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Z OLD Molecules, Genes and Disease > Amino acids and proteins > Flashcards

Amino acids and proteins Flashcards

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Organic Chemistry 101 flashcards
1
Q

What are the 12 components of a eukaryotic cell?

A

Plasma membrane, Lysosome, Basal bodies, Golgi complex, Vacuole, Nucleus, Rough endoplasmic reticulum, Cytosol, Free ribosomes, Mitochondria, Smooth endoplasmic reticulum

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2
Q

What does the nucleus consist of?

A
  • Nucleur envelope
  • Nucleolus
  • Chromosomes
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3
Q

What causes differences in cell types?

A

Proteins expressed

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4
Q

How does the DNA in every cell differ?

A

All the same, but not all genes expressed

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5
Q

What does differential expression of DNA mean?

A

Not all proteins are made

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6
Q

Give 5 examples of specialised cell types

A
  • Nerve cells
  • Adipocytes
  • Red blood cells
  • Muscle cells
  • Epithelial cells
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7
Q

What is the simplest cell type?

A

Prokaryotic cell

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8
Q

What are the 8 components of a prokaryotic cell?

A
  • Capsule
  • Cell wall
  • Plasma membrane
  • Flagella
  • Ribosomes
  • Cytosol
  • Nucleoid
  • Pilli
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9
Q

What is the advantage of the differences between eukaryotic and prokaryotic cells?

A

Can target these differences in the use of antibiotics

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10
Q

What differences can be targeted in the use of antibiotics?

A
  • Bacteria have no separate nucleus
  • Bacteria contain cell wall and plasma membrane
  • Bacteria lack most organelles
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11
Q

What are the levels of structure in a cell?

A

Cell/organelle → macromolecular complex → macromolecles → monomeric units

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12
Q

How are monomeric units joined together?

A

Covalent bonds

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13
Q

How are macromolecules/complexes held together?

A

By non-covalent interactions

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14
Q

Of what nature are most interactions between biomolecules?

A

Electrostatic

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15
Q

What do electrostatic interactions involve?

A

Some sort of charge

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16
Q

What type of interactions are present between biomolecules?

A
  • Hydrogen bonds
  • Ionic interactions
  • Hydrophobic interactions
  • Van der Waals interactions
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17
Q

Where do hydrogen bonds occur?

A

Between C=O and O-H, and peptide bonds (C=O and N-H)

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18
Q

Why do hydrogen bonds arise?

A

Because of polarised bonds

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19
Q

Why is the O-H bond polarised?

A

The hydroxyl group has very strong electronegative oxygen atom that pulls electrons towards it from H

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20
Q

Where do ionic interactions occur?

A

Between fully charged molecules

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21
Q

Are ionic interactions attraction or repulsion?

A

Can be either

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22
Q

What do hydrophobic interactions involve?

A

Exclusion of water

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23
Q

Are van der Waals forces strong or weak?

A

Weak

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24
Q

Why are van der Waals forces significant?

A

Because there are lots of them

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25
Q

What does the formation of macromolecules and complexes require?

A

Weak interactions

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26
Q

What is the result of multiple weak interactions?

A

They increase the stability of complexes

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27
Q

What is the result of breaking interactions between macromolecules and complexes?

A

Loss of structure and function

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28
Q

What does solubility depend on?

A

Ability to form hydrogen bonds

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29
Q

Essentially, what is the ability to be soluble?

A

The ability to interact with water, not necessarily to form hydrogen bonds

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30
Q

What kind of molecules can form hydrogen bonds?

A

Polar

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31
Q

Give 3 examples of polar molecules

A

NAME?

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32
Q

Why is glucose highly soluble?

A

Because it has lots of -OH groups, which can form hydrogen bonds with water

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33
Q

Are non polar molecules soluble?

A

No, because they cannot form H bonds

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34
Q

What kind of molecules are insoluble?

A

Fat like molecules

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35
Q

Why are fat like molecules insoluble?

A

Because C-C bonds cannot interact with water

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36
Q

Can carbonyl groups interact with water?

A

Yes, the O can

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37
Q

Why does the presence of a carbonyl group in fats not necessarily mean they are soluble?

A

Because it doesn’t have much impact compared to the rest of the molecule

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38
Q

What is hydrophilicity?

A

How much something likes water

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39
Q

What are amphipathic molecules?

A

Molecules with both polar and non-polar regions

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40
Q

Give an example of amphipathic molecules

A

Phospholipids

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41
Q

What is the result of amphipathic molecules having both polar and non-polar regions?

A

One side is very hydrophobic and one side is very hydrophilic

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42
Q

What happens when amphiphatic molecules are placed in water?

A

Hydrophobic regions cluster together and hydrophilic regions interact with water, forming micelles

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43
Q

Describe a micelle

A

The hydrophobic groups away from water, with an ordered shell of hydrophilic head groups that interact with water

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44
Q

Why are micelles formed?

A

Because they are energetically favourable

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45
Q

What model do biological membranes follow?

A

Fluid mosaic model

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46
Q

What are biological membranes made up of?

A

Lipid bilayer with proteins embedded in it

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47
Q

How are the proteins associated with the bilayer?

A

Can be associated on outside or span the membrane

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48
Q

What is it important that membranes have the right amount of?

A

Fluidity

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49
Q

What regulates membrane fluidity?

A

Cholesterol

50
Q

Where do proteins play a crucial role?

A

Virtually all biological processes

51
Q

Give 8 roles of proteins

A
  • Catalysts
  • Transporters
  • Structural support
  • Machines
  • Immune protection
  • Ion channels
  • Receptors
  • Ligans in cell signalling
52
Q

What are protein catalysts called?

A

Enzymes

53
Q

What do enzymes do?

A

Speed up rate of reaction

54
Q

Give an example of a transporter protein

A

Haemoglobin

55
Q

What proteins give structural support?

A

Collagens in skin and bone

56
Q

What proteins provide immune protection?

A

Immunoglobulins

57
Q

What are protein receptors for?

A

Hormones, neurotransmitters etc

58
Q

Give an example of a signalling ligand

A

Growth factors

59
Q

What kind of molecules are proteins?

A

Polypeptides

60
Q

What are polypeptides?

A

Macromolecules made up of amino acids covalently bonded by peptide bonds to give sequence of protein

61
Q

Technically, what are amino acids in proteins

A

Amino acid residues

62
Q

What is the amino acid sequence encoded for by?

A

The nucleotide sequence of a gene

63
Q

What do you have to have to make a protein

A

A gene

64
Q

What can each gene make?

A

More than one protein

65
Q

How can each gene make more than one protein?

A

Alternative splicing also transcription of mRNA in different ways

66
Q

What does the polypeptide chain fold into?

A

A complex and highly specific 3D struture

67
Q

What is the folding of a protein determined by?

A

The amino acid sequence

68
Q

What does the shape of a protein determine?

A

Function

69
Q

What happens to a denatured protein?

A

It looses its function

70
Q

What does folding depend on?

A

The physical and chemical properties of amino acids

71
Q

Does anything else help proteins fold?

A

Yes

72
Q

Where does the ability to fold in the right shape come from?

A

Solely from amino acid sequence

73
Q

What are amino acids?

A

The building blocks of proteins

74
Q

What is the amino acid made up of?

A

An amino group, a H, a carboxylic acid and a side chain covalently bonded to the α-carbon

75
Q

What is the ionised form of an amino acid called?

A

Zwitterion

76
Q

What happens to the amino acid in its ionised form>

A

The amino acid and carboxyl group are ionised, forming NH 3 + and COO -

77
Q

What is the overall charge on a zwitterion?

A

None

78
Q

What acts as the base in a zwitterion?

A

NH 2

79
Q

What acts as the acid in a zwitterion?

A

COOH

80
Q

Why can amino acids show stereochemistry?

A

Because there are 4 different functional groups attached to each central carbon

81
Q

Which isomer is found in humans?

A

L

82
Q

What would happen if there was a mixture of isomers in the human body?

A

Wouldn’t be able to form protein structure

83
Q

What are amino acids classified according to?

A

Chemical properties of the R groups

84
Q

Why are we only really interested in the R groups of amino acids?

A

Because when amino acids are joined together, we lose the amine group and carboxyl group in peptide bonds, leaving only one α-NH 3 + at N terminal end and one α-COO - at C terminal end, so only R groups impact properties

85
Q

What do R groups determine?

A

Acid base behaviour

86
Q

What kind of things affect an R groups properties?

A

NAME?

87
Q

What does aliphatic mean?

A

Long chains of C’s

88
Q

What does aromatic mean?

A

Rings of C’s

89
Q

Why does size affect properties?

A

Bulky side chains can cause problems with folding

90
Q

What are the 3 major types of amino acids?

A
  • Non-polar (hydrophobic)
  • Polar, uncharged (hydrophilic)
  • Polar, charged (hydrophilic)
91
Q

Why does the sulphur in methionine not cause polarity?

A

Because it’s in the middle of the chain

92
Q

What happens to prolines side chain?

A

It loops back

93
Q

What is the result of the polar groups in polar, uncharged amino acids?

A

They are able to interact with water

94
Q

What do charged amino acids have?

A

Whole charges on side chains

95
Q

Why is histidine classed as a polar, charged amino acid?

A

Despite having no charge, it’s acid dissociation constant means it’s classed as a positively charged molecule

96
Q

What is the pK a ?

A

The acid dissociation constant

97
Q

What does the acid dissociation constant tell you?

A

How likely a group is to dissociate/release a proton

98
Q

What happens if the pH of the solution

A

The group is protonated, resulting in a positive side chain

99
Q

What happens when the pH of the solution > the pK value?

A

The group is deprotonated

100
Q

What happens in peptide bond formation?

A

2 amino acids are linked by the removal of water

101
Q

What is meant by peptide bonds being planar?

A

C α , C, O, N and H all lie in the same plane

102
Q

What happens to the R groups when peptide bonds are formed?

A

They point up and down in different directions

103
Q

What is the advantage of the R groups pointing up and down alternately?

A

It allows when to form H bonds

104
Q

What does the C-N bond of proteins have?

A

Partial double bond characteristics

105
Q

What is the advantage of the C-N bond being short?

A

It means it’s stronger

106
Q

Why does the C-N bond being short mean its stronger?

A

Because electrons in the carbonyl bond delocalise across the bond

107
Q

What is the result of the delocalisation of the carbonyl groups electrons?

A

Makes the bond rigid and planar

108
Q

What different ways can peptide bonds be seen?

A

NAME?

109
Q

What happens to the R groups in trans formation?

A

The R groups are on opposite sides

110
Q

What orientation are peptide bonds in naturally occurring proteins?

A

Trans

111
Q

Why are peptide bonds only found in trans formation in naturally occurring proteins?

A

Prevents steric clashes

112
Q

What does the amino acid sequence determine?

A

NAME?

113
Q

What is the isoelectric point a protein?

A

The pH at which there is no overall net charge

114
Q

What is the pI of a basic protein?

A

> 7

115
Q

What does a basic protein contain?

A

A lot of positively charged (basic) amino acids

116
Q

What is the pI of an acidic protein?

A
117
Q

What does a acidic protein contain a lot of?

A

A lot of negatively charged (acidic) amino acids

118
Q

What happens if pH

A

Protein is protonated

119
Q

What happens if pH > pI?

A

Protein is deprotonated

120
Q

How many amino acids are in peptides/oligopeptides?

A

Few-

121
Q

How many amino acids are in polypeptides/proteins?

A

Many

122
Q

What are conjugated proteins?

A

Proteins covalently linked to chemical component in addition to amino acids

Z OLD Molecules, Genes and Disease (14 decks)

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