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Molecules, Genes, and Cells > Structure and Function of Proteins > Flashcards

Structure and Function of Proteins Flashcards

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Organic Chemistry 101 flashcards
1
Q

What are the 5 groups of amino acids?

A

Hydrophobic, aromatic, polar, negatively charged, positively charged

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2
Q

Do hydrophobic acids contain polar groups?

A

No

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3
Q

Where are hydrophobic amino acids found?

A

the hydrophobic core of proteins

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4
Q

Which amino acid group does glycine belong to?

A

Hydrophobic

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5
Q

What is the one letter code for glycine?

A

G

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6
Q

What is the three letter code for glycine?

A

Gly

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7
Q

Which amino acid group does alanine belong to?

A

Hydrophobic

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8
Q

What is the one letter code for alanine?

A

A

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9
Q

What is the three letter code for alanine?

A

Ala

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10
Q

Which amino acid group does valine belong to?

A

Hydrophobic

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11
Q

What is the one letter code for valine?

A

V

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12
Q

What is the three letter code for valine?

A

Val

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13
Q

Which amino acid group does leucine belong to?

A

Hydrophobic

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14
Q

What is the one letter code for leucine?

A

L

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15
Q

What is the three letter code for leucine?

A

Leu

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16
Q

Which amino acid group does isoleucine belong to?

A

Hydrophobic

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17
Q

What is the one letter code for isoleucine?

A

I

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18
Q

What is the three letter code for isoleucine?

A

Ile

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19
Q

Which amino acid group does methionine?

A

Hydrophobic

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20
Q

What is the one letter code for methionine?

A

M

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21
Q

What is the three letter code for methionine?

A

Met

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22
Q

Which amino acid group does proline belong to?

A

Hydrophobic

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23
Q

What is the one letter code for proline?

A

P

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24
Q

What is the three letter code for proline?

A

Pro

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25
Q

Name the 7 hydrophobic amino acids

A

Glycine, Alanine, Leucine, Isoleucine, Valine, Methionine, Proline

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26
Q

What do all aromatic amino acids contain?

A

A ring of delocalised electrons

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27
Q

Which amino acid group does phenylalanine belong to?

A

Aromatic

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28
Q

What is the one letter code for phenylalanine?

A

F

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29
Q

What is the three letter code for phenylalanine?

A

Phe

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30
Q

Which amino acid group does tyrosine belong to?

A

Aromatic

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31
Q

What is the one letter code for tyrosine?

A

Y

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32
Q

What is the three letter code for tyrosine?

A

Tyr

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33
Q

Which amino acid group does tryptophan belong to?

A

Aromatic

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34
Q

What is the one letter code for tryptophan?

A

W

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35
Q

What is the three letter code for tryptophan?

A

Trp

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36
Q

Are polar amino acids hydrophilic or hydrophobic?

A

Hydrophilic

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37
Q

Where are polar amino acids usually found?

A

On the surface of proteins

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38
Q

Which amino acid group does serine belong to?

A

Polar

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39
Q

What is the one letter code for serine?

A

S

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40
Q

What is the three letter code for serine?

A

Ser

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41
Q

Which amino acid group does threonine belong to?

A

Polar

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42
Q

What is the one letter code for threonine?

A

T

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43
Q

What is the three letter code for threonine?

A

Thr

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44
Q

Which amino acid group does cysteine belong to?

A

Polar

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45
Q

What is the one letter code for cysteine?

A

C

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46
Q

What is the three letter code for cysteine?

A

Cys

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47
Q

Which amino acid group does asparagine belong to?

A

Polar

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48
Q

What is the one letter code for asparagine?

A

N

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49
Q

What is the three letter code for asparagine?

A

Asn

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50
Q

Which amino acid group does gluamine belong to?

A

Polar

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51
Q

What is the one letter code for gluamine?

A

Q

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52
Q

What is the three letter code for gluamine?

A

Gln

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53
Q

Name the 3 aromatic amino acids

A

Phenylalanine, tyrosine, tryptophan

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54
Q

Name the 5 polar amino acids

A

Serine, threonine, cysteine, asparagine, gluamine

55
Q

Which amino acid group does aspartate belong to?

A

Negatively charged

56
Q

What is the one letter code for aspartate?

A

D

57
Q

What is the three letter code for aspartate?

A

Asp

58
Q

Which amino acid group does glutamate belong to?

A

Negatively charged

59
Q

What is the one letter code for glutamate?

A

E

60
Q

What is the three letter code for glutamate?

A

Glu

61
Q

Name the 2 negatively charged amino acids

A

Aspartate, glutamate

62
Q

Which amino acid group does lysine belong to?

A

Positively charged

63
Q

What is the one letter code of lysine?

A

K

64
Q

What is the three letter code of lysine?

A

Lys

65
Q

Which amino acid group does arginine belong to?

A

Positively charged

66
Q

What is the one letter code for arginine?

A

R

67
Q

What is the three letter code for arginine?

A

Arg

68
Q

Which amino acid group does histidine belong to?

A

Positively charged

69
Q

What is the one letter code for histidine?

A

H

70
Q

What is the three letter code for histidine?

A

His

71
Q

Name the 3 positively charged amino acids

A

Lysine, arginine, histidine

72
Q

Name the 7 uses of proteins

A 
catalysis
transport and storage
motion
mechanical support
immune protection
signal transduction
growth and development control
73
Q

Which amino acid is the most common replacement in mutation?

A

Alanine (she fit)

74
Q

Why is hydrogen bonding limited in proline?

A

Lack of hydrogen on the nitrogen

75
Q

What is the largest amino acid?

A

Tryptophan

76
Q

Which amino acid contains an imidazole ring?

A

Histidine

77
Q

Name the two processes by which protein structures can be determined

A

X-ray crystallography and Nuclear Magnetic Resonance (NMR)

78
Q

What are the three types of protein structure?

A

Globular, Membrane, and Fibrous

79
Q

Are globular proteins soluble in water?

A

Yes

80
Q

What makes globular proteins soluble in water?

A

They have a hydrophobic core and a hydrophilic surface

81
Q

What are possible protein structures limited by?

A

Properties of the peptide bond

82
Q

What is the hierarchy of protein structure?

A

Primary: amino acid sequence
Secondary: secondary structure elements and motifs
Tertiary: whole protein/domain structure
Quaternary: whole protein structure

83
Q

Can rotation occur around a peptide bond?

A

No

84
Q

Which amino acid can form cis bonds?

A

Proline

85
Q

Which bond is between C(alpha) and the amide group?

A

Phi

86
Q

Which bond is between the carbonyl carbon and the C(alpha)

A

Psi

87
Q

What does a Ramachandran plot show?

A

Which Phi and Psi bond combinations are possible

88
Q

What types of bonding are in proteins?

A
  • ionic interactions: between acidic and basic side chain groups of opposite charge
  • hydrogen bond: between donor and acceptor groups
  • disulphide bridges
  • hydrophobic interactions: between aliphatic and aromatic side chain groups
  • pi stacking between aromatic groups
89
Q

What are domains built from?

A

Motifs

90
Q

What can domains be stabilised by?

A

Disulphide bondes

91
Q

What are two ways in which proteins can be post translationally modified?

A

Covalent and non-covalent

92
Q

What are some examples of covalent modification?

A

Disulphide bridge formation, cleavage of peptide bonds, the N-terminus, the C-terminus, amino acid residues (side chains)

93
Q

What are some examples of non-covalent modification?

A

Addition of metals, addition of cofactors

94
Q

Why are proteins modified?

A

Stability, regulation of activity, localisation, ageing

95
Q

Are alpha helices left-handed or right handed?

A

Right-handed

96
Q

Do protein adopt the most thermodynamically stable or unstable structure?

A

Stable

97
Q

Name the four methods of denaturation

A

Chemical denaturants, heat, acid/base, force/kinetic energy

98
Q

What do protein disulphide isomerases (PDI) do?

A

Accelerate the formation of native disulphide bridging arrangements allowing disulphide shuffling and attacks incorrectly formed disulphide bonds

99
Q

What do Peptidyl Prolyl Cis-Trans Isomerases (PPIs) do?

A

Catalyse the rotation around peptide bonds preceding proline

100
Q

What do molecular chaperones do?

A

Prevent the improper folding and aggregation of proteins and prevent or reverse improper associations between proteins

101
Q

What are the two types of molecular chaperones?

A

DnaK/DnaJ/GrpE (or Hsp70) family and chaperonin family (GroE chaperonin)

102
Q

What do the DnaK/DnaJ/GrpE (or Hsp70) family do?

A

Prevent premature folding: bind to growing polypeptide chains while they are being synthesised on ribosomes

103
Q

What do the chaperonin family do?

A

Bind to the solvent-exposed hydrophobic surfaces of an unfolded or aggregated protein and release them

Assist post-translational folding

104
Q

What are proteopathies?

A

Diseases caused by misfolded proteins

105
Q

What are the two classes if proteopathies?

A

Hereditary and acquired

106
Q

Define hereditary proteopathies

A

Mutation causes loss of function or gain of function leading to disease

107
Q

Define acquired proteopathies

A

Infectious prion disease caused by exposure to misfolded proteins from other organisms

108
Q

Give two examples of a hereditary proteopathy

A

Cystic fibrosis and Alzheimer’s disease

109
Q

Give two examples of an acquired proteopathy

A

Bovine spongiform encephalopathy (BSE) and vCJD

110
Q

Why is Alzheimer’s disease associated with neuronal loss?

A

Due to deposition of amyloid plaques

111
Q

What did Anfinsen’s experiment on Ribonuclease A demonstrate about protein folding?

A
  1. All of the information for folding to the correct structure is in the amino acid sequence
  2. Proteins will fold to the most thermodynamically stable conformation
112
Q

Give 3 reasons why proteins might need to be purified

A

Protein characterisation, use in drugs & diagnostics, for commercial use esp. enzymes

113
Q

Give 3 examples of when protein characterisation might be needed

A

Assay to investigate function, investigate post-translational modifications, to study structure-function relationships

114
Q

What are the two sources of proteins?

A

Native (extracted from host organism) and heterologous protein expression systems

115
Q

How do heterologous protein expression systems work?

A
  1. Gene cloned into a vector
  2. Inserted into an organism
  3. Produces the protein via constitutive expression or inducible expression (AraBAD promoter and arabinose)
116
Q

Name the 6 characteristics used to separate proteins

A 
Size
Charge
Specific binding 
Specific epitope
Purification tag
Hydrophobicity
117
Q

How are proteins separated by size?

A

Size exclusion chromatography

118
Q

How are proteins separated by charge?

A

Ion exchange chromatography

119
Q

How are proteins separated by specific binding?

A

Affinity chromatography

120
Q

How are proteins separated by specific epitope?

A

Affinity chromatography

121
Q

How are proteins separated by purification tag?

A

Affinity chromatography

122
Q

How are proteins separated by hydrophobicity?

A

Hydrophobic interaction chromatography

123
Q

How can proteins be engineered for purification and detection?

A
  1. Add signal sequence that causes secretion into culture medium
  2. Add sequence of protein that helps the target protein fold and stay soluble
  3. Add a sequence that aids detection
  4. Add an affinity tag
124
Q

How does hydrophobic interaction chromatography work?

A
  1. Add bacterial lysate to column matrix in high salt buffer (hydrophobic proteins will stick to column)
  2. Wash less hydrophobic proteins from column with low salt buffer (less hydrophobic proteins elute from column)
  3. Elute protein from column by adding salt-free buffer
125
Q

What are the two techniques for analysing protein size?

A

Gel electrophoresis and mass spectrometry

126
Q

What is the difference in the mass given by gel electrophoresis vs mass spectrometry?

A

Gel electrophoresis gives approximate mass; mass spectrometry gives accurate mass

127
Q

What is the aim of polyacrylamide gel electrophoresis (PAGE)?

A

Separating mixtures of proteins by their relative rates of migration through a matrix in an electrical field

128
Q

What type of PAGE should be used for denatured protein?

A

SDS-PAGE

relative migration rate based on mass of protein

129
Q

What type of PAGE should be used for native proteins?

A

Native PAGE

relative migration rate based on both mass of protein and charge at the pH used

130
Q

What is isoelectric focusing (IEF) used for?

A

To separate proteins according to their overall charge

131
Q

What are the three basic components of a mass spectrometer?

A

Ioniser, mass analyser, detector

132
Q

What is the proteome?

A

The primary sequence of all proteins

133
Q

How can proteins be identified in complex mixtures?

A

Proteomics

  1. extract mixture of proteins from cells/tissue and 2D-PAGE
  2. extract proteins from gel and digest with trypsin
  3. identify by peptide mass fingerprinting

Molecules, Genes, and Cells (4 decks)

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