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Draft Outcomes for Lectures in Biology 1002B

2012

Biology 1002B Outcomes


The following list of Outcomes indicates, in general, what you can be expected to do in order to achieve a high grade on the Mid-term Tests and Final Exam in this course. The list is not necessarily exhaustive but students who command these ideas are much more likely to do well. Notice that there is an expectation to know the relevant vocabulary.

Note: Outcomes in italics are testable but were not directly addressed in lecture. Lecture 1: Making a Photosynthetic Animal
In multiple choice format questions, identify what is Elysia, what is Vaucharia what is meant by the terms heterotroph, autotroph. life cycle of Elysia What happens to the chloroplasts ingested by Elysia meaning of kleptoplasty

Lecture 2: Origin of Life


In multiple choice format questions, identify meaning of stromatolite, abiotic synthesis, prebiotic evolution, redox terminology, chirality, enantiomers, teratogen, racemic, polymerization, transcription, translation, RNA world, ribozyme, micelle, vesicle, basic characteristics of life (Chapter 2) general timing of the appearance of various life forms over geologic time stages of prebiotic evolution physical/chemical conditions of primordial earth with respect to atmosphere, energy etc. basic principles of oxidation/reduction chemistry basic design and results of Miller-Urey experiment

Draft Outcomes for Lectures in Biology 1002B whether or not abiotic synthesis can occur in the modern atmosphere possible explanations for homochirality in life which homochiral form of sugars and amino acids are used in life relationship between homochirality and enzyme activity stages of biological evolution evidence for various roles of RNA in early biological evolution reasons why DNA is preferred over RNA as an information storage molecule role of clay particles in formation of organic polymers and first cells

2012

Lecture 3: Drake Equation


In multiple choice format questions, identify meaning of Proxima Centauri, SETI, galaxy, extrasolar planet, habitable zone, cohesion, heat capacity, heat of vapourization, hydration shell, sublimation, Fermi paradox, all of the terms (and the rationale underlying their suggested values) of the Drake Equation. What is the Kepler observatory. mechanism by which the transit method detects extrasolar planets characteristics of the habitable zone that promote life the chemical characteristics of liquid water that give rise to its emergent physical properties role of hydration shells in chemistry of life evidence for water on Mars possible resolutions of the Fermi paradox

Lecture 4: LEGO of life: Biochemistry


In multiple choice format questions, identify meaning of constitutive vs induced vs repressed expression, Northern blot, Western blot, peptide bond, amino, carboxylic & R groups, aqueous, polarity, hydrophobic, hydrophilic, primary, secondary, tertiary and quaternary structure, helix, sheet, hydrogen, ionic, disulfide VanderWaals bond, nascent peptide, native conformation, in vitro vs in vivo, urea, denaturation, macromolecular crowding, chaperones, prosthetic group, cofactors process by which Northern and Western blots measure transcript and protein abundance relationship between polarity and +/- charge with respect to interaction with water how to measure transcript or protein abundance

Draft Outcomes for Lectures in Biology 1002B

2012

factors that influence mRNA transcript abundance size of typical peptide difference between peptide and protein main factors that contribute to primary, secondary, tertiary and quaternary structure physico-chemical conditions leading to protein folding . . . physico-chemical conditions leading to denaturation examples of denaturants mechanisms underlying denaturation factors or conditions required for proper protein folding relative timing of protein folding relative to translation factors that drive protein folding relationship between folding and free energy (G) of a protein conformation consequences of denaturation for exposure of hydrophobic amino acids and protein activity role of chaperones in promoting proper folding

Lecture 5: Energy and Thermodynamics


In multiple choice format questions, identify meaning of potential, kinetic, chemical energy, closed, open vs. isolated systems, First Law of Thermodynamics, Second Law of Thermodynamics, entropy, spontaneous reaction, enthalpy (H), H, exothermic, endothermic, Gibbs Free Energy, exergonic, endergonic, G, stability, work capacity, phosphoryl group transfer potential, equilibrium, characteristics that distinguish open systems from closed and isolated systems characteristics of First and Second Law of Thermodynamics relationship between entropy change and open, closed and isolated systems conditions needed for reactions to be spontaneous components of Gibbs Free Energy equation whether or not a given reaction will be spontaneous, given G relationship between phase changes and entropy role of enzymes in coupling ATP hydrolysis with other reactions why ATP breakdown is not ATP hydrolysis in coupled reactions relationship between life and the Second Law of Thermodynamics why life needs to consume energy

Draft Outcomes for Lectures in Biology 1002B

2012

Lecture 6: Enzymes
meaning of catalyst, rate of reaction, energy of activation (EA), transition state, kinetic stability, active site, turnover rate, enzyme kinetics, substrate, reaction velocity, Vmax, Km, enzyme/substrate affinity, competitive vs. non-competitive inhibition, penicillin, peptidoglycan, transpeptidase, covalent inactivation, Chlamydomonas, nitrate reductase, prosthetic group, cofactor, apoprotein, molybdenum cofactor (Moco) role of enzymes in endergonic vs. exergonic reactions relationship between activation energy and rate of reaction. how enzymes increase rate of chemical reactions. why biological systems need enzymes. characteristics of active sites. 3 mechanisms by which enzymes may mimic the transition state and lower activation energy. (graphical) relationship between [S] and velocity. relationship between Vmax and Km. mechanism of competitive vs. non-competitive inhibition. effect of competitive inhibition on velocity at increasing substrate concentration effect of competitive inhibition on Vmax and Km mechanism of action of penicillin. examples of prosthetic groups. Overcoming moco biochemical pathway block in humans.

Lecture 7: Membranes
In multiple choice format questions, identify meaning of amphipathic, hydrophilic, hydrophobic, fatty acid, saturated, membrane fluidity, hydrogenation, desaturase, membrane permeability, transmembrane protein, simple diffusion, facilitated diffusion, active transport, ATP-Binding Cassette (ABC) transporter, cystic fibrosis, Cystic Fibrosis Transconductance Regulator (CFTR), F508, chaperone protein, ER quality control, proteosomes role of fatty acids in membrane structure. cis vs. trans unsaturation. relationship of fatty acid saturation levels on membrane fluidity. relationship of temperature on membrane fluidity.

Draft Outcomes for Lectures in Biology 1002B

2012

relationship of fluidity to membrane functions such as transport. type of fat in common foods such as margarine and butter. properties of saturated vs. unsaturated fats. role of desaturases in fatty acid biosynthesis. relationship of bacterial desaturase expression vs. temperature. role of size and charge in movement of molecules across biological membranes. characteristics of transmembrane proteins that enable them to interact with hydrophobic core of membrane. basic structure of ABC transporter. genetics underlying cystic fibrosis. cystic fibrosis phenotype. physiological function of CFTR and sodium transporter. relationship of CFTR synthesis and folding in the intra-cellular secretory system. what happens to the deltaF508 form of CFTR role of chaperone proteins role of proteosomes

Lecture 8: Photosynthesis I: Light Dependent Reactions


In multiple choice format questions, identify meaning of oxygenic vs. anoxygenic photosynthesis, phytoplankton, fluorescence, thylakoid lumen, pigment, conjugated system, color, absorption, membrane and stroma, light-harvesting complexes, reaction center, antenna pigments, resonance energy transfer, photosynthetic electron transport, photosystem I vs. II, p680, p680*, p680+,

Fundamentals of light absorption by pigment molecules What is so special about light? Structure and function of different parts of a photosystem mechanism of transfer of energy in pigments associated with reaction center components of photosynthetic electron transport Use of light energy to drive electron transport characteristics of p680+ comparison of oxygenic vs. anoxygenic photosynthesis

Draft Outcomes for Lectures in Biology 1002B

2012

Lecture 9: Photosynthesis II: Light-Independent reactions


In multiple choice format questions, identify meaning of light-independent reactions, Calvin cycle, carbon fixation rate, light saturation curve, light compensation point, rubisco, photorespiration, carbonic anhydrase, C4 metabolism, PEP carboxylase, transpiration, stomata, transpiration ratio terrestrial vs. aquatic primary production factors that influence phytoplankton distribution role of iron in marine primary production Global carbon production Role of phytoplankton and what limits there abundance Iron release experiment carbon stoichiometry of the Calvin Cycle Calvin cycle intermediates, ATP and NADPH inputs Production vs. consumption of oxygen and carbon dioxide for respiration vs. photosynthesis How to determine respiration rate in plants/phytoplankton How to determine the light compensation point Relationship between light compensation point and growth (increase in mass) Reaction catalyzed by rubisco Effect of oxygen on rubisco activity Implications of photorespiration for growth Relative Affinity (Km) of rubisco for oxygen vs. CO2 Relative atmospheric/aquatic concentration of oxygen vs. CO2 Evidence for evolution of rubisco specificity for CO2 Various CO2 concentrating mechanisms (to reduce photorespiration) Examples of C4 plants cost of C4 metabolism explain global distribution of C4 vs. C3 plants relationship between gas solubility and water loss vs temperature