Final BIOCHEM TEST TERMS
Terms in this set (114)
The _________ describes the relation between interatomic distances, electronic charge, solution dielectric and free energies
Van der Waals interaction
Protein __________ structure defines the relation among subunits in a multisubunit lattice
Protein _____ structure defines amino acid sequence
Protein ______ structure defines packing of helices, sheets, turns, etc.
Protein ______ structure defines the motifs formed by short-range interactions between amino acids
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
Know form of B-sheet/ a-helix/disulfide bond
_________ is used to determine the sequence of a protein based on sequential chemical reactivity
A ___________ induces denaturation of proteins by disturbing the hydrophobic effect
what are examples?
A ____________________ is a graph of the conformational torsion angles ψ,Ф for the residues in a protein or peptide, a map of the structure of the polypeptide backbone
What do the angles stand for?
A ___________ has two charges which neutralize each other
The _______________ is the primary "force" of protein structural stabilization
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
What's the equation?
An act of ________ does not change an enzyme and lowers the transition state free energy of the associated reaction
What are requirements of enzymatic catalysis
The _______________ of an enzymatic catalysis reaction is the rate achieved when it is saturated with substrate
The ______________ (or double reciprocal) equation defines parameters that are used to characterize the kinetics of an enzyme
Km is the substrate concentration when Vo = Vmax/2, or ________________
What is Michaelis-Menten equation?
A _________________ is the enzyme-substrate combination formed during an enzyme catalysis event
The catalytic rate constant of an enzyme is abbreviated as ____________
__________ of enzyme catalysis occurs when an inhibitor binds to the active site of the enzyme
___________ of enzyme catalysis occurs when the inhibitor only binds to the enzyme-substrate complex
The _____________ postulates that a constant input feed of substrate is supplied whose rate equals that of product formation
steady state approximation
Two internal factors that limit the velocity of an enzymatic reaction are _________ and _________
Hydrophobic effect, H-bonding, disulfide bonds, van der Waals froces, ionic bonds or dipole-dipole interactions
Two external factors that limit the velocity of an enzymatic reaction are _______ and _________
pH, solvent polarity, temperature, salt concentrations/types, presence of chaotropes, osmolytes
What amino acid and functional group in the esterase site of acetylcholine esterase reacts with the substrate
Know structure of acetylcholine
Pyridine aldoximine methiodide (PAM) reactivates acetylcholine esterase, functioning as a ________
nerve gas antidote
What kind of reaction produces the reactivated enzyme?
The bisubstrate-enzyme ________ reaction is used by transaminases in the exchange of an amino group for a carbonyl group between two progessively binding substrates
An ________ works by amplifying an initial signal via several linked protease cleavage reaction stages (ie. blood clotting)
A _______ is a protein that is converted from inactive to active forms by a covalent modification, typically protease cleavage
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 ______________
____________ involves binding of a regulatory moelcule at a site other than the active site
_________ and ________ reactions, involving phosphate addition and removal respectively, regulate both glycolysis and the Krebs Cycle
Kinase / Phosphatase
__________ regulates entry and exit from mitosis by catalyzing a covalent modification reaction
Which two amino acids are modified in the reactions catalyzed by the enzyme in last question?
Tyrosine / Threonine
Two examples of reversible factors that control the catalytic capability of an enzyme are _________, ___________
non covalent modifications, pH/pKa changes, salt changes
Two examples of irreversible factors that control the catalytic capability of an enzyme are ________, ________
covalent modification, proteolysis, irreversible inhibitors
The _______________ accounts for the temperature dependence of the rate of a reaction
List two "chemical modes of catalysis"
List the two "binding modes of catalysis"
Proximity effect, transition-state stabilization
A ___________ attacks an electropositive site in its role in a chemical (enzymatic) reaction
A common process used to produce the species in this is __________
The most common amino acid used by enzymes to carry out acid-base catalysis is _________
A catalytic triad of amino acids is typically present in __________
The amino acids collaborate to accomplish ________
The most typically cited currency of energy in metabolism is ________
__________ is typically required to achieve optimal activity with ATP-cosubstrate enzyme reactions
A coenzyme is either a loosely bound cosubstrate or strongly bound ______
The heavy metal molybdenum is used to facilitate the biochemical reaction in _________, a key enzyme in purine catabolism.
When ATP used in some biochemical applications it yields AMP and _________
The (vitamin) __________ is required to synthesize coenzyme NAD+ for use in metabolic redox reactions
The other key redox coenzyme is abbreviated _____
The coenzyme ___________ often forms a Schiff base with the amino group of a lysine residue in the enzyme
What chemical group does coenzyme A typically carry in the course of its biochemical function?
The ______-avidin noncovalent binding interaction is used to capture ligand-binding entities in the "affinity capture" technique
The coenzyme ___________________ is required to incorporate the methyl group in thymidine, a necessary prerequisite for the production of DNA
Our understanding of this function can be used in a strategy for (treatment technique)
N5, N10 methylenetetrahydrofolate
The coenzyme bound carbohydrates __________ and glucose are required to synthesize lactose
Know structure of this and lactose
Cis-retinal functions in __________ the signal of a photon of light into a chemically recognizable form?
The two important straight-chain forms of carbohydrate structure are the ______ and ________
ketose and aldose
The two important ring forms of carbohydrates are the _________ and ________
pyranose and furanose
The two important ring conformations of Beta-D-glucopyranose are the _________ and ________
chair and boat
The cyclohexane ring containing the compound ___________ is released by phospholipase C in the phospholipid signal transduction mechanism
The acronym NAG is used to abbreviate the name of the compound ___________
What does NAG-a(1->6)-NAM-a(1_>4)-glc-B(1->4)-gal mean?
The key polysaccharide in starch is __________
The key polysaccharide in the liver is ___________
The antibiotic _________ selectively inhibits cell wall peptidylglycan synthesis in bacteria
Extra-cellular surface _______ regulate the osmotic pressure around cells
Phospholipase C produces two different second messengers in the phospholipid signal transduction pathway. The lipid-containing second messenger is ______________
The compound chondroitin sulfate ________ cartilage and skeletal joints
________________ Fatty acids of the same length have a lower melting temperature (Tm)
Lipid Tm values monitors the transforamtion from _________ to dispersed forms
Lipid _______ are composed of two face-to-face monolayers while lipid _______ form a biphasic sphere
The most popular model for a biological membrane is called the ___________
fluid mosaic model
The four nucleic bases in RNA are _______
adenine, guanine, cytosine, and uracil
The two normal base pairs in DNA and RNA are called ___________ base pairs
The _________ bond in a nucleoside connects the base to sugar
The __________ at ________ can be used to determine if 2 single strands of DNA or RNA form a double helix
absorbance at 260 nm
The face-to-face interaction between nucleic acid bases is called ___________
Counterions bind all nucleic acids and are required to neutralize the ________________
Protein complexes called _______ serve this counterion function in the case of most chromosomal DNAs
___________ base pairs are less stable than _________ base pairs
AT or AU less stable than GC
Two differences between A and B forms of DNA are:
3' endo sugar conformation
base pairs titled 20 degrees from helix
central axial cavity in the helix
2' endo sugar
base pairs perpendicular to helix
base pairs cross center of helix
longer, narrower helix
The 2'-hydroxyl group catalyzes __________ of RNA, a good example of anchiomeric assitance in a non-protein biomolecular mechanism
Why isn't DNA subject to this mechanism?
An antisense oligonucleotide functionally inactivates a mRNA for use in translation by a ribosome by forming a double helix with it and precluding ___________ binding
Name the two most prevalent of the four classes of RNA
ribosomal RNA and transfer RNA
other classes are:
Two distinctive features of most eukaryotic mRNAs are ________ and ___________
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
______________ are required to produce, manipulate, and clone specific pieces of DNA
The two functional ends of transfer RNA are the anticodon and _____________
amino acid acceptor
The three most central catabolic pathways of intermediary metabolism are _________
glycolysis, Krebs cycle, electron transport/oxidative phosphorylation
The four major compunds in which energy is captured in a chemically usable form by metabolic reaction pathways are _________
ATP, NADH, FADH2, and Coenzyme QH2
The ________ (Q) corrects for deviations from standard state concentrations (1M)
mass action ratio
_______ steps in glycolysis control most of the flux through the pathway under actual cellular conditions
What do these reactions have in common?
Know the enzymes responsible
In contrast, the rest of the reactions are
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 glyceraldehyde-3-phosphate
dihydroxyacetone phosphate DHAP
When citrate negatively regulates (discourage) the phosphofructokinase-1 reaction, the general name for this phenomenon is ______
When fructose-1,6-bisphosphate stimulates the pyruvate kinase reaction, the general name for this phenomenon is ________
The three possible catabolic fates of pyruvate are ______, _____, _______
acetyl CoA, ethanol, lactate
The enzyme alcohol dehydrogenase converts __________ to ethanol
_______________________ uses the coenzyme lipoic acid in fueling the Krebs Cycle
Dihydrolipoamide acetyl transferase
What symport reaction accompanies import of pyruvate into the mitochondrion and waht enzyme catalyzes the reaction?
The two oxidative decarboxylation reactions of the Krebs Cycle are catalyzed by
isocitrate dehydrogenase and
List the reactions, coenzymes, cofactors, and enzymes inovled in the substrate level phosphorylation reaction of the Krebs Cycle
Succinyl CoA synthetase
The enzyme _______ and malate dehydrogenase fix a carbonyl group on succinate in the production of oxaloacetate
What crucial 2 carbon compound is then fixed to oxaloacetate (OAA)
What amino acid and what product of pyruvate metabolism are the principle substrates for gluconeogenesis in mammals?
Alanine and lactate
What energy sources are used to produce the protonmotive force
NADH, CoQH2, FADH2
What enzyme complex uses this phenomenon as the driving energy for ATP synthesis in oxidative phosphorylation?
F0F1 ATP Synthase (ATPase)
How does electron transport drive production of the protonmotive force?
Exports H+ from mitochondrion (which creates a gradient, making them predisposed to flowing back in)
How many reactions does each round of B-oxidation of a fatty acid require
(oxidation #1, hydration, oxidation #2, thiolysis)
What are the products of one round of B-oxidation and whats the tally in terms of ATP equivalents of energy conserving products?
1 CoQH2, 1 NADH, H+, 1 Acetyl CoA, 1 fatty acid (minus 2 Cs)
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 Beta - oxidation. Write down the names of the four cofactors involved in this siphon
CoA, FAD/FADH2, Fe-S 2+/3+, CoQ/CoQH2
Which three steps of the Krebs Cycle do the first three steps of the fatty acid B-oxidation cycle resemble?
Succinate dehydrogenase, fumarase, malate dehydrogenase
most common phospholipid in cell membranes
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