DANYLO HALYTSKY
LVIV NATIONAL MEDICAL UNIVERSITY
DEPARTMENT OF BIOLOGICAL CHEMISTRY
GUIDE FOR INIVIDUAL WORK
ON BIOLOGICAL CHEMISTRY
for students of medical faculty
PART ІI
LVIV – 2015
1
Methodical instructions prepared by:
Prof. Sklyarov A.Ya., M.D., Ph.D.
Fomenko I.S., Ph.D.
Klymyshin D.O, PhD.
Nasaduk Ch.M., M.D., PhD
Editor: prof. Sklyarov A.Ya., M.D., Ph.D.
Reviewed by: prof. Pinyazhko O.R., M.D., PhD
2
Sense module № 12. Principles of molecular biology.
Topic № 1. Biochemical composition and biosynthesis of purine and pyrimidine
nucleotides. Biochemical function of nucleotides and nucleic acids.
Objective: to study chemical structure of nucleotides, structure and function of
nucleic acids. To make qualitative reactions for detection of nucleoprotein
compounds.
Actuality of the theme: Nucleoproteins are proteins that are associated with
nucleic acids. They can serve functional roles as enzymes, for example, telomerase in
modifying the nucleic acid, or structural ones, as with histones in packaging
chromatin.
Specific objectives:
 To interpret chemical structure of nucleoprotein compounds, structure and function
of nucleic acids, their role in protein biosynthesis.
 To know methods of isolation of nucleoproteins from tissues and qualitative
reactions for detection of their components: a) biuret test for polypeptides, b)
Trommer test for sugars (pentoses), c) silver probe for purine bases, d)
molybdenum probe for phosphates.
1.
GUIDE FOR THE INDEPENDENT STUDY OF THE TOPIC:
Questions:
References:
U.,
Chakrapani
U.
Biochemical functions of nucleic 1. Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
acids and nucleotides. Formation
P. 69-74.
of nucleic acid chain from
2. Harper′s Biochemistry. 27th edition / R. K.
nucleotides.
Murray, Daryl K. Granner, Peter A.
 Biochemical functions of
Mayes, Victor W. Rodwell, 2006.- P. 311nucleic acids;
314.
 Biochemical functions of
3. https://www2.chemistry.msu.edu/faculty/r
nucleotides;
eusch/virttxtjml/nucacids.htm;
 Formation of nucleic acid
4. Lecture notes.
chain from nucleotides
2.
U.,
Chakrapani
U.
Constituents of nucleotides and 1. Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
nucleosides. Minor nitrogenous
P. 69-73.
bases and nucleotides:
2. Lecture notes.
 Constituents of nucleotides;
5. Harper′s Biochemistry. 27th edition / R. K.
 Constituents of nucleosides;
Murray, Daryl K. Granner, Peter A.
 Minor nitrogenous bases and
Mayes, Victor W. Rodwell, 2006.- P. 294nucleotides
298.
3.
U.,
Chakrapani
U.
Free biologically active nucleotides 1. Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
and their biochemical functions:
3
P. 137-141, 223-224.
participation
in
metabolic
reactions (ATP, NAD, NADP, 2. Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A.
FAD, FMN, CTP, UTP) and in
Mayes, Victor W. Rodwell, 2006.- P. 297their regulation (cyclic nucleotides
298.
– cAMP, cGMP):
 biochemical functions of free 3. Lecture notes.
biologically active nucleotides;
4.
Nucleic
acids:
structure,
properties, stages of investigation.
Primary structure of nucleic acids,
polarity
of
polynucleotides,
specific features of DNA and RNA
structure:
 Structure of nucleic acids;
 Properties of nucleic acids;
 Stages of investigation of nucleic
acids;
 Primary structure of nucleic
acids;
 Specific features of DNA and
RNA structure
1. Satyanarayana
U.,
Chakrapani
U.
“Biochemistry”, Third Edition. – 2006. –
P. 73-82.
2. http://en.wikipedia.org/wiki/Nucleic_acid;
3. http://en.wikipedia.org/wiki/DNA;
4. http://en.wikipedia.org/wiki/RNA;
5. Lecture notes.
5.
Structure,
properties
and
biological significance of DNA.
Experimental proves of DNA
significance
in
heredity
(phenomenon of transformation):
 Structure of DNA;
 Properties of DNA;
 Biological significance of DNA;
 Experimental proves of DNA
significance in heredity
1. Satyanarayana
U.,
Chakrapani
U.
“Biochemistry”, Third Edition. – 2006. –
P. 73-79.
2. Lecture notes.
3. Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A.
Mayes, Victor W. Rodwell, 2006.- P. 311314.
4. http://en.wikipedia.org/wiki/Avery–
MacLeod–McCarty_experiment
5. http://en.wikipedia.org/wiki/Transformatio
n_(genetics)
6.
Secondary structure of DNA, role
of hydrogen bonds in stabilization
of secondary structure (Chargaff
rule,
Watson-Crick
model),
antiparallelism of chains:
 Secondary structure of DNA;
 Role of hydrogen bonds in
stabilization
of
secondary
structure;
1. http://en.wikipedia.org/wiki/Chargaff's_rul
es
2. http://en.wikipedia.org/wiki/DNA
3. http://www.nature.com/scitable/topicpage/
discovery-of-dna-structure-and-functionwatson-397
4. Lecture notes.
5. Satyanarayana
U.,
Chakrapani
U.
“Biochemistry”, Third Edition. – 2006. –
P. 73-75.
4
 Antiparallelism of chains.
7.
Tertiary structure of DNA.
Physical-chemical properties of
DNA:
denaturation
and
renaturation of DNA:
 Tertiary structure of DNA;
 Physical-chemical properties of
DNA
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
74-77
2. Lecture notes.
3. Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A. Mayes,
Victor W. Rodwell, 2006. - P. 312-314.
8.
Structure,
properties
and
biological functions of RNA. Types
of RNA: mRNA, tRNA, rRNA,
snRNA; specific features of
structure (secondary and tertiary)
of different RNA types:

Structure,
properties
and
biological functions of RNA;

Types of RNA;

Specific features of structure
of different RNA types.
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
79-82.
2. Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A. Mayes,
Victor W. Rodwell, 2006. - P. 314-320.
3. Lecture notes.
Comprehension questions:
1. Name the structures represented below.
x1 - ?
x2 - ?
x3 - ?
x4 - ?
2. DNA is a polymer of ________________. It is composed of monomeric units
namely ______________ (dAMP), ______________ (dGMP), ______________
5
(dCMP) and ______________ (dTMP). The monomeric deoxvnucleotides in
DNA are held together by ______________ bridges.
Make a daughters DNA strand using the template represented below. What
nucleic acids do not obey Chargaff's rule.
3. Name the structures represented below.
x1 - ?
x2 - ?
x3 - ?
x4 - ?
Examples of multi-choice questions:
Examples of tests „ Crock–1”
6
1. From nitrates, nitrites and nitrosamines in organism is formed nitrous acid which
causes oxidative deamination of nitrogene bases of nucleotides. This induce a point
mutation by replacement of cytosine to...
A. Uracil
B. Thymine
C. Adenine
D. Guanine
E. Inosine
2. 5’-bromouracil inhibits the biosynthesis of one from the listed below compounds. Chose
this compound
A. DNA
B. Protein
C. mRNA
D. rRNA
E. Histones
3. Into human body were incorporated mercury ions. This led to the increase in rate
of transcription of the gene, responsible for detoxification of heavy metals. What
protein gene amplification is in the background of this process?
A. Metallothioneine
B. Ceruloplasmin
C. Interferone
D. Transferrin
E. Ferritin
4. In a patient was recognized endemic goiter. What type of post-translational
modification of thyroglobuline is damaged in a patient?
A. Iodination
B. Phosphorylation
C. Methylation
D. Acetylation
E. Glycosylation
5. The samples of blood of a child and of a supposed father were directed for affiliation
to medical forensic examination. Which chemical components need to be identified in
the explored samples of blood?
A. DNA
B. tRNA
C. rRNA
D. mRNA
E. mnRNA
Individual independent work of students
1. Structure, properties and biological significance
of nucleoproteins,
phosphoproteins, lipoproteins, glycoproteins
7
2. Peculiarities in synthesis and in degradation of nucleoproteins, glycoproteins
and proteoglycans.
1.
2.
3.
4.
Additional literature:
Lehninger A. Principles of Biochemistry. – New York. – W.H.Freeman and
Company. – 2005. – 1010 p.
Mardashko O.O., Yasinenko N.Y. Biochemistry. Texts of lectures.-Odessa. The
Odessa State Medical University, 2003.-416p.
Devlin T.M., ed. Textbook of Biochemistry with Clinical Correlations, 5th ed.
New York: Wiley-Liss, 2002.
MCQs / Prof. Sklyarov A.Ya., Lutsik M.D., Fomenko I.S., Klymyshin D.O.,
Nasadyuk C.M.. – 2012. – 308 p.
Topic № 2. Catabolism of purine nucleotides, determination of end products of
their metabolism. Hereditary disorders of nucleotide metabolism.
Objective: To learn reactions of synthesis and degradation of purine and
pyrimidine nucleotides in normal conditions and in hereditary enzymopathias of this
metabolic pathways. To learn the method of determination of uric acid in biological
fluids and to interpret the obtained results.
Actuality of the theme: Uric acid is the end product of purine metabolism in
humans. The normal concentration of uric acid in the serum of adultsis in the range of
3-7 mg/dl. In women, it is slightly lower (by about 1 mg) than in men. The daily
excretion of uric acid is about 500-700 mg. Hyperuricemia refers to an elevation in
the serum uric acid concentration. This is sometimes associated with increased uric
acid excretion (uricosuria). Gout is a metabolic disease associated with
overproduction of uric acid. At the physiological pH, uric acid is found in a more
soluble form as sodium urate. In severe hyperuricemia, crystals of sodium urate get
deposited in the soft tissues, particularly in the joints. Such deposits are commonly
known as tophi. This causes inflammation in the joints result in a painful gouty
arthritis. Sodium urate and/or uric acid may also precipitate in kidneys and ureters
that results in renal damage and stone formation.
Specific objectives:
 To analyze the sequence of reactions of metabolism of purine nucleotides,
disorders in uric acid metabolism and biochemical principles of gout development.
 To analyze the sequence of reactions of biosynthesis and catabolism of pyrimidine
nucleotides.
 To conduct quantitative determination of uric acid in biological fluids and to
interpret the obtained results.
GUIDE FOR THE INDEPENDENT STUDY OF THE TOPIC:
1.
Questions:
References:
U.,
Chakrapani
U.
Biosynthesis of purine nucleotides; 6. Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
scheme of reactions of IMP
P. 387-392.
synthesis; synthesis of AMP, GMP,
ATP, GTP. Regulation of purine 7. Harper′s Biochemistry. 27th edition / R. K.
8
nucleotides synthesis on a principle
of feedback inhibition:
 Biosynthesis
of
purine
8.
nucleotides;
 Scheme of reactions of IMP
synthesis;
 Synthesis of AMP, GMP,
ATP, GTP;
 Regulation
of
purine
nucleotides synthesis
Murray, Daryl K. Granner, Peter A.
Mayes, Victor W. Rodwell, 2006.- P. 301304.
Lecture notes.
2.
U.,
Chakrapani
U.
Biosynthesis
of
pyrimidine 3. Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
nucleotides: reactions, regulation:
P. 398-399.
 Reactions of biosynthesis of
4. Lecture notes.
pyrimidine nucleotides;
th
 Regulation of biosynthesis of 5. Harper′s Biochemistry. 27 edition / R. K.
Murray, Daryl K. Granner, Peter A.
pyrimidine nucleotides;
Mayes, Victor W. Rodwell, 2006.- P. 305307.
3.
U.,
Chakrapani
U.
Biosynthesis
of 4. Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
deoxyribonucleotides. Formation
P. 392; 399.
of thymidyl nucleotides; inhibitors
of dTMP biosynthesis as antitumor 5. Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A.
drugs:
Mayes, Victor W. Rodwell, 2006.- P. 302;
 Biosynthesis
of
304-305.
deoxyribonucleotides;
 Formation
of
thymidyl 6. Lecture notes.
nucleotides;
 Inhibitors of dTMP biosynthesis
as antitumor drugs
4.
U.,
Chakrapani
U.
Catabolism of purine nucleotides; 6. Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
hereditary disorders of uric acid
P. 392-397.
metabolism.
Biochemical
background of hyperuricemia, 7. Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A.
gout, Lesch-Nyhan syndrome:
Mayes, Victor W. Rodwell, 2006.- P. 302;
 Catabolism
of
purine
307-308.
nucleotides;
 Hereditary disorders of uric acid 8. Lecture notes.
metabolism;
 Biochemical background of
hyperuricemia;
 Biochemical background of
gout;
9

5.
Biochemical background of
Lesch-Nyhan syndrome
U.,
Chakrapani
U.
Catabolism
of
pyrimidine 6. Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
nucleotides:
P. 400.
 Regulation of catabolism of
7. Harper′s Biochemistry. 27th edition / R. K.
pyrimidine nucleotides;
Murray, Daryl K. Granner, Peter A.
 Reactions of catabolism of
Mayes, Victor W. Rodwell, 2006.- P. 302;
pyrimidine nucleotides
308-309.
8. Lecture notes.
Comprehension questions:
Examples of multi-choice questions:
1. Many compounds contribute to the purine ring of the nucleotide. Name the sources
of individuat atoms in purine ring.
1–?
2–?
3–?
4–?
5–?
6–?
7–?
8–?
1. A 44-year-old woman who recently lost her job because of absenteeism, presents
to her physician complaining of loss of appetite, fatigue, muscle weakness, and
emotional depression. The physical examination reveals a somewhat enlarged liver
that feels firm and nodular, and there is a hint of jaundice in the sclerae and a hint of
alcohol on her breath. The initial laboratory profile included a hematological analysis
that showed that she had an anemia with enlarged red blood cells (macrocytic). A
bone marrow aspirate confirmed the suspicion that she has a megaloblastic anemia
because it showed a greater than normal number of red and white blood cell
precursors, most of which were larger than normal. Further analyses revealed that her
serum folic acid level was 2.9 ng/mL (normal = 6 to 15), her serum B12 level was
153 pg/mL (normal = 150 to 750), and her serum iron level was normal.
The patient’s megaloblastic anemia is most likely caused by which of the
following? Explain your answer.
A. A decreased synthesis of methionine
B. A decreased conversion of dUMP to dTMP
C. A decrease in the synthesis of phosphatidyl choline
D. A decrease in the levels of succinyl CoA
E. A decreased synthesis of dUTP
10
2. A patient presents with a urinary tract infection and is prescribed a combination
drug containing trimethoprim and sulfamethoxazole.
These drugs are effective because they do which of the following? Explain your
answer.
A. Bind to operons to prevent synthesis of bacterial mRNA
B. Block transport across bacterial cell walls
C. Inhibit bacterial synthesis of cobalamin (B12)
D. Inhibit bacterial synthesis of THF
E. Inhibit synthesis of phospholipids in bacteria
3. Leukemia patients are often given the compound Leucovorin (N5-formyl THF)
following treatment with the drug methotrexate. Why is Leucovorin useful as part of
this treatment protocol? Explain your answer.
A. It facilitates the uptake of methotrexate by cells
B. It can be converted to THF by bypassing DHFR
C. It acts as an activator of thymidylate synthase
D. It prevents the uptake of methotrexate by normal cells
E. It stimulates cells of the immune system
1.
2.
3.
4.
Additional literature:
Lehninger A. Principles of Biochemistry. – New York. – W.H.Freeman and
Company. – 2005. – 1010 p.
Mardashko O.O., Yasinenko N.Y. Biochemistry. Texts of lectures.-Odessa.
The Odessa State Medical University, 2003.-416p.
Devlin T.M., ed. Textbook of Biochemistry with Clinical Correlations, 5th ed.
New York: Wiley-Liss, 2002.
MCQs / Prof. Sklyarov A.Ya., Lutsik M.D., Fomenko I.S., Klymyshin D.O.,
Nasadyuk C.M. – 2012. – 308 p.
Topic № 3. Replication of DNA and transcription of RNA. Analysis of
mutations and mechanisms of DNA reparations.
Objective: To learn general principles of nucleic acids synthesis; stages of these
processes; mechanisms of mutations and reparations of damaged DNA; development
of hereditary diseases. To interpret mechanisms of action of antibiotics and other
inhibitors of nucleic acids biosynthesis. To conduct quantitative determination of
DNA in biological material.
Actuality of the theme: The biological information flows from DNA to RNA,
and from there to proteins. This is the central dogma of life. It is ultimately the DNA
that controls every function of the cell through protein synthesis. In the process of
nucleic acids biosynthesis may occur various disorders in nucleotide sequence under
the action of physical (ionizing and corpuscular irradiations), chemical (mutagens)
and biological (viruses) agents. Pharmaceutical preparations are widely used in
medical practice that can inhibit biosynthesis of nucleic acids in eukaryotes and
retard tumor cells proliferation in oncologic patients.
Specific objectives:
11
 To conduct quantitative determination of DNA in biological material.
 To interpret molecular mechanisms of storage and transfer of genetic information,
role of enzymatic systems, which provide semiconservative mechanism of DNA
replication in prokaryotes and eukaryotes.
 To explain mechanism of action of enzymatic system of RNA transcription.
 To interpret biochemical mechanisms of gene recombination, gene amplification,
specific features of regulation of gene expression in eukaryotes.
 To analyze consequences of genomic, chromosomal and gene mutations,
mechanisms of action of the most known mutagens, biological significance and
mechanisms of DNA reparations (reparation of UV-induced gene mutations).
1.
GUIDE FOR THE INDEPENDENT STUDY OF THE TOPIC:
Questions:
References:
U.,
Chakrapani
U.
Biological significance of DNA 9. Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
replication. The sense of J.Watson
P. 523-524.
and F.Crick discovery (1953).
Semiconservative mechanism of 10.https://www.youtube.com/watch?v=mpnh4
f6-vuA
replication,
the
scheme
of
Meselsohn's
and
Stahl's
experiment:
 Significance
of
DNA
replication;
 Semiconservative mechanism
of replication;
 The scheme of Meselsohn's
and Stahl's experiment.
2.
General scheme of DNA synthesis.
Mechanisms of DNA replication in
prokaryotes and eukaryotes:
 Scheme of DNA synthesis;
 DNA replication in prokaryotes
and eukaryotes.
6. Satyanarayana
U.,
Chakrapani
U.
“Biochemistry”, Third Edition. – 2006. –
P. 524-528.
2. https:// www.youtube. com/watch?v
=27TxKoFU2Nw.
11.http://www.johnkyrk.com/DNAreplication.
html
12.Lecture notes.
13.Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A.
Mayes, Victor W. Rodwell, 2006.- P. 333143.
3.
U.,
Chakrapani
U.
General scheme of transcription. 7. Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
Stages and enzymes of RNA
P. 543-547.
synthesis in prokaryotes and
8. https://www.youtube.com/watch?v=ysxtZJ
eukaryotes:
UeTCE&list=PLEDBny3Wyp5hOYdMP7
 Scheme of transcription;
HIpKpYf3usYYceV.
 Stages of RNA synthesis;
12
 Enzymes of RNA synthesis.
4.
Posttranscriptional modifications
of RNA.
5.
Inhibitors of replication and
transcription as medical drugs;
their mechanisms of action:
 Inhibitors of replication as
medical drugs;
 Inhibitors of transcription as
medical drugs.
Regulation of gene expression in
prokaryotes. Structure of Lacoperon of Escherichia coli:
structural and regulatory genes,
promotor, operator, regulator;
repression and induction of Lacoperon function:
 Regulation of gene expression in
prokaryotes;
 Structure of Lac-operon of
Escherichia coli;
 Repression and induction of Lacoperon function.
6.
7.
Peculiarities of structure and
functioning of eukaryotic genome.
Molecular organization of DNA in
eukaryotes
(exones,
intrones,
repeated
sequences).
Nuclear
chromatin and chromosomes of
eukaryotes:
 Structure and functioning of
eukaryotic genome;
 Molecular organization of DNA
in eukaryotes;
 Nuclear
chromatin
and
chromosomes of eukaryotes.
9. https://www.youtube.com/watch?v=TSvRq5C3K8.
10.https://www.youtube.com/watch?v=D3fO
Xt4MrOM.
11.Lecture notes.
9. Satyanarayana
U.,
Chakrapani
U.
“Biochemistry”, Third Edition. – 2006. –
P. 547-549.
10. https://www.youtube.com/watch?v=MbE
jQX4Im7Y.
11. Lecture notes.
9. Satyanarayana
U.,
Chakrapani
U.
“Biochemistry”, Third Edition. – 2006. –
P. 528.
10.Lecture notes.
1. https://www.youtube.com/watch?v=tS9FH
_ZbAps
2. https://www.youtube.com/watch?v=Yk4v
T3CWmUo
3. Lecture notes.
4. Satyanarayana
U.,
Chakrapani
U.
“Biochemistry”, Third Edition. – 2006. –
P. 567-569.
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
392-397
2. Lecture notes.
3. Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A. Mayes,
Victor W. Rodwell, 2006. - P. 326-330.
13
8.
9.
10.
Mutations:
genomic,
chromosomal,
gene
(point
mutations), their significance in
appearance of enzymopatias and
human hereditary diseases:
 Genomic mutations;
 Chromosomal mutations;
 Gene mutations(point mutations).
Biochemical mechanisms of action
of chemical mutagens – analogs of
nitrogenous bases, ultraviolet and
ionizing radiation:
 Biochemical mechanisms of
action of chemical mutagens;
 Biochemical mechanisms of
action of ultraviolet and
ionizing radiation.
Biological
significance
and
mechanisms of DNA reparation.
Reparation
of
UV-induced
mutations.
Xeroderma
pigmentosum:
 Mechanisms of DNA reparation;
 Reparation
of
UV-induced
mutations;
 Xeroderma pigmentosum.
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
535-537.
2. Lecture notes.
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
534-535.
2. Lecture notes.
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
537-539.
2. Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A. Mayes,
Victor W. Rodwell, 2006.- P. 343-346.
3. Lecture notes.
Comprehension questions:
1. Nitrogen is a major constituent of DNA. 14N is by far the most abundant
isotope of nitrogen, but DNA with the heavier (but non-radioactive) 15N isotope
is also functional. According to this information explain the results of the
Meselsohn - Stahl experiment depicted on the figure below.
14
a. What hypotheses for the method of replication of DNA had been proved by the
Meselsohn - Stahl experiment?
2. Point mutation is a random mutation in the DNA that occurs at one
point. Point mutations usually take place during DNA replication. DNA
replication occurs when one double-stranded DNA molecule creates two single
strands of DNA that is a template for the creation of the coinciding strand. A
single point mutation can change the whole DNA sequence. Changing one purine
or pyrimidine may change the amino acid that the nucleotides code for.
a. Name the types of point mutations using the scheme below.
b. What are the ways for point mutations to occur?
3. a.
Explain the process of transcription indicated in a figure below. Name stages of
transcription.
b. How many types of RNA can be transcribed from DNA? Name them.
15
c. Explain the role of the promoter site, RNA polymerase, sigma factor and
terminator in transcription.
d. What types of termination of RNA transcription do you know? Explain their
mechanisms of action.
e. What are the main differences between transcription in eukaryotic and
prokaryotic cells?
f. What compounds inhibit transcription in eukaryotes?
4. A special structure with a phosphate bond between 5' and 5' is added to
the 5' end of mRNA is depicted below. Name this structure and explain its role
in mRNA processing in eukaryotes
16
5. If a double-stranded DNA molecule undergoes two rounds of replication in an
in vitro system that contains all of the necessary enzymes and nucleoside
triphosphates that have been labeled with 32P, which of the following best
describes the distribution of radioactivity in the four resulting DNA molecules?
A. Exactly one of the molecules contains no radioactivity.
B. Exactly one of the molecules contains radioactivity in only one
strand.
C. Two of the molecules contain radioactivity in both strands.
D. Three of the molecules contain radioactivity in both strands.
E. All four molecules contain radioactivity in only one strand.
6. A 48-year-old man has had a lengthy history of skin cancer. In the past 6
years he has had over 30 neoplasms removed from sun-exposed areas and has
been diagnosed with xeroderma pigmentosum. Which of the following best
describes the enzymatic defect in patients with xeroderma pigmentosum?
A. DNA polymerase α
B. DNA polymerase γ
C. DNA ligase
D. Excision repair enzymes
E. RNA polymerase III
Examples of multi-choice questions:
Examples of tests „ Crock–1”
1. From nitrates, nitrites and nitrosamines in organism is formed nitrous acid which
induces oxidative deamination of nitrogenous bases nucleotides. It can result in a
point mutation by changing of cytosine into…
A. Uracil
B. Thymine
C. Adenine
D. Guanine
17
E. Inosine
2. A patient suffers from AIDS. RNA of AIDS virus invades leucocytes and using the
enzyme revertase cause synthesis of viral DNA in the cell. This occurs due to the
next process...
А. Reversal transcription
B. Derepression of operon
C. Repression of operon
D. Convariant replication
E. Reversal translation
3. For the treatment of urogenital infections are used quinolones – inhibitors of
enzyme DNA-gyrase. What process is altered first of all under the action of
quinolones?
A. Replication
B. Translation
C. Reverse transcription
D. Reparation
E. Gene recombination
4. Salts of mercury were acidentally introduced to human body. It resulted the
increase in frequency of transcription of gene, providing heavy metals detoxication.
Gene amplification of of what protein takes place in this case?
A. Metallothionein
B. Ceruloplasmin
C. Interferon
D. Transferrin
E. Ferritin
5. The structural analysis of hemoglobin in patient suffering from anemia revealed a
replacement of 6–Glu to 6–Val in β–chain. What is the molecular mechanism of this
pathology?
A. Gene (point) mutation
B. Chromosome mutation
C. Genome mutation
D. Gene amplification
E. Gene transduction
Individual independent work of students
Modern methods of DNA and RNA investigation, their clinical significance.
Additional literature:
1. Lehninger A. Principles of Biochemistry. – New York. – W.H.Freeman and
Company. – 2005. – 1010 p.
2. Mardashko O.O., Yasinenko N.Y. Biochemistry. Texts of lectures.-Odessa.
The Odessa State Medical University, 2003.-416p.
18
3. Devlin T.M., ed. Textbook of Biochemistry with Clinical Correlations, 5th ed.
New York: Wiley-Liss, 2002.
4. MCQs / Prof. Sklyarov A.Ya., Lutsik M.D., Fomenko I.S., Klymyshin D.O.,
Nasadyuk C.M.. – 2012. – 308 p.
Sense module № 13. Bases of molecular genetics.
Topic № 4. Biosynthesis of proteins on ribosomes, initiation, elongation and
termination in synthesis of polypeptide chain. Inhibiting effect of antibiotics.
Pprinciples of gene engineering and gene cloning, their application in modern
medicine.
Objective: To learn general principles of protein synthesis, stages of this
process, possible mechanisms of appearance and development of hereditary diseases.
To interpret the mechanisms of antibiotics action as well as other inhibitors of protein
synthesis. To know principles of gene engineering and gene cloning, its application in
modern medicine. To learn principle of polymerase chain reaction (PCR), its
applications in diagnostics.
Actuality of the theme:
There are wide variations in the cells with respect to the quality and quantity of
proteins synthesized. This largely depends on the need and ability of the cells.
Erythrocytes lack the machinery for translation, and therefore cannot synthesize
proteins. In general, the growing and dividing cells produce larger quantities of
proteins. Some of the cells continuously synthesize proteins for export. For instance,
liver cells produce albumin and blood clotting factors for export into the blood for
circulation. The normal liver cells are very rich in the protein biosynthetic machinery,
and thus the liver may be regarded as the protein factory in the human body. Due to
gene engineering technology the production of interferon, human insulin,
somatotropin, somatostatin, protein preparations for diagnostics of AIDS is achieved.
In particular, in recent years in diagnostics of many diseases and detection of bacillicariers is used an special method – polymerase chain reaction.
Specific objectives:
 To interpret the conception of protein synthesis on the ribosomes.
 To explain biochemical processes of posttranslational modification of
proteins.
 To explain the influence of physiologically active substances and antibiotics
on translation.
 To explain biochemical and molecular biology principles of methods used in
recombinant DNA technologies, recombinant gene technology and formation
of hybrid DNA molecules.
 To explain principles of gene cloning for production of drugs with
biotechnologies methods.
1.
GUIDE FOR THE INDEPENDENT STUDY OF THE TOPIC:
Questions:
References:
U.,
Chakrapani
U.
Features of genetic code; triplet 14. Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
structure, its properties:
19
2.
3.
4.
5.
P. 551-552.
 Features of genetic code;
th
 Triplet structure of genetic 15.Harper′s Biochemistry. 27 edition / R. K.
Murray, Daryl K. Granner, Peter A.
code;
Mayes, Victor W. Rodwell, 2006.- P. 365 Properties of genetic code.
367.
3. Lecture notes.
U.,
Chakrapani
U.
Protein synthesis on the ribosomes. 7. Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
Components of protein synthesis
P. 554-560.
system:
 Protein
synthesis
on
the 8. Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A.
ribosomes;
Mayes, Victor W. Rodwell, 2006.- P. 375 Components of protein synthesis
378.
system.
2.https://www.youtube.com/watch?v=D3f
OXt4MrOM.
3. Lecture notes.
Transfer RNA and, aminoacyltRNA synthetase:
 Transfer RNA and amino acid
activation;
 Aminoacyl-tRNA synthetase.
Stages and
mechanisms of
translation: initiation, elongation,
termination.
Initiating
and
terminating codons of mRNA:
 Stages of translation;
 Mechanisms of translation;
 Initiating and terminating codons
of mRNA.
Post-translational modification of
polypeptide chains. Regulation of
translation.
Molecular
mechanisms of translation control
on example of globin synthesis:
 Post-translational modification
of polypeptide chains;
 Regulation of translation.
 Molecular
mechanisms
of
translation control
12.Satyanarayana
U.,
Chakrapani
U.
“Biochemistry”, Third Edition. – 2006. –
P. 554-555.
13.Lecture notes.
12. Satyanarayana
U.,
Chakrapani
U.
“Biochemistry”, Third Edition. – 2006. –
P. 554-560.
13. Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A.
Mayes, Victor W. Rodwell, 2006.- P. 375378.
14. https://www.youtube.com/watch?v=MbEj
QX4Im7Y.
15. Lecture notes.
11.Satyanarayana
U.,
Chakrapani
U.
“Biochemistry”, Third Edition. – 2006. –
P. 560-562.
12.Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A.
Mayes, Victor W. Rodwell, 2006.- P. 378.
13.https://www.youtube.com/watch?v=7bKpx
REMiOI.
14.Lecture notes.
20
6.
The influence of biologically active
compounds
on
translation.
Antibiotics as inhibitors of
transcription and translation in
prokaryotes and eukaryotes, their
biomedical application:
 The influence of biologically
active
compounds
on
translation;
 inhibitors of transcription and
translation in prokaryotes and
eukaryotes.
1. Lecture notes.
2. Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A. Mayes,
Victor W. Rodwell, 2006.- P. 378-379.
7.
Gene engineering or : general
principles, biomedical significance.
The employment of enzymes. Gene
cloning for obtaining of medicinals
and diagnostic tools using methods
of
biotechnology
(hormones,
enzymes, antibiotics, antigens,
interferons etc.):
 Recombinant DNA technology;
 Gene cloning.
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
578-597.
2. Lecture notes.
8.
Polymerase chain reaction, its
biomedical
application
in
diagnostics of contagious and
hereditary diseases, identification
of a person (DNA-diagnostics).
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
535-537.
2.https://www.youtube.com/watch?v=eEcy9k
_KsDI.
3.
https://www.youtube.com/watch?v=2KoLnIw
oZKU.
4.
https://www.youtube.com/watch?v=HMC7c2
T8fVk
2. Lecture notes.
Comprehension questions:
1. The conversion of codon information into proteins is conducted by transfer
RNA. Each transfer RNA (tRNA) has an anticodon which can base pair with a
codon. Some anti-codons have modified bases that can pair with more than one
codon, specifying the same amino acid; this means that we don't need 61 different
tRNA molecules for all 61 codons.
a. What do the other three codons specify?
b. Using the figure below explain the structure of tRNA.
c. What is the role of the unusual inosine base?
21
d. Explain "wobble hypothesis".
2. The polymerase chain reaction (PCR) is a biomedical technology in molecular
biology used to amplify a single copy or a few copies of a piece of DNA across
several orders of magnitude, generating thousands to millions of copies of a particular
DNA sequence. Typically, PCR consists of a series of 20-40 repeated temperature
changes, called cycles, with each cycle commonly consisting of 2-3 discrete
temperature steps, usually three (Figure below).
Name the cycles of PCR.
What enzyme catalyze step 3?
Explain clinical application of the PCR.
22
3. What stages of translation are inhibited by the antibiotics represented below.
4. Ribosomes are the factories of the cell. Each is very complex, containing over 50
different proteins and several segments of ribosornal RNA (rRNA). Ribosomes use
mRNA to direct the assembly of a protein. In the diagram indicate the ribosomal
subunits and ribosomal sites. Explain their functions in protein translation.
x1 - ?
x2 - ?
x3 - ?
x4 - ?
x5 - ?
x6 - ?
Examples of multi-choice questions:
1. Diphtheria causes inhibition of translation process in human cells due to a loss the
factor of elongation (еEF-2) ability to carry out translocation of peptide residue
from A- on the P-site of ribosoms. What enzyme is a reason of еEF-2 blocking?
A. Peptidyl transferase
B. eIF-2-proteinkinase
C. ADP-ribosyltransferase
23
D. Peptidyl translocase
E. Hypoxantine-guanine phosphoribosyltransferase
2. For the treatment of infectious bacteria diseases are used antibiotics (streptomycin,
neomycin, kanamycin, etc). What stage in the protein synthesis do they inhibit?
A. Translation
B. Transcription
C. Replication
D. Processing
E. Splicing
3. What enzyme is involved in the pathway of synthesis of different genes carried out
from mRNA and DNA in the gene engineering (this enzyme catalyze a process,
discovered in some RNA–containing of viruses)?
A. Reverse transcriptase
B. Exonuclease
C. Endonuclease
D. DNA-ligase
E. Helicase
4. Patient who lives on specific geochemical territory has a diagnosis – endemic
goiter. What type of posttranslational modification of thyroglobulin is violated in the
organism of a patient?
A. Iodation
B. Methylation
C. Acethylation
D. Phosphorylation
E. Glycosylation
5. The inherited information is saved in DNA. What process does provide the
realization of the inherited information in a polypeptide chain?
A. Translation
B. Transcription
C. Translocation
D. Replication
E. Transformation
Individual independent work of students
Transcription processes in normal and pathological conditions. Programmed cell
death- apoptosis. Biochemical mechanisms of apoptosis.
Gene engineering. An application of gene engineering methods in modern
medicine.
Additional literature:
1. Lehninger A. Principles of Biochemistry. – New York. – W.H.Freeman and
Company. – 2005. – 1010 p.
24
2. Mardashko O.O., Yasinenko N.Y. Biochemistry. Texts of lectures.-Odessa. The
Odessa State Medical University, 2003.-416p.
3. Devlin T.M., ed. Textbook of Biochemistry with Clinical Correlations, 5th ed.
New York: Wiley-Liss, 2002.
4. MCQs / Prof. Sklyarov A.Ya., Lutsik M.D., Fomenko I.S., Klymyshin D.O.,
Nasadyuk C.M. – 2012. – 308 p.
Sense module № 14. Molecular mechanisms of hormones action on target cells.
Topic № 5. Molecular mechanisms of the effect of hormones of protein and
amino acid nature on target cells.
Objective: To learn biochemical and physiological function of hormones in a
system of intercellular integration in the organism. To learn structure of hormones of
protein and amino acid nature, derivatives of amino acids and steroid hormones,
mechanisms of their action upon the target cells, role of secondary messengers in cell
response to the hormones of protein or amino acid nature.
Actuality of the theme: Understanding of biochemical mechanisms of
realization of hormones effect on functioning of cell systems allows explaining
mechanisms of development of pathological states, caused by disorders in
functioning of endocrine glands and target cells as well as it also forms in students
considerations about the correction of hypo- or hyperfunction of endocrine glands.
Specific objectives:
 To interpret the biochemical and physiological functions of hormones and
bioregulators in a system of intercellular integration of vital functions of human
organism.
 To analyse and to explain correspondence between the structure of protein and
peptide hormones to their function and mechanism of action on target cells.
 To interpret the molecular mechanisms of action of hormones of protein and
peptide nature, derivatives of amino acids (catecholamines) up on target cells
with involvement of signaling mediator molecules.
 To interpret the molecular mechanisms of direct regulatory effect of steroid
hormones on the genome of targets cells.
1.
2.
GUIDE FOR THE INDEPENDENT STUDY OF THE TOPIC:
Questions:
References:
U.,
Chakrapani
U.
Hormones in a system of 16. Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
intercellular
integration
of
P. 427-428.
physiological functions in human
organism.
Classification
of 17.Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A.
hormones.
Mayes, Victor W. Rodwell, 2006.- P. 442446.
3. Lecture notes.
U.,
Chakrapani
U.
Regulation of synthesis and 14.Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
secretion of hormones. Cyclic
25
P. 427-429.
nature of hormone secretion,
transport of hormones in blood. 2. Lecture notes.
Factors, influencing the secretion
and effect of hormone action:
 Regulation of synthesis and
secretion of hormones;
 Cyclic nature of hormone
secretion.
 Transport of hormones in blood.
 Factors, influencing the secretion
and effect of hormone action
3.
4.
Targets of hormonal action; types
of cell response to the hormone.
Membrane and cytosol receptors
of hormones in the cell:
 Targets of hormonal action;
 Types of cell response to the
hormone;
 Membrane and cytosol receptors
of hormones in the cell
Mechanisms of hormonal action amino acid derivatives, peptide
and protein hormones, steroid
hormones. Regulatory sites in
DNA, which interacts with
hormone-receptor
complexes.
Messenger function of cyclic
nucleotides, Ca/calmodulin system
phosphoinositides.
Serine,
threonine
and
tyrosine
proteinkinases
in
effectory
response of the cell:

Mechanisms of hormonal
action;

Messenger function of cyclic
nucleotides;
 Ca/calmodulin
system
phosphoinositides;

Serine, threonine and tyrosine
proteinkinases in effectory
response of the cell
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
428-429.
15.Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A.
Mayes, Victor W. Rodwell, 2006.- P. 443444.
16.Lecture notes.
16.Satyanarayana
U.,
Chakrapani
U.
“Biochemistry”, Third Edition. – 2006. –
P. 428-431.
17.Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A.
Mayes, Victor W. Rodwell, 2006.- P. 464380.
18. Lecture notes.
26
5.
U.,
Chakrapani
U.
Hormones
of
hypothalamus. 15.Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
Mechanism of their action:
P. 431-437.
 Hormones of hypothalamus;
 Mechanism of action of 16.Lecture notes.
hypothalamus.
6.
Tropic hormones of the anterior
pituitary:
 Group
"growth
hormone
(somatropin) - prolactin Chorionic somatomamotropin";
pathological
processes
associated with impaired growth
hormone,
somatomedin,
prolactin;
 a group of glycoproteins –
pituitary trophic hormones
(TSH, gonadotropins, FSH,
LH), chorionic gonadotropin;
 POMK hormones – processing
products
of
POMK
(adrenokortykotropin,
lipotropin, endorphins).
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
432-437.
2. Lecture notes.
7.
Hormones
of the
posterior
pituitary: vasopressin (antidiuretic
hormone)
and
oxytocin.
Mechanism of action. The use of
oxytocin in medical practice:
 vasopressin
(antidiuretic
hormone);
 oxytocin.
 Application of oxytocin in
medical practice
Characteristics
of
pancreatic
hormones:
 Endocrine function of the
pancreas (insulin, glucagon,
somatostatin,
pancreatic
polypeptide);
 Insulin – structure, biosynthesis
and secretion; characterization
of insulin receptors, molecular
mechanisms of action (effect
on
metabolism
of
carbohydrates, lipids, amino
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
437.
2. Lecture notes.
8.
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
669-676.
2. Lecture notes.
27
9.
acids and proteins);
 Gucagon – the chemical nature
and the biological effect of the
hormone.
Catecholamines:
epinephrine,
norepinephrine,
dopamine.
Chemical nature, biological effect,
receptors. Their role in the stress
response:
 Epinephrine
 Norepinephrine
 Dopamine
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
444-445.
2. Lecture notes.
Comprehension questions:
1. Insulin plays a key role in the regulation of carbohydrate, lipid and protein
metabolisms. It exerts anabolic and anticatabolic influences on the body metabolism.
Fulfill the table (a) and indicate net effect of insulin on carbohydrate, lipid and
protein metabolisms using the diagram (b) represented below. How is insulin secreted
from the pancreas?
a.
Metabolism
Glycolysis
Net effect
Increased
Effect on enzyme/s
Glucokinase↑
Phosphofructokinase↑
Pyruvate kinase↑
Gluconeogenesis
Glycogenesis
Glycogenolysis
HMP shunt
Lipogenesis
Lipolysis
Ketogenesis
Protein synthesis
Protein degradation
b.
28
2. Indicate steps of catecholamine biosynthesis and enzymes involved in this process.
3. A diagrammatic view of pituitary gland is represented below. Name hormones that
are produced by the anterior and posterior pituitary glands.
?
?
Examples of multi-choice questions:
1. The formation of a secondary mediator is obligatory in membrane-intracellular
mechanism of hormone action. Point out the substance that is unable to be a
29
secondary mediator:
A. Glycerol
B. Diacylglycerol
C. Inositol-3,4,5-triphosphate
D. cAMP
E. Ca2+
2. On some diseases it is observed aldosteronism with hypertension and edema due to
sodium retention in the organism. What organ of the internal secretion is affected on
aldosteronism?
A. Adrenal glands
B. Testicle
C. Ovaries
D. Pancreas
E. Hypophysis
3. A typical symptom of cholera is body water loss and sodium ions loss. The
biochemical mechanism of unfavorable action of cholera toxin consists in:
A. Activation of adenilate cyclase activity of enterocytes
B. Activation of synthesis of atrial natriuretic factor
C. Decrease of synthesis of antidiuretic hormone in hypothalamus
D. Stimulation of rennin secretion by the cells of kidneys glomerular arteriolae
E. Activated oxidation of aldosterone in the cells of adrenal glands
4. A women with low arterial pressure after the parenteral introduction of a certain
hormone showed the essential rise of arterial pressure as well as blood levels of
glucose and lipids. What hormone was administered to the patient?
A. Adrenaline
B. Insulin
C. Glucagon
D. Progesterone
E. Estradiol
5. Biologically active substances, especially hormones, are products of hydrolysis and
modification of certain proteins. From which of the listed below proteins do
lipotropin, cortcotropin, melanotropin and endorphins appear in hypophisis?
A. Proopiomelanocortin (POMC)
B. Neuroalbumins
C. Neurostromin
D. Neuroglobulin
E. Thyreoglobulin
Individual independent student’s work
1. Transformations of arachidonic acid in human organism and the influence of
products on metabolic processes.
30
Additional literature:
1. Lehninger A. Principles of Biochemistry. – New York. – W.H.Freeman and
Company. – 2005. – 1010 p.
2. Mardashko O.O., Yasinenko N.Y. Biochemistry. Texts of lectures.-Odessa. The
Odessa State Medical University, 2003.-416p.
3. Devlin T.M., ed. Textbook of Biochemistry with Clinical Correlations, 5th ed.
New York: Wiley-Liss, 2002.
4. MCQs / Prof. Sklyarov A.Ya., Lutsik M.D., Fomenko I.S., Klymyshin D.O.,
Nasadyuk C.M.. – 2012. – 308 p.
Sense module № 15. Biochemistry of hormonal regulation.
Topic № 6. Molecular and cellular mechanisms of steroid and thyroid hormones
action upon target cells.
Objective: To analyze changes in carbohydrate, lipid and protein metabolism
which occur in endocrine glands dysfunction and to interpret prognostic significance
of distinct disorders. To learn mechanisms of hormonal regulation of calcium
homeostasis: distribution of Ca+2 in organism, fractions of calcium in human blood
plasma, the role of bone tissue, intestines and kidneys in support of calcium
homeostasis. To know biochemical mechanisms of pathological processes
development and typical manifestations in endocrine diseases, with special attention
to thyroid gland dysfunction.
Actuality of the theme: Hormones play an important role in mechanisms of
homeostasis. These substances regulate the activity of enzymes in cells, influence the
expression of cell genome and change the intensity of metabolism in target cell and in
the body as well. The knowledge of mechanisms of the neurohumoral regulation of
metabolism gives basis for diagnostics and rational therapy at endocrinological
disorders.
Specific objectives:
 To analyze metabolic changes and biochemical indexes, which characterize the
carbohydrate metabolism, metabolism of proteins and lipids in disorders of
endocrine glands and to summarize the prognostic estimation of these disorders.
 To interpret the mechanisms of hormonal regulation of calcium homeostasis:
distribution of calcium in the body, fractions of calcium in human blood plasma,
the role of bone tissue, small intestine and kidneys in support of calcium
homeostasis.
 To explain the biochemical mechanisms of development and manifestation of
pathological processes and typical disorders of endocrine system.
1.
GUIDE FOR THE INDEPENDENT STUDY OF THE TOPIC:
Questions:
References:
The mechanism of action of 1. Satyanarayana U., Chakrapani U.
thyroid hormones (cytosolic) of “Biochemistry”, Third Edition. – 2006. – P.
31
2.
3.
4.
thyroid
gland
and
steroid
hormones (cytosolic and nuclear
receptors).
 The mechanism of action of
thyroid hormones;
 The mechanism of action of
steroid hormones
429-432.
2. Lecture notes.
Thyroid hormones:
 the structure and biosynthesis of
thyroid hormones;
 biological effects of T4 and T3;
 • pathology of the thyroid gland;
features of metabolic disorders in
conditions
of
hyperand
hypothyroidism;
 mechanisms of endemic goiter
formation and its prevention
Steroid hormones: nomenclature,
classification.
Scheme
of
biosynthesis
of
the
steroid
hormones from cholesterol:
 Nomenclature
of
steroid
hormones;
 Classification
of
steroid
hormones;
 Biosynthesis of the steroid
hormones from cholesterol
Steroid hormones of the
adrenal cortex (C21-steroids):
 the structure, physiological and
biochemical
effects
of
glucocorticoids
(cortisol,
corticosterone), the role of
cortisol in the regulation of
metabolism
(carbohydrates,
proteins, lipids);
 biochemical basis of antiinflammatory properties of
glucocorticoids;
 the structure, physiological and
biochemical
effects
of
mineralocorticoids
(e.g.
aldosterone); role of aldosterone
in the regulation of water
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
437-441.
2. Lecture notes.
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
441-449.
2. Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A. Mayes,
Victor W. Rodwell, 2006.- P. 444-445.
3. Lecture notes.
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
441-444.
2. Lecture notes.
32
5.
6.
metabolism;
 Cushing's disease, Adison’s
disease, aldosteronism, Cohn's
disease.
Steroid hormones of the
gonads:
 female hormones: estrogen estradiol, estrone (C18-steroids),
progesterone
(C21-steroids);
physiological and biochemical
effects; connection with the
phases of the menstrual cycle;
regulation of synthesis and
secretion;
male sex hormones (androgens)
testosterone,
dihydrotestosterone
(S19steroids); physiological and
biochemical effects, regulation
of synthesis and secretion;
clinical application of hormone
analogues
and
antagonists
gonads.
The mechanism of action of
parathyroid
hormone
and
calcitonin. Parathyroid hormone structure. Calcitriol: biosynthesis;
effect on the absorption of Ca2 +
and phosphate in the intestine.
Calcitonin - structure, impact on
calcium and phosphate:

The mechanism of action of
parathyroid
hormone
and
calcitonin;

Structure
of
parathyroid
hormone;
 Biosynthesis; effect on the
absorption of Ca2 + and
phosphate in the intestine of
calcitriol;
 Calcitonin - structure, impact on
calcium and phosphate
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
445-449.
2. Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A. Mayes,
Victor W. Rodwell, 2006.- P. 448-453.
3. Lecture notes.
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
407-408, 437-441.
2. Lecture notes.
33
7.
8.
9.
10.
Clinical
and
biochemical
characteristics of disorders of
calcium
homeostasis
(rickets,
osteoporosis). Distribution of Ca2+
in the body; molecular forms of
calcium in the blood plasma. The
role of bone, small intestine and
kidney in calcium homeostasis:
 Clinical
and
biochemical
characteristics of disorders of
calcium homeostasis;
 Distribution of Ca2+ in the body.
 molecular forms of calcium in
the blood plasma
 The role of bone, small intestine
and kidney in calcium
homeostasis
General
characteristics
of
hormone-like
substances.
Biochemical basis of hormonal
regulation of digestion. Gastrin.
Cholecystokinin. Secretin:

General characteristics of
hormone-like substances;

Biochemical basis of hormonal
regulation of digestion;
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
408-409.
2. Lecture notes.
Biogenic amines with hormonal
and neurotransmitter properties:
structure,
biosynthesis,
physiological effects, biochemical
mechanisms of action (serotonin,
melatonin, histamine). Receptors
of biogenic amines; receptor action
of drugs, histamine receptor
antagonists:

Structure,
biosynthesis,
physiological
effects,
biochemical mechanisms of
action (serotonin, melatonin,
histamine) of the biogenic
amines;

Receptors of biogenic amines
The : general characteristics;
nomenclature
(prostaglandins,
prostacyclins,
thromboxanes,
1. Lecture notes.
2.
Harper′s Biochemistry. 27th edition / R.
K. Murray, Daryl K. Granner, Peter A. Mayes,
Victor W. Rodwell, 2006.- P.275-277.
1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. – P.
449-450.
2. Lecture notes.
1. Harper′s Biochemistry. 27th edition / R. K.
Murray, Daryl K. Granner, Peter A. Mayes,
Victor W. Rodwell, 2006.- P.204-208.
34
2. Lecture notes.
leukotrienes):

The
biosynthesis
of
prostaglandins
and
thromboxanes;
their
biological
and
pharmacological properties;

Leukotriene biosynthesis; 5lipoxygenase, their biological
properties;

Clinical
application
of
eicosanoids, aspirin and other
nonsteroidal
antiinflammatory
drugs
as
inhibitors of prostaglandin
synthesis.
Comprehension questions:
1. a. Name the stages of the synthesis and secretion of thyroid hormones represented
on the diagram below.
1–
2–
3–
4–
5–
6–
7–
b. Thyroid hormones are synthesized in follicular cells of the thyroid gland from
tyrosine residues within the thyroglobulin molecule. T4 and T3 molecules are then
cleaved and released into the circulation. T3, the physiologically active form of
thyroid hormone, can also be formed from the monodeiodination of T4. T4 is
converted to T3 predominantly by type I iodothyronine deiodinase. Abbreviations:
D1, type I iodothyronine deiodinase; D2, type II iodothyronine deiodinase; D3, type
III iodothyronine deiodinase; rT3, reverse T3.
What is the role of pituitary gland in biosynthesis of thyroid gland.
2. Biosynthesis of steroid hormones is represented on the diagram below. Name the
hormones and enzymes of this pathway.
35
x1 - ?
x2 - ?
x3 - ?
x4 - ?
Examples of multi-choice questions:
1. Pregnant women
have a requirement in the promoted amount of
cholecalciferol; one of its metabolite is a powerful synergist of parathormone,
which stimulates the process of bone resorbtion and output of calcium and
phosphates in blood. name this metabolit?
A. 1,25-Dihydroxycholecalciferol
B. 1-hydroxycholecalciferol
C. Cholecalciferol
D. Ergocalciferol
E. 25-Hydroxycalciferol
2. In blood of a patient a hypercalcemia, hypophosphatemia, in urine –
hyperphosphaturia is observed. What is a possible cause of this state?
A .Enhanced secretion of parathyroid hormone
B. Suppression of parathyroid hormone synthesis
C. Enhanced secretion of calcitonine
D. Suppressed calcitonine secretion
E. Enhanced thyroxine secretion
3. Arachidonic acid as essential nutrient is needed for normal growth and
developement. It is precursor of biologically active substances. Indicate what
compounds are synthesized from arachidonic acid
A . Prostaglandine E1
36
B. Noradrenalin
C. Ethanolamine
D. Triiodothyronine
E. Choline
4. Prostaglandins comprise a family of oxygenated lipid signaling molecules
derived from polyunsaturated fatty acids such as arachidonic acid. They are
involved in regulating a number of cellular processes. Some of the
prostaglandins act to increase vasodilation and levels of cAMP in cells, whereas
others increase vaso- and bronchoconstriction and smooth muscle contraction.
In the conversion of arachidonic acid to prostaglandins, the oxygenation step is
accomplished by the enzyme that synthesizes which of the following compounds?
A. Prostaglandin H2
B. Prostaglandin E2
C. Prostaglandin F2α
D. Prostaglandin D2
E. Prostaglandin I2
5. Signaling via prostanoids begins by interaction of the prostanoid with its
receptor. The receptor involved is usually located in which part of the cell?
A. Plasma membrane of a cell near the cell making the prostanoid
B. Nucleus of a cell in a different organ from the cell making the prostanoid
C. Endoplasmic reticulum of the cell making the prostanoid
D. Lysosomes of a cell circulating in the blood
E. Golgi of a cell circulating in the blood
6. The formation of a secondary mediator is obligatory in membraneintracellular mechanism of hormone action. Point out the substance that is
unable to be a secondary mediator:
A. Glycerol
B. Diacylglycerol
C. Inositol-3,4,5-triphosphate
D. cAMP
E. Ca2+
Individual independent student’s work
2. The role of hormone-receptor interaction in the development of hormonal effect.
Additional literature:
1. Lehninger A. Principles of Biochemistry. – New York. – W.H.Freeman and
Company. – 2005. – 1010 p.
2. Mardashko O.O., Yasinenko N.Y. Biochemistry. Texts of lectures.-Odessa. The
Odessa State Medical University, 2003. – 416p.
3. Devlin T.M., ed. Textbook of Biochemistry with Clinical Correlations, 5th ed.
New York: Wiley-Liss, 2002.
37
4. MCQs / Prof. Sklyarov A.Ya., Lutsik M.D., Fomenko I.S., Klymyshin D.O.,
Nasadyuk C.M.. – 2012. – 308 p.
Topic № 7. Biochemistry of nervous tissue. Pathobiochemistry of psychotic
disorders.
Objective: To learn the composition and peculiarities of metabolism in nervous
tissue, its functioning in normal conditions and in certain diseases. To use practically
a method of cholinesterase activity determination.
Specific objectives:
 To explain peculiarities of chemical composition of white and grey matter of
brain.
 To analyze differences between cerebrospinal fluid and blood plasma.
 To interpret specific features of metabolism in brain tissue.
 To explain the role of neurotransmitters in regulation of functions of organs and
cells.
 To analyze changes in cholinesterase activity in different diseases.
GUIDE FOR THE INDEPENDENT STUDY OF THE TOPIC:
Questions:
Peculiarities
of
biochemical
composition and metabolism of
nervous tissue:
 Chemical composition of brain
tissue
 Neurospecific proteins and lipids
(gangliosides,
cerebrosides,
cholesterol)
 Peculiarities
of
aminoacid
composition of brain tissue
 Role of glutamic acid system.
References:
17.Guide “Biochemistry of the nervous
system”
18.Power point lecture “Biochemistry of the
nervous system”
19.http://neurotransporter.org/glutamate.html
20.http://learn.fi.edu/learn/brain/proteins.html
2.
Energetic metabolism in human
brain tissue.
 The significance of aerobic
oxidation of glucose
 Changes in condition of
physiological sleep and narcosis.
1.Guide “Biochemistry of the nervous
system”
2.Power point lecture “Biochemistry of the
nervous system”
3.http://cdn.intechopen.com/pdfswm/32399.pdf
1.
3.
Neurotransmitters
(acetylcholine, 1.Guide “Biochemistry of the nervous
noradrenalin, dopamine, serotonin, system”
excitatory and inhibitory amino 2.Power point lecture “Biochemistry of the
1.
38
acids).
nervous system”
3. http://learn.fi.edu/learn/brain/proteins.html
4.http://thebrain.mcgill.ca/flash/i/i_01/i_01_
m/i_01_m_ana/i_01_m_ana.html
4.
Receptors for neurotransmitters and 1.Guide “Biochemistry of the nervous
physiologically active substances.
system”
2.Power point lecture “Biochemistry of the
nervous system”
3.http://www.learner.org/courses/biology/text
book/neuro/neuro_7.html
5.
Peptideergic system of brain.
6.
Opioid
peptides
(enkephalins, 1.Guide “Biochemistry of the nervous
endorfines, dynorphines).
system”
2.Power point lecture “Biochemistry of the
nervous system”
3.http://pubs.niaaa.nih.gov/publications/arh21
-2/132.pdf
Molecular principles of bioelectric 1.Guide “Biochemistry of the nervous
processes on neuron membranes.
system”
2.Power point lecture “Biochemistry of the
nervous system”
3.http://www.whatislife.com/reader2/membra
ne_bioelectricity.htm
4. http://www.bem.fi/book/02/02.htm
5.http://www.dummies.com/howto/content/understanding-the-transmission-ofnerve-impulses.html
6.http://www.cliffsnotes.com/sciences/anatom
y-and-physiology/nervoustissue/transmission-of-nerve-impulses
7.
1.Guide “Biochemistry of the nervous
system”
2.Power point lecture “Biochemistry of the
nervous system”
8.
Disorders
in
metabolism
of 1.Guide “Biochemistry of the nervous
neuromediators and modulators in system”
brain during psychoses.
2.Power point lecture “Biochemistry of the
nervous system”
9.
Neurochemical
mechanisms
of
action of psychotrope factors
(neuroleptics,
antidepressants,
anxiolytics, nootropics).
1.Guide “Biochemistry of the nervous
system”
2.Power point lecture “Biochemistry of the
nervous system”
39
10
Enzymes involved in biosynthesis 1.Guide “Biochemistry of the nervous
and degradation of neurotransmitters. system”
2.Power point lecture “Biochemistry of the
nervous system”
Comprehension questions:
1. Sign the following neurotransmitters and biologically active compounds
and write the reactions of their formation:
2. Sign the structural parts of a neuron:
3. Sign the following psychotropic compounds and explain their mechanism
of action and application in medicine:
40
4. Sign the constituents of the synapse:
5. Patients with insufficiency of thiamine usually shows several neurological
symptoms: loss of reflexes, excitability, loss of consciousness. Explain, why
does lack of thiamine deficiency affect brain functions?
6. It is known that glycogen which provides the energetic metabolism in the body
is accumulated in liver and muscules, but not in such important tissue as brain,
which preferentially utilizes glucose. Explain, why glycogen is not
accumulated in brain?
Examples of multi-choice questions:
1. Tetanus toxin causes tonic contraction of skeletal muscles because it supress
release from nerve endines the next neurotransmitter:
A. GABA
B. Noradrenalin
C. Acethylcholine
D. Glycine
E. Glutamate
2. Parkinson disease a dofaminergic transmission is altered and that in
treatment is used precursor of dofamin – L-DOPA. In order to decrease side
affects and dosis, L-DOPA is used in combination with:
A. Inhibitor of aromatic amino acids decarboxylase
B. Activator of aromatic amino acids decarboxylase
C. Inhibitor of monoaminoxidase
D. Activator of monoaminoxidase
E. Blockators of dofamin receptors
41
3. In brain of schizophrenia patients an increase in the amount of the next
receptors is observed:
A. Dopamin receptors
B. Serotonin receptors
C. Adrenalin receptors
D. Cholin receptors
E. GABA receptors
4. Disorder in process of myelinization of nerve fibres results in heavy
neurological disorders and mental disfunction. Such clinical status is caused by
inherited defects in metabolism of the next compound:
A.
Neutral fats
B.
Cholesterol
C.
Sphingolipids
D.
Glycerophospholipids
E.
Lipoproteins
Additional literature:
1. Guyton&Hall Textbook Of Medical Physiology. Saunders; 12th edition.- 2010.
– 1120 p.
2. Color Textbook of Histology by Leslie P. Gartner, James L. Hiatt. Saunders; 3
edition. – 2006. – 592 р.
3. Sanacora
G, Zarate
CA, Krystal
JH, Manji
HK.
Targeting the glutamatergic system to develop novel, improved therapeutics fo
r mood disorders. Nat Rev Drug Discov. 2008 May;7(5):426-37.
4. MCQs / Prof. Sklyarov A.Ya., Fomenko I.S., Klymyshin D.O., Nasadyuk C.M.
– 2012. – 308 p.
Sense module № 16. Biochemistry of muscular tissue and mechanism of its
contraction.
Topic № 8. Biochemistry of muscular tissue and the mechanisms of muscle
contraction.
Objective: To learn the composition and peculiarities of metabolism in muscular
tissue, its function in normal and pathological conditions. To perform a quantitative
determination of creatinine and creatine in urea and its diagnostic significance in
certain diseases.
Specific objectives:
 To analyze biochemical composition of muscles and the role of proteins in
formation of myocytes.
 To explain biochemical mechanisms of contraction and relax of muscular fiber.
 To analyze pathways of energetic support of muscular contraction, role of ATP
and creatine phosphate in these processes.
42
GUIDE FOR THE INDEPENDENT STUDY OF THE TOPIC:
Questions:
References:
1 Fine structure and biochemical 1.
Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. –
composition of myocytes; structural
P. 490-496
organization of sarcomers. Myofibril
Harper′s Biochemistry. 26th edition / R.
proteins:
myosine,
actin, 2.
K. Murray, Daryl K. Granner, Peter A.
tropomyosine, troponine complex.
Mayes, Victor W. Rodwell, 2003.- P.556Molecular organization of thick and
579
thin filaments.
3.
http://www.rtmsd.org/page/1790
2 Nitrogen-containing and nitrogen- 1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. –
free
water
soluble
organic
P. 493-494
compounds: structure and functional
significance. Molecular mechanisms 2. Harper′s Biochemistry. 26th edition / R. K.
Murray, Daryl K. Granner, Peter A.
of muscular contraction: modern
Mayes, Victor W. Rodwell, 2003.- P.557data on interaction of muscular
2+
572
filaments. Role of Ca
ions in
regulation of contraction and relax of 3. https://www.youtube.com/watch?v=BMT
4PtXRCVA
striated and smooth muscles.
4. https://www.youtube.com/watch?v=BMT
4PtXRCVA
5. ftp://ftp.mpimfheidelberg.mpg.de/pub/Ken.Holmes/Geeve
s_Holmes_05.pdf
3 Modern ideas on energetics of 1. Satyanarayana U., Chakrapani U.
“Biochemistry”, Third Edition. – 2006. –
muscular contraction and relaxation.
P. 490-495
Macroergic compounds of muscles.
Structure, production and role of 2. Harper′s Biochemistry. 26th edition / R.
K. Murray, Daryl K. Granner, Peter A.
ATP, creatine phosphate, creatine
Mayes, Victor W. Rodwell, 2003.- P.572phosphokinases, sources of ATP in
574
muscular cells; role of creatine
phosphate in energetic supply of
contraction.
4 Cell organization and peculiarities of 1. Harper′s Biochemistry. 26th edition / R.
K. Murray, Daryl K. Granner, Peter A.
bioenergetic
processes
in
Mayes, Victor W. Rodwell, 2003.- P.566
myocardiocytes and regulation of
2. https://tspace.library.utoronto.ca/bitstrea
their contraction.
m/1807/17464/21/Greenhalgh_Catherine_
A_200903_PhD_thesis.pdf
3. http://ceaccp.oxfordjournals.org/content/
7/3/85.full
5 Peculiarities of smooth muscles 1. http://www.rtmsd.org/page/1790
43
function. Molecular mechanisms in 2. https://www.youtube.com/watch?v=Hy8
RW0Szi68
regulation of tonus of vessels and
3. http://www.cvphysiology.com/Blood%20
bronchi.
Pressure/BP026.htm
4. http://www.jbc.org/content/277/3/2186.fu
ll
5. http://www.uic.edu/classes/phyb/phyb516
/smoothmuscleu3.htm
6. file:///C:/Users/Hrustuna/Downloads/Hor
owitz1996PhysiolRev76(4)9671003%20Mechanisms%20of%20Smooth
%20Muscle%20Contraction.pdf
U.,
Chakrapani
U.
6 Biochemical changes of blood plasma 1. Satyanarayana
“Biochemistry”, Third Edition. – 2006. –
enzymes in different periods of
P. 112-113
myocardial infarction and other
2. http://www.patient.co.uk/doctor/cardiacheart diseases.
enzymes-and-markers-for-myocardialinfarction
7 Heart
as
endocrine
organ. 1. http://www.eolss.net/samplechapters/c03/e6-54-05-04.pdf
Cardiopeptides, their functional
2. http://ajpheart.physiology.org/content/290
significance.
/1/H17
8 Biochemical changes and diagnosis of 1. Harper′s Biochemistry. 26th edition / R.
K. Murray, Daryl K. Granner, Peter A.
muscular dystrophies.
Mayes, Victor W. Rodwell, 2003.- P.565566
2. http://www.webmd.com/children/underst
anding-muscular-dystrophy-treatment
9 Pathobiochemistry of muscles – 1. Harper′s Biochemistry. 26th edition / R. K.
Murray, Daryl K. Granner, Peter A.
myopathias. Metabolic myopathias.
Mayes, Victor W. Rodwell, 2003.- P.565Disturbance of metabolism in skeletal
566
muscles in aging.
2. http://www.ninds.nih.gov/disorders/myopa
thy/myopathy.htm
3. http://emedicine.medscape.com/article/759
487-overview
Comprehension questions:
1. Fill in the table timeline of biochemical markers of myocardial infarction:
№
Marker
Timeline, hours
from
to
1. Myoglobin
44
2.
3.
4.
5.
6.
7.
Troponin T
MB creatine phosphokinase (CPK)
Total creatine phosphokinase (CPK)
Aspartate aminotransferase (AST)
Lactate dehydrogenase (LDH1,2)
Alanine aminotransferase (ALT)
2. Sign the structuctural elements of the muscular fiber:
3. Sign and explain which fibers presented below belong to the smooth,
skeletal and cardiac muscle tissue:
4. Sign the ultrastructural constituents of the muscle fiber, presented below:
45
5. Sign structural elements, presented on the picture below and biochemical
processes (indicated with numbers) of the process of muscular contraction:
6. It is known that the main feature of bronchial asthma is a spasm of smooth
muscles of bronchioles. What causes manifestation of such symptoms?
7. Patient has vitamin E hypovitaminosis. How will it influence the function of
muscles?
8. Patients with insufficiency of thiamine usually have a series of neurological
symptoms: loss of reflexes, excitability, loss of consciousness. Explain, why
does thiamine deficiency affect the brain functions?
Examples of multi-choice questions:
1. For early diagnostics of muscular distrofy is the most informative an increase in
activity of certain enzyme in blood plasma. Note it.
A. Lactate dehydrogenase
B. Alanine aminotransferase
C. Aspartate aminotransferase
D. Creatinkinase
E. Alfa-amylase
2. In a patient with progressive muscular dystrophy a biochemical investigation of
urine was conducted. Appearance of what compound in great amount in urine can
support diagnosis of muscle disease in this patient?
A. Hippuric acid
B. Creatin
C. Porphyrins
D. Carbamide
E. Creatinine
3. People which for a long time were in a state of hypodynamia, have intensive pains
in musclesafter the physical load. What is most reliable cause of this symptom?
A. Decrease of lipids in muscle
B. Increase of ADP in muscles
46
C. Accumulation of cretine in muscles
D. Increase of muscule proteins disintegration
E. Accumulation of lactic acid in muscules
4. For synthesis of ATP in skeletal muscles and myocardium are used different
substrats. One of them is utilized in myocardium, but not in skeletal muscles.
A. Glycogen
B. Glucose
C. Lactic acid
D. Fatty acids
E. Keton bodies
5. The most rapid mechanism of ATP regeneration in case of intensive physical load
in muscles is the next:
A. Generation of ATP from creatinphosphate
B. Aerobic glycolysis
C. Glycogenolysis
D. Anaerobic glycolysis
E. Oxidation of triglycerides
Individual independent students work
1. Multi-enzyme complexes and their advantages.
2. The employment of enzymes in biochemical investigations.
Additional literature:
1. Lehninger A. Principles of Biochemistry. – New York. – W.H.Freeman and
Company. – 2005. – 1010 p.
2. Mardashko O.O., Yasinenko N.Y. Biochemistry. Texts of lectures.-Odessa.
The Odessa State Medical University, 2003.-416p.
3. Devlin T.M., ed. Textbook of Biochemistry with Clinical Correlations, 5th ed.
New York: Wiley-Liss, 2002.
4. Toy E.C., Seifert W. E., Strobel H.W., Harms K.P. “Case Files in
Biochemistry. 2nd edition” – 2008. – 488 p.
5. MCQs / Prof. Sklyarov A.Ya., Fomenko I.S., Klymyshin D.O., Nasadyuk
C.M.. – 2012. – 308 p.
47