Chapter 2, page: Atoms and Molecules: The Chemical Basis of Life Csaba Bödör,

Carbon (C), hydrogen (H), oxygen (O), nitrogen (N) are responsible for more than 96% of the mass of most organisms.

ELEMENTS are substances that can not be broken down into simpler substances by normal chemical reactions each element has a chemical symbol (C: carbon, O: oxygen) Carbon (C), hydrogen (H), oxygen (O), nitrogen (N) are responsible for more than 96% of the mass of most organisms. Others also important in smaller quantities (sodium, potassium, calcium, phosphorus) 92 naturally occurring elements Trace elements: needed in a very small amount (iodine, copper)

Function of elements in organisms

ELEMENTS > ATOMS atom: is the smallest portion of an element that retains it chemical properties subatomic particles: electron (e - ): carries a negative charge neutron (n): is an uncharged particle proton (p + ): carries a positive charge protons + neutrons > atomic nucleus electrons move rapidly in orbitals In a neutral atom: numer of e - and p + is equal

ATOMS an atom is identified by its number of protons > known as atomic number ( 1 H, 8 O) elements are arranged in the periodic table in order by atomic number protons and neutrons determines atomic mass the mass (weight) of subatomic particles is exceedingly small Special units: atomic mass unit also known as Dalton The mass of electrons is ignored, its too small 8 O 16 1 H 1

1 ATOMS most elements consists of a mixture of isotopes Isotopes are different forms of atoms of the same element contain the same number of electrons and protons, but the number of neutrons varies 1 H 2 3 Hydrogen, Deuterium, Tritium Carbon Isotopes 6 C6 C C6 C 1414 radioisotopes break down and emit radiation research, diagnostics

Autoradiography

Electrons move in orbitals orbitals: specific 3D regions around the atomic nucleus each orbital contains maximum of 2 electrons electrons in orbitals with similar energies are at the same principal energy level, they make up an electron shell 1 st energy level 2 nd energy level 2 e -

Electrons move in orbitals max 8 e - max.2 e - Bohr-models

Electrons move in orbitals electrons distant from the nucleus have greater energy most energetic electrons are the valence electrons on valence shell valence shell is represented as the outermost concentric ring Valency: the power of an atom to combine with others changes in electron energy levels are important (up and down)

Chemical reactions chemical behavior of an atom is determined by the number of valence electrons the valence shell of most atoms is full when is contains 8 electrons when it is not full, the atom tends to loss, gain or share electrons in order to achieve the full outer shell. Noble gas full outer shell (8e - ) unreactive Valence shell full when contains 2 e - basis for chemical reactions !!!

Chemical reactions Atoms form compounds and molecules Compound: consists of atoms of two or more different elements combined in a fixed ratio (example: H 2 O, NaCl) Molecule: two or more atoms joined strongly, a stable particle (example: H 2, O 2 ) Molecular mass: sum of the atomic masses of component atoms Molecular mass of water and sodium chloride (glucose) ? Molecular or atomic mass can be converted to grams > mole Atomic mass of oxygen: 16 amu Molecular mass of water: 18 amu 1 mole of any substance contains the same number of units (atoms/molecules) (6,022 x units – Avogadro’s number) 1 mole of oxygen = 16 grams 1 mole of water = 18 grams

Chemical reactions … are described by chemical equations CO 2 + H 2 O H 2 CO 3 REACTANTSPRODUCTS Carbon-dioxidewaterCarbonic acid C 6 H 12 O O 2 6 CO H 2 O + energy Quantitatively precise way !!!

Chemical bonds are forces of attraction that hold atoms of a compound together Bond energy: the energy necessary to break a chemical bond 2 basic types of strong chemical bonds: covalent and ionic bonds In covalent bonds electrons are shared Each atom has a full valence shell Example: Hydrogen gas molecule (H 2 ) Single bond: when one pair of electrons is shared

Covalent bonds Oxygen gas molecule (O 2 ) Double bond: when two pairs of electrons are shared Triple bond: when three pairs of electrons are shared : ? Why are the electrons shared? H 2 O, CH 4, NH 3 Lewis structure, Structural formula

Shape of molecules Molecules that consist of two atoms are linear

Shape of molecules Molecules composed of more than 2 atoms have more complicated geometry (3D structure) (optimal distance) Methane CH 4

Polar and Nonpolar bonds Electronegativity: a measure of an atom’s attraction for shared electrons in covalent bonds Nonpolar bonds: atoms with similar electronegativity bonded together Electrons are shared equally Polar bonds: between atoms that differ in electronegativity

Polar and Nonpolar bonds Very electronegative elements: Oxygen, Fluorine, Chlorine, Nitrogen CO 2 One end with partially positive charge, one end with partially negative charge H2OH2O

Ionic bonds Ion: particle with one or more units of electric charge Cation: positively charged ion Anion: negatively charged ion lose or gain of electrons Cl and Cl - Na, K, Ca Important in many biological processes such as muscle contraction, neural signal transmission

Ionic bonds … are formed due to an attraction between a cation and an anion Ionic compounds: cations and anions bonded together NaCl: sodium chloride Na: electron donor Cl: electron acceptor Electron completely transferred from Na to Cl

Ionic bonds Are strong in the absence of water Compounds joined by ionic bonds have the tendency to dissociate (separate) into their components, when placed in water in H 2 O Water in an excellent solvent: many substances can be dissolved in water, > A dissolved substance is referred to as a solute See figure 2-10 in the book hydration

COVALENT and IONIC BONDS

Hydrogen bonds … are WEAK interactions !!!, very important in organisms … are formed between an atom with partial negative charge and a hydrogen covalently bonded to oxygen or nitrogen easy to form and break them individually weak Important role in the structure of proteins and nucleic acids (Chapter 3)

Hydrogen bonds

van der Waals interactions weak, transient interactions (not „real” bonds)

REDOX reactions Redox reactions: reduction and oxidation Redox reactions involve electron transfer Important in energy conversion in cells Oxidation: chemical process in which atom, ion or molecule loses electrons Reduction: chemical process in which atom, ion or molecule gains electrons Reduction and Oxidation occur simultaneously

ACIDS, BASES and SALTS Water has a slight tendency to ionize (dissociate) H 2 O H + OH - Hydroxide ion Concentration of H + and OH - in pure water are equal (10 -7 mol/liter) Such a solution is said to be neutral Acid is a substance that dissociates in a solution into H + and an anion Acid H + + anion An acid is a proton donor HCl H + + Cl - Base is a substance that dissociates in a solution into OH - and a cation NaOH Na + + OH - A base is defined as proton acceptor OH - + H + H 2 O pH: measure of acidity, pH= -log 10 (H + ) pure water = 7

ACIDS, BASES and SALTS Neutral solution: pH=7 Acidic solution: pH < 7 Base solution pH > 7 Acid H + + anion HCl H + + Cl - NaOH Na + + OH - OH - + H + H 2 O An acid and a base react to form a salt plus water HCl + NaOH NaCl + H 2 O Salt is a compound in which the H + ion is replaced by some other cation

Logarithmic scale