BIOCHEMISTRY - SYLLABUS



BIOCHEMISTRY AND MOLECULAR BIOLOGY

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 chains and biological values

2. Peptides;

the primary structure of polypeptide chain

the characterization of the peptide bond

biologically active peptides such as glutathione, angiotensin, enkephalins,

endorphin, insulin, glucagon, parathyroid hormone or calcitonin

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 the human body.

ENZYMES AND BIOLOGICAL OXIDATIONS

ENZYMES

1. Enzyme overview (general concepts). Structure of enzymes.

2. Enzymes features.

3. Enzymes classification. Six classes of enzymes.

4. Structure and properties of an active site. Models explaining the binding of

a substrate to an enzyme (lock-and-key model and induced fit model).

5. Changes of free energy during a reaction. Activation energy (Ea).

The transition state.

6. Types of catalytic mechanisms (General acid-base catalysis. Covalent

catalysis. Metal ion catalysis. Proximity and orientation effects. Preferential

binding of the transition state intermediates).

7. Coenzymes. Apoenzyme. Holoenzyme. Classification of coenzymes

(Organic coenzymes. Cofactors. Prosthetic groups. Activated groups).

8. Enzyme Kinetics. Michaelis-Menten plot and Lineweaver-Burk plot. Initial

rate of reaction (V0). Maximal velocity (Vmax). Michaelis constant (Km).

Michaelis-Menten equation. Order of reaction.

9. Units of enzyme activity (International enzyme unit. Katal. Specific activity.

Turnover number).

10. Factors Affecting Enzyme Activity (Concentration of a substrate and

an enzyme. Temperature. pH. Inhibitors. Activators).

11. Enzyme inhibitors. Reversible inhibitors (Competitive inhibitors.

Non-competitive inhibitors. Uncompetitive inhibitors. Mixed inhibitors).

Irreversible inhibitors.

12. Regulation of enzymes. Allosteric regulation. Covalent modification.

Zymogen activation (limited proteolysis). Enzyme compartmentalization.

Binding of protein activators and inhibitors. Formation of multienzyme

complexes.

13. Enzymes used in clinical diagnosis. Enzyme inhibitors used as therapeutic

agents. Enzymes used as therapeutic agents.

BIOLOGICAL OXIDATIONS

1. Catabolic reactions. Anabolic reactions. Metabolic fuels.

2. Thermodynamics. The first law of thermodynamics. Internal energy (U) of

a system. The second law of thermodynamics. Entropy (S), Gibbs free

energy (G), and enthalpy (H) of a system. Exergonic and endergonic

reactions.

3. Relationship between Gibbs free energy and equilibrium constant of

a reaction.

4. Energy rich compounds.

5. Pyruvate dehydrogenase complex. Reactions. Coenzymes. Regulation.

6. The Tricarboxylic Acid Cycle (TCA cycle, Krebs cycle, citric acid cycle).

Biological role of the TCA cycle. Reactions and regulation of the TCA

cycle.

7. Electron transport chain (ETC). Biological role of the ETC. Redox potential

(E). Complexes of ETC (names, coenzymes, and function). Inhibitors of

ETC.

8. Oxidative phosphorylation. Chemiosmotic hypothesis. P/O ratio. Regulation

of ETC. Uncouplers. Non-shivering thermogenesis.

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.

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

6. Characteristics of phospholipids – classification, functions, occurrence,

synthesis and degradation, phospholipases

7. Glycosphingolipids - classification, functions, occurrence, synthesis

and degradation

8. Sphingolipidoses – general description, examples.

9. Fatty acid synthesis – substrates, products, enzymes, stages,

regulation

10. Fates of palmitate and activation of fatty acids

11. Carnitine shuttle – substrates, products, enzymes, regulation,

functions of carnitine

12. 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

13. Ketogenesis – substrates, products, enzymes, regulation

14. Eicosanoids – description, classification, synthesis, regulation,

inhibitors of their synthesis

15. Diabetes mellitus and obesity – characteristics, description, treatment

16. Cholesterol – description, structure, functions, synthesis, regulation of

synthesis

17. Bile acids – description, structure, synthesis, functions

18. Lipoproteins – description, structure and composition of lipoproteins,

apolipoproteins, metabolism, functions

19. Functions of various lipid components in diet – saturated and

unsaturated fatty acids, cholesterol, triacylglycerols

20. Main disorders of plasma lipoproteins – examples

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 (most 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 and substrate specificity.

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. Transamination reactions

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. The role of glutamate, glutamine and alanine 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. Propionyl-CoA metabolism – methylmalonic aciduria

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

6. 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)

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 function: 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

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

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