Molecular Biology of the Cell 2 Flashcards
Where does glycolysis, TCA cycle and Oxidative phase occur, are they aerobic or anaerobic
Glycolysis in the cytosol and is anaerobic, TCA cycle is in mitochondrial matrix and Oxidative phase in the mitochondrial inner membrane and are both aerobic.
TCA cycle doesn’t require oxygen fo reactions but only runs when its present
What enzyme in glycolysis regulates the rate
Phosphofructokinase which turns fructose-6-phosphate into fructose-1,6-phosphate
Regulates the rate through allosteric inhibition, when ATP is low or ADP is high phosphofructokinase will be high. If ATP or citrate is high it inhibits this enzyme
What enzyme is needed for the first step of glycolysis and why is it important
Hexokinase converts glucose to glucose-6-phosphate
it is an irreversible step and commits the glucose to glycolysis
Without what enzyme would we lose half of the ATP made in glycolysis
Triose phosphate isomerase, TPI enzyma- needed to create the second triode phosphate/ glycerol aldehyde-3
What is the NET gain or loss of glycolysis
2NADH and 2ATP
lose 2ATP at beginning but gain 4 later
From glycolysis pyruvate is made, what are the 3 possible fates it can have
Alcoholic Fermentation- anaerobic, makes ethanol, makes NAD+ so glycolysis can continue
Lactate Generation- anaerobic, makes lactate which is produced by muscle in exercise, makes NAD+ so glycolysis can continue
Acetyl CoA formation- aerobic conditions needed, happens in mitochondria and will be committed to TCA cycle
Since ATP in muscle is depleted quickly, what do muscles store to sustain contraction
Creatine phosphate is stored in muscles so it can become creatine and ATP, providing energy
What enzyme catalyses Acetyl CoA generation from pyruvate and what disorder can affect this enzyme
Pyruvate dehydrogenase causes this reaction and makes an NADH as it does so.
BERI BERI is a deficiency of thiamine, this damages the PNS as the brain needs thiamine nd causes low cardiac output and weak muscles
What is the NET production of one turn of the Krebs cycle
2CO2, 3NADH, GTP, FADH
How can amino acids enter the Krebs cycle and what reaction creates amino acids that the cycle can utilise
can enter by removing the amino group and feeding the carbon skeleton in, all of Krebs cycle can be made from degradation of Amino Acids just not citrate.
glycogenic AAs enter in cycle or at pyruvate, ketogenic AAs enter at acetyl COA
transamination reaction is used to swap NH3+amine and =O ketone group so it can be used in the cycle.
The mitochondrial membrane is impermeable to NADH, how does it move in?
Glycerol-Phosphate shuttle: Dihydroxyacetone becomes Glycerol-3-phosphate and donates NADH in the form of electrons to DHAP, DHAP can then transfer these electrons to FAD inside the mitochondria to make FADH2 which CO-Q (part of the electron transport chain can use)
Malate-Aspartate shuttle- Oxeloacetate cannot cross the membrane so binds to NADH to become malate, malate then enters the mitochondria and reduced NAD to NADH+ within. Oxeloacetate then binds with glutamate to become aspartate and alpha-ketoglutarate, these move out of the cell and do the reverse reaction
How much ATP does one turn of the Krebs cycle make
12 ATP
NADH = 3 ATP, FADH2= 2ATP
How can Fatty acids enter the TCA cycle, explain
Beta Oxidation to create acetyl CoA
Fatty acid + ATP with ACYL COA SYNTHASE to make an Acyl CoA and AMP, this occurs on the outer mitochondria membrane
Acyl CoA will bind to carnatine to make Acyl carnatine which is catalysed by carnatine acyltransferase1 and then translocated in.
Within the cell Acyl carnatinewill become acetyl CoA and carnatine again via carnatine acetyltransferease II, carnatine will be tranlocased back out.
The acyl species then undergoes oxidation (FADH2 will be made), hydration, oxidation (NADH made) and thiolysis to make and Acetyl CoA and Acyl CoA species that’s two carbons shorter
How would a 16C fatty acid become Acetyl CoA and what would it produce
16C + 7FAD + 7NAD + 7H2O -> 8 Acetyl CoA + 7FADH2+ 7NADH
what condition can affect the conversion of an Acyl CoA species into an Acetyl CoA
Medium chain acyl CoA dehydrogenase deficiency
To become an Acetyl species the Acyl CoA has to undergo oxidation which happens through different Acyl CoA dehydrogenases aka short chain, medium, long very long.
This medium chain acyl con dehydrogenase deficiency is autosomal recessive and means the person cannot get energy from fatty acids that are larger than C12 so need a high carb diet. I.V glucose if vomiting or lose appetite
On what condition will the Acetyl CoA from Fatty acid metabolism enter the TCA cycle
if carbohydrate metabolism and beta oxidation are balanced as oxeloacetate is needed to bind with Acetyl CoA to begin TCA cycle.
If fat breakdown predominates what does Acetyl CoA become
acetoacetate, D-3 hydroxybutyrate, acetone
ALL KETONE BODIES
What deficiency/ problem can affect whether Acyl CoA can move into the mitochondria
primary carnatine deficiency
autosomal recessive, mutations result in reduced ability for cells to take up carnatine so it cannot move in, need to take. carnatine supplement
Describe fatty acid synthesis and where it occurs
occurs in the liver, adipose tissue and lactating breast
Acetyl CoA undergoes elongation due to ACETYL COA CARBOXYLASE enzyme to become Malonyl CoA. MAlonyl CoA regulates carnatine acetyltransferase and blocks so no more aftty acid can be broken down.
then undergoes reduction (NADP+), dehydration, reduction (NADPH+, condensation then linked to an Acyl carrier protein
To make a C16 fatty acid what would be needed and what would be the products
Acetyl CoA + 7 Malonyl CoA + 7H+ + 14NADPH -> C16 + 7Co2 + 6H2O + 14NADP++ 8 CoA-SH
What is the difference between beta oxidation and synthesis
Beta oxidation : in mitochondrial matrix, acyl group undergoes oxidation, hydration, oxidation, thiolysis. CoA is the carrier, FAD/NAD+ is the reducing power
Fatty acid synthesis : in the cytoplasm, Acetyl CoA undergoes reduction, dehydration, reduction, condensation, ACP is the carrier, NADPH is the reducing power
If a person is fasting and has low plasma glucose, what will happen to avoid hypoglycaemic coma
liver glycogen stores will release glucose, adipose tissue will release free fatty acids, Acetyl CoA will be made into ketone bodies.
eventually glucose store will be depleted so pyruvate provided by lactate or amino acids will start to become glyceralaldehyde 3 phosphate, glycerol released from adipose tissue releasing free fatty acids and glycerol will turn it into fructose 1,6 bisphosphate and glucose eventually made
What molecule is an indicator of cell death/damage
Creatine Kinase
What are the three dimetric isoenzymes of creatine kinase and where are these dimers found
MM - skeletal muscle, MM will move furthered towards negative cathode
BM - cardiac muscle/ myocardium
BB- brain
How would Creatine Kinase activity be measured
coupled assay to measure NADPH formation
What are other markers of myocardial damage
BM dimer of creatine kinase
Cardiac Troponin- enters bloodstream fast
Seum Glutamate Oxeloacetate Transaminase- 2 days after for 5 days total
Lactate Dehydrogenase- late marker 2-3 days, stays longer due to inflammation
describe what junctions pores keep cells together or allow them to communicate
tight junctions- occludin interacts and seals them together
adherens junctions and demosomes- have cadherin and keep cells together (cell-cell anchoring)
gap junction- pores between cells (channel forming)
hemidesmosomes- integrins that connect cell to basal membrane
What are the different functional types of epithelium and their features
TRANSPORTING EPITHELIA- lots of ion transporters and mitochondria
ABSORPTIVE EPITHELIUM- carriers on brush border membrane, villi and microvilli, nutrients build in cytoplasm then down conc gradient into basal interstitial space.
SECRETORY EPITHELIUM- tubules and glands arrangement. can be endocrine (secretory granules by basal membrane) or exocrine (secretory granules by apical membrane)
What are the different types of secretion
Constitutive secretion- secretory vesicles move to plasma membrane and release directly as formed
Stimulated secretion- secretory vesicles need a stimulant to fuse with membrane
Epithelial cells are replace how and what problems can occur if this process is inhibited or increased
Replaced by proliferation of stem cells
stem cells in crypts replace lost villi tips, so if proliferation is inhibited a flattened mucose=a will occur
stem cells replace cells out at the top of Strat squampous. if hyerproliferation occurs then will caused a thickened layer, papilloma virus induces this and creates a wart
What are the three sources that fats are derived from
The diet
De novo biosynthesis in the liver
storage deposits in adipose
A lack of bile salts results in what
fat passing through the gut and being unabsorbed leading to steatorrhea
Where are bile salts made and stored
made in the liver and stored in the gallbladder
What do bile salts do
Emulsify fats so dietary fats can be absorbed and fat soluble vitamins ADEK can be absorbed
What medication treats obesity and how does it work? what are the side effects?
Orlistat. treats obesity, reduces fat absorption by inhibiting pancreatic and gastric lipase.
abdominal pain, urgency to defecate, increased flatus, steatorrhea
As bile salts have what feature
amphipathic
How are chylomicrons formed and what is their overall structure
enterocytes on the brush border absorb lipids, they are re-synthesised into triglycerides and then put into chylomicrons which travel via lymphatics and blood stream. In the bloodstream they acquire apoproteins from High Density Lipoproteins.
Hydrophobic inside with triglycerides and cholesterol esters encased by acyl chains of phospholipid.
Hydrophilic outside with polar group of phospholipids and apoproteins, has cholesterol in too
How are chylomicrons used by tissues
Chylomicrons travel from lacteals of intestine to thoracic duct to subclavian vein
Lipoprotein lipase on capillary endothelial cell membranes recognises the apoprotein and breaks down chylomicrons, the fatty acids undergo beta oxidation and glycerol is retuned to liver
What is cholesterol
A steroid, increases or decreases stiffness of membrane
Polar head group, rigid planar steroid ring structure, non polar hydrocarbon tail
How is cholesterol made
2 acetyl CoA make acetoacetyl CoA.
Acetoacetyl CoA joins with another Acetyl CoA tome 3-hydroxy-3-methylglutaryl CoA (HMG-CoA) this is done by HMG CoA synthase
HMG-CoA is reduced to make mevalonate by HMG CoA reductase
mevalonate makes isopentenyl pyrophosphate, 6 molecules of this condensed to make squalene. undergoes cyclisation and demethylation to make cholesterol
What enzyme in cholesterol biosynthesis is important, and what looks similar to it
HMG CoA reductase because cholesterol and mevalonate both feed back negatively to inhibit its actions
statins look similar to this and are competitive inhibitors.
What do isoprene units do
isoprene units make molecules lipophilic and keep Co-Q (ubiquinone) to the inner mitochondrial membrane
From cholesterol what three things can be synthesises
Pregnenolone which makes all other steroid hormones
Vitamin D
Bile Salts- Glycocholate and taurocholate
What do lipoproteins carry to pack the contents closer together
Cholesterol esters
Cycle of lipoproteins
Liver produces VLDL and releases into circulation
VLDL give off glycerol, FFA and cholesterol to tissues that recognise apoprotein.
after giving its contents its called a lipid depleted remnant
Liver and small intestine synthesises HDL which have the lipids and cholesterol from tissues take the apoproteins from the lipid depleted remnant to go back to the liver. the removal of triglycerides leaves an Intermediate density lipoprotein
HDL then donates cholesterol esters to IDL to make LDL which has lots of cholesterol and macrophages take up. The rest of LDL is taken up by liver
what is the difference in HDL and LDL’s jobs
HDL lowers serum cholesterol taking it from tissues to liver
LDL transport cholesterol that liver synthesises to tissues and high levels can lead to atherosclerosis
What disorder can affect serum cholesterol levels, symptoms and
Familial hypercholesterolaemia
serum cholesterol -2-3 times more if inherit one gene, if inherit both then 5 times
will see orange/yellow xanthomas and plaque in arteries.
They lack functional LDL receptors Class I- no LDLR Class II- Low surface expression of LDLR Class III- LDL doesnt bind well to LDLR Class IV- LDL-LDLR doesn't cluster in clathrin coated pits Class V- LDLR doesn't release LDL
LDLR are supposed to bind to LDL, enter a clathrin pit and be endocytose as a clathrin covered vesicle, take off this coat of clathrin to fuse with endoscope which released the LDL to lysosome and make free cholesterol inside the cell
Two ways to control hypercholesterolaemia
Statins - HMG-CoA Reductase inhibitors stop mevalonate pathway so stops more cholesterol being made
Resins- make bile acid-cholesterol complexes to stop intestine reabsorbing them, lowers LDL and raises HDL
Explain the electron transport chain
NADH donates electrons to Complex I, this causes it to become supercharged and pump H+ inter the inter membrane space. With this energy it donates protons to CoQ.
FADH donates electrons to Complex II (succinate dehydrogenase), this Complex cannot become supercharged as is only on one side of the membrane so donates its electrons to CoQ
CoQ becomes CoQH2 after these donations
CoQH2 passes these electrons to Cytochome B in Complex III where the electron donated turns Fe3+ to Fe2+, this supercharge the complex and pumps H+ into the inter membrane space. It then donates it’s protons to Cytochrome C which has the same Fe3+ to 2+ process. Cytochrome C donates to Complex IV which becomes supercharged and also pumps protons to the inter membrane space. Complex IV then passes its electrons to oxygen which splits to make two water molecules. Ultimate electron acceptor is oxygen.
ATP Synthase takes advantage of proton gradient and protons move through, this energy causes the F0 subunit to create rotation creating potential energy to put ADP and Pi together to make ATP
what is chemiosmosis
protons moving from high to low concentration through ATP Synthase
What is redox couple and redox potential
A redox couple is something that can exist in oxidised and reduced forms
a redox potential is the ability of a redox couple to accept or donate electrons: if it is -Eo then its a reducing agent and donates electrons, if it is +Eo then It accepts electrons and oxidising agent
What controls the uptake of oxygen by the mitochondria
The amount of ADP that is available
Which metabolic poisons affect the ATP Synthase
Oligomycin inhibits the F0 subunit to stop ATP formation
2,4, Dinitrophenol (DNP) creates a hydrophobic pore and uncouples oxidative phosphorylation from ATP concentration, H+ move through to pore and no ATP- will see rise in temperature due to higher metabolic rate
babies have brown adipose tissue that creates thermogenin which creates a pore and uncouples to make heat for them
Glucose, citrate, different metabolic poisons what effect do they have on oxygen consumption
glucose or adding ADP+Pi will not speed up as the mitochondria can’t metabolise
citrate will increase oxygen consumption
Antimycin, Cyanide, CO, Oligomycin will stop O2 consumption
2,3 DNP (dinitrophenol) will increase oxygen consumption as it uncouples it from ATP production
How are collagen fibres formed
Prolines and lysine are hydroxylated to form procollagen which has an N and C terminal, if its becoming a fibrillar collagen these domains are removed before secretion (post translational modification). ITs then secreted becoming collagen (3 alpha chains) This condenses to a fibril by cross linking then aggregation to a fibre.
Not all collagens form fibrils- type IX and XII associate with fibrillar collagens and regulate organisation
What is extracellular matrix and what is its key functions
Network of proteins and carbohydrates filling space between cells
provides physical support, determines mechanical and psysicochemical properties if the tissue, influences growth adhesion and differentiation status of cells and tissues, essential for development tissue function and organisation
what are the components of connective tissues
Collagens: I,II,III are fibrillar, IV is basement membrane
Multi-adhesive glycoproteins: Fibronectin, fibrinogen. laminins in basement membrane
Proteoglycans: aggrecan, versican, decorin. perlecan in basement membrane
What is collagen, describe its arrangement, how many genes code for each type
Fibrous proteins, lots in bone, tendon and skin
skin collagen layers are at right angles to each other to resist tensive force
has three alpha chains making a triple helix: Type I is a heterotrimer having chains from two genes, Type II and III are homotrimers
In the triple helix every third position has a glycine
