Course Notes for Biology 101

Course Logistics

  • Exam Announcement

    • Dr. Bell will arrive within 7-8 minutes, will sit down, and wrap up exam logistics shortly thereafter.

    • Names will be read out to distribute exams.

  • Grade Updates

    • Average grades have increased across the board, indicating improved student performance.

    • Many students have significantly improved their scores through consistent effort.

    • Peer Tutoring: Available three times a week for additional help, offering individualized and group support.

    • Tutors will be emphasized every meeting; there is no excuse for not seeking help given the readily available resources.

  • Office Hours

    • Dr. Phalen and myself will hold back-to-back office hours on Thursdays for four hours, providing ample opportunity for student consultations.

    • If students can't attend scheduled office hours, we can arrange alternative appointments to ensure everyone gets necessary support.

    • Serious discussions regarding academic progress or concerns can be scheduled one-on-one when needed for privacy and focused attention.

  • Group Study Sessions

    • Dr. Phelan has organized group study for biology in the Science Center, fostering collaborative learning.

    • Schedule: Saturdays from 2 PM to 4 PM and Monday nights from 8 PM to 10 PM, offering flexible options for attendance.

  • Content for Today

    • Review Chapter 16: Focus on mutations and their molecular basis.

    • Transition into Chapter 17: Topics include transcription and translation, essential processes of gene expression.

    • The third exam is coming up next week on Friday (not Tuesday), so prepare accordingly.

    • Plan to clear any lingering confusion from Chapters 15, 16, and 17 during this session to ensure a strong understanding before the exam.

Chapter 16: Mutations

  • Types of Mutations

    • Mutations are classified as either point mutations (small-scale changes in a single nucleotide pair) or chromosomal mutations (large-scale alterations affecting chromosome structure or number).

    • Examples of point mutations include:

      • Silent Mutations: A nucleotide change that results in no change to the amino acid sequence, often due to the degeneracy (redundancy) of the genetic code. For instance, changing TAT to TAC both code for tyrosine.

      • Missense Mutations: A nucleotide change that alters a single amino acid in the protein sequence. The impact on protein function can range from negligible (conservative missense) to severe (non-conservative missense), depending on the chemical properties of the substituted amino acid.

      • Nonsense Mutations: A nucleotide change that introduces a premature stop codon (UAA, UAG, or UGA) into the mRNA sequence, leading to a truncated, and typically non-functional, protein product. These proteins are often targeted for degradation.

      • Frameshift Mutations: Results from the addition or deletion of nucleotides not in multiples of three, thereby altering the reading frame of the mRNA. This typically leads to a completely different amino acid sequence downstream of the mutation, often producing nonfunctional proteins due to premature stop codons or extensive missense changes.

  • DNA Replication Proofreading

    • During DNA synthesis, DNA polymerase not only adds nucleotides but also corrects mistakes through its 3' to 5' exonuclease activity, acting as a proofreader to remove incorrectly paired bases.

    • Repair enzymes, such as those involved in the Mismatch Repair (MMR) system, fix any mismatches that are not caught by DNA polymerase's initial proofreading. MMR recognizes, removes, and replaces mistakenly added bases after replication is complete, drastically reducing the overall error rate.

Chapter 17: Transcription

  • Overview

    • Focus on how RNA is synthesized from a DNA template. This process differs significantly between prokaryotes (bacteria and archaea) and eukaryotes (organisms with a cell nucleus).

    • Distinctions include the location (cytoplasm in prokaryotes, nucleus in eukaryotes), the complexity of RNA polymerases, and the extent of post-transcriptional RNA processing required in eukaryotes.

  • RNA Polymerase Functionality

    • RNA polymerase synthesizes a new RNA strand by extending it from the 3' end, using ribonucleoside triphosphates (NTPs: ATP, UTP, CTP, GTP) as precursors, unlike deoxyribonucleoside triphosphates (dNTPs) used in DNA synthesis.

    • Crucially, RNA polymerase does not require a primer to initiate RNA synthesis, unlike DNA polymerase.

    • The process of transcription proceeds through three main stages: initiation, elongation, and termination.

  • Initiation

    • Promoter Recognition: In bacteria, a sigma factor subunit helps the core RNA polymerase enzyme recognize and bind to specific DNA sequences called promoters. Key promoter sequences include the -35 box (consensus sequence 5'–TTGACA–3') and the -10 box (Pribnow box, consensus sequence 5'–TATAAT–3'), located upstream of the transcription start site.

    • The +1 site marks the first nucleotide that is transcribed into RNA, considered downstream of the promoter region.

    • After RNA synthesis is successfully initiated, the sigma factor is typically released from the core enzyme, allowing elongation to proceed.

  • Elongation

    • RNA polymerase moves along the DNA template strand in a 3' to 5' direction, adding complementary RNA nucleotides to the growing RNA strand in a 5' to 3' direction.

    • As the polymerase unwinds a short segment of DNA, forming a