Exam 2 Study Guide

Unit 2.1: DNA Structure and Replication

Key Concepts

1. DNA Structure

   • Double helix: Structure formed by two strands of nucleotides twisted around each other.

   • Nucleotides: Comprised of a phosphate group, a sugar (deoxyribose), and a nitrogenous base (Adenine (A), Thymine (T), Cytosine (C), Guanine (G)).

   • Base pairing rules:

     • Adenine (A) pairs with Thymine (T) via 2 hydrogen bonds.

     • Cytosine (C) pairs with Guanine (G) via 3 hydrogen bonds.

   • DNA functions:

     • Carries genetic information

     • Replicates itself

     • Generates genetic variation

2. DNA Replication

   • Helicase: Unwinds the DNA double helix.

   • SSBs (Single-strand binding proteins): Stabilize the single-stranded DNA during replication.

   • Primase: Adds a short RNA primer to the DNA template to start replication.

   • DNA polymerase: Enzyme that adds complementary nucleotides to the growing DNA strand, working in the 5’ to 3’ direction.

   • Okazaki fragments: Short segments of DNA synthesized on the lagging strand.

   • Ligase: Seals the gaps between Okazaki fragments by forming phosphodiester bonds.

3. DNA Packaging

   • Nucleosome: DNA wrapped around histone proteins.

   • Chromatin: Complex of DNA and proteins that forms chromosomes during cell division.

   • Chromosomes: Condensed chromatin visible during mitosis.

4. Central Dogma of Biology

   • Process: DNA → RNA → Protein.

   • DNA encodes the instructions for protein synthesis.

5. Mutations

   • Point mutations: A single nucleotide change (e.g., sickle cell anemia due to a single base substitution).

   • Frameshift mutations: Insertions or deletions that shift the reading frame, potentially leading to nonfunctional proteins.

Key Terms to Know

• Double helix: Twisted ladder structure of DNA.

• Nucleotide: Building block of DNA.

• Base pairing (A-T, C-G): Specific pairing of nitrogenous bases in DNA.

• Helicase: Enzyme unwinding the DNA double helix.

Unit 2.2: Transcription, Translation, and Gene Regulation

Key Concepts

1. Transcription

   • RNA polymerase: Enzyme that transcribes DNA into mRNA.

   • Pre-mRNA: Initial RNA transcript with both exons (coding) and introns (non-coding).

   • Spliceosome: Removes introns and joins exons to produce mature mRNA.

   • 5’ cap and 3’ poly-A tail: Modifications added to mRNA for stability and translation.

2. Translation

   • Ribosome: Reads mRNA and assembles amino acids into proteins.

   • tRNA: Transfers amino acids to the ribosome based on mRNA codons.

   • Codon: Sequence of three nucleotides coding for a specific amino acid.

3. Gene Regulation

   • Operon: Group of genes regulated together (e.g., lac operon in E. coli).

   • Inducible genes: Activated by specific molecules (e.g., lactose activates the lac operon).

   • Repressible genes: Deactivated by specific molecules (e.g., tryptophan turns off trp operon).

4. DNA Repair Mechanisms

   • Mismatch repair: Corrects base-pairing errors.

   • Base excision repair: Removes damaged bases and replaces them.

   • Nucleotide excision repair: Repairs DNA from UV-induced damage.

   • Homologous recombination: Repairs double-strand breaks using homologous templates.

   • Non-homologous end joining: Repair by directly ligating broken ends.

Key Terms to Know

• RNA polymerase: Enzyme transcribing DNA into RNA.

• Pre-mRNA: Initial transcript before processing.

• Exon: Coding region of a gene.

• Intron: Non-coding region removed during processing.

• Spliceosome: Complex joining exons in pre-mRNA.

• 5’ cap: Modified nucleotide for mRNA protection.

• 3’ poly-A tail: Stabilizing adenine stretch added to mRNA.

• Ribosome: Cellular machinery synthesizing proteins.

• tRNA: Transfers amino acids during translation.

• Codon: Set of three nucleotides coding for an amino acid.

• Operon: Group of regulated genes in prokaryotes.

• Lac operon: Operon controlling lactose metabolism.

• Mismatch repair: Corrects DNA base-pairing errors.

• Base excision repair: Removes damaged bases from DNA.

• Nucleotide excision repair: Removes DNA segments damaged by UV.

• Homologous recombination: Repairs DNA breaks with similar sequences.

• Non-homologous end joining: Directly repairs DNA ends.

Unit 2.3: Gene Regulation in Eukaryotes and Epigenetics

Key Concepts

1. Gene Regulation in Eukaryotes

   • Enhancers and silencers: Regulatory DNA sequences that influence gene expression.

   • Transcription factors: Proteins that bind to DNA and modulate transcription.

   • Alternative splicing: Enables multiple mRNA variants from a single gene.

   • RNA interference (RNAi): Small RNA molecules that silence gene expression.

2. HOX Genes

   • HOX genes: Control body plan development and are conserved across species.

3. Epigenetics

   • Epigenetics: Study of heritable gene expression changes not involving DNA sequence alteration.

   • Methyl groups: Chemically modify DNA to suppress gene activity.

   • Histones: Proteins that DNA wraps around, influencing gene activity.

   • Environmental factors can impact epigenetic changes.

Key Terms to Know

• Enhancer: DNA sequence enhancing gene transcription.

• Silencer: DNA sequence inhibiting gene transcription.

• Transcription factor: Protein regulating gene expression.

• Alternative splicing: Creation of multiple mRNA forms from a single gene.

• RNA interference (RNAi): Process silencing gene expression.

• miRNA: MicroRNA regulating gene expression.

• siRNA: Small interfering RNA that silences specific genes.

• HOX genes: Developmental control genes.

• Epigenetics: Gene expression changes not due to DNA sequence alteration.

• Methyl groups: Chemical modifications repressing gene expression.

• Histones: Protein complexes structuring nucleosomes.

Unit 2.4: Genomes and Genetic Diseases

Key Concepts

1. Human Genome Project

   • Completed the sequencing of the entire human genome.

   • Identified approximately 21,000 genes, with 1.5% coding for proteins.

   • Remaining 98.5% includes control regions, noncoding DNA, and repetitive DNA.

2. ENCODE Project

   • Demonstrated that 80% of the genome has a biochemical function, challenging the notion of "junk DNA".

   • RNA plays a significant role in gene regulation.

3. Genetic Diseases

   • Nondisjunction: Chromosome separation failure during meiosis, leading to conditions like Down syndrome (trisomy 21) and Turner syndrome (monosomy X).

   • Autosomal dominant disorders: Diseases from one dominant allele (e.g., Huntington's disease).

   • Autosomal recessive disorders: Requires two recessive alleles for condition expression (e.g., Galactosemia).

   • X-linked disorders: Genetic disorders due to mutations on the X chromosome (e.g., Hemophilia, color blindness).

Key Terms to Know

• Human Genome Project: International sequencing initiative.

• ENCODE Project: Functional element identification effort.

• Nondisjunction: Chromosome separation failure during meiosis.

• Trisomy: Extra chromosome presence (e.g., trisomy 21).

• Monosomy: Absence of a chromosome (e.g., monosomy X).

• Down syndrome: Genetic disorder from trisomy 21.

• Turner syndrome: Genetic disorder from monosomy X.

• Autosomal dominant disorders: Genetic disorders from a dominant allele.

• Autosomal recessive disorders: Disorders requiring two recessive alleles.

• X-linked disorders: Disorders from mutations on the X chromosome.

Unit 2.5: Personalized Medicine and Cancer

Key Concepts

1. Personalized Medicine

   • Integrates genomics, proteomics, and epigenomics for tailored treatments.

   • SNPs (Single Nucleotide Polymorphisms): Genetic variations that help predict disease risk.

   • Pharmacogenomics: Assesses genetic profiles to forecast drug effectiveness.

2. Cancer

   • Result of mutations in oncogenes and tumor suppressor genes.

   • EGFR: Oncogene related to cell division.

   • BRCA1/BRCA2: Tumor suppressor genes linked to breast cancer.

   • Targeted therapies: Approaches like hormone therapy, angiogenesis inhibitors, and immunotherapy.

Key Terms to Know

• Personalized medicine: Custom medical treatments based on genetics.

• SNPs: Genetic variations predicting disease risk.

• Pharmacogenomics: Study of genetics in drug response.

• Oncogene: Gene whose mutation can cause cancer.

• Tumor suppressor gene: Gene whose mutations can lead to cancer.

• EGFR: Oncogene pertinent to cell growth.

• BRCA1/BRCA2: Tumor suppressor genes linked to breast cancer.

• Targeted therapy: Specific treatments aimed at certain genes/proteins in cancer.

Unit 2.6: Emerging Technologies and Infectious Diseases

Key Concepts

1. Stem Cells

   • Embryonic stem cells: Highly versatile, can differentiate into any cell type.

   • Induced pluripotent stem cells (iPSCs): Adult cells engineered to behave like embryonic stem cells.

2. CRISPR

   • Gene-editing tool utilizing the Cas9 protein and guide RNA.

   • Capable of silencing, deleting, or inserting genes.

3. Emerging Infectious Diseases

   • Zoonotic diseases: Infectious diseases transmitted from animals to humans (e.g., Ebola, COVID-19).

   • RNA viruses: High mutation rates (e.g., HIV, SARS-CoV-2).

Key Terms to Know

• Stem cells: Cells capable of forming various cell types.

• Embryonic stem cells: Derived from embryos, can differentiate universally.

• Induced pluripotent stem cells (iPSCs): Adult cells reprogrammed to act as stem cells.

• CRISPR: Gene-editing technology using Cas9 and guide RNA.

• Cas9: Protein used in CRISPR to cut DNA.

• Zoonotic diseases: Infections transmitted from animals.

• RNA viruses: Viruses with RNA genomes, characterized by high mutation rates.