Chemistry 160 Protein Structure Homework Key
1. Give three roles of proteins in an organism.
nutrition, structure, motility, enzymes, regulatory, defense, recognition....
2. What are prosthetic groups?
non amino acid parts of a protein (heme in hemoglobin, for example)
3. What are glycoproteins and lipoproteins?
glycoproteins are proteins with sugar moieties. lipoproteins have lipids attached.
4. Describe the 4 levels of protein structure.
primary: amino acid sequence
secondary: simple folding...α helix, β sheet
supersecondary: structural motifs of secondary structures
tertiary: folded 3-D structure
quarternary: subunit interactions
5. Describe 3 types of interactions that stabilize protein structure.
disulfide linkages, electrostatic interactions...between oppositely charged side chains
H- bonding, metal chelation...+ metal ion sticking to - amino acids, nonpolar
forces
6. What drives protein folding?
increase of entropy of surroundings when water of hydration is displaced from nonpolar
amino acids when they are brought together.
7. Give two ways amino acid sequences are determined.
1. from the DNA sequence.
2. from purification and enzymatic cleavage followed by sequential Edman degradation
8. A small protein was cleaved in two separate experiments by chymotrypsin and by
trypsin. The chymotrypsin fragments were:
MAVKTMPW, ATF, AMERTPC, GMRTSSY
the trypsin fragments were:
ATFGMR, TPC, TSSYMAVK, TMPWAMER
What is the sequence of the protein?
ATFGMRTSSYMAVKTMPWAMERTPC
9. Describe an α helix. Be sure to describe what stabilizes it and where the R groups are.
right handed helix 3.6 aa/turn. intrachain backbone H-bonding between amino hydrogen
and carbonyl oxygen 4 aa away. meaning carbonyl O from aa-1 bonded to amino
nitrogen from aa #5.. side chains perpendicular to helix
10. Why does proline not fit into an α helix.
no free rotation between α c and amino nitrogen within the aa due to ring structure.
11. Why do we not see amino acids of the same charge 4 residues apart in a helix.
side chains very close together so in helix so there is repulsion
12. Describe a β sheet. Be sure to describe what stabilizes it and where the R groups are.
parallel or antiparallel chains forming a pleated sheet. intrachain H-bonding between
amino H and carbonyl O on adjacent chains. R-groups perpendicular to sheet with Rgroups pointed away from pleats
13. What is tertiary structure? How is it determined?
3-D structure. determined by x-ray crystallography and NMR
14. What is supersecondary structure? Give some examples.
supersecondary structure is a structural pattern. usually a pattern of secondary structures.
examples βαβ, β barrels, saddles etc.
15. Show with structures, how a pH change can disrupt protein structure.
+ amino acid sticks to - amino acid....like a lysine sticking to an aspartate (see below)
R
O
N
O
R
H3N+
O
R
O
N
R
If the pH, for example, drops, the aspartate will be protonated and then there will be no
negative charge to stick to the lysine (see below)
R
O
R
N
OH
H3N+
O
R
O
R
N
16. Discuss how proteins are purified.
Depends on the protein, but usually start with some crude source and then a
centrifugation step to remove debris. After that, a couple of chromatography steps to
purify.
17. What is specific activity? Briefly describe how it is determined.
Activity/mg protein. Determined by two assays. 1st is an assay for activity. Depends on
the protein, for an enzyme, it would be rate of reaction. 2nd is total protein.
18. Discuss what antibodies are and their use in affinity chromatography and ELISA.
antibodies are proteins that are produced by B-cells in the immune system. They bind
specifically to certain structures. They can be used to isolate a protein in affinity
chromatography as they will fish the protein out of a solution. (proteins run over a
column made of antibodies against that protein will stick to the column. The column can
be eluted by changing the pH>
In an ELISA, (Enzyme Linked ImmunoSorbent Assay) antibodies against the protein are
incubated with a solution putatively containing the protein. The antibodies are covalently
linked to a marker enzyme that will turn a certain substrate a color. If the protein is
present, a color change will be seen.
Pp. 110 – 111: 5, 7, 20, 21,22,28,40,41,42
Pp. 128 – 129: 11,12,13,15,19,26,34, 43, 47