quiz #4/5. #4: glycolysis (tuesday, feb 20 th ) #5: tca cycle (monday, mar 5 th ) pathways are in...
TRANSCRIPT
Quiz #4/5
Quiz #4/5• #4: Glycolysis (Tuesday, Feb 20th)
• #5: TCA cycle (Monday, Mar 5th)
• Pathways are in the books
• Quiz will have the entire pathway:–All cofactors will be present–Random intermediate and enzymes removed
• You fill in the missing names
–Draw the structure for 1 intermediate• Indicated by a larger box
Enzyme Regulation
Conditions Affecting Enzyme Activity
pHtemperature
pH
Effects of pH on Enzyme Activity
• Protonation state of side chains
– Variation in protein structure
– Substrate binding
– catalysis
• Ionization of substrate
– Substrate binding
Temperature
RelativeActivity
ba
Temperature
Protein unfolding
Control of Enzyme Availability
Principles of Genetic Regulation
Types of Enzymes“Control of Gene Expression”
• Constitutive Enzymes: e.g. glycolytic enzymes and gluconeogenic enzymes
• Inducible Enzymes: e.g. -galactosidase
• Repressible Enzymes: e.g. ten enzymes of histidine biosynthesis
Negative Regulators[Bind to operators or upstream repression
sequences (URS)]
O
O
–I nducer
I nducible
e.g. lactose operonRegulator
(Repressor)Complex
–Corepressor
Regulator(Aporepressor)
Complex(Repressor)
Repressible
e.g. trp operon
Positive Regulators[Bind to promoters, enhancers or upstream
activation sequences (UAS)]
O
O +I nducer
I nducible
e.g. cAMPRegulator Complex
"Activator"
+Corepressor
Regulator"Activator"
Complex
Repressible
e.g. nit-2
Regulation of Enzyme Catalytic Activity
Covalent ModificationAllosteric Enzymes
Principles Governing Controls of Enzyme Catalytic
Activity
• Regulatory Enzymes
– Enzyme catalyzing committed, rate-limiting step (often first step)
– Thermodynamically highly favorable reaction
• Outcomes of Regulation
– Feedback inhibition (fbi) of biosynthetic pathways
– Modulation of metabolic flux
Reversible Covalent Modification
Page 390
Protein Modification(Phosphorylation/Dephosphorylation)
Non-covalent Modification
Effectors or Ligands
Positive: activatorsNegative: inhibitors
Allosteric Enzymes(Modulation of Enzyme Catalytic
Activity)
• Substrate Binding
• Catalytic Rate
• Both
Allosteric (Regulatory) Enzymes
R (Active)(I nactive)
SubstratesActivators
I nhibitor
T
Homotropic Effects
VO
[S]
posit ive cooperativity
negative cooperativity
M—M (Simple Enzyme)
Heterotropic Effects
positive ef fector
negative ef fector
no ef fectorVo
[S]
Figure 12-16
Glycogen Phosphorylase
Regulation of Biosynthetic Pathways
Rationale for Regulation
CentralMetabolite
Product(e.g. Amino Acid)
Biosynthesis
Catabolism
Macromolecules
Nutrient
Efficiency and Flexibility
Biological Efficiency
• Biosynthesis– Synthesize precursors not available in diet– Cease synthesis when precursors become
available in diet (pre-existing enzymes)– Produce precursors and macromolecules at
appropriate rates
• Catabolism– Degrade most appropriate nutrients at
appropriate rates
Biological Flexibility
• Adaptaton to Dietary Changes– Need for biosynthetic products– Catabolism of new nutrients– Control of pre-existing enzymes
• Metabolic Flux– Rates of metabolism reflecting needs
for energy and macromolecular synthesis
Competing Reactions: Regulation
A
B C
Enzyme 1 Enzyme 2
Control Mechanisms
• Control of Enzyme Availability
– Induction/repression
• Control of Enzyme Activity
– Covalent/Non-covalent
• Control of Substrate Availability
Types of Regulation
• Specific: pathway’s substrate or product
• General: needs for C or N sources or growth rates (e.g. energy charge)
Signals Mediating Regulation
Availability ofSubstrates or Products
(Ligands)
Regulatory Proteins
Biosynthetic Pathways
CentralMetabolite
Product(Amino Acid)
ATP ADP + Pi
Simple Feedback Inhibition
X
ATP
CentralMetabolite
Product(Amino Acid)
ADP + Pi
Complex Feedback Inhibition
CentralMetabolite
Product 1
Product 2
XX
X
Mechanisms of Complex Feedback Inhibition
• Cumulative: sum of individual inhibitions
• Concerted: both end products required for inhibition
• Isoenzyme: two enzymes, each inhibitable by different end product
Cumulative Feedback Inhibition
A
GF
EDCBA
GF
EDCB
A
GF
EDCB
Concerted Feedback Inhibition
A
GF
EDCBA
GF
EDCB
A
GF
EDCB
Isozymes
A
GF
EDCBA
GF
EDCB
A
GF
EDCB
Modulation of Metabolic Flux
Energy Charge
Energy Charge(Daniel Atkinson)
Steady-State E.C. = 0.93
ATP, ADP and AMP = Regulatory Ligands
Energy Charge 12
2ATP + ADP ATP + ADP + AMP
=
Energy Charge
Anabolic pathways
(Biosynthesis)
• Require ATP
• Activated– High EC (ATP)
• Inhibited– Low EC (AMP)
Catabolic Pathways
(Degradation)
• Produce ATP
• Activated– Low EC (AMP)
• Inhibited– Hig EC (ATP)