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Biomolecules of life > Introduction to amino acids and protein folding - week 1 > Flashcards

Introduction to amino acids and protein folding - week 1 Flashcards

1
Q

What abbreviation options are there for amino acids?

A

full name, letter code, letter

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2
Q

Ala - A

A

Alanine

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3
Q

Arg - R

A

Argeinine

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4
Q

Asn - N

A

Asparagine

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5
Q

Asp - D

A

Aspartic acid

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6
Q

Cys - C

A

Cysteine

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7
Q

Glu - E

A

Glutamic acid

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8
Q

Gln - Q

A

Glutamine

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9
Q

Gly - G

A

Glycine

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10
Q

His - H

A

Histidine

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11
Q

Ile - I

A

Isoleucine

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12
Q

Leu - L

A

leucine

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13
Q

Lys - K

A

Lysine

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14
Q

Met - M

A

Methionine

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15
Q

Phe - F

A

Phenylalanine

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16
Q

Pro - P

A

Phenylalanine

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17
Q

Ser - S

A

Serine

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18
Q

Thr - T

A

Threonine

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19
Q

Trp - W

A

Tryptophan

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20
Q

Tyr - Y

A

Tyrosine

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21
Q

Val - V

A

Valine

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22
Q

what are amino acids?

A
  • building blocks of proteins
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23
Q

How many principle amino acids are found in proteins?

A

20, but other non-protein amino acids are found in all organisms

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24
Q

What do proteins consist of?

A
  • chiral alpha-carbon
  • amine group (NH2/NH3+)
  • carboxyl group (COOH/ COO-)
  • hydrogen atom
  • R-group
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25
Q

What is a zwitterion?

A
  • at neurotral pH amino acids exist as dipolar ions
  • amino groups is protonated, carboxyl group is depronated
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26
Q

Is the amino group of a zwitterion protonated?

A

Yes

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27
Q

Is the carboxyl group of a twitter ion protonated?

A

No - its deprotonated

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28
Q

What happens to the end groups at a ph of lower than 4? (properly at 2)

A

Both groups protonated

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29
Q

What happens to the end groups at a ph of higher than 6? (properly at 10)

A

both groups deprotonated

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30
Q

What pH allows for the highest concentration of zwitterions?

A

3 to 8

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31
Q

What is the aC in amino acids?

A

chiral

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32
Q

In what two forms which mirror each other can amino acids exist?

A

L and D isomers

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33
Q

Where is the NH3+ group on an L isomer in comparison to a D isomer?

A

left side on L, right side on D

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34
Q

Where is the COO group on an L isomer in comparison to a D isomer?

A

right side on L, left side on D

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35
Q

What four things makes the properties of L and D amino acids vary in certain conditions?

A
  • different shape alters biological activity
  • D-isomer cannot be digested
  • cannot interact with tRNA (steric hinderance)
  • can be found in some portions in both Pro and Eukaryotes
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36
Q

Which form of isomer is almost exclusively found in proteins?

A

L-isomer

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37
Q

what defines the properties of the amino acid?

A

Chemical nature of R group

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38
Q

Name the 6 key features of R groups in amino acids

A

size
shape
charge
hydrogen bonding capacity
hydrophobicity
chemical reactivity

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39
Q

What amino acids have a negative charged side chain?

A

Asp, Glu

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40
Q

What amino acids have a positive charged side chain?

A

arg, Lys, His

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41
Q

What amino acids have an uncharged polar side chain?

A

Asn, Gln, Ser, Thr, Tyr

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42
Q

What amino acids have a nonpolar side chain?

A

Ala, Gly, Val, Leu, Ile, Pro, Phe, Met, Trp, Cys

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43
Q

What amino acids are hydrophilic?

A

proteins with a negative, positive, and uncharged polar side chain

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44
Q

What amino acids are hydrophobic?

A

proteins with non polar side chains

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45
Q

Describe glycine

A
  • smallest amino acid
  • R group is a hydrogen atom
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46
Q

What do Glycine, alanine, valine, leucine, isoleucine and methionine have in common?

A

all have aliphatic R groups of increasing size

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47
Q

What increases with an increasing allopathic chain?

A

hydrophobicity

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48
Q

Where are hydrophobic amino acids often found?

A

on the inside of proteins away forms he aqueous cellular environment

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49
Q

What does methionine contain?

A

a thioether (-s-) group which contains a sulphur atom

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50
Q

list alanine, glycine isoleucine, leucine, valine and methionine from increasing size and hydrophobicity

A

glycine, alanine, valine, isoleucine and methionine

51
Q

What type of R group does proline have?

A

cyclic aliphatic

52
Q

What is unique about Proline’s R group?

A
  • bonded to amino group and aC
  • more structurally restricted
  • often found in bends in proteins
53
Q

List the three so called Aromatic amino acids

A

phenylalanine, tyrosine, tryptophan

54
Q

what do phenylalanine, tyrosine, tryptophan have in common?

A
  • all contain a phenyl ring
  • all hydrophobic
55
Q

Why do tyrosine and tryptophan have some hydrophilic properties?

A

-OH and -NH groups respectively

56
Q

What part of tyrosine is quite reactive

A

-OH group

57
Q

List Phenylalanine, Tryptophan, Tyrosine from increasing to decreasing size

A

Phenylalanine, Tyrosine, Tryptophan

58
Q

Describe cysteine

A
  • similar to serine
  • contains reactive thiol group -SH
  • Paris of thiol groups come together to form disulphide bond
59
Q

Describe lysine and arginine

A
  • basic amino acids
  • contain side chains that are positively charged at neutral pH
60
Q

Describe histidine

A
  • basic amino acid
  • contains imidazole ring
  • has pKA of 6 so can be charged or uncharged at pH near to neutral
61
Q

Where is histidine often found at?

A

the active site of enzymes where it can bind and release protons

62
Q

What enzyme is an important buffer of pH in blood?

A

histidine

63
Q

Is the pKa of histidine in haemoglobin different from that of free histidines? and why?

A

Yes - neighbouring groups affect the pKA

64
Q

What is the pKA for oxyhemoglobin?

A

6.8

65
Q

What is the pKA for deoxyhaemoglobin?

A

7.8

66
Q

Name two acidic amino acids

A

aspartic acid and glutamic acid

67
Q

What are aspartic acid and glutamic acid also called?

A

aspartate and glutamate

68
Q

What charge do aspartic acid and glutamic acid have at physiological pH?

A

negative

69
Q

Where are the carboxyl groups located in aspartic acid and glutamic acid?

A

at the end of a side chain

70
Q

What are asparagine and glutamine?

A

uncharged derivatives of aspartate and glutamate

71
Q

What is different after the conversion of aspirate and glutamate into asparagine and glutamine?

A

NH2 groups replaces O in carboxyl group

72
Q

What is the role of proteins?

A
  • carry out the mechanical, structural and transport functions of the body
  • play a crucial role as enzymes
  • have a wide variety of shapes and sizes
73
Q

Name structural proteins

A

collagen, keratin, amelogenin

74
Q

name movement proteins

A

actin, myosin

75
Q

name enzymes and catalyst proteins

A

trypsin, DNA pol

76
Q

name transport proteins

A

haemoglobin, transferrin

77
Q

name membrane transport proteins

A

Na+/Ka+ pump

78
Q

name hormone proteins

A

insulin

79
Q

name receptor proteins

A

acetylcholine receptor

80
Q

name defence proteins

A

antibodies, clotting factors

81
Q

name gene regulation proteins

A

histones, transcription factors

82
Q

name chromosome sorting proteins

A

tubulin

83
Q

What is the unit of mass for molecular measurements?

A

Dalton (Da)

84
Q

What is the equivalent to one Da?

A

the molecular weight of 1 Hydrogen atom

85
Q

What is the unit of distance?

A

Angstrom
1A= 1(-10)m= 0.1 nm

86
Q

From how many 3D structures is the portion structure made up of?

A

4 levels

87
Q

What is the primary sequence made up of?

A

sequence of aa in peptide chain including any disulphide linkages

88
Q

What os the secondary sequence made up of?

A

folding/ coiling of peptide chain (alpha helix or beta pleated sheet)

89
Q

What is the tertiary sequence made up of?

A

peptide chain folds upon itself

90
Q

What is the quaternary sequence made up of?

A

folded peptide chains join together

91
Q

Do polypeptides have direction (polarity) ?

A

Yes

92
Q

In what way Is the order of residues read?

A

from the amino (N) terminal to the carboy (C) terminal

93
Q

What is the order of amino acid residues in a protein called?

A

sequence

94
Q

What bond links two amino acids together?

A

peptide bond

95
Q

Describe protein assembly

A
  • hydrogen removed from amino group
  • oxygen (or hydroxide) group from carboxyl group
  • water released = condensation reaction
  • resulting covalent bond = peptide bond
96
Q

Describe the peptide bond

A
  • double bond characteristics
  • ring bond, prevents rotation
  • distance between CH and NH groups shortened (1.32 A)
  • planar (ie. 2 peptides 6 atoms lie in the same plane )
97
Q

In what forms can the peptide bond exist?

A

trans and cis form

98
Q

In protein bond its almost always cis-form

A

No- always trans-form (H of amino group trans to O of carboy group)

99
Q

When are cis peptide bonds long seen?

A

where the bond is between proline and any other amino acid

100
Q

In X-pro are trans or cis configurations possible? and why?

A
  • due to steric problems BOTH possible
101
Q

What forms polypeptides?

A

many amino acids joined together

102
Q

What are residues?

A

the amino acids in a polypeptide

103
Q

Is the amino terminal residue (NH3+) left or right?

A

left

104
Q

Is the carboxyl terminal residue left or right (COO-)?

A

right

105
Q

What is the main chain?

A

the regular repeating part of a polypeptide

106
Q

What is the main chain often referred to?

A

the backbone

107
Q

What are variable regions of an amino acid formed from?

A

side chains (R groups)

108
Q

Are side chains involved in peptide bonds?

A

No

109
Q

What is a naturally occurring example of a dipeptide?

A

aspartame (Asp-Phe): artificial sweetener

110
Q

What is an example of a tripeptide?

A

glutathione (Glu-Cys-Gly): natural antioxidant

111
Q

What is an example of a short polypeptide (10-40 aa)?

A
  • peptide hormones eg. glucagon (29 aa)
  • neurotransmitter eg. substances P (10 aa)
112
Q

How many amino acids are in a large polypeptide?

A

> 40 aa

113
Q

What is an example of a large protein?

A

dystrophin (3684 aa, 427 kDa)

114
Q

Are other covalent linkages contributing to protein structure?

A

Yes

115
Q

Name an example for other covalent linkages that contribute to protein structure?

A

disulphide (S-S) bridges between two Cys residues (joining subunits tithe eg. insulin)

116
Q

What is the protein conformation?

A

3D arrangement of protein atoms in its structure

117
Q

What does the protein conformation depend on?

A

confirmation is independent of the number of chains in a protein

118
Q

What is the native structure of a protein?

A

3D structure of a protein under physiological conditions

119
Q

When do proteins fail to work?

A

if they are not in their correct 3D conformation

120
Q

In what form are proteins translated?

A

in linear arrays

121
Q

Describe Anfinsens experiment

A
  • 1950
  • used solutions containing 8M urea or 6M guanidine hydrochloride (makes proteins denature into random coils)
  • used beta-mercaptoethanol (reducing agent and breaks disulphide bonds)
  • dissolved RNAse in solution of beta-mere and 8M urea
  • RNAse loses all activity (denatures)
  • then removed urea and mere using dialysis
  • RNAse spontaneously regains all enzyme activity (RNAse renautre)
122
Q

What was Anfinsen’s conclusion of his first experiment?

A
  • aa sequences of RNase provides all info required to specify its native structure (final conformation)
123
Q

What was anfinsen’s further experiments?

A
  • denatured RNAse in urea and merc
  • removed mercury but left urea
  • observed RNase regained 1% of original activity
  • bc only 1 combination of correct disulphide bonds but 105 possible combinations
  • urea disulphide bonds form randomly in 1 out of 105 possible combinations to correct bonds pattern is obtained 1/105 = ~ 1%
  • then added back traces amounts of mercury to scrambled RNAse (104 incorrect forms of RNAse)
  • after ~10 h of RNAse has completely regained its activity
124
Q

What was Anfinsen’s conclusion for his further experiments?

A
  • correct disulphide bonds were in a lower free energy state and are more energetically favourable
  • thermodynamically most stable structure of RNAse is its native conformation - true for all proteins

Biomolecules of life (10 decks)

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