ch 9

Study Guide - Smart Notes

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Genetics of Bacteria and Archaea

Overview

This chapter explores the mechanisms of genetic variation and exchange in bacteria and archaea, focusing on mutation types, gene transfer processes, and microbial immunity. Emphasis is placed on bacterial genetics, with key terms and processes defined and compared.

Key Concepts and Vocabulary

Auxotroph: An organism that requires an additional nutrient not needed by the wild type, usually due to mutation.
Conjugation: Gene transfer between prokaryotic cells requiring direct cell-to-cell contact.
Frameshift Mutation: Insertion or deletion of nucleotides that alters the reading frame of mRNA, often resulting in a nonfunctional protein.
Genotype: The complete genetic makeup of an organism.
Hfr Cell: A bacterial cell with the F plasmid integrated into its chromosome, enabling high-frequency recombination.
Induced Mutation: Mutation caused by external agents (mutagens) such as chemicals or radiation.
Insertion Sequence (IS): The simplest transposable element, carrying only genes for transposition.
Missense Mutation: A point mutation resulting in a codon that codes for a different amino acid.
Mutagen: An agent that increases the mutation rate.
Mutant: An organism with a heritable change in its DNA sequence.
Mutation: A heritable change in the base sequence of an organism's genome.
Nonsense Mutation: A mutation that converts a codon for an amino acid into a stop codon.
Phenotype: Observable characteristics of an organism resulting from genotype and environment interaction.
Point Mutation: A mutation affecting a single base pair.
Recombination: Rearrangement of DNA fragments to create new genetic sequences.
Reversion: A genetic change that restores the original phenotype or genotype.
Rolling Circle Replication: A mechanism for replicating circular DNA, involving strand nicking and unrolling.
Silent Mutation: A DNA sequence change that does not affect the phenotype.
SOS Repair System: An error-prone DNA repair system activated by extensive DNA damage.
Spontaneous Mutation: Mutation occurring naturally without external mutagens.
Transduction: Transfer of bacterial genes by a virus (bacteriophage).
Transformation: Uptake of free DNA from the environment by bacteria.
Transition: Mutation where a purine replaces a purine or a pyrimidine replaces a pyrimidine.
Transposable Element: DNA sequence that can move within the genome.
Transposon: A transposable element carrying additional genes beyond those for transposition.
Transversion: Mutation where a purine is replaced by a pyrimidine or vice versa.
Wild-Type Strain: The standard or most common form of an organism found in nature.

Mutation and Mutants

Definition and Types

Mutation: A heritable change in the nucleotide sequence of DNA.
Selectable Mutation: Confers a trait that can be easily identified or selected for (e.g., antibiotic resistance).
Non-Selectable Mutation: Does not provide an obvious advantage or selectable trait in laboratory conditions.

Mutant vs. Wild Type

Mutant: Organism with a genetic change compared to the wild type.
Wild Type: The typical form found in nature or used as a reference.
Examples: Antibiotic-resistant bacteria, yeast unable to synthesize an amino acid, fruit flies with altered eye color.

Screening vs. Selection

Screening: Identifies mutants by examining many organisms for a trait; does not confer a growth advantage.
Selection: Only mutants with a specific trait survive under selective conditions, making isolation easier.

Auxotrophic Mutants

Definition: Organisms unable to synthesize a required nutrient due to mutation.
Screening: Grow on minimal medium lacking the nutrient; auxotrophs fail to grow.

Types of Mutations

Point Mutations

Missense Mutation: Alters one amino acid in a protein.
Nonsense Mutation: Converts an amino acid codon to a stop codon, truncating the protein.
Silent Mutation: Changes DNA sequence without altering the amino acid sequence.

Frameshift Mutations

Caused by insertions or deletions not in multiples of three nucleotides.
Shifts the reading frame, altering all downstream codons and often resulting in a nonfunctional protein.

Comparing Mutation Types

All three (missense, nonsense, silent) are point mutations but differ in their effects on protein structure and function.
Frameshift mutations generally have more severe consequences than missense mutations because they disrupt the entire downstream protein sequence.

Genotype and Phenotype

Genotype: The DNA sequence of an organism.
Phenotype: Observable traits resulting from genotype and environment.
Phenotype does not always change with genotype (e.g., silent mutations).
Phenotype can change without genotype change (e.g., environmental effects).

Mutagenesis and DNA Repair

Mutagens

Physical or chemical agents that increase mutation rates.
Mechanisms include base alteration, DNA intercalation, and strand breaks.

Ionizing vs. Non-Ionizing Radiation

Type	Mechanism	Effects
Ionizing (X-rays, gamma rays)	Removes electrons, creates ions	Breaks DNA strands, generates reactive oxygen species, causes large deletions/insertions
Non-Ionizing (UV light)	Forms abnormal bonds (thymine dimers)	Distorts DNA helix, blocks replication/transcription, leads to repair errors

SOS Repair System

Activated by extensive DNA damage in bacteria.
Uses error-prone DNA polymerases to bypass lesions, allowing survival but increasing mutation rate.
Regulated by RecA (promotes repair) and LexA (represses repair until damage is detected).

Genetic Exchange in Bacteria

Transformation

Uptake of free DNA from the environment by competent cells.
Steps: DNA release, uptake by recipient, recombination into genome.
Competence: The ability of a cell to take up DNA; can be natural or induced.

Transduction

Transfer of bacterial genes by bacteriophages.
Transducing Particle: Virus-like particle carrying bacterial DNA; cannot initiate new phage infections.
Infectious Bacteriophage: Contains only phage DNA; can infect and lyse bacteria.

Generalized vs. Specialized Transduction

Type	Genes Transferred	Mechanism
Generalized	Any part of the genome	Random DNA fragments packaged during lytic cycle
Specialized	Specific genes near phage integration site	Incorrect excision of lysogenic phage with adjacent bacterial genes

Conjugation

Direct transfer of DNA between bacteria via cell-to-cell contact.
Donor cell produces a sex pilus to attach to recipient, forming a mating bridge for DNA transfer.

Rolling Circle Replication in Conjugation

Donor nicks plasmid DNA and transfers one strand to recipient.
Both donor and recipient synthesize complementary strands, resulting in complete plasmids in both cells.

F+ vs. Hfr Conjugation

Feature	F+ Conjugation	Hfr Conjugation
F Plasmid Location	Free in cytoplasm	Integrated into chromosome
Genes Transferred	F plasmid only	Chromosomal genes (adjacent to F site)
Recipient Becomes F+	Yes	Rarely
Chromosomal Gene Transfer	Rare	Common

Mobile Genetic Elements

Insertion Sequences vs. Transposons

Both are mobile genetic elements with inverted repeats and transposase genes.
Both can cause mutations by inserting into new genomic locations.
Transposons carry additional genes (e.g., antibiotic resistance), while insertion sequences do not.

Microbial Immunity: CRISPR System

CRISPR as Adaptive Immunity

CRISPR allows bacteria and archaea to recognize and remember invading genetic elements (e.g., viruses).
Invader DNA is stored as spacers in the CRISPR array, providing a genetic memory.

CRISPR Process

Adaptation: Viral DNA is captured and inserted as a new spacer in the CRISPR region.
Expression: CRISPR region is transcribed and processed into crRNAs, each containing a spacer.
Interference: crRNA guides Cas proteins to matching viral DNA, which is then cleaved and destroyed.

Summary Table: Mechanisms of Genetic Exchange

Mechanism	Agent	DNA Source	Key Features
Transformation	None (free DNA)	Environment	Requires competence; direct uptake of DNA
Transduction (Generalized)	Bacteriophage	Random bacterial DNA	Any gene can be transferred
Transduction (Specialized)	Bacteriophage	Specific bacterial genes	Only genes near phage integration site transferred
Conjugation (F+)	Plasmid	Donor cell	Transfers F plasmid; recipient becomes F+
Conjugation (Hfr)	Integrated F plasmid	Donor chromosome	Transfers chromosomal genes; recipient rarely becomes F+

Additional info: This guide focuses on bacterial genetics, with less emphasis on archaea as per the study guide instructions. For further details on archaea, consult the main textbook chapter.