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

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

Measuring units in Biology. Lecture 2

Constants 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 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 particles. Measuring units in Biology Lecture 2

6,02 x = the Avogadro number, chemical constant; the number of atoms which make up 12 grams of carbon. 22,4 liters = molar volume of gases, the volume, which is filled by a mole of every gaseous molecule or atom. Amadeus Avogadro ( ) – an italian chemist, who made an observation that gases react with each other in definite volume proportions. 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 0 o C = 32 o F; 100 o C = 212 o F F = (9/5 x C) Human body temperature in F degrees = 98,6 o Measuring units in Biology. Lecture 2

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 o C) Measuring units in Biology.

The bulk of cell’s mass is made up by water. Water evaporates upon heating the cells, dry weight remains. Chemical composition of the cell, tha main biogenic elements. Lecture 2

Carbon containing compounds are degraded to CO 2 and H 2 O by combustion, mineral compounds (ash) remain Chemical composition of the cell, tha main biogenic elements. Lecture 2

Organic chemistry – chemistry of carbon containing compounds. Biochemistry – chemistry of life, composition of and chemical reactions within the cells and organisms. Chemical composition of the cell, tha main biogenic elements. Lecture 2

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). Chemical composition of the cell, tha main biogenic elements. Lecture 2

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. Chemical composition of the cell, tha main biogenic elements. Lecture 2

THE MAIN TYPES OF MACROMOLECULES THAT MAKE UP THE LIFE Chemical composition of the cell, tha main biogenic elements. Lecture 2

Chemical composition of the cell, tha main biogenic elements. Lecture 2 THE MAIN TYPES OF MACROMOLECULES THAT MAKE UP THE LIFE

Chemical composition of the cell, tha main biogenic elements. Lecture 2 THE MAIN TYPES OF MACROMOLECULES THAT MAKE UP THE LIFE

Chemical composition of the cell, tha main biogenic elements. Lecture 2 THE MAIN TYPES OF MACROMOLECULES THAT MAKE UP THE LIFE

The concentration (%) of most important elements (macroelements) in human body Chemical composition of the cell, tha main biogenic elements. Lecture 2

Presentation of the main elements in the structural formulae of biologic macromolecules Chemical bounds (valencies) Chemical composition of the cell, tha main biogenic elements. 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. Lecture 2

The size of an atom depends on the element. The carbon atom has a diameter of nanometres (1 nm = m). The size dimension of the nucleus is m (10 femtometres; 1 fm = 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. The principles of atomic structure. Lecture 2

Isotopes Different mass versions of the same element. The principles of atomic structure. Lecture 2

THE STRUCTURE OF THE ELECTRON SHELLS Shells and sub-levels are filled by electrons consecutively, the lower levels are occupied first The principles of atomic structure. Lecture 2 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 (2n 2 ) and eventual number (=n) of energetic sub-levels (s,p,d,f)

THE STRUCTURE OF THE ELECTRON SHELLS The principles of atomic structure. Lecture 2

THE STRUCTURE OF THE ELECTRON SHELLS 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 (2n 2 ) = 8 The principles of atomic structure. Lecture 2

ATOMIC STRUCTURE OF BIOGENIC MACROELEMENTS One energy level - hydrogen, 1 H. Two energy levels - carbon, 6 C; nitrogen, 7 N; oxygen, 8 O. Three energy levels - phosphorus, 15 P; sulphur, 16 S. The principles of atomic structure. 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

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 Lecture 2 92 elements are found in nature, still other 17 elements are synthesised in laboratories (element # 109 – Meitnery).

Periodic Table and the elements that make up the Life Lecture 2 Sr

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 Periodic Table and the elements that make up the Life Lecture 2

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. Ultramicroelements: arsine (As) and gold (Au) – regulation of growth and metabolism. Periodic Table and the elements that make up the Life Lecture 2

Chemical bond When forming chemical bonds, atoms donate, acquire, or share electrons. Lecture 2

Chemical bond : ionic bond Particles, which are formed when atoms donate or acquire electrons are called ions. Lecture 2

Chemical bond : ionic bond Lecture 2 - e - Atoms with sparsely filled outer electron shell will donate the electrons easily. Donation of electron, decrease of electronegativity - oxidation.

Chemical bond : ionic bond Lecture 2 + e - Atoms with nearly saturated outer electron shell will acquire the electrons easily. Acquisition of electron, increase of electronegativity - reduction.

Chemical bond : ionic bond Lecture 2 The reactions of oxidation and reduction are interconnected - redox reactions. The oxidant becomes reduced, the reducing agent is oxidised.

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

Amino group Reduced amino group Chemical bond : ionic bond Lecture 2

Ionised groups participate in the formation of the secondary structure of the proteins Chemical bond : ionic bond Lecture 2