MINISTRY OF EDUCATION AND SCIENCE

OF THE RUSSIAN FEDERATION

FEDERAL STATE BUDGETARY

EDUCATIONAL INSTITUTION
OF HIGHER PROFESSIONAL EDUCATION
“TAMBOV STATE UNIVERSITY
NAMED AFTER G.R. DERZHAVIN”

Romantsova S.V., Panasenko A.I.,

Sheina O.A., Rosenbloom L.V.

BIOORGANIC CHEMISTRY

IN QUESTIONS AND ANSWERS

It is recommended to printing by
Publishing Committee of Tambov State
University named after G.R. Derzhavin
as higher school-book for students of
specialization 060101 – “Medicine”

Tambov 2013
 УДК 547.(075.8)
ББК 24.2 я73
Р

Reviewers:
Doctor of medical sciences, professor Osmanov E.M.;
Candidate of chemical sciences, assistant professor Knyaseva L.G.
Translated into English by Candidate of Philology,
Assistant professor Bannikova S.V.

Romantsova S.V., Panasenko A.I.

R Bioorganic chemistry in questions and answers. Higher
school-book for students of medical specializations at
Universities/A.I. Panasenko, S.V. Romantsova, O.A.
Sheina, L.V. Rosenbloom; Ministry of Education and
Science of RF; FSBEI HPE “Tambov State University
named after G.R. Derzhavin”. Tambov: Publishing House of
TSU named after G.R. Derzhavin, 2013. 108 pp.

This Higher school-book is written according to

education programme “General and Bioorganic chemistry”
for students with specialization “Medicine”. There are
answers to most widely spread questions which occur at
students during this subject. There are explanations of
classification, nomenclature and general laws of reaction
ability belonging to organic compounds, structure and
properties of biological macro-molecules and their
structural components.

УДК 547.
(075.8)
ББК 24.2
я73

© FSBEI HPE Tambov State University

2
 named after G.R. Derzhavin, 2013

CONTENTS

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1. Biologically important organic compounds classification
and nomenclature. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2. Organic compound structure. . . . . . . . . . . . . . . . . . . . . . . . 16
3. General laws of organic compound reaction ability . . . . . 26
4. Amino acids, peptides, proteins. . . . . . . . . . . . . . . . . . . . . 36
5. Carbohydrates: mono-, di- and poly-saccharides. . . . . . . . 58
6. Nucleotides and nucleic acids. . . . . . . . . . . . . . . . . . . . . . 88
7. Lipids and low-molecular bio-regulators. . . . . . . . . . . . . . 97
8. Organic compound identification. . . . . . . . . . . . . . . . . . . . 103
Literature. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

3
 INTRODUCTION

Aim of bioorganic chemistry as a subject is system knowledge

formation about interconnection between structure and chemical
properties of biologically important classes of organic compounds,
biopolymers and their structural components as basis to understand
life processes on modern molecular level.
At bioorganic chemistry teaching much attention is paid to
students’ independent work. This Higher school-book has detailed
answers on students’ questions at bioorganic chemistry. Using this
detailed information students study on their own to have general
approach and logic which facilitates writing tests.

4
 1. BIOLOGICALLY IMPORTANT ORGANIC
COMPOUNDS CLASSIFICATION AND NOMENCLATURE

Question 1. What is the basis to classify organic compounds?

Answer. At organic compounds classification basis there is
carbon skeleton structure and functional groups.
According to carbon skeleton organic compounds are subdivided
into hydrocarbons (in which structure there are only carbon and
hydrogen atoms) and hetero-cyclic compounds (in molecule cyclic
part in addition to carbon atoms there are some other atoms, for
example, nitrogen, sulfur or oxygen). Hydrocarbons, in their turn,
could be aliphatic (with open carbon chain) and cyclic (with closed
carbon chain). Both hydrocarbon types and hetero-cyclic compounds
could be saturated (in the molecule there are only single bonds) and
unsaturated (in the molecule there is one or more double or triple
bonds).
Aliphatic hydrocarbons:
СН3 СН2 СН2 СН3 СН СН СН СН СН СН СН СН
saturated unsaturated
3 3 3 3

alkanes alkenes (double bond) alkynes (triple bond)

Cyclic hydrocarbons:
Н2С СН2 НС СН НС СН
Н2С СН2 Н С СН
Н 2С СН2
СН2 2
СН
2
О
2
saturated unsaturated heterocyclic compound
Classification according to functional groups:
- halogen-derivatives R–Hal: СН3СН2Cl (chloro-ethane);
- alcohols and phenols R–ОН: СН3СН2ОН (ethanol);
- thiols R–SH: СН3СН2SН (ethane-thiol);
- ethers R–О–R: СН3–О–СН3 (di-methyl ether),
- esters R–СОО–R: СН3СН2СООСН2СН3 (acetic acid ethyl
ester; ethyl acetate);
- carbonyl compounds: aldehydes R–СНО: ketones R–СО–R:
О
СН3–С –Н 5
 (ethanal, aldehyde),СН3СОСН3 (propanon, ketone),

- carboxylic acids R - СООН: О (acetic acid);

СН3–С–ОН
- sulpho-acids R–SО3Н: СН3SО3Н (methane-sulpho acid);
- amines R–NH2: СН3СН2NH2 (ethyl-amine);
- nitrocompounds R–NO2: СН3СН2NО2 (nitro-ethane);
- metalorganic compounds: СН3СН2Nа (ethyl sodium).
Question 2. What organic compound nomenclature types are
used at present?
Answer. There are three types of organic compounds
nomenclature: trivial (historical), rational and systematic. Trivial
nomenclature is the system of historical names for compounds.
People who know Greek could easily understand that acetic acid
means something sour, and glycerol means something sweet. These
names do not give any information about structure of these
compounds. Due to increased synthesis of organic compounds new
nomenclatures were created, they reflected organic substance
structure.
Rational nomenclature makes compound name from easier
compound structure (first member of homologues series). СН3ОН –
carbinol, СН3СН2ОН – methyl-carbinol, СН3СН(ОН)СН3 – di-
methyl-carbinol etc.
At present this nomenclature type is very rare.
According to international (systematic) nomenclature organic
substance name is based on the name of corresponding hydrocarbon
with prefixes and suffixes which belong to this compound class
(homologues series).
Question 3. In what way is it proper to give a name to organic
compound according to systematic nomenclature?
Answer. To give proper name to an organic compound according
to systematic nomenclature it is necessary:
1) to choose the longest carbon chain as main carbon skeleton
and give it a name taking into consideration saturation or
unsaturation degree of the compound;

6
 2) to find all functional groups;
3) to denote what group is the group of the highest priority (table
1), this group name is reflected in compound name as suffix and it is
located at the end of the name; other groups are used as prefixes;
Table 1. Names of functional groups (groups are presented
according to their priority degree from top to bottom according to
priority decrease)
Compound Functional Prefix Suffix or ending
class groups
Acids СООН Carboxy- -oic acid
Sulpho-acids – SO3H Sulpho- Sulphonic acid
Nitryls –CN Cyan- -nitryl
Aldehydes СНО Oxo- -al
Ketones -С=О Oxo- -on
Alcohols ОН Hydroxy- -ol
Thiols – SH Mercapto- -thiol
Amines NН2 Amino- -amine
Alkenes -С=С-  -ene
Alkynes С≡С  -yne
Halogen- Br, I, F, Bromo-, -bromide, iodide,
derivatives Cl iodo-, fluro-, fluoride, chloride
chloro-
Nitro NO2 Nitro- 
compounds
4) to give numbers to carbon atoms in the main chain, giving
smaller number to a group of the highest priority (i.e. chain is
enumerated from the end which functional group with the highest
priority is closer to, in the case of hydrocarbons it is enumerated
from the end to which multiple bond or branch is closer);
5) to enumerate prefixes in alphabetic order (multiplying
prefixes as di-, tri-, tetra- etc. are not taken into consideration);
6) to make complete name of the compound.
You should remember:

7
 – in alcohols, aldehydes, ketones, carboxylic acids, amides,
nitryls, halogen-anhydrides names, suffix defining class follows
unsaturation degree suffix, for example, 2-butenal;
– compounds containing other functional groups are called as
hydrocarbon derivatives. These functional group names are placed as
prefixes at the beginning of hydrocarbon name, for example, 1-
chloro-propane.
Names of acid groups, for example, sulpho-acids or phosphine
acid are placed after hydrocarbon skeleton name, for example,
benzene-sulpho-acid.
Aldehyde and ketone derivatives are named according to the
name of initial carbonyl compound.
Esters are named as initial acid derivatives. Ending -oic acid is
changed into –oate, for example, methyl-propionate is propionic acid
methyl ester.
To mark the fact that substitute is attached to nitrogen atom from
primary structure capital N is used at the beginning of the substitute
name, for example, N-methyl-alanine.
Thus, start with main structure, you should know the names of
first 10 members of alkane homologues series by heart (methane,
ethane, propane, butane, pentane, hexane, heptane, octane, nonane,
decane). You should also know radicals formed from them, ending –
ane is changed into –yl.

Question4. What principles are at the basis of organic substance

classification?
Answer. At the basis of organic substance classification there
are two principles: structure of the carbon chain and functional group
origin.
Question 5. What class of organic compounds does
hydrocarbon belong to and what is its proper name according to
international (systematic) nomenclature?

СН3 СН СН СН3
2
СН СН
3
СН3
8
 Answer. 1) It is necessary to find what bond types are there in the
compound: single bonds, double bonds or triple bonds. In our case
there are only single bonds, it means that our compound belongs to
alkanes (saturated) hydrocarbons.
2) We should find the longest carbon chain. In this compound
there are two equally long chains containing 5 carbon atoms. They
could be enumerated in the following way:
3 4 5 3 4 5
СН3 СН СН СН СН3 СН СН СН
2 3 2 3
2 СН 1 2 СН
СН3 СН3
СН3 1СН
3
Enumeration is started from the end to which radical (branch) is
closer. That is why the following enumeration is a mistake:

3 2 1
СН3 СН СН СН3
2
4 СН
СН3
5СН
3

In the longest chain there are 5 carbon atoms, thus, the root is
“pentane”.
3) We find radicals attached to the main carbon chain. In the
compound there are same two methyl radicals. In the name they are
reflected by prefix “methyl” with multiplying prefix “di-”. Thus, the
compound name is di-methyl-pentane.
4) It is necessary to mark numbers of carbon atoms to which
hydrocarbon radicals are attached.
As a result we have 2,3-di-methyl-pentane.
Do not forget that between numeral and letter part of the name
you should write a dash.
Question 6. What is the name of this hydrocarbon and what is
its class of organic compounds?
СН3 СН С С СН СН3
2
СН3

9
 Answer. 1) It is necessary to define bond types at the
compound: single, double, triple. In the molecule there is a triple
bond, it means that compound belongs to alkynes.
2) We should find the longest carbon chain. It contains 6 carbon
atoms. Enumeration is started from the end with multiple bond. In
this compound triple bond is located in the centre of the molecule. In
this situation enumeration is started from the end to which
hydrocarbon radical is closer.
6 5 4 3 2 1
СН3 СН2 С С СН СН3
СН3
Alkane name with 6 carbon atoms is “hexane”. In the molecule
there is a triple bond, that is why, ending “-ane” is changed into
ending “-yne”.
3) We define carbon atom number with the triple bond. We
receive 3-hexyne.
4) We define radicals attached to main chain. In this compound
there is one methyl radical. In the name it is used as prefix “methyl-”
adding carbon atom number to which it is attached. As a result we
receive: 2-methyl-3-hexyne.
Question 7. What is following compound class and name
according to systematic nomenclature:
СН3 СН СН2 СН СН3
ОН СН3
Answer. To define the class of organic compound we need to
find functional groups. In this case there is hydroxyl group, thus, the
class of compounds is alcohols. In the molecule there is only one
such group then, it is mono-alcohol.
In the chain there are 5 carbon atoms, there are no multiple
bonds, then the root is “pentane”. Functional group is only one and
we name it as suffix “-ol” and note carbon atom number to which
hydroxyl group is attached. Chain enumeration starts from the end
with functional group.
1 2 3 4 5
СН3 СН СН2 СН СН
3
ОН СН3

10
 We receive 2-pentanol. What is left is to add radical name –СН3
(methyl) and carbon atom number to which it is attached. We receive
4-methyl-2-pentanol.
Let’s give a name to di-alcohol.
СН3 СН СН2 СН2
ОН ОН
In the chain there are 4 carbon atoms, there are no multiple
bonds, thus, the root is “butane”. Two the same functional groups are
marked in the form of suffix “-ol” and add multiplying prefix “di-”,
mark carbon atom numbers to which hydroxyl groups are attached.
Thus, we receive 1,3-butane-diol.
Algorithm is the same for tri-alcohol but we should take into
consideration the fact that multiplying prefix for three groups is “tri”,
then we receive the following name: 1,2,3-butane-triol.
Question 8. What is the class of organic compounds and name
according to systematic nomenclature for the following compound:
СН3 СН СН СООН
СН3 NН2
Answer. To define class of organic compounds we should find
functional groups in the compound. In the compound there are two
functional groups: carboxylic and amino group, then, the class of
organic compounds is amino acids. Carboxylic group is the group of
the highest priority, then, we start enumeration of the carbon chain
from carbon atom attached to carboxylic group:
4 3 2 1
СН3 СН СН СООН
СН3 NН2
All in all there are 4 carbon atoms in the chain, then, the root is
“butane”. Group of the highest priority is marked in the form of
ending “-oic acid”. Second functional group is used as prefix
“amino-” marking carbon atom number to which this group is
attached. We receive the name 2-amino-butanoic acid. What is left,
is to give the name to radical –СН3 (methyl) attached to the third
carbon atom. Radical name is used as prefix. Prefixes are enumerated
in alphabetic order. The name is 2-amino-3-methyl-butanoic acid.
Question 9. What is the class and name according to systematic

11
(international) and rational nomenclatures for the following
compounds:
СН3 О СН3 СН3 О СН2 СН3
I II
Answer. To define the class of organic compounds we should
analyze the structure. Both substances have similar structure: two
hydrocarbon radicals are attached to each other through oxygen
atom. This structure is typical of ethers. According to systematic
(international) nomenclature these compounds are alkoxy-alkanes.
Root is defined by the longest alkyl group. According to this
nomenclature rules the first compound is called metoxy-methane and
the second is called metoxy-ethane.
According to rational nomenclature rules ethers are called on
radicals attached to oxygen atom and the word “ether” is added. First
compound is called di-methyl ether, the second compound is called
methyl-ethyl ether. We could enumerate radicals according to their
priority or alphabetically.
Question 10. What is the formula and name of secondary
alcohol which contains 4 carbon atoms?
Answer. 1) It is necessary to write main carbon chain. In this
situation it should comprise 4 carbon atoms.
2) We define what functional group should be at this compound.
For alcohols it is hydroxyl group: –ОН.
3) We state what carbon atom is hydroxyl group attached to.
According to the wording of the task our alcohol is secondary, thus,
hydroxyl group is attached to secondary carbon atom (this is atom
directly attached to two other carbon atoms).
1 2 3 4
С С С С
ОН
In this situation this is second carbon atom.
4) We add hydrogen atoms to carbon atoms so that each carbon
atom valency is four. As a result we receive the following formula:
1 2 3 4
СН3 СН СН2 СН3
ОН

12
 We make the name of the compound. In the chain there are 4
carbon atoms, there are no multiple bonds, thus, the root is “butane”.
There is one functional group, that is why, it is marked as suffix “ol”
and mark carbon atom number with hydroxyl group. Name is 2-
butanol.
If we were asked to write down primary alcohol structure,
according to the same algorithm we receive 1-butanol:
4 3 2 1
СН3 СН2 СН2 СН2 ОН
Question 11. Write down the formula and name (according to
international nomenclature) to thiol containing 3 carbon atoms and
mark secondary carbon atom in the structure.
Answer. 1) First we write down main carbon chain. In this case
it has 3 carbon atoms.
2) We define what functional group should be in the compound.
Thiols and thio-alcohols are characterized by –SН group. According
to the wording of the task it is clear what carbon atom should have
thiol group. There are two formulas corresponding to the task:
3 2 1 1 2 3
СН3 СН2 СН2 SН СН3 СН СН3
SН
First formula is primary thiol as thiol group is attached to
primary carbon atom, in the second formula we have secondary thiol
as thiol group is attached to secondary carbon atom (atom which is
directly attached to two other carbon atoms). It means that secondary
carbon atom here is carbon atom number 2.
Now we make compound name. In the chain there are 3 carbon
atoms, there are no multiple bonds so the root is “propane” for both
substances. There is only one functional group so we mark it in the
form of suffix “-thiol” and mark carbon atom number to which it is
attached. We receive 1-propane-thiol and 2-propane-thiol.
Question 12. What is the formula and acid amide name which
has 4 carbon atoms?
Answer. First we should write down the formula of carboxylic
acid containing 4 carbon atoms.

13
 1) Write down main carbon chain. In this situation it
should have 4 carbon atoms.

2) Define functional group in this compound. This is

carboxylic group –СООН. We should add hydrogen
atoms to carbon atoms so that each carbon atom valency
is four. We receive the following formula:
4 3 2 1 О
СН3 СН2 СН2 С
ОН
Amide is carboxylic acid derivative in which –ОН group at
carboxylic group is substituted by amino group. Let’s write down
corresponding formula:
4 3 2 1 О
СН3 СН2 СН2 С
NН2
This compound is called butanoic acid amide (butane-amide).
According to trivial nomenclature it is called butter acid (butyric) (as
it is at butter in the form of ether with glycerol, in free form it is at
rotten butter), correspondingly, amide could be called butyric acid
amide (butyramide).
Amide bond is at biologically important polymers, for example,
proteins, in which structure it is called peptide bond.
Question 13. Choose formula with mistake in it.
Answer. It is necessary to analyze compound structure and
define whether written atom valency corresponds to real atom
valency. Let’s analyze two compounds:
1 2 3 4 4 3 2 1 ОН
а) СН С СН СН b) СН3 СН2 СН2 С
2 2 Н
You can see that in alkyne (a) three first carbon atoms valency is
four (each of them forms four bonds with other carbon and hydrogen
atoms) and fourth carbon atom has only three bonds (one is formed
with the third carbon atom and two are formed with hydrogen
atoms). It means that 1-butyne formula is not correct. In compound
(b) all carbon atom valency is four but oxygen atom valency is three
but not two. In this compound hydrogen attached to carbonyl carbon

4 14 3 2 1 О
b) СН3 СН2 СН2 С
Н
atom is extra and if it is omitted then we receive correct butanal
formula. So correct formulas are:
1 2 3 4
а) СН С СН СН
2 3
Question 14. Choose name with a mistake:
а) 1-methyl-butane; b) 2-methyl-butane; c) 2,2-di-methyl-butane; d)
2,3-di-methyl-butane
Answer. You should write down formulas of the compounds
according to their names and compare formula and suggested name.
All four names have the same root “butane”, it means that main
chain consists of four carbon atoms. Let’s enumerate chain and add
methyl radical to the first carbon atom in the first compound, methyl
radical is added to the second carbon atom in the second compound.
In two last compounds according to multiplying prefix “di-”, there
are two methyl groups. In the third compound, two groups are
attached to second carbon atom, in the fourth case they are attached
to second and third carbon atoms. Now we should add hydrogen
atoms according to carbon atom valency (4).
1 2 3 4 1 2 3 4
СН2 СН2 СН2 СН3 СН3 СН СН2 СН3
СН3 СН3
I II
СН3
1 2 3 4 1 2 3 4
СН3 С СН2 СН3 СН3 СН СН СН3
СН3 СН3 СН3 IV
III
At formula and name analysis it is clear that there is a mistake in
the first compound name as the longest (the only) chain has not four
but five carbon atoms and proper name is “pentane”.
Question 15. Does the name 2-methyl-4-butanol correspond to
international nomenclature?
Answer. To define whether the name is correct, let’s try to make
formula of the compound. The root is “butane” and it means that
there are 4 carbon atoms in the main chain. Let’s enumerate chain
and add hydroxyl group (-OH) corresponding to suffix “-ol” and
radical methyl (–СН3) at corresponding carbon atoms. We receive
the following compound:1 2 3 4
СН3 СН СН2 СН2 OН
СН3
15
 At analysis we could see a mistake: main carbon chain is not
properly enumerated. Numeration should start with the end to which
functional group is closer. 4 3 2 1
СН3 СН СН2 СН2 OН
СН3

Correct name of this compound is 3-methyl-1-butanol.

2. ORGANIC COMPOUND STRUCTURE

Question 16. What is the definition of the term: organic compound

structure?
Answer. Term organic compound structure is molecule structure
complete description. It comprises two levels at molecule
description: chemical structure and space (three-dimensional)
structure. Chemical structure is order (succession) of bonds between
atoms according to their valency. Chemical structure does not take
into consideration space localization of atoms making a molecule.
Space structure is studied at special chemistry branch which is called
stereo-chemistry. Modern development level of science and
technology allows stating space structure of very complex molecules.
Space structure is connected to physical, chemical properties and
biologic activity.
Question 17. What substances could be called isomers?
Answer. Isomers are compounds with the same qualitative and
quantitative content but which differ from each other in chemical or
space structure and which have different physical, chemical or
biological properties.
Question 18. What substances are called structural isomers or
isomers on structure?
Answer. Structural isomers or isomers on structure are
compounds with the same qualitative and quantitative content but

16
which differ from each other in chemical structure (succession
between atom bonds).
Question 19. What substances are called stereo-isomers?
Answer. Stereo-isomers (three-dimensional isomers) are
compounds in which molecules there is the same succession of
chemical bonds between atoms but they have different atom
localization in relation to each other in space.
Question 20. What are the types of structural isomerism?
Answer. There are three types of structural isomerism:
1– Carbon chain isomerism (isomers on carbon chain): butane
and 2-methyl-propane; 1 2 3
СН3 СН2 СН2 СН3 СН3 СН СН3
butane СН3 2-methylpropane

2– isomerism on position of functional group (or position of

multiple bonds):
1-butanol and 2-butanol or 1-butene and 2-butene;
4 3 2 1 1 2 3 4
СН3 СН2 СН2 СН2 ОН СН3 СН СН2 СН3
1-butanol ОН 3 2-butanol
1 2 3 4 1 2 4
СН2 СН СН2 СН3 СН3 СН СН СН3
1-butene 2-butene
3– isomerism on functional group (interclass): di-ethyl ether and
1-butanol.
4 3 2 1
СН3 СН2 О СН2 СН3 СН3 СН2 СН2 СН2 ОН
di-ethyl ether 1-butanol
Question 21. What are the types of space isomerism (stereo-
isomerism)?
Answer. Stereo-isomerism could be subdivided into
conformation and configuration.
Configuration isomers include geometric (cis- and trans-)
isomerism: cis-2-butene and trans-2-butene, and enantiomerism
(optical and mirror reflection isomerism): D- and L-lactic acids:
СООН СООН
Н3С СН3 Н СН3 НО Н Н ОН
С С С С
Н Н НС Н СН3 СН3
3
Cis-2-butene Trans-2-butene L-lactic acid D-lactic acid
17
 Conformation isomers comprise isomers received at molecule
rotation in relation to single bond. They are called eclipsed and
staggered conformations:
СН3 Н Н
СН3 СН3
Н Н СН3
Н Н Н Н
butane butane
eclipsed conformation staggered conformation
Question 22. What is molecule configuration?
Answer. Configuration is atom localization succession at space
without taking into consideration differences which appear as a result
of rotation around single s-bonds. For example, 2-butene has two
configuration isomers: cis-2-butene and trans-2-butene. Lactic acid
could also exist in the form of two configuration isomers: D-lactic
and L-lactic acid.
Question 23. What is molecule conformation?
Answer. Molecule conformations are its different geometric
forms which appear as a result of its rotation around single s-bonds.
Conformation isomers are stereo-isomers which are formed at
molecule separate parts rotation around single bonds.
Question 24. What is homologues series?
Answer. Homologues series is rank of similar structured
compounds which have similar chemical properties. In the series
members differ from each other on one or more -СН2-group.
At members of homologues series majority of reaction goes on
in the similar way (exception is only the first members of the series).
Thus, if you know chemical reactions for only one member of the
homologues series you can state that similar transformations are
typical of other members of homologues series.
A general formula could be written for any homologues series. It
reflects relation between carbon atoms and hydrogen atoms at the
members of the homologues series; this formula is called

18
homologues series general formula. For example, СпН2п+2 is formula
for alkanes, СпН2п+1ОН is formula for aliphatic mono-alcohols.
Question 25. Write down butanoic acid homologue, it should have
two more carbon atoms.
Answer. First, let’s write butanoic acid formula. The root is
“butane”, so in the molecule there are four carbon atoms.
Step one: write down main carbon chain consisting of four
carbon atoms.
Step two: define what functional group should be in the
compound. According to the ending “-oic acid” it is carboxylic group
–COOH. Add hydrogen atoms to each carbon atom so that carbon
atom valency is four. We receive the following formula:
4 3 2 1 О
СН3 СН2 СН2 С
ОН
Homologue should belong to the same class of organic
compounds, i.e. it is aliphatic acid with one carboxylic group and un-
branched hydrocarbon radical.
Step three: define what is the difference between initial acid and
homologue. According to the task, homologue should have two more
carbon atoms in the structure. It means that two –CH 2 groups should
appear in the hydrocarbon radical, in other words homologue
molecule should have not 4 but 6 carbon atoms. Let’s write main
carbon chain comprising 6 carbon atoms, the first carbon atom
belongs to carboxylic group –COOH. Let’s add hydrogen atoms to
each carbon atom so that carbon valency is four.
6 5 4 3 2 1 О
СН3 СН2 СН2 СН2 СН2 С
ОН
Let’s give name to the compound. In the main (and the only)
carbon chain there are 6 carbon atoms, then the root is “hexane”.
There is one functional group in the compound, it is marked in the
form of ending “-oic acid”. Carbon atom number is not marked here
as it is clear that it could be only the first. Homologue name is
hexanoic acid.
Question 26. Write down butanal homologue formula, it should have
four hydrogen atoms less.

19
 Answer. First of all let’s write butanal formula. The root is
“butane”, it means that there are four carbon atoms in the molecule.
Step one: write main carbon chain comprising four carbon
atoms.
Step two: define what functional group should be in the
compound. Suffix “-al” shows that there is aldehyde group –COH.
Now add hydrogen atoms to each carbon atom so that carbon
valency is four. We receive the following formula:
4 3 2 1 О
СН3 СН2 СН2 С
Н
Homologue should belong to the same class of organic
compounds, i.e. it should be an aldehyde.
Step three: define what is the difference between homologue and
initial aldehyde. According to our task in its molecule there are four
hydrogen atoms less. Four hydrogen atom decrease is the same as
decrease in two –CH2-groups, i.e. in homologue there are two carbon
atoms less in the carbon chain. Thus, homologue molecule contains
not 4 but 2 carbon atoms. Let’s write main carbon chain consisting of
two carbon atoms, first carbon atom belongs to aldehyde group –
CHO. Now we add hydrogen atoms to carbon atoms so that carbon
atom valency is four.
2 1 О
СН3 С
Н
Let’s give name to the compound. In the main (and the only)
chain there are 2 carbon atoms, thus, the root is “ethane”. There is
one functional group in the compound, we name it in the form of a
suffix “-al”. Carbon atom number in the carboxylic group is not
marked in this compound as it could be only the first. Homologue
name is ethanol. This compound is also called acetic aldehyde or
acetaldehyde.
Question 27. Write down pentanoic acid isomer on the carbon chain
structure.
Answer. First of all write down pentanoic acid formula. We
understand from the name that in the basis there is un-branched
(direct) chain consisting of five carbon atoms. Initial acid formula is:

20
 5 4 3 2 1 О
СН3 СН2 СН2 СН2 С
ОН
According to the term “isomer on the structure of the carbon
chain”, pentanoic acid isomer chain should have different structure
as compared to pentanoic acid carbon chain structure. In this
situation it could be only branched chain. For five carbon atoms there
are three variants of carbon chain structure:
4 3 2 1 О
СН3 СН2 СН С СН3
ОН 3 2 1 О
СН3 СН3 С С
I ОН
О СН3
4 3 2 1
СН3 СН СН2 С III
ОН
СН3
II
Let’s give names to the compounds. In compounds I and II the
longest carbon chain has four carbon atoms, thus, root is “butane”, as
there is carboxylic group the ending is “-oic acid”. In both molecules
there is one methyl radical which is attached to different carbon
atoms. Radical name and number of its carbon atom is given as
prefix. Carbon chain enumeration is started from functional group.
Thus, compounds I and II are called 2-methyl-butanoic acid and 3-
methyl-butanoic acid respectively. In compound III the longest
carbon chain has three carbon atoms, so the root is “propane” and
ending is “-oic acid”. This molecule has a more branched structure:
there are two methyl radicals (it means that there is multiplying
prefix “di-”), both radicals are attached to the second carbon atom (in
the name this number is repeated twice). Name of the third isomer is
2,2-di-methyl-propanoic acid.
The content of all three isomers and initial compound is the
same: С5Н10О2, but chemical structure is different.
Question 28. Write down 1-pentene isomer on the position of the
multiple bond.
Answer. Let’s start with writing 1-pentene formula. It is evident
that in molecule basis there is un-branched (direct) chain consisting
of five carbon atoms. Ending “-ene” shows that there is double bond.

21
Number 1 shows double bond position: it is between the first and
second carbon atoms. Initial alkene formula is:
1 2 3 4 5
СН2 СН СН2 СН2 СН3
1-pentene
According to the term “isomer on the position of the multiple
bond” in isomer formula multiple bond should be located between
other different carbon atoms. Theoretically it could have the
following form:
1 2 3 4 5 1 2 3 4 5
СН3 СН СН СН2 СН3 СН3 СН2 СН СН СН3
I II
1 2 3 4 5
СН3 СН СН2 СН СН2
III
At first glance, we could conclude that these are different
compounds. At giving names to compounds according to systematic
nomenclature, it turns out that it is impossible to have the same chain
enumeration as compared to initial compound, as chain enumeration
is started from the end with double bond. Following this rule we get:
1 2 3 4 5 5 4 3 2 1
СН3 СН СН СН2 СН3 СН3 СН2 СН СН СН3
I II
5 4 3 2 1
СН3 СН СН2 СН СН2
III
It is evident that formulas I and II correspond to one and the
same compound: it is 2-pentene, and formula III corresponds to
initial compound: it is 1-pentene.
Thus, there are only two isomers which follow the same general
formula С5Н10 and differ on chemical structure, to be more particular
they differ on the position of the double bond. These are 1-pentene
and 2-pentene.
Question 29. Write down butanal isomer on functional group.
Answer. Let’s start with butanal formula writing. It is clear from
the name that in the basis there is un-branched (direct) chain with
four carbon atoms. Suffix “-al” shows that one carbon atom belongs
to aldehyde group: 4 3 2 1 О
СН3 СН2 СН2 С
Н

22
 According to the term “isomer on functional group” at butanal
isomer formula there is some other (not aldehyde) functional group.
It could be, for example, keto-group: 4 3 2 1
СН3 СН2 С СН3
О
Both isomers content is the same: С4Н8О, but chemical structure
is different, in molecules there are different functional groups, in
other words, these substances belong to different classes of organic
compounds.
Let’s give name to new compound. The longest carbon chain has
four carbon atoms so the root is “butane”, suffix is “-on” as there is
keto-group. Name is 2-butanon. It is not necessary to mark number 2
as this is the only position of the functional group in the compound.
Carboxylic acid isomers on functional group are esters.
3 2 1 О 2 1 О
СН3 СН2 С СН3 С
ОН О СН3
Propanoic acid Acetic acid methyl
ester
Alcohol isomers on functional group are ethers.
СН3 СН2 ОН СН О СН3 3
ethanol di-methyl ether
Amino acid isomers on functional group are esters and hydroxyl
acid amides.
3 2 1 О 3 2 1 О
СН3 СН С СН3 СН С
ОН NН2
NН2 ОН
2-amino-propanoic 2-hydroxy-propanoic
acid (alanine) acid amide

Question 30. Serine (2-amino-3-hydroxy-propanoic acid) in L-

isomer form takes part at protein molecule formation. Write down
structural formula of its isomer and enantiomer.
Answer. Let’s write down serine formula:
3 2 1 О
СН2 СН С
ОН
ОН NН2
2-amino-2-hydroxy-
propanoic acid (serine)

23
 Second carbon atom is asymmetric (it is attached to four
different substitutes: carboxylic group, amino group, hydrogen atom
and third carbon atom in the carbon chain).This is first condition of
optical activity. Second condition is asymmetry at molecule
elements. Thus, compound is optically active and could exist in the
form of two enantiomers – space isomers, which are each other
mirror reflections.
To show enantiomers relative configuration, carbon chain is
drawn vertically, substitute of the highest priority is at the top;
substitutes at asymmetric carbon atom are located to the right and to
the left in relation to carbon chain:
1СООН 1СООН
СООН СООН
2 2
Н2N С Н Н С NН2 Н2N Н Н NН2
3 3
СН2ОН СН2ОН СН2ОН СН ОН2
L-serine D-serine L-serine D-serine

If amino group is located to the left in relation to carbon chain,

then isomer belongs to L-isomers. To write D-isomer, substitutes at
asymmetric carbon atom are drawn in mirror reflection. In our
situation they are at second carbon atom. Amino group is located on
the right in relation to carbon chain. Asymmetric carbon atom is not
marked by any chemical sign, it is supposed to be at line crossing
which shows corresponding bonds.
Question 31. What types of isomers are oleic and elaidic acids.
Answer. We should write down formulas of these acids. Oleic
and elaidic acids are un-saturated carboxylic acids with one double
bond, they are cis- and trans-isomers.
Н3С(СН2)7 (СН2)7СООН Н (СН2)7СООН
С С С С
Н Н Н3С(СН2)7 Н
Oleic acid Elaidic acid
Thus, these acids are space (geometric) isomers, as they differ in
atom and group localization in space in relation to double bond.

24
 Question 32. What is isomer type of butanoic acid and
propanoic acid methyl ester?
Answer. We should write formulas of these compounds. Root is
“butane”, it means there is un-branched carbon chain containing four
carbon atoms, one of which is in the structure of carboxylic group. In
propanoic acid molecule there are three carbon atoms; as ester is
methyl it is formed at interaction between propanoic acid and methyl
alcohol. Compound formulas are: 3 2 1 О
СН СН С
4 3 2 1 О 3 2 О СН3
СН3 СН2 СН2 С Propanoic acid methyl ester
ОН
Butanoic acid

General formula of both compounds is the same: С4Н8О2, but

chemical structure is different. These compounds belong to different
classes as they have different functional groups. We can conclude
that they are isomers on functional group.
Question 33. What is isomer type of 1-butanol and 2-butanol?
Answer. We should write these compound formulas. The root is
“butane”, it means that in the molecule there is un-branched carbon
chain having four carbon atoms. At both compounds there is suffix
“-ol”, both of them belong to one class, it is alcohols. At alcohol
molecule there is hydroxyl group (-OH). In the first compound this
group is attached to first carbon atom, in the second compound it is
attached to second carbon atom. Formulas of compounds are:
4 3 2 1 4 3 2 1
СН3 СН2 СН2 СН2 ОН СН3 СН2 СН СН3
1-butanol 2-butanol ОН
4 3 2 1 1
СН3 СН2 СН2 СН2 ОН 4 3 2
СН3 СН2 СН СН3
1-butanol
2-butanol ОН
Both compounds general formula is the same: С4Н9ОН, but
chemical structure is different. It means that they are structural
isomers. They belong to the same class and differ from each other
only by position of functional group. They are isomers on position of
the functional group.
Question 34. Are leucine and iso-leucine isomers?

25
 Answer. First of all, let’s write down these compounds
formulas. These are amino acids in the structure of proteins. Their
chemical names are 2-amino-4-methyl-pentanoic acid and 2-amino-
3-methyl-pentanoic acid.
The root at both substances is “pentane”, it means that there are
five carbon atoms in the main carbon chain, one of those carbon
atoms is in the structure of carboxylic group. In both molecules there
are amino groups attached to second carbon atom (next to carboxylic
group) and methyl radical (-CH3) attached to fourth and third carbon
atoms respectively. Compound formulas are:
5 4 3 2 1 О
5 4 3 2 1 О СН СН СН СН С
СН3 СН СН2 СН С 3 2 ОН
ОН СН NН
СН3 NН2 Iso-leucine 3 2
leucine
General formula of both compounds is the same: С6Н13О2N, but
carbon chain structure is different. These compounds are isomers on
carbon chain structure.

3. GENERAL LAWS OF ORGANIC COMPOUND REACTION

ABILITY

Question 35. What type of reactions is more typical of

compounds belonging to some class of organic compounds?
Answer. We are speaking not about all reactions but about more
typical of some class.
Alkanes practically reject one type of chemical reactions. It is
addition. Other reactions are quite possible for alkanes (taking into
consideration reaction conditions and reagent type). Most widely-
spread reactions for alkanes are substitution reactions. In alkane
molecules there is equal electron density distribution. That is why,
possibility of electrophilic particle or nucleophilic particle attack is
very low. Most typical reactions for alkanes are radical substitution
reactions.
Molecules containing p-bonds in the structure of double or triple
bond there is increased electron density which is higher and lower in
relation to molecule plane. It leads to the fact, that positively charged

26
ions or polar molecules by their positive pole (electrophilic particles)
are attracted to double bond. As a result of following interaction
there is reagent addition on the place of multiple bond. Most typical
reactions for alkenes and alkynes are electrophilic addition reactions.
In molecules containing functional groups there is electron
density displacement from carbon atom to hetero-atom from
functional group (for example, to halogen atom at halogen
derivatives or to oxygen atom at alcohols, etc.). As a result there is
partial positive charge on carbon atom. Thus, reagent attacking
carbon atom, should have partial or complete negative charge
(nucleophilic particle). As a result of interaction there is functional
group substitution by nucleophilic reagent. Halogen derivatives and
alcohols are characterized by nucleophilic substitution reactions.
Question 36. What is the type of chemical reaction according to
its equation?
Answer. It is necessary to know differential signs of reactions
belonging to different types.
1. According to reagent electron nature reactions are
subdivided into nucleophilic, electrophilic, free radical reactions.
Nucleophilic reagents are mono- and multi-anions or
molecules which have centres with increased electron density. They
include such anions and molecules as HO -, RO-, Cl-, Br-, RCOO-,
CN-, R-, NH3, C2H5OH, etc.
Electrophilic reagents are cations, simple or complex
molecules which have increased affinity to electron pair or affinity to
negatively charged molecule centres. They include cations H +, Cl+,
+
NO2, +SO3H, R+ and molecules with free orbitals AlCl3, ZnCl2, etc.
Free radicals are electro-neutral particles which have un-
shared electron, for example, Cl·, ·NO2.
2. According to particle number change during reaction there
are substitution, addition, elimination, degradation and redox
reactions.
In the case of substitution reaction in the molecule one atom
(or atom group) is substituted by another atom (or atom group), new
compounds are formed as a result. In this situation number of initial
substances equals number of reaction products.

27
 СН3–СН3 + С12 ® СН3–СН2С1 + НC1
In the case of addition reaction from two (or several)
molecules, one new substance is formed:
CH2 = CH2 + HBr → CH2Br–СH3
As a result of elimination reaction new organic substance is
formed with a multiple bond:
СН3–СН2С1 + NaOH(alcohol solution) ® СН2 = СН2 + NaC1 + Н2О
Degradation reaction leads to one substance formation from
two or more substances with more simple structure:
НСООН → СО2 + Н2
If in the molecule of initial substance there are two or more
carbon atoms, degradation reaction usually goes with carbon-carbon
bond breaking.
For example, under enzymatic action malic acid could degrade
and lactic acid is formed:
НООССН2СН(ОН)СООН ® СН3СН(ОН)СООН + СО2
3. In organic chemistry there are a lot of reactions which are
defined according to panial (additional) principles:
- hydration is water addition on the place of double bond
carbon-carbon or carbon-hetero-atom:
СН3–CH = CH2 + H2О ® СН3–CH(ОН)–CH3;
- dehydration is water elimination with unsaturated compound
formation:
СН3–CH(ОН)–CH3 ® СН3–CH = CH2 + H2О;
- hydrogenation is hydrogen addition on the place of the
double bond carbon-carbon or carbon-hetero-atom:
СН3–CH = CH2 + H2 ® СН3–CH2–CH3,
СН3–CО–CH3 + H2 ® СН3–CH(ОН)–CH3;
- dehydrogenation is hydrogen elimination with unsaturated
compound formation:
СН3–CH2–CH3 ® СН3–CH = CH2 + H2
- hydrolysis is interaction between complex substrate with
water with more simple compounds formation:
6 6 6
СН2ОН СН2ОН СН2ОН
5 5 5
О Н Н О Н О Н
Н Н Н Н Н
+ Н2О
4
ОН Н
1
О
4
ОН Н
1
2 4
ОН Н ОН
1

НО ОН НО
Н
3
ОН
2
Н ОН
3
28
2
Н
3
ОН
2

a-D-glucopyranosil-(1®4)- a-D-glucopyranose a-D-glucopyranose

(maltose) Maltose is reducing di-saccharide
 - nitration is interaction with nitric acid as a result hydrogen
atom at substrate molecule is substituted by nitro-group:
СН3–CH3 + HNO3 ® СН3–CH2NO2 + H2O;
- sulfonation is interaction with sulfuric acid or oleum as a
result hydrogen atom at substrate molecule is substituted by sulfo-
group:
СН3–CH3 + H2SO4 ® СН3–CH2SO3H + H2O;
- halogenation is interaction with halogen as a result hydrogen
atom at substrate molecule is substituted by halogen atom or halogen
atoms are added on the place of multiple bond:
СН4 + С12 ® СН3С1 + НC1
CH2 = CH2 + Br2 ® CH2Br – CH2Br;
- dehalogenation is halogen molecule elimination with
multiple bond or cyclic compound formation:
CH2Br – CH2Br ® CH2 = CH2 + Br2;
- hydro-halogenation is interaction with halogen-hydrogen as a
result hydrogen and halogen atoms are added on the place of the
multiple bond:
CH2 = CH2 + HBr ® CH2Br–СH3;
- dehydro-halogenation is halogen-hydrogen molecule
elimination with multiple bond formation:
CH2Br–СH3 ® CH2 = CH2 + HBr;
- carboxylation is reaction which result is carboxylic group
formation. For example, if there is ATP then pyruvic acid is
transformed into aceto-acetic acid in the organism:
СН3–СО–СООН+СО2+АТP ® НООС–СН2–СО–СООН+АDP+
Н3РО4;
- decarboxylation is reaction which result is carboxylic group
elimination from substrate, it is in the form of CO2:
R–CH(NH2)–COOH ® R–CH2NH2 + CO2;
- deamination is amino group elimination from substrate
molecule, as a result unsaturated, hydroxy- or oxo-compounds could

29
be formed according to reaction conditions or enzymatic conditions.
Thus the following reactions could be in vivo (in the organism):
- oxidative deamination, as a result amino group is
substituted by oxo-group:
R–CH(NH2)–COOH + [O] ® R–СО–CООН + NH3;
- hydrolytic deamination, as a result amino group is
substituted by hydroxyl group:
R–CH(NH2)–COOH + H2O ® R–СН(ОН)–CООН + NH3;
- intra-molecular deamination, as a result unsaturated
compound is formed:
R–CH2–CH(NH2)–COOH ® R–CH=CH–CООН + NH3;
- reductive deamination, as a result amino group is
substituted by hydrogen atom:
R–CH(NH2)–COOH + [Н] ® R–CH2–CООН + NH3;
- deamination in vitro (in the test-tube) is under nitrous acid
action with hydroxyl-compounds formation:
R–CH(NH2)–COOH + НNО2 ® R–СН(ОН)–CООН + N2 + H2O;
- isomerisation is substrate transformation into its isomer
which has the same quantitative or qualitative content but different
structure:

In organic chemistry reduction reactions include hydrogenation

reaction (hydrogen addition), and oxidation reaction includes
dehydrogenation reaction (hydrogen elimination) and reactions
which result is oxygen atom addition to substrate molecules.
Enzyme names, catalyzing reactions, are connected to reaction
classification according to additional principles. Enzymes catalyzing
redox reactions are called oxido-reductases; enzymes catalyzing
hydrogen elimination (dehydrogenation) are called dehydrogenases;

30
decarboxylation reactions are catalyzed by decarboxylases;
deamination reactions are catalyzed by deaminases; isomerization
reactions are catalyzed by isomerases; hydrolysis reactions are
catalyzed by hydrolases.
Question 37. Write down equation of reaction properly and
define its mechanism.
Answer. You should know organic substance classification and
be able to write their formulas (questions 1, 9-11) and study
characteristic principles of different reaction types (questions 35, 36).
For example you should write reaction between 2-butenoic acid
and hydrogen. In the first turn we should write formulas of substrate
and reagent: СН3–СН=СН–СООН and Н2
Let’s analyze substrate molecule structure. In molecule structure
there is carboxylic group (this is acid) and hydrocarbon radical
containing double bond (butEnoic but nor butAnoic acid).
Unsaturated compounds are characterized by addition reaction on the
place of the multiple bond. In this situation the most possible
reaction is hydrogen addition on the place of the double bond. And
p-bond is broken, hydrogen atoms add to the second and the third
carbon atoms:
СН3–СН=СН–СООН + Н2 ® СН3–СН2–СН2–СООН
Reaction product is butanoic acid.
In such compounds it is easier to attack electron density of the
p-bond and attacking particle should have positive charge. Thus, this
reaction mechanism is electrophilic addition. This reaction could
belong to reduction reactions, according to panial principles it is
hydrogenation reaction.
Let’s analyze one more example. Let’s try to write reaction
between bromo-ethane and sodium hydroxide aqueous solution and
define its mechanism.
Let’s write formulas of reacting substances: CH 3–CH2Br and
NaOH.
Let’s analyze bromo-ethane molecule structure. Bromine atom is
more electro-negative than carbon atom. Carbon-bromine bond is
polarized, carbon atom has partial positive charge. It means that
attack should be done by negatively charged reagent. Such

31
negatively charged particle is in the solution: it is hydroxyl-anion
ОН–, which is formed at sodium hydroxide dissociation in water.
This anion attacks carbon atom with partial positive charge and
forces out bromine anion from bromo-ethane molecule. Thus, there
is nucleophilic substitution reaction with ethanol formation:
CH3–CH2Br + NaOH ® CH3–CH2OH + NaBr
Question 38. What product is predominantly formed at
bromination reaction of 3-methyl-pentane?
Answer. All carbon atoms at 3-methyl-pentane are in the state
of sр3-hybridisation. In the molecule there are non-polar C-C and low
polar C-H s-bonds. It determines their participation at radical
substitution reactions SR: if there are primary, secondary and tertiary
carbon atoms, bromination predominantly goes on tertiary carbon
atom (the least solid C-H bond and the most solid intermediate bond
– tertiary radical). It means that predominant reaction product is 3-
bromo-3-methyl-pentane.
Br
CH3–СН2–СН–СН2–СН3 + Br2 ® СН3–СН2–С–СН2–СН3 + HBr
СН3 СН3
3-methyl-pentane 3-bromo-3-methyl-pentane

Question 39. Give name to reaction product at reaction between

propene and 2-butenoic acid with bromo-hydrogen if there is
hydrogen peroxide and there is no hydrogen peroxide in the mixture.
Answer. Halogen-hydrogen electrophilic addition goes
according to Markovnikov rule: hydrogen atoms are added mainly
to the most hydrogenated carbon atom. For example, at interaction
between propene and bromo-hydrogen there is mainly 2-bromo-
propane formed.
СН3СН=СН2 + НВr ® СН3СНВr–СН3
propene 2-bromo-propane
At 2-butenoic acid both carbon atoms with double bond have
equal hydrogen atoms number. In this case Markovnikov rule is used
in more general form: non-symmetric reagent addition to non-
symmetric alkene according to ionic mechanism goes in the direction
of more stable cation formation.

32
 Electron density of the p-bond is attacked by positively charged
particle Н+. As a result of hydrogen addition to the double bond in
the acid СН3СН=СНСООН two carbo-cations could be formed:
СН3®+СН–СН2®СООН (I) and СН3СН2®+СН®СООН (II)
In cation (I) near to positively charged carbon atom there is electron
donor methyl group which has positive inductive effect which leads to
positive charge delocalization and cation stability. In cation (II) methyl
group is farther from positively charged carbon atom, its effect is
weaker (inductive effect decreases going along the chain). Electron
acceptor carboxylic group due to its negative inductive effect,
destabilizes cation; but in cation (I) it is located farther and its
destabilizing action is lower than in secondary cation (II). As a result
charge distribution in cation (I) is more equal and this particle is more
stable, reaction goes on along the direction of its formation. Addition
would follow Markovnikov rule in its general form:
СН3СН=СНСООН + НВr ® СН3СНВrСН2СООН
2-butenoic acid 3-bromo-butanoic acid
If there is peroxide, addition reaction has radical mechanism and
does not follow Markovnikov rule (goes against Markovnikov rule):
СН3СН=СН2 + НВr(there is Н2О2) ® СН2ВrСН2СН3
propene 1-bromo-propane
СН3СН=СНСООН + НВr(there is Н2О2) ® СН3СН2СНВrСООН
2-butenoic acid 2-bromo-butanoic acid
Question 40. In the metabolic process in living organisms
fumaric acid is transformed into malic acid. In what way is it
possible to receive malic acid from fumaric acid in vitro?
Answer. Fumaric acid is unsaturated di-based acid (trans-
butene-diovic acid). Malic acid is saturated di-based hydroxyl acid
(hydroxyl-butane-diovic acid).
Fumaric acid transformation in to malic acid could be performed
with the help of water addition on the place of the multiple bond, i.e.
with the help of hydration reaction. Alkene hydration is performed at
strong acid aqueous diluted solution, for example, it could be sulfuric
acid. Acid is the source of electrophilic particle – proton Н+.
Reaction mechanism is electrophilic addition АЕ.
Electron density of carbon-carbon p-bond at fumaric acid

33
molecule is decreased due to two carboxylic groups electron acceptor
action. That is why fumaric acid hydration is performed at
comparatively severe conditions (heating with diluted aqueous
solution at temperature 150-200 °С).
НООС Н ОН
+
С=С + Н2О (Н ) ® НООС–СН–СН2–СООН
Н СООН Malic acid
Fumaric acid
Fumaric acid hydration in vitro leads to racemic mixture
formation (racemic mixture is mixture of equal amount of malic acid
enantiomers). In organism this reaction is catalyzed by an enzyme
which is called fumarase which has strict space specificity which
leads to only one stereo-isomer formation, it is L-malic acid.
Question 41. R-2-bromo-butane could react to sodium
hydroxide aqueous solution according to S N1 and SN2 mechanisms.
Describe stereo-chemical reaction result in each case.
Answer. Secondary halogen derivative could have mono- or bi-
molecule mechanism. Reaction product is 2-butanol, difference is
only in the optical activity of products. If reaction follows mono-
molecular mechanism (SN1), intermediate product is secondary
carbo-cation СН3НС+СН2СН3. Nucleophilic reagent (hydroxyl
group) attack on cation has equal direction possibility, as a result
racemic mixture is formed which contains R- and S-2-butanols with
equal amount in moles. Mixture has optically active components but
generally racemic mixture is optically inactive.
If reaction follows bi-molecular mechanism (S N2), intermediate
product is complex containing substrate and reagent molecules and
nucleophilic reagent attack is possible only at the side opposite to
halogen atom. Result is rotation of the configuration, we get S-2-
butanol which is optically active.
Question 42. At high doses of hydrasine or its derivatives action
on organism there are nervous disorders. What is the chemical basis
of hydrasine action if it is known that it reacts with co-enzyme
pyridoxalphosphate?
Answer. Pyridoxalphosphate is hetero-cyclic compound which
has aldehyde group in the cycle together with other substitutes.

34
Hydrasine as nucleophilic reagent reacts with carbonyl carbon atom.
Н О Н N–NH2
С ОН С ОН
НО СН2–О–Р=О + NH2–NH2 ® НО СН2–О–Р=О + H2O
ОН hydrasine ОН
НС3
НС3
pyridoxalphosphate pyridoxalphosphate hydrason
Final product at addition-elimination reaction is
pyridoxalphosphate hydrason.
Hydrason formation leads to aldehyde group blocking at
pyridoxalphosphate which breaks its interaction as co-enzyme with
glutamic acid amino group. This reaction is one stage of glutamic
acid transformation in the organism into g-amino-buteric acid. Co-
enzyme blocking by hydrosine leads to g-amino-buteric acid
deficiency which slows nervous impulse transmission.
Question 43. Methyl alcohol coming into organism leads to
severe poisoning which is accompanied by eye-sight loss. Its reason
is methanol oxidation product influence on eye cornea. Write down
the scheme of methanol oxidation.
Answer. At methanol poisoning in the organism under alcohol-
dehydrogenase action there is formaldehyde (methanol) and formic
acid formation which are more toxic than methanol. This is an
example of lethal synthesis (when less toxic substances due to
metabolic process are transformed in to more toxic compounds).
Alcohol-dehydrogenase О О
СН3–ОН Н–С + Н–С
Н ОН
methanol methanal formic acid

Ethyl alcohol C2H5OH has better reaction with the enzyme

which is called alcohol-dehydrogenase. It slows methanol
transformation into methanal and formic acid. Methanol is
discharged at initial form. That is why ethanol drinking immediately
after methanol poisoning decreases the severity of poisoning.
Question 44. What are the signs of interaction between sodium
oleate and bromine water?
Answer. Let’s analyze substrate structure in this reaction.
Sodium oleate is oleic acid sodium salt. Oleic acid is higher

35
unsaturated acid. Bromine water is bromine solution in water.
Bromine is brown liquid, bromine water is coloured from brown to
light-yellow according to concentration. Double bond in oleic acid
radical participates in reaction with bromine:
СН3(СН2)7СН=СН(СН2)7СООН+Br2®СН3(СН2)7СНBr–
СНBr(СН2)7СООН
As a result of the reaction bromine concentration in water is
decreased and bromine water turns lighter or there is complete
discoloration. Bromine water discoloration is the sign of qualitative
reaction on unsaturated compounds.

4. AMINO ACIDS, PEPTIDES AND PROTEINS

Question 45. What compounds belong to a-amino acids? What

is a-amino acid role in living organism functioning?
Answer. a-Amino acids are hetero-functional compounds which
contain two functional groups: carboxylic group (–СООН) and
amino group (–NH2), both groups are attached to one and the same
carbon atom. a-Amino acids are named according to International
nomenclature, and carbon atom with amino group is the second
carbon atom. Many a-amino acids, especially those in the protein
structure, are used in their trivial names according to trivial
nomenclature.

3 2 1 О О 4 3 2 1 О
СН3–СН–С С–СН2–СН–С
ОН НО ОН
NН2 NН2
2-amino-propanoic acid, alanine 2-amino-butane-diovic acid
Aspartic acid

Numerous peptides and proteins at living organisms are built

from twenty a-amino acid residues. All a-amino acids contain one
and the same fragment, H2N–СН–СООН group, second carbon atom
is attached to hydrocarbon radical –R. Hydrocarbon radical could
have different chemical nature.

36
 Modern rational amino acid classification is based on radical
polar character, i.e. their ability to react with water at physiological pH
(which are close to pH 7,0). Amino acids could have the following
radicals: 1) non-polar (hydrophobic); 2) polar (hydrophilic); 3)
aromatic; 4) negatively charged and 5) positively charged. There are
amino acid structural formulas, their names according to trivial
nomenclature, abbreviated English names and one-letter symbols
which are accepted in foreign and Russian literature.
a-Amino acids with non-polar (hydrophobic) radical
О О О
Н–СН–С СН3–СН–С СН3–СН–СН2–СН–С
ОН ОН ОН
NН2 NН2 СН3 NН2
Glycine Gly, G Alanine, Ala, A Leucine, Leu, L
О О О
СН3–СН2–СН–СН–С СН3–СН–СН–С С
ОН ОН ОН
СН3 NН СН3 NН N–Н
2 2
Isoleucine, Ile, I Valine, Val, V Proline, Pro, P
a-Amino acids with polar un-charged radical
О О О О
СН2–СН–С СН2–СН–С С–СН2–СН2–СН–С
ОН ОН Н2N ОН
ОН NН2 SН NН2 NН2
Cystein, Cys, C Glutamine, Gln, Q
Serine, Ser, S
О О О О
CH3–СН–СН–С СН2–СН2–СН–С С–СН2–СН–С
ОН ОН Н2N ОН
ОН NН2 S–CH3 NН2 NН2
Threonine, Thr, T Methionine, Met, М Asparagine, Asn, N
a-Amino acids with polar negatively charged radical
О О О О
С–СН2–СН–С С–СН2–СН2–СН–С
НО ОН НО ОН
NН2 NН2
Aspartic acid, Asp, D Glutamic acid, Glu, E
a-Amino acids with polar positively charged radical
О О
СН2– СН2–СН2–СН2–СН–С H–N CH2–CH– С
ОН ОН
NН2 NН2 N NН2
Lysine,Lys, K О Histidine, His, H
HN=C–NН–СН2–СН2–СН2–СН–С
ОН
NН2 NН2
Arginine, Arg, R
37 aromaticОradical
a-Amino acids with
О –СН2–СН–С О
–СН2–СН–С ОН –СН2–СН–С
ОН NН2 OН– ОН
NН2 N–Н NН2
Phenylalanine, Phe, F Tryptophan, Trp, W Tyrosine,Tyr, Y
 a-Amino acids are colourless crystals, soluble in water under
normal conditions.
Protein synthesis in the organism is possible only all twenty a-
amino acids are presented in the organism. Main source of a-amino
acids is food proteins. Some a-amino acids could be synthesized in the
organism (from other amino acids or other metabolic products), but
some part of a-amino acids is not synthesized at human organism and
could come only with food, that is why balanced protein nutrition is
very important for human beings. Such a-amino acids are called
essential: valine, leucine, isoleucine, lysine, threonine, methionine,
phenylalanine, tryptophan.
At some diseases non-essential amino acids could become
essential. For example, at phenylketonuria organism stops
synthesizing tyrosine.
Many a-amino acids are used at Medicine. For example, glycine
is used to make metabolic process in brain tissues and muscles
better. Glutamic acid is used as a treatment of central nervous system
dis-orders, methionine and histidine are used for cure hepatic
diseases etc.
Question 46. Write formulas of stereo-isomers (enantiomers)
for a-amino acids. Are all natural a-amino acids optically active?
Answer. At all natural a-amino acid molecules, except for
glycine, one and the same carbon atom (the second) is attached to
four different substitutes: carboxylic group (–СООН), amino group
(–NH2), hydrocarbon radical R and hydrogen atom, i.e. at least one

38
carbon atom from all carbon atoms in these compounds is
asymmetric (chiral). At all natural a-amino acids there are no
elements of symmetry, thus, all a-amino acids (except glycine) are
optically active compounds and could exist in the form of two
enantiomers. To write enantiomers properly we should locate carbon
chain vertically. Group of the highest priority (carboxylic) is located
at the top. Two other substitutes (amino group and hydrogen atom) at
second (asymmetric) carbon atom are located at the right and at the
left in relation to carbon chain. In standard Fischer’s formula L-
configuration corresponds to amino group location at the left from
the carbon chain, in D-configuration amino group is located in the
right:
СООН СООН
Н NН2 Н2N Н
R R
D-a-amino acid L-a-amino acid
Amino acids isoleucine and threonine have two asymmetric carbon
atoms (second and third) in the molecule, thus, they could exist in the
form of two enantiomer pairs:
СООН СООН СООН СООН
Н2N Н Н NН2 Н NН2 Н2N Н
Н ОН НО Н Н ОН НО Н
СН3 СН3 СН3 СН3
L-threonine D-threonine D-allothreonine L-allothreonine
СООН СООН СООН СООН
Н2N Н Н NН2 Н NН2 Н2N Н
Н СН3 Н3C Н Н СН3 Н3C Н
СН2 СН2 СН2 СН2
СН3 СН3 СН3 СН3
L-alloisoleucine D-alloisoleucine D-isoleucine L-isoleucine

From all four isomers only one is used in human organism to

build proteins: L-threonine and L-isoleucine.

39
 Other a-amino acids in the protein structure are in L-form. a-
Amino acids of D-form are in peptide structure at some micro-
organisms and bacteria.
Question 47. What is acid-base property expression and
amphoteric character at a-amino acids? What a-amino acid
properties determine their ion structure?
Answer. a-Amino acids form salts with both alkali and acids as
they are amphoteric compounds, as in their molecules there are acid
(-COOH) and base (-NH2) functional groups:
О + HCl О + NaOH О
R–СН–С Cl–
¬¾ R–СН–С ¾ ® R–СН–С
ОН ОН – H O ОNa
NН3+ NН2 2 NН2
a-amino acid a-amino acid a-amino acid
chloride sodium salt
With heavy metal cations a-amino acids form inner-salts of
chelate (claw-like) type:
О + Cu(OH) О C О NH
·· 2
R
R–СН–С ¾¾® 2 CH
ОН – 2 H O Cu
HC · ·
NН2 2
R NH О C О
2
a-amino acid a-amino acid chelate complex

Arrow directed from nitrogen atom to copper atom in chelate

formula stands for chemical bond formed according to donor-
acceptor mechanism. Nitrogen atom donates its electron pair to form
a bond, it is a donor, and copper atom providing vacant (free) orbital
is an acceptor.
At aqueous solutions amphoteric a-amino acids exist in the form
of balanced mixture of di-polar ion, cation and anion forms:
О + H+ О + OH– О
R–СН–С ¾
¬¾® R–СН–С – ¬¾® ¾ R–СН–С
ОН О О–
NН3+ NН3 + NН2
a-amino acid cation di-polar ion a-amino acid anion
form form

At strong acid solutions (рН = 1-2) cation form predominates, at

strong alkaline solutions (рН = 13-14) anion form predominates.
When solid a-amino acids exist in the form of di-polar ions. At

40
equation of reactions with a-amino acids they are written in non-
ionized form.
Ionic structure of a-amino acid molecules determines their high
melting temperatures (higher than 200 °С), non-volatility, water-
solubility, non-solubility at organic solvents. Solubility in water
provides a-amino acid biological functions: absorption, transmission
in the organism etc.
Question 48. What is the medium reaction at a-amino acid
dissolving at distilled water?
Answer. Solution рН, received at a-amino acid dissolving
depends on functional group nature at acid hydrocarbon radical, to be
more particular it depends on number of acid and base groups.
Let’s analyze amino acids with non-polar hydrocarbon radical.
In the molecule there is one acid group (–СООН) and one basic
group (–NH2). In aqueous solutions these amino acids are ionized.
Distilled water used for solutions does not have excessive amount of
Н+ ions, and ОН– ions, medium is neutral (рН = 7,0), thus, ion forms
in the solution are formed due to Н+ ions transition from acid group
(–СООН) to basic group (–NH2). Practically all amino acid
molecules exist in the form of di-polar ions and medium could be
considered close to neutral.
At glutamic and aspartic acid molecules there are two acid
carboxylic groups (–СООН) and one basic group (–NH2). At
solution there is also Н+ ion transition from carboxylic group to
amino group in a-position. Proton formed at second carboxylic
group dissociation transits to solution. Thus, excessive amount of Н+
ions is accumulated in the solution, medium is acid (рН < 7).
Amino acids lysine, arginine and histidine have one carboxylic
group and two basic amino groups. In the solution there is Н+ ion
transition from carboxylic group to amino group at a-position. At
second amino group interaction with water in the solution there is
excessive amount of ОН– accumulation, so medium is alkaline (рН >
7).
Question 49. What is a-amino acid isoelectric point? In what
way a-amino acids move in the electric field?

41
 Answer. Medium рН, at which practically all amino acid
molecules exist in the form of bi-polar ions, is called amino acid
isoelectric point for this amino acid and is marked as рI. At
isoelectric point total charge on a-amino acid molecule is zero. Di-
polar ions do not move in the electric field, thus, at medium рН
which is рI, amino acid solution does not conduct electric current.
If medium рН is lower than рI, amino acid exists predominantly
as cation. Under the action of constant electric field, for example, at
electrophoresis, amino acid cation moves to negatively charged
electrode (cathode).
If medium рН is higher than рI, amino acid predominantly exists
in the form of anion. Under the action of constant electric field, for
example, at electrophoresis, amino acid anion moves to positively
charged electrode (anode).
At acid medium a-amino acid is cation, moves to cathode and is
reduced there. At basic medium (alkaline) a-amino acid is anion,
moves to anode and is oxidized there.
With the help of electrophoresis it is possible to separate
individual amino acids at a-amino acid mixture.
For example, there is mixture of three acids: alanine (рI = 6,1),
lysine (рI = 9,7) and glutamic acid (рI = 3,2). Let’s try to define their
movement direction if electrophoresis is performed at рН = 6,1.
For lysine medium electrophoresis рН is lower than рI (6,1 <
9,7), thus, in the solution lysine predominantly exists in the form of
cation and under the action of electric field it moves to cathode.
For glutamic acid medium electrophoresis рН is higher than рI
(6,1 > 3,2), Thus, in the solution glutamic acid predominantly exists
in the form of anion and under the action of constant electric field it
moves to anode. As alanine isoelectric point is 6,1 then it will stay at
the start line (it will not move anywhere).
Question 50. Write down valine structural formula. Name this
amino acid according to international nomenclature. Write down
isomers on position of functional group, carbon chain structure,
functional group. Is valine optically active? If it is optically active
write and name its enantiomers. What is medium pH of this amino
acid solution at distilled water? What is ion form of this amino acid

42
at gastric juice (рН = 1)? What is medium pH when this amino acid
solution does not conduct electric current?
Answer. To give valine a name according to international
nomenclature we should find the longest carbon chain, enumerate it
starting from functional group with the highest priority (carboxylic
group). In the chain there are four carbon atoms then it is butanoic
acid, which has amino group at the second carbon atom and which
has methyl group at the third carbon atom. Carbon chain is branched,
to write isomer on the structure of the carbon chain it is enough to
locate all carbon atoms as a line and we get an isomer: 2-amino-
pentanoic acid. To write an isomer on position of the functional
group it is possible to transmit amino group to the third carbon atom
and transmit methyl group to the second carbon atom. We receive 3-
amino-2-methyl-butanoic acid. To write the third isomer it is
necessary to change some functional group, for example, at changing
–ОН group on to amino group we receive 2-hydroxy-3-methyl-
butanoic acid amide.
Valine is optically active as in its structure there is asymmetric
(chiral) carbon atom (С2) and there are no symmetry elements, thus,
this compound could be represented as two absolute configurations
(R- and S-isomers), and in the form of two relative configurations
(L- and D-isomers).
In molecule structure there is one carboxylic group and one
amino group, valine is amphoteric compound, and its solution in
distilled water has neutral medium. At strong acid medium (рН = 1)
valine is protoned on amino group and it is cation. рН, at which
amino acid solution does not conduct electric current is called
isoelectric point; for valine it is 6,0.

43
4 3 2 1 4 3 2 1 4 3 2 1
СН3 СН СН СООН СН СН СН СООН СН3 СН СНСОNН2
3
СН3 NН2 NН2 CН3 СН3 OН
valine 3-amino-2-methyl- 2-hydroxy-
2-amino-3-methyl- butanoic acid 3-methyl-butanoic
butanoic acid valine isomer on acid amide
functional group valine isomer on
position functional group
5 4 3 2 1
СН3 СН2СН2СН СООН
NН2 2 2
СООН СООН
2-amino-pentanoic 4 4
acid С Н С Н
valine isomer on (СН3)2CH NН2 Н2N CH(СН3)2
carbon chain 3 1 1 3
structure S-valine R-valine
СOOН СOOН
СН3 СН СН СООН
Н2N Н Н NН2
Н3C +NН3
СН СН
valine as cation
Н C СН3
3
Н C СН3
3 (рН=1)
L-valine D-valine
Question 51. What reaction could transform isoleucine into 3-
methyl-2-pentenoic acid? What reaction could transform serine into
2-amino-ethanol?
Answer. Let’s write down formulas of initial compound and
first reaction product.

О 5 4 3 2 1 О
СН3–СН2–СН–СН–С СН3–СН2–С=СН–С
ОН ОН
СН3 NН СН3
2
Isoleucine 3-methyl-2-pentenoic acid
It is obvious that to receive 3-methyl-2-pentenoic acid we need
removing amino group from isoleucine. If we remove amino group
then at second carbon atom there is one bond released:
О О
СН3–СН2–СН–СН–С ® СН3–СН2–СН–СН–С
ОН ОН
СН3 NН –NН2 СН3
2
44
 To form double bond between the second and third carbon
atoms we need one free bond at the third carbon atom. Methyl group
in this situation (–СН3) should be preserved at a molecule. It could
be done eliminating hydrogen atom from the third carbon atom:
5 4 3 2 1 О 5 4 3 2 1 О
СН3–СН2–СН–СН–С ® СН3–СН2–С=СН–С
ОН –Н ОН
СН3 СН3
Thus, to receive 3-methyl-2-pentenoic acid isoleucine molecule
should lose amino group and hydrogen atom. In free form these
particles are not stable and form ammonia molecule NН3. If
ammonia molecule is discharged from amino acid molecule with
unsaturated acid formation, then these are the signs of intra-
molecular deamination reaction (question 36). Final equation of
reaction could be written in the following way:
О О
СН3–СН2–СН–СН–С ® СН3–СН2–С=СН–С + NН3
ОН ОН
СН3 NН СН 3
2

Now let’s write down serine and 2-amino-ethanol molecules:

О
СН2–СН–С СН2 –СН2
ОН
ОН NН ОН NН
2 2
serine 2-amino-ethanol

Comparing formulas we come to decision that to solve our

problem we need removing carbon atom and two oxygen atoms from
carboxylic group. During reaction serine should lose carboxylic
group. This type of reaction is called decarboxylation, carboxylic
group is discharged in the form of carbon tetra-oxide.
In the organism a-amino acid decarboxylation goes on under
enzyme action which is called decarboxylase. Equation of reaction
could be written in the following way:
О decarboxylase
СН2–СН–С ¾¾¾¾® СН2 –СН2 + СО2
ОН
ОН NН ОН NН
2 2
serine 2-amino-ethanol
45
 Question 52. What compound is formed at serine reductive
deamination and glutamic acid oxidative deamination? Do oxidative
deamination products differ from each other in vivo (in the
organism) and in vitro (in the test tube)?
Answer. At a-amino acid reductive deamination hydrogen atom
in the second position is substituted. One more hydrogen atom adds
amino group with ammonia molecule formation:
О 2 [H] 3 2 1 О
СН2–СН–С ¾® СН2–СН2–С + NH3
ОН ОН
ОН NН ОН
serine 2 3-hydroxy-propanoic acid

As a result 3-hydroxy-propanoic acid is formed.

a-Amino acid oxidative deamination in living organism has two
stages. At the first stage under the action of enzymes dehydrogenases
there is dehydrogenation (hydrogen elimination) of initial a-amino
acid and imino acid is formed. At the second stage due to imino acid
hydrolysis (interaction with water) there is a-keto acid and ammonia
formation. For glutamic acid these stages have the following form:

НООС–СН2–СН2–СН–СООН ® НООС–СН2–СН2–С–СООН
– Н2
NН2 NН
Glutamic acid a-imino-glutaric acid
+НО
НООС–СН2–СН2–С–СООН ¾®2 НООС–СН2–СН2–С–СООН
– NН3
NН О
a-imino-glutaric acid a-keto-glutaric acid
At laboratory conditions oxidative deamination is performed
with the help of nitrous acid. There is a-hydroxy acid formation and
gas nitrogen discharge:
+ НNO2
НООС-СН2-СН2-СН-СООН ¾¾® НООС-СН2-СН2-СH-СООН
– N2
NН2 –НO OН
Glutamic acid 2 a-hydroxy-glutaric acid

46
 Question 53. What compounds are formed in the organism at
interaction between valine and pyruvic acid?
Answer. Let’s write down initial compound formulas:
О О
СН3–СН–СН–С СН3–С–С
ОН ОН
СН NН О
3 2
valine Pyruvic acid

Valine is a-amino acid, pyruvic acid is a-keto acid. In the living

organism under the action of enzymes which are transaminases, there
is transamination reaction, i.e. amino group transition. Amino group
donor is a-amino acid and its acceptor is a-keto acid. a-Amino acid
is transformed into a-keto acid and a-keto acid due to reaction is
transformed into a-amino acid with corresponding radical structure
(amino group and keto group exchange their positions).
At interaction between valine and pyruvic acid there is the
following reaction:
СН3СН–СН-СООН +СН3–С–СООН ® СН3СН–С-СООН+ СН3-СН-СООН
СН3 NН2 О СН3 О NН2
valine Pyruvic acid 2-oxo-3-methyl- alanine
butanoic acid
Reaction products are 2-oxo-3-methyl-butanoic acid and 2-amino-
propanoic acid (alanine). This reaction is used in the organism to
synthesize non-essential amino acids and to remove excessive amount
of un-necessary amino acids and connection is formed between protein
and carbohydrate metabolism.
Question 54. What are peptides? What is their difference from
proteins? What reaction forms peptide in the organism?
Answer. Peptides and proteins are compounds built from a-
amino acid residues. It is considered that peptides could have up to
100 amino acid residues and proteins could have more than 100
amino acid residues. Peptides are subdivided into oligopeptides (low-
molecular peptides) which contain less than 10 amino acid residues.
Peptides containing higher number of amino acid residues are called
poly-peptides. For macro-molecules with amino acid residues
number close to 100 or excessing 100, term peptide practically
corresponds to protein. Poly-peptide and protein chains are formed as

47
a result of a-amino acid poly-condensation reaction with peptide
(amide) bond formation (–СО–NH–) between monomer parts:
О О О
H2N–СН–С + H–N–СН–С ® H2N–СН–С–N–СН–С
ОН ОН ОН
R H R R О H R
a-amino acid a-amino acid dipeptide

Poly-peptide (poly-amide) chains at peptides and proteins, as a

rule, have unbranched structure. Terminal of the chain with amino
acid with free amino group is called N-terminal of the peptide
(protein), the other terminal with amino acid with free carboxylic
group is called C-terminal of peptide (protein).Peptide and protein
chains are written starting with N-terminal. Peptides are in all living
organisms. In opposition to proteins they have more varied amino
acid content which sometimes includes D-amino acids. They could
have cyclic fragments, branched chains, etc. Peptides having high
physiologic activity regulate different biological processes.
According to bio-regulatory action peptides are subdivided into
several groups:
– compounds characterized by hormonal activity (glucagon,
oxytocine, vasopressine, etc.);
– compounds regulating digestive process (gastrin, gastric
inhibiting peptide, etc.);
– peptides regulating appetite (endorphins, neuropeptide-Y,
leptin, etc.);
– compounds having pain relieving effect (opioid peptides);
– substances regulating higher nervous activity, biochemical
processes, connected to memory, education processes, fear, anger
appearance etc.;
– peptides regulating arterial pressure and vascular tone
(angiotensin II, bradicardine, etc.).
This subdivision is conditional as various peptides action is not
limited by only one direction. For example, vasopressine in addition
to vaso-constricting and anti-diuretic action also makes the memory
better.
All enzymes have protein nature.

48
 Question 55. Write down tri-peptide formula which condensed
marking is ala-lys-asp? What is this tri-peptide name? What is the
process of enzymatic hydrolysis under the enzyme trypsin which
splits only peptide bonds formed by carboxylic group of lysine or
arginine?
Answer. Amino acids have markings containing three letters
which are first three letters in their trivial name. Аla stands for
alanine, lys stands for lysine, asp stands for aspartic acid. According
to the wording of the task N-terminal is amino group from alanine,
C-terminal is carboxylic group from aspartic acid. To write peptide
properly all three amino acids should be located near each other so
that on the one line there is amino group, a-carbon atom and
carboxylic group. Amino acid radicals are located vertically (up or
down). Carboxylic group of one amino acid takes part at peptide
bond formation (–ОН group is discharged from it) and a-amino
group of the second amino acid (hydrogen atom is discharged from
it). Carboxylic and amino groups which are in hydrocarbon radical
do not take part at peptide bond formation.
О О О
H2N–СН–С + H–N–СН–С + H–N–СН–С ®
ОН ОН ОН
СН3 H (СН2)4 H СН2
alanine
NН2 СООН
lysine Aspartic acid
О H О H О
® H2N–СН–С–N–СН–С–N–СН–С
ОН
СН3 (СН2)4 СН2
NН СООН
2
Tri-peptide alanyl-lysyl-aspartic acid

Peptide names are made due to successive enumeration of amino

acid residues starting from N-terminal of the chain. And ending “-
ine” at the trivial acid name is changed into “-yl”, exception is amino
acid which is C-terminal (its name is not changed). In our case tri-
peptide is called alanyl-lysyl-aspartic acid.
As trypsin splits only peptide bonds formed by lysine carboxylic
group (there is no arginine at or peptide) then equation of enzymatic
hydrolysis has the following form:
О H О О
H2N–СН–С–N–СН–С + H2N–СН–С
49 СН ОН
СН
ОН
3
(СН )
2 4 2
Di-peptide alanyl-lysine NН СООН
2 Aspartic acid
 О H О H О trypsin
H2N–СН–С–N–СН–С–N–СН–С ¾¾®
ОН
СН3 (СН )
2 4
СН2
NН СООН
2
Tri-peptide alanyl-lysyl-aspartic acid

Question 56. Characterize primary, secondary, tertiary and

quaternary protein structure.
Answer. Primary protein structure is succession of alterations
between a-amino acids at poly-peptide chain (figure 1):
А-chain

B-chain

Figure 1. Insulin primary structure.

Amino acids are attached to each other by peptide bonds.

Primary structure can be identified due to successive terminal a-
amino acid splitting and their defining.
Secondary structure is represented by two conformations (figure
2). One structure from secondary protein structures is helix (this
structure is also called a-structure or a-helix). This poly-peptide
chain conformation is right-wind spiral. It is possible to imagine it as
poly-peptide chains winds around cylinder surface clock-wise (to the
right). One round of spiral contain average number of 3,6 amino acid
residues (36 residues at 10 rounds); spiral step (distance between two
neighboring rounds) is 0,54 nm; diameter is 0,5 nm. Planes of
neighboring peptide groups have the angle 105°, lateral radicals of

50
a-amino acids are located on spiral external side, in other words,
they are directed away from imaginary cylinder surface.
Main role at a-helix stabilization is played by hydrogen bonds
which are formed between carbonyl oxygen atom of each first amino
acid residue and hydrogen atom from –NH–group of every fifth
amino acid residue (hydrogen bonds are formed between peptide
bonds which are located at neighboring spiral rounds). Hydrogen
bonds are practically parallel to a-helix axis. Usually protein chains
are not completely spiral and a-helices alternate with linear parts.
Other secondary structure of poly-peptides is b-structure
(pleated sheet or pleated layer). Elongated poly-peptide chains are
located in pleated sheets. Chains are connected to each other by
numerous hydrogen bonds between peptide groups.

Figure 2. Protein secondary structure: A – helix, B- pleated structure.

Protein tertiary structure is determined by general poly-peptide
chain space localization, which includes secondary structures
elements. Globular (spherical) and fibrous (elongated threads)
protein structures are differentiated.

51
Figure 3. Protein tertiary structure: globular and fibrous.
At tertiary structure formation poly-peptide chains are curved
and lateral radicals of a-amino acid residues could react with each
other, which are located too far from each other in un-curved chains.
Several bond types play important role at protein tertiary structure
formation and stabilization.
Hydrogen bonds appear between functional groups at lateral
radicals (for example, between serine and threonine hydroxyl groups
or between hydroxyl and carbonyl groups at glutamine and
asparagine), and also between functional groups at lateral radicals
and peptide bond atoms.
Ion bonds are formed due to electro-static interaction between
ionic (able to form ion) radicals. For example, at aspartic acid radical
there is carboxylic group which does not take part at peptide bond
formation. At its dissociation negatively charged –СОО– group is
formed. At lysine radical there is amino group which does not take
part at peptide bond formation. It could accept proton and acquire
positive charge (–NH3+). Between these charged groups ion bond is
formed. Negatively charged group could be formed by glutamic acid,
positively charged groups could be formed by arginine and histidine.
Hydrophobic interaction (non-polar bonds) appears due to
mutual attraction of non-polar radicals (which do not contain
functional groups) due to Van der Waals forces. This type of bond is
typical of alanine, valine, leucine, isoleucine radicals, etc.
Disulfide bonds are formed between mercapto-groups which are
at cysteine radical. –SH groups are easily oxidized with disulfide
bridges formation. Disulfide bonds are especially numerous at keratine
(hair and wool protein). Main bond types are presented at figure 4.

52
Figure 4. Formation scheme of ion (1) bonds, hydrogen bonds (2),
hydrophobic bonds (3), disulfide bonds (4) between amino acid
radicals at tertiary structure formation.

Protein quaternary structure is complex containing several poly-

peptide chains. Each chain (sub-unit) keeps typical primary,
secondary and tertiary structures. Quaternary structure is stabilized
due to hydrogen bonds and hydrophobic interactions between sub-
units. Protein with quaternary structure performs biological functions
which are not typical of separate sub-units. Not all proteins are
characterized by quaternary structure. An example of this protein is
hemoglobin which main biological function is oxygen transition
from lungs to organs and tissues. Quaternary structure of this protein
is represented by four conjugated protein complex which comprises
poly-peptide chain (globin) and non-protein part (hem).

Figure 5. Hemoglobin quaternary structure.

Question 57. What is protein classification?

53
 Answer. There is no unified classification which takes into
consideration different protein parameters. Usually classifications are
based on one principle. Proteins could be classified according to:
– molecular form (globular and fibrous);
– molecular mass (low- and high-molecular);
– content or chemical structure (if there is non-protein part or
not);
– functions;
– cellular localization (nucleus, cytoplasmic, lysosomal etc.);
– localization in the organism (blood proteins, hepatic proteins
etc.);
– possibility to regulate these proteins amount: proteins with
constant synthesis rate (constitutive) and proteins which synthesis
rate could be increased due to external environment factors
(inducible);
– life period in the cell (quickly renovated proteins with half-
transformation period less than 1 hour, slowly renovated proteins
with half-transformation period up to weeks and months);
– similar parts at primary structure and similar functions (protein
families).
Globular proteins have relation between longitudinal and
transverse axis which does not exceed 1:10, and in more often cases
it is 1:3 or 1:4, i.e. protein molecule has the form of ellipse. Majority
of human proteins belongs to globular proteins. They have compact
structure, at globule formation hydrophobic radicals are directed
inside the molecule, and hydrophilic radicals are on the globule
surface, so their majority is well soluble in water. Examples are egg
white (albumin), myoglobin, hemoglobin, many enzymes.
Fibrous proteins have elongated, thread-like structure, in which
relation between longitudinal and transverse axis is more than 1:10.
Fibrous proteins include collagen, elastin, keratine performing
structural function at human body, and also myosin taking part at
muscle constriction, and fibrin which is protein at blood coagulating
system.
According to their structure all proteins are subdivided into
unconjugated (simple) and conjugated (complex). Unconjugated

54
proteins contain only a-amino acid residues. Conjugated proteins in
addition to a-amino acid residues contain additional component with
non-protein nature (prosthetic group). It could be organic substance,
phosphoric acid, metal ion etc.
Proteins containing phosphoric acid residue in their structure
(usually in the form of ester with serine hydroxyl group) are called
phosphor-proteins: it is milk casein; vitellin, vitellinin and phosvitin,
discharged from egg yolk; ovalbumin, discovered at egg white;
ichtulin which is in fish caviar, etc.
Carbohydrates are prosthetic group at glycoproteins (these are
components of blood serum - immunoglobulins, transferrins etc.);
blood group substances; many viral antigens; some hormones and
enzymes.
Lipids are in the structure of lipoproteins. Lipoproteins are
subdivided into free or water soluble (blood plasma lipoproteins,
milk, yolk lipoproteins etc.), and non-soluble or structural (cellular
membrane lipoproteins, myelin cover of nervous tissues, chloroplasts
at plants).
Nucleoproteins have nucleic acids: deoxyribonucleoproteins
(DNP) and ribonucleoproteins (RNP).
Proteins perform many biological functions at cells. They could
be subdivided into large groups:
– enzymes (specialized proteins catalyzing chemical reactions);
– regulating proteins (protein-hormones taking part at keeping
internal organism medium constant, they act on special target-cells);
– receptor proteins (serve to transmit hormonal signal);
– transport proteins (take part at specific ligand transport from
one organ to another, usually at complex with proteins molecules
which are not dissolving in water are transported: blood plasma
albumin transports fatty acid and bilirubin (hem degradation product)
and erythrocyte hemoglobin transports О2 from lungs to tissues etc.);
– structural proteins (give form, create support, define mechanic
properties of a tissue: for example, tendon and cartilage main
component is fibrous protein called collagen, which has high
solidity; other structural protein (elastin) due to its structure provides

55
particular tissues (vessels, lungs) property to stretch in all
directions);
– protective proteins (for example, immunoglobulins have
ability to recognize and bind foreign molecules, viral particles and
bacteria as a result there is their neutralization; protective properties
belong to proteins from blood coagulating system, for example,
fibrinogen, thrombin: they take part at thrombus formation, which
obstructs damaged vessel and prevents blood loss);
– constriction proteins (they give a cell ability to constrict or to
move: actin and myosin are fibrous proteins taking part at skeletal
muscle constriction; tubulin is important element, building material
of cell organelles (micro-tubes which are important elements of cilia,
with which help cells move).
There is a large number of proteins which have unique functions
not covered at this classification.
Example is protein family: myoglobin family which includes, in
addition to myoglobin itself, all types of hemoglobin.
Question 58. What qualitative reactions are used to identify
amino acids and proteins?
Answer. General for all α-amino acids and proteins reaction is
ninhydrin reaction which is blue-violet colour formation at amino
acid or protein solution interaction with ninhydrin (organic reagent).
To find peptide bonds at peptides and proteins biuret reaction is
used. It is red-violet colour formation at peptide or protein solution
interaction with copper sulfate solution at alkaline medium. Violet
colour could have different variations (red, blue). Reaction is
determined by peptide bonds –СО–NН–, which connect amino acid
residues. All peptides and proteins which have at least two such
bonds, have positive reaction.
There are also specific reactions to find separate α-amino acids
or relative amino acid groups. To find aromatic and hetero-cyclic α-
amino acids (phenylalanine, tyrosine, histidine, tryptophan) xanto-
protein reaction is used. For example, at action with nitric acid on
amino acid tyrosine (or protein solution, in which structure there is
tyrosine residue) nitro-compound is formed which is yellow. At

56
adding alkaline solution colour is orange. At this reaction tyrosine
aromatic radical is transformed, peptide bond is not affected.
Amino acids containing sulfur are found with the help of Fall’s
reaction (with lead acetate). First protein solution is heated with
concentrated alkaline solution (protein is partially hydrolyzed, sulfur
is discharged in the form of ion S 2–), after that lead acetate solution is
added (СН3СОО)2Pb and observe black precipitate formation of lead
sulfide PbS:
(СH3COO)2Pb + 2 NaOH ® Pb(OH)2 + 3 CH3COONa
Pb(OH)2 + 2 NaOH ® Na2PbO2 + 2 H2O
Na2PbO2 + Na2S + H2O ® PbS¯ + 4 NaOH
If there is small amount of sulfur in the protein then instead of
precipitate yellow-brown colour appears.
Sulfur ion S2– could be found if to heated solution of protein and
alkali we add sodium nitro-prusside solution Na 2[Fe(CN)5NO]; there
is red colour determined by complex salt formation:
Na2S + Na2[Fe(CN)5NO] ® Na4[Fe(CN)5NOS]
Question 59. Is it possible to differentiate phenylalanine from
tyrosine with the help of xanto-proteic reaction (with nitric acid)? If it is
possible then what is the difference? If it is impossible explain why.
Answer. Xanto-proteic reaction is coloured reaction with its
help it is possible to find amino acids with aromatic hydrocarbon
radical, that is why, it is impossible to differentiate phenylalanine
and tyrosine as in both of them there are benzene rings. At nitric acid
action in both cases there is nitro-compound formed which has
yellow colour.
Question 60. What amino acid was in the solution if at
interaction with lead acetate in alkaline medium black precipitate
was formed: a) alanine; b) serine; c) histidine; d) tryptophan; e)
cysteine; f) tyrosine?
Answer. Reaction with lead acetate (Fall’s reaction) is aimed at
sulfur containing amino acids. Among all enumerated α-amino acids
only one amino acid cysteine contains sulfur. And it was in the
solution.

57
 5. CARBOHYDRATES: MONO-, DI- AND POLY-
SACCHARIDES
Question 61. What compounds are called carbohydrates?
Answer. Carbohydrates are class of natural organic substances
which are hetero-functional compounds containing simultaneously
carbonyl and hydroxyl functional groups (i.e., they are multi-atom
aldehydo- or keto-alcohols or their condensation products). The term
“carbohydrates” appeared in the middle of 19 th century as in their
molecules relation between hydrogen atoms and oxygen atoms is the
same as in water molecule, in other words, two hydrogen atoms
correspond to one oxygen atom and carbohydrate molecule could be
represented as build from carbon (coal) and water. For example,
glucose molecule (С6Н12О6) has the following form С6(Н2О)6,
sucrose formula (С12Н22О11) could be written as С12(Н2О)11, and in
general form it is Сn(Н2О)m. Later natural carbohydrates were
discovered which do not correspond to the general formula
(Сn(Н2О)m), but the term “carbohydrates” is used at present together
with the term “saccharides” or “sugars”.

Question 62. What are carbohydrate functions?

Answer. Carbohydrates are formed at plants as a result of photo-
synthesis from carbon di-oxide and water. Animal organisms are not
able to produce carbohydrates and receive them with plant food.
Thus, carbohydrates are in the structure of all living organisms and
they are most widely-spread organic substances on Earth.
Carbohydrate functions:
– structural and supportive functions (cellulose is main structural
element of cellular walls at plants, chitin has similar function at
fungus and provides solid character of exo-skeleton at arthropod and
similar animals);
– protective function (at some plants there are protective formations:
thorns, prickles etc. which are made from dead cells cellular walls;
– energy function (at 1 gr of carbohydrate oxidation 4,1 kcal of
energy is discharged);

58
– plastic function (they are in the structure of complex molecules, for
example, ribose and deoxyribose, take part at ATP, DNA and RNA
structure);
– keeping function (carbohydrates store nutrition substances:
glycogen at animals, starch and inulin at plants);
– osmotic function (they take part at osmotic pressure regulation in
the organism, including blood);
– receptor function (they are in the structure of perceiving part at
many cellular receptors).
Many carbohydrates and their derivatives are used at pharmacy
and medicine. Carbohydrates are initial substances for paper,
artificial fibers, explosives, ethyl alcohol production etc.

Question 63. What is carbohydrate classification?

Answer. Carbohydrates are subdivided into two classes: un-
conjugated (simple) and conjugated (complex). Unconjugated
carbohydrates (mono-saccharides, monoses) are not hydrolyzed with
more simple carbohydrate formation. Unconjugated carbohydrates
are, for example, glucose (С6Н12О6), ribose (С5Н10О5), fructose
(С6Н12О6). О
С
Н СН2ОН О
Н ОН С
НО Н С=О Н
Н ОН НО Н Н ОН
Н ОН Н ОН Н ОН
Н ОН Н ОН
СН2ОН
СН2ОН СН2ОН
D – glucose D – fructose D – ribose

Unconjugated carbohydrates containing keto-group are called

ketoses, containing aldehyde group are called aldoses. According to
carbon atom numbers monoses are subdivided into trioses (three
carbon atoms), tetroses (four carbon atoms), pentoses (five carbon
atoms), hexoses (six carbon atoms) and heptoses (seven carbon
atoms).

59
 For example, glucose contains aldehyde group and six carbon
atoms, it is called aldohexose. Fructose has carbonyl group (it is
poly-keto-alcohol) and six carbon atoms, it is called keto-hexose.
Ribose is aldopentose. Natural monoses, as a rule, have un-branched
carbon chains.
Conjugated carbohydrates can be hydrolyzed with more simple
carbohydrate formation. If at conjugated carbohydrate hydrolysis
from 2 to 10 un-conjugated carbohydrates molecules are formed then
such conjugated carbohydrate is called oligo-saccharide. If at oligo-
saccharide hydrolysis two unconjugated carbohydrate molecules are
formed then it is called di-saccharide, if there are three molecules
then it is called tri-saccharide, etc. The most widely-spread di-
saccharide is sucrose (at hydrolysis fructose and glucose are formed),
maltose and cellobiose (at their hydrolysis two glucose molecules are
formed), lactose (at its hydrolysis galactose and glucose are formed).
If at carbohydrate hydrolysis large amount of unconjugated
carbohydrates are formed (up to several thousands) then these
carbohydrates are called poly-saccharides. Poly-saccharides are high-
molecular compounds. They include starch and cellulose (cellular
tissue). Conjugated carbohydrates could be looked at as mono-
saccharide poly-condensation products.
If poly-saccharides have one mono-saccharide residues then it
is called homo-poly-saccharide, if there are different mono-
saccharide residues then they are called hetero-poly-saccharides.
Biologically important homo-poly-saccharides are starch,
glycogen and cellulose. Biologically important hetero-poly-
saccharides are algene acids, agar which is in the structure of sea
weeds. Poly-saccharides of connective tissue are chondroitin-
sulfates, hyaluronic acid, and heparin).
Carbohydrate molecules are in the structure of mixed
biopolymers (glyco-proteins, proteo-glycanes) or carbon-lipids
(glyco-lipids).

Question 64. Are mono-saccharides optically active compounds?

Write enantiomers for mono-saccharides.

60

D – фруктоза
 Answer. Mono-saccharide molecules (except di-oxy-acetone)
have chirality centres (contain asymmetric carbon atoms) which is
the reason for their stereo-isomers existence. For example,
aldohexose has four asymmetric carbon atoms and it has 16 stereo-
isomers (24 = 16), forming 8 pairs. At aldopentose there are three
asymmetric carbon atoms and it has 8 stereo-isomers (2 3 = 8),
forming 4 pairs.
Members of one pair are antipodes or enantiomers (their
molecules refer to each other as an object and its mirror reflection).
Enantiomers have one and the same name but one of them belongs to
D-series and another belongs to L-series. Enantiomers could be
represented in the form of open Fischer’s formulas, for example:

1С
О О
1С
О О
2 Н 2 Н 1С 1С
Н ОН НО Н Н Н
3 3 2 2
Н ОН НО Н Н ОН НО Н
4 4 3 3
Н ОН НО Н Н ОН НО Н
5 5 4 4
Н ОН НО Н Н ОН НО Н
6 6 5 5
СН2ОН СН2ОН СН2ОН СН2ОН
D - allose L - allose D - ribose L - ribose
At Fischer’s formulas carbon chain is written vertically and
enumeration starts from the end to which aldehyde or keto-group is
closer, i.e. from highest carbon atom. Asymmetric carbon atoms are
not marked by symbol “C”, it is supposed that they are located on the
crossing of vertical and horizontal lines.
Keto-pentose molecule has two asymmetric carbon atoms (the
third and the fourth) and forms two pairs of enantiomers:
1СН ОН 1 СН
ОН 1 СН 1СН
2 2
ОН 2
ОН2
2 2С = О 2 2С
С=О С=О =О
Н3 ОН НО 3 Н НО 3 Н Н3 ОН
Н4 ОН НО 4 Н Н4 ОН НО 4 Н
5 5СН ОН 5 5СН ОН
СН2ОН 2
СН2ОН 2
D – ribulose L – ribulose D – xylulose L – xylulose
Isomer belonging to D- or L-series is determined by
configuration comparison: it is the farthest asymmetric carbon atom

О
61
С О
Н С
Н ОН Н
НО Н
СН2ОН СН2ОН
located in relation to carbonyl group, it is compared to isomer
configuration of glycerol aldehyde which is considered to be the
standard. Glycerol aldehyde has one asymmetric carbon atom in the
molecule and has only two enantiomers:

D – glycerol aldehyde L – glycerol aldehyde

Let’s analyze fructose isomers as an example:
1 СН ОН 1СН ОН
2 2
2С = О 2
С=О
3
НО 3 Н Н ОН
4
Н 45 ОН НО 5
Н
Н ОН НО Н
6СН ОН 6СН ОН
2 2
D – fructose (1) L – fructose (2)

In each formula there are three asymmetric (chiral) carbon

atoms. These are atoms 3, 4 and 5. The farthest from keto-group
(С=О) are chiral atoms with number 5. At formula (1) fifth carbon
atom configuration corresponds to chiral atom configuration at D-
glycerol aldehyde (ОН group is located at the right, hydrogen atom
is located at the left). Thus, first isomer belongs to D-series, it is D-
fructose. Fifth carbon atom configuration at formula (2) corresponds
to L-glycerol aldehyde configuration, it is L-fructose. Majority of
natural mono-saccharides belongs to D-series.

Question 65. Are there free mono-saccharides at natural

conditions?
Answer. The most widely-spread natural mono-saccharide is D-
glucose - grape sugar or dextrose from Latin “dexrus” - right, as
usual natural D-glucose has specific rotation + 52,5 о, i.e. rotates the
polarization plane of plane-polarized light to the right on 52,5 о .
In free form it is at blood being energy substrate for brain.
Glucose constant level is kept with the help of insulin hormone,
which decreases glucose concentration in blood and also there is

62

D – fructose
glucagon, adrenalin and other hormones which increase its
concentration. At diabetes mellitus insulin is produced at pancreas
and its amount is not sufficient which leads to glucose concentration
increase in blood.
It is interesting that L-glucose being usual natural D-glucose
enantiomer is also sweet but it is not utilized in the organism that is
why, it could not be used as sugar substitute.
Free glucose is at green plant parts, at different fruits and honey.
It is in starch, glycogen, cellulose, hemi-cellulose, dextranes,
sucrose, maltose and many other glycoside structures.
D-fructose is fruit sugar or levulose from Latin “laevus” - left as
D-fructose aqueous solutions have specific rotation - 92,4 o.
Fructose is at green plant parts, flowers, fruits and honey. It is in
the structure of sucrose and many poly-saccharides.
D-galactose. In free crystal form it is discharged at ivy fruit. It is
used as part at some di-saccharides (lactose) and poly-saccharides
(chondroitin, agar-agar, mucosa, hemi-cellulose).

Question 66. Write down galactose L-isomer if D-isomer

formula is known.
Answer. To write down enantiomer formula it is necessary to
write mirror reflection of all substitutes at all asymmetric carbon
atoms. Let’s write down D-galactose formula taking it from the
scheme, which is located lower, and change substitute location (–Н
and –ОН) at 2, 3, 4 and 5 carbon atoms:

63
 As a result we get D-galactose enantiomer:
1С
О О
1С
2 Н 2 Н
Н ОН НО Н
3 Н 3 ОН
НО Н
НО 4 Н 4 ОН
Н
Н 5 ОН НО 5 Н
6СН2ОН 6
СН2ОН
D – galactose L – galactose
Enantiomer name is L-galactose.

Question 67. What is the difference in dia-stereomers, epimers

and enantiomers?
Answer. Carbohydrate stereo-isomers which differ from each
other in configuration of only one or several asymmetric carbon atoms
are called dia-stereomers, for example, D-allose and D-mannose; D-
fructose and L-tagatose etc.
Epimers and enantiomers are certain cases of dia-stereomers.
Dia-stereomers which refer to each other as object and its mirror
reflection are called enantiomers. Enantiomers have same physical
and chemical properties but they differ from each other only by
polarization plane rotation direction of plane-polarized light.
Enantiomer biological activity is also different.

64
 If dia-stereomers differ in configuration of only one asymmetric
carbon atom then they are called epimers. If configuration differs at
second carbon atom then such dia-stereomers are called just epimers;
if difference is at some other atoms then this atom number is added
to the name.
For example, D-ribose and D-arabinose differ from each other in
configuration of the second carbon atom and they are epimers.
D-allose and D-glucose differ from each other in configuration
of the third carbon atom that is why, they are 3-epimers; D-allose
and D-gulose are 4-epimers.
Epimers have different physical and chemical properties and
different biological activity.

Question 68. Are D-allose and L-idose dia-stereomers?

Answer. To answer the question it is necessary to write these
aldoses formulas. D-allose formula is represented in the table
(question 6). L-idose is D-idose enantiomer, i.e. their molecules refer
to each other as an object and its mirror reflection. If you know D-
idose formula it is easy to write down L-idose formula (question 6):
According to definition dia-stereomers should differ from each
other in configuration at one or several asymmetric carbon atoms.
Analyzing D-allose and L-idose formulas we conclude that they have
same configurations at the second and the fourth carbon atoms (at D-
allose formula and at L-idose formula OH groups are located at the
right and hydrogen atoms are located at the left).
1С
О 1 О 1 О
С С
2 Н 2 Н 2 Н
НО Н Н ОН Н ОН
3 3 Н 3
Н ОН НО Н ОН
4 4 4
НО Н Н ОН Н ОН
5 5 5
Н ОН НО Н Н ОН
6 6 6
СН2ОН СН2ОН СН2ОН
D – idose L – idose D – allose
Configuration at the third and fifth carbon atoms is different (at
D-allose molecule OH groups are located at the right in relation to
carbon chain and at the molecule of L-idose they are located at the
left). Thus, D-allose and L-idose differ in configuration of two

65
asymmetric carbon atoms: the third and the fifth, and they are dia-
stereomers.

Question 69. Are D-glucose and D-mannose epimers?

Answer. To answer this question it is necessary to write down
these aldoses formulas. They are represented at the scheme (question
6). 1
О О
С 1
С
2 Н Н
Н ОН НО 2
3 Н
НО Н НО 3 Н
4 4
Н 5
ОН Н ОН
Н ОН 5
6 Н ОН
СН2ОН 6
СН2ОН
D – glucose D – mannose

Epimers are certain cases of dia-stereomers and, according to

definition, should differ at only one asymmetric carbon atom
configuration. Analyzing D-glucose and D-mannose formulas we
conclude that at the third carbon atom at both molecules hydrogen
atom is located at the right and hydroxyl group is located at the left;
at the fourth and the fifth carbon atoms at both molecules hydrogen
atom is located at the left and hydroxyl group is located at the right;
thus, configurations at the third, fourth and fifth asymmetric carbon
atoms at D-glucose and D-mannose are the same.
Configuration at the second carbon atom differs (at D-glucose
molecule OH group is located at the right in relation to carbon chain
and at D-mannose formula it is located at the left). Thus, D-glucose
and D-mannose differ from each other in only one asymmetric
carbon atom configuration and, thus, they are epimers.

Question 70. What is the mechanism of mono-saccharide cyclic

form formation?
Answer. Mono-saccharide cyclic forms are formed at intra-
molecular interaction between carboxylic and hydroxyl groups. These
forms are thermo-dynamically more stable than open forms at
carbohydrate molecules. Usually five-membered (furanose) and six-
membered (pyranose) cycles appear. At space aldehyde (or ketone)

66
 groups and hydroxyl group at the fourth or fifth position (for aldoses)
or fifth and sixth position (for ketoses) are close to each other. Due to
their interaction there is cycle closing at mono-saccharide molecules.
Six-membered pyranose cycle is formed at interaction between
aldehyde group and fifth atom at aldopentoses or aldohexoses; and
also at interaction between keto-group with the sixth atom at keto-
hexoses.
Н О 1 1
1С Н ОН НО Н
2 2 2
Н ОН НО Н НО Н
НО 3 Н НО 3 ОН + НО 3 ОН
НО 4 Н Н 4 ОН Н 4 ОН
5
Н 5 ОН Н О Н5 О
6 6
6 СН2ОН СН2ОН
СН2ОН
D-galactose -D-galacto-pyranose -D-galactopyranose
Fischer’s projection Transformed Fischer’s projection
Five-membered furanose cycle is formed at interaction between
aldehyde group and the fourth atom at aldotetroses, aldopentoses and
aldohexoses; and also at interaction between keto-group and fifth
atom at ketopentoses and ketohexoses.
1СН ОН
2
2С 1 1
=О НО 2 СН2ОН НОН2С ОН
2
3 3
НО 3 Н
Н 4 ОН
НО Н
Н 4 ОН + НО Н
Н 4 ОН
5
Н
5
ОН Н О Н5 О
6 6 6
СН2ОН СН2ОН СН2ОН
D-fructose -D-fructo-furanose -D-fructofuranose
Fischer’s projection Transformed Fischer’s projection
As a result of cycle formation at aldohexose molecule at the first
carbon atom instead of aldehyde group there is hydroxyl group (at
ketoses at the second carbon atom). This hydroxyl group is called
glycoside (hemi-acetal) hydroxyl group (glycoside hydroxyl). At the
name of cyclic forms ending “pyranose” is added to six-membered
cycles or “furanose” is added to five-membered cycles.

67
 In mono-saccharide cyclic molecule, number of asymmetric
carbon atoms increases as carbon atom being at aldehyde group or
keto-group turns to be asymmetric too. In the case of galactose this is
the first carbon atom, at fructose it is the second carbon atom. This
carbon atom is called anomer carbon atom. Additional asymmetric
carbon atom appearance leads to the increase in two times in number
of optical isomers, corresponding to cyclic form in comparison to
open form. Thus, for aldohexose this number is not 16 but 32
isomers. Each isomer with open form correlates to two isomers at
cyclic form (anomers).
At α-anomer, anomer centre configuration is the same as
asymmetric carbon atom configuration defining carbohydrate
belonging to D- or L-series, and at β-anomer it is opposed. At
Fischer’s projections at mono-saccharides belonging to D-series at α-
anomer glycoside hydroxyl is at the right and at β-anomer it is
located at the left in relation to carbon chain; situation is opposite for
L-isomers, at α-anomer glycoside hydroxyl is at the left and at β-
anomer it is located at the right in relation to carbon chain. Anomers
are dia-stereomers and differ from each other in their properties (for
example, on melting temperatures). Anomers are narrow cases of
epimers.

Question 71. Write down mono-saccharide cyclic forms as

Haworth’s perspective formulas.
Answer. According to Haworth cycles are drawn as plane
pentagons or hexagons which are located perpendicular to drawing
plane, that is why lines corresponding to front part of the ring are
thick. Oxygen atom is at pyranose cycle in the farther right angle, at
furanose cycle oxygen atom is at farther right angle or in the middle
of back cycle part of the ring. Hydroxyl groups and hydrogen atoms
are located perpendicular to cycle plane. Symbols of carbon atoms
are not usually written in the cycles.

СН2ОН НОСН2 О ОН
О Н
Н Н Н Н ОН
НО СН2ОН
НО Н
ОН Н НО СН2ОН
ОН 68
-D-fructo-furanose Н
-D-gluco-pyranose
 To write down Haworth’s formula it is necessary to write
Fischer’s formula first and rotate it on 90о to the right (clockwise):
1
О
С
2 Н Н Н ОН ОН О
НО Н 6
3 НОСН2 5 4 3 2 1С
НО Н
4 Н
Н ОН ОН ОН Н Н
5
Н ОН D-mannose
6
СН2ОН
D-mannose
It is necessary to rotate carbon atom attached to hydroxyl group
on 90о, this hydroxyl group takes part at cyclization reaction. At
manno-furanose formation this is the fourth carbon atom, at manno-
pyranose formation it is the fifth carbon atom. As a result of this
rotation –OH group should be on one line with main carbon chain.
That is why, for D-isomer –СН2ОН group is at the top and for L-
isomer it is located at the bottom:
1
О
С
2 Н 6
НО Н 6
Н Н ОН ОН О НОН2С Н ОНОН О
3 1 1
НО
4
Н НОСН25 4 3 2 С НО 5 4 3 2 С
Н ОН ОН ОН Н Н Н Н ОН Н Н Н
5
Н ОН
6 D-mannose D-mannose transformed
СН2ОН projection
D-mannose
1
О
С
Н
Н 2 ОН 6 Н ОН
ОН ОН Н О Н ОН Н Н О
Н6 3 ОН НОСН
6 5 4 СН 3 2 2 1С 5 4СН32ОН2 1
СН
4 2ОН 5 ОН НО С
НО Н Н 2
Н НН ОН ОН Н 6 О Н
НОНН2С Н Н ОН ОН ОН
НО 55 4 Н3ОН2ОН 1 О Н 1 О
НО 6СН ОН С 4 С L-mannose transformed
Н ОН
L-mannose
2 Н Н Н НО ОН НО
D-mannose
3 2 Н НО ОН НО Н
projection
D-mannose transformed
Н
After that chain is closed and Haworth’s
projection Н
Н projection is received: Н
-D-manno-pyranose
Н Н
5 ОН О
Н ОН Н Н О НО 6 69 ОН НО СН ОН ОН
2 1С СН2ОН О О
НО 5 4 3 НН
4 1С 2
О Н
6 Н
СН ОН
Н Н Н Н
НОН2С Н ОНОН Н Н 3 22 Н
L-mannose transformed Н О
СН2ОН
projection ОН НО
Н ОН НО
ОНН О
Н -L-маннопираноза
 In the name of the cyclic form we should mark: anomer type (
or ), after that we mark belonging to stereo-chemical series: D- or
L-; after that mono-saccharide name, which derivative this cyclic
form is, but it should be without ending “-se”, in other words we
should preserve gluco-, manno, fructo- etc., finally we mark cyclic
form type (pyranose or furanose).
At D-series of aldohexoses in pyranose form (and at D-series of
aldopentoses and ketohexoses in furanose form) СН2ОН group is
always located above cycle plane which is the formal sign of D-
series. For L-series this group is located under cycle plane. Glycoside
group –ОН at -anomers for D-series aldoses is under the plane and
for -anomers it is above cycle plane. For L-series glycoside
hydroxyl at -anomers it is located above the plane and for -
anomers it is located below cycle plane.
According to these rules we can write Haworth’s formulas for
ketoses at furanose and pyranose forms, for example, for fructose:
1СН ОН
2
2С 6СН ОН
=О 6СН
ОН 2
2
Н ОН 1 5 ОН
НО 3 Н
НО 5 4 3 2С СН2ОН Н Н
Н 4 ОН О
Н ОН Н О 4 ОН 2С
Н 5 ОН НО СН2ОН
6 3 1
СН2ОН Н
D-fructose D-fructose transformed projection

70
 СН2ОН СН2ОН
О О
Н Н ОН + Н Н СН2ОН
ОН ОН
НО СН2ОН НО ОН
Н Н
-D-fructofuranose -D-fructofuranose

1СН ОН2 Н Н
2С 5 6
=О С–ОН
Н Н ОН 1 Н
НО 3 Н 6 5 4 3 2С СН ОН
ОН Н
НОСН 4
Н 4 ОН 2
НО ОН Н О
2
НО ОН О
5 3 2
Н ОН С
6 Н СН2ОН
СН2ОН 1
D-fructose Н Н
6 О 6 О 1
Н Н ОН Н Н СН2ОН
5 2
НО СН ОН
5 + 2
НО Н НО Н
2
НО ОН
4 1 4
3 3
ОН Н ОН Н
-D-fructopyranose -D-fructopyranose

Question 72. What are predominant forms (open or cyclic) of

mono-saccharides in solid state and in the solution?
Answer. At solid position mono-saccharides are in cyclic form
(mainly pyranose). At solutions there is balance between open form
and two pairs of cyclic anomers (cyclic-oxo-tautomeric balance or
cyclic-chain tautomerism). Different molecule forms which are
balanced are called tautomers. In tautomer mixtures pyranose form
predominates. Open forms and furanose cycles are in small amounts.
- or -anomer dominance depends on monose nature, solvent,
concentration and other external conditions.
Carbohydrate tautomeric forms could transform in to one
another which leads to some form increasing due to its utilization at

71
some process. Balance between all forms is dynamic. If, for example,
glucose anomer is dissolved in water, it gradually transforms in to
another anomer, until balanced mixture containing two anomers is
formed, this mixture contains small amount of open form. This
transition is accompanied by change in solution optical rotation, as
each tautomer is characterized by its own plane-polarized rotation
angle of plane-polarized light. This phenomenon is called mono-
saccharide mutarotation.
НОСН2 О СН2ОН НОСН2 О ОН

Н Н НО ОН Н Н НО СН2ОН

ОН Н ОН Н
-D-fructo-furanose -D-fructo-furanose
Н Н
5 6
С–ОН
Н ОН Н
4
НО ОН
3 2
О
С
Н Н СН2ОН Н
6 1
О 1 6 О
Н Н СН2ОН Н Н ОН
5 2 5 2
НО Н НО ОН НО Н НО СН ОН
2
4 4 1
3 3
ОН Н ОН Н
-D-fructo-pyranose -D-fructo-pyranose
Question 73. Write -furanose and -pyranose forms of L-
arabinose. Draw their anomers in Fischer’s projections.
Answer. It is necessary to take D-arabinose as initial compound.
Let’s write its formula and draw its enantiomer formula (question 6).
L-arabinose is aldopentose. Its furanose form is formed due to
interaction between aldehyde group and hydroxyl group at the fourth
carbon atom; and its pyranose form is formed due to interaction
between aldehyde group and hydroxyl at the fifth carbon atom. At
cyclization process hydrogen from hydroxyl group (С5 or С4) is
added to oxygen from aldehyde group due to -bond С–О breaking,
forming hemi-acetal or glycoside hydroxyl (which is in the frame).

72
Oxygen from hydroxyl group at С4 or С5 after hydrogen elimination is
attached to carbon at aldehyde group at С1. There is oxygen bridge
formed between С1–С4 and it locks five-membered cycle, or С1–С5
and it locks six-membered cycle.
О О НО Н Н ОН
1
С–Н С–Н C С
НО Н Н 2 ОН H ОН H ОН
Н ОН НО 3 Н HO Н HO Н
Н ОН НО 4 Н О Н О Н
СН2ОН 5
СН2ОН СН2ОН СН2ОН
D-arabinose L-arabinose -L-arabino-furanose -L-arabino-furanose

О О НО Н Н ОН
1
С–Н С–Н C С
НО Н Н 2 ОН H ОН H ОН
Н ОН НО 3 Н HO Н HO Н
Н ОН НО 4 Н НО Н НО Н
СН2ОН 5
СН2ОН О СН2 О СН2
D-arabinose L-arabinose -L-arabino-pyranose -L-arabinopyranose
At hemi-acetal form the first carbon atom is transformed into
asymmetric carbon atom. As a result, at cycle closing from one open
aldehyde form (oxo-form) there are two cyclic hemi-acetal forms
appearance which differ from each other by the position of hemi-
acetal hydroxyl.
Cyclic form with hemi-acetal hydroxyl located at one side (at
cis- position) with hydroxyl defining monose configuration
(belonging to D- or L-series) is called -form. Cyclic form at which
hemi-acetal hydroxyl is at trans- position with hydroxyl defining
configuration is called -form. - and -forms are dia-stereomers
and they are called anomers.

Вопрос 74. What compounds are received at D-glucose and D-

fructose reduction?
Answer. At mono-saccharide reduction poly-alcohols are
received (polyols) which are called alditols. Reduction is usually
performed by hydrogen and there are metal catalysts (palladium,
1
О
nickel) or sodium
С bor-hydride. Hydrogen
1
СН is
ОНadded on the1СН
placeОН
of the
Н 2 2
Н 2 ОН 73Н
2
ОН НО 2 Н

3
НО 4 Н Н2 НО 3 Н НО 3 Н
Н 5 ОН Pd Н 4
ОН Н 4 ОН
5 5
Н 6 ОН Н ОН НО 6 Н
6СН ОН СН2ОН
СН2ОН 2
D – глюкоза D – глюцит L – сорбит
double bond between carbon-oxygen at carbonyl group. At aldose
reduction only one product is received (polyol), for example, at D-
glucose reduction six-atom alcohol is received which is D-glucitol
(L-sorbitol):

D-glucitol as well as D-glucose is optically active compound as in

its molecule there are four asymmetric carbon atoms (2, 3, 4, 5) and
there are no symmetry elements.
Glucose reduction into sorbitol is the first stage of ascorbic acid
chemical synthesis. Sorbitol is oxidized using micro-organism
Acetobacter suboxydans; L-sorbose which is formed is transformed
into ascorbic acid at several stages.
СН2ОН О=С
СН2ОН
Acetobacter C=O С–ОН О
НО Н suboxydans
НО Н НО Н … С–ОН
Н ОН Н ОН Н–С
НО Н НО Н НО–С–Н
СН2ОН СН2ОН
СН2ОН
L – sorbitol L – sorbose Ascorbic acid
At ketose reduction there is mixture containing two polyols, as
carbon atom which is in the keto-group structure, after reduction
turns into asymmetric and double localization of OH group and
hydrogen atom is possible in the space (on the left or on the right in
relation to carbon chain). For example, for D-fructose we have the
following case:
1СН ОН 1СН ОН 1СН ОН
2 2 2
2С = О 2 2
Н – С – ОН НО – С – Н
Н2
НО Н3

Н 4 ОН Pd
НО 3 Н
Н 4 ОН
+ НО 3 Н
Н 4 ОН
5 5
Н ОН Н 5 ОН Н ОН
6 6 6
СН2ОН СН2ОН СН2ОН
D-fructose 74
D – glucitol D – mannitol
 D-glucitol and D-mannitol are optically active.
Poly-alcohols which are received at mono-saccharide reduction
are crystal substances, well-soluble in water; they have sweet taste
and could be used as sugar substitutes at diabetes mellitus (xylitol,
sorbitol).

Question 75. At what aldose reduction optically inactive six-

atom alcohols are formed?
Answer. At D-galactose and D-allose reduction we receive six-
atom alcohols dulcitol and allitol respectively. These alcohols have
symmetry plane which is between the third and fourth carbon atoms,
thus, these polyols do not have optical activity.

1
О
С 1
СН2ОН
2 Н 2
Н ОН Н ОН
3 Н2 3
Н 4
ОН Н ОН
4
Н 5
ОН Pd Н ОН
5
Н 6
ОН Н ОН
6СН ОН
СН2ОН 2
D – allose allitol
1
О
С 1
СН2ОН
Н
Н 2 ОН Н 2
ОН
НО 43 Н Н2 НО 3 Н
4
НО 5 Н Pd НО Н
5
Н 6 ОН Н ОН
6СН ОН
СН2ОН 2
D – galactose dulcitol
Question 76. What compounds are formed at L-galactose
oxidation? Are they optically active?
Answer. Oxidation reaction is used at biochemical analysis (for
example, blood count and urinalysis on sugar). Mono-saccharide
oxidation product content and structure depends on monose nature and

75
oxidation conditions (first of all it depends on oxidizer strength).
Aldoses are easier oxidized than ketoses.
Under the action of weak oxidizers (silver oxide ammonia
solution, copper hydroxide, bromine water) aldoses are transformed
into aldonic acids (aldehyde group is oxidized into acid carbonyl
group).
А) silver mirror test (Tollence’s reaction):
1
О О
С 1С
Н ONН
Н 2 ОН
4
Н 2 ОН
3 3
НО 4 Н 2[Ag(NН3)2]OH НО Н + 2Ag + 3NH + H O
4
НО 5 Н t o НО Н 3 2

Н 6 ОН Н 5 ОН
СН2ОН 6СН ОН
2
D – galactose D-galactonic acid ammonia
salt
External sign of this reaction is metal silver layer formation on
test tube walls.

B) reaction with copper hydroxide (II):

1
О О
С 1С
Н OН
Н 2 ОН to Н 2 ОН
3 3
НО 4 Н + 2Cu(OН)2 НО Н + Cu O + 2H O
4
НО 5 Н Blue НО Н Red 2precipitate 2
Н 6 ОН precipitate Н 5 ОН
6СН ОН
СН2ОН 2
D – galactose D –galactonic acid
External sign of this reaction is copper hydroxide (II) blue
precipitate transformation into copper oxide (I) red precipitate.
C) oxidation by bromine water (external sign of reaction is
bromine solution discoloration):

1
О О
С 1С
Н OН
Н 2 ОН Н 2 ОН
3
НО 4 Н + Br + Н О НО 3 Н + НBrО
НО 5 Н 2 2 НО 4 Н
Н 6 ОН Н 5 ОН
СН2ОН 6СН ОН
2
D – galactose D –galactonic acid
76
 With the help of strong oxidizer (dissolved nitric acid) aldose
terminal groups (aldehyde and primary alcohol group) are
simultaneously oxidized into carboxylic groups, forming aldaric
(sugar) acids, for example:
1
О
С 1СООН
2 Н
Н ОН Н 2 ОН
3
НО 4
Н HNO 3 НО 3 Н
НО 5
Н НО 4 Н
Н 6
ОН Н 5 ОН
СН2ОН 6
СООН
D – galactose D –galactaric (mucous) acid
This reaction could be used to find galactose as mucous acid is
practically not soluble in water. It should be taken into consideration
that though in the mucous acid molecule there are four asymmetric
carbon atoms (2, 3, 4, 5), it is optically inactive as it has plane of
symmetry.
In the organism with the help of enzymes primary alcohol group
could be oxidized and aldehyde group is preserved un-oxidized.
Reaction products in this situation are uronic acids:

1
О О
С 1С
Н Н
Н 2 ОН Н 2 ОН
3 enzyme НО 3 Н
НО 4 Н
НО 5 Н НО 4 Н
Н 6 ОН Н 5 ОН
СН2ОН 6СООН
D – galactose D – galacturonic acid
In the organism uronic acids play an important role: they form
water soluble glycosides with medical substances and their
transformation products (metabolites) and toxic substances and they
discharge these glycosides with urine; this is the origin of these acids
name (latin urina is urine). D-glucuronic and L-iduronic acids and
their derivatives are poly-saccharide structural elements (pectin
substances, heparin, hyaluronic acid, chondroitin etc.). At the process

77
of uronic acid metabolism ascorbic acid is synthesized (it is not
synthesized at human beings).

Question 77. What compounds are received at D-fructose

oxidation? Are they optically active?
Answer. Ketose oxidation is performed under strong oxidizers
action and it is accompanied by carbon chain destruction. Bond
breaking could appear by two methods: between the first and the
second and between the second and the third carbon atoms. All
terminal carbon atoms are oxidized with carboxylic group formation.
At D-fructose oxidation four reaction products are formed. At
bond breaking between the first and the second carbon atoms formic
and D-arabinaric acids are formed. At bond breaking between the
second and the third carbon atoms oxalic and meso-tartaric acids are
formed.
1СН ОН 1СООН
2 НСООН
2С = О 2 Formic acid
СООН
[O] Oxalic acid 2 СООН
НО 3 Н
Н 4 ОН
3
СООН + НО 3 Н
Н 4 ОН Н 4 ОН
Н 5 ОН 5
6 Н ОН Н 5 ОН
СН2ОН 6 6
СООН СООН
D-fructose Meso-tartaric acid D-arabinaric acid
Oxalic and formic acids are optically inactive as there are no
asymmetric carbon atoms in their molecules. Meso-tartaric acid
contains two asymmetric carbon atoms but it has plane of symmetry
that is why, it is not optically active. D-arabinaric acid follows all
requirements to be optically active compound: in the molecule there
are three asymmetric carbon atoms and there are no symmetry
elements.

Question 78. What compounds are called glycosides?

Answer. Monose cyclic forms are built at interaction between
aldehyde group or keto-group with alcohol group, as they are
hemiacetals (hemi-ketals). Hemiacetals (hemiketals) at interaction
with alcohols at acid medium give acetal (ketal):
ОН
R–СН–OC2H5 + C2H5OH  R–СН–OC
ОC2Н5 2H5 + H2O
78
 Hemiacetal acetal
Mono-saccharides also form acetals (ketals) which are called
glycosides:
СН2ОН СН2ОН
О О
Н Н ОН CН ОН, dry HCl Н Н О–CН3
3

НО ОН НО Н – Н2О НО ОН НО Н

Н Н Н Н
-D-manno-pyranose О-methyl--Dmannopyranoside
Glycosides are not only carbohydrate acetals formed at alcohol
interaction. Glycosides are also products of hemi-acetal hydroxyl
interaction with other compounds. Bond which is formed by hemi-
acetal hydroxyl is also called hemi-acetal bond.
Glycosides could be classified according to the fact what
aglycone atom is connected to saccharide part of glycoside: C-
glycosides, O-glycosides, N-glycosides, S-glycosides.
According to the cycle type glycosides are subdivided into
pyranosides and furanosides.
Glycoside non-carbohydrate part is called aglycone (could be
translated as non-sugar). At this example it is metoxy group: methyl
alcohol residue (marked by italics). Glycoside names are built in the
following way: aglycone + glycoside. Carbohydrate ending “-ose” is
changed into “-oside”. At the beginning they mark atom through
which aglycone is attached to carbohydrate part.
Example of C-glycoside is pseudo-uridine, example of S-
glycoside is sinigrin which is in mustard. Nucleosides are ribose and
deoxyribose N-glycosides with nucleic bases which are nucleotide,
DNA and RNA components.
O O

NH

N O
НОН2С О НОН2С О
Н НН Н НН
Н Н
ОН ОН ОН ОН
uridine – N-glycoside 79
Pseudo-uridine – С-glycoside
 СН2ОН
О
Н Н S–С=N–CН2–CН=CH2
ОSO3Н
НО ОН Н Н

Н ОН
sinigrin – S-glycoside
Question 79. What is the process of ester formation from mono-
saccharides?
Answer. Esters could be received by organic acid anhydrides
action on mono-saccharides. For example, with acetic anhydride acetyl
mono-saccharide derivatives are received.
СН2ОН СН2О–СО–СН3
О О О О
Н Н Н 5 СН –С–О–С–СН Н Н Н
3 3

НО ОН Н ОН Н3С–ОС–О ОСОСН3 Н ОСОСН3

Н ОН Н О–СО–СН3
-D-glucopyranose 1,2,3,4,6-penta-О-acetyl- -D-glucopyranose

Esters are hydrolyzed at acid and alkaline medium.

Phosphoric acid esters are very important, they are called
phosphates and they are at all plant and animal organisms. They
include D-glucose phosphates: D-glucose 1-phosphate is received at
glycogen hydrolysis with the help of enzyme called phosphorylase;
glucose 6-phosphate is formed at glycolysis first stage (glucose
catabolism in the organism).
6СН ОН НО
2 6
5 О О=Р–О–СН2
Н Н Н
4 ОН 1
НО 5 О
Н
Н Н
НО ОН Н О–Р=О 4 1
3 2 НО ОН Н ОН
ОН
Н ОН 3 2
-D-glucopyranose 1- Н ОН
phosphate -D-glucopyranose 6-phosphate
80
 After that there is glucose 6-phosphate isomerization into D-
fructose 6-phosphate, which, in its turn, is phosphorylated into D-
fructose 1,6-phosphate with the help of ATP.
D-ribose and 2-deoxyribose phosphates are structural elements
of nucleic acids and several co-enzymes.
Sulfuric acid esters – sulfates – are in structure of poly-
saccharides at connective tissue.

Question 80. Write di-saccharide structural formula, it is formed

by -D-galactose two residues which are attached to each other by
1,4-glycoside bond. Write structural formula of di-saccharide
interaction product with methyl alcohol if there is chlorine-hydrogen
in the mixture. Could these compounds participate at “silver mirror
test”? Write necessary equations of reactions.
Answer. -D-galactose molecules could form bonds between
each other with the participation of 1st and 4th carbon atoms:

6СН 6СН 6СН ОН

ОН
2 2
ОН 2
5 О 5 О 5 О
НО Н ОН НО Н О Н ОН*
4 1 4 1 4 1
Н ОН Н Н Н ОН Н Н Н ОН Н Н
3 2 3 2 3 2
Н ОН Н ОН Н ОН
-D-galacto-pyranose -D-galactopyranosyl-(14)--D-galacto-pyranose

Glycoside hydroxyl is marked with a star, it can be substituted

by –ОСН3 group at interaction with methanol:
6СН 6СН ОН
ОН
2 2
5 О 5 О
НО Н О Н О–СН3
4 1 4 1
Н ОН Н Н Н ОН Н Н
3 2 3 2
Н ОН Н ОН
Due to glycoside hydroxyl this di-saccharide could be
transformed in linear form with aldehyde group at aqueous solution,

81
so, it can give positive silver mirror test (equation is given in
simplified form):
С12Н22О11 + Аg2О NH3 С12Н22О12 + 2Ag
Di-saccharide -D-galactose mono-methyl ether does not have
glycoside hydroxyl and could not exist at linear form and it cannot
participate at silver mirror test.

Question 81. What is sucrose molecule structure?

Answer. At hydrolysis sucrose molecule splits into α-D-gluco-
pyranose molecule and β-D-fructo-furanose molecule, thus, it is di-
saccharide, in other words it comprises two mono-saccharide
residues:
6СН ОН
2 1
5 О НОСН2 О ОН
Н Н Н 2 5
4 1
НО ОН Н О Н НО СН2ОН
6
3 2 3 4
Н ОН ОН Н
-D-glucopyranosyl--D-fructofuranoside–sucrose
These residues are attached to each other by glycoside bond
between hydroxyl groups at anomer carbon atoms (1 st atom at α-D-
glucopyranose and 2nd atom at β-D-fructofuranose).
At sucrose molecule there are no free OH-groups at 1 st carbon
atom at α-D-glucose residue and at 2nd carbon atom at β-D-fructose
residue (hemi-acetal or hydroxyl hydroxyls). That is why, sucrose
molecule could not transform into open (aldehyde) form and give
positive silver mirror test, and also it could not be oxidized by copper
hydroxide, i.e. it does not reduce silver and copper, it is non-reducing
carbohydrate.
Sucrose sources are sugar cane, beet root, plant and fruit juices.

Question 82. Is sucrose the sweetest substance?

Answer. Carbohydrate sweet taste makes our life brighter and
tastier. The sweetest substance is not sucrose and it is not
carbohydrate at all. Sweeter carbohydrate in comparison to sucrose is
fructose. If relative sweet taste of sucrose is 100 than fructose taste is

82
173, glucose sweetness is 74, maltose and galactose taste is 32 and
lactose sweetness is 16.
Mono-saccharides could be tasteless and even bitter and non-
carbohydrate substances could be sweet. For example, beryllium and
lead compounds could be sweet. Lead acetate is called lead sugar,
but it is not recommended to use it as sugar due to lead compounds
high toxicity.
Many organic substances also have sweet taste but they have
nothing in common with sugars, for example, saccharin which
sweetness exceeds sucrose sweetness 500 times. 4-Etoxy-phenyl-
urae (dulcin) 200 times sweeter than sucrose and it was used as
sucrose substitute until it was discovered that it is harmful for the
organism.
Acesulphame and aspartame (di-peptide L-aspartyl-L-phenyl-
alanine methyl ester) is 200 times sweeter than sucrose. L-aspartyl-
amino-malonic acid methyl-phenchyl ester is 33000 times sweeter
than sucrose and sucronic acid is 200000 times sweeter than sucrose.
Some proteins have very strong sweet taste. For example,
protein monellin from tropic plant Dioscoreophyllum cumminsii is
3000 times sweeter than sucrose and protein taumatin from tropic
plant Thaumacoccus daniellii is 750-1000 times sweeter than sugar
and its complex with aluminium ions – tallin – is 35000 times
sweeter than sucrose. Protein miraculin from Synsepalum dulcificum
does not have sweet taste but could change sour taste of products into
sweet.

Question 83. What oligo-saccharides are most-widely spread in

nature?
Answer. Sucrose (cane sugar, beet root sugar) is widely spread
at plants. It is non-reducing di-saccharide.
Maltose (malt sugar) is made from two -D-gluco-pyranose
residues which are attached to each other by -1,4–glycoside bond.
Maltose is formed at starch hydrolysis under the action of enzyme
called amylase; if you are chewing bread for a long time you can feel
maltose sweet taste, it is formed from bread starch under the action
of saliva amylase. It is reducing di-saccharide.

83
 Cellobiose is made from two -D-gluco-pyranose residues
which are attached to each other by -1,4-glycoside bond. It is
structural element of cellular tissue (cellulose). At free form it is at
some plant juice. It is reducing di-saccharide.
Lactose (lactic sugar) is made from -D-galacto-pyranose
residues and -D-gluco-pyranose residues which are attached to each
other by -1,4-glycoside bond. Lactose is only at mammal milk and
it is reducing di-saccharide.
In the organism lactose hydrolysis is performed with the help of
enzyme which is called lactase. If there is small amount of lactase
produced in the organism then there is lactase deficiency and inability
to digest lactose. That is why, at milk use at people with lactase
deficiency lactose is not digested but there is its putrefaction with
intestinal micro-flora with unpleasant consequences (flatulence,
diarrhea). At majority of people and mammals lactase gene is switched
off due to maturation. This fact is explained by information that
mammals use milk only at early age and later there is no use spending
energy and amino acids on lactase synthesis. As a result of mutation at
one of regulatory genes which product switched off lactase gene, this
enzyme (lactase) started synthesizing all though the life cycle. About
70% of European people can digest milk at mature age, though in
Africa, Oceania and Central Asia only 30% of all people can
synthesize lactase at mature age. Peoples from Africa with
traditionally high milk use (tutsy, tuaregs etc.) do not have any
problems with lactose digestion.
Tregalose (fungus sugar) comprises two -D-gluco-pyranose
residues attached to each other by hemi-acetal hydroxyl groups, thus,
tregalose is non-reducing di-saccharide.
It is at fungus and some plants. At yeast tregalose amount
reaches 18% on dry substance.
Other di-saccharides such as melibiose, hentibiose, turanose,
primverose etc. are rare.
Tri-saccharides are rare. Tri-saccharide rafinose which
comprises galactose, glucose and fructose is at sugar beet root. It is
non-reducing tri-saccharide. Other tri-saccharides (hencianose,
melecitose, manninotriose, cellotriose, planteose) are very rare.

84
 Tetra-saccharide stachyose is made from two galactose residues
and one glucose residue and one fructose residue. Stachyose is at
Stachys roots, at yellow-gold, soya, pea seeds and it is non-reducing
tetra-saccharide.
Cyclic oligo-saccharides – cyclo-dextrins (Shardinger’s
dextrins) are formed at starch hydrolysis under the action of amylase
from Bacillus macerans. They contain 6-10 D-glucose residues
attached to each other by -1,4-glycoside bonds. Cyclo-dextrins
have catalyst properties, for example, they are able to catalyze
phenol ester hydrolysis. They form coloured complexes with iodine
and iodine molecules are inside cyclo-dextrin cavity.

Question 84. What carbohydrates are called poly-saccharides?

Answer. Poly-saccharides or polyoses are high-molecular
carbohydrates. According to their chemical nature poly-saccharides
are poly-glycosides.
At poly-saccharide molecule there are many mono-saccharide
residues which are attached to each other by glycoside bonds. To form
a bond with previous residue, each new residue gives alcohol hydroxyl
group usually at 4th or 6th carbon atoms. To form a bond with each new
residue, each previous residue gives glycoside (hemi-acetal) hydroxyl.
At poly-saccharides with plant origin there are mainly (14)- and
(16) bonds. Poly-saccharide chains could be branched and non-
branched (linear).
Poly-saccharides are hydrolyzed at acid medium and are not
exposed to hydrolysis at alkaline medium. Complete hydrolysis leads
to mono-saccharide formation or their derivatives formation, whereas
incomplete hydrolysis leads to intermediate oligo-saccharides
formation, including di-saccharides.

Question 85. What is the difference between homo-poly-

saccharides and hetero-poly-saccharides?
Answer. Poly-saccharides are subdivided into two large groups:
homo-poly-saccharides and hetero-poly-saccharides.
Homo-poly-saccharides are made from one mono-saccharide
residues, for example, starch, cellulose, glycogen etc.

85
 Starch is a mixture of two poly-saccharides made from -D-
gluco-pyranose residues: amylose (10-20 %) and amylopectin (80-90
%).
Amylose chain is un-branched, it comprises 200-1000 glucose
residues (molecular mass is 160000).
6 6
СН2ОН СН2ОН 6
СН2ОН
5
5
О Н О 5
О
Н Н Н Н Н Н Н Н
4 1 4 1 4 1
О ОН ОН
НО ОН Н Н О… Н ОН
3 2 3 2 3 2
Н ОН Н ОН Н ОН
amylose
Amylose molecules wind in spiral, inner channel could be
occupied by particular-sized molecules (for example, iodine
molecules), forming complexes which are called intrusion
complexes. Amylose complex with iodine is blue. It is used as
qualitative reaction on starch (iodine-starch reaction).
Amylopectin, in opposition to amylose, is branched spiral. At its
main chain α-D-gluco-pyranose resides are attached to each other by
α(14)-glycoside bonds and at branch points they are attached by
α(16)-glycoside bonds. Between branch points there are 20-25 α-
D-gluco-pyranose residues. Amylopectin molecular mass is several
millions.
6 6
СН2ОН СН2ОН
5
О 5
О Н
Н Н Н Н
4
Н 1 4 1
…О ОН Н О… ОН Н
3 2 3 2 О
Н ОН Н НО
Amylopectin lateral chain
6 6 6
СН2ОН СН2О СН2ОН
5
5
О Н О Н 5
О Н
Н Н Н Н Н
4
Н 1 1
4 1 4
О ОН ОН
…О ОН Н Н О… Н О…
3 2 3 2 3 2
Н ОН Н ОН Н ОН
Amylopectin main chain

Starch is white amorphous substance. It is not dissolved at cold

water, at hot water it is swelling and dissolves only partially.
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 Starch is formed at plants at photosynthesis process and it is
accumulated at roots, tubers and seeds. At digestive tract there is
starch hydrolysis under the action of enzymes, hydrolysis final
product is α-D-glucose.
Glycogen is plant starch structural and functional analogue
which is at animal organisms. Glycogen is similar to amylopectin in
its structure but it has more branched character of its chains. Between
branch points usually there are 10-12 glucose parts, sometimes this
number is 6. Glycogen molecular mass is really high (up to 100
millions). In the organism glycogen is reserve carbohydrate. If it is
necessary enough, amount of glucose splits from it and energy
reserve is increased in the organism. Amylopectin plays the role of
reserve poly-saccharide at plants.
Cellulose or cellular tissue is the most-widely spread plant poly-
saccharide. It plays supportive function at plants. At cotton there is
about 100% of cellulose and in wood it is about 50-70 %.
Cellulose is made of β-D-gluco-pyranose residues which are
attached to each other by β(14)-glycoside bonds. The chain is not
branched, it has 2500-12000 β-D-glucose residues (molecular mass
is 0,4-2 million).
6 6
СН2ОН СН2ОН СН2ОН
5
5
О О О Н
Н Н Н Н Н Н
4 1 О 4 О… 4 1
ОН
НО ОН Н Н Н Н Н ОН
3 3 2 3 2
Н ОН ОН
cellulose
Cellulose linear structure is supported by hydrogen bonds which
are formed inside carbohydrate chains and between separate chains.
Cellulose is not digested at human gastro-intestinal tract and could
not be nutrition substance but it is necessary for normal nutrition, as
it facilitates gastro-intestinal tract regulation and it stimulates large
intestine peristalsis.
Pectin substances are at fruits and vegetables. If there are
organic acids these substances form jelly which is applied at food
industry. Pectin substance molecules include pectic-poly-
galacturonic acid which is made of D-galacturonic acid residues

87
attached to each other by a-(1®4)-glycoside bond.
Some pectin substances have anti-ulcer action and form the basis
of some medicines, for example, plantaglucide produced from
plantain.
6 6 6
СООН СООН СООН
5
5
О О 5
О
НО Н Н Н
Н Н Н
4 1 О 4 1 О… 4 1
ОН Н ОН Н Н ОН Н ОН
Н Н
2 3 2 3 2
3
Н ОН Н ОН Н ОН
Poly-galacturonic acid

Hetero-poly-saccharides are made from different mono-

saccharide residues. Hetero-poly-saccharides are attached to proteins
in the organism and form complex supra-molecular complexes.
Examples of hetero-poly-saccharides are hyaluronic acid and
heparin.
Hyaluronic acid is made from D-glucuronic acid residues and N-
acetyl-D-glucosamine attached to each other by β-(13)-glycoside
bond.
6
6
СООН СН2О 6 6
СООН СН2О
5
5
О
5
Н О 5
О Н О
Н Н Н Н Н Н Н Н
О 4 1 …
…О 4 1 О 4 1 О 4 1
ОН Н Н Н Н ОН Н Н Н Н
НО НО 2
2 3 2 2 3
3 3
Н ОН Н NНСОСН3 Н ОН Н NНСОСН3
Hyaluronic acid
Hyaluronic acid has high molecular mass and high viscosity. It
provides connective tissue impermeability for pathogenic micro-
organisms. Usually hyaluronic acid is not presented at free form, it is
usually attached to poly-peptide chains. Mixed biopolymers are the
basis for cells and liquids at animal organisms.
Heparin biopolymer structure contains D-glucosamine residues
and two uronic acid residues: D-glucuronic acid and L-iduronic acid.
L-iduronic acid predominates in quantity. Amino group at majority
of glucosamine residues is sulfonated (contains SО3Н-group), at
some residues it is acetylated (attached to СН3СО-group). In addition
there are SО3Н groups at some L-iduronic acid residues. Heparin and
its derivative – heparitine sulfate – in the organism are attached to

88
protein. Heparin prevents blood coagulation, heparitine sulfate is in
the structure of blood vessel walls.
6. NUCLEOTIDES AND NUCLEIC ACIDS

Question 86. What compounds are nucleic acid monomers?

Answer. Nucleic acids (poly-nucleotides) are biological
polymers which monomer parts are nucleotides.
Nucleotide is not an individual compound, it comprises
nucleoside and phosphoric acid residue.
Nucleoside is not individual compound also, it is formed at
interaction between carbohydrate (ribose or deoxyribose) and hetero-
cyclic base.

Question 87. What is carbohydrate form in the structure of

nucleic acids?
Answer. At DNA structure there is ribose at cyclic furanose
form - -D-ribofuranose, RNA molecules contain 2-deoxyribose at
furanose form – 2-deoxy--D-ribofuranose.
5 5
НОН2С О ОН НОН2С О ОН
4 1 4 1
Н Н Н Н Н Н Н Н
3 2 3 2
ОН ОН ОН Н
-D-ribofuranose 2-deoxy--D-ribofuranose
Question 88. What hetero-cyclic bases could be at nucleic acid
structure?
Answer. Nucleic bases are nitrogen-containing hetero-cyclic
compound derivatives – purine (adenine and guanine) and
pyrimidine: thymine (only DNA), uracil (only RNA) and cytosine:
O NH2 NН2
О
Н3С O N
Н N
NH N N NН
O NH 6
N N O N N NН2
NH N N
H N O 5 О Н Н guanine
Н adenine
thymine Н
H
O cytosine Н
N
uracil

89
 Question 89. What is the difference between DNA and RNA
structure?
Answer. DNA and RNA differ from each other in the type of
carbohydrate component (at DNA structure there is -D-ribo-
furanose and in the structure of RNA there is 2-deoxy--D-ribo-
furanose) and in content of pyridine bases (at RNA structure there is
uracil and cytosine, and at DNA structure there is thymine and
cytosine). In addition DNA exists in the form of double helix which
contains two separate molecules. RNA molecules are shorter and
mainly they are one-stranded.

Question 90. Define bond type between separate compounds

and fragments in nucleic acid structure.
Answer. Nucleic acids are long monomer chains – nucleotides.
Nucleotide is a complex compound comprising nucleoside and
attached phosphoric acid residue. Nucleoside, in its turn, is product
of reaction between carbohydrate (ribose or deoxyribose) and hetero-
cyclic base. Hetero-cyclic base –NН–group participates at reaction
with carbohydrate hemi-acetal hydroxyl. As a result N-glycoside
bond is formed:
O
O
5 NH
НОН2С О ОН
NH O
4 1
+ 5
НОН2С
N
Н Н Н Н
O – Н2 О О
3 2 N 4 1
ОН ОН Н Н Н Н Н
3 2
-D-ribo-furanose Uracil
ОН ОН
Uridine (U)
As the form of carbohydrate at nucleic acids is -D-furanose
then the bond is called -N-glycoside bond. This type of bond is
formed by both pyrimidine and purine hetero-cyclic bases.
After that alcohol hydroxyl group at carbohydrate nucleoside at
5’ or 3’ position should react with phosphoric acid according to
esterification reaction. Ester is formed, thus, this bond can be called
ester bond. As ester is formed at reaction with phosphoric acid then

90
there is one more name of this bond – phospho-ester bond.
When nucleotides are attached to each other there is one more
esterification reaction between phosphoric acid residue at nucleotide
and alcohol hydroxyl group at carbohydrate at 5’ or 3’ position. It is
possible to say that nucleotides are attached to each other by 3’,5’-
ester bond or phosphor-di-ester bond.
At secondary structure formation (double helix) in DNA
between complimentary hetero-cyclic bases there are hydrogen
bonds providing molecule helix structure existence.

Question 91. What is nucleic acid primary structure?

Answer. Nucleic acid primary structure is nucleotide content
and nucleotide succession, i.e. it is alternation order of nucleotide
elements at nucleic acid molecule. Nucleotide content is stated
studying nucleic acid hydrolytic degradation products.
RNA is easily hydrolyzed in soft conditions at alkaline medium
to nucleotides which, in their turn, are able to eliminate phosphoric
acid residue at alkaline medium with nucleoside formation. At acid
medium nucleosides are hydrolyzed to hetero-cyclic bases and
carbohydrates.
DNA chemical analysis is not practically used due to
complication by additional processes. More preferable procedure is
enzymatic hydrolysis under the action of nucleases.

Question 92. What is DNA secondary structure?

Answer. DNA secondary structure is poly-nucleotide chain
space organization. Its model was suggested in 1953 by G. Watson
and P. Crick. According to this model, DNA has the form of right-
wind spiral formed by two poly-nucleotide chains which are twisted
in relation to each other and around common axis. DNA model is
represented at figure 6. You can see that distance between rounds
(spiral step) is 3,4 nm. This distance has 10 nucleotide residues, one
nucleotide size is 0,34 nm; bi-spiral molecule diameter is 1,8 nm.

91
 Figure 6. Double-stranded DNA molecule scheme:
а – according to Watson and Crick (“с” is deoxy-ribose residue, “р” is
phosphoric acid residue); б – DNA A-form; в – DNA B-form.

DNA double-stranded molecule configuration is changed

according to water quantity and solution ionic strength. It is proved
that there are at least 6 DNA forms, which are called А-, В-, С-, D-,
Е- and Z-forms. Configuration of two of them in the simplest form is
presented at figure 6. At A-form there is some basic pairs
displacement from molecule centre to periphery which is reflected in
the size (one round length is 2,8 nm, there are 11 mono-nucleotides
instead of 10; distance between nucleotides is also changed etc.). If
A- and B-forms are right-wind spirals then Z-form (zigzag-like) has
left-wind configuration, in which phosphor-di-ester base is located as
zigzag along molecule axis. It is supposed that at A-form DNA plays
the role of matrix at transcription process (RNA synthesis on DNA
molecule) and B-form is used as matrix at replication process (DNA
synthesis on DNA molecule).
Nucleic base residues are directed inside the spiral. To provide
more stability to this structure hydrogen bonds are formed between
nitrous bases. Their number should be maximal. It is reached by
certain correspondence between residues at one strand in relation to
residues in the other strand: thymine groups at one strand should be
located in front of adenine groups at other strand (two hydrogen
bonds are formed between them), cytosine groups should be located
in front of guanine groups (three hydrogen bonds are formed
between them). These bases make complimentary base pairs.

92
Hydrogen bonds are formed between amino group of one base and
carbonyl group at another base, between amide and imine nitrogen
atoms.

Question 93. What is DNA tertiary structure?

Answer. At cell DNA forms super-helices which provide its
packing compact character. DNA with 4 cm length is located at
chromosome which size is up to 5 nm. DNA length is decreased up to
100 thousand times. Eukaryotic DNA tertiary structure is formed due
to interaction with nuclei protein and at certain stage of cell cycle it
acquires chromosome form (figure 7).

Figure 7. Scheme of DNA tertiary structure formation.

Question 94. What is RNA secondary structure?

Answer. In opposition to DNA, ribonucleic acid molecule is
made of one poly-nucleotide chain. Separate parts of RNA chain are
formed by spiral loops due to hydrogen bonds between
complimentary nitrous bases adenine-uracil and guanine-cytosine.
RNA chain parts at such spiral structures are anti-parallel and they
are not always complimentary, there are un-paired nucleotide
residues and one-stranded loops which do not correspond to double
helix. Spiral parts are typical of all RNA types.

а 93
b
 Figure 8. Scheme of RNA secondary structure formation:
а – scheme of bond formation between complimentary bases; b – transport
RNA scheme.

Transport RNA comprises four spiral parts and three (sometimes

four) one-stranded loops. To draw such a structure on plane special
“clover-leaf” figure is used.

Question 95. What is RNA tertiary structure?

Answer. One-stranded RNA molecules are characterized by
compact and ordered tertiary structure which appears due to
interaction between spiral elements of the secondary structure. Thus,
additional hydrogen bonds formation is possible between nucleotide
residues located at distance from each other or bonds between OH-
groups at ribose residues and bases. RNA tertiary structure is
stabilized by di-valent metal ions, for example, Mg 2+, which form
bonds not only with phosphate groups but also with bases.

Question 96. What base is complimentary to thymine? Write

down this complimentary pair structure and mark hydrogen bonds.
Answer. Base complimentary to thymine is adenine. They form
two hydrogen bonds.
O Н–NН
Н3С О 6 7
5 N
С NH 1 N
Н2 О НO 2
8

N 4 N9
С Н1 N
H 3 H
НThymine-adenine
3
О (
Н С
Question 97. What base is complimentary
Н to cytosine? Write
down this complimentary pair structure
3 and mark hydrogen bonds.
Answer. Base complimentary С to cytosine is adenine. They form
О
three hydrogen bonds. )
2
Н–N–H О
О 7
6
N НN
1
94 5 N
8
2
O НN 4 N9
N N
H 3 H
H
Cytosine-adenine
из
 ы

то

Question 98. What biopolymer

fragment is at figure 9? What structure
is represented (primary, secondary)?
Are there any mistakes at this
fragment? What is this biopolymer
role at human organism? ОН

Answer. To define what biopolymer is

at the figure we should analyze its
structure. At the figure we could see
ОН
nucleic acid fragment comprising
three nucleotides.

ОН
Figure 9. Biopolymer scheme.
Carbohydrate component here is ribose as at 2’ position there is
hydroxyl group. Thus, at the figure we can see RNA fragment. The
structure is primary (nucleotide succession at nucleic acid chain).
Nucleotide at the top has hetero-cyclic base thymine and not uracil
(there is –СН3 group). Thus, in the figure at RNA fragment there is a
mistake. Its role is to transmit hereditary genetic information and to
take part at protein synthesis.

Question 99. What biopolymer

fragment is at figure 10? What
structure is represented (primary,
secondary)? Are there any mistakes at
this fragment? What is this
biopolymer role at human organism?
Answer. To define what biopolymer is
represented on the figure we should
analyze its structure. At the figure we
95
can see nucleic acid fragment
comprising three nucleotides.

Figure 10. Biopolymer scheme.

Carbohydrate component here is deoxyribose as at 2’position
there is no hydroxyl group. Thus, at the figure there is DNA
fragment. This is primary structure (nucleotide succession at nucleic
acid chain). Nucleotide at the top has hetero-cyclic base which is
thymine (there is –СН3 group). Thus, in DNA fragment there are no
mistakes. Its role in the organism is to store and transmit genetic
information.

Question 100. What RNA types are there?

Answer. There are several RNA types.
Ribosomal RNA molecules (rRNA) are in the structure of
ribosomes being their structural basis. Their molecule completeness
is necessary for protein biosynthesis on ribosomes.
Transport RNA (tRNA) biological role is addition of activated
amino acid residues and their transport on ribosomes, i.e. to the place
of poly-peptide chain synthesis.
Information or matrix RNA (iRNA, mRNA) plays the role of
matrix (platelet) at protein biosynthesis during translation process
(reading nucleotide code and its translation into amino acid
succession at protein poly-peptide chains).
The problem to differentiate the following types of RNA is
being debated: low-molecular (small) nucleic, antisense and viral.
Small nucleic RNA (snRNA) is RNA class which is located at
eukaryotic cell nucleus. They take part at such important processes
as splicing (intron removing from immature mRNA), regulating
transcription factors or RNA-polymerase and keeping complete
telomers.
Antisense RNA is one-stranded RNA which are complimentary
to mRNA. Antisense RNA are introduced into cells to inhibit
complimentary mRNA translation due to fact that antisense RNA
make pair with mRNA-target and physically prevent translation
complex formation. This effect is stechiometric.
96
 Viral RNA is structural element of viral or phague
ribonucleoproteins, it has all information necessary for virus cell
proliferation at host-organism cells.

7. LIPIDS AND LOW-MOLECULAR BIOREGULATORS

Question 101. What is organic compound class of lipids?

Answer. Lipids (from Greek lipos – fat) are natural fat-similar
substances which are not practically soluble in water but soluble at
non-polar organic solvents.
Lipids do not belong to one organic substance class and they do
not have any common structural features. In majority of cases they
are esters of higher fatty acids with glycerol and other alcohols (for
example, sphingosine). At lipid structure the following substances
could be: phosphoric acid, amino alcohols or carbohydrates.

Question 102. Are lipids biopolymers?

Answer. Lipids are not biopolymers but in the organism they
could be attached to other biopolymers, for example, proteins.

Question 103. What functions are performed by lipids in the

organism?
Answer. The most important of lipid biological functions are:

97
 1. Building (structural) – lipids take part at cellular membrane
formation. Phospholipids, glycolipids and lipoproteids are in the
structure of cellular membranes. Lipids take part at many
biologically important compounds formation.
2. Energy function – at lipid oxidation a large amount of energy
is discharged. At 1gr of fat degradation to СО2 and Н2О about 38,9
kJ (9,5 kcal) of energy is discharged which is twice as much as at
protein and carbohydrate degradation. Lipids provide 25-30 % of
energy necessary to organism.
3. Storing function – calorie-rich character and insolubility in
water make fats and oils ideal components to store energy. This is
important for animals which sleep at winter or migrate for a long
time through the area without food supply. Plant seeds contain fat
necessary to provide energy for fetus to grow.
4. Thermic regulatory function – fats are very poor at heat
conducting, that is why, subcutaneous fat layer at mammals helps
them keep heat.
5. Protective mechanical function – amortization of
subcutaneous fat protects organs, for example, kidneys from
mechanical damage.
6. Catalytic function – it is connected to fat-soluble vitamins (А,
D, Е, К), which molecules have lipid basis. Vitamins as they are do
not have any catalytic activity but they are in the structure of
enzymes and without them enzymes could not perform their
functions.
7. Source of metabolic fluid – one of fat oxidation products is
water. This metabolic water is very important for creatures living at
deserts. Thus, fat which is at camel hump is not the source of energy
but the source of water in the first place.
8. Protection from excessive water amount and from too large
water loss – fat discharge from sebaceous glands helps skin and wool
being water-proof. Wax cuticle at insects and plants decreases water
evaporation, as water could not cross non-dissolvable lipid layer.
9. Regulatory function – sex hormones, testosterone,
progesterone and corticosteroids and also other hormones are
cholesterol derivatives. Vitamin D, cholesterol derivatives play an

98
important role at calcium and phosphorus metabolism. Bile acids
take part at food digestion (fat emulsification) and also at higher
carboxylic acid absorption.
10. Electric isolation – myelin which is discharged by Shwann’s
cells contains 70-75% of lipids which isolate some neurons in such a
way that impulse transduction is faster.

Question 104. What is the difference between saponificated and

un-saponificated lipids?
Answer. Saponificated lipids contain ester bonds and they are
able to be split at hydrolysis process. If hydrolysis goes on at alkaline
medium then soaps are produced among reaction products. Soap is
higher carboxylic acid salt. Un-saponificated lipids do not have ester
bonds and are not exposed to hydrolysis.

Question 105. What lipids belong to saponificated lipids?

Answer. Saponificated lipids are subdivided into two groups:
simple (unconjugated) and complex (conjugated). Unconjugated
lipids are esters and are made by fatty acid residues and alcohol
residues (mono-alcohols, di- or tri-alcohols), they include waxes, fats
and ceramides. In the structure of conjugated lipids there are higher
fatty acid residues and alcohols with substituted groups, phosphoric
acid residues and mono-saccharides. Conjugated saponificated lipids
include phospholipids, glycolipids and sphingolipids.

Question 106. What compounds belong to un-saponificated

lipids?
Answer. Un-saponificated lipids are not esters, that is why they
are not hydrolyzed at alkaline medium with fatty acid formation and
they do not give soap.
Many un-saponificated lipids are:
– low-molecular regulators (thromboxanes, leukotrienes,
prostaglandins, prostacyclins);
– vitamins (all fat-soluble vitamins);
– hormones (steroid sex hormones, glucocorticoids and
mineralocorticoids);

99
 – plant hormones (hibberellins, abscisic acid, ethylene);
– pigments (carotine, licopene);
– smelling substances (geraniol, geranial, menthol, mircen);
– pheromones (citral, grandisol).

Question 107. What alcohol residue is at plant oils?

Answer. Plant oils belong to un-conjugated saponificated lipids,
to be more particular they belong to liquid fats. In the structure of
liquid fats (as well as in the structure of solid fats) there are tri-
alcohol (glycerol) residues.

Question 108. What carboxylic acid residues are at plant oils?

Answer. In the structure of plant oils there are mainly glycerol
and higher carboxylic unsaturated acid esters. Most widely-spread
acids are oleic acid С17Н33СООН, linoleic acid C17H31COOH and
linolenic acid C17H29COOH. All these acids have 18 carbon atoms, at
oleic acid radical there is one double bond (in the middle of the
molecule), at linoleic acid radical there are two double bonds
separated by –СН2– group, at the linolenic acid radical there are
three double bonds separated by methylene groups (–СН2–).
О
СН3 (СН2)7 СН СН (СН2)7 С
ОН
Oleic acid О
СН3 (СН2)4 СН СН СН2 СН СН (СН2)7 С
ОН
Linoleic acid
О
СН3 СН2 СН СН СН2 СН СН СН2 СН СН (СН2)7 С
ОН
Linolenic acid

Question 109. What carboxylic acid residues are in solid fat

structure?
Answer. At solid fat structure there are mainly esters of glycerol
and higher fatty saturated acids. Most widely-spread acids are
palmitic acid C15H31COOH and stearic acid С17Н35СООН:

О О
СН3 (СН2)14 С СН3 (СН2)16 С
ОН ОН
Palmitic acid Stearic acid

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 Question 110. What configuration in relation to multiple bond is
typical of unsaturated acids which are in the structure of natural fats?
Answer. At plant oil structure there are mainly higher
carboxylic unsaturated acid residues containing one or several double
bonds at radical at cis-configuration. Hydrocarbon radical at an acid
has curved and shortened form, molecule has large volume and at
crystal formation it is packed more loosely than trans-isomers. It
determines difference in melting temperature and aggregate
conditions of acids. Thus, oleic acid at room temperature is liquid
and its trans-isomer, elaidic acid, is solid.
Н3С–(СН2)7 (СН2)7–СООН Н (СН2)7–СООН
С=С С=С
Н Н Н3С–(СН2)7 Н
Oleic acid Elaidic acid

Cis-configuration of unsaturated acids is less stable than trans-

configuration. This fact makes food fats more exposed to catabolism,
it is easier to digest them.

Question 111. Write down tri-oleyl-glycerol formula.

Answer. Tri-oleyl-glycerol is ester of glycerol and three oleic
acid molecules:
СН2–О–СО–(CH2)7–СН=СН–(СН2)7–CH3
СН – О–СО–(CH2)7–СН=СН–(СН2)7–CH3
СН2–О–СО–(CH2)7–СН=СН–(СН2)7–CH3
Tri-oleyl-glycerol
At the scheme thick letters stand for glycerol residue.

Question 112. Write down 1-oleyl-2-stearyl-3-palmityl-

glycerol.
Answer. 1-Oleyl-2-stearyl-3-palmityl-glycerol is ester of
glycerol and three different acid molecules: oleic, stearic and
palmitic acids. Carbon atoms at glycerol fragment are enumerated
starting from the top down, it means that oleic acid residue should be
located at the top, lower stearic acid residue is placed and palmitic
acid residue should be at the bottom.

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 СН2–О–СО–(CH2)7–СН=СН–(СН2)7–CH3
СН – О–СО–(CH2)16–CH3
СН2–О–СО–(CH2)14–CH3
1-oleyl-2-stearyl-3-palmityl-glycerol

Question 113. What reagent transforms liquid fats into solid

fats? Write down reaction scheme.
Answer. At liquid fat tri-acyl-glycerols there are mainly
unsaturated acid residues, in the structure of solid fats there are
mainly saturated acid residues. Thus, liquid fats could be
transformed into solid fats due to reduction reaction by hydrogen
with metal catalysts. Reaction scheme with tri-oleyl-glycerol has the
following form:
СН2–О–СО–(CH2)7–СН=СН–(СН2)7–CH3
Ni
СН – О–СО–(CH2)7–СН=СН–(СН2)7–CH3 + 3 Н2 
СН2–О–СО–(CH2)7–СН=СН–(СН2)7–CH3
Tri-oleyl-glycerol

СН2–О–СО–(CH2)7–СН2–СН2–(СН2)7–CH3
 СН – О–СО–(CH2)7–СН2–СН2–(СН2)7–CH3
СН2–О–СО–(CH2)7–СН2–СН2–(СН2)7–CH3
Tri-stearyl-glycerol

Question 114. What reagents could give soap?

Answer. Soaps are higher fatty acid salts. They are formed at
neutralization reaction between higher carboxylic acid and base or
alkaline hydrolysis reaction of fats (saponification reaction).
СН3(СН2)7СН=СН(СН2)7СООН + NaOH 
 СН3(СН2)7СН=СН(СН2)7СООNa + H2O

СН2–О–СО–(CH2)7–СН=СН–(СН2)7–CH3 СН2–ОH
СН – О–СО–(CH2)16–CH3 + 3 NaOH  СН – ОH +
СН2–О–СО–(CH2)14–CH3 СН2–ОH
1-oleyl-2-stearyl-3-palmityl-glycerol glycerol
О О
+ СН (СН ) С +
СН3 (СН2)7 СН СН (СН2)7 С 3 2 16 ОNa
ОNa Sodium stearate
Sodium oleate 102
О
СН3 (СН2)14 С
ОNa
Sodium palmitate
 +

Question 115. How many benzene rings are there at cholesterol

molecule?
Answer. To answer this question it is necessary to write
cholesterol molecule and analyze its structure.

It is evident that at cholesterol molecule there are three six-

membered rings, two of them are saturated and one is unsaturated,
but there are no aromatic benzene rings.

8. ORGANIC COMPOUND IDENTIFICATION

Question 116. At three test tubes there are gelatin, glucose and
starch solutions (there is one substance at one test tube). In what way
is it possible to identify substances?
Answer. Identification is stating equality of some unknown
substance with other substance which is known. Usually substance
properties are correlated using qualitative reactions typical of this
class. Gelatin is protein, glucose is mono-saccharide and starch is
homo-poly-saccharide.
Qualitative reaction on starch is blue colour at iodine solution
addition. From each test tube it is necessary to pour some part of
solution in to new test tubes (pour 1 ml in to clean test tubes). We
should add 1-2 drops of iodine solution in to each test tube. At one

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test tube solution turns blue, it means that starch is in the test tube
from which this sample was taken.
Let’s take samples from two left test tubes, add silver oxide
ammonia solution to them and heat them on water bath. In the
sample with glucose there is silver precipitate – “silver mirror” – it is
qualitative reaction on glucose.
So, we identified two substances and we can conclude that in the
third test tube there is gelatin. To check our conclusion we should
add sodium hydroxide solution to the third test tube and a few drops
of copper sulfate (biuret reaction), in the test tube there is violet
colour.
You should remember that you should not have qualitative
reactions with all initial amount of substances, as after the first
reaction there is no substance left for the next qualitative reaction or
repeating some reaction if it was not correctly performed.

Question 117. At three test tubes there are oil, glycerol and
maltose solutions (in one test tube there is one substance). In what way
is it possible to identify these substances?
Answer. We should use qualitative reactions to identify these
compounds. Oil is tri-acyl-glycerol, containing higher unsaturated
fatty acid residues, maltose is reducing di-saccharide and glycerol is
tri-alcohol.
Qualitative reaction on multiple bonds is bromine water
discoloration or potassium permanganate solution discoloration. We
do not know what is the test tube with oil, that is why, we should
pour some part of solution from each test tube into new clean test
tubes (i.e. we should take samples to perform reactions). To each
sample we add 1 ml of bromine water (or potassium permanganate
solution) and mix it. At one of the test tubes there is bromine water
or potassium permanganate solution discoloration, it means that this
sample is oil.
Let’s take sample once again from two test tubes left, to both of
them add silver oxide ammonia solution and heat at the water bath.
At the sample with maltose there is silver precipitate – “silver

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mirror” – it is qualitative reaction on compounds with aldehyde
group.
We identified two substances and can come to conclusion that in
the third test tube there is glycerol. To check we should mix sodium
hydroxide solution and copper sulfate solution at the test tube, as a
result copper hydroxide (II) precipitate is formed. After adding few
drops of glycerol precipitate is dissolved and there is bright blue
colour of the solution, it is glycerol copper complex.

Question 118. At three test tubes there are ethanol, sodium oleate
and tartaric acid solutions (in one test tube there is one substance). In
what way is it possible to identify these compounds?
Answer. For identification we should use qualitative reactions.
Ethanol is saturated mono-alcohol, sodium oleate is higher fatty acid
salt, tartaric acid is hetero-functional compound containing two
carboxylic groups and two hydroxyl groups at viscenal position (at
neighboring carbon atoms).
Qualitative reaction on multiple bonds is bromine water or
potassium permanganate discoloration. We do not know what is the
test tube with sodium oleate, that is why, from each test tube we
should take some part of solution in to three other clean test tubes
(i.e. we take samples). To each sample we should add 1 ml of
bromine water or potassium permanganate solution and mix. At one
test tube there is bromine water or potassium permanganate
discoloration, it means that in this test tube there is sodium oleate.
СН3(СН2)7СН=СН(СН2)7СОONa + Br2  СН3(СН2)7СНBr-CHBr(СН2)7СОONa
Oleic acid sodium salt 9,10-di-bromo-stearic acid sodium salt
Once again let’s take samples of two left substances and add 2-3
ml of chrome mixture to them. In the sample with ethanol as a result
of redox reaction and chrome oxidation degree change there is
orange color transformation into green, reaction mass is becoming
warmer and there is ethanol oxidation product specific smell.
Acetaldehyde has green apple smell.
3С2Н5ОН + K2Cr2O7 + 4H2SO4  3СН3CHO + K2SO4 + Cr2(SO4)3 + 7H2O
We identified two substances and can conclude that in the third
test tube there is tartaric acid. To check our conclusion we add several

105
drops of potassium hydroxide to the sample from this test tube, shake
it intensively and could see gradual formation of white crystal
precipitate of potassium hydro-tartrate. To this precipitate we add
sodium hydroxide solution in drops until precipitate is completely
dissolved. Double tartaric acid potassium-sodium salt solution is
formed (signet salt):
COOH COOK COOK
H – C – OH + KOH H – C – OH + NaOH H – C – OH
H – C – OH -H2O H – C – OH -H2O H – C – OH
COOH COOH COONa
Tartaric acid tartaric acid potassium salt moderate potassium-
sodium salt of tartaric acid
After that we should put several drops of copper sulfate solution
in to clean test tube, add sodium hydroxide solution till copper
sulfate (II) blue precipitate formation, add received precipitate from
tartaric acid (signet salt). Precipitate is dissolved and violet colour of
copper complex appears in the test tube:
CuSO4 + 2NaOH  Cu(OH)2↓+ Na2SO4
COOK H
HC – OH K+ -OOC – CH – O O – CH – COO- K+
2 + Cu(OH)2 Cu
HC – OH -2H2O Na+ -OOC – CH – O O – CH – COO- Na+
COONa H
Question 119. At three test tubes there is acetone, fructose
solution and cysteine solution. In what way is it possible to identify
substances?
Answer. For identification we use qualitative reactions on these
substances. Acetone is ketone, fructose is ketohexose, and cysteine is
sulfur-containing amino acid.
Qualitative reaction on ketohexoses is red colour formation at
heating with Selivanov’s reagent.
We do not know what test tube is with fructose, so, we should
pour some part of solution from each test tube in to new clean test
tubes (we take samples to perform reactions). To each sample we
should add 1 ml of Selivanov’s reagent, heat the mixture and after
heating let the samples stay for 5 minutes. At one of the test tubes

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there is red colour, it means that test tube with red colour has
fructose solution.
Once again we should take samples from two left test tubes and
add to each of them 0,5 ml of 2,4-di-nitro-phenyl-hydrasine saturated
solution. In the sample with acetone there is yellow precipitate
formation of acetone 2,4-di-nitro-phenyl-hydrason.
O O2N O2N
СH3–C + NH2–NH NO2 СH3 – C N–NH NO2+ H2O
СН3 СН3
Acetone 2,4-di-nitro-phenyl-hydrason
We identified two substances, so, we can conclude that the third
test tube contains cysteine solution. To check our conclusion we add
twice as much sodium hydroxide solution, mix the solution and boil
it for 1-2 minutes. To the alkaline solution we add several drops of
lead acetate (II) and boil it again. There is black precipitate
formation.

Question 120. In three test tubes there are solutions of albumin,

tyrosine and salicylic acid. In what way is it possible to identify these
compounds?
Answer. For identification we use qualitative reactions on these
substances. Albumin is a protein, tyrosine is amino acid with
aromatic hydrocarbon radical, salicylic acid is aromatic hydroxyl
acid containing phenol fragment.
It is well-known that phenols form coloured complexes with iron
chloride (III). We do not know what test tube has salicylic acid
solution, so, we take samples from each test tube and pour them to
new clean test tubes. To each test tube we should add 1 ml of iron
chloride (III) and mix. At one test tube solution gets intensively violet,
it means that in this test tube there is salicylic acid solution.
Qualitative reaction on amino acids with aromatic hydrocarbon
radical is xanto-protein reaction. Once again we take samples of two
left substances, add 2-3 drops of concentrated nitric acid, heat it
constantly shaking. At one test tube there is yellow colour. Cool the
test tube and add 2-3 drops of 1 aqueous solution of sodium
hydroxide. Bright orange colour proves tyrosine presence at the

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solution.
We identified two substances and it means that in the third test
tube there is albumin solution (egg white). To prove our conclusion
we should add sodium hydroxide solution to the third test tube and
we should add several drops of copper sulfate solution (biuret
reaction on proteins), in the test tube there is violet colour.

LITERATURE

1. Тюкавкина Н.А. Биоорганическая химия: учеб. для вузов /

Н.А. Тюкавкина Н. А., Ю.И. Бауков. – М.: Дрофа, 2006.
2. Овчинников Ю. А. Биоорганическая химия: учеб. для
вузов / Ю.А. Овчинников. – М.: Просвещение, 1987.
3. Руководство к лабораторным занятиям по
биоорганической химии / под редакцией Н.А.Тюкавкиной. – М.:
Дрофа, 2006.

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