Clinical Microbiology and Toxicology Lecture Notes

Announcements and Reminders

• First test is next Thursday.
• One exam approximately every three weeks.
• SI sessions with Olivia:
  • Wednesdays from 1 to 2 PM.
  • Room to be determined; check for class email.
• In-person labs next week: Attendance is mandatory.
  • Half credit deduction for non-attendance.
  • Lab material will cover exam content.
• Tutoring is available in addition to SI sessions.

Assignments Due

• Week one and two assignments due tomorrow at 5:00 PM.
• Submit assignments with enough time.

Extra Credit Opportunity

• Practice test is posted at the top of the page.
• Due tomorrow at 5:00 PM.
• Ensure device compatibility with testing software.
• Reduce stress for next Thursday's exam.
• Only 26 students have completed the practice test.
• If webcam is broken, schedule the exam with testing services for next Thursday at 9 AM.

Exam Resources

• Practice worksheet:
  • Multiple choice, true/false questions.
  • Suggested activities to practice exam material.
  • Work on independently as exam prep.
  • Olivia will use it during SI sessions.
  • In-class review sessions.
• Review Handout: Bring handout to review session.
  • The handout will be used as a PowerPoint, for filling in notes, drawings, and multiple-choice scenarios.

Exam Guidelines

• Exam is remote but is a real test; treat it as an in-person exam.
• No supplemental materials:
  • No notes or outside resources are allowed.
  • No additional course materials or help from others.
  • Remote proctoring software will restrict access to other websites.
• No hats, hoodies, earbuds, or phones.
• No talking, background TV, or music (will flag the exam).
• Remote proctoring records video and audio of the entire testing period.
• The software uses algorithms to detect suspicious activity, including eye movements.
• Remain seated and avoid excessive movements.

Exam Proctoring Details

• The proctoring software is sensitive to sounds and movements.
• Keep head still during the environmental check.
• Unusual events (sneezing, family interruptions) will be reviewed for context.
• Questions about anatomy during the exam are acceptable and won't be flagged.
• Lock animals in another room, if possible.
• Be appropriately clothed.

Review of Chemical Bonds

• Covalent bonds are used to construct biological molecules.
• Ionic bonds are relatively weak.
• Hydrogen bonds maintain the shape of proteins and DNA.
• Van der Waals forces are weak and result from electron cloud fluctuations.

Water as a Solvent

• Water is a universal solvent in the body.
• Solutes are mixed in water-based solutions.
• Drugs are administered in water-based solutions.

Measuring Solute Concentration

• Solute concentration can be measured by weight or by the number of solute particles.
• Physiologically relevant measurement: number of solute particles.
• Molarity: Measures the number of molecules.
• Physiological effects depend on the number of molecules:
  • Amount of glucose in the blood or urine.
  • Effective drug dosage in bodies of variable sizes.

Molarity and Physiological Importance

• Physiological effects are based on the number of molecules in a solution, not the weight.
• Molarity: Physiological importance.
• Equivalent molarities mean the same number of particles.

Chemical Reactions in the Body

• Chemical reactions are written with reactants forming products.
• Some reactions are reversible.
• All chemical reactions in the body are collectively referred to as metabolism.

Metabolism: Catabolism and Anabolism

• Metabolism = Catabolic + Anabolic Reactions
• Catabolic Reactions:
  • Breaking down larger reactants into smaller products.
  • Breakdown reactions.
  • Energy-releasing (exergonic).
• Anabolic Reactions:
  • Building larger products from smaller reactants.
  • Making reactions.
  • Energy-consuming (endergonic).

Organic Molecules

• Four types of organic molecules:
  • Carbohydrates
  • Lipids
  • Proteins
  • Nucleotides and nucleic acids
• Carbs, lipids, and proteins will be the main focus.
• Nucleic acids will be addressed in a separate chapter.

Organic Molecule Overview

• Carbohydrates:
  • Examples: glucose, glycogen.
  • Function: Energy (usable and storage forms).
• Nucleic Acids:
  • Examples: DNA, RNA, ATP.
  • DNA: hereditary material and genetics.
  • RNA: protein synthesis.
  • ATP: energy.
• Proteins:
  • Building blocks: amino acids.
  • Functions: structural materials, support, storage, movement, defense, transport.
• Lipids:
  • Examples: saturated vs. unsaturated fats, triglycerides, phospholipids, steroids.
  • Saturated fats: unhealthy.
  • Unsaturated fats: healthy.
  • Phospholipids: cell membrane component.
  • Steroids: hormones (testosterone, estrogen), cholesterol.

Carbon Chemistry

• Carbon: can bind to four other atoms.
• Perfect linker molecule.
• Functional Groups:
  • Hydroxyls: sugars, lipids.
  • Methyl: lipids, many.
  • Carboxyl and amino: amino acids.
  • Phosphates: DNA and RNA.

Monomers and Polymers

• Repeating units: monomers.
• Monomers linked together: polymer.
• Polymerization: process of building polymers.
• Glycogen and starch: polymers built from glucose.
• Proteins: polymers of multiple amino acids.

Dehydration Synthesis

• Monomers linked by dehydration synthesis.
• Removal of water (H2O) to form a covalent linkage.
• Also called condensation reaction.
• Anabolic reaction.

Hydrolysis

• Breaking down polymers by adding water (H2O).
• Water is added to break the covalent linkage between the monomers.
• Catabolic reaction.

Carbohydrates: Sugars

• Hydrophilic.
• General formula: $Cn H{2n} O_n$ (2:1 ratio of hydrogen to oxygen).
• Suffix: "-ose" indicates a sugar.
• Glucose: six-carbon ring ($C6 H{12} O_6$).

Glucose, Disaccharides, and Function

• Glucose is the absorbable and usable form of sugar.
• Main function of carbohydrates: energy.

Storage of Glucose

• Excess glucose is stored as glycogen.
• Starch is the storage form in plants.
• Cellulose is fiber in plants.
• Glycogen is the storage form of glucose in animals and humans.

Glycogen Synthesis

• Excess glucose taken in via ingestion is helped by insulin to be moved into our cells, after which it is stored as glycogen.

Carbohydrate Functions

• Main function: energy (ATP production).

Lipids: Fats

• Hydrophobic.
• High hydrogen-to-oxygen ratio.
• Examples:
  • Fatty acids
  • Triglycerides.
  • Phospholipids
  • Steroids
  • Icosanoids.

Fatty Acids

• Linear chains of 4 to 24 carbons.
• Saturated fats (unhealthy): no vacancies for hydrogens; every carbon bond is occupied.
• Unsaturated fats (healthy): vacancies where hydrogens could be added; double covalent linkages between carbons.
• Unsaturated fats do not form plaques and are heart-healthy. Saturated fats are stickier and form plaques.

Alcohol structures.

• Alcohol structures typically have a hydroxyl group stuck on the end, but are much shorter than the fat structures.

Triglycerides: Fat Storage

• Glycerol + three fatty acid tails.
• Connected through the process of dehydration synthesis
• Function:
  • Energy storage.
  • Shock absorption.
  • Insulation.

Phospholipids Amphipathic Nature

• One fatty acid replaced by a phosphate head.
• Amphipathic: both hydrophilic and hydrophobic regions.
• Function:
  • Cell membrane structure.
  • Fatty acid tails: hydrophobic (water-loathing).
  • Phosphate group: hydrophilic (water-loving).

Steroids and Cholesterol

• Ring-based structure (four rings).
• Steroids (cortisol, progesterone, estrogen, testosterone) are derived from cholesterol.
• Cholesterol is a type of lipid.
• Cholesterol is produced by the liver and is a component of cell membranes.
• Hormones that are lipids are acting as hormones when they bind to the receptors that exist in the surface of our cells.

Proteins: Function and Structure

• Structure and transport.
• Catalyze chemical reactions (enzymes).
• Monomer: amino acids.

Amino Acids

• Central carbon bound to:
  • Hydrogen
  • Carboxyl group (-COOH)
  • Amino group (-NH2)
  • R group (radical group; varies among amino acids).

Peptide Bond Formation

• Carboxyl group of one amino acid connects to the amino group of another.
• Reaction: condensation or dehydration synthesis (anabolic reaction).

Protein Shape and Structure

• Shape (conformation) is critical.
• Shape is what is known as its conformation.
• Four levels of protein structure:
  • Primary
  • Secondary
  • Tertiary
  • Quaternary

Protein Denaturation

• Heat and changes in pH can denature (alter) protein shape.
• Maintaining regular temperature and optimal pH is critical for protein function.

Protein Functions

• Structure (hair, nail, muscle).
• Movement.
• Transport.
• Enzymes: catalyze chemical reactions.
• Enzymes, which are typically proteins, facilitate chemical reactions given contact with it's specific substrate.

Enzymes: Biological Catalysts

• Enzymes are proteins that catalyze specific chemical reactions.
• Enzymes reduce the energy needed to occur or increase the rate of it's reaction.
• Substrate binds to the enzyme's active site.

Nucleotides: Monomers of DNA and RNA

• Form genetic messages (DNA and RNA).
• Monomers:
  • Nitrogenous base
  • Sugar (ribose)
  • Phosphate group

Plasma Membrane or Cell Membrane

• Forms the outer barrier of the cell.
• Allows for materials to move in and out of the cell.
• Main structure is the phospholipid bilayer.
• All of the phosphate heads are facing out while all of the fatty acid tails are facing in.

Phospholipid Organization

• The orientation that has the parts of the structure that is hydrophilic in nature facings out, and the hydrophobic portions facing out to the inside.
• Based on the amphipathic nature of phospholipid molecules.
  • Hydrophilic head: faces out, interacts with extracellular and intracellular fluid.
  • Hydrophobic tails: face the interior.

Glycocalyx: Cell Surface Coating

• Surface sugars (carbohydrates) on the cell surface.
• Functions:
  • Protection.
  • Transplant compatibility.
  • Immune system recognition of healthy vs. foreign/cancerous cells.