BASIC CELL
BIOLOGY
I CHEMISTRY of LIFE
STRUCTURE OF ATOMS, PERIODIC
TABLE OF ELEMENTS
Lecture 2
ATOMIC STRUCTURE, PERIODIC
TABLE OF ELEMENTS
 Measuring units
 Chemical composition of the cell, the main
biogenic elements.
 The principles of atomic structure.
 Periodic Table of elements, the elements
which make up the Life.
 Chemical Bonds: Ionic Bond
Measuring units in Biology.
Lecture 2
Multiple
Prefix
exa
peta
tera
giga
mega
kilo
hecto
deca
Symbol
E
P
T
G
M
k
h
da
Power
1018
1015
1012
9
10
106
103
102
10
Measuring units in Biology.
Lecture 2
Submultiple
Prefix
deci
centi
mili
micro
nano
pico
femto
atto
Symbol
d
c
m
 (mk)
n
p
f
a
Power
10-1
10-2
-3
10
10-6
10-9
10-12
10-15
-18
10
Measuring units in Biology
Lecture 2
Constants
Avogadro
NA
6,02 ·1023
number
Molar
VMol 22,4 l/gmol
volume
p+/e- mass
1836,2
ratio
Electron rest me
9,1·10-28 g
mass
Speed of
c
3·108 m/s
the light
Atomic mass
1.66 ·10-24 g
unit
number of molecules in
one mole
volume of one gram-mole
of gaseous substance
Measuring units in Biology
Lecture 2
Atomic mass unit: 1/12 of the carbon atom
mass; approximates the mass of proton.
Molecular mass – sum of the masses of the
atoms that make up the molecule .
The equivalent of the atomic mass unit:
Dalton (Da) ~ 1,66 x 10-24 grams.
Measuring units in Biology
Lecture 2
When making chemical bonds atoms interact
with each other in simple numerical
proportions: one atom with one, two, or three
other atoms, but not with 1,5 atoms
(stechiometry).
The unit of measurement of atoms (also ions
and molecules) is mole.
One mole of every atom (molecule, ion)
contains 6,02 x 1023particles.
Measuring units in Biology
Lecture 2
6,02 x 1023 = the Avogadro number, chemical
constant; the number of atoms which make up
12 grams of carbon.
Amadeus Avogadro (1776 - 1856) – an italian
chemist, who made an observation that gases
react with each other in definite volume
proportions.
22,4 liters = molar volume of gases, the
volume, which is filled by a mole of every
gaseous molecule or atom.
http://dbhs.wvusd.k12.ca.us/Mole/MolarMass.html
http://ask.yahoo.com/ask/19991123.html
Measuring units in Biology.
Lecture 2
The origin of some non-systemic units
which are used in Biology
Celsius (Centigrade, C) temperature scale:
0 point – freezing point of water; 100
degrees – boiling of water.
Fahrenheit (F) temperature scale 0oC =
32oF; 100oC = 212oF
F = (9/5 x C) + 32.
Human body temperature in F degrees
= 98,6o
Measuring units in Biology.
Atmosphere – the pressure of the Earth
atmosphere at the sea level.
Calorie – amount of energy (warmth) needed to
warm up by one degree Celsius one gram of pure
water. (from 14,5 to 15,5 oC)
Lecture 2
Chemical composition of the cell, tha main biogenic elements.
The bulk of cell’s mass is made up by water.
Water evaporates upon heating the cells, dry weight
remains.
Lecture 2
Chemical composition of the cell, tha main biogenic elements.
Carbon containing compounds are degraded to
CO2 and H2O by combustion, mineral compounds
(ash) remain
Lecture 2
Chemical composition of the cell, tha main biogenic elements.
Organic chemistry – chemistry of carbon
containing compounds.
Biochemistry – chemistry of life, composition of
and chemical reactions within the cells and
organisms.
Lecture 2
Chemical composition of the cell, tha main biogenic elements.
Element- – chemical substance which can not be
changed in CHEMICAL reactions.
Atom – the smallest crop of the element which still
retains it’s properties.
Compound – a substance which is made by different
(sometimes one) elements which are combined in
definite proportions.
The properties of the compound can not be deduced
from the properties of the involved elements (emergent
properties).
Lecture 2
Chemical composition of the cell, tha main biogenic elements.
Molecule – the smallest crop of the compound which still
retains it’s properties.
Molecules of the compounds that are typical for
life are made from long chains of carbon atoms.
Lecture 2
Chemical composition of the cell, tha main biogenic elements.
THE MAIN TYPES OF MACROMOLECULES THAT
MAKE UP THE LIFE
Lecture 2
Chemical composition of the cell, tha main biogenic elements.
THE MAIN TYPES OF MACROMOLECULES THAT
MAKE UP THE LIFE
Lecture 2
Chemical composition of the cell, tha main biogenic elements.
THE MAIN TYPES OF MACROMOLECULES THAT
MAKE UP THE LIFE
Lecture 2
Chemical composition of the cell, tha main biogenic elements.
THE MAIN TYPES OF MACROMOLECULES THAT
MAKE UP THE LIFE
Lecture 2
Chemical composition of the cell, tha main biogenic elements.
The concentration (%) of most important elements
(macroelements) in human body
Elements Symbols
%
Oxygen
O
65
Carbon
C
18
Hydrogen
H
10
Nitrogen
N
3
Calcium
Ca
1,5
Phosphorus
P
1,0
Sulphur
S
0,25
Lecture 2
Chemical composition of the cell, tha main biogenic elements.
Presentation of the main elements in the structural
formulae of biologic macromolecules
Chemical bounds (valencies)
Lecture 2
The principles of atomic structure.
Subatomic particles
Particle
Proton (p+)
Neutron (n0)
Electron (e-)
Relative
charge
+1
0
-1
Relative mass
1
1
1/1840
Protons + neutrons = nucleus of the atom
The electrons surround the nucleus in energy levels
or shells.
The principles of atomic structure.
Lecture 2
The size of an atom depends on the element.
The carbon atom has a diameter of 0.154 nanometres
(1 nm = 10-9 m). The size dimension of the nucleus is
10-14 m (10 femtometres; 1 fm = 10-15 m)
The principles of atomic structure.
Lecture 2
Atomic number – the number of protons or electrons of
the atom, its number in the periodic table.
Mass number of the atom ~ total number of protons
and neutrons in the nucleus.
Lecture 2
The principles of atomic structure.
13
14
6
6
6
6
7
8
12
13
14
6C
6C
98,9%
1,1 %
Traces
Half-time
of decay
6C
Frequency
nature
Mass
number
12
Neitron
number
Carbon
Proton
number
Element
Isotope
in
Isotopes
Different mass versions of the same element.
Stable
Stable
5730 y.
The principles of atomic structure.
Lecture 2
THE STRUCTURE OF THE ELECTRON SHELLS
The region where an electron may be found with a
certain probability is called the electron shell
The structure and placement of the electron shells
is characterised by four quantum numbers
The main quantum number n (1,2, 3…) determines
the energetic level of the electron, the maximal
number of the electrons in each shell (2n2) and
eventual number (=n) of energetic sub-levels
(s,p,d,f)
Shells and sub-levels are filled by electrons
consecutively, the lower levels are occupied first
The principles of atomic structure.
THE STRUCTURE OF THE ELECTRON SHELLS
Lecture 2
The principles of atomic structure.
THE STRUCTURE OF THE ELECTRON SHELLS
Lecture 2
The principles of atomic structure.
Lecture 2
The distribution of elestrons in the shells and
sub-levels of the carbon atom: 1s2; 2s2,2p2
Maximal number of the electrons in the second shell
(2n2) = 8
The principles of atomic structure.
Lecture 2
ATOMIC STRUCTURE OF BIOGENIC MACROELEMENTS
One energy level - hydrogen, 1H.
Two energy levels carbon, 6C; nitrogen,
7N; oxygen, 8O.
Three energy levels phosphorus, 15P;
sulphur, 16S.
Periodic Table and the elements that make up the Life
Lecture 2
Periodic Table and the elements that make up the Life
Lecture 2
Periodic Table and the elements that make up the Life
Lecture 2
Periodic Table and the elements that make up the Life
Lecture 2
92 elements are found in nature, still other 17
elements are synthesised in laboratories
(element # 109 – Meitnery).
Living objects are composed of 25 – 26
elements; another 10 – 15 elements may be
found within pharmacological ant toxic
substances.
Periodic Table and the elements that make up the Life
Sr
Lecture 2
Periodic Table and the elements that make up the Life
Element
Symbol
%
Potassium
K
0,2
Sodium
Na
0,15
Chlorine
Cl
0,15
Magnesium
Mg
0,05
Others
Lecture 2
0,75
Iron (Fe) – the most abundant microelement 0,0050 –
0,0075 % of the human body mass or 4 – 5 g within the
body of a person whose weight is 70 kg .
Periodic Table and the elements that make up the Life
Lecture 2
Approximate amounts of important microelements within
the 70 kg mass human body
Element
Iron
Symbol
Fe
Amount
4–5g
Tin
Zn
Copper
Cu
Manganese
Mn
Molybdenu
m
Cobalt
Mo
Role in the organism
Red-ox
reactions;
oxygen
transportation within erythrocytes
1,4 – 2,3 g Regulation of the growth and
development, synthesis of hormones
and proteins (hair, skin).
75 – 150
Oxidation reactions, biosynthesis of
mg
the skin pigment melanin
12 – 20 mg Formation of skin and mucous
layers, development of blood cells
5 – 9 mg Red-ox reactions at respiration
Co
1 – 1,5 mg
Chromium
Cr
0,6 – 1,4
mg
Metabolic processes, the component
of vitamin B12
Sugar turnover, action of insulin
eriodic Table and the elements that make up the Life
Lecture 2
Other important microelements:
lithium (Li)
selenium (Se)
fluorine (F)
iodine (I)
– regulation of nerve functions;
– protein biosynthesis, hair;
– development of bones and teeth;
– hormone biosynthesis, neural regulation.
Ultramicroelements:
arsine (As) and gold (Au) – regulation of growth and metabolism.
Chemical bond
Lecture 2
When forming chemical bonds,
atoms donate, acquire, or share
electrons.
Chemical bond : ionic bond
Lecture 2
Particles, which are formed
when atoms donate or acquire
electrons are called ions.
Lecture 2
Chemical bond : ionic bond
- e-
Atoms with sparsely filled outer electron shell will
donate the electrons easily.
Donation of electron, decrease of electronegativity
- oxidation.
Lecture 2
Chemical bond : ionic bond
+ e-
Atoms with nearly saturated outer electron shell
will acquire the electrons easily.
Acquisition of electron, increase of electronegativity
- reduction.
Chemical bond : ionic bond
The reactions of oxidation and
reduction are interconnected redox reactions.
The oxidant becomes reduced,
the reducing agent is oxidised.
Lecture 2
Chemical bond : ionic bond
Lecture 2
The electron from the
outer shell of sodium
atom is transferred to the
outer shell of the chlorine
atom.
The
number
of
the
electrons which can be
donated
or
accepted
determine the valence of
the atom.
Sodium and chlorine are
monovalent atoms.
Chemical bond : ionic bond
Lecture 2
In solid state the structure of the sodium chloride is
formed by electrostatic forces among oppositely
charged ions.
Electrostatic attraction between the oppositly
charged ions is ionic bond
Energy: 4 – 7 kcal/mole
Chemical bond : ionic bond
Lecture 2
Not only the atoms, also functional groups can
be ionised through donation or acceptance of
the proton.
Carboxyl group
Oxidised carboxyl group
Chemical bond : ionic bond
Amino group
Lecture 2
Reduced amino group
Chemical bond : ionic bond
Lecture 2
Ionised groups participate in the formation of the
secondary structure of the proteins