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BCH Final
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192
Biochemistry
Undergraduate 4
11/28/2012

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Term
The _____ describes the relation between interatomic distances,electronic charge, solution dielectric, and free energies.
Definition
Van der Waals Interaction
Term
Protein ____ defines relation among subunits in a multisubunit lattice.
Definition
Quaternary structure
Term
Protein ____ defines amino acid sequence
Definition
Primary structure
Term
Protein ___ defines packing of helices, sheets, turns, etc.
Definition
Tertiary Structure
Term
Protein ___ defines the motifs formed by short-range interactions between amino acids
Definition
Secondary Structure
Term
A ___ interaction involves polar O, N, or both and the atom for which it is named, and constitutes one of the most important protein stabilization elements
Definition
Hydrogen bond
Term
____ is used to determine the sequence of a protein based on sequential chemical reactivity.
Definition
Edman Degradation
Term
A ____ induces denaturation of proteins by disturbing the hydrophobic effect.
Definition
Chaotropic Agent
Term
A ____ is a graph of the conformation torsion angles ɸ and ᴪ for the residues in a protein or peptide, a map of the structure of the polypeptide backbone.
Definition
Ramachandran Plot
Term
A ____ has two charges which neutralize each other.
Definition
Zwitterton
Term
The ____ is the primary "force" of protein structural stabilization.
Definition
Hydrophobic effect
Term
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
Definition
initial rate
Term
An act of ____ does not change an enzyme and lowers the transition state free energy of the associated reaction.
Definition
catalyst
Term
The _____ of an enzymatic catalysis reaction is the rate achieved when it is saturated with substrate.
Definition
maximum velocity
Term
The _____ (or double reciprocal) equation defines parameters that are used to characterized the kinetics of an enzyme.
Definition
Lineweaver-Burk
Term
Km is the substrate concentration when V0 = Vmax/2, or _____
Definition
Michaelis-Menten constant
Term
A _____ is the enzyme-substrate combination formed during an enzyme catalysis event.
Definition
Michaelis complex
Term
The catalytic rate constant of an enzyme is abbreviated as ____
Definition
kcat
Term
_____ of enzyme catalysis occurs when an inhibitor binds to the active site of the enzyme.
Definition
competitive inhibition
Term
_____ of enzyme catalysis occurs when the inhibitor only binds to the enzyme-substrate complex.
Definition
Uncompetitive inhibition
Term
The _____ postulates that a constant input feed of substrate is supplied whose rate equals that of product formation.
Definition
Steady State approximation
Term
Two internal factors that limit the velocity of an ezymatic reaction are ___ and ___
Definition
hydrophobic effect, H-bonding, disulfide bonds, van der Waals force, ionic bonds (salt bridge), or dipole-dipole interactions
Term
Two external factors that limit the velocity of an enzymatic reaction are ___ and ___
Definition
pH, solvent polarity, temperature, salt concentration(s), and types, presence of chaotropes, osmolytes, others)
Term
What amino acid and functional group in the esterase site of acetycholine esterase reacts with the substrate?
Definition
serine, hydroxylate
Term
Pyridine aldoximine methiodide (PAM) reactivates acetycholine esterase, functioning as a ____
Definition
nerve gas antidote
Term
What kind of reaction produces the reactivated enzyme?
Definition
nucleophilic substitution
Term
The bisubstrate-enzyme ____ reaction is used by transaminase in the exchange of an amino group for a carbonyl group between two progressively binding substrates.
Definition
Ping-pong
Term
An _____ works by amplifying an initial signal via several linked protease cleavage reaction stages (ie blood clotting)
Definition
enzyme cascade
Term
A ____ is a protein that is converted from inactive to active forms by a covalent modification, typically protease cleavage
Definition
zymogen
Term
A decrease 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 _____
Definition
feedback inhibition
Term
____ involves binding of a regulatory molecule at a site other than the active site.
Definition
Allosterism
Term
____ and ____ reactions, involving phosphate addition and removal respectively, regulate both glycolysis and Krebs Cycle
Definition
Kinases and Phosphatase
Term
____ regulates entry and exit from mitosis by catalyzing a covalent modification reaction.
Definition
Cyclin kinase
Term
Which two amino acids are modified in the reactions catalyzed by enzyme in Cyclin Kinase?
Definition
Tyrosine and Threonine
Term
Two examples of reversible factors that control the catalytic capability of an enzyme are: ____ and _____
Definition
noncovalent modifications, pH and pKa changes, [salt] changes, others
Term
two examples of irreversible factors that control catalytic capability of an enzyme are: ____ and ____
Definition
covalent modifications, proteolysis, irreversible inhibitors, others
Term
The ____ accounts for the temperature dependence of a rate of a reaction.
Definition
Arrhenius equation
Term
List the two "chemical modes of catalysis"
Definition
acid-base, covalent
Term
List the two "binding modes of catalysis"
Definition
proximity effect, transition-state stabilization
Term
A ____ attacks an electropositive site in its role in a chemical (enzymatic) reaction
Definition
nucleophile
Term
A common process used to produce a nucleophile is ____
Definition
acid-base catalysis
Term
The most common amino acid is typically present in (enzyme class name)____
Definition
serine proteases
Term
The amino acids collaborate to accomplish____
Definition
acid-base catalysis
Term
The most typically cited currency of energy in metabolism is ___
Definition
ATP
Term
____ is typically required to achieve optimal activity with ATP-cosubstrate enzyme reactions?
Definition
Mg2+
Term
A coenzyme is either a loosly bound cosubstrate or strongly bound ____
Definition
prosthetic group
Term
The heavy metal molybdenum is used to facilitate the biochemical reaction in _____, a key enzyme in purine catabolism.
Definition
xanthine oxidase
Term
When ATP is used in some biochemical applications, it yields ____ and ____
Definition
AMP and pyrophosphate
Term
The (vitamin) ____ is required to synthesize coenzyme NAD+ for use in metabolic redox reactions.
Definition
nicotinamide
Term
The other key redox coenzyme is abbreviated ____
Definition
FAD
Term
The coenzyme ____ often forms a Schiff base with the Ɛ-amino group of a lysine residue in the enzyme.
Definition
pyridoxal phosphate
Term
What chemical group does coenzyme A typically carry in a course of its biochemical function?
Definition
acetate
Term
The ____-avidin noncovalent binding interaction is used to capture ligand-binding entities in the "affinity capture" technique.
Definition
biotin
Term
The coenzyme _____ is required to incorporate the methyl group into thymidine, a necessary prerequisite for the production of DNA
Definition
N5,N10 methylenetetrahydrofolate
Term
Our understanding of this function can be used in a strategy (treatment technique) ____
Definition
anticancer chemotherapy
Term
The coenzyme bound carbohydrates ____ and ____ are required to synthesize lactose.
Definition
UDP-galactose and glucose
Term
Cis-retinal functions in ____ the signal of a photon of light into chemically recognizable form?
Definition
transducing
Term
The two important straight-chain forms of carbohydrate structures are the ____ and ___
Definition
ketose and aldose
Term
The two important ring conformations of B-D-glucopyranose are the ___ and ___
Definition
chair and boat
Term
The cyclohexane ring containing the compound ____ is released by phospholipase C in the phospholipid signal transduction mechanism
Definition
inositol triphosphate
Term
The acronym NAG is used to abbreviate the name of compound ____
Definition
N-acetyl glucosamine
Term
The key polysaccharide in starch is ____
Definition
amylopectin
Term
the key polysaccharide in the liver is ____
Definition
glycogen
Term
The antibiotic ___ selectively inhibits cell wall peptidylgycan synthesis in bacteria
Definition
penecillin
Term
Extra-cellular surface _____ regulate the osmotic pressure around cells
Definition
carbohydrates
Term
Phospholipase C produces two different second messengers in the phopholipid signal transduction pathway. the lipid-containing second messenger is _____
Definition
diacylglycerol
Term
The compound condroitin sulfate ___ cartilage and skeletal joints
Definition
lubricates
Term
Saturated/Unsaturated (circle one) fatty acids of the same length have a lower melting temperature (Tm)
Definition
unsaturated
Term
Lipid Tm values monitor the transformation from ____ to dispersed form
Definition
liquid crystal
Term
Lipid ____ are composed of two face-to-face monolayers while lipid ___ form a biphasic sphere.
Definition
bilayers, micelles
Term
The most popular model for a biological membrane is called the ____
Definition
fluid mosaic model
Term
The four nucleic acid bases in RNA are ___, ___, ___, and ___
Definition
adenine, guanine, cytosine, and uracil
Term
The two normal base pairs in DNA and RNA are called ____ base pairs
Definition
Watson-Crick
Term
The ____ bond in a nucleoside connects the base to the sugar
Definition
glycosidic
Term
The _____ can be used to determine if 2 single strands of DNA or RNA form a double helix
Definition
absorpbance of 260nm
Term
The face-to-face interaction between nucleic acid bases is called ____
Definition
base stacking
Term
Counterions bind all nucleic acids and are required to neutralize the _____
Definition
phosphodiester phosphates
Term
Protein complexes called ____ serve this counterion function in the case of most chromosomal DNAs
Definition
Histones
Term
G*C/A*T(or A*U)(circle one) base pairs are less stable than G*C/A*T(A*U) base pairs.
Definition
A*T(or A*U), G*C
Term
The 2'-hydroxyl group catalyzes _____ of RNA, a good example of anchiomeric assistance in a non-protein biomolecular mechanism.
Definition
alkaline hydrolysis
Term
An antisense oligonucleotide functionally inactivate a mRNA for use in translation by a ribosome by forming a double helix with it and precluding ____ binding
Definition
tRNA anticodon
Term
Name the two most prevalent of the four classes of RNA
Definition
ribosomal RNA and transfer RNA
Term
Two distinctive features of most eukaryotic mRNAs are ____ and ____
Definition
m7G (5'-5') cap, monocistronic, contains introns and exons, poly(A) tail
Term
A ______ is used to detect the presence of a specific complementary nucleic acid sequence.
Definition
DNA probe
Term
_______ are required to produce, manipulate, and clone specific pieces of DNA.
Definition
Restriction endonucleases
Term
Two function ends of transfer RNA are the anticodon and ____
Definition
amino acid acceptor
Term
The three most central catabolic pathways of intermediary metabolism are ____, ____, and ____
Definition
Glycolysis, Krebs Cycle, and Electron Transport/Oxidative Phosphorylation
Term
The four major compounds in which energy is captured in a chemically usable form by metabolic reaction pathways are ___, ___, ___, and ___
Definition
ATP, NADH, FADH2, Coenzyme QH2
Term
The _____ (Q) corrects for deviations from standard state concentrations (1M)
Definition
mass action ratio
Term
____ (number) steps in glycolysis control most of the flux through the pathway under actual cellular conditions.
Definition
3
Term
What do the reactions in the 3 steps of glycolysis have in common?
Definition
metabolically irreversible
Term
In contrast, the rest of the reactions are _____
Definition
near equilibrium
Term
The kinetics of an enzyme reaction are most easily controlled when Km is approximately equal to the ____
Definition
actual concentration of the reactant
Term
The enzyme triose phosphate isomerase converts ___ into glyceraldehyde-3-phosphate
Definition
dihydroxyacetone phosphate
Term
When citrate negatively regulates (discourage) the phosphofructose-1 reaction, the general name for this phenomenon is ____
Definition
feedback inhibition
Term
When fructose-1,6-bisphosphate stimulates the pyruvate kinase reaction, the general name for this phenomenon is ____
Definition
feed forward activation
Term
The three possible catabolic fates of pyruvate are ___, ___, and ___
Definition
acetyl Coa, ethanol, and lactate
Term
________ uses the coenzyme lipoic acid in fueling Krebs Cycle.
Definition
Dihydrolipoamide acetyl transferase
Term
What symport reaction accompanies import of pyruvate into the mitochondrion and what enzyme catalyzes the reaction?
Definition
pyruvate translocase
Term
The two oxidative decarboxylation reactions of the Krebs Cycle are catalyzed by _____ and _____
Definition
isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase
Term
List the reactions, coenzyme(s), cofactor(s), and enzymes involved in the "substrate-level" phosphorylation in Krebs Cycle
Definition
Succinyl CoA Synthetase
Term
The enzymes ____ and ____ dehydrogenase "fix" a carbonyl group on succinate in the production of OAA
Definition
fumarase and malate dehydrogenase
Term
What crucial 2 carbon compound is then "fixed" to OAA?
Definition
acetate
Term
What amino acid and what product of pyruvate metabolism are the principle substrates for gluconeogenesis in mammals?
Definition
Alanine and Lactate
Term
What energy sources are used to produce the proton motive force?
Definition
NADH, CoQH2, FADH2(indirectly)
Term
What enzyme complex uses this phenomenon as the driving energy for ATP synthesis in oxidative phophorylation?
Definition
F0F1 ATP Synthase (ATPase)
Term
How does electron Transport drive production of the protomotive force?
Definition
exports H+ from mitochondrion (which creates a gradient, making them predisposed to flowing back in)
Term
How many reactions does each round of beta-oxiation of a fatty acid require?
Definition
four (oxidation 1, hydration, oxidation 2, thiolysis
Term
What are the products of one round of beta-oxidation and what's the tally in terms of ATP equivalents of energy conserving products?
Definition
1 CoQH2, 1 NADH, H+, 1 acetyl CoA, 1 fatty acid (minus 2 Cs)
Term
A set of coupled cofactor regneration cycles siphon off reducing equivalents then fix them into coenzyme Q in reactions that are coupled to the first oxidative step of fatty acid Beta-oxidation. Write down the names of the four cofactors involved int his siphon
Definition
CoA, FAD/FADH2, Fe-S2+/3+, CoQ/CoQH2
Term
Which three steps of Krebs Cycle do the first three steps of the fatty acid B-Oxidation cycle resemble?
Definition
Succinate dehydrogenase, fumarase, malate deydrogenase
Term
The Van der Waals interaction describes the relation between ____, ____, ____, and ____
Definition
interatomic distances,electronic charge, solution dielectric, and free energies.
Term
Protein quaternary structure defines relation among subunits in a ____ ____.
Definition
multisubunit lattice
Term
Protein Primary structure defines ____ ____ ____.
Definition
Amino Acid sequence
Term
Protein tertiary structure defines packing of ___, ___, ___, etc.
Definition
helices, sheets, turns
Term
Protein Secondary structure defines the motifs formed by ____ ____ ____ between amino acids
Definition
short-range interactions
Term
A Hydrogen bond interaction involves ___ ___, __, or both and the atom for which it is named, and constitutes one of the most important protein stabilization elements
Definition
polar O, N
Term
A Chaotropic Agent induces _____ of proteins by disturbing the hydrophobic effect.
Definition
denaturation
Term
A Chaotropic Agent induces denaturation of proteins by disturbing the ____ ____.
Definition
hydrophobic effect
Term
A Zwitterton has two charges which ____ each other.
Definition
neutralize
Term
An act of catalyst does not change an enzyme and lowers the ____ ____ free energy of the associated reaction.
Definition
transition state
Term
__ is the substrate concentration when V0 = Vmax/2, or Michaelis-Menten constant
Definition
Km
Term
Km is the substrate concentration when _____(equation), or Michaelis-Menten constant
Definition
V0 = Vmax/2
Term
The ___ ___ ___ of an enzyme is abbreviated as kcat.
Definition
catalytic rate constant
Term
Competitive inhibition of enzyme catalysis occurs when an inhibitor binds to the ___ ___ of the enzyme.
Definition
active site
Term
Uncompetitive inhibition of enzyme catalysis occurs when the inhibitor only binds to the ____ ____ complex.
Definition
enzyme-substrate
Term
Amino acid serine and functional group hydroxylate in the ____ site of ____ ____ reacts with the substrate?
Definition
esterase, acetycholine esterase
Term
____ ____ ____ reactivates acetycholine esterase, functioning as a nerve gas antidote
Definition
Pyridine aldoximine methiodide (PAM)
Term
Pyridine aldoximine methiodide (PAM) reactivates _____ _____, functioning as a nerve gas antidote
Definition
acetycholine esterase
Term
Nucleophilic substitution produces the _____ enzyme.
Definition
reactivated
Term
The bisubstrate-enzyme ping-pong reaction is used by _____ in the exchange of an amino group for a carbonyl group
Definition
transaminase
Term
The bisubstrate-enzyme ping-pong reaction is used by transaminase in the exchange of an amino group for a ____ group
Definition
carbonyl
Term
An enzyme cascade works by amplifying an initial signal via several linked ____ ____ reaction stages (ie blood clotting)
Definition
protease cleavage
Term
A zymogen is a protein that is converted from inactive to active forms by a ____ modification, typically protease cleavage
Definition
covalent
Term
A zymogen is a protein that is converted from inactive to active forms by a ____ ____.
Definition
Protease cleavage
Term
Kinases and Phosphatase reactions, involving phosphate addition and removal respectively, regulate both ____ and _____
Definition
Glycolysis and Krebs Cycle
Term
Cyclin Kinse regulates entry and exit from _____ by catalyzing a covalent modification reaction.
Definition
mitosis
Term
Cyclin Kinse regulates entry and exit from mitosis by catalyzing a ____ ____ reaction.
Definition
covalent modification
Term
Amino acids Tyrosine and Threonine are modified in the reactions catalyzed by enzyme in ____ ____?
Definition
Cyclin Kinase
Term
The Arrhenius equation accounts for the ____ dependence of a rate of a reaction.
Definition
temperature
Term
Acid-base catalysis is a common process to produce ____
Definition
nucleophiles
Term
A coenzyme is either a loosly bound ____ or strongly bound prosthetic group
Definition
cosubstrate
Term
The heavy metal ____ is used to facilitate the biochemical reaction in xanthine oxidase, a key enzyme in purine catabolism.
Definition
molybdenum
Term
The heavy metal molybdenum is used to facilitate the biochemical reaction in xanthine oxidase, a key enzyme in ____ ____.
Definition
purine catabolism
Term
When ____ is used in some biochemical applications, it yields AMP and Pyrophosphate
Definition
ATP
Term
The (vitamin) nicotinamide is required to synthesize coenzyme ____ for use in metabolic redox reactions.
Definition
NAD+
Term
The coenzyme pyridoxal phosphate often forms a ____ ____ with the Ɛ-amino group of a lysine residue in the enzyme.
Definition
Schiff Base
Term
The coenzyme pyridoxal phosphate often forms a Schiff Base with the Ɛ-amino group of a ____ residue in the enzyme.
Definition
lysine
Term
_____ ____ typically carries acetate in a course of its biochemical function
Definition
Acetyl Coa
Term
The biotin-avidin noncovalent binding interaction is used to capture ligand-binding entities in the "____ ____" technique.
Definition
affinity capture
Term
The coenzyme N5,N10 methylenetetrahydrofolate is required to incorporate the methyl group into thymidine, a necessary prerequisite for the production of ___
Definition
DNA
Term
The coenzyme N5,N10 methylenetetrahydrofolate is required to incorporate the ____ group into thymidine, a necessary prerequisite for the production of DNA
Definition
methyl
Term
The coenzyme N5,N10 methylenetetrahydrofolate is required to incorporate the methyl group into _____, a necessary prerequisite for the production of DNA
Definition
thymidine
Term
The coenzyme bound carbohydrates UDP-galactose and glucose are required to synthesize ____.
Definition
lactose
Term
______ functions in transducing the signal of a photon of light into chemically recognizable form?
Definition
Cis-retinal
Term
The two important ring conformations of B-______ are the chair and boat
Definition
B-D-glucopyranose
Term
The key polysaccharide in ____ is amylopection
Definition
starch
Term
the key polysaccharide in the _____ is glycogen
Definition
liver
Term
The antibiotic penecillin selectively inhibits ____ ____ ____ synthesis in bacteria
Definition
cell wall peptidyglycan
Term
Extra-cellular surface carbohydrates regulate the ____ ____ around cells
Definition
osmotic pressure
Term
______ produces two different second messengers in the phopholipid signal transduction pathway. the lipid-containing second messenger is diacyglycerol
Definition
Phospholipase C
Term
Phospholipase C produces two different second messengers in the ____ ____ ____ pathway. the lipid-containing second messenger is diacyglycerol
Definition
Phospholipid Signal Transduction
Term
The compound ____ ____ lubricates cartilage and skeletal joints
Definition
condroitin sulfate
Term
Unsaturated fatty acids of the same length have a ____ melting temperature (Tm)
Definition
lower
Term
Lipid __ values monitor the transformation from liquid crystal to dispersed form
Definition
Tm
Term
In _____ ______, the inhibitor binds to both the enzyme and the Enzyme-substrate complex.
Definition
Non-competitive inhibition
Term
The four nucleic acid bases in DNA are ___, ___, ___, and ___
Definition
adenine, guanine, cytosine, and thymine
Term
When base pair contains imino tautomer adenine and syn conformation Guanine, it is called ___ base pair
Definition
Hoogsteen
Term
A-DNA characters are ____, ____, ____, and ____
Definition
1. C-3' endo sugar pucker
2. 20 degree inclination of base pair to helix axis
3. shorter and wider helix
4. has central-axial cavity
Term
B-DNA characters are ____, ____,____, and _____
Definition
1. C-2' endo sugar pucker
2. base pairs perpendicular to helix axis
3. longer more narrow helix
4. no central axial cavity
Term
The glycosidic bond in a nucleoside connects the base to the ____
Definition
sugar
Term
The absorbance at 260nm can be used to determine if 2 single strands of DNA or RNA form a ___ helix
Definition
double
Term
______ bind all nucleic acids and are required to neutralize the phosphodiester phosphates
Definition
Counterions
Term
The _____ group catalyzes alkaline hydrolysis of RNA, a good example of anchiomeric assistance in a non-protein biomolecular mechanism.
Definition
2'-hydroxyl
Term
The 2'-hydroxyl group catalyzes alkaline hydrolysis of RNA, a good example of _____ assistance in a non-protein biomolecular mechanism.
Definition
anchiomeric
Term
An ____ ____ functionally inactivate a mRNA for use in translation by a ribosome by forming a double helix with it and precluding tRNA anticodon binding
Definition
antisense oligonucleotide
Term
An antisense oligonucleotide functionally inactivate a ____ for use in translation by a ribosome by forming a double helix with it and precluding tRNA anticodon binding
Definition
mRNA
Term
An antisense oligonucleotide functionally inactivate a mRNA for use in translation by a ribosome by forming a ____ ____ with it and precluding tRNA anticodon binding
Definition
double helix
Term
The Mass action ratio(Q) corrects for deviations from ____ ____ concentrations (1M)
Definition
Standard state
Term
The kinetics of an enzyme reaction are most easily controlled when __ is approximately equal to the actual conc. or the reactant
Definition
Km
Term
The enzyme ____ ____ ____ converts dihydroxyacetone phosphate into glyceraldehyde-3-phosphate
Definition
triose phosphate isomerase
Term
The enzyme triose phosphate isomerase converts dihydroxyacetone phosphate into _____
Definition
glyceraldehyde-3-phosphate
Term
When ____ negatively regulates (discourage) the phosphofructose-1 reaction, the general name for this phenomenon is feedback inhibition
Definition
citrate
Term
When citrate negatively regulates (discourage) the _____ reaction, the general name for this phenomenon is feedback inhibition
Definition
phosphofructose-1
Term
When _______ stimulates the pyruvate kinase reaction, the general name for this phenomenon is feed forward activation
Definition
fructose-1,6-bisphosphate
Term
When fructose-1,6-bisphosphate stimulates the _____ ____ reaction, the general name for this phenomenon is ____
Definition
pyruvate kinase
Term
The three possible catabolic fates of _____ are ethanol, lactate, and acetyl CoA
Definition
pyruvate
Term
Dihydrolipoamide acetyl transferase uses the coenzyme _____ _____ in fueling Krebs Cycle.
Definition
lipoic acid
Term
Dihydrolipoamide acetyl transferase uses the coenzyme lipoid acid in fueling ____ ____.
Definition
Krebs Cycle
Term
Succinyl CoA Synthetase is involved in ____ _____ ____.
Definition
Substrate level phophorylation
Term
Alanine and Lactate are princple substrates for _____ in mammals.
Definition
gluconeogenesis
Term
NADH, CoQH2, and FADH2(indirectly) are used to produce ____ ____ force
Definition
proton motive
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