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Protein Theme > Chapter 1 > Flashcards

Chapter 1 Flashcards

0
Q

What is FRET?

A

Fluorescence resonance energy transfer

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1
Q

What is fluorescence microscopy used for?

A

Visualisation of interactions in living cells

Can also view co-localisation

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2
Q

What can close proximity also be achieved by?

A

A common partner, not necessarily direct interactions

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3
Q

What does co-immunoprecipitatation show?

A

That two molecules interact

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4
Q

How do you capture the protein in co-immunoprecipitation?

A

A/G Sepharose gel

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5
Q

What does the dissociation constant show?

A

The stability of the complex

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6
Q

What happens if the dissociation constant is too quick?

A

Pull down assays will not work

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7
Q

What does the equilibrium dissociation constant relate to?

A

Strength of interactions

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8
Q

The smaller the Kd the …

A

More negative the deltaG association

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9
Q

What are the limitations of the ligand binding assay?

A

Stability of complex during washing
Detection and separation may be difficult
Non specific binding
Limited to low receptor concentration

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10
Q

What shape is the saturation curve?

A

Hyperbola

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11
Q

What does a competition assay allow the comparison of?

A

Many ligands using the same assay format

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12
Q

When May a competition assay not work?

A

When the Kc is lower than the Kd as the sensitivity is too low

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13
Q

What does isothermal calorimeters measure?

A

DeltaH directly from heat released or absorbed

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14
Q

Describe isothermal calorimeters

A

Label free technique
Can measure very low Kds from competition (can’t measure them directly)
Need relatively high concentrations of ligand and receptor
Ligand does not have to be small it can be large

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15
Q

What can you determine in ITC?

A

Enthalpy
Entropy
Reaction stoichiometry
Kd

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16
Q

To what accuracy using MS are proteins and biomolecules measured?

A

0.01%

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17
Q

To what accuracy are peptides and small molecules measure to?

A

5ppm (very accurate)

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18
Q

What are the three main sections of MS?

A

Ionisation source
Analyser
Detecter

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19
Q

What are the two forms of ionisation?

A

MALDI: matrix assisted laser desorption ionisation

Electro spray ionisation

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20
Q

Describe electrospray ionisation.

A

The sample can be directly injected into the ionisation source of the MS or the MS can be coupled to a high pressure liquid chromatography column to the sample is separated into a series of components that enter the mass spec sequentially

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21
Q

Between MALDI and electrospray ionisation which can add more than one proton to high Mr’s?

A

Electrospray ionisation

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22
Q

In MALDI what is the laser shone on to?

A

The crystalline solid

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23
Q

Is the analyser under high pressure/vacuum?

A

Yes

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24
Q

What does the analyser separate based on?

A

Mass to charge ratio

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25
Q

Give two types of MS analyser.

A

Time of flight analyser

Quadruple analyser

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26
Q

What does the Detecter do?

A

Amplifies the ion current from the analyser

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27
Q

What is the equation used to determine m/z?

A

((M+(nx1))/n

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28
Q

What does tandem MS show?

A

Structural information

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29
Q

What type of analyser is required for tandem MS?

A

A multi analyser eg Q-Tof, Q-Q, Tof-Tof

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30
Q

In MS/MS what is present in the collision cell?

A

Argon gas: inert, no reaction just collisions

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31
Q

What are the three different types of bond which can fragment along an amino acid backbone?

A

NH-CH
CO-NH (most common)
CO-CH

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32
Q

If trypsin cleaved at arginine what would the fragment m/z be?

A

175

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33
Q

If trypsin cleaved at lysine what would the m/z be?

A

147

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34
Q

What is the m/z reading for phosphate group?

A

79

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35
Q

Describe the steps of proteomics.

A

1) 2D gel
2) Excise protein from the gel
3) Digest with trypsin
4) Search database, MS to get masses
5) MS/MS: peptide sequences
6) Protein identification

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36
Q

What are non-covalent interactions dependent on?

A

pH
Temperature
Ionic strength

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37
Q

What is the reaction order definition?

A

The number of molecules needed to collide and from the activated complex

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38
Q

What is the equation for the first order reaction?

A

K=ln2/half life

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39
Q

In a mixed second order reaction what happens when B is kept constant?

A

The reaction is pseudo first order reaction in A

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40
Q

What type of reaction order is ligand binding?

A

Second order with pseudo first order conditions

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41
Q

What does the resonance in surface plasmon resonance depend on?

A

The Mr: when a bound receptor binds to a ligand the Mr increases and hence a different deflection and resonance occurs

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42
Q

When you measure the deflection in SPR what do you generate?

A

A sensogram

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43
Q

What does mass transport do?

A

Slows the rate of apparent kinetics

The rate depends on the flow rate

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44
Q

What yields Kd?

A

The steady state

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45
Q

What factors lead to rate enhancement in enzymes?

A 
Nucleophilic catalysis
Orientation and proximity
Acid base catalysis 
Strain
Cofactors
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46
Q

Which type of reaction proceeds quicker: intramolecular or intermolecular?

A

Intramolecular as the reactants are already in close proximity and therefore their effective concentration is greater

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47
Q

What is the Iimited pH range for acid/base catalysis?

A

5-9

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48
Q

What is the pKa range for amino acid side chains able to participate in acid base catalysis?

A

4-10 however this can be extended by the environment

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49
Q

In acid catalysis is the pKa greater or lower than the pH?

A

Greater

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50
Q

What happens in general acid catalysis?

A

The substrate is protonated by a catalytic residue

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51
Q

What happens in general base catalysis?

A

The substrate is de protonated by a catalytic residue

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52
Q

What does strain do?

A

Causes the substrate to better resemble the transition state structure so that it does not need to undergo unfavourable structural changes during the catalytic steps

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53
Q

What metal ion cofactors have a single oxidation state?

A

Magnesium, calcium and zinc
Small ionic radii
Divalent
Highly polarising

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54
Q

What metal ion cofactors have a single oxidation state?

A

Mn, Fe, Ni and Cu

They can all gain/lose electrons

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55
Q

What are the organic co-factors?

A 
Vitamins
TPP
FMN and FAD
NAD
CoA
PLP
Biotin
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56
Q

What is the transition state?

A

The highest energy state and the least populated state

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57
Q

What is the rate determining step in enzyme reactions?

A

Decomposition rate of the transition state

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58
Q

What happens to the reaction rate as the energy barrier gets lower?

A

The rate increases exponentially

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59
Q

When is a reaction catalysed?

A

When the deltaG(catalysed) is less than the deltaG(uncatalysed)

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60
Q

What must happen for catalysis to occur?

A

The enzyme binds the transition state more tightly than it binds the substrate

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61
Q

What is an example of ordered sequential bi bi reactions?

A

NADH linked dehydrogenases

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62
Q

What are the two mechanisms for a ternary complex?

A

Ordered sequential bi bi and random mechanism

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63
Q

What are the two none ternary mechanisms?

A

Bi bi ping pong and theorell chance

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64
Q

Give an example of bi bi ping pong

A

PLP a dependent transaminases

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65
Q

Give an example of theorell chance mechanisms

A

Horse lover alcohol dehydrogenase

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66
Q

What does the slope graph of the ordered sequential bi bi tell you?

A

Y=Ka/Vmax

Slope=Ka’Kb/Vmax

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67
Q

What does the intercept graph of both ordered sequential bi bi and bi bi ping ping tell you?

A

Y=1/Vmax

Slope=Kbps/Vmax

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68
Q

What do partial reactions for bi bi ping pong show?

A

That it is a bi bi as only one product is produced

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69
Q

What is rule one in product inhibition pattern?

A

The ordinate intercept will change if the enzymes are different

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70
Q

What does rule 2 of the product inhibition pattern state?

A

The slope will change if the enzymes are the same or connected by reversible steps

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71
Q

Which dehydrogenases are A specific?

A

Malate
Lactate
Alcohol

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72
Q

Which dehydrogenases are B specific?

A

Glutamate

Glyceryl delude-3-phosphate

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73
Q

What is the inhibitor of Pyruvate?

A

Oxamate

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74
Q

What is the inhibitor of lactate?

A

Oxalate

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75
Q

What are the two domains of lactate dehydrogenase?

A

N-terminal domain and C-terminal domain

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76
Q

What is the N terminal domain also known as? And what does it bind?

A

Rossmann fold and is a dinucleotide binding domain

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77
Q

What does the C-terminal bind and what is it composed of?

A

Substrate

2 x 3 anti parallel sheets

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78
Q

What is the N-terminal domain composed of?

A

6 stranded beta sheet

4 alpha helices

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79
Q

What is the composition of the Rossmann fold?

A

(Beta alpha beta alpha beta)^2

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80
Q

How was the rate of loop closure determined?

A

Site directed mutagenesis, add a fluorescent tryptophan into the loop at amino acid number 106.
The amount of fluorescent changes depending on whether it is In solvent or not, and therefore this can be studied.
Loop closure in lactate dehydrogenase is the rate determining step

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81
Q

What is the specificity constant defined as?

A

Kcat/Km

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82
Q

When changing the specificity of an active site what would you look at?

A

Overall charge balance in active site
Substrate vs active site volumes
Direct electrostatic complementarity

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83
Q

When changing LDH specificity to malate how would you change some of the charges?

A

Alter the amino acids in the active site to get the ideal charge of 0

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84
Q

What is glutathione reductase specific for?

A

NADH (catabolic) or NADPH (anabolic)

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85
Q

What family of enzymes is glutathione reductase part of?

A

Flavoprotein disulphide oxidoreductase

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86
Q

What residue is conserved in NADPH reactions?

A

Arginines

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87
Q

What is the NADPH binding consensus sequence?

A

GxGxxAxxxA

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88
Q

What is the binding consensus sequence for NADH?

A

GxGxxGxxxG

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89
Q

How many subunits are in LDH?

A

4: tetrameric and there are two subunit types (alpha and beta)
There are five different conformations of the subunits

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90
Q

What type of conformation of LDH is found in heart muscle?

A

Alpha4

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91
Q

What type of conformation of LDH is found in skeletal muscle?

A

Beta4

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92
Q

What mechanism does LDH a follow?

A

Ordered sequential bi bi

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93
Q

What did affinity labels in LDH a discover?

A

Residue His195
By altering Pyruvate to bromopyruvate it enabled nucleophilic attack and inactivation within the active site and as a consequences labelling of a specific residue (His195). When the enzyme was broken down, sequences and purified it could determine the specific residue.

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94
Q

What chemical modifies histidines?

A

DEPC
If you treat the enzyme with DEPC and you discover inactivation of he enzyme you know that a histidine is present in the active site.

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95
Q

Which chemical modifies arginine residues?

A

Phenylglyoxal
As you can’t break down the protein and purify to a specific reside you look at the effect of activity with just the enzyme, the enzyme and substrates and phenylglyoxal and finally just phenylglyoxal. This showed substrate protection

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96
Q

What chemical modifies cysteines?

A

NEM
showed substrate protection also
HOWEVER be careful
Cysteine was actually in the loop and when the loop is open NEM can modify the cysteine preventing the substrate from getting in however if you add the substrate first the NEM can’t then access the cysteine residue

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97
Q

What does bidirectional BLAST show?

A

Orthologs

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98
Q

What is BLAST bad at detecting?

A

Distant homologs

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99
Q

What is the order of enzymes?

A

OTHLIL

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100
Q

What does BLAST do?

A

Annotates genomes

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101
Q

What are PRIAM sequence profiles?

A

Multiple alignments of protein sequences

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102
Q

What is the malaria parasite?

A

Half plant and half animal

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103
Q

What does SHARK hunt do?

A

Annotation of raw genome sequence

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104
Q

In molecular networks what do the vertices represent?

A

Proteins

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105
Q

In molecular networks what do the edges represent?

A

The physical interaction between proteins

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106
Q

What are the macronutrients?

A

Carbohydrates, protein and fat

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107
Q

What are the micronutrients?

A

Vitamins and minerals

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108
Q

What is the reference nutrient intake?

A

The amount of nutrient needed to meet the needs of 97.5% of the population

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109
Q

What type of compound are vitamins?

A

Organic

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110
Q

What type of compound are minerals?

A

Inorganic

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111
Q

What are the fat soluble vitamins?

A

E, K, A and D

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112
Q

What is vitamin B1?

A

Thiamine (TPP)

  • required in Pyruvate dehydrogenase and alpha ketoglutarate dehydrogenase
  • in Pyruvate dehydrogenase nucleophilic attack occurs by the acidic carbon onto Pyruvate causing attachment of Pyruvate to the thiazolium ring
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113
Q

What does a deficiency in thiamin cause?

A

Beri beri

  • muscles are weak caused by nerve damage
  • the heart can be affected
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114
Q

What is vitamin B2?

A

Riboflavin which is found in FMN and FAD

Deficiency is rare

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115
Q

What is vitamin B3?

A

Niacin
Component of NAD(P)H
Can be synthesised in the body from tryptophan
Deficiency leads to pellagra which has the four D’s as symptoms
Rare in the developed world however it is sometimes seen in anorexia sufferers

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116
Q

What is vitamin B5?

A

Component of coenzyme A

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117
Q

What is the role of biotin?

A

It is used in carboxylases: acetyl CoA carboxylase and Pyruvate carboxylase
It is a carrier for CO2
Intracellular biotin is converted by holo carboxylase synthetase into either carboxylase biotinylation or histone biotinylation
Biocytin is converted back to intracellular biotin by biotinidase

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118
Q

What is vitamin B6?

A

Pyridoxane (PLP)
Used in transaminases and glycogen phosphorylase
Other roles include: haem synthesis, NT synthesis, modulates the actions of steroid hormones, inverse relationship between B6 levels and risk of cancer

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119
Q

What ion does vitamin B12 contain?

A

Cobalt (III) ion
Large and complex
Two enzymes which use this vitamin are L-methylmalonyl-CoA-mutase and methionine synthase
Only found in food sources

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120
Q

What caused pernicious anaemia?

A

Lack of vitamin B12 or an inability to process B12

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121
Q

What can pernicious anaemia lead to?

A

Neurological symptoms (due to myelin not being produced properly) such as an altered gait and tingling of fingers and toes or macrocytic anaemia

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122
Q

What part of folic acid is responsible for biological activity?

A

The pteridine ring

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123
Q

What is folic acid key in?

A

One carbon transfer

Vital for DNA synthesis

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124
Q

What are one carbon transfers needed for?

A

The synthesis of: methionine, serine, glycine, choline, purine nucleotides and dTMP

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125
Q

What enzyme converts N5-N10 THF into DHF?

A

Thymidylate synthase

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126
Q

What enzyme converts DHF into THF?

A

Dihydrofolate reductase

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127
Q

What enzyme converts THF into N5-N10 THF?

A

Serine hydroxymethyl transferase

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128
Q

What can folate deficiency cause?

A

Megaloblastic anaemia: large immature erythrocytes

Neural tube defects

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129
Q

What is needed for the recycling of folate?

A

B12

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130
Q

What vitamins are linked in DNAI methylation?

A

Folate, B12 and B6

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131
Q

What is vitamin C also known as?

A

Ascorbic acid

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132
Q

What is vitamin C a coenzyme for?

A

Proyly hydrolase (hydrogen bond formation) and lysyly hydroxylase (attachment sites for sugar residues, cross linking)
Bile synthesis and adrenalin synthesis
Antioxidant properties
Role in regeneration of reduced form of vitamin E

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133
Q

What can vitamin C deficiency lead to?

A

Scurvy

Abnormally weak collagen

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134
Q

What is the main role of vitamin E?

A

Protects from free radicals and against lipid peroxidation

Protects the nervous system

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135
Q

What is vitamin A derived from?

A

Dietary beta carotene

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136
Q

What is vitamin A also known as?

A

Retinol

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137
Q

What is the role of vitamin A?

A

Antioxidant and involved in sight (all trans retinol initially enters the epithelial cells and then the photoreceptor cells … cis-retinal combines with opsin to make rhodopsin)

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138
Q

What is retionoic acid involved in?

A

Gene regulation

Receptors for vitamin D and thyroid hormone which are involved in growth and differentiation of cells

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139
Q

What is the main role of vitamin K?

A

Koagulation
Vitamin K dependent carboxylases convert glutamate into gamma-carboxyglutamate residues which are found in clotting factors

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140
Q

What enzymes does warfarin inhibit?

A

Quinone reductase

Vitamin-K-epoxidase reductase

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141
Q

What is the precursor of vitamin D?

A

Cholesterol

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142
Q

What does a lack of vitamin D cause?

A

Bone disease
Autoimmune diseases
Cancer

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143
Q

What is vitamin D a transcriptional regulator of?

A

Calcium homeostasis and bone growth

Causes increase in calcium and phosphate absorption from the intestine

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144
Q

What are the roles of iron?

A

Electron carriers

Component of haem

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145
Q

What does iron deficiency cause?

A

Microcytic anaemia

146
Q

What caused muscle cramps and spasms?

A

Hypocalcaemia

147
Q

What are plasma calcium levels controlled by?

A

Vitamin D and parathyroid hormone

Stimulated when calcium levels drop

148
Q

What is the role of iodine?

A

Synthesis of thyroid hormone (basal metabolic growth and essential for normal growth)

149
Q

What does iodine deficiency cause?

A 
Growth and mental retardation
Thyroid enlargement (goitre)
150
Q

What controls iron absorption?

A

Hercipidin

151
Q

What type of wave are X-Rays?

A

Electromagnetic waves

152
Q

What happens to an electron when hit by X-Rays?

A

Start to vibrate at the same frequency

Secondary beams will be scattered

153
Q

What is the scattering from a molecule dependent on?

A

The number of and distances between electrons

154
Q

What do we need in order to determine the structure of a molecule?

A

Amplitude and phases

155
Q

What are the three different ways of crystal growth?

A

Sandwich drop
Sitting drop
Hanging drop

156
Q

What is a unit cell?

A

The minimum unit able to translocated in a 2D array

157
Q

What is an asymmetric unit?

A

Rotatable, smaller structure in 3D

158
Q

What must the packing symmetry be?

A

Less than 6 p, but it cannot be 5 fold

159
Q

What does Braggs law state?

A

Scattered beams in phase will add up and those out of phase will cancel each other out

160
Q

Why do you get a diffraction pattern produced in spots from an X-Ray?

A

No lens can focus an X-Ray

161
Q

How are the diffraction patterns interpreted?

A

Using the Fourier transform

162
Q

In diffraction patterns where is the best resolution?

A

The further out you go

163
Q

What is lost with the detector in X-ray crystallography?

A

Phases

For small molecules you can determine them from the amplitudes however for big molecules you need another method

164
Q

What are the phasing techniques?

A

Multiple isomorphous replacement
Molecular replacement
Single wavelength anomalous dispersion
Multi wavelength anomalous dispersion

165
Q

What happens in isomorphous replacement?

A

You soak an atom to form a heavy atom and introduce into the crystal structure
You then look at how the diffraction pattern have altered and determine the positions of the heavy atoms and from them the phases

166
Q

What does the intercept in MIR give you?

A

The phase angle

167
Q

In MAD what happens?

A

You get more than one diffraction pattern and you compare them

168
Q

What happens in molecular replacement?

A

Only applicable if a similar structure already exists

You combine the phases of the known structure with intensities of unknown structure

169
Q

What are phases?

A

They are the thing which contributes most to the electron density map
Contain the most important information

170
Q

What is the R factor?

A

Difference between known and unknown structure

171
Q

What is the atomic B factor?

A

Measure of the average displacement of an atom

172
Q

What is the structure F factor?

A

Intensities from the diffraction pattern

173
Q

What undergoes small vibrational and conformational changes in a protein?

A

Atoms

174
Q

What undergoes large movements relative to each other upon ligand binding?

A

Large multi domain proteins

175
Q

Can proteins undergo transient but complete unfolding? If yes, give an example.

A

Yes

When oxygen is released from oxyhemoglobin

176
Q

Can both external and internal residues be quenched?

A

Yes

177
Q

What is the rate Ki?

A

The rate for unstructured tripeptide

178
Q

What is rate Ko?

A

Rate of opening of a region of protein

179
Q

What is rate Kc?

A

Rate of closing

180
Q

What solvent are proteins put into during hydrogen exchange?

A

D2O

181
Q

How can hydrogen exchange be observed by NMR?

A

A deuteron has a different magnetic resonance frequency to a proton and therefore as a proton is exchanged you will see the signal disappear

182
Q

What does the rate of HX depend on?

A

pH
Location of the amide and degree of burying
Hydrogen bonds
Frequency of partial unfolding

183
Q

When the protein is very big what must you combine hydrogen exchanged with?

A 
2D NMR: this reduced overlapping signals
Isoelectric focussing (pI) and SDS-PAGE (mass)
184
Q

How are overlapping hydrogen resonances of the amide bond resolved?

A

Measuring the chemical shift of nitrogen on the same amide bond
HSQC medium
This generates a fingerprint of all NH groups

185
Q

Which residues are able to rotate giving an averaged spectra?

A

Tyrosine and phe

186
Q

Which residues are unable to rotate as they are too big and therefore are classed as different hydrogens and give two peaks?

A

Histidine and trp

187
Q

How do you obtain 3D structures from NMR?

A

Measure through space interactions/distances between NMR active nuclei. These are used as restraints when calculating structure

188
Q

Do dynamic areas show low or high constraints?

A

Few constraints

189
Q

What does the B factor in X-ray crystallography show?

A

The extent of smearing is given by the temperature factor B

190
Q

Describe molecular dynamics.

A

Atoms of known structure are given a set velocity and random motion, after a short time the magnitude of force acting on each of the atoms is calculated and from that you can work out the new positions of each atom.

191
Q

In molecular dynamics what is the force described as?

A

Sum of terms which includes bonded and non-bonded interactions

192
Q

What occurs more often, atomic fluctuations or collective motions?

A

Atomic fluctuations

193
Q

What are the four main classes of proteases?

A

Serine, cysteine, aspartic and metalloproteinases

194
Q

Where does trypsin cleave?

A

C-terminal to a charged side chain

195
Q

Where does pepsin cleave?

A

C-terminal to a hydrophobic side chain

196
Q

Where does cleavage commonly occur?

A

In dynamic regions such as domain functions and loops, however fully folded native domains can be highly resistant to degradation

197
Q

What are the two solutions for how to degrade a protein?

A

The proteolytic active sites are enclosed within a chamber and you use the energy to unfold the protein at a slower rate than intrinsic rate

198
Q

What are the five bacterial proteases?

A

ClpXP/ClpAP
FeSH
HSIUV
Lon

199
Q

Which bacterial proteases have the unfoldase and protease on the same peptide?

A

FeSH and Lon

200
Q

What is the ClpXP composed of?

A

The ClpP is 2 stacked rings of heptamers and can bind two AAA+ proteins. Each monomer has a serine protease active site.
The ClpX/A site is a ring like hexamer that can bind each end of the ClpP, this protein has one AAA+ domain.

201
Q

What does AAA stand for?

A

ATPases associated with various cellular activities

202
Q

What do AAA+ proteins participate in?

A

Protein degradation
Protein disaggregation
Protein complex remodelling
Utilises ATPASES to catalyse the unfolding of the substrate proteins

203
Q

How does ClpXP a recognise substrates?

A

It binds specific sequences/tags
Eg AADENYALAA which has two binding motifs
LAA is recognised by loop regions
AADENYAL is recognised by the adapted protein called SspB

204
Q

What are the two common methods to measure the force applied to/by a biomolecules?

A

Atomic force microscope and laser traps

Both measure the displacement of a spring with known stiffness

205
Q

What is AFM good at measuring?

A

Mechanical forces over short distances

206
Q

What are laser traps good at measuring?

A

Small forces over longer distances

207
Q

What are the two types of mode of AFM?

A

Tapping mode and contact mode

208
Q

What are the advantages and disadvantages of contact mode?

A

Any type of tip can be used and it is easy to do

You can get sample damage and high lateral forces can cause displacement

209
Q

What are the advantages and disadvantages or tapping mode?

A

A very sharp tip must be used however you reduce the lateral force and therefore reduce the damage

210
Q

How can you make a blunt tip, sharper?

A

Place a carbon nanotube tip on the end

211
Q

What does the surface area of a folding funnel describe?

A

The entropy

212
Q

In a folding funnel, where is the most stable section?

A

The bottom

213
Q

What do proteins fold from and to?

A

From: low enthalpy and high entropy
To: high enthalpy and low entropy

214
Q

What factors determine whether a protein can be folded reversibly?

A

pH, temperature and adding/diluting the chaperones

215
Q

What did the leviathan paradox show?

A

Proteins can’t fold at random as it would take far too long, there must be a protein folding pathway.

216
Q

What did ranganathan show?

A

That there is co-evolution and conservation
He showed that amino acids are not conserved independently
Carried out statistical coupling analysis

217
Q

Out of the 36 amino acids in WW domain how m ay were needed to fold and define?

A

8

218
Q

What do WW domains bind?

A

Proline rich sequences

219
Q

What did Ptitsyn show?

A

He looked at partially folded states by using mild de maturing conditions to define the species as molten globule

220
Q

How does a lysozyme refold?

A

Via parallel pathways with many intermediates

221
Q

Describe the structure of the hen lysozyme.

A 
Small with 139 amino acids 
45 disulphide bonds 
Enzyme glycosidase
Soluble, globular protein
Mixed alpha beta fold
222
Q

How was folding kinetics studied?

A

Stopped flow methods

223
Q

What does Far UV show?

A

Secondary structure information

190-240nm

224
Q

What does Near UV show?

A

Tertiary structure information

240-300nm

225
Q

Is the denatured state more or less fluorescent than the native state?

A

More

226
Q

Is folding cooperative?

A

Yes

227
Q

What else can contribute to far UV?

A

Aromatic residues - can give rise to an “over shoot” in the CD

228
Q

In pulsed hydrogen exchange how do you stop hydrogen exchange?

A

Quench at a low pH

229
Q

In pulsed hydrogen exchange what do the hydrogens start as?

A

Deuteron & an unfolded state

230
Q

What did pulsed quench flow of lysozyme folding show about the alpha helices?

A

They fold quicker and cooperatively compared to beta

231
Q

Describe the small proteins folding funnel.

A

Smooth
Intermediates are not populated
Few contacts are needed to define the native fold

232
Q

Describe the folding funnel for large proteins.

A 
Rough landscape
Intermediates are highly populated
Multiple pathways 
Fold by domains 
The hen lysozyme shows existence of distinct intermediates
233
Q

What happens straight away once the protein starts re folding?

A

Hydrophobic collapse

234
Q

What happens during hydrophobic collapse?

A

Exclusion of water
Short interactions
Molten globule state

235
Q

Is folding uni molecular or bimolecular?

A

Uni

236
Q

Is aggregation uni molecular or bimolecular?

A

Bi

237
Q

How can you prevent aggregation occurring and favour folding over aggregation?

A

It is concentration dependent and therefore you can decrease the concentration of the unfolded state

238
Q

How does expression of molecular chaperone usually come about?

A

Heat shock

239
Q

What do molecular chaperones bind?

A

Any non-native protein

240
Q

How do cells protect the polypeptide as soon as they can?

A

Ribosomal protein L23: specific chaperone binding site
TF and NAC: Chaperone the nascent chain as it leaves the ribosome
Hsp70/40: bind the nascent chain

241
Q

How do heat shock proteins work?

A

They act as a buffer of protein aggregation: they reversibly bind misfolding proteins and therefore prevent aggregation

242
Q

What does Hsp90 bind?

A

ATP and other proteins

243
Q

What is Hsp90 involved in?

A

Raf-1 signalling pathway and steroid hormone receptor activation
Acts on protein conformation (modulated protein conformations)

244
Q

What role of Hsp100 chaperones have?

A

Involved in protein disaggregation

245
Q

What are the advantages of linking an unfoldase to a protease?

A

Efficient and safe: gated access to a potentially damaging protease activity

246
Q

What is Hsp70 known as in Ecoli?

A

DnaK

247
Q

What does Hsp70 work with?

A

Hsp40 and a nucleotide exchange factor

248
Q

Which out of Hsp70 and Hsp40 binds ATP?

A

Hsp70

249
Q

Which out of Hsp70 and Hsp40 has an affinity for non-native polypeptides?

A

Hsp70

250
Q

What are Hsp70 and Hsp40 involved in?

A

ATP binding and release

251
Q

Is GroEL essential for the viability of Ecoli under all growth conditions?

A

Yes

252
Q

What is GroEL homologous to?

A

Rubisco binding protein

253
Q

What is GroES homologous to?

A

Hsp60 in mitochondria

254
Q

What is Hsp60 and what is Hsp10?

A

Hsp60: GroEL
Hsp10: GroES

255
Q

Which out of GroEL and GroES has ATPase activity and has affinity for non-native proteins?

A

GroEL

256
Q

What must be present in order for GroES to bind GroEL?

A

ATP/ADP

257
Q

What are cyro-EM structures?

A

Imagining macromolecule complexes in a solution state

258
Q

What did cyro-EM structures show about the ternary complex?

A

When ATP binds there is an enormous conformational change where the structure grows much taller

259
Q

What does projection theorem do?

A

Relates the 2d image to the 3D object

States that the Fourier transform of the 2D projection image is a central slice through the 3D transform

260
Q

When is ATP binding positively cooperative?

A

Within a ring

261
Q

What happens when ATP a binds GroE?

A

There is rotation within domains

262
Q

How many continuous subunits do you need to GroEL to work?

A

4

263
Q

What state is GroES release primed in?

A

Cigs

264
Q

What state is GroES release triggered in?

A

Trans

265
Q

What is type II Hsp60?

A

CCT

266
Q

What is a replisome?

A

Assembly of enzymes and molecular motors that are involved with DNA replication
Coordinates synthesis of lagging and leading strand

267
Q

Which direction does the polymerase move?

A

5’ to 3’

268
Q

What is T7 phage polymerase processivity factor?

A

Thioredoxin

269
Q

What are the two modes of processivity with the helices even?

A

Processive replication

Waiting for rebidding whilst loosely attacked to the helicase C-terminus

270
Q

Which is the slowest step within the replisome?

A

The primate

271
Q

What is key to coordination between the primase and helicase?

A

Zinc binding domain

272
Q

What do the two magnesium ions of the RNA polymerase do?

A

Activation of the 3’-OH

Brings in the incoming NTP

273
Q

Newly added nucleotides bias the motion of the polymerase in the forward direction

A

What is the brownish Ratchet model?

274
Q

What are the helicase superfamilies and which are hexameric and which are monomeric?

A

SF1, SF2, SF3, SF4, SF5 and SF6
1 and 2: monomeric
3,4,5 and 6: hexameric

275
Q

What is the inchworm model?

A

Hand over hand mechanism

276
Q

What did Koch postulate?

A

A series of descriptions for defining an organism

277
Q

How can the natural flora become infectious?

A

Can gain extra virulence or gain access to deep tissues by trauma, surgery etc.
Or the patient might be immunocompromised and become an easy target of the natural flora

278
Q

What does the natural flora do?

A

Provides colonisation resistance
Can contaminate species
Major source of disease

279
Q

What are endogenous infections?

A

Caused by the natural flora

280
Q

What is zoonosis?

A

The movement of diseases from an animal to a human

281
Q

What are the two types of infection caused by tuberculosis?

A

Latent vs active

282
Q

What bacteria can cause bacterial pneumonia?

A 
Staphylococcus aureus 
Klebsiella pneuomniae
Streptococcus pneumoniae
Haemophilus influenzae
Pseudomonas aeruginosa
283
Q

What does pneumonia affect?

A

Oxygen transport through the alveoli

284
Q

What are the two types of food borne disease?

A

Toxin mediated and infectious

285
Q

What do the two subunits of cholera do?

A

Subunit B binds GM1 glycolipids and is the delivery portion
Subunit A causes ADP ribosylation of Gs unit meaning excessive cAMP is produced and ions are moved into the lumen affecting the osmotic balance

286
Q

What causes endotoxin and septic shock?

A

Lipopolysaccharide

287
Q

What are the symptoms of septic shock?

A

Fever
Hypertension
Coagulation

288
Q

What is the plant cell wall made up of?

A

Cellulose

289
Q

What is the bacterial cell wall made up of?

A

Peptidoglycan

290
Q

What is the primary function of a cell wall?

A

Structural

291
Q

What does a cell wall also do?

A

Act as anchoring points for components of the bacteria that interact with the environment eg MSCRAMMS
Supporting and protective mesh

292
Q

Why is the bacterial cell wall important to us?

A

Role in virulence
Antigenic (recognised by the immune system)
Unique to bacteria (drug target)
Fundamental biological interest

293
Q

What is the glycan strand composed of?

A

NAM and NAG

From NAM extends stem peptides which cross link glycan strands

294
Q

What form of amino acids are used?

A

D-amino acids

295
Q

What is found in position 3 of the stem peptide?

A

Meso-diaminopimelate this contains two amino groups and therefore can form a peptide bridge

296
Q

What is position 4?

A

It is always D-alanine

297
Q

What replaces position 3 in S.aureus?

A

L-lys: also has two amino groups

298
Q

When synthesised how many amino acids does the stem peptide contain?

A

5

299
Q

What are the source of peptidoglycan precursors?

A

D-alanyl-D-alanine: which is an alanine racemase & D-ala-D-ala ligase
D-glutamate: glutamate racemase

300
Q

In peptidoglycan synthesis what happens in stage 1?

A

UDP-MurNAC pentapeptide is made in the cytoplasm

Involves MurA-F (C-F: ligases)

301
Q

In peptidoglycan synthesis what happens in stage 2?

A

Moves to the membrane
MurY converts it into lipid 1 by swapping UDP for UCP
MurG adds NAG to lipid 1

302
Q

In peptidoglycan synthesis what happens in stage 3?

A

Transglycosylation (polymerisation of the glycan strands) and transpeptidation (cross linking between glycan strands)
Transglycosylation occurs first carried out by PBPs

303
Q

What is the difference between gram positive and gram negative?

A

Negative has two membranes: not good for tethering

304
Q

What are the other constituents of gram negative?

A

Lipoproteins
Coordinates the cell wall and outer membrane
Gives rigidity

305
Q

What other constituents are found in positive?

A

Teichoic and lipoteichoic acids

Teichoic are bound to peptidoglycan whereas lipoteichoic are bound to the plasma membrane

306
Q

What is the peptidoglycan substitute in archaebacteria?

A 
S-layer
Thick layer of proteins
Smaller than 8nm can fit through
Structural rigidity 
Does contain NAM and N-acetyltalesminuronic acid
307
Q

What is the peptidoglycan substitute in chylamydiae?

A

P-layer: large cysteine residues

Can target PG synthesis with antibiotics

308
Q

What type of immune system detects the peptidoglycan cell wall?

A

Innate immune system
By extracellular recognition
Intracellular recognition
Soluble peptidoglycan recognition molecules

309
Q

What enzymes disrupt the cell wall?

A

Lysozyme: breaks the cell wall
Lysostaphin: metallopeptidase which targets the pentaglycine brige

310
Q

What is the beta lactam ring a structural analog of?

A

D-alanyl-D-alanine

311
Q

What enzyme does beta lactams bind to?

A

PBPs and causes inactivation

312
Q

What does vancomycin do?

A 
Prevents transglycosylation (steric hindrance)and transpeptidation 
Forms hydrogen bonds with D-alanyl-D-alanine of the stem peptide
313
Q

What are the mechanisms of antibacterial action?

A

Substrate analogues
Steric hindrance
Enzyme inactivation
Disruption or subversion

314
Q

What agents target cell wall synthesis?

A

Beta lactams and glycopeptides (vancomycin and teicoplanin)

315
Q

What drugs treat tuberculosis?

A

Ioniazoid and ethionamide
They block mycolic acid synthesis (both inhibit enoyl ACP reductase)
They are pro drug

316
Q

What agents target the membrane?

A

Daptomycin: causes membrane depolarisation

Polymysin B and E: leakage of cell content

317
Q

Which agents target nucleotide metabolism?

A

Sulfamethoxazole and trimethoprim
Sulfa drugs: competitive inhibitors and alternate substrates for DHPs
Does or effect mammalian cells as we do not make tetrehydrofolate
Trimethoprim: blocks DHF being converted to THF

318
Q

Which agents target DNA?

A

Quinolones and fluoroquinolones

Effect DNA gyrae and topoisomerase

319
Q

Which drugs effect transcription?

A

Rifampicin
Transcription inhibitor
Binds the beta subunit of prokaryotic RNAP
Interferes with initiation

320
Q

Which agents target protein synthesis?

A

Fusidic acid and linezolid

Bacteriostatic

321
Q

What does mupirocin do?

A

Inhibits the formation of isoleucyl tRNA

322
Q

What are the two types of antibiotic resistance?

A

Intrinsic and acquired (spontaneous mutation or horizontal gene transmission)

323
Q

What are the mechanisms of antibacterial resistance?

A 
Altered target site (mutation of target, increased quantities of target, modification of target)
Decreased uptake (efflux or reduced permeability)
Enzyme inactivation/modification (destruction or modification)
Target bypass (acquisition of alternative target)
324
Q

Give an example of modification of target.

A

Vancomycin in enterococci: makes an alternative stem peptide which vancomycin doesn’t bind as easily

325
Q

Give an example of enzyme inactivation of modification.

A

Amino glycosidases: enzyme modifies the drug preventing interaction with target 16S rRNA
Beta lactams: cyclic amide bonds are hydrolysed and can’t bind to target site

326
Q

Give an example of target bypass.

A

Methicillin resistance in S.aureus

327
Q

What are immunoglobulins secreted by?

A

B lymphocytes

328
Q

What is the function of immunoglobulins?

A

Bind to antigens and mediate humoral immunity

329
Q

What is the process called where gene fragments are shuffled around?

A

Somatic recombination of combinational joining

This shuffling gives lots of different variable regions

330
Q

What sections are joined with low fidelity to give junctional diversity?

A

V, D and J

331
Q

Which region binds to the immune system components?

A

The constant region

332
Q

Which region binds to epitopes?

A

The variable region

333
Q

What is the structure of an antibody?

A

Dimer of dimers

Two heavy chains and two light chains connected by disulphide bonds

334
Q

Which domains mediate antigen binding?

A

Vh and Vl domains, the loops which project from these domains form the antigen binding sites and is where the sequence variation is concentrated.

335
Q

What are the Vh and Vl loops known as?

A

Complementarity determining regions and hypervariable loops

336
Q

What type of interactions are made between antigens and antibodies?

A

Reversible, weak non-covalent bonds

337
Q

What are the five different immunoglobulin classes?

A

IgM, IgG, IgA, IgD, IgE

338
Q

Which immunoglobulin is present in the primary response?

A

IgM

339
Q

How can immunoglobulins act?

A

Neutralise antigens preventing entry into the cell
Opsinisation for uptake by phagocytosis
Activate the classical complement cascade
Antibody dependent cell mediated cytotoxicity

340
Q

Which heavy chains have four CH domains?

A

IgM and IgE

341
Q

How many antigen binding sites does IgM have?

A

Pentameric and therefore 10 binding sites

342
Q

What does the J chain in IgM do?

A

Promotes IgM polymerisation

343
Q

Where is IgM mainly found?

A

Due to its size it is mainly found in the vascular system

344
Q

Does IgM have low of high affinity for antigens?

A

Low affinity but high avidity

345
Q

What response does IgM bring about?

A

Classical complement pathway through neutralisation

346
Q

Which immunoglobulin has four different isotopes?

A

IgG, 1-4

347
Q

How does IgG bring about a response?

A

Opsonisation and activates the classical complement cascade

348
Q

What is IgA secreted onto?

A

Mucosal epithelial surfaces

349
Q

What is IgA’s principal function?

A

Neutralise antigens and prevents infection in the first place

350
Q

Where and how is IgA transported?

A

Across the epithelium into the mucus layer by binding to Ig receptors, they are then cleaved on the luminal surface releasing IgA

351
Q

What is IgE an immune response for?

A

Worms and parasites and a few antigens

Type 1 hypersensitivity reactions

352
Q

What happens in class switching?

A

As the immunoglobulin matures it changes the expression

Starts of expressing IgM and IgD and then goes on to express IgG, IgE and IgA

353
Q

How is the vast repertoire of B cells generated?

A

Somatic rearrangement
Affinity maturation
Class switching

354
Q

What are polyclonal antibodies?

A

More than one B cell is isolated

Mixture of antibodies that respond to different parts of the protein

355
Q

What are monoclonal antibodies?

A

Homogenous antibodies which respond to the same epitope of a protein

356
Q

What is splicing driven by?

A

RNA

357
Q

What did Cech show?

A

That splicing still occurs in simple cell extracts

358
Q

What did Miller and Urey show?

A

That the prebiotic soup was: amino acids, biopolymers and nucleotide bases

359
Q

What do you need in order for splicing to occur?

A

Unspliced RNA, a G nucleotide and divalent metal ions

360
Q

What role do the divalent metal ions have?

A

Acid base catalysis

Two metal ion catalysis

361
Q

What is the hammerhead ribozyme?

A

Viroids that do not code for any gene products and are not long
They kill by continuous replication (hijack cells enzymes etc) and messing up cellular metabolism
Consist of ssRNA

362
Q

What is the mechanism of ribonucleotide reductase?

A

Ribonucleotides are made first and then converted into 2’-deoxynucleotides in a highly conserved reaction

363
Q

What is SELEX?

A

Systematic evolution of ligand by exponential enrichment

Protein Theme (1 decks)

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