Comprehensive Exam Review 12/03/2009. Structure & Properties of Water Bent geometry, O-H bond length...
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Comprehensive Exam Review12/03/2009
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Structure & Properties of WaterBent geometry, O-H bond length of 0.958Å
Can form Hydrogen bonds
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Henderson - Hasselbalch equation
][
]][[
HA
AHK
From
][
][][
A
HAKHRearrange
Take (-)Log of each][
][loglog
HA
AKpH
][
][log
HA
ApKpH
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The 6 step approach
1. Write the Henderson + Hasselbalch equation.
2. Write the acid base equation
3. Make sure either an H+ or OH- is in the equation.
3. Find out what you are solving for
4. Write down all given values.
5. Set up equilibrium conditions.
6. Plug in H + H equation and solve.
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What is the pH of a solution of that contains 0.1M CH3COO- and 0.9 M CH3COOH?
1) pH = pK + Log [A-] [HA]
2) CH3COOH CH3COO- + H+
3) Find pH
4) pK = 4.76 A- = 0.1 M HA = 0.9 M
5) Already at equilibrium
6) X = 4.76 + Log 0.1 0.9
Log 0.111 = -.95 X = 4.76 + (-.95) X = 3.81
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Amino Acids
You must know Table 4.1 p76-77:
Their namesTheir structureTheir three letter codeTheir one letter code
Tyrosine, Tyr, Y, aromatic, hydroxyl
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The Fischer Convention
Absolute configuration about an asymmetric carbon
related to glyceraldehyde
(+) = D-Glyceraldehyde
(-) = L-Glyceraldehyde
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Newman ProjectionThreonine and Isoleucine
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Nucleophiles
R NH2 + H+ R N+ H
H
H
R NH2 O
R'
R''
R N C OH
R''
R'H
Basic reaction of amine
Nucleophilic reaction of an amine
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Biologically important nucleophiles
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R NH2 O
R'
R''
R N C OH
R''
R'
H
R
N
H R'
R''+
Amine Ketone or aldehyde
Carbinolamine intermediate
Imine
Movement of an electron pair from a position and pointing to the electron deficient center attracting the pair.
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Common biological electrophiles
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Group transfer reactions
Acetyl group transfer
Nucleophile attack on an acyl carbonyl to form a tetrahedral intermediate
Peptide bond hydrolysis
Phosphoryl group transfer
nucleophile attack on a phosphate to yield a trigonal bipyramid intermediate
Kinase reactions involving transfer of phosphate from ATP to organic alcohols
Glycosyl group transfers
substitution of one group at the C1 carbon of a sugar for another
Y + A X Y A + X
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Thioesters (Acetyl-coenzyme A)
High energy compound
Carrier of acetyl and acyl groups
Can be used to drive exogenic processes
e.g. GTP from GDP
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Oxidations and reductionsOxidation : Loss of Electrons
Reduction: Gain of ElectronsMany redox reactions involve the breaking of a C-H bond and the loss of two bonding electrons
Y + H O C
R
R
H
N
R
NH2
OH
+
Y H
R
NH2
O
R
R
O
HH
+ +
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Electron transfer reactions to oxygen undergo transfer of one electron at a time (Pauli exclusion principle)
Oxidations to oxygen from NADH require two electron steps to be changed to one electron steps. Stable radical structures like FMN or FAD and cytochromes are involved.
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Reduction of NAD+ to NADH
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Electron transfer reactions
BABA redred
n n
oxox
red
nox
nox
red0
B
B
A
AlnRTG G
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Half-cell reactions either donate or accept electrons
Electron donor (reducing agent)
Electron acceptor (oxidizing agent)
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Work is non -pressure volume work or
G = -w’ = -welec
Welec = nFE
or
G = -nFE
red
nox
nox
redo
B
B
A
Aln
nF
RT - E E
F = Faraday constant = 96,485 Coulombs per mole of electrons
E0 = standard reduction potential or midpoint potential
Nernst Equation- electromotive force -EMF- reduction potential
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Measuring potentials
red-n
ox red-n
oxB ne B and A neA
nox
red0AA A
ALn
nF
RT - E E
o
donor -eo
acceptor -eo E - E E
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However, there is no absolute potential to reference!
(g)H 2e 2H 2-
At equilibrium and in contact with a platinum electrode and at 1 M H+ and STP this is defined as zero potential. At pH of 7.0 this is -0.421 V = Eo´. Prime means that it is at pH 7.0.
Every thing is referenced to this potential
See Table in FOB pg 473 for standard potentials
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Example of each level of protein structure
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Binding of the O2 on one heme is more difficult but its binding causes a shift in the 1-2 (& 2-1) contacts and moves the distal His E7 and Val E11 out of the oxygen’s path to the Fe on the other subunit. This process increases the affinity of the heme toward oxygen.
The 1-2 contacts have two stable positions .
These contacts, which are joined by different but equivalent sets of hydrogen-bonds that act as a binary switch between the T (deoxy) and the R (oxy) states
Hemoglobin structure-monomers are related by 2-fold symmetry (same is true for )Note changes in structure:
between -monomers – see big double-headed arrowsat points of contact – see small arrows
DeoxyHb
oxyHb
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The Fe iron is about 0.6 Å out of the heme plane in the deoxy state. When oxygen binds it pulls the iron back into the heme plane. Since the proximal His F8 is attached to the Fe this pulls the complete F helix like a lever on a fulcrum.
The positive cooperativity of O2 binding to Hb The effect of the ligand-binding state of one heme on
the ligand-binding affinity of another.
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Binding causes a shift in the 1-2 contacts and moves the distal His E7 and Val E11 out of the oxygen’s path to the Fe on the other subunit. This process increases the affinity of the heme
toward oxygen.
The 1-2 contacts have two stable positions with different but
equivalent sets of hydrogen bonds to act as binary switch between the
T and the R states
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General Properties of Enzymes
•Increased reaction rates sometimes 106 to 1012 increase
Enzymes do not change G between the reactants and products.
They increase reaction rates (catalysts).
•Milder reaction conditions
•Great reaction specificity
•Can be regulated
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Mechanism of lysozyme
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Bovine Trypsin
Serine proteases
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Enzyme Kinetics: The double reciprocal plot
maxmax
M
V
1
S
1
V
K1
ov
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Competitive Inhibition
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Competitive Inhibition: Lineweaver-Burke Plot
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Uncompetitive Inhibition
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Uncompetitive Inhibition: Lineweaver-Burke Plot
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Mixed inhibition
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Monosaccharides (D-aldoses)
Epimers
Not Epimers
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Carbohydrates are classified as to the nature of the carbonyl group : ketone = ketose aldehyde = aldose
Triose
Tetrose
Pentose
Hexose
2(n-3) stereoisomers of ketoses
c.f. 2(n-2)
stereoisomers of aldoses
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Glycolysis Review• Stage I: Energy investment
(rxns. 1-5), glucose phosphorylated and cleaved to yield 2 G3P and consumes 2 ATP
• State II: Energy recovery (rxns. 6-10), G3P converted to pyruvate with generation of 4 ATP
• Net profit of 2 ATP per glucose
Glucose + 2NAD+ + 2ADP +2Pi 2NADH + 2pyruvate + 2ATP + 2H2O + 4H+
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The five reactions of the pyruvate dehydrogenase multi enzyme complex
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Comprehensive Exam
Tuesday December 15, 11:00 AM – 2:00 PM