DNA structure chapter 5

Course Schedule

  • Week of January 20

    • Wed, Jan 20

    • Chapter 1: Introduction to BIOL 213

    • Fri, Jan 22

    • Mon, Jan 25

    • Chapter 2: Chemical Components of Cells

    • Wed, Jan 27

    • Chapter 2: continued

    • Fri, Jan 29

    • Chapter 3: Energy, Catalysis and Biosynthesis

    • Mon, Feb 1

    • Chapter 3: continued

    • Wed, Feb 3

    • Chapter 4: Protein Structure and Function

    • Fri, Feb 5

    • Chapter 4: continued

    • Mon, Feb 8

    • Exam 1: Chapters (1, 2, 3, 4)

    • Chapter 11: continued

    • Chapter 12: Membrane Transport

  • Week of March 1

    • Mon, Mar 1

    • Chapter 13: How Cells Obtain Energy from Food

    • Wed, Mar 3

    • Chapter 13: continued

    • Fri, Mar 5

    • Chapter 14: Energy Generation in Mitochondria and Chloroplasts

    • Mon, Mar 8

    • Chapter 14: continued

    • Wed, Mar 10

    • Chapter 5: DNA and Chromosomes

    • Fri, Mar 12

    • Exam 2: Chapters (11, 12, 13, 14)

    • Mon, Mar 15

    • Chapter 5: continued

    • Wed, Mar 17

    • Chapter 6: DNA Replication, Repair and Recombination

    • Fri, Mar 19

    • Chapter 6: continued

    • Mon, Mar 22

    • Chapter 7: From DNA to Protein

    • Wed, Mar 24

    • Chapter 7: continued

    • Fri, Mar 26

    • Chapter 7: continued

    • Mon, Mar 29

    • Wed, Mar 31

    • Spring Break and Faculty and Staff Holiday

    • Fri, Apr 2

    • Chapter 8: Control of Gene Expression

    • Mon, Apr 5

    • Chapter 9: How Genes and Genomes Evolve

    • Wed, Apr 7

    • Chapter 9: continued

    • Fri, Apr 9

    • Chapter 15: Intracellular Compartments and Transport

    • Mon, Apr 12

    • Exam 3: Chapters (5, 6, 7, 8, 9)

    • Wed, Apr 14

    • Chapter 15: continued

    • Fri, Apr 16

    • Chapter 17: Cytoskeleton

    • Mon, Apr 19

    • Chapter 17: continued

    • Wed, Apr 21

    • Chapter 16: Cell Communication

    • Fri, Apr 23

    • Chapter 16: continued

    • Mon, Apr 26

    • Chapter 18: Cell Cycle Control and Cell Death

    • Wed, Apr 28

    • Chapter 18: continued

    • Fri, Apr 30

    • Chapter 19: Sexual Reproduction, Genetics and Human Disease

    • Mon, May 3

    • Chapter 19: continued

    • Wed, May 5

    • Chapter 20: Cancer

    • Fri, May 7

    • Chapter 20: continued

  • Summary of Topics Covered:

    • Cell constituents: Polysaccharides, Proteins, Lipids

    • Membrane Studies: Structure, Energy, Transport

    • DNA and Gene Expression Regulation

    • Cell Biology Concepts

Chapter 5: DNA and Chromosomes

Learning Objectives

  • Be able to:

    • Write a complementary DNA strand, labeling 3' and 5', given a single strand sequence

    • Describe, explain, and sketch the Avery/MacLeod/McCarty experiment

    • Predict the outcome of the A/M/M experiment if genetic information was protein or RNA

    • Describe, explain, and sketch the Hershey-Chase experiment

    • Design two experiments to determine the carrier of genetic information in a new organism infecting human cells

    • Sketch the Central Dogma, naming the molecules and processes involved

    • Compare DNA compaction in eukaryotes and prokaryotes

    • Sketch the arrangement of DNA on histones

    • Predict the effect of histone modifications (affecting histone charge) on histone-DNA binding tightness and provide justification

Outline of Chapter 5:

  1. Experimental demonstration that DNA contains genetic information

    • The Griffith experiment

    • The Avery-MacLeod-McCarty experiment

    • The Hershey-Chase experiment

  2. Structure of DNA

  3. The Genome

  4. Compaction of DNA, chromatin, and nucleosomes

Key Experiments in Demonstrating DNA as Genetic Material

Griffith Experiment

  • Frederick Griffith (1928) conducted studies on Streptococcus pneumoniae pathogenicity, showing transfer of material from heat-killed virulent strain to non-virulent strain, rendering the latter virulent: This process is termed transformation.

Avery, MacLeod and McCarty Experiment (1944)

  • Key Idea: A mixture’s effect on something can be tested by separating components.

  • Method: Enzyme treatments were used to destroy specific components of the mixture, which were then tested for their ability to transform R-strain cells using the following enzymes:

    • RNase

    • Protease

    • DNase

    • Lipase

    • Amylase

  • Results: This proved DNA to be the transforming principle.

Hershey-Chase Experiment (1952)

  • Investigated whether genetic information was carried by protein or DNA in phage viruses.

  • Method:

    • Labeling of phage DNA with 32P^{32}P and phage proteins with 35S^{35}S, followed by infection of bacteria and separation of components post-infection.

  • Finding: Post-experiment analysis showed that infected bacteria contained labeled DNA (32P^{32}P) but not the proteins (35S^{35}S).

Structure of DNA

Chargaff's Rule (early 1950s)

  • Erwin Chargaff revealed variation in base composition across species:

    • A = T and G = C, establishing equimolar amounts of A and T as well as G and C, leading to the conclusion that A+T<br>eqG+CA + T <br>eq G + C.

Watson-Crick Model (1953)

  • James Watson and Francis Crick proposed a double helical structure for DNA based on X-ray diffraction data from Rosalind Franklin and Maurice Wilkins.

  • Structural Aspects:

    • Two strands wrapped in a right-handed helix

    • Antiparallel strands with sugar-phosphate backbones outward, bases inward forming stable hydrogen bonds

    • Key Features:

    • Diameter uniform due to consistent base pair widths

    • 10 bases per helical turn

    • Presence of major and minor grooves, significant for protein interactions

Implications of the Watson-Crick Model

  • The linear arrangement of nucleotides enables storage of genetic information.

  • Complementarity in base pairing provides a replication mechanism for genetic information.

  • Nevertheless, aspects regarding the expression of genetic information remain an open question, prompting further investigation.

Central Dogma of Molecular Biology

  • Outlines the flow of genetic information in cells:

    • DNA Replication (5' to 3' direction)

    • Transcription to RNA

    • Translation to Protein

The Genome

  • Definition: The entire DNA complement of an organism.

  • Correlation: Complexity of the organism is often linked to genome size; more complex organisms typically have larger genomes.

  • Bioinformatics tools analyze sequenced genomes, identifying and quantifying genes.

  • The genome can be haploid, diploid, or polyploid, containing all information necessary for an organism's biology.

Compaction of DNA, Chromatin, and Nucleosomes

Organization of DNA in Chromosomes

  • Genomic DNA is organized into chromosomes that are elongated, single DNA strands associated with proteins, leading to a compact structure.

  • Packaging Ratio: Chromatin undergoes 10,000-fold compaction.

Nucleosomes

  • Basic units of eukaryotic chromatin structure.

  • Composed of histone octamers:

    • H2A, H2B, H3, H4 (core)

    • H1 (required for 30 nm fiber level packing)

  • Histones are positively charged, rich in lysine and arginine, and are conserved across species.

Levels of Chromosomal Organization

  • Nucleoid structure in prokaryotes lacks nucleosomes, featuring compact circular DNA.

  • Eukaryotic chromosomes demonstrate a multiscale organization:

    • 30 nm fiber formed by nucleosomal packing

    • Each DNA molecule packaged into mitotic chromosomes that are dramatically shorter than their extended forms.

Histone Modifications and Chromatin Remodeling

  • Chromatin remodeling complexes facilitate alterations in chromatin structure.

  • Modification of histone tails (e.g., trimethylation, acetylation) impacts gene expression and is fundamental to epigenetic regulation.