Block 2 - energy and proteins Flashcards
1
Q
what is the difference between an endergonic and exergonic reaction
A
endergonic reactions require energy whereas exergonic reactions release energy
2
Q
what is the condition required for endergonic and exergonic reactions to be coupled
A
the energy released by the exergonic reaction needs to be greater than the energy required by the endergonic reaction
3
Q
define gibbs free energy
A
the amount of energy available from a particular compound
4
Q
the gibbs free energy of an endergonic reaction is negative/positive
A
positive
5
Q
the gibbs free energy of an exergonic reaction is negative/positive
A
negative
6
Q
what are the components of ATP
A
adenosine (adenine + ribose) + 3 phosphates
7
Q
describe the two methods of ATP hydrolysis
A
ATP –> ADP and an inorganic phosphate
OR
ATP –> AMP and pyrophosphate. the pyrophosphate is then split into single phosphates
8
Q
describe the energetic differences between the 2 mechanisms of ATP hydrolysis
A
the ATP –> AMP method releases more energy than the ATP –> ADP mechanism but also requires more energy to reverse
9
Q
give 3 examples of what ATP can be used for
A
chemical work, transport and movement
10
Q
why does the ATP turnover need to be so fast
A
we need much more ATP per day than what is stored in our body (100-250g stored - need 50-75kg). ATP needs to be turned over around 500 times per day to meet the daily requirement
11
Q
describe the energy sources during 100m sprinting, where ATP turnover is not enough to sustain the body
A
stored ATP - 1 sec
creatine phosphate - 4 sec
fermentation of glucose - rest of race
12
Q
which product of anaerobic metabolism can be very painful
A
lactic acid
13
Q
high/low [ATP] inhibits catabolic reactions and stimulates anabolic reactions
A
high
14
Q
why is it sterically difficult to attach a phosphate to ADP
A
we need to overcome the repulsive negative charges of the other phosphates
because of this a lot of energy is released when a P is released
15
Q
give examples of reactions that require phosphate from ATP
A
FA –> phospholipid
synthesis of RNA/DNA - nucleoside monophosphate activation
protein synthesis - amino acid activation
post translational activation/deactivation by phosphorylation
16
Q
what doe kinases do
A
they phosphorylate
17
Q
what do phosphatases do
A
they dephosphorylate
18
Q
describe the nitrogen sensor in plants
A
NRTI.I nitrate sensor/transporter in plants - P site in thr 101nprovides a switch between high and low affinity nitrogen uptake
19
Q
describe calcium active transport
A
Ca pumps maintain low cytoplasmic concentration to allow fast transient signals (requires ATP)
20
Q
what is the first internal messenger in guard cells and what does it do
A
intracellular calcium - it opens channels so that ca can be released very quickly
21
Q
describe the myosin and actin motion in muscle and the involvement of ATP
A
myosin movement relies on reversibly binding to the actin filament and the unbinding requires ATP
22
Q
what are the 2 ways that ATP can be synthesised
A
substrate level (P group transfer) or oxidative phosphorylation (H gradient, ATP synthase)
23
Q
to make ATP the substrate needs to have more or less energy than ATP
A
more
24
Q
why do p groups have high energy
A
because they are attached in different types of bondages which are energy rich
25
give an overview of the ETC
NADPH brings energy rich e- that have been harvested through metabolism and they go down the chain towards the final electron acceptor (O2). the energy released is harvested by a proton gradient (matrix --> intermembrane space). H flow down their concentration gradient through ATP synthase, making ATP
26
describe mitochondria
numerous in ATP consuming tissues and closely associated with ATP consuming organelles
contains membrane protein complexes that are important in respiration
27
describe the structure and function
- rotor - spins clockwise when H flows past
- stator - holds rotor and knob in position
- rod - turns with rotor and causes a conformation change that activates the knob
- knob - catalytic sites join Pi + ADP making ATP
ATP synthase is made by separate proteins encoded by different genes
28
how does cryo EM work and why is it useful for visualising ATP
solubilized protein spotted on gold coated grid and freezing - then normal EM
it can be used to look at ATP in different dynamic structures
29
describe ATP synthase F1 structures
different Beta subunit forms have different affinities for ATP and ADP
alpha subunit rotation changes beta subunit conformation
the alpha subunit depends on shaft position for conformation - one conformation binds ATP, one makes it and one releases it
ATP drive the pump counter clockwise
30
describe the reversibility of ATP synthase
in low [ATP] ADP + Pi --> ATP
| in high [ATP] ATP --> ADP + Pi
31
what issue could the reversible nature of ATP synthase pose if it is not controlled properly
we need to avoid the ATP being generated being removed again due to the reversible nature. to avoid this ATP is quickly removed after being generated
32
what does the ADP-ATP exchanger do
it keeps [ATP] low in the mitochondrial matrix by removing ATP and adding ADP
33
what does the Pi/H cotransporter do
uses energy of the H gradient to import Pi
34
what is the overall reaction in glycolysis
glucose --> 2x pyruvate
35
what is pyruvate transformed into which is then used in the citric acid cycle
acetyl coA
36
when in respiration does oxidative phosphorylation occur
in the ETC and chemiosmosis
37
in respiration how many ATP are produced and by what means
2ATP by substrate level phosphorylation
| 32/34ATP by oxidative phosphorylation using ATP synthase and the proton gradient
38
what do NAD FAD and NADH all have in common
they can all reversibly uptake electrons
they can be oxidised - no electrons
they can be reduced - with electrons
39
how does NAD+ change to form NADH
double bonds are altered to accommodate the electrons (2e- + H+)
40
write the equation for a basic redox reaction
Xe- + Y --> X +Ye-
41
what is the redox potential
relative affinities of atoms to their outer shell e-
| the differences in the redox potential provide a source of energy
42
describe reducing sugars
those that want to get rid of electrons - we harvest the potential energy being released by allowing e- to move from the sugars to O2 ultimately
43
molecules that have very -ve redox potential have a lot/little free energy
lots
44
why are the mitochondrial membrane protein complexes important
they enable e- transfer and harvest energy to pump protons from the matrix into the intermembrane space which is used to drive chemiosmosis driven
45
describe the transfer of energy in 3 steps in respiration
redox energy --> electrochemical energy --> ATP
46
describe the electron transfer from NADH to O2
NADH e --> NADH reductase (first electron carrier protein complex) --> ubiquinone (Q) (first electron acceptor which now becomes reduced) --> cytochrome C (electron acceptor) (catalysed by the second protein complex - cytochrome reductase) --> O2 (catalysed by cytochrome oxidase)
energy released throughout the process is used to pump protons
47
what is the dual action of the protein pumps in the respiration ETC
they are redox enzymes and proton pumps
48
what are the 3 protein complexes in the respiration ETC
NADH reductase
cytochrome reductase
cytochrome oxidase
49
how do we measure redox potential
measured as voltage using voltmeter
50
what are all the redox reactions in the respiration ETC
```
NADH NAD+ + H+ +2e-
reduced Q oxidised Q + 2H+ + 2e-
reduced cyt c oxidised cyt c + e-
H2O 1/2O2 + 2H+ 2e-
this process is energetically downhill and there is progressive increase in redox potential and decrease in free energy
```
51
what is the energetic difference approximately between NADH and oxygen in respiration
over 1 V
52
what is the equation used to work out free energy using the redox potentially measured experimentally
deltaGo = - n(0.023)deltaEo(mv)
where n is the number of electrons involved
and Eo is the redox potential
53
how is FADH2 involved in transferring electrons to the ETC in respiration
it passes electrons to succinate Q reductase which then passes electrons to ubiquinone (Q)
54
is succinate Q reductase a proton pump
no
55
what are the prosthetic groups of the 3 protein proton pump complexes and succinate Q reductase of the ETC in the order in which they are involved in the pathway
NADH reductase - FMN, FeS
succinate Q reductase - FAD, FeS
cytochrome reductase - Heme (b,c), FeS
cytochrome oxidase - Heme (a), Cu
56
why do we get less energy from FAD than NAD
because succinate Q reductase is not a proton pump
57
describe the common redox groups
flavins e.g. FMN, FAD - ring structures with double bonds
quinone e.g. ubiquinone
heme group e.g. cyt c - ring structure with central Fe (5 different heme groups in the ETC
FeS clusters - either 2Fe-2S or 4Fe-4S, both have only 1e- (7 different FeS clusters in the ETC)
58
why is it useful that the redox groups are coloured
they can be monitored easily by looking at the colour change upon oxidising or reducing
59
what happens to complexes when ETC blockers are applied
they are usually in a mixed state but will become fully oxidised or reduced depending on their position relative to where the blocker acts
if they act before the blocker they will become fully reduced due to electron build up and if they act after they will become fully oxidised because electrons have been blocked from flowing to them
60
what happens to protein complexes in the ETC when oxygen is removed and why can removing O2 then adding it back be useful
they all become fully reduced
when O2 is added back the protein complex closest to O2 will change colour and oxidise firs because it loses its electrons
61
describe NADH reductase
- a large portion of it is in the membrane
- the alpha helices are in the membrane
- soluble blob has FeS prosthetic groups
- Q binds at the interface of the blob and the intermembrane part
- NADH brings electrons to the top of the enzyme
- it has some flavin groups
62
describe cytochrome reductase
- dimer
- intermembrane part and blob
- heme groups
- Q delivers 2e- but complex can only carry 1 (problem - alone they are radicals - can damage other molecules by stealing e-) radicals are held deep in the core to safeguard the environment
63
describe cytochrome oxidase
- 1 e- delivered from cyt c but 4 needed for O2. e- are stored until there are 4
- conserved structure
64
describe the Q cycle
- Q gives one e- to cyt c and the other is buried in cyt c reductase by another Q molecule. the second e- pair comes along from another Q and one binds to the radical, the other electron goes to cyt c. reduced Q is released
other explanation
- e- transfer from Q (2e-) to cyt c (1e-). it requires a repetitive cycle in which radical intermediate is held inside the enzyme in a Q molecule buried in the structure. the next Q goes into the chain and transfers one e- to be buried and the other pairs with the previous radical.
65
where did photosynthesis originate and what did it result in
it originated in cyanobacteria and this lead to atmospheric oxygenation
66
in a basic explanation how did chloroplasts come about
early photosynthetic bacteria were engulfed by eukaryotic cells and transformed into chloroplasts
67
name 2 photosynthetic organisms only found in the top layer of the ocean
phytoplankton and seaweed
68
why is wild vegetation better at capturing carbon than agricultural vegetation
we don't grow crops throughout the year in agriculture and we don't exploit the whole 3D space
69
there is a loss/gain of carbon stock upon land conversion from wild to agricultural
loss
70
to sustain the growing population we need to intensify ……..., not expand land
fixation
71
describe chloroplasts
made from membranous structures that carry photosystems
2 membranes - outer belongs to the plant, inner is of bacterial origin
thylakoids - stacks of membranes called grana. inner membrane invaginations were cut off to become thylakoids
interior - stroma
move towards light and communicate with each other
72
highlight some differences between mitochondria and chloroplasts
- chloroplasts are larger
- different sub compartmental structures
- chloroplasts capture light to make ATP whereas mitochondria use NADH to make ATP
73
highlight some similarities between mitochondria and chloroplasts
- inner membranes carry redox enzymes
- both have ATP synthase - in the mitochondria the knob sits in the matrix and the protons accumulate in the intermembrane space. in chloroplasts the knob sits in the stroma and the protons accumulate in the thylakoids
- they both have their own DNA but are no longer self sufficient
74
what is the overall role of photosynthesis
to use light to fix CO2 into organic molecules
75
what do photosynthesis and respiration have in common
- they both have an ETC, redox reactions and H pumps
76
what are the two main steps of photosynthesis
1. energy capture (ATP, NADPH production) - the photosystems in the thylakoids use sunlight to extract an e- from water
2. build up of organic carbon molecules from CO2 (ATP, NADPH consumption)
77
the calvin cycle can only operate in the dark true or false
false
the calvin cycle can occur in the light or the dark it just so happens that it is referred to as the dark cycle because light is not a requirement
78
describe the electron flow in photosynthesis
- plastoquinone --> plastocyanin (energetically downhill, energy harvested in pH gradient)
- PS2 - light energy --> photoexcited e- --> plastoquinone (electron void in PS2 allows it to pull an electron from water)
- PS1 - receives e- and promotes them to a higher energy state using light, e- shuttled to ferrodoxin then NADP
79
electron void in PS2 allows it to pull an electron from water. what is the opposite of the this step
it is the opposite to the final step of respiration
80
in respiration electrons lose free energy going uphill/downhill to oxygen
downhill
81
describe the z scheme
this is the energy scheme seen in photosynthesis
it is composed by and uphill movement followed by a downhill movement followed by another uphill movement
there is an overall increase in energy
82
describe chlorophyll
- sit in the centre of PS
- ring structure, double bonds, Mn4 allows reversible e- uptake
- absorbs blue/red light
- hydrophobic tails plant it in the membrane
- there are different forms with different absorption spectra
83
what is a PS made up of
antenna complex - protein and chlorophyll array
| reaction centre - contains special pair of chlorophyll molecules
84
what is the role of the antenna complex
collects and funnels energy to the reaction centre
| it expands the light capture range
85
what is the role of the reaction centre
produces high energy electrons and passes them to quinone
86
what is decay by resonance transfer
it is what chlorophyll molecules do in the antenna complex
| they pass on the excitement only
87
what is decay by successive electron transfer
it is what electrons do in the reaction centre - they pass e- to e- acceptor
88
what are the 3 types of photosystem
P900 - bacteria
P680 - PS2
P700 - PS1
89
how do the different types of PS differ from each other
the size of the antenna complex and the initial e- acceptor differ as well as the maximal absorbance
90
describe the electron flow in the purple bacteria reaction centre
special chlorophyll --> chlorophyll --> pheophytin --> tightly bound quinone --> free quinone (leaves PS so e- can't drop back down (speed also prevents this))
91
describe the electron flow in the reaction centre of plants
light energy to P680 Mn4 --> special chlorophyll --> chlorophyll --> pheophytin (first e- acceptor) --> plastoquinone --> exchangeable plastoquinone --> (PSII-->PSI) --> plastocyanin --> chlorophyll (first e- acceptor) --> quinone --> FeS complex --> ferrodoxin
see 1st year notes for full process
92
how can the ATP : e- be changed in photosynthesis
by changing from the z scheme to cyclic phosphorylation to make more ATP (electrons are passed back to quinone)
93
what are the functional protein classes (7)
```
structural
scaffold
enzymes
membrane transport
motor
regulatory
molecular machines
```
94
give an examples of a protein that belongs to several functional classes
insulin receptor - membrane transport, regulatory, enzyme
95
describe structural proteins
they determine the cell shape and contribute to the extracellular environment
96
give an example of structural proteins and their role in the cell
actin and tubulin - movement and shape
97
what are microfilaments made of
actin monomers
98
what are intermediate filaments made from
rope like assemblies of fibrous protein e.g. keratin
99
what are microtubules made of
cylinders made tubulin dimers of alpha/beta tubulin
100
describe scaffold proteins
they bring proteins into ordered complexes e.g. bring kinases together, formation of enzymes, molecular machines. they are often bound to adaptors to direct them to a specific point
101
describe membrane transport proteins
they are embedded in the membrane and recognise specific classes of molecules
102
give an example of structural proteins and their role in the cell
actin and tubulin - movement and shape
103
what are microfilaments made of
actin monomers
104
what are intermediate filaments made from
rope like assemblies of fibrous protein e.g. keratin
105
what are microtubules made of
cylinders made tubulin dimers of alpha/beta tubulin
106
describe scaffold proteins
they bring proteins into ordered complexes e.g. bring kinases together, formation of enzymes, molecular machines. they are often bound to adaptors to direct them to a specific point
107
describe membrane transport proteins
they are embedded in the membrane and recognise specific classes of molecules
108
describe regulatory proteins and give examples
they alter functions of other proteins e.g. receptors and signalling proteins
109
describe motor proteins and give examples
they move proteins, cells, organelles and organisms e.g. actin, myosin, kinesin ( head walks along microtubules, moving transport vesicles anchored to the tail - ATP dependent)
110
increased concentration increases/decreases collision frequency
increases
111
most collisions and successful/unsuccessful and why
unsuccessful - non covalent interactions are weak and transient
112
describe the 2 different types of dimerization
same protein dimerises
| protein-ligand dimerization
113
list non covalent interactions in order of decreasing strength
ionic bonds
H bonds
hydrophobic interactions
van der waals
114
what is the approximate strength of a covalent bond
~200kJ/mol
115
more non covalent bonds --> more tightly bound --> higher/lower affinity
higher
116
why does the actin and myosin interaction need to be carefully balanced
it needs to be tight to withstand forces but loose enough to be reversed
117
higher affinity interactions require more/less energy to break
more
118
describe the 2 different types of dimerization
same protein dimerises
| protein-ligand dimerization
119
what is a dialysis chamber and how is it used to study the R2C2 complex
it is a chamber with sides separated by a semi permeable membrane
- radioactive cAMP (can pass) is put in one side and R2C2 in the other (cant pass). we then measure the [cAMP], the lower the concentration at equilibrium the higher the affinity (keep R2C2 concentration constant.
120
what is induced fit
enzymes permit small latitude in structure of substrate leading to induced fit where the protein changes conformation when the ligand binds
121
describe the structure and mechanism if the cAMP dependent protein kinase
- it has 2 regulatory and 2 catalytic subunits. the regulatory subunits have the cAMP binding sites and the catalytic sites have the kinase activity
- the subunits form the R2C2 complex held together by non covalent interactions
- R masks the kinase active site
- when [cAMP] rises it is bound by the R subunits which leads to a conformation change (allosteric regulation) weakening the R2-C2 interaction. the C subunits dissociates and catalytic activity resumes
- the system is dependent on binding and is reversible if cAMP is removed
122
what is Kd
the binding dissociation complex
[P][L]/[PL]
Koff/Kon
123
how do we measure Kd
we either measure the equilibrium concentrations and calculate or we measure the kinetics of dissociation/association and calculate
124
what is the relationship between Kd and affinity
lower Kd = higher affinity, lower [L] needed to bind 1/2 P
125
what is a dialysis chamber and how is it used to study the R2C2 complex
it is a chamber with sides separated by a semi permeable membrane
126
what information is important to understand binding
structural information
127
what is the primary structure of a protein
sequence of amino acids connected by peptide bonds in a polypeptide chain
128
what is the secondary structure of a proteins
alpha helices, beta sheets and beta turns formation mediated by H bonding in the backbone
129
what is the tertiary structure of proteins
folding into the 3D shape by interactions between R groups
130
what is the quaternary structure of a protein
multiple polypeptide chains coming together
131
how can the peptide bond be best described
- as resonance structures - there are 2 resonance structures
- polar
- electrons are delocalised
- rotation around the C-N bond is restricted
132
describe the alpha helix
- common structural motif mediated by H bonding
- H bonding between the N-H and the C=O of a residue 4 residues away
- there are 3.6 residues per turn
- always right handed
- R groups point outwards
- proline residues are helix breakers (disrupts helical structure
133
describe beta sheets
- formed by H bonds between protein strands rather than within strands
- R groups alternate above and below the plane of the sheet
- amino acids are more extended than in the alpha helix
- sheets can be parallel or anti parallel
134
most common chains can form ……. ……… and …….. ………..
alpha helices and beta sheets
135
describe the beta turn
- they allow polypeptide chains to turn and go in the opposite direction
- they allow proteins to attain a compact (globular) shape
- proline glycine are commonly found in the structures
136
why are proline and glycine commonly found in the beta turn structures
proline because it is cyclic - 5N ring - connects to backbone twice which facilitates turns/kinks
glycine because of its small side chain - can fit wherever it is required
137
list some tertiary structure R group interactions
```
H bonding
ionic bonding
van der waals
hydrophobic interactions
disulphide bonds
```
138
describe tertiary protein structure hydrophobic interactions
hydrophobic R groups cluster in the inside of the protein leaving hydrophilic amino acids on the outside
139
describe the tertiary structure disulphide bonds
covalent linkages between S containing side chains of cysteine residues
these are stronger than the other types of tertiary bonds and they bring the peptide round to fold
140
which level of protein structure contains all the folding information
primary structure
141
proteins fold to the lowest/highest free energy conformation
lowest
142
what happens to free energy and entropy as proteins folding proceeds
they both decrease to a minimum
143
why do linear amino acid chains have high entropy
because they have multiple possible conformations
144
most proteins begin to fold in ………….
translation
145
what is the molten globule
a partially folded state which conserves native-like secondary structure content without the tightly packed protein interior
it has intermediate energy and entropy
146
describe the change between native, molten globule and denatured proteins
native protein (slow) molten globule (fast) denatured
147
which protein state has the lowest free energy and entropy
the native state - fully folded
148
how are van der waals useful in proteins
they help atoms in a protein pack together
149
why are alpha helices and beta sheets highly conserved
natural selection favours protein sequences with a single conformation which forms easily and seldom makes mistakes
150
describe the hydrophobic effect
it is the tendency of non polar molecules to aggregate in water
- water has flickering cluster structure, it H bonds with 7 or 8 other water molecules. the hydrophobic effect is an indirect effect resulting form water H bond exchange rate being 1011s-1
- non polar molecules result in less H bond opportunities for water and longer H bond lifetime (ice structure) --> decreased entropy
- at the interface water is rotationally and translationally constrained
- to minimise the effect of water on entropy, molecules that are hydrophobic cluster in the interior to minimise entropy loss
151
give 2 examples of diseases that are caused by aberrant protein folding
mad cow disease and Alzheimer's
152
describe how aberrant protein folding leads to Alzheimer's
molten globule --> self association of globules --> amyloid fibril core structure --> protofilament of partially folded amyloid proteins
153
what is a domain
it is a conserved part of the protein structure that can evolve, function and exist independently
they are the building blocks of proteins
many proteins consist of different domains linked together
154
why is the fact that domains fold independently key
it means that they can be easily moved between proteins by evolution or by genetic engineering
155
what is the chicken sarcoma
it is caused by the rous sarcoma virus which contains the src viral oncogene (tyrosine kinase) which has 3 domains: SH3, SH2, and kinase
156
what do SH3 domains bind to
polyproline motifs
157
what do SH2 domains bind to
p-tyr residues
158
describe the SH2 domain
structurally conserved and autonomously fold - they all exhibit the same arrangement of alpha helices and beta sheets and also have conserved regions of primary structure
they are important in signal transduction
159
what is a bromodomain
- a domain that binds acetylated lysine residues
- key residues have been identified in addition to the acetylated lysine
- they all bind slightly different acetylated lysines
- different bromodomains control different bromodomains control different aspects o histone reading activity. although they have similar folding and homologous structures they are sufficiently different to be targeted by different inhibitors
160
how is a motif different from a domain
it doesn't depict a functional role although it can sometimes indicate towards function
it isn't independently stable
domains tend to relate more to structural units
161
what is a motif
it can often define functional characteristics and are usually predictive of belonging to particular groups
they can be used to predict families e.g. kinase motifs
162
what is the walker motif
ATP binding site
163
exon ……….. in evolution contributed to shaping of eukaryotic proteomes
shuffling
164
what is the difference between the folding of big and small proteins
small proteins fold on their own but big proteins have domains which fold when synthesised and are independently stable while the rest of the protein is still being synthesised
165
what do the linker regions between domains do
they are often unstructured and act like a flexible hinge
166
why are active sites structurally difficult too determine
because the residues may be spread out in the primary sequence which may be close together in the folded protein
167
what are in silico approaches
computerised approaches
168
how can we use genome sequencing to predict protein structure
we can infer the sequence of amino acids and form this the structure
169
what is a blast search
basic local alignment search tool
| algorithm for comparison of sequence data
170
what is an MSA
multiple sequence alignment
sequence alignment of 3 or more sequences
used to assess conservation of protein domains, secondary and tertiary and secondary structures and even individual amino acids
171
……………………... analysis can assess the shared evolutionary origins
phylogenetic
172
what are atypical protein kinase Cs
they are a subfamily of kinases composed of two members with 72% identity
173
what does the structure of a protein provide that gives an insight into function
it allows an understanding of 3D arrangement and an insight into mechanism
174
describe X ray crystallography
a form of microscopy for the visualisation of protein structure at atomic level
the visual detail is limited by the electromagnetic wavelength
electron density is used to determine the atomic conditions
175
what are the steps in X ray crystallography
the protein first needs to be purified and crystallised then X rays are fired through the sample, producing a diffraction pattern which is interpreted by a computer and a crystallographer
176
what is the problem with X ray crystallography
many proteins only crystallise at non-physiological pH or [salt] hence can be difficult to crystallise
177
apart from S ray crystallography what are other methods used to determine protein structure
NMR and EM
178
what information does NMR provide
provides structural information under more physiological conditions (in aqueous buffer)
179
what information does EM provide
it provides the overall molecular shape but gives less of a sense of the individual atoms
180
we can use ………… information in designing inhibitors/activators/targeted drugs
structural
181
what are ACE inhibitors
- angiotensin converting enzyme inhibitors
- angiotensin usually converts angiotensin I to angiotensin II but the ACE inhibitors prevent angiotensin II production acting to lower bp
182
what is meant by design of "better" drugs
less side effects
increased efficacy
less need for combination therapy
183
what are the different methods of drug discovery
- go through a chemical library and see what will act as a ligand, docking to the protein
OR
- reverse docking - take already existing drug and add proteins from target database. for proteins that bind it may be an effective drug for them.
184
what is homology modelling
it is based on the observation that 2 proteins belonging to the same family with similar protein structures will have similar 3D structures. this is used frequently in the pharma industry
185
the degree of 3D structure conservation in a family is much less/greater then sequence conservation
greater
186
why do proteins in the lab need to be kept on ice and with protease inhibitors
proteins are susceptible to protease degradation and are also affected by other environmental conditions
187
when cells are broken open what environmental factors need to be controlled for to maintain confirmation
[salt] and pH
188
what is size exclusion chromatography
- protein solution run in column of gel beads (small proteins move into channels and pores getting stuck and larger proteins will elute first)
- it works best on water soluble proteins
- it is easy and cheap and begins to fractionate the mixture
189
why can we separate proteins based on charge
at the isoelectric point a protein has not net charge. at a pH above the pI a protein has a negative charge and below a positive charge
we can make the desired protein have a particular charge so it can be isolated, or at least purified more
190
describe anion exchange chromatography
we have a positively charged resin or beads that binds negatively charged proteins
191
describe cation exchange chromatography
we have a negatively charged resin or beads that binds positively charged proteins
192
describe affinity chromatography
a protein mix is added to a column containing polymer bound ligand specific for the protein of interest. unwanted proteins wash through. to elute the protein of interest that has bound we need to wash the column with the ligand. this is a more specific method but we need to know the ligand
193
what is isoelectric focusing gel
it is based on SDS page. proteins have first been separated on an ion exchange strip which separates proteins based on pI and pH gradient. each spot represents and individual protein
194
what is proteomics
large scale analysis of proteins, in particular complex mixtures e.g. cells, organelles, viruses.
195
what advances have lead to proteomics becoming a large area of study
it is enabled by the accumulation of DNA and protein databases, improvement of computer algorithms and mass spec
196
list the transcriptome, proteome and genome in increasing order of complexity
genome --> transcriptome --> proteome
197
what is mass spec
It involves measuring the mass : charge ratio of each amino acid.
small vaporised peptides are passed through magnets which causes bending. the bend extent depends on the mass : charge. the detector measures ionic collisions and readouts give the peptide sequence
198
enzymes work by decreasing/increasing activation energy
decreasing
199
do enzymes change the equilibrium of a reaction
no
200
enzymes are usually highly specific for particular substrates true or false
true
201
give examples of enzyme uses in industry
- biological washing powder contain lipases and proteases to remove protein and FA stains respectively
- many drinks and prepared food have high fructose corn syrup (starch is broken down by amylases and glucose --> fructose by xylose isomerase)
202
what did frances Arnold do
she induced mutations through error prone PCR and selected enzymes with better properties
203
what is the rate equation
rate = k[A][B] where k = the rate constant
204
the half life of an enzyme is long/short if it is stable
long
205
progress curves allow measurement of ………. ………..
initial rate
206
what is a progress curve
it shows the disappearance of reactant or the appearance of product over the time course of the reaction
207
how can we infer the initial rate from the progress curve
the initial rate is the slope of the initial line. formation of product is initially linear with time.
208
initial rate is directly proportional to ………… ……………..
enzyme concentration
209
reactions proceed via the ……….. …………...
transition state
210
what is the transition state
an intermediate state where the nucleophile and the leaving group are bound
211
what are the 2 requirements for a collision to be successful
the reactants need to have correct orientation and thermal energy
212
…….…… stabilise the transition state
enzymes - they lower Ea
213
what is a Boltzmann distribution curve
it shows the kinetic energy on the x axis and on the y axis the number of molecules with each kinetic energy
214
what happens to the Boltzmann distribution curve when temperature of a reaction is increased
it shift lower and to the right
215
what is the Arrhenius equation
k = Aexp(-Ea/RT)
r is the gas constant
k is the rate constant
T is the temperature in K
216
in an lnk vs. 1/T plot what is the slope representative of
-Ea/R
217
enzymes are usually more/less stable in the cold. with increasing temperature they usually ……………..
more
| denature
218
initial rate increases roughly ……………. for every 10 C increase in temperature
double
219
why is optimal temperature a meaningless concept
because rate can go up but the enzyme might denature
220
why do pepsin and trypsin have different optimal pHs
because they function in different places. pepsin (pH 1.5) functions in the stomach so needs to tolerate very acidic conditions but trypsin functions in the intestine which is a more neutral environment so its optimal pH is around 7
221
what groups does the active site contain
groups that bind to the substrate in a defined orientation and groups that help catalyse the reaction
222
the ………. ………… stabilises the transition state
active site
223
enzymes are larger/smaller than their substrate
much larger
224
…….……. ………….. can lead to different enzymes with similar mechanisms
convergent evolution
225
give an example where convergent evolution has occurred in enzymes
chymotrypsin is a mammalian serine protease and subtilisin is a bacterial serine protease. they have very different structures but similar mechanisms
226
how is enzyme activity calculated
see summary notes for calculation example
227
what is enzyme kinetics
the study of how fast an enzyme catalyses its reaction and what factors affect this - it can provide information on mechanism and function
228
what is the linweaver burk plot
1/V vs 1/[S]
| - it can be used to measure Vmax and Km
229
what is turnover number
kcat or k2
it is how fast an enzyme can work
the number of molecules of S-->P by one enzyme active site at substrate saturation per unit time
230
the initial rate of an enzyme catalysed reaction increases with …….. …………...
substrate concentration - the curve get closer and closer to Vmax
231
in an uncatalyzed reaction rate increases …………. with [S}
linearly
232
what is the michaelis menten equation
V = (Vmax[S])/(Km +[S])
| where E + S (K1 forward, K-1 back) ES --> (K2) E +P
233
what is Vmax
the reaction rate when the enzyme is fully loaded with substrate
234
Vmax is directly proportional to the ………… …………..
enzyme concentration
235
what is Km
the substrate concentration required to give Vmax/2
236
Km is dependent/independent of [E]
independent
237
what is the michaelis menten reciprocal
1/v = 1/Vmax + Km/Vmax x 1/[S]
| 1/Vmax is where the line crosses the Y axis
238
what is the equation for Kd
Kd = koff/kon
239
what is the equation for Km
Km = (k-1 +k2)/k1
240
when would Km = Kd
when the catalysis is very slow relative to the binding and dissociation
241
explain how Km values are relevant to function
control of glycolysis in the liver and muscle cells are different
the liver is freely permeable to glucose so cytosolic [glucose] varies around 5mM according to fed/fasted states. Glucokinase Km ~ 10mM
muscle is not freely permeable to glucose soo cytosolic [glucose] is low. hexokinase Km ~0.1mM
242
…….….. …………….. can bind activators or inhibitors. these enzymes often show ……..... kinetics, not hyperbolic kinetics
allosteric sites
| sigmoid kinetics
243
phosphofructokinase is allosterically activated by …………. and ………… and inhibited by ……….... and ……………….
F 2,6 BP and AMP
| ATP and citrate
244
in the liver F 2,6 BP is made when blood glucose is high/low which controls glycolysis
high
245
at saturation what does Vmax equal
Vmax = Kcat[Etotal]
246
how is turnover number calculates
see notes for example calculation
247
what is Kcat/Km
the specificity constant - how efficiently does an enzyme convert its substrate to product
248
lactate dehydrogenase has very high/low malate dehydrogenase activity. why is this and how can we change it
low
malate has one more Ch2 group and one more -ve charge than lactate
there are 3 mutations (single amino acid changes that increase active site volume, remove a -ve charge and add a +ve charge) which together convert lactate dehydrogenase to malate dehydrogenase by redesigning the enzyme specificity
249
lower Km = higher/lower affinity
higher
250
higher Kcat = better/worse catalysis
better
251
what happens when NAD binds to lactose dehydrogenase
it involves many interactions i.e. ionic interactions, H bonds, hydrophobic interactions
252
why is NADP+ not a substrate of lactose dehydrogenase
interaction of 2'-OH explains why NADP+ isn't a substrate. NAD enzymes cant use NADPH and vice versa
253
describe competitive inhibitors
- they resemble the substrate and bind reversibly (weakly/non-covalently) to the active site
- increase Km by a factor of 1 + [I]/Ki
- there is no change in Vmax
- with inhibition 1/V is higher so rate is lower
254
describe irreversible inhibition and give an example
- inhibitors react covalently with active site group essential for catalysis
- chymotrypsin is irreversibly inactivated by reaction with DIPF which reacts with ser195. the OH of serine reacts with DIPF causing fluoride displacement and covalent bond formation between DIPF and ser195
255
why do we know that the enzyme stabilises the transition state
it binds to it better than the substrate or product
it lowers the transition state energy level
this is how Ea is reduced
256
name 5 other ways in which a chemical reaction can be accelerated other than stabilising the transition state by reducing Ea
- acid-base catalysis
- acid catalysis
- base catalysis
- covalent catalysis
- metal ion catalysis
257
what is acid-base catalysis
speeding up the reaction by residues with charged side chains (also N/C terminal)
the acid or base is not itself consumed in the chemical reaction
258
what is acid catalysis
donation of a proton
259
what is base catalysis
accepting a proton
260
what is covalent catalysis
Nu attack by unprotonated His, Lys, OH, SH, COO- to produce a covalent intermediate which is transiently covalently attached to the enzyme - provides an alternate pathway to an uncatalyzed reaction
261
what is metal ion catalysis
metal ions stabilise the developing -ve charge on an O atom in the transition state
262
describe he amide hydrolysis transition state
when the OH and the O are both bound to the C and the NH2 leaving groups is also still attached
263
how are catalytic Abs used in amide hydrolysis
the antigen is a transition state analogue and the Abs against it hydrolyse the amide, increasing uncatalyzed rate dramatically. the rate is increased but not to as much as if the native transition state was used
264
apoenzyme (protein portion) + cofactor (non protein portion) --> ………………..
haloenzyme (whole enzyme)
265
what is pyridoxal phosphate
cofactor required for catalysis by glycogen phosphorylase, aminotransferases and other enzymes
266
what are chymotrypsin, trypsin and elastase
they are proteases stored as zymogens in the pancreas and are activated by proteolysis on release into the small intestine
they all use the same mechanism as water hydrolysis
267
what is the role of chymotrypsin
it hydrolyses peptide bonds after aromatic amino acids
268
what is the role of trypsin
it hydrolyses peptide bonds after basic amino acids
269
what is the role of elastase
it hydrolyses peptide bonds after small neutral amino acids
270
what does DIPF do to chymotrypsin
it reacts with ser195 to inactivate chymotrypsin
271
what are the key structures of chymotrypsin
Asp 102
His57
ser195
272
what are the six steps in the chymotrypsin mechanism
1. ser195 of the chymotrypsin protease attacks the carbonyl group of the substrate. His57acts as a base catalyst, removing the proton from the ser OH group to form an alkoxide ion
2. the oxyanion (alkoxide) intermediate is stabilised by H bonding to the backbone groups in the oxyanion hole
- covalent catalysis - enzyme covalently attached to substrate
- TS stabilised
- only get bonding with transition state
- O- stabilised by H bonding
3. C-N bond is broken. N terminal part (R1COO-) is attached to ser195 - the acyl enzyme. C terminal part (R2NH2) is still in the active site. H bonded to His57
- acid catalysis
- NH2 is part of the product (replaced by water)
- acyl enzyme - substrate acyl transiently attached to serine hydroxy group of enzyme
4. the C terminal part of the substrate leaves
5. H2O replaces the C terminal part and attacks the acyl enzyme
6. the second oxyanion intermediate is established by the oxyanion hole, then His57 acts as an acid catalyst to release the N terminal product
(try learn this but use the full wiki mechanism for understanding)
273
what is a catalytic triad
group of 3 amino acids found in the active sites of proteases, involved in catalysis. it is a common motif for generating a Nu residue for covalent catalysis (ser is the Nu)
274
what does the catalytic triad do
it removes a proton from ser195 making it a very strong Nu. ser195 becomes covalently attached to the substrate in the acyl enzyme (covalent catalysis)
275
the ………. ………… makes favourable interactions with the oxyanion hole that neither the substrate or product can make
transition state
276
how does the substrate binding pocket determine substrate specificity
the specificity pocket binds the sidechain and the pockets are specific in that they will only bind certain sidechains
277
describe the specificity pocket of the 3 proteases
chymotrypsin - made of np groups that make hydrophobic interactions - aromatic side chain can fit
trypsin - aspartate vesicle chain only accepts +ve side chains
elastase - only fits small hydrophobic sidechains
278
what are statins
competitive inhibitors of HMGCoA reductase that lower cholesterol and are used in prevention/treatment of heart disease
279
what is the normal pathway in the production of cholesterol and where do statins act
acetyl coA --> HMGCoA --> mevalonate --> cholesterol
| statins act in the conversion to mevalonate by blocking the HMGCoA reductase
280
describe nerve gases
- irreversible inhibitors
281
what is the effect of sarin
it is a nerve gas
- it inactivates acetylcholine esterase at neuromuscular junctions and looks similar to DIPF which inactivates chymotrypsin
- acetylcholine esterase breaks down neurotransmitters allowing muscles to relax but sarin inhibits this causing constant contraction making you unable to breath
- sarin reacts with one ser residue
282
what are the 2 types of serine protease
chymotrypsin of subtilisin like
283
how do artificial arms work
they feed signals to the brain that allow movement
284
how can frog muscles be active outside the body
when they are brushed with different solutions this results in action potentials being generated
285
what happens when a plant is wounded
an electric signal is transmitted through the entire plant
286
separated charges have ………… ……..
potential energy
287
ions on opposite sides of the membrane with opposite charges create ……….. …………
membrane potential
288
describe the resting membrane potential
it is negative inside cells
289
how can resting potential be measured
using a voltmeter - one electrode in the cell and one in the extracellular fluid
290
what is diffusion
the net movement of molecules from high concentration to low concentration due to thermal motion
291
…….….. particles reach equilibrium before we have equal concentration
charged
292
if there is a concentration gradient for X+ and the membrane is selectively permeable for X+ there will always be an ………… ………….. across the membrane
electrical potential
293
describe the main concentration gradients in animal cells and plant cells and what is the basis for these
animal - less Na inside than out, more k, less Cl, more organic components
plant - more Na inside than out, more K, more Cl, more organic components
they are all based on NaK and ATP proton pumps
294
ATP pumps protons in/out of the cell
out
295
what are the 3 types of secondary transport
antiport, symport, cotransport
296
if the membrane is 100% selective for K+ then the membrane potential = ………… ……………..
equilibrium potential
297
concentration gradient does/doesn't matter if the membrane isn't permeable
doesn't matter - voltage depends only on those things that are permeable
298
what is the Nernst equation and what is it used for
it describes the equilibrium potential for an ion at room temperature
Ex = Z(-60mV)log10([Xin]/[Xout])
see notes for example
299
what is the PM more permeable to Na or K
K
300
what si the membrane potential and why
resting potential for a typical neuron is -60mV this is closer to the equilibrium potential for K (-90) than Na (+60) because the membrane is more permeable to K so it has more of an effect on the membrane potential
301
membrane potential is determines by the …… ……….. and the ………….. of each ion
equilibrium potential
| permeability
302
membrane potential can be represented as a circuit - describe how this is shown
permeability = conductance (1/resistance)
equilibrium potential = battery
voltage across the circuit measured by batteries in parallel
conductance changes - changes membrane potential
ion channels are tuneable conductors
303
describe the action potential generation
generated by transient changes in Na and K permeability due to opening and closing of channels
1. resting - more K open than Na channels (-ve)
2. depolarisation - opening of Na channels (-ve --> +ve)
3. repolarisation - closure of Na and opening of K channels (back to -ve)
4. hyperpolarisation - K channels remain open after resting potential reached
304
what direction does Na move in through the Na channels
into the cell
305
what direction does K move in through the K channels
K moves out
306
Na/K channels are stronger in defining the final voltage
Na
307
what is patch clamp and describe the method
it is a method used to study ionic current sin individual isolated living cells, tissue sections or patches of a cell membrane (even individual channels)
- fill pipette with solution connected to electrode with amplifier. Put pipette on top of cell and suck - seal created between electrode and membrane - take measurements and see channels opening and closing from the readings
308
what are the 3 different modes of patch clamp
cell attached, whole cell or excised patch
309
what is membrane potential
the difference between the electrical potential of interior and exterior of the cell - determined by the equilibrium potential and permeability of each ion
310
what creates a concentration gradient
primary pumps and secondary transport
311
alpha helices allow proteins to arrange amino acid sidechains so that they ……….... ……… ………. ………... but these structures on their own are not enough to constitute a ……...…….. …………...…… because soluble proteins also have alpha helices
compensate each others charge
| transmembrane protein
312
what does the hydropathy index indicate
the hydrophobicity of an amino acid (kJmol-1). it gives the energy for the transfer of an amino acid from a hydrophobic to a hydrophilic environment
-ve - release energy - hydrophilic
+ve - invest energy - hydrophobic
0 - amphiphilic
313
describe the Na channel topology
24 Tm domains each consisting of a large number of hydrophobic amino acids linked by hydrophilic linker domains. there are 6 domains per repeat. between 5 and 6 the protein dips into the membrane
314
what does the gradient of a plot showing current vs voltage tell us
```
steep = high conductance
flatter = low conductance
```
315
what does excised patch allow for
individual channel current measurement, control of ion concentrations on both sides of the membrane, and control of membrane potential
316
what is reversal potential
voltage where current = 0. we compare it with the equilibrium potential to infer selectivity of an ion for a particular channel
317
what is open probability
frequency of opening
318
what changes the open probability
gating - by voltage (inward rectifying, outward rectifying) or ligands
319
describe the shaker K channel
only one 6 domain unit
320
describe the prokaryotic transmembrane channel
has domains S5-6 only so only has pore (between 5-6 the protein dips into the membrane - selectivity filter
321
describe the K channel pore and how ions pass through
3 Armstrong's in diameter which is wide enough for K and Na but is still selective for K. 4 units of protein determine the size of the pore. the narrowest part is determined by the partial transmembrane domains. the ions need to strip off their hydration shell t pass through the pore
322
which ion is smaller Na or K and how does size affect the hydration shell
Na is smaller and binds to water more tightly due to the charge being more concentrated in a smaller ion
323
what is the TVGYG motif
it is a well conserved selectivity filter favourable for K
324
why is the K channel selective for K and not Na
K gains more energy in the domain than is used to remove the hydration shell (for Na its the opposite) so the pore is favourable for K and not Na
325
how many binding sites does K channel have and how is this useful
4 binding sites - ions push one another up one site due to the electrostatic repulsion. there are K in the binding sites a any one time. high rate of transport
326
the K channel is voltage/ligand gated - what triggers it to open
voltage - it opens due to depolarisation. when voltage changes the domains change which leads to opening or closing of the pore
327
why do we need to look at the mammalian K channel to study voltage gating
without all 6 domains we don't see voltage gating (prokaryotic channel only has the pore domains)
328
the S4 domain has a lot of ...….. amino acids and can sense voltage change because of this
charged
329
how is the K channel inactivated
the N terminal is critical. when voltage stays the same the current still disappears. the last 20 amino acids are positively charged and attached to a flexible segment of the polypeptide chain. when the channel opens the ball (20aa) is attracted to the pore and occludes it. the channel only conducts for a short period of time
330
describe the acetylcholine receptor
it is a ligand gated ion channel gated by acetylcholine. it is a non selective cation channel. it is a pentameric channel with transmembrane domains. 5 units come together to form the pore
331
describe acetylcholine receptor channel opening and what effect does this have on the cell
channel opening results in a small depolarisation of the membrane potential which triggers an action potential. as action potential arrives at the neuron end, this leads to acetylcholine release from the synaptic vesicles at the synaptic cleft. receptors in the next neuron perceive the signal, opening the channel, generating an action potential in the neuron
332
describe the difference in structure between the open and closed acetylcholine receptor
closed - 2 rings don't fit well into each other
| open - twisting mechanism caused by acetylcholine - achieved by rotating M12 TM helix by 15 degrees
333
give an example of a P-type ATPase
Ca ATPase (SERCA) - pumps Ca from the cytoplasm into the sarcoplasm reticulum of muscle cells
334
muscle contraction is triggered by low/high Ca concentration in the muscle cytoplasm
high
335
how do we get muscles to relax after contraction
Ca is pumped from the cytoplasm into the SR which requires ATP
336
describe the process of muscle contraction initiation in terms of the Ca pump
action potential arrives and the Ca channel opens due to being voltage gated. Ca rushes into the cytoplasm and this results in muscle contraction. this is very quick because initial cytoplasmic Ca is very low
ATP --> ADP at the N domain and phosphate is transferred to the P domain (Asp351). ATP binding and phosphorylation rearranges the A, P, N domains and subsequently domains so that 2Ca are released into the SR. dephosphorylation of the P domain converts protein to its original state
337
High/low Ca affinity (take from cytoplasm) --> (conf change) High/low Ca affinity (go into SR)
high
| low
338
name and describe a method used for structure-function analysis
mutation and electrophysiological experiments e.g. heterologous expression of membrane proteins in Xenopus oocytes
1. clone channel in E.coli
2. carry out in vitro transcription
3. inject RNA into oocytes and measure ion currents - the protein gets put into the membrane by the oocyte
339
the citric acid cycle harvest electrons through …….. which are then fed into the ETC to set up a ……….. ……….. used by …………… …………. to make ATP
NADH
proton gradient
ATP synthase
340
where do the sugars in our food come from
they ultimately come from that produced by plant photosynthesis
341
how is excess glucose stored
glycogen
starch
fat
proteins etc
342
what is the main plant store of excess glucose
starch - can be converted to ATP when required
343
how do bacteria and lower organisms adjust their work/energy supply balance
they detect nutrient availability in the environment. they move towards nutrient and can adjust reproduction and metabolism
344
how do plants adjust their work/energy supply balance
they adjust metabolism/growth in response to nutrient availability
345
how do higher organisms adjust their work/energy supply balance
they detect internal nutrient/energy status and environment status
346
what is another name for transporter receptors
transceptors
347
describe chemoreceptors of prokaryotes
they are usually histidine kinase systems and detect and respond to ligands and adjust accordingly
348
what are 2 roles of the plant vacuole
store of nutrients and the site of autophagy
349
what is autophagy
breakdown to recover building blocks
350
what organelle of animals acts in a similar way to the vacuole of plants
lysosomes
351
as well as the current and surrounding levels, higher animals can sense ………… levels of nutrients and adjust to changes
storage
352
does a high energy status promote anabolic or catabolic pathways
anabolic
353
what does AMPK detect
the AMP : ATP
354
how do we respond to high AMP
high AMP --> AMPK activated --> stimulate catabolism --> energy homeostasis
355
how do we respond to low AMP
low AMP --> AMPK not activated --> stimulate anabolism --> energy homeostasis
356
what happens to ATP levels when the first ETC protein complex is blocked with berberine and how does this compare to what is expected and explain the situation
we expect reduced ATP and ADP build up. the ATP decrease is actually minor and the ADP increase is lower than expected. we see a large AMP increase. adenylate kinase maintains ATP in the short term by transforming ADP to ATP and AMP
357
what is the chemical equation for transforming ADP to AMP and ATP
2ADP --> ATP + AMP when ADP:ATP high
ATP + AMP --> 2ADP when ADP:ATP low
catalysed by adenylate kinase
358
AMP detection rather than ATP allows very early detection of ATP production proteins, why is this
AMP is increasing before ATP levels go down. the early change is AMP increase and the late change is that ATP goes down
359
what happens when AMP:ATP is high
AMPK is activated by being phosphorylated by an upstream kinase, and upregulates the energy supply and downregulates energy expenditure
360
describe AMPK structure and the function of each of the subunits
it is a heterotrimer
- alpha subunit - catalytic - contains the kinase domain and is the site where AMPK is phosphorylated (conformation change moves the autoinhibitory domain away from the catalytic domain to activate the enzyme)
- beta subunit - linker - detects other types of stimuli
- gamma subunit - regulatory - binds ATP, AMP, ADP
the subunits are each encoded by their own gene
361
describe the triple mode of AMPK activation
1. AMP binds, promoting AMPK thr172 phosphorylation by LKB1
2. binding of AMP inhibits thr172 dephosphorylation
3. AMP binding causes allosteric activation
all 3 effects are antagonised by ATP
362
why isn't AMPK regulation described as on/off
because expression is controlled/regulated according to the AMP/ATP ratio
363
list some AMPK outputs
signalling pathways regulate processes in glucose metabolism, lipid metabolism, protein synthesis, anti-inflammatory, anti-ageing, redox regulation
364
list some inputs for AMPK
targeted by signalling pathways e.g. calorific restriction, overnutrition, obesity/inflammation, and exercise/contraction. some involve AMP/ATP pathways but other don't
365
what is SnRK1
it is found in plants and is a kinase very similar to AMPK. it regulates energy metabolism in plants. it is partially regulated by AMP and directly targeted by environmental stress. it helps balance how much energy they put into growing and defence
366
insulin detects …… ……...
blood sugar
367
what happens during long term starvation
1. decrease in blood glucose and increase in glucagon and glycogenolysis. once glycogen is depleted we see gluconeogenesis. glucose prioritised to the brain and ketone bodies to other tissues. BMR increases for a period of hyperactivity then decreases again
2. ketone bodies used by the brain. less energy expenditure, body temp, heart rate, bp and respiration, brain activity, protein synthesis, immune activity. muscle weakness. GIT organ atrophy
3. loss of 40-50% body weight. proteins of organs, muscle, cell membrane, blood are used for energy. see dehydration, oedema, cardiac arrhythmia. paralysis --> death
368
in plants starch breakdown occurs when and how is it adjusted
at night
it is adjusted to the amount of starch made during the day. they use all the starch before the next day to optimise growth. the starch degradation is adjusted to anticipate night length - its adjusted to the 24h cycle
369
what happens if plants use up their starch at night too early
if used too early they will starve and there will be a delay in starch production the next day
370
many plants mutants in the use of starch at night also have defects in the ………… ...…….
circadian clock
371
what chemically promotes breakdown of starch in plants
phosphorylation of the starch granule
