BIOCHEMISTRY AND MOLECULAR BIOLOGY
SYLLABUS
PART I
STRUCTURES. PROPERTIES AND FUNCTIONS OF AMINO ACIDS.
PEPTIDES AND PROTEINS.
1. Amino acids of mammalian tissues;
general structure,
physicochemical properties,
classification related to the type of side chain and biological values
2. Peptides;
the primary structure of polypeptide chain
characteristic of the peptide bond
biologically active peptides such as glutathione, angiotensin, enkephalin,
endorphin, insulin, glucagon, parathyroid hormone or cacitonin
3. Proteins of mammalian tissues;
protein structures and interactions which stabilize all of them;
the secondary structure (α-helix, β-pleated sheet, β-bends),
the tertiary structure, domains
the quaternary structure
physicochemical properties,
classification related to structures, physicochemical properties,
biological values
4. Chaperones in protein folding.
5. Myoglobin and hemoglobin structures. Sickle cell disease.
6. Collagen and elastin formation, structures
7. Different roles of proteins in humans
PART II
ENZYMES AND BIOLOGICAL OXIDATIONS
ENZYMES
1. Enzyme overview (general concepts).
Apoenzyme. Holoenzyme. Coenzyme. Active site (substrate binding site,
catalytic site). Allosteric site.
2. Enzyme nomenclature. Classification of enzymes. Six classes of enzymes.
3. General properties of enzymes. Enzyme specificity (substrate specificity,
functional specificity) and catalytic efficiency.
4. Coenzymes and cofactors which cooperate with enzymes.
5. Mechanism of enzyme action.
Energy changes during the reaction. Free energy of activation.
Rate of reaction. Chemistry of an active site. Complementarity of substrate
and enzyme. Substrate strain. Acid- base catalysis. Covalent catalysis.
Entropy effect.
6. Factors affecting reaction velocity.
Enzyme concentration. Substrate concentration. Temperature, pH,
activators, inhibitors.
7. Kinetics of enzyme-catalyzed reactions.
Michaelis-Menten plot and Michaelis-Menten equation.
Velocity of a reaction (V). Initial velocity (Vo). Maximal velocity (Vmax).
Turnover number (kcat). Characteristics of Km. Lineweaver-Burk plot.
Order of reactions. Units of enzyme activity.
8. Inhibition of enzyme activity.
Competitive inhibition and its effect on Vmax and Km. Noncompetitive
inhibition and its effect on Vmax and Km. Uncompetitive inhibition and its
effect on Vmax and Km.
9. Regulation of enzyme activity.
Enzyme compartmentation. Allosteric effectors (homotropic, heterotropic).
Covalent modification. Limited proteolysis.
10. Enzymes in clinical diagnosis. Isoenzymes. Enzymes and enzyme inhibitors
used as drugs.
BIOLOGICAL OXIDATIONS
1. Energy-producing and energy-utilizing systems.
2. Thermodynamic relationships and energy-rich compounds.
Thermodynamic laws, free energy (G), enthalpy (H) and entropy (S).
The classification of energy-rich compounds.
3. Sources and fates of acetyl~CoA.
Metabolic sources of pyruvate. Pyruvate dehydrogenase: reactions,
coenzymes, regulation.
4. The tricarboxylic acid cycle (TCA cycle, Krebs cycle, citric acid cycle).
Significance of the TCA cycle. Reactions of the TCA cycle. Regulation of
the activity of TCA cycle.
5. Structures of mitochondrial membranes and their functions.
Transport systems of the inner mitochondrial membrane. Substrate
shuttles transporting reducing equivalents across the inner mitochondrial
membrane. Citrate shuttle.
6. Electron transfer chain (ETC).
Oxido-reduction (redox) reactions. Free energy changes in redox reactions.
The multicomponent system of the mitochondrial ETC. Inhibitors of ETC
and sites of their action.
7. Oxidative phosphorylation.
The coupling of ATP synthesis to electron transport in ETC. P:O ratio.
The chemiosmotic coupling hypothesis. Generation of the proton gradient,
membrane potential and ATP synthesis. The uncoupling agents and
inhibitors of oxidative phosphorylation. Nonshivering thermogenesis.
PART III
PROPERTIES AND METABOLISM OF CARBOHYDRATES
1. Definition of carbohydrates
a. Classification of carbohydrates
b. Physicochemical properties
c. Isomerism
d. Reductive properties of sugars
2. Monosaccharides and their derivatives (as components of
glycosaminoglycans, nucleic acids and their intermediates).
3. Oligosaccharides – function and structure.
4. Polysaccharides (homo- and heteroglycans).
5. Carbohydrates as an element of the diet (starch, cellulose, sucrose,
lactose)
a. Digestion of carbohydrates
b. Absorption of monosaccharides: facilitated diffusion, the Na+/K+
cotransport system
c. Transport of hexoses into the cells
6. Conversion of D-galactose and D-fructose to D-glucose in the liver.
7. Glycolysis.
8. Reactions of glycolysis connected with phosphorylation at “the substrate
level” .
9. Energy yield of glycolysis in anaerobic and aerobic conditions.
10. Reactions of glycolysis (and their meaning) catalyzed by hexokinase,
glucokinase, phosphofructokinase and phosphoenolpyruvate kinase.
Regulative factors of their activities.
11. Fates of glycolytic metabolites in anaerobic and aerobic conditions.
Tissues releasing lactate to the blood (erythrocytes, skeletal muscle, brain).
12. Regulatory enzymes of glycolysis.
13. Fates of pyruvate.
14. Gluconeogenesis, the principal substrates for gluconeogenesis.
The Cori cycle and the alanine cycle.
15. Regulation of gluconeogenesis.
16. Common and separate reactions of glycolysis and gluconeogenesis.
17. The pentose phosphate pathway as a source of reduced NADP (NADPH)
and ribose.
18. Glycogen distribution in tissues. Glycogenesis and its regulation.
19. Glycogenolysis in liver and muscle – a role of enzymes, regulation of
glycogenolysis.
20. Synthesis of fructose from glucose in seminal vesicle cells (aldose
reductase, ketose reductase, sorbitol reductase). Fructose in glycolysis.
21. Metabolism of galactose.
22. Synthesis of the active nucleotide uridinediphosphate glucose (UDPG),
reactions occuring with it.
23. Hormonal regulation of glucose level in the blood (insulin, glucagon,
adrenalin, glicocorticoid hormones).
24.Tissular specificity of glucose metabolism (liver, erythrocytes, brain
adipocytes, muscle).
25. Disorders in metabolism of carbohydrates:
a. diseases of glycogen storage
b. disorders in metabolism of fructose and galactose
c. disorders in metabolism carbohydrates in erythrocytes
26. Glycoproteins and proteoglycans – structure and their biological functions.
PART V
PROPERTIES AND METABOLISM OF LIPIDS.
1. Classification and general description of lipids
2. Fatty acids – classification, characteristics, functions
3. Triacylglycrols – synthesis, characteristics, functions
4. Activity of hormone sensitive lipase in the adipose tissue
5. Process of lipid digestion – stages, regulation, enzymes, products
emulsification, absorption of lipids, formation of chylomicrons and
their functions, activity of lipoprotein lipase in tissues
7. Characteristics of phospholipids – classification, functions, occurrence,
synthesis and degradation, phospholipases
8. Glycosphingolipids - classification, functions, occurrence, synthesis
and degradation
9. Sphingolipidoses – general description, examples.
10. Fatty acid synthesis – substrates, products, enzymes, stages,
regulation
11. Fates of palmitate and activation of fatty acids
12. Carnitine shuttle – substrates, products, enzymes, regulation,
functions of carnitine
13. Oxidation of fatty acids – types of different oxidations, stages of
β- oxidation, substrates, products, enzymes, regulation, diseases
involved with oxidation of fatty acids, formation of ATP during
β- oxidation
14. Ketogenesis – substrates, products, enzymes, regulation
15. Eicosanoids – description, classification, synthesis, regulation,
inhibitors of their synthesis
16. Diabetes mellitus and obesity – characteristics, description, treatment
17. Cholesterol – description, structure, functions, synthesis, regulation of
synthesis
18. Bile acids – description, structure, synthesis, functions
19. Lipoproteins – description, structure and composition of lipoproteins,
apolipoproteins, metabolism, functions
20. Functions of various lipid components in diet – saturated and
unsaturated fatty acids, cholesterol, triacylglycerols
21. Main disorders of plasma lipoproteins - examples
PART V
NUTRITION. VITAMINS. MINERALS. HORMONES.
INTEGRATION OF METABOLISM.
I. FORMING A PLAN FOR GOOD NUTRITION
1. Essential nutrients
2. Calories
3. Protein
4. Carbohydrates
5. Fats
6. Fiber
7. Water
8. Dietary guidelines
9. Other nutrition concerns
II. VITAMINS
1. Definition
2. Sources of vitamins
3. Classification
4. Deficiency
5. The water-soluble vitamins (structure, nutritional requirements, function,
deficiency)
a. The vitamins of the B complex:
thiamin (vitamin B1), riboflavin (vitamin B2), pantothenic acid (vitamin
B5), niacin (vitamin B3), pyridoxine (vitamin B6), biotin, cobalamin
(vitamin B12)
b. Folic acid ( pteroylglutamin acid)
c. Vitamin C (ascorbic acid)
6. The lipid-soluble vitamins (structure, nutritional requirements, function,
deficiency)
a. Vitamin A (retinol)
b. Vitamin D (cholecalciferol)
c. Vitamin E (tocopherol)
d. Vitamin K (phylloquinones, menaquinones)
III. Minerals
1. Essential minerals (macrominerals).
Nutritional requirements, metabolic role and deficiencies of calcium,
chloride, magnesium, phosphorus, potassium, sodium.
2. Trace minerals (microminerals).
Nutritional requirements, metabolic role and deficiencies of cobalt,
copper, iodine, manganese, molybdenum, selenium, zinc, iron.
IV. CHEMICAL SIGNALING IN THE BODY. THE MECHANISMS OF
SIGNAL TRANSDUCTION. STRUCTURE AND FUNCTION OF
HORMONES.
1. General characteristics of the signaling molecules:
a. Endocrine hormones
b. Growth factors and cytokines
c. Neurotransmitters
2. The hormones release control. How is the release of signaling molecules
controlled?
3. Hormones classification according to
site of synthesis, chemical structure, water solubility (solubility
properties), location of receptor. Nature of the signaling used to mediate
action within the cell.
4. How does ligand binding result in cellular responses?
a. Membrane receptor-mediated responses
b. Intracellular receptor-mediated responses
5. The membrane receptor-mediated responses overview
6. Classes of cell-surface receptor protein (membrane-bound receptors)
a. Ion channel-linked
b. G protein-linked
c. Enzyme-linked
7. Hormonal action mediated by surface receptor
a. Hormone-receptor interaction
b. The second messenger concept
c. Signaling via G protein-linked cell-surface receptors:
- cAMP mediated pathways
- the phosphatidylinositol cascade
- function of calcium as an intracellular messenger
- diacylglicerol (DAG) function as an intracellular messenger
d. Signaling via enzyme-linked cell-surface receptors:
- receptor quanylyl cyclase and c GMP as an intracellular mediator
- hormone receptors that are transmembrane tyrosine kinase
8. Hormonal action mediated by intracellular receptors
9. Biosynthesis of hormones. Storage and secretion. Hormones in the
blood. Degradation.
10. Hormones of anterior pituitary gland. Regulation of anterior pituitary
function.
11. Salt and water balance. Hormonal regulation of water and electrolytes
balance.
a. Antidiuretic hormone
b. Aldosterone
c. Atrial natriuretic peptide
12. Integrated compensatory responses to changes in salt and water
13. Thyroid gland. Regulation of thyroid function. Thyroid hormones.
(thyroxin and triiodothyronine)
a. Synthesis
b. Regulation of secretion
c. Function
d. Disorder
14. Distribution of calcium in the body. Hormonal regulation of calcium
metabolism.
a. Parathormon
b. The vitamin D3 endorcine system
c. Calcitonin
d. Other hormones that affect calcium balance
15. Integrated actions of calcitropic hormones. Response to a hypo- and
hypercalcemic challenge
16. Adrenocorticotropic hormone (ACTH) and glucocorticoids
a. Regulation of glucocorticoids secretion
b. Genaral functions of glucocorticoids
c. Disorders of adrenal glands hormones
17. Endorcine pancreas. Chemistry, secretion, metabolism and biochemical
actions and disorders
a. Insulin
b. Glucagon
c. Somatostatin
18. Hormonal control of nutrient metabolism
19. Function of gastrointestinal hormones
V. INTEGRATION OF METABOLISM
1. Metabolic fuels;
a. definition
b. caloric value of metabolic fuels
c. body stores of metabolic fuels
d. use of metabolic fuel
2. The major categories of metabolic pathways
a. catabolic pathways
b. anabolic pathways
c. amphibolic pathways
3. The location and integration of the metabolic pathways
a. the tissue and organ level
b. the subcellular level
4. The basic strategy of metabolism
5. No hormonal regulation of metabolic pathways
a. metabolic control by regulation of the activities of the enzyme in
the cell
- allosteric regulation of mainstream metabolic pathways:
glycolysis and gluconeogenesis
glycogenesis and glycogenolysis
fatty acid synthesis and degradation
citric acid cycle
control of nitrogen metabolism
b. control of enzyme activity by covalent modification (enzyme level)
c. respiratory control
d. substrate supply (availability)
e. compartmentalization of metabolic pathways in the cell
f. the flow of key metabolic intermediates between different pathways\
- key junction: glucose-6-phoshate, acetyl-CoA, pyruvate
6. Metabolism of specialized tissues
a. brain
b. liver
c. adipose tissue
d. skeletal muscle
e. heart muscle
7. Metabolic relationships of tissues in various nutritional and hormonal
states
a. obesity
b. insulin-dependent diabetes mellitus
c. non-insulin-dependent diabetes mellitus
d. stress
PART VI
STRUCTURES, PROPERTIES AND METABOLISM OF NUCLEIC ACIDS.
PROTEIN SYNTHESIS.
1. Overview and structure of nucleotides – subunits of nucleic acids.
Structure and nomenclature of the components of nucleic acids:
nitrogenous bases, nucleosides and nucleotides.
Common and unusual pyrimidine and purine nitrogenous bases and
nucleosides.
2. Structure and biological role of DNA and RNA.
a. DNA structure and properties:
double stranded antiparallel helix structure, A, B and Z structures,
denaturation and melting temperature.
b) RNA structures and properties:
Primary and secondary structures of RNA. Types of RNA (rRNA, hnRNA,
mRNA, tRNA). Ribonucleoproteins.
c) Comparison of DNA with RNA in respect to:
chemical composition and properties, molecular weight, structure of
the molecule, cellular localisation, biological role.
3. Nuleic acids`metabolism
a. Nucleic acids as components of the diet. Digestion of nucleic acids in the
gastrointestinal tract. Degradation and catabolism of nucleic acids. Final
products of catabolism of nucleic acids. Catabolism of pyrimidine
nucleotides. Catabolism of purine nucleotides. Structure and properties of
uric acid. The gout. Salvage pathway for purines and the Lesch-Nyhan
syndrome.
b. De novo pyrimidine nucleotide synthesis. Formation of orotic acid.
Synthesis of UMP and other pyrimidine nucleotides.
c. De novo purine nucleotide synthesis. Sources of atoms in the purine ring.
Steps in the purine ring synthesis, formation of inter mediates. Inhibitors
of purine nucleotides synthesis Conversion of IMP (the “parent” purine
nucleotide) to AMP and GMP. Synthesis of diphospho- (NDP) and
triphospho- (NTP) nucleosides.
Synthesis of thymine. Synthesis of deoxynucleotides. Regulation of
pyrimidine and purine nucleotides synthesis.
4. DNA synthesis (replication)
a. Steps in prokaryotic and eukaryotic DNA synthesis; semiconservative
mode of replication. Initiation of the replication (separation of the two
strands, formation of the replication fork, formation of primosome). Chain
elongation during replication (DNA polymerases, direction of DNA
replication, leading and lagging strands, Okazaki fragments). Termintion
of the replication.
b. Fidelity of the replication and DNA repairing systems.
5. RNA synthesis (transcription).
a. Steps in prokaryotic and eukaryotic RNA synthesis. RNA polymerases and
their function. Initiation of transcription. Elongation of the RNA chain.
Termination of transcription.
b. Posttranscriptional modification of RNA: rRNA, mRNA and tRNA
modifications.
c. Inhibitors of transcription
5. Genetic code and protein synthesis.
a. Characteristics of the genetic code (its specificity, universality,
redundancy, nonoverlapping and commalessness).
b. Protein synthesis (translation of the genetic code). The role of aminoacyl
tRNA synthetases and tRNAs (specificity of the enzymes, activation of
amino acids).
Ribosomes` structure and their role in translation. Sources of energy for
translation. Steps of translation: initiation of translation, elongation of
translation
and termination of translation. Posttranslational polypeptide modification.
Inhibitors of protein biosynthesis (antibiotics, toxins)
PART VII
CATABOLISM OF PROTEINS. METABOLISM OF AMINO ACIDS.
DISEASES CONNECTED WITH DYSFUNCTIONS OF THESE
PROCESSES.
Protein catabolism
I. Catabolism of dietary proteins
1. Dietary proteins and their biological values;
a. proteins with high biological values (animal proteins with exception of
collagen) as sources of all kinds amino acids (essential and nonessential
amino acids)
b. proteins with low biological values (plant proteins)
c. disturbances connected with protein deficiency in food (kwashiorkor,
marasmus).
2. Classification of proteolytic enzymes (representatives);
a. endopeptidases and exopeptidases
b. aspartate proteases, serine proteases, cysteine proteases, threonine
proteases, metalloproteases.
3. Digestion of dietary proteins in the gastrointestinal tract and its regulation.
a. Components of gastric juice involved in the digestion of dietary
proteins
- hydrochloric acid (HCl) in gastric digestion of dietary proteins
- carbonic anhydrase in synthesis of (HCl) in parietal cells of
the stomach,
- the activation of pepsinogen
- pepsin activity.
b. Components of pancreatic juice involved in the digestion of
dietary proteins
- the role of bicarbonate ions
- the activation of trypsinogen
- the action of trypsin (the activation of other pancreatic proteolytic
enzymes and the digestion of products of pepsin activity)
- the substrate specificities of trypsin, chymotrypsin, elastase,
carboxypeptidases A and B.
c. The substrate specificity of aminopeptidase.
4. Systems of transport of free amino acids from the gastrointestinal tract
II. Catabolism of body proteins
1. Protein turnover, a dynamic balance between protein degradation and
protein synthesis.
a. Main factors of the regulation of protein turnover
b. Intracellular and extracellular proteins half-lives
c. Significance of the body protein turnover
d. Diseases connected with disturbances of protein turnover
2. Protein degradation in lysosomes.
a. The transport of proteins into lysosomes.
b. Characteristics and activity of lysosomal proteolytic enzymes
3. Protein degradation in proteasomes.
a. The structure of proteasome
b. The process of protein preparation for degradation in
proteasomes
c. Characteristics and activity of enzymes of proteasomes
4. Amino acid pool
5. Interorgan amino acid exchanges
III. Amino acids metabolism
Amino acids catabolism
1. Processes of nitrogen removal from amino acids.
a. The transamination reaction
b. Oxidative deamination reactions
c. Nonoxidative deamination reactions
2. Diagnostic values of the determination of plasma aminotransferases
3. Ammonia metabolism
a. Ammonia toxicity for the human body
b. Glutamate and glutamine roles in ammonia metabolism
c. Reactions and location of the urea cycle
d. The regulation of the urea cycle
e. Disorders of the urea cycle
4. Nitrogen balance
a. Positive nitrogen balance and its causes
b. Negative nitrogen balance
5. Catabolic pathways and final products of
- glycine and serine
- alanine
- threonine
- proline
- methionine
- cysteine
- arginine
- histidine
- lysine
- tryptophan
- phenylalanine and tyrosine
- asparagine and aspartic acid
- glutamine and glutamic acid
- valine, leucine, isoleucine
6. Fates of final products of amino acid catabolism
a. Glucogenic amno acids
b. Ketogenic amino acids
c. Glucogenic and ketogenic amino acids
d. Amino acids as energy sources
IV. Pathways of amino acid conversion to specialized products and
their roles in the human body
1. The formation of physiologically active amines
- ethanolamine,
- cysteamine,
- taurine,
- γ-aminobutyrate (GABA),
- dopamine, norepinephrine, epinephrine,
- serotonin, melatonin,
- histamine,
- puterscine, spermidine, spermine
2. Melanin formation
3. Nitrogen oxide formation
4. Niacin formation
5. Creatine phosphate formation
6. Glutathione formation
7. Amino acids as sources of one-carbon units and the role of
tetrahydrofolic acid
V. Pathways of biosyntheses of amino acids nonessential for
humans including the synthesis of
- glycine and serine
- glutamic acid
- glutamine
- aspartic acid
- asparagine
- arginine
- alanine
- cysteine
- tyrosine
- hyroxyproline and hydroxylysine
VI. Metabolic disorders of amino acid metabolism
a. Penylalanine and tyrosine metabolism
- phenylketonurias
- tyrosinemias
- alkaptonuria
- albinism
b. Methionine metabolism - homocystinuria
c. Histidine metabolism - histidinemia
d. Lysine metabolism - lysinemia
e. Glycine metabolism - nonketotic hyperglycinemia
f. Valine, leucine and isoleucine metabolism
- maple syrup urine disease
g. The conversion of propionyl-CoA into succinyl-CoA – methylmalonic
aciduria
PART VIII
BIOCHEMISTRY OF THE BLOOD AND THE KIDNEY.
ACID-BASE EQUILIBRIUM.
1.Blood – general information
a. Biological role of the blood
b. Blood red cells
- metabolism of erythrocytes
- the function of hemoglobin
- synthesis and catabolism of heme
- pathology in heme metabolism (porphyria, icterus)
c. Constituents of plasma
- biological role of plasma proteins
- physiological nonprotein constituents of serum
- iron and copper – transport and storage
d. Hemostasis – biochemical aspects of coagulation and fibrinolysis
- general information about clots forming
- the role of platelets, vitamin K and calcium
- anticoagulants
- coagulation disturbances – von Willenbrand disease, hemophilias,
2. Kidneys – general information
a. Urine production
b. Physiological and pathological constituents of the urine
c. Hormonal role of kidneys
d. The role of kidneys in the oedema development
3. Acid-Base Equilibrium
a. Buffers of the human body
b. The main role of kidneys and lungs in the maintaining of acid-base
balance
c. Other organs involved in the maintaining of acid-base balance (bones,
liver, digestive system)
d. Metabolic and respiratory acidosis and their causes
e. Metabolic and respiratory alkalosis and their causes