Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MBB266 > Proteins > Flashcards

Proteins Flashcards

1
Q

What three things do you need to fully describe a protein?

A
  1. the structure of the protein. 2. The reaction that is catalysed. 3. The mechanism of action.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What isomer of amino acids are all proteins made up from?

A

L.

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

What type of side chains are hydrophobic?

A

Non charged.

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

Amino acids are either hydrophobic or hydrophilic. True or False?

A

False. They can have hydrophobic and hydrophilic parts. For example the oh group on tyrosine is hydrophilic whereas the benzene ring is hydrophobic.

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

What two amino acids are carboxylic?

A

Aspartate and glutamate.

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

What pH is histidine rarely found at?

A

Above 14. Then it becomes a amidizole ring with a net negative charge.

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

What charge is histidine most commonly found at?

A

Neutral. This is between pH 6 and pH14.

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

Why are peptide bonds rigid?

A

Electron localisation.

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

The bottom right hand corner of a Ramachandran plot is disallowed for all amino acids. True or false?

A

False. Glycine is allowed.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Beta strands are helical. True or false?

A

True.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

How many residues are there per turn in a beta sheet?

A

2.

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

How many residues are there per turn in an alpha helix?

A

3.6.

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

What is formed in a protein when the same phi-psi angles are found in succession?

A

The proteins secondary stucture- alpha helices and beta sheets.

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

What does this define? ‘The arrangement of all atoms in the subunit, arrangement of the alpha-helices and beta sheets, side chains an any additional co factors.’

A

The tertiary structure.

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

What is the definition of a proteins structure motifs?

A

Arrangement of a few helices and/or strands that occur often in different structures.

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

Where is the helix-turn-helix often found?

A

DNA binding proteins.

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

What is the definition of a domain?

A

Distinct sub division of a protein.

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

What super-secondary structure is found in the TIM barrel?

A

Beta-alpha-beta unit.

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

What are the two types of oligomers are found in quaternary structures?

A

Homo-oligomers and hetero-oligomers.

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

What are dimers, timers and 24ers all examples of?

A

Homo-oligomers.

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

What is ferritin an example of?

A

24mer.

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

What is the definition of a hetero-oligomer?

A

Where copies of different chains assemble.

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

What is the main technique used to see the structure of a protein?

A

X ray diffraction.

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

Why can you see an electron density map of a proteins structure via x-ray crystallography?

A

The x-rays interact with the electrons.

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

Apart from X ray diffraction from protein crystals what are the other two methods to determine the structure of a protein?

A

NMR spectroscopy and high resolution cryo-electron microscopy.

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

What percentage of protein structure have been determined by x-ray crystallography?

A

90%.

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

What is being described here? Crystals of the highly purified target molecules are grown and exposed to X-rays to give diffraction patterns.

A

X ray crystallography.

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

What is the definition of resolution?

A

Level of detail that can be seen in a given map.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What does 1A equal in nm?

A

0.1

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

How much resolution do you need to see two bonded carbon atoms?

A

1.5A (the distance between two carbon atoms.)

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

How many A’s are used in a low resolution map?

A

6.

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

How many A’s are used in a medium density resolution map?

A

3.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What can you see in a low resolution map?

A

Sausages of helical density but no detail of side chains or atomic interactions.

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

What can you see in a medium density electron map?

A

Turns of a helix and side chains of blobs but not individual atoms.

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

How many A’s can you see in a high resolution map?

A

1.6.

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

What can you see on a high resolution map?

A

Holes in aromatic rings and can almost see individual atoms.

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

What is the energy of interaction between atoms also known as?

A

Enthalpy.

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

Why are there few ionic interactions in a protein?

A

Because there are few charged amino acids.

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

What do ionic interactions depend on?

A

Distance.

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

Where are ionic interactions strongest?

A

In the centre.

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

Where are charged groups mainly found in the protein and why?

A

On the surface so they can interact with water.

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

What is the dielectric constant in the centre of a protein?

A

4.

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

What is the dielectric constant in water?

A

80.

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

Are ionic bonds or hydrogen bonds highly directional?

A

Hydrogen.

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

What do hydrogen bonds bind to on the exterior of a protein?

A

H20, ligands and the surface of other proteins.

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

What do hydrogen bonds depend on?

A

Distance and angle.

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

What do disulphide bonds do in hostile environments?

A

Add stability.

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

Why do you not find disulphide bonds in the interior of a protein?

A

There is reducing conditions.

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

What is the difference between delta H in a folded and unfolded protein?

A

0.

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

In a folded protein there are numerous VDW and H bonding interactions. What interactions are present in an unfolded protein?

A

The Hydrogen groups form hydrogen bonds with water and the rest of the chain makes VDW with water.

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

What is the key to protein folding?

A

Entropy.

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

What entropy change of protein folding is important?

A

The entropy of the water molecules.

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

Water molecules form cage like structures around unfolded proteins. What are these called?

A

Clathrates.

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

How are hydrophilic and hydrophobic residues arranged in a beta sheet?

A

They alternate.

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

How are the hydrophobic groups arranged in an alpha helix?

A

On the inside face.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

For a novel protein is it quicker to predict the structure by using hydrophobic residues or by determining them experimentally?

A

Determining them experimentally.

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

What do groups of hydrophobic residues on the surface of a protein result in?

A

Sticky patches that can interact with hydrophobic ligands/ patches on other proteins.

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

How do basic amino acids interact with phosphate groups?

A

Ionic interactions.

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

What gives strands and helices specific shapes?

A

Hydrogen bonds.

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

What do enzymes allow?

A

Regulation.

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

How many reactions can each enzyme catalyse?

A

Generally only one.

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

How much do enzymes enhance the reaction rate by?

A

10^8 10^12

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

Are intermediates or transition states short lived?

A

Transition states.

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

What three things do enzymes do to molecules?

A
  1. Bring substrates close together. 2. Allow them to be at optimal orientation. 3. Stabilize transition states and intermediates.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

What do most enzyme reactions involve?

A

Hydrogen ion transfer.

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

What is the definition of acid-base catalysis?

A

When a proton is transferred going to or from the transition state.

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

What’s the difference between a base and a nucleophile?

A

The bond formed when a nucleophile donates an electron is usually something other H.

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

What does RNase cleave?

A

Single stranded ribonucleic acids.

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

What type of enzyme is RNase?

A

A digestive enzyme.

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

Where is RNase produced?

A

The pancreas.

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

Where does RNase act?

A

The lower intestine.

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

RNase was worked on extensively in the 1980’s because it was abundant. Where was it abundant?

A

Beef pancreas.

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

What is RNase S?

A

A clipped form of RNase.

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

Where in RNase do you clip to make RNase S?

A

Between residues 20 and 21.

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

Is RNAse active?

A

Yes.

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

Why was RNase S used in early mutagenesis experiments?

A

As the first 20 polypeptides could be replaced.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
77
Q

What type of base will RNase cut after?

A

Pyrimidines (U and C).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
78
Q

What bond does RNase cleave?

A

P-O5’ bond.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
79
Q

What isotope of oxygen is the solution used for the RNase reaction enriched with?

A

O18.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
80
Q

What key catalytic intermediate is found in the RNase reaction which can unusually be isolated and characterised ?

A

2’-3’ cyclic nucleotide.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
81
Q

The 2’-3’ catalytic intermediate splits the RNase reaction into two steps. What are these steps?

A
  1. The formation of the 2’-3’ cyclic compound. 2. Cleavage.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
82
Q

The RNase reaction has two steps. What step is easier to study and revealed the pH dependance of the reaction?

A

The second step (the cleavage step).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
83
Q

What did the pH profile or Vmax show with the RNase reaction?

A

Two intersecting curves- this showed that two groups of a pka of roughly 7 were present. These groups were suspected to be histidine.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
84
Q

What is the principle behind chemical modification?

A

Reactive compounds chemically modify key groups in the enzyme.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
85
Q

One chemical modifier used to try and determine the structure of RNase was iodoacetate. What group did was this wrongly thought to chemically modify?

A

The SH groups or cysteine.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
86
Q

What chemical modifier was used to try and determine the structure of RNase?

A

Iodoacetate.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
87
Q

What method showed that cysteine was not an essential amino acid in RNase?

A

Cysteine.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
88
Q

What is special about the histidine residues in RNase?

A

They are unusually nucleophillic.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
89
Q

What are the key residues in the active site of RNase?

A

His12 and His119.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
90
Q

Why is only one His residue modified at a time in RNase?

A

As they are close together.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
91
Q

What do the two his residues act as in RNase?

A

One as an acid and one as a base.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
92
Q

The histidine residues in the active site of RNase are always hyper reactive. True or false?

A

False. They are only hyper reactive when the protein is folded.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
93
Q

Where was it determined that the modifying agent should lie in RNase?

A

Between the two histidine residues.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
94
Q

RNase was the forth protein to have its structure determined. When was it determined?

A

1967.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
95
Q

How was the structure of RNase determined?

A

X ray crystallography.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
96
Q

What does the polypeptide chain of RNase fold into?

A

A 3-stranded V-shaped anti-parallel beta sheet.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
97
Q

What is the polypeptide chain of RNase cross linked by?

A

4 disulphide bridges.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
98
Q

What shape is the active site in RNase?

A

A deep cleft.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
99
Q

Where is the catalytic residue His12 found in RNase?

A

The N terminal.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
100
Q

What is the role of Lys41 in the specificity pocket of RNase?

A

Stabilises the -ve phosphate group in the intermediate.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
101
Q

What two other basic residues asset with binding in RNase?

A

Lys and Arg.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
102
Q

What residue in the specificity pocket of RNase makes VDW contacts with the RNA base?

A

Phe 120.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
103
Q

What two residues in the RNase are involved in H bonding?

A

Ser123 and Thr45.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
104
Q

Why can the purines not bind to RNase?

A

The pocket is too small.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
105
Q

Different hydrogen bonding occurs with RNase and U and RNase and C. Why this is possible?

A

Ser and The can both be donors and acceptors.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
106
Q

Dinucleotides and longer molecules were cleaved by RNase when they entered the specificity site, meaning you can not visualise how the two interact. What useful non- cleavable analogue was used to allow visitation of this interaction?

A

UpCH2A.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
107
Q

What are the three active site residues in RNase?

A

Lys 41, His 12, His 119.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
108
Q

What are the three specificity pocket residues in RNase?

A

Phe 120, Thr 45, Ser 123.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
109
Q

What type of catalysis happens in the RNase enzyme?

A

General acid base.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
110
Q

What his residues acts as the acid in the first half of the RNase reaction?

A

His 119.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
111
Q

What residue acts as a base in the RNase reaction?

A

His 12.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
112
Q

How does the second half of the RNase reaction work?

A

The system is attack by water and the whole thing is reversed.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
113
Q

How many classes of RNase are there roughly?

A

100.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
114
Q

Most classes of RNase are related to RNase A. True or false?

A

False.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
115
Q

What is the function of RNase H?

A

Cleaves RNase in RNA/DNA duplexs.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
116
Q

What is the function of RNase L?

A

Destroys all RNA in the cell (innate anti-viral and apoptosis.)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
117
Q

What is function of RNase P?

A

Riboenzyme involved in processing tRNAs.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
118
Q

What is angiogein?

A

A homologue of ribonuclease A.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
119
Q

How similar is angiogein to ribonuclease A?

A

33%

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
120
Q

What does angiogenin do?

A

Promotes development of blood vessels in healthy cells and in tumours.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
121
Q

How is it though that angiogenin works?

A

Translocated to the nucleus of endothelial cells where it cleaves tRNA and RNA molecules involved in signalling.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
122
Q

What is special about the binding inhibitor angiogenin?

A

It is one of the tightest binding inhibitors known.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
123
Q

What product is made after RNase cleavage?

A

5’ OH and 3’ P.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
124
Q

Where is the key oxygen on a deoxyribose ring?

A

3.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
125
Q

RNA has an extra hydroxyl group attached to the ribose ring. What position is this in?

A

2.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
126
Q

What carbon of the sugar ring is the phosphate group attached to?

A

5.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
127
Q

What distances are hydrogen bonds usually?

A

2.8A-3.2A.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
128
Q

Sometimes you can get hydrogen bonds shorter than the average hydrogen bond (you can never get them larger.) How short can these bonds be?

A

2.4A.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
129
Q

Due to repulsion hydrogen bonds are fairly linear. How much variation is there on this?

A

20 degrees or 30 CHECK

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
130
Q

Are purines or pyrimidines larger?

A

Purines.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
131
Q

How many carbons are in the purine rings?

A

5/6.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
132
Q

How many carbons are in the pyramidines rings?

A

6.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
133
Q

What is different between U and T?

A

Thymine has an extra methyl group.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
134
Q

C, U and T are all pyrimidines with the same hydrogen bonding potential. True or false?

A

False, T/U have a different hydrogen potential to C.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
135
Q

By knowing the covalent structure of the bases we also know the 3D structure. True or false?

A

False.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
136
Q

The 3D structure of each nucleotide is determined by __ conformational angles.

A
  1. The value of these three angles= the 3D structure.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
137
Q

What was the main source of evidence for Watson and Cricks DNA structure?

A

X-ray fibre diffraction.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
138
Q

What 5 methods were used to determine the structure of DNA?

A
  1. Electron microscopy and light scattering. 2. Chargaff’s rules… ratio of bases. 3. X-ray fibre diffraction. 4. Titration of DNA. 5. Model-building studies.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
139
Q

How big is the diameter of DNA?

A

20A. Most proteins are roughly 50A.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
140
Q

Why can you not see DNA without a microscope?

A

Visible lights wavelength is about 500A. You need 1.5A.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
141
Q

X rays are the ideal wavelength to visualise DNA however they can’t be used. Why?

A

There is no suitable lens to view them with meaning the diffraction pattern will not be seen.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
142
Q

What are used as lenses in an electron microscope?

A

Magnets.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
143
Q

In the 1950’s electron microscopes were not very good meaning that could not show the overall molecule shape. What could they show?

A

The overall molecule shape, which was a long thin molecule with a diameter of 20nm.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
144
Q

What other method showed that DNA was the same structure as electron microscopes had previously done?

A

Light scattering- some light hits the protein/ nucleic acid and is scattered.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
145
Q

What did Chargaff discover?

A

A=T and C=G.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
146
Q

G/C +A/T =?

A

1.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
147
Q

Although diffraction patterns from X-ray fibre diffraction can not be seen with lenses they can be seen with ______ _____.

A

Photographic film.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
148
Q

What is the X Ray passed though in X ray fibre diffraction ?

A

1000s of aligned DNA molecules pulled through a fibre.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
149
Q

What does X ray diffraction results show?

A

A regular structure.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
150
Q

X ray diffraction patterns showed repeating distances of 3.4A. Why was this relevent?

A

3.4A is the thickness of an aromatic ring. (Stack of pennies.)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
151
Q

In the 1950’s Franklin and Wilson placed DNA fibres in controlled humidity chambers. What two humidities did they use?

A

Less than 75% and 92%.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
152
Q

What form of DNA is found in 92% humidity?

A

B.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
153
Q

Type A DNA is found in

A

A.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
154
Q

Did Franklin or Watson/ Crick concentrate on B form DNA (

A

Watson and Crick.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
155
Q

What pattern was showed in the B type DNA?

A

Double diamond with 2 fold symmtery- this showed a helix.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
156
Q

All forms of DNA are clockwise (right handed). True or false?

A

False. Z form is anti-clockwise.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
157
Q

Is A or B DNA shorter and fatter?

A

A.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
158
Q

How are the base pairs arranged in B strand DNA?

A

Perpendicular.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
159
Q

What angle are the base pairs at in A DNA?

A

20 degrees.

160
Q

How many bp to As does Type A DNA have?

A

11bps in 28A.

161
Q

How many base pairs to As does type B DNA have?

A

10bps in 34A.

162
Q

How are the bases arranged in A and B DNA?

A

They are stacked.

163
Q

What type of DNA isn’t neatly stacked and is ‘hollow’?

A

A.

164
Q

What way does A DNA turn?

A

Towards.

165
Q

What way does B DNA turn?

A

Away.

166
Q

Does changing from type A to type B DNA require bond breaking?

A

No.

167
Q

Is the A or B form of DNA rare?

A

B.

168
Q

What can cause the DNA sequence to be slightly twisted?

A

The sequence of proteins.

169
Q

Most DNA in the cell is free. True or false?

A

False.

170
Q

What RNA was used to determine is structure?

A

RNA from reovirus.

171
Q

What is the only type of RNA you get?

A

A.

172
Q

Why can you not get B form RNA?

A

RNAs hydroxyl group can not fit into the B structure.

173
Q

Why can’t RNAs hydroxyl group fit in the B structure?

A

Steric clashes with the next base.

174
Q

A DNA can form DNA/RNA complex. What is it hence involved in?

A

Transcription.

175
Q

B DNA can not form a DNA/RNA complex as it can only pair with a B strand. What is B DNA hence involved in?

A

Replication.

176
Q

How many types of DNA were used in fibre diffraction?

A

All of them.

177
Q

What is single crystal diffraction also called?

A

Crystallography.

178
Q

What two words can describe DNA crystallography?

A

Detailed and simple.

179
Q

The downside of crystallography is that you can not mathematically interpret the data. True or false?

A

False. You can.

180
Q

What is used instead of a lense in x-ray crystallography?

A

A computer.

181
Q

Is there ambiguity in X ray crystallography?

A

No.

182
Q

What was the problem with X ray crystallography in the 1970’s?

A

It was not poogen

183
Q

When was the ‘Z form’ of DNA found?

A

1979.

184
Q

What sequence was found in Z DNA?

A

GCGCGC- repeated purines/ pyrimidines.

185
Q

What shape is the backbone for Z DNA?

A

Zig Zag.

186
Q

How long is Z DNA?

A

Very short.

187
Q

How manu bp/ A is there in Z DNA?

A

12bp and 45A.

188
Q

Where was Z DNA found in 1999?

A

Human editing enzyme.

189
Q

What was found in 2003 with Z DNA?

A

DNA/RNA binding proteins, some found in tumour response and viral pathogenicity.

190
Q

Although unclear, what may regions of Z DNA be involved in?

A

Unwinding/ supercoiling.

191
Q

Has Z DNA with a top half of A or B been found?

A

B.

192
Q

B DNA with a bottom of Z has been found. What is found at this junction?

A

AT base pair.

193
Q

Who proposed tRNA?

A

Crick.

194
Q

How many types of tRNA are there?

A

More than 20.

195
Q

tRNAs are quite big and easy to purify. True or false?

A

True.

196
Q

What was the tRNA base structure worked out in in 1965?

A

Yeast analine.

197
Q

Why was it thought that tRNA might base pair with itself?

A

Complementary parts of the sequence.

198
Q

tRNA is made out of 4 B DNA ‘arms’. True or false?

A

False. It is made out of 4 B DNA arms.

199
Q

What arm is found on the left side of tRNA?

A

D.

200
Q

What arm is found on the right side of tRNA?

A

A.

201
Q

Where do amino acids attach to in tRNA?

A

Tha aa arm.

202
Q

Where do anticodons attach to in tRNA?

A

The ac arm.

203
Q

What percentage of bp in tRNA pair in a Watson/Crick manner?

A

55%.

204
Q

How does the ribosome bind to the tRNA?

A

Through the T loop in the top left corner (third corner.)

205
Q

Unusual base triplets are found in tRNA, what do this add?

A

Extra stability.

206
Q

95% if the aromatic bases in tRNA are stacked on top of each other?

A

That base stacking is a major force of stability in tRNA.

207
Q

What causes the bases to stack in A/B DNA and in tRNA?

A

The edges of the bases are rich in N and O, allowing hydrogen bonds to form. This means they want to form hydrogen bonds with water/ each other.

208
Q

What part of bases is hydrophobic and what does this cause?

A

IThe face/ the aromatic rings. These then stack on top of each other to avoid water, resulting in stacking.

209
Q

In X ray fibre diffraction what does big spacing on the pattern correlate to?

A

Small spacing in the molecule.

210
Q

What group in DNA can always be titrated?

A

Phosphates.

211
Q

What pH do the phosphates in DNA titrate at?

A

2.

212
Q

What pH do the bases titrate at?

A

It varies depending on the base.

213
Q

You can titrate the bases in DNA easily?

A

False. They can only be titrated in extreme circumstances as they are not exposed.

214
Q

Watson and Crick used model building studies to determine the structure of DNA. What did they use to make these?

A

Known information on stereochemistry of phosphates, sugars and the bases.

215
Q

What were the four key features of Watson and Crick’s model of DNA?

A
  1. Helical stacking. 2. Base stacking. 3. Two chains. 4.Regular sugar phosphate backbone.
216
Q

What evidence did Watson and Crick use to support helical stacking?

A

Diffraction pattern.

217
Q

What evidence did Watson and Crick use to support base stacking?

A

3.4A repeats in diffraction pattern.

218
Q

What evidence did Watson and Crick use to support two chains?

A

Density measurements and x ray patterns.

219
Q

What evidence did Watson and Crick use to support the regular- sugar phosphate backbone?

A

The backbone was shown to be the same in DNA from different species. It also did not depend on base composition.

220
Q

Why did Watson and Crick think the bases were hydrogen bonded to each other?

A

As titration experiments showed they were buried from water.

221
Q

Watson and Crick determined that DNA contained hydrogen bonds through titration experiments. How did they work out that they were between the two chains?

A

As hydrogen bonds are linear and meaning they can not be present between the same chain.

222
Q

Watson and Crick determined that the hydrogen bonds in DNA had to be between two different chains. What other restriction was there?

A

The x ray diffraction patterns had shown the the base pair composition could not be affected by the base pairs.

223
Q

Why did Watson and Crick conclude that the base pairs had to be Pu:PY?

A

As Purines are larger than pyrimidines meaning that if the bases were paired as Pu:Pu and Py:Py the distances would not be the same (Pu:Pu larger) and due to the random incorporation of the bases the backbone would not be universal.

224
Q

AT and GC have almost identical geometry provided the chains run in opposite directions. True or False?

A

False. It is identical.

225
Q

What did thermal denaturation of DNA provide information on and why?

A

The base pairs due to the fact that GC has 3 hydrogen bonds which correlates to a higher melting point.

226
Q

Why was the determination of different size DNA grooves important?

A

As this provided vital information later on to determine protein/drug DNA interaction.

227
Q

How long is a turn in DNA?

A

34A.

228
Q

How long is a repeat unit in DNA?

A

3.4A.

229
Q

What is the role of the base pairing in DNA?

A

Carries genetic information.

230
Q

What is the role of the sugar-phosphate backbone in DNA?

A

Stability.

231
Q

What is the lysozyme enzyme involved in?

A

The first line of defence against bacterial attack.

232
Q

Where are lysozyme found in humans?

A

Bodily secretions.

233
Q

Lysozyme are small enzymes. How many amino acids are they made up of?

A

129.

234
Q

How many SS bridges are there in lysozyme?

A

4.

235
Q

Bacteriophages have lysozymes related to human lysozymes in both chemistry and structure . True or false?

A

False, their chemistry is the same but the structure is different.

236
Q

Lysosomes are part of what huge group of enzymes?

A

Glycosidase enzymes.

237
Q

What is the main role of glycosides enzymes?

A

They hydrolyse sugars.

238
Q

What type of bacteria have a thick peptidoglycan cell wall?

A

Gram positive.

239
Q

What two alternating sugars are peptidoglycan molecules made up of?

A

NAM and NAG.

240
Q

From what sugar does peptidoglycan cross link?

A

NAM.

241
Q

Where does the lyzosome cleave the peptidoglycan?

A

Between NAM and NAG where they aren’t too many cross links.

242
Q

What two unusual amino acids are found in the peptidoglycan cross link?

A

D-ala and D-glu.

243
Q

What does the side chain of D-Glu bind to with an unusual link in peptidoglycan?

A

Main chain of lys.

244
Q

What does the side chain of lys bind to with an unusual linkage in peptidoglycan?

A

Main chain of Gly.

245
Q

What enzymes synthesis peptidoglycan cross links and are also targets of penicillin and related antibiotics?

A

D-Ala-D-Ala transpeptidase.

246
Q

What linkage does the lysozyme cleave?

A

NAM B(1-4) NAG linkage in peptidoglycan.

247
Q

When the NAM NAG linkage is cleaved where does the O molecule go?

A

To NAG. H20 then turns this and the exposed group on NAM into two H20 molecules.

248
Q

How long is a typical peptidoglycan sugar chain?

A

25-35 disaccharide units.

249
Q

How many domains do lysozymes have?

A

2 separated by a deep cleft.

250
Q

What does the left domain of the lysozyme contain?

A

A small Beta sheets made mainly of hydrophobic residues.

251
Q

What does the right domain of the lysozyme contain?

A

A hydrophobic core surrounded by a short alpha helices.

252
Q

What substrate was observed binding to the top half of the cleft/active site of the lysozyme?

A

triNAG.

253
Q

What did the rate of hydrolysis of NAG show?

A

That the active site will bind 6 sugars.

254
Q

What sites did triNAG bind to?

A

ABC.

255
Q

Why could NAM only be found in sites B, D and F?

A

Because it is bigger.

256
Q

What is hexaNAG cleaved into?

A

(NAG)4 and (NAG)2.

257
Q

What pattern of interactions was found in the lysozyme active site?

A

H bonds to O and N on the edges of the sugar rings and hydrophobic/ VDW interactions on the faces of the sugars.

258
Q

What sites is the NAM/NAG cleavage site found between?

A

D and E.

259
Q

What are the only two amino acids in the D/E region of the enzyme that can accept/donate protons meaning they are the catalytic groups?

A

Asp52 and Glu35.

260
Q

Glu35 and Asp52 both have carboxylic acid functional groups, however at pH 6 they are not both found as carboxylate ions. Why?

A

Glu is in a hydrophobic microenvironment which makes it protonated (uncharged).

261
Q

What method showed that Glu35 is found in its protonated state in the lysozyme?

A

Neutron diffraction.

262
Q

What intermediate was proposed in the now wrong Phillips mechanism?

A

Carbonium intermediate.

263
Q

What was the role of Asp 52 in Phillips mechanism?

A

Stabilises the distorted carbonic ion intermediate in the D site.

264
Q

What was the main reason that the Phillips mechanism was disregarded?

A

Carbonium ion is high energy and isn’t a likely intermediate.

265
Q

What bond was involved in the second proposed mechanism of the lysozyme?

A

enzyme-glycosol covalent bond.

266
Q

What acts as a nucleophile in the second proposed mechanism for the lysozyme?

A

Asp52.

267
Q

Nucleophilic attack by _____ forms covalent ___________ intermediate. ____ (_____) donates a proton and E-F diffuses away, making the first product. Attack by ______. OH added to C1 of D and a proton to _____. A-B-C-D is the second product.

A

Asp52, glycosyl-enzyme, Glu35 buried, water, Glu35.

268
Q

What type of evolution are lysozymes thought to have followed and why?

A

Convergent evolution as they have no sequence similarity but all their mechanisms use two carbonyl groups.

269
Q

Name 5 types of glycosidases.

A
  1. Lysozymes. 2. Lactases. 3. Amylases. 4. Cellulases. 5. Neuraminidases.
270
Q

What do cellulases do?

A

Break down cellulose to glucose.

271
Q

What is the purpose of neuramindases?

A

Used by viruses and bacteria to penetrate cell walls in a process called pathogenesis.

272
Q

Glu 35 is protonated in the lysozyme. What can this also be known as?

A

Glutamic acid.

273
Q

What are the three steps of the lysosome mechanisms?

A
  1. Nucleophilic attack by ASP52 to create a covalent glycosyl-enzyme intermediate. 2. Glu35 donates a proton. 3. Water attacks.
274
Q

What are 6 examples of DNA BP?

A
  1. Proteins that regulate gene expression. 2. DNA packaging proteins. 3. Restriction enzymes. 4. Polymerases. 5. Repair proteins. 6. Unwinding proteins.
275
Q

Why are DNA binding proteins often positive?

A

As the DNA backbone is negative due to the phosphates.

276
Q

What fits easily into the major groove?

A

The edges of bases (specific sequences can be detected easily).

277
Q

Can the edges of bases be seen by the minor groove?

A

Yes.

278
Q

DNA is always found in is low energy A and B forms. True or false?

A

False. It can bend away from the structure and some sequences are more likely to do this then others.

279
Q

When were the first DNABP established?

A

1980’s.

280
Q

Do DNABP react with the phosphate group specifically?

A

No.

281
Q

What two bases are involved in specific binding with adenine in the major groove?

A

Asn and Gln.

282
Q

What other reactions are involved with DNABP?

A

Non polar interactions, hydrophobic interactions, non hydrogen bonding contacts.

283
Q

After hydrogen bonds between bases have been taken into consideration how many other options of Hydrogen bonds can be made in the major groove?

A

3.

284
Q

After hydrogen bonds between bases have been taken into consideration how many other options of Hydrogen bonds can be made in the minor groove?

A

2.

285
Q

What is the pattern of donors and acceptors between A and T in the major groove?

A

ADA.

286
Q

What is the pattern of donors and acceptors between A and T in the minor groove?

A

AA.

287
Q

What is the pattern of donors and acceptors between G and C in the major groove?

A

AAD.

288
Q

What is the pattern of donors and acceptors between G and C in the minor groove?

A

DA.

289
Q

What base has a methyl group that proteins/ residues?

A

Thymine.

290
Q

What fits neatly in the major groove into the B DNA?

A

Alpha helix

291
Q

What amino acid is in the turn in the helix turn?

A

Glycine as it fits well into the B groove of DNA.

292
Q

What is the zinc finger model made up off?

A

2 beta strands and 1 alpha helix.

293
Q

How are the zinc finger motifs usually arranged?

A

In strings.

294
Q

Why are zinc fingers not normally found on their own?

A

They don’t give much specificity.

295
Q

The tilt of the helix relative the the groove of DNA doesn’t change. True or false?

A

False.

296
Q

What amino acids are present in the zinc finger model?

A

2 cysteines on the beta strand and 2 histidines.

297
Q

When is the basic leucine zipper motif used?

A

In non DNAbp polymerisation.

298
Q

How are the helices arranged in the leucine zipper motif?

A

At the same height.

299
Q

The basic leucine zipper motif is one continuous helix. True or false?

A

False, it can be one continuous helix but it can also double back on itself in a loop.

300
Q

How are B ribbons formed?

A

By two beta strands.

301
Q

Where does the beta ribbon fit into and what does it do?

A

It fits into the major groove of DNA and the side chains of the strand interact with the edges of the bases.

302
Q

What type of contacts can be made by a b strand and the minor groove of DNA in packaging?

A

Non specific contacts.

303
Q

How may degrees does DNA rotate onto itself?

A

180.

304
Q

Where is the symmetry in DNA?

A

Through and between every base pair (approximately, ignore the base pairs).

305
Q

What is the only DNA sequence that has true 2 fold?

A

Palindromic.

306
Q

Where are palindromic sequences often found?

A

Binding sites.

307
Q

What do most prokaryotic repressors and activators recognise?

A

Palindromic DNA sequences.

308
Q

When is the basic leucine zipper used?

A

Non DNABP in a polymerisation/ dimerisation fashion.

309
Q

The basic leucine zipper motif is always a continuous helix. True or false?

A

False. It can be double back on itself in a loop.

310
Q

When were ribozymes discovered?

A

1983.

311
Q

What are ribozymes made from?

A

RNA.

312
Q

Where was the first example of a ribozyme found?

A

In the protozoan Tetrahymena.

313
Q

What part of the mRNA makes up the ribozyme?

A

Intron.

314
Q

What are the three main points regarding the ribozymes structure?

A
  1. The majority of base pairs form WC pairs in A-form double helices. 2. Almost all bases are stacked, even if they aren’t paired. 3. Base triplets and metal ions can link bits o the structure together.
315
Q

What forms the 3D structure in the ribozymes?

A

H bonds.

316
Q

What drives the folding of the ribozymes?

A

Base stacking of hydrophobic surfaces.

317
Q

What is the probable ancestor of the spliceosome?

A

Self splicing intron.

318
Q

What are the catalytic triads in the group 2 ribozymes?

A

CGC or AGC.

319
Q

What do the catalytic triads (CGC and AGC) bind to in the group 2 ribozymes?

A

2 Mg2+ ions.

320
Q

What two things do RNA enzymes need to do/have?

A
  1. They need to specifically bind substrates. 2. Have groups with unusual activity that can catalyse reactions.
321
Q

How do RNA enzymes bind their substrates?

A

They have unpaired bases which can bind complementary sequences in DNA and RNA.

322
Q

Why do ribozymes have much less scope for reactivity than proteins do?

A

They only have four bases.

323
Q

Ribozymes are only made up of 4 bases so they are less chemically reactive than protein enzymes. What two methods can increase their reactivity?

A
  1. Bound metal ions can give unusual reactivity. 2. Nucleobases in unusual 3D environments can give unusual chemical properties.
324
Q

What are ribozymes thought to be the remainder of?

A

RNA world.

325
Q

Why is it thought that most cofactors have a nucleotide in their structure?

A

They may have originally been cofactors to ribozymes.

326
Q

What is the definition of a riboswitch?

A

mRNA segments that can fold up and bind small target molecules and affect the transcription of the mRNA.

327
Q

What do riboswitches demonstrate?

A

That RNA can regulate gene synthesis.

328
Q

What do riboswitches show in regards to RNA?

A

That they can bind small molecules.

329
Q

When could riboswithes be descended from?

A

RNA world (pre protein regulatory machinery.

330
Q

What can riboswitches be?

A

Potential antibiotic targets.

331
Q

Riboswitches are mainly found in bacteria but they have recently been found in some eukaryotes. What are these?

A

Plants and fungi.

332
Q

How many Svedborg units is the prokaryotic ribosome made out of?

A

70s. 50s large 30s small

333
Q

What is the overall size of the prokaryotic ribosome in megadaltons?

A

2.7 megadaltons.

334
Q

What is the overall size of the small prokaryotic ribosome subunit in megadaltons?

A

1.0 mega daltons.

335
Q

What is the overall size of the large prokaryotic ribosome subunit in megadaltons

A

1.7 mega daltons.

336
Q

Both subunits in the prokaryotic ribosome are made up of two pieces of RNA. True or false?

A

False. The small subunit only has one.

337
Q

How many proteins are in the large subunit of the prokaryotic ribosome?

A

34.

338
Q

How many proteins are in the small subunit of the prokaryotic ribosome?

A

21.

339
Q

What main method was used to determine the structure of the ribosome?

A

Neutron scattering.

340
Q

In the 1980’s Ada Yonath tried to crystallise ribosomes from many bacterial species, including T thnermophlillus. What were her results?

A

She obtained poor quality crystals which resulted in weak diffraction patterns (spots were too close to be distinguised between.)

341
Q

In the 1990s technological advances helped with the determination of the structure of the ribosome. What are 5 examples of these improvements?

A
  1. Synchrotron radiation ( 1000x stronger than conventional sources.) 2. Improved detector technology ( increases diffraction intensities) 3. Cryocooling (prevents radiation damage). 4. Improvements in computer power ( Improved date processing.) 5. EM structures present.
342
Q

What happened in 1999 in regards to the ribosomes structure?

A

Low resolution gave the overview of the structure. 6A gave the structure of both subunits. The structure of the complete ribosome and the tRNAS were done at 8A.

343
Q

At a low resolution what was determined about the structure of the ribosome?

A

The overall shape of the protein/ RNA maintain but no detail of side chains or bases.

344
Q

When did the detailed structure of the small and large ribosomal subunits become available?

A

August 2000.

345
Q

Were all components of the DNA and the proteins determined in the August 2000 model of the ribosome?

A

Yes.

346
Q

What is the purpose of the large ribosomal subunit?

A

Catalyses peptide bond formation.

347
Q

How many domains are in the larger piece of RNA in the large subunit?

A

6

348
Q

What is thought to form the core of the ribosome?

A

Complex 3D jigsaws of RNA.

349
Q

A few proteins are found close to the active site of the ribosome. True or false?

A

False, no proteins are close to the active site. the N and C tails of some proteins however are.

350
Q

What is the core of the large subunit made from?

A

Tightly packed mass of RNA helices.

351
Q

What stabilises interactions between RNA domains?

A

Ribosomal proteins on the outside of the domains.

352
Q

What is the active site for protein synthesis in the ribosome made form?

A

100% RNA.

353
Q

What can the ribosome also be called?

A

A ribozyme.

354
Q

How was the active site of the ribosome located?

A

Soaking crystals with known inhibitors.

355
Q

The proposed catalytic mechanism for the active site of the ribosome is complex. What does it involve?

A

A crucial adenine in an unusual 3D environment very close to a phosphate group. This unusual environment results in abnormal protonation.

356
Q

What is the peptide exit tunnel is bounded by?

A

RNA domains.

357
Q

What is the small ribosomal subunit responsible for?

A

Decoding genetic information during translation.

358
Q

What does the small subunit bind?

A

mRNA and tRNA (to read the mRNA).

359
Q

How many proteins/ nucleotides is the small subunit made from?

A

20/ 1518.

360
Q

All 20 proteins in the small subunit have been identified. What proportion of the nucleotides have been identified?

A

96%.

361
Q

What is the decoding centre in the small subunit made from?

A

100% RNA.

362
Q

What are the three key parts of the ribosome?

A
  1. Decoding centre 2. Peptide tunnel 3. Peptidyl active site.
363
Q

The eukaryotic ribosome is larger than the prokaryotic ribosome. What is its size?

A

4200 KDA.

364
Q

Is translation more complex in eukaryotes?

A

Yes.

365
Q

The ribosomes of both prokaryotes and eukaryotes are very closely related. True or false?

A

False. They are only closely related in the active site.

366
Q

Several classes of antibiotics are directed against the bacterial ribosome. What two antibiotics are directed at the small subunit?

A

Tetracycline. Streptomycin.

367
Q

Several classes of antibiotics are directed against the bacterial ribosome. What two antibiotics are directed to the large subunit?

A

Chloramphenicol. Erythromycin.

368
Q

Do AB bind to the RNA or the protein in the ribosome?

A

RNA.

369
Q

What is tetracycline used for?

A

Respiratory tract infections.

370
Q

What is chlorampheniocal used for?

A

Bacterial meningitis.

371
Q

What do palindromic base sequences allow?

A

2-fold protein to interact symmetrically with bases as well as the backbone.

372
Q

What are the three main DNA binding proteins in bacteria?

A
  1. CAP. 2. CRO. 3. Lambda repressor.
373
Q

The three main DNABP in bacteria are CAP, CRO and the lambda repressor. These all have very different structures but are similar in two ways. What are these ways?

A
  1. All dimers. 2. All have a helix-turn-helix motif.
374
Q

What is the purpose of CAMP in the CAP/DNA complex?

A

It switches on DNA binding.

375
Q

In the CAP/DNA complex the recognition helixes bind to the major grooves in the DNA. What happens to the DNA molecule?

A

It bends around the cap complex to maximise interactions.

376
Q

When is the trp repressor active?

A

When trp can act as the co repressor.

377
Q

At low trp concentrations the repressor is not active. How much mRNA is hence transcribed to make trp?

A

5 pieces corresponding to 5 enzymes.

378
Q

When trp is bound to the trp repressor how far apart are the helices?

A

34A. (Can bind)

379
Q

When trp is not bound to the repressor how far apart are the helices?

A

26A. (Can not bind).

380
Q

Endonuclease EcoR1 and DNAP1 (Klenow fragment) both cleave DNA. Which one is a dimer?

A

EcoR1.

381
Q

Endonuclease EcoR1 and DNAP1 (Klenow fragment) both cleave DNA. Which one is a monomer?

A

DNAP1 klenow fragment.

382
Q

Endonuclease EcoR1 and DNAP1 (Klenow fragment) both cleave DNA. Which one only cleaves palindromic sequences?

A

EcoR1.

383
Q

Endonuclease EcoR1 and DNAP1 (Klenow fragment) both cleave DNA. Which one cleaves all sequences?

A

DNAP1 klenow fragment.

384
Q

Endonuclease EcoR1 and DNAP1 (Klenow fragment) both cleave DNA. Which one is described to ‘embrace DNA’?

A

EcoR1.

385
Q

Endonuclease EcoR1 and DNAP1 (Klenow fragment) both cleave DNA. Which one is described as a ‘ large circular cleft that wraps around the DNA like a hand.’

A

DNAP1 klenow fragment.

386
Q

Structure of the p53 core domain complexed with DNA revealed critical contacts. What were these (3)?

A
  1. Zn2+ ion stabilising binding loops (p53) 2. Strand loop helix motif of P53 fits into B DNA major groove. 3. Arg248 contacts backbone in minor groove.
387
Q

How often is the Arg 248 residue of P53 mutated in cancer patients?

A

10% of cancer causing mutations.

388
Q

What do the 6 most common P53 mutations normally affect?

A

Non specific DNA binding.

389
Q

What are the 6 most common P53 mutations resulting in 40% of the p53 derived tumours?

A
  1. 2 arginines- sugar phosphate backbone. 2. 3 arginines- H bond within the protein structure and stabilise protein conformation. 3. Gly245 stabilises structure of the loop in the minor groove.
390
Q

60% of P53 tumours have mutations of residues close to the protein-DNA interface. What two things does this cause?

A
  1. Disruption of sequence specific interactions. 2. Proteins no longer recognise correct DNA target sequence.
391
Q

What shape is p53?

A

A tetramer.

392
Q

Some anticancer drugs work by blocking DNA replication. How?

A

Disrupt DNA-protein interactions and prevent transcription.

393
Q

What three types of cancer drug are there?

A
  1. Intercalating. 2. Major groove binding. 3. Minor groove binding.
394
Q

What type of drug is actinomycin?

A

Intercalating.

395
Q

What type of drug is cisplatin?

A

Major groove binding.

396
Q

What type of drug is neutrospin?

A

Minor groove biding.

397
Q
A

MBB266 (7 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions