Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

Molecules, Genes And Cells > Proteins > Flashcards

Proteins Flashcards

1
Q

What are enzymes function?

A

Catalyse covalent bond breakage or formation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are the function of structural proteins

A

Provide mechanical support to cells and tissues

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is the function of motor proteins

A

Generate movement in cells and tissues

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is the function of signal proteins?

A

Carry extra cellular signals from cell to cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is the function of transport proteins?

A

Carry small molecules or ions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is the function of gene regulatory proteins?

A

Bind DNA to switch genes on or off

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is the function of receptor proteins?

A

Detect signals and transmit them to the cells machinery

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is the function of special purpose proteins?

A

Their function is highly variable. For example proteins can act as messengers, antibodies, pumps and channels

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

How do proteins differ?

A
  • Chemical composition (amino acid sequence)
  • Structure / shape
  • Functions e.g. transport, structural, enzymatic etc
  • Name (haemoglobin, insulin)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are proteins made of?

A
  • Alpha amino acids
  • Amino acid are linked end to end by covalent bonds in linear chain
  • Amino acid chain known as a polypeptide
  • Polypeptide is folded into specific 3D shape
  • One or more folded polypeptides = protein
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the primary structure of an amino acid?

A

Linear amino acid sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the secondary structure of a protein?

A

Polypeptide folding into regular shapes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the tertiary structure of a protein?

A

Tertiary structure - arrangement of one/ multiple domains
3D structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is the quaternary structure of a protein?

A

Arrangement of multiple polypeptides
Protein complex (multi-subunits)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

General formula for amino acids?

A

R-CH(NH2)COOH

R = side chain
COOH = carboxyl group
NH2 = amino group
C = alpha carbon
H = alpha proton

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What differs between the 20 naturally occuring amino acids in nature?

A

Side chains (R group)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is an amino acids at PH 7?

A

Zwitteron - it has both positive and negative charges

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Which is the only amino acid that is not chiral? Why?

A

Glycine
The side chain of glycine is H

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Isomers of amino acids?
Which is found in proteins in nature?

A

L and D
L are found in proteins in nature

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Which are ‘small and simple’ amino acids?

A

Glycine and alanine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Which amino acids have hydrophobic side chains?

A

Valine (Val, V)
Leucine (Leu, L)
Isoleucine (IIe, I)
Methionine (Met, M)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What can the amino acids Cystetine do?

A

Thiol group (-SH) can form disulphide bonds (S-S)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Which amino acids have aromatic (ring) side chains?

A

Phenylalanine (Phe, F)
Tyrosine (Tyr, Y)
Tryptophan (Trp, W)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Which amino acids have polar side chains?

A

Serine (Ser, S)
Threonine (Thr, T)

(Contains -OH group)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Which amino acids are positively charged / basic?
What property does this give them?

A

Lysine (Lys, K)
Arginine (Arg, R)
Histidine (His, H)

Hydrophilic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Which amino acids are negatively charged / acidic?

A

Aspartate (Asp, D)
Glutamate (Glutamate, E)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Which amino acids are charged?

A

Aspartate (Asp, D)
Glutamate (Glu, E)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What is different about the amino acid proline?

A
  • Side chain forms a five membered ring by bonding to the nitrogen atom
  • It is an Imino acid NOT amino acid
  • Proline side chain is often rigid and forces a sharp ‘bend’ in the main chain
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What bond are amino acids joined together with?
Where is the bond?

A

Covalent
Carbonyl group of one amino acids joins together the amino group on the next

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What type of reaction is polymerisation?
What is the reverse?

A

Condensation reaction
Reverse = hydrolysis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What bond is between the C and N of two different amino acids in a polypeptide?

A

Peptide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

When / where do disulphide bonds occur?

A
  • Between side chains of two cysteine under oxidising condition
  • Tend to be found in proteins that are present extracellularly
  • Disulphide bonds can b cleaved by reduction with a reducing agent such as B-mercaptoethanol
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What can effect an amino acids properties?

A

Size
Charge
Hydrophobicity
Polar / non-polar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What is sickle-cell anaemia caused by?

A

-Mutation that affects single amino acids joins together residue in haemoglobin B
- Glu and Val mutation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What is cystic fibrosis caused by?

A

Deletion of single amino acid (Phenylalanine) in te transmembrane conductance regulator (CFTCR)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What is the configuration of the majority of peptide bonds?

A

Trans

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What does trans configurations allow for peptide bonds?

A

Allows amino acid side chain to be spaced far apart meaning no/less steric hinderance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What can happen when peptide bonds are in cis configuration

A

Steric hinderance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

What is steric hinderance?

A

The repulsion or resistance that occurs when atoms or groups within a molecule are positioned close together. This can prevent chemical reactions from taking place / affect the reactivity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

What is different about X-proline?

A

-X can be any amino acid
-steric clashes occur in bot cis and trans configurations
-X-proline bond can be present in cis more frequently than any other peptide bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

Why are atoms in peptide units in the same lane? How many atoms?

A

Six atoms are in the same plane due to the double-bond characteristics of the peptide bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

Which peptide bonds are rigid in the peptide units?

A

C-N peptide bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Which bonds in peptide units can rotate? What does this mean?

A

C alpha - C
N - C alpha

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

What is rigid in a polypeptide backbone?

A

Peptide bond and amide plane

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

Which bonds are free to rotate in a polypeptide backbone?

A

N - C alpha
C alpha - CO

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

What is Phi ø?

A

Torsion angle of N - C alpha bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

What is psi?

A

Torsion angle of C alpha - CO

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

What does the conformation of the polypeptide backbone depend on?

A

Phi and psi

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

What are phi and psi restricted by?

A

Steric constraints:
-size of side chain (R)
-planarity of peptide unit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

Why is the peptide backbone only partially flexible?

A

Only a certain combination of phi and psi are energetically favoured (stable)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

Which angles are favoured in secondary structures?

A

B sheets and right handed alpha helix. These are on the right hand side of the ramachandran plot

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

What can protein structures be stabilised by?

A

Non-covalent interactions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

Are non-covalent bonds stronger or weaker than covalent bonds?

A

20-100 times weaker

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

Three non-covalent bonds?

A

1- hydrogen bonds
2- salt bridges (electrostatic interaction)
3- van der waals’ interactions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

What is a hydrogen bonds?

A
  • Non-covalent bond that occurs when a donor atom donates its covalently bonded H atom to an electronegative acceptor atom
  • H-bond is strongest (most stable) when the acceptor, hydrogen and donor lie in a straight line
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

When does hydrogen bonds occur in proteins?

A

H = partial positive
O, N = partial negative

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

What are hydrogen bonds needed for in proteins?

A

Crucial for folding and formation of secondary structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

What does salt bridges form from?

A

Oppositely charged atoms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

Which amino acids form salt bridges?

A

Positive:
- arginine
- lysine

Negative:
- glutamic acid
- aspartic acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

What is van der waals’ interactions?

A

A non specific attractive force when two atoms are 3-4 Å apart

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

What do van der waals result from?

A

Transient shift in electron density

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

What happens when two atoms get too close (van der waals)

A

Repulsion

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

What happens to NH and CO is the backbone?

A

Neutralise each other via H bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

What does the polypeptide form in an alpha helix?

A

Regular right handed spiral structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

How many amino acid residues form from five turns of the helix?

A

18 amino acid residues

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

What is the vertical rise per residue in an alpha helix?

A

0.15nm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

How to calculate vertical rise per turn?

A

Number of residues per turn x vertical rise per residue

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

Length of helical stretches of polypeptide?

A

4-40 amino acid residues in length

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

What is the length of a typical alpha helix?

A

Ten amino acid residues = 1.5nm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

What are the angles of psi and phi in alpha helix’s?

A

Phi = 60 degrees
Psi = 50 degrees

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
71
Q

What direction do side chains face in an alpha helix?
Why?

A

Outwards
- inwards would cause steric hinderance and electrostatic interactions
- Maximises hydrophobic and hydrophilic reactions
- hydrogen bonds keep the helix stable

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

What do amino acid residues in an alpha helix do?

A

Determines the properties and how it interacts with protein domains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

What do alpha helixes drawn as a helical wheel show?

A

Spatial distribution of side chains in an alpha helix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
74
Q

What shape do polypeptides in a beta sheet form?

A

Flat, extended structure (zig zag) that is free from steric clashes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
75
Q

What is the vertical rise per residue for beta sheets?

A

0.33nm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
76
Q

What is the ‘pitch’ (rise per turn) for beta sheets?

77
Q

What is the typical length of a beta strand?

A

4-20 amino acid residues

78
Q

What is the average length of a beta strand?

A

8 amino acid residues (2nm)

79
Q

Phi and psi for a beta sheet?

A

Phi = -119 degrees
Psi = +132 degrees

80
Q

How are beta sheets formed form beta strands?

A
  • H bonds occur between N-H
81
Q

What are adjacent, anti parallel strands connected by in beta sheets?

A

Hairpin turns or loops

82
Q

What do turns / loops do in beta sheets?

A

Permit the change of direction of peptide chains

83
Q

What does the curve of beta sheets mean?

A

Can make barrel structures

84
Q

What are the common features of turns / loops in beta sheets?

A
  • Variable lengths
  • May be stabilised by local H bonds
  • Present at the surface of molecule
  • Often rich in charged / polar side chains
  • Often act as binding sites
85
Q

What are the common features of turns / loops in beta sheets?

A
  • Variable lengths
  • May be stabilised by local H bonds
86
Q

Which form of a protein is more stable?

A

Folded form

87
Q

What do polypeptide chains do in an aqueous environment?

A

Fold spontaneously

88
Q

Change in Gibbs free energy (delta G) = ?

A

Delta G = delta H -T delta S
Delta H = change in enthalpy (heat)
Delta S = change in entropy (disorder)
T - temperature

89
Q

Does the change inGibbs free energy need to be to positive or negative occur spontaneously?

90
Q

What is enthalpy associated with?

A

The internal energy change due to the formation of non-covalent bonds such as H bonds and Van der waals interactions

91
Q

What is conformation entropy?

A

A measure of the degree of conformational freedom available to a polypeptide chain

92
Q

What happens if the hydrophobic groups are folded towards the core (away from water)?

A

Entropy of the water molecules in the surrounding increases

93
Q

What do hydrophobic groups lead to in polypeptides?

A

A decrease in the number of H bonds that nearby water molecules can form with each other, meaning lower entropy

94
Q

What is the hydrophobic effect of polypeptides? What does it promote?

A

Increased ordering (decreased entropy) due to the packing of side chains in protein ‘core’ is partially offset by decreased ordering of surrounding water molecules
-Drives the formation of hydrophobic core

95
Q

What does increasing the entropy of water molecules do?

A

Provides the driving force for the hydrophobic effect?

96
Q

What does the hydrophobic effect promote?

A

Tertiary structure formation

97
Q

What can disrupt a folded polypeptide chain?
What will happen?
Is it reversible?

A
  • High temperature
  • Extreme pH
  • Detergents etc.

Protein will unfold and denature

If denaturants are removed, the polypeptides can refold

98
Q

What do folding pathways do?

A

Bypass random sampling of all possible conformations

99
Q

What are chaperones?

A

Proteins that enhance the rate at which other proteins fold

100
Q

How do chaperones assist folding?

A
  • Catalyse the cis/trans isomerisation of X pro bonds
  • Catalyse the interchange of disulphide bonds
  • Acting as components in which single polypeptide can fold, isolated from other polypeptide molecules
101
Q

What are neurodegenerative diseases typically caused by?

A

Amyloid plaques (misfolding of prion proteins)

102
Q

What are domains?

A

Bundles of secondary structures that are able to fold independently of the remainder of the protein

103
Q

What are features within a domain?

A
  • Hydrophilic groups are exposed
  • hydrophobic groups are buried (the side chains form a hydrophobic core which is closely packed)
104
Q

What are the three classes of domain structures?

A

1- Alpha helical domains
2- Beta sheet domains
3- Alpha / beta domains

105
Q

What does an alpha helical domain look like?

A

Pair of helixes, connected by a short loo, packed together in an anti parallel arrangement

106
Q

How does the helixes in an alpha helical domain fit together?

A

Ridges of one helix fit into the grooves of its partner, creating a large complementary surface and numerous Van der waals contacts

107
Q

What is a beta sandwich?

A
  • Two beta sheets packed together
  • Sandwich stabilised by the filling - hydrophobic side chains
  • Beta sheets are often twisted
108
Q

What is a beta barrel?

A
  • 8 beta strands that forms a barrel like structure
  • Usually has hydrophobic residues orientated towards the centre of the barrel (for proteins in an aqueous environment)
109
Q

What is an alpha helical domain/ beta barrel?

A

Parallel strands for a closed beta barrel and alpha helices are located on outside only

110
Q

What is an open twisted beta sheet?

A

?
Alpha helices pack against both sides of sheet
Alpha beta repeats

111
Q

What is quaternary structure?

A

When more than one polypeptide chains fold together
Can be the same polypeptide (homo) or different (hetero)

112
Q

What does only 20 amino acids mean?

A

Limited number meaning they cannot form all tasks required - they have to ‘recruit’ other types of chemistry

113
Q

What is innate immunity?

A

Rapid but non-specific
Evolutionarily conserved

114
Q

What is adaptive immunity?

A

Slow but specific
Immunological memory

115
Q

What is immunoglobulin (Ig) / antibody

A

Y shaped globular proteins, produced by b cells

116
Q

What are the 5 types of antibody?

A

IgA
IgD
IgE
IgG
IgM

117
Q

What do antibodies recognise?

A

Unique epitope or antigenic determinant on an antigen

118
Q

What does an antigen do?

A

Stimulates production of antibodies and is a target for an antibody

Recognise and bind to invaders, but not the host

119
Q

What do Immunoglobulins bind to?

A

Epitopes through complementary surfaces

120
Q

How does antibodies specify?

A

With their antigen binding site

121
Q

What does immunological memory depend on?

A

Lymphocyte differentiation and clonal expansion

122
Q

Process of lymphocyte differentiation and clonal expansion

A

1- proliferation and B cell diversification in bone marrow
2- antigen binding to specific B cell in peripheral lymphoid organ
3- proliferation (clonal expansion) and differentiator

123
Q

How does C1 work? What does it do?

A

1- Binding of Ig to antigen stimulates binding of C1
2- C1 triggers amplification cascade
3- 1000’s of molecules of membrane attack complex formed
—> these punch holes in membranes

124
Q

How does histamine release occur? (Hay fever example)

A
  • IgE cells bind to receptors on mast cell
  • multivalent antigen cross links adjacent IgE molecules
  • Histamine release by phagocytosis
125
Q

What must an immunoglobulin process?

A

Constant region (Fc) - that is recognised by complement C1 and by receptors (Fc receptors)

Variable domains - able to recognise an almost infinite range of antigens

Multivalency - form immune complexes

Flexibility - adjust to different spacing of antigenic determinants

126
Q

Description of an antibody

A

Each antibody molecule is made of two identical light chains, and two identical heavy chains, so the two antigen binding sites are identical

127
Q

What is the ‘anatomy’ of an immunoglobulin protein?

A

2 heavy chains
2 light chains
Linked by disulphides
2 arms
Symmetrical
Arms are flexible

128
Q

How many residues does a heavy and light chain have?

A

Heavy - 446 residues
Light - 219 residues

129
Q

How is the sequence divided in a heavy and light chain?

A

Heavy - 4 equal domains (3 are similar)
Light - 2 equal domains

130
Q

How many c terminals are the same in heavy and light chains?

A

Heavy - 337 residues Light
Light - 110

131
Q

What is the X ray structure of a constant domain?

A
  • Beta sandwich
  • 4 beta strands of anti parallel beta sheet form one fae and 3 strands from other
  • domains are liked together end to end - hinge between CH1 and CH2
132
Q

What is the x ray structure of a variable domain?

A
  • beta sandwich but has 9 beta strands
  • 4 beta strands form one face and 5 form the other
  • hyper variable regions all located in loops between beta strands
133
Q

How does each IgG have a distinct surface available for binding?

A
  • 6 variable regions in sequence
    -10^9 species of IgG, each with different HVR’s
134
Q

What can the surface be on an IgG?

A
  • flattish: suitable for binding to another protein
  • a cleft for binding a small molecule
135
Q

What forces stabilise the complex between Ab and Ag?

A

Van der Waals
Ionic interactions
The burial of hydrophobic surfaces
Hydrogen bonds
-complementary binding ensures the binding is plentiful and tight - bonds are weak on there own

136
Q

What is the structure of the variable region bound to a lysozyme?

A
  • classical crystal structure of complex between one arm of Ab and lysozyme
  • 17 amino acid residues from Ab make contact with a total of 16 lysozyme residues
    —> combined surface area = 1000A
  • all six hyper variable regions contribute to the Ab-Ag formation
137
Q

Where is hyper variable regions?

A

Ends of the ‘arms’

138
Q

How are antibodies used as molecular flags?(microscope detection)

A

1- specific antigens are coupled with dye / gold / tag
dye = fluorescent microscope
Gold = electron microscope

139
Q

How are antibodies used as molecular flags? (Biochemical detection)

A

1- antigen A separated from other molecules by electrophoresis
2- incubation with the labeled antibodies that bind to antigen A allows the position of the antigen to be determined
3- second antibody binds the first antibody

140
Q

How do you use antibodies to purify molecules?

A

Immunoprecipitation and immuno affinity column chromotography

141
Q

How does immunoprecipitation work?

A

1- add specific antigens-A antibodies to the mixture of molecules
2- collect aggregate of A molecules and anti-A by centrifugation

142
Q

How does immuno affinity column chromatography work?

A

1- beads coated with anti-A antibodies
2- column packed with the beads
3- mixture of molecules through the column - anti a molecules bind to beads
4- elute antigen A from beads to get pure antigen A

143
Q

What is meant by protein purification?

A

Techniques tailored to isolate and analyse specific proteins
Starts containing many different protein and ends in a sample containing one type of protein

144
Q

How to purify a protein?

A

1- grow / obtain cells (ideally abundant in protein)
2- lose cells to release protein. Mechanical - homogenisation, sonication, high pressure disruption. Non-mechanical - detergents, organic solvents, freeze thaw cycles
3- centrifuge to remove cell debris- soluble and insoluble
4- fractionation methods
Chromatography methods

145
Q

How to purify a protein based of properties of the proteins?

A

Solubility - salt fractionation
Charge - ion exchange, isoelectric focussing
Size / shape - centrifugation, size exclusion chromatography
Ability to bind various other molecules - affinity chromatography

146
Q

What is the general principle of differential fractionation?

A

Reduce solubility of the protein by changing the properties of the solution (eg ph, temperature, ionic strength)

147
Q

Disadvantage of salt fractionation?

A

Unlikely to get rid of all the unwanted molecules / proteins
Makes it a multi step process

148
Q

How does column chromatography work?

A

1- proteins separate as they pass through the column
2- solvent continuously applied to the top of the column
Fractionated molecules eluded and collected

149
Q

What is ion exchange chromatography

A

Protein has a net charge allowing it to interact with opposite charge

150
Q

What is size exclusion chromatography / gel filtration?

A

Protein size in a native state. May be a multimer

151
Q

What is affinity chromatography?

A

Binding of ligands
Protein specifically recognises molecule

152
Q

What happens when you separate a protein using heat?

A

Solution is heated
Protein comes out of solution as it is heat labile
-protein of interest must be heat stable for this

153
Q

How does ion exchange chromatography work?

A
  • Positively charged protein binds to negatively charged bead
  • Negatively charged protein flows through
  • Increase salt concentration or change buffer pH to elute the bound protein. Gradient allows more separation
154
Q

What is 1 band on a gel?

A

1 linear polypeptide chain

155
Q

How are proteins separated by polyacrylamide gel electrophoresis?

A

-Sodium dodecyl sulphate (SDS) - detergent added to protein in natural state
-Protein denatured by SDS
-Reducing agents break disulphide bonds (less structural support)
-SDS gives negative charge. Moves through gel only based on size

156
Q

How do you know what gel is in fraction?

A

Chromatogram using absorbance

157
Q

What are the purification steps on the gel?

A

Lane M - molecular weight marker
Lanes 1- 4 - purification steps before chromatography columns
Lanes 5 - 6 - after affinity column
Lane 7 - after size exclusion column (final purification product)

158
Q

What does gel electrophoresis do?

A

Separates proteins based on their size and charge

159
Q

What does the surface charge of a protein depend on?

160
Q

What does it mean if:
PH &laquo_space;pI
pH = pI
pH&raquo_space; pI

A

PH &laquo_space;pI protein positively charged
pH = pI no net charge
pH&raquo_space; pI protein negatively charged

161
Q

What does the charge of amino acid side change depend on?

162
Q

How doe size exclusion chromatography work?

A
  • Carbohydrate polymer beads - small molecules Exeter the aqueous spaces within beads
  • Large molecules cannot enter the beads
163
Q

What is a native PAGE?

A

Protein not denatured (no SDS) and disulphide bridges not reduced (no reducing agents)

Protein retains its tertiary and quaternary structure

164
Q

What is a homotrimer?

A

3 identical subunits (polypeptide chains)

165
Q

What is isoelectric focusing?

A

Proteins separated based on their pI - pH at which proteins net surface charge is 0

166
Q

What happens to soluble proteins in analytical ultracentrifugation?

A

Due to their thermal (brownian) motion which keeps them evenly distribute throughout the solution

167
Q

What does light do with proteins?

A

Light scatters from different parts of the protein will have different intensities
This is due to constructive and destructive interference of the scattered light
Intensity of scattered light will vary with angle 0

168
Q

What happens to light when put through a sample?

A

Interaction with sample results in a change to emitted light which we measure

169
Q

How to calculate energy in protein absorption spectroscopy?

A

E =hv

E = energy
h = Plancks constant 6.626 x 10^-34
v = frequency (c / lambda)

170
Q

How to calculate absorbance?

A

A = E cl
l = light path length (corvette width) = 1cm
c = protein concentration (unknown)
E =molar extinction coefficient of a protein

171
Q

What do myoglobin and haemoglobin have in common?

A

Similar protein folds

172
Q

What does the affect on affinity depend on?

A

Coordinating histidine that allows the Fe2+ to fit into the ring

173
Q

What does myoglobin and oxygen do?

A

Myoglobin binds molecular oxygen tightly and releases little under physiological conditions

174
Q

What does the His residue movement do?

A

Tracks movement of a helix, which bind to a dimer interface

175
Q

How does haemoglobin achieve cooperativity?

A

By having two conformational states differing in affinity for oxygen

176
Q

What does the concerted modal show?

A

Two states of the protein are in equilibrium, and that O2 binding stabilises one over the other

177
Q

What is the T state and R state?

A

T state: Lower affinity for oxygen - deoxyhaemoglobin
R state: higher affinity - oxyhaemoglobin

178
Q

What is the Bohr effect?

179
Q

What does chrymotrypsin cleave after?

A

Aromatic or long non-polar side chain

180
Q

What does trypsin cleave after?

A

Arginine, lysine

181
Q

What defines the peptide that can be bound?

A

The residues lining the binding pocket?

182
Q

What are proteases?

A

Enzymes that catalyse peptide bond hydrolysis

183
Q

What are the steps of two dimensional electrophoresis?

A

1- Separation of proteins by pI value
2- Soaking the gel in SDS solution and fitting it on an SDS PA gel
3- Separating the proteins by molecular mass with SDS page

184
Q

How are peptides analysed?

A

Mass spectrometry

185
Q

How are proteins identified?

A

Peptide fragment ion spectra are matched to theoretical databases to identify the peptides which are the used to identify the protein

186
Q

Steps for the catalysis of DIPF

A

1 - covalent bond between serine and enzyme
2- removal… enzyme is slowed down until free enzyme is available
3- catalytic triad makes Ser195 more reactive
4- attack by Ser195 forms a tetrahedral intermediate (stabilised by oxyanion hole)

187
Q

What does a serine protease do?

A

Uses serine hydroxyl group as the attacking group

188
Q

What happens when you smoke to cause emphysema?

A
  • Neutrophils secrete elastase to cross elastin in the lungs
  • Elastase is inhibited outside the lungs

Smoking oxidises the inhibitor

Molecules, Genes And Cells (4 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions