Microbial Genetics

Genetics and Genomes

Genetics is the study of inheritance and inheritable traits as expressed in an organism’s genetic material. The genome is the entire genetic complement of an organism, including its genes and nucleotide sequences.

Genome: All genetic material in a cell.

Gene: Segment of DNA coding for a functional product.

Nucleotide: Building block of nucleic acids, composed of a phosphate, pentose sugar, and nitrogenous base.

The Structure of Nucleic Acids

Nucleic acids are polymers of nucleotides. DNA and RNA differ in their nitrogenous bases and sugars. The length of DNA is expressed in base pairs.

DNA: Double-stranded, contains adenine (A), thymine (T), guanine (G), cytosine (C).

RNA: Single-stranded, contains adenine (A), uracil (U), guanine (G), cytosine (C).

Base pairing: A-T (DNA), A-U (RNA), G-C (both).

Prokaryotic and Eukaryotic Genomes

Prokaryotic genomes consist mainly of a single circular chromosome located in the nucleoid. Eukaryotic genomes are typically linear, sequestered within the nucleus, and often diploid.

Prokaryotes: Haploid, circular chromosome, may contain plasmids.

Plasmids: Small, independently replicating DNA molecules; types include fertility, resistance, bacteriocin, and virulence plasmids.

Eukaryotes: Linear chromosomes, diploid, nuclear and extranuclear chromosomes (mitochondria, chloroplasts).

DNA Replication

Semiconservative Replication

DNA replication is semiconservative, meaning each new DNA molecule consists of one original and one daughter strand. The process requires triphosphate deoxyribonucleotides for both monomers and energy.

Key concept: Complementary structure of DNA strands enables accurate replication.

Bacterial DNA Replication

Bacterial DNA replication begins at the origin and proceeds bidirectionally. DNA polymerase synthesizes DNA only in the 5′ to 3′ direction. The leading strand is synthesized continuously, while the lagging strand is synthesized discontinuously.

Enzymes: Gyrases and topoisomerases remove supercoils; DNA is methylated for regulation and protection.

Eukaryotic DNA Replication

Eukaryotic DNA replication is similar to bacterial replication but uses four DNA polymerases, thousands of replication origins, and produces shorter Okazaki fragments.

Gene Function

Genotype and Phenotype

The genotype is the set of genes in the genome, while the phenotype refers to the physical features and functional traits of the organism.

Central dogma: DNA is transcribed to RNA, which is translated to form polypeptides.

Transcription

Transcription is the process by which information in DNA is copied as RNA. Six types of RNA are transcribed: RNA primers, messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), regulatory RNA, and ribozymes.

Steps: Initiation, elongation, termination.

Location: Occurs in nucleoid (prokaryotes), nucleus/organelles (eukaryotes).

Eukaryotic mRNA processing: Capping, polyadenylation, splicing.

Translation

Translation is the process in which ribosomes use genetic information in mRNA to synthesize polypeptides. Participants include mRNA, tRNA, ribosomes, and rRNA.

Stages: Initiation, elongation, termination.

Energy: Initiation and elongation require GTP.

Differences: Eukaryotic initiation uses 5′ guanine cap; first amino acid is methionine.

Regulation of Genetic Expression

Gene Regulation

Most genes are expressed at all times, but some are regulated to conserve energy. Regulation typically halts transcription or stops translation directly.

Prokaryotic Operons

An operon consists of a promoter and a series of genes, controlled by a regulatory element called an operator. Operons can be inducible (activated by inducers) or repressible (deactivated by repressors).

Lactose operon: Regulates lactose catabolism; activated by CAP and deactivation of repressor.

Tryptophan operon: Regulates tryptophan synthesis; repressed when tryptophan is available.

Regulatory RNAs

Regulatory RNAs, such as microRNAs (miRNAs), small interfering RNAs (siRNAs), and riboswitches, can control translation by binding to mRNA or changing shape.

Mutations of Genes

Types of Mutations

A mutation is a change in the nucleotide base sequence of a genome. Mutations are rare and usually deleterious, but occasionally beneficial.

Point mutations: Affect one base pair; include substitutions and frameshift mutations.

Gross mutations: Include inversions, duplications, and transpositions.

Mutagens

Mutagens are agents that increase the mutation rate. They include radiation (ionizing and nonionizing) and chemical mutagens (nucleotide analogs, nucleotide-altering chemicals, frameshift mutagens).

DNA Repair

Cells have several methods for repairing damaged DNA: direct repair, single-strand repair, and error-prone repair. Error-prone repair is a last resort and may introduce mutations.

Identifying Mutants, Mutagens, and Carcinogens

Mutants are descendants of cells that do not repair a mutation. Wild-type cells are those normally found in nature. Methods to recognize mutants include positive selection, negative (indirect) selection, and the Ames test.

Genetic Recombination and Transfer

Genetic Recombination

Exchange of nucleotide sequences often occurs between homologous sequences, resulting in recombinants—cells with DNA molecules containing new nucleotide sequences.

Horizontal Gene Transfer Among Prokaryotes

Horizontal gene transfer involves the transfer of genetic material from a donor to a recipient cell. Three types are transformation, transduction, and bacterial conjugation.

Transformation: Uptake of DNA from the environment; cells must be competent.

Transduction: Transfer of DNA via bacteriophage; can be generalized or specialized.

Conjugation: Transfer of DNA requiring physical contact; donor cell remains alive.

Transposons and Transposition

Transposons are segments of DNA that move from one location to another, causing frameshift insertions. They contain palindromic sequences at each end. Insertion sequences are the simplest transposons, while complex transposons contain additional genes.