I. Matter and Energy
- Matter is anything
that takes up space and has mass
- Three states of matter exist (solid
liquid and gas)
- The fundamental units of matter are
elements which are composed of atoms that are subdivided into subatomic
- Elements are
substances that cannot be broken down into other substances by ordinary
- Each element is represented by
letters (e.g. H = hydrogen, C = carbon, etc...)
- There are six elements that
frequently occur in organic matter: CHNOPS = Carbon, Hydrogen,
Nitrogen, Oxygen, Phosphorus, and Sulfur: Diagram
- Elements are organized into
compounds and molecules:
- Molecules - two or more of the
same element held together by chemical bonds. (e.g. O2)
- Compounds - two or more
different kinds of elements held together by chemical bonds. (e.g.
C. Organization of Matter
- Atoms are the smallest possible
amount of an element.
- Atoms of the same element share
similar chemical properties.
- Atoms are composed of subatomic
- Electrons (e-,
negatively charged) high energy, low mass
- Protons (p+,
positively charged) low energy, high mass
- Neutrons (n0,
neutral charge) low energy, high mass
- Protons and neutrons are packed into
a dense core called a nucleus
- Positively charged protons are
attracted to negatively charged electrons, but electrons have high
amounts of energy, defying attraction to protons and spins around the
- The three dimensional space
electrons are found is called an orbital.
- Elements are defined by the atomic
number and mass number.
- Atomic number =
the number of protons in an atom
- Mass number =
the number of protons and neutrons in an atom
- Examples - helium represented as He
- Atomic number = 2 (two protons)
- Mass number = 4 (two protons and
- Isotopes - atoms of
an element that have the same atomic number but different mass number. Diagram
II. Energy and Energy Levels
- Energy is the
ability to do work (types = mechanical, chemical, thermal, and
- Energy is defined as being either
potential or kinetic:
- Kinetic energy
- energy of motion which is directly proportional to the speed of that
motion. (e.g. electrons moving within an orbital)
- Potential energy
- energy stored by matter as a result of its location or spatial
arrangement. Different states of potential energy of electrons in an
atom is referred to as an energy level. The more an energy an
electron possesses, the further away (thus high energy level) the
electron will be from the nucleus
III. Element's Chemical
Properties and Chemical Bonds
- Chemical behavior of an atom is
determined by the electron configuration of the outermost electron
- Electron configuration
is the distribution of electrons in each atom's energy level: Diagram
- Electron configuration rules:
- Electrons must first occupy
lower electron levels before the higher levels can be occupied.
- The first energy level of an
atom has only two electrons and all higher energy levels have eight
- If an atom doesn't have enough
electrons to fill all energy levels, the outermost level will be the
only one partially filled with valence electrons
(electrons in outermost energy level).
- Octet Rule - with the
exception of the first energy level, the valence level is complete when
it contains eight electrons.
- As a result of incomplete valence
levels, atoms fill those levels by interacting with each other forming chemical
bonds (attractions that hold molecules together)
- There are three general types of
chemical bonds: ionic, covalent, and hydrogen: Diagram
- Covalent bonds
- chemical bond between atoms formed by sharing a pair of electrons.
- Covalent bonds may be
single, double, or triple.
- example --> hydrogen gas
- H2 (molecular
formula = # and types of elements)
- H-H (structural formula = #
of elements & bonding)
- Ionic bonds -
bond formed by the attraction after the complete transfer of an
electron from a donor atom to an acceptor.
- Such a relation ship forms
an ion (charged atom).
- There are two types of ions:
- Anion - an atom
that has gained one or more electrons from another atom and has become
- an atom that has lost one or more electrons and has become more
- Hydrogen bonds
- bond formed between a slightly positive hydrogen and a slightly
IV. Chemical Reactions
- Chemical Equation: Reactant +
Reactant ---------- Product(s)
- May be reversible
- Tends toward equilibrium
- Types of Reactions:
- Synthesis reactions (A +
B --> AB), usually anabolic, requires energy (endergonic) to build
- Decomposition reaction
(AB --> A + B), usually catabolic, releases energy (exergonic) to
break down compounds. Diagram
- Exchange/displacement reaction
(AB + CD ---> AD + CB), may or may not require\release energy. Diagram
- Redox reactions -
compounds may gain or lose electrons:
- oxidized - reactant loses an
- reduced - reactant gains an
- Chemical reactions are effected by
particle size, temperature, concentration, catalysts, etc...
V. Inorganic and Organic
i. Inorganic compounds
- Compounds that contain no carbon or
if containing carbon, may also contain elements other than HNOPS
- Examples: water, salts, acids, and
- Water and Its Properties:
- High heat capacity
- absorb/release large amounts of heat energy without changing in
- High heat of
vaporization - heat energy to cause transformation (disrupt
hydrogen bonds) of water from liquid to gas.
- Polarity -
unequal distribution of electrons causing slightly positive hydrogens
and slightly negative oxygens.
- Solvent -
water dissolves solutes (therefore compounds are dissociated in water).
- Reactant -
involved in hydrolysis reactions and dehydration synthesis reactions.
absorber (e.g. joints and cerebral spinal fluid)
- Salts are ionic compounds
consisting of cations other than H+. The dissociation of
salts with water forms electrolytes which are ions that conduct
electrical current in solution.
- Acids and bases...
- Acids -
hydrogen ion (H+ = proton) donors
- Bases -
- pH -
measure of protons in solution. (scale 0.0-14.0) Diagram
- reacting acids with bases yielding a water and a salt.
ii. Organic compounds
- Compounds containing carbon but may
also contain hydrogen and oxygen
- Biologically organic compounds may
contain (in addition to C,H,O) nitrogen, phosphorus, and sulfur.
- Types of organic compounds
- Carbohydrates - composed of
units called saccharides
- Lipids - composed of units
called fatty acids
- Proteins - composed of units
called amino acids
- Nucleic acids - composed of
units called nucleotides
A. Carbohydrates Diagram
- Compounds containing carbon,
hydrogen, and oxygen in exact ratios (CnH2nOn)
- Carbs are divided into two classes
called simple sugars (monosaccharides and disaccharides) and complex
sugars (oligosaccharides and polysaccharides).
- Monosaccharides - one
saccharide, made up of 5 (pentose) and 6 (hexose) carbons. e.g. ribose
(pentose) is component of RNA and DNA & glucose, fructose,
and galactose all hexoses are biologically important in the
production of energy.
- Disaccharides - two saccharides
formed from a synthesis (dehydration/synthesis) reaction. egs. sucrose
(glu + Fru), lactose (glu + gala), and maltose (glu +
- Polysaccharides - starches (in
plants) and glycogen (in animals), both composed of many glucoses.
- Carbohydrates provide cellular fuel;
glucose is oxidized in body cells and bond energy released during
oxidation is transferred and trapped in the bonds of ATP molecules
(adenosine triphosphate). ATP is then used in subsequent endergonic
(energy requiring reactions).
B. Lipids Diagram
- Lipids are composed of fatty acids
- Fatty acids are compounds containing
long chains of carbons and glycerol is a compound containing a small
chain of three carbons
- Lipids are divided into three
classes: Triglycerides, Phospholipids, and Sterols.
- Triglycerides - considered the
most usable form of energy in the body and is composed of three fatty
acids bound to one glycerol by dehydration synthesis. Triglycerides may
be saturated or unsaturated.
- Phospholipids - component of
cell membranes and is composed of one glycerol, two fatty acids. and a
- Sterols (steroids) - isoprene
units (rings of carbon) egs. cholesterol and sex hormones.
C. Proteins Diagram
- Proteins are composed of long chains
of amino acids.
- Peptide - short chain of amino acids
- Polypeptide - long chain of amino
- Structural Levels:
- Primary = sequence of amino acids
- Secondary = coiling of primary
due to hydrogen bonding
- Tertiary = folding of secondary
due to hydrogen and sulfur bonds
- Quaternary = many tertiary
proteins bonded together
- Biological structures: Fibrous and
- Fibrous - strand-like
appearance, mostly secondary structure, and referred to as structural
- Structural/mechanical -
collagen, keratin, and elastin
- Movement - actin and myosin
- Globular - compact
spherical tertiary proteins referred to as functional proteins
- Functional proteins may
- Example of globular proteins
- catalysts - enzymes
- transport - hemoglobin
- pH regulation - plasma
- metabolism regulation -
peptide and protein hormones
- body defense -
- Enzymes - globular
proteins that act as biological catalysts of reactions and are made up
of protein and a cofactor/coenzyme (helpers of enzymes).
- Mechanism of enzyme action:
- Enzyme-substrate complex
formation --> enzyme binds substance (substrate) on which it acts to
a special site (active site) on the enzyme.
- Enzyme-substrate complex
undergoes an internal rearrangement that forms a product. Diagram
- Enzyme releases the product
of the reaction and now can catalyze another reaction.
- Enzymes lower a reactions activation
energy which is the energy required by compounds in order to react.
D. Nucleic Acids Diagram
- Nucleic Acids (DNA and RNA) are
composed of nucleotides
- Nucleotide are the basic building
blocks of our genetic information (chromosomes)
- Each nucleotide contains three
- Phosphate group
- Nitrogenous base (adenine, guanine, cytosine,
thymine found in DNA and adenine, guanine, cytosine,
uracil found in RNA)
- Note: cytocine complimentarily binds to guanine and andenine complimentarily binds to thymin/uracil