FPT DNA

Introduction to DNA

  • What is DNA? An overview of DNA as the genetic material.

DNA Structure

  • Deoxyribonucleic acid (DNA)

    • Definition: DNA is a polynucleotide.

    • Components of a nucleotide:

    • A nitrogen base which can be:

      • Adenine (A)

      • Guanine (G)

      • Cytosine (C)

      • Thymine (T)

    • A pentose sugar: deoxyribose.

    • A phosphate group.

  • Bonds in DNA:

    • Phosphodiester bond links the sugar and phosphate of adjacent nucleotides.

    • Hydrogen bonds hold the two strands of DNA together:

    • A always binds to T (2 H bonds).

    • C always binds to G (3 H bonds).

  • Structural specifics of the sugar:

    • The 5th carbon (C) of the deoxyribose sugar has a phosphate group attached (called 5 prime or 5’).

    • The 3rd carbon has a hydroxyl group attached (called 3 prime or 3’).

Purine and Pyrimidine Bases

  • Purines:

    • Adenine (A)

    • Guanine (G)

  • Pyrimidines:

    • Cytosine (C)

    • Thymine (T) (found only in DNA)

    • Uracil (U) (found only in RNA)

Key Concepts in Base Pairing

  • Important bindings between nitrogenous bases:

    • A → T (2 H bonds).

    • C → G (3 H bonds).

  • DNA has an anti-parallel structure where one strand runs from 5’ to 3’ and the other from 3’ to 5’.

Differences between DNA and RNA

  • DNA:

    • Sugar: deoxyribose

    • Bases: G, C, A, T

    • Structure: double-stranded, long

    • Location: nucleus only

  • RNA:

    • Sugar: ribose

    • Bases: G, C, A, U (uracil)

    • Structure: single-stranded, short

    • Location: nucleus and cytoplasm

Historical Discovery of DNA

  • Alfred Hershey & Martha Chase (1952): Demonstrated DNA as the genetic material through experiments. Won the Nobel Prize in 1969.

  • James Watson & Francis Crick (1953): Discovered the double helical structure of DNA, for which they, along with Maurice Wilkins, received the Nobel Prize in 1962.

  • Rosalind Franklin: Significant contributions through X-ray crystallography that demonstrated DNA’s helical structure.

  • Matthew Meselson & Franklin Stahl (1958): Revealed DNA replication as a semi-conservative process.

DNA Replication

  • Types of DNA replication:

    • Conservative: Both strands remain intact after replication.

    • Semiconservative: Each new DNA molecule consists of one old strand and one new strand.

    • Dispersive: New DNA consists of strands from both old and new.

  • Replication Mechanics:

    • Initiation: Separation of strands, creation of a replication bubble.

    • Enzymes involved: DNA gyrase (topoisomerase), DNA helicase, single-stranded binding proteins (ssB’s).

Steps in DNA Replication

  1. Initiation:

    • DNA gyrase unwinds DNA.

    • DNA helicase breaks H-bonds between strands.

    • ssB’s prevent strand re-annealing.

  2. Elongation:

    • RNA primase adds RNA primer for DNA polymerase to build upon.

    • DNA polymerase III synthesizes DNA in the 5’ to 3’ direction.

    • Continual strand (leading) versus discontinuous (lagging) with Okazaki fragments.

  3. Termination:

    • DNA polymerase II proofreads and terminates replication as two separate entities.

Mutation

  • Definition: An alteration in the DNA sequence that can alter gene function or protein product.

  • Causes:

    • Chemical agents, ultraviolet radiation, or natural causes.

    • Errors during DNA replication or protein synthesis.

  • Examples of mutagens: Dyes, tobacco smoke, UV rays, benzene, and some viruses.

  • Telomeres: Repetitive DNA segments at chromosomal ends preventing genetic information loss during replication.

Telomere Research and Implications

  • Elizabeth Blackburn: Discovered telomeres and the enzyme telomerase.

    • Overactive telomerase links to cancer risk; underactive leads to cell death.

Protein Synthesis Overview

  • Definition: The process of making proteins from DNA instructions.

    • Transcription occurs in the nucleus, translation occurs in the cytoplasm.

  • Process:

    1. Synthesis of mRNA from the DNA template.

    2. mRNA moves to cytoplasm through nuclear pore.

    3. Protein synthesis at ribosome.

Transcription Process

  1. Initiation: RNA polymerase binds to the DNA promoter region.

  2. Elongation: RNA strands are synthesized in a 5’ to 3’ direction, using the 3’ to 5’ DNA template strand.

  3. Termination: Done upon RNA polymerase reaching a terminator sequence.

Translation Process

  • The conversion of mRNA into a protein:

  1. mRNA structure: Codons read by ribosome.

    • The start codon is AUG. The end codons (UAA, UAG, UGA) signal termination.

  2. Ribosome Function: Composed of rRNA and proteins; facilitates mRNA reading.

  3. tRNA Function:

    • Each tRNA carries an anticodon which matches mRNA codons, bringing appropriate amino acids.

    • For each amino acid addition, ATP is required.

Gene Expression

  • Stages:

    • Transcription to mRNA in the nucleus.

    • Translation to protein in the cytoplasm.

    • Proteins are functional units consisting of amino acids sequenced per the mRNA.

    • Alternative splicing can create diverse protein products from a single gene.

Mutations Explained

  • Types of mutations:

    • Point mutations: Can be substitutions, deletions, or insertions, impacting the resulting protein sequences (silent, missense, nonsense).

    • Chromosomal mutations: Involves larger-scale alterations such as translocation and inversion.

Practice Questions and Activities

  • Familiarize with mutation examples, DNA structure modeling using simulation, gene expression mapping, and practice transcription and translation exercises.