biochemistry S2 Y1 Flashcards
(283 cards)
1
Q
Role of non-photosynthetic energy conversion pathways?
A
Catabolise carbon-based fuels (fats, carbs and proteins) to reduce O2
2
Q
What does the inner mitochondrial membrane contain to enable the ETC to occur?
A
Complexes for electrons to pass through
3
Q
Why is there a proton gradient across the inner-mitochondrial membrane?
A
Electrochemical movement of protons from area of high conc. to low conc. to produce ATP (due to redox running electron motive force)
4
Q
2 things the proton gradient establishes?
A
- pH gradient that forms chemical potential energy
- Electrical difference that forms electrical potential energy
5
Q
Why is low pH created in mitochondrial matrix?
A
Protons then move into the matrix through ATP synthase to form ATP (proton flow = electric current, ATP synthase = resistor)
6
Q
Why is low pH created in chloroplasts’ cytosol?
A
Photosystems move protons into thylakoids and then they move out to produce ATP
7
Q
What is H+ uncoupling?
A
Generation of heat rather than ATP
8
Q
What are blocking effects?
A
Blockers shutting down H+ flow to cause cell death as DPH and DY increase
9
Q
When is proton uncoupling used?
A
In hibernation, newborn mammals, cold-adapted animals and bodybuilders to generate heat
10
Q
Why have humans used 2,4-DNP?
A
It is an uncoupler that causes rapid weight loss
11
Q
How was the chemiosmotic theory proven?
A
Using an artificial membrane containing a bacteriorhodopsin protein (much like a photosystem - light lets H+ through) and a mitochondria - ATP WAS SYNTHESISED
12
Q
What carry out oxidative phosphorylation?
A
Four protein complexes (I-IV), cytochrome C, ATP synthase
13
Q
What provide channels for small molecules across outer membranes?
A
Porin proteins
14
Q
Role of translocase proteins?
A
Shuttle ATP, ADP, Pi across inner-mitochondrial membrane
15
Q
- Number of H+ translocated at the start of the ETC?
- How many reenter per ATP?
A
- 10
- 4 (3 via ATP synthase, 1 via phosphate translocase)
16
Q
What happens to the electron donor whilst transferring to acceptor (the oxidant)?
A
It is oxidised (acts as a reductant)
17
Q
Do oxidation and reduction occur simultaneously or at different times?
A
Simultaneously (as shown by half-equations, oxidised form on LHS)
18
Q
4 ways electrons are transferred from donor to acceptor?
A
- Directly as electrons
- As hydrogen atoms
- As a hybride ion (:H-)
- Direct combination with oxygen
19
Q
- What depends on redox potential?
- How is standard redox potential of a couple measured?
- Role of strong reducing agent (e.g. NADH)?
- Role of strong oxidising agent (e.g. Fe3+)?
A
- Tendency of a redox couple accepting and donating
- Using electrochemical cell relative to standard hydrogen electrode
- Poised to donate electrons (has negative redox potential)
- Ready to accept electrons (has positive redox potential)
20
Q
What is E°’?
A
Potential of a redox couple in which reduced and oxidised species are present at 1M, 25°C, pH7
21
Q
- Where do electrons flow in a spontaneous reaction?
- ΔG°’ and ΔE°’ in spontaneous reaction?
A
- From redox couple of lower potential to redox couple of higher potential
- ΔG°’ is negative
ΔE°’ is positive
22
Q
Equation for work done when an electron is moved in an electric field?
A
Work done = electron charge x potential
23
Q
Equation for ΔG°’?
A
ΔG°’ = -n x F x ΔE°’
n = no. of electrons transferred
F = Faraday constant (96.5)
ΔE°’ = difference in standard reduction potentials between 2 redox couples (V)
24
Q
What is the Nernst equation?
A
E’ = ΔE°’ + (2.303 RT / nF) log10 ([e- acceptor] / [e- donor])
- At 25°C, (2.303 RT / nF) = 0.059 for 1 electron transfer, 0.0295 for 2
25
Mitochondrial electron transport system:
- What is it?
- Where do electrons from NADH flow?
- How many H+ translocated concomitantly?
- A series of coupled redox reactions
- Enter complex I, then CoQ, complex III and complex IV
- 10
26
Mitochondrial electron transport system:
- Where electron pairs derived from FADH2?
- How many H+ translocated concomitantly?
- Complex II, ETF-Q oxidoreductase or glycerol-3-phosphate dehydrogenase
- 6
27
Complex I (NADH-ubiquinone oxidoreductase):
- What is coupled?
- How many Fe-S carrying e- at a time?
- What can Fe-S clusters change?
- How many H+ translocated into intermembrane space?
- NADH oxidation (releases 2e-) and FMN reduction (forms semiquinone intermediate if it is 1e- and FMNH2 if it is 2e-)
- 7
- Redox potential from -0.5 to 0.4V (depending on protein microenvironment)
- 4
28
Coenzyme Q (ubiquinone):
- 3 roles?
1. Mobile, lipid-soluble e- carrier that transports electrons in membrane from complex I to III
2. Entry point into ETC for e- pairs from CAC, fatty acid oxidation and glycerol-3-phosphate dehydrogenase
3. Converts 2e- transport system in complexes I and II to 1e- system in complex III (which then passes electrons to cytochrome C one at a time)
29
Complex II (succinate dehydrogenase):
- What is it linked to?
- Role?
- CAC
- Oxidises succinate to fumarate (coupled to FAD/FADH2) -- electron pair then used to reduce Q to QH2 via Fe-S and a haem -- electrons move through Fe-S clusters and cytochrome b560 (FADH2 then oxidised)
30
Complex III (ubiquinone-cytochrome c oxidoreductase):
- What 2 binding sites?
- What are its prosthetic groups for?
- Role?
- What kind of complex?
- Why does CoQ utilise the Q cycle?
- Q binding sites (Qp and QN)
- Function as electron carriers
- Reduces cytochrome c and translocates 4H+
- Dimeric (2x11 subunits)
- Converts 2e- process into 2 x 1e- transfers
31
Haems and cytochromes:
- How is cytochrome c haem group linked to protein?
- What does a type a haem have?
- Covalently through thiol groups from cysteine residues
- Long hydrophobic tail
32
Complex IV (cytochrom c oxidase):
- Role?
- What is electron transport though?
- What happens to 4 H+?
- Cytochrome c oxidation
- Through one monomer of homodimer (culminating O2 reduction to form H2O)
- 2H+ translocated into inter-membrane space, 2H+ used top form H2O
33
What do complexes I-IV all have?
Transmembrane regions and functional domains protruding into the matrix (III and IV have functional domains that protrude into the intermembrane space to interact with cyt c)
34
How many H+ does NADH oxidation starting at complex I translocate?
10
35
How many H+ does CoQ + FADH2 oxidation starting at complex II translocate?
6
36
Why must CoQ and cyt c make 2 trips to transfer 2e- from NADH and FADH2?
Can only transfer 1e- at a time
37
Reactions for reactive oxygen species and H+ making water?
O2-. + 2H+ <--> O2 + H2O2 (SOD catalyses)
2 H2O2 <--> O2 + H2O (catalase catalyses)
38
Equation for the transfer of 2e- from NADH through respiratory chain to O2?
ΔG°' = -nFΔE°' = -nF[E°'(acceptor) - E°'(donor)]
39
Equation for ΔG available from H+ gradient across mitochondrial membrane?
ΔG = RT ln (c2/c1) + ZFΔΦ
- Z is absolute value of its charge
- F is faraday constant
- Φ is electrical potential difference across
membrane
40
ΔpH and ΔΦ in actively respiring mitochondria?
ΔpH = 0.75
ΔΦ = -0.15V
41
Is more free energy available from H+ gradient derived from ΔpH or ΔΦ?
ΔΦ
42
What subunits do all ATP synthases have?
3 alpha and 3 beta
43
What is different about bacterial ATP synthase?
Has gamma subunit that associates with F1 component as the 3 alpha and beta subunits
44
What is different about yeast ATP synthase?
Has the gamma subunit, 3 alpha and beta, a delta subunit homologous to bacterial gamma subunit and an OSCP subunit
45
What are the F0 and F1 components for in ATP synthase?
F0 is a H+ channel, F1 is for catalytic activity
46
What is the stator of ATP synthase?
Subunit with half-channels for H+ to enter and exit AND a stabilising arm (b, d, h + OSCP)
47
What is the rotor of ATP synthase?
c + g + d + e rotate as H+ enter and exit the c-ring
48
What is the headpiece of ATP synthase?
Hexameric a3b3 unit responsible for ATP synthesis
49
What are the 3 basic principles of ATP synthase?
1. Gamma directly contacts all 3 beta subunits, but each interaction is distinct (gives rise to 3 different beta conformations)
2. ATP binding affinities of the 3 beta subunits are T, L, O (tight = ATP bound, loose = ADP + Pi bound, open = ATP released)
3. H+ flow through F0 cause rotation of gamma subunit counter-clockwise during ATP synthesis - each 120° rotation cuases beta subunits to go fro, L --> T --> O --> L etc
50
What direction does ATP synthase rotate in?
In reverse conditions that favour ATP hydrolysis
51
How can ATP synthesis be catalysed?
a3b3 headpiece simply as the function of the g subunit is imposed by electromagnets
52
What are disaccharides attached by?
O-glycosidic bonds
53
What do alpha and beta glucose react to form?
Maltose
54
2 examples of reducing sugars?
Maltose and lactose
55
Example of non-reducing sugar?
Sucrose
56
What are the two types of oligosaccharide?
1. 2-8 linked monosaccharides (disaccharides included)
2. 3-8 saccharide molecules (low abundance)
57
What are polysaccharides?
>8 saccharides for structure or storage
58
2 examples of structural polysaccharides?
1. Cellulose (beta (1-4) linked glucose units)
2. Chitin (beta (1-4) linked N-acetylglucosamine units that are linked and unbranched)
59
What does beta 1-4 linkage of glucose form?
Straight chains whereby hydrogen bonds can form with adjacent molecules to add further stability
60
2 examples of polysaccharides for storage?
1. Starch - alpha amylose (unbranched alpha 1-4 glucose polymer) and amylopectin (branched and linked alpha 1-6 glucose polymer)
2. Glycogen (similar to amylopectin but branches 3x more)
61
What do alpha 1-4 linkages cause?
Coiled chains (twist around one another)
62
Glycosaminoglycans (GAGs):
- What are they?
- Major role?
- Example?
- Polymers composed of repeating disaccharide units
- Component of ground substance (holds tissue types together)
- Hyaluronic acid
63
Hyaluronic acid:
- Where?
- Made up of?
- How are disaccharides attached?
- Characteristics?
- Ground substance, synovial fluid, vitreous humour of eyes
- D-glucuronic acid and N-acetyl-D-glucosamine
- Beta 1-4
- Rigid, highly hydrated, viscous, absorbs shock and shearing forces
64
What are glycoproteins?
Proteins modified through the addition of carbohydrates without strict genetic control
65
What determines the carbohydrate added to proteins?
Enzymes available at the time = microheterogenity
66
2 types of carbohydrate attachment to proteins in glycoprotein formation?
1. N-linked
- Needs amino acid side chain with N
- E.g. N-linked-N-acetylglucosamine is beta
linked to nitrogen of Asn
2. O-linked
- OH group of Ser or Thr (sometimes
HyrdroxyLys) attachment
- More variable than N-linked
67
What is glycogen composed of?
Alpha 1-4 linked chains and alpha 1-6 linked branches
68
What does the glycogen chain start with?
Glycogenin proteins (where A and B chains begin)
THERE ARE TWO IDENTICAL PROTEINS
Act as primer for glycogen formation
69
What are the inner and outer regions of glycogen?
Inner = B-chains with 2 branch points
Outer = A-chains that aren't branched
70
How does glycogen branch?
When 13 residues have been added to growing strand, branching enzyme recognises this and make a branch to grow a new chain
71
Why are the outermost chains of glycogen unbranched?
Makes glucose more easily accessible (outermost tier always contains 34.6% of glucose in structure)
72
What are other proteins associated with glycogen for?
Synthesis and breakdown
73
How does glycogenin act as a catalyser of glucose addition?
First glucose added to Tyr195 and then subsequent glucoses are added to growing chain (until 10-20 residues when glycogen synthase takes over)
74
What do glycogenin and glycogen synthase utilise?
Activated precursors (UDP-glucose in eukaryotes, ADP-glucose in bacteria and plants)
UTP + glucose-1-phosphate --> UDP-glucose
CATALYSED by UDP-glucose pyrophosphorylase
75
Role of UDP-glucose pyrophosphorylase?
Cleaves alpha and beta phosphate in UTP
76
Role of inorganic pyrophosphatase?
Hydrolyses the phosphates released from UTP in the cytoplasm to prevent the reverse reaction
77
What type of reaction is UDP-glucose addition?
Glycosyl transfer with the release of UDP via double nucleophilic substitution or intramolecular nucleophilic substitution
78
What is the glycogen branching enzyme and what does it do?
Amylo-(1,4 --> 1,6) transglycosylase
Transfers terminal chain section (around 7 residues) to the C6-OH of another glycogen chain
79
What enzymes degrade glycogen?
Glycogen phosphorylase
Glycogen debranching enzyme Phosphoglucomutase
80
- What does glycogen phosphorylase do?
- Mechanism?
- Hydrolyses 1-4 bond which releases alpha-D-glucose-1-phosphate and glycogen
- Via a carbocation (Sn1) --> carbocation stabilised by pyridoxal phosphate which is covalently linked to the enzyme (PLP is active for of vitamin B6)
81
Debranching enzyme:
- 2 functions? (bifunctional)
- Mechanism in notes, but what is the result?
- Transferase and alpha-1,6-glucosidase
- No branch
82
Phosphoglucomutase:
- Role?
- Fates of glucose-6-phosphate?
- What happens in periods of plentiful glucose?
- Converts glucose-1-phosphate to glucose-6-phosphate
- Enters glycolysis OR dephosphorylated to form glucose in the liver
- G-6-P formed by hexokinase to change the equilibrium position so that the enzyme converts G-6-P into G-1-P that can form UDP-glucose for glycogen synthesis
83
How does the relationship between the synthetic capacity and the degrative capacity vary between the liver and muscle?
Liver = roughly equal
Muscle = degradation can be 300x faster
84
How is glycogen metabolism regulated?
Through synthesis (using glycogen synthase) and degradation (using glycogen phosphorylase) --> regulated by phosphorylation and dephosphorylation
85
Signalling cascade of glycogen metabolism?
1 signal molecule --> 10 second messengers --> 100 molecules activated --> 1000 glucose released
86
How does insulin lower blood glucose?
Increases glycogen synthase activity (increases conversion from phosphorylated b form to dephosphorylated ACTIVE a form)
It does this by binding to an insulin receptor, phosphorylating insulin receptor substrate which interacts with PI3K to for PIP3 that signals the target GSK3 molecule and phosphorylates ut to deactivate it so glycogen synthase is activated
87
Glycogen synthase kinase 3 (GSK3):
- How does it inactivate glycogen synthase?
- When can the P be added?
- Phosphorylates serine side chains (has site where it recognises primed phosphate and a site where it adds the phosphate)
- After priming reaction that occurs via casein kinase II action
88
What catalyses dephosphorylation of glycogen synthase?
Phosphoprotein phosphatase 1 (PP1)
- acts quicker if G-6-P is bound to glycogen
synthase
89
What does PP1 activate and what does it inactivate?
Activates glycogen synthase
Inactivates glycogen phosphorylase and phosphorylase kinase
90
How is glycogen phosphorylase regulated?
As it is more active when it is phosphorylated, it is phosphorylated by phosphorylase kinase and dephosphorylated by phosphorylase phosphatase 1
91
2 ways glycogen is signalled to be degraded?
1. Glucagon signals liver to release glucose into blood
2. Adrenaline signals muscles to release glucose for energy production
92
5 steps of mechanism for signal for glycogen degradation?
1. Either molecule signals GDP to GTP conversion
2. GTP interacts with adenylate cyclase
3. ATP converted to cAMP
4. cAMP causes protein kinase A to activate phosphorylase kinase
5. Glycogen phosphorylase is activated
93
2 way muscle glycogen phosphorylase is activated?
1. Ca2+ released into muscles to induce contraction which stimulates phosphorylase kinase
2. AMP builds up if not enough ATP is produced
94
What inhibits liver glycogen phosphorylase?
Glucose - glycogen phosphorylase acts as a glucose sensor - bound phosphates more exposed to removal by PP1
95
PP1:
- What does it increase?
- What does it decrease?
- What is it inhibited by?
- What is it bound to?
- Attached to?
- Glycogen synthase activity by dephosphorylation
- Glycogen phosphorylase by dephosphorylation
- PKA
- Glycogen with GS, PK and GP
- Glycogen-targetting protein
96
How are carbohydrate and lipid metabolisms regulated?
Co-ordinately
- Signalling factors have co-ordinated effects on glycogen synthesis and breakdown and glycolysis AS WELL AS lipid synthesis and breakdown
97
Why are simple lipids less common than complex ones?
Simple have more specific functions (e.g. cholesterol) and complex ones have greater range (e.g. phospholipids)
98
What are complex lipids made up of?
Smaller components - fatty acid is major component
99
What are fatty acids composed of?
Saturated/unsaturated long chain hydrocarbon (most double bonds are cis), and a carboxyl group (pKa = 4.5) and is ionised at most physiological pHs
100
What is the nomenclature of fatty acids?
Number of carbons in chain + 'oic acid' or 'oate' if ionised
101
Are all the R groups in triacylglycerols the same?
No, the differences determine the type of fat or oil
102
How does the structure of phospholipids differ from triacylglycerols?
Has a polar (hydrophilic) head group
103
How does chain length affect inter-chain interactions?
Longer chains create more interactions
104
How do double bonds affect inter-chain interactions?
More double bonds = less interactions
105
What does the extent of inter-chain interactions affect?
Fluidity levels
106
What are amphipathic molecules also known as?
Schizophrenic
107
Examples of amphipathic molecules?
Free fatty acids, phospholipids, glycolipids, sphingolipids and ceramides
108
- What do amphipathic molecules naturally form?
- What does vigorous shaking cause?
- Monolayers and sometimes bilayers
- Micelle formation (driven by entropy)
109
3 sources of fatty acids?
1. Diet
2. Adipose storage
3. De novo synthesis
110
Where does fat digestion begin?
In the small intestine and uses the pancreas+liver
111
What produces and releases bile and what is its role?
Liver produces, gall bladder releases
As it is made from bile acids and salts derived from cholesterol, it acts as a dtergent (emulsifies lipids to form fat droplets)
112
What does the pancreas produce?
Digestive enzymes and bicarbonate solution
113
What enzyme does the pancreas release for fat digestion and how does it work?
Lipase
Breakdown micelles into monoglycerides and fatty acids, these are then incorporated into the ER as they move down the concentration gradient from the gut into cells --> triglycerides then synthesised, chylomicrons formed --> enter blood via lymphatic vessel
114
Role of pancreatic lipases?
Catalyses hydrolysis of triaglycerols at 1+3 positions
Triaglycerol --> 1,2-diacylglycerol + fatty acid --> 2-acylglycerol + fatty acid
115
Role of phospholipase A2?
Removes fatty acid residue from phospholipids at C2 position to aid digestion, to form lysophospholipid
116
How are lipids transported in the bloodstream?
Lipoprotein complexes (e.g. chylomicrons, VLDL, LDL, HDL) - lipid droplets surrounded by proteins and phospholipids so they are soluble
117
How are some fatty acids solubilised so they can be transported in the blood?
Through serum albumin binding
118
What happens to chylomicrons once they have been formed?
Enter the blood and then the liver, turned into VLDLs and re-released into the blood --> these activate and interact with lipoprotein lipase and are broken down in blood to enter cells surrounding the capillaries
119
Lipoprotein lipase:
- Where?
- What activates it?
- Capillary surfaces of tissues that absorb lipid from blood
- Apo-CII component of chylomicrons
120
What do triacylglycerols breakdown into?
Fatty acids and monoacylglycerols
121
How was beta-oxidation of fatty acids discovered?
Fatty acids labelled at methyl end with phenyl group (blocks degradation) were fed to dogs -- excretion products examined in urine
- Odd-chain lengths formed benzoate
- Even-chain lengths formed ohenyl acetate as the beta carbon was attacked
121
3 stages of beta oxidation?
1. Activation
2. Transport
3. Oxidation
122
Activation in beta oxidation:
- What forms?
- Where?
- 2 ways?
- Fatty acid chain bound to CoA (acyl-CoA)
- Outer mitochondrial surface
- 1. Catalysed by acyl-CoA synthase
RCOO- + CoA + ATP --> Acyl-CoA + AMP +
PPi
2. Catalysed to the right by
pyrophosphatase (irreversible)
RCOO- + CoA + ATP +H2O --> Acyl-CoA +
AMP + 2Pi + 2H+
123
Transport in beta-oxidation:
- Where to?
- How does acyl-CoA enter matrix?
- Mitochondria via transporter protein
- Converted to acylcarnitine so it can move through the transporter - reconverted back in matrix
124
What are the four steps of oxidation in beta oxidation of fatty acids?
1. Oxidation I
2. Hydration
3. Oxidation II
4. Thiolytic cleavage
125
Oxidation I of beta oxidation:
- What forms?
- Enzyme?
- Enoyl-CoA (C=C between beta and alpha C)
- Acyl-CoA dehydrogenase
126
Hydration of beta oxidation:
- What forms?
- Enzyme?
- Alcohol called hydroxy-acyl-CoA (H2O added over C=C in enoyl-CoA)
- Enoyl-CoA hydratase
127
Oxidation II of beta oxidation:
- What forms?
- Enzyme?
- Ketoacyl-CoA (ketone)
- Beta-hydroxyacyl-CoA dehydrogenase
128
Thiolytic cleavage of beta oxidation:
- What forms?
- Enzyme?
- Acetyl-CoA
- Thiolase
129
What do glycogen storage diseases (GSDs) cause?
Increased or decreased glycogen (mainly affects liver and muscle as most of the glycogen in stored there)
130
How does the liver receive blood and why is it important it sees all this blood?
From aorta via the hepatic artery and the small intestine via the portal vein
- Liver sees everything that enters mouth and can regulate things like glucose
131
GSD type I (Type I glycogenosis):
- Cause?
Glucose-6-phosphatase deficiency as the multicomponent enzyme is responsible for catalysing terminal steps of gluconeogenesis and glycogenolysis
132
6 steps of the Cori cycle?
1. Lactate generation in muscle
2. Lactate enters the blood
3. Lactate converted to pyruvate
4. Pyruvate becomes glucose
5. Glucose returns to muscle
6. Glucose becomes glycogen
133
4 biochemical characteristics of GSD type I?
1. Hypoglycaemia (reduced glycogen)
2. Hyperlacticacidaemia (increased lactate)
3. Hyperlipidaemia (increased lipid)
4. Hyperuricaemia (increased uric acid)
134
Where is the glucose-6-phosphatase enzyme located?
ER of liver, intestinal and kidney cells (facing in)
135
As glucose-6-phosphate is in the cytoplasm, how does it enter the ER?
Transport protein on ER membrane, inside it is converted to glucose
136
How does glucose get out of the ER lumen?
GLUT2 transporters
137
What stabilises the reaction glucose-6-phosphatase catalyses?
Stabilising protein
138
2 roles of hepatocytes?
1. Metabolic function
2. Present G6Pase
139
Role of cholangiocytes in the liver?
Transport bile
140
6 cells that make up intestines?
1. Enterocytes (absorption, produce G6P)
2. Goblet cells (produce mucous, protect from acid, lubricate)
3. Enteroendocrine cells
4. Paneth cells (produce bacterialcidal lysozyme)
5. Pit cells
6. Stem cells
141
Kidney:
- Where is G6Pase found?
- How is G6Pase involved in gluconeogenesis?
- Glycogen breakdown?
- Proximal convoluted tubule
- Pyruvate turned into PEP --> reverse glycolysis to form F-1,6-P2 then F-G-P into G6P THEN G6PASE CONVERTS THIS INTO GLUCOSE + Pi
- Glycogen phosphorylated to glycogen and glucose-1-phosphate which becomes G6P THEN G6PASE CONVERTS THIS TO GLUCOSE
142
Where is the G6Pase gene and what regulates its expression?
- Chromosome 17
- Glucocorticoids
143
What are glucocorticoids produced from?
Cholesterol
144
What is the action of glucocorticoids?
Pass through lipid membrane, bind to glucocorticoid receptors, this complex binds to glucocorticoid response elements in the promoters of genes
145
What are GSD ___:
- 1a?
- 1b?
- 1c?
- 1aSP?
- Cataylytic subunit
- T1 G6P
- T2 Pi
- Stabilising protein
146
3 symptoms of GSD1?
1. Protruding abdomen (due to enlarged liver (hepatomegaly) -- high glycogen storage)
2. Fasting-induced hypoglycaemia
3. Growth failure
147
How does fasting-induced hypoglycaemia work?
G6Pase is removed and glucose is not formed so there is more G6P and glycogen
148
3 autonomic and 5 impaired brain function symptoms of hypoglycaemia?
Autonomic = sweating, hunger, tremor
Brain = parasthesia, personality change, fatigue, seizures, coma/death
149
What is hyperlacticacidaemia?
Increased lactate as normally glycogen is converted to lactate in muscle, this then enters the blood, converted to glucose in the liver and reconverted to glycogen in the muscle --> in this condition glucose is not generated so direction of glycolysis is towards pyruvate and lactate
150
What is hyperlipidaemia?
Increased lipid levels
151
What can GSD1 in puberty cause?
Xanthoma (external lipid storage e.g. on elbows)
152
Why is there increased glycerol in GSD1?
G6P is not converted to glucose which means there is increased fructose-6-phosphate that PFK converts to F-1,6-P2 which is converted to GAP and DHAP by aldolase and DHAP is converted to glycerol-3-phosphate by glycerol-3-phosphate dehydrogenase, this is then converted to glycerol by glycerol kinase
153
Why does GSD1 cause increased fatty acids?
Increased G6P causes increased pyruvate = increased acetyl-CoA = increased citrate
Citrate leaves mitochondria, converted back to acetyl-CoA in cytoplasm by ATP citrate lyase and acetyl-CoA is converted to malonyl-CoA by acetyl-CoA carboxylase and this forms fatty acids
154
What does increased glycerol and fatty acids mean?
Increased triglycerides (lipids)
155
2 contributing factors to hyperuricaemia?
1. Increased purine catabolism
2. Increased uric acid clearance from kidneys
156
How does increased purine catabolism cause hyperuricaemia?
Increased G6P is converted to NADPH/purines via the pentose phosphate pathway --> purines are converted to xanthine which is converted to uric acid
157
2 ways of treating GSD1?
1. Frequent feeding e.g. nasogastric tube
2. Liver transplant (orthotopic)
158
How is liver transplant going to have to change?
Tissue will have to be developed from stem cells due to organ shortages
159
Overall reaction of beta oxidation of fatty acids?
Cn-Acyl-CoA + FAD + NAD+ +H2O + CoA --> C(n-2)-Acyl-CoA + FADH2 + NADH + H+ + acetyl-CoA
160
2 pathways for acetyl-CoA?
1. Enters the CAC
2. Made into ketone bodies
161
Why must acetyl-CoA enter the CAC?
There will be a shortage of carbohydrate or a lot of fatty acid metabolism for gluconeogenesis
162
Equation for the CAC?
Acetyl-CoA + 3NAD+ + FAD + GDP + Pi + 2H2O --> 2CO2 + 3NADH + 3H+ + FADH2 + GTP + CoA
163
- How many acetyl-CoA, FADH2 and NADH+H+ does palmitate produce?
- From CAC (GTP, no acetyl-CoA)?
- 8 acetyl-CoA, 7 FADH2, 7 (NADH + H+)
- 8 GTP, 8 FADH2, 24 (NADH + H+)
164
What are 8 GTP equal to?
8 ATP
(GTP + ADP <---> ATP + GDP)
165
NADH+H+ and FADH2 produce from oxidative phosphorylation (theoretical and measured)?
NADH+H+ = 3, but 2.5 measured
FADH2 = 2, but 1.5 measured
166
How many ATP are generated from palmitate?
131 (but 2 are used so 129 are available)
- 31 NADH/H+ generates 91
- 15 FADH2 generates 30
- 8 GTP generates 8
167
How many times greater is the energy captured from palmitate than the free energy of the hydrolysis of one phosphate from ATP?
129
168
- What is the standard free energy of oxidation of palmitate?
- Proportion of energy captured?
-9790 kJ/mol
- 40% (-3999/-9790)
169
- Yield per carbon oxidised to CO2?
- For glucose?
- 129 (no. of ATP) / 16 (no. of C) = 8.2
- 6.3
170
- What is oxaloacetate needed for?
- Where is it produced?
- Uses?
- Qualities for why it is taken up by heart and renal cortex for energy?
- Acetyl-CoA to enter the CAC
- The liver
- Gluconeogenesis and is a major site for key enzymes for ketone body synthesis
- Energy rich and water soluble
171
First step of ketone body formation (in mitochondria)?
2 acetyl-CoA <---> acetoacetyl-CoA
Uses thiolase enzyme and releases CoA-SH
172
Second step of ketone body formation (in mitochondria)?
Acetoacetyl-CoA ---> beta-hydroxy-beta-methylglutaryl-CoA
Uses HMG-CoA synthase (and acetyl-CoA + H2O --> CoA-SH)
173
Third step of ketone body formation (in liver)?
Beta-hydroxy-beta-methylglutaryl-CoA ---> acetoacetate
Uses HMG-CoA lyase and releases acetyl-CoA
174
What is beta-hydroxy-beta-methylglutaryl-CoA used for?
Precursor for cholesterol synthesis
174
Fourth step of ketone body formation (in liver) (2 parts)?
1. Acetoacetate ---> acetone (CO2 released)
2. D-beta-hydroxybutyrate (NADH/H+ converted to NAD+)
175
How does acetone leave the body?
Via the lungs as it cannot be metabolised (volatile)
176
Ketone body utilisation:
- Where do they go?
- Steps of utilisation?
- Out of blood into heart + renal cortex
- D-beta-hydroxybutyrate --> acetoacetate --> acetacetyl-CoA (uses B-ketoacyl-CoA transferase and converts succinyl-CoA to succinate) --> acetyl-CoA (by thiolase)
177
What are complex lipids made up of?
Triacylglycerols (act as principle membrane component)
178
Roles of complex lipids made of triacylglycerols?
Specialised signalling molecules at low concentration, involved in synthesis and breakdown of fatty acids
179
What does breakdown release and synthesis require?
Energy and reducing equivalents
180
What is 8% of body's basal O2 consumption for?
Fatty acid biosynthesis
181
What is the major biosynthetic product from fatty acids?
Palmitic acid
182
What does the biosynthetic process do to growing fatty acids?
Adds 2 carbon units
183
Fatty acid synthesis:
- Where?
- What is involved?
- What is needed?
- Cytoplasm
- NADP+/NADPH
- CO2 as HCO3-
184
Fatty acid breakdown:
- Where?
- What is involved?
- What is NOT needed?
- Mitochondria
- NAD+/NADH
- CO2
185
How was fatty acid biosynthesis discovered?
Tissue was homogenised and centrifuged at 100000 x g to form pellet (nuclear material, mitochondrial fragments, all membranous debris) and a soluble fraction (no membrane fraction, only soluble fractions)
186
What happens to soluble fraction?
Undergoes protein precipitation with ammonium sulphate (water required to dissolve -- taken from soluble protein), as the concentration increases, different proteins are precipitated out (fractions)
187
Why do 2 fractions combined have fatty acid present and not single fractions?
One of the fractions will contain biotin so fatty acid biosynthesis will be supported
188
Stage one of fatty acid biosynthesis:
- What happens?
- 2 required substances?
- What catalyses it?
- Reversible or irreversible?
- 2 steps?
- Acetyl-CoA carboxylated to form malonyl-CoA
- Biotin and HCO3-
- Acetyl-CoA carboxylase
- Irreversible
- 1. Biotin + HCO3- --> Biotin-CO2- (biotin carboxylase used and ADP released)
2. Biotin-CO2- --> CO2-CH2CO-S-CoA (transcarboxylase used, biotin converted to acetyl-CoA)
189
Stage two of fatty acid biosynthesis:
- What happens?
- What primes the reaction?
- Reaction?
- Enzyme?
- Chain elongation as long chain fatty acids are formed from acetyl-CoA + malonyl-CoA by successive additions to a growing chain
- Acetyl-CoA (becomes methyl terminus of fatty acid chain)
- Acetyl-CoA + 7 malonyl-CoA + 14 NADPH/H+ --> CH3CH2(CH2-CH2)6CH2COOH (palmitate) + 7CO2 + 14NADP+ + 8CoA + 6H2O
- Fatty acid synthase
190
Fatty acid synthase:
- How many reactions does it catalyse?
- Where?
- What does it require?
- What don't accumulate?
- 7 (each has a separate active site)
- Cytosolic fraction of cells
- Malonyl-CoA, acetyl-CoA, NADPH, 4-phosphopantetheine
- Free, unbound intermediates
191
What are the 7 enzymatic steps of fatty acid synthase?
1. Acetyl-CoA attached to acyl carrier protein
2. Malonyl transacylase transfers a malonyl group to ACP
3. Condensation reaction catalysed by ketoacyl-ACP synthase to which acetyl is bound and CO2 is released
4. Reduction catalysed by ketoacyl ACP reductase
5. Dehydration using hydroxyacyl-ACP dehydrase (removes water and forms a double bond)
6. Reduction catalysed by enoyl-ACP reductase
7. Palmitoyl-ACP ---> palmitate + ACP-SH (catalysed by palmitoyl thioesterase)
192
Enzymatic step one of fatty acid synthase:
- Reaction?
- Where is acetyl then transferred?
- Acetyl-CoA ---> acetyl-ACP + CoASH (catalysed by acetyl transferase)
- To the beta-ketoacyl ACP synthase protein
193
Reaction for enzymatic step four of fatty acid synthase?
CH3C(=O)CH2C(=O)~S-ACP <---> CH3CHCH2C(=O)~S-ACP
(NADP+ released from forward, NADPH/H+ from reverse)
194
Reaction for enzymatic step 5 of fatty acid synthase?
Beta-hydroxyacyl-ACP <---> alpha,beta-trans-enoyl-ACP
195
Enzymatic step six of fatty acid synthase:
- Reaction?
- How does it work?
- Alpha,beta-trans-enoyl-ACP ---> acyl-ACP
- Acyl group is transferred to beta-ketoacyl synthase domain of protein, this frees the ACP to bind to another malonyl group to form C6 acyl, this repeats until C16 acyl group is bound to ACP
196
Acetyl-CoA carboxylase:
- Role?
- What is linked to lysine residue?
- Role of biotin carboxylase?
- What can the bound CO2 do?
- Regulates fatty acid reduction
- Biotin coenzyme
- Adds CO2 to acetyl group on biotin
- Move to different spatial regions e.g. interact with transcarboxylase
197
3 components of acetyl-CoA carboxylase?
1. Biotin carboxyl carrier protein
2. Biotin carboxylase
3. Carboxyl transferase
198
Why are all the components of acetyl-CoA carboxylase activated together?
Genes arranged in an operon
199
What is the animal enzyme of acetyl-CoA carboxylase?
Single multifunctional protein that is found as a dimer with one biotin per subunit (but must polymerise to become active)
200
- How many activities occur in fatty acid synthase?
- How does this vary in bacteria/plants, yeast and vertebrates?
- 7
- Bacteria/plants occurs in 7 separate polypeptides, yeast occurs in 2 polypeptides, vertebrates occurs in 1 large polypeptide
201
Why do plants have many peptides in fatty acid synthase?
So they can make many different products
202
Why does fatty acid synthase have covalent substrate linkage?
So intermediates are not released to make process more efficient
203
Role of beta-ketoacyl ACP synthase in fatty acid synthase?
Holds position of growing chain before condensation with malonyl-ACP AND the -SH group of a cysteine amino acid acts as an attachment site for a priming group
204
Role of acyl carrier protein (ACP) in fatty acid synthase?
-SH group of a 4-phosphopantetheine which is linked to a serine side chain of ACP
205
Final product from animal enzyme?
Palmitate (and stearate to lesser amount)
206
What does yeast enzyme mainly release?
Palmitoyl-CoA
207
What does bacterial/plant enzyme produce?
20% palmitoyl-CoA/palmitoyl-ACP
70% vaccenate-CoA
208
What is the precursor of fatty acid synthesis?
Cytosolic acetyl-CoA
209
Where is acetyl-CoA synthesised?
In the mitochondria
210
How is acetyl-CoA transported out of the mitochondria?
Use of citrate transporter, citrate reacts with CoA to form oxaloacetate and acetyl-CoA
211
What are the two pathways of malate (from oxaloacetate)?
1. Enters malate-alpha-ketoglutarate transporter to become oxaloacetate again in mitochondria
2. Becomes pyruvate which enters mitochondria to release ATP and then become oxaloacetate
212
3 fates of acetyl-CoA?
1. Utilisation of 2 ATP with conversion of one NADH to NADPH with transfer of CO2 from mitochondria to cytosol
2. Utilisation of 1 ATP and no net change in NAD+/NADH (favoured by low energy conditions)
3. Pentose phosphate pathway that generates NADPH and converts G6P to ribulose-5-phosphate
213
What is compartmentalisation?
Oxidative reactions occur in mitochondria, reductive in cytosol
214
4 factors affecting acetyl-CoA carboxylase (ACC) activity?
1. Hydroxytricarboxylic acid levels (e.g. citrate) SHORT TERM
2. Presence/absence of long chain acyl-CoA SHORT TERM
3. Phosphorylation status SHORT TERM
4. Enzyme synthesis/degradation LONG TERM
215
Hydroxytricarboxylic acid levels:
- What are they?
- What do high levels increase?
- When are citrate levels high?
- What does citric act as?
- What does a cytosolic [citrate] of 0.3-1.9mM create?
- Precursors of acetyl-CoA
- Activity
- When there is excess energy
- A positive feed-forward activator
- Half maximal activity of acetyl-CoA carboxylase
216
Presence/absence of long-chain acyl-CoA:
- What do they act as?
- What are the most and least effective inhibitors?
- What is inhibition competitive with?
- What is inhibition non-competitive with?
- What is the inhibition constant for C16?
- Negative feedback inhibitors
- Most = saturated 16-20C
Least = unsaturated fatty acids
- Citrate
- Acetyl-CoA, ATP, bicarbonate ions
- 5.5nM
217
Phosphorylation status:
- How many sites does ACC have for phosphorylation?
- When is ACC inactivated?
- What remove Pi?
- How is it controlled?
- Effect of citrate?
- Effect of acyl-CoA and phosphorylation?
- 6 (hydroxyl groups of serine side chains)
- When phosphorylated
- Phosphatase 1C/2A
- Allosterically (dimer (inactive) <---> polymer (active))
- Activates (moves equilibrium to polymer)
- Inactivate (moves equilibrium to dimer)
218
Enzyme synthesis/degradation:
- Main way of controlling?
- Level of control?
- What is this controlled by?
- Rate of synthesis
- Transcriptional level
- Transcription factors (e.g. SREBP1c) that are controlled by unesterified fatty acid levels
219
What do insulin and glucagon do?
Regulate carbohydrate, amino acid and fat metabolism
220
What catalyses acetyl-CoA carboxylase phosphorylation?
AMP-activated protein kinase (activated when dephosphorylated)
221
Role of insulin on AMP activated protein kinase?
Increases rate of dephosphorylation
222
Role of glucagon on acetyl-CoA carboxylase?
Increases cAMP which increases action of kinase kinase so more phosphorylation of AMP activated protein kinase occurs
223
Effect of fatty acyl-CoAs?
Negatively impact acetyl-CoA carboxylase and increase kinase kinase activity
224
What is endosymbiosis?
Mitochondria and chloroplasts becoming part of eukaryotic cells
225
What shows the diversity of bacteria?
Environmental PCR (and only 5-10% have been cultured)
226
Why is catabolic diversity higher in prokaryotes than eukaryotes?
Higher diversity of substrates used and metabolic pathways
227
2 main energy source type organisms?
1. Chemotrophs (use chemical compounds for energy source)
2. Phototrophs (use of light for energy source)
228
2 subtypes of chemotrophs?
1. Chemolithotrophs (use inorganic chemicals)
2. Chemoorganotrophs (use organic chemicals)
229
2 subtypes of chemolithotrophs with different carbon sources?
1. Chemolithoautotrophs (C=CO2)
2. Mixotrophs (C=organic)
230
2 subtypes of phototrophs with different carbon sources?
1. Photoautotrophs (C=CO2)
2. Photoheterotrophs (C=organic)
231
What is an example of a chemolithoautotroph primary producer in black smoker geothermal vents?
Riftia pachyptila that live in tubeworms and use iron to fix CO2 from the water, they are then eaten by tubeworm, which is then eaten by other organisms
- COULD have been origin of life
232
Energy transduction:
- 6 reasons it is needed?
- What does it do?
- What is the key?
- 2 ways energy is conserved?
- Growth, maintainence, reproduction, biosynthesis, transport, motility
- Converts energy source into usable energy
- Redox reactions
- 1. Energy rich chemical bonds
2. Concentration gradient
233
Difference between exergonic and endergonic reactions?
Exergonic = -ΔG and free energy leaves
Endergonic = +ΔG and free energy is gained
234
What does ΔG vary depending on?
Concentration, temperature and pressure
235
What can electrons not be in solution?
Free
236
What reactions are coupled?
Oxidation and reduction half reactions
237
What do different e- donor and acceptor couples generate?
Different levels of energy
238
What is the terminal e- acceptor in aerobic respiration?
Oxygen
239
Chemoorganotrophy (organic energy):
- How is ATP produced?
- What does carbon flow result in?
- What occurs?
- What is released?
- Electrons go out to create electron flow which causes proton motive force = ATP
- CO2 released
- Biosynthesis
- O2
240
Chemolithotrophy (inorganic energy):
- How is ATP produced?
- 2 types?
- Same as chemoorganotrophy
- 1. Mixotrophy or chemolithoheterotroph
2. Autotrophy or chemolithoautotroph
241
6 sources of energy for chemolithotrophic organisms?
1. Hydrogen
2. Sulphur compounds
3. Ammonia
4. Nitrites
5. Iron
6. Arsenite
242
Terminal electron acceptor for facultative anaerobes?
Nitrate or nitrite
243
Terminal electron acceptor for obligate anaerobes?
Sulphate (SO4 2- --> H2S)
244
Terminal electron acceptor for methanogens?
CO2
245
What is the difference between photoheterotrophy and photoautotrophy?
Photoheterotrophy = organic C for biosynthesis
Photoautotrophy = inorganic C (CO2) for biosynthesis
246
What do chemolithotrophs still need?
ATP and NAD(P)H
247
Pathway of e- in chemolithotrophs that have inorganic e- donors with redox potentials higher than NAD(P)+ and NAD(P)H?
E- are transferred to coenzyme Q or a cytochrome
- some generate proton motive force
when passed to a terminal e- acceptor
(forward e- transport)
- some are passed to NAD(P)+ to make
NAD(P)H using proton motive force
(reverse e- transport)
248
How does nirtospira generate NADPH and ATP?
Complex chemolithotrophic pathways using reverse electron pathway embedded in cyto bc1 complex
249
Autotrophy:
- What does it use?
- How is cell material created?
- Calvin cycle
- Reverse CAC results in acetyl-CoA production, the new cell material is then created via the reductive acetyl-CoA pathway or the 3-hydroxypropionate bi-cycle
250
What is campylobacter jejuni?
A prokaryote that cannot eat glucose and uses H2 and SO3 2- as an e- donor, causes gastroentritis
251
What happens when there is insufficient oxygen for respiration?
Fermentation and lactic acid is produced
252
What happens when lactic acid builds up?
Lactic acidosis and hyperactive neurons
253
Common anaerobic environments?
Water, soil, food, tissues, GI tract
254
2 types of anaerobic metabolism?
1. Anaerobic phototrophy
2. Anaerobic respiration (an e- transport chain delivers e- to a non-O2 e- acceptor, electron transport chain phosphorylation generated by ATP)
3. Fermentation
255
Fermentation:
- Where?
- What are bacteria called that only use this?
- What organisms is it limited to?
- What are reduced and recycled?
- Endo or exogenous?
- Environments where there is no terminal e- acceptor or iron for e- transport chain
- Obligate fermentators
- Chemoorganotrophs
- E- carriers (NAD and FAD)
- Endogenous
256
What is the e- acceptor in fermentation said to be?
Organic and internally supplied
257
What is excreted from fermentation?
Reduced product
258
Equation of fermentation substrate level phosphorylation?
Phosphoenolpyruvate + ADP <---> pyruvate + ATP (electrons are transferred)
259
Difference in ATP produced from lactate fermentation and lactate respiration?
LF = 2 ATP
LR = 38 ATP
260
What are coenzymes (cofactors)?
Small organic molecules that interact with an apoenzyme to form an active holoenzyme
261
Role of NAD, FAD, NADP and FMN?
They are water-soluble coenzymes that carry electrons from oxidation reactions and donate them to reduction enzymes
262
Difference between NAD+NADP and FAD+FMN?
NAD and NADP are free moving from one enzyme to another
FAD and FMN are tightly bound to enzymes (flavoproteins) covalently or noncovalently
263
Difference between simple (linear) and complex (split/branched) pathways?
Simple generate reductive products and less ATP
Complex generate reductive and oxidative products and more ATP
264
What is glycolysis said to be?
A type of fermentation that uses 2 ATP and releases 4 ATP
265
What does glycolysis do?
Reduces pyruvate to fermentation products, balances redox and regenerates ATP
266
What does a lot of substrates being fermented mean?
A lot of fermentation products
267
How do organisms generate different fermentation products?
Using many different pathways and substrates
268
Examples of substrates?
Sugars, polyalcohols, organic acids, amino acids, purines, pyrimidines, acetyene, citrate, glyoxylate, succinate, oxalate, malonate
269
What rare substances can some bacteria ferment?
Xenobiotic compounds (anthropogenic and unknown in natural ecosystems)
270
Difference between homofermentative and heterofermentative?
Homo = one product e.g. lactobacillus spp. (lactate)
Hetero = more than one product e.g. bifidobacterium spp. (lactate, acetate, ethanol)
271
How does fermentation with no substrate level phosphorylation work?
No external e- acceptor is used and ion pumps are used to produce a potential difference
272
2 ways of carrying out fermentation with no substrate-level phosphorylation?
1. Ion-coupled end-product efflux via a symport
2. Decarboxylation driven ion transport
273
What is 2,3-butanediol fermentation?
A type carried out by some bacteria that can occur in aerobic conditions whereby high energy phosphate from ATP is added (no net ATP produced)
274
As fermentation produces ATP, what do some processes directly use?
A proton motive force
275
What do some strict fermentative bacteria do to generate proton motive force?
Use ATP to run ATPase in reverse
276
What do primary fermentors use?
High level substrate
277
What are secondary fermentors?
Fermentors that are usually needed by primary fermentors and use the fermentation products of higher organisms
278
When do fermentation pathways go from being endergonic to exogonic?
When reaction products concentration is low
279
What happens if fermentation product does not diffuse away?
Reaction pathways gets backed up and stops
280
What is the relationship between primary and secondary fermenters?
Syntrophy (primary is syntrophic)
281
