biochemistry of enzymes

what are enzymes?

Proteins that act as catalysts for biochemical reactions

what are the properties of enzymes?

not consumed during the reaction most effective catalysts Most enzymes are globular proteins

what is the the delta G of a spontaneous reaction?

delta G of product is less that delta G of substrate

what does the rate of reaction depend on?

transition state Signup and view all the answers

what is the transition state?

state btwn the substrate and the product that the substrate has to undergo before becoming a product Signup and view all the answers

what is the delta G or energy of activation?

The energy difference between the transition state and the substrate Signup and view all the answers

the higher the delta G?

the higher the energy requirement for the reaction to proceed Signup and view all the answers

how does an enzyme lower the energy of activation?

by forming the temporary enzyme-substrate complex Signup and view all the answers

what are simple enzymes?

enzymes composed only of protein (amino acid chains) Signup and view all the answers

what is a conjugated enzyme?

enzymes that have non-protein and protein parts apoenzymes, cofactor, holoenzymes Signup and view all the answers

what is an apoenzyme

protein part of a conjugated enzyme Signup and view all the answers

what is a cofactor?

non-protein part of a conjugated enzyme Signup and view all the answers

what is a holoenzyme?

biochemically active conjugated enzyme Signup and view all the answers

what are prosthetic groups, cofactors and coenzymes?

small molecules or metal ions that participate directly in substrate binding or catalysis Signup and view all the answers

what are the properties of cofactors?

small inorganic metal ions that activate enzymes located near active site helps in binding to the substrate Signup and view all the answers

what are the properties of coenzymes?

large, non-protein, organic molecules that activate enzymes have no catalytic activity But it helps catalyze reactions by donating/accepting electrons transferring functional groups form/break covalent bonds provide functional groups Signup and view all the answers

what are some common coenzymes and what do they do?

Lipoic acid (decarboxylate alpha-keto acid) NAD/NADP, FAD (redox reaction transfer of electrons, dehydrogenation transfer of H+) CoASH (Krebs cycle, beta-oxidation) vitamins (do not provide energy but help unlock energy by acting as co-enzymes) Signup and view all the answers

what forms the complete enzyme?

AKA holoenzyme is formed by the apoenzyme + cofactor Signup and view all the answers

what are the properties of the apoenzyme?

inactive form of enzymes can bind to substrates w/ an affinity comparable to holoenzyme Signup and view all the answers

how are enzymes named?

with reference to their function (focal point is type of reaction catalyzed and name of substrate) Signup and view all the answers

what is the suffix that identifies a substance as an enzyme?

-ase exception: suffix -in is used in some digestive enzymes Signup and view all the answers

what is often used as a prefix when naming enzymes?

type of reaction catalyzed by an enzyme eg, oxidase enzymes do oxidation Hydrolase does hydrolysis Signup and view all the answers

what else is used when naming an enzyme in addition to type of reaction?

identity/ name of substrate Signup and view all the answers

how are enzymes classed?

based on the types of reactions they catalyze Signup and view all the answers

what are the classes of enzymes?

<ol> <li>oxidoreductases oxidation-reduction reactions</li> <li>transferases functional group of transfer reactions</li> <li>hydrolases hydrolysis reactions</li> <li>lyases addition or removal of groups to form double bonds</li> <li>isomerase isomerization reactions</li> <li>ligases reactions involving bond formation w/ the participation of ATP</li> </ol> Signup and view all the answers

what do oxidoreductases require?

a coenzyme that is oxidized or reduces as the substrate is reduced or oxidized Signup and view all the answers

what are the subtypes of transferases?

transaminase- catalyzes the transfer of an amino group from one molecule to another kinase- catalyzes the transfer of a phosphate group from ATP tp give ADP and a phosphorylated product Signup and view all the answers

what does hydrolase do? and what process is it crucial for?

adds a water molecule to a bond causing it to break central to digestion Signup and view all the answers

what is a lyase?

catalyzes the addition or removal or a group to form a double bond in a manner that does not involve hydrolysis or oxidation Signup and view all the answers

what are the classes of lyases?

dehydratase- effects the removal of the components of water from a double bond hydratase- effects the addition of the components of a water to a double bond Signup and view all the answers

what is an isomerase?

aka mutases catalyzes the isomerization (rearrangement) of a substrate in a reaction Signup and view all the answers

what is a ligase?

catalyzes the formation of a bond btwn two molecules w/ the participation of ATP Signup and view all the answers

why is atp required in ligase reactions?

these reactions are energetically unfavorable Signup and view all the answers

what is the active site? how is it formed?

small part of the enzyme's structure that is involved in catalysis formed due to the folding and bending of the protein Signup and view all the answers

what is the lock and key model?

enzyme's substrate fits perfectly w/ the active site Signup and view all the answers

what are the limitations and reality of the lock and key model?

limitation: implies enzymes are very rigid reality: enzymes are flexible limitation: 1 enzyme w/ 1 substrate reality: enzymes are not strictly specific in binding to a substrate Signup and view all the answers

what is the induced fit model?

initially there is no perfect fit btwn the active site and the substrate, the substrate induces a change in the active site (conformational change), eventually achieving a perfect fit Signup and view all the answers

what are the properties of induced fit model?

implies that substrate changes enzyme implies that enzyme changes substrate explains why enzymes act on wide range of related substrates Signup and view all the answers

what are the forces that assist substrate binding?

electrostatic interactions, hydrogen bonds, hydrophobic interactions Signup and view all the answers

what are the 4 types of enzyme specificity?

absolute specificity/ group specificity/ linkage specificity/ stereochemical specificity Signup and view all the answers

what is absolute specificity?

enzyme will catalyze only one reaction/ most restrictive and is not common/ eg. catalase Signup and view all the answers

what is group specificity?

enzyme will act only on molecules that have a specific functional group/ eg. carboxypeptidase cleaves AA Signup and view all the answers

what is linkage specificity?

enzyme will act on a particular type of chemical bond, rest of the molecular structure is not considered/ most general of the common specificities Signup and view all the answers

what is stereochemical specificity?

enzyme will act on particular stereoisomers/ chirality is inherent in an active site Signup and view all the answers

what are the 4 mechanisms of enzyme catalysis?

catalysis by proximity/ acid-base catalysis/ catalysis by strain/ covalent catalysis Signup and view all the answers

what is catalysis by proximity?

for molecules to interact they must come w/in bond forming distance Signup and view all the answers

what is acid-base catalysis?

reactions for which the only participating acid or base are protons or hydroxide ions Signup and view all the answers

what is catalysis by strain?

enzymes that catalyze lytic reactions (involve breaking a covalent bond) bind their substrates in a conformation that is somewhat unfavorable for the bond targeted for cleavage Signup and view all the answers

what is covalent catalysis?

formation of a covalent bond between the enzyme and one or more substrates Signup and view all the answers

what are the types of AA that should be found in the active site of enzymes for covalent catalysis to take place?

polar amino acids: serine/threonine/cysteine/histidine/arginine/lysine Signup and view all the answers

what mechanism of enzyme catalysis follows a ping pong mechanism?

covalent catalysis Signup and view all the answers

what are the factors affecting enzyme activity?

temperature/ph/substrate concentration Signup and view all the answers

what is enzyme activity?

measure of the rate at which an enzyme converts substrate to products in a biochemical reaction Signup and view all the answers

how does higher temperature affect enzyme activity?

Higher temp --> higher kinetic energy (molecules move faster and collide more frequently) Signup and view all the answers

what is optimum temperature?

temperature at which enzymes exhibit maximum activity (37) an increase in temp above this initiates enzyme denaturation Signup and view all the answers

how does ph affect enzyme activity?

small changes in ph can result in denaturation of proteins Signup and view all the answers

what is optimum ph?

ph at which an enzyme exhibits maximum activity (most enzymes 7.0-7.5) Signup and view all the answers

what is the optimum ph of pepsin and trypsin?

pepsin: 2.0 trypsin: 8.0 Signup and view all the answers

how does substrate concentration affect enzyme activity?

At a constant enzyme concentration, the enzyme activity increases with increased substrate concentration Signup and view all the answers

what is the limit of substrate saturation?

when substrate concentration reaches its maximum rate and all the active sites are full Signup and view all the answers

what is turnover number?

number of substrate molecules converted to product per minute by one enzyme under optimum temperature, pH, and saturation Signup and view all the answers

how does enzyme concentration affect enzyme activity?

at a constant substrate concentration, enzyme activity increases w/ the increase in enzyme concentration Signup and view all the answers

what are the things that come under enzyme kinetics?

rate (speed, velocity, measure of change over a period of time)/ reaction rate (formation of products over a period of time) Signup and view all the answers

what is a zero order reaction?

the reaction rate is constant even if the reactant concentration is increased/ the reaction rate is INDEPENDENT of the reactant concentration (flat part of graph) Signup and view all the answers

what is a first order reaction?

The reaction rate increases as the concentration of the reactants increases/ the reaction rate is dependent on the reactant concentration/ there is a direct proportional relationship between the reactant concentration and the reaction rate Signup and view all the answers

in the michaelis-menten curve, very low substrate concentration indicates which order?

1st order reaction Signup and view all the answers

when the substrate conc increases this means?

reaction rate increases Signup and view all the answers

when the substrate conc is very high this indicates?

zero order Signup and view all the answers

what is mixed order?

the transition from first to zero order Signup and view all the answers

what is vmax?

the velocity at which it is zero order Signup and view all the answers

what is vmax1/2?

halfway thru vmax Signup and view all the answers

what is km?

AKA michaelis constant, Km is substrate concentration at vmax 1/2 Signup and view all the answers

what does michaelis constant represent?

enzymes affinity to the substrate Signup and view all the answers

low km means?

enzyme has high affinity to substrate (high rate of reaction w/ lower substrate) Signup and view all the answers

high km means?

enzyme has low affinity with the substrate (rate or reaction needs higher substrate concentration for same rate of reaction) Signup and view all the answers

what is the formula for the michaelis-menten curve?

v0= vmax [s]/km +[s] Signup and view all the answers

what is the formula for the Lineweaver-Burk plot?

1/v0= km/vmax[s]+1/vmax Signup and view all the answers

what is an enzyme inhibitor?

substance that slows down or stops the normal catalytic function of an enzyme by binding to it Signup and view all the answers

what is a competitive inhibitor?

molecule that resembles an enzyme substrate in shape and charge distribution Signup and view all the answers

what is a noncompetitive inhibitor?

binds to the enzyme at a location other than the active site Signup and view all the answers

what is reversible competitive inhibition?

competitive inhibitor that binds reversibly to the active site Signup and view all the answers

what is reversible noncompetitive inhibition?

decreases enzyme activity by binding to a site on an enzyme other than the active site/ causes a change in the structure of the enzyme/ prevents catalytic groups at the active site from properly affecting their catalyzing action Signup and view all the answers

how does increasing concentration of substrate effect inhibition in reversible noncompetitive inhibition?

does not completely overcome inhibition Signup and view all the answers

how does increasing concentration of substrate effect inhibition in reversible competitive inhibition?

inhibition is reduced by increasing substrate conc Signup and view all the answers

what are examples of reversible noncompetitive inhibitors?

lead, silver, mercury Signup and view all the answers

what is a reversible uncompetitive inhibitor?

Inhibitor does not bind to the free enzyme/ binds to an allosteric site Signup and view all the answers

give the summary of lineweaver-burke plots in inhibitors

competitive: km increase, vmax unaffected & uncompetitive: km decrease , vmax decrease & noncompetitive km unaffected, vmax decrease Signup and view all the answers

what is irreversible enzyme inhibition?

inactivated enzymes by forming a strong covalent bond to an amino acid side chain group with the enzymes active site Signup and view all the answers

how does substrate concentration affect inhibition in irreversible inhibition?

increasing substrate conc does not reverse inhibition process/ enzyme is permanently inactivated Signup and view all the answers

what are the properties of allosteric enzymes?

have quaternary structures/ have at least 2 kinds of binding sites/ active and regulatpry binding sites are distinct from each other in both location and shape Signup and view all the answers

what happens when molecules bind at the regulatory site of allosteric enzymes?

changes in the 3d structure of the enzyme Signup and view all the answers

what happens with the binding of a positive and negative regulator?

positive regulator increases enzyme activity vice versa Signup and view all the answers

what are regulators of allosteric enzymes? (feedback control)

products of different pathways of reaction within the cell/ compounds produced outside the cell (hormones) Signup and view all the answers

what is a proteolytic enzyme?

enzymes that catalyze the breaking of peptide bonds Signup and view all the answers

what are zymogens?

pro enzymes, activated at the appropriate time and place (most digestive and blood clotting enzymes) Signup and view all the answers

how to turn a zymogen (proenzyme) into a proteolytic enzyme (active enzyme)

removing a peptide fragment Signup and view all the answers

what is covalent modification?

process in which enzyme activity is altered by covalently modifying the structure of the enzyme Signup and view all the answers

what is an example of a common covalent modification?

addition and removal of phosphate groups (phosphorylation/dephosphorylation) Signup and view all the answers

During phosphorylation/dephosphorylation, what amino acids are the phosphate groups added to/removed from?

the R groups of serine, tyrosine or threonine Signup and view all the answers

what are extremozymes?

microbial enzymes that are active at rly hot and rly cold places Signup and view all the answers

what are: 1. acidophiles, 2. alkaliphiles, 3. halophiles, 4. hyperthermophiles, 5. piezophiles

<ol> <li>acidophiles: optimal pH 3.0 or below, 2. alkaliphiles: optimum pH 9.0 or above, 3. halophiles: live in highly saline conditions, 4. hyperthermophiles: hot temperature 80- 122 °C, 5. piezophiles: grow under high hydrostatic pressure</li> </ol> Signup and view all the answers

what are the steps for gathering commercially successful enzymes?

<ol> <li>Samples are gathered from extreme environment 2. extremophile DNA is extracted and processed 3. marcoscopic amounts of dna are produced by polymerase chain reaction 4. genes responsible for extremozyme production are identified 5. genetic engineering processes are applied to produce extremozymes thru bacteria 6. extremozymes are commercially produced</li> </ol> Signup and view all the answers

what are the applications of extremozymes?

biotechnology industry/ laundry detergents/ petroleum drilling Signup and view all the answers

what are the enzymes lactate dehydrogenase (LDH) and creatine kinase (CK) used for in medical diagnostics?

used to diagnose and monitor myocardial infarction Signup and view all the answers

what are the enzymes, pancreatic amylase and pancreatic lipase, used for in medical diagnostics?

used to diagnose and monitor acute pancreatitis Signup and view all the answers

what are the enzymes urokinase and streptokinase used for in medical therapeutics?

as thrombolytics. used to lyse blood clots in patients w/ STEMI and CVA (cerebrovascular accident) Signup and view all the answers

what are examples of prescription drugs that work by inhibiting enzymes?

ACE inhibitors [blood pressure regulation], sulfa drugs, and penicillin Signup and view all the answers

what is angiotensin and how do ACE inhibitors work?

Angiotensin: increases bp by narrowing blood vessels. ACE converts angiotensinogen to angiotensin in the blood. ACE inhibitors block ACE and lower bp Signup and view all the answers

what AA are removed in turning angiotensinogen to angiotensin?

histidine and leucine Signup and view all the answers

what are sulfa drugs?

Derivatives of sulfanilamide, exhibit antibiotic properties Signup and view all the answers

what is sulfanilamide? how is it antibiotic?

competitive inhibitor of enzymes that convert PABA [needed by bacteria to produce folic acid] to folic acid --> folic acid deficiency --> retards bacterial growth and kills them Signup and view all the answers

how does penicillin inhibit transpeptidase?

covalent modification of serine residue Signup and view all the answers

how are enzymes used in research?

make genes soft and easily accessible to other enzymes Signup and view all the answers