CH. 2 Basic Chemistry

Types of Energy Types of energy: Kinetic: energy associated with motion Potential: stored (inactive) energy Electrical : results from the movement of charged particles (Na+, K+)

Matter and Composition of Matter Matter is anything that has mass and occupies space Matter is made up of elements Elements are pure substances that cannot be broken down by ordinary chemical means; composed of atoms

The Atomic Structure N Atoms Have Three Important Particles: Neutrons No charge, in atomic nucleus 1 atomic mass unit (amu) Protons Positive charge, in atomic nucleus 1 amu Electrons Negative charge, orbit nucleus (in up to 7 shells) 0 amu Equal in number to protons in atom N

Identifying Elements Atoms of each element contain a unique number of protons Compare hydrogen, helium and lithium The atomic number is equal to the number of protons The mass number is equal to the number of protons and neutrons

Hydrogen (H) Helium (He) Lithium (Li) Proton Neutron Electron Figure 2.2

Chemical Bonds A molecule is two or more atoms chemically bound together (H2 or C6H12O6) Octet rule: Except for the first shell which is full with two electrons, atoms interact in order to have eight electrons in their outermost energy level or valence shell

(a) Chemically inert elements Valence shell complete 8e 2e 2e Helium (He) Neon (Ne)

Chemically Reactive Elements Atoms whose valence shell is not fully occupied by electrons with interact with other atoms forming a chemical bond. To form a chemical bond, atoms lose, gain or share electrons with other atoms to achieve stability

(b) Chemically reactive elements Valence shell incomplete 4e 1e 2e Hydrogen (H) Carbon (C) 1e 6e 8e 2e 2e Oxygen (O) Sodium (Na) Figure 2.4b

Oppositely charged ions are attracted resulting in an ionic bond Ionic Bonds Ions are formed by: The loss or gain of electrons Anions (–) have gained one/more electrons Cations (+) have lost one/more electrons Oppositely charged ions are attracted resulting in an ionic bond

+ – Sodium atom (Na) Chlorine atom (Cl) Sodium ion (Na+) Chloride ion (Cl–) Sodium chloride (NaCl) Figure 2.5

Covalent Bonds Covalent bonds form when valence electrons are shared Allows each atom to fill its valence shell at least part of the time

+ Reacting atoms Resulting molecules or Hydrogen atoms Carbon atom Molecule of methane gas (CH4) (a) Formation of four single covalent bonds: Figure 2.7a

+ Reacting atoms Resulting molecules or Oxygen atom Oxygen atom Molecule of oxygen gas (O2) (b) Formation of a double covalent bond: Figure 2.7b

+ Reacting atoms Resulting molecules or Nitrogen atom Nitrogen atom Molecule of nitrogen gas (N2) (c) Formation of a triple covalent bond:. Figure 2.7c

Sharing of electrons may be equal or unequal Covalent Bonds Sharing of electrons may be equal or unequal Equal sharing of valence electrons produces nonpolar covalent bonds

Covalent Bonds Unequal sharing of valence electrons by atoms with different electron-attracting abilities produces polar covalent bonds Ex. H2O

+ – Hydrogen bond + + – – – + + + – (a) The slightly positive ends (+) of the water molecules become aligned with the slightly negative ends (–) of other water molecules. Attractive force between a positive hydrogen of one molecule and an electronegative atom of another molecule Figure 2.8

Synthesis Reactions A + B  AB Always involve bond formation Anabolic Endergonic

(a) Synthesis reactions Smaller particles are bonded together to form larger, molecules. Example Amino acids are joined to Form protein. Amino acid molecules Protein molecule Figure 2.9a

Decomposition Reactions AB  A + B Opposite of synthesis reactions Involves breaking bonds Catabolic Exergonic

(b) Decomposition reactions Bonds are broken in larger molecules, resulting in smaller, less complex molecules. Example Glycogen is broken down to release glucose units. Glycogen Glucose molecules Figure 2.9b

Classes of Compounds Inorganic compounds Organic compounds Do not contain carbon (ex. Water, salts, and many acids and bases) Organic compounds Contain carbon, usually large, covalently bonded (ex’s. carbohydrates, fats, proteins, nucleic acids)

Water 60%–80% of the volume of living cells Most important inorganic compound in living organisms because of its properties

Salts Ionic compounds that dissociate into ions in water Ions (electrolytes) conduct electrical currents in solution

Acids : Proton (H+) donors (release H+ in solution) HCl  H+ + Cl–

Bases: Proton acceptors (take up H+ from solution) NaOH  Na+ + OH–

Acid-Base Concentration Acid solutions contain higher amounts of H+ As [H+] increases: acidity increases Basic solutions contain higher concentrations of OH– As [H+] decreases (or as [OH–] increases): alkalinity increases pH = measure of the acidity/bascisity of a solution

Acid-Base Concentration Neutral solutions: pH = 7 Contains equal numbers of H+ and OH– Acidic solutions  [H+],  pH pH = 0–6.99 Basic solutions  [H+],  pH pH= 7.01–14

Ribonucleic Acid (RNA) Four bases: adenine (A), guanine (G), cytosine (C), and uracil (U) Single-stranded PLAY Animation: DNA and RNA

Adenosine Triphosphate (ATP) Adenine-containing RNA nucleotide with two additional phosphate groups

High-energy phosphate bonds can be hydrolyzed to release energy. Adenine Phosphate groups Ribose Adenosine Adenosine monophosphate (AMP) Adenosine diphosphate (ADP) Adenosine triphosphate (ATP) Figure 2.19

Function of ATP Phosphorylation: The chemical energy contained in the high energy phosphate bonds can be used to perform cellular work

Figure 2.20 Solute + Membrane protein (a) Transport work + Relaxed smooth muscle cell Contracted smooth muscle cell (b) Mechanical work + (c) Chemical work Figure 2.20

Carbohydrates Functions Polymers of monosaccharides Three classes Monosaccharides -Simple sugars containing three to seven C atoms Ex. Glucose Disaccharides -Double sugars fructose, sucrose, maltose Polysaccharides –many monosaccharides linked together ex., starch, glycogen, cellulose Functions Cellular fuel Provide structure in RNA and DNA

Carbohydrates: Polysaccharides

Lipids Mainly insoluble in water Several Classes of Lipids Triglycerides Phospholipids Steroids

Triglycerides Triglycerides—solid fats and liquid oils Three fatty acids bound to glycerol (3:1) Functions Energy storage Insulation Protection

Phospholipids Two fatty acids bound to glycerol (2:1), bound to a phosphate group “Head” and “tail” regions have different properties Main component of cellular membranes

Steroids Composed of four fused carbon rings Ex’s. Cholesterol, vitamin D, steroid hormones, and bile salts

Polymers of amino acids All 20 amino acids have same basic structure Proteins Polymers of amino acids All 20 amino acids have same basic structure Amino acids are held together by peptide bonds (polypeptides)

Denaturing Natural Folding https://www.youtube.com/watch?v=yZ2aY5lxEGE (protein folding animation 2m 19 s) start around 1:11

Nucleic Acids Two examples: DNA and RNA Contain C, O, H, N, and P Polymers of nucleotides: nucleotides have 3 parts: a N-containing base, a pentose sugar, and a phosphate group

Sugar-phosphate backbone Nucleotide Base pair Base pair Figure 3.16C DNA double helix. Sugar-phosphate backbone

Deoxyribonucleic Acid (DNA) Four bases: adenine (A), guanine (G), cytosine (C), and thymine (T) Double-stranded, helical Replicates before cell division, ensuring genetic continuity Provides instructions for protein synthesis

Ribonucleic Acid (RNA) Four bases: adenine (A), guanine (G), cytosine (C), and uracil (U) Uracil replaces thymine in RNA Single-stranded Mainly active outside of nucleus