Untitled Quiz

Exam Information

• Exam date: Friday December 13th, 10:30 AM CST
• Exam duration: 75 minutes; officially closes at 3pm
• Location: Canvas, "Quizzes" tab, same as previous exams
• Exam format: ALL multiple choice questions, no free response questions
• Content breakdown: 50% Weeks 12, 13, and 14; 50% Weeks 1-11
• Point value: 106 points (21.2% of total grade)
• Number of questions: 53, each worth 2 points

Content Review by Weeks

• "Unit 4": Weeks 12, 13, 14
• Unit 1: Weeks 1-4
• Unit 2: Weeks 5-8
• Unit 3: Weeks 9-11

Week 12: Cell Communication and Signaling

• Cell signaling: communication between cells, ligand binding to a receptor causes a response
• Signal transduction: how the signal is transmitted within the cell

Cellular Messaging

• Cell signaling: communication between cells
• Simplest explanation: ligand binding to a receptor which causes responses
• Seen in prokaryotes and eukaryotes

Local Signaling

• Autocrine signaling: cell targets itself, often related to negative feedback
• Direct contact: through cell junctions, cell junctions allow communication between the cytoplasm of neighboring cells
• Gap junctions: animals
• Plasmodesmata: plants/algae
• Paracrine signaling: a signaling molecule targets nearby cells, only works with cells in close proximity because signal spreads via diffusion

Long Distance Signaling

• Endocrine signaling: animals use hormones that move through bloodstream
• Bloodstream carries message to target cell in a remote part of the body
• The message (hormone) will only bind to the cell with the correct receptor in the body

Synaptic Signaling

• Synaptic signaling: neurotransmitter (chemical message) is converted into electrical signal in neurons; allows for responses
• Outside the cell: high Na+ and Cl-; inside the cell: high K+
• At rest, inside of the cell is negative; outside is positive
• Charges shift during signal transmission; inside temporarily becomes more positive
• At end of signal transduction, influx of Ca2+ allows for release of neurotransmitter to pass signal onto next neuron.
• Signal released: Neurotransmitter
• Signal received by: neurons, creates a response

3 Stages of Cell Signaling

• Reception: binding of signal molecule to receptor à conformational change of receptor & activation of enzymes
• Transduction: relayed through the cell, proteins change shape in a cascade
• Response: activation of cellular response

Receptors to Know

• G-protein coupled receptors: ligand binds, converts GDP → GTP, GTP activates an enzyme that starts the cascade
• Receptor tyrosine kinases: Dimerization (two signaling molecules bind), cytoplasmic regions become phosphorylated, activating relay proteins
• Ion channel receptors: signaling molecule binds, opens channel, ions move across, causes cellular response
• Steroid receptors (intracellular): steroid hormones cross membrane to reach intracellular receptors, some bind directly to DNA (non-polar/lipid-soluble messengers), ex: estrogen to different receptors

Transduction: Phosphorylation/Dephosphorylation

• Phosphorylation (add phosphate group via kinase) à changes conformation/becomes active
• Dephosphorylation (via phosphatase) à restores the protein to inactive form
• Phosphorylation cascade (multiple relays of phosphorylation)

Transduction: Second Messengers

• Small, non-protein molecules: diffuse freely through the cell
• Participate in GPCRs and RTKs
• Ex: Ca2+ (normally at very low levels inside cell; when enters cell, can act as 2nd messenger)

Signal Regulation

• Specificity: ligand-receptor specificity; same molecule at same location, different response based on proteins
• Amplification: make a signal bigger (megaphone analogy); same molecule binds to different receptors, different responses (tissue specialization)
• Diversity; overall efficiency of response - proteins in pathway grouped by scaffolding proteins
• Termination/control of signal: resetting by removing stimuli or degrading components

DNA/Chromosomal Structure

• Chromatin: loose form of DNA and proteins, present when cell is not dividing
• Chromosomes: condensed/tightly packed form of DNA, found only during cell division
• Chromatids: singular copy of a chromosome, sister chromatids (two copies via duplication), connected at the centromere.

The Cell Cycle

• Interphase: cell spends most time here, includes G1 (growth, protein synthesis), S (synthesis, DNA replication), G2 (growth prep for division)
• M phase: mitosis and cytokinesis
• Prokaryotes: Binary fission - DNA replication → chromosome segregation → cytokinesis (2 exact copies)

Mitosis

• Eukaryotic nuclear division, chromosome number is constant across daughter cells
• Prophase: chromatin condenses, mitotic spindle forms, nucleolus dissolves
• Prometaphase: nuclear envelope fragments, spindle "grabs" chromosomes at kinetochores
• Metaphase: spindle complete, chromosomes align at metaphase plate
• Anaphase: chromatids separate, pulled toward opposite poles
• Telophase: daughter nuclei form, mitotic spindle disappears
• Cytokinesis: division of cytoplasm, cleavage furrow (animal) or cell plate (plant)

Human Ploidy

• Somatic cells: diploid (2n) - Two copies of genetic material subdivided into chromosomes; any cell that's not a reproductive cell
• Human somatic cells: 22 pairs of autosomes and 2 sex chromosomes
• Autosome: anything not a sex chromosome
• Gamete cells: haploid (n) - single copy of each chromosome (unpaired)
• Allele: alternative version of a gene; may produce different phenotypes

Diploid vs Haploid

• Diploid cells (2n): two copies of each chromosome
• Haploid cells (n): one copy of each chromosome
• Meiosis results in 4 haploid cells (from one diploid cell)
• In mitosis, a diploid cell gives rise to 2 diploid daughter cells

Homologous Chromosomes

• "Homologous" refers to similarity between structures, one from mom, one from dad
• NOT genetically identical
• Similar in size and shape, genes in same order, but can be different alleles

Meiosis

• Cell division, sexually-reproducing organisms, consists of 1 replication and 2 divisions producing gametes.
• Meiosis I separates homologous chromosomes. Meiosis II separates sister chromatids
• Prophase I: duplicated chromosomes pair with homologs (synapsis). Crossing over
• Metaphase I: homologous pairs line up facing poles
• Anaphase I: pairs of homologs separate to poles
• Telophase I: each half cell is haploid
• Prophase II: spindle apparatus forms, chromosomes condense
• Metaphase II: sister chromatids at plate
• Anaphase II: sister chromatids separate and cohesin separates
• Telophase II: nuclei form; chromosomes decondense

Crossing Over

• Reciprocal exchange of genetic material between two non-sister chromatids during prophase I of meiosis
• Non-sister chromatids broken at corresponding positions
• DNA breaks are repaired, joining DNA from one non-sister chromatid to the corresponding position of another

Independent Assortment

• Random arrangement of pairs of homologous chromosomes at the center of the cell during metaphase I
• Meiosis allows for novel combinations of traits not seen in the previous generation (genetic variation)

Animal Life Cycle

• Haploid gametes (egg and sperm) produced by meiosis
• Two gametes fuse during fertilization => diploid zygote
• Zygote goes through mitosis to form a multicellular body
• Other eukaryotic life cycles: plants/algae have alternation of generations; fungi/protists have spores; many life cycles spent as haploid

Week 14: Genomes and Biotechnology

• Recombinant DNA: Plasmids (vehicles) are non-chromosomal DNA, easy to isolate and manipulate
• Ways to introduce: natural genetic recombination, adding methyl groups to nucleotides
• Retroviruses (RNA viruses): insert DNA into a cellular chromosome (reverse transcriptase).

Polymerase Chain Reaction (PCR)

• PCR used to amplify DNA (make copies); exponential generation
• Cycle 1 consists of 3 steps: Denaturation, Annealing, Extending

DNA Technology (Probes/FISH)

• Probes/FISH: single-stranded RNA or DNA sequence used to search for its complement in a sample genome; fluorescence allows visualization; identifies presence or location of specific mRNAs
• Reverse-Transcriptase-Polymerase Chain Reaction (RT-PCR): uses RNA as template for reverse transcription to complementary DNA (cDNA) for PCR amplification and gene detection.

Gel Electrophoresis

• Separates and visualizes DNA according to molecular size
• DNA negatively charged (travels towards anode)
• Smaller fragments travel further; larger fragments closer to cathode.

DNA Microarrays

• Used to study the expression of all genes in different tissues at different times or under different conditions
• Microarray consists of tiny amounts of many single-stranded genes fixed to glass slide

CRISPR-Cas9 system

• Gene editing technology
• Cas9 enzyme cuts both strands of DNA complementary to guide RNA
• After cut, DNA is repaired, and nucleotides may be introduced.
• Also used to disable/knock out the target gene for studying.

Small Nucleotide Polymorphism (SNPs)

• Each SNP represents a difference in a nucleotide
• 3 million SNPs in human genome
• Majority of variation in human genomes is in noncoding regions (rarely directly involved in disease)

Stem Cells

• Embryonic (pluripotent): Undifferentiated à any cell type, obtained from embryos
• Adult: Limited number of cell types
• Induced pluripotent stem cells: reprogrammed adult cells to act like embryonic cells; used for therapeutic treatments

Cloning

• Therapeutic cloning: use of cloned embryos as source for stem cells to treat disease
• Cloning plants (using single cell cultures, easy to genetically engineer)
• Cloning animals (fusing nucleus of differentiated body cell into an unnucleated egg cell)
• Only a small percentage of cloned embryos normally develop to birth; many show defects, epigenetic changes can conflict with developmental needs, flaws with mtDNA

Genomics and Bioinformatics

• Forensic applications: every individual's genetic profile is unique due to highly repetitive STRs (short tandem repeats); STRs help in solving cold cases
• Bioinformatics: use of computer programs/mathematical models to organize biological data

Transposable Elements

• Transposable elements: stretches of DNA that can move within genomes in prokaryotes and eukaryotes
• Makes up ~75% of human repetitive DNA
• Helps to facilitate recombination and may facilitate recombination, carry genes to new positions
• May create sites for RNA splicing – genome evolution

Comparing Genomes

• Chromosome sets contribute to diversity, chromosomal mutations, some genes diverged, multigene families.
• Comparing genome sequences provides clues to evolution and development; comparing highly conserved genes
• Branch points on a phylogenetic tree represent divergence from a common ancestor; genome size and organism complexity are unrelated.

Week 1-2: Chemical Bonds, Water, and Carbon

• Covalent bonds: sharing of valence electrons (nonpolar is equal; polar is unequal); ionic bonds: electron transfer (cations and anions); Intermolecular forces (Van der Waals and hydrogen bonds); Isomers: same molecular formula, different structure/properties
• Water: hydrogen bonds, hydroxide (OH) and hydronium (H3O⁺) ions, cohesive, adhesive, high specific heat, evaporative cooling, excellent solvent
• Hydrogen bonds in water result inability to break up other compounds (sugars, Amino Acids) compared to Lipids (non-polar).

Week 3: Monomers and Macromolecules

• Carbohydrates: monosaccharides, dehydration synthesis forms glycosidic linkages; disaccharides, polysaccharides (storage, structural)
• Lipids: not true polymers; fats (ester bond of glycerol and fatty acids), phospholipids (2 fatty acids and 1 glycerol); steroids (4-ring structure); saturated vs. unsaturated
• Proteins: amino acids joined by peptide bonds (four levels of structure - primary, secondary, tertiary, quaternary), enzyme structure and function; shape dictates function
• Nucleic acids: nucleotides joined by phosphodiester bonds; DNA (double stranded, A-T and C-G, deoxyribose), RNA (single stranded, A-U and C-G, ribose).

Aquaporins

• Proteins embedded in plasma membrane allow water movement between extracellular and intracellular spaces
• Key features of shape: amphipathic (hydrophilic/hydrophobic regions) to interact with both aqueous and hydrophobic regions
• Amino acid characteristics: charged/polar amino acids on top and bottom interacting with water; hydrophobic regions interact with phospholipid tails

Week 4: Prokaryotes and Eukaryotes, Origins, and Cell Structure

• Prokaryotes vs. Eukaryotes: differences in cell structure, presence/absence of organelles and nucleus
• Large surface area to volume ratio important for prokaryotes

Week 5: Membrane Structure and Function and Gradients

• Plasma membrane structure (selective permeability, temperature, cholesterol, types of fatty acids)
• Types of transport: passive (no ATP needed, ex: osmosis, diffusion) vs. active (ATP needed); osmosis vs. diffusion
• Tonicity: hypertonic (higher solute outside cell), hypotonic (lower solute), isotonic (equal)
• Membrane proteins: integral, peripheral, transmembrane; functions of membrane proteins

Week 6: Energy Transformation, ATP, and Enzymes

• Gibbs Free Energy (G), endergonic (requires energy), exergonic (releases energy), ΔG; Spontaneous vs. non-spontaneous reactions
• Enzymes = catalysts, decrease activation energy; specific temp & pH
• Enzyme inhibitors (competitive, non-competitive, allosteric)
• Enzyme-substrate interactions (lock-and-key, induced fit model); ATP role in energy coupling; cell respiration and photosynthesis

Week 7: Cellular Respiration

• Redox reactions (oxidation, reduction, hydrogen atoms)
• Types of phosphorylation: substrate-level, oxidative phosphorylation)
• 3 types of catabolic pathways: aerobic respiration (36-38 ATPs), anaerobic respiration (varied outcome, less ATP), fermentation (2 ATPs)
• Cellular respiration stages: Glycolysis, Pyruvate Oxidation, Citric Acid Cycle (Krebs cycle), Oxidative Phosphorylation
• Lactic acid fermentation, alcoholic fermentation

Week 8: Photosynthesis

• Stages of photosynthesis (light reactions, Calvin cycle)
• Electron transport pathways: linear, cyclic electron flow, role in ATP/NADPH production
• Calvin cycle stages (carbon fixation, reduction and sugar formation, regeneration of RuBP)
• Alternative mechanisms of carbon fixation (photorespiration; C3, C4, and CAM)

Week 9: DNA Structure, Replication, and Heredity

• Different experiments leading to understanding of DNA (Morgan, Griffith, Avery, McCarthy, MacLeod, Hershey, Chase, Chargaff, Wilkins, Franklin, Watson, Crick, Meselson)
• Semiconservative replication model, steps and enzymes (replication, DNA polymerase I vs III, prokaryotes vs. eukaryotes, DNA repair, mismatch repair and nucleotide excision repair)

Week 10: The Genetic Code, Transcription, Translation, and Mutations

• Universal genetic code (redundant, not ambiguous, start/stop codons)
• Transcription (DNA → mRNA, RNA polymerase, template vs coding strand)
• Translation (mRNA → protein, initiation, elongation, termination, wobble, signal-recognition particle)
• Prokaryotic vs. eukaryotic processes (polyribosome, coupling, transcription complex)
• Mutations (frameshift, substitution mutations: silent, missense, nonsense)

Week 11: Gene Regulation and Expression

• Prokaryotic gene regulation (operons: lac operon, trp operon, inducible and repressible)
• Eukaryotic Gene regulation (Chromatin structure, Transcriptional regulation, RNA processing, post-translational modifications, embryonic development-cytoplasmic determinant, induction, Cancer development-mutation of proto-oncogenes/tumor suppressor genes like p53)

Question about Chromatin Condensation

• Increased chromatin condensation requires decreased histone acetylation or increased methylation.