DNA, RNA, and Gene Expression: Study Guide for Exam 3

Structure and Function of DNA and RNA

DNA and RNA Structure

DNA and RNA are nucleic acids composed of nucleotide monomers. Their structure determines their function in genetic information storage and transfer.

• 5'-to-3' Directionality: Nucleic acid strands have directionality, defined by the 5' (five-prime) and 3' (three-prime) carbon atoms of the sugar in their backbone. New nucleotides are always added to the 3' end.

• Antiparallel Nature: In double-stranded DNA, the two strands run in opposite directions (one 5'→3', the other 3'→5').

• Stability Differences: DNA is more chemically stable than RNA due to the absence of a 2'-hydroxyl group in deoxyribose, making RNA more prone to hydrolysis.

Example: The sequence 5'-ATCG-3' pairs with 3'-TAGC-5' in DNA.

Discovery of DNA as the Hereditary Molecule

Historical Experiments and the "RNA World" Hypothesis

DNA was identified as the hereditary material through experiments such as those by Avery, MacLeod, and McCarty, and Hershey and Chase. The "RNA world" hypothesis suggests that RNA may have been the original genetic material in early life forms due to its ability to store information and catalyze reactions.

• Key Experiments: Transformation in bacteria (Griffith), DNA as transforming principle (Avery et al.), and bacteriophage labeling (Hershey & Chase).

• RNA World: RNA can act as both genetic material and as a catalyst (ribozymes).

DNA Replication

Leading and Lagging Strands

During DNA replication, the two strands are copied differently due to their antiparallel orientation.

• Leading Strand: Synthesized continuously in the 5'→3' direction toward the replication fork.

• Lagging Strand: Synthesized discontinuously as Okazaki fragments, away from the replication fork.

Example: If the replication fork moves right, the lower strand (3'→5') is the template for the leading strand.

Role of the 3'-OH and Primase

• 3'-OH Group: DNA polymerase adds nucleotides to the free 3'-OH group of the growing strand.

• Primase: Synthesizes a short RNA primer to provide a 3'-OH for DNA polymerase to begin synthesis.

Equation: $\text{(dNMP)}_n + dNTP \rightarrow \text{(dNMP)}_{n+1} + PP_i$

Mutation Prevention and Repair

• Mutations: Changes in DNA sequence can disrupt gene function and cause disease.

• Safeguards: Proofreading by DNA polymerase, mismatch repair, and excision repair mechanisms help maintain DNA integrity.

Transcription and RNA Processing

Transcription: From DNA to RNA

• Template vs. Coding Strand: The template strand is used to synthesize RNA; the coding strand matches the RNA sequence (except T→U).

• Promoter Directionality: The orientation of the promoter determines which DNA strand is transcribed.

Example: Given a DNA template 3'-TAC-5', the RNA produced is 5'-AUG-3'.

RNA Processing in Eukaryotes

• 5' Cap: A modified guanine nucleotide added to the 5' end for stability and ribosome recognition.

• Poly(A) Tail: A string of adenines added to the 3' end for stability and export from the nucleus.

• Splicing: Removal of introns and joining of exons; alternative splicing allows one gene to produce multiple proteins.

Translation and the Genetic Code

Reading Frame and Protein Synthesis

• Reading Frame: The way nucleotides are grouped into codons (sets of three) determines the amino acid sequence.

• Predicting Protein Sequence: Use the mRNA sequence and the genetic code to determine the amino acid sequence.

Example: mRNA 5'-AUGGCC-3' codes for Met-Ala.

Mechanism of Translation

• Ribosome: Site of protein synthesis; has A, P, and E sites for tRNA binding.

• Peptide Bond Formation: Occurs in the ribosome's large subunit between amino acids carried by tRNAs.

Equation: $\text{Amino acid}_1 + \text{Amino acid}_2 \rightarrow \text{Dipeptide} + H_2O$

Gene Expression and Regulation

Differential Gene Expression

All cells contain the same DNA, but different genes are expressed in different cell types due to regulatory mechanisms.

• DNA Accessibility: Chromatin structure (e.g., histone modification) affects whether genes are accessible for transcription.

• Transcriptional Regulation: Activators and repressors bind to regulatory elements to increase or decrease transcription.

Post-Transcriptional and Post-Translational Regulation

• Post-Transcriptional: mRNA splicing, editing, transport, and degradation affect gene expression.

• Post-Translational: Protein folding, modification (e.g., phosphorylation), and degradation regulate protein activity.

Regulatory Elements: Activators vs. Repressors

Element	Function
Activator	Increases transcription by helping RNA polymerase bind to the promoter
Repressor	Decreases transcription by blocking RNA polymerase or recruiting silencing complexes

Additional info: This guide covers core concepts from chapters on the molecular basis of inheritance, gene expression, and regulation (Ch. 16–18). For exam preparation, practice predicting sequences and identifying regulatory mechanisms using sample DNA and RNA sequences.