biol3010 exam 1 review

Exam Preparation Overview

  • Location and Time

    • Exam scheduled for tonight at 07:15.

    • Either in assigned classroom or classroom 2402.

  • Seating Arrangement

    • Students should sit in every other seat for spacing.

    • Availability of seats in the front for those comfortable with it.

Exam Format and Requirements

  • Exam Type

    • Grading scope with topology to fill in.

  • Identification

    • Clearly write name and computing ID on exam paper.

    • 5 different versions of the exam; bubble in the version taken at the top right corner of the sheet.

  • Duration

    • 90 minutes total, though it’s acceptable not to use the full time.

  • Submission

    • Turn in both paper exam and bubble sheet once completed.

  • Materials

    • Bring a pencil; electronic devices are not allowed.

    • Calculator not necessary for math problems.

Office Hours

  • Additional Support

    • Office hours available from 4-5 PM with TA assistance for further clarification on questions not answered in class.

DNA Repair Mechanisms Overview

Single-Stranded DNA Repair

  • Mismatch Repair (MMR)

    • Mechanism used during DNA replication to fix incorrectly inserted bases.

    • Endogenous proofreading activity of DNA polymerase can sometimes correct errors independently; MMR is a backup.

  • Base Excision Repair

    • Enzymes called DNA glycosylases identify specific lesions (e.g., deaminated cytosine) and initiate repair.

    • Subsequent repair steps include activation of AP endonucleases and exonucleases to remove damaged nucleotides and fill them with new nucleotides using DNA polymerase.

    • Enzyme DNA ligase seals the final nick in the DNA backbone, requiring ATP for this action.

Nucleotide Excision Repair

  • Recognition of Damage

    • Identifies issues such as thymine dimers, often resulting from UV irradiation.

    • Specific proteins recognize and nick the damaged DNA segment leading to repair.

  • Repair Process

    • Similar to base excision repair: damaged segments are chewed back, filled in by DNA polymerase, and sealed by DNA ligase.

Differentiation of Enzymes

  • Endonucleases vs. Exonucleases

    • Endonucleases cleave DNA at specific sites within the strand.

    • Exonucleases remove nucleotides from the ends of the DNA strand.

Importance of Template in DNA Repair

  • Need for a Primer

    • DNA polymerase requires a 3' hydroxyl group to fill gaps; does not necessarily require a primer if such a group is already present.

Meiosis and Genetic Diversity

Homologous Recombination

  • Crossing Over

    • Occurs during meiosis I when homologous chromosomes pair, leading to genetic diversity through chiasmata formation.

    • Sister chromatids are consolidated; recombination occurs between non-sister chromatids.

Double-Stranded Break Repair

  • Repair Mechanisms

    • Homologous recombination is preferred to use sister chromatids to ensure accurate repair.

    • Non-sister chromatids may be used in some cases, which can lead to less favorable genetic outcomes, especially in heterozygous individuals.

DNA Damage Types and Repair Challenges

  • Interstrand Cross-Links

    • Covalent bonds that can form between nucleotides of opposite DNA strands lead to halting of the DNA replication machinery.

    • These cross-links need to be repaired to prevent double-stranded breaks during DNA replication.