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Biochemistry > Amino acids and proteins > Flashcards

Amino acids and proteins Flashcards

1
Q

What groups are on the basic structure of an amino acid?

A

Amino group, carboxyl group, hydrogen and R which surround an alpha carbon

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2
Q

What configuration is prominent in proteins and peptides, trans or cis?

A

Trans, so they don’t interfere with eachother

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3
Q

How many different amino acids are there in proteins?

A

20

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4
Q

What is the main carbon in an amino acid called?

A

Alpha carbon

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5
Q

What is the most simple amino acid?

A

Glycine

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6
Q

What is the r group in glycine?

A

Hydrogen

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7
Q

Symbol for glycine

A

Gly, G

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8
Q

What is the R in asparagine?

A

CH2 and CONH2

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9
Q

Symbol for asparagine

A

Asn, N

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10
Q

What is the R group in glutamic acid?

A

CH2, CH2 and COOH

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11
Q

Symbol for glutamic acid

A

Glu, E

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12
Q

What is the R group in Tyrosine?

A

CH2, phenyl group, OH

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13
Q

Symbol for tyrosine

A

Tyr, Y

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14
Q

How to tell L from D amino acids?

A

Read clockwise, if CO->R->N then it is L

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15
Q

What does it mean that amino acids are amphoteric?

A

They have both acid and basic group

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16
Q

What does pKa tell you?

A

Strength of an acid

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17
Q

Does a strong acid have a high or low pKa?

A

Low, less than zero
The lower the stronger

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18
Q

What is the definition of pH

A

Measure of the concentration of hydrogen ions in an aqueous solution

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19
Q

What is a zwitterion?

A

Ion with two functional groups, both a positive and negative

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20
Q

Why does the line not increase linearly during titration?

A

Because of buffer

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21
Q

What is the pI?

A

The isoelectric point

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22
Q

What is the electric charge of the molecules at the isoelectric point?

A

Net charge is zero

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23
Q

What is the second most simple amino acid?

A

Alanine

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24
Q

What is the pI? (Definition)

A

The pH where the average charge of all the amino acid species in solution is zero

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25
Q

Why can an amino acid act as a buffer?

A

Because it can react with added acid and bases to keep the pH nearly constant

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26
Q

What is the pKa 1 because of?

A

The carboxyl group

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27
Q

What is the pKa 2 because of?

A

The amino group

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28
Q

Why do some amino acids have 3 pKa?

A

Because the have 2 amino groups

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29
Q

What bond forms between 2 amino acids?

A

Peptide bonds

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30
Q

What reaction happens when bond forms between 2 amino acids?

A

Dehydration or condensation reaction (elimination of water molecule)

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31
Q

What is a peptide formed by 2 amino acids called?

A

Dipeptide

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32
Q

What are the 8 classifications of the R group?

A

Hydrophobic, hydrophilic, aromatic, aliphatic, polar, neutral, positively charged, negatively charged

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33
Q

2 amino acids with OH group

A

Serine and Threonine

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34
Q

What can amino acids with OH be?

A

Phosphorylated

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35
Q

Most common amino acid with a sulfur group?

A

Cysteine

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36
Q

3 amino acids that can be phosphorylated?

A

Serine and Threonine and Tyrosine

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37
Q

What decides if the charge of an amino acid is postive or negative?

A

The pH

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38
Q

What happens to the positive and negative charge in a protein in an aqueous solution?

A

The hydrophobic aminoacid go in the middle and the hydrophilic go to the outside, called the hydrophobic effect

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39
Q

What is the hydrophobic effect ?

A

Folding of protein because the hydrophobic goes away from the water

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40
Q

Most important concept in folding of proteins?

A

The hydrophobic effect

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41
Q

What is the fisher projection useful for seeing?

A

Stereoisomers

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42
Q

When do strong hydrophobic interaction occur?

A

When aromatic groups are stacked in the phenylalanine side chains

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43
Q

What are covalent disulphide bonds formed between?

A

2 molecules of cysteine or cysteine residues in a protein

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44
Q

Where does the electrostatic interaction happen?

A

Between the positively charged side chain and negatively charged side chain

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45
Q

How many essential amino acids are there?

A

9

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46
Q

How do we get the essential amino acids?

A

Through the diet, we don’t produce them ourselves

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47
Q

What makes proline different from other amino acids?

A

The side chain is a pyrrolidine ring which includes both the alpha amino group and the alpha carbon

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48
Q

What forces are bend in a polypeptide chain?

A

Proline

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49
Q

What can the bend in a polypeptide chain do?

A

Change the direction of the chain

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50
Q

What links together 2 chains of insulin?

A

Disulphide bridges

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51
Q

Antioxidant which helps prevent damage due to reactive oxygen species

A

Glutathione

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52
Q

What decides the degree of rotation?

A

The R group

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53
Q

Is the peptide bond always a double bond?

A

No but it has a tendency to forma a double bond

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54
Q

Can the alpha carbon rotate?

A

Yes

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55
Q

What part of the protein rotate?

A

The alpha carbon

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56
Q

What charge does a phosphate group have?

A

Negative

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57
Q

What is the most common type of regulatory modification?

A

Phosphorylation

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58
Q

Which amino acid has an uncharged side chain under physiological conditions?

A

Threonine

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59
Q

Which amino acid has a side chain whose pKa is closest to neutral pH?

A

Histidine

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60
Q

Which is the favoured conformation of peptide bonds?

A

The sequential alpha carbon is in trans

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61
Q

What is the alpha helix?

A

Is a right handed helix where the peptide bonds are located on the inside of the chain

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62
Q

How many aa/turn (amino acids/turn) does the alpha helix have?

A

3.6 aa/turn

63
Q

Which amino acid is found most frequently at beta turns in the secondary structure of proteins?

A

Proline

64
Q

Which secondary structure is most likely to be found in the membrane embedded portion of a protein?

A

An alpha helix comprised entirely of hydrophobic residue

65
Q

What interactions contributes most to the thermodynamic stabilisation of a protein’s native structure?

A

Hydrophobic interactions

66
Q

What determines a protein’s native structure?

A

The protein’s linear amino acid sequence

67
Q

What is the molecular interaction called “the hydrophobic effect”?

A

The tendency of non-polar molecules to avoid interactions with water and thus aggregate

68
Q

What is disulphide bonds characterised by?

A

A covalent linkage

69
Q

What does the process of protein folding involve?

A

Progressive stabilisation of correct secondary structural intermediates and unfolding of incorrect structures until the final structure is attained

70
Q

What functional group is the peptide bond?

A

Amide

71
Q

What decides if an amino acid donates a proton or accept a proton (if they are acidic or basic)?

A

The pH of the medium

72
Q

What does the ionisable proton become in low pH?

A

Protenated

73
Q

What does the ionisable proton become in high pH?

A

Deprotenated

74
Q

Two definitions of pKa

A

pKa= pH at which the non-ionised fraction= the ionised fraction
pKa= pH at which the protonated fraction= deprotonated fraction

75
Q

Is the pKa a constant?

A

Yes

76
Q

In an acidic medium which fraction is the largest, the more or less acidic? (pKa>pH)

A

The more acidic, the protonated

77
Q

In a basic medium which fraction is the largest, the more or less acidic? (pKa<pH)

A

The less acidic, the deprotonated

78
Q

What are L and D amino acids?

A

L= amino acid group on left
D= amino acid group on right

79
Q

What does the Ramachandran plot show?

A

At which angles the protein structures are stable and which are psi og phi angles

80
Q

How can you tell if an alpha helix is right handed or left handed?

A

If you have a helix in front of you, imagine a staircase inside it, the actual helix being the handrail: if you go up the stairs, which hand would you put on the handrail? If the handrail is on your right, that’s a right-hand helix, otherwise it’s a left-handed helix.

81
Q

Difference between peptides and proteins

A

Peptides are smaller and contain less amino acids (2-50) where proteins are larger and contain more amino acids (>50)

82
Q

How many amino acid in a peptide?

A

2-50

83
Q

How many amino acids make up a protein?

A

50 or more

84
Q

What determines the charge, polarity and hydrophobicity of proteins?

A

Side chains

85
Q

Are L and D enantiomers superimposable or non superimposable?

A

Nonsuperimposable

86
Q

Why is glycine not a chiral molecule?

A

Because the R group is a H so the carbon doesn’t have 4 different groups

87
Q

Which amino acids are chiral molecules?

A

All but glycine

88
Q

Which forms can all the chiral amino acids exist in?

A

D and L

89
Q

What is Ka?

A

Acid dissociation constant

90
Q

What does Ka measure?

A

How completely an acid dissociates in an aqueous solution

91
Q

Relationship between Ka and strength of acid

A

The higher the Ka the stronger the acid (the more it dissociates)

92
Q

Relationship between pKa and Ka

A

pKa=-log(Ka)

93
Q

What does pKa predict?

A

What a molecule will do at a specific pH

94
Q

What kind of reaction does the amino acids join together in?

A

Condensation reaction or dehydration reaction

95
Q

Do amino acids accept or donate H+ ions?

A

They can do both as they both an acid and a base group

96
Q

What happens to an amino acid when it becomes a zwitterion?

A

Internal acid base reaction: the carboxylic acid group loses H+ ion and the amino group gains the H+ ion

97
Q

What determines wether an amino acid is acidic, basic or a zwitterion?

A

The pH of the solution they are in

98
Q

Do zwitterions form at the same pH for all amino acids?

A

No it forms at different pH

99
Q

What is the isoelectric point?

A

pH of the solution where zwitterions form and exists

100
Q

What is CO2 produced from cellular metabolism converted to in the red blood cells?

A

Bicarbonate and H+

101
Q

What buffers H+ in the red blood cells?

A

Hemoglobin (Hb)
Phosphate (HPO42-)

102
Q

Which amino acid has 3 pKa values?

A

Histidine

103
Q

How many pKa values do most amino acids have?

A

2

104
Q

What denotes the pH at which half the molecule of an amino acid in solution have side chains that are charged?

A

pKa

105
Q

What is a peptide bond formed between?

A

N of the amino group and C of the carboxyl group

106
Q

Possible chemical characteristics of amino acid R groups

A

Hydrophobic
Polar
Positively charged
Negatively charged

107
Q

5 aliphatic amino acids

A

Glycerine
Alanine
Valine
Leucine
Isoleucine

108
Q

4 aromatic amino acids

A

Phenylalanine
Tyrosine
Tryptophan
Proline

109
Q

4 neutral amino acids

A

Serine
Throenine
Asparagine
Glutamine

110
Q

2 sulfur containing amino acids

A

Cysteine
Methionine

111
Q

2 acidic amino acids

A

Aspartic acid
Glutamic acid

112
Q

3 basic amino acids

A

Histidine
Lysine
Arginine

113
Q

What is the disulfide compound called?

A

Cystine

114
Q

Is insulin highly variable between specie?

A

No it is highly conserved, only very few amino acid substitutions and none in the regions that affect activity

115
Q

What is the precursor molecule of insulin?

A

Proinsulin

116
Q

How is proinsulin converted into insulin?

A

Proteolytic cleavage of certain peptide bonds

117
Q

Are the chains in the active insulin molecule identical or nonidentical?

A

Nonidentical

118
Q

Which amino acid can exist in cis-configuration in peptides?

A

Proline

119
Q

What are peptide units?

A

Effectively rigid groups that are linked to a chain by covalent bonds at the alpha carbon

120
Q

How many degrees of freedom does each peptide unit have?

A

2

121
Q

What is the rotation around the alpha C-N bond in a peptide unit called?

A

Phi

122
Q

What is the rotation around the alpha C-N bond in a peptide unit called?

A

Psi

123
Q

What is the confirmation of the main chain atoms determined by?

A

The values of the Phi and Psi angles in the peptide units

124
Q

What is the peptide torsion angle?

A

The values of the Phi and Psi angles in the peptide units

125
Q

Where can post-translational modification occur?

A

On the amino acid side chains

126
Q

How do post-translational modifications extend the chemical repertoire of the 20 standard amino acids?

A

By modifying an existing functional group or introducing a new one

127
Q

What is glycosylation?

A

The addition of carbohydrates to a molecule

128
Q

What are oligosaccharides bound to serine or threonine residues by in O-glycosylation?

A

O-linkages

129
Q

What are carbohydrates bound to the amide nitrogen of asparagine by in N-glycosylation?

A

N-linkage

130
Q

What is fatty acylation?

A

Addition of lipids to a molecule

131
Q

What does prenylation involve the addition of?

A

The farnesyl group (C15) or geranylgeranyl groups (C20)

132
Q

What are the farnesyl group (C15) and geranylgeranyl groups (C20) synthesised from?

A

The five-carbon isoprene unit (isopentenyl pyrophosphate)

133
Q

What is the primary structure of amino acids?

A

Polypeptide chain

134
Q

What is the secondary structure of amino acids?

A

Alpha helix and beta pleated sheets

135
Q

What is the tertiary structure of amino acids?

A

Folded sheets and helixes

136
Q

What is the quaternary structure of amino acids?

A

Subunits attached

137
Q

Which enantiomer of amino acids are found in proteins, L or D?

A

L-amino acids

138
Q

Why are there 2 different pKa when titrating amino acids?

A

Because there is the amino group and the carboxylic acid group

139
Q

At what pH does the zwitterion occur?

A

Around neutral pH

140
Q

Name of the starting point of amino acids

A

N-terminus

141
Q

Name of the ending point of amino acids

A

C-terminus

142
Q

Which side is N-terminus on?

A

Left

143
Q

Which side is C-terminus on?

A

Right

144
Q

What makes amino acids more hydrophobic?

A

Long side chains

145
Q

Why is cysteine very reactive?

A

Because of the presence of S in its side chain

146
Q

What kind of bonds are peptide bonds?

A

Covalent bonds

147
Q

Is cystine strong or weak?

A

Very strong

148
Q

How is a sequence of amino acid written?

A

Left to right
From amino terminal to carboxyl terminal

149
Q

How many amino acids are the 2 chains of insulin made up of?

A

A chain: 21
B chain: 30

150
Q

What is glutathione made up of?

A

Glutamyl
Cysteinyl
Glycine

151
Q

Why is trans confirmation the most common in amino acids?

A

Because the confirguration is mor linear and the R chains are far away from eachother so they don’t interact

152
Q

Which 2 metals are the typical intrinsic metal ions?

A

Iron and zinc

153
Q

3 types of post-translational modifications of amino acids in proteins

A

Glycosylation
Lipid addition
Prenylation

Biochemistry (28 decks)

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