Substrates Pathway

1,3-Bisphosphoglycerate Glycolysis
2-Phosphoglycerate Glycolysis
3-Phosphoglycerate Glycolysis
Acetoacetate Ketone Bodies
Acetyl-CoA TCA, FAO, FAS, AAD, Ketone Bodies
Alpha-Ketoglutarate TCA, AAD
AMP Purine Synthesis
Arginine AAS
Arginnosuccinate AAS
Aspartate AAS
Carbamoyl Phosphate AAS
Citrate TCA
Citrulline AAS
CO2
Dihydroxy Acetone Phosphate Glycolysis
Erythrose-4-Phosphate PPP
Fructose-1,6-Bisphosphate Glycolysis, Gluconeogenesis
Fructose-6-Phosphate Glycolysis, Gluconeogenesis, PPP
Fumarate TCA, AAD, AAS
Glucose Glycolysis, Gluconeogenesis
Glucose-1-Phosphate Glycogen Synthesis
Glucose-6-Phosphate Glycolysis, Gluconeogenesis, PPP
Glutamate AAD
Glyceraldehyde-3-Phosphate Glycolysis, PPP
GMP Purine Synthesis
Isocitrate TCA
Lactate Fermentation (Animal Cells)
Malate Gluconeogenesis, TCA
Malonyl-CoA FAS,
NH4+ AAD, AAS
Ornithine AAS
Oxaloacetate Gluconeogenesis, TCA, AAD
Phosphoenolpyruvate Glycolysis, Gluconeogenesis
PRPP Purine Synthesis
Pyruvate Glycolysis, Gluconeogenesis, TCA, AAD
Ribose-5-Phosphate PPP
Ribulose-5-Phosphate PPP
Succinate TCA
Succinyl-CoA TCA, FAO, AAD
UMP Pyrimidine Synthesis
Urea AAS
 Path
Enzymes Activates Inhibits
way
Citrate, Dephosphorylated Fatty acyl-CoA,
Acetyl-CoA (Insulin) Phosphorylated (Glucagon)
Carboxylase FAS

Acyl-CoA
Synthetase FAO
Alpha- AMP NADH, Succinyl-CoA
Ketoglutarat
e
Dehydrogena
se TCA

Aminotransf
erases AAD
ATP, NADH, Succinyl-
Citrate CoA
Synthase TCA

Fatty Acid
Synthase FAS
Fructose-1,6- Citrate F-2,6-B, AMP
Bisphosphata
se GLU
"Substrate-level control"
Glucose-6- high Km for G6P
Phosphatase GLU
Glucose-6- High NADPH & Acetyl-
Phosphate CoA
Dehydrogena
se PPP
Glutamate
Dehydrogena
se AAD
Glycogen GLY AMP, Phosphorylation High Glucose,
Phosphorylas C (Glucagon & Epinephrine) Dephosphorylation
e DEG (Insulin)
GLY Dephosphorylated Phosphorylated (Glucagon
Glycogen C (Insulin) & Epinephrine)
Synthase SYN
 Path
Enzymes Activates Inhibits
way
G6P
Hexokinas
GLY
e
Isocitrate ADP (lowers Km for NADH, ATP
Dehydrog TCA isocitrate), NAD+
enase
Lactate
FER
Dehydrog
M
enase
PEP
Carboxyki GLU
nase
AMP, ADP ATP, Citrate
Phosphofr
GLY
uctokinase
Pyruvate Acetyl-CoA, ATP
Carboxyla GLU
se
Pyruvate Pyruvate, NAD+, CoA, ATP, NADH, Acetyl-CoA,
Dehydrog Dephosphorylation Phosphorylation
TCA
enase
Complex
AMP, F-1,6-B ATP, Acetyl-CoA, Alanine
Pyruvate
GLY
Kinase
Ribonucle
NUC
otide
SYN
Reductase
Thioredox NUC
in SYN
Thioredox
NUC
in
SYN
Reductase
Regulation of glycolysis

hexokinase: is inhibited by glucose-6-P (product inhibition)

phosphofructokinase: is inhibited by ATP and citrate (which signals the abundance of citric acid cycle
intermediates). Probably this mechanism prevents the cell from using all its ATP stock in the phosphofrutokinase
reaction, which would prevent glucose activation by hexokinase. It is stimulated by its substrate (fructose-6-
phosphate), AMP and ADP (which signal the lack of available energy), etc.

pyruvate kinase: inhibited by ATP, alanine, free fatty acids and acetyl-CoA. Activated by fructose-1,6-bisphosphate
and AMP

Regulation of gluconeogenesis

Flow is regulated in the gluconeogenesis-specific reactions.

Pyruvate carboxilase is activated by acetyl-CoA, which signals the abundance of citric acid cycle intermediates, i.e.,
a decreased need of glucose.

Regulation of the citric acid cycle

The citric acid cycle is regulated mostly by substrate availability, product inhibition and by some cycle
intermediates.

pyruvate dehydrogenase: is inhibited by its products, acetyl-CoA and NADH

citrate synthase: is inhibited by its product, citrate. It is also inhibited by NADH and succinyl-CoA (which signal
the abundance of citric acid cycle intermediates).

isocitrate dehydrogenase and a-ketoglutarate dehydrogenase: like citrate synthase, these are inhibited by NADH
and succinyl-CoA. Isocitrate dehydrogenase is also inhibited by ATP and stimulated by ADP. All aforementioned
dehydrogenases are stimulated by Ca2+. This makes sense in the muscle, since Ca2+ release from the sarcoplasmic
reticulum triggers muscle contraction, which requires a lot of energy. This way, the same "second messenger"
activates an energy-demanding task and the means to produce that energy.

Regulation of the urea cycle

Carbamoyl-phosphate sinthetase is stimulated by N-acetylglutamine, which signals the presence of high amounts of
nitrogen in the body.

Regulation of glycogen metabolism

Liver contains a hexokinase (hexokinase D or glucokinase)with low affinity for glucose which (unlike "regular"
hexokinase) is not subject to product inhibition. Therefore, glucose is only phosphrylated in the liver when it is
present in very high concentrations (i.e. after a meal). In this way, the liver will not compete with other tissues for
glucose when this sugar is scarce, but will accumulate high levels of glucose for glycogen synthesis right after a
meal.

Regulation of fatty acids metabolism

Acyl-CoA movement into the mitochondrion is a crucial factor in regulation. Malonyl-CoA (which is present in the
cytoplasm in high amounts when metabolic fuels are abundant) inhibits carnitine acyltransferase, thereby preventing
acyl-CoA from entering the mitochondrion. Furthermore, 3-hydroxyacyl-CoA dehydrogenase is inhibited by NADH
and thiolase is inhibited by acetyl-CoA, so that fatty acids wil not be oxidized when there are plenty of energy-
yielding substrates in the cell.
Regulation of the pentose phosphate pathway

Metabolic flow through the pentose phosphate pathway is controled by the activity of glucose-6-phosphate
dehydrogenase, which is controlled by NADP+ availability.

Metabolic profiles of key tissues

Brain

Usually neurons use only glucose as energy source. Since the brain stores only a very small amount of glycogen, it
needs a steady supply of glucose. During long fasts, it becomes able to oxidize ketone bodies.

Liver

The maintenance of a fairly steady concentration of glucose in the blood is one of the liver's main functions. This is
accomplished through gluconeogenesis and glycogen synthesis and degradation. It synthesizes ketone bodies when
acetyl-CoA is plenty. It is also the site of urea synthesis.

Adipose tissue

It synthesizes fatty acids and stores them as triacylglycerols. Glucagon activates a hormone-sensitive lipase, which
hydrolizes triacylglycerols yielding glycerol and fatty acids. These are then released into the bloodstream in
lipoproteins.

Muscle

Muscles use glucose, fatty acids, ketone bodies and aminoacids as energy source. It also contains a reserve of
creatine-phosphate, a compound with a high phosphate-transfer potential that is able to phosphorilate ADP to ATP,
thereby producing energy without using glucose. The amount of creatine in the muscle is enough to sustain about 3-
4 s of exertion. After this period, the muscle uses glycolysis, first anaerobically (since it is much faster than the citric
acid cycle), and later (when the increased acidity slows phosphofrutokinase enough for the citric acid cycle to
become non-rate-limiting) in aerobic conditions.

Kidney

It can perform gluconeogenesis and release glucose into the bloodstream. It is also responsible for the excretion of
urea, electrolytes, etc. Metabolic acidosis may be increased by the action of the urea cycle, since urea synthesis
(which takes place in the liver) uses HCO3-, thereby further lowering blood pH. Under these circunstances, nitrogen
may be eliminated by the joint action of kidney and liver: excess nitrogen is first incorporated in glutamine by
glutamine synthetase. Kidney glutaminase then cleaves glutamine in glutamate e NH3, which the kidney
immediately excretes. This process allows nitrogen excretion without affecting blood bicarbonate levels.

Hormone control

Hormone control is mainly effected through the action of two hormones synthesized by the pancreas: insulin and
glucagon. Insulin is released by the pancreas when blood glucose levels are high, i.e., after a meal. Insulin stimulates
glucose uptake by the muscle, glycogen synthesis, and triacylglyceride synthesis by the adipose tissue. It inhibits
gluconeogenesis and glycogen degradation. Glucagon is released by pancreas when blood glucose levels drop too
much. Its effects are opposite those of insulin: in liver, glucagon stimulates glycogen degradation and the absorption
of gluconeogenic aminoacids. It inhibits glycogen synthesis and promotes the release of fatty acids by adipose
tissue.
PENTOSE PHOSPHATE PATHWAY
Enzymes in cytosol of liver & adipose, absent in muscle (G6P -> G)
Oxidative: NADPH

R5P: Rev NonOx - (2)F6P+G3P->(3)R5P

NADPH: Recycle R5P -> G3P + F6P
NADPH&ATP: PPP&Glycolysis

Fate of G6P
Phosphofructokinase: Low energy
G6P dehydrogenase: Inhibited by NADPH & Acetyl-CoA (biosynthetic needs are met)

KETONE BODIES:
Most Acetyl-CoA -> TCA
Some converted to acetone, acetoacetate (ketone bodies)
Ketone bodies synthesized primarily in liver, but imp as fuel for tissues (brain, heart, skeletal muscle)
Synthesized in mitochondrial matrix

2 Acetyl-CoA condensed -> Acetoacetyl-CoA + CoA

Acetate group (from another Acetyl-CoA) added -> HMG-CoA
Acetoacetate cleaved
Acetoacetate reduced to beta-hydroxybutyrate

Acetoacetate & beta-HDB transport from liver through blood

Ketone body easy way to transport FA w/o using serum albumin or other FA binding proteins as
transporter

Diabetes: Lack of insulin, glucose not transported to cells results in gluconeogenesis which uses
oxaloacetate, breakdown of fat produces a lot Acetyl-CoA, but low level of oxaloacetate no TCA

GLYCOGEN:
Glycogen phosphorylase
+(a) high AMP, phosphorylaion
-(b) high glucose, dephosphorylation

Glycogen synthase
+(a) dephosphorylated (G6P no effect), insulin (liver&muscle)
-(b) phosphorylated (activated by G6P)

Blood glucose rise - insulin

Increase in glucose transport & G -> G6P
Phosphorylation & inactivation of GSK3
Stimulates PP1

Low blood glucose - glucagon & epinephrine

Activates phosphorylase kinase (phosphorylates GlyPho & GlySyn)
Ez: Glycogen phosphorylase breaks glycogen from nonreducing end -> g-1-p + glycogen (n-1)
Breaks 1,4 bonds stops 4 residues away from branch, leftover branched strands are limit dextrins

Synthesis: Activation - G1P + UTP -> UDP-G + pyroP

PyroP + 2H2O -> 2Pi Ez: UDP-G pyrophosphorylase

First 4 G residues joined to protein glycogenin, units added by enzyme glycogen synthase. Transfers G
from UDP-G to C4 at nonreducing end

FATTY ACID SYNTHESIS

*Committed step of F.A.S.
Acetyl-CoA + CO2 + ATP -> Malonyl-CoA + ADP
Enzyme: Acetyl-CoA Carboxylase
+ Citrate. Dephosphorylation (insulin)
- Fatty acyl-CoA. Phosphorylation (glucagon)

Malonyl-CoA + Acetyl-CoA + 2NADPH + 2H -> 4C-Fatty Acid + 2NADP+ + CO2

*Cytosol
*CoE: NADP+/NADPH
*Acyl Carrier Protein

Malonyl-CoA inhibits FAO by preventing fatty acyl-CoA from entering mitochondria.

Higher level of Malonyl-CoA stimulates FAS

Enzyme: Fatty acid synthase (chain)

Cytosolic Acetyl-CoA - Amino acid degradation

Mitochondrial Acetyl-CoA - Glycolysis, FA oxidation

Acetyl-CoA + Oxaloacetate -> Citrate: mitochondria --> cytosol: Citrate -> Acetyl-CoA + Oxaloacetate
by ATP-citrate lyase
-oxaloacete can convert to pyruvate or malate and back to mitochondrial matrix

Cytosolic NADPH
1. PPP
2. Oxaloacetate + NADH + H -> Malate + NAD+
THEN Malate + NADP+ -> pyruvate + CO2 + NADPH + H

HDL/LDL in blood indicative of arterial plaque development

FATTY ACID OXIDATION

Tricylglycerol lipase - break down stored triacylglycerols
+Glucagon inadipocytes

Mitochondria

*Activation
FA + CoA + (2)ATP -> Fatty acyl-CoA
Ez: Acyl-CoA synthetase
Short/Med: In mitochondria
Long: Activated outside, convert to O-acylcarnitine bycarnitine acyl transferase I, transported through
inner membrane by translocase, O-acylcarnitine -> acyl-CoA by carnitine acryltransferase II.

*Beta-Ox - Even
Fatty acyl-CoA + FAD + NAD+ -> FADH2 + NADH + Fatty acyl-CoA + Acetyl-CoA

*Beta-Ox - Odd
Product: Acetyl-CoA + Propionyl-CoA

Propionyl-CoA + ATP -> Succinyl-CoA

Monounsaturated: Isomerase
Polyunsaturated: Isomerase + Reductase (reduce bond w/ NADPH)

AMINO ACID SYNTHESIS

Plants - Nitrogen Assimilation:
NO3- + 2H + 2e -> NO2- + H2O
NO2- + 8H + 6e -> NH4+ + 2H2O
Enz: Reductase

Bacteria - Nitrogen fixation:

N2 + 10H + 8e -> 2NH4+ + H2
Enz: Nitrogenase

Get NH4+ into cells

1.NH4 + a-KG + NADPH + H -> glutamate + NADP + H2O
Enzyme: GDH

2.Glutamate + NH4 + ATP -> glutamine + ADP + P

Enzyme: Glutamine synthetase

Source of intermediates
a-KG, Asp, Pyruvate, 3-P, PEP&E4P

a-KG -> Glu -> Gln / Pro / Arg

Asp: Asp -> Asn / Met(E) / Lys(E) / Thr -> Isl(E)
Pyruvate: Pyruvate -> Ala / Val (E) / Leu (E)
PEP&E4P: PEP&E4P -> Phenylala(E) / Tyr (E) / Trypt(E)
Chorismate is key intermediate for Phenylalanine or Tyrosine

Regulated by feedback inhibition. Final product inhibits enzyme for committed step

AMINO ACID BREAKDOWN

AA breakdown
1. Amino group removed
2. Carbon skeleton metabolized to glucose, TCA intermediate or Acetyl-CoA
Intermediates: pyruvate, a-KG, succinyl-CoA, fumarate, oxaloacetate, Acetyl-CoA, Acetoacetyl-CoA
(Gly, TCA, FAO)

a-AA + a-KG -> a-KA + glutamate

Enzyme: Aminotransferase
Glutamate + NAD+ + H2O -> a-KG + NADH + NH4+
Enzyme: glutamate dehydrogenase (GDH)

Ketogenic
Leucine ->-> Acetyl-CoA + acetoacetate
Lysine -> acetoacetyl-CoA

PURINES
R5P + ATP -> PRPP + AMP
Enzyme
(-) ADP, GDP
PRPP is rate limiting in purine syn

PRPP -> phosphoribosyl-beta-amine

Enzyme: Glutamine PRPP amino transferase
'A site' (-) AMP, ADP, ATP
'G site' (-) GMP, GDP, GTP

PRPP -> IMP (+10 rxn, +5 ATP)

IMP -> AMP, EZ (-) by AMP. GTP provides energy for AMP synthesis

De novo synthesized AMP & GMP -> ATP & GTP by sucessive phosphorylation

AMP + ATP -> 2ADP (adenylate kinase)

ADP -> ATP (oxidative phosphorylation)

GMP + ATP -> GDP + ADP (guanylate kinase)

GDP + ATP -> GTP + ADP (nucleoside disphosphate kinase)

Nucleic acid degraded in cell are salvaged.

Bases adenine, guanine, hypoxanthine(base in IMP) by
Base + PRPP <-> nucleoside-5-phosphate + PPi
by phosphoribotransferases (APRT and HGPRT)
Acts on base to form AMP, GMP and IMP

Dietary purines -> uric acid.

Purine base released from sugar by PNP, guanine or hypoxanthine -> xanthine (by guanine deaminase or
xanthine oxidase)
xanthine -> uric acid (xanthine oxidase)

Absence of enzyme that turn dietary purine to uric acid.

deoxyadenosine not converted to uric acid, salvaged and dATP higher than normal
dATP feedback inhibitor of deoxynucleotide synthesis. DNA won't replicate and divide

Missing salve enzyme (HGPRT). No salvage, purine de novo increases, dietary purine converts to uric
acid
symptoms: elevated PRPP, purine denovo syn & uric acid

PYRIMIDINE
Pyrimidine synthesis
1. Carbamoyl phosphate + aspartate
2. PRPP added -> OMP
3. CO2 removed from OMP -> UMP

UMP + ATP -> UDP + ADP (UMP kinase)

(-) UDP, UTP
(+) PRPP, ATP
UDP + ATP -> UTP + ADP (nucleoside diphosphate kinase)
UTP animated at position 6 -> CTP (CTP synthetase using glutamine as amine donor)

DEOXYRIBONUCLEOTIDE
Ribonucleotide reduction by ribonucleotide reductase -> deoxyribonucleotides

Enzyme: ribonucleotide reductase

Substrate specificity site: ATP, dATP, dGTP, dTTP

Overall activity site: ATP, dATP
Active site: ADP, CDP, DP, GDP
(+) ATP bound, active
(-) dATP bound, inactive

Proteins: thioredoxin and thioredoxin reductase

Transfer reducing equivalents from NADPH to enzyme

Overall activity site regulated to need of dNTP