Bio - Molecular Genetics


  • Nucleoside: A ribose sugar coupled with a nitrogenous base.

  • Nucleotide: Comprises a ribose sugar, a nitrogenous base, and a phosphate group.

  • Purines:

    • Double-ringed nitrogenous bases that include:

    • Adenine (A)

    • Guanine (G)

  • Pyrimidines:

    • Single-ringed nitrogenous bases that include:

    • Cytosine (C)

    • Thymine (T)

    • Uracil (U)

  • Nucleosomes:

    • Complexes consisting of DNA wrapped around histone proteins.

  • Histone proteins:

    • Negatively charged proteins accommodating negatively charged DNA, facilitating proper binding.

Chromatin

  • Euchromatin:

    • Loosely packed nucleosomes, making DNA readily accessible for transcription.

  • Heterochromatin:

    • Tightly packed nucleosomes, with DNA not easily accessible and hence mostly inactive.

  • Acetylation:

    • Process where positive charges are removed, relaxing DNA-histone attraction to allow transcription.

  • Deacetylation:

    • Increases positive charges, tightening DNA-histone attraction and decreasing transcription.

  • Methylation:

    • The addition of methyl groups which can either suppress or enhance transcription.

Bio-DNA Replication

  • Origin of replication:

    • Site where DNA strands first separate to initiate replication.

    • Bacteria (with circular DNA) have a single origin of replication, while humans (with linear DNA) have multiple origins.

  • Replication process:

    • Involves semiconservative replication (one new strand plus one old strand).

    • Initiation occurs at AT-rich segments due to easier splitting (fewer hydrogen bonds) compared to GC pairs.

    • DNA helicase: Unzips DNA by breaking hydrogen bonds, creating a replication fork.

    • Leads to supercoiling, creating tension ahead of the replication fork.

  • DNA elongation:

    • Single-strand binding proteins: Bind to uncoiled DNA to keep strands separate.

    • Topoisomerase: Nicks DNA ahead of helicase to mitigate tension and supercoiling.

    • Primase: Places RNA primers on the template strands for 3' end nucleotide addition.

    • Sliding clamp proteins: Hold DNA polymerase onto the template strand for adding free nucleoside triphosphates.

  • Strands dynamics:

    • Leading strand: Synthesized continuously as its 3' end faces the replication fork.

    • Lagging strand: Synthesized discontinuously needing multiple RNA primers to create Okazaki fragments.

    • DNA polymerase replaces RNA primers with DNA.

    • DNA ligase: Connects separated DNA fragments.

  • Termination of DNA replication:

    • Occurs when the replication fork cannot proceed.

    • Telomeres: Non-coding, repeated nucleotide sequences at the ends of linear chromosomes to avert DNA loss, extend via telomerase.

Bio-DNA Replication - Diagram

  • Diagram illustrates:

    • Original (template) DNA

    • Free nucleotides

    • DNA polymerase: Extends DNA in the 5' to 3' direction.

    • Replication fork, leading and lagging strands.

Bio-Transcription

  • Process where DNA is transcribed to produce single-stranded messenger RNA (mRNA).

  • In prokaryotes: Transcription and translation occur simultaneously in the cytosol.

  • Transcription steps:

    • Initiation: Activated by a promoter next to a gene to recruit RNA polymerase.

    • Elongation: Forms a transcription bubble where RNA polymerase moves 3' to 5' on the template strand, producing RNA in a 5' to 3' direction.

    • Termination: Occurs when RNA polymerase encounters a termination sequence, signaling to stop transcription.

    • The template strand: Known as the antisense/non-coding strand.

    • The other strand is referred to as the coding/sense strand, closely resembling the mRNA (except for T to U variations).

Prokaryotic Transcriptional Control

  • Operons: Groups of genes functioning as a single unit controlled by one promoter.

  • Regulation:

    • Repressors bind to operator regions and activators bind to promoter sites to modulate transcription.

Eukaryotic Transcriptional Control

  • Transcription factors are necessary for RNA polymerase binding to promoters.

  • TATA box: An A-T rich sequence in many promoters recognized by transcription factors.

  • Enhancers: DNA sites for activator proteins to increase transcription of genes.

  • Silencers: DNA sites for repressor proteins that decrease gene transcription. Both can be distant from genes.

  • Poly-A signal: Added in eukaryotes during termination to create a poly-A tail.

Bio-Transcription Continued

  • Regulatory proteins in both prokaryotes and eukaryotes possess DNA binding motifs that recognize and bind to the major groove of regulatory sequences without unwinding the helix.

    • Motifs include:

    • Zinc finger

    • Helix-turn-helix

    • Homeodomain

    • Leucine zipper

Eukaryotic Post-Transcriptional Modifications

  • Converts pre-mRNA into processed mRNA:

    • 5' Capping: Addition of a guanine cap to protect from degradation during elongation.

    • 3' polyadenylation: Addition of a poly-A tail at the 3' end to prevent degradation.

    • Intron Splicing: Removal of introns (noncoding sequences) from pre-mRNA by spliceosomes.

    • Alternative splicing: A single pre-mRNA can yield multiple spliced mRNA products, allowing for various proteins.

    • miRNA (MicroRNA): Small RNA molecules that silence mRNA expression through base-pairing, inhibiting translation.

Bio-Lac Operon/Trp Operon in Prokaryotes

  • Lac Operon: Encodes proteins necessary for lactose metabolism through three genes - lacZ, lacY, lacA.

    • It's an inducible operon, activated when glucose is scarce and lactose needs metabolizing.

    • Control:

    • The Lac repressor protein (always expressed) binds to the operator, blocking transcription.

    • Lactose converts into allolactose, which detaches the repressor, allowing transcription to occur.

    • cAMP levels: Inversely related to glucose levels; when glucose is scarce, cAMP levels are high, facilitating the attachment of CAP (catabolite activator protein) near the lac promoter to promote transcription.

  • Trp Operon: Produces tryptophan via coding for tryptophan synthetase.

    • Repressible operon, always active except when tryptophan is in the environment.

    • Control:

    • Tryptophan binds to the trp repressor, activating it to bind the operator, preventing further production.

    • When tryptophan is absent, the trp operon undergoes transcription as the repressor remains inactive.

Bio-Translation

  • Translation: Process converting mRNA into protein products.

  • Ribosomes: Composed of rRNA and proteins, consisting of:

    • Eukaryotes: Small (40s) and large (60s) subunits form an 80s ribosome.

    • Prokaryotes: Small (30s) and large (50s) subunits form a 70s ribosome.

  • Codon: A sequence of 3 mRNA bases (A, U, G, or C) coding for an amino acid or terminating translation.

    • Start Codon: AUG (methionine).

    • Stop Codon: UAA, UAG, UGA (terminates translation).

    • Open reading frame: Sequence between start and stop codons.

    • Anticodon: A sequence of three tRNA bases that pairs with the codon, with each tRNA carrying an amino acid.

  • Aminoacyl-tRNA: A tRNA molecule linked to an amino acid.

Ribosome Binding Sites

  • A site: Aminoacyl-tRNA enters the ribosome.

  • P site: Contains the growing polypeptide; transfers to the tRNA in A site during bond formation.

  • E site: Exiting site for tRNA post-pairing.

  • Translation Initiation: The start codon (AUG) pairs with methionine-tRNA at the P site.

  • Elongation: Aminoacyl-tRNAs enter the A site; peptide bonds form, facilitated by the ribosome.

  • Translocation: Shifting of tRNAs among sites (A-P-E sequence).

  • Termination: Occurs when a stop codon pairs with release factors and the polypeptide is released.

  • Chaperonins: Assist newly synthesized polypeptides in folding correctly.

Bio-Mutations

  • DNA mutation: A modification in the nucleotide sequence.

    • Mutations in germ cells can be inherited, while those in somatic cells affect only the individual.

Types of DNA mutations:

  • Base Substitution Mutations: One nucleotide replaced by another.

    • Silent Mutations: No change in amino acid sequence, often due to 3rd base wobble.

    • Missense Mutations: Single amino acid change which can be either:

    • Conservative: Similar amino acid.

    • Non-conservative: Different amino acid.

    • Nonsense Mutations: Change resulting in a stop codon and early termination of protein.

  • Frameshift Mutations: Shift in the reading frame's interpretation due to:

    • Insertion: Addition of nucleotides.

    • Deletion: Removal of nucleotides.

    • Null Mutation: Produces a non-functional allele lacking normal allele function.

  • Causes of DNA mutations: DNA polymerase errors during replication, DNA loss during crossing over, chemical damage, radiation, transposons.

  • Prevention mechanisms:

    • DNA polymerase proofreads during replication.

    • Mismatch repair machinery checks uncaught errors.

    • Nucleotide excision repair substitutes damaged DNA with correct bases through complementary base pairing.

Bio-Mutations Continued

  • Chromosomal mutations: Affect the entire chromosome rather than individual nucleotides.

    • Deletion: Loss of a chromosome segment, leading to a shorter arm.

    • Duplication: Replication of a chromosome segment, resulting in an elongated arm and atypical banding pattern.

    • Inversion: Reversal of a chromosome segment, which changes the orientation but not the length.

    • Translocation: Attachment of chromosome segments to another, affecting both chromosomes with abnormal banding patterns.

Bio-Molecular Genetics of Viruses

  • Capsid: Protein coat made of capsomeres.

  • Phospholipid envelope: Lipid bilayer acquired from host cell membranes, aiding in host cell attachment.

  • Viral replication process: Includes:

    • Attachment: Binding to the host cell.

    • Penetration: Crossing the host's cell membrane.

    • Uncoating: Disassembly of the viral capsid by host enzymes.

    • Replication: Duplication of the viral genome and manufacturing of capsid components.

    • Assembly: Formation of the complete viral capsid.

    • Release: Exit from the host cell.

Viral Life Cycles

  • Lysogenic Cycle: Virus integrates its genome into the host's genome, remaining dormant and replicated alongside host DNA.

  • Lytic Cycle: Virus hijacks the host for replication, potentially lysing the host to infect new cells.

Retroviruses

  • Contain RNA genomes that infect host cells, employing reverse transcriptase to convert their RNA into complementary DNA, integrating this into the host genome, often entering the lysogenic cycle.

Bio-Molecular Genetics of Bacteria

  • Bacteria reproduce asexually via binary fission, inheriting genes from one parent without genetic diversity improvement via reproduction.

  • Horizontal Gene Transfer:

    • Gene transfer between organisms includes:

    • Conjugation: Utilization of pili to copy and transfer specialized plasmids (fertility factor plasmid).

    • Transformation: Uptaking of extracellular DNA by competent bacteria, which may be induced through electroporation.

    • Transduction: Viruses (bacteriophages) transfer bacterial DNA between hosts during their life cycles by integrating bacterial DNA into the host genome.

  • R-factors: Extrachromosomal plasmid DNA containing antibiotic resistance genes.