Exam (elaborations)
MCBM 1- (3) Amino Acids, Peptides, and Protein Structures Questions with 100% Correct Answers
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MCBM 1- (3) Amino Acids, Peptides, and Protein Structures Questions with 100% Correct Answers
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1 of 21Term
Discuss peptide bonds. What specifically is reacting with what? What
is the reaction called? What is a byproduct? What are the ends
called?
Give this one a try later!
Loose domain formations --> high density protein formation
Two or more domains included.
, After this process, proteins have acquired final structure and FULL
function. An example of this would be a catalytic domain being able to
function if a substrate binding domain is near it.
They stabilized by hydrogen bonds between peptide strands.
Intrachain=same peptide chain
Interchain=different peptide chains
Parallel strands have N and C termini on the same side, anti parallel
have them on different sides.
Formed by an alpha carboxyl and alpha amino group via
condensation reaction. Water is a byproduct to form a peptide
bond. End is called N or C terminal dependent on whether it is a
carboxyl or amino group.
1) Energetically favorable to avoid contact with water and the
hydrophobic groups.
2) The resulting hydrophobic interactions stabilize the structure, but
not by much.
3) Initial shape formation.
HYDROPHOBIC EFFECT IS THE MOST IMPORTANT FACTOR IN
INITIAL PROTEIN FOLDING!
Don't know?
2 of 21
Term
, Discuss the location of nonpolar and polar amino acids in soluble
and membrane proteins.
Give this one a try later!
Acidic and basic side chains found in the active site of an enzyme.
Triad typically has an acidic, basic, and nucleophilic component.
Acidic side chain has a negative charge, and is responsible for aligning
and polarizing the basic molecule.
The polarization of the basic amino acid helps de-protonate the
nucleophilic amino acid and makes it very reactive.
In a linear soluble protein, nonpolar amino acids aggregate in
the interior of, polar amino acids aggregate on the surface.
In a membrane protein, nonpolar amino acids aggregate on the
surface (in contact with the hydrophobic tails of the bilayer).
Polar amino acids are in contact with the cellular and extra
cellular matrix.
1) Energetically favorable to avoid contact with water and the
hydrophobic groups.
2) The resulting hydrophobic interactions stabilize the structure, but
not by much.
3) Initial shape formation.
HYDROPHOBIC EFFECT IS THE MOST IMPORTANT FACTOR IN
INITIAL PROTEIN FOLDING!
Binding site either forms hydrogen or ionic bonds with the substrate.
The binding site needs to be complementary to the substrate. This is
the very basis of binding specificity.
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