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Biochem Final
Sample Final Exam
111
Chemistry
Undergraduate 4
12/10/2009

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Term
van der waals interaction
Definition
The _____ describes the relation betwee ineratomic distances, electronic charge, solution dielectric and free energies
Term
Quaternary structure
Definition
Protein ____ defines the realtion among subunits in a multisubunit lattice
Term
Primary Structure
Definition
Protein ____ defines the amino acid sequence
Term
Tertiary Structure
Definition
Protein ____ defines the packing of helices, sheets, turns, etc.
Term
Secondary Structure
Definition
Protein ____ defines the motifs formed by short-range interactions between amino acids
Term
Hydrogen bond
Definition
a ____ interaction involves polar O, n, or both and the atom for which it is named, and constitutes one of the important protein stabilization elements
Term
Edman degredation
Definition
___ is used to determine the sequence of a protein based on sequential chemical reactivity
Term
chaotropic agent
Definition
a _____ induces denaturation of proteins by disturbing the hydrophobic effect
Term
ramachandran plot
Definition
A _____ is a graph of the conformational torsion angles phi and psy for the residues in a protein or peptide, a map of the structure of the polypeptide backbone
Term
zwitterion
Definition
A _____ has two charges whch neutralize each other
Term
hydrophobic effect
Definition
the _____ is the primary force of protein structural stabilization
Term
initial rate
Definition
the _____ is the characteristic speed of an enzyme's kinetics extrapolated to the time when a defined amount of substrate is added to the enzyme solution
Term
catalysis
Definition
an act of _____ does not change an enzyme and lowers the transition state free energy of the associated reaction
Term
maximum velocity
Definition
the _____ of an enzymatic catalysis reeaction is the rate achieved when it is saturated with substrate
Term
Lineweaver-Burk
Definition
the _____ (or double reciprocal) equation defines parameters that are used to characterize the kinetics of an enzyme
Term
Michaelis-Menten constant
Definition
Km is the substrate concentration when v0=vmax/2, or _____
Term
kcat
Definition
the catalytic rate constant of an enzyme is abbreviated _____
Term
competitive inhibition
Definition
_____ of enzyme catalysis occurs when an inhibitor binds to the active site of the enzyme
Term
uncompetitive inhibition
Definition
_____ of enzyme catalysis occurs when the inhibitor only binds to the enzyme-substrate complex
Term
steady state approximation
Definition
the _____ prostulates that a constant input feed of substrate is supplied whose rate equals that of product formation
Term
hydrophobic effect, H-bonding, disulfide bonds, van der waals forces, ionic bonds (salt bridges) or dipole-dipole interactions
Definition
two internal factors that limit the velocity of an enzymatic reaction are _____ and _____
Term
pH, solvent polarity, temperature, salt concentration, and presence of chaotropes, osmolytes
Definition
two external factors that limit the velocity of an enzymatic reaction are _____ and _____
Term

serine, hydroxylate
Definition
What amino acid and functional group in the esterase site of acetylcholin esterase reacts with the substrate?
Term
nerve gas antidote
Definition
Pyridine aldoximine methiodide (PAM) reactivates acetylcholine esterase, functioning as a _____
Term
nucleophilic substitution
Definition
What kind of reaction produces the reactivated enzyme? (acetylcholine esterase)
Term
ping-pong
Definition
the bisubstrate-enzyme _____ reaction is used by transaminases in the exchange of an amino group for a carbonyl group between two progressively vinding substrates
Term
enzyme cascade
Definition
an _____ works by amplifying an initial signal via several linked protease cleavage reaction stages. (eg, blood clotting)
Term
zymogen
Definition
a _____ is a protein that is converted from inactive to active forms by a covalent modification, typically protease cleavage
Term
feedback inhibition
Definition
a decrase in the activity of an enzyme as a result of binding of a product from the reaction in question or subsequent reactions is referred to as _____
Term
allosterism
Definition
_____ involves binding of a regulatory moleculte at a site other than the active site
Term
kinase and phosphatase
Definition
_____ and _____ ractions, involving phosphate addition and removal respectively, regulate both glycolysis and the kreb's cycle
Term
cyclin kinase
Definition
_____ regulates entry and exit from mitosis by catalyzing a covalent modification reaction
Term
tyrosine , threonine
Definition
What two amino acids are modified in the reactions catalyzed by cyclin kinase?
Term
noncovalent modifications, pH and pKa changes, salt changes
Definition
Two examples of reversible factors that control the catalytic capability of an enzyme are _____ and _____
Term
covelent modifications, proteolysis, irreversible inhibitors
Definition
Two examples of irreversible factors that control the catalytic capability of an enzyme are _____ and _____
Term
arrhenius equation
Definition
the _____ accounts for the temperature dependence of the rate of a reaction
Term
acid-base, covalent
Definition
List the two chemical modes of catalysis
Term
proximity effect, transition-state stabilization
Definition
List the two binding modes of catalysis
Term
nucleophile
Definition
a _____ attacks an electropositive site in it's role in a chemical (enzymatic) reaction
Term
acid/base catalysis
Definition
a commmon process used to produce a nucleophile is _____
Term
histidine
Definition
probably the most common amino acid used by enzymes to carry out acid/base catalysis is _____
Term
serine proteases
Definition
a catalytic triad of amino acids is typically present in _____
Term
acid/base catalysis
Definition
the amino acids colloborate to accomplish _____
Term
ATP
Definition
the most typically cited currency of energy in metabolism is _____
Term
Mg2+
Definition
_____ is typically required to achieve optimal activity with ATP cosubstrate enzyme reactions
Term
prosthetic group
Definition
a conenzyme is either loosely bound cosubstrate or tightly bound _____
Term
xanthine oxidase
Definition
the heavy metal molubdenum is used to fascilitate the biochemical reaction _____, a key enzyme in purine cataboism
Term
pyrophosphate
Definition
when ATP used in some biochemical applications it yields AMP and _____
Term
nicotinamide
Definition
the (vitamin) _____ is required to synthesize coenzyme NAD+ for use in metabolic redox reactions
Term
FAD
Definition
the other key redox coenzyme is abbreviated _____
Term
pyridoxal phosphate
Definition
the enzyme _____ often forms a schiff base with the e-amino group of a lysine residue in the enzyme
Term
acetate
Definition
What chemical group does coenzyme A typically carry in the couse of its biochemical function?
Term
biotin
Definition
the _____-avidin noncovalent binding interaction is used to capture ligand-binding entities in the affinity capture technique
Term
N5, N10 tetrahydrofolate
Definition
the coenzyme _____ is required to incorporate the methyl group into thymidine, a necessary prerequisite for the production of DNA
Term
anti-cancer chemotherapy
Definition
our understanding of DNA production can be used in a strategy for _____
Term
UDP-Galactose
Definition
The coenzyme bound carbohydrate _____ and glucose are required to synthesize lactose
Term
transducing
Definition
Cis-retinal functions in _____ the signal of a photon of light into a chemically recognizable form
Term
ketose and aldose
Definition
the two important straight -chain forms of carbohydrate structures are the _____ and _____
Term
pyranose and furanose
Definition
the two important ring forms of carbohydrates are the _____ and _____
Term
chair and boat
Definition
the two important ring coformations of B-D-glucopyranose are the _____ and _____
Term
inositol triphosphate
Definition
the cyclohexane ring containing compoind _____ is released by phospholipase C in the phospholipid signal transductoin mechanism
Term
N-acetyl galactosamine
Definition
the acronum NAG is used to abbreviate the name of the compound _____
Term
amylopectin
Definition
the key polysaccharide in starch is _____
Term
glycogen
Definition
the key polysaccharide in the liver is _____
Term
penicillin
Definition
the antibiotic _____ selectively inhibits cell well peptidylglycan synthesis in bacteria
Term
carbohydrates
Definition
extra-cellular surface _____ regulate the osmotic pressure around cells
Term
diacylglycerol
Definition
phospholipase C produces two differnt second messengers in the phospolipid signal transduction pathway.  The lipi containing second messenger is _____
Term
lubricates
Definition
the compound chondroitin sulfate _____ cartilage and skeltal joints
Term
unsaturated
Definition
saturated/unsaturated fatty acids of the same length have a lower melting temp (Tm)
Term
Liquid crystal
Definition
Lipid Tm values moitor the transformation from _____ to dispersed forms
Term
bilayer, micelles
Definition
lipid _____ are composed of two face-toface monolayers while lipid _____ form a biphasic sphere
Term
fluid mosaic
Definition
the most popular model for a biological membrane is called the_____ model
Term
adenine, guanine, cytosine, and uracil
Definition
the four nucleic acid bases in RNA are _____, _____, _____, and _____
Term
Watson-Crick
Definition
The two normal base pairs in DNA and RNA are called _____ base pairs
Term
glycosidic
Definition
the _____ bond in a nucleoside connects the base to the sugar
Term
absorance at 260 nm
Definition
The _____ can be used to determine if a double helix forms from 2 single strands of DNA or RNA
Term
base stacking
Definition
the face-to-face interaction between nucleic acids is called _____
Term
phosphodiester phosphates
Definition
counterions bind all nucleic acids and are required to neutralize the _____
Term
histones
Definition
the proteins called _____ are counterions that bind and neutralize nucleic acids in the case of the most chromosomal DNA's
Term
AT (or AU), GC
Definition
GC/AT (or AU) base pairs are less stable than GC/AT (or AU) base pairs
Term
alkaline hydrolysis
Definition
the 2'-hydroxyl group catalyzes _____ of RNA, a good exmaple of anchiomeric assistance in a non-protein biomolecular mechanism
Term
tRNA anticodon
Definition
an antisense oligonucleotide functionally inactivarte a mRNA for use in translation by a ribosome by forming a double helix with it and precluding _____ binding
Term
m7G+ (5'-5') cap, monocistronic, contains introns and exons, poly(A) tail
Definition
two distinctive features of most eukaryotic mRNAs are _____ and _____
Term
DNA probe
Definition
a _____ is used to detect the presence of a specific complementary nucleic acid sequence
Term
restriction endonucleases
Definition
_____ are required to produce, manipulate, and clone specific peices of DNA
Term
amino acid acceptor
Definition
the two functional ends of transfer RNa are the anticodon and _____
Term
glycolysis, Krebs cycle, and electron transport/oxidative phosphorylation
Definition
the three most central catabolic pathways of intermediary metabolism are _____, _____, and _____
Term
ATP, NADH, FADH2, and Coenzyme QH2
Definition
the four major compounds in which energy is captured in a chemically usable form by metabolic reaction pathways are _____, _____, _____, and _____
Term
mass action ratio
Definition
the _____ (Q) corrects for deviations from standard state concentrations (1M)
Term
three
Definition
_____ (number) steps in glycolysis control most of the flux through the pathway under actual cellular conditions
Term
metabollically irreversible
Definition
What do the three steps in glycolysis have in common?  They are all _____
Term
near equilibrium
Definition
Most of the reactions in glycolysis are _____
Term
the actual concentration of the reactant
Definition
the kinetics of an enzyme reaction are most easily controlle when Km is approximately equal to  _____
Term
dihydroxyacetone phosphate
Definition
the enzyme triose phosphate isomerase converts _____ into glyceraldehyde-3-phosphate
Term
feedback inhibition
Definition
when citrate negatively regulates (discourages) the phosphofructokinase-1 reaction, the general name for this phenomenon is _____
Term
feedforward activation
Definition
when fructose-1,6-bisphospahte stimulates the pyruvate kinase reaction, the general name for this phenomenon is _____
Term
acetyl CoA, ethanol, and lactate
Definition
the three possible catabolic fates of pyruvate are _____, _____, and _____
Term
acetaldehyde
Definition
the enzyme alcohol dehydrogenase converts _____ to ethanol
Term
dihydrolipoamide acetyl transferase
Definition
_____ uses the coenzyme lipoic acid in fueling the kreb's cycle
Term
pyruvate translocase
Definition
What symport reaction accompanies import of pyruvate into the mitochondrion and what enzyme catalyzes the reaction?
Term
isocitrate dehydrogenase and a-ketoglutarate dehydrogenase
Definition
the two oxidative decarboxylation reactions of the kreb's cycle are catalyzed by _____ and _____
Term
succinyl CoA synthetase
Definition
list the reaction, coenzymes, cofactors, and enzymes involved in the substrate level phosphorylation reaction of the kreb's cycle
Term
fumarase
Definition
the enzymes _____ and malate dehydrogenase fix a carbonyl group on succinate in the production of oxaloacetate
Term
acetate
Definition
what crucial 2 carbon compound is fixed to oxaloacetate?
Term
alanine and lactate
Definition
what amino acid and what product of pyruvate metabolism are the principle substrates for gluconeogenisis in mammals?
Term
NADH, FADH2, CoQH2
Definition
What energy sources are used to produce the protomotive force?
Term
f0f1 ATP synthase
Definition
what enzyme complex uses protonmotive force as the driving energy for ATP synthesis in oxidative phosphorylation?
Term
four (oxidaiton 1, hydration, oxidation 2, and thiolysis)
Definition
How many reactions does each round of b-oxidation of a fatty acid require?
Term
1 CoQH2, 1 NADH, 1 H+, 1 acetyl CoA, 1 fatty acid (minus 2 C's)
Definition
What are the products of one round of b-oxidation and what's the tally in terms of ATP equivalents of energy conserving products?
Term
CoA, FAD/FADH, FE-S2+/3+, CoQ/CoQH2
Definition
A set of coupled cofactor regeneration cycles siphon off reducing equivalents then fix them into coenzyme Q in reactions that are coupled to the first oxidative step of fatty acid B-oxidation.  Write down the names of the four cofactors involved in this siphon
Term
succinate dehydrogenase, fumarase, malate dehydrogenase
Definition
Which three steps of the Kreb's cycle do the first three steps of the fatty acid b-oxidation cycle resemble?
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