Protein I and II

Question 1

What bond is used to polymerize amino acids? Describe it!

Answer 1

Peptide bonds! Formed between the alpha carboxyl group and the alpha amino group. Loses water in this formation.

Amino acids are build N terminus -> C terminus

Question 2

Name the amino acids that are charged polar

Answer 2

Acidic (negative charge)
Glutamic Acid
Aspartic Acid

Basic (positive charge)
Lysine
Arginine
Histidine

Question 3

Name the amino acids that are Neutral Polar (uncharged)

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Answer 3

Glutamine
Asparagine
Cysteine
Serine
Tyrosine
Threonine

Question 4

Name the nonpolar amino acids (most are very hydrophobic)

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Answer 4

Methionine
Valine
Leucine
Isoleucine
Proline
Tryptophane
Phenylalanine
Alanine
Glycine

Question 5

What are zwitterions?

Answer 5

When free amino acids have a pH of 7. They are dipolar with + and - charges

Question 6

What happens when pH= pKa

Answer 6

Side chain is 50% protonated

Question 7

What does the isoelectric point determine?
pI = pH -> ?
pI > pH = ?
pI

Answer 7

Helps determine the net charge on a certain polypeptide sequence at a particular pH. Proteins precipitate out of solution at their isoelectric point.
pI = pH -> no charge
pI > pH = positive charge
pI

Question 8

Describe Hydrogen bond and important qualities

Answer 8

Hydrogen bonds: occur between side chains. Important because the distance between the donor and acceptor is fixed; all atoms are co-linear; water can form hydrogen bonds with proteins.

Question 9

Salt bridges: Describe and important qualities?

Answer 9

Occur between opposite charged groups..

Few geometric constraints on salt bridges only the distance and not the direction of participants

Question 10

Van der Waals

Answer 10

Weak interactions that occur between any two adjacent atoms that don’t repel. It is energetically favorable for atoms to pack up against each other.

Question 11

Hydrophobic interactions

Answer 11

Hydrogen residues segregate in the interior of the protein to remove them from the aqueous environment. The greater amount of hydrophobic surface area buried upon folding of a protein leads to more energetically favorable process.

Question 12

What features stabilize the alpha helix?

Answer 12

1. R groups point out away from the helix
2. The helix is right handed and has a 3.6 amino residue per turn
3. The backbone is maximally hydrogen bonded

Question 13

What features disrupt the alpha helix?

Answer 13

A stretch of adjacent like charges (electrostatic repulsion)
A proline residue (promotes a bend in the chain because you can’t have free rotation around the peptide bond) and lack a backbone amino-proton to make a hydrogen bond with the preceding carboxy oxygen.

Question 14

What does SDS-PAGE (PolyAcrylamide Gel Electrophoresis) do?

Answer 14

Proteins are separated by mass (the proteins are denatured so that charge is negligent). Small proteins move through the gel more rapidly than the larger ones

Question 15

What is UREA PAGE?

Answer 15

Urea (uncharged) is used to denature the protein. This leaves the charge on it. The total charge on the protein will determine whether it runs on the gel towards the anode or cathode.

Question 16

Protein identification by mass spectrometry

Answer 16

Uses the masses of proteolytic peptides as input to a search of a database of predicted masses that would arise from digestion of a list of known proteins. If a protein sequence in the reference list gives rise to a significant number of predicted masses that match the experimental values, there is some evidence that this protein was present in the original sample.

Question 17

What amino acids are found in proteins?

What amino acids are found in proteins?

Answer 17

Only L-amino acids