Molecular Biology: Nucleic Acids, Gene Expression, and Regulation

Chapter 4: Nucleic Acids and the RNA World

Nucleotides in DNA and RNA

Nucleotides are the building blocks of nucleic acids. DNA and RNA differ in their nucleotide composition:

• DNA Nucleotides: Deoxyribose sugar, bases: Adenine (A), Thymine (T), Cytosine (C), Guanine (G)

• RNA Nucleotides: Ribose sugar, bases: Adenine (A), Uracil (U), Cytosine (C), Guanine (G)

Key Difference: DNA contains thymine, while RNA contains uracil. DNA has deoxyribose; RNA has ribose.

Primary Structure of DNA

The primary structure of DNA is its sequence of nucleotides joined by phosphodiester bonds, forming a sugar-phosphate backbone.

• Directionality: 5' to 3' end, based on the numbering of carbon atoms in the sugar.

• Sequence: The order of bases encodes genetic information.

Secondary Structure of DNA

The secondary structure is the famous double helix, described by Watson and Crick.

• Double Helix: Two antiparallel strands held together by hydrogen bonds between complementary bases (A-T, C-G).

• Base Pairing: A pairs with T (2 H-bonds), C pairs with G (3 H-bonds).

Tertiary Structure of DNA

Tertiary structure refers to the higher-order folding of DNA, such as supercoiling and packaging into chromosomes.

• Supercoiling: DNA twists upon itself to fit inside the cell.

• Chromatin: In eukaryotes, DNA wraps around histone proteins to form nucleosomes.

Structure-Function Relationship in DNA

• Stability: Double helix protects genetic information.

• Replication: Complementary base pairing allows accurate copying.

• Storage: Linear sequence encodes instructions for proteins.

Primary, Secondary, and Tertiary Structure of RNA

• Primary: Single-stranded sequence of ribonucleotides.

• Secondary: Intramolecular base pairing forms structures like hairpins and loops.

• Tertiary: Complex 3D shapes, enabling catalytic activity (ribozymes).

Functional Versatility of RNA

• Information Carrier: mRNA conveys genetic code from DNA to ribosomes.

• Catalysis: Some RNAs (ribozymes) catalyze reactions.

• Structural: rRNA forms part of ribosomes.

• Regulation: Small RNAs regulate gene expression.

Chapter 15: DNA Synthesis and Repair

Structure of DNA

DNA is a double helix with antiparallel strands, each composed of nucleotides with a deoxyribose sugar, phosphate group, and nitrogenous base.

Origin of Replication

• Definition: Specific sequence where DNA replication begins.

• Prokaryotes: Single origin per chromosome.

• Eukaryotes: Multiple origins per chromosome.

Leading and Lagging Strand Synthesis

• Leading Strand: Synthesized continuously in the 5' to 3' direction.

• Lagging Strand: Synthesized discontinuously as Okazaki fragments, later joined by DNA ligase.

Replication of Chromosome Ends

• Problem: DNA polymerase cannot fully replicate the 3' ends of linear chromosomes.

• Solution: Telomerase extends telomeres, preventing loss of genetic material.

Role of Telomerase

• Function: Adds repetitive DNA to chromosome ends (telomeres).

• Importance: Maintains chromosome integrity during cell division.

Effect of Telomere Length on Cell Division

• Short Telomeres: Limit cell division, leading to cellular aging (senescence).

• Long Telomeres: Allow more divisions; cancer cells often have active telomerase.

DNA Damage Repair Mechanisms

• Proofreading: DNA polymerase corrects errors during replication.

• Mismatch Repair: Enzymes fix incorrectly paired bases after replication.

• Nucleotide Excision Repair: Removes bulky DNA lesions (e.g., thymine dimers).

Chapter 16: How Genes Work

Genotype and Phenotype

• Genotype: Genetic makeup (DNA sequence).

• Phenotype: Observable traits, resulting from gene expression.

• Link: Genes encode proteins that determine phenotype.

Flow of Genetic Information

• Central Dogma: DNA → RNA → Protein

$\text{DNA} \xrightarrow{\text{transcription}} \text{RNA} \xrightarrow{\text{translation}} \text{Protein}$

Role of RNA in Protein Production

• mRNA: Carries genetic code from DNA to ribosome.

• tRNA: Brings amino acids to ribosome.

• rRNA: Forms core of ribosome's structure and catalyzes protein synthesis.

Genetic Code

• Triplet Code: Three nucleotides (codon) specify one amino acid.

• Redundancy: Multiple codons can code for the same amino acid.

• Universality: Nearly universal among organisms.

Applying the Genetic Code

• Given an mRNA sequence, use the codon table to determine the amino acid sequence.

Types of Mutations

• Point Mutations: Change in a single nucleotide (substitution, insertion, deletion).

• Chromosome Mutations: Large-scale changes (deletions, duplications, inversions, translocations).

Effects of Mutations on Fitness

• Beneficial: Increase fitness.

• Neutral: No effect on fitness.

• Deleterious: Decrease fitness.

Chapter 17: Transcription, RNA Processing, and Translation

Transcription Phases

• Initiation: RNA polymerase binds to promoter, DNA unwinds.

• Elongation: RNA polymerase synthesizes RNA strand.

• Termination: RNA polymerase releases RNA and detaches from DNA.

Transcription in Eukaryotes vs. Bacteria

• Bacteria: Single RNA polymerase, simple promoters, simultaneous transcription and translation.

• Eukaryotes: Multiple RNA polymerases, complex promoters, transcription in nucleus, RNA processing required.

RNA Processing in Eukaryotes

• 5' Cap: Modified guanine added to 5' end; protects mRNA and aids ribosome binding.

• Poly(A) Tail: Series of adenines added to 3' end; stabilizes mRNA and aids export from nucleus.

• Splicing: Removal of introns, joining of exons.

Translation: Decoding mRNA

• Ribosomes: Site of protein synthesis; composed of rRNA and proteins.

• mRNA: Provides the template.

• tRNA: Matches amino acids to codons via anticodon loop.

Translation Phases

• Initiation: Ribosome assembles at start codon (AUG).

• Elongation: Amino acids added one by one to growing polypeptide.

• Termination: Stop codon reached; release factor frees polypeptide.

Post-Translational Modification

• Definition: Chemical modifications after translation (e.g., phosphorylation, glycosylation).

• Function: Alters protein activity, stability, or location.

Chapter 18: Control of Gene Expression in Bacteria

Mechanisms of Gene Regulation

• Transcriptional Control: Regulates whether a gene is transcribed.

• Translational Control: Regulates mRNA translation.

• Post-Translational Control: Regulates protein activity after synthesis.

lac Operon Regulation

• Negative Control: Repressor binds operator, blocks transcription (lac repressor).

• Positive Control: Activator (CAP-cAMP) increases transcription when glucose is low.

trp vs. lac Operon

• trp Operon: Repressible; repressor active when tryptophan is present.

• lac Operon: Inducible; repressor inactivated by allolactose (lactose present).

Global vs. Single Operon Regulation

• Global Regulation: Controls multiple genes/operons simultaneously (e.g., catabolite repression).

• Single Operon Regulation: Controls one operon at a time.

Chapter 19: Control of Gene Expression in Eukaryotes

Chromatin Structure and Condensation

• Chromatin: DNA + histone proteins; can be condensed (heterochromatin) or open (euchromatin).

• Active Genes: Found in less condensed (euchromatin) regions.

• Chromatin Remodeling: Enzymes modify histones or DNA to change accessibility.

RNA Processing in Eukaryotes

• Alternative Splicing: Produces different mRNAs from the same gene, increasing protein diversity.

Regulatory DNA Elements

• Core Promoter: Site where RNA polymerase binds.

• Promoter-Proximal Elements: Regulatory sequences near promoter; bind specific transcription factors.

• Enhancers: Distant regulatory sequences; increase transcription when bound by activators.

Transcription Factors and DNA Recognition

• Transcription Factors: Proteins that bind DNA and regulate transcription.

• Specificity: Recognize specific DNA sequences via structural motifs (e.g., helix-turn-helix).

Translation and Post-Translational Control

• Translational Control: Regulates mRNA translation efficiency or stability.

• Post-Translational Control: Modifies proteins after synthesis (e.g., phosphorylation).

Gene Regulation and Cancer

• Tumor Suppressor Genes: Inhibit cell division; mutations can lead to cancer (e.g., p53).

• Proto-Oncogenes: Promote cell division; mutations can create oncogenes, driving cancer.

• p53: Mutations in p53 remove cell cycle control, promoting uncontrolled division.

Comparison: Gene Expression in Bacteria vs. Eukaryotes

Feature	Bacteria	Eukaryotes
Chromatin Structure	Absent	Present
Transcription/Translation	Coupled	Separated (nucleus/cytoplasm)
RNA Processing	Minimal	Extensive (capping, splicing, polyadenylation)
Regulation	Mainly at transcription	Multiple levels