BIOL 151 Lecture - DNA Structure and Replication

BIOL 151 Lecture Notes - DNA Structure and Replication Basics

Date: 10/6/25
Starter Clicker Question of the Day

  • Question: What should you do if the cops show up at a party you’re attending next weekend?

    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.

  • Students are encouraged to use the lecture slides during discussion.

p53 Protein and DNA

  • p53:

    • Function: Activated in the presence of DNA Damage.

    • Triggers DNA Repair:

    • If DNA repair is successful, the cell continues to live.

    • If DNA damage remains, the cell undergoes apoptosis (programmed cell death).

p53 Binding Domain

  • p53 contains a DNA-binding core domain that binds to specific DNA base sequences.

p53 Tetramer Formation

  • p53 molecules bind to each other to form a tetramer.

  • Each p53 molecule features a DNA binding domain that interacts with specific DNA base sequences.

  • p53 binding to DNA activates the expression of p21, a cyclin-dependent kinase inhibitor (CDKI) that blocks:

    • CDK4/6

    • CDK2

  • Overall effect: Block the cell cycle.

MDM2 Role

  • MDM2:

    • Binds to p53 tetramers and attaches Ubiquitin to p53, tagging it for degradation.

Cancer Driver Genes and Mutations Overview

  • Important driver genes and 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.

    • Includes statistics on mutation prevalence and significance in various cancers.

Cancer Mutation Insights

  • TP53 mutations:

    • Notable for being prevalent in several cancers, including lung cancer, where mutations cluster at specific codons (157, 248, and 273).

  • Implications:

    • Significant evidence used in litigation against the tobacco industry linking lung cancer to smoking.

Smoking and Lung Cancer

  • Cigarette sales and lung cancer correlations:

    • Strong historical trends showing a delay of about 25 years between cigarette use and lung cancer diagnosis.

    • Data indicates a decline in smoking correlated with a drop in lung cancer mortality over time.

Chemical Carcinogenic Mechanism

  • Benzo(a)pyrene (BP):

    • Known carcinogen linked to tobacco smoke.

    • Activates through a metabolic pathway that ultimately forms DNA adducts by binding to p53 gene DNA at codons 157, 248, and 273.

DNA Replication Overview

  • Occurs during the S phase of the cell cycle, necessitating several key proteins and processes:

    • Key readings include:

    • DNA Structure: How Life Works Chapter 3

    • DNA Replication: How Life Works Chapter 12

Applications of DNA Synthesis and Repair

  • Applications:

    • PCR for DNA analysis (medicine, forensics)

    • Molecular cloning and mutagenesis

    • DNA editing (e.g., CRISPR/Cas9)

    • DNA sequencing for genomic analysis

Cell Cycle Regulation

  • Cyclins and checkpoints in the cell cycle include:

    • Cyclin D: Activated by initial growth signals, increases CDK4/6 activity.

    • Cyclin E: Further increases in CDK2 activity, leading to phosphorylation of Rb protein and activation of S phase genes.

    • After S phase, Cyclin A is induced, deactivating CDK2 and preventing further S phase gene activation.

DNA Replication Mechanics

  • Strands of DNA:

    • Unidirectionally synthesized from 5’ to 3’.

    • Leading strand synthesized continuously, lagging strand consists of Okazaki fragments.

Key Enzymes Involved in DNA Replication

  1. Helicase: Unwinds the DNA double helix.

  2. Single-Stranded Binding Protein (SSB): Stabilizes unwound DNA strands.

  3. Primase: Synthesizes RNA primers providing 3’OH for DNA polymerase.

  4. DNA Polymerase III: Main enzyme synthesizing new DNA strands, requiring existing strand for base pairing.

  5. DNA Polymerase I: Replaces RNA primers with DNA nucleotides.

  6. DNA Ligase: Joins DNA fragments by forming phosphodiester bonds.

Process of DNA Synthesis

  • DNA polymerases work to elongate the new DNA strand.

  • New nucleotides are incorporated into the growing chain through:

    • Formation of phosphodiester bonds between the 3’ hydroxyl of the last inserted nucleotide and the 5’ phosphate group of the new nucleotide.

  • DNA replication is semi-conservative, retaining one original strand within each double-stranded DNA molecule post-replication.

Checking for Errors

  • Proofreading by DNA Polymerase III:

    • 3’ - 5’ exonuclease activity to remove incorrect bases.

    • Correct base inserted with 5’ - 3’ polymerase activity.

Conclusion

  • DNA is flexible, forming various shapes due to twists in the sugar-phosphate backbone.

  • The most common form is the right-handed double helix (B-DNA), with occasional formations of left-handed helices (Z-DNA).

  • Various types of nucleotides (purines vs pyrimidines) play crucial roles in the base pairing rules that stabilize DNA structure during replication.

Future Directions

  • Advance studies on the biochemical pathways of DNA damage repair as it relates to cancer therapy and genetic engineering applications.