Comprehensive Notes on Bacterial and Eukaryotic Genetics, Transcription, Translation, and Cell Division

BACTERIAL TRANSCRIPTION

  • Transcription is divided into 3 distinct processes:     * 1. INITIATION: The enzyme synthesizing RNA does so in the 5′→3′5' \rightarrow 3' direction. RNA polymerase binds to the DNA at the promotor sequence, at which point the DNA unwinds and separates.     * 2. ELONGATION: The RNA polymerase moves along the 3′→5′3' \rightarrow 5' strand (template strand) and synthesizes RNA in the 5′→3′5' \rightarrow 3' direction. It is explicitly noted that only one strand of DNA is used to synthesize the RNA.     * 3. TERMINATION: The RNA polymerase dissociates from the DNA, and the transcript is complete.

GENE STRUCTURE

  • Promoter: A sequence specifying where transcription starts.
  • Gene: The RNA-coding sequence.
  • Terminator: A sequence indicating the end of mRNA creation.

EUKARYOTE TRANSCRIPTION

  • Eukaryotes differ by having more than one RNA polymerase. In transcription specifically, RNA polymerase II is used to synthesize pre-mRNA.
  • 1. INITIATION: Requires transcription factors, which are proteins that help to bind RNA polymerase to the DNA. Transcription factors bind to certain regions in the promoter, such as the TATA box. This binding triggers RNA polymerase II.
  • 2. ELONGATION: RNA polymerase II reads the template strand and synthesizes pre-mRNA in the 5′→3′5' \rightarrow 3' direction.
  • 3. TERMINATION: The RNA is cut free.
  • 4. RNA PROCESSING: The pre-mRNA is modified in 3 major ways before being considered mature:     * 5′5' cap: A guanine is added to the 5′5' end. This protects mRNA from degradation by hydrolytic enzymes, helps in distinguishing mRNA from other RNA, and assists in the transport of mRNA from the nucleus.     * Poly-A-tail: Consists of 50 to 25050 \text{ to } 250 adenine nucleotides added to the 3′3' end. This protects the mRNA from degradation and assists in export.     * Splicing: Carried out by spliceosomes, which are complexes of proteins and small RNA molecules called ribozymes. Splicing removes introns and joins exons.     * Alternative splicing: This occurs when pre-mRNA is put together differently to produce different mature mRNAs from the same sequence, which increases the rate of transcription diversity.

EPIGENOME AND DNA PACKAGING

  • DNA Packaging: DNA is packed into the nucleus as chromatin. Environments can influence which genes are expressed through this packaging.     * Euchromatin: Loosely packed chromatin where genes are expressed.     * Heterochromatin: Tightly packed chromatin where genes are usually not expressed.
  • Histones: Proteins that are positively charged and responsible for first-level DNA packaging.
  • Nucleosomes: Structures formed when DNA coils around 88 histones.
  • N-terminal: The tails of the histones involved in gene expression.
  • Chromatin Modification: Acetyl groups are added to histones to loosen chromatin and increase transcription rates.

RIBOSOME STRUCTURE AND SITES

  • Ribosomes: Made in the nucleolus. These are the sites of protein synthesis (translation); in prokaryotes, this occurs in the cytoplasm.
  • Composition: Made up of rRNA and protein. It contains 22 subunits: Small and Large. These assemble only in the presence of mRNA.
  • Binding Sites:     * P site (Peptidyl-tRNA binding site): Holds the tRNA that carries the growing polypeptide chain.     * A site (Aminoacyl-tRNA binding site): Holds the tRNA that carries the next amino acid to be added to the chain.     * E site (Exit site): The location where discharged tRNAs leave the ribosome.     * mRNA binding site: Located on the small subunit.     * Exit tunnel: Part of the large subunit through which the polypeptide emerges.
  • Codon Reading: The ribosome reads 33 bases (called a codon) at a time.

TRANSLATION PROCESS

  • Translation is the process of using mRNA to make proteins. All 33 stages require protein factors to assist the process.
  • 1. INITIATION: The mRNA binds to the small ribosomal subunit near the start codon. The ribosome identifies the start codon: AUGAUG. A tRNA carrying the anticodon UACUAC enters the P site. The large ribosome subunit then binds to form the full ribosome. The initiation complex is formed when the mRNA, tRNA, and subunit are assembled with the help of initiation factors.
  • 2. ELONGATION: A new tRNA enters the A site with a specific anticodon. A peptide bond forms between the amino acids. The growing chain moves from the tRNA in the P site to the A site. Translocation occurs, moving the ribosome one codon forward along the mRNA.
  • 3. TERMINATION: The ribosome reaches a stop codon (UAA,UAG, or UGAUAA, UAG, \text{ or } UGA). A Release factor enters the A site to trigger the release of the finished polypeptide. The ribosome then dissociates.
  • Energy Requirements: Translation requires energy in the forms of GTPGTP and ATPATP.
  • Polyribosome: Many ribosomes can translate the same mRNA at the same time, shaped like a chain along the mRNA.
  • WOBBLINING: A phenomenon where there are fewer tRNAs than codons. While the first 22 bases of a codon are strict in their pairing, the last one is flexible. This flexible pairing is called "wurdbing" or wobbling.

MUTATIONS

  • Definition: A change in the DNA sequence. Their function is to create genetic variety.
  • Large-scale mutations: Affect large chromosome regions (e.g., deletions, inversions).
  • Small-scale mutations: Affect one or a few nucleotides. A one-nucleotide change is called a point mutation.
  • Types of Substitutions (Point Mutations):     * Silent mutation: The codon changes, but the amino acid produced stays the same.     * Missense mutation: The codon changes and a different amino acid is produced.     * Nonsense mutation: A codon changes into a stop codon.
  • INDELS (Insertions & Deletions): These add or remove nucleotides and result in frameshift mutations.
  • Causes of Mutations: Mutations are caused by replication errors (where DNA polymerase inserts the wrong bases during mitosis/meiosis) or mutagens (external factors like smoking, industrial chemicals, or UV radiation) which increase the rate of chemical changes.
  • Case Study: Sickle-cell Anemia:     * Result of a single nucleotide mutation in the gene encoding for the β\beta-globin polypeptide of haemoglobin.     * Leads to the production of an abnormal protein.     * Red blood cells become sickle-shaped, causing reduced oxygen levels and fatigue.

CHROMOSOME STRUCTURE AND GENETICS

  • Genome: All the DNA in a cell.
  • Chromosome: One DNA molecule within the genome. During cell division, DNA is replicated, and chromosomes condense into visible structures.
  • Chromosome Anatomy:     * Sister chromatids: Replicated halves of a chromosome.     * Centromere: The attachment point of sister chromatids.     * p arm: The short arm.     * q arm: The long arm.     * Telomere: The tips of the chromosome.
  • Chromosome Shapes: Metacentric, Acrocentric, Sub-metacentric, Telocentric.
  • Genetic Terminology:     * Phenotype: Description of physical traits.     * Genotype: The genetic makeup.     * Locus: Where a gene is located on the chromosome.     * Allele: A variant form of a gene.

KARYOTYPES

  • Humans have 2323 pairs of chromosomes.
  • Karyotype: An ordered display of chromosome pairs, grouped according to length and size. They are captured during metaphase because chromosomes are maximally condensed and visible.
  • Homologous chromosomes: The two chromosomes in each pair. They have the same length and shape and carry genes controlling the same inherited characters (e.g., eye color), though they may have different alleles (e.g., brown eyes vs blue eyes).
  • Classification:     * 22 Autosomes (Pairs 1 to 221 \text{ to } 22).     * 23rd pair: Sex chromosomes (XX and YY).     * Group A: Largest chromosomes.     * Group G: Very short chromosomes.
  • Polyploidy: Common in plants; instead of being diploid (2n2n), they are 3n,4n3n, 4n, etc.

MITOSIS AND THE CELL CYCLE

  • Mitosis: The division of the nucleus that produces two genetically identical daughter cells. Functions include growth and repair. It is distinct from meiosis, which is for sperm/egg production.
  • The Cell Cycle:     * Interphase (Cell growth and preparation):         * G1G_1: Cell grows, makes proteins, and produces organelles.         * S phase: DNA replication occurs. The chromosome number stays the same, but the number of chromatids doubles.         * G2G_2: Cell grows more and prepares for mitosis.     * Mitotic (M) phase:         * Mitosis: Nucleus division (PMAT).         * Cytokinesis: Cytoplasm division.
  • Steps of Mitosis:     * 1. Prophase: Chromosomes condense, 22 sister chromatids become visible. The nucleolus dissapears. The spindle fiber (made of 22 centrosomes and microtubules) forms.     * 2. Prometaphase: A transition stage where spindle fibers access chromosomes. They attach to a protein attachment called a kinetochore.     * 3. Metaphase: Chromosomes line up in the middle at the imaginary metaphase plate.     * 4. Anaphase: Chromatids separate. Cohesins are broken by the enzyme separase.     * 5. Telophase: Nuclear envelopes form and nucleoli reappear.     * 6. Cytokinesis: A cleavage furrow forms, and a contractile ring pinches the cell into two.