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Flashcards in ch 8 Deck (52):

qualities of enzymes

1. efficient-
2. specific
- stereo-specific can tell between 2 isomers
3. regulated
4. saturable
5. inhibitable


what are different versions of the same enzymes called? and how are the made?

isoenzymes or isozymes. made by alternative splicing


what are the 4 types of enzyme specificity?

1. absolute - enzyme catalyzes only one reaction
2. group specific - enzyme acts only on molecules having particular functional group
3. linkage specific - enzyme acts on a particular type of chemical bond
4. stereo-chemical specific- enzyme acts on a particular stereo or optical isomer


what does the action of an enzyme depend primarily on?

tertiary and quaternary structure


what part of enzyme sturcture acts on substrate

active site


what are cofactors?

other compounds or ions that enymes require before their catalytic activity can occur
non-protein sbstance which may be organic (vitamins)


what is the protein portion of an enzyme referred to?



what is an enzyme with the cofactor called



what is an indactive form of an apoenzyme?

proenzyme or zymogen. may contain several exra amino acids which are removed to allow final specific tertiary structure fo be formed in order to be ativated


3 types of cofactors

1. coenzyme: a non protein organic substance that is loosely attached to the enzyme; detachable molecules that function to carry chemical groups or electons between molecules
2. prostetic group: non protein organic substance that is firmly attached to enzyme (heme group)
3. metal ion activators


what must the chemical substrate go through to form the product?

tansition state with higher free energy than either S or P


what is the transition state?

a transient molecular structure that is no longer the substrate bit is not yet the product


what is a major reason enzymes can catalyze reactions?

they can birng substrates into close proximity with reactive groups


what are the three reasons we known the ES complex exists

1. at constant enzyme concentration, reaction rate increases until a maximal velocity is reached. at this point enzyme is saturated and reaction rate stops increasing. uncatalyzed reactions do not show this saturation effect

2. x-ray crystallography has revealed that the atomic structures substrates bound to the active sites of enzymes.

3. spectroscopy: largest peak is the ES complex


if active site is made only of a few amino acids why are enzymes so big

extra amino acids serve as a scaffold to properly orient the active site residues. residues next to each other are sterically constrained from forming an active site. extra motifs may have other functions


what functions may extra motifs have

channeling substrate to active site
contain regulatory sites
participate in binding to other proteins or nucleic cadis


microenvironment of active sit

when substrate binds to active site awter is usually excluded
acive site is nonpolar environment that enhances binding and catalysis
polar residues can be found in the active site


how do enzymes bind to substrates?

multiple weak attractions
. noncovalent interactions
- weak reversible interactions comprised of hydroen bonds, van der waals forces, electrostatic and hydrophonic interactions


how do hydrogen bond help substrates bind to enzymes properly

hydrogen bonds have a directional character conferring to high specificity


how does the induced fit model help explain how enzymnes lower activation energy

inexact fit puts stress on certain bonds of the substrate to lower energy to break them


why does the enzyme remain unchanged?

does not form any chemical bond with susbtrate


why does rate increase at low substrate concentrations

many active sites available to be ocupied


what is k1?

constant for the formation of ES


what is K-1

constant for the converstion of ES to E+S


what is K2?

constant for product formation K2= Kcat


what is turnover number a measure of?

turnovernumber (kcat) is a measure of catalytic activity.

catalytic production of product under saturating substrate conditions

the maximum number of substrate molecules converted to product per enzyme pmolecule per unit of time (under conditions of fully saturated sbstrate)


values of kcat range from?

1 per second to many millions per second


how do you calculate kcat



how do you calculate catalytic efficiency



what does catalytic efficiency allow you to see?

comparison of an enzyme's effectiveness toward different substrates


when [S] > Km rate of catalysis is:
when [S] << Km rate of catalysis is :

when [S] > Km rate of catalysis is: equal to vmax
when [S] << Km rate of catalysis is : less than kcat


when enzymes have values approaching the upper limit of catalytic efficiency, what does this mean?

catalytic velocities are only restricted by rate at which they encounter substrate in solution (catalytic perfection)
almost every encounter between enzyme and substrate results in product


how do you find km and vmax on a lineweaver burke plot?

x intercept: -1/km
y intercept: 1/vmax

x axis 1/vo
y axis 1/[s]


3 types of reversible inhibition

mixed (noncompetitive)


what do you call the increased km of competitive inhibition?

apparent km


what is uncompetitive inhibition

inhibitor only binds to the enzyme susbtrate complex


what is noncompetitive inhibitor

inhibitor and susbtrate can bind simultaneously to enzyme. noncompetitive inhibitor acts to reduce turnover number of the enzyme. does not prevent binding of susbtrate to the enzyme.


what are the three categories of irreversible inhibitors

1. group specific reagents
2. reactive substrate analogs
3. suicide inhibitors


what do group specific reagents do?

react with specific side chains of amino acids


what are examples of group specific reagents?

DIPF (nerve gas) modifies serene residues
Iodoacetamide modifies cysteine residues


what are reactive substrate analogs

molecules that are similar to the substrate for the enzyme and covalently bind to the active site residues. much more specific than group specific. also called affinity labels


what is a substrate analog for chymotrypsin



suicide inhibitors?

modified substrates that are the most specific reagents for modifying residues within the active site. binds to the enzyme and is processed by normal catalytic mechanism.action upon suicide inhibitor results in the genration of a reactive intermediate which inactiavtes the enzyme through covalent modification. enzme participates in its own inactivation


what are transition state analogs

compounds that resemble the transition sate and should be effective inhibitors


utilization of transition state analogs

1. sources of insight into catalytic mechanisms
2. they are potent and specific inhibitors of enzymes
3. can be used as immunogens to generate catalytic antibodies


penicillin function

interferes with cell wall synthsis in bacteria


penniciillin structure

thiazolidine ring fused to beta-lactam ring. beta lactam ring very unstable and labile


peptidoglycan structure

Peptidoglycan consists of linear
polysaccharide chains that are crosslinked
by short peptides


peptidoglycan use?

prevents bacteria from bursting from osmotic shock


penicillin does what to prevent cel lwall cyntehsis

blocks formation of peptide linkages between sugar chains


how does a cross link form?

amino group at one end of a pentaglycine chain attacks the peptide bond between 2 d-alanine residues to form a cross link. catalyzed by glycopeptide transpeptidase


transpeptidase normally forms a covalent acyl intermediate with glycopeptide transpeptidase, however penicillin:

is welcomed into active site because it resembles susbtrate, reacts with a serine rsidue at the active site forming an inactive enzyme complex. irreversible suicide inhibitor