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

🧪 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)

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

🧠 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

• 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

🧪 Conceptual Question from Slides

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