Biochemistry semester 2 Flashcards
(301 cards)
1
Q
What is actin an example of?
A
A microfillament.
2
Q
Is tubulin or actin branched?
A
Actin.
3
Q
How long is actin?
A
8nm
4
Q
How long is tubulin?
A
25 nm.
5
Q
How many genes encode actin?
A
6
6
Q
What forms of actin encode muscle actin?
A
4 alpha
7
Q
What forms of actin encode non muscle actin?
A
Beta and gamma.
8
Q
What form of actin acts as a monomer?
A
G (globular) actin.
9
Q
What state will all actin be at equilibrium?
A
F (filamentous state)
10
Q
What actin form forms a cleft to bind ATP?
A
G (globular) form.
11
Q
Which end is actin added too?
A
The barbed end.
12
Q
Which end is actin removed from?
A
The pointed end.
13
Q
What angle does myosin heads bind to F actin at?
A
45 degrees.
14
Q
When does the rate of actin polymerisation increase?
A
Once a trimer has formed.
15
Q
Why does actin growth require no ATP?
A
MgATP is bound.
16
Q
What causes actin to unravel?
A
The hydrolysis of bound ATP.
17
Q
What is present to allow stability of F actin?
A
Capping proteins.
18
Q
What is the role of thymyosin?
A
Catches actin in the cell to prevent its polymerisation.
19
Q
What is the purpose of profilin?
A
Promotes nucleotide exchange and filament formation.
20
Q
What does the longest human gene encode for?
A
Dystrophin.
21
Q
What end of actin is anchored to the membrane?
A
The C terminus.
22
Q
What type of MD is more severe, Duchenne MD or Becker MD?
A
Duchenne MD.
23
Q
What is Fimbirin?
A
An actin binding protein which binds it’s N and C terminus to form strong ladders.
24
Q
What is the purpose of filamin?
A
Forms G network and helps the membrane maintain it’s structure.
25
What is the purpose of Gelosin?
It binds to the barbed end preventing the binding of any other actin. This cause the filament to unravel and be reused. This prevents blood clots.
26
What degrees does actin bind at?
70 degrees.
27
Where is myosin 2 found?
Muscles, sacromeres and involved in cell division.
28
What forms of myosin are involved in hearing?
6 and 7.
29
What end does myosin vary at?
C end.
30
What type of interaction is contraction?
Transient.
31
In transport contact of myosin and actin is ______.
Maintained.
32
What type of coil is in myosin 2?
A complete coil coil.
33
Why can myosin 2 make a complete coil coil?
It contains no proline.
34
What is the filamentous structure of myosin 2 held together by?
Charged interactions.
35
What do dimers of myosin 2 contain?
Two heads and 2 tails.
36
What type of coil is in myosin 5?
A part coil coil.
37
What can myosin 5 form?
Dimers.
38
What can myosin 5 not form?
Filaments as it's coil coil is not complete.
39
What are Nebulin and Titun?
Giant proteins.
40
What does Nebulin define?
The number of actins.
41
What does Titun do?
It compresses when muscles shorten. It is a type of elastic protein.
42
Why does myosin get stuck on actin?
The hydrolysis of ATP causes a phosphate ion to form.
43
How is hydrolysis in muscle contraction completed?
Myosin binding to actin causing the jaw of myosin to open and the ATP to fall out.
44
What regulatory proteins are bound to the actin for regulation in striated muscles?
Tropomyosin and troponin.
45
What instantly releases muscle inhibition?
The release of calcium ions.
46
What can myosin and actin mutations result in?
Inherited heart disease.
47
What form of myosin is at the leading end?
1.
48
What form of myosin is at the rear?
2.
49
What is tubulin an example off?
Microtubule.
50
Where are stable microtubules found?
Non differentiating cells.
51
Where are transient microtubules found?
Cells that divide.
52
How many protofilliments are found in a microtubule?
13, all with the same orientation.
53
Is kinesin or dyenin processive?
Kinesin.
54
What are microtubules used for?
Tracks.
55
What myosin precisely delivers cargo?
Myosin 5.
56
Can myosin hydrolyse ATP when kinesin is carrying cargo?
No.
57
What two domains do microtubule associated proteins have?
A projection and a MT binding domain. The arm binds to the membrane or other filaments controlling length of adjacent microtubules.
58
What is taxol used for?
Cancer treatment. It stabilises microtubules in all cells inhibiting there shortening.
59
What does colchicine do?
Causes depolymerisation of microtubules making them stuck in mitosis.
60
What motor protein does axonome use?
Dynein.
61
What highly elastic substance contexts adjacent microtubules?
Nexin.
62
What does Kartegens symptoms result in?
Non motile sperm and no transport in oviduct or bronchial tract. Also causes Situs Invertes.
63
'Is the hand over hand' or 'inchworm' theory correct?
Hand over hand.
64
What can a single point mutation in axonemal dynein result in?
No ATP binding and no motor activity/ cilia function.
65
How do heterotrophs obtain energy?
Oxidising reduced carbon.
66
Is NADH formation favourable or unfavourable?
Unfavourable.
67
When NADH is produced during glycolysis where have the electrons usually come from?
A carbon atom.
68
How much energy is required to form ATP?
30.5 kj.
69
Is more glucose produced when the system is coupled or uncoupled?
Coupled.
70
Is the formation of ATP energetically favourable?
Unfavourable.
71
What is the purpose of the first step of glycolysis?
To trap glucose by turning it into glucose 6 phosphate so it can not leave the cell.
72
What enzymes phosphorylates glucose in the first step of glycolysis?
Hexokinase.
73
Where does glycolysis occur?
The cytosol.
74
What is the third intermediate in glycolysis?
Fructose 6 phosphate.
75
What type of reaction is step 4 in glycolysis?
Cleavage- fructose 1-6 bisphospahte is turned into Glyceraldehyde 3 phosphate and dihydroxyacetone phosphate.
76
Step four converts an aldo sugar into what?
A Keto sugar.
77
What is dihydroxyacetone phosphate, produced in the first stage of glycolysis, turned into?
Fats.
78
What ratio is Glyceraldehyde 3 phosphate and dihydroxyacetone phosphate produced at?
4:96
As more G3P carries on through the cycle the equilibrium position moves to counteract this
79
What enzyme converts between Glyceraldehyde 3 phosphate and dihydroxyacetone phosphate?
Triose phosphate isomerases.
80
Which two steps in the first half of glycolysis require ATP?
Step 1 and step 3.
81
In glycolysis are the delta positive G steps coupled?
No. As intermediates are shares the delta negative G steps can pull them through via product removal.
82
What is Glyceraldehyde 6 phosphate turned into?
1-3 bisphosphoglycerate.
83
What two reactions happen in the conversation of Glyceraldehyde 3 phosphate to 1-3 bisphosphate glycerate?
Oxidation (aldehyde to carb acid) and phosphorylation.
Oxidation is energetically favourable while phosphorylation is not. The whole step ends up with a positive delta G overall.
84
What enzyme carries out the conversation of Glyceraldehyde 3 phosphate into 1-3 bisphosphate glycerate?
G3P dehydrogenase.
85
What amino acids are in the binding site of G3P dehydrogenase?
Cysteine and histidine.
86
What two steps occur in the G3P dehydrogenase enzyme?
1. Nucleophilic attack.
Cysteine forms a triester intermediate with oxidised G3P
2. Phosphate attacks triester.
87
What two steps of glycolysis produce ATP?
7 and 10.
1,3 bisphosphate glycerate to 3 phosphoglycerate
Phosphoenol pruvate to pyruvate.
88
Is it energetically favourable to hydrolyse a phosphoanhydride bond?
Yes. This happens in step 7 of glycolysis and ATP is formed.
89
What is the link reaction?
Pyruvate into acetyl coA.
90
What does the term redox imbalance mean?
With no oxygen present NADH can not be re oxidised meaning there is a deficient of NAD+ and glycolysis is inhibited.
91
What does NADH reduce pyruvate into when no oxygen is present in muscle tissue?
Lactate.
92
What does NADH reduce pyruvate into when no oxygen is present in bacteria?
Pyruvate is first decarboxylated into 2 molecules of acetylaldehyde. This is then reduces to ethanol.
There is a net production of 2 ATP.
93
Is pyruvate oxidised or reduced in the link reaction when oxygen is present?
Oxidised.
94
What enzyme is involved with pyruvate oxidation in the links reaction?
The pyruvate dehydrogenase complex in the mitochondrial matrix.
95
How many molecules of NADH does each molecule of pyruvate produce when it is oxidised for links?
1.
96
What is coenzyme A?
An activated carrier molecule. It contains an acetyl and CoA linkage which is energetically favourable to hydrolyse.
97
What is the first step of links when oxygen is present?
Decarboxylation of pyruvate.
98
What does the decarboxylation of pyruvate produce?
An hydroxethyl group.
99
What can the hydroxethyl group produced by decarboxylation of pyruvate bind to?
The thiamine phosphate group cofactor of pyruvate dehydrogenase?
100
What is the second step of the link reaction when oxygen is present?
The oxidation of the hydroxyethyl group generated by the decarboxylation of pyruvate.
101
What cofactor oxidises the hydroxyethyl group in links?
Lipoamide cofactor (of dihydrolipoyl transacetylase)
102
Lipoamide is used to oxidise the hydroxyethyl group formed in the link reaction. This group is then reduced by?
The transforming of the acetyl group to CoA.
103
What is the third step of the link reaction?
The reduction of NAD+.
104
What reduces NAD+ in the link reaction?
Lipoamide is first oxidised by FAD which then reduces NAD+.
105
What does the protein environment in E3 create?
A FAD molecule with a more negative redox potential.
106
What does the flexible domain (E2) in PDH contain?
Lipoamide cofactor.
This carries substrates from E1 - E2 - E3.
107
What activates fatty acid beta oxidation?
The linkage of CoASH. This requires the formation of AMP.
108
How many enzymes oxidise fatty acids?
4.
109
Is oxidation of fatty acids spontaneous?
Yes. It is coupled to the formation of NADH and FADH2.
110
How many NADH molecules are produced in krebs?
3.
111
In krebs CO2 is produced. Where do the oxygen atoms come from?
Glucose or water.
112
Is the Krebs cycle catabolic or anabolic?
Both.
113
What can citrate be made into?
Fatty acids and sterols.
114
What can alpha Keto-glutarate be made into?
Amino acids and purines.
115
What can succinate CoA be made into?
Porphyrins, heme, chlorophyll.
116
What can oxaloacetate be made into?
Aspartate, amino acids and purines/ pyrdimines.
117
What step in krebs is citrate formed?
1.
118
Are the decarboxylation reactions oxidation or reduction reactions?
Oxidation.
119
In what step in krebs is ATP formed?
5.
120
In what steps in krebs is succinate oxidised?
6.
121
What step in the Krebs cycle involves fumerate hydration?
7.
122
What step in krebs involves malate oxidation?
8.
123
What happens in citrate formation?
Citrate synthase removes a proton from the methyl group of acetyl CoA. The CH2- nucleophile then attacks the carbon oxaloacetate. This reaction is energetically favourable and is driven by the hydrolysis of COA.
124
How is the unstable intermediate inocitrate formed in krebs?
The movement of the hydroxyl group from C5 to C4.
125
What happens in decarboxylation 1 of krebs?
The unstable inocitrate looses a molecule of CO2. Oxidation then occurs at carbon four which is catalysed by isocitrate dehydrogenase. The hydroxyl group is converted into a carbonyl group and NADH is produced.
126
What happens in the second decarboxylation in krebs?
Alpha Keto dehydrogenase catalyses the oxidation of carbon 5 by decarboxylation. Carbon 4 is then oxidised from +2 to +3. NADH is formed.
127
What happens in ATP formation in krebs?
Succinyl CoA synthatase hydrolyses the thioester bond and replaces it with a phosphate ester bond.
128
What does Succinyl CoA mechanism involve?
Coenzyme A is displaced by PI forming succinyl phosphate. Histidine removes this phosphate from succinate and phosphohisdine is formed. The phosphate then gets transferred to ADP.
129
what is succinate dehydrogenase and how does it work?
Succinate dehydrogenase is a transmembrane protein that uses the cofactor FAD to oxidise succinate. NADH is also produced.
130
What enzyme is involved in the hydration of fumerate?
Fumerase.
131
What is the role of malate dehydrogenase in krebs?
It converts the hydroxyl group of malate to a carboxylate group forming oxaloacetate. NAD+ is used in this process.
132
Are mitochrondrian always smaller than chloroplasts?
Yes.
133
Where are cristae found?
The inner membrane.
134
What does the outer membrane of the mitochondria contain?
Channel folding porins.
135
What does the DNA in the mitochondria encode for?
13 respiratory chain proteins and bacterial type MRNA/TRNA.
136
In terms of redox potentials, what way do electrons flow?
Negative to positive.
137
What redox potential is NAD+/NADH at?
-30mv.
138
What redox potential is O2/H2O at?
+820mv.
139
What is ubiquine reduced too?
Ubiquinol.
140
What compex is FADH a cofactor for?
Complex 2.
141
If the redox potential of a compound is more negative what is it more likely to do?
Donate an electron.
142
How are redox potentials measured?
Using equimolar amounts of a compound in it's oxidised and reduced states in one half cell and 1 atmosphere of H2/ 1M of H+ in the other.
143
If the electrons flow from the hydrogen half cell to the substance what does this mean?
That the substance has a more positive redox potential.
144
What is the salt bridge normally soaked in?
KCl.
This neutralises charges.
145
How much energy does one mole of ATP cost to form?
57 kj.
146
What is found at complex one?
NADH dehydrogenase.
147
How many protons are transported at compex one?
4.
148
What does the matrix arm at complex one bind?
One molecule of FMN. FMN oxidise NADH.
149
What is oxidised at complex one?
NADH.
150
What is the membrane domain used for at complex one?
Proton pumping.
151
Are t 7 or 9 iron clusters used in the complex one found in humans?
7 are used in humans and 9 in bacteria, however there are 9 clusters in both.
152
How many subunits make up complex one?
46 protein subunits.
153
What is bound to the membrane arm at complex one?
Ubiquinone.
154
Can iron sulphur clusters undergo redox reactions without releasing protons?
Yes.
155
What is Ubiquinol?
A lipid soluble electron carrier which allows the translocation of protons.
156
What enzyme is found at complex 2?
Succinate dehydrogenase.
157
What is reduced and what is oxidised at complex 2?
FAD+ is reduced to FADH2
Succinate is oxidised to fumerate.
158
How many iron sulphur clusters are at complex 2?
3.
159
What is found in the electron transferring flavoprotein?
FADH2
160
Electrons are passed from the electron transferring flavoprotein to ________.
ETF dehydrogenase.
They are then passed on to Ubiquinone making Ubiquinol.
161
How does ETF dehydrogenase transfer electrons?
Via bound cofactors called flavin and 4Fe4S.
162
The inner mitochondrial membrane is impermeable to NADH. How are electrons hence passed to ubiquinone?
The G3P shuffle and the malate aspartate shuffle.
163
Where is the glycerol 3 phosphate shuffle used?
Rapidly respiring tissue.
164
Why is less ATP produced from the G3P shuffle?
NAD+ is rapidly recycled.
165
In the G3P shuffle what does NADH reduce to make G3P?
DHAP.
166
What is the role of G3P dehydrogenase in the G3P shuffle?
It oxidises G3P.
Note, FAD has to be reduced before ubiquinone.
167
Which shuffle is more common?
The aspartate malate shuffle, which is especially common in the liver and heart.
168
How many enzymes and antiporters are involved in the malate- aspartate shuffle?
4 enzymes and 2 antiporters.
169
What is oxaloacetate reduced to in the malate-aspartate shuffle?
Malate. The reduction is carried our by NADH.
170
When malate travels across the membrane is the malate-aspartate shuffle what is it exchanged for?
alpha- keto glutarate.
171
What enzyme is used to convert malate back to oxaloacetate in the malate aspartate shuffle?
Malate dehydrogenase.
This is an oxidation reaction and NADG is produced in the matrix.
172
What transformation takes place to allow oxaloacetate to re enter the cytoplasm in the malate aspartate shuffle?
An amine group is transferred from glutamate. this produces aspartate and alpha ketoglutarate.
173
In the malate aspartate shuffle where does reverse transformation occur?
The cytoplasm.
174
What is found at complex 3?
Cytochrome bc1.
175
What happens at complex 3?
Uniquinol is oxidised with it's electrons going to cytochrome C.
176
Complex 3 is a homodimer consisting of how many subunits?
11.
177
What cofactors are involved at complex 3?
3 heam cofactors and one iron sulphur cluster.
178
What are Qp and Qn and where are they found?
They are ubiquinone binding sites found in each homodimer in complex 3.
Each monomer also has a cyt c binding site.
179
How are the cofactors ( 3 heam and one iron sulphur cluster) bound to complex 3 where they are found?
Via histidine, cysteine and methionine side chains.
180
Where does the Q cycle occur and what does it do?
The Q cycle is found in complex 3 and doubles the amount of H+ transferred per ubiquinol present. No protons are directly pumped in the process.
181
How many subunits are in complex 4?
13.
182
What is found at complex 4?
Cytochrome C oxidase.
183
How many protons are pumped at complex 4?
4.
184
How many molecules of cytc are needed to reduce oxygen into two water molecule at complex 4?
4.
185
In complex four oxygen is reduced to water. Where are the protons taken up to do this?
At the haem a3 cub site.
The protons come from the matrix.
186
Where is the cub cofactor embedded at complex four and how?
It is embedded in the membrane domain and is coordinated by 3 histidine side chains, one of which is covalently modified by a tyrosine linkage.
187
Where does cytochrome C reside?
The intermembrane space.
188
Who proposed oxidative phosphorylation?
Peter Mitchell.
189
Electron microscopy showed that during respiration the ratio of the volume of the matrix and inter-membrane space dramatically changed. What did this show that electron transport was coupled too?
Osmotic potential.
190
What do uncouplers do?
Abolish the proton gradient so chemiosmosis can not occur.
191
What to things contribute to the proton motor force?
Membrane potential and the proton concentration gradient.
192
How many protons are carried in one full turn of the F0 ring found in ATP synthase.
12.
193
One full turn of ATP synthase makes how many molecules of ATP?
3.
194
What domain of ATP synthase protrudes out of the inner membrane into the matrix?
The F1 domain.
195
How many subunits is the F1 domain made off?
9.
196
Where is the F0 domain found in ATP synthase?
Embedded in the membrane.
197
What subunits comprise the F0 domain?
12c ,1a and b2.
198
What subunit in the F0 domain acts as the stator?
B2.
199
What subunit of ATP synthase accepts protons and how?
The C subunit of the F0 domain. The protons are accepted by an aspartate residue.
200
What does the rotation of the C subunit in ATP synthase cause?
The rotation of the gamma subunit in F1.
201
What subunits in ATP synthase bind ATP?
The 3 beta subunits in the F1 domain.
202
The gamma subunit in F1 changes the conformation of the beta subunits in F1. What are the possible conformations of the beta subunits?
Tight, open and loose.
In that order.
203
What does a larger proton motor force mean?
Fewer moles of protons are required to make ATP.
204
Why do the number of C subunits vary between species?
Different species have different size proton motor forces.
205
How many molecules of ATP are produced altogether in respiration per glucose molecule?
30.
206
Why doe NADH produced in the cytosol yeild less ATP than NADH produced in the matrix.
Because the inner membrane space in impermeable to NADH and transferring NADH into the matrix for it to come in contact with NADH dehydrogenase requires energy.
207
What does the proton motor force drive apart from chemiosmosis?
Metabolite exchange
Eg pyruvate, ADP and Pi.
208
Rotation of ____ causes rotation in _____ which causes ATP synthesis in _____ in ATP synthase.
C , gamma , beta.
209
What is transduction?
The conversion of a signal/ information from one form to another.
210
Between what steps in the signalling pathway does amplification take place?
Reception and transduction.
211
What do good signals need to be?
Made and turned over quickly.
212
Auxins and adrenaline are examples of what type of signal?
Modified amino acids.
213
Steroid hormones are an example of what type of signal?
Lipid.
214
Glycogen is an example of what type of signal?
Peptide.
215
Are ligands metabolised when they act as first messengers?
No.
216
What does ligand binding lead to?
Conformational change.
217
Is endocrine signalling long or short distant?
Long.
218
Is paracrine signalling long or short distance?
Short.
219
Are hormones used more in endocrine or paracrine signalling?
Endocrine. They act on long distances and have a different effect on different cells. An example is insulin.
220
Are growth factors used in paracrine or endocrine signalling?
Paracrine as they tend to act on neighbouring cells.
221
What is the target of NO ?
Blood vessel lining. It is a paracrine signal.
222
What is the target of histamine?
Mast cells. It is a paracrine signal.
223
What is an example of specialised paracrine signalling?
Neuronal signalling.
224
What targets does acetylcholine act on?
Skeletal muscle where it causes contraction.
Heart muscle where it reduces contraction.
Salivary glands where it causes the release of saliva.
225
Where do contact dependant signals stay?
The membrane of the signalling cell. Often used in early development.
226
What cells produce the delta signal?
All cells.
227
Delta signal is produced in prospective neurones. What are the receptors called that this cell binds to to prevent other cells from producing delta signals?
Notch.
228
What type of receptor does NO bind to?
Intracelluar.
229
What type of molecules do surface receptors bind?
Bigger signals such as peptide signals and hydrophilic signals.
230
What three things can NO do to the body?
1. Relax smooth muscle.
2. Cause blood vessels to expand.
3. Increase blood flow.
231
What is cyclic GMP an example of?
A second messenger.
232
Cyclic GMP relaxes smooth muscle and is normal degraded after being used as a signal. What drug blocks this degradation?
Viagra.
233
What can intracellular receptors regulate?
Gene transcription.
234
Steroid hormones are carried in the blood and can diffuse into the membrane where they activate a receptor. Where does this complex then travel to and why?
The nucleus where it binds to DNA and altered gene expression.
A shape change can uncover the nucleus and localise the signal.
235
When acetylcholine binds to a receptor on the neuromuscular boundary what happens?
The transmembrane helix rotates 15 degrees to open the gate and allow sodium into the cell.
236
What makes up a single pass?
A extracelluar ligand binding domain, one transmembrane helix and a cytoplasmic domain.
237
Which domain in the single pass has enzymatic activity?
The cytoplasmic domain.
238
When the ligand binds what happens to the receptors?
They dimerise.
239
What enzymes reverses the activity of the kinases?
Phosphatates.
240
How are receptor kinases activated?
Dimerisation and transphosphorylation.
241
Seven pass receptors are found in which type of receptors?
G protein receptors.
242
What produces second messenger cAMP?
Adenylate cyclase.
243
What activates PLC enzyme?
Adenylate cyclase.
244
When a G protein is bound to GTP it will dissociate from the receptor and bind other proteins/ enzymes for example _______.
Adrenaline.
245
What two types of receptors can ligand bind too?
G protein coupled receptor
| Enzymes.
246
What type if messenger is calcium ion release?
Second messenger.
247
What three changes can be brought about through signalling?
Enzyme activity, cytoskeleton and gene expression.
248
What follows transphosphorylation?
The receptor phosphates themselves.
249
During transphosphorylation/ phosphorylation what can the phosphate group then act as?
Docking sites.
250
What can docking sites have specificity to?
Phosphotryosine.
251
Receptor kinase activity activates which two processes?
Kinase cascades and calcium release.
252
When the RAS switch is bound to GDP is it on or off?
Off.
253
How does the RAS switch turn itself off?
It's own GTPase activity.
254
How does the RAS switch get turned on?
Activated receptor kinase.
255
If RAS mutates and can not be switched off what happens?
Downstream pathways involved in cell signalling are permanently on.
256
Kinases are often found in groups of what?
Threes.
257
Longer pathways allow more specificity, complicated signals and amplification. True or false?
True.
258
Is calcium releases dependant or independent of RAS?
Independent.
259
What does phospholipase C do and how is it activated?
It cleaves phospholipids and is activated by G protein receptors or kinases.
260
When a membrane phospholipid is cleaved by phospholipase C what is produced?
DAG and inositol trisphosphate (IP3)
261
What does IP3 allow?
Calcium to enter the cytoplasm from the ER. This can increase the activity of calcium activated proteins and activate other proteins such as kinases.
262
What is calmodulin?
A calcium activated protein.
263
What cell also carries phospholipase C?
A sperm cell.
264
What catalyses the production of IP3?
PLC.
265
In the activation of cAMP in a response to adrenaline do you need ATP?
Yes.
266
Adneylate produces cAMP. What does cAMP mainly do?
Activates cAMP dependant protein kinases.
267
If a unimolecular reaction once the reaction has happened there is a high chance it will undo itself. True or false?
False. There is almost a 0 chance.
268
If a molecular can only be in an open or closed form, with an abrupt transition what type of reaction is it?
Unimolecular.
269
If the ends of a protein have come together and they haven't bounded yet what state is it in?
Translation state.
270
What can the activation energy measure in terms of transition state?
Measures how unlikely a molecule is to be in a transition state. It combines the potential energy and entropy.
271
What is the rate of change of a molecule changing from a and b?
-kNa.
272
If the rate of change of a to b is -kNa what is the rate of change of b to a?
+kNa
Expressed in terms of concentration and not moles.
273
For a system of a fixed volume the concentration is in molar style units. What is this proportional too?
Number of molecules.
274
What are rate equations written in terms of?
Concentrations.
275
What does K show the ratio off?
A:B
276
If the activation energy of A-B is less than B-A which rate constant is greater?
A-B.
277
K shows the ratio of A:B. What do you actually want to know?
The actual amount in each state.
278
What is K equal to in terms of k?
k1/k-1.
279
When you know concentrations but not a K value what would K be equal to in terms of proteins being unfolded and folded at equilibrium?
[U]eq/[F]eq.
This will tell us the concentration ratios but you will more often want to know the proportion as a percentage.
280
How would you work out the fraction of proton folded in a mixture of folded and unfolded protein?
[F]/ Ptotal.
281
If there are K times as many molecules in B to A, what two equations could you use to work out the fractions of B and A?
Fraction of B = K/1+K
Fraction of A 1/ 1+K
282
What type of system is P+L > PL?
Second order.
283
What are the units of k?
s^-1. This is the unit on all first order reactions.
284
A+B =C
| What is the chance that B will react with A in a given time period, from A's perspective?
k[B].
285
Many biological and chemical systems involve the binding of ligands. What are 5 examples of when a ligand has to bind?
1. Metal ions binding to EDTA
2. Signalling molecules binding to receptors
3. A drug molecule binding to a target
4. Transcription factors binding to DNA
5. Substrate binding to an enzyme.
286
In terms of binding, what makes paracetamol, ibuprofen and asprin different to other drugs?
They bind to an enzyme and not a receptor.
287
If the forward reaction is a second order reaction then the reverse will be also. True or false?
False. It depends on how many products and reactants you have. For example with A + B =C the forward reaction is second order as it relies on the concentration of A and B, whereas the reverse is first order as it only relies on the concentration of C.
288
For the reaction P + L = PL what equation represents the system at equilibrium (with the forward reaction being described as 'on' and the reverse being described as 'off'.)
kon{P}{L} = koff[PL]
289
What is KD also known as?
The equilibrium dissociation constant.
290
What are the units for KD?
Concentration.
291
What equation represents KD?
koff/ kon or ([P]eq[L]eq)/[PL]eq.
292
If you want a ligand to bind better to its receptor, do you want the KD value to be smaller or larger and why?
Smaller. This is because you want the reverse reaction to be at the lowest rate as possible (koff) and the forward reaction to be at the highest rate possible (kon). This will result in a smaller fraction.
293
Ideally for tighter binding you want the KD value to be as low as possible. In theory this can be achieved by altering the rate of kon and koff. In practice you can only really change one of these values. Which one can you change?
koff. You make increase binding so PL will dissociate at a slower rate but it is difficult to make P and L react at a faster rate.
294
How much of a protein is bound when free ligand concentration is equal to KD?
1/2.
295
How would you work out the total amount of protein bound?
[PL]/Ptot.
296
If the total protein concentration is 1um and [PL] is 1um what is the system said to be?
Saturated.
297
In a simple system when A is turned into B without the catalyst there is no limit on the rate of production of B, as long as the concentration of A keeps increasing. True or false?
True. There is a directly proportional relationship in this type of system.
298
What does this following equation represent?
S+E = ES -- P + E
A system that is catalysed by an enzyme.
299
In a system catalysed by an enzyme why can you ignore the concentration of E bound to S?
As it is assumed that the concentration of enzyme is so low that the value of ES becomes insignificant.
300
What do lipases do?
Break down fatty acids into fats and glycerol.
301
Are fats or sugars more reduced?
Fats.
