Flashcards in Chapter 3 protein function Deck (34):
How many molecules can proteins bind to?
proteins are usually very specific in their binding and bind to one molecule
What is the molecule that proteins bind to?
What is binding of a protein to a ligand made possible by?
the weak noncovalent interactions of protein and ligand
What are the weak noncovalent interactions?
van der waals
What type of fit does the proteins have for their ligands?
like a hand to glove
What is the region that associates with the ligand?
ligands binding site
What does the binding site of protein consist of?
a cavity with different arrangements of amino acids
what does the neighboring parts of a polypeptide chain keeps away from the binding site?
water can form hydrogen bonds within the ligand binding site
What can alter the reactivity of of proteins?
clustering of neighboring polar amino acids
how does the clustering of neighboring polar amino acids alter proteins activity?
If folding forces together negatively charged side chains, this increases the affinity for a positive molecule.
When side chains react with each other through hydrogen bonding unreactive side groups become reactive
Why does two different conformations differ in chemistry?
chemical reactivity depends on which amino acids are exposed and orientation relative to one another
What is similar in protein domain families?
3D structure (tertiary and quaternary structures)
What are enzymes?
enzymes are proteins that speed up reactions by breaking and making bonds
name the parts in the steps of protein reaction?
Substrate and enzyme
Enzyme and product
What are characteristics of and Enzyme?
not consumed or destroyed by chemical reaction
may be localized to specific region or compartment
do not change delta G
only present in low concentrations
increase probabilty of a reaction occurring/increase reaction rate
enzye activity can be regulated
What is the activity of a hydrolase?
catalyze hydrolytic cleavage reactions
What is the activity of nucleases?
break down nucleic acids
What is the activity of proteases?
breakdown proteins by cleaving peptide bond
What is the activity of sythases?
Used in anabolic reaction to polymerize two molecules
What is the activity of kinases?
catalyze addition of phosphate group to a molecule
protein kinases add PO4 to a protein
What is the activity of phosphotases?
Catalyze the removal of a phosphate group
What is the activity of ATPases
What is the Michaelis-Menten kinetics equation
V= Vmax *[S]/Km + [S]
What is Km?
Is the substrate concentration when the Velocity is equal to 0.5Vmax
What is velocity equal to when Substrate concentration is less than Km?
What is the rate of the reaction dependent on when the substrate concentration is less than Km?
it is substrate dependent
What is the velocity equal to when substrate concentration s greater than Km?
Velocity = Vmax
What is the rate of reaction dependent on if substrate concentration is greater than Km?
it is enzyme dependent
What is velocity equal to when substrate concentration is equal to Km?
velocity = 0.5Vmax
How are the enzyme activity regulated in the cell?
-effect enzyme concentration
-regulation by covalent modifications
how is enzyme activity regulated with regulatory molecules?
competition for active site
feedback control (positive or negative)
how is enzyme activity regulated by covalent modifications?
How does competitive inhibition changes Vmax and Km?
no change in Vmax