Biology Exam 1 Study Notes

Meeting 1: An Introduction to Biology

Resources

A Chemistry primer (Bialecki slides)
A review of the atom (Bialecki lecture video)
Themes of Biology (Bialecki slides)
Themes of Biology 1 (Bialecki lecture video)
Themes of Biology 2 (Bialecki lecture video)

A Chemistry Primer

Table Completion and Questions:

Atom	Atomic #	Mass #	# of Protons	# of Neutrons	# of Electrons	Net charge
A	8	16	8	8	10	-2
B	8	18	8	10	8	0

Are these two atoms from the same or different elements?
- They are from the same element.
- Reason: They have the same atomic number, which is determined by the number of protons.
What term would you use to define the relationship between these two atoms?
- These are isotopes.
- Reason: They are atoms of the same element (same number of protons) but have different numbers of neutrons, resulting in different mass numbers.
What special term could you apply to atom A?
- Atom A is an ion, specifically an anion.
- Reason: It has a net charge of -2, meaning it has gained electrons and is thus an ion with a negative charge.
What is the valence number atom B?
- The valence number for atom B is 6.
- Reason: Atom B has 8 protons and 8 electrons. Its electron configuration would be 2 (inner shell) and 6 (outer/valence shell). The valence number indicates the number of electrons in the outermost shell.
Which atom is more electronegative, atom B or a carbon atom?
- Atom A is referred to in the transcript, not B: The outer shell would have a fuller shell, which would be Atom A, since the outer shell would have max 8 and the inner shell is max 2.
- Clarification: The question asks to compare atom B (which is neutral Oxygen with 8 valence electrons, so 6 in its outer shell) with a carbon atom (which has 4 valence electrons). Oxygen is significantly more electronegative than Carbon because its outer shell is closer to being full (needs 2 more electrons for a total of 8, while Carbon needs 4 more).

Themes of Biology

Is all variation heritable? Give an example of human variation that is not heritable.
- Not all variation is heritable.
- Definition of Variation: Any way two people differ from each other.
- Variations can be heritable (obtained from parents and passed down) or non-heritable (acquired during an individual's lifetime and not passed to offspring).
- Non-heritable variations can be random and could look different for different individuals.
- Example of non-heritable human variation: A scar from an injury or a specific haircut (not passed onto offspring).
Describe the concept of "Structure determines function" as it applies to proteins.
- The concept "Structure determines function" is fundamental in biology, especially for proteins.
- Core Idea: The specific three-dimensional shape (structure) of a protein dictates its biological role (function).
- Examples:
  - Hemoglobin: Its specific globular structure allows it to bind and transport oxygen.
  - Melanocortin 1 Receptor: Its specific membrane-bound structure allows it to bind a signaling molecule, influencing pigmentation.
  - Insulin: Its precise structure enables it to act as a hormone, signaling cells to take up glucose.
  - Enzymes: These are proteins with highly specific active sites. The unique shape of an enzyme's active site creates a pocket that only fits a particular type of molecule (its substrate), ensuring precise catalytic function.
What might knowing the structure of the active site of an enzyme allow you to predict?
- Knowing the structure of an enzyme's active site allows one to predict its function.
- Reason: The active site's shape is complementary to its specific substrate(s). Understanding this shape can reveal what molecules the enzyme will bind to and what type of reaction it will catalyze.
Read about how structure determines function in the normal and disease versions of the HBB protein involved in hemoglobin.
- Normal HBB Protein (involved in hemoglobin): The normal structure of the HBB protein leads to the correct folding of hemoglobin. This allows hemoglobin to efficiently carry oxygen throughout the body by binding it reversibly.
- Disease Version of HBB Protein (involved in hemoglobin): In diseases like sickle cell anemia, a single amino acid change in the HBB protein alters its structure. This altered structure causes hemoglobin molecules to aggregate into stiff rods under low oxygen conditions, distorting red blood cells into a sickle shape. This new, abnormal structure impairs their ability to carry oxygen and causes them to block blood vessels, leading to disease symptoms.
Examine the figure above. The structure of a protein is dependent on its sequence of amino acids. What determines the amino acid sequence of a protein?
- The sequence of amino acids within a protein determines how it folds into its specific three-dimensional structure.
- This protein structure, in turn, determines the protein's function.
- The amino acid sequence of a protein is determined by the expression of genetic information, specifically by genes in our DNA.
- Process (as depicted in the figure):
  - A crystallin gene (a section of DNA) contains the information.
  - Transcription: The DNA sequence is used to make (transcribe) a specific mRNA molecule.
  - Translation: The information in the mRNA nucleotide sequence is translated to make a chain of linked amino acids.
  - Protein Folding: This chain of amino acids then folds into the specific shape of the crystallin protein.
  - The correctly folded crystallin proteins can then pack together transparently, allowing the eye's lens to focus light.
What does it mean when one says that the genetic code is universal?
- The genetic code is universal means that the same set of correspondences between codons (sequences of three mRNA nucleotides) and amino acids is shared among nearly all organisms on Earth.
- Example:
  - The RNA sequence that codes for phenyl alanine amino acid is the same across all organisms.
  - The codon AAC will always encode for the asparagine amino acid in virtually every organism.
Briefly describe transcription.
- Transcription is the process where a cell uses the information in the sequence of DNA nucleotides to synthesize (transcribe) a specific RNA molecule, known as messenger RNA (mRNA).
Briefly describe translation.
- Translation is the process where the cell takes the information contained in the sequence of mRNA nucleotides and uses it to synthesize a protein, which is a series of linked amino acids.
Describe how mutations can cause new traits.
- Mutations are random changes in DNA sequences.
- While some mutations have no effect, those that do can alter the flow of genetic information:
  1. Change in DNA sequence (mutation).
  2. This change can affect the transcript (mRNA).
  3. The altered mRNA can lead to a change during translation.
  4. This results in a change in the amino acid sequence of the protein.
  5. The altered amino acid sequence can cause the protein to fold differently, leading to a change in its shape.
  6. A change in protein shape often results in a new function or a modified function for the protein.
  7. If this new protein function leads to a noticeable characteristic, it manifests as a new heritable trait.
Describe the three components of evolution.
- Evolution, as described by Darwin, involves three key components:
  1. Random Heritable Variations:
    - These originate from mutations, which are random changes in DNA sequences.
    - A mutation can lead to a change in the amino acid sequence of a protein, which in turn changes the protein's structure and potentially its function.
    - These altered proteins can generate new heritable traits. The expression of genetic information (DNA) determines the sequence of amino acids in a protein and its structure.
  2. Natural Selection:
    - This is a non-random process, determined by the environment.
    - Principles:
      - Organisms produce more offspring than can survive in a given environment.
      - Offspring within a population compete for limited resources (e.g., food, land, water).
      - Not all offspring will survive to reproduce.
      - Individuals with advantageous heritable variations (traits that make them better suited to their environment) are more likely to survive and produce more offspring.
      - Over generations, the proportion of individuals with these advantageous traits increases in the population.
    - Example: If black mice are more easily seen by predatory birds than brown mice in a particular environment, the brown mice (with advantageous camouflage) will survive more often and produce more offspring. Consequently, the population will shift to have more and more brown mice over time.
  3. Time:
    - Evolution is a process that requires immense spans of time.
    - The Earth's history (3.8 billion years since the origin of life) has provided ample time for the incredible diversity of life we see today to arise and for significant evolutionary changes to occur, including those in humans.
Which of the components in the previous question is random?
- The random heritable variations (resulting from mutations) are the random component of evolution.
At what point in the hierarchy of biological organization does life emerge?
- Life emerges at the level of molecules.
- When the right types of molecules (proteins, carbohydrates, lipids, nucleic acids) are organized in specific ways, the organized group of molecules exhibits properties that define life, which are greater than the sum of their individual parts.
What is the cause of emergent properties?
- The cause of emergent properties is organization.
- When individual parts are arranged and interact in a specific, complex way, new and novel characteristics (emergent properties) arise that were not present in the isolated parts themselves.
Does the energy from the sun cycle or flow? Explain.
- The energy from the sun flows, it does not cycle.
- Explanation:
  - The sun is the ultimate source of energy for most life on Earth.
  - This solar energy is used by producers (e.g., plants) to create organic molecules through photosynthesis.
  - This energy stored in organic molecules is then transferred through food webs.
  - Organisms use this energy to perform cellular work, often by converting it into ATP.
  - During these conversions and metabolic activities, a significant portion of the energy is lost as heat energy into the environment.
  - This heat energy cannot be recaptured and reused by organisms in the same way, meaning the energy flow is unidirectional (from sun to Earth and ultimately out as heat), rather than a continuous cycle.
Most examples of feedback inhibition rely on inhibiting the first enzyme of a multi-enzyme pathway. Why?
- Scenario: Consider a metabolic pathway where reactant A is converted to B, then C, and finally to product D (A
  ightarrow B
  ightarrow C
  ightarrow D).
- Each step is catalyzed by a specific enzyme (e.g., Enzyme 1 for A
  ightarrow B).
- Negative Feedback Inhibition: Product D (which has useful functions in the cell) binds to and inhibits Enzyme 1 (the first enzyme in the pathway).
- Reason for inhibiting the first enzyme:
  - Efficiency: If the cell has enough of product D and it inhibits the first enzyme, it effectively shuts down the entire pathway at the earliest possible step.
  - Resource Conservation: This prevents the unnecessary expenditure of energy and resources on producing intermediates (B, C) that would eventually lead to an oversupply of D.
  - Avoid Intermediate Accumulation: If an enzyme later in the pathway (e.g., Enzyme 3 for C
    ightarrow D) were inhibited, intermediates B and C would still be produced and accumulate unnecessarily within the cell (assuming the organism doesn't use these intermediates for other important processes).
- Mechanism: As the concentration of D increases beyond the cell's need, more D molecules bind to Enzyme 1, inactivating it and thereby shutting down further production of D.

Meeting 2: Chemical Bonding, Water, pH, and Buffers

Resources

Bialecki Lecture Videos and Slides
- Chemical bonding, properties of water, buffers, and pH slides
- Weak interaction slides
- Chemical bonding
- Weak interactions
- Properties of water
- pH and buffers
Polar and Nonpolar Covalent bonds: Video

What is electronegativity and what determines how electronegative an atom will be?
- Electronegativity: It is the measure of an atom's affinity (attraction) for electrons in a chemical bond.
- What determines electronegativity:
  - Atoms with nearly full outer (valence) shells (e.g., halogens, oxygen, nitrogen) are highly electronegative because they strongly attract electrons to complete their octet.
  - Atoms with nearly empty outer (valence) shells (e.g., alkali metals) have lower electronegativity because they tend to lose electrons rather than gain them.
  - Electronegativity generally increases across a period (left to right) and decreases down a group (top to bottom) in the periodic table.
What’s the difference between a covalent bond and an ionic bond?
- Covalent Bond:
  - Formed by the sharing of electrons between two atoms.
  - Typically occurs between two nonmetals (e.g., H_2O).
  - Generally results in molecules with lower boiling points.
  - Do not conduct electricity well in water (as they don't dissociate into free ions).
- Ionic Bond:
  - Formed by the transfer of electrons from one atom to another.
  - Typically occurs between a metal and a nonmetal (e.g., NaCl).
  - Involves the attraction between oppositely charged ions.
  - Generally results in compounds with higher boiling points.
  - Conduct electricity when dissolved in water (as they dissociate into free ions).
What is the difference between an ion and a molecule with a partial charge like water?
- Ion:
  - Has either a full positive (cation) or negative (anion) charge.
  - This full charge results from the gain or loss of one or more whole electrons.
  - Examples: Na^+ (lost an electron), Cl^- (gained an electron).
- Molecule with a partial charge (like water):
  - Has regions with unequal distribution of electrons due to differences in electronegativity between the atoms in the covalent bond.
  - No full electrons are gained or lost; instead, electrons are unevenly shared.
  - These partial charges are denoted by delta (\delta), such as \delta^- (slightly negative) and \delta^+ (slightly positive).
  - Example: In H_2O, oxygen is more electronegative, so it pulls electrons closer, becoming \delta^-, while hydrogen atoms become \delta^+. The molecule as a whole is neutral.
Are hydrocarbons polar? Explain.
- No, hydrocarbons are nonpolar.
- Explanation: Hydrocarbons are composed solely of carbon (C) and hydrogen (H) atoms. The electronegativity difference between carbon and hydrogen is very small, meaning the electrons in C-H bonds are shared almost equally. This even distribution of electrons, combined with the often symmetrical structure of hydrocarbons, results in no significant partial positive or negative charges across the molecule. Therefore, hydrocarbons are nonpolar.
Why are ionic bonds weaker in an aqueous solution?
- Ionic bonds are weaker in an aqueous solution due to water's polarity and its ability to form hydration shells.
- Explanation: When an ionic compound (like NaCl) is placed in water, the polar water molecules surround the individual ions.
  - The partially negative oxygen atoms (\delta^-) of water molecules are attracted to and surround the positive ions (Na^+).
  - The partially positive hydrogen atoms (\delta^+) of water molecules are attracted to and surround the negative ions (Cl^-).
- These attractions between water molecules and ions overcome the strong electrostatic attraction between the positive and negative ions of the ionic compound. The water molecules effectively pull the ions apart, weakening the ionic bond and causing the compound to dissolve.

Compare methanol (left) to methane (right) and answer the following questions.

Methanol: CH_3OH
Methane: CH_4

Which molecule contains covalent bonds?
- Both methanol and methane contain covalent bonds.
- Reason: Covalent bonds are present in all the C-H, C-O, and O-H linkages within both molecules.
Which molecule contains ionic bonds?
- None of these molecules contain ionic bonds.
- Reason: Ionic bonds typically form between metals and nonmetals, and both methanol and methane are composed entirely of nonmetal atoms (Carbon, Hydrogen, Oxygen).
Which molecule contains at least one polar covalent bond?
- Methanol contains at least one polar covalent bond.
- Reason: The O-H bond and the C-O bond in methanol are polar due to the significant electronegativity difference between oxygen and hydrogen, and between oxygen and carbon.
Explain how you figured this out using the concept of electronegativity.
- Explanation: Covalent bonds involve the sharing of electrons. A bond is considered polar if there's an unequal sharing of electrons due to a difference in electronegativity between the bonded atoms. Oxygen is significantly more electronegative than both carbon and hydrogen. Therefore:
  - In methanol, the oxygen atom pulls electrons more strongly in both the C-O and O-H bonds, creating partial negative charges on oxygen and partial positive charges on the carbon and hydrogen atoms bonded to it.
  - In methane, the electronegativity difference between carbon and hydrogen is very small, leading to essentially nonpolar C-H bonds.
Which molecule has atoms that have partial negative and positive charges? On what atoms do these partial charges reside?
- Methanol has atoms with partial negative and positive charges.
- In methanol (CH_3OH):
  - The oxygen (O) atom has a partial negative charge (\delta^-) because it is more electronegative and pulls electrons from both the carbon and the hydrogen it is bonded to.
  - The hydrogen (H) atom bonded to the oxygen has a partial positive charge (\delta^+).
  - The carbon (C) atom bonded to oxygen also has a partial positive charge (\delta^+).
Are either of the molecules considered an ion? If so, which one?
- No, neither methanol nor methane are considered ions.
- Reason: An ion has a full positive or negative charge due to the gain or loss of electrons. While methanol has partial charges, it does not have a net positive or negative charge and has not gained or lost electrons.
If two atoms have very different electronegativities, what kind of bond would they most likely form, ionic or covalent?
- If two atoms have very different electronegativities, they would most likely form an ionic bond.
- Explanation: A large difference in electronegativity means one atom has a much stronger pull on electrons than the other. This typically leads to a complete transfer of electrons from the less electronegative atom to the more electronegative one, resulting in the formation of oppositely charged ions that attract each other to form an ionic bond. (As noted in the transcript, ionic bonds are often between a metal and a nonmetal because these typically have large electronegativity differences.)
Can the hydrogen attached to the carbon in methanol (left) form a hydrogen bond with the carbon in methane? Explain.
- No, the hydrogen attached to carbon in methanol cannot form a hydrogen bond with the carbon in methane.
- Explanation: For a hydrogen bond to form, the hydrogen atom must be covalently bonded to a highly electronegative atom (like Oxygen, Nitrogen, or Fluorine). Hydrogens bonded to carbon are not sufficiently positive (due to the small electronegativity difference between C and H) to participate in hydrogen bonding. Additionally, carbon atoms typically don't act as hydrogen bond acceptors because they lack the necessary lone pair of electrons and sufficient electronegativity.
Can the hydrogen attached to the oxygen in methanol form a hydrogen bond with the carbon in methane? Explain.
- Yes, the hydrogen attached to the oxygen in methanol can form a hydrogen bond.
- Explanation: In methanol, the O-H bond is highly polar due to oxygen's high electronegativity. This makes the hydrogen atom bonded to oxygen very partially positive (\delta^+), allowing it to act as a hydrogen bond donor. It could form a hydrogen bond with a suitably electronegative atom that has a lone pair of electrons (e.g., oxygen or nitrogen in another molecule). However, the question asks about forming a hydrogen bond with the carbon in methane. Carbon is typically not an acceptor for hydrogen bonds. It's more likely this question implies forming a bond with another methanol or water molecule, rather than with methane itself.
- Re-evaluation: The question is specifically asking if the H on methanol's O can form an H-bond with the carbon in methane. The answer is No. A hydrogen bond requires a partially positive hydrogen (bonded to O, N, or F) and a partially negative atom with a lone pair (O, N, or F). Carbon, even if it had a partial negative charge in some context, does not typically serve as a hydrogen bond acceptor because it is not sufficiently electronegative and its lone pairs are not readily accessible for this type of interaction. The previous thought about it acting as a donor is correct, but it must interact with an appropriate acceptor.
Can the hydroxyl group (-OH) in methanol form hydrogen bonds with water? Explain.
- Yes, the hydroxyl group (-OH) in methanol can form hydrogen bonds with water.
- Explanation: The hydroxyl group contains both a hydrogen atom bonded to a highly electronegative oxygen (making it a hydrogen bond donor) and an oxygen atom with lone pairs (making it a hydrogen bond acceptor). Water molecules also possess these properties. Therefore, methanol can readily form multiple hydrogen bonds with water, contributing to its solubility.
Which of the two molecules, methanol (left) or methane (right) is more soluble in water? Explain.
- Methanol is more soluble in water.
- Explanation: Methanol has a polar hydroxyl (-OH) group. This group allows methanol to form hydrogen bonds with water molecules (as explained in Q15). The ability to form hydrogen bonds with water makes a molecule hydrophilic (water-loving) and therefore more soluble in water. Methane, being a nonpolar hydrocarbon, cannot form hydrogen bonds with water and is thus hydrophobic (water-fearing) and largely insoluble in water.

The Properties of Water: Video

Describe the components of a hydrogen bond.
- To form a hydrogen bond, two main components are required:
  1. A partially positive hydrogen atom (\delta^+) that is covalently bonded to a highly electronegative atom. This highly electronegative atom is typically Oxygen (O), Nitrogen (N), or Fluorine (F). The electronegative atom pulls electrons away from hydrogen, leaving the hydrogen atom with a partial positive charge, making it capable of attracting another electronegative atom.
  2. A partially negative highly electronegative atom (\delta^-) with a lone pair of electrons. This atom is also typically Oxygen (O), Nitrogen (N), or Fluorine (F). This partially negative atom is attracted to the partially positive hydrogen atom from another molecule or different part of the same molecule.
Can hydrocarbons be involved in hydrogen bonds? Explain.
- No, hydrocarbons cannot be involved in hydrogen bonds.
- Explanation:
  - Hydrocarbons consist only of carbon (C) and hydrogen (H).
  - The electronegativity difference between carbon and hydrogen is very small, so C-H bonds are essentially nonpolar.
  - This means hydrogen atoms in hydrocarbons do not develop a significant partial positive charge (\delta^+) required to act as a hydrogen bond donor.
  - Furthermore, carbon atoms do not have the necessary high electronegativity or readily available lone pairs of electrons to act as hydrogen bond acceptors.
  - Consequently, hydrocarbons are nonpolar and hydrophobic, unable to participate in hydrogen bonding.
Must water be one of the molecules involved in a hydrogen bond? Explain.
- No, water does not necessarily have to be one of the molecules involved in a hydrogen bond.
- Explanation: Any molecule that contains a hydrogen atom covalently bonded to a highly electronegative atom (O, N, F) can act as a hydrogen bond donor. Similarly, any molecule containing a highly electronegative atom (O, N, F) with a lone pair of electrons can act as a hydrogen bond acceptor. While water is an excellent example and forms extensive hydrogen bonds, other molecules like ammonia (NH3), hydrogen fluoride (HF), alcohols (ROH), and amines (RNH2) can also form hydrogen bonds with themselves or with each other, without water necessarily being present.
What aspect of water’s structure is responsible for the molecule’s emergent properties?
- The polarity of the water molecule and its resulting ability to form extensive hydrogen bonds are responsible for its emergent properties.
- Explanation: Water's bent shape and the significant electronegativity of oxygen create a permanent dipole (partial positive H's and partial negative O). This allows each water molecule to form up to four hydrogen bonds with other water molecules, leading to cohesion, adhesion, high specific heat, high heat of vaporization, and its role as a universal solvent.
On a summer day, Newport beach is always cooler than Santa Ana. Why?
- Newport Beach is cooler than Santa Ana on a summer day due to water's high specific heat.
- Explanation:
  - Water has a high specific heat capacity, meaning it can absorb and release a large amount of heat energy with only a small change in its own temperature.
  - The large body of water at Newport Beach (the Pacific Ocean) absorbs a considerable amount of solar energy during the day without dramatically increasing its temperature.
  - It also releases heat slowly at night.
  - This moderating effect of the ocean keeps coastal areas like Newport Beach cooler than inland areas like Santa Ana, which are heated much more rapidly by the sun and lack a large body of water to absorb and regulate temperature.
Define solute, solvent, and solution. How is a solution different from a suspension?
- Solute: The substance that is being dissolved in a solvent.
- Solvent: The substance that does the dissolving of the solute.
- Solution: A homogeneous mixture formed when a solute is completely dissolved in a solvent.
- Difference between a Solution and a Suspension:
  - Solution: In a solution, the solute particles are very small, completely dissolved, and evenly distributed, making the mixture appear clear and homogeneous. The particles will not settle out over time.
  - Suspension: In a suspension, the particles of the dispersed substance are larger and typically insoluble. They remain suspended for a while but will eventually settle out over time (e.g., sand in water). Suspensions are heterogeneous mixtures.
Why is water such a good solvent?
- Water is an excellent solvent (often called the "universal solvent") primarily because of its polarity and its ability to form hydration shells.
- Explanation:
  - Being a polar molecule, water has partially positive hydrogen atoms and a partially negative oxygen atom.
  - This allows water to dissolve ionic compounds (like NaCl) by orienting its partially negative oxygen towards positive ions and its partially positive hydrogens towards negative ions. It surrounds these ions, pulling them away from each other and preventing them from re-associating.
  - Water also dissolves many polar molecules (like sugars, alcohols) by forming hydrogen bonds with their polar functional groups.
What property must molecules have in order to be dissolved by water?
- Molecules must be polar or ionic in nature to be dissolved by water.
- Explanation: Water, being a polar solvent, dissolves