THE CHEMISTRY OF LIFE I: ATOMS, MOLECULES, AND BONDS BIO 2, Lecture 3 THE CHEMISTRY OF LIFE I: ATOMS, MOLECULES, AND BONDS  – + H O H2O

Matter is made up of elements A substance that cannot be broken down to other substances by chemical reactions 92 naturally-occurring elements (periodic table) A compound is a substance consisting of two or more elements in a fixed ratio (e.g. NaCl, MgCl2) A compound has characteristics different from those of its elements

Sodium Chloride Sodium Chloride

About 25 of the 92 naturally-occurring elements are essential to living organisms on Earth

Dwarfing of plants due to nitrogen deficiency Goiter due to iodine deficiency

Each element consists of unique atoms An element’s chemical behavior and properties depend on the structure of its atoms Each element consists of unique atoms An atom is the smallest unit of matter that still contains the behavior and properties of an element Atoms are composed of a nucleus containing protons (+) and (usually) neutrons, and electrons (-) that inhabit defined energy shells around the nucleus

Cloud of negative charge (2 electrons) Nucleus Electrons (b) (a) Figure 2.5 Simplified models of a helium (He) atom

Atoms of the various elements differ in number of subatomic particles they contain An element’s atomic number is the number of protons in its nucleus An element’s mass number is the sum of protons plus neutrons in the nucleus Atomic mass, the atom’s total mass, can be approximated by the mass number (since electrons are so light)

All atoms of an element have the same number of protons but may differ in number of neutrons Isotopes are two atoms of an element that differ in number of neutrons Radioactive isotopes decay spontaneously, giving off particles and energy

Isotopes of hydrogen: 1H Protium 1 0 Stable 2H Deuterium 1 1 Stable Symbol Name # protons # neutrons Half-life 1H Protium 1 0 Stable 2H Deuterium 1 1 Stable 3H Tritium 1 2 12.3 yrs 4H Lab only 1 3 Very low* 5H Lab only 1 4 Very low* 6H Lab only 1 5 Very low* 7H Lab only 1 6 Very low* * less than 10-22 seconds

Some applications of radioactive isotopes in biological research are: Dating rocks and fossils Tracing atoms through metabolic processes to learn about those processes Diagnosing medical disorders

Stable Daughter Product Currently Accepted Half-Life Values Parent Isotope Stable Daughter Product Currently Accepted Half-Life Values Uranium-238 Lead-206 4.5 billion years Uranium-235 Lead-207 704 million years Thorium-232 Lead-208 14.0 billion years Rubidium-87 Strontium-87 48.8 billion years Potassium-40 Argon-40 1.25 billion years

Compounds including radioactive tracer (bright blue) Human cells Incubators 1 2 3 4 5 6 7 8 9 50ºC 45ºC 40ºC 25ºC 30ºC 35ºC 15ºC 20ºC 10ºC Human cells are incubated with compounds used to make DNA. One compound is labeled with 3H. The cells are placed in test tubes; their DNA is isolated; and unused labeled compounds are removed. DNA (old and new) Figure 2.6 Radioactive tracers

3 The test tubes are placed in a scintillation counter. Figure 2.6 Radioactive tracers 3 The test tubes are placed in a scintillation counter.

Counts per minute ( 1,000) Temperature (ºC) 10 20 30 40 50 Temperature (ºC) Optimum temperature for DNA synthesis Figure 2.6 Radioactive tracers

Cancerous throat tissue

Energy is the capacity to do work (fight entropy) Atoms have mass and therefore have potential energy; E = mc2 Part of this energy is stored in the nucleus of the atom and part is stored in the energy levels of the electrons An electron’s state of potential energy is called its energy level, or electron shell

(a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons Third shell (highest energy level) Second shell (higher energy level) Energy absorbed First shell (lowest energy level) Atomic nucleus (b) lost Figure 2.8 Energy levels of an atom’s electrons

The chemical behavior of an atom is determined by the distribution of electrons in electron shells The periodic table of the elements shows the electron distribution for each element Valence electrons are those in the outermost shell, or valence shell Elements with filled valence shells are inherently stable and don’t readily combine with other elements

1H 2He 3Li 4Be 5B 6C 7N 8O 9F 10Ne 11Na 12Mg 13Al 14Si 15P 16S 17Cl Hydrogen 1H 2 Atomic number Helium 2He He Atomic mass 4.00 First shell Element symbol Electron- distribution diagram Lithium 3Li Beryllium 4Be Boron 5B Carbon 6C Nitrogen 7N Oxygen 8O Fluorine 9F Neon 10Ne Second shell Sodium 11Na Magnesium 12Mg Aluminum 13Al Silicon 14Si Phosphorus 15P Sulfur 16S Chlorine 17Cl Argon 18Ar Figure 2.9 Electron-distribution diagrams for the first 18 elements in the periodic table Third shell

Each electron shell consists of a specific number of orbitals An orbital is the three-dimensional space where an electron is found 90% of the time Each electron shell consists of a specific number of orbitals 1S (1 orbital; 2 electrons) 2S (1 orbital; 2 electrons) 2P (3 different oribitals; 6 electrons) The shell is designated by the number, the orbitals by the letter Atoms seek filled shells above all else

Electron-distribution diagram (a) Separate electron orbitals Neon, with two filled shells (10 electrons) First shell Second shell 1s orbital 2s orbital Three 2p orbitals (c) Superimposed electron 1s, 2s, and 2p orbitals x y z Figure 2.10 Electron orbitals

Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms These interactions usually result in atoms staying close together, held by attractions called chemical bonds A covalent bond is the sharing of a pair of valence electrons by two atoms In a covalent bond, the shared electrons count as part of each atom’s valence shell

e- Hydrogen atoms (2 H) Both atoms unstable (unfilled valence shells) molecule (H2) e- Both atoms unstable (unfilled valence shells) Atoms stable, share electrons so both have filled valence shells Figure 2.11 Formation of a covalent bond

A molecule consists of two or more atoms held together by covalent bonds A single covalent bond, or single bond, is the sharing of one pair of valence electrons A double covalent bond, or double bond, is the sharing of two pairs of valence electrons

COVALENT BONDS Name and Molecular Formula Electron- distribution Diagram Lewis Dot Structure and Structural Space- filling Model (a) Hydrogen (H2) (b) Oxygen (O2) (c) Water (H2O) (d) Methane (CH4) COVALENT BONDS Figure 2.12 Covalent bonding in four molecules

Covalent bonds can form between atoms of the same element or atoms of different elements A compound is a combination of two or more different elements Bonding capacity is called the atom’s valence

Electronegativity is an atom’s attraction for the electrons in a covalent bond The more electronegative an atom, the more strongly it pulls shared electrons toward itself In a nonpolar covalent bond, the atoms share the electron equally In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally

Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule (e.g. water)  – + H O H2O The oxygen nucleus has more protons and attracts the shared electrons more strongly than the hydrogen nuclei

An example is the transfer of an electron from sodium to chlorine Rather than sharing electrons, atoms sometimes transfer electrons to their bonding partners because it fills their valence shells (makes them stable) An example is the transfer of an electron from sodium to chlorine After the transfer of an electron, both atoms have charges A charged atom (or molecule) is called an ion Ions with opposite charges attract to form ionic bonds

IONIC BOND Na Cl Sodium atom Chlorine atom Na+ Sodium ion (a cation) Chloride ion (an anion) Sodium chloride (NaCl) Figure 2.14 Electron transfer and ionic bonding IONIC BOND

Compounds formed by ionic bonds are called ionic compounds, or salts Salts, such as sodium chloride (table salt), are often found in nature as crystals because they stack easily Na+ Cl–

Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules Weak chemical bonds, such as ionic bonds and hydrogen bonds, are also important Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other

A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom In living cells, the electronegative partners are usually oxygen or nitrogen atoms Hydrogen bonding is important in water, DNA and RNA, proteins, and many other molecules important for life

HYDROGEN BOND   Water (H2O) Ammonia (NH3) + Figure 2.16 A hydrogen bond