lecture 6- protein

Question 1

Distinct regions of a protein that fold independently of one another and often function in a semi-independent manner are called:

Answer 1

domains

Question 2

molecular chaperones

Answer 2

may prevent growing proteins from making random, nonselective interactions with other proteins in various cellular compartments

Question 3

the first protein whose tertiary structure was determined

Answer 3

myoglobin

Question 4

denaturation of protein can be caused by

Answer 4

detergents, organic solvents, heat, certain chemical compounds, or radiation

Question 5

the unfolding or disorganization of protein

Answer 5

denaturation

Question 6

amino acid sequence will fall into the sequence that has the

Answer 6

lowest energy

Question 7

a secondary structure will not have a noncovalent interaction with the

Answer 7

side chain

secondary structures will have interactions with the main chain!

Question 8

stabilization of a tertiary structure of a protein will always be with

Answer 8

a side chain

Question 9

beta sheets are very strong because of

Answer 9

hydrogen bonding

Question 10

Protein (3 main concepts)

Answer 10

-mediate nearly all the processes in a cell
-diverse structure and function
-all the proteins use the same set of 20 amino acids

Question 11

8 types of proteins

Answer 11

enzymes, structural proteins, motor proteins, receptor proteins, transport proteins, storage proteins, signal proteins, gene regulatory proteins

Question 12

what is the only differing thing about amino acids?

Answer 12

the side chains (R)

all 20 amino acids are categorized based on their side chain properties

Question 13

amino acid side chain categories

Answer 13

nonpolar, polar uncharged, acidic, basic

(all fairly hydrophobic)

Question 14

hydrophobic side chains packed together (hydrophobic effect)

Answer 14

put amino acid sequence in water, hydrophobic side chains pack together, forms a pseudo 3D structure (the multenglobun??)

the pseudo 3D structure does not have noncovalent interactions!!!!

Question 15

peptides

Answer 15

2+ amino acids joined by peptide bonds

Question 16

peptides are held together by

Answer 16

peptide bonds formed as a result of a condensation rxn

Question 17

peptide directionality convention

Answer 17

N-terminus to C-terminus (left to right)

Question 18

shape of a protein is dictated by

Answer 18

amino acid sequence

side chains dictate unique properties of the amino acid which affect how the protein folds

Question 19

Secondary structure: 2 most common

Answer 19

alpha helix= side chain outside helix (H bonding stabilizes)
beta helix= same direction or different directions

Question 20

Alpha helix

Answer 20

• peptide backbone wraps around imaginary axis
• R group phases outwards
• intrachain H bonds stabilizes alpha helixes

Question 21

how to determine is an amino acid is right or left handed?

Answer 21

use the right hand rule!!
follow amino acid in the way your thumb is pointing. helix should curve in same direction as your fingers

Question 22

amino acid R-groups affect alpha helix stability

Answer 22

1. electrostatic/steric interactions between adjacent side chains can affect stability of an alpha helix
2. electrostatic/steric interactions between amino acids 3-4 residues away can affect the stability of an alpha helix
3. proline and glycine are not usually found in helices

Question 23

why is proline not found in helices?

Answer 23

-the nitrogen of proline is in a rigid ring which sterically interferes w the backbone

-proline in a peptide bond lacks an amide hydrogen to form hydrogen bonds

Question 24

why is glycine not found in helices?

Answer 24

glycine is very flexible, allows for conformations that do not suit alpha helices

glycine is so small that is can’t protect the backbone hydrogen bonds from the aqueous environment

(don’t use the textbook for this info, he is the expert in this?)

Question 25

proline and glycine are seen as

Answer 25

“helix breakers”

Question 26

amphipathic helices

Answer 26

one side is hydrophobic, the other side is hydrophilic

Question 27

proteins with alpha helices are

Answer 27

very strong
coils can form around eachother
(ex. keratin)