BY160 Ch. 11 Lecture Slides

Page 1: Title Introduction

  • Nucleic Acids structure & function, DNA Replication, and Chromosomes

  • Quote: "The DNA test is back. You're guilty and part collie." - Karen

Page 2: Overview of Topics

  • Introduction

    • Focus on DNA structure; RNA structure will be covered in the next chapter.

    • Topics include

      • DNA replication - essential for cell division and reproduction.

      • Chromosome structure and DNA organization in prokaryotic and eukaryotic cells.

Page 3: Nucleic Acid Structure Overview

  • Part 1 - Nucleic Acid Structure

Page 4: Importance of Nucleic Acid Structure

  • Structure-function relationship demonstrates how:

    • DNA and RNA store, replicate, and transmit information. Also hereditary and can replicate itself.

    • Variations in DNA and RNA structure arise through mutation, contributing to evolutionary processes.

Page 5: Levels of Complexity in DNA

  • DNA Structure (Exam Essay Question!!)

    • Nucleotides: Building blocks (monomers) of nucleic acid polymer.

    • DNA Strand: Formed by covalent linking of nucleotides into a single strand.

    • Double Helix: Two DNA strands in an antiparallel orientation.

    • Chromatin: Complex of DNA and associated proteins for packaging in the nucleus.

    • Genome: Total genetic material within a cell, including chromosomes and organelles like chloroplasts and mitochondria.

      • Mitochondrial DNA: Circular DNA found in mitochondria, distinct from nuclear DNA, and inherited maternally.

      • Nuclear DNA: Genetic material found within the nucleus of eukaryotic cells, organized into chromosomes and responsible for encoding the majority of an organism's genes.

Page 6: Components of DNA Nucleotides

  • DNA Nucleotides: All are composed of three main components

    • Phosphate group: Forms the DNA/RNA backbone, conferring an overall negative charge.

    • Pentose Sugar (5-carbon):

      • DNA contains deoxyribose.

      • RNA contains ribose.

    • Nitrogenous Base:

      • Purines: double-ring structure (Adenine (A), Guanine (G)).

      • Pyrimidines: single-ring structure (Thymine (T), Uracil (U), Cytosine (C)).

Page 7: Nucleotide Orientation and Structure

  • Nucleotide Structure

    • Important orientation component with a numbering system for sugar carbons (1’, 2’, 3’, 4’, 5’ positions).

    • Base attached at the 1’ position; phosphate attached to the 5’ position.

    • Comparison between sugars: RNA has an –OH; DNA has an –H at the 2’ position.

Page 8: DNA Strand Characteristics

  • DNA Strand

    • Linear chain of nucleotides linked by covalent phosphodiester bonds forming the DNA backbone.

    • Phosphate groups connect the 5’ of one sugar to the 3’ of the next.

    • DNA primed in either 3’ to 5’ or 5’ to 3’ direction is crucial for the synthesis of new DNA strands, as DNA polymerases can only add nucleotides to the 3’ end of a growing strand.

    • 5’ end has a phosphate group, and the 3’ end has an –OH group.

Page 9: Sequence Importance in DNA

  • DNA Sequence

    • Specific base sequences are crucial for information storage.

    • Directionality indicated with 5’ and 3’ labels: e.g., 5’ - TACG - 3’, with complement 3’ - ATGC - 5’.

Page 10: DNA Double Helix Structure

  • DNA Double Helix

    • Formed by bonding of two complementary DNA strands. Each strand runs in opposite directions, known as antiparallel orientation, which is crucial for the proper pairing of nucleotide bases.

    • Strands held by hydrogen bonds between bases. The major and minor grooves of the helix provide binding sites for proteins that regulate DNA functions, allowing for essential processes such as replication and transcription.

    • Base pair rules: Purines pair with pyrimidines (A pairs with T; G pairs with C). The structure of the double helix not only stabilizes the genetic information but also facilitates the unwinding of strands during replication, ensuring that each daughter cell receives an accurate copy of the DNA.

    • Antiparallel orientation: one strand 5’ to 3’, other 3’ to 5’.

Page 11: Structural Elements of DNA

  • Features of the DNA Helix

    • Diameter of 2 nm, with a complete turn every 3.4 nm.

    • Illustration of nucleotide structures and bonds (A, T, C, G bases; sugar-phosphate backbone).

Page 12: Structural Grooves in DNA Helix

  • Grooves in Helix

    • Major and minor grooves provide accessibility for replication and gene expression. These grooves are essential for protein binding, allowing transcription factors and other regulatory proteins to interact with the DNA and influence gene activity.

    • Approximately 10 bases per helical turn.

Page 13: Transition to DNA Replication

  • Part 2 - Overview of DNA Replication

Page 14: Complementary DNA Replication Model

  • DNA Replication

    • Complementary model allows replication using parent strands as templates to build identical daughter strands.

    • Semi-conservative mechanism: each new strand has one parent and one daughter strand.

Page 15: DNA Replication Steps

  • Steps of DNA Replication

    • Separation of parent strands by breaking hydrogen bonds.

    • Synthesis of complementary daughter strands following AT/GC pair rules.

    • Role of DNA polymerases and processivity differences: leading strand (5’ to 3’) vs. lagging strand (3’ to 5’).

Page 16: Molecular Mechanism of DNA Replication

  • Part 3 - Molecular Mechanism of DNA Replication

Page 17: Origin of Replication

  • Origin of Replication (ori)

    • Designated starting point for DNA replication; bidirectional process from ori.

    • Site of replication activity (replication fork).

    • Forks join to complete replication.

Page 18: Differences in Prokaryotic and Eukaryotic Replication

  • Prokaryotes vs. Eukaryotes

    • Prokaryotes have a single ori; eukaryotes have multiple oris due to more DNA and multiple chromosomes.

Page 19: Functions of Key Enzymes

  • Replication Fork Enzymes

    • DNA helicase: separates DNA strands by breaking hydrogen bonds.

    • DNA topoisomerases: relieve tension from unwinding DNA.

    • Single-stranded binding proteins: prevent re-bonding of exposed bases.

Page 20: Synthesis of New Strands

  • New Strand Synthesis

    • Function of DNA polymerases: build complementary strands by bonding deoxynucleoside triphosphates.

    • Adherence to AT/GC base pairing rules.

Page 21: Priming Synthesis

  • DNA Primase Role

    • DNA polymerase requires a primer; DNA primase synthesizes short RNA primers at ori.

    • Primers prepare the DNA template strand for replication.

Page 22: Directionality in DNA Synthesis

  • Directionality in DNA Synthesis

    • DNA polymerase moves only in the 5’ to 3’ direction.

    • Leading strand: synthesized continuously (5’ to 3’).

    • Lagging strand: synthesized discontinuously (3’ to 5’).

Page 23: Lagging Strand Synthesis

  • Lagging Strand Synthesis

    • Synthesized in Okazaki fragments; requires various DNA polymerases (I, II, III).

    • Polymerase I: synthesizes lagging strand; polymerase II: proof-reading; polymerase III: leading and lagging strand synthesis.

Page 24: Joining Lagging Strand Fragments

  • Fragment Joining

    • Okazaki fragments initiated by RNA primers; removed by DNA polymerase I.

    • Gaps filled in by additional DNA synthesis using DNA ligase to covalently link fragments.

Page 25: Roles of Key Enzymes in Replication

  • Key Enzymes Functions

    • DNA helicase: separates DNA strands.

    • Single-strand binding protein: stabilizes single-stranded DNA.

    • Topoisomerase: releases supercoiling ahead of replication fork.

    • DNA primase: synthesizes RNA primers.

    • DNA polymerase: synthesizes DNA, removes primers, fills gaps.

    • DNA ligase: links adjacent Okazaki fragments.

Page 26: Accuracy in Replication

  • Accuracy of DNA Replication

    • High fidelity; errors are rare (1 mistake per 100 million nucleotides in bacteria).

    • Accuracy attributed to:

      • Base pairing kinetics (AT/GC specificity).

      • Active site specificity in DNA polymerase.

      • Proof-reading ability of DNA polymerases.

Page 27: Introduction to Telomeres

  • Part 4 - Telomeres and Telomerase

Page 28: Structure of Telomeres

  • Telomeres in Prokaryotes and Eukaryotes

    • Prokaryotes: single circular chromosome with no ends.

    • Eukaryotes: linear chromosomes with telomeres (non-coding sequences at ends).

    • Human telomere sequence: 5’–GGGTTA–3’.

Page 29: Issues with Telomere Shortening

  • Lagging Strand Issues

    • Lagging strand ends in 3’ overhang due to RNA primer placement; DNA polymerase cannot replicate tips.

    • Consequence: chromosomes shorten with each replication cycle.

Page 30: Role of Telomerase

  • Telomerase Function

    • Prevents telomere shortening by extending the DNA molecule.

    • Telomerase activity is upregulated in 90% of cancers; of interest to the anti-aging field.

Page 31: Chromosome Molecular Structure Overview

  • Part 5 - Molecular Structure of Eukaryotic Chromosomes

Page 32: Eukaryotic Chromosome Structure

  • Eukaryotic Chromosomes

    • Composed of multiple linear chromosomes; multiple DNA double helices.

    • Humans are diploid with 23 pairs of chromosomes (46 total).

    • Chromosomes consist of two copies, one inherited from each parent.

Page 33: Nucleosome Formation

  • Nucleosomes

    • How to fit 1 m of DNA into each cell:

      • DNA wrapped around histones (146 base pairs).

      • Nucleosomes form repeating structures with linker regions (20-100 bp) between them.

      • H1 histone binds linker regions.

Page 34: Higher Strucutre of Chromatin

  • 30 nm Fibers

    • Nucleosomes further condensed into a 30 nm fiber, forming coiled structures.

    • Combined action of histones, nucleosomes, and fibers contributes to 50x compaction of DNA.

Page 35: Chromatin Configuration

  • Chromatin Loops

    • Radial loop domains contain 25,000 - 200,000 bp, anchored to the nuclear matrix (nuclear lamina).

    • Non-uniform compaction observed in heterochromatin (highly condensed) versus euchromatin (expressed DNA).

Page 36: Chromosomal Territory Organization

  • Chromosomal Territories

    • In non-dividing cells, chromosomes occupy distinct territories influenced by nuclear lamina interactions.

Page 37: Compaction During Cell Division

  • Further Compaction

    • Maximum DNA compaction occurs during cell division (mitosis/meiosis).

    • Chromosomes condense into X-shaped structures with identical copies linked at centromeres.