Microbio exam 2 notes

Microbiology Chapter 4: DNA and RNA Process

Nucleotide Bonds

• Cytosine to Guanine has 3 hydrogen bonds.

• Thymine to Adenine has 2 hydrogen bonds.

DNA Transcription

1. Processes:

   • Initiation: DNA binds to promoter region.

   • Elongation: RNA polymerase adds nucleotides to the growing RNA strand.

   • Termination: Polyadenylation (addition of a poly-A tail) occurs and released by poly(A) polymerase.

2. Role of Polymerases:

   • DNA polymerase unwinds the double-stranded DNA.

   • RNA polymerase synthesizes RNA in the 5’ to 3’ direction.

DNA Translation

1. Processes:

   • Initiation: mRNA binds to ribosome at acceptor, peptide, and exit sites.

   • Elongation: tRNA binds to the P site; a peptide bond forms between amino acids.

   • Termination: Stop codon (UAA, UAG, UGA) is recognized, leading to protein release to the Golgi apparatus.

DNA Supercoiling

• DNA Gyrase:

  • Creates double-stranded breaks, allowing unbroken helix to pass through.

  • Produces negative supercoils.

Replication Origin

1. Eubacteria: one replication origin (theta structure).

2. Eukaryotes: multiple origins of replication.

3. Steps in Replication:

   • DNA gyrase unwinds supercoils.

   • Helicase exposes DNA to polymerases.

   • Primase synthesizes a primer.

RNA Types in Eukaryotes

• Three types: mRNA, tRNA, rRNA.

• RNA polymerase requires a DNA template; initiates at promoter sequence.

Key Features of Transcription and Translation

• Codon Degeneracy:

  • Multiple codons can encode a single amino acid.

• Termination:

  • Intrinsic terminators (stem-loop followed by uracils).

  • Rho-dependent termination: Rho protein binds to RNA and displaces RNA polymerase.

Amino Acid Activation

1. Activation Steps:

   • Amino acid is attached to tRNA; requires ATP.

   • Aminoacyl tRNA synthetase catalyzes the reaction:

     1. Enzyme binds amino acid and ATP.

     2. ATP is hydrolyzed; amino acid binds to AMP.

     3. Forms aminoacyl-AMP; binds to tRNA to form charged tRNA.

2. Recognition:

   • Anticodon on tRNA pairs with codon on mRNA.

Chapter 5: Microbial Growth Phases

1. Growth Phases:

   • Lag phase → Exponential phase → Stationary phase → Death phase.

2. Counting Methods:

   • Spread Plate Method: Sample spread onto surface of agar.

   • Pour Plate Method: Sample mixed with sterile medium and incubated.

   • Dilution Series: Ex: 1 mL to 9 mL creates a series of dilutions.

Microbial Classification Based on Temperature and Salinity

• Psychrophiles: Optimal growth at 4°C (cold-loving).

• Mesophiles: Optimal growth at 39°C (E. coli).

• Thermophiles: Optimal growth at 60°C.

• Hyperthermophiles: Optimal growth at 88-106°C.

• Halotolerant: Can tolerate high salinity (e.g., Staphylococcus aureus).

• Halophiles: Thrives in high salt concentrations.

Oxygen Requirements

• Categories of Oxygen Utilization:

  • Facultative anaerobes: Can respire with or without oxygen.

  • Oxygen Intermediates: Toxic byproducts of oxygen respiration.

Chapter 7: Gene Expression and Regulation

Overview of Gene Expression

• The process of converting genetic information into functional proteins.

• Enzyme activity is regulated according to environmental conditions.

Types of Gene Regulation

1. Constitutive Genes: Constantly expressed; "always on".

2. Inducible Genes: Expression activated by specific signals.

Regulatory Mechanisms

1. Control of Enzyme Activity:

   • Negative Control: Involves repressors that inhibit transcription.

   • Induction: Repressor falls off operator, allowing transcription to occur (e.g., lac operon in E. coli).

   • Repression: Corepressor binds to repressor and promotes operator binding, stopping transcription.

2. Positive Control: Activator proteins promote transcription at DNA binding sites.

Specific Case: Lac Operon

• Involves both positive and negative controls:

  • Repression when glucose is present, induction when glucose is absent.

• Allolactose acts as the inducer, allowing transcription to proceed when bound to the repressor.

Two-Component Regulatory Systems and Quorum-Sensing

• Two-Component Systems: Involve signal transduction via phosphorylation.

  • Kinase activity and phosphatase function regulate transcription.

• Quorum-Sensing: Bacteria communicate based on population density, ensuring efficient resource use.