Chapter 4 - Protein

Question 1

What is alpha-amino acid?

Answer 1

its the molecule with amino group, carboxylate (COO^-) with side chain (R) and H

Question 2

How many chiral amino acids are there? Which one is the exception?

Answer 2

19/20 except Glycine (gly, G)

Question 3

Entiomer

Answer 3

The stereoisomer that has non-superimposable mirror image

(D and L are enantiomer)

Question 4

What is zwitterion? What is the example of this?

Answer 4

The dipolar molecules (positive and negative charge at the same time)

Amino Acid under physiological pH=7.4 (deprotonated COO^- and protonated NH³⁺)

Question 5

What is the amphoteric molecule?

Answer 5

the molecule that can act as acid and base (Histidine, H)

Question 6

What is AA of 20 AAs that has constrained conformation angle?

Answer 6

Proline (Pro, P) due to the ring structure

Question 7

What is AA of 20 AAs that has most free conformation angle?

Answer 7

Glycine (Gly, G) due to small size

Question 8

What is special about HIstidine?

Answer 8

It can act as base or Acid based on the external pH

(pH < pKa: acid (+) charge ) and (pH>pKa: base - neutral charge)

Question 9

What is important about primary structure?

Answer 9

It determines the chemical and physical properties of protein (protein’s conformation and folding process)

Question 10

How many possible sequences for n -residues?

Answer 10

20ⁿ possible sequences

Question 11

Peptide

Protein

Answer 11

< 40 residues and doesn’t have distinct 3D structure (linked many amino acids)

>40 residues

Question 12

Characteristics of Peptide Bond?

Answer 12

Have limitations on rotation

Have resonance at double bond C=O

Question 13

Dalton (D)

1 residue equal to (D)?

Answer 13

g/mol

110D

Question 14

Beside peptides, proteins also have?

Answer 14

metal ions or organic molecules as cofactos

Question 15

alpha-helix

of residues per turn? length/ turn?

Answer 15

one polypeptide strand in helix formation

3.6 residues and spans 5.4 Å/turn

Question 16

How is alpha-helix structure held?

Answer 16

by the backbone of hydrogen bonds between C=O bond at n residue and N-H bond of n+4 residue

Question 17

What are the conditions that don’t favor the alpha-helix formation?

Answer 17

Proline (helix breaker)

Glycine (too many conformations)

bulky or large/ branched side chain (I, Y, Trp)

Interactions between two same charges side chains

Question 18

Where is the position of R-groups in alpha-helix conformation?

Answer 18

they extend outward from helix

Question 19

What force hold together the beta-sheet?

Answer 19

the H-bonds backbone (C=O and NH)

Question 20

Where does R-groups locate in beta-sheet?

Answer 20

above and below the sheet

Question 21

Which one is more stable than? antiparallel or parallel?

Answer 21

antiparallel because it has smaller # of strands and thus less distorted bonds than in parallel (higher # of strands)

Question 22

What technique can be used to determine 3D structure of protein?

Answer 22

X-ray crystallography

Question 23

Tertiary structure

Answer 23

the folding 2nd structure of polypeptides and the “absolute configuration” of side chains (R)

Question 24

What does 3D structure of protein have?

Answer 24

hydrophobic core and hydrophilic surface

Question 25

What stabilize that 3D protein structure?

Answer 25

hydrophobic effect hydrogen bonds salt bridge disulfide bonds inorganic ions crosslink

Question 26

salt bridge disulfide bond inorganic ion crosslink

Answer 26

ionics bonds btw acid and base covalent bond Zn (2+) interactions with R-group

Question 27

polypeptide loops irregular 2nd structures

Answer 27

the hairpin turn that connect secondary structures of beta-sheets or alpha-helix backbone conformation is not defined

Question 28

WHat solven can use to denature protein?

Answer 28

salt, urea

Question 29

Can protein has more than one conformation?

Answer 29

Yes, depend on pH of cellular, charged state of other side chains

Question 30

pKa of C-terminus Asp Glu His Cys N-terminus Tyr Lys Arg

Answer 30

3. 5 3. 9 4. 1 6. 0 8. 4 9. 0 10. 5 10. 5 12. 5

Question 31

What is PI? How to calculate PI?

Answer 31

the pH at which molecule is in neutral state (0) or no electric charge equal to 1/2 of the Pka on either side of neutral species

Question 32

pH \< PI pH \> PI

Answer 32

the species is protonated species is deprotonated

Question 33

What is the PI of most uncharged polar and nonpolar AAs?

Answer 33

6.25

Question 34

Functions of amino acids?

Answer 34

neurotransmitter metabolic activities hormones enzyme components

Question 35

beta-turn

Answer 35

n residue (C=O) hydrogen bond to (NH) of n+3 residue

Question 36

Orientation of C=O and NH in alpha-helix

Answer 36

all C=O groups point in the same direction all N-H groups point in the same direction but opposite of C=O bonds

Question 37

Orientation of side chain in alpha-helix

Answer 37

point toward the N-terminus

Question 38

This is what type of beta-sheet?

Answer 38

parallel

Question 39

type of beta-sheet?

Answer 39

antiparallel

Question 40

How do you know you are looking at a beta-sheet?

Answer 40

look for the opposite side chains on two secutive residues

Question 41

What is the length between R group in one strand of beta-sheet?

Answer 41

7 Å

Question 42

Where is Proline found in alpha-helix?

Answer 42

at the beginning or the end of alpha-helix and not in the middle