🦠Microbiology Unit 10 – Biochemistry of the Genome

Key Concepts and Terminology

• Genome encompasses all genetic material of an organism, including DNA and RNA
• Nucleotides serve as building blocks of nucleic acids (DNA and RNA) consist of a sugar, phosphate group, and nitrogenous base
• Complementary base pairing dictates specific hydrogen bonding between nucleotides (adenine-thymine, guanine-cytosine in DNA; adenine-uracil in RNA)
• Central dogma of molecular biology describes flow of genetic information from DNA to RNA to proteins
• Genetic code refers to correspondence between codons (triplets of nucleotides) and amino acids they specify
• Mutations involve changes in DNA sequence can be beneficial, neutral, or deleterious to an organism
• Genetic diversity arises from mutations and recombination contributes to adaptability and evolution of species

DNA Structure and Function

• DNA (deoxyribonucleic acid) stores and transmits genetic information in cells
• Double helix structure proposed by Watson and Crick consists of two antiparallel polynucleotide strands wound around a central axis
  • Strands held together by hydrogen bonds between complementary base pairs (A-T and G-C)
  • Sugar-phosphate backbone provides structural stability and polarity to the molecule
• Genetic information encoded in sequence of nucleotide bases (A, T, G, C) determines amino acid sequence of proteins
• DNA packaging into chromatin and chromosomes allows efficient storage and regulation of genetic material
  • Histones are proteins that help compact and organize DNA in eukaryotic cells
• DNA replication ensures accurate transmission of genetic information to daughter cells during cell division
• DNA serves as a template for RNA synthesis (transcription) and ultimately protein synthesis (translation)

RNA Types and Roles

• RNA (ribonucleic acid) is a single-stranded nucleic acid involved in various cellular processes
• Messenger RNA (mRNA) carries genetic information from DNA to ribosomes for protein synthesis
  • Codons in mRNA specify amino acid sequence of proteins
• Transfer RNA (tRNA) molecules deliver amino acids to ribosomes during translation
  • Anticodon on tRNA complementary to codon on mRNA ensures accurate amino acid incorporation
• Ribosomal RNA (rRNA) is a structural and catalytic component of ribosomes essential for protein synthesis
• Small nuclear RNAs (snRNAs) participate in splicing of pre-mRNA to remove introns and generate mature mRNA
• Regulatory RNAs (e.g., microRNAs, siRNAs) play crucial roles in gene expression regulation and silencing
• RNA can also function as enzymes (ribozymes) catalyze chemical reactions (e.g., self-splicing introns)

Replication Process

• DNA replication is semiconservative each daughter molecule contains one original and one newly synthesized strand
• Replication initiates at specific sites called origins of replication
• DNA helicase unwinds double helix and separates strands to form replication forks
• Single-stranded binding proteins stabilize separated strands and prevent reannealing
• DNA primase synthesizes short RNA primers complementary to template strand
  • Primers provide a starting point for DNA synthesis by DNA polymerase
• DNA polymerase III extends primers and synthesizes new DNA strands in 5' to 3' direction
  • Leading strand synthesized continuously; lagging strand synthesized discontinuously as Okazaki fragments
• DNA polymerase I replaces RNA primers with DNA and fills gaps between Okazaki fragments
• DNA ligase seals nicks between adjacent DNA fragments to create a continuous strand

Transcription and Gene Expression

• Transcription is the synthesis of RNA from a DNA template catalyzed by RNA polymerase
• Promoter regions upstream of genes contain recognition sites for RNA polymerase and transcription factors
• Transcription factors are proteins that regulate gene expression by binding to specific DNA sequences
  • Activators enhance transcription; repressors inhibit transcription
• RNA polymerase binds to promoter, unwinds DNA, and initiates RNA synthesis at the transcription start site
• Elongation involves the addition of nucleotides to the growing RNA chain complementary to the template strand
• Termination occurs when RNA polymerase encounters a termination signal releases the newly synthesized RNA
• Post-transcriptional modifications (e.g., 5' capping, 3' polyadenylation, splicing) generate mature mRNA
• Alternative splicing allows production of multiple protein isoforms from a single gene

Translation and Protein Synthesis

• Translation is the process of synthesizing proteins based on the genetic code in mRNA
• Ribosomes are the sites of protein synthesis composed of rRNA and proteins
• mRNA binds to the small ribosomal subunit; tRNAs deliver amino acids to the ribosome
• Codons in mRNA are read sequentially by complementary base pairing with anticodons on tRNAs
• Initiation involves the assembly of the ribosome, mRNA, and initiator tRNA at the start codon (AUG)
• Elongation occurs as the ribosome moves along the mRNA, adding amino acids to the growing polypeptide chain
  • Peptide bonds form between adjacent amino acids catalyzed by the ribosome
• Termination happens when the ribosome reaches a stop codon (UAA, UAG, or UGA) releasing the completed polypeptide
• Post-translational modifications (e.g., folding, cleavage, addition of functional groups) generate functional proteins

Genetic Mutations and Repair Mechanisms

• Mutations are changes in the DNA sequence can arise from errors during replication or exposure to mutagens
• Point mutations involve single nucleotide changes (substitutions, insertions, or deletions)
  • Silent mutations do not change the amino acid sequence; missense mutations result in a different amino acid; nonsense mutations introduce a premature stop codon
• Frameshift mutations (insertions or deletions) alter the reading frame and can have significant effects on protein function
• Chromosomal mutations involve large-scale changes (e.g., deletions, duplications, inversions, translocations)
• DNA repair mechanisms maintain genetic integrity by correcting errors and damage
  • Mismatch repair corrects errors during replication; nucleotide excision repair removes damaged bases; double-strand break repair fixes broken DNA strands
• Mutations in DNA repair genes can lead to increased mutation rates and genomic instability associated with various diseases (cancer)

Applications in Microbiology

• Genetic analysis of microorganisms helps understand their pathogenicity, antibiotic resistance, and evolution
• Recombinant DNA technology allows the insertion of foreign genes into microorganisms for various applications
  • Production of recombinant proteins (e.g., insulin, vaccines) in bacterial or yeast hosts
  • Development of genetically modified microorganisms for bioremediation, agriculture, or industrial processes
• Polymerase chain reaction (PCR) amplifies specific DNA sequences for rapid detection and identification of microorganisms
• DNA sequencing technologies enable whole-genome sequencing of microorganisms for comparative genomics and epidemiological studies
• CRISPR-Cas9 is a powerful gene-editing tool derived from bacterial adaptive immune systems used for precise genetic modifications
• Metagenomics involves sequencing and analysis of DNA from environmental samples to study microbial communities and discover novel genes or organisms
• Understanding the genetics of microorganisms is crucial for developing strategies to combat infectious diseases, antibiotic resistance, and bioterrorism