Microbiology Exam 1 Study Guide: Metabolism, Genetics, and Gene Transfer

Exam Information and Format

• Date/Location: October 14, Tuesday, 2 PM–3:15 PM (REM 112)

• Format:

  • ~40 multiple-choice and true/false questions (84%)

  • 4 short and specific answer questions (16%)

  • Emphasis on understanding major concepts from each class

• Preparation: Review homework, practice questions, lecture notes, and recommended textbook pages.

Lecture 7: Bioenergetics and Introduction to Metabolism

Fundamental Requirements for Cellular Life

• Water: Essential solvent and medium for biochemical reactions.

• Nutrients: Provide building blocks and energy sources.

• Free Energy: Required to drive cellular processes.

• Reducing Power: Electrons needed for biosynthetic reactions. (NADH)(NADPH)-electron donors

Free Energy in Cellular Life

• Free Energy (ΔG): The energy available to do work in a system.

• Types: Chemical, transport, and mechanical work.

• Cells use free energy to drive endergonic (energy-requiring) reactions.

Thermodynamics in Metabolism

• First Law: Energy cannot be created or destroyed, only transformed.

• Second Law: Entropy (disorder) increases in spontaneous processes.

• Cells couple exergonic and endergonic reactions to maintain order.

Change in Free Energy (ΔG°')

• ΔG°' is the standard free energy change under standard conditions.

• Negative ΔG°': Reaction is exergonic (releases energy, spontaneous).

• Positive ΔG°': Reaction is endergonic (requires energy input).

• Equation: $\Delta G = \Delta G^{\circ'} + RT \ln Q$

Equilibrium and Reaction Direction

• Equilibrium Constant (Keq): Ratio of product to reactant concentrations at equilibrium.

• ΔG can predict if a reaction will proceed forward or backward.

Major Types of Metabolism

• Catabolism: Breakdown of molecules to release energy.

• Anabolism: Synthesis of complex molecules from simpler ones.

• Cells balance catabolic and anabolic reactions for growth and maintenance.

ATP and Energy Conservation

• ATP (Adenosine Triphosphate): Universal energy currency of the cell.

• High-energy phosphate bonds store potential energy.

• Hydrolysis of ATP releases energy for cellular work.

ATP Synthesis Mechanisms

• Substrate-level phosphorylation: Direct transfer of phosphate to ADP during glycolysis and TCA cycle.

• Oxidative phosphorylation: ATP synthesis using energy from electron transport chain (ETC).

• Photophosphorylation: ATP synthesis using light energy (in phototrophs).

Redox Reactions and Electron Carriers

• Redox Reaction: Transfer of electrons from donor to acceptor.

• Reduction Potential (E0'): Tendency of a compound to accept electrons.

• Electron carriers (e.g., NAD+/NADH) shuttle electrons in metabolic pathways.

• Donor always has a lower reduction potential than the acceptor.

General Aspects of Metabolism

• Metabolic pathways are interconnected and regulated.

• Energy flow and electron transfer are central to metabolism.

Lecture 8: Microbial Metabolism 1

Metabolic Classes of Microorganisms

• Phototrophs: Use light as energy source.

• Chemotrophs: Use chemicals as energy source.

• Chemoorganotrophs: Use organic compounds.

• Chemolithotrophs: Use inorganic compounds.

Glycolysis (Embden–Meyerhof–Parnas Pathway)

• Substrate: Glucose (6 carbons).

• End Products: 2 pyruvate, 2 ATP (net), 2 NADH per glucose.

• Preparatory Phase: Consumes 2 ATP.

• Payoff Phase: Produces 4 ATP and 2 NADH.

• Fermentative microbes regenerate NAD+ for glycolysis.

Catabolic Fate of Pyruvate

• Pyruvate can enter TCA cycle (aerobic/anaerobic respiration) or fermentation (anaerobic conditions).

• Fermentation: Regenerates NAD+, produces organic acids/alcohols.

Citric Acid Cycle (TCA/Krebs Cycle)

• Entry: Acetyl-CoA combines with oxaloacetate to form citrate.

• Outputs per cycle: 2 CO2, 3 NADH, 1 FADH2, 1 GTP/ATP.

• Net effect: Complete oxidation of acetyl groups, generation of reducing power.

Electron Transport Chain (ETC)

• Located in bacterial cell membrane or mitochondrial inner membrane.

• Transfers electrons from NADH/FADH2 to O2 (or other acceptors), generating proton motive force (PMF).

• PMF drives ATP synthesis via ATP synthase.

Oxidative Phosphorylation

• ATP synthesis coupled to electron transport and PMF.

• O2 is the final electron acceptor in aerobic respiration; other acceptors used in anaerobic respiration.

Lecture 9: Microbial Metabolism 2

Fermentation vs. Respiration

• Fermentation: Anaerobic, organic molecules as electron acceptors, low ATP yield (2 ATP/glucose).

• Respiration: Aerobic/anaerobic, inorganic/organic electron acceptors, high ATP yield (up to 38 ATP/glucose in aerobic).

Autotrophy and Carbon Fixation

• Autotrophs: Use CO2 as carbon source.

• Calvin Cycle: Main pathway for CO2 fixation; three phases: carboxylation, reduction, regeneration.

• 6 CO2 + 18 ATP + 12 NADPH → 1 glucose (overall reaction).

Reverse/Reductive TCA Cycle

• Some bacteria use reverse TCA to fix CO2 and generate acetyl-CoA.

Pentose Phosphate Pathway

• Generates NADPH and pentoses for biosynthesis.

Nitrogen Metabolism

• Sources: Ammonia (NH3), nitrate (NO3-), atmospheric N2.

• Nitrogen fixation: Conversion of N2 to NH3 (requires nitrogenase, ATP, and reducing power).

• Assimilation: Incorporation of NH3 into amino acids (e.g., via glutamine synthetase).

Glyoxylate Cycle

• Bypasses decarboxylation steps of TCA cycle, allowing net synthesis of C4 dicarboxylic acids from acetyl-CoA.

Lecture 11: Microbial Genetics and Replication

Genetic Vocabulary

• DNA: Deoxyribonucleic acid, genetic material.

• RNA: Ribonucleic acid, involved in gene expression.

• Gene: DNA segment encoding a functional product.

• Nucleotides: Building blocks of nucleic acids (dNTPs for DNA, NTPs for RNA).

DNA Structure

• Pentose sugar: Deoxyribose in DNA, ribose in RNA.

• Phosphate group: Attached to 5' carbon.

• Nitrogenous base: Attached to 1' carbon (A, T, G, C for DNA; U replaces T in RNA).

• Phosphodiester bond: Links 5' phosphate to 3' OH of adjacent nucleotide.

Base Pairing

• G–C: 3 hydrogen bonds (higher melting point).

• A–T: 2 hydrogen bonds.

• High G–C content stabilizes DNA in thermophiles.

Double-Stranded DNA Structure

• Antiparallel strands, right-handed helix, major and minor grooves.

• Binding sites for proteins and enzymes.

Supercoiling and DNA Gyrase

• Supercoiling compacts DNA to fit inside the cell.

• DNA gyrase introduces negative supercoils (unique to prokaryotes).

Central Dogma and DNA Replication

• Central Dogma: DNA → RNA → Protein.

• Replication: Semiconservative, 5'→3' synthesis, requires DNA polymerase, primase, helicase, ligase.

• Leading strand: Continuous synthesis.

• Lagging strand: Discontinuous synthesis (Okazaki fragments).

• Primers removed and fragments joined by DNA ligase.

Polymerase Chain Reaction (PCR)

• Invented by Kary Mullis.

• Amplifies DNA using cycles of denaturation, annealing, and extension.

• Uses thermostable DNA polymerase (e.g., Taq polymerase).

Lecture 12: Horizontal Gene Transfer (HGT)

Mechanisms of HGT

• Transformation: Uptake of free DNA from environment.

• Transduction: DNA transfer via bacteriophages (viruses).

• Conjugation: Direct transfer of DNA between cells via pilus.

Mobile Genetic Elements (MGEs)

• Transposons, insertion sequences, plasmids, and integrons.

• Facilitate gene movement within and between genomes.

Significance of HGT

• Rapid genetic change and adaptation in bacteria.

• Spread of antibiotic resistance genes.

• Impacts evolution, biotechnology, and genetic engineering.

Bacteriophages

• Viruses that infect bacteria.

• Can mediate gene transfer (transduction).

Lecture 13: Bacterial Transcription and Translation

Transcription

• DNA is transcribed to mRNA by RNA polymerase.

• Promoter regions (-35 and -10) recognized by sigma factor.

• Termination: Rho-dependent or Rho-independent mechanisms.

• Monocistronic mRNA: Encodes one protein.

• Polycistronic mRNA: Encodes multiple proteins (operons).

Translation

• mRNA is translated into polypeptide by ribosomes.

• Genetic code: 64 codons (61 for amino acids, 3 stop codons).

• tRNA: Cloverleaf structure, anticodon pairs with mRNA codon, carries specific amino acid.

• Ribosome: 70S in prokaryotes (50S + 30S subunits).

• Initiation, elongation, and termination steps.

Protein Secretion Systems

• Sec and Tat systems: Transport proteins across membranes.

• Different systems for different types of proteins and destinations.

Additional info:

• Some content inferred and expanded for clarity and completeness based on standard microbiology curricula.