question

A reaction may be thermodynamically favored, but ____________ ___________.

answer

Extremely slow Not a useful time scale for the reaction to occur.

question

Enzymes

answer

1. Highly specialized molecules that have high catalytic power. 2 High degree of specificity for substrates 3. They accelerate chemical reactions

question

T/F: All enzymes are proteins.

answer

False; All enzymes are proteins, WITH THE EXCEPTION of a small group of catalytic RNA molecules. Not ALL enzymes are proteins

question

What is essential for a protein's enzyme catalytic activity?

answer

A proteins primary, secondary, tertiary and quaternary structures of protein enzymes are essential for their catalytic activity. 1. If an enzyme is broken down into its components, denature or dissociated into subunits, the enzyme catalytic activity is destroyed.

question

Simple enzyme

answer

A simple enzyme is an enzyme that requires no chemical groups for their catalytic activity, only their AA residues.

question

Cofactor

answer

An enzyme that requires an additional chemical component for catalytic activity of 1) one or more inorganic ions (Fe2+, Mg2+, Mn2+, Zn2+)

question

Coenzyme

answer

An enzyme that requires an additional chemical component of catalytic activity of: 1) A complex organic or metalloorganic molecule.

question

Some enzymes require BOTH a coenzyme and one or more metal ions for activity (cofactor).

answer

...

question

Prosthetic Group

answer

A coenzyme or metal ion that is TIGHTLY or even covalently bound to the enzyme protein.

question

What is another name for a prosthetic group?

answer

A prosthetic group may also be called: 1. Cofactor 2. Coenzyme

question

Holoenzyme

answer

A complete, catalytically active enzyme together with its bound coenzyme and/or metal ions

question

Apoenzyme

answer

Aka Apoprotein

question

Apoenzyme

answer

The protein portion of an enzyme; protein portion of an enzyme without its prosthetic group (coenzyme or cofactor)

question

Holoenzyme

answer

whole protein enzyme + prosthetic group

question

Holoenzyme

answer

Complete or catalytically active enzyme

question

______ act as transient carriers of specific functional groups

answer

Coenzymes

question

Some enzyme proteins may be ________ ______.

answer

COVALENTLY MODIFIED. Phosphorylation Glycosylation Other processes

question

What does covalently modification do to enzyme proteins?

answer

Covent modification of enzyme proteins causes alterations to activate/inactivate regulation of enzyme activity.

question

Glycosylation

answer

A type of covalent modification; which is the addition of a sugar.

question

Phosphorylation

answer

A type of covalent modification; which is the addition of a phosphate group.

question

-ase suffix

answer

Most enzymes end in "-ase" suffix, but not all enzymes. Some enzymes were named prior to the adoption of this process.

question

Exceptions to proteins ending in "-ase"

answer

Pepsin, trypsin, lysozyme

question

-"ase"

answer

suffix to name enzymes; added to the name of their substrate or to a word or phase describing their activity.

question

urease catalyase

answer

enzyme, functions for hydrolysis of urea

question

DNA polymerase

answer

enzyme that catalyzes the polymerization of nucleotides to form DNA

question

Why do not all enzymes end in "ase"?

answer

Some enzymes were named by their discovers for a broad function, before the specific reaction catalyzed was known.

question

Pepsin

answer

Enzyme named not using typical "ase" suffix. Acts in digestion of foods.

question

Lysozyme

answer

Enzyme named not using typical "ase" suffix. Named for the ability to lyse bacterial cell walls.

question

Trypsin

answer

Enzyme named not using typical "ase" suffix. Named based on greek word tryein "to wear down"; the name was obtained based of function of rubbing pancreatic tissue with glycerin.

question

EC

answer

Enzyme Commission

question

EC system

answer

Enzyme commission system -divides enzymes into six classes; each with a subclass Based on the type of reaction catalyzed. -each enzyme is assigned a four-part classification number and a systematic name, which identifies the reaction it catalyzes.

question

Purpose of EC system

answer

Enzyme commission system names an enzyme based on the class of enzyme and type of the reaction they catalyze (identify the reaction it catalyzes).

question

Each enzyme has a _____-part classification number and systematic name.

answer

Each enzyme has a FOUR-part classification number. 6 Classes of enzymes.

question

Class 1 of enzyme

answer

Oxidoreductases

question

Class 2 of Enzyme

answer

Transferases

question

Class 3 of enzyme

answer

Hydrolases

question

Class 4 of enzyme

answer

Lyases

question

Class 5 of enzyme

answer

Isomerases

question

Class 6 of enzyme

answer

Ligases

question

Oxidoreductases

answer

Class 1 enzyme

question

Transferases

answer

Class 2 Enzyme

question

Hydrolases

answer

Class 3 enzyme

question

Lysases

answer

Class 4 enzyme

question

Isomerases

answer

Class 5 enzyme

question

Ligases

answer

Class 6 enzyme

question

Reaction Type: Electron transfer (H atoms)

answer

Oxidoreducatase

question

Reaction Type: Group Transfer

answer

Transferases

question

Reaction Type: Hydrolysis (transfer of functional groups to water)

answer

Hydrolases

question

Reaction Type: Formation of double bonds by removal of groups or addition to double bonds

answer

Lysases

question

Reaction Type: Isomerizations (transfer of groups within molecules to yield isomeric forms)

answer

Isomerases

question

Reaction Type: Condensations (formation of C-C, C-S, C-O and C-N bonds coupled to ATP cleavage)

answer

Ligases

question

L-lactate dehydrogenase (example of EC naming)

answer

Catalyzes the oxidation of lactate to pyruvic acid. EC 1.1.2.3 1=oxioreductase 1=oxidation involves conversion of OH to ketone 2=cytochrome acts as electron acceptor in oxidation 3=identified L-lactate as enzymes substrate

question

D-Lactate dehydrogenase

answer

EC 1.1.2.4. Different from L-lactate dehydrogenase, in which it uses D-lactate for the substrate of the enzyme instead of L-lactate.

question

International system used to classify enzymes

answer

Enzyme Commisssion System (EC)

question

Some enzymes are composed only of amino acids, while others may contain additional components beside the peptide chain

answer

The additional entity is known as a prosthetic group: -which may be organic or organometallic (coenzyme) or -cofactor (catalytic activity may require an inorganic ion)

question

Cofactor

answer

Requires an inorganic ion for the catalytic activity of the enzyme. Often a divalent metal cation is required (Mg2+, Fe2+)

question

Holoenzyme

answer

a complete catalytically active enzyme

question

Apoenzyme

answer

aka apoprotein The protein part of a holoenzyme

question

Sometimes a protein must undergo _____ ______ a one of its side chain functional groups in order to be catalytically active, or block catalysis

answer

...

question

Example of catalytic modification

answer

Addition of phosphate or sugar group to OH of amino acid serene.

question

Enzymes

answer

Protein (usually) molecules that catalyze the vast majority of reactions that occur in living organisms.

question

Classifications in EC

answer

Six different categories depending on the type of reaction catalyzed by the particular enzyme.

question

Enzyme that catalyzes the oxidation of lactic acid to pyruvic acid

answer

lactate dehydrogenase

question

In the absence of a catalyst, what would occur with most reactions?

answer

In the absence of a catalysts, most reactions would occur extremely slow; even though they may be thermodynamically favored.

question

Without an enzyme, most reactions would occur extremely slow, even though they may be ________ ___________.

answer

Thermodynamically favored

question

Conversion of Glucose to CO2 and Water

answer

Absence of catalysis= This conversion would take an extremely long time to occur under biologically relevant conditions. Presence of catalysis= This conversion would take place very fast, with a lot of intermediates in between and able to get energy from the reaction.

question

What is the function of enzymes?

answer

Enzymes function to provide the means to vastly INCREASE the RATE of a reaction.

question

Enzymes are highly _______.

answer

SPECIFIC So specific we need to name them in a systematic way.

question

In biologically relevant conditions, do uncatalyzed reactions occur?

answer

Yes they occur, but are very slow. Biological molecules are quite stable in our cells (neutral pH, mild temp. and aqueous environment)

question

Many common reactions in biochemistry are _____ or ______ to occur in the cellular environment.

answer

Unfavorable Unlikely to occur But enzymes provide a SPECIFIC environment in which a given reaction may occur more rapidly.

question

Active Site

answer

Pocket on the enzyme where the enzyme-catalyzed reaction may take place; outside the unfavorable cellular environment.

question

the molecule that is bound in the active site and acted upon by the enzyme

answer

substrate

question

Surface of the active site...

answer

amino acid residues with substituent groups that bind the substrate and catalyze its chemical transformation.

question

When a substrate binds to the active site....

answer

the active site encloses a substrate, removing it completely from solution

question

Portion of enzyme in which the reaction occurs, usually a pocket or receive on the enzyme's surface.

answer

the active site

question

the molecule that binds to the active site and is acted upon by the enzyme

answer

a substrate

question

amino acid residues that constitute the active site

answer

...

question

E S P

answer

Enzyme (E) Substrate (S) Product (P)

question

E+S-->ES--->EP--->E + P

answer

A enzymatic reaction (all reversible=equilibrium reaction)

question

Catalyst function to ___________. Catalyst do not affect the ______ _____.

answer

Increase the RATE of the REACTION REACTION EQUILIBRIUM

question

____ and ____ are transient complexes of the enzyme with the substrate and with the product.

answer

ES and EP

question

Reaction Coordinate diagram

answer

any reaction may be described using the energy changes during a reaction. X=reaction coordinate (time) Progress of reaction in which S is converted to P Y=free energy of system

question

Ground state

answer

The starting point for either the forward or the reverse reaction.

question

If A can't be converted to B under any circumstance, an enzyme....

answer

an enzyme may never make it occur either. It must be possible for the enzyme to work.

question

Activation energy

answer

Delta G double dagger

question

The energy required to reach the transition state before the system goes on to product

answer

Activation energy

question

Biochemical standard free energy change that occurs when S is converted to P at pH of 7.0

answer

biochemical standard free energy change ΔG0'

question

equilibrium between S and P reflects....

answer

the differences in the free energies of their ground states.

question

_________ reduce the activation energy required to reach the transition state.

answer

Enzymes

question

_____ and _____ are intermediate states which occupy minima along the reaction coordinate

answer

ES and EP

question

The ______ and ______ of equilibrium in a reaction coordinate are NOT affected by any catalyst (enzyme.

answer

Position Direction

question

Catalyst will create a ______ activation energy of the reaction, lowering the ______ ______

answer

lower transition state

question

In a reaction there are often distinct intermediates along the way.

answer

...

question

A favorable reaction doesn't mean that the conversion of S---> will occur at a _______ rate.

answer

detectable

question

A rate of a reaction and whether a reaction is favorable or not are TWO SEPARATE things.

answer

...

question

The point at which decay to the S or P state is equally probable, it is downhill either way.

answer

Transition State

question

The _____ ______ is not a chemical species with any significant stability and should not be confused with ES or EP.

answer

Transition state.

question

The difference between the energy levels of the ground state and the transition state

answer

activation energy

question

The rate of a reaction reflects this activation energy; a higher activation energy corresponds to a _____ reaction, while a lower activation energy corresponds to a ______ reaction.

answer

Slower Faster

question

How may reaction rates be increased?

answer

The rate of a reaction may be increased with: 1. increasing the temp. 2. catalyst

question

Catalyst

answer

a catalyst enhances the reaction rate by lowering the activation energy.

question

Function of catalyst

answer

lower activation energy, increase reaction rate

question

The rate of the reaction will ______ by increasing the temperature.

answer

Increase; increasing the temp will increase the number of molecules with sufficient energy to overcome the energy barrier.

question

Enzymes _____ (do/don't) affect the reaction equilibrium.

answer

DON'T.

question

T/F: Enzymes are used up in reactions.

answer

F: Enzymes are not used up in the reaction. and the equilibrium point is unaffected.

question

The role of enzymes is to ________ the interconversion between S and P.

answer

ACCELERATE

question

Is the equilibrium rate affected by an enzyme?

answer

No the equilibrium rate of an enzyme is NOT affected The rate of reaction is increased with an enzyme, so the reaction reaches equilibrium much faster when the appropriate enzyme is present.

question

Different enzymes enhance the rate of different reactions at different levels, so much more than others.

answer

...

question

Enzymes generally enhance reaction rates anywhere from _____ to _____ orders of magnitude.

answer

5 to 17 orders of magnitude

question

What are two fundamental models that have been developed to explain the substrate specificity of enzymes?

answer

1. Lock and Key 2. Induced Fit

question

First postulated by Emil Fischer in 1954

answer

Lock and Key Model

question

The Lock is the ____ and the key is the ____, in the lock and key model.

answer

Lock=enzyme Key=substrate

question

Only the correctly sized key (_____) may fit into the key hole (_______) of the lock (______)

answer

Only the correctly sized key (substrate) may fit into the key hole (active site) of the lock (enzyme)

question

Lock and key model assumes...

answer

a certain rigidity in the shape of the active site, a shape that is complementary to that of the substrate.

question

First postulated by Daniel Koshland in 1958

answer

Induced-Fit model

question

the enzyme's active site has sufficient flexibility to accommodate the substitute in order to form the enzyme-substrate complex.

answer

induced-fit model

question

this model is analogous to a glove whose shape is altered somewhat by a hand which fits into it.

answer

induced-fit model

question

this model infers rigidity of the shape of the active site

answer

lock and key model

question

DHFR

answer

dihydrofolate reductase (enzyme) -important target for the actions of certain anticancer and anti parasitic drugs.

question

What are the substrates for DHFR?

answer

The enzyme dihydrofolate reductase (DHFR), the substrates are: 1. dihydrofolate 2. NADP+

question

Each substrate binds at a specific location within the enzymes's ______ ______ in such a way that the two molecules are able to interact.

answer

ACTIVE SITE In DHFR enzyme, dihydrofolate and NADP+ bind to two separate locations within the enzymes active site so the molecules are able to interact

question

What is essential in order to develop drugs to effect the enzyme's actions?

answer

To develop drugs to effect an enzymes action, one must know: 1. Knowledge of the active site of the enzyme 2. All molecular interactions within substrate

question

Rate-limiting step

answer

the overall rate is determined by the step with the highest energy, when several steps occur in a reaction.

question

_________ step is the highest-energy point in the interconversion S and P

answer

Rate limiting step

question

Enzymes are very specific, readily discriminating between substrates with quite similar structures.

answer

...

question

Delta GB

answer

binding energy

question

binding energy

answer

major source of energy used by enzymes to lower the activation energies of reactions.

question

the energy derived from the enzyme substrate interactions

answer

binding energy

question

___________ identifies the structure and function of enzymes

answer

X-ray crystallography

question

How can enzymes be enormous and highly selective rate enhancements be explained?

answer

1. Covalent bonds during enzyme-catalyze reactions: substrate and enzyme functional groups (aa side chains, metal ions and coenzymes) 2. non covalent bonds between enzymes and substrate-->allows energy to lower activation energy

question

the ability to distinguish between a substrate and a competing molecule

answer

specificity

question

Once a substrate is bound to an enzyme, properly positioned catalytic functional groups aid in the cleavage and formation of bonds by a variety of mechanisms:

answer

1. general acid-base catalysis 2. covalent catalysis

question

_____ and _____ involve transient covalent interaction with a substrate or group transfer to or from a substrate.

answer

1. general acid-base catalysis 2. covalent catalysis 3. Metal ion catalysis Differs from mechanisms based on binding energy (non-covalent bonds)

question

proton transfers mediated by other classes of molecules

answer

general acid-base catalysis

question

In ________ __________, a covalent bond is formed during the transition from substrate to product

answer

covalent catalysis

question

Describe the reaction with a catalyst: A-B--H20--->A + B

answer

A-B +X:-->A-X + B:--H20-->A + X: + B X: nucleophilic group of an enzyme within the ACTIVE SITE A-X ( a discrete intermediate), in the end X goes back to its original form

question

X:

answer

a nucleophilic group of an enzyme within the ACTIVE SITE

question

______ is a nucleophile, which may be 1. a group in one of the side chains observed in general-acid base catalysis. 2. contained in an enzyme's cofactor

answer

X:

question

In covalent catalysis, hydrolysis of the bond ____ and ____ results in the formation of product B.

answer

A and X A-X + B:--> A + X: +B

question

A metal ion pulls on the electrons of a carbonyl group, rendering carbon atoms more positive and subject to nucleophilic attack.

answer

Metal Ion catalysis

question

REVIEW 3 types of catalysis

answer

Enzymatic reactions take a variety of mechanistic ways, it is important to understand when developing inhibitors.

question

Enzymes: 1. 2. 3. 4.

answer

1. greatly enhance reaction rates by lowering activation energy without affecting equilibrium 2. form complex with substrate within the active site 3. have high degree of specificity for substrate (lock and key and induced fit) 4. multiple weak noncovalent interactions that result in lowering of binding energy, stabilizing the transition state.

question

chymotrypsinogen

answer

an inactive zymogen from the pancreas

question

zymogen

answer

a precursor of an active enzyme

question

Many enzymes are produces in the cell as inactive precursors, or ________

answer

zymogens

question

most enzymes utilize a combination of several catalytic strategies to bring about a rate enhancement.

answer

...

question

What is a good example of the use of both covalent catalysis and general acid-base catalysis?

answer

Reaction catalyzed by chymotrysin

question

pancreatic chymotrypsin is a ______ (a type of enzyme)

answer

a protease, an enzyme that catalyzes the hydrolytic cleavage of peptide bonds.

question

What does pancreatic chymotrypsin specifically do?

answer

Chymotrypsin functions as a protease specific for peptide bonds adjacent to aromatic AA residues (Typ, Phe, Tyr)

question

Pancreatic chymotrypsin cleaves peptide bonds adjacent to aromatic AA residues of ___, ____ and _____.

answer

Typ Phe Tyr

question

Chymotrypsin enhances the rate of peptide bond hydrolysis by a factor of at least _____

answer

10^9

question

Chymotrypsin doesn't catalyze a direct attack of water on the peptide bond....instead

answer

a transient covalent acyl-enzyme intermediate is forme.

question

The chymotrypsin reaction has two distinct phases:

answer

1. acylation phase 2.deacylation phase

question

in _____ phase, the peptide bond is cleaved and an ester linkage is formed between the peptide carbonyl carbon and the enzyme.

answer

acylation phase of chymotrypsin

question

in _____ phase, the ester linkage is hydrolyzes and the nonacylated enzyme is regenerated

answer

deacylation phase of chymotrypsin

question

What is a classic example of general acid-base catalysis and covalent catalysis?

answer

Chymotrypsin mechanism

question

____ mechanism involves acylation and deacylation of a ____ residue

answer

Chymotrypsin mechanism involves acylation and deacylation of a Ser residue

question

Alpha-chymotrypsin

answer

A protease produced by the pancreas and secreted in the small intestine.

question

Chymotrypsinogen

answer

the inactive precursor (of alpha-chymotrypsin) produced in the pancreas

question

Chymotrypsinogen is a _____ chain with _____ disulfide bonds.

answer

Chymotrypsinogen is a SINGLE chain with FIVE disulfide bonds.

question

Formation of alpha-chymotrypsin from chymotrypsinogen results in _______________.

answer

Formation of the active protease involves the loss of two dipeptides (residues 14/15 and 147/148) through enzymatic cleavage.

question

What are key active residue sites in alpha-chymotrypsin?

answer

Ser 195, His 57 and Asp 102

question

The hydroxyl of _______ attacks the _____ group of the substrate.

answer

Ser 195 carbonyl

question

What is the specific role of alpha-chymotrypsin?

answer

The specific role of alpha-chymotrypsin: Hydrolyzes the peptide bond in which one of the AA has an aromatic ring in its side chain (phenylalainine, tyrosine and tryptophan)

question

Alpha-chymotrypsin belongs to the _____ protease family of proteins.

answer

SERINE

question

The active site of alpha chymotrypsin...

answer

consists of 3 amino acids (catalytic triad): 1. histidine residue 57 2. aspartate residue 102 3. serine residue 195

question

How is the three amino acids consisting of the active site of chymotrypsin (catalytic triad) are so far away from each other?

answer

The three residues are far apart from each other in the primary sequence of the enzyme, but the 3-D conformation of the enzyme brings them into close proximity.

question

Imidazole ring of histidine (in chymotrypsin catalytic triad) simultaneously acts as ______ and ______

answer

proton donor proton acceptor Thus it may act as an acid or a base

question

Serine hydroxyl group acts as a ________

answer

proton donor

question

Serine ______ group acts as a proton donor to...

answer

Serine hydroxyl (OH) group acts a proton donor to result in an oxy anion attacks the carbonyl of the peptide bond.

question

Acyl part of the peptide bond is...

answer

covalently attached to the serene OH group as an ester, which is subsequently hydrolyzed to regenerate the catalytic triad.

question

Review mechanism of chymotrypsin slide 21

answer

...

question

Oldest and most important method of studying the mechanism of enzyme-catalyzed reactions.

answer

Enzyme kinetics

question

Measurement of the rate of an enzyme-catalyzed reaction and that rate changes in response to changes in experimental conditions.

answer

Enzyme kinetics

question

Studying the kinetic parameters of an enzyme can provide valuable insight into numerous biochemical processes, as well as the mechanisms of action for many drugs.

answer

...

question

Enzyme kinetics is widely used to get insight into the mechanism of which a particular enzyme works.

answer

...

question

Compound A converted to Product P, uncatalyzed

answer

Linear relationship between [A] and reaction velocity (V) The greater the concentration of A, the faster the reaction will be. As we increase the concentration of A, the reaction velocity will increase.

question

1st order reaction (uncatalyzed)

answer

velocity of reaction (rate of reaction) is PROPORTIONAL to the concentration of the substrate [A]

question

Initial rate

answer

aka initial velocity, Vo A measure taken when [S]>(much greater)[E] If [S] is present in five or six orders of magnitude or higher.

question

Michaelis-Menten Enzyme Reaction

answer

E+S-->ES-->P + E Reversible reaction so equilibrium constant is K1 and K-1, then K2 and K-2

question

If K2 is far larger than K-2, than

answer

one may say ES-->P+E is almost irreversible

question

First order reaction

answer

a linear relationship between [substrate] and the reaction velocity, v, is established and the slope of the line is directly proportional to the [substrate], the proportionality being defined by the rate constant K

question

In first order reaction, the ____ of the line is directly proportional to the [substrate], which is defined by ______.

answer

SLOPE The proportionality being defined by the RATE CONSTANT K

question

General theory of enzyme action

answer

1st proposed by Leonor Michaelis and Maud Menten in 1913.

question

Michaelis-Menton Model

answer

Based on the assumption that the enzyme (E) reversibly combined with the substrate (S) to form complex ES that breaks down to yield Product (P) and regenerate the enzyme

question

In M-M model, the formation of P is irreversible

answer

when K-2=0

question

Equilibrium constants in M-M model are

answer

associated with both forward and reverse reactions.

question

What occurs if one plots the [S] against the velocity, V, of an enzyme-catalyzed reaction?

answer

A line is obtained that tends to level off at high substrate concentrations.

question

The plateauing effect, that is seen at high substrate [}, occurs

answer

because all the enzyme's active sites have become saturated with substrate and the reaction cannot be speed up no matter how much more substrate is added.

question

When the line levels off at high [substrate],

answer

the enzymes active sites are saturated with substrate and the reaction rate may not increase, not matter how much more substrate is added=Vmax

question

The point in the plot where a plateauing effect is seen at high [substrate] and the reaction is occurring at _________

answer

it's maximum velocity, Vmax

question

At Vmax, the rate of the reaction (is/isn't) dependent on the concentration of substrate and is said to be displaying ____ order kinetics.

answer

At Vmax, the rate of the reaction ISN'T dependent on the concentration of substrate and is said to be displaying ZERO order kinetics.

question

Michaelis-Menton Kinetics

answer

All reactions when plotted and the plateauing effect occurs when high [substrate] and Vmax is exhibited, are said to obey Michaelis-Menten kinetics

question

Enzymes which follow Michaelis-Menton Kinetics and are plotted, the plots is referred to as....

answer

Saturation curve or Michaelis Menten-Plot

question

Vo

answer

Initial velocity Measurement of velocity of the reaction immediately after the substrate and the enzyme are mixed (1 minute) at which the product [] is zero.

question

Why is Vo measurement taken 1 minute after substrate and enzyme are mixed?

answer

Vo is taken early, while the product [] is zero and the back reaction may be ignored.

question

At Vo, the [] of ______ is assumed to be constant.

answer

[ES] enzyme-substrate complex concentration is assumed to be constant.

question

What does it mean when [ES] is constant?

answer

At Vo, the [ES] is constant, which means the rate at which ES forms from E and S is the same as the rate at which ES disappears both by reforming E + S and forming E+P Such a system is said to have attuned steady-state condition

question

In a M-M plot, at low [substrate]...

answer

the formation of ES from E + S is first order; the rate of the reaction is directly proportional to the initial substrate concentration.

question

The rate of the reaction is directly proportional to the initial [substrate]

answer

first-order kinetics which is seen at low [substrate] in M-M plot

question

Km

answer

Michael Constant It is characteristic of each particular enzyme

question

Km

answer

the [substrate] at 1/2 the value of Vmax, which is constant of that particular enzyme.

question

Km

answer

value obtained by adding the rate constants K1 and K2 and dividing by K1

question

(K1+K2)/K1 Where K1, K2 are rate constants of the reaction.

answer

Km

question

1/2Vmax

answer

=Km

question

Km= the substrate concentration at 1/2 Vmax

answer

...

question

Michaelis-Menten equation

answer

may be used to determine Vo of an enzyme catalyzed reaction at any substrate [] if one knows the values of Vmax and Km.

question

Michaelis-Menton plot: Is it practical?

answer

The M-M plot is not practical, because there is no easy way to obtain the values of Km and Vmax. Using substrate [] sufficiently high to reach Vmax is difficult to obtain due to problems of substrate availability or cost.

question

What is way to avoid the high cost of a Michaelis-Menton plot?

answer

Manipulation of the Michaelis-Menton Equation is developed to overcome by: Hans Lineweaver and Dean Burk (1934)

question

What occurs if the reciprocal of the Michaelis-Menton equation is taken?

answer

If the reciprocal of the M-M equation is taken on both sides, it leads to y=1/vo (similar to y=mx + B)

question

Y= X= M= B=

answer

M=slope of the line, Km/Vmax X=reciprocal of the substrate [], 1/[S] b=y-intercept of 1/vmax y=1/vo

question

Lineweaver-Burk Plot

answer

A manipulation of M-M equation; which a straight-line relationship is derived when 1/Vo is plotted against 1/[S] Then Km and Vmax may be directly obtained from the double-reciprocal plot

question

1/Vo is plotted against 1/[S]

answer

Lineweaver-Burk plot aka double reciprocal plot

question

What may be obtained from a linesweaver-burk plot?

answer

Km and Vmax may be directly obtained from the plot.

question

Vo=Vmax[S]/ ((Km +[S]))

answer

Michaelis-Menton Equation at any point along the graph

question

KNOW Michaelis-Menten Equation

answer

...

question

Km (IMPORTANT DEFINITION)

answer

substrate [] at which an enzyme is working at 1/2 it's maximum velocity

question

y =m x + b 1/vo=km/vmax 1/[s] 1/vmax

answer

Reciprocal of Michaelis-Menton Equation, which produces a Linesweaver-Burke Plot

question

In a Linesweaver-Burke plot, y-axis? x-axis?

answer

x-axis= 1/[s] y-axis=1/[Vo]

question

In a linesweaver-burke plot, the y-intercept represents ___________ and the value of ____ may be obtained by extending the line to the x-intercept.

answer

y-intercept represent Vmax a line may be extended to x-intercept to obtain the value of Km

question

The importance of Km

answer

may be observed from the Michaelis-Menten Plot of two enzymes that catalyze the same reaction; because each enzyme has a characteristic Km value which is constant of that particular enzyme

question

______ and _______ are enzymes which catalyze the same reaction of conversion of glucose to glucose-6-phosphate (1st step in metabolism of glucose)

answer

Hexokinase Glucokinase Reaction that brings glucose into metabolic

question

Hexokinase

answer

an enzyme that is primarily in the brain and skeletal muscles; it catalyzes the reaction of conversion of glucose to glucose-6-phosphate

question

Glucokinase

answer

an enzyme that is primarily in the liver; it catalyzes the reaction of conversion of glucose to glucose-6-phosphate.

question

Glucokinase and Hexokinase are examples of __________

answer

isozymes; enzymes that catalyze the same reaction but have different properties and are encoded by different genes

question

Hexokinase has a Km of _____ mM for glucose, and its isozyme glucokinase, has a Km of ____ mM for glucose.

answer

0.005 mM for hexokinase 10 mM for glucokinase Km of Glucokinase is about 200 times greater than the Km of hexokinase.

question

Km of Glucokinase is about 200 times greater than the Km of hexokinase. What does this indicate?

answer

Since the normal blood glucose concentration is 5mM, it Indicates the brain enzyme (hexokinase) may operate with great efficiency to enable the metabolism of glucose at extremely low blood glucose levels, which helps maintain brain function under dire conditions.

question

Km of hexokinase would be less than Km of glucokinase, because Km is reached at very low [glucose] compared to glucokinase.

answer

...

question

Which enzyme be more efficient catalyst for the reaction: glucose--->glucose-6-phosphate?

answer

...

question

Hexokinase

answer

enzyme in brain; Km is very low so the enzyme is saturated with glucose at very low glucose levels.

question

Amount that catalyzes formation of one micro mole of product in one minute

answer

one enzyme unit

question

one enzyme unit

answer

Amount that catalyzes formation of one micro mole of product in one minute

question

Number of substrate molecules converted into product per enzyme molecule per unit time when the enzyme is saturated with substrate

answer

turnover number (Kcat)

question

Kcat

answer

turnover number

question

Kcat

answer

Number of substrate molecules converted into product per enzyme molecule per unit time when the enzyme is saturated with substrate

question

An enzyme at saturation, Kcat, is how many molecules are converted to product

answer

...

question

Kcat of a particular enzyme is a ______

answer

Kcat, turnover number, of a particular enzyme is CONSTANT

question

[Vmax]/total amount of enzyme in=

answer

Kcat (sec-1) expresses in units of reciprocal seconds

question

Kcat values of enzymes

answer

vary; a wide distribution.

question

Kcat describes....

answer

the limiting rate of any enzyme-catalyzed reaction at saturation. If a reaction has several steps and one is clearly the rate limiting step, Kcat is equivalent to the rate constant for that limiting step.

question

A large Kcat value indicates _______, while a small Kcat value indicates _________.

answer

...

question

Kcat allows us to compare the relatives velocities of catalysis of various enzymes, but doesn't tell us anything about the enzyme's affinity for its substrate. Km tells us about affinity, but nothing about velocity.

answer

...

question

What is enzyme activity affected by?

answer

1. Temperature 2. pH 3. Covalent modifications 4. Presence of inhibitors

question

How does pH affect enzyme activity?

answer

Each enzyme is optically active at a certain pH, which is generally near the pH of the medium in which the enzyme operates.

question

pH of the medium may be important in determining the efficiency of the enzyme

answer

The enzyme has a maximum efficiency at the pH of which it is found (in this case, the tissue in which it is found)

question

Pepsin

answer

enzyme that has maximum capacity at pH of 1-2; energineered to be maximum effective at a low pH

question

pH has an affect on an enzyme because the side chains may be ionized or unionized depending on the pH

answer

...

question

Salivary amylase

answer

enzyme found in the mouth that has the maximum capacity at pH of 5-7

question

Alkaline phosphatase

answer

enzyme found in bone and tissue and has the maximum capacity at pH of 9

question

Enzyme has an optimum pH (or pH range) at which their activity is maximal; at higher or lower pH, the activity decreases.

answer

...

question

Temperature on enzyme activity

answer

For most enzymes, we find maximum enzyme activity at/around body temp, or the environment they function in. If you increase temp. above body temperature, the enzyme is denatured and the active site will be affected.

question

Thermophilic organisms

answer

Thermus aquatics are organisms that thrive at high temperatures and possess enzymes that operate efficiently at high temps. Organism is the source of Taq DNA polymerse

question

Taq DNA polymerase

answer

Important enzymes in molecular biology due to it's use in PCR (polymerase Chain reaction) Organism Thermus aquatics is the source for Taq DNA polymerase

question

Most enzymes are subject to _____ _____, which may greatly influence their activity.

answer

Covalent modifications May be used to control an enzyme activity

question

Kinase

answer

aka phosphorylation enzyme that phosphorylates a substrate to activate or deactivate.

question

phosphatase

answer

an enzyme that removes a phosphate to activate or deactivate an enzyme.

question

Phosphorylation occurs especially on ____ groups, like _____, ______ and ______

answer

Phosphorylation occurs especially on the OH groups, like Threonine, Tyrosine, and Serine; which may affect the activity of an enzyme.

question

acetyl CoA carboxylase

answer

an enzyme involved in the production of FA in the cell; the enzyme may be inactivated by phosphorylation of a specific OH group by a particular type of kinase.

question

Acetyl CoA carboxylase by be (activated/inactivated) by phosphorylation by a kinase, and (activated/inactivated) by dephospho rylation by a phosphatase

answer

INACTIVATED by a kinase (addition of a phosphate group) ACTIVATED by a phosphatase (removal of a phosphate)

question

What are the various types of enzyme inhibition?

answer

1. Reversible -Competitive -Uncompetitive (uncommon/don't need to know) -Noncompetitive *Pure (uncommon) *Mixed (most noncompetitive enzyme inhibitors are mixed) 2. Irreversible (DISTINCT COVALENT BOND FORMATIO -Covalent bond formation -Suicide (mechanism-based) inactivators

question

What is the major difference between reversible and irreversible enzyme inhibition?

answer

Irreversible enzyme inhibition involves COVALENT BOND FORMATION, while reversible enzyme inhibition doesn't.

question

Suicide enzyme inactivator

answer

Special type of irreversible inhibitor in which the inhibitor is converted by the enzyme to an activated form, capable of forming a covalent bond within the active site.

question

Irreversible inhibitors

answer

Enzymes that bind covalently with or destroy a functional group on an enzyme that is essential for the enzyme's activity or those that form a particularly stable non covalent association.

question

In irreversible inhibition, ______________ is common.

answer

formation of a covalent link between an irreversible inhibitor and an enzyme are common.

question

Amino acids with key catalytic functions in the active site can sometimes be identified by determining which residue is covalently linked to an inhibitor after the enzyme is inactivated.

answer

...

question

A special class of irreversible inhibitors

answer

suicide inactivators.

question

What is one type of reversible inhibitor?

answer

A type of reversible inhibitor is COMPETITIVE inhibitor.

question

Competitive Inhibition

answer

A competitive inhibitor competes with the substrate for the active sit of an enzyme. When the inhibitor (I) occupies the active site, it prevents the binding of the substrate to the enzyme.

question

Many competitive inhibitors are compounds that resemble _______

answer

resemble the substrate and combine with the enzyme to form the EI complex, but without leading to catalysis.

question

The inhibitor (of competitive inhibition) often bears a structural resemblance to the substrate; however, the complex (EI) formed between enzyme and inhibitor doesn't lead to catalysis.

answer

...

question

A competitive inhibitor (I) binds to the enzyme's active site with it's own equilibrium constant (K1), preventing....

answer

the normal substrate from binding to the site.

question

Because inhibitor binds reversibly to the enzyme, the competition....

answer

can be biased to favor the substrate, by adding more substrate. When [S] far exceeds [I], the probability that an inhibitor molecule will bind to the enzyme is minimized and the reaction exhibits a normal Vmax.

question

How does competitive inhibition affect the M-M equation?

answer

In competitive inhibition, a normal Vmax may be seen when [S] far exceed [I]. BUT, the [S] at which Vo=1/2Vmax, the Km value will increases in the presence of an inhibitor by a factor of alpha.

question

In this type of inhibition, the Vmax remains normal, but the Km value will increase by a factor of alpha.

answer

Competitive Inhibition.

question

Vo=Vmax[S]/ (((alphaKm) + [S]))

answer

competitive inhibitor in the system; therefore, Km is increased by a specific amount (alpha)

question

K1=[E][I]/[E]

answer

Rate constant of a competitive inhibitor reaction

question

In a Michaelis-Menten plot, [S] (x-axis) is plotted against Vo for a competitive and noncompetitive inhibitor....

answer

Competitive inhibitor: -Vmax doesn't change compared to noncompetitive -Km, substrate concentration required to reach 1/2Vmax is increased in presence of competitive inhibitor Noncompetitive inhibitor:

question

the substrate concentration required to reach 1/2Vmax

answer

definition of Km

question

In the presence of a competitive inhibitor, compared to a noncompetitive inhibitor:

answer

1. The Vmax remains the same 2. Km is increased in the presence of a competitive inhibitor.

question

Why does Vmax remain the same in the presence of a competitive inhibitor, compared to a noncompetitive inhibitor?

answer

A Vmax doesn't change, because increase the [substrate] overwhelms the effect of the inhibitor so the maximum velocity of the reaction may still be achieved.

question

Why does Km change in the presence of a competitive inhibitor?

answer

The Km changes in the presence of a competitive inhibitor, because the substrate [] required to reach 1/2 vmax (aka Km) is increased in the presence of a competitive inhibitor.

question

In a competitive inhibitor, describe a typical lineweaver-burke plot.

answer

Competitive Inhibition: Lineweaver-Burke Plot 1. All have same y-intercept (1/Vmax); because the Vmax remains the same. 2. Km (x-intercept) is increased by a factor of the reciprocal of alpha (1/Km*alpha)

question

In a competitive inhibitor, describe a typical lineweaver-burke plot:

answer

Add more inhibitor, the slope line is increased and a steeper line occurs. Vmax is the same Km is increased

question

alpha=1 + [I]/K1

answer

...

question

How does competitive inhibition affect the Km?

answer

...

question

What is a classic example of competitive inhibition?

answer

A classic example of competitive inhibition is: Succinate Dehydrogenase

question

Succinate Dehydrogenase

answer

enzyme involved in step 8 of the citric acid cycle

question

Competitive inhibitor of succinate dehydrogenase

answer

Malonate

question

Malonate

answer

competitive inhibitor of succinate dehydrogenase

question

malonate

answer

bears an obvious structural resemblance to succinate substrate and is capable of binding reversibly to enzyme's active site.

question

Substrate, ______, and competitive inhibitor __________ compete to bind to the active site of the enzyme succinate dehydrogenase.

answer

Substate-succinate CI-Malonate

question

Malonate is an inhibitor of cellular respiration, because it binds to the active site of the succinate dehydrogenase in the citric acid cycle but does not react, thereby competing with succinate. For the oxidative phosphorylation reaction, Malonate is an inhibitor for complex II which, again, contains succinate dehydrogenase.

answer

...

question

Succinate Dehydrogenase (E) + Succinate (S)-->ES complex---> Fumarate (P) and Succinate dehydrogenase (E)

answer

In competitive inhibition, Succinate Dehydrogenase (E) + Malonate (S)-->ES complex---> No product is formed, nothing occurs malonate just physically takes up space in the active site.

question

ADH

answer

Alcohol dehydrogenase

question

Example of an enzyme subject to competitive inhibition

answer

Alcohol Dehydrogenase (ADH)

question

Methanol poising

answer

Liver enzyme converts methanol to formaldehyde (damaging to many tissues); blindness is often a result of methanol ingestion. Eyes are sensitive to formaldehyde.

question

ADH

answer

Ethanol and Methanol compete to occupy the active site of ADH (alcohol dehydrogenase)

question

Ethanol--ADH-->acetylaldehyde Methanol--ADH-->formaldehyde-->formic acif

answer

Ethanol competes much like a competitive inhibitor for ADH.

question

Methanol Poising: Treatment

answer

In methanol poising, methanol is converted in the body by ADH enzyme to formaldehyde. Formaldehyde is a toxic substance, which the eyes are extremely sensitive to and may cause blindness. Use ethanol to displace the methanol from the active site of ADH enzyme, by giving a slow IV infusion of ethanol at a rate that maintains a controlled concentration in the bloodstream for many hours.

question

Result of Methanol Poising Treatment

answer

Result: Slows the formation of formaldehyde, lessing the danger while the kidneys filter out the methanol to be excreted harmlessly in the urine.

question

The enzyme alcohol dehydrogenase is not specific as to which substrate it binds to; 1. ethanol or 2. methanol

answer

...

question

Acetylcholine

answer

know structure

question

a neurotransmitter widely found in the ANS and CNS

answer

acetylcholine

question

What are the neurotransmitter affects of acetylcholine?

answer

1.Stimulates skeletal muscle contractions 2. Inhibits cardiac muscle contractions 3. Stimulate GI secretions 4. Role in cognitive function (closely associated with alztimers)

question

Acetylcholinesterase

answer

aka cholinesterase, an enzyme

question

classic example of a enzyme that frequently has been the target in the development of drugs, by competitive inhibition

answer

acetylcholinesterase, aka cholinesterase.

question

substrate for acetylcholinesterase

answer

acetylcholine

question

the role of acetylcholine in cognition has....

answer

led to the development of cholinesterase inhibitors in the treatment of Alzheimer's disease.

question

ACh

answer

Acetylcholine

question

ACh

answer

a neurotransmitter in cholinergic neurons ACh is released by the pre-synaptic neuron and after interacting with the acetylcholine receptor on the post-synaptic neuron, its action is terminated by acetylcholinesterase.

question

ACh

answer

is cleaved by acetylcholinesterase on the post-synaptic neuron ACh receptor, into acetate and choline, which are then taken up by the pre-synaptic neuron for synthesis of more acetylcholine

question

Mechanism by which Acetylcholinesterase hydrolyzes acetylcholine involves:

answer

3 residues in the active site.

question

What are the 3 residues in the active site of acetylcholinesterase responsible of hydrolyzing acetylcholine?

answer

3 residues in active site: 1. Glu 334 2. Ser 203 3. His 447

question

+charged quaternary nitrogen atom of ACh is held in place by __________

answer

gluatamate residue (334) anionic site

question

All while the serine OH group attacks the ________ with the assistance of __________

answer

All while the serine OH group attacks the ESTER CARBONYL with the assistance of the IMIDAZOLE RING of the histidine residue (esteratic site)

question

The acetylated intermediate is then..

answer

hydrolyzed. Then the vacated anionic and esteratic sites are then free to accommodate another molecule of acetylcholine.

question

ACh has a high Kcat value

answer

...

question

A classic example of a cholinesterase inhibitor

answer

neostigmine

question

neostigmine

answer

a drug, cholinesterase inhibitor, which blocks the breakdown of acetylcholine in the synapse (synaptic cleft)

question

What is the result of neostigmine?

answer

Neostigmine, a cholinesterase inhibitor, blocks the breakdown of acetylcholine in the synapse--->cholinergic agent.

question

Cholinergic agent

answer

a drug that has effects are similar to that of ACh itself.

question

Why is neostigmine differ from ACh?

answer

Neostigmine occupies the same active site as ACh, and its carbonyl group (carbonate group) is subject to attack by the serine OH, just like ACh. BUT the intermediate carbamate ester is hydrolyzed MUCH MORE SLOWLY than is an ACETYL ESTER-->thus effectively blocking the active site.

question

Neostigmine occupies the same active site as acetylcholine and its carbonyl group is subject to attack by serine OH, just like ACh....but

answer

the intermediate carbamate ester of neostigmine is hydrolyzed MUCH MORE SLOWLY than is an acetyl ester-->thus effectively blocking the active site.

question

Trial by Ordeal

answer

Persons accused of crimes or witchcraft were given a Calabar bean to chew (which contains physostigmine). If death resulted (usually by respiratory depression), the person was deemed to be justifiably guilty. However, if the person's stomach rejected the agent, they were said to be proven innocent. To avoid death, one must vomit the Calabar bean up.

question

Physostigmine

answer

a naturally occuring reversible cholinesterase inhibitor with cholinergic effects; especially useful in treating glaucoma.

question

Found in Calabar bean (physostigma venenosum) a plant native to Nigeria

answer

Physostigmine, a naturally occuring reversible cholinesterase

question

used to treat glaucoma

answer

physostigmine (found in Calabar bean)

question

Bind to both the Enzyme (E) and the Enzyme-Substrate (ES) complex

answer

Noncompetitive inhibitors

question

In noncompetitive inhibition, the inhibitors (do/don't) bind at the same spot as the substrate, so the inhibitors effect (can/can't) be overcome by increasing [S]

answer

DON'T CAN'T

question

In ______ inhibition, binding of the inhibitor to the substrate INFLUENCES the binding of the substrate to the enzyme.

answer

NONCOMPETITIVE

question

Where are the binding sites in noncompetitive inhibition?

answer

In noncompetitive inhibition, the binding sites for inhibitor and substrate are separate on the enzyme, they may be near each other or the inhibitor may induce conformational changes in the enzyme that affect binding of the substrate to the enzyme.

question

In noncompetitive inhibition, the competitor in effect lowers the ____________

answer

concentration of the enzyme. Because an inhibitor may induce conformational changes in the enzyme, which affect binding of the substrate to the enzyme.

question

In noncompetitive inhibition, the Vmax is _____ and the Km is _____ in the presence of a noncompetitive inhibitor.

answer

Vmax is REDUCED Km is INCREASED

question

What are the types of noncompetitive inhibition?

answer

Two types of noncompetitive inhibition: 1. pure 2. mixed

question

Pure none competitive inhibition

answer

uncommon occurs when inhibitor binds to the E and ES with the same affinity (K1=K1')

question

Mixed competitive inhibition

answer

frequently occurs substrate and the inhibitor have different affinities for their respective binding sites K1 doesn't equal K1' (like pure noncompetitive)

question

Lineweaver-Burke plot of pure noncompetitive inhibitor

answer

Km is not affected by the inhibitor Vmax decreases

question

Lineweaver-Burke plot of mixed noncompetitive inhibitor

answer

Km effect depends Vmax decreases with increased concentrations of inhibitor.

question

Irreversible Inhibition

answer

similar to reversible inhibition, except in irreversible inhibition the inhibitor forms a covalent bond with the enzyme, which is indicated by *. EI*

question

Differentiate between reversible and irreversible inhibitors.

answer

Reversible inhibitors: non covalent bonds formed Irreversible inhibitors: covalent bonds formed with an enzyme and inhibitor, which are permeant bond to make the interaction irreversible!

question

On a lineweaver-burke plot, distinguish competitive and noncompetitive inhibition.

answer

Competitive inhibition: 1. Vmax is unchanged (y-intercept) 2. Km increases (x-intercept) 3. effect of inhibitor may be overcome by increasing [substrate] Noncompetitive: 1. Vmax decreases with increased concentration of inhibitor 2. Km increases 3. effect of inhibitor may not be overcome by increasing [substrate]

question

Examples of irreversible inhibition

answer

acetylcholinesterase enzyme: Irreversible inhibitors: phosphonate esters containing a good leaving group.

question

Phosphonate esters

answer

a irreversible inhibitor of acetylcholinesterase. Phosphonate ester is formed at serine OH group, such esters are extremely difficult to hydrolyze-->the enzyme's active site is irreversibly blocked.

question

The effect of an irreversible inhibitor can't be overcome by the addition of more substrate, just like _____ inhibitor

answer

noncompetitive reversible inhibitor.

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