Biology Exam Review: Cell Signaling

Exam Review

• Review is recorded on Sunday, Dec 8th, 2024
• Slides will also be posted.

Exam Information

• Exam date: Friday, December 13th at 10:30 AM CST
• Exam duration: 75 minutes (officially closes at 3 pm)
• Exam location: On Canvas under the "Quizzes" tab, same as previous exams.
• Exam format: ALL multiple choice questions; no free-response questions (FRQs).
• Content breakdown: 50% of the content from Weeks 12, 13, and 14, and 50% of the content from Weeks 1–11.
• Exam points: 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: ligand binding to a receptor, resulting in a cellular response
• Signal transduction: processes involved in signal transmission within the cell

Cellular Messaging

• Cellular signaling pathways
• Different stages of a signal transduction pathway
  • Ligand binding to receptor
  • Receptor activation of a protein at the membrane
  • Activation of protein in cytosol
  • Activation of a target protein within cell that triggers response

Local Signaling

• Autocrine signaling: cell targets itself
• Direct contact: through cell junctions, such as gap junctions(animal) and plasmodesmata(plants/algae).
• Paracrine signaling: cell targets nearby cells

Long Distance Signaling

• Endocrine signaling: animals use hormones that travel through the bloodstream to target cells in remote locations.
  • The message (hormone) binds to specific receptors to carry out the response.

Synaptic Signaling

• Neurotransmitters (chemical messages) converted to electrical signals in neurons.
• Movement of signal from outside of the cell (high Na+ and Cl-) to the inside of the cell (high K+), which creates a response.
• Influx of Ca2+ releases neurotransmitters to pass signal onto the next neuron
• Signal received by neurons creates a cellular response

3 Stages of Cell Signaling

• Reception: binding of signal molecule to receptor causing conformational change.
• Transduction: relaying the message via activation of enzymes. Cascades of protein activation in signal transduction pathway which also causes the shape of each protein to change.
• Response: activation of cellular response

Receptors

• G-protein coupled receptors: ligand binding converts GDP to GTP.
• Receptor tyrosine kinases: 2 signaling molecules binds to 2 receptors creating a dimer, and activating intracellular relay proteins.
• Ion channel receptors: signaling molecule binds to receptor, triggering ion movement.
• Steroid receptors (Intracellular): steroid hormones cross the membrane and interact with these intracellular receptors.
  • Some can directly bind to DNA.

Transduction: Phosphorylation/Dephosphorylation

• Phosphorylation: Adding phosphate group through kinase.
• Dephosphorylation: Removing phosphate group through phosphatase. Phosphorylation cascade involves multiple relays of phosphorylation by protein kinases.

Transduction: Second Messengers

• Small, non-protein molecules that diffuse freely through the cell.
• Participate in GPCRs and RTKs.
• Ex. Ca2+

Signal Regulation

• Specificity: Same signaling molecule but different responses based on cell's proteins.
• Amplification: making a signal bigger.
• Diversity: same molecule can bind to different receptors which enact differing responses in the cell.
• Overall efficiency: protein scaffolding in pathways.
• Termination: Removal of stimulus/degradation.

Week 13: Mitosis and Meiosis

• DNA/Chromosomal Structure
  • Chromatin: less-organized form of DNA found when cell is not dividing
  • Chromosomes: compact form of condensed DNA only seen during division.
  • Chromatids: singular copies of a chromosome - sister chromatids are connected at the centromere

The Cell Cycle

• Interphase: cell spends the majority of its time in this state. G1, S, and G2 phases: Growth; protein synthesis; DNA synthesis; organelles replicate
• M Phase: mitosis and cytokinesis
• Prokaryotes: Binary fission; DNA replication—chromosome segregation—cytokinesis
• Mitosis: Exact Copy of Cells Prophase, prometaphase, metaphase, anaphase, telophase, cytokinesis

Human Ploidy

• Somatic Cells: diploid (2n) two copies of each genetic chromosome
• Human somatic cell: 22 pairs of autosomes and 2 sex chromosomes
• Autosome: any chromosome that is not a sex chromosome
• Gamete Cells: haploid (n); one copy of each chromosome
• Allele: alternative version of gene

Diploids vs. Haploids

• Q1. In a diploid cell with 3 chromosome pairs (2n = 6) how many sister chromatids are found during metaphase of mitosis? 12
• Q2. What cell is produced by meiosis? 4 haploid cells
• Q3. Mitosis produces two identical daughter cells with 2n chromosomes (diploid)

Homologous Chromosomes

• Similar in size, shape
• Carry same genes in same order
• Not genetically identical – different alleles

Meiosis

• Cell division in sexually reproducing organisms (consists of 1 replication and 2 divisions ) resulting in half the number of chromosomes = gametes.
• Meiosis I: separates homologous chromosomes
• Meiosis II: separates sister chromatids

Meiosis Diagrams

• Prophase I, Metaphase I, Anaphase I, Telophase I and Cytokinesis, Prophase II, Metaphase II, Anaphase II, Telophase II and Cytokinesis
• Stages involved in meiosis

Crossing Over – Meiosis

• Reciprocal exchange of genetic material between non-sister chromatids
• During prophase I of meiosis
• DNA breaks are repaired

Independent Assortment – Meiosis

• Random arrangement of homologous chromosome pairs at the center of a cell during metaphase I.
• Meiosis gives rise to genetic variation in the offspring

Animal Life Cycle

• Haploid gametes (egg and sperm) are made by meiosis; fuse during fertilization → diploid zygote
• Zygote develops via mitosis to form a multicellular organism body

Week 14: Genomes and Biotechnology

• Recombinant DNA: Plasmids: Non-chromosomal DNA, easy isolation, manipulation.
  • Ways to add recombinant DNA
  • Natural genetic recombination
  • Modification of nucleotides
  • Retroviruses
• Polymerase Chain Reaction (PCR):
  • DNA cloning using cycles
  • Denaturation, annealing, extension
• DNA Technology:
  • Probes/FISH: single-stranded RNA/DNA sequences in a sample genome for its complementary sequence
  • Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR): Using RNA as template to reverse transcribing RNA into Complementary DNA (cDNA); Used to amplify cDNA for detection

Gel Electrophoresis

• Separates and visualizes DNA fragments according to size; DNA is negatively charged → travels to positive end
• smaller fragments travel further compared to larger fragments.

DNA Technology

• DNA Microarrays: used to study gene expression; consists of tiny amounts of single-stranded genes on a glass slide
• CRISPR-Cas9 System: Gene-editing technology
• Can cut both strands of DNA (complementary to guide RNA)
• Repair after cutting the DNA

Small Nucleotide Polymorphism (SNPs)

• Each SNP is a difference in a nucleotide in human genome
• 3 million SNPs
• Most SNPs in non-coding regions

Stem Cells

• Embryonic (pluripotent) stem cells: Undifferentiated; can become any cell type
• Adult stem cells: can only produce a limited number of cell type
• Induced pluripotent stem cells: adult cells reprogrammed back to embryonic-like state that allow development into variety of cell type

Cloning

• Therapeutic cloning: using cloned embryos as a source of stem cells to treat disease.
• Cloning of plants using single-cell cultures
  • Ease of cloning/genetic engineering, more ways to transfer recombinant DNA into a plant.
• Cloning of animals through nuclear transplantation.
  • Fuse nucleus of differentiated body cell to an unnucleated egg cell

Genomics and Bioinformatics

• Forensic applications: Highly repetitive and individually distinctive short tandem repeats (STRs); Help in cold cases: determine number of repeats
• Bioinformatics: use computer programs and mathematical models to organize and study large biological data

Transposable Elements

• The movement of DNA segments within a genome by prokaryotes & eukaryotes
• Makes up ~75% of human repetitive DNA
• Facilitates DNA recombination or creates new sites for RNA splicing.

Comparing Genomes

• Chromosome set contribution to species diversity
• Chromosomal mutations introduced by duplication
• Multigene family formation; similar protein functions in different species
• Conserved genes help reveal evolutionary relationships; phylogenetic tree branching points reflect divergence.
• Genome size is not directly correlated with organism complexity.

Week 1 - 2

• Covalent bonds (sharing electrons); non-polar (equal sharing), polar (unequal sharing).
• Ionic bonds (transfer of electrons); cations (+), anions(-).
• Intermolecular forces; Van der Waals, Hydrogen bonds.
• Water properties: Cohesion, adhesion, high specific heat; evaporative cooling, expansion upon freezing, a great solvent; dissociates to form H3O+ and OH¯
• Isomers: same molecular formula but different structures.

Week 5

• Membrane structure: selective permeability; types of transport proteins.
• Passive transport: osmosis and diffusion; active transport.
• Compare osmosis vs. diffusion
• Tonicity (isotonic, hypertonic, hypotonic)
• Membrane proteins
  • Integral, peripheral, transmembrane

Week 6

• Energy Transformation; ATP, and Enzymes; Thermodynamics.
• Entropy: measure of disorder; free energy = instability & energy availability.
• Exergonic/Endergonic reactions; G = free energy, ΔG = change in free energy
• Enzymes = protein catalysts
  • Lower the activation energy
  • Affect reaction rates by temperature, pH, pressure
• Enzyme Inhibitors: competitive, non-competitive, and allosteric

Week 7

• Cellular respiration
• Redox Reactions,
• Phosphorylation types:
  • Substrate level, Oxidative
• Catabolic pathways types: Aerobic respiration (36-38 ATPs), anaerobic respiration (2-36 ATPs), Fermentation (2ATPs);
• Stages of cellular respiration: Glycolysis, Pyruvate oxidation, Citric Acid (Krebs) cycle, & Oxidative phosphorylation
• Lactic acid fermentation vs. alcoholic fermentation

Week 8

• Photosynthesis
• Stages of photosynthesis:
  • Light-dependent reactions (light part)
  • PSII → PSI → Chemiosmosis
  • Calvin cycle (synthesis part)
• Electron flow pathways Linear & Cyclic electron flow
• Calvin cycle stages
  • Carbon fixation, reduction, sugar formation, RuBP regeneration
• Alternative carbon fixation mechanisms
  • Photorespiration, C3, C4, CAM plants

Week 9

• DNA Structure, Replication, and Hereditary
• Different experiments on DNA
  • T.H. Morgan, Frederick Griffith, Avery, McCarthy, MacLeod, Hershey & Chase, Chargaff's rule, Wilkins & Franklin, Watson and Crick, Meselson & Stahl
• Replication steps and enzymes
  • DNA polymerase, replication steps
• DNA repair: mismatch repair, nucleotide excision repair

Week 10

• The genetic code, transcription, translation, and mutations.
• Universal genetic code (redundant but not ambiguous)
• Transcription
  • Replication process; uses DNA as template; enzyme RNA polymerase
• Translation
  • Process of converting mRNA into proteins; involves tRNA, ribosomes
  • Wobble hypothesis
  • Prokaryotes vs. eukaryotes (polyribosome, coupling)
• Mutations
  • Frameshift, substitution (silent, missense, nonsense).

Week 11

• Gene Regulation and Expression
• Prokaryotic gene regulation: operons (lac and trp operons)
  • Inducible, repressible
• Eukaryotic gene regulation
  • Chromatin remodeling
  • Transcriptional regulation.
  • RNA processing
  • Post-translational modification
• Embryonic development; cytoplasmic determinant, induction.
• Cancer development; mutations

Questions

• Increase chromatin condensation : Increase methylation and decrease acetylation.

Q&A Session

Prepare for your upcoming biology exam with this comprehensive review focused on cell communication and signaling. The quiz covers material from Units 1 to 4, emphasizing key topics from Weeks 12, 13, and 14. Enhance your understanding of cellular signaling pathways and signal transduction before the exam on December 13th.