2

Small Molecules and the Chemistry of Life

2 Small Molecules and The Chemistry of Life

2.1 How Does Atomic Structure Explain the Properties of Matter? 2.2 How Do Atoms Bond to Form Molecules?

2.3 How Do Atoms Change Partners in Chemical Reactions? 2.4 What Makes Water So Important for Life?

2.1 How Does Atomic Structure Explain the Properties of Matter?

All matter is composed of atoms An Atom is composed of three types of particles Electronsnegligible mass; negative charge Protonshave mass; positive charge Neutronshave mass; no charge

2.1 How Does Atomic Structure Explain the Properties of Matter?

Neutrons and protons packed together in dense core Atomic Nucleus

Electrons located in a cloud or shell around the nucleus attracted to nucleus by positively charged protons

Figure 2.1 The Helium Atom

2.1 How Does Atomic Structure Explain the Properties of Matter?

Atoms have volume and mass. Mass of one proton or one neutron = 1 atomic mass unit (amu) or 1 dalton, or 1.7 1024 grams.

Mass of one electron = 9 1028 (usually ignored).

2.1 How Does Atomic Structure Explain the Properties of Matter?

Element: pure substance containing only one kind of atom. Elements are arranged in the periodic table. Each element has a unique chemical symbol.

2.1 How Does Atomic Structure Explain the Properties of Matter?

Each element has a unique chemical symbol. Symbol is usually 1 or 2 letters of its name (may be derived from Latin or German)
H = Hydrogen He = Helium Na = Sodium (Natrium) Fe = Iron (Ferrum)

Figure 2.2 The Periodic Table (Part 1)

2.1 How Does Atomic Structure Explain the Properties of Matter?

About 98% of every living organism is composed of 6 elements: Carbon, Hydrogen, Oxygen, Nitrogen, sulfur, and phosphorus

Figure 2.2 The Periodic Table (Part 2)

He from periodic table here

2.1 How Does Atomic Structure Explain the Properties of Matter?

The number of protons identifies an element Number of protons = atomic number. Written as a subscript to left of chemical symbol 2He, 8O, 16S, 26Fe, 11Na

Number of protons and electrons are generally the same an atom is electrically neutral

2.1 How Does Atomic Structure Explain the Properties of Matter?

All elements except hydrogen have one or more neutrons. Mass number = number of protons + number of neutrons. Mass number = mass of atom in daltons. Written as a superscript to left of

chemical symbol - 4He, 55Fe, 23 Na

16O,

32S,

2.1 How Does Atomic Structure Explain the Properties of Matter?

Number of Neutrons Mass number - Atomic Number = Number of neutrons

2.1 How Does Atomic Structure Explain the Properties of Matter?

Isotopes: forms of an element with different numbers of neutrons, and thus different mass numbers. Example:
12C 13C 14C

has 6 neutrons
has 7 neutrons

has 8 neutrons

2.1 How Does Atomic Structure Explain the Properties of Matter?

Isotopes of some elements, such as hydrogen, have special names.

2.1 How Does Atomic Structure Explain the Properties of Matter?

Atomic weight: average of mass numbers of isotopes in their normally occurring proportions.

Atomic weight of carbon = 12.011 Atomic weight of hydrogen = 1.0079

2.1 How Does Atomic Structure Explain the Properties of Matter?

Some isotopes are unstable: Radioisotopes give off energy in the form of alpha, beta, and gamma radiation from the nucleus.

This radioactive decay transforms the atom, including changes in the number of protons.

2.1 How Does Atomic Structure Explain the Properties of Matter?

The released radiation can be used to detect the presence of radioisotopes. Radioisotopes can be incorporated into molecules to act as a tag or label.

Figure 2.3 Tagging the Brain

Positron Emission Tomography or PET scan

2.1 How Does Atomic Structure Explain the Properties of Matter?

Radioisotopes are useful in research and in medicine, but radiation can damage cells and tissues. It is sometimes used to treat cancer.

2.1 How Does Atomic Structure Explain the Properties of Matter?

The number and location of electrons determines how atoms will interact. Chemical reactions involve changes in the distribution of electrons between atoms.

2.1 How Does Atomic Structure Explain the Properties of Matter?

Locations of electrons in an atom are described by orbitals. Orbital: region where electron is found at least 90% of the time.

Orbitals have characteristic shapes and orientations, and can be occupied by a maximum of two electrons.
Orbitals are filled in a specific sequence.

Figure 2.4 Electron Shells and Orbitals

2.1 How Does Atomic Structure Explain the Properties of Matter?

Orbitals occur in a series called electron shells or energy levels. First shell: one s orbital (holds 2 electrons) Second shell: 1 s and 3 p orbitals (holds 8 electrons) Additional shells: 4 orbitals (8 electrons)

2.1 How Does Atomic Structure Explain the Properties of Matter?

The further a shell is from the nucleus, the higher the energy level is for an electron occupying that shell

Figure 2.5 Electron Shells Determine the Reactivity of Atoms

2.1 How Does Atomic Structure Explain the Properties of Matter?

The outermost electron shell (valence shell) determines how the atom behaves. If the outermost shell is full, the atom is stable; it wont react with other atoms. Examples: helium, argon and neon Reactive atoms have unpaired electrons in their outermost shell.

2.1 How Does Atomic Structure Explain the Properties of Matter?

Atoms can share electrons, or lose or gain electrons, resulting in atoms bonded together to form molecules. Octet rule: the tendency of atoms to form stable molecules so that they have eight electrons in their outermost shells (however, hydrogen attains stability when 2 electrons are in its single shell)

2.2 How Do Atoms Bond to Form Molecules?

Chemical bond: attractive force that links atoms together to form molecules. There are several kinds of chemical bonds.

2.2 How Do Atoms Bond to Form Molecules?

Covalent bonds: atoms share one or more pairs of electrons, so that the outer shells are filled.

Figure 2.6 Electrons Are Shared in Covalent Bonds

2.2 How Do Atoms Bond to Form Molecules?

Compound: a molecule made up of two or more elements bonded together in a fixed ratio. Examples: Water: H2O = 2 Hydrogen : 1 Oxygen
Table salt: NaCl = 1 Sodium : 1 Chlorine

The molecular weight of a compound is the sum of the atomic weights of all atoms in the molecule.

2.2 How Do Atoms Bond to Form Molecules?

Organic Chemistry Study of carbon compounds Great variety of different compounds Versatility of carbon Atomic number = 6 Six protons and six electrons 4 valence electrons Forms 4 covalent bonds Arrangement of bonds is a tetrahedral shape

Figure 2.7 Covalent Bonding Can Form Compounds

Carbon can form four covalent bonds.

2.2 How Do Atoms Bond to Form Molecules?

Carbon forms bonds with several elements

Hydrogen (valence = 1) Oxygen (valence = 2) O Nitrogen (valence = 3) Carbon (valence = 4) C

Carbon can form single, double, and even triple bonds with other atoms IF they have the electrons to share

2.2 How Do Atoms Bond to Form Molecules?

Covalent bonds are very stronga lot of energy is required to break them. At temperatures in which life exists, the covalent bonds of biological molecules are quite stable, but this does not preclude change.

2.2 How Do Atoms Bond to Form Molecules?

Orientation of bonds: The length, angle, and direction of bonds between any two elements are always the same. Example: Methane always forms a tetrahedron.

methane tetrahedron here

2.2 How Do Atoms Bond to Form Molecules?

The shapes of three simple organic molecules

Name (a) Methane Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model

(b) Ethane

(c) Ethene (ethylene)

2.2 How Do Atoms Bond to Form Molecules?

Covalent bonds can be Singlesharing 1 pair of electrons C H Doublesharing 2 pairs of electrons C C

Triplesharing 3 pairs of electrons

N N

2.2 How Do Atoms Bond to Form Molecules?

Sharing of electrons in a covalent bond is not always equal. Electronegativity: the attractive force that an atomic nucleus exerts on electrons. It depends on the number of protons and the distance between the nucleus and electrons.

2.2 How Do Atoms Bond to Form Molecules?

A polar covalent bond results when electrons are drawn to one nucleus more than to the other, because one atom has more electronegativity.

Figure 2.8 Waters Covalent Bonds Are Polar

2.2 How Do Atoms Bond to Form Molecules?

Because of this unequal sharing, the bond has a slight negative charge on one end and a slight positive charge on the other. The bond is said to be polar and produce polar molecules or polar regions of large molecules.

2.2 How Do Atoms Bond to Form Molecules?

A nonpolar covalent bond results from the equal sharing of electrons between atoms This occurs when the atoms are close to each other in electronegativity Example: O2, H2

2.2 How Do Atoms Bond to Form Molecules?

When one atom is much more electronegative than the other, a complete transfer of electrons may occur. This results in two ions with fully paired electrons in their outer shells.

Figure 2.9 Formation of Sodium and Chloride Ions

2.2 How Do Atoms Bond to Form Molecules?

Ions: electrically charged particles when atoms lose or gain electrons

Cationspositive
Anionsnegative Ionic bonds are formed by the electrical attraction of positive and negative ions.

Salts (such as NaCl) are ionically bonded compounds.

2.2 How Do Atoms Bond to Form Molecules?

In a solid, ions are close together and the ionic bond is strong. In water, the ions are far apart and the attraction is much weaker.

Ions interact with polar molecules (e.g., salts dissolve in water).

Figure 2.10 Water Molecules Surround Ions

2.2 How Do Atoms Bond to Form Molecules?

Hydrogen bond: weak type of bond Attraction between the partially negative () end of one molecule and the partially positive (+) hydrogen end of another molecule. Hydrogen bonds form between water molecules, and are important in the structure of DNA and proteins.

2.2 How Do Atoms Bond to Form Molecules?

Although individually weak, collectively hydrogen bonds have considerable strength Hydrogen bonds are important in determining and maintaining the three dimensional structures of DNA and proteins

Figure 2.11 Hydrogen Bonds Can Form Between or Within Molecules

2.2 How Do Atoms Bond to Form Molecules?

Polar molecules that form hydrogen bonds with water are hydrophylic (water-loving). Nonpolar molecules such as hydrocarbons that interact with each other, but not with water, are hydrophobic (water-hating).

Figure 2.12 Hydrophilic and Hydrophobic

2.2 How Do Atoms Bond to Form Molecules?

van der Waals forces: attractions between nonpolar molecules that are close together. Individual interactions are brief and weak, but summed over a large molecule, can be substantial.

2.3 How Do Atoms Change Partners in Chemical Reactions?

Chemical reactions occur when atoms collide with enough energy to combine or change their bonding partners. In all chemical reactions, matter and energy are neither created nor destroyed. Energy: capacity to do work or the capacity for change. Energy usually changes form during chemical reactions.

 All of the atoms in the reactants must be accounted

for in the products The reaction must be balanced

2 H2 Reactants

O2 Reaction

2 H2O Products

Reactants

Products

In Photosynthesis (summarized reaction):

6 CO2 + 6 H2O

C6H12O6 + 6 O2

This is not what happens chemically, but is a balanced equation of the summarized reaction

2.4 What Makes Water So Important for Life?

Water has unique structure and special properties: Polar molecule Forms hydrogen bonds

Tetrahedral shape

2.4 What Makes Water So Important for Life?

Ice floats: Each molecule is hydrogenbonded to four other molecules in a rigid, crystalline structure. Solid water is less dense than liquid water.

Figure 2.14 Hydrogen Bonding and the Properties of Water

2.4 What Makes Water So Important for Life?

Water has high specific heatthe amount of heat energy required to raise the temperature of 1 gram of water by 1C. Water helps moderate climate because of its high heat capacity.

2.4 What Makes Water So Important for Life?

Water has a high heat of vaporization: the amount of heat energy required to change water from a liquid to a gas state. The basis of evaporative coolingheat must be absorbed from the environment in contact with the water.

2.4 What Makes Water So Important for Life?

Cohesion: water molecules resist coming apart from one another. Helps water move through plants Results in surface tension

Figure 2.15 Surface Tension

2.4 What Makes Water So Important for Life?

A solution is a substance (solute) dissolved in a liquid (solvent). Many important biochemical reactions occur in aqueous solutions.

2.4 What Makes Water So Important for Life?

Solvent - dissolving agent (water) Solute - substance that is dissolved (sugar) Aqueous solution - water is the solvent

2.4 What Makes Water So Important for Life?

Mole: The amount of a substance (in grams) that is numerically equal to its molecular weight. 1 mole of sodium ion Na+ = 23 g

1 mole of hydrogen gas H2 = 2 g

1 mole of table sugar (C12H22O11) = 342 g

2.4 What Makes Water So Important for Life?

The number of molecules in 1 mole is constant for all substances. One mole contains 6.02 1023 molecules = Avogadros number A 1 molar solution (1M) is 1 mole of a substance dissolved in water to make 1 liter of solution.

2.4 What Makes Water So Important for Life?

When acids dissolve in water, they release hydrogen ions: H+ (protons). H+ ions can attach to other molecules and change their properties.

Bases accept H+ ions.

2.4 What Makes Water So Important for Life?

HCl H Cl

HCl is a strong acid: the dissolution is complete.

2.4 What Makes Water So Important for Life?

Organic acids have a carboxyl group:

COOH COOH H

Weak acids: not all the acid molecules dissociate into ions.

2.4 What Makes Water So Important for Life?

NaOH is a strong base (it accepts H+). In water:

NaOH Na OH

OH H H 2O

2.4 What Makes Water So Important for Life?

Weak bases: Bicarbonate ion

HCO3 H H 2CO3
Ammonia

NH3 H NH 4

Compounds with amino groups

NH 2 H NH 3

2.4 What Makes Water So Important for Life?

Acid-base reactions may be reversible.

CH 3COOH CH 3COO H

Ionization of strong acids and bases is irreversible. Ionization of weak acids and bases is reversible.

2.4 What Makes Water So Important for Life?

Water has a slight tendency to ionize.

H 2O H OH

2.4 What Makes Water So Important for Life?

2.4 What Makes Water So Important for Life?

Water acts as both a weak acid and a weak base.

Ionization of water is important to all organisms because of the abundance of water in living systems, and the reactive nature of the H+ ions.

2.4 What Makes Water So Important for Life?

pH = negative log of the molar concentration of H+ ions.

pH log H

H+ concentration of pure water is 107 M, its pH = 7.

Lower pH numbers mean higher H+ concentration, or greater acidity.

2.4 What Makes Water So Important for Life?

1 M HCl solution: H+ concentration = 1 M

pH = 0

1 M NaOH solution: H+ concentration = 1014 M.

pH = 14

2.4 What Makes Water So Important for Life?

A solution with a pH of 7 is neutral

A solution with a pH of less than 7 is acidic (it has more H+ ions than OHions)
A solution with a pH of more than 7 is basic

Figure 2.16 pH Values of Some Familiar Substances

2.4 What Makes Water So Important for Life?

Living organisms maintain constant internal conditions (homeostasis). Buffers help maintain constant pH. A buffer is a weak acid and its corresponding base.

HCO3 H H 2CO3
Bicarbonate ion Weak base Carbonic acid Weak acid

pH / Buffers
Bicarbonate buffer - blood buffer

How it works. Response to a rise in pH

H2CO3

Response to a drop in pH

HCO3- + H+

H+ donor H+ acceptor (acid) equilibrium in human blood (base)

Carbonic acid and bicarbonate are in Hydrogen

ion

Human blood is maintained at pH 7.4