Welcome to Chemistry

If anyone wishes to search out

the truth of things in serious earnest, he
ought not to select one special science;
for all the sciences are conjoined with
each other and interdependent.
Descartes,
Rules for the Direction of the Mind

Prof. Natalya VODOLAZKAYA

V.N. Karazin Kharkov National University

Chemical Faculty
Department of Physical Chemistry
Central building of the University
Chemical side, 2nd floor
Laboratory 2-82
[email protected]
 Program of course “MEDICAL CHEMISTRY”
for the first-year students of the School of Medicine
Module 1. “Acid-base equilibria and complex formation in biological liquids”.
1. Biogenic s- and p- block elements: biological role, application in medicine.
2. Biogenic d- block elements: biological role, application in medicine.
3. Chemical bonding.
4. Solutions. Electrolytic dissociation.
5. Acid-base equilibrium in biological liquids.
6. Dissociation of water, pH scale. Buffer solutions.
7. Colligative properties of solutions.
Practice for Module 1: 5 seminars, 5 tests according to the material of
seminars, 4 laboratory exercises and final test.
Module 2. “Equilibrium in biological systems at the phase interface”.
1. Chemical thermodynamics. Thermochemistry.
2. Kinetics of biochemical processes.
3. Electrochemical phenomena in biological processes.
4. Colloidal solutions and colloid stability.
5. Electric double layer and electrokinetic phenomena. Adsorption. Chromatography.
6. Properties of polymer solutions.
Practice for Module 2: 5 seminars, 5 tests according to the material of
seminars, 5 laboratory exercises and final test.
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 Grades for Module 1 and 2
Work Grade
Laboratory exercise:
a) 5 points
a) working during experiment
b) 5 points
b) writing of the experiment and results in copybook
Working during seminar 5 points
Test according to the seminar material 10 points = 5 problems for 2 points
Final test 75 points = 15 problems for 5 points
For Module 1:
40 points = 4 lab. exercises for 10 points
25 points = 5 seminars for 5 points
60 points = 5 tests for 12 points
75 points = final test
All: up to 200 points
Total:
For Module 2:
50 points = 5 lab. exercises for 10 points
25 points = 5 seminars for 5 points
50 points = 5 tests for 10 points
75 points = final test
All: up to 200 points

Points Traditional Grade Two-level Grade

200 – 180 excellent credit
179 – 150 good credit
149 – 120 satisfactory credit
119 – 0 unsatisfactory not credited 3
 V.N. Karazin Kharkov National University
Medical Chemistry
Module 1. Lecture 1

Chemistry of biogenic
elements
Natalya VODOLAZKAYA
[email protected]
30 November 2020 Department of Physical Chemistry
4
 Lecture topics
√ Fundamentals of chemistry.
√ Classification of chemical elements.
√ Classification of biogenic elements.
√ Periodic law and Periodic table.
√ Three important atomic properties: the atomic and
ionic radii, the ionization energy, and the electron affinity.

5
 Fundamentals of chemistry
Chemistry is the study of matter, its composition, structure and properties,
and the chemical changes it undergoes.
Matter is anything that occupies space and has mass.
A substance is a form of matter that has a definite (constant)
composition and distinct properties. Examples are water, ammonia, sugar,
gold, oxygen, and etc.
Substances can be either elements or compounds. An element is a
substance that cannot be separated into simpler substances by chemical
means.

The symbols of some elements are derived from their Latin names – for example, Au from
aurum (gold), Fe from ferrum (iron), and Na from natrium (sodium) – whereas most of them
come from their English names.

On the basis of atomic theory, we can define an atom as the basic

unit of an element that can enter into chemical combination.
Atoms actually possess internal structure; that is, they are made up of
electrons, protons, and neutrons.
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 Fundamentals of chemistry
The atomic number (Z) is the number of protons in the nucleus of each
atom of an element. As atom is a neutral particle the number of protons is
equal to the number of electrons, so the atomic number also shows the
number of electrons in the atom.

The mass number (A) of an atom is the total number of neutrons and
protons present in the nucleus of an atom of an element. The number of
neutrons in an atom is equal to the difference between the mass number
and the atomic number.

A molecule is an aggregate of at least two atoms in a definite

arrangement held together by chemical forces (also called chemical bonds).
A molecule may contain atoms of the same element or atoms of two or more
elements joined in a fixed ratio.

An ion is an atom or a group of atoms that has a net positive or negative

charge. The loss of one or more electrons from a neutral atom results in a
cation, an ion with a net positive charge. The acceptance of electron(s) by
an atom results in an anion, a particle with a net negative charge.

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 Fundamentals of chemistry

Figure 1. The atom.

The protons and neutrons of an atom are packed in an
extremely small nucleus. Electrons are shown as ‘clouds’
around the nucleus.
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Classification of chemical elements
√ natural and artificial;
√ metals and nonmetals;
√ according to the structure of outer energy level (incompletely filled
subshells): s-, p-, d- and f-elements;
√ according to distribution on Earth's crust (widespread and rare). Of the
83 elements that are found in nature, 12 make up 99.7% of Earth’s crust by
mass. They are, in decreasing order of natural abundance, oxygen (O),
silicon (Si), aluminum (Al), iron (Fe), calcium (Ca), magnesium (Mg), sodium
(Na), potassium (K), titanium (Ti), hydrogen (H), phosphorus (P), and
manganese (Mn);
√ radioactive elements (atomic nuclei are unstable), e.g. astatine (At),
polonium (Po);
√ according to importance for human and animal organisms
(organogenic and biogenic).

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 Figure 2. Natural abundance of the elements .
(a) Natural abundance of the elements in percent by
mass.
(b) Abundance of elements in the human body in percent
by mass.
For example, oxygen’s abundance is 45.5 percent. This means that in a
100 g sample of Earth’s crust there are, on the average, 45.5 g of the
element oxygen.
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Classification of biogenic elements
√ Chemical elements essential to life forms can be broken down into four
major categories:

1) bulk elements (H, C, N, O, P, S);

2) macrominerals (Na, K, Mg, Ca, Cl);
3) trace elements (Fe, Zn, Cu);
4) ultratrace elements, comprised of nonmetals (F, I, Se, Si, As, B) and
metals (Mn, Mo, Co, Cr, V, Ni, Cd, Sn, Pb, Li).

√ Biological essentiality of these elements has been defined by certain

criteria:

1) a physiological deficiency appears when the element is removed from

the diet;
2) the deficiency is relieved by the addition of that element to the diet;
3) a specific biological function is associated with the element.

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 Bioelements can be divided for
physiological processes as following:
√ Elements for physiological processes in bioliquids (C, H, O, N, P, Cl, K,
Na, Ca, Mg).
√ Elements for metabolism (Fe, Zn, Cu, Mo, Co, I).
Of special interest are the trace elements, such as iron (Fe), copper (Cu), zinc
(Zn), iodine (I), and cobalt (Co), which together make up about 0.1 percent of the
body’s mass. These elements are necessary for biological functions such as
growth, transport of oxygen for metabolism, and defense against disease. There is
a delicate balance in the amounts of these elements in our bodies. Too much or too
little over an extended period of time can lead to serious illness, retardation, or
even death.

√ Elements decreasing generation and growth of microorganisms (As, Sb,

Ag).
√ Elements for regulation of redox reactions (Mn, Cu, Cr).

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 Periodic law and Periodic table
Recognition of periodic regularities in physical
and chemical behavior and the need to organize
the large volume of available information about the
structure and properties of elements and their
compounds led to the development of the periodic
law by Russian chemist D.I.Mendeleev.

The modern periodic law: the physical and

chemical properties of elements are periodic
functions of their atomic numbers.

Visual expression of the periodic law is the

periodic table – a chart in which elements having
Russian chemist
similar chemical and physical properties are grouped
D.I.Mendeleev
together.

The periodic table is a handy tool that correlates the properties of the
elements in a systematic way and helps us to make predictions about
chemical behavior.
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IUPAC – International Union of Pure and Applied Chemistry
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 Periodic Table of elements: the 1-18 group
designation has been recommended by the IUPAC

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 Periodic Table
√ In modern periodic table the elements are arranged by atomic
number in horizontal rows called periods and in vertical columns known
as groups or families, according to similarities in their chemical
properties.

√ All elements can be divided into three categories – metals,

nonmetals, and metalloids.

√ Elements are often referred collectively by their group number (Group

1A, Group 2A, and so on). However, for convenience, some element
groups have been given special names.
Group 1A elements (Li, Na, K, Rb, Cs, and Fr) are called alkali
metals.
Group 2A elements (Be, Mg, Ca, Sr, Ba, and Ra) are called alkaline
earth metals.
Elements in Group 7A (F, Cl, Br, I, and At) are known as halogens.
Elements in Group 8A (He, Ne, Ar, Kr, Xe, and Rn) are called noble
gases (or rare gases).

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 Three important atomic properties
The fitness of an element for a biological role is a consequence of
electronic structure.
We now need to understand how electronic structure affects atomic
and ionic radii, and the thermodynamic ability of an atom to release or
acquire electrons to form ions or chemical bonds.

Three important atomic properties:

√ the atomic and ionic radii,
√ the ionization energy,
√ and the electron affinity.

These properties are of great significance in chemistry and biology,

for they are controls on the number and types of chemical bonds the
atom can form.
Indeed, we can use these properties to reveal an important reason
for the unique role of carbon in biology.
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 Atomic and ionic radii
The atomic radius of an element is half the distance between the
centers of neighboring atoms in a solid (such as Cu) or, for nonmetals, in a
homonuclear molecule (such as H2 or S8).

If there is one single attribute of an element that determines its

chemical properties (either directly, or indirectly through the variation of
other properties), then it is atomic radius.
In general, atomic radii decrease from left to right across a period
and increase down each group.

The ionic radius of an element is its share of the

distance between neighboring ions in an ionic solid.
That is, the distance between the centers of a
neighboring cation and anion is the sum of the two
ionic radii.

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 Atomic and ionic radii
Table lists the radii of some ions that play important roles in
biochemical processes.

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 Ionization energy
The minimum energy necessary to remove an electron from a many-
electron atom is its first ionization energy, I1. The second ionization
energy, I2, is the minimum energy needed to remove a second electron
(from the singly charged cation):

The ionization energy of an element plays a central role in

determining the ability of its atoms to participate in bond formation.
After atomic radius, it is the most important property for determining an
element’s chemical characteristics.

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 Electron affinity
The electron affinity, Eea, is the difference in energy between a neutral
atom and its anion.
It is the energy released in the process
E(g) + e−(g) → E−(g) Eea = E(E) − E(E−)
The electron affinity is positive if the anion has a lower energy than the
neutral atom.
Further analysis of ionization energies and electron affinities can begin
to tell us why carbon is an essential building block of complex biological
structures.
Among the elements in Period 2, C has intermediate values of the ionization
energy and electron affinity, so it can share electrons (that is, form covalent bonds)
with many other elements, such as H, N, O, S, and, more importantly, other C
atoms.
As a consequence, such networks as long carbon–carbon chains (as in lipids)
and chains of peptide links can form readily. Because the ionization energy and
electron affinity of C are neither too high nor too low, the bonds in these covalent
networks are neither too strong nor too weak.
As a result, biological molecules are sufficiently stable to form viable organisms
but are still susceptible to dissociation (essential to catabolism) and rearrangement
(essential to anabolism). 21
 References
¾ Chang R. Chemistry. 10-th edition. NY: McGraw-Hill,
2010. 1170 p.
¾ Chang R. General Chemistry: The Essential Concepts. 6-
th edition. NY: McGraw-Hill, 2011. 853 p.
¾ Crichton R.R. Biological Inorganic Chemistry: An
Introduction. Amsterdam: Elsevier, 2008. 369 p.
¾ Roat-Malone R. M. Bioinorganic Chemistry: A Short
Course. John Wiley & Sons, 2002. 348 p.
¾ S. V. Eltsov, N. A. Vodolazkaya. Practical Medical
Chemistry: manual / Kh.: V. N. Karazin Kharkiv National
University, 2018. 196 p.

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