Proteins

Question 1

linear polymer formed by linking amino acid residues with peptide bonds
(polypeptide chains)

N to C terminus

Answer 1

Primary (1º) Structure

N to C terminus

Question 2

Peptide bonds link amino acids to form polypeptides by:

Answer 2

the alpha-carboxyl (COO) group of one amino acid to the alpha-amino group of another (NH3+)

Question 3

peptide bond characters:

Answer 3

• have double bond character at C-N
• are planar
• uncharged
• are usually trans

Question 4

amino acid residues are what weight:

Answer 4

110 g/mol

Question 5

a polypeptide with 50 amino acids weights what?

Answer 5

5500 g/mol

1 AA weights 110 g/mol

Question 6

Where can disulfide bonds occur?

Answer 6

between the thiols of cysteines (SH + SH) = S-S and 2H+ in a REDOX rxn

vertical bonds, not horizontal like peptide bonds

Question 7

whats an alpha helix?

Answer 7

a coiled rod-like structure with a tightly coiled backbone; stabilized by intrachain hydrogen bonds (R groups on outside)

Secondary structure

basically a coiled ribbon

Question 8

Where are the H bonds in an alpha helix?

Answer 8

CO group bonds with the NH group of the amino acid situated 4 residues ahead. all but N and C term. ones bonded

“hotdog fold”

Question 9

Whats the rise and rotation of each residue

Answer 9

Rise = 1.5 A
Rotation = 100º (3.6 AA’s per turn)

Question 10

What is a beta sheet made of?

Answer 10

2+ polypeptide chains called beta strands (side by side, linked through H bonds)

Question 11

Fully extended, beta strands have ____ A between AA’s?

Answer 11

3.5A between amino acids (alpha is 1.5A b/w adjacent AA’s)

Question 12

The side chains of adjacent amino acids point in ____ direction?

Answer 12

opposite

Question 13

Describe antiparallel vs parallel

Answer 13

anti = R chains point in opposite directions (N and C terminus line up)
parallel = side chains point in same directions (N and C terminus’s are opposite sides)

Question 14

can beta sheets be mixed between antiparrallel and parallel?

Answer 14

beta sheets can be parallel, antiparallel, or mixed.
- Usually 5-10+ B strands per sheet
- not flat, but usually twisted

Question 15

Whats a “motif” / supersecondary structure

Answer 15

specific combinations of secondary structure present in many proteins exhibiting similar functions

EX helix-turn-helix and beta-hairpin

Question 16

Whats a domain in tertiary protein?

Answer 16

a compact globular region of a protein (30-400 AA)

Question 17

stability in 3º structure through:

Answer 17

hydrophobic, hydrophillic and other residues (hydrophobic inside b/c no more H bond donors left)

Question 18

what is quartenary 4º structure?

Answer 18

In proteins containing more than one polypeptide chain, the spatial arrangements of those chains (subunits) and the nature of contacts among them.

Question 19

Interactions in 4º structire

Answer 19

VDW (side chains)
H bonds (C to N a-helix or b-sheet)
dipole dipole

Question 20

whats a subunit in 4º structure?

Answer 20

Any of the polypeptide chains in a protein that contains more than one such chain.

Question 21

Homo vs hetero-oligomer

Answer 21

homo = 2+ identical subunits
hetero = 2+ different subunits

Question 22

Dimer, Trimer, Teramer refers to:

Answer 22

number of subunits (polypeptides) in a protein

Question 23

What is denaturation?

Answer 23

When a protein is converted into a randomly coiled peptide without its normal activity (unfolded)

Cleavage of disulfide bonds b/w cystines, for example, into cysteines

Question 24

Sequence specifies conformation: native confirmation is most thermodynamically stable

Answer 24

the information needed to specify the catalytically active three-dimensional structure of ribonuclease is contained in its amino acid sequence.

Question 25

Ammonium sulfate precipitation sorts proteins by:

Answer 25

salting out; sort based on solubility in water

Question 26

How does affinity chromotography work?

Answer 26

protein has high afinity for specific molecule or group; binds said molecule to purify (reversible)

Question 27

gel filtration/ SDS-PAGE sorts by

Answer 27

mass; SDS denatures and gives proteins uniform charge/ unit mass [so sorts ONLY by mass]

Question 28

Specific activity = ?

Answer 28

total activity/ total protein (g)