Unit 2 Chemistry
Chemistry Note outline
See your notes periodic table, know how to find the element name of an atom, facts
about an element
Organization of Matter
A. Matter is anything that occupies space and has mass.
1. It includes solids, liquids, and gases.
2. Matter is made of some ninety-two naturally occurring elements; the four most
abundant in humans are: O, C, H, and N (in decreasing order).
a. Trace elements are present in very small, but critical, quantities.
b. The symbol designation for each element is the same the world over.
3. Compounds are substances in which two or more elements are combined in
fixed proportions.
B. The Structure of Atoms
1. A molecule is a bonded unit of two or more (same or different) atoms.
2. An atom is the smallest unit of matter that is unique to a particular element.
3. Atoms are composed of three particles:
a. Protons (p+) are part of the atomic nucleus and have a positive charge. Their quantity
is called the atomic number (unique for each element).
b. Neutrons are also a part of the nucleus; they are neutral. Protons plus neutrons
=
atomic mass.
c. Electrons (e–) have a negative charge. Their quantity is equal to that of the
protons. They move around the nucleus.
C. Isotopes
1. Atoms with the same number of protons (for example, carbon with six) but a different
number of neutrons (carbon can have six, seven, or eight) are called isotopes (12C,13C,
14C).
2. Some radioactive isotopes are unstable and tend to decay into more stable atoms.
a. They can be used to date rocks and fossils.
b. Some can be used as tracers to follow the path of an atom in a series of
reactions or to diagnose disease.
know what ions are and isotopes. Ionized and radioactive
II. Bonds Between Atoms
A. The Nature of Chemical Bonds
1. A chemical bond is a union between atoms formed when they give up, gain, or
share electrons.
2. Energy Levels
a. Electrons are attracted to protons but are repelled by other electrons.
b. Orbitals, orbits, valances or shells permit electrons to stay as close to
the nucleus and as far from each other as possible.
c. Each orbital contains one or two electrons.
d. Orbitals can be thought of as occupying shells around the nucleus.
1) The shell closest to the nucleus has one orbital holding a maximum of
two electrons.
2) The next shell can have four orbitals with two electrons each for a total
of eight electrons.
e. Atoms with “unfilled” orbitals in their outermost shell tend to be
reactive with other atoms.
B. Ionic Bonding
1. When an atom loses or gains one or more electrons, it becomes positively or negatively
charged—an ion.
2. In an ionic bond, (+) and (–) ions are linked by mutual attraction of opposite charges,
for example, NaCl.
C. Covalent Bonding
1. A covalent bond holds together two atoms that share one or more pairs of electrons.
2. In a nonpolar covalent bond, atoms share electrons equally.
3. In a polar covalent bond, because atoms share the electron unequally, there is slight
difference in charge between the two poles of the bond; water is an example.
D. Hydrogen Bonding
1. In a hydrogen bond, an atom or a molecule interacts weakly with a hydrogen atom
already taking part in a polar covalent bond.
2. These bonds impart structure to liquid water and stabilize nucleic acids and other large
molecules.
III. Properties of Water
A. Water is a polar molecule because of a slightly negative charge at the oxygen end and
a slightly positive charge at the hydrogen end. Water molecules can form hydrogen
bonds with each other.
B. Polar substances are hydrophilic (water-loving); nonpolar ones are hydrophobic
(water-dreading) and are repelled by water.
C. Water displays three properties:
1. Water tends to stabilize temperature because it can absorb considerable heat
before its temperature changes. This is an important property in evaporative and
freezing processes.
2. Hydrogen bonding of water molecules provides cohesion (capacity to resist
rupturing), which imparts surface tension and helps pull water through plants, for
example.
3. The solvent properties of water are greatest with respect to polar molecules
because “spheres of hydration” are formed around the solute molecules.
IV. Acids, Bases, and Salts
A. Acids and Bases
1. A substance that releases hydrogen ions (H+) in solution is an acid; for
example, HCl.
2. Substances that release ions such as OH– that can combine with hydrogen ions
are called bases.
B. The pH Scale
1. pH is a measure of the H+ concentration in a solution; the greater the H+ the
lower the pH scale.
2. The scale extends from 0 (acidic) to 7 (neutral) to 14 (basic).
3. The interior of living cells is near pH = 7.
C. Buffers
1. Buffer molecules combine with, or release, H+ to prevent drastic changes in
pH.
2. Carbonic acid is one of the body’s major buffers.
D. Dissolved Salts
1. A salt is an ionic compound formed when an acid reacts with a base; example:
NaOH + HCl Æ NaCl + H2O.
2. Salts dissociate into useful ions (examples: Na+ and Ca++) in body fluids.
Chemistry/biochemistry
Note outline
1. Cellular Composition The Chemistry of Life
2. Molecular Composition of the Cell = Major Macromolecules in the Cell
Macromolecule group
functions
Proteins
Structure, Enzymes(function)
Carbohydrates
Energy, structure
Lipids( Fats, Cholesterol
Structure, storage
Nucleic Acids
Information control systems
i. 1.5 Carbon Chemistry(Listen to lectures)
1. Important for understanding Biologically inportant molecules
2. Terminology Presented Not included in exams
ii. Carbohydrates
1. Energy source Glucose (C6H12O6)
2. Energy storage Glycogen (animals), Starch ( plants)
3. Macromolecular Building Blocks
a. Monosaccharide = simple sugar
Example: Hexoses = Glucose (only one used by the cell),
Galactose, Fructose
Not responsible for Trioses, linkage types
b. Disaccharides = 2 Monosaccharides joined together
Example: Maltose, Lactose, Galactose
c. Polysaccharides = Many Monosaccharides (polymers)
Example: Amylose (Starch), Glycogen, Not responsible for
Amylopectin
d. Structural Polysaccharides, some modified
i. Cellulose (Plant cell walls)
ii. Chitin (exoskeleton of Arthopods)
iii. Mucopolysaccharides (lubrication, found in mucus,
ets.)
iv. Pectin (cellular "glue") Impt for making jelly!
iii. Lipids
1. Water insoluble
2. Type: Fats (triglycerides), Phosplipids,
a. Fatty Acid
b. Glycerol
c. Saturated Fats
d. Unsaturated Fats
e. Phosplipids
3. Structure: all cell membranes (Fat = Phospholipid & Cholesterol),
4. Type: Cholesterol
a. Hormones, Steroids
b. In cell membrane and Myelin (nerves)
5. Functions:
a. Energy storage (Fat tissue, insulin converts excess sugar to
Fat)
b. Insulation of nerves (myelination)
c. Hormones, Steroids
6. Not responsible for Linkage types
iv. Nucleic Acids
1. Major Molecules DNA & RNA (Genetic Material)
2. Composed of nucleotides (Phosphate, Pentose (5C) Sugar,
Nitrogen Base)
a. Purines = Adenine, Guanine
b. Pyrimadines = Thymine, Cytosine, Uracil
3. Linear in Structure
4. Some RNA & circular DNA found in mitochondria & chloroplasts
(extranuclear)
5. DNA
a. Genetic Code, Inherited Information
b. Chromosome structure & function
c. Composed of deoxyribonucleotides (Adenine, Cytosine,
Guanine, Thymine)
d. Made in the nucleus, works in the nucleus
6. RNA
a. Translation of genetic information into protein structure
b. Composed of ribonucleotides (Adenine, Cytosine, Guanine,
Uracil)
c. Made in the nucleus, works in the cytoplasm
d. Types:
1. m-RNA, carries genetic code from the
nucleus to the cytoplasm
2. r-RNA, with protein forms structure of the
ribosome
3. t-RNA, specific ones for each amino acid,
carries amino acid to ribosome
v. Proteins
1. Structural = Collagen in bone & Muscle
2. Functional = Enzymes (Denatured by heat, will not work due to
shape change)
a. Catalyze every metabolic transformation
b. a b c enzymes
c. A ==> B ==> C ==> D
d. metabolic pathway
e.
f. A to B catalyzed by enzyme a
g. B to C catalyzed by enzyme b
i. C to D catalyzed by enzyme c, etc.
3. Building Blocks
a. Linear arrangement of Amino Acids (20)
b. Individual Proteins, different sequences of Amino Acids
c. Sequence of Amino Acids determined by DNA (genes)
d. Amino Acid sequence (primary structure) determines
foldings, shape etc. (tertiary structure)
e. Protein Function depends Amino Acid sequence and Shape
4. Protein Structure
a. Important for understanding Metabolism
b. Important for understanding Expression of Genetic
Information
c. Molecular organization
i. Primary Structure - sequence of amino acids,
specified by genetic code
ii. Secondary Structure - (Not important here)
iii. Tertiary Structure - folding Important for
understanding Enzyme Function
iv. Quaternary Structure - Important for understanding
Hemoglobin