System Simulation and Modelling with types and Event Scheduling
1 handout biokimia lanjut. p.ukun
1. INTEGRATION OF
METABOLISM
Metabolism consists of catabolism
and anabolism
Catabolism: degradative pathways
– Usually energy-yielding!
Anabolism: biosynthetic pathways
– energy-requiring!
2. Catabolism and
Anabolism
Catabolic pathways converge to a few end
products
Anabolic pathways diverge to synthesize
many biomolecules
Some pathways serve both in catabolism
and anabolism
Such pathways are amphibolic
3. Organization in Pathways
Pathways consist of sequential steps
The enzymes may be separate
Or may form a multienzyme complex
Or may be a membrane-bound system
New research indicates that multienzyme
complexes are more common than once
thought
5. Organization of Pathways
Linear
(product of rxns are
substrates for subsequent
rxns)
Closed Loop
(intermediates recycled)
Spiral
(same set of enzymes used
repeatedly)
6. Themes in Metabolic
Regulation
• Allosteric regulation
• Covalent modification
• Control of enzyme levels
• Compartmentalization
• Metabolic specialization of organs
7. Allosteric Regulation
End products are often inhibitors
Allosteric modulators bind to site other than
the active site
Allosteric enzymes usually have 4o structure
Vo vs [S] plots give sigmoidal curve for at
least one substrate
Can remove allosteric site without effecting
enzymatic action
8. Regulation of Enzyme Activity
(biochemical regulation)
1st committed step of a biosynthetic pathway or
enzymes at pathway branch points often regulated
by feedback inhibition.
Efficient use of biosynthetic precursors and
energy
B A C
1 3”
3’
2
E F G
4’ 5’
H I J
4” 5”
X
X
9. Vo vs [S] plots give sigmoidal curve
for at least one substrate
Binding of allosteric inhibitor or activator does not effect Vmax, but
does alter Km
Allosteric enzyme do not follow M-M kinetics
11. Allosteric T to R transition
Concerted model Sequential model
ET-I ET ER ER-S
I
I S
S
12. Allosteric modulators bind to site other than
the active site and allosteric enzymes have 4o
structure
Fructose-6-P + ATP -----> Fructose-1,6-bisphosphate + ADP
ADP
Allosteric Activator (ADP) binds
distal to active site
13. Regulation of Hexose Transporters
Intra-cellular [glucose] are much lower than
blood [glucose].
Glucose imported into cells through a
passive glucose transporter.
Elevated blood glucose and insulin levels
leads to increased number of glucose
transporters in muscle and adipose cell
plasma membranes.
14. Covalent Modification
• Covalent modification of last step in
signal transduction pathway
• Allows pathway to be rapidly up or down
regulated by small amounts of triggering
signal (HORMONES)
• Last longer than do allosteric regulation
(seconds to minutes)
• Functions at whole body level
15. Covalent modification
•Regulation by covalent modification is
slower than allosteric regulation
•Reversible
•Require one enzyme for activation and one
enzyme for inactivation
•Covalent modification freezes enzyme T or
R-conformation
16. Phosphorylation/dephosphorylation
•Most common covalent modification
•Involve protein kinases/phosphatase
•PDK inactivated by phosphorylation
•Amino acids with –OH groups are
targets for phosphorylation
•Phosphates are bulky (-) charged
groups which effect conformation
17. Enzyme Levels
• Amount of enzyme determines rates of
activity
• Regulation occurs at the level of gene
expression
• Transcription, translation
• mRNA turnover, protein turnover
• Can also occur in response to hormones
• Longer term type of regulation
18. Regulation of Gene Expression
AAAAAA5’CAP
mRNA
RNA Processing
RNA Degradation
Protein DegradationPost-translational
modification
Active
enzyme
21. Specialization of Organs
• Regulation in higher eukaryotes
• Organs have different metabolic roles
i.e. Liver = gluconeogenesis,
Muscle = glycolysis
• Metabolic specialization is the result of
differential gene expression
22. Brain
• Glucose is the primary fuel for the brain
• Brain lacks fuel stores, requires constant supply
of glucose
• Consumes 60% of whole body glucose in resting
state. Required too maintain Na and K
membrane potential in of nerve cells
• Fats can’t serve as fuel because blood brain
barrier prevents albumin access.
• Under starvation can ketone bodies used.
23. Muscle
• Glucose, fatty acids and ketone bodies are fuels
for muscles
• Muscles have large stores of glycogen (3/4 of
body glycogen in muscle)
• Muscles do not export glucose (no glucose-6-
phosphatase)
• In active muscle glycolysis exceeds citric acid
cycle, therefore lactic acid formation occurs
• Cori Cycle required
25. Muscle
• Muscles can’t do urea cycle. So excrete
large amounts of alanine to get rid of
ammonia (Glucose Alanine Cycle)
• Resting muscle uses fatty acids to meet
85% of energy needs
26. Heart Muscle
• Heart exclusively aerobic and has no
glycogen stores.
• Fatty acids are the hearts primary fuel
source. Can also use ketone bodies.
Doesn’t like glucose
27. Liver
• Major function is to provide fuel for the
brain, muscle and other tissues
• Metabolic hub of the body
• Most compounds absorb from diet must
first pass through the liver, which
regulates blood levels of metabolites
28. Liver: carbohydrate
metabolism
• Liver removes 2/3 of glucose from the blood
• Glucose is converted to glucose-6-phosphate
(glucokinase)
• Liver does not use glucose as a fuel. Only as a
source of carbon skeletons for biosynthetic
processes.
• Glucose-6-phosphate goes to glycogen (liver
stores ¼ body glycogen)
29. Liver: lipid metabolism
• Excess glucose-6-phosphate goes to glycolysis to
form acetyl-CoA
• Acetyl-CoA goes to form lipids (fatty acids
cholesterol)
• Glucose-6-phosphate also goes to PPP to
generate NADH for lipid biosynthesis
• When fuels are abundant triacylglycerol and
cholesterol are secreted to the blood stream in
LDLs. LDLs transfer fats and cholesterol to
adipose tissue.
• Liver can not use ketone bodies for fuel.
30. Liver: protein/amino acid
metabolism
• Liver absorbs the majority of dietary amino
acids.
• These amino acids are primarily used for protein
synthesis
• When extra amino acids are present the liver or
obtained from the glucose alanine cycle amino
acids are catabolized
• Carbon skeletons from amino acids directed
towards gluconeogenesis for livers fuel source
31. Adipose Tissue
Enormous stores of Triacyglycerol
Fatty acids imported into adipocytes from
chylomicrons and VLDLs as free fatty acids
Once in the cell they are esterified to
glycerol backbone.
Glucagon/epinephrine stimulate reverse process
32.
33. Well-Fed State
• Glucose and amino acids enter blood stream,
triacylglycerol packed into chylomicrons
• Insulin is secreted, stimulates storage of fuels
• Stimulates glycogen synthesis in liver and
muscles
• Stimulates glycolysis in liver which generates
acetyl-CoA for fatty acid synthesis
34. Refed State
• Liver initially does not absorb glucose, lets
glucose go to peripheral tissues, and stays in
gluconeogenesis mode
• Newly synthesized glucose goes to replenish
glycogen stores
• As blood glucose levels rise, liver completes
replenishment of glycogen stores.
• Excess glucose goes to fat production.
41. GLIKOLISIS
Glikolisis terdiri dari 2 fase:
Fase preparasi (preparatory phase), yaitu
fosforilasi glukosa dan konversinya
menjadi gliseraldehid 3-fosfat.
Fase pembayaran (payoff phase), yaitu
konversi oksidatif gliseraldehid 3-P
menjadi piruvat disertai pembentukan ATP
dan NADH.
44. • Seven steps of glycolysis are
retained
• Three steps are replaced
• The new reactions provide for a
spontaneous pathway (G
negative in the direction of
sugar synthesis), and they
provide new mechanisms of
regulation
46. Regulation of Hexokinase
Glucose-6-phosphate is an allosteric inhibitor of
hexokinase.
Levels of glucose-6-phosphate increase when down
stream steps are inhibited.
This coordinates the regulation of hexokinase with
other regulatory enzymes in glycolysis.
Hexokinase is not necessary the first regulatory
step inhibited.
47. Regulation of PhosphoFructokinase (PFK-1)
PKF-1 has quaternary structure
Inhibited by ATP and Citrate
Activated by AMP and Fructose-2,6-
bisphosphate
Regulation related to energy status of cell.
50. Regulation of fructose 1,6-bisphosphatase-1 (FBPase-1)
and phosphofructokinase-1 (PFK-1)
51. Regulation of PFK by
Fructose-2,6-bisphosphate
• Fructose-2,6-bisphosphate is an allosteric activator of PFK in
eukaryotes, but not prokaryotes
•Formed from fructose-6-phosphate by PFK-2
•Degraded to fructose-6-phosphate by fructrose 2,6-
bisphosphatase.
•In mammals the 2 activities are on the same enzyme
•PFK-2 inhibited by Pi and stimulated by citrate
52. Regulation of Pyruvate Kinase
Allosteric enzyme
Activated by Fructose-1,6-bisphosphate
(example of feed-forward regulation)
Inhibited by ATP
When high fructose 1,6-bisphosphate present
plot of [S] vs Vo goes from sigmoidal to
hyperbolic.
Increasing ATP concentration increases Km for
PEP.
In liver, PK also regulated by glucagon. Protein
kinase A phosphorylates PK and decreases PK
acitivty.
54. Deregulation of Glycolysis in Cancer Cells
Glucose uptake and glycolysis is ten times faster in
solid tumors than in non-cancerous tissues.
Tumor cells initally lack connection to blood supply
so limited oxygen supply
Tumor cells have fewer mitochondrial, depend more
on glycolysis for ATP
Increase levels of glycolytic enzymes in tumors
(oncogene Ras and tumor suppressor gene p53
involved)
55. Gluconeogenesis
• Synthesis of "new glucose" from common
metabolites
• Humans consume 160 g of glucose per day
• 75% of that is in the brain
• Body fluids contain only 20 g of glucose
• Glycogen stores yield 180-200 g of glucose
• The body must still be able to make its own
glucose
56. Gluconeogenesis
• Occurs mainly in liver and kidneys
• Not the mere reversal of glycolysis
for 2 reasons:
– Energetics must change to make
gluconeogenesis favorable (delta G of
glycolysis = -74 kJ/mol
– Reciprocal regulation must turn one
on and the other off - this requires
something new!
57. • Seven steps of glycolysis
are retained
• Three steps are
replaced
• The new reactions
provide for a
spontaneous pathway
(G negative in the
direction of sugar
synthesis), and they
provide new
mechanisms of
regulation
58. Regulation of Gluconeogenesis
• Reciprocal control with glycolysis
• When glycolysis is turned on,
gluconeogenesis should be turned off
• When energy status of cell is high,
glycolysis should be off and pyruvate, etc.,
should be used for synthesis and storage of
glucose
• When energy status is low, glucose should
be rapidly degraded to provide energy
• The regulated steps of glycolysis are the
very steps that are regulated in the reverse
direction!
59. Transaminasi
The first of the
bypass reactions
in gluconeogenesis
is the conversion
of pyruvate to
Phosphoenolpyruvate
(PEP)
Conversion of Pyruvate
to
Phosphoenolpyruvate
Requires
Two Exergonic
Reactions
61. Pyruvate Carboxylase
• The reaction requires ATP and bicarbonate as
substrates
• Biotin cofactor
• Acetyl-CoA is an allosteric activator
• Regulation: when ATP or acetyl-CoA are high,
pyruvate enters gluconeogenesis
62. PEP Carboxykinase
• Lots of energy needed to drive this reaction!
• Energy is provided in 2 ways:
– Decarboxylation is a favorable reaction
– GTP is hydrolyzed
• GTP used here is equivalent to an ATP
63. PEP Carboxykinase
Not an allosteric enzyme
Rxn reversible in vitro but irreversible in vivo
Activity is mainly regulated by control of
enzyme levels by modulation of gene
expression
Glucagon induces increased PEP carboxykinase
gene expression
65. Glucose-6-Phosphatase
• Presence of G-6-Pase in ER of liver and kidney cells makes
gluconeogenesis possible
• Muscle and brain do not do gluconeogenesis
• G-6-P is hydrolyzed as it passes into the ER
• ER vesicles filled with glucose diffuse to the plasma membrane,
fuse with it and open, releasing glucose into the bloodstream.
66. Regulation of Gluconeogenesis
• Reciprocal control with glycolysis
• When glycolysis is turned on, gluconeogenesis
should be turned off
• When energy status of cell is high, glycolysis
should be off and pyruvate, etc., should be used
for synthesis and storage of glucose
• When energy status is low, glucose should be
rapidly degraded to provide energy
• The regulated steps of glycolysis are the very steps
that are regulated in the reverse direction!
67. •Metabolites other than
pyruvate can enter
gluconeogenesis
•Lactate (Cori Cycle)
transported to liver for
gluconeogenesis
•Glycerol from Triacylglycerol
catabolism
•Pyruvate and OAA from
amino acids (transamination
rxns)
•Malate from glycoxylate cycle
-> OAA -> gluconeogenesis
68.
69. The Metabolism of Glycogen in
Animals
Glycogen granules in a hepatocyte
70. Hormonal Regulation of Glycogen Metabolism
Insulin
Secreted by pancreas under high blood [glucose]
Stimulates Glycogen synthesis in liver
Increases glucose transport into muscles and adipose
tissues
Glucagon
Secreted by pancreas in response to low blood [glucose]
Stimulates glycogen breakdown
Acts primarily in liver
Ephinephrine
Secrete by adrenal gland (“fight or flight” response)
Stimulates glycogen breakdown.
Increases rates of glycolysis in muscles and release of
glucose from the liver
71. Metabolism of Tissue Glycogen
• But tissue glycogen is an important energy reservoir - its
breakdown is carefully controlled
• Glycogen consists of "granules" of high MW
• Glycogen phosphorylase cleaves glucose from the nonreducing
ends of glycogen molecules
• This is a phosphorolysis, not a hydrolysis
• Metabolic advantage: product is a sugar-P - a "sort-of" glycolysis
substrate
72. •Glycogen phosphorylase cleaves
glycogen at non-reducing end to
generate glucose-1-phosphate
•Debranching of limit dextrin occurs
in two steps.
•1st, 3 X 1,4 linked glucose residues are
transferred to non-reducing end of
glycogen
•2nd, amylo-1,6-glucosidase cleaves 1,6
linked glucose residue.
•Glucose-1-phosphate is converted to
glucose-6-phosphate by
phosphoglucomutase
73. The catabolic pathways:
from glycogen to glucose 6-phosphate
(glycogenolysis) and
from glucose 6-phosphate to pyruvate (glycolysis)
The anabolic pathways:
from pyruvate to glucose (gluconeogenesis) and
from glucose to glycogen (glycogenesis)
76. Glycogen Synthase
• Forms -(1 4) glycosidic bonds in glycogen
• Glycogen synthesis depends on sugar nucleotides UDP-Glucose
• Glycogenin (a protein!) protein scaffold on which glycogen
molecule is built.
• Glycogen Synthase requires 4 to 8 glucose primer on Glycogenin
(glycogenein catalyzes primer formation)
• First glucose is linked to a tyrosine -OH
• Glycogen synthase transfers glucosyl units from UDP-glucose to C-
4 hydroxyl at a nonreducing end of a glycogen strand.
77. Branch synthesis in glycogen: The glycogen-branching enzyme
(also called amylo (1→4) to (1→6) transglycosylase or glycosyl-
(4→6)-transferase)
78. Coordinated Regulation of Glycogen
Synthesis and Breakdown
Glycogen Phosphorylase Is Regulated
Allosterically and Hormonally
Glycogen Synthase Is Also Regulated by
Phosphorylation and Dephosphorylation
79. Control of Glycogen Metabolism
• A highly regulated process, involving
reciprocal control of glycogen phosphorylase
(GP) and glycogen synthase (GS)
• GP allosterically activated by AMP and
inhibited by ATP, glucose-6-P and caffeine
• GS is stimulated by glucose-6-P
• Both enzymes are regulated by covalent
modification - phosphorylation
87. Lipoproteins
Transport water insoluble
TAG, cholesterol and
cholesterol-esters
throughout circulatory
system
Hydrophobic core
containing TAG and
cholesterol-esters
Hydrophillic surface made
of proteins (apoproteins)
and phospholipids)
88. Common membrane phospholipids
P
O
OO
O
H
CH2
H
CH2C
O O
C C OO
R1 R2
P
O
OO
O
CH2
CH2
H
CH2C
O O
C C OO
R1 R2
CH2
NH3
P
O
OO
O
CH2
CH2
H
CH2C
O O
C C OO
R1 R2
CH2
NH3
COO
P
O
OO
O
CH2
CH2
H
CH2C
O O
C C OO
R1 R2
CH2
NH3C CH3
CH3
Phosphatidate Phosphatidylethanolamine Phosphatidylserine Phosphatidylcholine
89.
90.
91. Fatty acids and MAG enter mucosal cells where
they are used to re-synthesize TAG
TAG is then packaged into lipoprotein transport
particles called chylomicrons (lipoprotein).
Chylomicrons are mainly composed of TAG and
apoprotein B-48. Also contain fat solubel vitamins
Chylomicrons enter the lymph system and then the
blood stream.
Chylomicrons bind to membrane bound lipoprotein
lipases at the surface of adipose and muscle cells.
92.
93.
94.
95.
96.
97.
98.
99. Lipoproteins
Several different classes of lipoproteins.
Chylomicrons deliver dietary fats to tissues
VLDL, IDL and LDL transport endogenously
synthesized TAG and cholesterol to tissues
HDLs remove cholesterol from serum and tissues and
transports it back to the liver.
VLDL, IDL, LDL, and HDL named based on their
density. Low density lipoproteins have high lipid to
protein ratios. High density lipoproteins have low lipid
to protein ratios.
100. Lipoproteins
Lipases in capillaries of adipose and muscle
tissues degrade TAG in VLDLs. VLDLs
become IDLs.
IDLs can then give up more lipid and
become LDLs.
LDLs are rich in cholesterol and
cholesterol-esters.
101. Apolipoproteins
VLDLs, IDLs, and LDLs all contain a large
monomeric protein called ApoB-100.
ApoB-100 forms amphipathic crust on lipoprotein
surface.
Chylomicrons contain analogous lipoprotein ApoB-
48.
VLDLs and IDLs also possess a number of small
weakly associated proteins that disassociate
during lipoprotein degradation.
Small apolipoproteins function to modulate the
activity of enzymes involved in lipid mobilization
and interactions with cell surface receptors.
102.
103. LDL Receptor
Binds to ApoB-100.
Found on cell surface of many cell types
Mediates delivery of cholesterol by inducing
endocytosis and fusion with lysosomes.
Lysosomal lipases and proteases degrade the LDL.
Cholesterol then incorporates into cell membranes
or is stored as cholesterol-esters.
104.
105.
106.
107. High LDL levels can lead to
cardiovascular disease.
LDL can be oxidized to form oxLDL
oxLDL is taken up by immune cells called
macrophages.
Macrophages become engorged to form foam cells.
Foam cells become trapped in the walls of blood
vessels and contribute to the formation of
atherosclerotic plaques.
Causes narrowing of the arteries which can lead to
heart attacks.
109. Absence of LDL Receptor Leads to
Hypercholesteremia and Atherosclerosis
Persons lacking the LDL receptor suffer from
familial hypercholesterolemia
Result of a mutation in a single autosomal gene
Total plasma cholesterol and LDL levels are
elevated.
Homozygous individuals have cholesterol levels
of 680 mg/dL. Heterozygous individuals = 300
mg/dL. Healthy person = <200 mg/dL.
Most homozygous individuals die of
cardiovascular disease in childhood.
110. LDLs/HDLs and Cardiovascular Disease
LDL/HDL ratios are used as a diagnostic tool for
signs of cardiovascular disease
LDL = “Bad Cholesterol”
HDL = “Good Cholesterol”
A good LDL/HDL ratio is 3.5
Protective role of HDL not clear.
An esterase that breaks down oxidized lipids is
associated with HDL. It is possible (but not
proven) that this enzyme helps destroy oxLDL
