Introduction to Molecular and Cell Biology, Biol. 220
Lecture 4: Protein Structure
| Index | CourseInfo LogIn | Syllabus | References | Other Resources |
| |
Introduction to Molecular and Cell Biology, Biol. 220 Lecture 4: Protein Structure |
||||
|
Enzymes
An enzyme is a catalyst that increases the rate of a reaction by lowering the activation energy and stabilizing transition-state intermediates.
What does that mean?
Demonstration: I need a volunteer.
What types of molecules can serve as enzymes?
Most enzymes are proteins but some are RNA.
How is an enzyme organized?
An enzyme contains an active site, which comprises two functional parts: a substrate-binding region and a catalytic region (Fig. 3.23).
Fig. 3.23 cAMP-dependent
protein kinase (cAPK).
The amino acids that make up the active site do not need to be adjacent in the polypeptide chain, but in fact can be from different regions of the chain that are brought together by protein folding (Fig. 3.24)
Fig. 3.24 Phosphorylation
mechanism of cAMP-dependent protein kinase (cAPK)
What are the environmental conditions necessary for an enzyme to function?
A cellular enzyme must be able to catalyze its reaction in an environment normally encountered in a cell, i.e., in aqueous solution, at pH 6.5 to 7.5, at 37C.
Are all enzyme functions, and therefore life, limited to these conditions?
Extremophiles
Two models for enzyme function
Lock and Key - substrate binding site fixed in shape.
Induced Model - change conformation in response to substrate binding (induced fit model) (Fig. 3.25) but after the product is released, the enzyme is the same as before binding the substrate.
Fig. 3.25 Conformational
changes in the catalytic subunit of cAPK.
What are the rate limiting steps of enzymes?
The rate at which an enzyme operates is dependent on the binding, catalysis and release constants:
binding catalysis
release
E + S <-> ES
<-> EP <-> E + P
If all enzyme sites are saturated with substrate, then an enzyme will function at its maximum velocity (Vmax, Fig. 3.26b).
Question: If you doubled the amount of enzyme that you added to a saturating amount of substrate, what would be the impact on the reaction rate?
Fig. 3.26b Substrate concentration
and affinity dependent reaction rates.
The substrate concentration at which the enzyme is running at half-maximal velocity is called the Km and is a combination of the rate limiting binding, catalysis or release constants (Fig. 3.26b).
The velocity or rate of reaction at any given substrate concentration can be determined by the equation:
velocity = Vmax * [S] / ( [S] + Km ), where [S] is the substrate concentration.
Question: If you were given an enzyme that had a Vmax of 300 units and a Km of 0.2 mM what would the velocity be if the substrate concentration were 0.3 mM?
Regulation of enzyme activity
Unlike inorganic catalyst, the rates of catalyst can be regulated or modulated to have decreased or increasted activity depending on the presense or absense of factors other than substrate in the environment.
Substrate concentration (Fig. 3.26b).
Allosteric release of catalytic subunits (Fig. 3.27a).
Fig. 3.27a Activation of
cAPK by cyclic AMP.
Allosteric transition between active and inactive states (Fig. 3.28).
Fig. 3.28 Allosteric regulation
of aspartate transcarbamoylase (ATCase). Orange catalytic subunits are
held together by green regulatory subunits. Binding of the blue CTP molecules
cause a conformational change in the regulatory subunits to an inactive state.
Cooperative binding of ligands (Fig. 3.29).
Fig. 3.29 Cooperative binding
of substrates (red line) in multisubunit proteins shows a greater response within
a narrow range of substrate concentrations as compared to single subunit proteins
(blue line). Example, Hemoglobin (red) and myoglobin (blue).
Protein phosphorylation and dephosphorylation (Fig. 3.30).
Fig. 3.30 Phosphorylation
and dephosphorylation are common mechanisms for regulating protein activity.
Proteolytic activation (Fig. 3.31).
Fig. 3.31 Activation of
chymotrypsinogen to chymotrypsin by excision of to peptide bonds.
Questions: Which type of regulation would you choose if you were designing an enzyme to:
A. Allosteric release of catalytic subunit
B. Allosteric transition between active and inactive states
C. Cooperative binding of ligands.
D. Cyclic phosphorylation and dephosphorylation.
E. Proteolytic activation
| Created 2004 by CA Rinehart• email CA Rinehart | Index • CourseInfo LogIn • Syllabus • References • Other Resources |