General Biology Study Guide: DNA, Central Dogma, Viruses, and Bacteria

Exam 2 Study Guide: DNA, Central Dogma, Viruses, and Bacteria

Overview

This study guide covers key concepts in molecular genetics, including the structure and replication of DNA, the central dogma of molecular biology, gene expression, the genetic code, mutations, and the genetics of viruses and bacteria. It is designed to help students prepare for a college-level General Biology exam.

DNA as Genetic Material

Discovery and Evidence

• Genetic Material Hypotheses: Early scientists debated whether DNA or protein was the genetic material of cells.

• Key Experiments:

  • Griffith's Experiment: Demonstrated transformation in bacteria, suggesting a 'transforming principle.'

  • Avery, MacLeod, and McCarty: Identified DNA as the transforming principle.

  • Hershey-Chase Experiment: Used bacteriophages to show DNA, not protein, is the genetic material.

• Model Organisms: Bacteriophages (viruses that infect bacteria) were crucial in these experiments due to their simplicity and clear genetic outcomes.

Structure of DNA

Determining DNA Structure

• Double Helix: DNA is a double-stranded helix, as determined by X-ray crystallography (Rosalind Franklin) and model building (Watson and Crick).

• Polynucleotide: DNA is a polymer made of nucleotide monomers.

• Nucleotide Structure: Each nucleotide consists of a phosphate group, a deoxyribose sugar, and a nitrogenous base.

• Nitrogenous Bases: Adenine (A), Thymine (T), Cytosine (C), Guanine (G). A pairs with T, C pairs with G (complementary base pairing).

• Antiparallel Strands: DNA strands run in opposite directions (5' to 3' and 3' to 5').

• Importance: The structure allows for accurate replication and storage of genetic information.

Table: DNA vs. RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Bases	A, T, C, G	A, U, C, G
Strands	Double-stranded	Single-stranded
Function	Genetic storage	Protein synthesis, regulation

DNA Replication

Process and Mechanisms

• Semiconservative Replication: Each new DNA molecule consists of one old and one new strand.

• Bidirectional Replication: Replication proceeds in both directions from the origin.

• Replication Origins: Eukaryotic chromosomes have multiple origins; prokaryotes usually have one.

• Replication Fork: The Y-shaped region where DNA is unwound and new strands are synthesized.

• Key Enzymes:

  • Helicase: Unwinds DNA.

  • DNA Polymerase: Synthesizes new DNA strands; proofreads for errors.

  • Primase: Synthesizes RNA primers.

  • Ligase: Joins Okazaki fragments on the lagging strand.

• Directionality: DNA is synthesized 5' to 3'.

• Proofreading: DNA polymerase corrects errors during replication.

Central Dogma of Molecular Biology

Overview

• Central Dogma: Information flows from DNA → RNA → Protein.

• Transcription: DNA is transcribed into messenger RNA (mRNA).

• Translation: mRNA is translated into a polypeptide (protein).

Gene Expression

Genes and Proteins

• Gene: A segment of DNA that codes for a functional product (usually a protein).

• One Gene-One Enzyme Hypothesis: Each gene codes for a single enzyme (now known to be an oversimplification).

• Transcription: Synthesis of RNA from a DNA template.

• Translation: Synthesis of protein from an mRNA template.

Genetic Code

• Codon: A sequence of three nucleotides in mRNA that specifies an amino acid.

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

• Start Codon: AUG (codes for methionine).

• Stop Codons: UAA, UAG, UGA (signal termination of translation).

Transcription

Process

• Initiation: RNA polymerase binds to promoter region.

• Elongation: RNA polymerase synthesizes RNA in the 5' to 3' direction.

• Termination: RNA polymerase releases the completed RNA transcript.

• Differences in Prokaryotes and Eukaryotes: Eukaryotic transcription involves RNA splicing (removal of introns), addition of 5' cap and 3' poly-A tail.

Translation

Process

• tRNA: Transfers amino acids to the ribosome during protein synthesis.

• Ribosome: Composed of rRNA and proteins; site of protein synthesis.

• Steps:

  1. Initiation: Ribosome assembles on mRNA.

  2. Elongation: Amino acids are added to the growing chain.

  3. Termination: Ribosome reaches a stop codon and releases the polypeptide.

• Polyribosome: Multiple ribosomes translating a single mRNA simultaneously.

Mutations

Types and Effects

• Silent Mutation: No change in amino acid sequence.

• Missense Mutation: Changes one amino acid.

• Nonsense Mutation: Introduces a premature stop codon.

• Frameshift Mutation: Insertion or deletion shifts the reading frame.

• Causes: Errors in replication, environmental factors, etc.

Viruses

Structure and Replication

• Virus: An infectious particle composed of nucleic acid (DNA or RNA) and a protein coat (capsid).

• Replication: Viruses reproduce only inside host cells.

• Bacteriophage: Virus that infects bacteria; can undergo lytic or lysogenic cycles.

• Animal Viruses: May have envelopes; replication cycles vary (e.g., retroviruses use reverse transcriptase).

• Emerging Viruses: New or previously uncommon viruses that can cause outbreaks (e.g., SARS, Ebola).

• Prions: Infectious proteins causing neurodegenerative diseases.

Bacterial Genetics

Gene Transfer

• Transformation: Uptake of naked DNA from the environment.

• Transduction: Transfer of DNA by bacteriophages.

• Conjugation: Direct transfer of DNA between bacteria via a pilus.

• Plasmids: Small, circular DNA molecules; can carry antibiotic resistance genes (R plasmids).

Table: Bacterial Gene Transfer Methods

Method	Description	Key Features
Transformation	Uptake of free DNA	Competent cells required
Transduction	DNA transfer by phage	Generalized or specialized
Conjugation	Direct cell-to-cell transfer	Requires F plasmid/pilus

Key Terms and Concepts

• Semiconservative Replication: Each new DNA molecule has one old and one new strand.

• Antiparallel: DNA strands run in opposite directions.

• Codon: Three-nucleotide sequence in mRNA.

• Mutation: Change in DNA sequence.

• Plasmid: Extra-chromosomal DNA in bacteria.

• Prion: Infectious protein.

Important Equations and Concepts

• Base Pairing Rule: $A = T$, $C = G$ in double-stranded DNA.

• Central Dogma: $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$

• Codon to Amino Acid Ratio: $\text{Number of codons} = 64$, $\text{Amino acids} = 20$

Example: If a DNA sequence is 5'-ATGCGT-3', the complementary RNA sequence is 5'-ACGCAU-3'.

Additional info: For a comprehensive understanding, students should refer to their textbook, lecture notes, and supplemental materials as this guide provides an overview of key concepts and topics.