Microbiology Exam 2 Study Guide: Bacterial Genome, Microbial Interactions, PCR, Microbiome, and Epidemiology

Chapter 13 – Bacterial Genome

Griffith’s Experiments on Transformation

Griffith’s experiments demonstrated that bacteria could acquire new genetic traits through a process called transformation.

• Key Point: Griffith used Streptococcus pneumoniae strains: one virulent (smooth, S) and one non-virulent (rough, R).

• Key Point: When heat-killed S strain was mixed with live R strain, mice died and live S strain was recovered, showing genetic material transfer.

• Example: This experiment suggested that a "transforming principle" could transfer virulence.

Contributions of Avery, MacLeod, McCarty, Hershey, and Chase

These scientists confirmed that DNA is the genetic material.

• Avery, MacLeod, McCarty: Demonstrated that DNA, not protein or RNA, was responsible for transformation in bacteria.

• Hershey and Chase: Used T2 phage and radioactive labeling to show that DNA, not protein, enters bacteria during infection.

• Example: Their experiments with bacteriophages provided definitive evidence that DNA stores genetic information.

Vocabulary and Concepts

• Genome: The complete set of genetic material in an organism.

• Genotype: The genetic makeup of an organism.

• Phenotype: Observable traits resulting from genotype and environment.

• Life Cycle of Virulent T2 Phage (Lytic Cycle): Virus infects host, replicates, and lyses cell to release new phages.

• Chemical Components of DNA: DNA is composed of nucleotides: deoxyribose sugar, phosphate group, and nitrogenous base (adenine, thymine, cytosine, guanine).

• Nucleotide Assembly: Nucleotides are linked by phosphodiester bonds between the 5' phosphate and 3' hydroxyl groups.

• History of DNA Structure: Watson and Crick proposed the double helix model, using data from Rosalind Franklin’s X-ray diffraction and Chargaff’s rules.

• Six Main Features of DNA Double Helix:

  1. Two antiparallel strands

  2. Right-handed helix

  3. Complementary base pairing (A-T, C-G)

  4. Major and minor grooves

  5. Uniform diameter (~2 nm)

  6. Hydrogen bonds stabilize base pairs

• Protein Structure: Proteins are polymers of amino acids, folded into primary, secondary, tertiary, and quaternary structures.

Chapter 13 Part 2 – Gene Expression

Central Dogma

The central dogma describes the flow of genetic information: DNA → RNA → Protein.

• Key Point: DNA is transcribed into RNA, which is translated into protein.

• Equation: $\text{DNA} \xrightarrow{\text{Transcription}} \text{RNA} \xrightarrow{\text{Translation}} \text{Protein}$

Types of RNA

• mRNA (messenger RNA): Carries genetic code from DNA to ribosome.

• tRNA (transfer RNA): Brings amino acids to ribosome during translation.

• rRNA (ribosomal RNA): Structural and catalytic component of ribosomes.

Gene Definition

• Gene: A segment of DNA that encodes a functional product, usually a protein or RNA.

Transcription in Prokaryotes

Transcription is the synthesis of RNA from a DNA template.

• Initiation: RNA polymerase holoenzyme binds to promoter, aided by sigma factor.

• Elongation: RNA polymerase synthesizes RNA in 5' to 3' direction.

• Termination: RNA synthesis stops at terminator sequence.

• Bacterial RNA Polymerase Holoenzyme: Core enzyme (α, β, β', ω) plus sigma factor.

• Promoters and Sigma Factors: Promoters are DNA sequences recognized by sigma factors, which guide RNA polymerase to start transcription.

• Factor-Independent Termination: Forms a hairpin loop in RNA, causing dissociation.

• Rho-Dependent Termination: Rho protein binds RNA and causes release from DNA.

Translation in Prokaryotes

Translation is the process of synthesizing proteins from mRNA.

• Universal Genetic Code: Specifies amino acids for each codon; nearly universal across organisms.

• Wobble Hypothesis: Flexibility in third base of codon allows fewer tRNAs to recognize multiple codons.

• Initiation Complex Formation: Small ribosomal subunit binds mRNA, initiator tRNA (fMet in bacteria), and large subunit assembles.

• Bacterial Ribosome Structure: 70S ribosome (30S + 50S subunits).

• Initiator tRNA: fMet-tRNAfMet is used in bacteria.

• A, P, E Sites:

  • A site: Accepts incoming aminoacyl-tRNA.

  • P site: Holds tRNA with growing polypeptide chain.

  • E site: Exit site for discharged tRNA.

Chapter 27 – Microbial Interactions

Types of Microbial Interactions

Microbes interact in various ways, affecting each other's survival and function.

• Mutualism: Both partners benefit (e.g., Buchnera aphidicola and aphids).

• Cooperation: Both benefit, but association is not obligatory.

• Commensalism: One benefits, other is unaffected (e.g., skin bacteria).

• Predation: One organism kills and consumes another (e.g., Bdellovibrio).

• Parasitism: One benefits, other is harmed but not killed immediately (e.g., tapeworms).

• Amensalism: One is harmed, other is unaffected (e.g., antibiotic production).

• Competition: Both compete for resources, may be harmed.

Symbiotic Interactions

• Symbiosis: Close association between two organisms.

• Examples:

  • Coral Bleaching: Loss of symbiotic algae (zooxanthellae) from coral, disrupting mutualism.

  • Buchnera aphidicola Mutualism: Provides essential amino acids to aphids.

  • Protozoan-Termite Relationship: Protozoa digest cellulose for termites.

  • Marine Invertebrates and Zooxanthellae: Algae provide nutrients via photosynthesis.

  • Tube Worm Riftia pachyptila: Bacteria fix carbon for worm.

Distinguishing Interactions

• Commensalism vs. Amensalism:

  • Commensalism: Example: Staphylococcus epidermidis on skin.

  • Amensalism: Example: Penicillium mold produces antibiotics harming bacteria.

• Predation vs. Parasitism:

  • Predation: Example: Bdellovibrio consumes other bacteria.

  • Parasitism: Example: Tapeworm in human intestine.

The Polymerase Chain Reaction (PCR)

Background and Steps

PCR is a technique to amplify DNA, invented by Kary Mullis.

• Key Steps:

  1. Denaturation: DNA strands separated by heat.

  2. Annealing: Primers bind to target DNA.

  3. Extension: DNA polymerase synthesizes new DNA.

• Outcome: Exponential amplification of target DNA sequence.

• Verification: PCR products are checked by gel electrophoresis.

• Applications: Diagnostics, cloning, forensics, research.

Chapter 34 – Microbiome

Definitions

• Microbiome: The collection of all microbial genomes in a particular environment.

• Holobiont: Host plus its associated microbiota.

• Microbiota: The community of microorganisms living in a specific environment.

• OTS: Operational Taxonomic Units, used to classify microbes based on DNA sequence similarity.

Early Colonization and Diversity

• Influences on Early Colonization: Mode of birth, diet, environment, antibiotics.

• Microbiome Variation: Different body sites have distinct microbiota; driven by pH, oxygen, moisture, and host factors.

Gut Microbe Communication with CNS

• Routes:

  1. Neural (vagus nerve)

  2. Immune signaling

  3. Metabolic (microbial metabolites)

Metabolic Syndrome and Endotoxemia

• Metabolic Syndrome: Cluster of conditions (obesity, high blood pressure, insulin resistance) increasing disease risk.

• Metabolic Endotoxemia: Presence of endotoxins in blood, often linked to gut microbiota imbalance.

Probiotics

• Probiotic: Live microorganisms that confer health benefits when administered in adequate amounts.

Chapter 36 – Epidemiology

Definition and Importance

Epidemiology is the study of disease distribution and determinants in populations.

• Purpose: To control and prevent disease outbreaks.

Outbreak, Epidemic, Pandemic

• Outbreak: Sudden increase in cases in a localized area.

• Epidemic: Widespread occurrence of disease in a community.

• Pandemic: Epidemic that spreads across countries or continents.

Father of Modern Epidemiology

• John Snow: Traced cholera outbreak to contaminated water, pioneering epidemiological methods.

Disease Frequency and Statistical Measures

• Sporadic Disease: Occurs occasionally and irregularly (e.g., typhoid fever).

• Endemic Disease: Constantly present in a population (e.g., malaria in some regions).

• Hyperendemic Disease: Persistent, high levels of disease occurrence.

• Reservoir Host: Organism that harbors pathogen without symptoms.

• Disease Frequency: Measurement of how often disease occurs.

• Statistical Measures:

  • Prevalence Rate: Proportion of population with disease at a given time.

  • Morbidity Rate: Incidence of disease in a population.

  • Mortality Rate: Number of deaths due to disease.

• Equation for Prevalence Rate: $\text{Prevalence Rate} = \frac{\text{Number of cases}}{\text{Total population}} \times 100$

• Equation for Morbidity Rate: $\text{Morbidity Rate} = \frac{\text{Number of new cases}}{\text{Population at risk}} \times 100$

• Equation for Mortality Rate: $\text{Mortality Rate} = \frac{\text{Number of deaths}}{\text{Total population}} \times 100$

Smallpox Success Story

• Key Point: Smallpox eradicated through global vaccination campaigns.

Pathways of Infection

• Infectious Disease: Caused by pathogenic microorganisms.

• Communicable Disease: Can be transmitted from person to person.

• Types of Epidemics:

  • Common Source Epidemic: Arises from a single source (e.g., contaminated water).

  • Propagated Epidemic: Spread from person to person.

Herd Immunity, Antigenic Drift, Antigenic Shift

• Herd Immunity: Resistance to disease spread in a population due to high immunity levels.

• Antigenic Drift: Gradual changes in viral antigens due to mutations.

• Antigenic Shift: Sudden, major changes in viral antigens, often leading to pandemics.

Emerging and Reemerging Infectious Diseases

• Reasons for Increase: Global travel, urbanization, antibiotic resistance, environmental changes.

Vaccines

• Types:

  • Live attenuated: Weakened pathogens.

  • Inactivated: Killed pathogens.

  • Subunit: Purified antigens.

  • Toxoid: Inactivated toxins.