Lecture Notes: Basic Chemistry I. Atoms, Molecules and Chemical Reactions

A) ____________________

(1) Anything that has mass and volume (2) Biotic (3) Abiotic (4) Composed of 92 naturally occurring elements (5) Most common elements found in biological specimens:

(a) ____________________

B) Atom

(1) The smallest amount of an atom that can enter into a chemical reaction (2) Structure

(a) Nucleus (b) orbit (or shell) (c) Note: most of an atom is empty space

(3) Subatomic particles

(a) ____________________ 1) negatively charged e¯ 2) orbit in shells 3) small

(b) ____________________

1) positively charged p⁺

2) nucleus 3) larger

(c) ____________________ 1) Electrically neutral n° 2) nucleus

3) about same size as p⁺

(d) The number of protons determines the element/type of atom

1) Carbon 6 p⁺

2) Hydrogen 1 p⁺

3) Oxygen 8 p⁺

4) Nitrogen 7 p⁺

(4) isotopes: variant forms of an atom of an element

(a) C-12 6 p⁺ and 6 n°

(b) C-13 6 p⁺ and 7 n°

(c) C-14 6 p⁺ and 8 n°

(d) note: how isotopes are used in the body allow for imaging, diagnosing and treatment

(5) ____________________

(a) number of p+ = number of e- (6) ____________________

(a) charged atom (or group of atoms) (b) p+ does not equal e- (c) example:

1) hydrogen ion H⁺

2) Sodium ion Na ⁺

3) Chloride ion Cl-

C) Molecules: 2 or more atoms held together by chemical bonds

(1) ____________________making, breaking or rearranging of chemical bonds

(a) Reactant � products

(b) ____________________ starting substance(s)

(c) Arrow: indicates chemical reaction occurred

(d) ____________________ ending substance(s)

(e) Change in energy with each chemical reaction ATP � ADP + P + Energy

(2) Energy: Ability to do work

(a) Potential Energy: energy due to an object’s position or in chemical bonds (b) Kinetic Energy: energy due to an objects movement or heat

(c) Forms of Energy 1) chemical: chemical bonds

a) Potential energy 2) electrical: movement of ions or e¯

a) Electrical impulse, muscle contractions 3) Mechanical: work

a) Directly involved moving matter 4) Radiant: energy that travels in waves

a) Vision, sunburn, vitamin D synthesis

(3) 1st Law of Thermodynamics: Energy is neither created nor destroyed, it only changes into a different form

(4) 2nd Law of Thermodynamics: During energy conversions, some energy is lost, usually as heat

D) Inorganic and Organic Molecules (1) Inorganic Molecules

(a) small/simple (b) lack Carbon (c) examples:

(d) exceptions:

(2) Organic Molecules (a) large/complex 1) biotic: carbohydrates, proteins, lipids, nucleic acids 2) abiotic: gas, motor oil, plastics

(b) _________________________________ (c) Biological molecules have chains or rings of Carbon atoms/carbon skeleton

E) Chemical Bonds atoms participate in chemical bonds to fill shells—stable

(1) __________________________________

(a) electrostatic attraction between oppositely charged ions

(b) __________________________________ 1) substance gains electron(s)

(c) __________________________________ 1) substance loses electron(s)

(d) Redox—occurs simultaneously

(2) __________________________________ (a) Sharing of pair(s) of electrons between atoms

(b) Single covalent bonds: 1) Share 1 pair of electrons 2) Hydrogen gas H-H

(c) Double covalent bonds: 1) share 2 pair of electrons 2) Oxygen gas O=O

(d) Triple covalent bonds: 1) share 3 pair of electrons 2) Nitrogen gas N≡N

(3) __________________________________ weak bond that forms between a H atom in a

covalent bond with an O or N atom in a different covalent bond

(a) water : holds water molecules in liquid form at room and body temperature

(b) protein responsible for protein shape (secondary, tertiary and quaternary structure)

(c) DNA holds the two strands together in a double helix

F) ________________________________ (1) large, complex molecules made from smaller, simpler molecules (2) Examples:

(a) Carbohydrates (b) Protiens (c) nucleic acids (d) Lipids

(3) ________________________________ (a) Repeating units (b) Examples: proteins, polysaccharides (starch)

(4) ________________________________ (a) small, simple molecules used to build macromolecules (b) Examples: Glucose or fructose

G) Dehydration Synthesis or Condensation Reaction: (1) Building reactions (2) Water product (3) Monomers joined by creating a covalent bond (4) Enzyme mediated

H) Hydrolysis Reaction: (1) Opposite of condensation reaction

(2) Reactants ∅ Products (3) Degradative reaction (4) Water reactant (5) Covalent bond between the monomers of a macromolecule are broken (6) Enzyme mediated

I) Factors that influence the rate of a chemical reactions

(1) temperature: optimum/body temp (2) particle size: larger particles move slower (3) Concentration of Reactants: lots of starting materials (4) presence of a catalyst: enzymes— speed up chemical reactions

II. Water, Acids & Bases

A) General Characteristics of Water

(1) Inorganic (2) Abundant (3) Polar (4) H-bonds

B) Properties of Water

(1) Liquid at room temperature (a) Cohesive (b) H-bonds (c) Dynamic (d) Allows other substances to move through

(2) Universal Solvent (a) Solution:

a) homogeneous mixture b) Uniform/same composition throughout

(b) ________________________ 1) Substance that does the dissolving 2) Substance in the greatest amount

(c) ________________________ 1) Substance that gets dissolved 2) Substance in the least amount

(d) Biochemistry 1) Chemical reactions that occur in water/life

(3) Participates in some chemical reactions

(a) hydrolysis reaction 1) Degradation/break covalent bonds 2) Water required as a reactant

(b) condensation reaction 1) synthesis/build—create covalent bonds 2) water produced as a product

(4) Cushions/protection

(a) CSF cerebrospinal spinal fluid (b) amniotic fluid

(5) Frozen water is less dense than liquid water

(a) floats—insulates water beneath (b) crucial to life in lakes/ponds/etc.

(6) Temperature of water rises and falls slowly

(a) Requires a lot of energy

(b) Prevents sudden/drastic changes

(7) High heat of vaporization

(a) H2O liquid � H2O vapor

(b) cooling effect

(8) Water molecules ionize

(a) most molecular

form (55 million Molecules)

(b) very few ionize (1 water molecule ionizes)

C) Acids & Bases

(1) ___________________________ (a) Any substance that releases hydrogen

ions in solution (b) HCl (Hydrochloric acid)� H+ + Cl –

(2) ____________________________ (a) Any substance that absorbs (removes)

hydrogen ions from solution OR releases hydroxide ions in solution

(b) NaOH (Sodium Hydroxide)� Na + + OH -

(3) pH Scale: Measure of the Hydrogen ion

concentration in solution

(a) Neutral pH

(b) Acidic pH

(c) Basic pH

(d) pure water

(4) ________________________: substance that absorbs/releases hydrogen ions in order

to maintain a constant pH

(a) dissociation adds more H+

(b) reformation removes H+

III. Carbohydrates

A) Elemental Composition (1) Carbon (2) Hydrogen (3) Oxygen (4) Ratio 1 C : 2 H : 1 O

B) Categories

(1) Monosaccharides (2) Disaccharides (3) polysaccharides

C) Monosaccharides

(1) General Characteristics

(a) Monomer (b) ‘simple sugars’ (c) Suffix ‘ose’ (d) Typically 3-7 Carbons

(2) Hexoses : 6-carbon sugar, C6H12O6

(a) ____________________ blood, energy

(b) ____________________ dietary, energy

(c) ____________________ Milk, energy

(3) Pentoses 5-carbon sugar

(a) ____________________ RNA component

(b) ___________________ DNA component

D) Disaccharide

(1) Mono + mono � disaccharide + water (2) Joined by condensation rxn

(3) ____________________

(a) Table sugar (b) glucose + fructose � sucrose + water

(4) ____________________

(a) milk sugar (b) glucose + galactose � lactose + water

(5) ____________________

(a) glucose + glucose � maltose + water

E) Polysaccharides

(1) ___________________________ (a) many glucose units (b) storage form of glucose in plants

(2) ___________________________

(a) many glucose units (different bonds) (b) cell wall/‘fiber’ provides no energy

(3) ___________________________

(a) many glucose units (b) storage form glucose in muscle and liver cells

IV. Lipids (Fats and oils)

A) Elemental Composition

(1) Carbon (2) Hydrogen (3) Oxygen (4) Sometimes Nitrogen and Phosphorus

B) General Characteristics

(1) Organic (2) Insoluble in water (3) variable

C) Categories

(1) Triglycerides (2) Fatty acids (3) Phospholipids (4) Sterols (5) waxes

D) Common Monomers

(1) ____________________________

(a) 3-Carbon molecule (b) other molecules attached

(2) ____________________________

(a) long chain carbons

(b) ___________________________ 1) single covalent bond 2) Solid at room temp 3) lard, animal fat

(c) ___________________________

1) one/more double covalent bonds 2) liquid at room temp 3) plant/veg oils

E) Triglycerides

(1) Monomers (a) glycerol (b) 3 FA (fatty

acids)

(2) Functions (a) long-term

energy storage

(b) Insulation (c) cushioning

F) Phospholipids

(1) monomers

(2) Function:

G) Sterols (1) structure

(a) complex C-ring structure (b) provides basic structure for other molecules

(2) sterols (a) cholesterol (b) some hormones (c) bile salts (d) vitamin D

H) Waxes

(1) structure: (really) Long chain fatty acid (2) function

(a) water proofing/prevent dehydration (b) protection

(3) examples: (a) waxy cuticle of plant leaf (b) cerumen (ear wax)

V. Nucleic Acids A) Elemental Composition

(1) Carbon (2) Hydrogen (3) Oxygen (4) Nitrogen (5) Phosphorus

B) Polymer of nucleotides

(1) Nucleotides are the monomers

(2) Nucleotides form strands (polymers)

C) Nucleotide

(1) pentose

(2) phosphate group

(3) N Base (a) adenine A (b) thymine T (c) cytosine C (d) guanine G

D) DNA (deoxyribonucleic acid)

(1) Function:

(2) DNA Structure 1) _______________________

a) each strand is a polymer of nucleotides

2) one strand a) nucleotides held together by covalent

bones b) sugar-phosphate backbone

3) two strands held together by______________________

4) Base pairing rules

5) Double helix

E) RNA (ribonucleic acid)

(1) Function: ______________________ (2) Structure:

(a) pentose: ribose

(b) N bases

(c) single stranded

G) ATP (Adenosine TriPhosphate)

(1) Function: ATP � ADP + P +

Energy

(2) Structure: (a) Nitrogen base-A (b) pentose (c) 3 Phosphate Groups

VI. Proteins A) Elemental Composition:CHON, sometimes S (Sulfur)

B) Monomers: ______________________

C) Amino Acid Structure:

(1) Central C atom (2) amine (N) group (3) acid group (4) H atom

D) ______________________

(1) Pept = protein (2) chain of amino acids (3) peptide bond-covalent bond between amino acids

E) ______________________ (1) function: provide structure or protection (2) examples:

(a) collagen (strength)-tendons and ligaments (b) elastin (stretch and recoil)-ear (c) keratin -skin, hair

F) _______________________________________ DO-ERS of the cell! 1) ____________________

a) carry out chemical rxns b) biological catalysts c) ‘ase’

2) ____________________ a) hemoglobin b) channel c) pump d) porin

3) ______________________

a) antibodies (immunity) b) blood clotting factors

4) ____________________

a) actin and myosin in muscle

5) ____________________ a) some hormones b) some neurotransmitters

G) Structure (Shape) = Function

H) Levels of Protein Structure

(1) Primary Structure: (a) sequence of amino acids coded by DNA (b) Polypeptide--chain/polymer of amino acids

(2) Secondary Structure:

(a) alpha-helix (b) pleated sheet (c) H-bonds hold polypeptide in shape

(3) Tertiary Structure: (a) polypeptide folds further upon itself, held by various types of chemical bonds (b) (may or may not be functional)

(4) Quaternary Structure:

(a) describes the structure of a functional protein that is composed of >1 polypeptides held together by various chemical bonds

I) ____________________________describes when a proteins shape is changed resulting in a

loss or cessation of function. (1) heat (2) pH

J) How Enzymes Work

(1) Enz binds substrate(s)

(2) Substrate undergoes chem rxn (3) Enz releases product(s) (4) (repeats)

K) Biochemical Pathways are Economical and

Efficient (1) Recycle (2) Enzymes are unique ����

(3) Enzymes may catalyze reaction in both

directions ATP ∅ ADP + P + Energy (4) Reactions can be controlled:

(a) environment or other molecules (b) amount of reactant/product available (c) pH (d) temperature