biochemistry exam 2

classes of lipids

free fatty acids, triacylglycerols, phospholipids, glycolipids, steroids

energy storage as carb vs fat

- triacylglycerols stored in anhydrous form
- polar glycogen binds water
- fat more reduced than carbs
- 1g anhydrous fat stores 6x as much energy as 1g hydrated glycogen

lipid droplet

compartment of TAG surrounded by a single layer of phospholipids in adipocytes

lipolysis steps

1. glucagon or epinephrine triggers activation of PKA through adenylyl cyclase and cAMP
2. PKA phosphorylates perilipin and hormone-sensitive lipase
3. perilipin restructures TAGs to be more accessible for degradation
4. perilipin phosphorylation triggers release of cofactor for adipose triglyceride lipase (ATGL)
5. ATGL binds to cofactor and degrades TAG into fatty acid and diacylglycerol
6. hormone-sensitive lipase degrades diacylglycerol into fatty acid and monoacylglycerol
7. monoacylglycerol lipase degrades monoacylglycerol into fatty acid and glycerol

triacylglycerol > diacylglycerol + fatty acid

- adipose triglyceride lipase (AGTL)
- activated by cofactor released after phosphorylation of perilipin

diacylglycerol > monoacylglycerol + fatty acid

- hormone-sensitive lipase
- activated by phosphorylation by PKA

monoacylglycerol > glycerol + fatty acid

monoacylglycerol lipase

hormones inducing lipolysis

glucagon and epinephrine

blood protein which transports fatty acids

albumin

glycerol > glycerol 3-phosphate

glycerol kinase

glycerol 3-phosphate > dihydroxyacetone phosphate

glycerol-3-phosphate dehydrogenase

dihydroxyacetone phosphate > glyceraldehyde 3-phosphate

triose phosphate isomerase

fatty acid + CoA-SH + ATP > acyl-CoA + AMP + PPi

fatty-acyl-CoA synthase

fatty acid activation for degradation

1. fatty acid reacts with ATP to form acyl adenylate, ATP is converted to AMP and pyrophosphate (PPi), AMP replaces O
2. sulfhydryl group of CoA attacks acyl adenylate, acyl-CoA and free AMP are formed
3. pyrophosphatase converts PPi into posphate (Pi)

pyrophosphate (PPi) + H2O > 2 orthophosphate (Pi)

- pyrophosphatase
- drives activation of fatty acids forward

complete reaction for fatty acid activation

fatty acid + CoA-SH + ATP + H2O > acyl-CoA + AMP + 2Pi

carnitine acyltransferase I (carnitine palmitoyl transferase I)

transfers acyl group from CoA to carnitine in mitochondrial intermembrane space

carnitine acyltransferase II (carnitine palmitoyl transferase II)

transfers acyl group from carnitine to CoA in mitochondrial matrix

why is ATP converted to AMP in fatty acid activation

so the pathway can be made irreversible by the hydrolysis of inorganic pyrophosphate (PPi)

acyl-CoA > enoyl-CoA

acyl-CoA dehydrogenase

enoyl-CoA > L-3-hydroxyacyl-CoA

enoyl-CoA hydratase

L-3-hydroxyacyl-CoA > 3-ketoacyl-CoA

L-3-hydroxyacyl-CoA dehydrogenase

3-ketoacyl-CoA > acetyl-CoA

3-ketothiolase

palmitate

C16:0

stereate

C18:0

laurate

C12:0

myristate

C14:0

arachidate

C20:0

palmitoleate

C16:1 (cis-9)

oleate

C18:1 (cis-9)

linoleate

C18:2 (cis-9,12)

acetyl-CoA > acetoacetyl-CoA

3-ketothiolase

acetoacyl-CoA > 3-hydroxy-3-methylglutaryl-CoA

hydroxymethylglutaryl-CoA synthase

3-hydroxy-3-methylglutaryl-CoA > acetoacetate

hydroxymethylglutaryl-CoA cleavage enzyme

acetoacetate > D-3-hydroxybutyrate

D-3-hydroxybutyrate dehydrogenase

ketone body breakdown

1. D-3-hydroxybutyrate converted to acetoacetate by dehydrogenase
2. acetoacetate converted to acetoacetyl-CoA by CoA transferase
3. acetoacetyl-CoA converted to 2 acetyl-CoA by thiolase

why does ketogenesis take place in the liver

liver cells lack CoA transferase needed for breakdown of acetoacetate so it can escape and be transported to other tissue

why can acetyl-CoA not be converted to glucose?

the carbon atoms of acetyl-CoA leave the citric acid cycle as CO2 before oxaloacetate is generated so there is no net synthesis of oxaloacetate which can be converted into pyruvate

acetyl-CoA + oxaloacetate > citrate

citrate synthase

citrate > acetyl-CoA + oxaloacetate

- ATP-citrate lyase
- activated by phosphorylation by PKB/Akt which is stimulated by insulin

what inhibits phosphofructokinase?

citrate in cytoplasm

oxaloacetate > malate

malate dehydrogenase

malate > pyruvate

malic enzyme

pyruvate > oxaloacetate

pyruvate carboxylase

acetyl-CoA > malonyl-CoA

- acetyl-CoA carboxylase I
- biotin-dependent

fatty acid synthesis

fatty acid synthase (FAS)

acetyl-CoA > acetyl-ACP/FAS

acetyl transacylase

malonyl-CoA > malonyl-ACP/FAS

malonyl transacylase

acetyl-ACP/FAS + malonyl-ACP/FAS > acetoacetyl-ACP/FAS

β-ketoacyl (condensing enzyme)

crotonyl-ACP/FAS > butyryl-ACP/FAS

enoyl-ACP/FAS reductase

how is fatty acid chain length determined

thioesterase acts selectively on C16-acyl so a C16 fatty acid is cleaved from FAS after it is produced

pyruvate > acetyl-CoA

pyruvate dehydrogenase

glucose 6-phosphate > 6-phosphogluconate

glucose 6-phosphate dehydrogenase

6-phosphogluconate > ribulose 5-phosphate

6-phosphogluconate dehydrogenase

ribulose 5-phosphate > ribose 5-phosphate

phosphopentose isomerase

ribose 5-phosphate > 2 fructose 6-phosphate + glyceraldehyde 3-phosphate

transketolase and transaldolase

what does glutathione (GSH) do?

- reduces reactive oxygen species (ROS) to harmless forms
- forms glutathione disulfide (GSSG) when oxidized
- must be reduced back to GSH by NADPH generated in PPP

reactive oxygen species (ROS)

superoxide anion (•O2-), hydrogen peroxide (H2H2), hydroxyl radical (•OH)

glutathione (GSH) + ROS > glutathione disulfide (GSSG) + H2O + O2

glutathione peroxidase

glutathione disulfide (GSSG) > glutathione (GSH)

glutathione reductase

heinz bodies

hemoglobin molecules cross-link with each other through disulfide bridges and form aggregates on red blood cell membrane, usually prevented by GSH keeping cysteine residues in reduced form

pentose phosphate pathway is also called

hexose monophosphate shunt, phosphogluconate pathway

α-amino acid + α-ketoglutarate > α-ketoacid + glutamate

aminotransferase/transaminase

glutamate > α-ketoglutarate + NH4+

glutamate dehydrogenase

which amino acids can be directly deanimated?

serine and threonine

serine > pyruvate + NH4+

serine dehydratase

threonine > α-ketobutyrate + NH4+

threonine dehydratase/deaminase

which amino acids cannot be deaminated in the liver?

branched amino acids: leucine, isoleucine, valine

glucose-alanine cycle steps

1. amino group of glutamate is transferred to pyruvate to form alanine in muscle
2. alanine is released into blood and taken up by liver
3. amino group is transferred back to glutamate and then into urea cycle
4. pyruvate is used for gluconeogenesis

glutamate + NH4+ > glutamine

glutamine synthetase

NH4+ + CO2 > carbamoyl phosphate

carbamoyl phosphate synthetase I

ketogenic amino acids

- degrade into acetyl-CoA or acetoacetate
- can give rise to ketone bodies or fatty acids but not glucose

glucogenic amino acids

- degrade into pyruvate or citric acid cycle intermediates
- can give rise to glucose through gluconeogenesis

asparagine > aspartate + NH4+

asparaginase

glutamine > glutamate + NH4+

glutaminase

phenylalanine + O2 > tyrosine + H2O

phenylalanine hydroxylase

what is carbamoyl phosphate synthetase I regulated by?

N-acetylglutamate which is synthesized when N-acetylglutamate synthase is activated by arginine

acetyl-CoA + glutamate > N-acetylglutamate

N-acetylglutamate synthase

carbamoyl phosphate + ornithine > citrulline

ornithine transcarbamoylase

citrulline + aspartate > argininosuccinate

argininosuccinate synthetase

argininosuccinate > arginine + fumarate

argininosuccinase

arginine > ornithine + urea

arginase

major sites of glycogen storage

liver and skeletal muscle

glycogen > glucose 1-phosphate

glycogen phosphorylase (transferase, α-1,6-glucosidase)

what is phosphorolysis?

cleavage of a bond by the addition of orthophosphate (Pi); e.g. phosphorolysis of glycogen

advantages of phosphorolytic cleavage of glycogen

- hydrolytic cleavage would yield glucose which would have to be phosphorylated before entering glycolysis
- muscle cells have no transporters for glucose 1-phosphate so it cannot be transported out

why can glycogen phosphorylase not carry out glycogen breakdown alone?

- glycogen phosphorylase can only cleave α-1,4 glycosidic bonds
- glycogen branch points have α-1,6 glycosidic bonds
- glycogen phosphorylase stops cleaving when it reaches a residue 4 residues away from a branch point

transferase (glycogenolysis)

shifts 3 glucosyl residues from one branch to another

α-1,6-glucosidase

hydrolyzes α-1,6 glycosidic bond to release free glucose (debranching enzyme)

glucose 1-phosphate > glucose 6-phosphate

phosphoglucomutase

glucose 6-phosphate > glucose

glucose 6-phosphatase (only present in liver)

activation of glycogen breakdown

1. glucagon (liver) or epinephrine (muscle) triggers activation of PKA through adenylyl cyclase and cAMP
2. PKA phosphorylates phosphorylase kinase (activates)
3. phosphorylase kinase phosphorylates glycogen phosphorylase (activates)
4. PKA phosphorylates glycogen synthase (inactivates)
5. PKA phosphorylates glycogen synthase phosphatase inhibitor (activates)

hormones stimulating glycogenolysis (breakdown)

glucagon and epinephrine; both for liver, epinephrine for muscle

cAMP > AMP

phosphodiesterase

glucose 1-phosphate + UTP > UDP-glucose + PPi

UDP-glucose phosphorylase

UDP-glucose > glycogen

glycogen synthase (glycogenin, branching enzyme)

glycogenin

catalyzes formation of α-1,4-glucose polymers of 10-20 glucosyl residues before glycogen synthase can add on

branching enzyme (glycogenesis)

breaks a α-1,4 glycosidic bond to form an α-1,6 branch in glycogen

activation of glycogenesis (synthesis)

1. insulin triggers phosphorylation of glycogen synthase kinase (GSK) (inactivates)
2. protein phosphatase 1 (PP1) dephosphorylates glycogen phosphorylase (inactivates)
3. PP1 dephosphorylates glycogen synthase (activates)
4. glycogen synthase is activated by glucose 6-phosphate

inhibition of glycogenesis

- glucagon and epinephrine trigger activation of PKA through adenylyl cyclase and cAMP
- PKA phosphorylates glycogen synthase (inactivates)
- PKA phosphorylates protein phosphatase 1 inhibitor (activates)