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MiMS > Biological macromolecules, protein structure and enzyme catalysis > Flashcards

Biological macromolecules, protein structure and enzyme catalysis Flashcards

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1
Q

What are the roles of sugars and polysaccharides within the cell?

A

Food molecules and energy storage

Structural support in plant and bacteria cell walls

Cell protection

Cell-cell adhesion and mobility

Cell signalling

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2
Q

What is a sugar?

A

Straight chain polyhydroxy alcohols

They include an aldehyde or ketone group

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3
Q

Why is the Haworth projection of glucose misleading?

A

Glucose is puckered not planar

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4
Q

Which bond links 2 monosaccharides?

A

Glycosidic

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5
Q

Why is the reducing end of a disaccharide more reactive?

A

Ring can be opened to produce a free reducing group (aldehyde)

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6
Q

How reactive is sucrose?

Why is this?

A

Relatively inert

No reducing end

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7
Q

What is chitin?

A

Structural polysaccharide used for cell walls of fungi and exoskeletons of arthropods

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8
Q

What is the nitrogen containing group in chitin?

A

N acetyl glucosamine

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9
Q

What are oligosaccharides?

What is their function?

A

Complex carbohydrates that coat proteins and lipids on the cell surface

Protection
Cell-cell adhesion
Signalling

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10
Q

Where are oligosaccharides added to proteins?

A

Endoplasmic reticulum

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11
Q

Which amino acid side chains are oligosaccharides linked to?

A

N-linked to asparagine

O-linked to serine or threonine

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12
Q

What is the function of RNA?

A

Working template involved in gene expression

Information store in some viruses

Structural and functional role in ribosomes

Involved in catalysis

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13
Q

What type of sugar is deoxyribose?

A

Aldopentose

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14
Q

Which part of deoxyribose is incorporated into the DNA?

A

Beta-anomer

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15
Q

How many rings are in a purine molecule?

A

2

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16
Q

How many rings are in a pyrimidine molecule?

A

1

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17
Q

Which bases are purine?

A

Adenine and guanine

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18
Q

Which bases are pyrimidine?

A

Cytosine, thymine and uracil

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19
Q

In which direction do DNA bases bind down the backbone?

A

3’ - 5’

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20
Q

Why do purines only bind to pyrimidines?

A

Same distance between all base pairs so keeps a regular structure

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21
Q

How often is there a complete turn in the double helix of DNA?

A

Every 3.4nm

10 bases per turn

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22
Q

What are major and minor grooves in the DNA helix?

What is the function of these grooves?

A

Spaces between 2 strands

Provide access to the bases for DNA binding proteins n

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23
Q

What does the ribosome consist of?

A

RNA and protein

mostly RNA

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24
Q

Which amino acids have hydrophobic side chains

A

Proline

Alanine

Leucine

Glycine

Isoleucine

Valine

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25
Which amino acids have charged side chains?
Histidine Aspartic acid Glutamic acid Arginine Lysine
26
Which amino acids have aromatic side chains?
Phenylalanine Tryptophan
27
Which amino acids have sulphur-containing side chains?
Cysteine Methionine
28
Which amino acid cannot form hydrogen bonds? Why?
Proline Side chain is covalently linked to the N in of the amino group
29
Where does rotation occur in a peptide bond?
Around the alpha carbon
30
Describe rotation in a peptide bond
Rotation of phi and psi around alpha carbon
31
What is amylose?
A polymer of maltose with repeating alpha glucose subunits
32
How is glycogen stored?
Granules in the liver
33
Can humans break down cellulose?
No
34
On which carbon is DNA deoxy?
2
35
Why do hairpin loops form in RNA? Give an example of this
Some regions of single stranded RNA can be complementary to other regions of the same single stranded molecule e.g. tRNA has 4 regions that are double stranded and forms a 3D structure recognisable by a ribosome
36
What form is the alpha carbon in the chiral centre?
L-form
37
When do amino acids form zwitterions?
At neutral pH
38
What can free cysteine side chains be involved in?
Metal binding
39
Do nucleotide bases point inwards or outwards?
Inwards
40
Is peptide bond planar or non-planar? Why is this?
Planar due to electron delocalisation
41
In what order is the primary structure numbered?
N-terminus to C-terminus
42
What is the primary structure of a protein?
The linear sequence of amino acid residues
43
What was the first protein to have its primary structure determined?
Insulin
44
Describe the experiment that shows how primary structure alone provides all the information required for folding and formation of the tertiary structure?
1. A pure sample of RNase was denatured in a test tube by adding urea and mercaptoethanol - urea breaks hydrogen bonds - mercaptoethanol reduces disulphide bonds 2. Denaturing agents removed and protein spontaneously refolds 3. Refolded structure was active showing that the native structure had reformed
45
What is the secondary structure?
Folding of regions of the protein into localised, regular arrangements of the backbone via hydrogen bonding between N-H and C=O groups
46
In what orientation is a hydrogen bond strongest?
Linear
47
What are the 2 main types of secondary structure?
Alpha helix and beta pleated sheet
48
How are secondary structures linked together?
Loop regions
49
What is shown by the Ramachandran plot?
All combinations of phi and psi angles found in proteins
50
What direction does the alpha helix turn?
Clockwise/right
51
How many amino acid residues are there per turn of the alpha helix?
3.5
52
Which form of the beta-sheet is more stable, parallel or anti-parallel?
Anti-parallel
53
What are the 5 types of interaction in the tertiary structure from strongest to weakest? What are the relative strengths of these interactions?
Disulphide bonding (350-450kj/mol) Ionic interaction (40-200kj/mol) Hydrogen bonding (2-20kj/mol) Hydrophobic interaction (3-10kj/mol) van der Waal's (0.4-4kj/mol)
54
Where do hydrogen bonds form between amino acids?
C=O and N-H groups Between R groups
55
What are hydrophobic interactions?
Hydrophobic groups cluster in the core of the protein and interact with each other to avoid contact with water which would be entropically unfavourable
56
What are 2 other terms for ionic interactions?
Electrostatic interactions Salt bridges
57
Why are ionic interactions stronger in the core of a protein?
No water to shield the charges
58
Why do vdW forces arise?
Asymmetric electron distribution induces a transient dipole in a neighbouring atom
59
What determines the strength of vdW forces?
Distance between atoms
60
Why don't intracellular proteins exhibit disulphide bonding
disulphide bonds cannot form inside the cell because it is a reducing environment
61
Describe fibrous proteins
Regular, ordered structures with a strong repeat unit
62
Give examples of fibrous proteins
Collagen and keratin
63
What is the function of collagen?
Provides strength to skin, bone, cartilage and tendons
64
Describe the structure of collagen
Each chain forms a helix which twists around 2 others to form a 'superhelix'
65
Why is collagen not an alpha helix?
It has only 3 residues per turn and is left handed
66
What are each of the 3 collagen chains made up of ?
Many copies of a 3 amino acid repeat: Gly-X-Y X is usually proline which causes tight bends in the backbone Y is usually hydroxyproline which is generated by enzymatic modification of proline
67
Describe the orientation of the chains and the helix formed in collagen
Each chain is a left handed helix The 3 chains are twisted into a right handed superhelix
68
What is the reason for the tensile strength of collagen?
Tightly packed triple helix structure
69
Where are the proline residues situated in collagen?
On the outside of the triple helix
70
Where is glycine situated in collagen? Why is this?
On the inside of the triple helix Its small size allows the 3 helices to pack closely
71
What is hydroxylation?
Addition of an -OH group
72
What is a collagen fibre made up of?
Many triple helices
73
What does proline hydroxylation enable?
Formation of another hydrogen bond (proline has no NH group)
74
How does a lack of vitamin C lead to scurvy?
The enzyme that makes hydroxyproline needs Fe2+ ions Vitamin C maintains Fe2+ in the reduced state, allowing the enzyme to work Scurvy is caused by a lack of vitamin C which leads to a lack of collagen This leads to bleeding skin and gums and loss of teeth
75
What is more common? Fibrous or globular proteins?
Globular
76
Describe the structure of a globular protein
Hydrophobic side chains cluster in the centre and drive folding Hydrophilic side chains are found on the surface and help to determine function
77
How is the b-a-b motif held together?
Hydrogen bonds between the strands and hydrophobic interactions between helix and strands
78
How are alpha helical hairpins held together?
Mostly by hydrophobic interactions, some ionic interactions
79
How are beta sheets in greek key motifs held together?
Hydrogen bonds between strands
80
What is a domain?
Part of a protein that forms a structurally independent unit with a hydrophobic core Composed of several motifs together
81
What size is insulin?
5.6kDa
82
What links the 2 chains in insulin?
Disulphide bonding
83
What is a multidomain protein?
A single polypeptide chain which folds into multiple domains with linkers between
84
Give an example of a multidomain protein
Glyceraldehyde-3-phosphate dehydrogenase 2 domains come together to form a single globular entity 1 domain binds to NAD Other domain contains active site
85
Describe the action of a DNA binding protein
Each domain independently binds to DNA by fitting into a separate place on the major groove
86
What is a multimeric protein?
A protein made up of many polypeptide chains (quaternary)
87
Give an example of a multimeric protein
HIV protease 2 subunits
88
What holds quaternary structures together?
Same interactions as tertiary
89
What do all antibody molecules contain?
4 polypeptide chains, 12 domains 4 light chain domains 8 heavy chain domains
90
What is a motif?
Commonly observed groupings of secondary structural elements
91
What stabilises the antibody tetramer?
Disulphide bonding (inter and intra)

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