Proteins

Question 1

Which amino acids are in the “greasy”, hydrophobic family?

Answer 1

1. Valine (Val, V)
2. Leucine (Leu, L)
3. Isoleucine (Ile, I)
4. Methionine (Met, M)

Question 2

Which amino acids are in the aromatic family?

Answer 2

1. Phenylalanine (Phe, F)
2. Tyrosine (Tyr, Y)
3. Tryptophan (Trp, W)

Question 3

Which amino acids are charged (basic)?

Answer 3

1. Lysine (Lys, K)
2. Arginine (Arg, R)
3. Histidine (His, H) – not usually charged in neutral pH

Question 4

What makes cysteine (Cys, C) special?

Answer 4

Contains a sulfhydryl (SH) group at the end of its side chain.

-SH group can form disulfide bridges between 2 cysteines to create tertiary structure.

Question 5

Which amino acids have polar side chains?

Answer 5

1. Aspargine (Asn, N)

2. Glutamine (Gln, Q)

Question 6

Which amino acids have side chains ending in hydroxyl (OH) groups?

Answer 6

1. Serine (Ser, S)

2. Threonine (Thr, T)

Question 7

What do hydroxyl groups on amino acids allow?

Answer 7

Attaching of a phosphate group to the OH by protein kinases (enzymes).

Question 8

Which amino acid has cyclic structure?

Answer 8

Proline (Pro, P)

Question 9

Which amino acids have side chains of carboxylic acids (negatively charged)?

Answer 9

1. Aspartate (Asp, D)

2. Glutamate (Glu, E)

Question 10

How is a peptide bond formed?

Answer 10

Linking of amino acids to form polypeptide chain requires formation of a covalent bond between the amino group of one amino acid and the carboxyl group of another amino acid.

In the cell, formation of the bond is carried out by the ribosome

Water must be removed to form the bond and added to cleave it.

Question 11

What is special about a peptide bond?

Answer 11

Bond has semi-planar characteristics because resonance (sharing) of electrons occurs across the peptide bond. Gives partial double bond character and prevents free rotation of the bond from occurring.

Question 12

What are the 3 protein secondary structures?

Answer 12

Helix (alpha is most common): coiled polypeptide chain
Beta sheet (parallel and anti-parallel): extended polypeptide chain
Beta turn

Question 13

What bonds form the alpha helix?

Answer 13

hydrogen bonds from peptide backbone (NOT from R-groups) between the CO group and the NH group.

N is always the bond donor; O is always the acceptor.

Question 14

How far apart are the residues that form the bonds of the helix?

Answer 14

4 amino acids apart

Question 15

What function do alpha helices play in the lipid bilayer?

Answer 15

Form parts of proteins that pass through plasma membrane.

Question 16

What is a beta turn?

Answer 16

turns the polypeptide chain 180 degrees; a minimum of 2 amino acids are involved in the turn.

Question 17

Properties of beta turns

Answer 17

1. Occur on surfaces of proteins
2. Often sites of glycolysation: where sugars are attached
3. Important sites of immunological recognition (to tell if something is foreign)
   - Antibodies like to look at beta turns
4. Somewhat predictable from the amino acid sequence

Question 18

What are some protein misfolding diseases?

Answer 18

1. Transmissible spongiform encephalopathies (Cruezfeldt-Jakob, mad cow disease, scrapie) where misfolded proteins called PRIONS are the infectious agent
2. Alzheimer’s disease

Question 19

Why are prions so dangerous?

Answer 19

Can convert additional molecules of the normal protein into prions. Prion versions of the protein also form aggregates (amyloid); amyloid aggregates disrupt normal cellular function and cause disease.

Question 20

What is a protein domain?

Answer 20

Unit of a protein’s 3D structure that folds autonomously, is formed from secondary structural elements connected by loops, has its own hydrophobic core, and has an independent functional or structural property.

Question 21

What are protein motifs?

Answer 21

Functional/structural units which occur within domains

Question 22

What are crosslinks?

Answer 22

Disulfide bonds S-S; on amino acids, these require CYSTEINES.

Most common covalent cross-link in proteins b/c very hard to break, so suitable for harsher conditions outside the cell.

Question 23

What does X-ray crystallography do?

Answer 23

Determines protein’s 3D structure.

Question 24

What are the steps of X-ray crystallography?

Answer 24

1. Must make a uniformly repeated lattice of molecules out of the protein to be studied (i.e. crystals)
2. Hit crystal w/ x-rays from various angles
3. Obtain a diffraction pattern
4. Fourier transformation of this pattern reveals an electron density map that can be converted to an atomic map.

Question 25

What is Nuclear Magnetic Resonance (NMR) Spectroscopy?

Answer 25

Way to determine protein’s 3D structure.

Question 26

What are the steps of NMR spectroscopy?

Answer 26

1. Apply magnetic field to protein in solution
   a. Works b/c atomic nuclei are magnetic
2. Magnetic field aligns the spin states of the nuclei
3. As the nuclei relax back to their original states, they emit radiation which provides structural information
4. Advantage: Structure of proteins in solution; Don’t require crystals
5. Disadvantage: Only good to about 100K MW (900 amino acids)

Question 27

What are homo and heteromeric quaternary structures?

Answer 27

Homomeric: all proteins making up quaternary structure are the same
Heteromeric: proteins making up quaternary structure are different