The Chemical Basis of Life Chapter 2 The Chemical Basis of Life Modified by C. Kerins

NATURE’S CHEMICAL LANGUAGE Chemicals play an important role in all organisms. Hormones send messages within an organism Other chemicals signal between organisms The rattlebox moth provides a good example of chemicals used in mating and defense.

Rattlebox Moth Froth found on moth is a noxious chemical that is distasteful to the spiders that prey on this moth. A male moth passes an extra dose of this defensive chemical to the female to supply additional protection for her and their offspring. Chemicals play many more roles in life than signaling…they are the very stuff making up our bodies, those of other organisms, and the physical environment.

2.1 ELEMENTS, ATOMS, AND MOLECULES At the base of the biological hierarchy are elements, atoms, and molecules. The properties of life emerge from the arrangement of its chemical parts into higher and higher levels of biological organization.

ELEMENTS, ATOMS, AND MOLECULES Living organisms are composed of about 25 chemical elements Elements are the basic chemical units that cannot be broken apart by typical chemical processes There are 92 naturally occurring elements 25 are required by living organisms 4 make up 96 % of the human body Oxygen, carbon, hydrogen, and nitrogen Main ingredients in biological molecules like proteins, carbohydrates, and lipids.

ELEMENTS, ATOMS, AND MOLECULES Other 4 % Calcium Phosphorus Potassium Sulfur Sodium Chlorine Magnesium These elements are involved in bone formation, nerve signaling, and DNA synthesis.

Trace elements are common additives to food and water Trace elements are essential in minute quantities for proper biological functioning Iodine is a trace element that prevents goiter. Many foods are fortified with trace elements and vitamins (which consist of two or more elements—they’re compounds…we’ll get there…).

TRACE ELEMENTS Fluoride is a form of fluorine added to water to reduce tooth decay Iron and other minerals are added to food to boost nutritional value

Elements can combine to form compounds Compounds contain two or more elements in a fixed ratio Different arrangements of the atoms of elements determine the unique properties of each compound The smallest unit of an element is an atom The physical and chemical properties of compounds are usually VERY different from those of their constituent atoms.

LE 2-3 Sodium Chlorine Sodium Chloride

Atoms consist of protons, neutrons, and electrons Subatomic particles Protons and neutrons occupy the central region (nucleus) of an atom—this is also where the mass of the atoms is located A proton has a positive charge A neutron is electrically neutral Electrons surround the nucleus An electron has a negative charge

Determining the number of P, N, and e- in an atom Differences in Elements All the atoms of a particular element have the same number of protons The atomic number (number of protons) defines the element's unique properties Atoms are neutral; therefore, the number of electrons is equal to the number of protons. An atom's mass number is the sum of its protons and neutrons Mass number – atomic number = # neutrons

LE 2-4a Electron cloud 6e– 2e– Nucleus 2 Protons 6 Protons Mass number = 4 Mass number = 12 2 Neutrons 6 Neutrons 2 Electrons 6 Electrons Helium atom Carbon atom

ISOTOPES Isotopes Isotopes are atoms with the same atomic number but different mass numbers (different number of neutrons) An element’s atomic mass is the weighted average of all of an element’s naturally occurring isotopes…usually NOT a whole number. ROUND the atomic mass to the nearest whole number and use it as the atom’s mass number.

Radioactive isotopes have nuclei that break down at a constant rate over time. They pose serious risk to living organisms They have many uses in biological research and medicine

Radioactive isotopes can help or harm us Radioactive isotopes are useful as tracers to study the fate of elements and molecules in living systems Radioactive tracer isotopes are often used in combination with sophisticated imaging instruments for medical diagnosis Uncontrolled exposure to radioactive material can harm living organisms

PET scanner

PET image of throat cancer

2.6 ELECTRON ARRANGMENTS IN ATOMS Electron arrangement determines the chemical properties of an atom Electrons in an atom are arranged in electron shells, which may contain different numbers of electrons The farther an electron is from the nucleus, the greater its energy. It is the number of electrons in the outermost shell (valence electrons) that determines the chemical properties of an atom.

Atoms want to have full or empty valence shells. 1st orbital holds two electrons 2nd orbital holds eight electrons 3rd orbital holds eight electrons Atoms form chemical bonds to complete their valence shells.

UNHAPPY ATOMS….  Atoms whose outer shells are not full share or transfer electrons to other atoms, forming molecules Two major types of chemical bonds between atoms form compounds Ionic bonds Covalent bonds

2.7 IONIC BONDS Ionic bonds are formed when one atom transfers one or more electrons to another atom. An ion is a charged atom that has lost or gained electrons in its outer shell A positively charged ion (cation) is an atom that has lost an electron A negatively charged ion (anion) is an atom that has gained an electron

Animation: Ionic Bonds SODIUM CHLORIDE An electrical attraction between ions with opposite charges results in an ionic bond Example: sodium chloride (table salt) results from an ionic bond between sodium and chlorine Animation: Ionic Bonds

Na Sodium atom Cl Chlorine atom LE 2-7a-1 Transfer of electron Na Sodium atom Cl Chlorine atom

Sodium chloride (NaCl) LE 2-7a-2 Note that the overall charge on the MOLECULE is neutral! Na+ Sodium ion Cl- Chloride ion Sodium chloride (NaCl)

LE 2-7b Na+ Cl-

Animation: Covalent Bonds Covalent bonds join atoms into molecules through sharing one or more PAIRS of electrons Covalently bonded atoms share one or more pairs of outer shell electrons, forming a molecule In a double bond, two pairs of electrons are shared…in a triple bond, three pairs of electrons are shared Covalent bonds can be represented in various ways Animation: Covalent Bonds

Unequal electron sharing creates polar molecules A molecule whose covalently bonded atoms share electrons equally is nonpolar (fats, oils, and waxes) A molecule whose covalently bonded atoms share electrons unequally is polar One part of the molecule is slightly positive, and one part is slightly negative… …like our friend water!

Polar Molecules Atoms in a covalently bonded molecule are in a constant tug-of-war for the shared electrons of their covalent bond. An atom’s attraction for its electrons, including shared electrons, is called its electronegativity. The more electronegative an atom, the more strongly it pulls shared electrons toward its nucleus.

Electronegativity Electronegativity increases as you move from left to right on the periodic table. Electronegativity decreases as you move down the periodic table.

LE 2-9 A water molecule

Hydrogen bonds are weak bonds important in the chemistry of life The attraction between slightly positive regions (hydrogen atoms) and slightly negative regions of polar molecules creates hydrogen bonds Hydrogen bonding occurs in many biologically important compounds Water DNA Proteins

LE 2-10 Hydrogen bond

2.11 Water’s Life-Supporting Properties Hydrogen bonds make liquid water cohesive Cohesion is the tendency of molecules to stick together Surface tension results from the cohesion of water molecules Animation: Water Transport

2.12 Water's hydrogen bonds moderate temperature When water is heated, the heat energy is absorbed, disrupting hydrogen bonds The water stores a large amount of heat while warming only a few degrees When water is cooled, heat energy is released as hydrogen bonds are formed The temperature of the water is lowered slowly

Water also moderates temperature by evaporative cooling The surface cools as the hottest molecules leave

2.13 Ice is less dense than liquid water Hydrogen bonds in ice create a stable, three-dimensional structure Ice is less dense than water, because it has fewer molecules in the same volume

Hydrogen bonds are stable constantly break and re-form Ice Liquid water Hydrogen bonds are stable Hydrogen bonds constantly break and re-form

2.14 Water is the solvent of life A solution is a homogeneous mixture of a liquid solvent and one or more dissolved solutes Because water is a polar molecule, it readily forms solutions with many other polar and ionic compounds A solution in which water is the solvent is an aqueous solution

LE 2-14 Ion in solution Salt crystal

2.15 The chemistry of life is sensitive to acidic and basic conditions A compound that releases H+ ions in solution is an acid A compound that accepts H+ ions in solution is a base Acidity is measured on the pH scale from 0 (most acidic) to 14 (most basic) The pH of most cells is kept close to 7 (neutral) by buffers that resist pH change

(Higher concentration of H+) (Lower concentration of H+) LE 2-15 pH scale H+ H+ OH H+ H+ Lemon juice, gastric juice OH H+ H+ H+ H+ Grapefruit juice, soft drink (Higher concentration of H+) Increasingly ACIDIC Acidic solution Tomato juice Human urine OH OH NEUTRAL [HOH-] Pure water H+ H+ OH OH OH Human blood H+ H+ H+ Seawater Neutral solution (Lower concentration of H+) Increasingly BASIC Milk of magnesia Household ammonia OH OH OH H+ OH Household bleach OH OH H+ Oven cleaner Basic solution

2.16 Acid precipitation threatens the environment CONNECTION 2.16 Acid precipitation threatens the environment Acid precipitation is formed when air pollutants from burning fossil fuels combine with water vapor in the air to form sulfuric and nitric acids Some ecosystems and structures are threatened by acid precipitation

2.17 Chemical reactions change the composition of matter In a chemical reaction, reactants interact, leading to products Atoms are rearranged, but the number of atoms stays constant on both sides of the equation

LE 2-17a + 2 H2 + O2 2 H2O

Living cells carry out thousands of chemical reactions that rearrange matter in significant ways

LE 2-17b Beta-carotene Vitamin A (2 molecules)