Flashcards in ch 8 Deck (52):
qualities of enzymes
- stereo-specific can tell between 2 isomers
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
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
what do you call the increased km of competitive inhibition?
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
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
interferes with cell wall synthsis in bacteria
thiazolidine ring fused to beta-lactam ring. beta lactam ring very unstable and labile
Peptidoglycan consists of linear
polysaccharide chains that are crosslinked
by short peptides
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