Genetics: Key Concepts and Definitions

Essential Terms in Microbial Genetics

• Genome: The complete set of genetic material in an organism, including all of its genes and non-coding sequences.

• Heritable: Traits or characteristics that can be passed from one generation to the next through genetic material.

• Gene: A segment of DNA that encodes information for the synthesis of a specific protein or functional RNA.

• Genotype: The genetic makeup of an organism; the specific set of genes it carries.

• Phenotype: The observable characteristics or traits of an organism, resulting from the interaction of its genotype with the environment.

• Chromosome: A DNA molecule with part or all of the genetic material of an organism; in eukaryotes, chromosomes are linear and associated with histones, while in prokaryotes, they are typically circular.

• Histones: Proteins found in eukaryotic cell nuclei that package and order DNA into structural units called nucleosomes.

• Plasmid: Small, circular, double-stranded DNA molecules found in bacteria and some eukaryotes, often carrying genes beneficial for survival (e.g., antibiotic resistance).

• Nucleic acids: Biomolecules (DNA and RNA) that store and transmit genetic information.

• Nitrogen base: Organic molecules (adenine, thymine, guanine, cytosine, uracil) that form the building blocks of nucleic acids.

• Purine: Nitrogenous bases with a double-ring structure (adenine and guanine).

• Pyrimidine: Nitrogenous bases with a single-ring structure (cytosine, thymine, and uracil).

• Mutation: A change in the nucleotide sequence of DNA, which can affect gene function.

• Enzyme: Biological catalysts that speed up biochemical reactions, including those involved in DNA replication and repair.

• Primosome: A protein complex that initiates DNA replication by synthesizing RNA primers.

• Helicase: Enzyme that unwinds the DNA double helix during replication.

• Primase: Enzyme that synthesizes short RNA primers needed for DNA polymerase to begin replication.

• Single-strand binding proteins: Proteins that stabilize unwound DNA strands during replication.

• DNA polymerase III: Main enzyme that adds nucleotides to the growing DNA strand during replication in prokaryotes.

• DNA polymerase I: Enzyme that removes RNA primers and replaces them with DNA nucleotides.

• Ligase: Enzyme that joins Okazaki fragments on the lagging strand by forming phosphodiester bonds.

• Okazaki fragments: Short DNA fragments synthesized discontinuously on the lagging strand during replication.

• Semiconservative DNA replication: Each new DNA molecule consists of one original (parental) strand and one newly synthesized strand.

• Protein synthesis: The process by which cells build proteins based on genetic instructions (includes transcription and translation).

• RNA polymerase: Enzyme that synthesizes RNA from a DNA template during transcription.

• Reverse transcription/Reverse transcriptase: The process (and enzyme) by which RNA is used as a template to synthesize DNA (e.g., in retroviruses).

• Intron: Non-coding sequence within a gene that is removed during RNA splicing in eukaryotes.

• Exon: Coding sequence within a gene that remains in mature mRNA after splicing.

• Silent mutation: Mutation that does not change the amino acid sequence of a protein.

• Substitution mutation: Replacement of one nucleotide with another in DNA.

• Insertion mutation: Addition of one or more nucleotides into a DNA sequence.

• Deletion mutation: Removal of one or more nucleotides from a DNA sequence.

• Reversion mutation: A mutation that restores the original sequence or function of a gene.

• Nonsense mutation: Mutation that introduces a premature stop codon, leading to a truncated protein.

• Missense mutation: Mutation that results in a different amino acid in the protein sequence.

• Frameshift mutation: Mutation caused by insertions or deletions that change the reading frame of the gene.

• Mutagen: An agent (chemical, physical, or biological) that increases the rate of mutation.

• Epigenome: The collection of chemical modifications to DNA and histone proteins that regulate gene expression without altering the DNA sequence.

• Transposons: DNA sequences that can change their position within the genome, sometimes causing mutations.

Structure and Features of DNA and RNA

Features of DNA

• Double-stranded helix composed of nucleotides (deoxyribose sugar, phosphate group, nitrogenous base).

• Bases: Adenine (A), Thymine (T), Guanine (G), Cytosine (C).

• Base pairing: A pairs with T, G pairs with C via hydrogen bonds.

• Antiparallel strands (5' to 3' and 3' to 5').

• Stores genetic information for all cellular processes.

Features of RNA

• Single-stranded molecule composed of nucleotides (ribose sugar, phosphate group, nitrogenous base).

• Bases: Adenine (A), Uracil (U), Guanine (G), Cytosine (C).

• Functions in protein synthesis and gene regulation.

Molecular Building Blocks

• DNA: Deoxyribose sugar, phosphate group, nitrogenous bases (A, T, G, C).

• RNA: Ribose sugar, phosphate group, nitrogenous bases (A, U, G, C).

The Central Dogma of Molecular Biology

The central dogma describes the flow of genetic information within a biological system:

• DNA is transcribed into RNA.

• RNA is translated into protein.

Equation:

DNA Replication

Overview of DNA Replication

• Replication is semiconservative: each new DNA molecule contains one parental and one new strand.

• Occurs in the 5' to 3' direction.

Leading vs. Lagging Strand

• Leading strand: Synthesized continuously toward the replication fork.

• Lagging strand: Synthesized discontinuously away from the replication fork in short segments called Okazaki fragments.

Main Enzymes and Their Actions

• Helicase: Unwinds the DNA double helix.

• Primase: Synthesizes RNA primers.

• DNA polymerase III: Adds nucleotides to the growing DNA strand.

• Single-strand binding proteins: Stabilize unwound DNA.

• DNA polymerase I: Removes RNA primers and replaces them with DNA.

• Ligase: Joins Okazaki fragments on the lagging strand.

Okazaki Fragments

• Short DNA segments synthesized on the lagging strand.

• Later joined by DNA ligase to form a continuous strand.

Protein Synthesis (Gene Expression)

Process and Regulation

• Transcription: DNA is used as a template to synthesize RNA (mRNA, tRNA, rRNA).

• Translation: mRNA is decoded by ribosomes to assemble amino acids into proteins.

• Regulation: Controlled at transcriptional, post-transcriptional, translational, and post-translational levels.

Main Types of RNA and Their Functions

• mRNA (messenger RNA): Carries genetic code from DNA to ribosomes for protein synthesis.

• tRNA (transfer RNA): Brings amino acids to the ribosome and matches them to the coded mRNA message via anticodons.

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

RNA Splicing

• In eukaryotes, introns are removed and exons are joined to form mature mRNA.

Protein Synthesis in Prokaryotes vs. Eukaryotes

• Prokaryotes: Transcription and translation occur simultaneously in the cytoplasm; no introns or RNA splicing.

• Eukaryotes: Transcription occurs in the nucleus, translation in the cytoplasm; mRNA undergoes splicing, capping, and polyadenylation.

Mutations and Their Consequences

Types of Mutations

• Silent mutation: No change in amino acid sequence.

• Missense mutation: Changes one amino acid in the protein.

• Nonsense mutation: Introduces a stop codon, truncating the protein.

• Frameshift mutation: Insertion or deletion shifts the reading frame, altering downstream amino acids.

• Substitution mutation: One base is replaced by another.

• Insertion mutation: Addition of one or more bases.

• Deletion mutation: Removal of one or more bases.

• Reversion mutation: Restores original sequence or function.

Categories of Mutagens

• Chemical mutagens: Chemicals that alter DNA (e.g., base analogs, alkylating agents).

• Physical mutagens: Physical agents like UV light or X-rays.

• Biological mutagens: Viruses or transposons that disrupt genetic material.

Epigenome and Gene Expression

• The epigenome consists of chemical modifications (e.g., DNA methylation, histone modification) that regulate gene expression without changing the DNA sequence.

• DNA methylation typically represses gene expression by preventing transcription factors from binding to DNA.

DNA Repair Mechanisms

Excision Repair

• Damaged DNA is recognized and removed by specific enzymes.

• The gap is filled in by DNA polymerase and sealed by DNA ligase.

Horizontal Gene Transmission Mechanisms

• Transformation: Uptake of free DNA from the environment.

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

• Conjugation: Direct transfer of DNA between bacteria via a pilus.

Genetic Code and Protein Synthesis

Using the Genetic Code Table

• DNA is transcribed into mRNA codons (triplets of nucleotides).

• Each codon specifies an amino acid or a stop signal.

• tRNA molecules have anticodons that pair with mRNA codons during translation.

Relationship Between Codons and Anticodons

• Codons: Found on mRNA; specify amino acids.

• Anticodons: Found on tRNA; complementary to mRNA codons.

Gene Regulation Mechanisms

Pre-Transcriptional Regulation

• Control of gene expression before transcription begins (e.g., DNA methylation, histone modification, transcription factor binding).

Post-Transcriptional Regulation

• Control after transcription (e.g., RNA splicing, mRNA stability, RNA interference).

Summary Table: Types of Mutations and Their Effects

Example: DNA to Protein Translation

• DNA sequence: 5'-ATG GAA TGA-3'

• mRNA sequence: 5'-AUG GAA UGA-3'

• Protein sequence: Met-Glu-Stop

Additional info: In prokaryotes, gene expression is often regulated by operons (e.g., lac operon), while in eukaryotes, regulation is more complex and involves chromatin remodeling and multiple regulatory elements.