Biochemistry Review Dr Hoda Alkholy

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Biochemistry Review Dr Hoda Alkholy

Table of contents :
......Page 1
......Page 3
1 Basic Concept of Metabolism
......Page 5
2 Electron Transport Chain
......Page 7
Hormones......Page 11
Insulin......Page 14
Glucagon......Page 17
Catecholamines......Page 18
steroid, thyroid hormones, active vitamin D (Calcitriol) and vitamin A or retinoic acid
......Page 21
Monosaccharides......Page 22
Disaccharides......Page 23
Homopolysaccharides......Page 24
Hyaluronic acid......Page 25
Heparin......Page 26
Carbohydrate (CHO) Metabolism......Page 27
Glycolysis......Page 30
Lactate......Page 38
Alcohol metabolism......Page 41
Citric acid cycle
......Page 43
Hexose Monophosphate Pathway (HMP) or (Pentose phosphate pathway)
......Page 46
Uronic Acid Pathway
......Page 50
Glycogenesis......Page 51
Glycogenolysis......Page 53
Gluconeogenesis......Page 56
Galactose Metabolism......Page 59
Fructose Metabolism......Page 60
Blood glucose
......Page 63
Hypoglycemia......Page 65
Diabetes Mellitus (DM)......Page 66
Type I diabetes mellitus......Page 67
Type 2 diabetes mellitus
......Page 69
Complications of DM
......Page 70
Glycosuria......Page 75
Protein Chemistry And Metabolism......Page 77
Amino acids......Page 78
Peptides......Page 80
Protein structure (folding)......Page 81
Protein Misfolding......Page 82
Collagen......Page 85
Amino acid pool......Page 88
Protein Turnover......Page 91
General metabolic pathways of amino acids
......Page 92
Metabolism of Ammonia......Page 96
Urea cycle......Page 100
Glutamine Metabolism......Page 102
Glycine......Page 103
Creatine Metabolism......Page 105
Glutathione......Page 107
Phenylalanine......Page 108
Catecholamine......Page 110
Melanin pigment......Page 112
Thyroid hormones......Page 113
Glutamic acid......Page 118
Tryptophan......Page 119
Serotonin metabolism......Page 120
Melatonin metabolism......Page 121
Arginine amino acid......Page 122
Serine amino acid metabolism......Page 123
Methionine amino acid......Page 124
Histidine amino acid......Page 126
Branched. chain amino acids......Page 127
Neurotransmitters......Page 128
Hemoglobin......Page 130
Myoglobin......Page 132
Biosynthesis of Hemoglobin......Page 133
Catabolism of Hemoglobin......Page 138
Hyperbilirubinemia and jaundice......Page 142
Sickle cell anemia (hemoglobin S disease)
......Page 146
Thalassemia......Page 148
Immunoglobulin......Page 150
Immunoglobulin A (IgA)......Page 151
Immunoglobulin D (lgD)......Page 152
Alcohols......Page 153
Steroid alcohol (cholesterol)
......Page 154
Chemical Classification......Page 155
Unsaturated Fatty Acids (PUFA)......Page 156
Simple lipids......Page 157
Glycerophospholipids......Page 158
Glycolipids......Page 159
Steroids......Page 160
Lipid Metabolism......Page 161
Disorders of lipid digestion and absorption......Page 164
......Page 165
Lipolysis......Page 166
Fatty acid synthesis......Page 168
Oxidation of Fatty Acids
......Page 169
Metabolism of Ketone Bodies......Page 174
Hormonal regulation......Page 177
......Page 178
Metabolism of Compound Lipids......Page 179
Eicosanoids......Page 180
......Page 181
......Page 184
Metabolism of Cholesterol......Page 185
Bile acids & Salts
......Page 188
Steroid Hormones
......Page 191
Plasma Cholesterol......Page 192
Plasma Lipoproteins......Page 193
Metabolism of Chylomicrons......Page 195
Metabolism of LDL......Page 198
Metabolism of HDL......Page 200
Fatty liver
......Page 203
Atherosclerosis and ischemic heart diseases......Page 205
Obesity......Page 209
Fed or the absorptive state
......Page 212
Liver in absorptive state
......Page 214
Resting skeletal muscles in absorptive state......Page 215
The liver during fasting state......Page 216
Adipose tissue in fasting......Page 217
Brain in fasting
......Page 218
Vitamins......Page 219
Vitamin A......Page 221
Vitamin D......Page 224
Vitamin E......Page 227
Vitamin K......Page 228
Thiamine (vitamin B1)
......Page 230
Niacin (vitamin B3) (Nicotinic acid)
......Page 232
Pyridoxine (Vitamin B6)
......Page 233
Folic Acid (Folate)......Page 234
Vitamin B12 (Cobalamin)
......Page 236
Ascorbic Acid (Vitamin C)
......Page 239
Free radicals......Page 241
Antioxidants......Page 244
Enzymes......Page 247
Factors affecting the enzyme activity......Page 249
Inhibition of enzyme activity......Page 251
Regulation of the enzyme activity......Page 253
Plasma enzymes in clinical diagnosis......Page 254
III) Lactate dehydrogenase (LDH)
......Page 255
VI) Lipase......Page 256
Biochemical Markers of Acute Myocardial Infarction......Page 257
Nitrogenous bases......Page 259
Pentose sugar......Page 260
Nucleic acid structure......Page 262
Chemistry of RNA (Ribonucleic acid)......Page 264
I-Messenger RNA (m RNA)
......Page 265
Ill-Transfer RNA (tRNA)......Page 267
DNA......Page 268
DNA synthesis (Replication)......Page 270
DNA damage and repair......Page 273
POST -transcription modifications of RNA......Page 277
GENETIC CODE......Page 280
Point mutation......Page 282
Frame-shift mutations......Page 283
Protein Synthesis (Translation)......Page 284
Post-translational modifications......Page 286
Antibiotics and Protein Synthesis......Page 288
Cell cycle......Page 289
GENE THERAPY......Page 291
Apoptosis (Cell Suicide)......Page 292
Polymerase chain reaction......Page 293
......Page 295
Adenosine deaminase deficiency
......Page 296
Lesch-Nyhan syndrome......Page 297
Calcium......Page 298
Phosphorus......Page 303
Sodium......Page 304
Sulfur......Page 305
Iron (Fe)......Page 306
Copper......Page 309
Iodine......Page 310
Selenium......Page 311
Bone Matrix......Page 312
Blood......Page 314
Urine......Page 317
Semen (Seminal fluid)
......Page 320
Milk......Page 321
Saliva......Page 324
Biochemistry Of Cancer......Page 325
Tumor markers......Page 326
pH scale......Page 329
Buffers......Page 330
Renal regulation of pH......Page 332

Citation preview

By Prof. Dr. Hoda Mohammed El· Kholy Biochemistry Department Faculty of Medicine (For Girls), AI Azhar University - Cairo


[ Review of Medical Biochemistry with Clinical Correlations

By Prof. Dr. Hoda Mohammed El-Kholy Biochemistry Department Faculty of Medicine (for Girls), AI Azhar University Cairo

Index Subject ----------- ------- --Basic concept of metabolism ----- -- -- ----------Electron transport chain ----------------Hormones Carbohydrate chemistry and metabolism--------- --------------------- -----Protein chemistry and metabolism ----------------------Neurotransmitters ------------------------Hemoproteins ------------------Immunoglobulin Lipid chemistry and metabolism - - - - - - - - - - - - - - - - ----------- --------Metabolicintegrations --------------Vita mins Free radicals and a n t i o x i d a n t s - - - - - - - - - - - - Enzymes Nucleic acids chemistry Nucleotide metabolism Minerals and electrolytes Extracellular matrix Body fiuids Biochemistry of cancer Acids and bases

Page 10 21 75 124 126 145 148 206 213 233 240 251 285 288

302 304

315 319

Preface and Acknowledgment This book has been done for dinical students. The main subjects that have been explained were chemistry and metabolism of carbohydrates, lipids,· proteins, _heme, nucleotides, and nucleic acids. Metabolic integrations, body fluids, metabolism of nervous system, vitamins, enzymes, minerals, biochemistry of cancer, and bioenergetics have been explained in brief. I will greatly appreciate receiving from teachers and students their comments, notice of errors and advices.

I wish to express my deep appreciation to all staff ~~mbers of biochemistry deparbnent Faculty of Medicine, AI-Azhar UniversitY (For Girls} for their comments and good help. Many thanks to my family who has pro~ided the assistance that have made the completion of this work possible.

Hoda Mohammed Elkholy

Email: [email protected]

[email protected] hotmail


Basic Concept of Metabolism Metabolic Pathways: • Metabolic pathways are series of enzymatic reactions occurring in consecutive steps, the product of one enzyme reaction becomes the substrate for the next reaction in the sequence. The successive products of the reaction are known as metabolites or metabolic intermediates. • Metabolism is the sum of chemical activities in an organism • Metabolic pathways occur in the cytoplasm, mitochondrial membrane and matrix, lysosomes and peroxisomes. Metabolism is divided into: 1. Anabolism (anabolic reactions). 2. Catabolism (catabolic reactions) 1. Anabolic reactions or anabolism: are processes that build complex molecules from simpler one. Theses reactions usually consume energy usually derived from ATP (They are called endergonic reactions).

Anabolic reactions Glucose




I+ I


y~ Glycogen

fatty acid






ADP+P ATP j. \ Simple compounds ( C02, monosaccharides, amino acids, ---~......;:a,-L.:;..._......::.,~ fatty acids )


Amino arid


Amino acid

y~ [YfPmin ..;;


Complex compounds (Polysaccharides, protein, lipids)

Energy required is provided by ATP hydrolysis

2. Catabolic reactions or catabolism: are processes that break down complex molecules into simpler ones. These reactions usually release energy in the form of ATP or exothermic in the surrounding environment. They!re called exergonic reactions. Catabolism occurs in three stages: 1. Stage I (hydrolysis of complex molecules: Polysaccharide are degraded to monosaccharides, proteins are degraded to amino acids and triacylglycerol to glycerol and fatty acids. 2. Stage II: These smaller molecules are further degraded to acetyl CaA. In this stage, some free energy is trapped as ATP.


3. Stage Ill: Is the final common pathway by which these molecules are oxidized to C02 and water and trap the available free energy as ATP. It consists of: a. The citric acid cycle. b. The electron transport chain.


StageD Breakdown of complex molecules to their component building blocks

Amino acids

Single sugars

Fatty acids,






Conversion of building blocks to acetyi-CoA (or other simple intermediates)

Stage E) Metabolism of acetyi-CoA to C02 and formation of ATP

Citric acid cycle (and Electron transport chain)


Electron Transport Chain (ETC) (Respiratory Chain) Glucose and lipids are energy-rich molecules. They are metabolized by a series of oxidation reactions usually yielding C0 2 and water. During oxidation of these compounds metabolic intermediates are produced. These intermediates carry electrons and donate these electrons to specific coenzymes-nicotinamide adenine dinucleotide (NAD•) and flavin adenine dinucleotide (FAD) to form the energy-rich reduced coenzymes, NADH+H and FADH 2. These reduced coenzymes can, in tum, each donate a pair of electrons to a specialized set of electron carriers, collectively called the electron transport chain. As electrons are passed down the electron transport chain, they lose much of their free energy. Part of this energy can be captured and stored by the production of ATP from AD P and inorganic phosphate (Pi). The remainder of the free energy not trapped as ATP is used to drive other reactions such as Ca 2• tr~nsport into mitochondria, and to generate heat. Definition of electron transport chain: Electron transport chain is system of electron carriers, which catalyze the transfer of electrons (also called reducing equivalent) derived from different fuels in the body (in the form of reduced coenzymes as NADH+W and FADH 2) to molecular oxygen to form H20. • It is called respiratory because the end acceptor of electrons and protons is oxygen. Site of electron transport chain: In the inner mitochondrial membrane. INNE'R UEMBRANE 1~ 10


MATRIX • TCA CWde en:rymes

• Gdd.a1Jon anzymac • nttDNA.. .eRHA • 'n \liS ribosomes

mosl $ Stimulates Insulin secretion.:::> Increases synthesis of the key regulatory enzymes (inducer) c:::> Enhances glycolysis


4. During fasting:tGiuca gon/ ratio, glucagon represses synthesis of the key regulatory enzymes (repressor).·

During fasting

tl- Blood glucose level Q

Inhibits insulin seaetion&stimulates glutagDD & glucocorticoid

seaetion c::> ~Synthesis of key regulatory enzymes of glycolysis& 1} Synthesis of the

1l 6iucoJieOgenesis. -

four enzymes that reverse glycolysis ..::::> ~of glyoolysis &

Sources and fate of Pyruvate: Sources of pyruvate are: 1. Glycolysis. 2. Lactate by lactate dehydrogenase. 3. Glycogenic amino acid e.g. alanine & serine. 4. From malate by NADP malic enzyme. Fate of pyruvate: 1. Lactate formation: Pyruvate is converted to lactate by lactate dehydrogenase. 2. Oxaloacetate formation: by pyruvate carboxylase enzyme. 3. Alanine formation: by transamination. 4. Acetyl CoA formation: by pyruvate dehydrogenase complex (PDH). 5. Reduction of pyruvate to ethanol by micro-organisms.

Lactate Sources of lactate are: • Anaerobic glycolysis (as in the exercising skeletal muscles and RBCs because they contain no mitochondria), • Lactate by lactate dehydrogenase enzyme.

Lactate E



ILactate dehydrogenase



Lactate dehydrogenas e: • Lactate dehydrogenase is composed of four subunits (tetramer.2H&2M). It has 5 isoenzymes: LDH-1 (4H}-in the heart ,RBC and brain ,elevated in myocardial infarction. LDH-2 (3H1 M):-in the reticuloendothelial system. LDH-3 (2H2M}-in the lungs. LDH-4 ( 1H3M}-in the kidneys, placenta, and pancreas. LDH-5 (4M}-in the liver and striated muscle. Elevated mainly in some liver diseases e.g. acute viral hepatitis.









Itill U\111



aa~ f.fli


nvn nvn


Causes of increased blood Lactate are: Physiological: {i} Glycolysis in RBCs, cornea and lens. {ii} Sever muscle exercise. Pathological: {i} Hypoxia in myocardial infarction, pulmonary embolism uncontrolled hemorrhage, in infancy during labor, and severe anemia are the common causes of high blood lactate. Explanation: • Failure to bring adequate amounts of oxygen to the tissues results in impaired oxidative phosphorylation and decreased ATP synthesis. To survive, the cells use anaerobic glycolysis as a backup system for generating ATP, producing lactic acid as end product. {ii} Tumor cells due to anaerobic glycolysis in tumor cells. {iii} Deficiency of thiamine as in alcoholics {because poor diet and alcohol which inhibits thiamine absorption). Fate of lactate: (Cori-cyclel or lactic acid cycle: Cori cycle: Is the the metabolic pathway in which lactate produced by anaerobic glycolysis in the muscles moves to the liver and is converted to glucose, which then returns to the muscles and is metabolized ... • Lactic acid passes from muscles ~To plasma--)- To liver. • In the liver lactate~ pyruvate which will be converted t~ glucose again by the reverse of glycolysis {gluconeogenesis}.

Lactic acid cycle Glucose -----:.-Glucose _ _,___ Glucose


t.Giuconeo J.·genesis

: +Glycolysis


-~. 't'



NAD:::t ..



.....:---+--·· Lactat:a....._-"~c-·· Lactate



Complications of excess lactate are: {i} Muscle_ fatigue. {ii} Lactic acidosis: Normal blood lactate levels are less than 1.2 mmoi/L, elevation of lactate above normal leads to lactic acidosis (blood lactate may reach 5 m moVL or more}. 38

Lactic acidosis: Definition: Elevated concentrations of lactate in the plasma. Causes of lactic acidosis: I. Increased production of lactate: • See causes of increased blood lactate. II. Decreased utilization due to: • Defective gluconeogenesis due to liver disease·. • Ethanol intake. • Excess use of hypoglycemia drug called metformin mainly in patients with renal failure because metformin inhibits Cori cycle. Normally, the excess lactate would be cleared by the kidneys, but in patients with renal failure, the kidneys cannot handle the excess lactic acid. . • Deficiency of pyruvate dehydrogenase enzyme. Ill. Decrease excretion of lactic acid as in diabetic ketoacidosis which affects functio~s of the kidney. Mechanism of lactic acidosis: 1. Lactate undergo ionization inside the cells with the release of excess hydrogen ions. 2. Hydrogen ions release into the circulation. 3. Plasma hydrogen ions are neutralized by Na bicarbonate buffer which when consumed cause acidosis.


Lactate+ Na bicarbonate ---~")1~ Na lactato +Carbonic acid/



Clinical application s of glycolysis: I. Pyruvate kinase deficiency: Cause: Inherited deficiency of pyruvate kinase. It is the second most common cause (after glucose 6-phosphate dehydrogenase deficiency) of enzyme deficiency related hemolytic anemia. Clinical picture: Clinical picture might appear since birth (congenital) in the form ot 1) Hemolytic anemia 2) Jaundice. Biochemica l basis: decrease of ATP production in the RBCs leads to impaired Na/k+-pump with accumulation of Na+ inside the RBCs ~ excess H20 influx by osmolarity ~ swelling then rupture of the RBCs i.e. Hemolysis, with release of excess heme. Catabolism of heme in the spleen gives ex~ss bilirubin and jaundice. · Treatment: Repeated transfusion of packed RBCs. II. Hexokinase deficiency: Cause: Inherited deficiency of hexokinase enzyme. Clinical picture: Hemolytic anemia & jaundice (due to .,1, ATP production - as in pyruvate kinase deficiency). · • Ill. Lactic acidosis: see above.


Alcohol metabolism Absorption: • Alcohol is rapidly absorbed from the stomach and the intestine. • The highest blood level occurs about 30 minutes from the time of the last drink. • Alcohol absorption is slowed by the presence of food in the stomach; however, once it reaches the small intestine, alcohol absorption is rapid. • Alcohol vapors can be inhaled· and absorbed by the lungs and can be a significant occupational hazard where used industrially. Excretion: It is excreted in the urine and breath, hence the utility of the taking breath samples to evaluate alcohol exposure. Metabolism of alcohol: • Most of alcohol in the bod,~ is metabolized in liver. • Metabolism of alcohol is done by two oxidation reactions: 1. Ethanol is first converted to acetaldehyde by alcohol dehydrogenase. 2. Acetaldehyae is subsequently oxidized to acetate by aldehyde dehydrogenase. 3. Both alcohol dehydrogenase and aldehyde dehydrogenase are NAD dependent _ ______ _ enzymes and both reactions lead to release of excess NADH+H•. _




\... L

Alcohol dehydrogenase




CH3-ct1o __ '=J.;;;;::H•-=-~--?• CH3 -COOH Acetaldehyde Acetate Acetaldehyde dehyrogenase


Complications of acetaldehyde in blood are: Acetaldehyde is toxic, and its accumulation will lead to: 1. Flushing. 2. Tachycardia. 3. Hyperventilation. 4. Nausea. 5. Excess acetaldehyde leads to death. Increased NADH+H+ leads to: 1. Reduction of pyruvate to lactate. The rise in lactate ~ lactic acidosis and, hyperuricemia {because lactate competes with urate for excretion by the kidney). 2. Reduction of oxaloacetate {OAA) ~ malate. 3. Excess NADH+H+ ~..1. the synthesis of glucose --+ hypoglycemia. Metabolic complications of alcohol intake are: 1. High levels of NADH in cytoplasm helps conversion of pyruVate to lactate with lactic acidosis. 2. lactic acidosis causes decreased excretion of uric acid resulting in acute attack of gout. . 3. Deficiency of pyruvate ~ depression of gluconeogenesis and hypoglycemia. 4. Decreased pyruvate and oxaloacetate and increased NADH leads to suppression of TCAcycle.


5. Suppression of TCA cycle leads to accumulation of acetyl CoA ~ fatty acid synthesis ~ fatty liver ~ Liver cirrhosis and liver cell failure. 6. High level of acetyl CoA ~ Ketogenesis. 7. Depression of central nervous system. 8. Accumulated toxic acetaldehyde in liver leads to cellular death and fibrosis. 9. Liver cell failure leads to hepatic coma. 10. Alcohol inhibits absorption of pyridoxal phosphate (86 ) (polyneuritis) and absorption of vitamin 81 ~ Wernicke's disease. Potential long-term effects of

Ethanol L arge consumption Brrun :--~----------------------------+-7-


lmpa~ red


- wem1cke-Korsakofi syndrome • Vision changes ' Ataxia • l mpa~red memory - Psychological • Cravmgs • lrntab1hty • AniiSOClahty • DepreSSion · Anxiety • PanJC · Psychosis • HaJiucmations • DeluS1ons • Sleep diSOrders

Mouth, trachea and esophagus: - Cancer Blood: -----------------... -Anemia H ean: ----------~~--,

-Alcoholic cardio· myopathy

~~~~~sis - H epanus Stomach: -Chronic ga!.UIIJS Pancreas:

{-------------=;o. =. :;-


- Pancreaulis Peripheral tissues: - Ina eased risk of d1abetes type 2


Mitochondrial pathways for complete oxidation of glucose 1. Oxidative decarboxylation of pyruvate by pyruvate dehydrogenase enzyme complex (PDH) to form acetyl CoA: • • •

Pyruvate {end of glycolysis under aerobic conditions) js transported at first to the inside of the mitochondria by special transporter. In the mitochondria, it is irreversibly converted to acetyl CoA by pyruvate dehydrogenase complex {PDH). -- - - -- -- - - Irreversibility of the reaction explain why glucose cannot be re-formed from acetyl CoA in gluconeogenesis.

COA7L J.f.


2 Pyruvate





2 Acetyl COA




Pyruvate dehydrogenase enzyme complex (PDHl: H is a complex formed of 3 enzymes and 5 coenzymes which are Thiamine pyrophosphate (Tpp), lipoic acid, CoA, FAD and

NAD. Energy yields from oxidative decarboxylation of two pyruvate molecules produced from glycolysis: • 2 NADH molecules are released during the process; they are -oxidized in the respiratory chain producing 5 molecules of ATP.

.Citric acid cycl~ Definition: It is sequences of reactions by which acetyl CoA is oxidized to C02, water and energy. • Citric acid cycle is the final common pathway for the oxidation of carbohydrate, lipid, and Site: All the steps of citric acid cycle occur in mitochondria. State: Under aerobic conditions in the presence of oxygen. Intracellular location of TCA cycle: All enzymes of the TCA cycle are present in the mitochondria except Succinate dehydrogenase which is bound to the inner mitochondrial membrane and acts as a component of respiratory chain. Steps: Citric acid cycle begins by condensation of acetyl CoA {2 carbons) produced from pyruvate with oxaloacetate (4 carbons) to form citrate (6 carbons) which is reconverted to oxaloacetate again by the end of the cycle. Energy produced from oxidation of 2 molecules of acetyl CoA: Oxidation of one molecule acetyl CoA in citric acid cycle produces {1 OATP) .• So, two molecules produce 20 ATP. Regulation of citric acid cycle: 1. It is stimulated by t ADP & NAD, both activates PDH complex, pyruvate carboxylase, citrate syntheses and isocitrate dehydrogenase. · • Activation of pyruvate carboxylase {enzyme responsible for conversion of pyruvate to oxaloacetate) and activation of PDH {enzyme responsible for conversion of pyruvate to acetyl CoA) increase the level of substrates. 42

2. It is inhibited by




citrate and by accumulation of end products. · -----·- ---·- ·-·· acetyi-CoA





citrate synthase

oxaloacetate ·





Citric_acid cycle

NAo+ isocitrate dehydrogenase





a-ketoglutarate dehydrog



sucdnyt-coA synthetase ~ 4 ~-e:. ·· --- --

·· -· ·-




Biomedical importances of citric acid cycle: TCA cyde is said to be amphibolic in nature i.e. has dual functions: ; I. Anabolic functions: The intermediates of the citric acid cyde such as citrate, a ketoglutarate, succinyl CoA and malate are used as prea.Jrsors in the biosynthesis of many compounds: 1. Synthesis of fatty acids from citrate. Excess citrate penetrates the mitochondria through citrate shuttle to cytosol and cleaved by an ATP dependent citrate lyase to oxaloacetate and acetyl CoA 2. Synthesis of ketone bodies and cholesterol from acetyl CoA. 3. Synthesis of glucose (gluconeogenesis) from intennediates of the cycle. 4. Synthesis of some non- essential amino acids: Pyruvate-. alanine Oxaloacetate-.Aspartate a- ketoglutarate-+Giutamate. 5. Synthesis of porphyrins & heme from succinyl CoA 43


Succinyl CoA +Glycine~ Heme. Catabolic functions: Common pathway for oxidation of carbohydrates, fatty acids and amino acids occur and the road of interconversion between carbohydrate, lipids and proteins.

Synthesis of ketone bodies &Cholesterol

carbohydrates, lipids &proteins Oxidation of carbohydrates lipids & proteins

functions of TCA cycle

Energy yields from complete oxidation of one glucose molecule: 1. Glycolysis: 5~7 ATP. 2. Oxidative decarboxylation of pyruvate (2 molecules of pyruvate):5 ATP 3. Oxidation of 2 acetyl CoA in the citric acid cycle: 20 ATP • So net energy= 30-32 ATP


Alternative pathways for glucose oxidation 1. Hexose monophosphate pathway (HMP). 2. Uronic acid pathway.

Hexose Monophosphate Pathway (HMP) or (Pentose phosphate pathway) Definition: ·It is the pathway by which glucose is converted to pentose phosphate with production of NADPH and C02 without consumption or production of ATP. It is multicyclic process because: 1. 3 molecules of glucose-6- phosphate enter the cycle producing 3 molecules of C02 ,6 molecules of NADPH and 3 molecules of 5 Carbon sugars. 2. S Carbon sugars are rearranged to give 2 molecules of glucose -6- P (re-enter the cycle) and one molecule glyceraldehyde -3- P. Site: It proceeds in all tissues that require NADPH such as: 1. Erythrocytes: It is most active site; it requires NADPH to keep glutathione in reduced form. 2. Liver, mammary glands, and adipose tissue where it supplies NADH+H+ for fatty acid synthesis (these are the sites for synthesis of fatty acids). 3. Adrenal cortex, ovaries and testes and placenta {supplies NADPH+H+ for synthesis of steroids, male and female sex hormones). 4. Tissues that requires ribose -5-p for nucleotide, nucleic acids and coenzyme synthesis. Intracellular location: The enzymes of this pathway are in the cytoplasm. Steps: Pentose phosphate pathway occurs in two phases: 1. Irreversible oxidative phase: it consists of three reactions that lead to the formation of ribulose 5-phosphate, C02, and two molecules of NADPH for each molecule of glucose 6phosphate. • Key enzyme is glucose-6- phosphate dehydrogenase (G-6-P). • NADP is the coenzyme. NAOP



~g++ 2

Glucose-6-P dehydrogenase






6- phosphogluconate

Gluconolactona hydrolase NAOP

Ribulose-5-Phosphate 2. Reversible non- oxidative phase: re-arrangement of the 3 molecules of ribulose-5phosphate to reform ribose -5- phosphate, and intermediates of glycolysis (fructose-6phosphate and glyceraldehyde _3- phosphate). • Transketolase and transaldolase are the enzymes of this phase. • Thiamine pyrophosphate (TPP) is the coenzyme of transketolase. 45

Ribulose-5-phosphate ~ RibU!ose-5-P

Rib~lose-5-P ~






Transketolase (TPP coenzyme} Sedaheptulose-7-phosphate

Glyceraldehyde 3-phosphate

Fructose &-phosphate



Fructose 6-phosphate



Hexose Monophosphate pathway (HMPl in muscles: In muscles, oxidative phase of HMP is not active due to deficiency of glucose-6-p dehydrogenase, so pentoses in muscles are formed by the reverse of the non- oxidative phase. Regulation: The key enzyme is glucose-6-phosphate dehydrogenase. 1. Insulin induces key enzyme synthesis. 2. It is strongly inhibited by excess NADPH. Functions of hexose monophosphat shunt are: 1. It provides the body with ribose-5-phosphate for the synthesis of nucleotides (ATP, ADP, AMP etc.) and nucleic acids (DNA and RNA), coenzymes (NAD, NADP) and some vitamins like vitamin 82. 2. It is the main source of NADPH: Importance of NADPH is: a. Synthesis of fatty acids, cholesterol, vitamin 03, steroid hormones and bile acids. b. Maintenance of the integrity of red blood cell membrane and prevent hemolysis: NADPH is essential for keeping of the reduced form of glutathione (G-SH). Reduced glutathione is essential for keeping the red blood cell wall intact by the following mechanism: • Keeping the iron of hemoglobin in ferrous state so ·prevent forl'!"ation of methemoglobin. • Keeping the globin of hemoglobin in native state. • Preventing accumulation of free radicals as H20 2 in RBCs so keeping RBCs wall intact. 46

c. Bactericidal effect: During the respiratory burst the macrophages synthesize H202 in order to kill bacteria, later on H202 is detoxicated by NADPH+H. d. NADPH is very important for vision (see visual cycle). e. Detoxifies foreign compounds such as peroxides, drugs and carcinogens. f. It is required for the synthesis of nitric oxide NO which acts as a vasodilator molecule and as a neurotransmitter.

Clinical application: Favism: Definition: It is genetic acute hemolytic anemia with hemoglobinuria in some persons with G6PD deficiency. • It is an inherited X-linked disease. It affects males only because the gene of glucose -6-p dehydrogenase enzyme is on the X chromosome. • It is a type of hemolytic anemia. • It the most common genetic defect. Cause: Deficiency of glucose- 6- phosphate dehydrogenase (G6PD) enzyme.

Glucose-6-Phosphate dehydrogenase







Precipitating factors of favism are: 1. Oxidant drugs: Antibiotics (for example, sulfa- methoxazole and chloramphenicol), Antimalarial drugs (for example, primaquine), and some antipyretics and Anti-inflammatory drugs (for example, acetanilide and aspirin). 2. The fava (broad) bean, a dietary staple in the Mediterranean region. The hemolytic effect of ingesting fava beans is not observed in aU individuals with G-6-PD deficiency, but all patients with favism have G-6-PD deficiency. 3. Infection: Infection is the most common precipitating factor of hemolysis in G6PD deficiency. The inflammatory response to infection resutts in the generation of free radicals in macrophages, which can diffu se into the red blood cells and cause oxidative damage. Biochemical bases (mechanism) of Favism: 1. NADPH in erythrocy~es is formed only by the pentose phosphate pathway. 2. NADPH converts oxidized glutathione (GSSG) to reduced glutathione (GSH). 3. Reduced glutathione is essential for detoxication of H20 2 . 4. G-6-PD deficiency ~ decrease NADPH production~ inh ibits generation of reduced glutathione ~ No detoxification of H2 0 2 . ~ Destruction of red cell membrane~ hemolysis.

Pathways of glucose 6-phosphate metaboism in the erythrocyte. HMP=hexose monophosphate pathway. Effects of H60 6 on red blood cells: 1. Lipid peroxidation: It affects cell membrane lipids by peroxidation leading to hemolysis. 2. Oxidation of iron in hemoglobin to ferric state so hemoglobin is converted to methemoglobin. Methemoglobin has no capability to carry oxygen. 3. Cause denaturation of globin part in hemoglobin. Symptoms and signs of favism: 1.Hemolytic anemia with hemoglobinuria 2. Neonatal jaundice appearing 1-4 days after birth. The jaundice, which may be severe, typically results from increased production of unconjugated bilirubin. 3. Chronicity and sever complications leads to death. • Treatment: • The only treatment is to avoid the above factors and by blood transfusion during the attack of hemolysis. 48

Uronic Add Pathway--- -- •

It is a minor alternative pathway for glucose oxidation in which glucose is converted to glucuronic acid. • This pathway occurs in the cytoplasm of liver mainly. Active form of glucuronic acid: is uridine diphosphate glucuronic acid (UDP-glucuronic acid). Functions of UDP-alucuronic acid: --~ _________ _ 1. Synthesis of glucosamines and glucosamine to form mucopolysaccharides. 2. Detoxification of drugs, chemicals, antibiotics and hormones it converts them to corresponding soluble glucuronides which are excreted. 3. Conjugation with bilirubin. Unconjugated biJirubin is conjugated with UDP-gluauonic acid and converted to soluble mono and diglucuronides. 4. Enters in hexoses monophosphate shunt ·- _;- -- 5. Synthesis of vitamin C but not in human. 6. Synthesis of Heparin, chondroitin sulphate and hyaluronic -acid. Clinical importance: · Essential pentosuria: • It is a rare asymptomatic genetic disorder. Cause: Inherited deficiency of NADPH dependent L-Xylulose reductase. L-xylulose L-XyluloseX reductast;. L-Xylitol Laboratory findings: • L-xylulose cannot be converted to xylitol ~ Accumulation of xylulose in blood. • Excretion of large amounts of L-xylulose in urine and gives positive benedict test_ N.B. major sources of phosphorylated Pentose in the body is HMP because there is no pentokinase in the body.



Glycogen Metabolism •

It is the storage form of gJucose in animals. It is highly branched homopolysaccharide formed of glucose monomers.· Glycogen is present mainly in: A. Liver (about 100 gm or Pr10% of its weight). B. Muscles (400 gm or 1-2%ofits weight) .. ·-·--·--· Functions of glycogen are: (1) Liver glycogen maintains normal blood glucose level during early stage of fasting (especially between meals). Glycogen stores are depleted after 12-18 hours of fasting. (2) Muscle glycogen: it ads as a source of energy during muscle contraction. Glycogen metabolism includes: ·....

(1) Glycogenesis: It is the synthesis of glycogen from glucose in the liver and muscles. (2) Glycogenolysis: It is the breakdown of glycogen into glucose in the liver and lactic acid iq muscles.

Glycogenesis Definition: Glycogenesis is the formation of glycogen from glucose in the liver and musdes. Substrates for glycogen svnthesis are: A) In liver: (1) Blood glucose. fructose and galactose. (2) Non- carbohydrate souroes as lactic acid. B) In muscles: From blood glucose only. Intracellular location: Cytoplasm of the liver and muscle cells. State: Well fed state . . Steps: See diagram. · I Key enzyme: glycogen synthase enzyme. N. B. • UTP= Uridine triphosphate. UDP = Uridine diphosphate. • Glycogen primer is either: A. Fragment of glycogen in cells whose glycogen stores are not totally depleted. B. Protein, called glycogenin. • Key enzyme is glycogen synthase. Regulation of glycogenesis: The key regulatory enzyme is glycogen synthase enzyme. Active form is dephosphorylat~d . form. Activation: It is activated by: • high level of G-6-P and ATP. • 1nsulin hormone which stimulate the phosphatase~ dephosphorylate glycogen synthase. Inhibition: It is inhibited by: • Glucagon and epinephrin~Phosphorylation of the enzyme.


G-0 1-+4- Ghu:osidic bond e UnlabeSed g!uoose msidu9 OfO 1-+6- Ghreosittic bond


~ gM:los9 msidua

The biosynthesis of glycogen. Glucose ~~~G-Iu_co_ki_nase _ _(l_n_INer_~)-....,


Hexokinase (in muscles)


JPhosphosJucomutasel Glucose-1-phosphate


~ ppa "f-



Giycogenin } UDP-Giucoso


Glycosenprimer UDP

Giycogon fragmont


..£.-... ~-



Glycosen synthase


oc (1 ~4) glucosyl units ~~B~ra-n-ch-=-:-ing-enzyme---.1

Glycogen oc (1--)..4) and -c. {1--)..&)slucosyl units


Steps of!"'cosenesis



Glycogenolysis Definition: It is the breakdown of glycogen into glucose in liver and lactate in muscles. • Glycogenolysis occurs in the liver during the fasting state (in between meals and at night, it starts approximately 4 hours after the last meal and lasts for 12"!'18 hours. Site: Cytoplasm of liver and muscles. --- • Small amount (1-3%) of glycogen is continuously degraded by the lysosomal enzyme, a (1 -... 4) glucosidase (acid maltase). Steps of glvcogenolvsis: 1. Glycogen phosphorylase (it requires PLP as a coenzyme) (Key enzyme) +transverse enzyme +Debranching enzyme~ glucose 1-phosphate. -- --- - -------------- -2. Glucose 1-phosphate is converted to glucose 6-phosphate by phosphoglucomutase. 3.. Fate of glucose-6- phosphate: · ··· A. In the liver: glucose 6-phosphate is converted to glucose by glucose 6-phosphatase. B. In the muscles: there is no glucose 6-phosphatase in muscles so, glucose-6-phosphate enters glycolysis, providing energy needed for muscle contraction. Glycogen

~~ ~ Glycogen:hosphorylase Transferase + Debranching enzyme

Free glucose

Glucose-1- phosphate


Glucose-6-phosphate HzO

No glucose-6- phosphatase


Glycolysis -----:i~~ Energy

in muscles

Glucose-6-phsphatase in liver

Pi Glucose

Key enzyme of glycogenolysis: Glycogen phosphorylase. Regulation of glycogen metabolism: • Glycogenesis _and glycogenolysis regulation is reciprocal i.e. when one is activated the other is inhibited. • In the liver, glycogenesis accelerates during periods well fed, whereas glycogenolysis accelerates during periods of fasting.


In skeletal muscle, glycogenolysis occurs during active exercise, and glycogenesis begins as soon as the muscle is again at rest 1.Hormonal regulation. • Insulin hormone releases in fed stat~ (After meai)-+Activation of glycogenesis and inhibition of glycogenolysis. • Glucagon (in fasting st~te) -+ activation of glycogenolysis and inhibition of glycogenesis. Blood glucose level tends to be increased. 2.Regulation by Calcium ions and calmodulin protein: Calcium released during muscle contraction binds to a protein called calmodulin -+Activated calmodulin -+ Activation of glycogenolysis and inhibition of glycogenesis. Disorders of glycogen metabolism: They include glycogen storage diseases. Glycogen storage diseases_are group of inherited congenital diseases characterized by the-accumulation of glycogem in tissues. The most important glycogen storage diseases are: (1) Von Gierke's disease (Type 1). (2) Pompe's disease (Type II). (3) Cori's disease (Type Ill). (4) Anderson's disease (Type IV). (5) Me Ardle disease (Type V). (6) Hers disease (typeV1) (1) Von Gierk's disease (the most common type): Causes: Inherited deficiency of glucose-6-phosphatase enzyme-+over load of the liver with glycogen (hepatomegaly) and may cause liver cirrhosis. Symptoms and signs: It occurs nearly at the age of one year. (1) Hepatomegaly. (2) Fasting hypoglycemia: deficiency of glucose-6 phosphatase will inhibit both gluconeogenesis and glycogenolysis on fasting. (3) Lactic acidosis due to decreased gluconeogenesis with accumulation of lactate. (4) Mental and growth retardation.



(6) Hyperuricemia as follow:

ttGiucose-6-p --+

tt ribose-5-p J,

t Purine nucleotide synthesis in the liver J,

tt Production of uric acid --+

Gouty arthritis

(N.B.): The patients die in childhood. (2) Pompe's Disease (Type II): Normally about 3% of cellular glycogen is hydrolyzed by the lysosomal a 1-4 glucosidase. Congenital deficiency of a 1-4 glucosidase -+ accumulation of glycogen in the lysosomes of many tissues including the heart -+ death before 2 years old due to heart failure. -


(3) Cori's Disease l!ype llll: His due to deficiency-of the debranching enzyme in the rwer-+ inhibit glycogenolysiS-+ mild fasting hypoglycemia and mild hepatomegaly. Gluconeogenesis is not affected by the debranching enzyme which has no role in gluconeogenesis. (4) Anderson's Disease l!ype IVl (Amvlopectinosisl: This type occurs due to deficiency of the branching enzyme --+ Synthesis of unbranched glycogen {formed of straight chain only) ~ liver fibrosis and early death. (5) Me Ardle's Svndrome l!ype Vl: It is due to deficiency of the muscle phosphorylase-+ . accumulation of glycogen in muscles with ..1. in ATP during muscle exercise. Decrease of ATP --+ painful muscle cramps on exercise ~ damage of muscle cells with increase in the serum level of muscle enzymes e.g. creatine phosphokinase {CPK) and lactate dehydrogenase (LDH). (6) Her's -~isease (Type VI): There is a genetic deficiency of hepatic phosphorylase -)>hepatomegaly and fasting hypoglycemia. S.ummary of glycogen storage diseases: Disease

Deficient enzyme

Organ Clinical features affected . Von Gierk's disease glucose-6Uver and Hypoglycemia, hepatomegaly, (Type I) phosphatase kidney Gout, mental and growth enzyme retardation Pompe's Disease lysosomal ex 1-4 All organs Enlarged organs as tongue and (Type II): heart leading to heart failure glucosidase Cori's Disease (Type Debranching Muscles and Hypoglycemia, hepatomegaly, Ill): enzyme hypotonia and sometimes affect liver the heart Anderson's Disease branching fibrosis· and Liver Uver (Type IV)· enzyme cirrhosis,hypotonia and death Me Ardle's Syndrome muscle Muscle weakness, fatigue and Muscles muscle cramps phosphorylase, and Hypoglycemia Her's Disease Uver hepatic hepatomegaly phosphorylase -


Gluconeogenesis Definition: It is the synthesis of glucose or glycogen from non-carbohydrate sources such as lactate, pyruvate, glucogenic amino acids, propionyl CoA and intermediates of citric acid cycle. Site: Liver (90%) and Kidney {10%) because both organs contain glucose -6- phosphatase enzyme. State: Fasting state with absence of insulin. It stars 6-8 hours fasting and reach maximum after 18 hours after complete exhaustion of glycogen in liver. Gluconeogenic substrates or precursors: Gluconeogenic precursors are molecules that can be used to produce a net synthesis of glucose, they include: 1. Lactate and pyruvate: Lactate is released into the blood by exercising skeletal muscle, and by cells that lack mitochondria, such as red blood cells. lactate diffuses into the blood-7taken up by the liver --7 pyruvate--7 glucose by gluconeogenesis~released back into the circulation. 2. Glucogenic amino acids: • Glucogenic amino acids: These are amino acids whose catabolism yields pyruvate or one of the intermediates of citric acid cycle e.g. Alanine,serine,aspartate,phenylalanine and tyrosine. • Alanine gives glucose in liver by glucose alanine cycle. (Glucose ___.. Pyruvate-. Alanine-. Pyruvate -> Glucose) glucose-alanine cycle: is the series of reactions in which amino groups and carbons from muscle are transported to the liver. 1t is quite similar to the Cori cycle in the cycling of nutrients between skeletal muscle and the liver.


- - --.;...._--'l-



2 Pyruvate

" " ' r,.,

Glucose - ------?-


- loss




Equilibrium Intake = Loss


-ve nitrogen balance Loss> intake


1. Equilibrium: This condition is present in normal adults.

I Nitrogen

intake- Nitrogen loss


2. Positive nitrogen balance: Nitrogen intake is more than nitrogen losses. Occurs in Conditions associated with increase in synthesis of tissue proteins. • In growing children. • Pregnancy and in lactating women . • Convalescence. 3. Negative nitrogen balance: Nitrogen loss is more than nitrogen intake in the following: • Low intake of proteins: in starvation, malnutrition , and gastrointestinal tract diseases. • In diseases associated with loss of tissue proteins like bums, hemorrhage and kidney diseases. • Diseases associated with high breakdown of tissue proteins such as diabetes mellitus, hyperthyroidism, fever and infection . Protein Turnover •

All the proteins in the body are in dynamic state, constantly degraded to their constituents of amino acids and re-synthesized again.


The rate of this turnover is variable. for different proteins in different tissues. For example, high rates of turnover have been shown in proteins of plasma, liver and kidneys while low rates have been shown in the muscles, skin and brain. hyperthyroidism, fever and infection.

General metabolic pathways of amino acids_ General metabolic pathways of amino acids-inclu-de: · (1) Transamination. (2) Dearl')ination. (3) Transdeamination. (4) Decarboxylation ofarrnno acids

(1) Transamination Definition: It is the transfer of a amino group from a amino acid to a Keto acid (usually a ketoglutarate) to fonn a new amino acid (nonessential amino acid} Jusua11y glutamate) and new a Keto acid. • It is only transfer of NH2 group and no free ammonia is released.

ITransaminase I

)- New amino aid+ new ~-Keto acid

Amino acid+ at -Keto acid ( • •

Transamination is a reversible reaction. All of the common amino acids except lysine, threonine, proline, and hydroxyproline participate in transamination. Intracellular location of transamination: Cytosol and mitochondria of cells throughout the body. (Major tissues are liver, heart, kidney, intestine, muscles and brain). Enzymes of transamination: They are called transaminases or aminotransferases. Coenzyme: It requires pyridoxal phosphate (PLP) as a coenzyme. Substrates: amino acids and Keto acids. There main three keto acids which acts as recipient molecules in transamination reactions are a Ketoglutarate, pyruvate and oxaloacetate. . Products: New a-Keto acid and new nonessential amino acid. • a-Ketoglutarate is the commonest a Keto acid utilized by transamination. It is converted to glutamate.

~ ~


R-C-mOH + 1




H Aminoatitl

et.· KetoGiutarate(KG)



keto dWI ...:.1

Examples of transaminases are: 1. Alanine transaminase. 2. Aspartate transaminase. 3. Glutamate transaminase. 1. Alanine transaminase or (ALT): •

It was previously called glutamate - pyruvate transaminase (GPT}.



H New amino acid

It catalyzes the transfer of the amino group from alanine to a ketoglutarate to form glutamate and pyruvate. The reaction is reversible. Pyridoxal phosphate (PLP)is the coenzyme.




Alpha koto slutorote


The enzyme is present mainly in the cytoplasm and mitochondria of the liver, heart, and skeletal muscles. • Normal serum level is 5-35 IU/l. 2. Aspartate transaminase (AST): • It was termed glutamate - oxaloacetate.transaminase (GOT). • AST transfers amino group from aspartate to a-ketoglutarate, forming oxaloacetate and glutamate. The reaction is reversible and pyridoxal phosphate (PLP) is the coenzyme. COOH






COOH Aspartate



I CH~ +

Aspal"hhte tnmsamln,._









[email protected] I


CH 2



o(. -Kooglutorotv


f"z crz



COOII Glutamate

The enzyme is present in the cytoplasm and mitochondria of the liver, heart, and skeletal muscles but mainly in the heart. • Normal serum value is 5-40 IU/L. Glutamate transaminase enzyme: . • It catalyzes the transfer of amino group from any amino acid (except lysine) to a Keto glutamate to form glutamic acid and the corresponding a Keto acid. • It is widely distributed in tissues. • The reaction is reversible. • PLP is the coenzyme. Diagnostic value of plasma aminotransferases: • Aminotransferases are normally intracellular enzymes, with the low levels found in the plasma representing the release of cellular contents during normal cell turnover. • The presence of elevated plasma levels of aminotransferases indicates damage to cells rich in these enzymes. For example. physical trauma or a disease process can cause cell lysis. resulting in release of intracellular enzymes into the blood. They are of diagnostic value in: 1. Hepatic diseases: • Serum AST and ALT are elevated in nearly all liver diseases, espetially in conditions that cause extensive cell necrosis, such as: a. Acute viral hepatitis. b. Toxic injury. 92

• ALT is more .specific than AST for liver disease. 2. Non- hepatic disease: • AST is more specific for myocardial infarctiol') and muscle diseases as myasthenia gravis. N. B. Myocardial infarction-+ t AST while Hepatitis & alcohol cirrhosis-+ t ALT & AST. Metabolic importance of transamina.tion: • It is important for synthesis of non-essential amino acids. • It prevents toxicity of ammonia as its not released as free ammonia. • In case of low energy, the organism depends on oxidation of a ketoacids produced by transamination for subsequent gluconeogenesis.

2- Deamination Definition: Removal of the amino group from an amino acid in the form of_ free a~J!lQnia with formation of a. - Keto acid.




There are two tvpes of deamination: Dearnination



Non- oxidative


Oxidative deamination: Definition: His removal of free ammonia from amino acid coupled with oxidation (removal of hydrogen). H liberates free NH 2 and a Keto acids. · Organ: Liver and kidney. Pathway: It has two pathways: 1. Major pathway: It is catalyzed by Glutamate dehydrogenase. 2. Minor pathway: It is catalyzed by one of the following enzymes: 1. L-amino acid oxidase acts on naturally occurring L-amino acids. Ravine mononucleoti~e (FMN) is the coenzyme). 2. D- armno acid oxidase acts on D-amino acids which found in plant food and cell wall of microorganisms. Oxidative deamination by L-alutamate dehydrogenase: 1. Glutamate dehydrogenase is zinc containing enzyme present in cytoplasm and mitochondria of most tissues mainly in liver and kidney. It is very active enzyme. 2. It deaminates glutamic acid to a Keto-glutarate with the release of free ammonia and a-keto acid (a-ketoglutarate). The reaction is reversible. Coenzyme: Glutamate dehydrogenase can use either NAD+ or NADP+ as a coenzyme. (I)

NAD+Hz 0






Glutomato dohydroaan.ase











(II) Non - oxidative deamination: It is deamination not coupled with oxidation. It is suitable for sulfur and hydroxy containing amino acids.

3.Transdeam ination Definition: It is combination between transamination (by glutamate transaminase) and oxidative deamination (by L-glutamate dehydrogenase). It is the most effective-method for deamination of amino acids. • The amino group of most amino acids is transferred to a ketoglutarate to form glutamate and new Kato acid (Transamination) then glutamate is deaminated by glutamate dehydrogenase with release of free ammonia (deamination).



-'-ketoglutarate + NH3

Products of deamination and transdeamination of amino acids: A. The carbon skeleton which goes to: 1. Glucogenic fate: i.e. synthesis of glucose by gluconeogenesis. 2. Ketogenic fate: only leucine and lysine. 3. Both glucogenic and ketogenic fate: mainly for phenylalanine, tyrosine, tryptophane, and isoleucine. B. Ammonia: see metabolism of ammonia.

Decarboxylation of amino acids Definition: It is the removal of alpha carboxyl group from amino acid by amino acid decarboxylase enzyme to produce corresponding amine. R-yH--~

Amino acid dcacarboxylasca


C0 2

NH 2 Amino acid

Examples: 1. Decarboxylation of histidine to histamine. 2. Decarboxylation of glutamic acid to GABA.



R-CH 2 -NH2 Amine

3. Decarboxylation of tyrosine to tyramine. 4. Decarboxylation of Ornithine to putrescine. 5. Decarboxylation of lysine to cadaverine by micro-organisms.

Metabolism of Ammonia Ammonia is produced by all tissues during the metabolism of a variety of compounds, and it is removed from the body mainly by formation of urea in the liver. • The level of ammonia in the blood must be kept very low, because even slightly elevated concentrations (hyperammonemia) are toxic to the central nervous system (CNS). • At physiological pH ammonia is present as NH4+ions. • Liver is the site of detoxification of ammonia into urea so in liver cell failure, ammonia increase in blood. Sources of ammonia: 1. Amino acids: by oxidative, non-oxidative deamination and by transdeamination in liver. 2. Glutamine: By the action of glutaminase enzyme in liver, kidney and intestine. •


I .

f0-NH 2

f H - N H2





I fH_-NH.z









COOH Glutarnarta

COOH Glutamlno

Hydrolyal• of alutamlna to form ammonia

3. By the action of bacterial enzymes in the intestine: Ammonia is formed by the action of bacterial urease enzyme on urea in the lumen of the intestine. 4. Monoamines e.g. epinephrine, give rise to ammonia by the action of mono amine oxidase. 5. From purines and pyrimidines: In the catabolism of purines and pyrimidines, amino groups attached to the rings are released as ammonia.


-..Keto acid



Acyi-CoA synthetase






Hippuric acid


l- Tyrosine

Dihydroblopterln + H20


Tyrosine hydroxylase


3.4 dihydroxyphenylalanlne (DOPA)

COz Dehydro ·ascorbate +Hzo


Phenylethanolamine N-methyltr.ansfer.ase

mRNA-I>Protein Blologlcallnfonnatlon flow DNA synthesis (Replication): Definition: Replication is the synthesis of daughter DNA from parental DNA. • Occurs during the S phase of the cell cycle, .takes about 9 hours in typical cell and is catalyzed by a complex of proteins. • It oecurs in both prokaryotes and eukaryotes.


parental DNA ~dUU:IL'I::I


Basic requirements for DNA synthesis are: 1. Substrates: deoxyribonucleoside triphosphates (dATP, dTTP, dCTP, and dGTP). All four deoxyribonucleoside triphosphate must be present for DNA elongation to occur. If one of the four is depleted, DNA synthesis stops. 2. DNA Template: It is single stranded DNA formed after separation of the DNA double helix. 3. Primers: Short strands of RNA approximately ten nucleotides long are synthesized first before elongation of strands occur, using the parent DNA strand as a template to direct the RNA synthesis. 4. RNA primase: It is the enzyme responsible for synthesis of the primers 5. DNA proteins. Dna A protein, DNA Helicase, single stranded binding proteins (SSBs}, and DNA topoisomerases. 6. DNA polymerases. In prokaryotes, there are three types of DNA polymerases mediating DNA replication: a- DNA polymerase Ill holoenzyme: "Team Captain". DNA polymerase Ill holoenzyme is the enzyme primarily responsible for DNA synthesis in E. coli. It encircles and travels along the template DNA strand laying down new nucleotides as it moves. b- DNA polymerase II: DNA polymerase II is essentially a proofreading and repair enzyme. C- DNA polymerase 1: fills in the small gaps during replication and repair.


Characteristic of replication: 1-Semi-conservativ e replication i.e. half of the parental DNA is conserved in each new double helix and paired with a newly synthesized complementary strand.

Sernicons ervative replicatio n




. .-18--0td

2-Bidirectional: Replication process starts from origin and proceeds in two opposite directions. Origin of replication i

3-High fidelity: It means that it is of high accuracy. 4-semi-continous: one newly formed strand is synthesized continuously while the other strand is discontinuing. Summary of steps of replication in prokarvotes: 1-lnitiation: 1- Determination of the origin of replication, its melting and binding to Dna A protein. 2- Helicase breaks the hydrogen bonds holding the base pairs of the parental strands together. 3- Unwinding of the parental strands and formation of two replication forks. 4- Prevention of reannealing of the strands by Single-stranded DNA-binding protein (SSB).


Ori~n of replication

_A_ ---v -

Replication r - bubble ---.,

~ Replication fork

Replication fork










ed ~d-nd s:_F'~\~~ing

DNA protein [558)

11-Eiongation: 1. Supercoil formation (during formation of replication fork), they are removed by topoisomerases. 2. Synthesis of primers by primase enzyme. 3. Attachment (annealing) of the primers to each parental strand according to base pairing rule. 4. Synthesis of new complementary strands by DNA polymerase Ill in the form of leading and lagging strands. They are synthesized in the 5' --+ 3' direction (Leading strand is synthesized continuously and the lagging strand is synthesized discontinuously as a series of small fragments known as Okazaki fragments ).

,. Parental duplex ~

fork progressi on

Ill-Termin ation: 1. After complete synthesis of the complementary strands RNA primers are removed by DNA polymerase I. 2. DNA polymerase I fills in the resulting gaps by synthesizing DNA, beginning at the 3' end of the neighboring Okazaki fragment. 3. Both DNA polymerase I and Ill can proofread their work by means of a 3' --+ 5' exonuclease activity 4 . DNA ligase seals the nicks between Okazaki fragments , converting them to a continuous strand of DNA. 5. Rewinding of the strands again.






T..o 't"I..CN.l-Mttrtt


1111111111111111111111 3' ATGT 5'



3. Lesch-Nyhan syndrome! • It is an inherited disorder presents at birth in baby boys. Cause: Deficiency of HGPRT.


hypoxanthine-g ~----------uanine --------------~ phosphoribosy l transferase


Guanine + PRPP ~ Guanylate+ PPi Hypoxanthine + PRPP~ lnosinata + PPi

Symptoms: 1. Sever gout. 2. Sever physical and mental problems. Biochemical bases: • Accumulation of PRPP ~ t De novo synthesis of purine ~ t uric acid formation ~ Hyperuricemia (The disease is associated with mental retardation, tt uric acid, which is · manifested by renal disease together with gout and renal stones). Metabolic disorders of pyrimidine metabolism: Orotic aciduria: • This hereditary condition is characterized by high levels of urinary orotic acid. Cause:_Deficiency of orotate phosphoribosyl transferase or orotate monophosphate decarboxylase. Clinical picture: retarded growth, and severe anemia.


Principal elements 1- Calcium Sources: 1. Animal sources: Milk, cheese & yoghurt are very rich sources. 2. Plant sources: Vegetables, fruits, and egg yolk are medium sources. Absorption: 30% of the dietary ca++ is absorbed. It is usually in the form of calcium phosphate or carbonate. Site: First and 2nd parts of the duodenum. Absorption requires a carrier protein; and energy. Factors increase Ca++ absorption are: (1) Vitamin D: Calcitriol(1-25dihydroxycholicalciferol) induces the synthesis of calcium bi~~ing protein in the intestinal epithelial cells. (2) Parathyroid hormone : It helps calcium absorption through activation of vitamin D. (3) Low pH (acidity), increases ca++ absorption because calcium salts in the form of calcium phosphate or carbonate are soluble in acidic solutions . (4) High protein diet: especially those contain arginine and lysine amino acids because they increase acidity and solubility of ca•• salts . (5)Sugars and organic acids: Microbial fermentation of sugars in the gut increase solubility of ca++ salts.

(6) Citric acid due to its high acidity. Factors decrease calcium absorption are: (1) Factors which reduce calcium solubility by the formation of insoluble Ca salts e.g.: • Excess phytic acid which present in cereals. • Excess oxalates in mango and green leafy vegetables. • Excess phosphate, as it precipitates ca++ as calcium phosphate (Ca: P ratio is 2:1 ). • High fat diet ~ insoluble ca++ salts. • Excess fibers interfere with its absorption. (2) Malabsorption syndrome reduce the absorption of calcium due to formation of insoluble calcium salts with fatty acids insoluble ca++ salts. (3) Alkaline medium due to formation of insoluble tricalcium phosphate, so excess alkali intake as in treatment of peptic ulcer decrease calcium absorption. (4) Glucocorticoids because it reduces intestinal calcium absorption. (5) Calcitonin hormone: it reduces intestinal calcium absorption indirectly inhibiting activation of vitamin (6) Advancing age and inflammatory intestinal conditions also decrease intestinal absorption. Distribution of Ca2+: Total body ca++ is from 1 to 2 kg in 70 kg body weight, they are disrupted as follow: 1-8keleton and teeth:99% are present in the skeleton and teeth in the form of hydroxyapatite Ca1o(P04)&(0H)2. 2-Tissues and body fluids (it is mainly extracellular), they contain 1%. N.B No Ca++ in RBCs.


Body calcium



Skeleton& teeth 99%

Tissues& body fluids

1% plasma calcium: plasma ca++ level is 9-11mg/dl. It exists in two forms: 1-Non-diffusible (45% l : is bound to albumin it is physiologically inactive form. It was found that every one gram decrease in albumin leading to decrease total plasma calcium about 0.9 mg/dl. 2-Diffusible calcium ( 55 °/o ) it may be ionized and non-ionized. a- Non -Ionizable form (5%): In the form of calcium citrate. 'It is physiologically inactive form. b- lonizableform (50%): Free ionized calcium is the only physiologically active form. If ionized calcium is decreased. tetany will occur. Plasma calcium



Non diffusible 45%

Diffusible 55%



Ionizable 50% Physiologically active


Non ionizable 5% Physiologically inactive

Regulation of plasma calcium: Regulation of plasma calcium (calcium homeostasis) depends on: I. Hormonal regulation: It depends upon three hormones act on three organs: 1- Three main hormones are: parathyroid hormone. calcitriol & calcitonin 2. Three main organs: bone. kidney and intestine. II. Non hormonal: Acidosis. alkalosis. hypoalbuminemia.

Regulation of plasma calcium

I Non hormonal Acidosis Alkalosis Hypoalbuminemia



Two hormones


plasma calcium (Parathyroid hormone& calcitriol)



One hormone ~ plasma calcium (Calcitonin)

Hormonal regulation : Hormones that increase blood calcium are: 1- parathyroid hormone: it increases calcium level & decrease phosphorous in blood through its action on: (1) bone: increases mobilization of calcium from bone to the blood through: • Increase the number and activity of osteoblasts so cause demineralization of bone. • Release of lactic acid to the surrounding medium which solubilize calcium. • Release of collagenase enzyme from osteoclasts which increase bone resorption with release of ca++ and phosphate from hydroxyapatite. (2) Kidney: a-t reabsorption of calcium and decrease absorption of phosphate from the renal tubules. b-Promote the production of 1-25 dihydroxycholicalciferol by stimulation of 1-hydroxylion of 25-hydroxylcalciferol to form 1-25 dihydroxycholicalciferol in the kidney. (3) Intestine: t of the ca++ absorp~ion from the intestine by activation of vitamin D which in turn increase of synthesis of calbindin protein that carry calcium. II-Vitamin 03 (Calcitriol): It increase plasma calcium and phosphate through its action on: 1-lntestine: It increase intestinal absorption of calcium and phosphate by increasing the synthesis of ca++ binding protein (calbindin protein) which is responsible for ca++ absorption. 2-Bone: Calcitriol together with parathyroid hormone increase the mobilization of calcium and phosphorus from bone. 3-Kidney:t of reabsorption of ca++ and phosphorus by renal tubules. Hormone that decrease blood calcium is calcitonin: Calcitonin hormone: It is a hormone secreted by the parafollicular cells of the thyroid gland. Its secretion is stimulated by the increase in serum ca++. & gastrin hormone. It is the only hormone that .J, b.lood calcium by its action on: 1-Bone: Itt the deposition of ca++ and phosphorus in bone by .J, in the activity of osteoclasts & tthe activity of osteoblasts. 2-Kidney: It decreases reabsorption of calcium and phosphorus and t excretion. 3-lntestine: It .J, ca++ absorption by decreasing the activity of vit. D.


N.B.: t of plasma ca++ ~ t the secretion of calcitonin & .J, secretion of PTH & vit 03. While .J, of plasma ca++ ~ -1- the secretion of calcitonin & t the secretion of PTH & vit 03. N.B.: Calcitonin in plasma is highly increased in cases of medullary carcinoma of the thyroid gland so. it acts as a tumor marker.


Thyroid gland release






ReducesCa uptake In kidneys


Non hormonal regulation: (1) hypoalbuminemia:~ of plasma albumin as in nephrotic syndrome decreases the total plasma Ca2+ with normal free ionized ca•• so no tetany. (2) Acidosis--)> t the free ionized Ca++. (3) Alkalosis --)> decrease of the free ionized ca++. N.B.: Rapid infusion of NaHC03 (alkali) during correction of acidosis -+.,t. of the ionized Ca++ --)> tetany will occur. while slow infusion of· alkali will t the free ionized Ca++ by release of the parathyroid hormone. N.B Glucocorticoids: decrease calcium absorption from intestine by anti-vitamin D action, increases its renal excretion. Functions of calcium in the bodv are: 1- Bone and teeth formation. 2- Nerve conduction: calcium is necessary for transmission of nerve impulses. 3- Calcium mediates excitation and contraction of muscles: • calcium interacts with troponin C protein to trigger muscular contraction. • Calcium activates ATPase, increases action of actin and Myosin and facilitate excitation contraction coupling. • Calcium decreases neuromuscular excitability.


4-Piays a very important role in blood coagulation, it is considered as factor IV in blood coagulation. It is very important for thrombin formation. 5-Activation of enzymes: • Calmodulin protein binds with 4 calcium to form calcium calmodulin complex. This complex activates phosphorylase enzyme that stimulate glycogenolysis. • _ca++ activates some enzymes e.g. lipase, ATP-ase, succinate dehydrogenase, enzymes of coagulation pathway and renin. 6-Second messenger: Calcium and cAMP are second messenger for hormones such as epinephrine. 7-Calcum prolongs systole in myocardium so in hypercalcemia cardiac arrest is seen in systole. Daily requirements: adults: 0.8 g /day. · Children: 1.2g I day while in pregnancy & lactation its about 1.5g/ day. Excretion: Mostly with stool and small amount with urine. Clinical applications: Hypercalcemia: It is the increase of Ca++ level above 11 mg /dl. Causes of hypercalcemia are: 1. Primary hyperparathyroidism because its associated with large amount of parathyroid hormone. 2. Cancers with bone metastases as multiple myeloma and lymphoma by releasing a group of cytokines that stimulate osteoclasts tc;> resorb bone, resulting in osteolytic lesions, diffuse osteopenia, or both. 3. Endocrine causes as acromegaly due to coexistence hyperparathyroidism but it is rare. Idiopathic hypercalcemia in infants. 4. Overdose of vitamin D or related conditions which increase level of vitamin D such as sarcoidosis, tl)berculosis and lung cancer. (II) Hypocalcemia: Decrease of calcium level below 8.8 mg/dl is called hypocalcemia Causes of hypocalcemia are: (1) Hypoalbuminemia as in nephrotic syndrome, if albumin concentration in serum is low the total calcium is low because the bound fraction is low. (2) Hypomagnesemia because magnesium is required for secretion of parathyroid hormone. (3) Hypoparathyroidism which result from surgery, idiopathic or due to magnesium deficiency. (4) Vitamin D deficiency which may be due to malabsorption, an inadequate intake or kidney disease which leads to improper activation of vitamin D. (5) Chronic liver disease leadiog to hypoalbuminemia... (6) Chronic renal disease with defect in hydroxylation of vitamin D. Effects of hypocalcemia: 1. )\cute deficiency of ionized calcium leads to tetany and carpopedal spasm. 2. Chronic deficiency leads to rickets in children and osteomalacia and osteoporosis in adults.


Phosphorus Sources: • Animal sources: Liver, kidney, heart, meat and fish, milk and cheese are rich sources. • Plant sources: In the beans and legumes group e.g. soybeans and lentils Absorption: Upper part of the small intestine. Factors affecting phosphorus absorption: the same as calcium. Distribution: total body phosphorus is about 800gm. 1-Skeleton: represents 80%. 2-Tissues & body fluids: 20% mainly intracellular. Blood phosphate: Phosphorus is present in: 1-ln RBCs: it is present in two forms: • Organic form: In molecules as Hexose and Pentose Phosphate. • Inorganic form: Potassium phosphate buffer. 2-ln plasma: Normal range is generally 2.4 to 4.1 mg/dl. • Organic form: Mainly phospholipids. • Inorganic form: Sodium phosphate buffer. Factors affecting plasma phosphorous: 1. Parathyroid hormone: it decreases absorption of phosphorus from renal tubules{phosphaturia). 2. Vitamin D:it causes mobilization of phosphate into bone. 3. Renal function: In renal failure, the level of phosphate in plasma. Functions of phosphorus are: 1. Mineralization of bone & teeth. 2. Component of DNA & RNA. 3. Many coenzymes contain phosphate as TPP & energy stores as ATP & GTP. 4.1mportant fn carbohydrate metabolism e.g. phosphorylation of glucose in glycolysis. 5. Activates enzymes (e.g. protein kinase) and inactivates enzymes (e.g. glycogen synthase). 6. Maintains pH (phosphate buffer). 7- Enter in synthesis of phospholipids and phosphoproteins. Clinical applications: Hypophosphatemia: it means that serum phosphorus is less than 2.4 mg/dl. Decreases of serum phosphorus level is accompanied by an increase of serum calcium. Causes of hypophosphatemia are: 1. Insufficient intake as in malnutrition and starvation. 2. Increased excretion in cases of hyperparathyroidism, malignancy, or use of antacids based on aluminum hy~roxide or magnesium. 3. Respiratory and metabolic alkalosis is the most common cause. Hypemhosphatemia: abnormally high serum phosphate levels above 4.5 .mg/dl. Causes of hyperphosphatemia: 1-lncreased phosphate intake as in excessive oral or intravenous phosphate administration. 2-Decreased phosphate excretion as in Primary hypoparathyroidism and renal failure (the most common cause).


3-Shifts of PO 4 into the extracellular space eg in excessive destruction of cells as in hemolytic. anemias and in treatment with chemotherapy, in diabetic ketoacidosis. N.B. Normal children: have higher levels of phosphate help to drive calcium into bone. Excretion: Mainly in stool and small amount in urine. Requirements: 0.8-1.0 gm/day increase to 1-2 in pregnant and lactating women.

Magnesium (Mg++) _ Sources: Animal sources: Liver, heart, kidney, meat, fish. Plant sources: Green leafy vegetables. Absorption: Upper part of the small intestine. Factors affecting absorption are: the same as calcium. Distribution: The total body magnesium is about 20 gm, distributed as follow: 1. Skeleton: bone contains 70% of total magnesium. 2. Tissues as muscles and body fluids: 30°k. It is present in high concentration in RBCs. • Normal serum range is: 1.7-2.4 mg/dl. Functions of magnesium are: 2- Muscle contraction. 1- Enter in the structure of bone. 3-Nerve impulse propagation. 4-Co factor in many enzymes like kinases phosphorylase and phosphates 5-Decrease neuromuscular excitability. Daily requirements: 0.3 gm/ day.

Sodium Sources: Mainly table salt (NaCI). Distribution: It is the main extracellular cation. • Normal plasma level of Na+ is 136 - 145 mmoi/L. Regulation of plasma sodium: 1. Aldosterone hormone: J, of the urinary sodium excretion. 2. Atrial natriuretic peptide hormone: t of the urinary Na+ excretion. Excretion: Mainly via the kidney, in sweat and in the stool (about 5 mmol). Functions of body sodium are: 1. It regulates the extracellular fluid volume. 2. Regulation of pH, osmotic pressure and acid base balance. 3. Maintains muscle and nerve excitability. 4. Formation of buffers. 5. Active transport of glucose, galactose and amino acids.


Potassium (~) Sources of K+: Fruits, vegetables, meat, liver and kidney. Distribution: Total body potassium is about 3.5-5 mmoi/L. It is the main intracellular cation. About 2% of the total body potassium is in the extracellular compartment. Functions of K+ are: a) Regulation of pH and intracellular osmotic pressure._ b) Muscle contraction. c) Neuromuscular excitability. d) Insulin secretion. e) Formation· of buffers.

Chloride (Cr) • It is the main extracellular anion. Soruces: Table salt. Body Chloride: Chloride present mainly in the· plasma (96-106 mmoi/L) and in CSF (125 mmoi/L). Chloride concentration in CFS is higher than any other body fluids. Excretion: Mainly through the. kidney (in urine). Control of chloride: a) Diet b) Aldosterone. Functions of chloride are: 1) Formation of HCI in gastric juice. 2) Cl- ions are involved in chloride shift. 3) Activation of some enzymes as salivary amylase, and pancreatic amylase. 4) Regulation of neuromuscular excitability.

Sulfur Sources: a-Sulfur containing amino acids. b- Sulfur containing vitamins. c-Sulfolipids. d-Mucopolysaccharides. Examples of sulfur containing compounds in the body are : 1. Sulfur containing amino acids and their derivatives as Glutathione and homocysteine, indoxyl potassium sulfate and skatoxyl potassium sulfate 2. Amino ethyl mercaptan in CoASH. 3. Thiocyanate in detoxification. 4. Urochrome present in urine. 5. Sulpholipids. 6. Sodium and potassium sulfate.7. Sulfated mucopolysaccharides. 8. Adenosine 5\ phosphosulphate. 9. Sulfur containing vitamins.


Trace elements Iron (Fe) Total body iron content is 3-5gm, 75% in the blood , and the rest is in the liver, bone marrow, muscles and plasma. Hb contains about 3.4 mg of iron/gm. Sources of iron are: •

1) Exogenous sources: The ~~ wurce of iron Is lean red ~at Iron can also be Animal sources: Liver, kidney, spleen , and meat are very rich found In chiCken, turl