Enzymes: Biochemistry

344 terms by mpaleno

Create a new folder

Advertisement Upgrade to remove ads

Abramson lecture

A reaction may be thermodynamically favored, but ____________ ___________.

Extremely slow

Not a useful time scale for the reaction to occur.

Enzymes

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

T/F: All enzymes are proteins.

False; All enzymes are proteins, WITH THE EXCEPTION of a small group of catalytic RNA molecules.

Not ALL enzymes are proteins

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

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.

Simple enzyme

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

Cofactor

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

Coenzyme

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

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

...

Prosthetic Group

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

What is another name for a prosthetic group?

A prosthetic group may also be called:

1. Cofactor
2. Coenzyme

Holoenzyme

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

Apoenzyme

Aka Apoprotein

Apoenzyme

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

Holoenzyme

whole protein enzyme + prosthetic group

Holoenzyme

Complete or catalytically active enzyme

______ act as transient carriers of specific functional groups

Coenzymes

Some enzyme proteins may be ________ ______.

COVALENTLY MODIFIED.

Phosphorylation
Glycosylation
Other processes

What does covalently modification do to enzyme proteins?

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

Glycosylation

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

Phosphorylation

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

-ase suffix

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

Exceptions to proteins ending in "-ase"

Pepsin, trypsin, lysozyme

-"ase"

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

urease catalyase

enzyme, functions for hydrolysis of urea

DNA polymerase

enzyme that catalyzes the polymerization of nucleotides to form DNA

Why do not all enzymes end in "ase"?

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

Pepsin

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

Lysozyme

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

Trypsin

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.

EC

Enzyme Commission

EC system

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.

Purpose of EC system

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

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

Each enzyme has a FOUR-part classification number.

6 Classes of enzymes.

Class 1 of enzyme

Oxidoreductases

Class 2 of Enzyme

Transferases

Class 3 of enzyme

Hydrolases

Class 4 of enzyme

Lyases

Class 5 of enzyme

Isomerases

Class 6 of enzyme

Ligases

Oxidoreductases

Class 1 enzyme

Transferases

Class 2 Enzyme

Hydrolases

Class 3 enzyme

Lysases

Class 4 enzyme

Isomerases

Class 5 enzyme

Ligases

Class 6 enzyme

Reaction Type: Electron transfer (H atoms)

Oxidoreducatase

Reaction Type: Group Transfer

Transferases

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

Hydrolases

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

Lysases

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

Isomerases

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

Ligases

L-lactate dehydrogenase (example of EC naming)

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

D-Lactate dehydrogenase

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.

International system used to classify enzymes

Enzyme Commisssion System (EC)

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

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)

Cofactor

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

Holoenzyme

a complete catalytically active enzyme

Apoenzyme

aka apoprotein
The protein part of a holoenzyme

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

...

Example of catalytic modification

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

Enzymes

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

Classifications in EC

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

Enzyme that catalyzes the oxidation of lactic acid to pyruvic acid

lactate dehydrogenase

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

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

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

Thermodynamically favored

Conversion of Glucose to CO2 and Water

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.

What is the function of enzymes?

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

Enzymes are highly _______.

SPECIFIC

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

In biologically relevant conditions, do uncatalyzed reactions occur?

Yes they occur, but are very slow.

Biological molecules are quite stable in our cells (neutral pH, mild temp. and aqueous environment)

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

Unfavorable
Unlikely to occur

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

Active Site

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

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

substrate

Surface of the active site...

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

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

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

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

the active site

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

a substrate

amino acid residues that constitute the active site

...

E
S
P

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

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

A enzymatic reaction (all reversible=equilibrium reaction)

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

Increase the RATE of the REACTION

REACTION EQUILIBRIUM

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

ES and EP

Reaction Coordinate diagram

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

Ground state

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

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

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

Activation energy

Delta G double dagger

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

Activation energy

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

biochemical standard free energy change
ΔG0'

equilibrium between S and P reflects....

the differences in the free energies of their ground states.

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

Enzymes

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

ES and EP

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

Position
Direction

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

lower
transition state

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

...

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

detectable

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

...

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

Transition State

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

Transition state.

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

activation energy

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.

Slower
Faster

How may reaction rates be increased?

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

Catalyst

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

Function of catalyst

lower activation energy, increase reaction rate

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

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

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

DON'T.

T/F: Enzymes are used up in reactions.

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

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

ACCELERATE

Is the equilibrium rate affected by an enzyme?

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.

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

...

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

5 to 17 orders of magnitude

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

1. Lock and Key
2. Induced Fit

First postulated by Emil Fischer in 1954

Lock and Key Model

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

Lock=enzyme
Key=substrate

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

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

Lock and key model assumes...

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

First postulated by Daniel Koshland in 1958

Induced-Fit model

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

induced-fit model

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

induced-fit model

this model infers rigidity of the shape of the active site

lock and key model

DHFR

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

What are the substrates for DHFR?

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

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

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

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

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

Rate-limiting step

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

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

Rate limiting step

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

...

Delta GB

binding energy

binding energy

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

the energy derived from the enzyme substrate interactions

binding energy

___________ identifies the structure and function of enzymes

X-ray crystallography

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

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

the ability to distinguish between a substrate and a competing molecule

specificity

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:

1. general acid-base catalysis
2. covalent catalysis

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

1. general acid-base catalysis
2. covalent catalysis
3. Metal ion catalysis

Differs from mechanisms based on binding energy (non-covalent bonds)

proton transfers mediated by other classes of molecules

general acid-base catalysis

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

covalent catalysis

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

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

X:

a nucleophilic group of an enzyme within the ACTIVE SITE

______ 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

X:

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

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

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

Metal Ion catalysis

REVIEW 3 types of catalysis

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

Enzymes:
1.
2.
3.
4.

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.

chymotrypsinogen

an inactive zymogen from the pancreas

zymogen

a precursor of an active enzyme

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

zymogens

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

...

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

Reaction catalyzed by chymotrysin

pancreatic chymotrypsin is a ______ (a type of enzyme)

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

What does pancreatic chymotrypsin specifically do?

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

See More

Please allow access to your computer’s microphone to use Voice Recording.

Having trouble? Click here for help.

We can’t access your microphone!

Click the icon above to update your browser permissions above and try again

Example:

Reload the page to try again!

Reload

Press Cmd-0 to reset your zoom

Press Ctrl-0 to reset your zoom

It looks like your browser might be zoomed in or out. Your browser needs to be zoomed to a normal size to record audio.

Please upgrade Flash or install Chrome
to use Voice Recording.

For more help, see our troubleshooting page.

Your microphone is muted

For help fixing this issue, see this FAQ.

Star this term

You can study starred terms together

NEW! Voice Recording

Create Set