Exam 2 Flashcards
Many diseases are caused by an excess of _____ or deficiency of a ______
product, substrate
Active site
region where catalysis occurs
Substrate
Reactant of the enzyme
Product
Molecules produced as the result of a reaction
Enzymes work best in what conditions
temps below 100 C and a neutral pH
How much faster is a catalyzed reaction than an uncatalyzed one
10^6-10^14 times faster
Why are side products rare in enzyme reactions
because enzymes are usually highly specific in terms of reaction selectivity
How are enzymes regulated (3 ways)
- covalent modification
- levels of enzyme synthesized
- allosteric regulation
Oxidoreductases
used in redox reactions
Transferases
used when functional groups are being transferred
Hydrolases
water cleaving bonds
Lyases
forms a double bond
Isomerases
intermolecular rearrangement
Ligases
creating a bond with ATP
How do enzymes work
by lowering the energy of activation
Rate enhancement
e^(ΔΔG‡/RT)
When ΔG‡ is larger, the reaction is
slower
At 298K, decreasing ΔG‡ by 5.7 kJ/mol, the speed of reaction increases
10 fold
Catalytical enzyme mechanisms (5 types)
- acid-base
- covalent
- metal ion
- proximity and orientation effects
- preferential binding of the transition state
Example of acid-base catalysis
RNAase A
Covalent catalysis
transient formation of an enzyme-substrate covalent bond
Covalent catalysis usually involves a reaction between ______ on the catalyst and the _____ group on the substrate
nucleophilic, electrophilic
What are the 4 amino acids that are typically used as substrates in covalent catalysis
ser, cys, his, lys
Metal ion participation in metal ion catalysis (3)
- binding to substrates to orient them properly
- Mediating redox reactions
- Electrostatic stabilization and shielding negative charges
What metal ion catalyzes carbonic anhydrase formation
zinc
What is the purpose of metal ion catalysis
to create a stronger nucleophile
Net reaction of glycolysis
- 1 molecule of glucose consumed
-2 molecules of ADP are converted to ATP
-2 molecules of NAD+ are reduced to NADH
Step 1 glycolysis
Hexokinase
Requires Mg2+
Generates G6P
G6P activates _____ and then _____
glucose, traps it in the cell
Step 3 glycolysis
Phosphofructokinase (PFK)
F6P-> 1,6 FBP
Hexokinase is a
transferase
Step 3 of glycolysis is
irreversible, critical regulatory point/committed step
PFK2 generates _____ which is a regulator for ______ and _____
2,6 FBP, gluconeogenesis, glycolysis
Irreversible steps of glycolysis
1, 3, 10
What steps in glycolysis use ATP
1 and 3
Step 4 of glycolysis
Aldolase
1,6 FBP -> 2 triose compounds
operates via aldol cleavage
Step 6 of glycolysis
GAPDH
NAD+ reduced to NADH
GAP -> 1,3-BPG
Step 6 of glycolysis is the only ________ step
oxidation
Step 7 glycolysis
Phosphoglycerate kinase (PGK)
1,3-BPG + ADP -> 3-PG + ATP
Steps 7 and 10 of glycolysis are examples of
substrate level phosphorylation
Step 10 of glycolysis
Pyruvate Kinase
Phosphoenol pyruvate (PEP)-> pyruvate
Catalytic triad
ASP - HIS- SER
High energy phosphates (4)
- acetyl phosphate
-1,3-BPG
-Phosphocreatine
-Phosphoarginine
Low energy phosphates (2)
- alpha-D-glucose-6-phosphate
- 1-glycerol-3-phosphate
Preferential binding of the transition state
this is the concept that the enzyme will bind tighter to the transition state so the complex is forced to complete the original reaction instead of reacting with a different compound
_____ bonds link the anomeric carbon to other compounds
Glycosidic
Why can humans not digest cellulose
We cannot digest the 1,4-beta linkages found in cellulose
True/False: A low Kcat/Km ratio is favorable because it indicates a higher enzyme efficiency
False. A high Kcat/Km ratio indicates a higher enzyme efficiency
____ Kcat is favorable, ______ Km is favorable
high, low
Competitive inhibitors bind to
enzyme only
Competitive inhibition increases _____ and does not affect ____
Km, Vmax
Catalytic mechanism by serine proteases
- preferential binding of transition state
- Covalent catalysis (Ser195 binds substrate)
- Proximity/orientation effects (Ser195 positioned for nucleophilic attack)
- Acid/base catalysis (His57 acts as both an acid and a base, Asp102 acts somewhat as a base)
Summary of lysozyme mechanism
- Binds hexasaccharide unit, distorts D residue
- Glu35 transfers proton to O1 bridging D and E rings
- Asp52 nucleophilically attacks C1 of D ring to form glycosyl-enzyme intermediate
- Water replaces E ring product in active site and Glu35 hydrolyzes covalent bond
Km=[S] when
V0=1/2Vmax
Enzymes with small Km achieve maximal efficiency at ____ substrate concentrations
low
Trypsin specificity pocket
Deep. Trypsin binds lysine and arginine
Chymotrypsin specificity pocket
binds aromatic compounds. specificity pocket is large
Elastase specificity pocket
Small uncharged residues
What is alpha in liveweaver-burke plots
a factor by which substrate concentration must be increased in order to overcome the effects of the inhibitor
Uncompetitive inhibitors bind
ES
T/F: Uncompetitive inhibition cannot be overcome by addition of S
true
Uncompetitive inhibition _____ Vmax and Km
decreases
Lines on uncompetitive lineweaver-burke are
parallel
Noncompetitive inhibitors bind
E and ES
Pure noncompetitive inhibition
Vmax decreases
Km stays the same
Mixed noncompetitive
If K1 is larger -> inhibitor favors binding enzyme, mimics competitive inhibition
If K1’ is larger -> inhibitor favors binding ES which mimics uncompetitive inhibition
Lines on Linewever-burke do not intersect on an axis
Vmax decreases
Inactivation of serine proteases
-irreversible
-DIPF inactivates
-Lovers Vmax but doesn’t affect Km
Enzymes that catalyze reactions near equlibrium (delta G near 0)
not good sites to control pathway flux
rate is almost entirely controlled by substrate/product concentrations
Enzymes that catalyze far from equilibrium (delta G«0)
-act as chokepoints that can be used to control entire pathway
