MCAT Biochemistry - Enzymes

hypertension

high blood pressure; increases risk of stroke, heart failure, kidney failure

angiotensin-converting enzyme (ACE) inhibitors

anti-hypertensive medication; inhibits ACE

angiotensin-converting enzyme (ACE)

catalyses a reaction that converts angiotensin I to angio tensin II

angiotensin II

causes constriction of blood vessels; stimulate sthe release of aldosterone

aldosterone

hormone that activates the kidneys to reabsorb more water into the blood stream; increase in blood volume increases blood pressure

enzymes

biological catalysts; used to regulate homeostatic mechanisms in every organ system and are highly regulated themselves by environmental conditions, activators, and inhibitors; may be naturally occurring or may be given as a drug

all catalytic properties +

• Are pH- and temperature-sensitive, with optimal activity at specific pH ranges and temperatures

• Are specific for a particular reaction or class of reactions

catalysts

• Lower the activation energy

• Increase the rate of the reaction

• Do not alter the equilibrium constant

• Are not changed or consumed in the reaction

• Do not affect the overall ΔG of the reaction

enzyme specificity

a given enzyme will only catalyze a single reaction or class of

reactions with these substrates

substrate

the molecules upon which an enzyme acts

urease

catalyses the breakdown of urea

chymotrypsin

cleaves peptide bonds around the amino acids that contain aromatic rings—phenylalanine, tryptophan, and tyrosine.

-ase

suffix for most enzymes

Oxidoreductases

catalyzes the transfer of electrons between molecules

electron carrier

often a cofactor for oxidoreductases

e.g. NAD+, NADP+

reductant

electron donor

oxidant

electron acceptor

dehydrogenase

name suggesting oxidoreductase (1)

reductase

name suggesting oxidoreductase (2)

oxidase

name suggesting oxidoreductase with oxygen as the final electron acceptor

transferases

catalyze the movement of a functional group from one molecule to another

aminotransferase

convert aspartate and α-ketoglutarate toglutamate and oxaloacetate by moving amino group →

kinase

catalyze the transfer of a phosphate group (esp. from ATP) to another molecule

hydrolases

catalyze the breaking of a compound into two using hydrolysis; using naed only for substrate

hydrolysis

breaking a compound/polymer using the addition of water molecules

phosphatase

hydrolase that cleaves a phosphate group

peptidases

hydrolase that cleaves a polypeptide

nucleases

hydrolase that cleaves a nucleic acid

lipases

hydrolase that cleaves a lipid

lyases

catalyze the cleavage of a single molecule into two products without water

may also be a synthase

synthase

catalyzes the synthesis of two (esp. small) molecules into a single one

may also be a lyase

isomerase

catalyze the rearrangement of bonds within a molecule; can be classified as another type of enzyme depending on mechanism

ligase

catalyze addition or synthesis reactions, generally between large similar molecules, often require ATP

e.g. nucleic acid synthesis

endergonic reaction

requires energy input (ΔG > 0)

exergonic reaction

energy is given off (ΔG < 0)

activation energy

the minimum amount of energy that must be available to reactants for a chemical reaction to occur; make it easier for substrates to achieve transition state

enzyme-substarte complex

the physical interaction between the enzyme and the molecule it acts upon; transition state

active site

teh location within the enzyme where the substrate is held during the chemical reaction

lock and key theory

active site is always in the appropriate conformation for the substrate to bind

induced fit theory

the substrate induces a change in the shape of the enzyme; conformation is endergonic, release is exergonic; enzymes return to original shape when not bound

Thiamine (Vitamin B1)

essential cofactor for enzymes in cellular metabolism and nerve conduction

defienciency from excess alcohol consumption, poor diet

Wernicke-Korsakoff syndrome

disease stemming from thiamine deficiency, esp. from alcoholism

symptoms: neurologic deficits, including delirium, balance problems, the inability to form new memories

cofactors

inorganic molecules or metal ions, often ingested as dietary minerals, that aid enzymes; small, bound to the active site of enzyme and participate in catalysis by carrying charge (ionization, (de)protonation); low concentrations in cells, recruited when needed

coenzymes

small organic groups, often vitamins or derivatives, that aid enzymes; small, bound to the active site of enzyme and participate in catalysis by carrying charge (ionization, (de)protonation); low concentrations in cells, recruited when needed

e.g. NAD+, FAD, coenzyme A

water-soluble vitamins

must be replenished regularly, easily excreted

e.g. B complex, ascorbic acid/C

fat-soluble vitamins

regulated by partition coefficients

e.g. A, D, E, K

partition coefficients

quantify the ability of a molecule to dissolve in a polar vs. nonpolar environment

apoenzymes

enzymes without necessary cofactors/coenzymes

holoenzymes

enzymes containing necessary cofactors/coenzymes

riboflavin (vitamin B2)

involved in energy metabolism, cellular respiration, and antibody production, as well as normal growth and development

niacin (vitamin B3)

converted within the body to NAD+

Pantothenic acid (vitamin B5)

synthesize coenzyme A (CoA), which is essential for cellular energy production and for the synthesis and degradation of proteins, carbohydrates, and fats

Pyridoxal phosphate (vitamin B6)

all transamination reactions, and in certain decarboxylation, deamination, and racemization reactions of amino acids

Biotin (vitamin B7)

involved in the catabolism of amino acids and fatty acids, synthesis of fatty acids, and gluconeogenesis

Folic acid/folate (vitamin B9)

required for the body to make DNA and RNA and metabolise amino acids necessary for cell division and maturation of blood cells

(Cyano)cobalamin (vitamin B12)

required for DNA synthesis, in both fatty acid and amino acid metabolism, the synthesis of myelin, and in the circulatory system in the maturation of red blood cells in the bone marrow

saturation

every enzyme is busy/occupied; increasing substrate concentration cannot increase velocity further

maximum velocity (v_max)

the highest rate of catalysis at a given concentration of enzymes can perform

synonymous with max activity/rate

Michaelis-Menten equation

As the amount of substrate increases, the enzyme is able to increase its rate of reaction until it reaches v_max; once v_max is reached, adding more substrate will not increase the rate of reaction.

v = v_max [S] / K_m + [S]

When rate = ½ v_max, K_m = [S]

v = k_cat[E][S] / K_m + [S] ≈ k_cat / K_m ([E][S])

Michaelis constant (K_m)

a measure of the affinity of the enzyme for its substrate; higher K_m = lower affinity for substrate, requires a higher substrate concentration to be half-saturated

substrate turnover (k_cat)

measures the number of substrate molecules converted to product per enzyme molecule per second

v_max=[E]k_cat

catalytic efficiency

the ratio of the k_cat / K_m of a particular enzyme

Lineweaver-Burk plot

double reciprocal graph of the Michaelis–Menten equation

x-intercept = −1/K_m

y-intercept = 1/v_max

Cooperativity

Binding of the substrate to one subunit encourages the transition of other subunits from the low affinity, tense (T) state to the high-affinity, relaxed (R) state, which increases the likelihood of substrate binding by these other subunits

sigmoidal (S-shaped) Michaelis-Menten plot

e.g. haemoglobin, phosphofructokinase-1 (glycolysis)

Hill’s coefficient

quantifies cooperativity, indicates the nature of binding by the molecule

>1 - positively cooperative binding

<1 - negatively cooperative binding

=1 - no cooperative binding

Enzymes and temperature

double in velocity per 10°C inc. until optimum temp. then activity falls sharply due to denaturation

optimal temp. is typically body temp. (37°C/98.6°F/310 K in humans)

tyrosinase

enzyme responsible for pigmentation

mutated in Siamese cats: ineffective @ body temperature, but active at cooler temperatures

Enzymes and pH

pH affects the ionization of the active site, also changes in pH can lead to denaturation of the enzyme

e.g. ideal blood pH 7.4, pepsin pH 2 (stomach), pancreatic enzymes pH 8.5 (small intestine)

Enzymes and salinity

Increasing levels of salt can disrupt hydrogen and ionic bonds, causing a partial change in the conformation of the enzyme and causing denaturation

feedback regulation

regulation by products further down a given metabolic pathway

feed-forward regulation

regulated by intermediates that precede the enzyme in the pathway

Feedback inhibition/negative feedback

helps maintain homeostasis; once we have enough of a given product, we want to turn off the pathway that creates that product rather than creating more; competitive inhibition

methanol (wood alcohol)

enzymatically converted to toxic metabolites in the body; may cause blindness or death

treatment: intravanous ethanol, with competes for active sites

competitive inhibition

occupancy of the active site; overcome by adding more substrate

binding site: active

K_m: increases

v_max: unchanged

noncompetitive inhibition

bind to allosteric site that induces a conformational change; no extra substarte with form a complex; less enzyme available to react

binding site: allosteric

K_m: unchanged

v_max: decreases

mixed inhibition

inhibitor can bind to either the enzyme or the enzyme–substrate complex, but has different affinity for each

binding site: allosteric

K_m: increases (favours enzyme) or decreases (favours complex)

v_max: decreases

On a Lineweaver–Burk plot, the curves for the activity with and without the inhibitor intersect at a point that is not on either axis

uncompetitive inhibition

inhibitors bind only to the enzyme–substrate complex and essentially lock the substrate in the enzyme, preventing its release

binding site: allosteric

K_m: decreases

v_max: decreases

On a Lineweaver–Burk plot, the curves for activity with and without an uncompetitive inhibitor are parallel

Allosteric site

non-catalytic regions of the enzyme that bind regulators

irrevirsible inhibition

the active site is made unavailable for a prolonged period of time, or the enzyme is permanently altered

e.g. aspirin

Acetylsalicylic acid (aspirin)

irreversibly modifies cyclooxygenase-1, which now can no longer bind its substrate (arachidonic acid) to make its products (prostaglandins), which are involved in modulating pain and inflammatory responses

Allosteric enzymes

alternate between an active and an inactive form

allosteric activators

result in a shift that makes the active site more available for binding to the substrate

allosteric inhibitors

result in a shift that makes the active site less available for binding to the substrate

phosphorylation/dephosphorylation

addition/removal of a phsophate group; depending on the enzyme, either could activate or deactivate it

glycosylation

the covalent attachment of sugar moieties can tag an enzyme for transport within the cell or can modify protein activity and selectivity.

zymogens

inactive form of an enzyme; often when enzymes are digestive; regulatory domain must be either removed or altered to expose the active site; often ends in -ogen

e.g. tyrpsinogen (→ trypsin), pepsinogen (→ pepsin)