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z - chm040 - biomolecules > Chapter 3: Protein Structure and Function (part 2) > Flashcards

Chapter 3: Protein Structure and Function (part 2) Flashcards

1
Q

where is alpha carbon attached to

A
  • carboxyl group (-COOH)
  • amino group (-NH2)
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2
Q

at pysiologic pH, the amino acid has what?

A
  • -COO-
  • -NH3+
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3
Q

neutral molecule with equal number of + and - charges

A

zwitterion

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4
Q

zwitterion is from the word what?

A

German “zwitter” = “hybrid” or “hermaphrodite”

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5
Q

what do the two charged groups at the two ends of the amino acid lead to

A

internal proton transfer, forming zwitterions

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6
Q

how do you affect the net charge on zwitterions

A

by changing pH

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7
Q

pH point at which there is no net charge on zwitterions

A

isoelectric point (pI)

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8
Q

pH 7

A

physiological pH

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9
Q

zwitterion

A

internal salt

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10
Q

what is internal salt

A

product of acid-base reaction between carboxylic acid and amine

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11
Q

At the isoelectric point, what will happen to the amino acid?

A

not migrate in an applied electric field

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12
Q

zwitterions have higher __ __

A

melting points

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13
Q

test done by applying a sample of amino acid to specially treated paper or gel and applying electric field at different pH values

A

electrophoresis

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14
Q

amino acid bearing a positive charge will migrate where

A

cathode (-)

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15
Q

amino acid bearing a negative charge will migrate where

A

anode (+)

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16
Q

weakly basic

A

carboxylate group

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17
Q

at an acidic enough pH, what will happen to the carboxylate group

A

protonated creating carboxylic acid

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18
Q

weakly acidic

A

ammonium group

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19
Q

at a basic enough pH, what will happen to the ammonium group

A

deprotonated creating amine

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20
Q

net charge of protonated of carboxylate group

A

+1

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21
Q

net charge of deprotonated ammonium

A

-1

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22
Q

isoelectric point represent the pH values of what concentration

A

acid = conjugate base

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23
Q

pI formula

A

pI= (pKa1 + pKa2) / 2

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24
Q

equation which states [HA] = [A-], pH = pKa

A

Henderson-Hasselbalch equation

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25
Q

indicates whether an acid is a strong acid or a weak acid

A

pKa

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26
Q

in an amino acid with acidic sidechain, where does positively charged form (+1) dominate

A

very low pH

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27
Q

in an amino acid with acidic sidechain, where does zwitterionic (neutral) form dominate

A

low pH

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28
Q

in an amino acid with acidic sidechain, where does negatively charged form (-1) dominate

A

intermediate pH

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29
Q

in an amino acid with acidic sidechain, where does doubly negatively charged form (-2) dominate

A

strongly basic pH

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30
Q

in an amino acid with acidic sidechain, the isolelectric point should be the average of what

A

pKa values of two most acidic groups

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31
Q

in an amino acid with basic sidechain, where does double positively charged form (+2) dominate

A

very low pH

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32
Q

in an amino acid with basic sidechain, where does positively charged form (+1) dominate

A

intermediate pH

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33
Q

in an amino acid with basic sidechain, where does the zwitterionic form (neutral) dominate

A

basic pH

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34
Q

in an amino acid with basic sidechain, where does the negatively charged form (-1) dominate

A

strongly basic pH

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35
Q

in an amino acid with basic sidechain, the isolelectric point should be the average of what

A

two most basic groups (pKa2 and pKa3)

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36
Q

the pI values of polar acidic amino acids are about what pH?

A

pH 3

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37
Q

analytical method for identifying amino acids by observing their migration as a function of pH under an applied electric field gradient

A

electrophoresis

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38
Q

Electrophoresis steps

A
  1. paper or gel (polyacrylamide) saturated with buffer solution
  2. soln. of AA is placed at center of paper
  3. electrodes are connected to ends and electric current is allowed to pass
  4. ninhydrin is sprayed
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39
Q

reacts with AAs to produce colored products, green/blue

A

ninhydrin

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40
Q

Western Blot Analysis

A
  1. sampling and protein extraction
  2. SDS-PAGE Gel Preparation
  3. Protein Fractionation
  4. Hybridization and Detection
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41
Q

amino acid carries a __ at pH<pI and migrates where?

A
  • positive charge
  • negative electrode (cathode)
42
Q

amino acid carries a __ at pH>pI and migrates where?

A
  • negative charge
  • positive electrode (anode)
43
Q
  • process for separating components of a mixture
  • the mixture is dissolved in a substance called the mobile phase, which carries it through a second substance called the stationary phase
A

Chromatography

44
Q

Three types of chromatography

A
  1. ion-exchange chromatography
  2. size-exclusion chromatography
  3. affinity chromatography
45
Q

technique for separating compounds based on their net charge

A

Ion exchange chromatography

46
Q

separates molecules based on their size by filtration through a gel

A

Size exclusion chromatography (SEC)

47
Q

separation method based on a specific binding interaction between an immobilized ligand and its binding partner

A

Affinity chromatography

48
Q
  • loss of organized structure of globular protein
  • does not alter primary structure
A

denaturation

49
Q

Examples of substances or process that cause denaturation

A
  1. heat and organic compounds
  2. acids and bases
  3. heavy metal ions
  4. agitation
50
Q

break apart H bonds and distrupt hydrophobic interactions

A

heat and organic compounds

51
Q

break H bonds between R groups and disrupt ionic bonds

A

acids and bases

52
Q

react with S-S bonds to form solids

A

heavy metal ions

53
Q
  • ex. whipping
  • stretches peptide chains until bonds break
A

agitation

54
Q
  • splits the peptide bonds to give smaller peptides and amino acids
  • occurs in digestion of proteins
A

protein hydrolysis

55
Q

what does the hydrolysis of peptide require when in the lab

A
  • acid or base
  • water
  • heat
56
Q

what does the hydrolysis of peptide require when in the body

A

enzymes

57
Q

Some practical aspects of protein denaturation `

A
  1. heat and UV
  2. salts of heavy metal ions esp. Hg2+, Pb2+, Ag+
  3. organic compounds such as soap, detergents, phenol, and aliphatic alcohol
58
Q

heat and UV

A
  • denaturation of egg white protein to become utilizable
  • sterilzation using UV and heat by steam to coagulate bacterial protein
59
Q

salts of heavy metal ions esp. Hg2+, Pb2+, Ag+

A
  • antiseptics in low concentrations
  • poisons at higher concentrations
60
Q

any agent that produces nausea and vomiting

A

emetic

61
Q

oragnic compounds such as soap, detergents, phenol, and aliphatic alcohol

A
  • hydrophobic portions interact with hydrophobic core of protein
  • hydrophilic portion H-bonded to aqueous environment
  • causes swelling and unfolding of protein
62
Q

Procedure in determination of amino acid sequence

A
  1. hydrolysis (by acid, alkali, or enzyme)
  2. identification of products
  3. fitting pieces together
63
Q

Three types of hydrolysis

A
  1. acid hydrolysis
  2. alkaline hydrolysis
  3. enzymatic hydrolysis
64
Q

involves heating in presence of 6N HCl in sealed tube at 110C for 10-100 hrs. depending on nature of protein

A

acid hydrolysis

65
Q

temperature and duration during acid hydrolysis

A

110C
10-100 hrs
(6N HCl)

66
Q

what is completely and partially destroyed during acid hydrolysis

A

completely
- trp

partially
- ser
- thr
- tyr

67
Q

heating in presence of 4N NaOH in sealed tube at 110C 10-100 hrs

A

alkaline hydrolysis

68
Q

what is used in alkaline hydrolysis

A

4N NaOH

69
Q

amino acids in alkaline hydrolysis

A

not damaged
- trp

completely destroys
- arg
- cys
- thr
- ser

70
Q

by proteases or peptidases

A

enzymatic hydrolysis

71
Q

Two types of peptidases

A
  1. exopeptidases
  2. endopeptidases
72
Q

enzyme that cleave external peptide bonds

A

exopeptidases

73
Q

Two types of exopeptidases

A
  1. aminopeptidases
  2. carboxypeptidases
74
Q
  • sequentially cleaves peptide bonds, beginning at the N-terminal end of the polypeptide
  • the liberated amino acids are identified one by one
A

aminopeptidases

75
Q

sequentially cleaves peptide bonds beginning at the C-terminal end of the polypeptide

A

carboxypeptidases

76
Q

cleaves internal peptide bonds

A

endopeptidases

77
Q

Five types of endopeptidases

A
  1. trypsin
  2. chymotrypsin
  3. elastase
  4. pepsin
  5. thermolysin
78
Q

cleaves peptide bonds at the carboxyl end of the two strongly basic amino acids

A

trypsin

79
Q

where does trypsin cleave

A

C-end
- arginine
- lysine

80
Q

cleaves peptide bonds at the carboxyl end of the three aromatic amino acids

A

chymotrypsin

81
Q

where does chymotrypsin cleave

A

C-end
- phenylalanine
- tryptophan
- tyrosine

82
Q

cleaves on the carboxyl side of Gly and Ala

A

elastase

83
Q

where does elastase cleave

A

C-end
- glycine
- alanine

84
Q

cleaves peptide bonds at the amino end of the three aromatic amino acids

A

pepsin

85
Q

where does pepsin cleave

A

N-end
- phenylalanine
- tryptophan
- tyrosine

86
Q

cleaves peptide bonds at the amino end of the three aromatic amino acids and amino acids with bulky nonpolar R groups

A

thermolysin

87
Q

where does thermolysin cleave

A

N-end
- Phe, Tyr, Trp
- Leu, Ileu, Val

88
Q

trypsin biological source

A

bovine pancreas

89
Q

Trypsin cleavage points

A

(C)
- Lys
- Arg

90
Q

mouse submaxillary gland

A

Submaxillarus protease

91
Q

Submaxillarus protease cleavage points

A

(C)
Arg

92
Q

chymotrypsin biological source

A

bovine pancreas

93
Q

chymotrypsin cleavage points

A

(C)
- phe
- trp
- tyr

94
Q

Staphylococcus aureus V8 protease biological source

A

bacterum S. aureus

95
Q

Staphylococcus aureus V8 protease cleavage points

A

(C)
- asp
- glu

96
Q

Asp-N-protease biological source

A

bacterium Pseudomonas fragi

97
Q

Asp-N-protease cleavage points

A

(N)
- asp
- glu

98
Q

pepsin biological source

A

porcine stomach

99
Q

pepsin cleavage points

A

(N)
- phe
- trp
- tyr

100
Q

endoproteinase Lys C biological source

A

bacterium Lysobacter enzymogenes

101
Q

endoproteinase Lys C cleavage points

A

(C)
lys

102
Q

cyanogen bromide cleavage points

A

(C)
met

z - chm040 - biomolecules (15 decks)

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