BIOL 151 Lecture Notes

Date: 10/6/25

Topic: DNA Structure and Replication Basics

Starter Clicker Question

• Question: What should you do if the cops show up at a party you’re attending next weekend? Possible answers:
  1. Ignore them.
  2. Listen and do what they say.
  3. Run away.
  4. Throw stuff at them.
  5. Ask yourself whether it’s worth being at that party.

Announcements

• Discussions do meet this week.
• Discussions DO NOT meet NEXT week.
• Please use the lecture slides during discussion.

p53 Protein

• Function:
  • Activated with DNA damage.
  • Triggers DNA repair.
  • If DNA repair is successful, the cell continues to live on.
  • If DNA damage persists, the cell is killed off through apoptosis.

p53 DNA-binding Core Domain

• Role:
  • Binds to specific DNA base sequences.

p53 Tetramer Formation

• p53 molecules bind to each other to form a tetramer.
• Each p53 molecule includes a DNA binding domain that directly binds to specific DNA base sequences.
• p53 binding to DNA activates the expression of p21, a Cyclin Dependent Kinase Inhibitor (CDKI) that blocks both CDK4/6 and CDK2, effectively blocking the cell cycle.

MDM2 and p53 Interactions

• MDM2 Role:
  • Binds to p53 tetramers and attaches Ubiquitin to p53, regulating its function and stability.

Cancer Driver Genes and Mutations

• List of genes related to cancer mutations:
  • EIF1AX, GNA11, SF3B1, BAP1, PBRM1, ATM, SETD2, NF2, KDM6A, CUL3, MET, SMARCA4, U2AF1, RBM10, STK11, NF1, IDH1, IDH2, PTPN11, MAX, ATRX, EGFR, TCF12, HIST1H1E, LZTR1, KIT, RAC1, ARID2, BRD7, BRAF, NRAS, RNF43, SMAD4, ARID1A, KRAS, APC, SMAD2, ACVR2A, GNAS, HRAS, STAG2, FGFR3, RHOA, CDKN1A, ERBB3, KANSL1, RB1, TP53, CDKN2A, KEAP1, CASP8, TGFBR2, HLA-B, MAPK1, NOTCH1, HLA-A, RASA1, EPHA2, NSD1, ZNF750, KMT2D, NFE2L2, KLF5, EP300, FAT1, PTEN, FBXW7, PIK3CA, RUNX1, DNMT3A, SMC1A, ERBB2, KMT2C, AKT1, MAP3K1, FOXA1, BRCA1, CDH1, PIK3R1, PPP2R1A, BCOR, ARHGAP35, FGFR2, CHD4, CTCF, CTNNB1, SPOP.

Tobacco-Related Carcinogen: Benzo(a)pyrene

• Carcinogenic Classification:
  • According to IARC, sufficient evidence shows that Benzo(a)pyrene (BP) is carcinogenic in laboratory animals and probably also in humans (Group 2A).
• Metabolic Activation Pathway:
  1. The formation of (7R,8S)-epoxy-7,8-dihydrobenzo(a)pyrene catalyzed by cytochrome P450 enzymes.
  2. Conversion to (7R,8R)-dihydroxy-7,8-dihydrobenzo(a)pyrene catalyzed by epoxide hydrolase (EH).
  3. Final step produces four possible isomers of 7,8-diol-9,10-epoxide, with (7R,8S)-dihydroxy-(9S,10R)-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene (BPDE) being the most important, which binds to DNA and produces BPDE-DNA adducts.

Binding of BPDE to p53 Gene

• BPDE binds to specific locations, including codons 157, 248, and 273 in the p53 gene in HeLa cells and bronchial cells from healthy, nonsmoking individuals.

DNA Replication

Overview of S Phase

• Readings:
  • DNA Structure - How Life Works Chapter 3
  • DNA Replication - How Life Works Chapter 12
• Applications of DNA Synthesis/DNA Repair:
  • PCR (Polymerase Chain Reaction) for DNA analysis in medicine and forensics.
  • Molecular cloning and mutagenesis.
  • DNA editing using CRISPR-Cas9.
  • DNA sequencing for genomic analysis.

Cell Cycle Regulation

• G1 Checkpoint Control System:
  • Involves Cyclins D and E, and CDK4/6 and CDK2 to regulate progression to S phase.
  • Growth signals increase Cyclin D levels, activating CDK4/6, which partially phosphorylates Rb.
  • Further signals increase Cyclin E levels, activating CDK2 and fully phosphorylating Rb, releasing E2F_DP1 which activates S phase genes and triggers DNA replication.

Components of DNA Replication

• Major enzymes involved:
  • Helicase: Unwinds the DNA double helix.
  • Single-Strand Binding Proteins: Stabilize single-stranded DNA (ssDNA).
  • Topoisomerase: Relieves unwinding tension in the double helix.
  • Primase: Lays down an RNA primer, providing a starting point for new DNA synthesis.
  • DNA Polymerases: Extend the DNA strand by adding nucleotides based on the template strand.
  • DNA Ligase: Seals gaps between Okazaki fragments on the lagging strand.

Characteristics of DNA Structure

• Composition of DNA:
  • DNA is a double helix composed of two complementary strands held together by base pairing (A::T and G:::C).
  • Each strand has a sugar-phosphate backbone and is polar (5' to 3' directionality).
• Base Pairing Rules:
  • Adenine pairs with Thymine, forming two hydrogen bonds.
  • Guanine pairs with Cytosine, forming three hydrogen bonds.

DNA Synthesis Process

• Synthesis occurs 5' to 3'. New nucleotides are added to the 3' hydroxyl (-OH) group of the preceding nucleotide.
• Proofreading: DNA polymerase III possesses a 3' to 5' exonuclease activity to correct base pair mismatches during replication.

Semi-Conservative Nature of DNA Replication

• DNA replication is semi-conservative:
  • Each new DNA molecule consists of one old (template) strand and one newly synthesized strand.
  • This ensures fidelity and continuity of genetic information.