers, it must also be taught about ethical decision making. Already Microsoft, Adobe, and IBM, along with smaller firms and start-ups, are developing ethical guidelines and best practices for their AI use. Type “gymnast” into Google’s image search and the vast majority of the top results are female, as are the results for “nurse.” The term “parents” shows almost exclusively heterosexual couples. The results of these searches are driven by AI, which isn’t explicitly taught to discriminate. Rather, these prejudices are the result of the data submitted to the AI algorithm. “There is increasing concern that algorithms used by modern AI systems produce discriminatory outputs, presumably because they are trained on data in which societal biases are embedded,” notes Madalina Vlasceanu, an Assistant Professor of Psychology at New York University, whose research explores biases in internet search algorithms and the potential impact of these biased search results on society. The Most Ethical Companies Each year, Ethisphere magazine (targeted toward top management and focused on ethical leadership) examines more than 5,000 companies in 30 separate industries, seeking the world’s most ethical companies. It then lists the top 100. The magazine uses a rigorous format to identify true ethical leadership. A few of the selected winners are shown in Table 3.1. Table 3.1 Selected Winners of the World’s Most Ethical Companies Company Industry Country 3M Industrial manufacturing USA Accenture Consulting Services Ireland Aflac Accident and life insurance USA Apple Technology USA Colgate-Palmolive Consumer products USA Dell Technology USA EDP Energy and utilities Portugal General Motors Company Automotive USA Illy Food, beverages, and agriculture Italy Kao Health and beauty Japan L’Oreal Health and beauty France Mastercard Payment Services USA Natura Health and beauty Brazil Parsons Engineering and design USA Salesforce Application software USA U.S. Bank Banks USA Workday Software & Services USA Source: “The 2022 World’s Most Ethical Companies Honorees List,” https://worldsmostethicalcompanies.com/honorees/ (accessed January 30, 2023).

know these transformations or get shoved in a locker

🦠 MICROBIOLOGY — WEEK 1 STUDY NOTES Microbiology Foundations Assigned reading: 1.1 What Our Ancestors Knew 1.2 A Systematic Approach 1.3 Types of Microorganisms 3.1 Spontaneous Generation 3.2 Foundations of Modern Cell Theor/y 1.1 What Our Ancestors Knew First: What is microbiology? Microbiology = the study of very small organisms and infectious agents. Microorganism / microbe = an organism that is generally too small to see without a microscope. Examples include: * Bacteria * Archaea * Fungi such as yeast and molds * Protozoa * Microscopic algae * Some parasites Viruses are also studied in microbiology, although viruses are acellular, meaning they are not made of cells. Important idea Microbes are NOT automatically bad. Many microbes are harmless or helpful. They: * help produce food * live naturally in and on our bodies * help ecosystems function * can be used to make medicines and other products Only some microbes cause disease. 🍞 Humans Used Microbes Before They Knew Microbes Existed Humans were using microorganisms for thousands of years before microscopes existed. One of the biggest examples is: Fermentation Fermentation = microorganisms change sugars/carbohydrates into substances such as: * alcohol * gases * organic acids Microbes involved can include: bacteria + yeast + molds Humans used fermentation to make: * bread * cheese * yogurt * beer * wine * pickled vegetables Easy example Yeast eats/metabolizes carbohydrates in bread dough. ↓ Yeast produces carbon dioxide (CO₂). ↓ Gas becomes trapped in the dough. ↓ Bread rises. Remember Fermentation = microbes changing sugars. ⸻ 🧊 Ötzi the Iceman Ötzi was a preserved human mummy approximately 5,300 years old. Scientists found evidence that he had: * Trichuris trichiura → a parasitic worm * Borrelia burgdorferi → bacterium that causes Lyme disease He also carried a fungus called Fomitopsis betulinus, which has laxative and antibiotic properties. Why does this matter? It shows that ancient people were trying to treat disease long before they understood microorganisms. ⸻ 🦠 Early Ideas About Disease Before microscopes, people didn’t know exactly what caused disease. Some cultures believed disease came from: * supernatural forces * angry gods * fate * bad air But some people began to realize that disease might spread between people. ⸻ Quarantine Ancient societies sometimes separated sick people from healthy people. This is called: Quarantine = separating potentially infected people to prevent disease spread. Even though they didn’t know what bacteria or viruses were, they understood that some diseases could spread. ⸻ 🚿 Sanitation Ancient civilizations also developed ways to improve sanitation. Examples included: * clean-water systems * drainage systems * sewers * aqueducts This was important because removing human waste and providing cleaner water can reduce disease transmission. ⸻ Important People From Early Medicine Hippocrates Who? Greek physician. Important idea: Disease had natural causes, rather than always being caused by supernatural forces. He is commonly called: “Father of Western Medicine.” Remember Hippocrates → disease has natural causes. ⸻ Thucydides Thucydides survived the Athenian plague. He noticed that people who survived the disease usually did not become sick from the same disease again while caring for infected people. This was an early observation of: Immunity Immunity = the body’s ability to resist a particular infection/disease. Remember Thucydides → early idea of immunity. ⸻ Marcus Terentius Varro Varro proposed that extremely tiny creatures that could not be seen might cause disease. He described tiny creatures entering the body through the: * mouth * nose This was an important idea because microscopes did not yet exist. Remember Varro → invisible tiny creatures may cause disease. ⸻ Ibn Sina / Avicenna Ibn Sina wrote the important medical work: Canon of Medicine He described ideas involving: * contagion * spread of disease * transmission through breath * isolation of sick people His work contributed to ideas that later became important for quarantine and infectious-disease control. ⸻ 🔬 Birth of Microbiology The development of the microscope completely changed science. For the first time, scientists could actually see microorganisms. ⸻ Antonie van Leeuwenhoek Extremely important name. In 1675, Antonie van Leeuwenhoek used powerful simple microscopes to observe tiny organisms. He called them: “animalcules” Today we know that some of the organisms he observed were: * bacteria * protists Remember Leeuwenhoek → first to describe bacteria/microorganisms seen through a microscope. Think: Leeuwenhoek = LOOKED at microbes. ⸻ ⭐ Golden Age of Microbiology Approximately: 1857–1914 During this period, scientists made major discoveries connecting microorganisms with: * fermentation * disease * medicine * infection Two huge names: Louis Pasteur and Robert Koch You are going to see both names repeatedly in microbiology. ⸻ Louis Pasteur Pasteur showed that microorganisms are responsible for fermentation. He also developed: Pasteurization Pasteurization = using controlled heat to kill/reduce microorganisms that cause spoilage or disease. He also worked on vaccines, including a vaccine against: rabies Pasteur will become especially important again in Section 3.1. Remember Pasteur → fermentation → pasteurization → vaccines → helped prove germ theory → disproved spontaneous generation ⸻ Robert Koch Koch showed that particular microbes could cause particular diseases. He identified microorganisms associated with diseases including: * anthrax * tuberculosis * cholera Remember Koch → specific microbe → specific disease. ⸻ 🧪 Basic Microbiology Laboratory Tools You don’t need to master these yet, but recognize the terms. Microscope → magnifies microbes. Stains/dyes → add color/contrast so microorganisms are easier to see. Growth media → nutrients/material used to grow microorganisms in the laboratory. Petri dish → shallow dish commonly used to hold growth media. Test tube → can contain liquid or solid/semi-solid growth media. Bunsen burner → flame that can be used during laboratory sterilization procedures. These will make much more sense once you start doing microbiology lab work. ⸻ 1.2 A Systematic Approach Now we move from discovering microbes to: “How do scientists organize and name all these different organisms?” ⸻ Taxonomy Definition Taxonomy = classification, description, identification, and naming of living organisms. Think: Taxonomy = biological organization system. ⸻ Carolus Linnaeus Linnaeus developed an important system for classifying organisms. The main levels used in classification include: Kingdom → Phylum → Class → Order → Family → Genus → Species A common memory trick: K P C O F G S King Philip Came Over For Good Soup You should know the order. ⸻ Species Species is the most specific/basic taxonomic level in this hierarchy. Example: Homo sapiens Homo = genus sapiens = species ⸻ Binomial Nomenclature Very important term. Binomial = two names. Every organism receives a scientific name consisting of: Genus + species Example: Homo sapiens Rules: Genus * first letter CAPITALIZED species * lowercase Both should normally be italicized when typed. Correct: Homo sapiens Not: Homo Sapiens ❌ homo sapiens ❌ Homo Sapiens ❌ ⸻ 🌳 Phylogeny Phylogeny = evolutionary relationship/history between organisms. Scientists can represent these relationships with a: Phylogenetic tree A phylogenetic tree shows how organisms are believed to be evolutionarily related. Organisms with a more recent common ancestor are considered more closely related. ⸻ Classification Changed Over Time Scientific classification did not stay the same. Linnaeus Originally divided nature into kingdoms including: * animals * plants * minerals The mineral kingdom was later abandoned. ⸻ Ernst Haeckel Added: Protista for many unicellular organisms. He later proposed Monera for organisms lacking nuclei. Remember: Haeckel → Protista ⸻ Robert Whittaker Developed a five-kingdom system: Animalia Plantae Fungi Protista Monera ⸻ 🧬 Carl Woese — VERY IMPORTANT Carl Woese used differences in: ribosomal RNA (rRNA) to study evolutionary relationships. His work helped establish the modern: THREE-DOMAIN SYSTEM 🟠 Bacteria 🟣 Archaea 🔵 Eukarya This is very important for your Week 1 material. Memorize: BAE Bacteria Archaea Eukarya ⸻ Bergey’s Manuals These are important references used in bacteriology. They help scientists: * classify bacteria * identify bacteria You probably don’t need every detail yet, but recognize the name: Bergey’s Manual ⸻ How Can Bacteria Be Identified? Scientists can identify microorganisms using things such as: Biochemical tests Look at chemical/metabolic characteristics. DNA/RNA analysis Examines genetic material. Serological tests Use reactions involving antibodies/antigens. ⸻ 1.3 Types of Microorganisms This section is VERY IMPORTANT. You need to understand the major groups. ⸻ 🌎 Three Domains of Life Again: 1. Bacteria 2. Archaea 3. Eukarya ⸻ Before We Continue: Two Big Cell Types You will hear these words constantly: PROKARYOTE vs EUKARYOTE Prokaryotic cells DO NOT have a membrane-bound nucleus. Bacteria = prokaryotic Archaea = prokaryotic Eukaryotic cells DO have a membrane-bound nucleus. Examples include: * animals * plants * fungi * protozoa * algae Super important: Prokaryote = NO nucleus Eukaryote = HAS nucleus ⸻ 🦠 BACTERIA Bacteria are: * unicellular * prokaryotic * found almost everywhere Some bacteria are helpful. Some bacteria can cause disease. Many bacteria have cell walls. You’ll learn much more about bacterial structures later. ⸻ 🌋 ARCHAEA Archaea are also: * unicellular * prokaryotic Like bacteria, they do not have a nucleus. BUT: Archaea ≠ Bacteria They differ in: * genetics * evolutionary history * metabolic pathways * cell membrane composition * cell wall composition Archaea occur in many environments. Important textbook point No archaea have been identified as human pathogens. Remember Bacteria + Archaea = Prokaryotes ⸻ 🔵 EUKARYA Eukaryotic microorganisms include: Algae Protozoa Fungi Helminths These have eukaryotic cells. ⸻ 🌿 ALGAE Algae can be: * unicellular * multicellular They are similar to plants in an important way: They perform photosynthesis. Photosynthesis = using light energy to make chemical energy/food. Remember: Algae → photosynthesis. ⸻ 🧫 PROTOZOA Protozoa are: * unicellular * eukaryotic * structurally more complex than bacteria Many are capable of movement. Remember Protozoa → single-celled eukaryotes, often motile. Motile = able to move. ⸻ 🍄 FUNGI Fungi studied in microbiology include: Yeasts Usually unicellular. Molds Usually grow as multicellular filament-like structures. Examples of fungi can be microscopic even though other fungi, such as mushrooms, are large. Remember Fungi → yeast + molds ⸻ 🪱 HELMINTHS Helminths = parasitic worms. You may think: “A worm isn’t microscopic. Why is it in microbiology?” Good question. Adult worms may be large enough to see. BUT their: * eggs * larvae can be microscopic. Therefore they are studied in microbiology. ⸻ 🦠 VIRUSES Viruses are different from cellular organisms. Viruses are ACELLULAR. Acellular = not made of cells. Viruses cannot reproduce independently. They require a: Host cell to reproduce. Remember Virus = acellular + requires host to reproduce ⸻ ⭐ Major Microorganism Comparison Group Cell type Nucleus? Important idea Bacteria Prokaryotic ❌ Some cause disease Archaea Prokaryotic ❌ Different from bacteria; no known human pathogens Fungi Eukaryotic ✅ Yeasts + molds Protozoa Eukaryotic ✅ Unicellular, often motile Algae Eukaryotic ✅ Photosynthesis Helminths Eukaryotic ✅ Parasitic worms Viruses Acellular No cell Need host to reproduce 🔥 This table is worth knowing very well. ⸻ 3.1 Spontaneous Generation This is mainly about one historical question: Where does life come from? People once believed: Spontaneous Generation Spontaneous generation = the belief that living organisms can arise from nonliving material. Examples people once believed: rotting meat → maggots mud → frogs old food → microorganisms Today we know this idea is incorrect. ⸻ Francesco Redi Redi tested whether maggots appeared spontaneously from meat. He compared meat that flies could reach with meat protected from flies. Result Maggots appeared when flies could access the meat. This suggested: Maggots came from flies — not directly from the meat. Remember Redi → meat + flies + maggots ⸻ John Needham Needham performed experiments with broth. He boiled broth and then observed microbial growth afterward. He interpreted this as evidence supporting: Spontaneous generation. Remember Needham → supported spontaneous generation. ⸻ Lazzaro Spallanzani Spallanzani disagreed. He boiled broth for longer and sealed the containers more carefully. The sealed broth did not show microbial growth. He argued that microbes came from contamination from the environment rather than being generated spontaneously. Remember Spallanzani → argued against spontaneous generation. ⸻ 🦢 Louis Pasteur’s Swan-Neck Flask Experiment This is VERY IMPORTANT. Pasteur used flasks with long curved necks. Why the curved neck? Air could enter the flask. BUT: Dust and microorganisms became trapped in the curved neck. So the broth remained uncontaminated. When microorganisms could reach the broth, microbial growth occurred. Conclusion Microorganisms did NOT spontaneously appear. They came from microorganisms already present in the environment. Pasteur helped establish the principle: “Life comes from life.” Exam memory Pasteur → swan-neck flask → disproved spontaneous generation. ⸻ 3.2 Foundations of Modern Cell Theory Now we move from: “Where do microbes come from?” to: “What is life made of?” Answer: CELLS ⸻ 🧬 Cell Theory The textbook describes the development of the idea that cells are the fundamental units of life. The central ideas are: 1. All living organisms are made of one or more cells. 2. The cell is the fundamental/basic unit of life. 3. Cells arise from pre-existing cells. Think: Life → cells → cells come from cells. ⸻ Robert Hooke In the 1660s, Robert Hooke examined cork with a microscope. He saw tiny compartments and called them: “cells” Remember Hooke → named/described cells. Don’t mix him up with Leeuwenhoek: Hooke → cells Leeuwenhoek → microorganisms ⸻ Matthias Schleiden Schleiden studied plants. He concluded that: Plants are made of cells. Remember: Schleiden → plants ⸻ Theodor Schwann Schwann studied animals. He concluded: Animals are made of cells. Remember: Schwann → animals ⸻ Robert Remak Remak provided evidence that cells form through the division of existing cells. ⸻ Rudolf Virchow Virchow strongly promoted the idea: Cells come from other cells. So: New cells do not spontaneously appear. ⸻ Easy Scientist Memory Hooke → saw/named cells Schleiden → plants Schwann → animals Remak/Virchow → cells come from existing cells ⸻ 🧬 Endosymbiotic Theory This sounds difficult, but the basic idea is simple. Endosymbiotic theory says: Mitochondria and chloroplasts were originally bacteria-like prokaryotic cells. A larger ancestral cell engulfed them. Instead of being destroyed, the cells developed a mutually beneficial relationship. Eventually, the engulfed bacteria evolved into: Mitochondria and Chloroplasts inside eukaryotic cells. ⸻ Evidence for Endosymbiotic Theory Mitochondria and chloroplasts have similarities to bacteria. They have: Their own DNA Their DNA resembles bacterial DNA. Their own ribosomes Their ribosomes resemble bacterial ribosomes. They reproduce through a process similar to binary fission Binary fission is a major way bacteria reproduce. Easy version Mitochondria and chloroplasts act strangely like bacteria because their ancestors were bacteria. ⸻ Lynn Margulis Lynn Margulis helped develop and promote the modern endosymbiotic theory. Remember Margulis → endosymbiotic theory ⸻ 🦠 Miasma Theory vs Germ Theory This distinction is very important. Miasma Theory Old idea: Disease comes from “bad air” associated with rotting material. Think: Bad smell → disease. This theory was eventually replaced. ⸻ Germ Theory Germ theory = many diseases are caused by microorganisms. Think: Microbe enters/infects body → disease Scientists whose work helped establish germ theory included: * Ignaz Semmelweis * John Snow * Louis Pasteur * Joseph Lister * Robert Koch ⸻ 🧼 Ignaz Semmelweis Semmelweis worked around childbirth. He noticed that patients treated by doctors and medical students had much higher rates of puerperal fever than patients cared for by midwives. Medical students often went from: autopsies → examining living patients without washing their hands. Semmelweis introduced handwashing with chlorinated lime solution. Result Maternal deaths fell dramatically. Remember Semmelweis → HANDWASHING ⸻ 💧 John Snow John Snow investigated cholera outbreaks in London. He connected cholera cases with: contaminated water. His work helped show that disease wasn’t simply coming from “bad air.” He is important in the history of: Epidemiology Epidemiology = study of disease patterns and spread in populations. Remember Snow → cholera + contaminated water + epidemiology ⸻ Joseph Lister Lister applied ideas about microorganisms to surgery. He promoted: * handwashing * cleanliness * sterilization * antiseptic techniques He used carbolic acid (phenol) to reduce infections during surgery. Result Surgical infections decreased. Remember Lister → antiseptic surgery ⸻ Robert Koch — Again Koch developed: Koch’s postulates These helped scientists determine whether a particular microorganism causes a particular disease. Basic idea: specific microorganism → specific disease You will learn Koch’s postulates in more detail later. ⸻ 🔥 WEEK 1 — PEOPLE YOU NEED TO KNOW Scientist/person Remember THIS Hippocrates Disease has natural causes Thucydides Early observation of immunity Varro Invisible creatures may cause disease Leeuwenhoek Observed microbes/bacteria Linnaeus Taxonomy + naming organisms Haeckel Added Protista Whittaker Five kingdoms Woese Three domains; used rRNA Redi Meat + flies + maggots Needham Supported spontaneous generation Spallanzani Evidence against spontaneous generation Pasteur Swan-neck flask; fermentation; germ theory Hooke Described/named cells Schleiden Plants are made of cells Schwann Animals are made of cells Remak/Virchow Cells come from cells Margulis Endosymbiotic theory Semmelweis Handwashing John Snow Cholera + contaminated water Lister Antiseptic surgery Koch Specific microbes cause specific diseases ⸻ 🚨 THE 15 THINGS I WOULD MEMORIZE FIRST Don’t try to memorize every paragraph tonight. Start here: 1. Microbiology = study of microorganisms. 2. Fermentation uses microbes to convert sugars into products such as alcohol, gases, or acids. 3. Leeuwenhoek observed microorganisms. 4. Pasteur and Koch were major scientists during the Golden Age of Microbiology. 5. Taxonomy = classification and naming of organisms. 6. Binomial nomenclature = Genus + species. 7. Three domains = Bacteria, Archaea, Eukarya. 8. Bacteria + Archaea = prokaryotes. 9. Prokaryote = no membrane-bound nucleus. 10. Eukaryote = has membrane-bound nucleus. 11. Virus = acellular and needs a host to reproduce. 12. Spontaneous generation = life arises from nonliving matter. 13. Pasteur’s swan-neck flask helped disprove spontaneous generation. 14. Cell theory = organisms are made of cells, cells are the basic unit of life, and cells come from existing cells. 15. Germ theory = microorganisms can cause disease. ⸻ 🧠 Super-Simple Week 1 Mental Map Think about the entire week’s reading as one story: PART 1 — Humans discover microbes People used microbes before knowing they existed. ↓ Leeuwenhoek sees them. ↓ Scientists begin studying them. ⸻ PART 2 — Scientists organize microbes Linnaeus → Taxonomy ↓ Woese → 3 domains ↓ Bacteria | Archaea | Eukarya ⸻ PART 3 — Scientists ask where life comes from People believed in spontaneous generation. ↓ Redi + Spallanzani question it. ↓ Pasteur disproves it. ↓ Life comes from existing life. ⸻ PART 4 — Scientists understand cells Hooke → cells ↓ Schleiden → plants Schwann → animals ↓ Remak/Virchow → cells come from cells ↓ Cell Theory ⸻ PART 5 — Scientists understand disease Old: Miasma = bad air causes disease ❌ ↓ New: Germ theory = microorganisms can cause disease ✅ ↓ Semmelweis → handwashing Snow → contaminated water Lister → antiseptic surgery Pasteur → microbes Koch → specific microbe causes specific disease