mid. 2 – Chemistry – Flashcards

Enzymes can accelerate reactions as much as 10²⁰ over uncatalyzed rates!

Urease is a good example:

Catalyzed rate: 3x104/sec

Uncatalyzed rate: 3x10 -10/sec

Ratio is:  !

The breakdown of glucose by ___  provides a prime example of a metabolic pathway. Ten enzymes mediate the reactions of glycolysis.

Enzymes are highly regulated at

      the ___ level

      the ____ level

      the ____  level

Oxidoreductases

Act on many chemical groupings to add or remove ____  atoms or ______.

Transferases

Transfer functional groups between ___  and _____  molecules.

Transferases

Hydrolases

Add water across a _____ , hydrolyzing it.

Lyases

Add ____,  _____ or _____ across double bonds, or remove these elements to produce double bonds or other cleavages involving electron rearragenement.

Lyases

Lyases

Add water, ammonia or carbon dioxide across ____ , or remove these elements to produce ______or other cleavages involving _____ rearragenement.

Isomerases

Carry out many kinds of isomerization: ____ isomerizations, mutase reactions (shifts of chemical groups) and others.

Isomerases

Isomerases

Carry out many kinds of isomerization: L to D isomerizations, ___ reactions (shifts of ____ ) and others.

Ligases

Catalyze reactions in which two chemical groups are  ____ (or ligated) usually with the use of energy from ____.

Act on many chemical groupings to add or remove hydrogen atoms or electrons.

Transfer functional groups between donor and acceptor molecules.

Add water across a bond, hydrolyzing it.

Add water, ammonia or carbon dioxide across double bonds, or remove these elements to produce double bonds or other cleavages involving electron rearragenement.

Carry out many kinds of isomerization: L to D isomerizations, mutase reactions (shifts of chemical groups) and others.

Catalyze reactions in which two chemical groups are joined (or ligated) usually with the use of energy from ATP.

Examples                  RXN

Oxidoreductasesà Alcohol Dehydrogenaseà turns ___ into ______.

Transferasesà Hexokinase à turns _____ into _____

Hydrolase à Carboxypeptidase à turns a molecule with a  _____ bond into a ____

Lyases à Pyruvate decarboxylase à turns ___  into ____

Ligases à Pyruvate Carboxylase à Turns  ___ into ____.

_______à Alcohol Dehydrogenaseà turns Ethanol into Acetaldehyde

_______à Hexokinase à turns D-Glucose into D-Glucose-6-phosphate

 ______à Carboxypeptidase à turns a molecule with a double bond into a single

 ______à Pyruvate decarboxylase à turns Pyruvate into Acetaldehyde

 ______à Maleate isomerase à Turns Maleate into Fumarate

 _______à Pyruvate Carboxylase à Turns Pyruvate into Oxaloacetate

ENZ.                 Optimum pH

Pepsin              _____

                     pH 

Catalase      _____ 

                 pH 

Trypsin     ______ 

                           pH 

Fumarase         ____

                                       pH

Ribonuclease               ____

Arginase                       ____

______ changes the rate of the catalyze reaction ( rate ___ as temperature goes up)

• Increasing temperature will eventually lead to _______.

Enzyme Kinetics

For a reaction taking place at constant temperature and pressure, e.g., in the body→  _____.

the change in free energy is represented by this rxn

___________________

An enzyme alters the rate of a reaction, but not its _____ change or position of _______

The rate of a reaction depends on its______ , DG°‡

The rate of a reaction depends on its activation energy, denoted as _____(or symbol is)?

a enzyme provides an alternative pathway with a ____ activation energy

The overall free energy change, _____  for a reaction is related

to the equilibrium constant

The free energy of activation, ____ for a reaction is related

to the rate constant

         In an enzyme-catalyzed reaction  S → P

substrate, S: a ______

 active site: the small portion of the _______ where the substrate(s) becomes bound by ______ forces, e.g.,  ______bonding, _______attractions, van der Waals attractions

Specificity is controlled by _____ - the unique fit of substrate with enzyme controls the selectivity for substrate and the product yield – all refered to as the  ______.

lock-and-key model: substrate binds to that portion of the enzyme with a __________.

induced fit model: binding of the substrate induces a______ in the ______  of the enzyme that results in a complementary fit

Two models have been developed to describe formation of the enzyme-substrate complex

_____: substrate binds to that portion of the enzyme with a complementary shape

______: binding of the substrate induces a change in the conformation of the enzyme that results in a complementary fit

 For the reaction-->

A + B ---> P

Rate = k[A] ^f[B]^g

Where k is a proportionality constant called the specific ________.

Order of reaction: the ______ of the exponents in the rate equation .

Chymotrypsin

Initial rate of an enzyme-catalyzed reaction versus substrate concentration...look at pic-->

for an enzyme-catalyzed reaction--> (rxn)-->

Michaelis-Menten Model

the rates of formation and breakdown of ES are given by these equations ---->

At the steady state the equation is-->

Michaelis-Menten Model

when the steady state is reached, the concentration of free enzyme is the total less that bound in ES----represented by equation-->

Michaelis-Menten Model

substituting for the concentration of free enzyme and collecting all rate constants in one term gives the equation--->

KM is called the _____  _____.

in the initial stages, formation of product depends only on the rate of breakdown of ES---represented by equa.--->

 Michaelis-Menten Model

if substrate concentration is so large that the enzyme is saturated with substrate [ES] = [E]T

_equa.-->

substituting k2[E]T = Vmax into the top equation gives  --->

Vmax is the constant rate reached when the enzyme is completely ______ with substrate, a value that frequently must be estimated from such a graph.

which has the form y = mx + b, and is the formula for a straight line . equation?

 Lineweaver-Burk Plot

a plot of 1/V versus 1/[S] will give a ___ line with slope of KM/Vmax  and y intercept of 1/Vmax

such a plot is known as a Lineweaver-Burk ______  ______  ______.

Lineweaver-Burk Plot

a plot of 1/V versus 1/[S] will give a straight line with slope of _______and y intercept of ______ such a plot is known as a Lineweaver-Burk double reciprocal plot

KM is the dissociation constant for ___ ; the greater the value of KM, the ____tightly S is bound to E

Vmax is the maximum ______

_____ is the dissociation constant for ES; the greater the value of ____ , the less tightly S is bound to E

 ____ is the maximum velocity

 Turnover Numbers

Vmax is related to the turnover number of enzyme:also called ______. 

 Turnover Numbers

Vmax is related to the turnover number of enzyme:also called kcat

Values for some typical enzymes

Reversible inhibitor: a substance that binds to an ____  to ____ it, but can be

 Enzyme Inhibition

competitive inhibitor: binds to the ___ ____ site and blocks access to it by ____.

 Enzyme Inhibition

noncompetitive inhibitor: binds to a site other than the _____ _______ ; inhibits the enzyme by changing its ___.

Irreversible inhibitor: a substance that causes inhibition that _____  _____ _____.

usually involves formation or breaking of  ___ ____ to or on the enzyme

__________: a substance that binds to an enzyme to inhibit it, but can be released

__________: binds to the active (catalytic) site and blocks access to it by substrate

___________: binds to a site other than the active site; inhibits the enzyme by changing its conformation

____________: a substance that causes inhibition that cannot be reversed

usually involves formation or breaking of covalent bonds to or on the enzyme

substrate must compete with inhibitor for the _____; more substrate is required to reach a given ________.

substrate must compete with inhibitor for the active site; more substrate is required to reach a given reaction velocity

substrate must compete with inhibitor for the active site; more substrate is required to reach a given reaction velocity

we can write a dissociation constant, KI for EI

Competitive Inhibition

In a Lineweaver-Burk double reciprocal plot of 1/V versus 1/[S], the  ______ (and the x intercept) changes but the y intercept does not _____.

 Competitive Inhibition

several equilibria are involved.....

because the inhibitor does not interfere with binding of substrate to the active site, KM is ______.

increasing substrate concentration cannot overcome ______  _______.

 Inhibitor Type

 Inhibitor Type

Competitive Inhibitor

Kinetic effect

Vmax is _______; Km, as defined by [S] required for 1/2 maximal activity, is increased.

 Inhibitor Type

Noncompetitive Inhibitor

Binds E or ES complex other than at the _____  site. Substrate binding ______, but ESI complex cannot form products. Inhibition ____ _____ reversed by substrate.

 Inhibitor Type

Noncompetitive Inhibitor

Km appears unaltered; Vmax is ________ proportionately to inhibitor _____________.

Uncompetitive- inhibitor _____ bind to the ES complex but not to free _____.   Vmax decreases and KM decreases.

Mixed- Similar to noncompetitively, but binding of I affects binding of S and vice versa.

Sigmoidal shape- characteristic of allosterism

Again Max. velocity reached, but different mechanism

Enzymes are highly regulated at

the activity level

Substrate-level Control; Product inhibition

What Factors Influence Enzymatic Activity

Rate slows as product ________.

Rate depends on ______  availability

________ effectors may be important

Feedback Control (inhibition)

The protein level

Enzymes can be modified _______: reversibly or irreversibly

Zymogens, isozymes and modulator proteins may play a role

Translation – to make more or less ______.

Protein turnover

Compartmentalization

the gene level

Genetic controls - induction and repression

Allosteric: Greek allo + steric, other shape

Allosteric enzyme: an _____ whose biological activity is affected by other ______ binding to it.

these substances change the enzyme’s activity by altering the conformation(s) of its _____.

allosteric ______ or an allosteric _______.

   __________    _____________.

Figure à Rate of ATCase catalysis vs substrate conc.

Figureà ATCase catalysis in presence of CTP; ATP

catalytic unit:  ___ subunits organized into  trimers ___

regulatory unit: 6 subunits organized into 3 trimers

The key to allosteric behavior is the existence of multiple forms for the ___ ___ of the enzyme.

 Allosteric Enzymes

allosteric effector: a substance that modifies the ____ of an allosteric enzyme

 Allosteric Enzymes

homotropic effects: allosteric interactions that occur when several ____ molecules are bound to the ____; e.g., the binding of ____  to _____

  Allosteric Enzymes

heterotropic effects: allosteric interactions that occur when ______ substances are bound to the ______ ; e.g., inhibition of ATCase by ____  and activation by ______.

________: a substance that modifies the 4° structure of an allosteric enzyme

__________: allosteric interactions that occur when several identical molecules are bound to the protein; e.g., the binding of aspartate to ATCase

 Allosteric Enzymes

________: allosteric interactions that occur when different substances are bound to the protein; e.g., inhibition of ATCase by CTP and activation by ATP

Action at "another site"

Enzymes situated at key steps in ______ are modulated by

_______effectors.

Action at "another site"

These effectors are usually produced _____ in the pathway

Action at "another site"

Effectors may be feed-forward ______ or feedback ____.

Kinetics are ____ ("S-shaped")

The ______ Model

The _______ Model

Wyman, Monod, and Changeux - 1965

The enzyme has two conformations

R (relaxed): binds _____  tightly; the active form

T (tight or taut): binds _____ less tightly; the inactive form

In the absence of substrate, most enzyme molecules are in the  _______ form.

 The Concerted Model

The presence of ____ shifts the equilibrium from the T (inactive) form to the R (active) form

 The Concerted Model

In changing from T to R and vice versa, all subunits change _________ simultaneously; all changes are concerted

Wyman, Monod, and Changeux - 1965

The enzyme has two conformations

________: binds substrate tightly; the active form

________: binds substrate less tightly; the inactive form

A ______ protein with two subunits

both change from ___ to ___ at the same time

Figureà Monod-Wyman-Changeaux model

Koshland - 1966

the binding of substrate induces a conformational change from the ___ form to the ____ form

Koshland - 1966

the change in conformation is induced by the fit of the  ______ to the enzyme, as per the induced-fit model of substrate binding

Koshland - 1966

the change in conformation is induced by the fit of the substrate to the enzyme, as per the _____ of substrate binding

Figureà Sequential model for cooperative binding of substrate to an allosteric enzyme

 Sequential Model

Figureà Allosteric activation and inhibition also occur by the induced-fit mechanism

_______ Modification

_______ Modification

the side chain -OH groups of Ser, Thr, and Tyr can form  _______ esters

phosphorylation by ATP can convert an inactive precursor into an ______ ______.

Irreversible Covalent Modifications:

Are known as ______

Zymogen: an _____ precursor of an ______; cleavage of one or more _____  ______ transforms it into the active enzyme

 Chymotrypsinogen

synthesized and stored in the _____

 a single polypeptide chain of 245 amino acid residues cross linked by five disulfide (-S-S-) bonds

when secreted into the small intestine, the digestive enzyme ______ cleaves a 15 unit polypeptide from the N-terminal end to give p-chymotrypsin

_________: an inactive precursor of an enzyme; cleavage of one or more covalent bonds transforms it into the active enzyme

1. Which amino acid residues on an enzyme are in the ____ _____  and  ____ the reaction?

2. What is the spatial relationship of the _______ ______ _______ residues in the active site?

3. What is the _________ by which the essential amino acid residues catalyze the reaction?

 The Active Site

As a model, we consider chymotrypsin, an enzyme of the digestive system that catalyzes the selective hydrolysis of peptide bonds in which the carboxyl group is contributed by Phe or Tyr

Trypsin, chymotrypsin, elastase, thrombin,  

subtilisin, plasmin, TPA

Enzyme and substrate become linked in a ______ ______at

one or more points in the reaction pathway

Trypsin, chymotrypsin, elastase, thrombin,  

subtilisin, plasmin, TPA

The formation of the ________ ______provides chemistry that

speeds the reaction

Trypsin, chymotrypsin, elastase, thrombin,  

subtilisin, plasmin, TPA

All involve a _______ in catalysis - thus the name

Trypsin, chymotrypsin, elastase, thrombin,  

subtilisin, plasmin, TPA

Ser is part of a "catalytic triad" of _____, _____, ______.

Trypsin, chymotrypsin, elastase, thrombin,  

subtilisin, plasmin, TPA

Serine proteases are _____ , but locations of the three

crucial residues differ somewhat

Trypsin, chymotrypsin, elastase, thrombin,  

subtilisin, plasmin, TPA

Enzymologists agree, however, to number them always as His-

57, Asp-102, Ser-195

Burst kinetics yield a hint of how they work!

Chymotrypsin

because Ser-195 and His-57 are required for activity, they must be close to each other in the active site

results of x-ray crystallography show the definite arrangement of amino acids at the active site

in addition to His-57 and Ser-195, Asp-102 is also involved in catalysis at the active site

Coenzyme: a  _____ organic molecule that takes part in an _____ reaction and is regenerated for further reaction

organic compounds, many of which are vitamins or are metabolically related to vitamins are ______ - molecules that bring unusual chemistry to the enzyme active site

Vitamins and coenzymes are classified as "___ ____" and "____ _____"

The water-soluble coenzymes exhibit the most interesting chemistry

Fat-soluble Vitamins:_____,_____,_____,_____.

Water-soluble Vitamins:

  B1 – Thiamine  C – Ascorbic acid

  B2 -  Riboflavin 

  B3 -  Niacin

  B5 -  Pantothenic Acid

  B6 -  Pyridoxal

  B7 – Biotin

  B9 -  Folic acid

  B12 - Cyanocobalamin

aka pyridine nucleotides

These coenzymes are _____ _____ ______

Nicotinic Acid and the Nicotinamide Coenzymes

They transfer _____ ____ ____  to and from substrates

Nicotinic Acid and the Nicotinamide Coenzymes

NAD+ is a ____ ____ oxidizing agent, and is reduced to ______.

 NAD+/NADH

NAD+ is involved in a variety of _____ ____ oxidation/reduction reactions.