Chapter 4 - Protein Flashcards Preview

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Flashcards in Chapter 4 - Protein Deck (42)
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1
Q

What is alpha-amino acid?

A

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

2
Q

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

A

19/20 except Glycine (gly, G)

3
Q

Entiomer

A

The stereoisomer that has non-superimposable mirror image

(D and L are enantiomer)

4
Q

What is zwitterion? What is the example of this?

A

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

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

5
Q

What is the amphoteric molecule?

A

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

6
Q

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

A

Proline (Pro, P) due to the ring structure

7
Q

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

A

Glycine (Gly, G) due to small size

8
Q

What is special about HIstidine?

A

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

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

9
Q

What is important about primary structure?

A

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

10
Q

How many possible sequences for n -residues?

A

20n possible sequences

11
Q

Peptide

Protein

A

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

>40 residues

12
Q

Characteristics of Peptide Bond?

A

Have limitations on rotation

Have resonance at double bond C=O

13
Q

Dalton (D)

1 residue equal to (D)?

A

g/mol

110D

14
Q

Beside peptides, proteins also have?

A

metal ions or organic molecules as cofactos

15
Q

alpha-helix

of residues per turn? length/ turn?

A

one polypeptide strand in helix formation

3.6 residues and spans 5.4 Å/turn

16
Q

How is alpha-helix structure held?

A

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

17
Q

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

A

Proline (helix breaker)

Glycine (too many conformations)

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

Interactions between two same charges side chains

18
Q

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

A

they extend outward from helix

19
Q

What force hold together the beta-sheet?

A

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

20
Q

Where does R-groups locate in beta-sheet?

A

above and below the sheet

21
Q

Which one is more stable than? antiparallel or parallel?

A

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

22
Q

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

A

X-ray crystallography

23
Q

Tertiary structure

A

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

24
Q

What does 3D structure of protein have?

A

hydrophobic core and hydrophilic surface

25
Q

What stabilize that 3D protein structure?

A

hydrophobic effect

hydrogen bonds

salt bridge

disulfide bonds

inorganic ions crosslink

26
Q

salt bridge

disulfide bond

inorganic ion crosslink

A

ionics bonds btw acid and base

covalent bond

Zn (2+) interactions with R-group

27
Q

polypeptide loops

irregular 2nd structures

A

the hairpin turn that connect secondary structures of beta-sheets or alpha-helix

backbone conformation is not defined

28
Q

WHat solven can use to denature protein?

A

salt, urea

29
Q

Can protein has more than one conformation?

A

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

30
Q

pKa of C-terminus

Asp

Glu

His

Cys

N-terminus

Tyr

Lys

Arg

A
  1. 5
  2. 9
  3. 1
  4. 0
  5. 4
  6. 0
  7. 5
  8. 5
  9. 5
31
Q

What is PI? How to calculate PI?

A

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

32
Q

pH < PI

pH > PI

A

the species is protonated

species is deprotonated

33
Q

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

A

6.25

34
Q

Functions of amino acids?

A

neurotransmitter

metabolic activities

hormones

enzyme components

35
Q

beta-turn

A

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

36
Q

Orientation of C=O and NH in alpha-helix

A

all C=O groups point in the same direction

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

37
Q

Orientation of side chain in alpha-helix

A

point toward the N-terminus

38
Q

This is what type of beta-sheet?

A

parallel

39
Q

type of beta-sheet?

A

antiparallel

40
Q

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

A

look for the opposite side chains on two secutive residues

41
Q

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

A

7 Å

42
Q

Where is Proline found in alpha-helix?

A

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