BIOL 190A Final Exam Study Guide: Genetics, DNA, and Gene Expression

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Chapter 13: The Molecular Basis of Inheritance

Discovery and Structure of DNA

The discovery of DNA as the genetic material and its structure was a pivotal moment in biology. Several key experiments and researchers contributed to our understanding.

Griffith's Experiment: Demonstrated transformation in bacteria, suggesting a 'transforming principle' (later identified as DNA).
Chargaff's Rules: Showed that in DNA, the amount of adenine equals thymine, and cytosine equals guanine (A=T, C=G).
Hershey & Chase: Used bacteriophages to confirm that DNA, not protein, is the genetic material.
Watson & Crick: Proposed the double helix model of DNA structure.
Rosalind Franklin: Provided X-ray diffraction images crucial for understanding DNA's helical structure.
Meselson & Stahl: Demonstrated that DNA replication is semiconservative.

DNA Structure:

DNA is a double helix with two antiparallel strands.
Each strand is a polymer of nucleotides (phosphate, deoxyribose sugar, nitrogenous base).
Bases pair via hydrogen bonds: A with T, C with G.
Phosphodiester bonds link nucleotides in a strand.

Example: The antiparallel nature means one strand runs 5' to 3', the other 3' to 5'.

DNA Replication

DNA replication ensures genetic information is accurately passed to daughter cells.

Meselson and Stahl Experiment: Used isotopes of nitrogen to show each new DNA molecule has one old and one new strand (semiconservative).
Replication Bubble and Forks: Replication begins at origins, forming bubbles and forks where DNA is unwound.
Leading and Lagging Strands: DNA polymerase synthesizes the leading strand continuously and the lagging strand in Okazaki fragments.
RNA Primers: Short RNA sequences provide a starting point for DNA polymerase.
Enzymes Involved: Helicase (unwinds DNA), primase (synthesizes RNA primer), DNA polymerase (adds nucleotides), ligase (joins fragments).
Prokaryotic vs. Eukaryotic Replication: Prokaryotes have a single origin; eukaryotes have multiple origins and more complex machinery.
Proofreading and Repair: DNA polymerases correct errors; repair enzymes fix mismatches and damage.
End Replication Problem: Eukaryotic chromosomes shorten with each replication; telomerase extends telomeres to prevent loss of genetic information.

Chromatin Organization: DNA wraps around histone proteins to form nucleosomes, further compacted into higher-order structures.

DNA Technology

Modern techniques allow manipulation and analysis of DNA.

Recombinant DNA: Combining DNA from different sources using cloning vectors (e.g., plasmids).
Transgenic Organisms: Organisms with foreign genes inserted into their genome.
PCR (Polymerase Chain Reaction): Amplifies DNA using Taq polymerase, enabling rapid DNA analysis.
DNA Fingerprinting: Identifies individuals based on unique DNA patterns.
DNA Sequencing: Determines the order of nucleotides in DNA.
CRISPR: Genome editing tool for targeted DNA modification (general concept only).

Chapter 14: Gene Expression: From Gene to Protein

Central Dogma and Flow of Genetic Information

The central dogma describes the flow of genetic information: DNA → RNA → Protein.

Prokaryotes vs. Eukaryotes: In prokaryotes, transcription and translation occur in the cytoplasm; in eukaryotes, transcription occurs in the nucleus and translation in the cytoplasm.
Key Molecules: mRNA (messenger), tRNA (transfer), rRNA (ribosomal).

Properties of the Genetic Code

The genetic code is universal, redundant (degenerate), and unambiguous.
Codons (triplets of nucleotides) specify amino acids.

Transcription

Steps: Initiation, elongation, termination.
Polarity: RNA is synthesized 5' to 3' using the DNA template strand (3' to 5').
Types of RNA: mRNA (codes for proteins), tRNA (brings amino acids), rRNA (forms ribosomes).
Prokaryotes vs. Eukaryotes: Eukaryotes have more complex regulation and RNA processing.

RNA Processing in Eukaryotes

5' Cap: Modified guanine nucleotide added to the 5' end.
3' Poly-A Tail: Series of adenine nucleotides added to the 3' end.
Splicing: Removal of introns (non-coding regions); exons (coding regions) joined together.

Translation

Steps: Initiation, elongation, termination.
Ribosome Binding Sites: A (aminoacyl), P (peptidyl), E (exit) sites.
Polarity: Polypeptides synthesized from N-terminus (amino) to C-terminus (carboxyl).
Protein Processing: Folding and modification occur in the cytoplasm or endoplasmic reticulum.

Mutations

Classification by Scale: Small-scale (point mutations), large-scale (chromosomal mutations).
Classification by Cell Type: Somatic (non-inheritable), germline (heritable).
Types of Point Mutations:
- Silent: No change in amino acid.
- Missense: Changes one amino acid.
- Nonsense: Introduces a stop codon.
- Frameshift: Insertion or deletion alters reading frame.

Chapter 15: Regulation of Gene Expression

Prokaryotic Gene Regulation: Operons

Operons are clusters of genes regulated together in bacteria.

Main Components: Promoter, operator, structural genes, regulatory gene.
Repressible Operon (Trp Operon): Usually on; can be turned off by a repressor (negative feedback).
Inducible Operon (Lac Operon): Usually off; can be turned on in the presence of an inducer (lactose).
Negative vs. Positive Control: Negative control involves repressors; positive control involves activators (e.g., CAP in lac operon).

Eukaryotic Gene Regulation

Differences from Prokaryotes: More complex, involves chromatin structure and multiple regulatory elements.
Chromatin Modification: Histone acetylation and DNA methylation affect gene accessibility.
Combinatorial Control: Multiple transcription factors and regulatory sequences determine gene expression.

Chapter 16: Development, Stem Cells, and Cancer

Types of Cloning

Cell Cloning: Producing identical cells from a single cell.
Gene Cloning: Making copies of a specific gene.
Organismal Cloning: Creating a genetically identical organism (e.g., Dolly the sheep).
Therapeutic Cloning: Producing embryonic stem cells for medical treatment.

Types of Stem Cells

Embryonic Stem Cells: Pluripotent; can become any cell type. Types include totipotent (can form all tissues, including placenta) and pluripotent (all body cells).
Adult Stem Cells: Multipotent; limited to certain cell types (e.g., hematopoietic stem cells).
Induced Pluripotent Stem Cells (iPS): Adult cells reprogrammed to pluripotency.

Molecular Basis of Cancer

Proto-oncogenes: Normal genes that promote cell division; mutations can convert them to oncogenes (cancer-causing).
Oncogenes: Mutated genes that drive uncontrolled cell division.
Types of Mutations: Point mutations, gene amplification, chromosomal translocations.
RAS Mutations: Lead to constant cell signaling and division.
Tumor Suppressor Genes: Inhibit cell division; loss-of-function mutations can lead to cancer.
p53 Mutations: p53 protein regulates cell cycle and apoptosis; mutations disable this control.
Cumulative Effects: Multiple mutations accumulate in genes (e.g., colorectal and breast cancer models) to cause cancer.

Gene Type	Normal Function	Cancerous Mutation Effect
Proto-oncogene	Promotes cell division	Becomes oncogene, overstimulates division
Tumor suppressor	Inhibits cell division	Loss of function, fails to stop division
DNA repair gene	Fixes mutations	Loss of function, mutations accumulate

Additional info: For diagrams (e.g., replication fork, operon structure), refer to textbook figures for visual reinforcement. Practice drawing chromosome configurations for mitosis and meiosis, and use Punnett squares for genetics problems.