Lecture 1

know what the chemcal properties of an amino acid R group are, if shown
         (e.g.  can it donate an H+, can is is positively charged, is it
         hydrophobic, etc.)

know what a peptide bond is, and the basic descriptors of a polypeptide (C
         terminal, N terminal,
a-carbon, peptide bond, etc.)
know the 20 amino acids by name, three letter code, one letter code, and be able to recognize
    as opposed to draw) the structures.
understand the different orders or levels of protein structure
understand what rate enhancement means
describe the energetics of catalysis in simple terms
know how enzymes (and other catalysts) affect activation energy
be able to express this using a reaction energy diagram
know how enzymes affect forward and reverse reaction rate and what this
    means
know the 4 main catalytic mechanisms of enzymes, in simple terms,  
    and be able to recognize which is occurring in an example

Lecture  2

know the relationship between activation energy and reaction rate, and understand the
    equation that describes this relationship
know how to use this equation to discern things about the effects of changes
    in various free energies on rates
be able to write and use the equation describing  simple binding of ligand to
    a binding site, using Kd and Bmax
understand the binding isotherms, or graphs, that result from this relationship
know the relationship of Kd and L, and the simple way that Kd is related to
    half-saturated binding
be able to describe the more complicated case of cooperative binding, and compare
    it to the simpler case of a constant Kd
understand the Michaelis-Menton equation, including what roles Km, Vmax and
    S play in the equation, and how Km relates to concentration of S at 50% saturation
know the meaning of k
cat, and how it is defined, and what it does and does not tell you
    about the rate plot and saturation behavior of an enzyme
know the features of a Lineweaver-Burk (double reciprocal) plot, and generally why they
    are useful
describe or compare two enzymes based on how their L-B plots look.
understand the features of the chymostrypsin active site and mechanism: be able to sketch
    the active site, including the catalytic triad. understand how these three residues act to
    allow proteolysis
know how a covalent inhibitor of an enzyme works, in simple, general terms
discuss the significance of sigmoidal rate curve in enzyme kinetics
describe the basic structural features of a cooperative enzyme
understand in basic terms the concept of allosteric effectors in enzyme action
describe and graph the effects of allosteric inhibitors or activators on an enzyme
be able to propose an allosteric solution to the problem of regulating a metabolic pathway
    by inhibition or activation
describe the general reactions of protein phosphorylation and dephosphorylation;  know the
    two classes of enzyme that add and remove phosphoryl groups from proteins

Lecture 3

be able to describe catabolism and anabolism in general terms, and with sufficient
    understanding to decide if a pathway is an example of one, the other, or both
know how enthalpy (heat) and entropy contribute to the general expression for the free
    energy change,
deltaG, or a process
know the meaning of "prime zero" in the superscripts of
deltaG
understand how
deltaG relates to the spontaneity of a process
know the relationship between
deltaG'0 and Keq; be able to write and use the equation that
    describes the
deltaG' as a function of deltaG'0
know the equation that describes the free energy for a real process as a function of reactant    
        and product concentrations and the
deltaG'0
be able to compute the free energy change for a set of reactions from the individual free
    energy changes
understand the idea of creating a good leaving group as a strategy to drive and otherwise
    non-spontaneous reaction
understand the importance of steps in metabolic pathways that have small changes in free
    energy and the differing importance of steps that have a big change in free energy, and       
     how this distinction can be used to predict how pathways are regulated

Lecture 4

know how to distinguish more and less oxidized carbon atoms in an organic molecule
understand the physical meaning of a half-cell potential
know the equation that relates actual half cell potential for a half reaction to the standard
    half cell potential and concentrations of reactants and products (Nernst equation)
understand how
E' can be used to predict spontaneity of reaction or half reaction
know how to compute
deltaE' o for a complete redox reaction from the pair of E' o reduction
    potentials for each half reaction
know the relationship between
deltaG for a process and E
understand how carbohydrate oxidation to CO2
and H2O can be thought of as a redox
    reaction, where electrons are removed from one reactant and gained by another
understand how the functional group of NAD
+ (or NADP+) is designed to accept carry
    electrons as a hydride ion ( no need to memorize structure, but you should be able to    
    recognize it and describe relevant chemistry
understand how the functional group of FAD (or FMN) is designed to accept carry
    individual electrons; no need to memorize structure, but you should be able to recognize
    it and describe relevant chemistry

Lecture 5

know the general layout of the glycolytic pathway, including preparatory phase, the payoff
    phase, and how the important components are regenerated
understand where ATP comes from in glycolysis, and why there is a net gain
know all the structures, and the 10 reactions that comprise the pathway.  The level of
    understanding should allow you to trace a carbon (or any other) atom at a particular
    position in one of the pathway molecules to the appropriate position, or positions, in
    another molecule further down the pathway. 
know the mechanisms that are highlighted in the lectures
be able to recognize the names of the enzymes involved, and any features of them have    
    been discussed in class. 
know how NAD is regenerated in anaerobic organisms or tissues, and why this is important
know the three usual fates of pyruvate (fermentation, lactate production, conversion to
    acetate, and the significance of each
understand the biological circumstance where glycolysis is the sole or main source of
    metabolic energy


Lecture 6


know how fructose is introduced into the glycolytic pathway
know how glucose is released by glycogen phosphorylase
understand the important role that glycolysis has in the anaerobic or hypoxic
    production of ATP from glucose, and be familiar with the various  
    examples I gave in class of glycoloysis in low-oxygen situations
know the two major pathways of fermentation that were mentioned in class
understand how the cofactor TPP works (no need to know the structure, but
    do understand how the chemistry at the "business end" works).
know the action of TPP in the pyruvate decarboxylase reaction, since it is a     
   very simple enzyme that allows understanding of TPP in more complex enzymes
    like pyruvate dehydrogenase
understand why, in chemical terms, TPP is so often involved in breaking and
    forming sigma bonds attached to carbonyl carbons
be able to describe how lactate is formed, why this is important for purely
    glycolytic organisms, and what the physiological importance of
    lactate is during intense exercise, whether it is coelacanths, crocodiles, sprinters,     
    or crocodiles chasing sprinters
know which glycolytic enzymes are regulated, and what molecules affect     
    their activities
understand why phosphofructokinase-1 (PFK-1) is so important for control  
    glycolysis. and what its allosteric regulators are
be able to describe, with structures and enzyme names, how ribose is produced from glucose by
    the oxidative steps of the pentose phosphate pathway.
understand, verbally but no need for structures, the non-oxidative portion of the
    pentose phosphate pathway.  The principle that many sugars are made by shuffling
    2 and 3 carbon units around with transketolase (2 carbon) and transaldolase (3 carbon).


Lecture 7


know the variety of ways the people write acetyl CoA, just so that you stay     
    stay sane.  And understand what an acetyl group is.
be able to describe in general terms where acetate groups come from for  
    entry into the Krebs cycle
be clear on the critical chemistry of the CoA carrier.  How does that sulfur  
    play its critical role in its action as a carrier?  What is the name of the linkage
    between sulfur and acetate?
be able to describe the net reaction of the PDH complex.  So substrates in,  
    and products out
be able to describe the role of the various cofactors that the PDH  
    employs to do its chemical magic on pyruvate
understand the chemistry of the lipoic acid cofactor.  Although you dont
    have to know the structure, you should be able to recognize "the business end", and
    be familiar with the way the oxidized and reduced forms of this portion of the molecule
    participate in the PDH reaction cycle.
know the PDH catalytic cycle (which is really a combination of the above 3 things).
know all the structures and the enzymes for the Krebs cycle.  Mechanisms that we have
    described in class are part of the extent of your knowledge
be able to describe in general terms what the Krebs is fed, and what it  produces. 
    What is its catabolic function(s)?
understand how a labeled carbon in citrate will go through the various
    Krebs cycle structures, that is, at what position or positions that label will end
    up in in any intermediate. 
understannd why aconitase can distinguish between the two CH3-CO2- groups in the substrate

Lecture 8

understand how the concept of prochiral pertains to the synthesis of
    isocitrate by aconitase, and to the synthesis of citrate as well
understand the general roles of Krebs cycle in anabolism
know the four anaplerotic (http://dictionary.oed.com/) reactions
understand the role of biotin as a cofactor in carboxylation reactions; you
     dont need to memorize structures, but you should be able to
    recognize them
know the regulation points for the production of acetate and its consumption by the Krebs cycle.     
    which enzymes are regulated?
understand the logic of the various regulators of these enzymes, such that
    if one is show to you, you would predict how it might regulate
    the Krebs cycle.
understand why the Krebs cycle can not be used to produce net glucose from
    fat- without the use of other sources of carbon
know how the glycoxylate cycle gets around this problem, and what the
    two new enzymes are that allow this alternate route for acetate
    anabolism

Lecture 9

 
know the key structures (that I listed) of the mitochondrion, and the
         biochemical properties and protein activities listed for each
understand the different types of electron carriers that participate in the
         respiratory chain.  No need to memorize structures, but understanding
         their action if presented with them is a good idea
know why an ordered series of E values can predict (but not prove) a chain
         of electron transport.  Be able to predict such a chain from a set of Es
         that you are presented with
understand how inhibitors can be used as an independent (from E values)
         way to evaluate the order of events in a chain of redox reactions like
         the respiratory chain

complexes I-IV
    names, where they work, substrates and products, order in RC
relevant carriers and cofactors in oxidative phosphorylation
proton gradient: deltapH and deltaY, relative importance in ATP production
understand the formula that describes these two components
structure of mitochondrion and how components of respirator chain are   
    arranged

Lecture 10

action and arrangement of the ATP synthase
know effects of following drugs on ATP synthesis, O2 consumption, proton
    gradient: : weak acid uncouplers, ATP synthase inhibitors, and inhibitors of
    individual complexes
other examples of rotary molecular motors

You are NOT RESPONSIBLE for the things listed below on the midterm,
but you will be responsible for them on the final:

malate/aspartate shuttle for moving electrons across inner membrane
glycerol-3P shuttle for moving electrons across the inner membrane
understand what thermogenin does and its role in brown adipose tissue
principle of acceptor control: why does ADP availability control the rate of   
    respiratory chain activity
know how respiratory chain, Krebs cycle, and glycolysis are all connected by
    key allosteric regulators