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Chapter 4 and 12.5

🧬 Chapter 4: Nucleic Acids and Information Flow


Section 1: Structure of DNA

🔑 Key Ideas

  • DNA stores genetic information and copies itself.

  • DNA is a double helix composed of repeating nucleotides.

🧱 Components of DNA:

  • Nucleotide = phosphate + deoxyribose (sugar) + nitrogenous base (A, T, C, G)

  • Nucleoside = base + sugar (no phosphate)

  • Phosphodiester bonds link nucleotides together (strong covalent bonds).

📐 Structure Discovery:

  • Griffith's experiment: transformation in S. pneumoniae

  • Avery, MacLeod, McCarty: DNA is the genetic material

  • Watson & Crick: used Franklin's X-ray crystallography and Chargaff’s rules to model DNA as a right-handed double helix

🔁 Base Pairing Rule:

  • A pairs with T (2 H-bonds), G pairs with C (3 H-bonds)

  • Explains DNA’s replication fidelity and mutation resistance

  • DNA strands are antiparallel: 5′ → 3′ and 3′ → 5′


Section 2: DNA vs RNA

Feature

DNA

RNA

Sugar

Deoxyribose

Ribose

Bases

A, T, C, G

A, U, C, G

Structure

Double-stranded

Single-stranded

Stability

Stable

Less stable

Function

Long-term storage

Many roles (messenger, enzymatic, etc.)

🧪 RNA World Hypothesis: RNA may have been the original molecule of life due to its catalytic ability and role in early evolution.


Section 3: The Central Dogma

mermaid

CopyEdit

graph LR A[DNA] -->|Transcription| B[mRNA] B -->|Translation| C[Protein]

  • Information flows from gene to protein

  • Transcription: DNA → RNA

  • Translation: RNA → Protein


Section 4: Transcription

🧬 Where it happens:

  • Prokaryotes: cytoplasm

  • Eukaryotes: nucleus (due to nuclear membrane)

🔎 Key Players:

  • RNA Polymerase: catalyzes RNA synthesis

  • Promoter: DNA sequence signaling start (e.g., TATA box)

  • Template Strand: strand RNA is copied from

  • Coding Strand: same as RNA sequence, but with T instead of U

Transcription Steps:

  1. Initiation:

    • RNA polymerase + transcription factors bind promoter

    • DNA unwinds locally (transcription bubble)

  2. Elongation:

    • RNA is synthesized 5′ → 3′

    • Complementary to template strand

  3. Termination:

    • RNA polymerase releases RNA

    • In prokaryotes: directly terminates

    • In eukaryotes: coupled to mRNA processing


Section 5: Post-Transcriptional Modification (Eukaryotes)

Modification

Purpose

5′ Cap

Ribosome binding, stability

Poly-A Tail (3′)

Export, stability, translation

Splicing

Removes introns, joins exons

Alternative splicing

Creates protein diversity


Section 6: Genome Packaging (Chapter 12.5)

🧬 DNA Organization

  • DNA wraps around histone proteins forming nucleosomes

  • “Beads on a string” appearance

  • Compacts DNA ~50,000x

🧱 Chromatin Types

Type

Description

Gene Expression

Euchromatin

Loosely packed

Active

Heterochromatin

Densely packed

Inactive

🧠 Eukaryotes vs Prokaryotes

  • Eukaryotes: linear chromosomes, histones, nucleus

  • Prokaryotes: circular genome, no histones, cytoplasm


🧠 Practice Questions

🔄 Base Pairing Practice

Template strand: 3′-TACCGGATA-5′
mRNA transcript: 5′-AUGGCCUAU-3′


🔍 Conceptual Questions

  1. How does histone binding influence gene expression?

  2. What would happen if the 5′ cap wasn't added to mRNA?

  3. How does base-pairing ensure accurate transcription and replication?


🔗 Connection Questions

  1. What’s the functional advantage of alternative splicing for a multicellular organism?

  2. How is RNA stability influenced by both ends of the transcript?


🧾 Vocabulary to Know

  • Nucleotide / Nucleoside

  • Phosphodiester bond

  • Base-pairing rule

  • Antiparallel strands

  • RNA Polymerase

  • Promoter

  • Template / coding strand

  • Transcription factors

  • 5′ cap / poly-A tail

  • Intron / exon / splicing

  • Euchromatin / heterochromatin

  • Nucleosome / histone

    Why does euchromatin show higher gene expression than heterochromatin?

    • A. It's more tightly packed

    • B. It has more histones

    • C. It's more accessible to RNA polymerase

    • D. It's located outside the nucleus

  • Given the template strand 3′-TACGGTACG-5′, what is the RNA transcript?

    • A. 5′-AUGCCAUGC-3′

    • B. 3′-AUGCCAUGC-5′

    • C. 5′-TACGGTACG-3′

    • D. 5′-UACGGUACG-3′

  • Which of the following is NOT a post-transcriptional modification?

    • A. Polyadenylation

    • B. Exon splicing

    • C. Addition of 5′ cap

    • D. DNA methylation

  • If RNA polymerase II continuously binds to a mutated enhancer, what would be the likely effect?

    • A. No transcription

    • B. Sporadic transcription

    • C. Continuous transcription

    • D. RNA degradation

  • Which component provides the energy for RNA polymerization?

    • A. ATP from mitochondria

    • B. GTP binding proteins

    • C. The phosphate bonds in incoming NTPs

    • D. RNA helicase


📦 Chapter 12.5 – Genome Packaging

📘 Learning Goal

Understand how DNA is compacted into chromosomes and how chromatin structure affects gene expression.


🧬 Eukaryotic Genome Organization

🧱 Nucleosome Structure

  • Definition: The basic unit of DNA packaging in eukaryotes.

  • DNA wraps around histone proteins (a histone octamer) forming nucleosomes.

  • This "beads on a string" structure allows long DNA molecules to fit inside the nucleus.

📏 DNA Condensation

  • Nucleosomes are further coiled and supercoiled into condensed chromosomes.

  • This hierarchical structure enables efficient storage and regulation of DNA.


🔄 Chromatin Types

Chromatin Type

Structure

Gene Activity

Euchromatin

Loosely packed

Transcriptionally active

Heterochromatin

Densely packed

Transcriptionally silent

  • The degree of DNA packing influences gene expression: less compact = more accessible to transcription machinery.


🧪 Key Structures

  • Histones: Small, positively charged proteins that DNA wraps around. Their modifications can regulate gene accessibility.

  • DNA with histones forms chromatin.

  • DNA without histones (rare in eukaryotes) is unstructured and not protected.


🧠 Comparison: Eukaryotes vs. Prokaryotes

Feature

Eukaryotes

Prokaryotes

DNA shape

Linear

Circular

Location

Nucleus

Cytoplasm

Packaging

Wrapped around histones (nucleosomes)

No histones, supercoiling only

Organization

Chromosomes

Single circular DNA molecule

Key distinction: "DNA wraps around histones in eukaryotes" — not in prokaryotes.


🧪 Conceptual Question from Slides

What is one key difference between eukaryotic and prokaryotic DNA packaging?

Correct answer:
C. DNA wraps around histones in eukaryotes.


🧾 Vocabulary

  • Nucleosome: DNA + histone complex

  • Chromatin: General term for DNA-protein complex

  • Histone: Protein core for nucleosome

  • Euchromatin: Loose, gene-active DNA

  • Heterochromatin: Tight, gene-inactive DNA