Amino acids

Question 1

what are the pka’s of carboxyl group, aspartate, glutamate, histidine, amino group, lysine, arginine

Answer 1

carboxyl: 2
glutamate and aspartate: 4
histidine: 6
amino: 9
Lysine: 10
Arginine: 12

Question 2

Name the 9 nonpolar amino acids and two with special properties.

Answer 2

glycine, alanine, valine, isoleucine, leucine, proline, methionine, tryptophan, phenylalanine.

glycine is achiral and proline is 15% of the time found in cis conformation and is stabilized.

Question 3

Name the 6 uncharged polar amino acids. and their one letter symbols

Answer 3

cysteine, serine, threonine, glutamine, asparagine, tyrosine.

GLUTAMINE IS LONGER THAN ASPARAGINE (glutton)

c, s, t, Q, N, Y

asparagine is N
Arginine the base is R

Question 4

Will you see disulfide bonds in the cytoplasm?

Answer 4

No, because the intracellular environment is reducing and disulfide bonds form under oxidation. So for example, it won’t be present in the active site. It adds stability to the protein but is not the driving force of the folding. Insulin is stabilized by disulfide bonds. Oxidize = remove electrons,

Question 5

What are the two amino acids with acidic side chains? Which is longer? Which is more acidic? What are the letter symbols?

Answer 5

glutamate and aspartate. Glutamate is longer and its pka is larger, wonder why bech.

GlutamatE = E
Aspartate = D 

negative ED

Question 6

what are the three basic amino acids and their one letter symbols. What is histidine special for?

Answer 6

Korean human resources

K = lysine
H=histidine
R=arginine.

If histidine is present then it is doing something important. It is great for pH sensing because it has a pKa close to physiological pH. We would say it is neutral and useful in a narrow range.

Question 7

How to determine buffer region?

Answer 7

+1 or minus 1 the pKa.

Question 8

phi and psi

Answer 8

There are only two sets of phi, psi angles that can be repeated without steric collisions. If you repeat one set over and over, you would get a coil. If you alternate sets you would get a beta. So these angles determine secondary structures.

Question 9

Describe the alpha helix stats

Answer 9

Right handed, 3.6 residues per turn,

5. 4 angstroms per turn
6. 5 angstroms per rise (per residue)

every turn is 360 degrees. Every turn has 3.6 residues. So at every 100 degrees there is a side chain sticking out.

Question 10

For an antiparallel beta sheet, how many angstroms per residue?

Answer 10

3.5 angstroms per residue, almost double the distance covered by the alpha helix residue

Question 11

Parallel vs antiparallel beta sheet

Answer 11

Parallel beta sheets are looped by an alpha helix. These sheets are usually buried in the protein interior, therefore, they are hydrophobic.

Antiparallel beta sheets and amphipathic, and exposed on the surface. They usually have a polar and non polar face. And they don’t need a linking motif.

All beta sheets make hydrogen bonds with their neighboring beta strands via backbone C=O and N-H

Question 12

Name the four motifs.

Answer 12

helix-loop helix (alpha chains) - can have packing perpendicular or parallel to itself.

beta -hairpin: beta chains

greek key: beta hair pins that folds back over.

Those two are antiparallel.

beta alpha beta motif - parallel beta sheet, covered by alpha chains.

Question 13

Which amino acids tend to be phosphorylated? Which amino acid functions as a nitrogen donor?

Answer 13

Serine, threonine, tyrosine. In metabolism, glutamic acid functions as a nitrogen donor in metabolism.

Question 14

Describe primary, secondary, tertiary and quartenary structures

Answer 14

Primary- the sequence which is defined by covalent bonds. Includes disulfide bonds.

Secondary - local arrangements of the peptide bond, defined by hydrogen bonds

Tertiary - arrangement of secondary structures into domains

Quartenary - multisubunit protein

Question 15

What is an up-down beta barrel

Transmembrane up down beta barrel

Greek key barrel

alpha beta singly wound barrel

doubly wound alpha beta.

Answer 15

The helix loop helix motif is found in alpha helix bundles (can be perpendicular)

It is an antiparallel beta sheet wrapping to form a barrel, protecting its nonpolar side.

The opposite. This beta barrel wants the polar on the inside because the membrane interior is a hydrophobic environment. (beta hairpin)

The more strands for each barrel, the larger the pore.

Greek key barrel: the greek key motif is unable to form the barrel structure. It forms more a sandwich around the molecule. Like the doubly wound barrel.

Alpha/beta singly wound barrel: small parallel beta sheet barrel, surrounded by amphipathic alpha helices. Helices are only on one side of the beta sheet.

alpha/beta doubly wound: shown like a sandwich. you have barrels on both sides of the beta sheet. The sheet just remains flat instead of curling around.

Question 16

what are characteristics of cis proline?

Answer 16

The peptide bond is planar, it is in L configuration, not common to secondary structures,

it is common in turns and therefore is often located on surfaces rather than interior of proteins.

Turns - non repetitive secondary structures, 4 residue beta bend is stabilized by a hydrogen bond. Now the functional property of a protein is due to the turns and loops. Cis proline always creates a turn in the backbone and so is found on surfaces of proteins.

Question 17

How many residues in an alpha helix that spans a lipid bilayer of 33 A?

Answer 17

1.5A per residue so 33/1.5 = 22 residues.

Can be polar residues but never charged.

Question 18

What would happen from an insertion of one additional amino acid into the strand of an anti-parallel beta sheet?

Answer 18

Insertion of any amino acids will disrupt the polar non polar alternation that creates the hydrophilic and hydrophobic faces.

Question 19

Where are hydrogen bonds formed in the alpha helix?

How about beta strands

Answer 19

Between the C=O and N-H of every residue n and n+4.

In beta strands its the C=O and H-N between strands and perpendicular to the side chains.