Smith-AminoAcids

Question 1

What is the pKa value of carboxylic acid (COOH)?

Answer 1

4.4

Question 2

What is the pKa of an amine (NH+)?

Answer 2

6.0

Question 3

What is the pKa of hydro-sulfur (SH)?

Answer 3

8.5

Question 4

What is the pKa of alcohol (-OH)?

Answer 4

10.0

Question 5

What is the pKa of a -NH3+ group?

Answer 5

10.0

Question 6

What is the pKa of the =NH2+ on arginine?

Answer 6

12.0

Question 7

What is the difference between pKa and pH?

Answer 7

pKa is an inherent property of a compound or a functional group which does not change while pH is the measurement of hydronium ions [H+] in solution at a given time.

Question 8

why is glycine an alpha helix breaker?

Answer 8

due to its overt flexibility (lack of stability) and small size

Question 9

Why is Proline an alpha chain breaker?

Answer 9

Due to its steric hinderance. Has no flexibility at all.

Question 10

What do Ramachandran Plots characterize?

Answer 10

The ability of R groups to rotate around their Psi and Phi bonds (angle rotation from -180 to +180

Question 11

list the organizational forms proteins can make (4) in increasing order

Answer 11

1. secondary structure
2. motif
3. domain
4. quaternary/tertiary structure

Question 12

define primary structure of protein

Answer 12

amino acid sequence

Question 13

what is secondary structure of proteins

Answer 13

angles and structure dictated by the amino acid composition

Question 14

What is a motif?

Answer 14

portion of a protein (e.g. a loop) that is repeated in other proteins

Question 15

What is a domain?

Answer 15

portion of a protein that is physically separate and often has a particular function

Question 16

What are the major differences between alpha and beta sheets? (two aspects for each)

Answer 16

Alpha Helices:
1. bonds within a singluar amino acid sequence
2. all side chains are point outwards
Beta Sheets:
1. separate amino acid sequences in one structure
2. side chains alternate up and down from the plane of the sheet

Question 17

What can govern how a protein folds? (4)

Answer 17

1. Thermodynamics (small proteins)
2. Kinetics/Translation Order
3. Helpers (chaperones and refolding proteins)
4. Heaven Only Knows (huge proteins that end up in rando places)

Question 18

What is PDI?

Answer 18

protein disulfide isomerase:
an enzyme found within the endoplasmic reticulum that catalyzes protein folding by forming and breaking disulfide bonds between cysteine residues within proteins as they fold.

Question 19

in what state is PDI active?

Answer 19

reduced (has donated electrons)

Question 20

What is peptidylprolyl isomerases?

Answer 20

an enzyme found in both eukaryotic and prokaryotic cells that interconverts the cis and trans isomers of proline peptide bonds

Question 21

Most amino acids have a strong energetic preference for the …… peptide bond confirmation due to ….. ……

Answer 21

trans
steric hinderance

Question 22

what types of proteins put sugars on proteins?

Answer 22

glycosilate proteins

Question 23

Where can glycans (sugars) be linked to your proteins?

Answer 23

1. N-linked glycans
2. O-linked glycans
3. Phospho-glycans

Question 24

N-linked glycans are linked to what amino acids typically?

Answer 24

asparagine
arginine

Question 25

O-linked glycans are linked to which amino acids typically?

Answer 25

serine, threonine, tyrosine, hydroxyproline, hydroxylysine

Question 26

Phospho-glycans are linked to which amino acids typically?

Answer 26

phosphoserine

Question 27

N-linked glycosylation requires participation of a special lipid called ..... ......

Answer 27

dolichol phosphate

Question 28

For what reasons would we need sugars on proteins?

Answer 28

1. to stabilize the protein 2. to increase the protein's solubility 3. for the protein's function 4. -in animals- to monitor the 'age' of proteins for degradation 5. for the protein's folding process

Question 29

What is the function of glycosilates?

Answer 29

to put sugars on proteins

Question 30

What are three important ways proteins can be post-translationally modified?

Answer 30

1. glycosylation 2. phosphorylation 3. lipidation

Question 31

What determines the fold of a protein?

Answer 31

amino acid composition

Question 32

What determines the function (stability) of a protein?

Answer 32

The amino acid composition and fold

Question 33

What is an example of a stable ('rock'-like) protein?

Answer 33

collagen