Exam Study Guide Notes

Cell Signaling (Chapter 9)

  • Essential elements in cellular communication.
  • Types of signals used by cells; secondary messengers.
  • Types of receptors: hormone receptors, ion channels, receptor kinases, G protein receptors.
  • Signaling cascades and examples.
  • Cells use different signaling pathways to determine actions.

Cytoskeleton (Chapter 10.2)

  • Structure and function of microtubules, microfilaments, and intermediate filaments.
  • Roles of kinesin, dynein, and myosin in cellular transport and movement.
  • Exoskeleton supports cells.

Meiosis and Mitosis (Chapter 11 and 14.1)

  • Binary fission process.
  • Five major phases of the cell cycle and events in each.
  • Interphase vs. M phase.
  • Key terms: chromatin, sister chromatid, chromosome, centromere, kinetochore, centrosome, centriole, spindle fibers.
  • DNA changes during mitosis phases (Prophase, Prometaphase, Metaphase, Anaphase, Telophase).
  • Cytokinesis.
  • DNA changes during Meiosis I and II.
  • Role and advantage of homologous chromosome crossing-over during Meiosis I.
  • Cells undergoing meiosis vs. mitosis.
  • Major control proteins of the cell cycle.
  • Cancer and protein mutations.

DNA Replication (Chapter 11)

  • Semi-conservative replication and discovery by Meselsehn and Stahl.
  • Enzymes: helicase, primase, DNA polymerase, single-stranded binding protein, nuclease, ligase.
  • Replication bubble: origin of replication, replication fork, leading/lagging strands, RNA primers, Okazaki fragments.

Chemical Foundations (Chapter 2)

  • Protons, neutrons, electrons, valence electrons in an atom.
  • Common atoms in the cell.
  • Difference between ion, atom, and isotope.
  • Bond prediction (ionic, covalent, polar covalent) using periodic table and electronegativity.
  • Dipole moment in polar-covalent bonds.
  • Water's properties due to polar-covalent bonds: universal solvent, liquid at high temperatures, ice floats.
  • Hydrogen bonds.
  • pH scale interpretation.
  • Acids donate H+H^+ (decrease pH), bases decrease H+H^+ (increase pH); acidic and basic functional groups.
  • Hydrophobic vs. hydrophilic molecules.
  • Hydrophobic interactions and entropy.
  • Carbon's importance in life.
  • Functional groups: carboxyl, carbonyl, hydroxyl, phosphate, amino groups.
  • Line drawings of carbon atoms.

Macromolecules

  • Four major groups: built from what monomers?
  • Sugars: monosaccharides, polysaccharides (ribose, glucose, fructose, deoxyribose, cellulose, starch, glycogen), ring formation in water.
  • Fatty acids: amphipathic, fatty acid, phospholipid, glycerol, micelles, membrane fluidity (saturated vs. unsaturated, short vs. long fatty acids).
  • DNA: nitrogenous base, nucleoside, nucleotide, sugars/bases in RNA/DNA, RNA vs. DNA, double helix (hydrogen bonds), base pairing, anti-parallel chains, phosphodiester bond.
  • Central dogma of molecular biology.
  • Amino acids/proteins: R group chemistry (hydrophobic, hydrophilic, acidic, basic).
  • Peptide bond.
  • Stanley-Miller Experiment: origin of life.

Chemical Reactions (Chapter 6)

  • Organism classification by energy and carbon use.
  • Cellular metabolism, anabolic vs. catabolic reactions.
  • Potential, kinetic, chemical energy examples.
  • First and second laws of thermodynamics.
  • Chemical reactions.
  • ΔG\Delta G: exergonic and endergonic reactions.
  • Energy diagrams and predicting ΔG\Delta G sign.
  • Energetic coupling for unfavorable reactions (positive ΔG\Delta G).
  • Activation energy.
  • Enzymes lower activation energy.
  • Enzyme characteristics: substrate specificity, reusability.
  • Enzymatic reaction steps: E+S→ES→EP→E+PE + S \rightarrow ES \rightarrow EP \rightarrow E + P
  • Competitive vs. non-competitive inhibitors.
  • Allosteric enzymes.
  • Biofeedback in metabolic cascades.

Molecular Foundations

  • Biology understanding through time and microscopes.
  • Griffith's experiment: DNA as genetic material.
  • Avery, Macleod, McCarty experiment.
  • Chargaff, Wilkins, Franklin, Watson, Crick: DNA structure.
  • Nucleotide percentage calculation (if T is 10%, what is %C?).
  • DNA in Eukaryotic vs. Prokaryotic cells.
  • Chromosome: packaging protein.
  • Central dogma.
  • Gene: three parts.
  • Transcription stages: initiation, elongation, termination.
  • DNA transcription regulation: activator, repressor.
  • Coding vs. template strand; RNA sequence prediction.
  • RNA types: tRNA, rRNA, mRNA, snRNA.
  • RNA world hypothesis.
  • Eukaryotic RNA processing steps to mRNA.
  • Intron vs. exon; splicing complex.
  • Alternative splicing.

Protein Structure and Function

  • Amino acid R group classification: hydrophobic, hydrophilic (polar uncharged, acidic, basic).
  • Primary structure: amino acid sequence.
  • Peptide bonds.
  • Secondary structure: stabilized by bonds.
  • Tertiary structure: stabilization.
  • Amino acid replacement impact on protein folding.
  • Quaternary structure.
  • Scientists determining protein structure from primary sequence.

Translation

  • mRNA sequence to protein decoding.
  • tRNA function and codon relationship.
  • Translation steps: tRNA charging, initiation, elongation, termination.
  • Proteins/RNAs: aminoacyl tRNA synthetase, ribosome (rRNA + protein), tRNA, release factors.
  • Silent and mismatch mutations.
  • Gene copies and alleles.

Cellular Foundations

  • Cell Membranes (Chapter 3.2):
    • Three major components of a cell membrane?
    • Why do cell membranes form in a bi-layer?
    • What does it mean that membranes are fluid? What happens if a membrane is not fluid enough or too fluid? What kinds of things can be added or subtracted from a cell membrane to make it more or less fluid? Are these things different in animal and plant cells? How does cholesterol work?
  • Cell Membrane Permeability (Chapter 3.3):
    • Membranes are semi-permeable. How does the chemistry of the lipid affect passive permeability? How do the types of proteins found in the membrane affect permeability?
    • Be able to rank how well molecules can diffuse through a membrane based on their chemistry.
    • Be able to predict the direction of osmosis of water when a cell is placed in a hypertonic vs. a hypotonic solution. Understand what isotonic means.
    • Understand what it means for a cell to undergo plasmolysis, crenation, or hemolysis?
    • Why is a watered plant turgid?
    • What two kinds of proteins facilitate membrane transport?
    • What is the difference between facilitated passive vs. active transport?
    • What is the difference between primary and secondary active transport?
    • What is the electrochemical gradient and how does it need to be taken into account during passive and active transport?
    • What is antiport and what is symport?
  • Cell Structure and Function (Chapter3)
    • What are the major features of a Prokaryotic Cell?
    • What are the major features of a Eukaryotic Cell?
    • What things are different between them? What things are similar?
    • What features are specific to a plant cell and are not found in an animal cell?
    • What are several purposes of the cytosketon of a eukaryotic cell? What are the three most predominate types of protein filaments found in the cytosketon? What kind of proteins are they made up of?
    • You should have a basic understanding of the structure and function of the following Eukaryotic organelles – Nucleus, Golgi, rough and smooth E.R., Mitochondria, Chloroplast, Vacuole, Lysosome, vacuole.
    • How may a Eukaryotic Cell have developed from an original prokaryotic cell? What is endosymbiosis?
    • What evidence is there that the chloroplast and mitochondria may have orginally been prokaryotic cells?
  • Protein Transport (Chapter 5.4)
    • What is an N-terminal protein localization signal?
    • If a protein doesn’t have an ER localization signal where is it translated?
    • If a protein has an ER N terminal localization signal where is it translated? What organelles or places might it eventually end up in?
    • What happens to a protein as it goes through the endomembrane system?
    • Be able to describe the pathway of a protein through the endomembrane system.
    • What is exocytosis and endocytosis?
    • How can exocytosis be controlled with Ca2+Ca^{2+}
    • Be able to explain how a protein destined for the lysosome or outside of the cell gets to the outside of the cell? (ie the endomembrane system)

Cellular Respiration

  • Net chemical reaction for cellular respiration.
  • Oxidation vs. reduction.
  • Oxidized and reduced substances during cellular respiration.
  • Electron carriers.
  • ATP creation methods.
  • Four major steps: glycolysis, pyruvate dehydrogenation, citric acid cycle, electron transport.
  • Glycolysis: location, net reactants/products, enzyme count.
  • Electron carrier fate with and without oxygen.
  • Fermentation products and need.
  • Pyruvate dehydrogenation products.
  • Organic molecules broken down into acetyl CoA.
  • Citric acid cycle: location, net products.
  • Glycolysis and Citirc Acid cycle: carbon source.
  • Electron transport: location.
  • Proton pumping and H+H^+ gradient.
  • ATP synthetase mechanism.
  • Uncoupling electron transport and H+H^+ gradient with DNP.

Photosynthesis

  • Plant biomass source and carbon source.
  • Major overall reaction for photosynthesis.
  • Reduced and oxidized substances in photosynthesis.
  • Calvin cycle inputs, products, and location.
  • Fate of 3-carbon sugar exiting the Calvin cycle.
  • Light reaction products needed for the Calvin cycle.
  • Light capture by photosystems.
  • Photosystem locations.
  • Two photosystems, water splitting, proton gradient, NADPH production.
  • Electron transport and H+H^+ pumping.
  • ATP creation location.
  • ATP generation for other chemical reactions.