BASIC CHEMISTRY

Matter

1. Matter - occupies space and has mass

2. Mass - amount of matter in something and; remains the same

3. Weight - varies with gravity; is used to approximate mass

4. States of matter

-a. Solid - has a definite shape and volume

-b. Liquid - can change shape, definite volume

-c. Gas - neither a definite shape of definite volume

Energy

1. Energy - capacity to do work or to put matter into motion

2. Measured – its effect on matter

3. Kinetic Energy - energy in action

-b. Potential Energy - stored or inactive energy; potential to do work

4. Forms of Energy - body uses energy in several forms

-a. Chemical energy - stored in the chemical bonds; food, ATP

-b. Electrical energy - movements of charged particles (ions); nerve, muscle, heart

-c. Mechanical energy - energy directly involved in moving matter

-d. Electromagnetic energy - travels in waves; UV Vitamin D; vision

5. Conversion - from one form to another

-a. Inefficient - some of the initial energy is always lost to the environment a heat

-b. Heat - mostly unusable; warm blooded; body temperature

COMPOSITION OF MATTER: ATOMS AND ELEMENTS

Basic Terms

1. Elements - unique substances, not into simpler substances by chemical methods

-a. Body – C, O, H, N 96%; 20 others in lesser, trace amounts

-b. Periodic table - A complete listing of known elements

2. Atoms - smallest particle of an element which retains its properties

-a. Atomic symbol - for each element; first one or two letter; Latin

Atomic Structure

1. Nucleus - central part of the atom which contains protons; 99% weight

-a. Protons - have a positive charge

-b. Neutrons - are neutral

-c. Atomic Mass Unit (amu) - considered the weight of one proton or neutron

2. Electron - a negative charge; equal in strength to the positive charge of the proton

3. Neutrality - number of electrons must equal the number of protons

4. Models – planetary (simple); orbital, region likely to find (accurate)

Identifying Elements

1. Atomic number – unique, number of protons in the nucleus of an

2. Isotope - atomic variants of an element; number protons, same; neutrons vary

3. Hydrogen isotopes - includes hydrogen (1H), deuterium (2H), and tritium (3H)

4. Radioisotopes - heavy isotopes; decompose; radiation; diagnosis, treatment

Molecules and Compounds

1. Molecules – two or more atoms held together by chemical bond

2. Compounds – two, more different kinds of atoms chemically bound to each other

-a. Unique – can have properties different from atoms which make it

-b. Molecule – the smallest subunit of a compound

3. Chemical bonds – must be broken; can not be separated by physical means

Mixtures

1. Mixtures – two, more components physically mixed; solutions, colloid, suspension

-a. Physical separation – chemical bonds do not have to be broken

2. Solutions - homogeneous mixture; does not scatter light

-a. Solvent - present in the greatest quantity; dissolving medium; usually liquids

-b. Solute - in smaller amounts

3. Colloids - heterogeneous mixture; particles larger; do not settle

4. Suspensions - heterogeneous mixtures; large particle; settle out; blood

The Role of Electrons in Chemical Bonding

1. Electron shell - space that the electron cloud around occupies; 1 to 7

2. Valence shell - outermost energy level; chemically reactivity

-a. Octet rule (Rule of Eight) - Atoms interact; eight electrons in valence shells

-b. Shell 1 - is an exception as it can contain only 2 electrons

3. Chemically inert – noble gases; helium (2); neon and all others (8)

4. Chemically reactive – have only 1 in inner shell or less than 8 in others

Types of Chemical Bonds

1. Ionic bonds – attraction between opposite charged; loss and gain of electrons

-a. Ions - electrons can be transferred; negative or positive charge

-b Anion - electron acceptor; negative charge

-c. Cation - electron donor; positive charge

-d. Table salt - ionic bond between sodium (Na) and chloride (Cl)

2. Covalent bonds - electron sharing and not transfer of electrons (as in ionic bonds)

-a. Single covalent bonds - 2 atoms share 1e-; Hydrogen gas; methane

-b. Double covalent bonds - 2 atoms share 2 e-; double line; oxygen gas

-c. Triple covalent bonds - 2 atoms share 3 e-; triple line; nitrogen gas

Polar and Nonpolar molecules

1. Nonpolar molecules - electrons shared equal between atoms; electrically balanced

-a. Symmetrical – molecules tend to be nonpolar

-b. Carbon dioxide – 2 oxygens pull equally on carbon’s electrons

2. Polar molecules – electrons not equally shared

-a. Asymmetrical – molecules tend to be

-b. Water – 1 atom of oxygen shares two electrons with 2 hydrogen atoms

3. Dipole - polar molecules, like water, have a positive side and a negative side

4. Hydrogen bonds – weak; do not form molecules; between + and – sides of dipoles

-a. Water – properties, like surface tension, result of hydrogen bonds

-b. Proteins – higher order structure result of hydrogen bonds

Chemical reactions

1. Chemical reactions – chemical bonds are made, broken, rearranged

2. Chemical equations - reactions can be written in

-a. Reactants - number and kind of reacting substances are found to the left

-b. Products - number and kind of substances formed and are found to the right

-c. Chemical formula - number of atoms, as subscripts on the right, in each molecule

-d. Balanced equations - show the relative proportion of reactants and products

3. Chemical reactions

-a. Synthesis - bond formation; anabolic; A + B → AB

-b. Decomposition - bonds are broken; catabolic; AB → A + B

-c. Exchange – both; redox; AB + C → AC + B

4. Energy flow - chemical bonds represent stored chemical energy

-a. Exergonic reactions - release energy; bonds broken; products less potential energy

-b. Endergonic reactions - energy absorbing; bond made; products more potential energy

5. Reversibility – some chemical reactions; many biological

-a. Double arrow – used to show

-b. Equilibrium - neither the reaction nor the reverse reaction is dominant

6. Reaction rate - increase chances and force of collisions of the atoms and molecules

-a. Temperature - increases the kinetic energy of particles and force of their collisions

-b. Particle size - smaller particles move more quickly; more force when colliding

-c. Concentration - more particles present, the greater their chances of colliding

-d. Catalysts – increase rate of reactions; do not changed; enzymes

BIOCHEMISTRY

Inorganic Compounds

Water

1. Abundance – most common compound in living material; 50 to 60 %

2. Heat capacity - absorb and release heat before changing; protects living systems

3. Heat of vaporization - much heat is required to break hydrogen bonds; perspiration

4. Universal solvent - biochemical reactions must take place in solution

5. Cushioning - around some organs; cerebrospinal fluid surrounds the brain

Salts

1. Salts - ionic compounds containing cations and anions

2. Dissociation - salts dissociate into ions in water; overcomes ionic bond

3. Electrolytes - conduct an electrical current in solution and include all ions

4. Importance – very important in body

-a. Calcium phosphates – hardness to bone

-b. Excitable tissue – Na, K, and Ca are all important

Acids and Bases

1. Electrolytes – like salts

2. Ions have to be formed before dissociation can occur

3. Acid - releases hydrogen ions [H] in detectable amounts; sour taste

-a. HCl – in water hydrogen ion dissociates

4. Bases - take up hydrogen atoms in detectable amounts; bitter

-b. NaOH – in water hydroxide ion dissociates; binds hydrogen ion

5. pH - relative concentration of hydrogen ions

-a. Acidic – more hydrogen ions than hydroxyl; below 7

-b. Alkaline (basic) – less hydrogen ions than hydroxyl; above 7

-c. Neutral - equals number; pH 7

-d. Logarithmic – pH 6, 10 times H ion as pH 7

Organic Compounds

Carbohydrates

1. Carbohydrates - include sugar and starches

2. Atomic composition – C, H, and O; 1:2:1 ration

3. Monosaccharides - single chains, rings; three to six carbons

-a. Deoxyribose - is an important pentose

-b. Glucose - blood sugar

-c. Isomers - same molecular formula, arranged differently

3. Disaccharides - two monosaccharides

-a. Dehydration synthesis - monosaccharides joined; removal of one water molecule

-b. Sucrose - glucose and fructose (table sugar)

-c. Lactose - glucose and galactose (milk sugar)

-d. Hydrolysis - reverse of dehydration synthesis; bond broken by the addition of water

4. Polysaccharides - long chains of simple sugars linked together by

-a. Monomer - a building block molecule such as glucose

-b. Polymer - a large molecule made up of many monomers

-c. Starch - polysaccharide produced by plants

-d. Glycogen - an important polysaccharide stored in liver and muscles

5. Functions – mostly fuel; some used in structures

Lipids

1. General – insoluble in water; fat soluble; H, C, and O; much less O; diverse

2. Neutral Fats - fats (solid) and oils (liquid)

-a. Fatty acids - a hydrocarbon chain with organic acid group at the end (COOH)

-b. Glycerol - modified three carbon sugar (sugar alcohol)

-c. Dehydration synthesis - attaching 3 fatty acids to 1 glycerol; E-like appearance

-d. Triglycerides (Triacylglycerols) - other name for neutral referring to three fatty acids

-e. Nonpolar - because of the long hydrocarbon chain; insoluble in water

-f. Energy storage - most concentrated; mostly beneath skin

-g. Saturated fats - only single bonds between carbons

-h. Unsaturated fats - some double bonds

-i. Monounsaturated fats - one double bond

-j. Polyunsaturated fats - more than one double bond

-k. Fats - tend to contain longer and saturated fatty acids

-l. Oils - tend to contain shorter and unsaturated fatty acids

3. Phospholipids - modified triglycerides phosphorus head and two fatty acid chains

-a. Polar head – phosphorous containing; attracts other polar molecules like water

-b. Nonpolar tail - interacts only with nonpolar molecules

-c. Cell membrane - unique characteristics; phospholipids making up the cell membrane

4. Steroids - flat molecules formed of four interlocking hydrocarbon rings

-a. Cholesterol - most important; cell membranes; hormones; vitamin D; bile salts

5. Eicosaniods - diverse group of lipids

-a. Arachidonic acid - a 20 carbon fatty acid; cell membranes; are derived

-b. Prostaglandin - most important; blood clotting, inflammation, and labor contraction

Proteins: general

1. Function – structure and function of body

-a. Structure - 10% to 30% of cell mass basic structural material

-b. Enzymes - biological catalyst; mostly proteins

-c. Other functions – blood clotting; hemoglobin; antibodies; etc.

2. Make up – C, H, O, and N (all); S and P (some)

3. Amino acids - building blocks of proteins; 20 different;

-a. Amine group (NH₂) – always on the carbon next to carboxyl group

-b. Organic Acid Group (COOH) – carboxyl group

-c. R- group - only part of the amino acids that differ; also to alpha carbon

4. Peptide bonds - dehydration synthesis; amine of one and the acid of another

-a. Mono, di, and tripeptides – 1, 2, and 3 amino acid chains

-b. Polypeptides - more than ten amino acids

-c. Proteins - contain more that 50 amino acids

-d. Macromolecules - most protein contains 100 to 1000 amino acids

Proteins: structural levels

1. Primary structure - linear sequence of amino acids; determines higher levels

2. Secondary structure - twisting and folding of primary structure; hydrogen bonding

-a. Alpha helix - primary chain is coiled; spiral structure held in place by hydrogen bonds

-b. Beta pleated sheet – chains linked side by side by hydrogen bonds undulating ribbon

3. Tertiary structure – folding secondary structure; R group interact with R groups, water

4. Quaternary structure - two or more polypeptide chains aggregate, in a regular manner

Proteins: fibrous and globular

1. Fibrous - have an extended stand like appearance

-a. Secondary structure - usually exhibit only one type

-b. Quaternary structure - found in some

-c. Properties - linear, insoluble in water, and are very stable

-d. Structural proteins - such as

-e. Collagen - most abundant and is found connective tissue

2. Globular - compact, spherical proteins

-a. Tertiary structure - at least

-b. Quaternary structure - in some

-c. Water soluble - mobile, chemically active molecules

-d. Functional proteins – very important hemoglobin, antibodies, enzymes

Proteins: denaturation

1. Denaturation - change in the three dimensional; loss of function

2. Globular proteins - most prone to denaturation

3. Causes – disrupt hydrogen bonds

-a. acidity – pH out of homeostatic limits; disrupts attraction between dipoles

-b. heat – out of normal body range; water molecules have more kinetic energy

4. Reversible – many are

5. Irreversible - from extreme pH or heat; coagulation of egg white (albumin)

6. Active sites - site of binding with other molecules; disrupted structure, role

Enzymes

1. Enzymes - globular proteins; catalysts; increase reaction rates by a factor of 1 million

2. Holoenzyme - enzyme that consists of two parts

-a. Apoenzyme - protein portion

-b. Cofactor - depending on the enzyme; metal ion; coenzyme (usually from vitamin)

3. Specificity – high degree; each enzyme, a single reaction or group of related reactions

4. -ase - enzymes end in this suffix

5. Named - for the reaction they catalyze; oxidase (add oxygen)

6. Enzyme activity - involve

-a. Substrate - substance acted upon by the enzyme

-b. Active site - substrate binding site on the enzyme

-c. Induced-fit model - enzyme recognition of proper substrate

-d. Internal rearrangement – enzyme substrate complex; reaction; ex. dehyd. synthesis

-e. Product – released; enzyme is unchanged

Nucleic Acids (DNA and RNA)

1. Nucleic acids - include

-a. Deoxyribonucleic acid - DNA

-b. Ribonucleic acid - RNA

2. Nucleotides - structural units of nucleic acids; three components

-a. Phosphate group

-b. Pentose sugar –ribose or deoxyribose

-c. Nitrogen containing base – purines or pyrimidines

3. Purines - two ring bases include

-a. Adenine - abbreviated as A

-b. Guanine - abbreviated as G

4. Pyrimidines - one ring bases include

-a. Cytosine - abbreviated as C

-b. Thymine - abbreviated as T; only in DNA

-c. Uracil - abbreviated as U; only in RNA

5. Dehydration synthesis - joins nucleotides together water molecule is removed to join

-a. Phosphate group - of one nucleotide; joined to

-b. Pentose sugar - of another nucleotide

6. DNA – carries, replicates genetic info; nucleus (mostly); double helix

-a. AT - adenine and thymine

-b. CG - cytosine and guanine

7. RNA – different types; protein synthesis; cytoplasm, nucleus; single strand

-a. Uracil - replaces thymine

Adenosine triphosphate (ATP)

1. Cellular respiration - captures energy produced during this

2. Adenine containing ribonucleotide – ribose sugar

3. Phosphate bond - releases energy when broken ATP becomes ADP

4. Cellular functions - use energy from this; membrane transport, muscle contractions