Chapter 2 Chemistry

II. Chemistry Comes Alive

1)   Basic chemistry

a)    Matter and energy

i)     Matter- anything that occupies space and had mass (weight)

ii)    Energy- the ability to do work (various forms):

(1)  Heat

(2) Chemical

(3) Electrical

(4) Mechanical

(5) Radiant

(6) Others…

b)   Composition of matter: Atoms and elements

i)     Basic terms

(1)  Elements- fundamental units of matter

(a)  96% of the body is made from four elements

(i)   Carbon

(ii)  Oxygen

(iii) Hydrogen

(iv)  Nitrogen

(2) Atoms- building blocks of elements

(3) Atomic symbols

ii)    Atomic structure (See Figs. 2.1& 2.2)

(1)  Nucleus

(a)  Protons (p+) (inside)

(b) Neutrons (n°) (inside)

(c)  Electrons  (eˉ) (outside)

(2) Isotopes

iii)  Major elements of the human body (See Table 2.1)

iv)   Identification of elements

(1)  Atomic number- equal to the number of protons that the atom contains

(2) Mass number- sum of the protons and neutrons

(3) Atomic weight- close to mass number of most abundant isotope

 - atomic weight reflects natural isotope variation

(4) Isotopes- have the same number of protons

   - vary in number of neutrons

(5) Radioactivity- process of spontaneous atomic decay

(6) Radioisotope: heavy isotope, tends to be unstable, decomposes to more stable isotope

c)    Molecules and Mixtures

i)     Molecules- two or more like atoms combined chemically

ii)    Compounds- two or more different atoms combined chemically

iii)  Mixtures

d)   Chemical bonds- atoms are united by chemical bonds

i)     Atoms dissociate from other atoms when chemical bonds are broken

ii)    Electrons occupy energy levels called electron shells

iii)  Electrons closest to the nucleus are most strongly attracted

iv)   Each shell has distinct properties

(1)  The number of electrons has an upper limit

(2) Shells closest to the nucleus fill first

v)    The role of electrons in chemical bonding

(1)  Electron shells

(2) Energy levels

(3) Filling of electron shells

(a)  Bonding involves interactions between electrons in the outer shell (valence shell)

(b) Full valence shells do not form bonds

(c)  Valence shell

(d) Rule of eight = rule of octet

(4) Inert elements (See Fig. 2.5a)

(a)  Atoms are stable (inert) when the outermost shell is complete

(i)   Shell 1 max- 2 electrons

(ii)  Shell 2 max– 8 electrons

(iii)Shell 3 max- 18 electrons

(5) Active elements

(a)  Valence shells are not full and are unstable

(b) Tend to gain, lose, or share electrons

(i)   Allow for bond formation, which produces stable valence

vi)   Types of chemical bonds

(1)  Ionic bonds (See Fig. 2.6)- when electrons are completely transferred from one atom to another

(a)  Ions – a charged particle

(i)   Anions- negative

(ii)  Cations- positive

(iii)Either donate or accept electrons

(2) Covalent bonds (See Fig. 2.7)

(a)  Atoms become stable through shared electrons

(b) Types

(i)   Single covalent bond- share one pair of electrons

(ii)  Double covalent bond- share two pairs of electrons

(iii)Triple covalent bond- share three pairs of electrons

(c)  Covalentky bonded molecules: carbon dioxide and water

(d) Polar and nonpolar molecules (See Figs. 2.8)

(i)   Polar: have a positive and negative side

(ii)  Non-polar: electrically neutral as a molecule

(iii)Electronegativity

(iv) Electropositivity

(3) Hydrogen bonds (See fig. 2.10)

(a)  Weak chemical bonds

(b) Hydrogen is attached to the negative portion of polar molecule

(c)  Provides attraction between molecules like a magnetic force

e)    Chemical reactions (See Fig. 2.11)

i)     Chemical equation

(1)  Reactants

(2) Products

ii)    Types

(1)  Synthesis (endergonic)

(a)  (A + B ® AB)

(b) Atoms or molecules combine

(c)  Energy is absorbed for bond formation

(2) Anabolic reactions (endergonic)

and

(3) Decomposition (exergonic)

(a)  (AB = A + B)

(b) Molecule is broken down

(c)  Chemical energy is released

(4) Catabolic reactions (exergonic)

and

(5) Exchange

(a)  (AB + C ® AC +B)

(b) Involves both synthesis and decomposition reactions

(c)  Switch is made between molecule parts and different molecules are made

(6) Displacement reactions

iii)  Reversibility of chemical reactions

iv)   Rate of chemical reactions

(1) temperature

(2) particle size

(3) concentration

(4) catalysts/enzymes

2)   Biochemistry

a)    Organic compounds

i)     Contains carbon

ii)    Most are covalently bonded

iii)  Example: C6H12O6 (glucose)

b)   Inorganic compounds;

i)     Lack carbon

ii)    Tend to be similar compounds

iii)  Examples:

(1)  Water (Fig. 2.8 & 2.9) (H2O)- most abundant inorganic compound

(a)  Vital properties: high heat capacity, polarity/solvent properties, chemical reactivity, and cushioning

(2) Salts (See Fig. 2.12)

(a)  Easily dissociate into ions in the presence of water

(b) Vital to many body functions

(c)  Include electrolytes which conduct electrical currents

iv)   Acids and bases (See Fig. 2.13)

(1)  Acids

(a)  Release hydrogen ions (H+)

(b) Are proton donors

(2) Bases

(a)  Release hydroxyl ions (OHˉ)

(b) Are proton acceptors

(3) pH (Fig. 2.12)

(a)  Acidic- pH below 7

(b) Basic- pH above 7

(c)  Neutral- pH 7

(d) Neutralization reaction- acids and bases react to form water and a salt

(e)  Measures relative concentration of hydrogen ions

(4) Buffers- chemicals that can regulate pH change

c)    Organic compounds

i)     Carbohydrates (See Figs. 2.13)

(1)  Contains carbon, hydrogen, and oxygen

(2) Includes sugars and starches

(3) Classified according to size

(a)  Monosaccharide = simple sugars

(b) Disaccharides = double sugars (two simple sugars joined by dehydration synthesis)

(c)  Polysaccharides = polymers of simple sugars (long- branching chains of linked simple sugars)

ii)    Lipids (See Fig. 2.15)

(1)  Contains carbon, hydrogen, and oxygen

(a)  Carbon and hydrogen outnumber oxygen

(2) Insoluble in water

(3) Neutral fats (triglycerides)

(a)  found in fat deposits

(b) Composed of fatty acids and glycerol

(c)  Source of stored energy

(4) Phospholipids

(a)  Form cell membranes

(5) Steroids

(a)  Includes cholesterol, bile salts, vitamin D, and some hormones

iii)  Proteins (See Fig. 2.16 & 2.17)

(1)  Made up of amino acids

(2) Contains carbon, oxygen, hydrogen, nitrogen, and sometimes sulfur

(3) Accounts for over half of the body’s organic matter

(4) Provide for construction materials for body tissues

(5) Play a vital role in cell function

(6) Act as enzymes, hormones, and antibodies

(7) Structural levels of proteins

(a)  Primary structure

(b) Secondary structure

(c)  Tertiary structure

(d) Quaternary structure

(8) Fibrous versus Globular proteins

(9) Protein denaturation

(10)Enzymes

(a)  Characteristics

(b) Mechanism of actions (See Fig. 2.18)

iv)   Nucleic acids (See Fig. 2.19)

(1)  Provide blueprint of life

(2) Nucleotide bases: (A) adenine, (G) guanine, (T) thymine, (C) cytosine, (U) uracil

(3) Nucleotides

(a)  Sugar

(i)   Ribose (RNA)

(ii)  Deoxyribose (DNA)

(b) Phosphate group

(4) Types

(a)  Deoxyribonucleic acid DNA

(b) Ribonucleic acid RNA

v)    Adenosine triphosphate ATP (See Figs. 2.20 & 2.21)

(1)  Chemical energy used by all cells

(2) Energy is release by breaking high energy phosphate bond

(3) ATP is replenished by oxidation of food fuels