Genetics Study Guide: DNA Replication, Transcription, Translation, Mutation, and Repair

DNA Replication

DNA Polymerases

DNA replication is the process by which a cell duplicates its DNA, ensuring genetic information is passed to daughter cells. Key enzymes are involved in this process:

• DNA Polymerase III: Main enzyme adding nucleotides in the 5'→3' direction in prokaryotes.

• DNA Polymerase I: Removes RNA primers and replaces them with DNA (5'→3' exonuclease activity).

Leading vs. Lagging Strands

• Leading strand: Synthesized continuously toward the replication fork.

• Lagging strand: Synthesized discontinuously away from the fork, forming Okazaki fragments.

Key Enzymes

• Helicase: Unwinds DNA.

• Primase: Synthesizes RNA primer.

• Topoisomerase: Relieves supercoiling ahead of the fork.

• Ligase: Seals nicks between Okazaki fragments.

Proofreading

• DNA polymerase has 3'→5' exonuclease activity for proofreading.

Transcription

Key Points

Transcription is the synthesis of RNA from a DNA template. It involves several steps and factors:

• RNA Polymerases:

  • Prokaryotes: Single RNA polymerase synthesizes all RNA types except 5S rRNA.

  • Eukaryotes: RNA Polymerase I (rRNA), II (mRNA, some snRNA), III (tRNA, 5S rRNA).

• Initiation:

  • Prokaryotes: Sigma factor recognizes -10 (Pribnow box) and -35 regions.

  • Eukaryotes: TFIID binds TATA box.

• Processing (Eukaryotes):

  • 5' capping

  • Polyadenylation (addition of poly-A tail at 3' end)

  • Splicing (removal of introns by spliceosome)

  • Alternate splicing (produces multiple mRNAs from one gene)

• Termination:

  • Prokaryotes: Rho-dependent or intrinsic (hairpin structure)

  • Eukaryotes: Cleavage at polyadenylation signal

Translation

Initiation

• Prokaryotes: Shine-Dalgarno sequence aligns mRNA with small ribosomal subunit.

• Eukaryotes: Small subunit binds 5' cap and scans for start codon (AUG).

tRNA & Aminoacyl-tRNA Synthetase

• tRNA attaches amino acid via ester bond.

Ribosomes

• Prokaryotic: 70S (50S + 30S)

• Eukaryotic: 80S (60S + 40S)

Elongation & Termination

• Peptide bond formation catalyzed by ribosome's peptidyl transferase activity.

• Termination occurs when stop codon reaches A site; release factors bind and disassemble the complex.

Gene Regulation

Promoters & Enhancers

• Promoters: DNA sequences where RNA polymerase binds.

• Enhancers: Regulatory sequences that increase transcription from a distance.

Operators

• DNA elements acting for repressors in prokaryotes.

Repressors

• Bind to operators, blocking transcription.

RecA Protein

• Damage-induced repair system in prokaryotes; promotes homologous recombination.

Mutations

Types of Mutations

• Silent Mutation: No amino acid change.

• Missense Mutation: One amino acid changed.

• Nonsense Mutation: Codon changed to stop codon.

• Frameshift Mutation: Insertion/deletion changes reading frame.

• Transition: Purine ↔ purine or pyrimidine ↔ pyrimidine.

• Transversion: Purine ↔ pyrimidine.

Effects of Mutations

• Loss-of-function: Protein loses activity.

• Gain-of-function: Protein gains new activity.

• Null mutation: Complete loss of function.

DNA Repair

Base Excision Repair (BER)

• DNA Glycosylase: Removes damaged base.

• Endonuclease: Cuts backbone.

• DNA Polymerase: Fills gap.

• Ligase: Seals nick.

Nucleotide Excision Repair (NER)

• Removes bulky lesions (e.g., thymine dimers).

Mismatch Repair (MMR)

• MutS recognizes mismatches.

• MutH cleaves newly synthesized strand.

Homologous Recombination

• Uses homologous DNA as template for repair.

• RecA facilitates strand invasion in prokaryotes.

Non-Homologous End Joining (NHEJ)

• Directly joins broken DNA ends.

Post-Transcriptional Modifications (Eukaryotes)

• 5' capping: Addition of methylated guanine cap for stability and translation initiation.

• Polyadenylation: Addition of poly-A tail at 3' end for stability.

• Splicing: Removal of introns, joining of exons.

• Alternate splicing: Generates multiple proteins from one gene.

Ribozymes

• Catalytic RNA molecules capable of acting like enzymes (e.g., peptidyl transferase activity).

Homologous Recombination and RecA

• RecA promotes strand invasion in prokaryotic recombination and DNA repair.

Key Terms and Definitions

• Consensus Sequence: The most common bases found at each position among many genes; serves as a recognition site for transcription factors.

• Shine-Dalgarno Sequence: Ribosome binding site in prokaryotic mRNA, aligns mRNA for translation initiation.

• Pribnow Box: -10 region in prokaryotic promoters, recognized by sigma factor.

• TATA Box: Eukaryotic promoter element, recognized by transcription factors.

• Polyadenylation Signal: Sequence in eukaryotic mRNA that signals addition of poly-A tail.

Example Table: Types of Mutations and Their Effects

Mutation Type	Definition	Effect on Protein
Silent	No change in amino acid	No effect
Missense	Change in one amino acid	Possible loss or gain of function
Nonsense	Change to stop codon	Truncated protein
Frameshift	Insertion/deletion shifts reading frame	Altered protein sequence downstream

Key Equations

• Central Dogma of Molecular Biology:

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

• Base Pairing:

$\text{A} = \text{T}, \text{G} = \text{C}$

• Genetic Code Table: (Additional info: Refer to standard codon table for translation of mRNA to amino acids.)

Additional info:

• Some context and definitions have been expanded for clarity and completeness.

• Examples and applications are provided to illustrate key concepts.