DNA, Chromosomes, and the Nucleus: Structure, Packaging, and Function

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Chapter 16: DNA, Chromosomes, and the Nucleus (Part 2)

Student Learning Outcomes

This chapter covers the molecular structure of DNA, the organization and packaging of chromosomes, and the structure and function of the nucleus. Students should be able to:

Describe the double helix structure and the bonds that hold DNA together.
Compare and contrast bacterial, mitochondrial, chloroplast, and eukaryotic nuclear genomes.
Explain the levels of eukaryotic DNA packaging and factors influencing chromosome condensation.
Describe the structure of the nucleus and nuclear pores.
Understand the mechanism for nuclear import/export.
Identify the main types of RNAs made in cells.
Explain the key characteristics of the genetic code and how to read it.
Describe the types of RNA processing in different cell types.
List the main cellular components required for translation.
Compare the composition and localization of bacterial/eukaryotic ribosomes.
Describe the steps in prokaryotic translation.
Explain co-translational import of polypeptides.
Describe how start and stop transfer sequences produce integral proteins.

DNA Structure

Discovery and Significance

Experiments established DNA as the molecule of inheritance, raising key questions about its replication and three-dimensional structure.

DNA is the hereditary material in cells.
Understanding DNA structure is essential for explaining how genetic information is stored and replicated.

Chargaff's Rules

Base Composition and Pairing

Erwin Chargaff's experiments revealed consistent relationships between the four DNA bases across species.

Proportion of Adenine (A) = Proportion of Thymine (T)
Proportion of Guanine (G) = Proportion of Cytosine (C)
These relationships are known as Chargaff's Rules.
The rules provided critical evidence for the double-helix model proposed by Watson and Crick.

Table: DNA Base Composition Data (from slide)

Organism	A (%)	T (%)	G (%)	C (%)	A/T Ratio	G/C Ratio
Human	28.4	28.4	21.1	22.1	1.00	0.95
Calf Thymus	28.1	28.4	22.5	21.0	0.99	1.07
Salmon	28.3	28.2	22.6	20.9	1.00	1.08
Yeast	31.3	32.9	18.7	15.1	0.95	1.06
Bacterium	36.9	36.9	14.0	12.8	1.02	1.09

Additional info: Table values show that A/T and G/C ratios are close to 1, supporting base pairing.

Watson-Crick Double Helix Model

Structural Features

The double helix model describes the physical structure of DNA and explains how genetic information is stored and replicated.

Sugar-phosphate backbone forms the outside of the helix.
Nitrogenous bases (A, T, G, C) are on the inside, paired via hydrogen bonds.
Base pairing: A pairs with T, G pairs with C.
DNA is a right-handed helix with about 10 nucleotide pairs per complete turn.
Diameter of the helix: ~2 nm; distance per nucleotide pair: 0.34 nm.

Replication Mechanism:

Strands separate during replication.
Each strand serves as a template for synthesis of a new complementary strand.

Structural Variants of DNA

Forms of DNA Helix

DNA can exist in several structural forms, each with distinct properties.

B-DNA: Right-handed helix; most common form in cells.
Z-DNA: Left-handed helix; biological significance not fully understood.
A-DNA: Right-handed helix; shorter and thicker than B-DNA; rare in nature, but common in RNA double helices.

Denaturation and Renaturation of DNA

Physical Properties

DNA strands are held together by hydrogen bonds, which can be disrupted under certain conditions.

Denaturation (melting): Separation of DNA strands by increasing temperature or pH.
Single-stranded DNA absorbs more UV light (260 nm) than double-stranded DNA.
Melting temperature (): The temperature at which half the DNA is denatured; increases with higher G+C content.
Renaturation (annealing): Reformation of the double helix when temperature is lowered.

Equation for melting temperature:

DNA Packaging

Challenges and Solutions

DNA must be efficiently packaged to fit within cells and to regulate gene expression.

Bacterial chromosomes are supercoiled and folded into loops, localized to the nucleoid.
Bacterial plasmids are small, circular DNA molecules that replicate autonomously.
Eukaryotic DNA is complexed with proteins to form chromatin.

Chromatin and Chromosomes

Organization in Eukaryotes

Eukaryotic DNA interacts with histone proteins to form chromatin, which condenses into chromosomes during cell division.

Histones: Small, basic proteins rich in lysine and arginine; positively charged to interact with negatively charged DNA.
Mass of histones ≈ mass of DNA in a chromosome.

Nucleosomes

Basic Unit of Chromatin Structure

Nucleosomes are the fundamental repeating units of chromatin, facilitating DNA packaging.

Nucleosome core particle: Histone octamer (2x H2A-H2B dimers, 2x H3-H4 dimers) + 146 bp of DNA wrapped around it.
Linker DNA: DNA between adjacent nucleosomes; length varies among organisms.
Histone H1: Not part of the octamer; helps compact nucleosomes into higher-order structures.

Higher-Order Chromatin Packaging

Levels of Condensation

Chromatin is further compacted into fibers and loops to fit within the nucleus.

10-nm fiber: "Beads-on-a-string" structure; least condensed state.
30-nm fiber: More condensed; facilitated by histone H1.
DNA loops: 50,000–100,000 bp; stabilized by cohesin and attached to a chromosomal scaffold.

Chromatin Remodeling and Histone Modification

Regulation of Gene Expression

Post-translational modifications of histone tails regulate chromatin structure and gene activity.

Methylation (by HMT): Can activate or repress transcription.
Acetylation (by HAT): Opens chromatin, making it transcriptionally active.
Deacetylation (by HDAC): Closes chromatin, repressing transcription.
Combinations of modifications create a "histone code" that influences gene expression.

Euchromatin and Heterochromatin

Types and Functions

Chromosomal DNA exists in two main forms, each with distinct properties and functions.

Euchromatin: Loosely packed, diffuse, transcriptionally active.
Heterochromatin: Highly compacted, transcriptionally inactive; includes constitutive (permanently compacted, e.g., centromeres, telomeres) and facultative (can convert to euchromatin).

Organelle Genomes: Mitochondria and Chloroplasts

Structure and Function

Mitochondria and chloroplasts contain their own DNA, distinct from nuclear DNA.

Organelle DNA is usually circular and lacks histones.
Encodes some proteins required for organelle function; most proteins are nuclear-encoded.
Human mitochondrial genome: 16,569 bp, encodes 37 genes.
Chloroplast genome: ~160,000 bp, encodes ~120 genes.

The Nucleus

Structure and Function

The nucleus is the defining organelle of eukaryotic cells, housing chromosomes and regulating gene expression.

Site of DNA replication and transcription.
Enclosed by a double-membrane nuclear envelope.
Outer membrane is continuous with the endoplasmic reticulum (ER).
Nuclear space (between membranes) shares contents with ER lumen.

Nuclear Matrix and Lamina

Structural Support

The nuclear matrix and lamina provide structural integrity and organization to the nucleus.

Nuclear matrix: Insoluble fibrous network maintaining nuclear shape.
Nuclear lamina: Dense meshwork of lamin proteins lining the inner nuclear membrane.
Mutations in lamin A gene can cause disease (e.g., progeria).

Nuclear Pores and Transport

Exchange of Molecules

Nuclear pores are specialized channels that regulate the movement of molecules between the nucleus and cytoplasm.

Formed by fusion of inner and outer nuclear membranes.
Contain nuclear pore complexes (NPCs) made of nucleoporin proteins.
Allow passive diffusion of small molecules (<10 nm diameter).
Large proteins and RNAs require active transport via nuclear localization signals (NLS) and nuclear export signals (NES).

Nuclear Import and Export Mechanisms

Transport Pathways

Specific signals and transport proteins mediate the import and export of macromolecules through nuclear pores.

Nuclear Localization Signal (NLS): Short amino acid sequence (often rich in lysine and arginine) that targets proteins for import into the nucleus.
Importin: Receptor that binds NLS-containing proteins and transports them into the nucleus via the Ran/importin pathway.
Nuclear Export Signal (NES): Sequence on adaptor proteins that targets RNA-protein complexes for export; recognized by exportins.

Example: The classic NLS sequence: Pro-Lys-Lys-Lys-Arg-Lys-Val

Additional info: The Ran-GTP/importin cycle ensures directionality of nuclear import/export.