Chapter 4 - Protein Flashcards Preview

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Flashcards in Chapter 4 - Protein Deck (42)
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1

What is alpha-amino acid?

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

2

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

19/20 except Glycine (gly, G) 

3

Entiomer

The stereoisomer that has non-superimposable mirror image 

(D and L are enantiomer)

4

What is zwitterion? What is the example of this?

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

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

5

What is the amphoteric molecule?

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

6

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

Proline (Pro, P) due to the ring structure

7

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

Glycine (Gly, G) due to small size

8

What is special about HIstidine?

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

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

9

What is important about primary structure?

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

10

How many possible sequences for n -residues?

20n possible sequences

11

Peptide

Protein

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

>40 residues 

12

Characteristics of Peptide Bond?

Have limitations on rotation

Have resonance at double bond C=O

13

Dalton (D)

1 residue equal to (D)?

g/mol

110D

14

Beside peptides, proteins also have?

metal ions or organic molecules as cofactos

15

alpha-helix

# of residues per turn? length/ turn?

one polypeptide strand in helix formation

3.6 residues and spans 5.4 Å/turn

16

How is alpha-helix structure held?

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

17

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

Proline (helix breaker)

Glycine (too many conformations)

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

Interactions between two same charges side chains

 

18

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

they extend outward from helix

19

What force hold together the beta-sheet?

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

20

Where does R-groups locate in beta-sheet?

above and below the sheet

21

Which one is more stable than? antiparallel or parallel?

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

22

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

X-ray crystallography

23

Tertiary structure

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

24

What does 3D structure of protein have?

hydrophobic core and hydrophilic surface

25

What stabilize that 3D protein structure?

hydrophobic effect

hydrogen bonds

salt bridge

disulfide bonds

inorganic ions crosslink

 

26

salt bridge

disulfide bond

inorganic ion crosslink

ionics bonds btw acid and base

covalent bond

Zn (2+) interactions with R-group

27

polypeptide loops

irregular 2nd structures

 

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

backbone conformation is not defined

28

WHat solven can use to denature protein?

salt, urea

29

Can protein has more than one conformation?

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

30

pKa of C-terminus

Asp

Glu

His

Cys

N-terminus

Tyr

Lys

Arg

3.5

3.9

4.1

6.0

8.4

9.0

10.5

10.5

12.5