BIOCHEM FINAL MONDAY

Protein _____ defines the relation among subunits in a multisubunit lattice

The _____ describes the relation between interatomic distances, electronic charge, solution dielectric and free energies

Protein _____ defines the amino acid sequence

Protein _____ defines the packing of helices, sheets, turns, etc.

Protein _____ 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

_____ is used to determine the sequence of a protein based on sequential chemical reactivity

A _____ induces denaturation of proteins by disturbing the hydrophobic effect

Name the following protein structure:

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

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

An act of _____ does not change an enzyme and lowers the transition state free energy of the associated reaction

The _____ of an enzymatic catalysis reaction is the rate achieved when it is saturated with substrate

The _____ equation defines parameters that are used to characterize the kinetics of an enzyme

Km is the substrate concentration when vo=vmax/2, or _____

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 an 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

Internal factors that limit the velocity of an enzymatic reaction are _____ (6)

External factors that limit the velocity of an enzymatic reaction are _____ (7)

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 _____

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 progressively binding substrates

An _____ works by amplifying an initial signal via several linked protease cleavage reaction stages (e.g. 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 molecule at a site other than the active site

_____ 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

What two amino acids are modified in the reactions catalyzed by the enzyme cyclin kinase?

Examples of reversible factors that control the catalytic capability of an enzyme are: (3)

Examples of irreversible factors that control the catalytic capability of an enzyme are: (3)

The _____ accounts for the temperature dependence of the rate of a reaction

The two "chemical modes of catalysis"

The two "binding modes of catalysis"

A _____ attacks an electropositive site in it's role in a chemical (enzymatic) reaction

A common process used to produce 'nucleophiles' is _____

Probably 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 (enzyme class name) _____

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 tightly 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 the metabolic redox reactions

The other key redox coenzyme is abbreviated _____

The coenzyme _____ often forms a Schiff base with the ε-amino group of a lysine residue in the enzyme

What chemical group does coenzyme A typically carry in the course of it's 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 into thymidine, a necessary prerequisite for the production of DNA

Our understanding of this function can be used in a strategy for (treatment technique) _____

The coenzyme bound carbohydrate _____ and glucose are required to synthesize 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 _____

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

The acronym NAG is used to abbreviate the name of the compound _____

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 produce two different second messengers in the phospholipid signal transduction pathway. The lipid-containing second messenger is _____

The compound _____ lubricates cartilage and skeletal joints

_____ fatty acids of the same length have a lower melting temperature (Tm)

Lipid Tm values monitor the transformation from _____ to dispersed forms

_____ are composed of two face-to-face monolayers while _____ form a biphasic sphere

The most popular model for a biological membrane is called the _____

The four nucleic acid bases in RNA are

The two normal base pairs in DNA and RNA are called _____

The _____ bond in a nucleoside connects the base to the sugar

The _____ can be used to determine if a double helix forms from 2 single strands of DNA or RNA

The face-to-face interaction between nucleic acid bases is called _____

Counterions bind all nucleic acids and are required to neutralize the _____

The proteins called _____ serve this function in the case of most chromosomal DNAs

_____ base pairs are less stable than _____ base pairs

Differences between A and B forms of DNA are

The 2'-hydroxyl group catalyzes _____ of RNA, a good example of anchiomeric assistance in a non-protein biomolecular mechanism

An antisense oligoculeotide functionally inactivate 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

Distinctive features of most eukaryotic mRNAs are _____ (4)

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 end of transfer RNA are the _____ and _____

The three most central catabolic pathways of intermediary metabolism are:

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)

_____ steps in glycolysis control most of the flux through the pathway under actual cellular conditions

In contrast to metabolically irreversible reactions, the rest of the reactions are _____

The kinetics of an enzyme reaction are most easily controlled when Km is approximately equal to _____

The enzyme triose phosphate isomerase converts _____ into _____

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 _____

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

What "symport" reaction accompanies import of pyruvate into the mitochondrion and what enzyme catalyzed the reaction?

The two "oxidative decarboxylation" reactions of the Krebs cycle are catalyzed by _____ and _____

List the reactions, coenzymes, cofactors, and enzymes involved in the "substrate-level phosphorylation" reaction of the Krebs cycle

The enzymes _____ and _____ "fix" a carbonyl group on succinate in the production of oxaloacetate

What crucial 2 carbon compound is "fixed" to oxaloacetate?

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?

How does electron transport drive production of the protomotive force?

How many reactions does each round of β-oxidation of a fatty acid require?

What are the products of one round of β-oxidation?

What are the 4 cofactors involved in the "siphon" of β-oxidation?

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

Which 3 steps of the Kreb's cycle do the first 3 steps of the fatty acid β-oxidation cycle resemble?