The Structure and Replication of Genomes: Microbial Genetics and Gene Function

The Structure and Replication of Genomes

Genetics and Genome

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 all its genes and nucleotide sequences.

• Genetics: Focuses on how traits are passed from one generation to the next.

• Genome: Includes both coding (genes) and non-coding sequences of DNA.

• Example: The human genome contains about 3 billion base pairs.

The Structure of Nucleic Acids

Nucleic acids (DNA and RNA) are polymers of nucleotides, each consisting of a sugar, phosphate group, and nitrogenous base. DNA is typically double-stranded and forms a double helix, while RNA is usually single-stranded.

• Base Pairing: Adenine (A) pairs with Thymine (T) in DNA, and with Uracil (U) in RNA; Guanine (G) pairs with Cytosine (C).

• Hydrogen Bonds: Hold the two DNA strands together.

• Example: The sequence ATCG in DNA pairs with TAGC on the complementary strand.

The Structure of Prokaryotic Genomes

Prokaryotic Chromosomes

Prokaryotic cells are typically haploid, containing a single, circular chromosome located in a region called the nucleoid.

• Haploid: Only one copy of each gene.

• Circular DNA: Most prokaryotic chromosomes are circular, not linear.

• Example: Escherichia coli has a single circular chromosome.

Plasmids

Plasmids are small, circular DNA molecules that replicate independently of the chromosome. They are not essential for normal cell function but can provide advantages such as antibiotic resistance.

• Types of Plasmids:

  • Fertility plasmids (F plasmids): Involved in conjugation.

  • Resistance plasmids (R plasmids): Provide resistance to antibiotics.

  • Bacteriocin plasmids: Encode toxins that kill other bacteria.

  • Virulence plasmids: Carry genes for pathogenicity.

• Example: R plasmids in Staphylococcus aureus confer resistance to methicillin.

The Structure of Eukaryotic Genomes

Nuclear Chromosomes

Eukaryotic chromosomes are linear and located within the nucleus. Eukaryotic cells are often diploid, containing two copies of each chromosome.

• Linear DNA: Unlike prokaryotes, eukaryotic chromosomes are linear.

• Diploid: Two sets of chromosomes (one from each parent).

• Example: Human cells have 46 chromosomes (23 pairs).

DNA Replication

Semiconservative Model

DNA replication is semiconservative: each new DNA molecule consists of one original strand and one newly synthesized strand.

• Process: Each parental DNA strand serves as a template for a new strand.

• Example: After one round of replication, two DNA molecules each have one old and one new strand.

Mechanism of DNA Replication

• Origin of Replication: Replication begins at a specific site called the origin.

• Bidirectional: Replication proceeds in both directions from the origin.

• Leading Strand: Synthesized continuously in the 5' to 3' direction.

• Lagging Strand: Synthesized discontinuously as Okazaki fragments.

• Key Enzymes: DNA polymerase, primase, ligase, gyrase, and topoisomerase.

• DNA Methylation: Addition of methyl groups to DNA, important for gene regulation and DNA repair.

Replication in Eukaryotes

• Uses four different DNA polymerases.

• Has thousands of origins of replication.

• Okazaki fragments are shorter than in prokaryotes.

Gene Function

Genotype and Phenotype

The genotype is the set of genes in the genome, while the phenotype is the physical and functional expression of those genes.

• Genotype: Genetic makeup (e.g., BB, Bb, bb).

• Phenotype: Observable traits (e.g., purple or white flowers).

The Central Dogma: Transcription and Translation

• Transcription: DNA is copied into RNA by RNA polymerase.

• Translation: Ribosomes use mRNA to synthesize polypeptides (proteins).

• Central Dogma: $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$

Transcription in Prokaryotes

• RNA polymerase binds to the promoter region of DNA.

• RNA polymerase synthesizes an RNA copy of the gene.

• Multiple RNA polymerases can transcribe a gene simultaneously.

• Six types of RNA: RNA primers, mRNA, rRNA, tRNA, regulatory RNA, ribozymes.

Transcription in Eukaryotes

• Occurs in the nucleus.

• mRNA is processed before translation: capping, polyadenylation, and splicing (removal of introns).

Translation

• Ribosomes use mRNA sequence to assemble amino acids into polypeptides.

• Participants: mRNA (instructions), tRNA (amino acid carriers), ribosomes (assembly machinery).

• Three stages: Initiation, Elongation, Termination.

• Requires energy in the form of GTP.

• Polyribosomes: Multiple ribosomes can translate a single mRNA simultaneously in prokaryotes.

Regulation of Genetic Expression

Gene Regulation

• Some genes are always expressed (constitutive genes).

• Other genes are regulated and only expressed when needed, conserving energy.

• Regulation can occur at transcription or translation.

Prokaryotic Operons

• An operon is a cluster of genes under the control of a single promoter and operator.

• Inducible operons (e.g., lac operon) are activated by inducers.

• Repressible operons (e.g., trp operon) are deactivated by repressors.

Operon Type	Example	Regulation
Inducible	lac operon	Activated by presence of inducer (lactose)
Repressible	trp operon	Deactivated by corepressor (tryptophan)

Mutations of Genes

Mutation

• A mutation is a change in the nucleotide sequence of DNA.

• Most mutations are rare and deleterious, but some can be beneficial.

Types of Mutations

• Point Mutations: Affect a single base pair (silent, missense, nonsense).

• Frameshift Mutations: Insertions or deletions that shift the reading frame, affecting all downstream codons.

Mutation Type	Description	Effect
Silent	Base change does not alter amino acid	No effect on protein
Missense	Base change alters amino acid	May affect protein function
Nonsense	Base change creates stop codon	Premature termination
Frameshift	Insertion/deletion shifts reading frame	Major changes in protein

Mutagens

• Radiation: UV light can cause thymine dimers.

• Chemical Mutagens:

  • Nucleotide analogs: Disrupt DNA/RNA replication.

  • Nucleotide-altering chemicals: Cause base-pair substitutions.

  • Frameshift mutagens: Cause insertions or deletions.

Genetic Recombination and Transfer

Horizontal Gene Transfer in Prokaryotes

Horizontal gene transfer is the movement of genetic material between organisms other than by descent. It increases genetic diversity in prokaryotes.

• Transformation: Uptake of naked DNA from the environment by competent cells.

• Transduction: Transfer of DNA by bacteriophages (viruses that infect bacteria).

  • Generalized: Random DNA transferred.

  • Specialized: Specific DNA sequences transferred.

• Bacterial Conjugation: Direct transfer of DNA via a pilus from donor to recipient cell.

Type	Mechanism	Example
Transformation	Uptake of free DNA	Streptococcus pneumoniae
Transduction	Phage-mediated transfer	Generalized or specialized
Conjugation	Direct cell-to-cell transfer	F plasmid transfer in E. coli