1

TYPE 2
DIABETES MELLITUS
BIOCHEMISTRY PORTFOLIO

KRISTEL DANA A. BADUA

University of the East
Ramon Magsaysay Memorial Medical Center
College of Medicine SY 2017-2018
Department of Biochemistry
Submitted to: Dra. Donato
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TABLE OF CONTENTS

I. Introduction…………………………………………………………………………….3
II. Type 2 Diabetes Mellitus……………………………………………………………..3
III. Case…………………………………………………………………………………….4
IV. Hormonal Regulation………………………………………………………………….6
V. Carbohydrate Metabolism…………………………………………………………....8
VI. Lipid Metabolism………………………………………………………………………17
VII. Protein Metabolism……………………………………………………………………26
VIII. Nucleic Acid Metabolism………………………………………………………….30
IX. Gene Expression………………………………………………………………………32
X. Integration of all Macromolecules……………………………………………………33
XI. Action of Insulin, Primary Manifestations, and Treatment of DM 2………..……..35
XII. Reflection……………………………………………………………………………….36
XIII. Evidences……………………………………………………………………………38
XIV. Appendices………………………………………………………………………….46
XV. References……………………………………………………………………………..47
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I. INTRODUCTION
I thought long and hard about the topic I would want to work on in
this portfolio. I wanted something interesting yet at the same time
something close to my heart. Then and there I thought about my
loving father. He suffered stroke 7 years ago and our family was
deeply devastated. Although he is well again now, he was never like
before.

Many people with stroke have other problems or conditions which

put them at higher risk such as hypertension, heart disease, smoking,
or diabetes [1]. My father has Type 2 Diabetes Mellitus, I aspire to
research more about it in the hopes that I can contribute to the
improvement of his quality of life.

Diabetes is a metabolic disorder characterized by

hyperglycemia (high blood glucose levels). Most of the food we eat
is broken down into glucose to give us energy. In order for glucose to
actually enter cells and provide energy, it needs a hormone called
insulin. Insulin In people who have diabetes, the pancreas does not
make insulin (Type 1 diabetes), or it makes too little insulin or the
cells in the muscles, liver and fat do not use insulin the right way
(Type 2 diabetes) [2].

What happens then is people with diabetes end up with too much
glucose in their blood, while their cells don’t receive enough energy.
Over time, this glucose can lead to increased fatty deposits or
clots on the insides of the blood vessel walls. These clots can
narrow or block the blood vessels in the brain or neck, cutting off the
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blood supply, stopping oxygen from getting to the brain and causing a
stroke [2].

II. CASE

Figure 1. Current Photo of my Father

Patient R.B. is a 57 year old male who suffered stroke seven years ago.
Worried that his health is further compromised by his Type 2 Diabetes Mellitus,
he was referred by his family to Jecsons Medical Center for further assessment
on his current state.

Past Medical History:

 Stroke or Transient Ischemic Attack
 He denies polyuria, polydipsia, and blurred vision

Current Medications:
 Aspirin
 Zynapse
 Metformin
 Insulin Glargine (Lantus ®)

Personal/ Social History:

 Doctor by profession, limited exercise
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 Non-smoker
 Non-alcoholic drinker

Family History: NON-REMARKABLE

Physical Examination:
 General Survey: no cardiopulmonary distress
 BP: 120/80  RR: 15/min
 HR: 76/min  T: 37°C
 Weight: 145 lbs; Height: 5’8”; BMI: 22 kg/m (normal)
2

Review of Systems: NON-REMARKABLE

Lab Results:

 Glucose (random): 170.96 mg/dl (normal range: <140 mg/dL)

 Creatinine: 1.11 mg/dl (normal range: 0.70–1.20 mg/dL)
 Sodium: 136 mg/dl (normal range: 135–155 meq/L)
 Potassium: 4.3 mg/dl (normal range: 3.40–5.60 mg/dl)
 Lipid panel:
 Total cholesterol: 151.54 mg/dl (normal: 150-200 mg/dl)
 HDL cholesterol: 36.15 mg/dl (normal: <64.61 mg/dl)
 LDL cholesterol: 71.54 mg/dl (normal: <99.61 mg/dl)
 Triglycerides: 219.30 mg/dl (normal: <201.75 mg/dl)
 Cholesterol-to-HDL ratio: 4.19 (normal: <4)
 ALT: 5 u/L (normal: 0–41 u/L)
 HBA1C: 11.30% (normal: 4.20–6.20%)

Assessment:
Based on R.B.’s medical history, records, physical exam, and lab results,
he is assessed as follows:
 Uncontrolled type 2 diabetes (A1C >7%)
 Self-care management/lifestyle deficits
 Limited exercise
 High carbohydrate intake
 High blood cholesterol and triglycerides
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III. HORMONAL REGULATION

 INSULIN and GLUCAGON

Figure 2. Insulin Secretion [3]

 Glucose goes inside pancreatic beta cell via GLUT2
 Glucose will undergo glycolysis in the cytosol, producing ATP
 ATP closes sensitive K+ channels
 Membrane becomes less negative causing depolarization
 Ca2+ goes inside the cell
 Insulin release through exocytosis

The level of circulatory glucose is the most important factor

determining the amount of glucagon or insulin produced. The release of
glucagon is precipitated by low levels of blood glucose, whereas high levels of
blood glucose stimulates cells to produce insulin.

Carbohydrate Metabolism:
Insulin is the major regulatory hormone for both Glycolysis and
Glycogenesis. Islet dysfunction and peripheral insulin resistance are both
present in type 2 diabetes and are both necessary for the development of
hyperglycemia. Consequent to insulin deficiency, glucagon
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concentrations rise [4]. Glucagon, on the other hand, is the major

regulatory hormone for Gluconeogenesis and Glycogenolysis.

Patient R.B. requires a constant administration of oral medications like

metformin along with insulin injection to maintain low blood glucose levels.
Metformin improves glycemic control by reducing rates of hepatic
gluconeogenesis and glycogenolysis [5]. Insulin works by binding to the
insulin receptor leading to the activation of GLUT 4 transporter which imports
glucose into the cell, thereby increasing glycolysis and glycogenesis.

Lipid Metabolism:
Insulin is the major regulatory hormone for TAG synthesis, fatty
acid synthesis, and cholesterol synthesis. It promotes storage of fat.
On the other hand, glucagon regulates both beta-oxidation of fatty
acids and ketone oxidation. It promotes ATP production. All the
pathways will be discussed in detail.

Protein Metabolism:
Insulin is the major regulatory hormone for protein synthesis while
glucagon is for proteolysis.
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IV. CARBOHYDRATE METABOLISM

 GLUCOSE

Figure 3. Structure of Glucose [6]

 Glucose (C6H12O6, also known as D-glucose, dextrose, or grape sugar)

 Highly elevated in people with Type 2 Diabetes Mellitus.
 It is a simple sugar (monosaccharide) which serves as a primary fuel for
energy production in higher animals.
 It is the sole source of ATP for the brain, RBC, cornea, adrenal medulla,
and testes.
 GLYCOGEN

Figure 4. Structure of Glycogen [7]

 Storage form of glucose.
 It is a very large, branched polymer of glucose residues that can be
broken down to yield glucose molecules when energy is needed.
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 Most of the glucose residues in glycogen are linked by α-1,4-glycosidic

bonds. Branches at about every tenth residue are created by α-1,6-
glycosidic bonds [8].

 DIGESTION and ABSORPTION OF CARBOHYDRATES

Figure 5. Digestion of Carbohydrates [9]

 Carbohydrate digestion starts in the mouth.

 The salivary glands release the enzyme salivary a-amylase, which
begins the process of breaking down the polysaccharides.
 The mixture enters the stomach where there will be no further digestion
because the stomach produces acid which stops the action of the salivary
a-amylase.
 In the duodenum, the pancreas releases the enzyme pancreatic a-
amylase, which breaks the polysaccharide down into a disaccharide.
 The small intestine then produces enzymes called lactase, sucrase and
maltase, which break down the disaccharides into monosaccharides [10].
 The monosaccharides are single sugars that are then absorbed in the
small intestine through the use of certain transporters. One of which is the
Na+ Dependent Transporters (SGLTs) that are located in the luminal
side. It enables the absorptive cells to concentrate glucose from the
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intestinal lumen. Another one would be Facilitative Glucose

Transporters (GLUT2) located in the serosal side of the cell wherein
glucose moves from a high to low concentration without utilizing ATP.

 GLYCOLYSIS

Figure 6. Glycolysis Pathway [11]

Glycolysis a.k.a. Embden Meyerhoff Pathway is the catabolism

of glucose in the cytosol to produce ATP. It consists of an energy-requiring
phase (Phase I) followed by an energy-releasing phase (Phase II) [12]. It
is stimulated by insulin.

In Phase I:
 Glucose will first be phosphorylated to produce glucose-6-
phosphate through the enzyme hexokinase (muscle) or
glucokinase (liver). (-1 ATP)
 Glucose-6-phosphate will then be isomerized to fructose-6-
phosphate by phosphoglucoisomerase.
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 Fructose-6-phosphate will then be phosphorylated to form

fructose-1,6-bisphosphate (F-1,6-BP) through the action of
phosphofructokinase-1 (PFK-1). (-1 ATP)
o PFK-1 is the rate limiting enzyme of Glycolysis. It
can be allosterically activated by AMP and F-2,6-
bisphophates and inhibited by ATP, citrate, and
anions.
 Aldolase will then cleave F-1,6-BP to dihydroxyacetone
phosphate (DHAP) and glyceraldehyde-3-phosphate (G-3-P).
 DHAP will then be interconverted to G-3-P through the
enzyme triose phosphate isomerase.

In Phase II:
 The two G-3-P produced will be oxidized to two 1,3-
bisphosphoglycerate (1,3-BPG) catalyzed by G-3-P
dehydrogenase. (+2 NADH++H+)
 The two 1,3-BPG will undergo the first substrate level
phosphorylation producing two 3-phosphoglycerate through
the enzyme phosphoglycerate kinase. (+2 ATP)
o Phosphoglycerate kinase is the only endergonic
and reversible kinase.
o ATP production is at a breakeven point because the
two molecules consumed in the energy investment
phase have been replenished in this process.
o This step is by-passed in the body’s erythrocytes,
and instead goes through the Rapoport-Luebering
Shunt for its energy production needs.
 The two 3-phosphoglycerate produced from the previous
reaction will then be isomerized to two 2-phosphoglycerate
by phosphoglycerate mutase.
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 It will then be followed by a dehydration reaction producing

two high energy phosphoenolpyruvate (PEP) through the
enzyme enolase.
 The two PEP will undergo the second substrate level
phosphorylation producing the final product of glycolysis
which is two pyruvates through the enzyme pyruvate kinase.
(+2 ATP)

Net ATP produced:

If aerobic glycolysis= 4 ATPs
If anaerobic glycolysis= 2 ATPs
(Additionally, 2 NADH compounds, two water molecules, and two
pyruvates are created.)

 GLUCONEOGENESIS
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Figure 7. Gluconeogenesis in contrast to Glycolysis Pathway [13]

Gluconeogenesis is the reverse of glycolysis. It refers to the

synthesis of glucose from non-carbohydrate sources such as lactate,
glycerol, glucogenic amino acids, and propionyl-CoA. It occurs in the liver
and kidneys during the fasted state. It is stimulated by Glucagon. In the
case where lactate is the source it is transported back to the liver where it
is converted into pyruvate, the first designated substrate of the
gluconeogenic pathway, by the enzyme lactate dehydrogenase. Aside
from the irreversible steps in glycolysis, the other steps in the pathway are
the same as reversed glycolysis.

 First irreversible step: Pyruvate to Oxaloacetate (-2 ATP)

o This reaction is catalyzed by pyruvate carboxylase.
o This reaction occurs in the mitochondria.
 Second irreversible step: Oxaloacetate to PEP (-2 GTP)
o Catalyzed by phosphoenolpyruvate carboxykinase.
o The malate shuttle allows free passage of this intermediate to
the cytosol, so that gluconeogenesis can be completed.
 Third irreversible step: F-1,6-BP to F-6-P
o Catalyzed by fructose-1,6-bisphosphatase.
o Rate-limiting step in gluconeogenesis.

The other step in gluconeogenesis consuming 2 ATPs is the conversion of

3-Phosphoglycerate to 1,2-bisphosphoglycerate (-2 ATP).

Liver only: Glucose-6-Phosphate to free glucose

o Catalyzed by glucose-6-phosphatase
o This does not occur in muscles, although muscles undergo
gluconeogenesis.
Net ATP consumed:
4 ATP + 2 GTP = 6 ATPs are used to make 1 glucose
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 GLYCOGENESIS

Figure 8. Glycogenesis [14]

Glycogenesis takes place when blood glucose levels are high to

allow excess glucose to be stored in liver and muscle cells. It is stimulated
by the hormone insulin. Insulin inactivates glycogen synthase kinase
(GSK inactivates glycogen synthase through phosphorylation). It begins
as glucose is converted into glucose 6-phosphate, the first substrate in
glycogenesis, by the enzyme hexokinase (muscle) or glucokinase (liver).

 Glucose-6-Phosphate to Glucose-1-Phosphate
o Catalyzed by phosphoglucomutase.
 Glucose-1-Phosphate ------> UDP-Glucose
o Catalyzed by UDP-glucose pyrophosphatase
o Pyrophosphatase: Cleaves the high-energy phosphoric
anhydride bond. This drives the formation of UDP-
Glucose and makes its formation irreversible.
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 Glycogenn + UDP-Glucose ------> Glycogenn+1 + UDP

o Catalyzed by glycogen synthase (makes only linear
glucose, connected in alpha-1,4 linkages)
o Glycogen synthase requires a primer. It will add another
glucose residue to an already-existing chain. If no primer
is present, a protein called Glycogenin is used.
o Rate-limiting step of Glycogenesis
 a(1,4) to a(1,6) glucosyl units
o Catalyzed by branching enzyme
o Once the glycogen chain is about 11 residues long, the
branching enzyme removes about 7 of the residues.
o It places the 7-residue chain in a 1,6-linkage, at least 4
residues away from any other branching point [15].

 GLYCOGENOLYSIS

Figure 9. Glycogenolysis [14]

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Glycogenolysis is a process wherein glycogen is broken down into

glucose to provide immediate energy during the fasting state. It occurs
primarily in the liver and is stimulated by the hormones glucagon and
epinephrine.

 Glycogenn to Glucose-1-Phosphate + Glycogenn-1

o Catalyzed by glycogen phosphorylase (takes any glucose
chain down to the last four residues before a branch point.
It does not cut beyond that.)
o Phosphorolysis reaction not hydrolysis
o Cleaves only the alpha-1,4 linkages
 Debranching Enzyme: Takes over when within four residues to
a branch point. It has two activities.

o 4-alpha-D-Glucanotransferase: Transfer 3 residues to

another chain on the polymer.
o Amylo-alpha-1,6-Glucosidase: Hydrolysis of the final
1,6 bond.
o This step creates free glucose not Glucose-1-Phosphate.
o This is a true hydrolysis reaction, not phosphorolysis.
 Glucose-1-Phosphate to Glucose-6-Phosphate
o Catalyzed by phosphoglucomutase

Liver only: Glucose-6-Phosphate to free glucose

o Catalyzed by glucose-6-phosphatase
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V. LIPID METABOLISM
 DIGESTION and ABSORPTION OF LIPIDS

Figure 10. Digestion and Absorption of Lipids [16]

 EMULSIFICATION: Physical breakdown of fats. They remain unchanged in

the stomach but undergo emulsification by bile acids in the small intestine.

Emulsification of lipids leads to mixed micelles. They are partially

degraded lipids with detergent-like properties. They contain bile acids,
dietary lipids, phospholipids, fat-soluble vitamins, cholesterol, etc. They
are formed in the duodenum and the nutrient-component is absorbed in
the jejunum through microvilli in the intestinal wall. The bile-acids
themselves are not absorbed until later (distal ileum).

 PANCREATIC LIPOLYTIC ENZYMES: Chemical breakdown; break down

triacylglycerols to individual fatty acids.

- Lipase degrades triacylglycerols. It is activated by co-lipase.

- Phospholipase A2 degrades phospholipids. It is activated by trypsin

and Ca+2.
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- Cholesteryl Ester Hydrolase degrades dietary cholesterol, usually

present in the form of cholesteryl esters. It is activated by bile salts.

 ABSORPTION: Individual fatty acids (not triacylglycerols) are absorbed

through the brush border.

 RE-ESTERIFICATION: Once inside intestinal enterocytes, triacylglycerols

and cholesteryl esters are reformed. From triacylglycerols using Acyl-CoA-
Synthetase and Acyltransferase.

 CHYLOMICRON ASSEMBLY: The newly formed triacylglycerol droplets

are then assembled into a chylomicron in the intestinal epithelial cells. It is a
form of lipoprotein.

 TRANSPORT: into the lymphatic system for the most part. They cannot
travel through the arteries because they can form plaques. Chylomicrons
are released into the intestinal lacteals by exocytosis, travels through the
thoracic duct, to the subclavian vein, circulating via the venous system.

- Short-chained fatty acids (up to 10 carbons): Majority are carried

through the portal circulation back to the liver.

- Long-chained fatty acids: (greater than 12 carbons): Majority are

carried through the lymphatic system.

 LIVER: Fats make their way back to liver. They then

utilize lipoproteins (VLDL, LDL, etc.) to get distributed to target tissues. At
the target tissue, fats are broken back down again, using lipoprotein
lipase (Triacylglycerol Monoacylglycerol + 2 Fatty Acids) [15].
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 TRIACYLGLYCEROL/ TAG SYNTHESIS

Figure 11. Fatty Acid Synthesis [15]

TAGs are comprised of a glycerol backbone and fatty acids.

Intestines: TAG synthesis occurs in intestinal cells following lipid

digestion. FFAs are first bound to CoA in an energy dependent process.
FA-CoAs can then be attached to the 2- MAG backbone by acyl
transferases.

Liver and Adipose Tissue: Glycerol must first be phosphorylated in

order to form TAGs. This occurs in the liver and adipose tissue in one of
two ways. Both tissue can convert glucose into glycerol 3-P through action
of glycerol-P dehydrogenase on DHAP, in the glycolysis pathway.

The liver can also phosphorylate glycerol directly, hence once

liberated in the blood (by hormone-sensitive lipase) it returns to the liver
for processing.

Glycerol phosphate combines with fatty acyl CoA from fatty acid
synthesis to yield a 1,2 diglyceride and finally a triglyceride [20].
 20

 FATTY ACID SYNTHESIS

Figure 12. Fatty Acid Synthesis [15]

Fatty acid synthesis mainly occurs at the liver in the cytoplasm of

cells. It is the process of combining eight 2-carbon fragments (acetyl
groups from acetyl CoA) to form a 16-carbon saturated acid palmitate [17].

 Acetyl-CoA + HCO3- + ATP Malonyl-CoA

- The enzyme which catalyzes this reaction is Acetyl CoA
Carboxylase with Biotin as co-factor. This is the rate-limiting step
of the pathway and is therefore irreversible.

4 STEPS:
CONDENSATION:
- Acetyl Unit (2C) + Malonyl Unit (3C) 4-carbon chain + CO2
REDUCTION:
- The beta-carbonyl from above is reduced to OH.
- NADPH NADP+ is concurrent oxidation.
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DEHYDRATION:
- The OH group is eliminated creating a double bond - alpha, beta-
unsaturated species.

- Loss of H2O
REDUCTION:
- Add H across the double-bond, fully saturating it.
- NADPH NADP+ is concurrent oxidation.
FINAL PRODUCT: Butyryl Unit - a 4-carbon acid.
 These reactions are repeated until 16-carbon FA palmitoyl-ACP is
assembled. Palmitate is therefore the predominant product of the
pathway [17].

 BETA-OXIDATION OF FATTY ACIDS

Figure 13. Beta-oxidation of Fatty Acids [15]

 ACTIVATION OF FATTY ACIDS: Fats are delivered to cells as free fats. They must
be activated before they can be burned.

Free Fat Acyl-CoA Thioester

- Catalyzed by Acyl-CoA Synthetase.

- ATP is required in the synthesis.

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 TRANSLOCATION OF FATTY ACYL-CoA THIOESTER INTO THE

MITOCHONDRIAL MATRIX

 Carnitine Intermediate: Only long-chain fatty acids are converted to carnitine as

an intermediate. Short-chain fatty acids can traverse the inner membrane directly:
o Intermembrane space: Carnitine Acyl Transferase I

Acyl-CoA Acyl Carnitine.

o Mitochondrial matrix: Carnitine Acyl Transferase II:

Acyl-Carnitine Acyl-CoA

o In the matrix the fat is esterified back to Coenzyme-A.

BETA-OXIDATION:

4 STEPS:

OXIDATION: Acyl-CoA Dehydrogenase catalyzes an elimination of

hydrogens on Palmitoyl CoA to form beta-unsaturated ∆2 -transenoyl CoA.
FAD FADH2 is the corresponding reduction.

HYDRATION: Add water across the double bond, creating an OH group on

the beta-Carbon. Unsaturated ∆2 -transenoyl CoA is hydrated to b-
hydroxyacyl CoA by enoyl CoA hydratase.

OXIDATION: b-hydroxyacyl CoA is oxidized to b-ketoacyl CoA via b-

hydroxyacyl CoA dehydrogenase. NAD+ NADH is the corresponding
reduction.

THIOLYTIC CLEAVAGE: b-ketoacyl CoA is cleaved via b-keto thiolase into

Acetyl-CoA and a fatty acyl CoA that is 2 carbons shorter than the original
molecule that entered the beta oxidation cycle. The shorter fatty acid chain
then undergoes another round of beta oxidation.
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All the Acetyl CoA formed will enter the Kreb’s Cycle for oxidation into ATP
[15].

 Net ATP produced and consumed:

o 8 Acetyl-CoA x 10 ATP
o 7 FADH2 x 1.5 ATP
o 7 NADH x 2.5 ATP
o Total 108 ATP
- 2 ATP (Thiokinase Reaction)
106 ATPs

 Glucose gives us about + 32 ATP per 6 carbons

 CHOLESTEROL SYNTHESIS

Figure 14. Structure of Cholesterol [15]

Cholesterol is a highly lipophilic substance. It is an alicyclic compound

whose basic structure includes the perhydrocyclopentanophenanthrene nucleus
which contains four fused rings. It has 27 carbon atoms and all of it is derived from
Acetyl-CoA. It is a very expensive substance to manufacture therefore its synthesis
occurs only in the fed state.
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Figure 15. Cholesterol Synthesis [19]

CONDENSATION

o 2 Acetyl-CoA Acetoacetyl-CoA
 Acetoacetyl-CoA Thiolase
o Acetoacetyl-CoA + Acetyl-CoA HMG-CoA
 HMG-CoA Synthase
o HMG-CoA Mevalonate
 HMG-CoA Reductase
 This step only occurs in the cytosol. In the mitochondria, ketone
bodies are made instead.
 Rate limiting step

POLYMERIZATION:

o Mevalonate (C6) Isopentyl Pyrophosphate (C5)

o Isopentyl Pyrophosphate (C5) Geranyl Pyrophosphate (C10)
o Geranyl Pyrophosphate (C10) Farnesyl Pyrophosphate (C15)
o Farnesyl Pyrophosphate + Farnesyl Pyrophosphate SQUALENE (C30)
 25

CYCLIZATION:

o Squalene + O2 Squalene Epoxide

o Squalene Epoxide Lanosterol
 Cyclization occurs at this step.

o Lanosterol Cholesterol
 C14 comes off as formic acid; Lose two carbons as CO2

 KETONE BODY SYNTHESIS/ KETOGENESIS

Figure 16. Ketone Bodies [18]

Ketone bodies originate from an intermediate of Cholesterol synthesis, 3-

Hydroxy-3-methylglutaryl-CoA (HMG-CoA). They are highly elevated in
people with Type 1 DM, but in the case of our patient, it is not.

 HMG-CoA Acetoacetate + Acetyl-CoA

o HMG-CoA Lyase
o This is a simple cleavage of the 6-carbon HMG-CoA.
o This occurs in the mitochondria only. In the cytosol, HMG-CoA is further
synthesized to cholesterol.

 KETONE BODY OXIDATION/ UTILIZATION

 Acetoacetate Acetoacetyl-CoA
o CoA-Transferase
 Acetoacetyl-CoA + Coenzyme-A 2 Acetyl-CoA
o Thiolase

All the Acetyl CoA formed will enter the Kreb’s Cycle for oxidation into ATP.
 26

VI. PROTEIN METABOLISM

Patient R.B. needs insulin in order to maintain his blood glucose level. Insulin is
synthesized by propeptides A, B, and C. C is cleaved away, and A and B get together
to form the final polypeptide.

 DIGESTION AND ABSORPTION OF PROTEINS

Figure 17. Digestion and Absorption of Proteins [21]

 Food enters stomach, activating parietal cells to secrete HCl

 Pepsinogen is converted to Pepsin by the action of acid (H+) from HCl.
o PEPSIN: Proteolytic digestive enzyme.
 The acid is secreted by parietal cells in the intestinal wall. The parietal cells
secrete acid whenever food enters the stomach from the esophagus.
 Auto-Catalytic

ENDOPEPTIDASES: Peptidases that cleave peptides within.

 TRYPSIN - Activated by enterokinase. It converts Trypsinogen to Trypsin. Auto-

Catalytic.
 CHYMOTRYPSIN - Activated by trypsin. It converts Chymotrypsinogen to
Chymotrypsin.
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 ELASTASE - Activated by trypsin. It converts Proelastase to Elastase

EXOPEPTIDASES: Cut the very last residue off a protein.

 CARBOXYPEPTIDASE: These are exopeptidases that cleave at the carboxy-

end. Activated by Trypsin just like above. Procarboxypeptidase to
Carboxypeptidase. It is secreted in the pancreas.

 AMINOPEPTIDASE: Exopeptidases that cut at the amino end of a peptide.

o This is secreted at the jejunum.
 DIPEPTIDASE: Cuts two acids at a time from the amino end of a peptide.
 At this point, the peptides are small enough that they can be absorbed by small
intestine and go, through portal circulation, to the liver.

SECRETAGOGUES: They stimulate the pancreas to release pancreatic enzymes.

 CHOLECYSTOKININ
 SECRETIN
 GASTRIN

TRANSEPITHELIAL AMINO ACID TRANSPORT:

In the brush border membrane, a Na+-dependent transport protein carries an

amino acid with it as it moves along a concentration gradient. Na+ is then pumped into
the serosal side by the Na+K+ ATPase system. The accumulated AA inside the cell is
brought to the liver via the portal vein for metabolism and distribution to other tissues.
 28

 SYNTHESIS OF INSULIN

Figure 18. Digestion and Absorption of Proteins [22]

Insulin is synthesized in significant quantities only in beta cells in the

pancreas. The insulin mRNA is translated as a single chain precursor called
preproinsulin, and removal of its signal peptide during insertion into the
endoplasmic reticulum generates proinsulin.

Proinsulin consists of three domains: an amino-terminal B chain, a

carboxy-terminal A chain and a connecting peptide in the middle known as the C
peptide. Within the endoplasmic reticulum, proinsulin is exposed to several
specific endopeptidases which excise the C peptide, thereby generating the
mature form of insulin [23].

 DEGRADATION OF PROTEINS
UREA CYCLE:

Figure 18. Urea Cycle [24]

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 Carbamoyl Phosphate + Ornithine Citrulline

o Rate-limiting step
o This step occurs in the mitochondria. Citrulline is then transferred from
mitochondria to the cytosol for the rest of the steps.
o Catalyzed by Ornithine Transcarbamoylas.
 Citrulline + Aspartic Acid Arginosuccinate
o Aspartate Aminotransferase.
o This step, and all subsequent steps, occurs in the cytosol.
 Arginosuccinate Arginine + Fumarate
o Catalyzed by Arginosuccinase
 Fumarate then goes through the TCA Cycle.
 Arginine Urea + Ornithine
o Catalyzed by Arginase.

CATABOLISM OF CARBON SKELETONS:

Figure 19. Anaplerotic Reactions [25]

GLUCOGENIC: Amino acids whose degradation results in pyruvate or

one of the intermediates of the TCA cycle. That means that those carbons can be
used to make glucose via gluconeogenesis, under the right metabolic
circumstances.
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KETOGENIC: Amino acids whose degradation results only in Acetyl-CoA

or Acetoacetyl-CoA. These carbon-skeletons can only be funneled into fat-
metabolism: aerobic respiration of acetyl-CoA, or fat-synthesis [15].

VII. NUCLEIC ACID METABOLISM

This topic won’t be tackled much because of its minimal relation with the case of Patient R.B.

 PURINE METABOLISM

SYNTHESIS OF PURINES: The basic purine is Inosinate (IMP), from which AMP and
GMP are made.

Figure 20. Purine Metabolism [26]

o PPRP 5-Phosphoribosyl-1-Amine
 Amidophosphoribosyl Transferase
 Rate-limiting step

SYNTHESIS OF AMP:

 Inosinate (IMP) + Aspartic Acid Adenylosuccinate

o GTP is required.
 Adenylosuccinate Adenylate (AMP) + Fumarate
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SYNTHESIS OF GMP:

 Inosinate (IMP) Xanthylate

o Concurrent reduction: NAD+ NADH
 Xanthylate + Glutamine Guanylate (GMP) + Glutamate
o ATP is required.

 PYRIMIDINE METABOLISM

Figure 21. Pyrimidine Metabolism [26]

 Glutamine + HCO3- Carbamoyl Phosphate + Glutamate

o Carbamoyl Phosphate Synthetase II is the primary regulated step of
Pyrimidine Biosynthesis.
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VIII. GENE EXPRESSION

Figure 22. Gene Expression [27]

This topic won’t be tackled much because of its minimal relation with the case of Patient R.B.
Gene expression is the complex process where a cell uses its genetic
information to make functional products like the hormone Insulin.

Each time a cell divides, each of its double strands of DNA splits into two
single strands. Each of them acts as a template for a new strand of
complementary DNA. Replication is controlled by the Watson-Crick pairing of
the bases and is directed by DNA polymerase enzymes. It proceeds in the 5′- to
3′-direction.

Transcription is the process by which DNA is copied to mRNA, which

carries the information needed for protein synthesis. First, pre-messenger RNA
is formed, with the involvement of RNA polymerase enzymes. The resultant
single strand of RNA is the reverse-complement of the original DNA sequence.
The pre-messenger RNA is then "edited" to produce the desired mRNA molecule
in a process called RNA splicing. The mRNA formed in transcription is
transported out of the nucleus, into the cytoplasm, to the ribosome. Here, it
directs protein synthesis. Messenger RNA is not directly involved in protein
synthesis − transfer RNA (tRNA) is required for this. The process by which
mRNA directs protein synthesis with the assistance of tRNA is called translation.
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The ribosome is a very large complex of RNA and protein molecules.

Each three-base stretch of mRNA is known as a codon, and one codon contains
the information for a specific amino acid. As the mRNA passes through the
ribosome, it interacts with the anticodon of a specific transfer RNA (tRNA)
molecule. This tRNA molecule carries an amino acid at its 3′-terminus, which is
incorporated into the growing protein chain. The tRNA is then expelled from the
ribosome [28].

IX. INTEGRATION OF ALL

MACROMOLECULES
The following metabolic pathways happen to patient R.B. depending on
his last meal intake, organized according to the different organs involved:

Well-Fed State (2-4 hours after a meal):

Liver: Gycolysis, Glycogenesis, Protein synthesis, Urea Cycle,
FA, TAG, Cholesterol synthesis
Brain: Glycolysis
RBC: Anaerobic Glycolysis
Skeletal Muscles: Glycolysis, Glycogenesis
Adipose Tissue: Glycolysis, FA and TAG synthesis
Early Fasted State (4-18 hours):
Liver: Glycogenolysis, Urea Cycle
Brain: Glycolysis
RBC: Anaerobic Glycolysis
Skeletal Muscles: Glycogenolysis, Proteolysis
Adipose Tissue: Glycolysis
 34

Fasted State (18-48 hours):

Liver: Gluconeogenesis, Ketone Body Synthesis,
Beta-oxidation of FA
Brain: Glycolysis, KB Oxidation
RBC: Anaerobic Glycolysis
Skeletal Muscles: Beta-oxidation of FA, KB Oxidation, Proteolysis
Adipose Tissue: Lipolysis, Beta-oxidation of FA, KB Oxidation
Starved State (2 days to weeks):
Liver: Gluconeogenesis, Ketone Body Synthesis,
Beta-oxidation of FA
Brain: Ketone Body Oxidation
RBC: Anaerobic Glycolysis
Skeletal Muscles: Beta-oxidation of FA
Adipose Tissue: Lipolysis, Beta-oxidation of FA
Early Re-fed State:
Liver: Gluconeogenesis (first few hours),
Glycogenesis (from lactate)
Brain: Glycolysis
RBC: Anaerobic Glycolysis
Skeletal Muscles: Glycolysis, Glycogenesis
Adipose Tissue: Glycolysis, FA and TAG synthesis
 35

Actions of Insulin:
GO STOP
Glucose uptake in muscles and adipose Gluconeogenesis
tissue via GLUT4
Glycolysis Glycogenolysis
Glycogen Synthesis Lipolysis
Protein Synthesis Ketogenesis
Uptake of ions (especially K+ and PO4-) Proteolysis

DIABETES MELLITUS TYPE 2:

Primary manifestations:
1. HYPERGLYCEMIA
- insulin level not sufficient to control gluconeogenesis (down-
regulation of PEPCK does not occur)
- glucose uptake by adipocytes and skeletal muscles impaired due
to decrease translocation of GLUT4 to plasma membrane
-normal increase of fructose-2,6-biphosphate

2. HYPERTRIACYLGLYCEROLENEMIA
- usually results in increase in VLDL without increase in
chylomicrons
- liver synthesis of FAs diverted to TAG and VLDL synthesis
TREATMENT:
Balanced Diet
Weight Control
Blood Glucose Lowering Drugs: Insulin, Metformin, Glipizide, Rosiglitazone

Ketoacidosis rarely develops because enough insulin is present to prevent

uncontrolled release of FA from adipocytes and FA reaching the liver or synthesized de
novo are directed in TAGs [29].
 36

X. REFLECTION

Figure 17. Me and my Father

Biochemistry is a very complicated yet meaningful subject. Before

medicine school, I never really understood most of it. But after all the
discussions and late night reviews, I began to appreciate its importance
more. It’s truly amazing how processes, even down to the molecular levels,
contribute to and ensure that our body has a constant supply of
energy in the form of ATP.

Working on this portfolio helped me integrate the theories I learned

in the classroom into a clinical setting. I realized that insulin is very
important regardless of one’s health condition. If inadequate, it could
significantly affect our health like in the case of my father. The cells will
lack fuel, and the body will suffer from lack of energy. I now know the
explanation why my father complains about being weak and tired all the
time.

I believe that his Type 2 Diabetes Mellitus also served as a

predisposing factor when he suffered stroke. That is the main reason why
 37

I chose this topic in the first place – so that somehow I’d know more about
the disease, help prevent the recurrence of any vascular complications,
and ultimately contribute to the improvement of his quality of life.

After finishing this portfolio, I’m more confident now about going
to second year. All the knowledge I gained and will continue to gain will
not only benefit me as a future doctor, but it will also benefit my father who
longs to live long enough to see her daughter become a good one
someday.
 38

XI. EVIDENCES
Evidence 1. Grades in Biochemistry for the 1st - 5th Grading Period
 39

Evidence 2. Worksheets/ BGD

 40

Evidence 3. Pathways that I worked hard on to help me study; discussed in the

hormonal regulation part (Insulin Secretion, GLUT4 Translocation,Stimulation of
Glycogenesis, Inhibition of Gluconeogenesis)

INSULIN
 41

Evidence 4. Pathways that I worked hard on to help me study; discussed in the

carbohydrate metabolism part (Glycolysis, Gluconeogenesis Glycogenesis,
Glycogenolysis)
GLYCOLYSIS

GLUCONEOGENESIS

GLYCOGENOLYSIS

GLYCOGENESIS
 42

Evidence 5. Pathways that I worked hard on to help me study (HMP Shunt, Uronic Acid
Pathway, PDH Cycle, TCA, ETC-Oxidative Phosphorylation)
HMP SHUNT URONIC ACID PATHWAY

TCA CYCLE
PDH CYCLE
 43
OXIDATIVE PHOSPHORYLATION

ELECTRON TRANSPORT CHAIN

 44
PURINE METABOLISM

PYRIMIDINE METABOLISM
 45

XII. APPENDICES
Appendix A. Laboratory Tests of Patient R.B. taken on January 23, 2017

Appendix B. Laboratory Tests of Patient R.B. taken on January 24, 2017

 46

XIII. REFERENCES
[1] The National Institute of Diabetes and Digestive and Kidney Diseases
Health Information Center (n.d.). Retrieved December 16, 2017 from
http://bit.ly/2yN3L1h
[2] National Stroke Association (2013). Retrieved December 16, 2017 from
www.stroke.org/sites/default/files/resources/DiabetesBrochure.pdf
[3] http://david-bender.co.uk/metabonline/CHO/MODY/images/secretion.png
[4] Giugliano, et al. (2008). Glucose metabolism and hyperglycemia. The American
Journal of Clinical Nutrition. 87(1): 217S-222S.
[5] Hundal, R. S., Krssak, M., Dufour, S., Laurent, D., Lebon, V., Chandramouli, V.,
Shulman, G. I. (2000). Mechanism by Which Metformin Reduces Glucose
Production in Type 2 Diabetes. Diabetes, 49(12), 2063–2069.
[6]https://themedicalbiochemistrypage.org/carbohydrates.php
[7]https://chem.libretexts.org/Under_Construction/Textmaps_and_Wikitexts/MVC%3A_C
hem_1406/Chapters/14%3A_Carbohydrates/14.7%3A_Polysaccharides
[8] Berg JM, Tymoczko JL, Stryer L. (2002). Glycogen Metabolism. Biochemistry 5th
edition. Chapter 21
[9]https://image.slidesharecdn.com/2-140707044444-phpapp02/95/digestion-and-
absorption-of-carbohydrates-4-638.jpg?cb=1502992122
[10] Kaiser,S. (n.d.) Retrieved December 16, 2017 from
http://healthyeating.sfgate.com/steps-digestion-carbohydrates-4053.html
[11] https://biochemist01.wordpress.com/tag/steps-in-glycolysis/
[12] Khan Academy (n.d) Retrieved December 16, 2017 from
https://www.khanacademy.org/science/biology/cellular-respiration-and-
fermentation/glycolysis/a/glycolysis
[13] http://www.biochemden.com/wp-content/uploads/2015/03/Gluconeogenesis.jpg
[14] http://biostudizz.weebly.com/uploads/6/0/8/1/60814701/5971725_orig.jpg
[15] Goodman, S. (1999). Carbohydrate Metabolism. Retrieved December 16, 2017 from
https://www.kumc.edu/AMA-MSS/Study/carbohydrates.htm
[16] https://image.slidesharecdn.com/digestionandabsorptionoflipids-150104110115-
conversion-gate01/95/digestion-and-absorption-of-lipids-22-
638.jpg?cb=1420369336
[17] Dr. Madarcos’ Finals Reviewer PPT
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[18] https://biologydictionary.net/ketone-bodies/
[19] https://med.libretexts.org/TextMaps/Book%3A_Intermediate_Nutrition_(Lindshield)/6
%3A_Macronutrient_and_Alcohol_Metabolism/6.3%3A_Lipid_Metabolism/6.3
5%3A_Cholesterol_Synthesis
[20] http://www.sharinginhealth.ca/cells_and_molecules/fats/transport_and_metabolism/
TAG_synthesis.html
[21] https://www.slideshare.net/nidhinbm5/digestion-and-absorption-41903619
[22] http://www.vivo.colostate.edu/hbooks/pathphys/endocrine/pancreas/proinsulin.gif
[23] http://www.vivo.colostate.edu/hbooks/pathphys/endocrine/pancreas/insulin.html
[24] http://newenglandconsortium.org/for-professionals/teachers-resources/an-
educators-guide-to-urea-cycle-disorders/
[25] https://www.pinterest.com/pin/45317539973932312/
[26] http://clinchem.aaccjnls.org/content/45/4/539/tab-figures-data
[27] http://b4fa.org/bioscience-in-brief/introduction-genes-crops/what-is-a-gene/gene-
expression/
[28] https://www.atdbio.com/content/14/Transcription-Translation-and-Replication
[29] Lecture notes of Dr. Mendoza on Integration to Metabolism II

Additional:
 [3,6,7,9,11,13,14] are images retrieved on December 16, 2017 from stated
websites.
 [16,18,19,20,21,22,23,24,25,26,27] are images retrieved on May 30, 2018 from
stated websites.
 Personal handouts in Biochemistry are also used as source of information in the
discussions.
 The pathways I made in the evidences section are also used as reference for the
explanation of the biochemical pathways.
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WORKSHEETS