Week 1 Flashcards
The function of _____ is to store high energy phosphate bonds in creatine for fast conversion to ATP, when there is a high demand for ATP.
Creatine kinase
This enzyme catalyzes the addition of water to CO2. It is an example of a metalloenzyme because it utilizes a zinc ion as part of its catalytic mechanism.
Carbonic anhydrase
describes the catalytic power of the enzyme. It is defined as the maximal number of substrate molecules converted to product by one enzyme molecule per second.
Turnover number
The general mechanisms of Catalysis are typically put in to 4 categories:
- Specific substrate interactions
- Binding the transition state optimally
- Providing covalent chemistry
- Providing acid/base chemistry
that is, only the substrate binds effectively. Other compounds do not bind as well, even if similar in structure.
Specific substrate interactions
If the enzyme binds the transition state well, even better than substrate, what will happen is that substrate will bind, and then deform a little, because of the binding interactions. This deformation will bend the substrate into something that looks more like the transition state. This effectively lowers the barrier to achieve the transition state and is caused by the binding interactions with the enzyme.
Binding the transition state optimally
Specificity is achieved not only by specific binding but also through subsequent changes in protein structure.
induced fit hypothesis.
has a small side chain that allows large hydrophobic residues to bind.
For aromatic or hydrophobic residues: Trp, Tyr, Phe, Leu
Chymotrypsin
has hydrophobic side chains that interact with small hydrophobic side
chainsinthe substrate.
-small hydrophobic residues: Gly, Val, Ala
Elastase
has a (-) charged aa side chain that forms an ionic bond with a (+) charged aa in the substrate.
For lys and Arg (cationic)
Trypsin
Facilitate redox chemistry.
Often involve NAD or FAD
NAD requiring enzymes are called dehydrogenases (if you see this name, you know its an NAD requiring oxido-reductase).
Oxido-reductases
move a group from one molecule to another.
A common example is kinases: They transfer a phosphate group from one molecule (ATP typically), to another. Example is protein kinase A, which will catalyze the transfer of phosphate from ATP, to regulated proteins.
Transfer ashes
These use water addition to break a chemical bond.
Proteins in this class include those that break peptide and ester bonds. For example, proteases, esterases, lipases.
Typically one molecule is cleaved into two new products.
Also included are nucleases, phosphodiesterases, helicases, DNA glycosylases. There are many others.
Hydrolases
Catalyze cleavage of C-C bonds, C-O bonds, C-N bonds, C-S bonds, and C-halide bonds. Also P-O bonds.
Decarboxylases are one example. Dehydratases are another (remove water; breaks C-O bond).
Pyruvate decarboxylase is part of the pyruvate dehydrogenase complex or acts alone to convert pyruvate to acetaldehyde and further conversion to ethanol during fermentation in yeast or bacteria.
Lyases
General examples:
- dehydratases
- decarboxylases
Lyases
Example:
Protease
Hydrolases
example: phosphoglucomutase
Isomerases
As the name implies, isomerases catalyze isomerization reactions, often among stereoisomers to racemize them.
Isomerases
Catalyze the formation of bonds: C-O, C-S, C-N, C-C and others.
Ligases
Example:
glutamine synthetase
Ligase
Used as an acyl carrier and is involved in many catabolic and anabolic reactions.
Coenzyme A
Examples of the two most common redox carriers:
NAD and FAD
help facilitate reactions where unique reactivity is required, or reactivity not readily supplied by the canonical set of 20 amino acids.
(Ex. Coenzyme A)
Cofactors
Vmax is unchanged
Km is increased
Overall: this is a slope effect. You can see that in the equation – only the slope is affected, not the y-intercept.
Competitive inhibitors
reflects the amount of enzyme present
vmax
reflects a concentration range that is relevant for the enzyme. It can be greater, close to (most typical) or higher than a typical substrate concentration. This depends on the purpose.
km
Vmax decreases
km is unchanged
non-competitive inhibition
Both Vmax and km decreased
uncompetitive inhibition
