MCBM 1- (3) Amino Acids, Peptides, and
Protein Structures Questions and
Answers
Discuss nonpolar amino acids. Which ones are in this group? What is special about
Methionine? What goes on in regards to proton gain/loss? What role do these play in protein
folding? Where do you find these amino acids in folded proteins? - ANSWER - Met has sulfur
and is the first one to be encoded.
These amino acids do not gain or lose protons; NONREACTIVE.
Since they are nonpolar, they are hydrophobic. The hydrophobic effect that they take part in
makes them interact with each other away from water, and thus they gather inside a folded
protein.
These amino acids do not have any hydrogen or ionic bonding!
Discuss the hydrophobic effect further. Discuss this in regards to energy, stability, and protein
shape considerations. - ANSWER - 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!
What are domains? - ANSWER - Domains are the functional and 3 dimensional structural units
of protein, built from combinations of motifs.
, Discuss tertiary folding. What is the goal of this folding? What is the result after tertiary folding? -
ANSWER - Loose domain formations --> high density protein formation
Discuss the location of nonpolar and polar amino acids in soluble and membrane proteins. -
ANSWER - 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.
Discuss amino acids with uncharged polar side chains. What bonds do they form? What is
special about cysteine? - ANSWER - Mostly can form hydrogen bonds. The disulfide bond that
Cysteine can form (because of thiol -SH) is VERY STRONG.
Discuss the acidic side chains, specifically their pK values. - ANSWER - Aspartic acid and
glutamic acid have very low pKs. This means they are fully ionized at physiological pH.
Hydrogen is disassociated from the side chain and therefore is negatively charged and can
have ionic interactions with any positively charged molecule.
Discuss the basic side chains. - ANSWER - Lysine and Arginine have very high pK values. At
pH of 7, they are fully ionized by accepting a proton. They can form ionic bonds with negatively
charged molecules.
Histidine is partially ionized. Weak base and conjugate acid form a buffer.
Discuss the catalytic triad. What are the components? What is important about each one? -
ANSWER - 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.
Protein Structures Questions and
Answers
Discuss nonpolar amino acids. Which ones are in this group? What is special about
Methionine? What goes on in regards to proton gain/loss? What role do these play in protein
folding? Where do you find these amino acids in folded proteins? - ANSWER - Met has sulfur
and is the first one to be encoded.
These amino acids do not gain or lose protons; NONREACTIVE.
Since they are nonpolar, they are hydrophobic. The hydrophobic effect that they take part in
makes them interact with each other away from water, and thus they gather inside a folded
protein.
These amino acids do not have any hydrogen or ionic bonding!
Discuss the hydrophobic effect further. Discuss this in regards to energy, stability, and protein
shape considerations. - ANSWER - 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!
What are domains? - ANSWER - Domains are the functional and 3 dimensional structural units
of protein, built from combinations of motifs.
, Discuss tertiary folding. What is the goal of this folding? What is the result after tertiary folding? -
ANSWER - Loose domain formations --> high density protein formation
Discuss the location of nonpolar and polar amino acids in soluble and membrane proteins. -
ANSWER - 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.
Discuss amino acids with uncharged polar side chains. What bonds do they form? What is
special about cysteine? - ANSWER - Mostly can form hydrogen bonds. The disulfide bond that
Cysteine can form (because of thiol -SH) is VERY STRONG.
Discuss the acidic side chains, specifically their pK values. - ANSWER - Aspartic acid and
glutamic acid have very low pKs. This means they are fully ionized at physiological pH.
Hydrogen is disassociated from the side chain and therefore is negatively charged and can
have ionic interactions with any positively charged molecule.
Discuss the basic side chains. - ANSWER - Lysine and Arginine have very high pK values. At
pH of 7, they are fully ionized by accepting a proton. They can form ionic bonds with negatively
charged molecules.
Histidine is partially ionized. Weak base and conjugate acid form a buffer.
Discuss the catalytic triad. What are the components? What is important about each one? -
ANSWER - 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.
