DNA function

Intended Learning Outcomes

  • Summarize the flow of genetic information in a cell, from DNA to protein: Understanding how the process of transcription and translation conveys information from the genetic code in DNA to the synthesis of proteins in cells.

  • Know how RNA and DNA are similar and how they differ: Recognition of similarities (both are nucleic acids, polymers of nucleotides) and differences (RNA is usually single-stranded, contains ribose sugar, and has uracil instead of thymine).

  • Explain why the genetic code is universal and how this reflects evolutionary history: The genetic code is nearly the same across all organisms, indicating a common evolutionary ancestor.

  • Identify similarities and differences between replication and transcription: Both involve template-based synthesis but differ in the products (DNA vs RNA) and enzymes used (DNA polymerase vs RNA polymerase).

  • Identify important molecules and mechanisms in transcription/translation: Understanding the roles of mRNA, tRNA, rRNA, ribosomes, and various enzymes in transcription and translation.

  • Understand and be able to explain ribosome function: Ribosomes are the molecular machines where translation occurs, facilitating the assembly of amino acids into proteins.

  • Sketch the steps involved in protein synthesis (initiation, elongation, termination): Familiarity with the stages of translation and the role of different molecules and enzymes in each stage.

  • Explain functional differences between bacterial and eukaryotic mRNA and the translation process: Recognizing that in bacteria, transcription and translation can occur simultaneously, whereas in eukaryotes they are separated by the nuclear envelope.

  • Understand the impacts of mutations: A comprehension of how mutations can affect protein synthesis, including silent, missense, and nonsense mutations, and their implications for evolution and genetics.

DNA to Protein Flow

  • Major Steps:

    1. Replication of DNA:

      • DNA double helix unwinds

      • Each strand acts as a template for new strands (semiconservative replication)

      • Enzyme DNA polymerase adds nucleotides to growing DNA strands

      • Additional proteins stabilize and unwind the DNA helix during replication.

    2. Transcription (DNA to RNA):

      • RNA polymerase synthesizes RNA by copying DNA

    3. Translation (RNA to Protein):

      • Ribosomes read mRNA sequences to assemble polypeptides (proteins) from amino acids.

Understanding DNA Replication

Overview of DNA Replication

  • Process:

    1. Two antiparallel strands unwind.

    2. Each parental strand serves as a template for new DNA strands (semiconservative replication).

    3. DNA polymerase adds new nucleotide subunits.

    4. Multiple enzymes and proteins unwind and stabilize the DNA helix.

Size and Speed of DNA Replication

  • E. coli Genome:

    • Size: ~5 million base pairs

    • Replication time: < 1 hour

  • Human Genome:

    • Size: ~6 billion base pairs (over 1000 times that of E. coli)

    • Comprises 46 chromosomes, arranged in pairs, each a single long DNA polymer

    • Despite genome size, replication takes only a few hours due to rapid mechanisms.

Origin of Replication

  • Initiation:

    • Starts at a specific base sequence known as the Origin of Replication.

    • Multiple origins allow for simultaneous replication of DNA strands.

Proteins Involved in DNA Replication

Key Enzymes and Their Functions

  • Origin Binding Proteins: Open up the DNA helix at the origin site.

  • Helicases: Unwind the double helix by breaking hydrogen bonds between base pairs.

  • Single Strand Binding Proteins (SSBs):

    • Keep strands apart.

    • Prevent annealing and protect against hydrolysis by nucleases.

  • Topoisomerase: Relieves strain ahead of the replication fork by cutting and rejoining DNA strands.

Base Pairing During Replication

  • Nucleotides are added according to base-pairing rules. E.g., a template strand sequence of 3'-GAATC-5' results in a new strand of 5'-CTTAG-3'.

Leading and Lagging Strands

Leading Strand

  • Synthesized continuously in the 5' → 3' direction toward the replication fork.

Lagging Strand

  • Synthesized discontinuously in short sections termed Okazaki fragments.

  • DNA polymerase must work away from the replication fork, leading to back-stitching of RNA primers.

Proofreading by DNA Polymerase

  • DNA polymerase is highly accurate (approx. 1 in 10^7 error rate).

  • If a mispairing occurs, polymerase can excise and replace incorrect nucleotides.

  • However, proofreading occurs in the 5' to 3' direction only.

Transcription Overview

  • Definition: Copying of information from DNA to RNA.

  • Steps:

    1. Initiation: RNA polymerase binds to promoter.

    2. Elongation: RNA polymerase synthesizes RNA in the 5’ to 3’ direction.

    3. Termination: RNA polymerase stops when it reaches a termination signal.

Types of RNA

  • mRNA (messenger RNA): Carries information for protein synthesis.

  • tRNA (transfer RNA): Brings amino acids to the ribosome, matching codons to their anticodons.

  • rRNA (ribosomal RNA): Structural component of ribosomes, facilitating translation.

Post-Transcriptional Modifications in Eukaryotes

  1. Capping of the 5’ End: Addition of a 7-methylguanosine cap, which helps protect mRNA and assist in ribosome binding.

  2. Polyadenylation: Addition of a Poly-A tail to the 3’ end, increasing stability of the mRNA molecule.

  3. Intron Removal: Splicing out of non-coding regions (introns) to yield mature mRNA that is ready for translation.

The Triplet Code

  • Codons: Sequences of three bases forming the genetic code.

  • Start Codon: AUG (codes for Methionine)

  • Stop Codons: UAA, UAG, UGA (indicate termination of protein synthesis).

Codon and Anticodon Relationship

  • Each tRNA has an anticodon that pairs with the mRNA codon, ensuring correct addition of amino acids during protein synthesis.

Translation Process

Steps of Translation

  1. Initiation:

    • The small ribosomal subunit binds to mRNA and the initiator tRNA recognizes the start codon (AUG).

  2. Elongation:

    • tRNAs bring amino acids to the ribosome; peptide bonds form between amino acids.

    • mRNA is read in codons, and the ribosome moves along the mRNA (translocation).

  3. Termination:

    • When a stop codon is reached, a release factor binds, and the newly synthesized polypeptide chain is released.

Mutations and Their Impact

Types of Mutations

  • Silent Mutations: Do not change amino acid sequence.

  • Missense Mutations: Change one amino acid in the polypeptide chain, which can lead to altered function.

  • Nonsense Mutations: Create a premature stop codon, often leading to nonfunctional proteins.

  • Frameshift Mutations: Occur with insertions or deletions not in multiples of three, altering the entire reading frame and potentially creating nonfunctional proteins.