1. Medical Chemistry (1st year) Lecture I

2. Why are the students of medicine forced to study chemistry?

3. Biochemistry = science studying chemical processes in living organisms
UNDERSTANDING ALL PROCESSES at MOLECULAR LEVEL
transformations of biomolecules
(metabolism, "metabolic pathways")
function of particular molecules
chemical composition

4. Chemical composition of human body
- it is already well known
- new discoveries are not probable, but not exluded at all
Surprising discoveries done recently
NO - nitric oxide
NO ?
toxic corrosive oxidizing
- many functions in human body
- signaling molecule
miRNA (microRNA)
- short RNA molecules (~22 nt)
- negative regulators of gene expression at the posttranscriptional level

5. Function of particular molecules
HEME
HEMOGLOBIN
- protein of the red blood cells for oxygen transport

6. Biotransformations (synthesis, degradation)

7. Biotransformations (synthesis, degradation)
HEM
HEMOGLOBIN

8. porphyria cutanea tarda
Clinical impact
Porhyria
- errors in biosynthesis of the HEME:
porphyria cutanea tarda
(skin lesions, blistering)
- errors in degradation of the HEME:
Jaundice
hyperbilirubinemia =

9. Ultimate goal of biochemistry
UNDERSTANDING ALL PROCESSES at MOLECULAR LEVEL
cellular biology, molecular biology
physiology
pathology, pathological physiology "pathobiochemistry"
pharmacology, immunology, microbiology, genetics, oncology
MODERN MEDICINE = more than hopeful wish to help !

10. tick-borne diseases: - Lyme disease - tick-borne encephalitis
(Ixodes ricinus)

11. Nettle
(Urtica dioica)
- painful sting
- histamine

12. = science studying the properties and behavior of matter
Chemistry
= science studying the properties and behavior of matter
Matter - anything that has mass and occupies space
- physical material of the universe
States of matter: gas (g)
liquid (l)
solid (s)

13. Pure substance – matter that has fixed composition
and distinct properties
2 categories of substances:
Elements - cannot be decomposed by chemical methods
into simpler substances (carbon, oxygen, iron)
- consist of one kind of atoms
Compounds - contain two or more kinds of atoms
(water – H2O sodium chloride – NaCl)

14. atom – the smallest particle of an element having its
Structure of the atom
atom – the smallest particle of an element having its
chemical properties
("atomos" = "indivisible")
3 types of elementary particles:
PROTONS
NEUTRONS
ELECTRONS
"nucleons"

15. Modern physics: Standard model of elementary particles

16. proton mass: 1.67 × 10-27 kilograms
Properties of the subatomic particals
Particle
Symbol
Relative charge
Relative mass
Proton p
positive +1 1
Neutron n
Electron e
negative -1
negligible *
* mass of the electron = only 1/1836 of the mass of the proton
proton mass: 1.67 × kilograms

17. Atoms have no overall charge
number of protons = number of electrons
ATOMIC number (Z) - the number of protons in the nucleus
- uniquely identifies a chemical element
Element = mixture of atoms with the same number of protons
- there can be various number of neutrons!

18. C Atomic number (Z) = number of protons
Every atom can be characterized by 2 numbers:
Atomic number (Z) = number of protons
- it determines the element = symbol: C, N, Fe
Mass (nucleon) number (A) = number of nucleons
(protons + neutrons)
mass number symbol of element
atomic number 12 C 6

19. Nuclide - specific atomic number and mass number
C U
most elements are mixtures of different nuclides !
(same atomic number, variation in mass numbers)
ISOTOPES of an element
- same number of protons, variation in number of neutrons
- identical chemical properties 12
238 6 92

20. H H H Isotopes of hydrogen proton neutrons hydrogen deuterium (D)1 H 2 3 H H 1 1 1
hydrogen
deuterium (D)
tritium (T)
water H2O
"heavy water" D2O

21. C C C C N + e Isotopes of carbon particle b = e 12 C 13 14 C C 6 6 6
Certain isotopes of some elements are radioactive!
Radioactive decay = unstable atomic nucleus "loses energy" by emitting:
particle a = He
particle b = e
g rays ( = high-energy photon) 4 2 -1 14 14 C N + e
+ antineutrino 6 7 -1
half life 5730 years

22. Cl Cl Isotopes of chlorine 35 Cl 37 Cl
stable 17 17

23. Electrons - surround the nucleus in energy levels (shells, orbits)
The chemical reactions - interaction of electrons from the
OUTERMOST orbit

24. Arrangement of electrons in the atom
4 quantum numbers:
1) n principle quantum number - determines energy level
- positive integral values 1, 2, 3, 4, ...
K, L, M, N, ...
2) l orbital quantum number - determines the shape of electron cloud
- values from 0 to (n-1) , 1, 2, 3, ...
s p d f
3) m magnetic quantum number - determines orientation of the
electron cloud in space
- integral values from –l to +l
4) s spin - determines the intrinsic state of an electron
- only 2 possible values: +½ or -½

25. s orbitals
p orbitals
d orbitals

26. The principal quantum number (s orbitals)

27. Rules that must be respected
1) The lowest "energy levels" are
occupied first.
2) Hund‘s rule:
No electron pairing in p, d, f
orbitals until each orbital of given
set contains one electron.
3) Pauli exclusion principle:
No TWO electrons in any given
atom can have exactly the same
set of all 4 quantum numbers.

28. Electron configurations
Electrons
Orbital diagram
1s2 2s1
1s2 2s2
1s2 2s2 2p1
1s2 2s2 2p2
1s2 2s2 2p3
1s2 2s2 2p6
1s2 2s2 2p6 3s1

29. The periodic properties of the elements
The elements with similar arrangement (configuration) of electrons
in the superficial shell have SIMILAR CHEMICAL PROPERTIES !
Periodic table
Dmitri Mendeleyev (1869) - Russian chemist
elements are listed in order of increasing atomic number
horizontal rows = PERIODS
vertical columns = GROUPS
elements in groups: the same number of electrons in outermost orbits
= similar chemical properties

33. Names of the groups Li, Na, K, Rb, Cs, Fr O, S, Se, Te, Po
Elements
I A
Alkali metals
Li, Na, K, Rb, Cs, Fr
II A
Alkaline earth metals
Be, Mg, Ca, Sr, Ba, Ra
VI A
Chalcogens
O, S, Se, Te, Po
VII A
Halogens
F, Cl, Br, I
VIII A (0)
Noble (rare, inert) gases
He, Ne, Ar, Kr, Xe, Rn

34. Chemical bonding
Covalent bond - sharing of one or more pairs of electrons
Coordinate covalent bond - both electrons of the bond belong to one atom, the other has empty orbital
(electron pair donor, electron pair acceptor)

35. Chemical bonding
Covalent bond sharing of one or more pairs of electrons
Coordinate covalent bond - both electrons of the bond belong to one atom, the other has empty orbital
Ionic bond - big difference of electronegativities
- IONS attracted by electrostatic forces Na+ Cl-

36. Hydrogen bonding
a weak electrostatic interaction between partially (+) charged hydrogen atom and partially (-) charged another atom (O, N, F)
H bonds
important in stabilizing the structures of: PROTEINS
NUCLEIC ACIDS

37. The EARTH Core (inner, outer) Mantle Crust Crust Lithosphere 93 %
Hydrosphere 7 %
Atmosphere %
Biosphere %

38. The elementary composition (mass %)
Earth crust
Human body O
49.5
62.4 Si
25.7 - Al
7.5 Fe
4.7
0.005 H
0.9
9.8 P
0.12
1.0 C
0.09
21.1 S
0.06
0.16 N
0.03
3.1
elementary composition of the human body is very
different from that of lithosphere !

39. Specific selection of elements for the biological uses
% in human body
% in the Earth crust C
243 N
103 H 11 P 8 S
2.7 O
1.26 Fe
0.001 Al Si
some chemical elements (C, H, N, O, ...) are "better" than
others to make up molecules of living organisms

40. most abundant elements of the Earth core: Fe, Ni
most abundant elements of the Earth crust: O, Si, Al, Fe
most abundant elements in living organisms: O, C, H, N
oxygen is the most abundant element both on the Earth surface and in human body

41. The atmosphere of the Earth
The dry air (% by volume)
Nitrogen 78 %
Oxygen 21 %
Argon %
Carbon dioxide 0.04 %

42. The oxygen cycle O2 CO2 H2O water 2 kg food 1.2 kg
Plants
PHOTOLYSIS of H2O
PHOTOSYNTHESIS
Animals, plants
RESPIRATION
CO2
H2O
Needs per day: air l [ 13.5 kg ]
water kg
food kg

43. The greenhouse effect
CO2 is a "greenhouse gas" - global warming

44. Comparison of inspired and expired air
21 %
15 %
CO2
0.04 %
5 % N2
78 %
CO2 is a waste product of respiration

45. The bioelements (summary)
Principal bioelements: O, C, N, H, P, S
(biomolecules: proteins, nucleic acids, lipids, saccharides)
Water and ions: ( H2O ) Na+, K+, Mg2+, Ca2+, Cl-, ( HCO3- , phosphates)
Mineral constituents of bones and teeth: calcium phosphate
Microelements (trace elements): Fe, Cu, Co, Zn, I, F, Se, ...
5) Contamination (intoxication): Hg, Al, ...