Metabolism Flashcards
What is a common property of Aspartate and Glutamate?
negative side chain?
Where is lysozyme formed and how does it provide defence against bacteria?
Tears and nasal secretions. Hydrolyses the bond between the repeating disaccharide NAG (N-acetylglucosamine) and NAM (N-acetyl muramic acid) in the bacterial cell wall making it lyse.
State the two essential residues in lysozyme.
Glu-35 an Asp-52
Describe the mechanism of action of lysozyme.
Glu-35 protonates the oxygen in the glycosidic bond thus breaking it.
Asp-52 stabilises the positively charged intermediate that’s formed.
Water becomes de protonated by Glu-35 which returns the Glu-35 to its original state.
The hydroxide ion then attacks the positively charged intermediate adding an OH to it.
What is the optimum pH of lysozyme and why?
5.0 because at this pH Glu-35 is unionised and Asp-52 is ionised
What type of reaction is NAD+ regularly involved in?
Dehydrogenation – it is able to readily accept one hydrogen and two electrons
Describe the action of NAD+ in Lactate Dehydrogenase.
In anaerobic respiration, pyruvate is converted to lactate which generates lots of NAD+. The lactate travels to the liver where the NAD+ converts the lactate back to pyruvate.
What are the net products of glycolysis?
Which steps of glycolysis use and produce ATP?
2 ATP + 1 NADH
Glucose G6P (-ATP)
Fructose-6-phosphate Fructose-1,6-bisphosphate (-ATP)
1,3-bisphosphoglycerate 3-phosphoglycerate (+ATP)
Phosphoenolpyruvate Pyruvate (+ATP)
Draw a flow chart showing all the steps in glycolysis including the enzymes involved.
.
What are the three fates of pyruvate?
Describe the reactions involved in each of the three steps.
Alcoholic fermentation
Generation of lactate
Generation of Acetyl-CoA
What does the pyruvate dehydrogenase complex consist of?
Lipoamide Reductase Transacetylase (Lipoamide)
Dihydrolipoyl Dehydrogenase (FAD)
Pyruvate Decarboxylase (Thiamine Pyrophosphate)
Other co-factors: NAD+ and CoA
Describe all the steps in the TCA cycle including enzyme and co-factors.
What are the products of one turn of the TCA cycle?
3 x NADH
1 x FADH2
1 x GTP
2 x CO2
Where are the Krebs’ Cycle enzymes found?
Which Krebs’ Cycle enzyme is not found in this location?
Mitochondrial Matrix
Succinate Dehydrogenase
What are the two ways of electrons from NADH entering the mitochondrial matrix? Where are these two transport mechanisms found?
Glycerol Phosphate Shuttle – skeletal muscle, brain
Malata-Aspartate Shuttle – liver, kidney, heart
Describe the glycerol phosphate shuttle
Cytoplasmic glycerol-3-phosphate dehydrogenase transfers electrons from NADH to dihydroxyacetone phosphate converting it to glycerol-3-phosphate
Glycerol-3-phosphate is converted by mitochondrial glycerol-3-phosphate back into Dihydroxyacetone phosphate and the electrons are passed via FAD to coenzyme Q
What different types of reactions are NADPH and NADH involved in?
NADPH = Anabolic NADH = Catabolic
Where are the Krebs’ Cycle enzymes found?
Which Krebs’ Cycle enzyme is not found in this location?and why is it positioned there?
Mitochondrial Matrix
Succinate Dehydrgenase – allows communication with coenzyme Q
What are the components involved in the malate-aspartate shuttle?
Malate (in) Alpha-ketoglutarate (out) Oxaloacetate (converted from malate) Glutamate (in) Aspartate (out)
Draw the malate-aspartate shuttle.
,
What type of genome do mitochondria have?
Circular molecule of DNA
Describe the action of cytochrome oxidase
Cytochrome oxidase receives two electrons from cytochrome C
Once it has 4 electrons in total, it transfers the four electrons along with 4 protons to Oxygen generating 2H2O
Describe the structure of ATP Synthase.
ATP Synthase has a F0 region (transmembrane)
And a F1 region (protruding into the matrix)
F0 consists of subunits = a, b + c
F1 consists of subunits = , +
Alpha and beta subunits CANNOT rotate because they are fixed in position by a + b subunits
How do redox potentials show that the ETC is energetically favourable?
Each successive membrane complex or carrier has a more positive redox potential than the previous – this means transfer of electrons from one complex to the next is energetically favourable
How does ATP synthase generate ATP?
The gamma subunit rotates forcing the beta subunits to undergo conformational changes which alters their affinities for ADP and ATP
Torsional energy flows from the catalytic subunit to the ADP and inorganic phosphate to promote formation of ATP
How does cyanide act as a metabolic poison?
Cyanide binds to Fe3+ in the cytochrome oxidase complex and blocks the flow of electrons through the ETC and consequently, the production of ATP
How does malonate act as a metabolic poison?
Competitive Inhibitor of Succinate Dehydrogenase – slows down the flow of electrons from succinate to ubiquinone by inhibiting the oxidation of succinate to fumarate by succinate dehydrogenase
How does oligomycin act as a metabolic poison?
Binds to the stalk of ATP synthase and inhibits oxidative phosphorylation
It blocks the flow of protons through ATP synthase and so causes a backlog of protons in the intermembrane space. The intermembrane space eventually becomes saturated with protons meaning that protons can no longer be pumped into the space by the ETC components. This means that the flow of electrons through the ETC, and hence respiration, stops.
How does dinitrophenol act as a metabolic poison?
Uncouples oxidative phosphorylation from ATP production by transporting protons across the mitochondrial membrane
What is non-shivering thermogenesis?
Thermogenin (UCP-1) channel can be activated in response to a drop in body temperature – like DNP, it allows protons to bypass ATP synthase thereby releasing heat from the dissipation of the proton gradient
What are the three parts of the Golgi Apparatus?
Cis, medial and trans
What are the two types of secretory pathways and what is the difference between them?
Constitutive – it is unregulated and acts as a shuttle vesicle to the membrane
Regulatory – it is regulated. Vesicles in this pathway must receive a signal (e.g. a hormone or neurotransmitter) before the material in the vesicles can be exocytosed. Found in excitatory cells.
What are the different types of modification that take place within the ER?
Folding, Glycosylation, proteolytic cleavages, disulphide bond formation
Describe the passage of lysosomal enzymes in the secretory pathway.
Lysosomal hydrolase precursors move from the ER to the cis Golgi
The mannose on the lysosomal hydrolase is phosphorylated by phosphotransferase
The phosphorylated sugar acts as a tag
It moves through the Golgi apparatus and binds to mannose-6-phosphate receptors in the trans Golgi
Once bound, the vesicles move to the late endosome
The late endosome has a proton pump which pumps protons into the late endosome thus making it acidic
The acidity allows the dissociation of the M6P receptor
Phosphohydrolases remove the phosphate from the lysosomal hydrolase – meaning it can’t return to the Golgi
Lysosomal hydrolases accumulate in the late endosome and it matures into a lysosome
What are the three fates of endocytosed material?
Degradation, transcytosis and recycling
Give an examples of something that uses the degradation pathway.
LDL binds to LDL receptors and form clathrin-coated vesicles
These vesicles move to the early endosome (clathrin coat is removed along the way)
From there, the LDL receptors are recycled back to the cell surface and LDL is transported to the lysosome where it is degraded to form free cholesterol
Give an example of a disease of endocytosis.
Familial Hypercholesterolaemia – caused by mutation in the LDL receptor
What is cholesterol synthesised from?
Acetyl-CoA
What are the three main parts of cholesterol biosynthesis?
Generation of isopentyl pyrophosphate from acetyl-CoA
Generation of squalene from 6x isopentyl pyrophosphate
Generation of cholesterol from squalene
Describe the synthesis of cholesterol up to isopentyl pyrophosphate.
.
Describe the synthesis of cholesterol from isopentyl pyrophosphate to squalene.
.
Describe the synthesis of cholesterol from squalene.
.
What steroid hormone precursor is derived from cholesterol?
Pregnenolone – gives rise to all 5 types of steroid hormone
What Vitamin is synthesised from cholesterol?
Vitamin D
What breakdown products of cholesterol are used as bile salts?
Taurocholate
Glycocholate
Describe the role of cholesterol in signalling.
Cholesterol and sphingolipids form lipid rafts that are involved in localising proteins involved in signalling
What do the phospholipid monolayers of lipoproteins consist of?
Phospholipids
Cholesterol
Apoproteins
What is contained in the core of a lipoprotein?
Cholesteryl ester
Triacylglycerols
How are lipoproteins categorised?
Based on density :
Chylomicrons, Very Low, Intermediate, Low, High
Where is lipoprotein lipase found and what does it do?
It is found in capillary endothelial cells.
Hydrolyses triacylglycerols to glycerol and fatty acids.
Fatty acids are then used in beta-oxidation.
What is the role of apoproteins in lipoproteins?
Allows the lipoprotein to be recognised by tissues
What are the clinical features of familial hypercholesterolaemia?
High risk of severe atherosclerosis and coronary. infarction in adolescence
What mutation causes FH?
LDLR (LDL receptor)
How do statins reduce the accumulation of cholesterol? Give an example.
Statins are HMG-CoA Reductase inhibitors. Lovastatin – competitively inhibits HMG-CoA Reductase
What do Resins and Sequestrants do?
Hide bile acid-cholesterol complexes and prevents reabsorption by the intestines. Lowers LDL levels. Raises HDL levels
What is the general structure of a fatty acid?
.
What are the three main fat sources?
.
Describe emulsification by bile.
.
Describe fat absorption and digestion
.
Where does Beta-Oxidation take place?
.
What is the first step of beta oxidation?
Where does this first reaction take place?
.
How do the products of the first reaction enter the mitochondrial matrix?
.
Describe the Beta-Oxidation cycle.
What is generated by the Beta-Oxidation cycle?
.
What is an important thing to remember when calculating the number of ATP produced by the beta-oxidation of a fatty acid?
.
What condition needs to be in place for the Acetyl-CoA from beta-oxidation to enter the TCA cycle?
.
If fat breakdown predominates, what does Acetyl-CoA form?
.
What two enzymes are involved in lipogenesis?
.
Describe the general process of lipogenesis.
.
After each round of elongation, the fatty acid undergoes reduction and dehydration by the sequential action of which three enzymes?
.
