Genetics Exam 2 Study Guide: DNA, Chromosomes, Replication, Transcription, Translation, Mutation, and Chromosome Aberrations

Module 6: DNA and Chromosome Structure

Discovery and Structure of DNA

The discovery of DNA as the hereditary material was a pivotal moment in genetics, leading to the elucidation of its double helical structure and its role in storing genetic information.

• DNA Structure: DNA is a double helix composed of two antiparallel strands of nucleotides.

• Importance: DNA encodes genetic information, allowing for inheritance and variation.

• Key Experiments: Griffith, Avery-MacLeod-McCarty, and Hershey-Chase experiments established DNA as the genetic material.

• Watson and Crick Model: Proposed the double helix structure based on X-ray diffraction data from Rosalind Franklin.

Structural Characteristics of DNA and RNA

• Nucleotides: The building blocks of nucleic acids, each consisting of a phosphate group, a five-carbon sugar (deoxyribose in DNA, ribose in RNA), and a nitrogenous base.

• DNA vs. RNA: DNA contains deoxyribose and thymine; RNA contains ribose and uracil.

• Full Molecules: DNA is typically double-stranded; RNA is usually single-stranded but can form complex secondary structures.

Purines vs. Pyrimidines

• Purines: Adenine (A) and Guanine (G); double-ring structures.

• Pyrimidines: Cytosine (C), Thymine (T, in DNA), and Uracil (U, in RNA); single-ring structures.

• Base Pairing: A pairs with T (or U in RNA), G pairs with C via hydrogen bonds.

Chemical Bonding in Nucleic Acids

• Phosphodiester Bonds: Link nucleotides in a strand (3' to 5').

• Hydrogen Bonds: Hold complementary bases together between strands.

• Stacking Interactions: Stabilize the double helix via hydrophobic interactions between bases.

Genome Size and Trends

• Prokaryotes: Generally have smaller, circular genomes (e.g., E. coli ~4.6 Mb).

• Eukaryotes: Larger, linear genomes with significant non-coding DNA (e.g., human genome ~3.2 Gb).

Virus and Viral Genome Types

• Genome Types: DNA or RNA, single- or double-stranded, linear or circular.

• Retroviruses: RNA viruses that reverse transcribe their genome into DNA (e.g., HIV).

Human Genome Architecture and Repetitive DNA

• Repetitive DNA: Includes satellite DNA, minisatellites, microsatellites, and transposable elements.

• Transposons: Mobile genetic elements that can move within the genome.

LTR Retrotransposons

• Structure: Long Terminal Repeats (LTRs) flank coding regions; transpose via RNA intermediate.

Telomeres and Telomerase

• Telomeres: Repetitive DNA sequences at chromosome ends, protecting them from degradation.

• Telomerase: Enzyme that extends telomeres, especially active in germ cells and cancer cells.

Supercoiling and Associated Enzymes

• Supercoiling: Over- or under-winding of DNA; affects compaction and accessibility.

• Topoisomerases: Enzymes that relieve supercoiling by cutting and rejoining DNA strands.

Levels of DNA Packaging in Eukaryotes

• Nucleosome: DNA wrapped around histone octamers.

• Chromatin: Higher-order structures formed by nucleosome folding.

• Chromosome: Most condensed form, visible during cell division.

Histone Structure

• Core Histones: H2A, H2B, H3, H4 form the nucleosome core; H1 is the linker histone.

Module 7: DNA Replication

DNA Replication Mechanisms

DNA replication is the process by which a cell duplicates its DNA before cell division, ensuring genetic continuity.

• Enzymes: DNA polymerases, helicase, primase, ligase, single-strand binding proteins.

• Directionality: DNA synthesis occurs in the 5' to 3' direction.

• Bacterial vs. Eukaryotic Replication: Bacteria have a single origin of replication; eukaryotes have multiple origins.

Replication Forks

• Structure: Y-shaped region where DNA is unwound and replicated.

• Leading Strand: Synthesized continuously.

• Lagging Strand: Synthesized discontinuously as Okazaki fragments.

DNA Polymerases

• Bacteria: DNA Pol III (main replicative), DNA Pol I (removes RNA primers).

• Eukaryotes: DNA Pol α (primase activity), δ and ε (main replicative).

Telomerase and Chromosome Ends

• Problem: Linear chromosomes lose DNA at ends after each replication.

• Solution: Telomerase extends telomeres using an RNA template.

PCR and Taq Polymerase

• PCR (Polymerase Chain Reaction): Amplifies specific DNA sequences in vitro.

• Taq Polymerase: Heat-stable DNA polymerase from Thermus aquaticus.

Sanger Sequencing

• Method: Uses dideoxynucleotides (ddNTPs) to terminate DNA synthesis at specific bases.

• Application: Determining the nucleotide sequence of DNA fragments.

Module 8: Transcription and RNA Processing

tRNA Structure and Function

• Structure: Cloverleaf secondary structure with anticodon loop and amino acid attachment site.

• Function: Delivers specific amino acids to the ribosome during translation.

rRNA Function

• Role: Structural and catalytic component of ribosomes; facilitates peptide bond formation.

Transcription Mechanisms

• Initiation: RNA polymerase binds promoter; DNA unwinds.

• Elongation: RNA strand synthesized 5' to 3'.

• Termination: RNA polymerase releases the completed RNA transcript.

• Directionality: RNA is synthesized 5' to 3'; template DNA is read 3' to 5'.

Promoter Sequences and Architecture

• Promoter: DNA sequence upstream of gene; recognized by RNA polymerase and transcription factors.

• Consensus Sequences: -10 (TATA box in prokaryotes), -35 regions.

RNA Processing

• Introns: Non-coding sequences removed from pre-mRNA.

• Exons: Coding sequences joined to form mature mRNA.

• Other Modifications: 5' capping, 3' polyadenylation.

Module 9: Translation and Protein Structure

The Genetic Code

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

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

• Start Codon: AUG (methionine).

• Stop Codons: UAA, UAG, UGA.

Ribosome Structure and Activity

• Subunits: Large and small; composed of rRNA and proteins.

• Function: Catalyze peptide bond formation and ensure correct codon-anticodon pairing.

Translation Mechanisms

• Initiation: Assembly of ribosome on mRNA at start codon.

• Elongation: Sequential addition of amino acids.

• Termination: Release of polypeptide at stop codon.

• Directionality: Polypeptide synthesized from N-terminus to C-terminus.

2-D Electrophoresis

• Purpose: Separates proteins based on isoelectric point and molecular weight.

Shine-Dalgarno and Kozak Sequences

• Shine-Dalgarno (prokaryotes): Ribosome binding site upstream of start codon.

• Kozak Sequence (eukaryotes): Consensus sequence surrounding start codon, enhancing translation initiation.

Amino Acid and Protein Structure

• Levels of Structure: Primary (sequence), secondary (α-helix, β-sheet), tertiary (3D folding), quaternary (subunit assembly).

Module 10: Mutation, Repair, and Recombination

Types of Mutation

• SNPs: Single nucleotide polymorphisms.

• Indels: Insertions or deletions of bases.

• Point Mutations: Change in a single base pair.

• Somatic vs. Germ-line: Somatic mutations occur in body cells; germ-line in gametes.

• Forward vs. Reverse: Forward changes wild-type to mutant; reverse restores wild-type.

• Transitions: Purine to purine or pyrimidine to pyrimidine.

• Transversions: Purine to pyrimidine or vice versa.

Trinucleotide Repeat Disorders

• Definition: Expansion of three-nucleotide repeats causes disorders (e.g., Huntington's disease).

Mutagens

• Definition: Agents that increase mutation rate (e.g., chemicals, radiation).

DNA Repair Mechanisms

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

• Translesion DNA Synthesis: Specialized polymerases replicate past DNA lesions.

• Non-homologous End Joining (NHEJ): Repairs double-strand breaks by directly ligating ends.

• Synthesis-Dependent Strand Annealing (SDSA): Error-free repair using homologous sequences.

Holliday Junctions

• Structure: Cross-shaped DNA structure formed during homologous recombination.

• Resolution: Leads to crossover or non-crossover products.

The Ames Test

• Purpose: Detects mutagenic potential of chemicals using bacteria.

Module 11: Chromosome Aberrations and Transposition

Nondisjunction, Aneuploidy, and Gene Dosage

• Nondisjunction: Failure of chromosomes to separate properly during cell division.

• Aneuploidy: Abnormal number of chromosomes (e.g., trisomy 21).

• Gene Dosage: Changes in gene copy number affect phenotype.

Polyploidy

• Definition: More than two complete sets of chromosomes.

• Examples: Common in plants (e.g., wheat is hexaploid).

G-banding

• Technique: Chromosome staining method revealing characteristic banding patterns.

Chromosome Structural Changes

Type	Description
Translocation	Exchange of segments between non-homologous chromosomes
Deletion	Loss of a chromosome segment
Inversion	Reversal of a chromosome segment; can form tetravalent complexes during meiosis

Transposable Elements

Class	Mechanism	Example
Class I (Retrotransposons)	Copy and paste via RNA intermediate	LTR retrotransposons
Class II (DNA transposons)	Cut and paste via DNA intermediate	Bacterial insertion sequences

• Maize 'Jumping' Genes: Discovered by Barbara McClintock; first evidence of transposable elements.

• Replicative Transposition: Transposon is copied to a new site, original remains.

Gene Duplication and Pseudogenes

• Gene Duplication: Creation of extra gene copies; source of genetic novelty.

• Pseudogenes: Nonfunctional gene copies arising from duplication or retrotransposition.

Additional info: This guide expands on the listed topics with definitions, examples, and context to provide a comprehensive review for genetics students preparing for Exam 2.