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Chapter 5 The Central Dogma: What is the central dogma? DNA → RNA →Protein What is the exception? Viruses (not alive) DNA Structure: What are DNA's building blocks? Nucleotides. How are DNA strands linked? Phosphodiester bonds (5’ -> 3’). What are...

Chapter 5 The Central Dogma: What is the central dogma? DNA → RNA →Protein What is the exception? Viruses (not alive) DNA Structure: What are DNA's building blocks? Nucleotides. How are DNA strands linked? Phosphodiester bonds (5’ -> 3’). What are the DNA bases? A, T, G, C. What bonds hold bases together? Hydrogen bonds. What is complementary base pairing? A-T (2 H-bonds), G-C (3 H-bonds). Why is base pairing important? It enables DNA replication. Chromosomes: How is DNA stored in bacteria? Single circular DNA. Where is DNA stored in eukaryotes? Nucleus. How many chromosomes do humans have? 23 pairs (46 total). Genes: What is a gene? A region of DNA specifying a protein.  What is intragenic DNA? Non-gene DNA that regulates genes. Cell Cycle: What happens in G1? Cell grows and functions. What happens in S phase? DNA replication. What happens in G2? Prepares for division. What happens in M phase? Cell division. Chromosome Replication: What happens in interphase? DNA is long and thin. What happens in S phase? DNA duplicates (sister chromatids). What happens in M phase? DNA becomes dense ("X" shape). Chromosome Structure: What are telomeres? Caps at chromosome ends. What is the centromere? Where sister chromatids connect. What is ori? Replication origin. DNA Visualization: What are two DNA stains? Hoechst and Ethidium Bromide.  What does FISH do? Visualizes DNA sequences. What is a karyotype? Chromosome display. Chromatin & Nucleosomes: What is chromatin? DNA-protein complex. What is a nucleosome? DNA wrapped around histones. What is chromatin remodeling? Moves DNA on histones. Heterochromatin vs Euchromatin: What is heterochromatin? Closed, gene-off. What is euchromatin? Open, gene-on. Epigenetics: What is epigenetics? Gene expression changes without DNA changes. What are acetylation and methylation? Acetylation opens, methylation closes. What is epigenetic inheritance? Inherited chromatin structure. Chapter 6 DNA Replication & Cell Division When does DNA replication occur? During S-phase of the cell cycle. Why is DNA replication necessary? To copy DNA for each new cell. What is the speed and accuracy requirement? Must be fast and perfect to ensure functionality. DNA as a Template What is complementary base pairing? A-T (2 H-bonds), G-C (3 H-bonds). What is semi-conservative replication? New DNA contains one original strand. DNA Replication Process Where does DNA replication start? At origins (Ori). What forms during replication? 2 replication forks. What is unique about the strands? They are antiparallel. Why are A-T regions easier to break? Fewer hydrogen bonds. Key Replisome Proteins What is the role of DNA polymerase? Synthesizes DNA 5’ to 3’. What does helicase do? Unwinds DNA. What does primase add? RNA primer for initiation. What does nuclease do? Breaks down RNA primer.  What does repair polymerase do? Replaces RNA with DNA. What is the function of ligase? Joins DNA fragments. 5' to 3' Synthesis How does DNA polymerase add nucleotides? To the 3' end (hydroxyl group). What happens to incoming nucleotides? Lose 2 phosphates, forming the backbone. Leading vs. Lagging Strand What is the leading strand? Continuous replication at the 3' end. What is the lagging strand? Discontinuous (Okazaki fragments), joined by ligase. DNA Proofreading How does DNA polymerase proofread? Adds bases 5’ to 3’, checks 3’ to 5’. What does proofreading fix? Errors from shape distortions in base pairing. Key Replisome Proteins (Continued) What are sliding clamps (PCNA)? Stabilize DNA polymerase. What do single-strand binding proteins (SSBs) do? Keep the lagging strand straight. Topoisomerases  What does Topoisomerase I do? Breaks one backbone to untwist DNA, then reseals it. What does Topoisomerase II do? Untangles DNA by breaking and resealing both backbones. What is a drug that affects Topoisomerase I? Camptothecin. What is a drug that affects Topoisomerase II? Doxorubicin. Telomerase What is the function of telomerase? Elongates telomeres in reproductive and cancer cells. Why is telomerase not active in adult cells? It leads to aging. DNA Replication Importance What can imperfect replication lead to? Mutations. How do accumulated mutations affect cancer risk? Increase risk with age. Mismatch Repair What do mismatch repair proteins do? Fix errors missed by DNA polymerase. Base Damage Types What is depurination? Loss of a purine base (A or G). What is deamination? Loss of an amine group, causing base changes. What are thymine dimers? Fusion of 2 thymines, often caused by UV radiation. Excision Repair What does nuclease do in excision repair? Cuts damaged base. What role does DNA polymerase play? Repairs the base. What does DNA ligase do? Seals the nick. Double-Stranded Break Repair What is non-homologous end-joining? A fast repair method that may lose bases. What is homologous recombination? Uses a homologous chromosome template for repair. Diseases from Defective DNA Repair What are symptoms of defective repair? Cancer, sun sensitivity, accelerated aging. What is an example of accelerated aging? Werner Syndrome. What increases cancer risk? BRCA1/2 defects. Chapter 7 Depurination When? Randomly during cell life. Why? Loss of a purine base (A or G). Deamination When? Occurs spontaneously. Why? Loss of an amine group, causing a base change. Thymine Dimers When? After exposure to UV radiation (e.g., tanning beds). Why? Thymine bases fuse together, potentially leading to skin cancer. Excision Repair When? When a base is damaged. Why? To remove damaged bases and repair DNA. Non-homologous end-joining (NHEJ) When? After a double-stranded DNA break. Why? Quick fix, but may cause some base loss. Homologous Recombination (HR) When? After a double-stranded break in coding regions. Why? Uses a homologous chromosome as a template to repair the break. Diseases from Defective DNA Repair When? When DNA repair pathways fail. Why? Leads to cancer, sun sensitivity, and accelerated aging (e.g., Werner Syndrome, BRCA 1/2 defects). Chapter 8 Differentiation What? Cells become specialized. Example: Cloning shows all cells have full genetic instructions. Gene Expression & Regulation Housekeeping Proteins Always on in all cells. Examples: Repair proteins, RNA Polymerase, Ribosomes. Differential Gene Expression What? Genes turn on/off based on cell type. Gene Expression Regulation 1. Transcriptional Control – How often a gene is read. 2. mRNA Degradation – Breaks down mRNA. 3. Post-Translational Control – Activates/deactivates proteins. Transcriptional Control Chromatin Acetylation: Opens DNA for transcription. Deacetylation: Closes DNA to stop transcription. Promoter Region What? Where RNA Polymerase binds to start. Transcription Factors What? Control gene expression. Types: ○ Activators: Increase gene expression. ○ Repressors: Decrease expression. Gene Activation  1. Chromatin opens. 2. Activators bind to regulatory sequences. 3. General factors bind to the promoter. 4. DNA bends to start transcription. Gene Deactivation What? Repressors condense chromatin, blocking transcription. Combinatorial Control What? Multiple factors control gene expression. Result? Creates different cell types. Feedback & Inheritance Positive Feedback: Activators increase more activators. Epigenetic Inheritance: Chromatin structure passed to new cells. Histone Modifications Acetylation: Opens genes. Methylation: Closes genes. Maintenance Methyltransferase What? Transfers methylation to new DNA to silence genes. Chapter 18 Cell Growth & Preparation  When does cell growth occur? During G1 phase; to grow and function. When does DNA replication happen? During S-phase; to duplicate DNA. When is DNA checked for errors? During G2 phase; to prepare for division. When does cell division occur? During Mitosis; to divide genetic material. What happens during cytokinesis? It forms two separate cells after Mitosis. Chromosome Changes When are chromosomes loose? During Interphase; for cell functions. When do chromosomes condense? During Mitosis; to pack DNA for division. Flow Cytometry When is flow cytometry used? During cell analysis; to measure DNA levels. Cyclin-Dependent Kinases (Cdks) When are Cdks activated? When Cyclins bind; to progress the cycle. When are Cdks deactivated? When Cyclins degrade; to stop the cycle. P53 (Guardian of the Genome) When is p53 activated? When DNA is damaged; to stop the cycle. What does p21 do? Blocks Cdks; halts the cycle for repair.  Chapter 20 Dysregulation, Cancer, Drugs, and Diseases What are cancer cells? Cells that grow uncontrollably and ignore cell cycle rules. How do cancer cells spread? They invade and colonize other areas, like teratomas. Cancer Development How does cancer develop? Through the accumulation of mutations that disrupt normal function. DNA Damage What is deamination? A change of a DNA base. What is depurination? The loss of a DNA base. Genetic Instability When does genetic instability occur? When mutations interfere with DNA replication. What are the consequences? Sensitivity to carcinogens, cancer, and incorrect chromosome numbers. P53 Mutation What happens to p53 in cancer cells? It is often mutated, allowing uncontrolled replication. Oncogenes  What are oncogenes? Genes that cause cancer, originating from proto-oncogenes. What changes create oncogenes? 1. Mutation in coding sequence 2. Gene amplification 3. Chromosome rearrangement What is the result? Increased gene/protein function; some anti-cancer drugs target these pathways. Gleevec What is Gleevec? An anti-cancer drug that blocks oncogene kinase activity. How does Gleevec work? It binds to the kinase site, preventing hyperactivity. Dysregulation in Cells What is dysregulation? When cell systems malfunction, potentially causing diseases like cancer. Antibiotics, Viruses, and Other Pathways How do antibiotics work? They block gene expression in bacteria. How do viruses replicate? They inject DNA into our cells, using our machinery. What do pesticides/herbicides do? They target gene expression pathways to manipulate cell division.