Home assignments on biochemistry for medical students: Методическое пособие

52 Pages·2018·1.303 MB·Russian

by  Danilova L. A.

БИБЛИОТЕКА ПЕДИАТРИЧЕСКОГО УНИВЕРСИТЕТА

L.A. DANILOVA, L.A. LITVINENCO
N.A. CHAYKA, O.B. BASHARINA
E.N. KRASNICOVA, N.P. RAMENSKAYA

HOME ASSIGNMENTS
ON BIOCHEMISTRY
FOR MEDICAL STUDENTS

Санкт-Петербург
0
Министерство L.A. DANILOVA
здравоохранения
Российской Федерации L.A. LITVINENCO

N.A. CHAYKA

O.B. BASHARINA

E.N. KRASNICOVA
N.P. RAMENSKAYA

HOME
Санкт-Петербургский
Государственный
ASSIGNMENTS
Педиатрический
Медицинский
ON BIOCHEMISTRY
Университет
FOR MEDICAL
STUDENTS

Методическое САНКТ-ПЕТЕРБУРГ
пособие 2018

1
УДК 577.1
ББК 28.707.2
Д66

Д66 Home assignments on biochemistry for medical students. / Danilova L.A.,
Readers: Litvinenco L.A., Chayka N.A., Basharina O.B., Krasnicova E.N.,
Ramenskaya N.P. — St.-Petersburg: SPbSPMU, 2018. – 52 pp.

ISBN 978-5-907065-12-3

“Home assignments” is based on our teaching experience in biochemistry acquired
during a long time. It is the second English edition of Professor Danilova L.A.,
Readers: Litvinenco L.A., Chayka N.A., Basharina O.B., Krasnicova E.N.,
Ramenskaya N.P.
Common editing has been made by Litvinenco L.A.
This book is designed to develop in student ability to learn the concepts in
Biochemistry independently in a logical and stepwise manner. It incorporates control
questions, protocol forms, list of necessary formulas, home exercises, selected
reading for all practical lessons, and multiple choice questions for the testing lessons
and examination programme. It’s important that there are home exercises. They will
stimulate the students to think rather than merely learn the subject.

УДК 577.1
ББК 28.707.2

Утверждено учебно-методическим советом Государственного бюджетного
образовательного учреждения высшего профессионального образования
«Санкт-Петербургский государственный педиатрический медицинский
университет» Министерства здравоохранения Российской Федерации

ISBN 978-5-907065-12-3 © СПбГПМУ, 2018
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General biochemistry course is divided into two parts: the former is the lecture course
which you will have to attend. The latter is the practical training which is compulsory
for your attending too.
For the successful learning all students have to do their homework asking on control
questions using lectures and supplementary materials such as biochemistry textbooks
and other selected books.
The fluent control of student knowledge level will be both orally or by test control.
All classes are obligatory for attending. If student would be absent he must
compensate the missed classes.

SAFETY PRECAUTIONS

1. All students must attend practical training only in special clothes (white coats).
2. All reactives that students take by hand must have a labels.
3. Do not test reagents by tongue or by hands.
4. Make reactions only according instruction.
5. Make all reactions with toxic and concentrated reagents only in hood.
6. Measure all reagents by pipettes or burettes.
7. Measure the biological liquids (blood, urine, serum) only by automatic pipettes.
8. If you burn of acid, wash up this place by water as long as you can then
neutralize by 3 % Na CO solution. Wash up alkaline burn by water and
2 3
neutralize by 3 % CH COOH.
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9. Labor place must be clean after laboratory work.
10. Wash your hands after laboratory work.
11. Don’t eat in classes during the work.
12. If fire happens in laboratory you must use fire-fighting tools such a as sand
(That is in the corridor box near the rooms), fire-extinguisher.

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Chemistry of simple and compound lipids

Control questions:
1. The features of chemical structure of lipids. The solubility properties.
Distribution of lipids in human organism.
2. Classification of lipids.
3. Fatty acids. Physical and chemical properties. Biological functions. Essential
fatty acids.
4. Neutral lipids (mono-, di-, triacylglycerols). Their structure, physical and
chemical properties. The localization in the human organism. Biological role.
5. Glycerophospholipids. The chemical structure of different groups,
representatives. Biological functions.
6. Sphingolipids. Their physical and chemical features of structure. Biological
functions.
7. Steroids. Cholesterin and cholesteryl esters. Structure, physical and chemical
properties. Biological important steroids.
____________________________________________________________________
Necessary formulas:
fatty acids such as butyric, palmitic, stearic, palmitoleic, oleic, linoleic, linolenic.
Glycerin, mono-, di-, triacylglicerides. Phosphatidic acid, glycerophospholipids.
Sphingomyelin, cerebrozides, gangliozides.
____________________________________________________________________

Selected readings: U.Satyanarayana. Biochemistry. Kolkata, India. Reprinted
2004. pp. 29-44. Pamela C. Champe , Richard A.Harvey., Biochemistry.
Lippincott’s Illustrated Reviews. USA.1994. pp. 171-173,179,180,191-192, 194-
196,199-201, 205,206. L.Stryer. Biochemistry. USA. New York. 1988. pp. 284-
290, 469-471.

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The biologically important properties of amino acids

Control questions:
1. Classification of amino acids, formulas of 20 amino acids.
2. The ionization states of amino acids depend on pH; acid-base concepts.
3.The reactions can occur with α-amino groups of amino acids.
4.The reactions can occur with carboxyl groups of amino acids.
5.The reactions can occur with radical of amino acids.
6. Protens are built from the 20 L- amino acids. Formation of the peptide
bonds. Nomenclature for peptides and polypeptides.
7. Biochemical methods employed in studying the protein composition of
amino acids:
a)specifical reactions (colored reactions of protein) ;
b) methods of chromatography.
____________________________________________________________________
Necessary formulas: 20 proteinogenic amino acids.
____________________________________________________________________

Selected readings: U.Satyanarayana. Biochemistry. Kolkata, India. Reprinted
2004. pp. 45-53. Pamela C. Champe , Richard A.Harvey., Biochemistry.
Lippincott’s Illustrated Reviews. USA.1994. pp. 1-10. L.Stryer. Biochemistry.
USA. New York. 1988. pp. 16-23.

Protein Structure and Function

Control questions:
1. Protein functions.
2. Molecular weight of proteins and methods of its determining.
3. Primary structure of protein (structure of the peptide unit).
Methods employed in studies the protein primary structural organization.
Hydrolysis of peptide bonds in different sites of proteins. Kinds of hydrolysis.
4. Secondary structure of proteins. α – Helix. β–Structure.
5. Tertiary structure. Bonds responsible for protein tertiary structure. Protein
molecule shape.
6. Quaternary structure of proteins. Characteristics of bonds involved in structural
organization.
7. Using of protein hydrolysis in medical practice.

____________________________________________________________________
Necessary formulas:
20 proteinogenic amino acids.
____________________________________________________________________

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Home exercises. Fill in the following tables:

Table № 1 Conditions of different kinds of hydrolysis

Acidic Alkali Enzymic
№ Conditions
Hydrolysis Hydrolysis Hydrolysis
1. Concentration of
- acid (HCl, H SO )
2 4
- base (NaOH, KOH)
Features of enzymes
2. The ratio between protein and
reagent
3. Reaction temperature
4. Duration
5. Lacks

Table № 2 The methods for estimation protein hydrolysis degree

Partially- Full-
Non-hydrolyzed
№ Methods hydrolyzed hydrolyzed
protein
protein protein
1. Qualitative reactions
a) Ninhydrin reaction
b) Biuret reaction
c) Reaction with 10% TCA

d) Boiling

2. Quantitative method (amino
nitrogen determination)

____________________________________________________________________

Selected reading : U.Satyanarayana. Biochemistry. Kolkata, India. Reprinted 2004.
pp. 45, 53–64. Pamela C. Champe, Richard A.Harvey. Biochemistry. Lippincott’s
Illustrated Reviews. USA. 1994, pp. 13–23, 231–233. L.Stryer. Biochemistry.USA.
New York. 1988. pp. 7–11, 15, 16, 23–40, 49–68.
________________________________________________________________

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Physical and chemical properties of proteins

Control questions:
1. Colloidal and osmotic properties of proteins.
2. Proteins as amphoteric electrolytes. Effect of the medium pH on a charge of
protein. Buffering properties. Isoelectrice point, properties of protein in this
condition.
3. Hydration of proteins and factors affecting protein, solubility.
4. Salting-out, mechanism. Separation of proteins by salting-out.
5. Denaturation of proteins. The factors producing denaturation. Properties of
denaturated proteins.
6. Methods of protein separation, based on physical-chemical properties.

____________________________________________________________________
Necessary formulas: 20 proteinogenic amino acids.
____________________________________________________________________

Home exercises. Determine the net charge of neutral protein in acidic and alkaline
pH using the following scheme:
NH
Pr 2
← + H+ + OH- →
COOH

Selected reading : U.Satyanarayana. Biochemistry. Kolkata, India. Reprinted 2004.
pp. 51, 64–67. Pamela C. Champe, Richard A.Harvey. Biochemistry. Lippincott’s
Illustrated Reviews. USA.1994, pp.5–9, 18–19. L.Stryer. Biochemistry.USA. New
York. 1988. pp. 32–34, 43–50.

Classification of proteins. Simple proteins. DNA, RNA proteins.
Phosphoproteins.Lipoproteins.
Structure and Functions.

Control questions:
1. Biological functions of proteins.
2. Classification of proteins.
3. Simple proteins. The main representatives of simple proteins: albumins,
globulins, protamines, gistones, prolamines, glutelins, fibrous proteins
(collagens, elastins, keratins). Features of structure, biological functions.
4. Nucleoproteins. Chemical structure. Characteristics of bond between
nucleic acids and protein.
5. DNA. Purine and pyrimidine nucleotide and nucleoside structure. Structure
of DNA. The Watson-Crick model of DNA double helix.
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6. RNA. Several kinds of RNA. Structure and biological role.
7. Phosphoproteins. Structure, characteristics of bond between protein and residues
of phosphate. Biological role.
8. Lipoproteins. Localization and biological functions. Classification of serum
lipoproteins and its composition.

Necessary formulas:
Adenine, guanine, cytosine, thymine, uracil, nucleoside, nucleotide, dinucleotide,
phosphoserine, serine, threonine.

Selected reading: U.Satyanarayana. Biochemistry. Kolkata, India. Reprinted 2004.
pp. 67-71. Pamela C. Champe , Richard A.Harvey., Biochemistry. Lippincott’s
Illustrated Reviews. USA.1994, pp. 57, 208, 213, 214, 333-344, 357-379. L.Stryer.
Biochemistry, USA. New York. 1988. pp. 71-78, 179, 560-561, 825-830.

Glycoproteins. Chromoproteins. Structure and Functions

Control questions:
1.Structure of glycoproteins. Heteropolysaccharides of irregular structure.
Localization and biological functions of glycoproteins.
2. Proteoglycans. Structure and functions of glycosaminoglycans.
3.Classification of chromoproteins. Hemoproteins. Structure of heme. Non-
enzymic hemoproteins (hemoglobin and myoglobin). Enzymic hemoproteins
(cytochromes, catalase, peroxidase). Flavoproteins.
4. Metalloproteins.

________________________________________________________________

Necessary formulas (by cyclic forms):
D-Glucose, glucuronic acid, glucosamine, acetylglucosamin, acetylglucosamin 4-
sulfate, acetylglucosamin 6-sulfat, D-Galactose, galacturonic acid, galactosamine,
acetylgalactosamin, acetylgalactosamin 4-sulfate, acetylgalactosamin 6-sulfate, L-
fucose, neurominic acid, sialic acid (N-acetyl-neurominat), structural formulas of the
repeating disaccharide units of hyaluronate, chondroitin 6-sulfate, chondroitin 4-
sulfate, heme.
________________________________________________________________

Selected reading: : U.Satyanarayana. Biochemistry. Kolkata, India. Reprinted
2004. pp. 23-26, 199-207. Pamela C. Champe , Richard A.Harvey., Biochemistry.
Lippincott’s Illustrated Reviews. USA.1994, pp. 25-32147-162. L.Stryer.
Biochemistry. USA. New York. 1988. pp. 275-277, 298-299, 343-347,143-152.
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Testing lesson

Part 1. Test control (it is included 15 questions from 57 which you can look over to
the appendix 1). Find in «Home Assigments».
Part 2. Theoretical question. One of the following control questions:
1. Standard amino acids (structure and classification). Levels of protein
structure.
2. Protein hydrolysis (kinds of hydrolysis, conditions of hydrolysis, a use of
hydrolysates in the clinical practice).
3. Physical and chemical properties of proteins.
4. Classification of proteins. Structure and functions of simple proteins.
5. Classification of proteins. Structure and functions of glycoproteins.
6. Classification of proteins. Structure and functions of hemoproteins.
7. Classification of proteins. Structure and functions of nucleoproteins.
8. Classification of proteins. Structure and functions of the lipoproteins.

Appendix
The questions for the test control. Choose one or more correct answers.
1. The protein is well soluble in the water if:
1. It contains many residues of amino acids with charged side chains.
2. It has residues of aliphatic amino acids with non-polar side chains.
3. Its net charge is zero.
4. It has a globular form.
5. It contains the uncharged polar amino acids.
2. Which one of the following statements about physical-chemical properties of
protein is correct?
1. The denaturation of proteins always leads to irreversible loss of
secondary and tertiary structure.
2. Low viscosity is characteristic of protein solution.
3. Proteins diffuse across semipermeable membrans.
4. Solubility of proteins is determined by presence in it amino acids
with non-polar side chains.
5. Proteins have high diffusion rate.

3. The protein at the isoelectric point is characterized by:
1. Maximal solubility.
2. Minimal solubility.
3. Minimal electrophoretic mobility.
4. Maximal sedimentation.
5. Zero net charge.
4. Proteins:
1. Are amphoteric polyelectrolytes.
2. Exhibit buffering properties.
3. May form gels.
4. May separate by cellophane membrane.
5. Have high osmotic pressure in solution.
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