Molecular Genetics and Regulation of Gene Expression: Study Guide

Chapter 4: Nucleic Acids and Their Structure

Structure of Nucleosides and Nucleotides

• Nucleoside: Consists of a pentose sugar (ribose or deoxyribose) bonded to a nitrogenous base (purine or pyrimidine) without any phosphate group.

• Nucleotide: A nucleoside with one or more phosphate groups attached to the 5' carbon of the sugar.

• Pentose sugars: Ribose (in RNA) and deoxyribose (in DNA; lacks an oxygen atom at the 2' position).

• Bases in DNA: Adenine (A), Thymine (T), Cytosine (C), Guanine (G).

• Bases in RNA: Adenine (A), Uracil (U), Cytosine (C), Guanine (G).

Scientific Discoveries and Researchers

• Key experiments (e.g., Avery, Hershey-Chase, Watson & Crick, Chargaff) built the foundation for understanding DNA structure and function.

• Scientific progress is cumulative; each discovery leads to new questions and experiments.

Chargaff’s Rule and Base Pairing

• Chargaff’s Rule: In DNA, the amount of A = T and G = C.

• Base pairing: A pairs with T (or U in RNA) via 2 hydrogen bonds; G pairs with C via 3 hydrogen bonds (stronger pairing).

Phosphodiester Linkages

• Phosphodiester bond: Covalent bond linking the 3' carbon of one sugar to the 5' phosphate of the next nucleotide.

• Formed via a condensation reaction, releasing water.

Purines vs. Pyrimidines

• Purines: Double-ring structures (Adenine, Guanine).

• Pyrimidines: Single-ring structures (Cytosine, Thymine, Uracil).

• Significance: Purine-pyrimidine pairing maintains uniform DNA width.

Antiparallel Strands and Directionality

• DNA strands run in opposite directions: one 5' → 3', the other 3' → 5'.

• Nucleotides are always added to the 3' end during synthesis.

Chapter 15: DNA Replication and Repair

Base Pairing and Nucleotide Addition

• Purines (A, G) pair with pyrimidines (T/U, C).

• DNA replication is anabolic and endergonic; energy is provided by hydrolysis of dNTPs (e.g., dATP, dCTP).

• Hydrolysis of pyrophosphate ($dNTP \rightarrow dNMP + PP_i$) drives the reaction forward.

Semi-Conservative Replication

• Each new DNA molecule consists of one parental and one newly synthesized strand.

Origin of Replication

• Prokaryotes: Single origin of replication.

• Eukaryotes: Multiple origins of replication per chromosome.

Enzymes in DNA Replication

• Helicase: Unwinds the DNA double helix.

• Topoisomerase: Relieves supercoiling ahead of the replication fork.

• Primase: Synthesizes short RNA primers to provide a 3' OH group.

• DNA Polymerase III: Main enzyme for DNA synthesis (prokaryotes).

• DNA Polymerase I: Removes RNA primers and replaces them with DNA.

• Ligase: Seals nicks between Okazaki fragments.

RNA Primer and DNA Elongation

• DNA polymerases can only add nucleotides to an existing 3' OH group.

• Elongation occurs in the 5' → 3' direction.

Leading vs. Lagging Strands and Okazaki Fragments

• Leading strand: Synthesized continuously toward the replication fork.

• Lagging strand: Synthesized discontinuously away from the fork in short segments called Okazaki fragments.

DNA Replisome

• Complex of proteins and enzymes that carry out DNA replication.

Telomeres and Telomerase

• Telomeres: Repetitive DNA sequences at chromosome ends; protect against loss of genetic information.

• Telomerase: Enzyme that extends telomeres; active in germ cells, stem cells, and some cancer cells.

DNA Repair Mechanisms

• Mutagen: Agent that causes DNA mutations (e.g., UV light, chemicals).

• Thymine dimer: Covalent linkage of adjacent thymines, often caused by UV light.

• Mismatch repair: Corrects errors missed by DNA polymerase proofreading.

• Nucleotide excision repair: Removes bulky lesions (e.g., thymine dimers) and replaces with correct nucleotides.

Chapters 16 & 17: The Central Dogma and Gene Expression

The Central Dogma of Molecular Biology

• Information flows from DNA → RNA → Protein.

• Transcription: DNA is transcribed into RNA.

• Translation: RNA is translated into protein.

The Genetic Code and Codons

• Genetic code: Set of rules by which nucleotide sequences specify amino acids.

• Codon: Sequence of three nucleotides in mRNA that codes for a specific amino acid.

• Start codon: AUG (methionine); Stop codons: UAA, UAG, UGA.

Transcription and Translation in Prokaryotes vs. Eukaryotes

• Prokaryotes: Transcription and translation occur simultaneously in the cytoplasm.

• Eukaryotes: Transcription occurs in the nucleus; translation in the cytoplasm.

Mechanism of Transcription

• RNA polymerase: Synthesizes RNA from DNA template.

• Transcription factors: Required for initiation in eukaryotes; bind to promoter regions (e.g., TATA box).

• Promoter: DNA sequence where RNA polymerase binds to initiate transcription.

• TATA box: Conserved promoter sequence in eukaryotes; helps position RNA polymerase.

• Template strand: DNA strand used as a template for RNA synthesis.

• RNA is synthesized 5' → 3' (nucleotides added to 3' end).

mRNA Processing in Eukaryotes

• 5' cap: Modified guanine nucleotide added to 5' end for stability and ribosome binding.

• Poly-A tail: String of adenines added to 3' end for stability and export from nucleus.

• Splicing: Removal of non-coding introns; exons are joined to form mature mRNA.

• Introns: Non-coding sequences removed during splicing.

• Exons: Coding sequences retained in mature mRNA.

Translation: tRNA, Ribosomes, and the Genetic Code

• tRNA: Transfers amino acids to ribosome; contains anticodon complementary to mRNA codon.

• Aminoacyl-tRNA synthetase: Enzyme that attaches correct amino acid to tRNA.

• Ribosomes: Composed of rRNA and proteins; sites of protein synthesis.

• Three sites: A (aminoacyl), P (peptidyl), E (exit).

• Peptide bonds form between amino acids during elongation.

Mutations and Their Effects

• Point mutations: Change in a single nucleotide.

• Silent mutation: No change in amino acid sequence.

• Missense mutation: Changes one amino acid.

• Nonsense mutation: Introduces a premature stop codon.

• Insertions/Deletions: Addition or loss of nucleotides; may cause frameshift mutations, altering downstream amino acid sequence.

Chapters 18 & 19: Regulation of Gene Expression

Importance of Gene Regulation

• Allows cells to respond to environmental changes and differentiate during development.

Transcriptional Regulation

• Primary control point, especially in bacteria.

Prokaryotic Regulation: Operons

• Operator: DNA segment where regulatory proteins bind.

• Operon: Cluster of genes under control of a single promoter and operator.

• Negative control: Repressor protein binds operator to block transcription.

• Repressible operon: Usually on; can be turned off (e.g., trp operon).

• Inducible operon: Usually off; can be turned on (e.g., lac operon).

• Inducer: Molecule that inactivates repressor (e.g., allolactose for lac operon).

• Co-repressor: Molecule that activates repressor (e.g., tryptophan for trp operon).

• Activator protein: Increases transcription when bound to DNA (e.g., AraC with arabinose).

Examples of Prokaryotic Operons

Operon	Type	Regulatory Molecule	Pathway Regulated
lac operon	Inducible	Inducer (allolactose)	Lactose metabolism
trp operon	Repressible	Co-repressor (tryptophan)	Tryptophan synthesis
ara operon	Inducible	Activator (AraC + arabinose)	Arabinose metabolism

Eukaryotic Regulation: Chromatin and Transcription Factors

• Chromatin: DNA-protein complex; "beads on a string" structure (beads = nucleosomes, string = DNA).

• Histones: Proteins around which DNA is wrapped to form nucleosomes.

• Chromatin compaction reduces gene expression by limiting access to DNA.

• DNA methylation: Addition of methyl groups to DNA; generally represses gene expression.

• Regulatory transcription factors: Bind to enhancers; increase or decrease transcription (distinct from basal/general transcription factors).

• Enhancer: DNA sequence bound by activators to increase transcription.

Alternative RNA Splicing and Post-Transcriptional Control

• Alternative splicing: Different combinations of exons can be joined to produce multiple mRNAs from one gene.

• mRNA and protein degradation rates affect gene expression levels.

• Proteasome: Protein complex that degrades unneeded or damaged proteins.

Additional info:

• Gene regulation is essential for cellular differentiation and adaptation.

• Mutations in regulatory regions can have significant effects on phenotype.