Lecture 10: Substrate binding Flashcards
Oxidoreductases and carriers
Move electrons in redox reactions
NADH, NADPH, FADH2, FMNH2
Transferases ATP and pyridoxal phosphate
Transfer phosphate functional groups
Transferases SAM, THF, 5’-DAC
Transfer methyl groups
Hydrolases
Break a chemical bond by added water across it (hydrolysis)
Isomerases
Rearrange order of atoms in a molecule (isomerization)
Lyases
Break a chemical bond without using water
Ligases
Paste two pieces together using ATP
TPP
+/- aldehyde group
CoASH, lipoamide
+/- Acyl group
Biotin
+/- CO2 group
Carbonyl condensation
Change number of carbons
Elimination
Increase bond order
Active site structure
Only consists of a few residues out of the protein
3-D pocket creating unique microenvironment
How does active site determine specificity and what type of interactions occur
Specificity determined by size and charge
Contacts substrate through non-covalent interactions
Allosteric binding
Does NOT occur at the active site, but follows same rules
Involves second substrate that can be inhibitor or activator
Apoenzymes
Incomplete
Inactive
Lack cofactor/coenzyme
Holoenzymes
Whole
Active
Contain cofactor/coenzyme
Require allosteric activation
Kd
Dissociation constant for E x Sn complexes
Equal to the concentration of ligand where 1/2 the available binding sites are full
When the receptor is half-saturated
Hill equation (n=1)
Y= [S] / Kd + [S]
When Y= 0.5, what does [S] equal
Kd
When n=1 what are the values of the slope, y-intercept and x-intercept
Slope= -1/Kd y-intercept= 1/Kd x-intercept= [E]t
Cooperativity
Binding of each subsequent ligand influences the affinity of the next ligand to bind active site
Hill equation (n>1, perfectly cooperative)
0(with dash through middle) =
[S]^n / (Kd + [S]^n)
n= number of binding sates
Slope and y-intercept values for Hill plot when n>1
Slope= n(h) y-intercept= log(1 / Kd)
Interpretations of hill equation
n(h)=1
n(h)>1
0 < n(h) < 1
nh=1 means no cooperativity (sites are independent)
nh>1 means positive cooperativity (affinity increases)
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