-
Protein _____ defines the relation among subunits in a multisubunit lattice
quaternary sturcture
-
The _____ describes the relation between interatomic distances, electronic charge, solution dielectric and free energies
van der Waals interaction
-
Protein _____ defines the amino acid sequence
primary structure
-
Protein _____ defines the packing of helices, sheets, turns, etc.
tertiary structure
-
Protein _____ defines the motifs formed by short-range interactions between amino acids
secondary structure
-
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
hydrogen bond
-
_____ is used to determine the sequence of a protein based on sequential chemical reactivity
Edman degradation
-
A _____ induces denaturation of proteins by disturbing the hydrophobic effect
chaotropic agent
-
Name the following protein structure:
- R1-CH2-S-S-CH2-R2
- disulfide bond
-
A _____ is a graph of the conformational torsion angles Φ and Ψ for the residues in a protein or peptide, a map of the structure of the polypeptide backbone
Ramachandran plot
-
A _____ has two charges which neutralize each other
zwitterion
-
The _____ is the primary "force" of protein structural stabilization
hydrophobic effect
-
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
initial rate
-
An act of _____ does not change an enzyme and lowers the transition state free energy of the associated reaction
catalysis
-
The _____ of an enzymatic catalysis reaction is the rate achieved when it is saturated with substrate
maximum velocity
-
The _____ equation defines parameters that are used to characterize the kinetics of an enzyme
Lineweaver-Burh (or double reciprocal)
-
Km is the substrate concentration when vo=vmax/2, or _____
Michaelis-Menten constant
-
A _____ is the enzyme-substrate combination formed during an enzyme catalysis event
Michaelis complex
-
The catalytic rate constant of an enzyme is abbreviated as _____
kcat
-
_____ of enzyme catalysis occurs when an inhibitor binds to the active site of the enzyme
Competitive inhibition
-
_____ of enzyme catalysis occurs when an inhibitor only binds to the enzyme-substrate complex
Uncompetitive inhibition
-
The _____ postulates that a constant input feed of substrate is supplied whose rate equals that of product formation
steady state approximation
-
Internal factors that limit the velocity of an enzymatic reaction are _____ (6)
- hydrophobic effect
- H-bonding
- disulfide bonds
- van der Waals forces
- ionic bonds (salt bridges)
- dipole-dipole interactions (actually underlying all of the others)
-
External factors that limit the velocity of an enzymatic reaction are _____ (7)
- pH
- solvent polarity
- temperature
- salt concentrations and types
- presence of chaotropes
- osmolytes
- others
-
What amino acid and functional group in the esterase site of acetylcholine esterase reacts with the substrate?
-
Pyridine aldoximine methiodide (PAM) reactivates acetylcholine esterase, functioning as a _____
nerve gas antidote
-
What kind of reaction produces the reactivated enzyme?
nucleophilic substitution
-
The bisubstrate-enzyme _____ reaction is used by transaminases in the exchange of an amino group for a carbonyl group between two progressively binding substrates
ping-pong
-
An _____ works by amplifying an initial signal via several linked protease cleavage reaction stages (e.g. blood clotting)
enzyme cascade
-
A _____ is a protein that is converted from inactive to active forms by a covalent modification, typically protease cleavage
zymogen
-
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 _____
feedback inhibition
-
_____ involves binding of a regulatory molecule at a site other than the active site
Allosterism
-
_____ and _____ reactions, involving phosphate addition and removal respectively, regulate both glycolysis and the Krebs cycle
-
_____ regulates entry and exit from mitosis by catalyzing a covalent modification reaction
Cyclin kinase
-
What two amino acids are modified in the reactions catalyzed by the enzyme cyclin kinase?
tyrosine, threonine
-
Examples of reversible factors that control the catalytic capability of an enzyme are: (3)
- noncovalent modifications
- pH and pKa changes
- [salt] changes
- possibly others
-
Examples of irreversible factors that control the catalytic capability of an enzyme are: (3)
- covalent modification
- proteolysis
- irreversible inhibitors
- possibly others
-
The _____ accounts for the temperature dependence of the rate of a reaction
Arrhenius equation
-
The two "chemical modes of catalysis"
-
The two "binding modes of catalysis"
- proximity effect
- transition-state stabilization
-
A _____ attacks an electropositive site in it's role in a chemical (enzymatic) reaction
nucleophile
-
A common process used to produce 'nucleophiles' is _____
acid-base catalysis
-
Probably the most common amino acid used by enzymes to carry out acid-base catalysis is _____
histidine
-
A "catalytic triad" of amino acids is typically present in (enzyme class name) _____
serine proteases
-
The amino acids "collaborate" to accomplish _____
acid-base catalysis
-
The most typically cited currency of energy in metabolism is _____
ATP
-
_____ is typically required to achieve optimal activity with ATP-cosubstrate enzyme reactions
Mg2+
-
A coenzyme is either a loosely bound cosubstrate or tightly bound _____
prosthetic group
-
The heavy metal molybdenum is used to facilitate the biochemical reaction in _____, a key enzyme in purine catabolism
xanthine oxidase
-
When ATP used in some biochemical applications it yields AMP and _____
pyrophosphate
-
The (vitamin) _____ is required to synthesize coenzyme NAD+ for use in the metabolic redox reactions
nicotinamide
-
The other key redox coenzyme is abbreviated _____
FAD
-
The coenzyme _____ often forms a Schiff base with the ε-amino group of a lysine residue in the enzyme
pyridoxal phosphate
-
What chemical group does coenzyme A typically carry in the course of it's biochemical function?
acetate
-
The _____-avidin noncovalent binding interaction is used to capture ligand-binding entities in the "affinity capture" technique
biotin
-
The coenzyme _____ is required to incorporate the methyl group into thymidine, a necessary prerequisite for the production of DNA
N5, N10 tetrahydrofolate
-
Our understanding of this function can be used in a strategy for (treatment technique) _____
anti-cancer chemotherapy
-
The coenzyme bound carbohydrate _____ and glucose are required to synthesize lactose
UDP-galactose
-
Cis-retinal functions in _____the signal of a photon of light into a chemically recognizable form
transducing
-
The two important straight-chain forms of carbohydrate structure are the _____ and _____
-
The two important ring forms of carbohydrate are the _____ and _____
-
The two important ring conformations of β-D-glucopyranose are the _____ and _____
-
The cyclohexane ring containing compound _____ is released by phospholipase C in the phospholipid signal transduction mechanism
inositol triphosphate
-
The acronym NAG is used to abbreviate the name of the compound _____
N-acetyl glucosamine
-
The key polysaccharide in starch is _____
amylopectin
-
The key polysaccharide in the liver is _____
glycogen
-
The antibiotic _____ selectively inhibits cell wall peptidylglycan synthesis in bacteria
penicillin
-
Extra-cellular surface _____ regulate the osmotic pressure around cells
carbohydrates
-
Phospholipase C produce two different second messengers in the phospholipid signal transduction pathway. The lipid-containing second messenger is _____
diacylglycerol
-
The compound _____ lubricates cartilage and skeletal joints
chondroitin sulfate
-
_____ fatty acids of the same length have a lower melting temperature (Tm)
Unsaturated
-
Lipid Tm values monitor the transformation from _____ to dispersed forms
liquid crystal
-
_____ are composed of two face-to-face monolayers while _____ form a biphasic sphere
- Lipid bilayers
- Lipid micelles
-
The most popular model for a biological membrane is called the _____
fluid mosaic model
-
The four nucleic acid bases in RNA are
- adenine
- guanine
- cytosine
- uracil
-
The two normal base pairs in DNA and RNA are called _____
Watson-Crick base pairs
-
The _____ bond in a nucleoside connects the base to the sugar
glycosidic
-
The _____ can be used to determine if a double helix forms from 2 single strands of DNA or RNA
absorbance at 260 nm
-
The face-to-face interaction between nucleic acid bases is called _____
base stacking
-
Counterions bind all nucleic acids and are required to neutralize the _____
phosphodiester phosphates
-
The proteins called _____ serve this function in the case of most chromosomal DNAs
histones
-
_____ base pairs are less stable than _____ base pairs
-
Differences between A and B forms of DNA are
A: 3'endo sugar conformation, Base pairs tilted 20° from helix axis, "Doughnut hole" in center of helix, Shorter squatter helix
- B: 2'endo sugar, Base pairs perpendicular to helix axis, Base pairs
- cross center of helix, Longer narrower helix
-
The 2'-hydroxyl group catalyzes _____ of RNA, a good example of anchiomeric assistance in a non-protein biomolecular mechanism
alkaline hydrolysis
-
An antisense oligoculeotide functionally inactivate a mRNA for use in translation by a ribosome by forming a double helix with it and precluding _____ binding
tRNA anticodon
-
Name the two most prevalent of the four classes of RNA
ribosomal RNA and transfer RNA
-
Distinctive features of most eukaryotic mRNAs are _____ (4)
- m7G+ (5'-5') cap
- monocistronic
- contains introns and exons
- poly(A) tail
-
A _____ is used to detect the presence of a specific complementary nucleic acid sequence
DNA probe
-
_____ are required to produce, manipulate and clone specific pieces of DNA
Restriction endonucleases
-
The two functional end of transfer RNA are the _____ and _____
- anticodon
- amino acid acceptor
-
The three most central catabolic pathways of intermediary metabolism are:
- glycolysis
- Krebs cycle
- electron transport/oxidative phosphorylation
-
The four major compounds in which energy is captured in a chemically usable form by metabolic reaction pathways are:
-
The _____ corrects for deviations from standard state concentrations (1 M)
mass action ratio (Q)
-
_____ steps in glycolysis control most of the flux through the pathway under actual cellular conditions
metabolically irreversible (3)
-
In contrast to metabolically irreversible reactions, the rest of the reactions are _____
near equilibrium
-
The kinetics of an enzyme reaction are most easily controlled when Km is approximately equal to _____
the actual concentration of the reactant
-
The enzyme triose phosphate isomerase converts _____ into _____
- dihyroxyacetone phosphate
- glyceraldehyde-3-phosphate
-
When citrate negatively regulates (discourage) the phosphofructokinase-1 reaction, the general name for this phenomenon is _____
feedback inhibition
-
When fructose-1,6-bisphosphate stimulates the pyruvate kinase reaction, the general name for this phenomenon is _____
feedforward activation
-
What are the 3 possible catabolic fates of pyruvate?
-
The enzyme alcohol dehydrogenase converts _____ to _____
-
_____ uses the coenzyme lipoic acid in "fueling" the Krebs cycle
dihydrolipoamide acetyl transferase
-
What "symport" reaction accompanies import of pyruvate into the mitochondrion and what enzyme catalyzed the reaction?
pyruvate translocase
-
The two "oxidative decarboxylation" reactions of the Krebs cycle are catalyzed by _____ and _____
- isocitrate dehydrogenase
- α-ketoglutarate dehydrogenase
-
List the reactions, coenzymes, cofactors, and enzymes involved in the "substrate-level phosphorylation" reaction of the Krebs cycle
- succinyl CoA to succinate
- Enzyme: succinyl CoA synthetase
- Cofactors: Pi (bonded to histidine), GDP or ADP-->GTP or ATP CoA-SH
-
The enzymes _____ and _____ "fix" a carbonyl group on succinate in the production of oxaloacetate
- fumarase
- malate dehydrogenase
-
What crucial 2 carbon compound is "fixed" to oxaloacetate?
acetate
-
What amino acid and what product of pyruvate metabolism are the principle substrates for gluconeogenesis in mammals?
-
What energy sources are used to produce the "protomotive force"?
-
What enzyme complex uses protomotive force as the driving energy for ATP synthesis in oxidative phosphorylation?
- f0f1 ATP synthase (or ATPase)
- ("synthetase" not accepted)
-
How does electron transport drive production of the protomotive force?
- exports H+ from mitochondrion
- (which creates a gradient, making them predisposed to flowing back in)
-
How many reactions does each round of β-oxidation of a fatty acid require?
- four
- (oxidation 1, hydration, oxidation 2, thiolysis)
-
What are the products of one round of β-oxidation?
- and What's the tally in terms of ATP equivalents of energy conserving products?
- 1 CoQH2=1.5 ATP
- 1 NADH=2.5 ATP, H+
- 1 acetyl CoA=10 ATP
- 1 fatty acid (minus 2 Cs)
-
What are the 4 cofactors involved in the "siphon" of β-oxidation?
- CoA
- FAD/FADH2
- Fe-S2+/3+
- CoQ/CoQH2
-
A set of coupled cofactor regeneration cycles siphon off _____ then fix them into _____ in reactions that are coupled to the first _____ step of fatty acid β-oxidation
- reducing equivalents
- coenzyme Q
- oxidative
-
Which 3 steps of the Kreb's cycle do the first 3 steps of the fatty acid β-oxidation cycle resemble?
- succinate dehydrogenase
- fumarase
- malate dehydrogenase
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