STRUCTURE OF ATOMS, PERIODIC TABLE OF ELEMENTS

1
BASIC CELL BIOLOGY
I CHEMISTRY of LIFE
STRUCTURE OF ATOMS, PERIODIC TABLE OF ELEMENTS
2
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

3
Lecture 2
Measuring units in Biology.
4
Lecture 2
Measuring units in Biology.
5
Measuring units in Biology
Lecture 2
Constants
6
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.
7
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.
8
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 ht
tp//ask.yahoo.com/ask/19991123.html
9
Lecture 2
Measuring units in Biology.
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
10
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)
11
Lecture 2
Chemical composition of the cell, tha main
biogenic elements.
The bulk of cells mass is made up by water.
Water evaporates upon heating the cells, dry
weight remains.
12
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
13
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.
14
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 its 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).
15
Lecture 2
Chemical composition of the cell, tha main
biogenic elements.
Molecule the smallest crop of the compound
which still retains its properties.
Molecules of the compounds that are typical for
life are made from long chains of carbon atoms.
16
Lecture 2
Chemical composition of the cell, tha main
biogenic elements.
THE MAIN TYPES OF MACROMOLECULES THAT MAKE UP THE
LIFE
17
Lecture 2
Chemical composition of the cell, tha main
biogenic elements.
THE MAIN TYPES OF MACROMOLECULES THAT MAKE UP THE
LIFE
18
Lecture 2
Chemical composition of the cell, tha main
biogenic elements.
THE MAIN TYPES OF MACROMOLECULES THAT MAKE UP THE
LIFE
19
Lecture 2
Chemical composition of the cell, tha main
biogenic elements.
THE MAIN TYPES OF MACROMOLECULES THAT MAKE UP THE
LIFE
20
Lecture 2
Chemical composition of the cell, tha main
biogenic elements.
The concentration () of most important elements
(macroelements) in human body
21
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)
22
Lecture 2
The principles of atomic structure.
Subatomic particles
Protons neutrons nucleus of the atom The
electrons surround the nucleus in energy levels
or shells.
23
Lecture 2
The principles of atomic structure.
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)
24
Lecture 2
The principles of atomic structure.
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.
25
Lecture 2
The principles of atomic structure.
Isotopes Different mass versions of the same
element.
26
Lecture 2
The principles of atomic structure.
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
27
Lecture 2
The principles of atomic structure.
THE STRUCTURE OF THE ELECTRON SHELLS
28
Lecture 2
The principles of atomic structure.
THE STRUCTURE OF THE ELECTRON SHELLS
29
Lecture 2
The principles of atomic structure.
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
30
Lecture 2
The principles of atomic structure.
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.
31
Lecture 2
Periodic Table and the elements that make up the
Life
32
Lecture 2
Periodic Table and the elements that make up the
Life
33
Lecture 2
Periodic Table and the elements that make up the
Life
34
Lecture 2
Periodic Table and the elements that make up the
Life
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.
35
Lecture 2
Periodic Table and the elements that make up the
Life
Sr
36
Lecture 2
Periodic Table and the elements that make up the
Life
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
.
37
Lecture 2
Periodic Table and the elements that make up the
Life
Approximate amounts of important microelements
within the 70 kg mass human body
38
Lecture 2
Periodic Table and the elements that make up the
Life
Other important microelements lithium (Li)
regulation of nerve functions selenium (Se)
protein biosynthesis, hair fluorine (F)
development of bones and teeth iodine (I)
hormone biosynthesis, neural regulation. Ultramic
roelements arsine (As) and gold (Au)
regulation of growth and metabolism.
39
Lecture 2
Chemical bond
When forming chemical bonds, atoms donate,
acquire, or share electrons.
40
Lecture 2
Chemical bond ionic bond
Particles, which are formed when atoms donate or
acquire electrons are called ions.
41
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.
42
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.
43
Lecture 2
Chemical bond ionic bond
The reactions of oxidation and reduction are
interconnected - redox reactions. The oxidant
becomes reduced, the reducing agent is oxidised.
44
Lecture 2
Chemical bond ionic bond
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.
45
Lecture 2
Chemical bond ionic bond
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
46
Lecture 2
Chemical bond ionic bond
Not only the atoms, also functional groups can be
ionised through donation or acceptance of the
proton.
Carboxyl group Oxidised carboxyl group
47
Lecture 2
Chemical bond ionic bond
Amino group Reduced amino group
48
Lecture 2
Chemical bond ionic bond
Ionised groups participate in the formation of
the secondary structure of the proteins