Biochem Exam #2 Study Guide Flashcards
Enzymes
proteins that catalyze specific reactions
Each Enzyme is
unique
catalyze specific reactions
speed up reactions
What attracts an enzyme to a substrate?
intermolecular forces
Active Site
catalytic center where the substrate fits into the enzyme
What happens when the enzyme undergoes a conformational change?
- creates tighter induced fit
- bring chemical groups in position to catalyze the reaction
When S binds to E
- there is a conformational change
- transition state is stabilized
- create environment for rxn
cofactor
any organic or inorganic molecule that aids in catalysis
What are the 2 types of cofactors? Protein or Non-protein?Organic or inorganic?
coenzyme & prosthetic group
nonprotein
organic
How do the 2 cofactors bind?
coenzyme: binds with IMFs
prosthetic group: bind with covalent bond
Holoenzyme vs. Apoenzyme
holoenzyme: has cofactor
apoenzyme: does not have cofactor
Oxidoreductase (dehyrogenase)
cataylze redox reactions
Transferases
transfer functional group
G+ATP->G6P+ ADP
Hydrolase
use H20 to break covalent bonds
Lyase
adds or removes covalent bond without H2O
Isomerase
creates an isomer (molecule with same EF but arranged differently)
Ligase
make covalent bond and use energy (ATP)
What does enzyme kinetics give us? (5)
info on: purity of enzyme catalytic efficiency specificity inhibition
Lock & Key Theory
Enzyme binds S like a lock fits a key
Induced Fit
S binds to E, but “fit” to accommodate transition state
The conformational change during cataylsis allows for what?
Stabilization of the transition state
How does an enzyme speed up a reaction?
by lowering its activation energy
What are the 2 things we need to know about the enzyme?
- how good the substrate binds (km)
2. Production of product
k1 is; k-1
the association of S to E; disassociation of S from E
Rate=____: which is?
Velocity: the quantity of S that disappears and quantity of P that appear in a specific time
1st order rate
exponential
rate depends on substrate concentration
Zero order rate
horizontal line
rate does not depend on substrate concentration; there is no difference
ka
rate constant
indicator of strength of acid
2nd order rate
sigmodial
rate depends on concentration of both substrate 1 and 2
Steady State Assumption was created by?
Briggs Haldene
Steady State
As the [S] decrease the [P] increases, but the ES complex is still the same
Vmax
theoretical max rate of an enzyme that is never reached
Km
“affinity”
concentration of S at 1/2 Vmax
Small Km=
High Km=
small=tight fit (better affinity)
high=weak fit
Kcat;equation
“turnover number”
-number of S molecules converted to P
the bigger the number the more product made
-Kcat=Vmax/[Et]
Kcat/Km
catalytic efficiency
Types of Inhibition
Competitive
Noncompetitive
Uncompetitive
Competitive Inhibition: reversible?
-inhibitor binds the to the same place that the substrate binds
reversible
-can be overcome by adding more substrate
Affects of competitive inhibitor
Lowers the Km, but Km will appear to increase
Noncompetitive Inhibition:reversible?
- inhibitor binds to a spot on the enzyme other than the active site
- can not be overcome by adding more substrate
Affects of noncompetitive inhibitor
Vmax is decreased; Km is unchanged
Uncompetitive Inhibitor
inhibitor binds to ES only
prevents S from detaching or become P
Affects of uncompetitive inhibitor
Km & Vmax are decreased
Cleland Notations
for enzymes with 2 substrates
What are the 2 types of notations for cleland diagrams
sequential & double displacement
Ordered Sequential
S1:S2:P1:P2
order matters
Double Displacement
S1:P1:S2:P2
catalytic residue (2)
- amino acid side chains in active site that are involved in the mechanism
- alter pka
- stabilize transitional state
Acidic Residue
want charge: pka decrease (-)
not want charge: pka increases (+)
Basic Residue
want charge: pka increase (+)
not want charge: pka decreases (-)
Nu
nucleus loving
has extra electrons
reacts with + or partial +
E+
electron loving
has lack of electrons
react with - or partial -
proteases
enzyme the cut peptide bonds
Acid Catalysis
uses a strong E+
a molecule other than water acts as an acid
positive charge pulls on oxygen
Base Catalysis
uses a strong Nu
a molecule other than water acts as a base
negative charge pulls on hydrogen
Acid/Base Catalysis
uses both strong E+ and Nu
Carboxypeptidase A
CPA
metalloprotease
cuts off C-terminal residue
uses Zn+2 for catalytic activity
MetalloPR
uses a metal for catalytic mechanism
metal acts as E+
Mechanism of CPA (6)
- Substrate binds to active site
- Zn attacks the double bonded oxygen
- Glu takes H+ from water
- Attack N-term leaves
- Tetrahedral intermediate forms
- Enzyme resets
CPA: substrate binds active site
Arg attacks the C term
CPA:Zn attacks double bonded oxygen
makes carbon better E+(acts as an acid)
CPA:Glu take H+ from water
water acts as a base
CPA:Tetrahedral intermediate form
Transition state stabilized by Tyr
Tyr acts as an acid
CPA: Enzyme reset
Tyr accepts H from Glu
Chymotrypsin
Serine PR
has a catalytic triad
cuts after WMFYL
What amino acids are in the catalytic triad?
aspartic acid
histidine
serine
Mechanism of Chymo (9)
- substrate binds active site and activates catalytic triad
- Asp takes H+ from His, then His takes from Ser
- Nu attack bu Ser
- Tetrahedral intermediate formed
- Reform pi bond
- 2nd Nu attack
- Shiff N of His gives es to water
- Attack on tetrahedral intermediate
- N term released
Cutting locations of chymo
WMFYL
Cutting locations of trypsin
K and R
Cutting locations of elastase
A and G
Feed forward activation
ATP binds Enz to make go
Feedback inhibition
E binds Enz to make slow
Enzyme catalyze with step in the pathway
rate limiting step-committing step
T State
Active site is blocked; little S bind
R State
Active site open; S bind readily
What types of domains do enzymes have?
active site domain
regulatory domain
Effector binds the _____ domain
w/ + effector=
w/ - effector=
regulatory domain
activator (more in R)
inhibitor (more in T)
Isozymes
2 enzymes
Zymogen
inactive precusor
ex.chymotrypsiongen
post translational modifications
“after protein made change”
Kinase
- enzyme that catalyze the transfer of a phosphate from ATP to an aa side chain in an enzyme
- reversed by phosphatases
