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1

What is the smallest unit in which an element can exist?

An atom

2

What are the subatomic particles of an atom and give their relative charges.

Electron -1
Proton +1
Neutron 0

3

What is an Anion?

Has gained electrons. Has more electrons than protons and therefore has a negative charge.

4

What is a Cation?

Losses electrons. So has more protons than electrons. Has a positive charge.

5

What is the name of a positively charged ion?

Cation

6

What is the name of a negatively charged ion?

Anion

7

What are each of the atomic orbitals labelled as?

s, p, d, f

8

Which atomic orbitals are present in shell 1 of an atom?

S

9

How many electrons does an 'S' atomic orbital hold?

2

10

Which atomic orbitals are present in shell 2 of an atom?

S and P

11

How many electrons can the P atomic orbital of an atom hold?

6

12

Which atomic orbitals are in shell 3 of an atom?

S, P, D

13

How many electrons does the 'D' atomic orbital of an atom hold?

10

14

How many electrons does the 'F' atomic orbital of an atom hold?

14

15

What does the atomic number of an atom tell us?

The number of protons and therefore electrons that an atom has.

16

Write out the order in which electron shells are filled by electrons. (Up to 4d).

1s, 2s, 2p, 3s, 3p, 4s, 3d, 4p,5s, 4d.

17

Potassium has an atomic number of 19, write out its electron configuration.

1S2, 2S2, 2P6, 3S2, 3P6, 4S1

18

How can you identify the atomic number of an atom given its electron configuration?

Add all of the numbers in the superscript. These tell you the number of electrons in the atom and therefore the number of protons in an atom too.

19

What are valency electrons?

Electrons which are furthest away from the nucleus and which are likely to be involved with bonding with other atoms.

20

What are the electrons that are furthest away from the nucleus called?

Valency electrons

21

How many amino acids exist?

20

22

What do amino acids derive from?

Carboxylic acids

23

What causes 'Alpha' amino acids?

They have a central alpha carbon.

24

Name some properties of amino acids.

Cause cellular changes in pH.
Have changes in charge distribution.
Catalyse enzymes.
They are important in metabolism and cellular activities.

25

What form are amino acids in at low pH?

Ion form with a positive charge.

26

When are amino acids in ion form?

At low or high pH

27

What form are amino acids in at neutral pH?

Zwitterion form

28

When are amino acids in their Zwitterion form?

At neutral pH

29

What form are amino acids in at high pH?

Ion form with a negative charge.

30

What is a Zwitterion ?

A ion with separate positively and negatively charged groups.

31

When are the polar side chains of amino acids hydrophilic?

At neutral pH

32

When are the non polar side chains of amino acids hydrophobic?

At neutral pH

33

Are polar side chains of amino acids hydrophobic or hydrophilic?

Hydrophilic

34

Are the non-polar side chains of amino acids hydrophilic or hydrophobic?

Hydrophobic

35

What are amino acids classified based on?

The chemical properties of their 'R' groups.

36

What are the classifications of amino acids?

Hydrophobic amino acids.
Polar amino acids.
Positively charged amino acids.
Negatively charged amino acids.

37

How are hydrophobic amino acids categorised?

They have non-polar 'R' groups.

38

How are polar amino acids categorised?

They have neutral R groups with an uneven charge distribution.

39

How are positive charged amino acids classified ?

They have 'R' groups with a positive charge at pH 7.4

40

How are negatively charged amino acids classified?

They have a negatively charged 'R' group at pH 7.4

41

Describe the general structure of the amino acid 'Proline' and how this occurs.

A confirmationally restricted ring structure. Due to aliphatic side chains which are bonded to both alpha carbon and 'Nitrogen' atoms of other amino acids.

42

Describe the structure of the amino acid 'Phenylanine' and how this occurs.

Phenyl ring structure due to aromatic rings in the side chains being hydrophobic.

43

Describe the structure of the amino acid 'Tryptophan' and why this occurs.

Indole ring.
Because aromatic rings in the side chains are hydrophobic and so cluster away from water.

44

What are the overall characteristics of the amino acids 'Serine', 'Theronine' and 'Tyrosine'?

They all have 'OH' groups which makes them hydrophilic.

45

Why are Serine, Theronine and Tyrosine amino acids all hydrophilic?

They have an OH group.

46

What is meant by -SH?

Has a thiol or a slufhydryl functional group.

47

What is the effect of an amino acid having an -SH functional group?

This is a reactive functional group so works to stabilise the protein structure by making covalent disulphide bonds.

48

Name an amino acid with a -SH functional group.

Cysteine

49

Outline some of the characteristics of negatively charged amino acids.

They have acidic side chains which are ionisable.

50

What are the benefits of an amino acid having an ionisable side chain?

This allows them to form ionic bonds by accepting or donating electrons to facilitate reactions.

51

What are the 2 different enantiomers of Thalidomide?

R and S

52

How does the composition of Thaldomide change within the body?

During metabolism, Thalidomide undergoes racemization. So instead of one pure enantiomer existing, both enantiomers are present in an equal mixture.

53

What is a racemic mixture?

Equal quantities of each enantiomer of a molecule are present.

54

What is racemization?

The use of heat or chemicals to convert one pure enantiomer into an equal mixture of both enantiomers.

55

Which enantiomer of Thalidomide has negative effects?

S

56

What are enantiomers?

Molecules that are exact mirror images of each other.

57

What are molecules that are exact mirror images of each other called?

Enantiomers

58

What type of reaction joins amino acids together?

Condensation

59

What are 2 amino acids chemically bonded called?

Dipeptide

60

Which parts of each amino acids bond to form a dipeptide?

The carboxyl group of one Amino acid group reacts with the amine group of another amino acid to form a peptide bond and remove water.

61

What type of bonds join amino acids?

Peptide

62

Draw a peptide bond

-

63

Draw the structure of an amino acid

-

64

Draw the structure of a carboxylic acid

-

65

Draw the structure of glycerol

-

66

Draw the structure of an ester bond

-

67

Draw the structure of a peptide bond

-

68

What is it called when many amino acids are joined?

Polypeptide

69

What is the primary structure of a protein?

The specific sequence of amino acids which are joined by peptide bonds.

70

How can amino acids be identified by their primary structure?

Identified by the N terminus amine group and the C terminus carboxyl group.

71

What is the secondary structure of proteins?

The folding of the amino acids in to alpha helices and beta pleated sheets using hydrogen bonding.

72

What is the tertiary structure of proteins?

The bonding between alpha helices and beta pleated sheets to form a 3D globular structure.
Using hydrogen bonding, ionic interactions and disulphide bridges.

73

What is the quaternary structure of proteins?

More or one polypeptide chain or the presence of prosthetic groups.

74

How can changing one amino acid in the primary structure affect Haemoglobin?

Changing one amino acid may cause large fibrous aggregates to form. This means fibres form across the cell and cause cellular distortion. This cellular distortion causes swelling in the extremities of the body. This is painful and can lead to a high risk of infection.

75

What are cell aggregates?

Cells that are loosely grouped together. Not grouped tightly enough to form a tissue.

76

How can chaining one amino acid in the primary structure of a protein lead to Cystic Fibrosis?

If there is a change in the structure of the Cystic Fibrosis Transmembrane Conductance Regulator Protein, mucus production won' be regulated. This means that proteins will have abnormal transport across cell membranes. Mucus will build up and infections e.g cystic fibrosis.

77

Describe some of the features of peptide bonds.

They are flexible but restricted.
Planar.
Partial double bond character.
Uncharged.
Can be Cis or Trans.
Have angles of rotation.

78

What is meant by a molecule being planar?

6 atoms on the same plane.

79

What occurs when a molecule has carbon-carbon double bonds?

No rotation can occur around carbon carbon double bonds so geometric isomers are formed.

80

What type of isomers are formed due to the presence of carbon-carbon double bonds?

Geometric

81

Are peptide bonds charged or uncharged?

Uncharged

82

What is a 'Cis' molecule?

Side chains with the largest Mr are on the same side of the c-c double bond. (Vertical split)

83

What is a 'Trans' molecule?

Side chains with the largest Mr's are on opposite sides of the c-c double bond. (vertical split)

84

What are the purposes of angles of rotation in bonds.

Used to prevent steric clashes

85

What are steric classes?

The un-natural overlap of two non-bonding atoms in a protein molecule.

86

What type of bonding are alpha helices stabilised by?

Hydrogen

87

How many Amino acids are present per turn of the alpha helix?

3.6

88

Alpha helices can have left or right handed screws, but which are more favourable?

Right screws are more energetically favourable.

89

Why don't the amino acids Valine, Theronine and Isoleucine make Alpha helices?

They have steric clashes and therefore don't fit the alpha helix structure.

90

How does the presence of alpha helices in the secondary structure of a protein affect its solubility?

Alpha helices increase solubility.

91

What are amphipathic helices ?

Hydrophilic outwards and hydrophobic inwards.

92

Name some molecules which beta pleated sheets are present in.

Collagen
Alpha keratin

93

How many polypeptides are needed to form an alpha helices ?

1

94

How many polypeptides are needed to form a beta pleated sheet ?

2 or more

95

How are beta pleated sheets formed?

Beta stranded are arranged side by side and are stabilised by hydrogen bonding between the the carbonyl oxygen of one amino acid and the amine hydrogen of the adjacent amino acid on the beta strands.

96

Are beta pleated sheets with parallel or anti-parallel beta strands more stable?

Anti-parallel are more stable

97

What causes side chain interactions in the tertiary structure of proteins?

The amino acids in the primary structure are pulled closer together and caused to interact.

98

What the of bonds stabilise the tertiary structure of proteins?

Non-covalent interactions between side chains.

99

What type of bonding is present in the tertiary structure of proteins?

Hydrogen
Ionic interactions
Disulphide bridges

100

What are 'Motifs' in terms of protein structure?

A combination of alpha helices, beta strand and loops.

101

What are 'domains' in the tertiary structure of domain and describe their structure.

Compact units which are independent of each other but are joined at the primary structure level. They each have 30-300 amino acids and their own hydrophobic core. They can also have secondary structure elements.

102

How many amino acids are in a tertiary structure 'domain'?

30-300

103

How do tertiary structure 'domains' group?

Into families with similar sequences.

104

What is the purpose of having specific indentations in the tertiary and quaternary structures of proteins?

Allows for specific interactions between the protein to other proteins, DNA or RNA.

105

Do all proteins have a quaternary structure?

No

106

What is an oligomer in terms of proteins?

A protein with multiple different polypeptide subunits (the subunits can have the same or different functions).

107

What type of bonding is the quaternary structure of proteins stabilised by?

Non-covalent hydrophobic interactions.
Electrostatic forces

108

What are charge to charge interactions between proteins?

Electrostatic attraction between 2 charged particles.

109

What distance do Van Der Waals forces act over?

Short

110

Describe the magnitude of van Der Waals forces.

Small

111

When do hydrophobic interactions occur between proteins?

Occur between relatively non-polar molecules.

112

Order these bond types from strongest to weakest: Van Der Waals, covalent bonds, hydrophobic interactions.

Covalent bonds
Hydrophobic interactions
Van Der walls

113

What is meant by a molecule being in its native form?

In its original form

114

How do chemical , heat and pressure denaturants affect proteins?

They cause disruption to the interactive bonds within a protein.

115

Does denaturation or renaturation require more energy?

Renaturation

116

Can all proteins be renatured spontaneously ?

No, but some can.

117

What features are used to fold proteins into an 'N' shape and why is this done.

Energy funnels or energy wells are used. Makes the protein very stable because there are many intermediate structures in the folding pathway.

118

What are proteins folded into an 'N' very stable?

They have many intermediate structures in their folding pathway.

119

How must proteins fold to achieve their lowest energy state?

Spontaneously

120

What are the 3 main types of protein side chain modification?

Hydroxylation
Glycosylation
Phosphorylation

121

When does hydroxylation of a protein side chain occur?

Immediately after the amino acid chain is formed.

122

What does hydroxylation of a protein side chain required?

Vitamin C

123

Give and example of where hydroxylation of an amino acid side chain is necessary.

Essential in the production of collagen.

124

What is glycosylation of a protein side chain?

Adding a sugar chain

125

When does glycosylation of amino acid side chains occur?

Immediately after the Amino acid is formed.

126

Which type of proteins does glycosylation of side chains mainly occur in?

Proteins that have been secreted or are on the surface of cells.

127

what is the purpose of glycosylating side chains of a protein?

Stabilises the protein's structure.

128

What is phosphorylation of a protein side chain?

Adding a phosphate group.

129

What is the purpose of phosphorylation of an Amin acid side chain?

Helps control enzyme activity.

130

Is phosphorylation of amino acid side chains reversible or not?

Yes

131

How many times during the life of a protein can phosphorylation of a side chain occur?

Many

132

What is a chiral centre?

An atom which has 4 different groups chemically bonded to it and has a non-superimposable mirror image

133

Define atomic orbital

Specific areas in which electrons are able to move within the electron cloud.

134

How many electrons can each atomic orbital hold?

s = 2
p = 6
d = 10
f = 14

135

What are the shapes of each atomic orbital?

s = sphere
p = dumbell
d = double dumbell

136

Define electron configuration.

The most stable way that an atom will arrange its electrons around the nucleus.

137

In what order do electrons fill the atomic orbital shells?

1s, 2s, 2p, 3s, 3p, 4s, 3d, 4p, 5s, 4d, 5p, 6s, 4f, 5d, 6p, 7s, 5f, 6d, 7p

138

What are the 2 exceptions to electron configuration?

Copper and chromium

139

How are the electron configurations of copper and chromium different to the normal rule?

They fill the 3d before the 4s

140

Why do copper and chromium fill the 3d before the 4s?

It is more stable for them to have a completely or half 3d orbital. So electrons from the 4s rise to the 3d.

141

Define Zwitterion.

Amino acids with both positive and negative charged areas but with an overall neutral charge.

142

Why is the changing change of amino acids in different environments important?

Allows chemical reactions to continue (especially metabolic).

143

Identify some methods of purifying/ identifying amino acids.

High performance Liquid Chromatography.
Gas chromatography.
Mass spectrometry.

144

Draw a peptide bond

-

145

What are positively charged amino acids?

Amino acids with side chains that can accept H+

146

Are positive charged amino acids acidic or basic ?

Basic

147

What enables the zwitterion capabilities of amino acids?

The amine and carboxyl groups.

148

How does the amine group of an amino acid change when it becomes the zwitter ion form?

Changes from NH2 to NH3+

149

How does the carboxyl group of an amino acid change when it becomes the Zwitter ion form?

It changes from COOH to COO-

150

What is the overall charge of a zwitter ion?

Neutral

151

Draw a trans peptide bond

-

152

Draw a cis peptide bond

-

153

What are amino acids joined by peptide bonds now called?

Amino acid residues

154

What is the end polypeptide that ends in NH2 called?

N terminus

155

what is the end polypeptide that ends in COOH called?

C terminus

156

In an alpha helix, where do stabilising hydrogen bonds form?

Between the C=O of one amino acid residue and the N-H of another on the same polypeptide chain.

157

In a beta pleated sheet, where do the stabilising hydrogen bonds form?

O of one amino acid residue and the N-H of another on a different polypeptide chain.

158

Outline the structure of a beta turn in the secondary structure of a protein?

Causes the chain to double back on itself as a Hydrogen bond forms between the C=O of one amino acid residue and the N-H of another amino acid 3 spaces down the polypeptide chain.

159

Name amino acids which are helix disrupters?

Glycine and Proline

160

How does Proline affect the structure of an Alpha helix?

Causes it to kink and therefore can't form stabilising hydrogen bonds.

161

Where do the stabilising hydrogen bonds form in a beta barrel (tertiary structure)?

The first and last beta strand

162

How many alpha helices need to associate to form a coiled coil tertiary structure?

2 or more

163

What are the 2 main classifications of quaternary structure?

Globular
Fibrous

164

Describe the structure of globular quaternary structures.

Highly folded polypeptides

165

What are the advantages of globular proteins to cells?

Give integrity and strength

166

Describe the structure of fibrous quaternary structures.

Elongated with little folding

167

Why are hydrophobic and hydrophilic interactions beneficial to the structure of proteins ?

Stabilise the 3D structure