Anatomy and physiology

Chapter 2
Chemistry

Energy
Has no mass, does not take up
space, can be measured by its
capacity to do work.
Two types of nrg.
Kinetic
Potential

Forms of energy
Chemical: energy stored in the bonds of
chemical substances
i.e. ATP when you release a P during
cellular respiration energy is released

Electrical energy
Flow of charged particles: electrons
CNS, muscles

Mechanical: directly involved in

moving matter
Radiant energy: the sun and all the
different light waves: i.e our retinas,
skin

Energy conversion:
Energy can be easily converted from one
form to another:
Law of conservation of energy: energy can
not be created nor destroyed BUT it can
change form. It is often lost in two
forms________,_______

What is Matter?

The stuff in which the known

universe is made.

Characteristics of matter:

Matter has mass

Matter occupies space. volume

The matter we know is shown

as elements in the periodic
table.

Matter can be broken down in to

smaller subunits called atoms. Atoms
are the smallest units of matter

Subatomic particles: protons, neutrons,

electrons.

Atomic number = # of protons

Neutral atoms Protons=electrons
Mass number = protons + nuetrons
Isotopes = same # of protons diff. #
neutrons.

Atomic mass: this number is the number of

protons plus the average number of
neutrons in that element. The number is
called the atomic weight or atomic mass.

The atomic weight is the average of all

Isotopes and their relative weights

Radioisotopes
An isotope that exhibits
radioactive behavior, because of
its deterioration.
Releasing alpha , beta or gama
particles

Molecules
The combination of
two or more atoms by
chemical bonds.

Atoms of each
element can be
combined to form a
new distinguishable
substance known as
a compound, a
compound is made by

 Mixture: physically intermixed

Type 1: solution: a homogeneous mixture of
gasses, liquids, or solids.
Solvent: dissolving medium
Solute: dissolved substance

Type 2: Colloids: a heterogeneous mixture

Sol-gel: start as a solution transform to a gel
Jello Cytosol in cells
Type 3: suspensions: heterogeneous
mixture with large visible solutes.

http://www.klast.net/bond/

 Ionic bonds: bonding by the attractive forces of

electrons/protons
Covalent bonds: bonds formed by the sharing
of electrons.
H-bonds: relatively weak, seen in proteins and
DNA

Chemical Reactions
Chemical reactions occur whenever bonds
are formed, rearranged or broken.
Chemical equations: tell you what is
happening in a reaction. They also tell the
proportion of reactants and products.

Patterns of chemical reactions:

Synthesis (combination): larger molecules
are formed from smaller molecules
Decomposition reaction: large molecules
are broken down into smaller molecules.
Exchange (displacement): both synthesis
and decomposition occur.
Oxidation and Reduction: decompositions
reactions in which electrons are exchanged
between the reactants. ( the breakdown of
food)

Energy flow:
exergonic reactions release
energy as a product:

endergonic reactions absorb

energy.
Hot and cold packs work this way.

Reversibility of Chemical Reactions

All chemical reactions are theoretically
reversible.
When the rate of reaction forward is
equal to the rate of reaction reverse,
the reaction has reached equilibrium.
A+B

AB

Factors influencing chemical reactions.

Temperature: this increases the
movement in molecules, increasing
collisions, increasing the reaction rate.
Concentration: the more the
reactants the faster a reaction can go.
Increasing the odds of collision.

Particle size: the smaller the

particle size the faster they move.
Thus increasing the rate of
reaction.
Catalysts: something that
increases the reaction rate without
being changed itself. Enzymes
work this way.

Biochemistry
Two major classes:
organic: covalently bonded
molecules, Large associated with
C
Inorganic: All others

Inorganic Compounds:
Water:
the most important inorganic
molecule; it is 60-80% of living
cells.
Has a high heat capacity.
(absorbs a lot of heat energy
before it changes temperature)

Water has a high heat of vaporization: it

will absorb a lot of NRG before the
bonds break.
Polar and the universal solvent
An important reactant in many
reactions.
Forms a protective cushion around
many organs of the body. i.e. Brain

Salts:
Salts are ionic compounds
containing Cat-ions other that H+ and
Anions other than OH-.
When they are dissolved in water
the dissociate into their component
ions. Known as electrolytes

Acids and Bases:

Acids: aka proton donors,they
dissociate in water to give H+ ions and
anions. HCl
H+ + ClBases: aka proton acceptors, they
absorb H+ ions
OH- + H+

H2O

The pH scale:the relative concentration

of H+ ions
0-14 with 7 being neutral
Logarithmic: the change in one pH is
ten fold.
More H+ more acidic number drops
Fewer H+ less acidic Number rises

Neutralization occurs when an acid

and a base are mixed together.
They go through a displacement
reaction to form a salt and water.
HCl + NaOH

Buffer: a substance that resists large

fluctuations in pH that would be
damaging to living tissue. ( proteins,
carbonic acid/bicarbonate system in
blood)

Organic Compounds
Defn: substances containing C
exception: Carbon dioxide,carbon
monoxide carbides
Why is carbon so cool? It is
electroneutral. It will share electrons at
all four binding sites

A. Carbohydrates:
Carbos contain CHO, generally the H
and O are in a 2:1 ratio.
Classified by the number of sugars.
Monosaccharides: simple sugars
single ringed structures. With a
CHO ratio of 1:2:1 (CH2O)n
n= number of carbons

Disaccharides:
double sugar: formed by the process of
dehydration synthesis. i.e glucose +
fructose= sucrose + water
These are too big to get into the cell so
we break them apart by hydrolysis.

Polysaccharides: many sugars

joined by dehydration synthesis.
Carbo functions: energy for the
cell.

More organic compounds:

B. Lipids: insoluble in water
Neutral fats: known as fat when
solid and oil when liquid.
composed of fatty acids and
glycerols. Saturated and
unsaturated
Phospholipids: diglycerides with a P
containing group.

Steroids: flat molecules made up of four

interlocking hydrocarbon rings. Fat
soluble and contain little oxygen.

testosterone

Estradiol

estrogen

Eicosanoids: diverse lipids derived from

arachidonic acid: used in blood
clotting,inflamation.

C. Proteins
Proteins compose 10-30 % of cell
mass.
basic structural material of the body
vital in cellular function

Proteins are long chains of amino acids

connected by peptide bonds.(bonds
that join the amine group to the
carboxyl group)
Proteins have four structural levels.
1. linear sequence of AAs is the
primary structure.( helix)
2. twisting is the secondary
structure.( pleated sheet)

3. Tertiary structure is the folding upon itself.

4.Quarternary results from two or more
polypeptide chains grouped together to form
a complex protein. (hemoglobin)

Fibrous/globular proteins:
Fibrous: extended and strand-like,
structural proteins. Generally
secondary structure. stable
globular: compact,spherical, water
soluble,chemically active,play important
roles in vital body functions(immunity)
will denature

Protein Denaturation:
The loss of 3-d structure. The activity
of a protein is specific to its structure.

Molecular Chaperins: globular proteins

that help in achieving the 3-d shape.

Enzymes:
Globular proteins that act as
biological catalysts
Can be pure protein or two subunits
called a Holoenzyme(apoenzyme +
cofactor)
Enzymes are chemically specific.
lower the activation nrg

Nucleic acids: DNA, RNA

The largest molecules in the
body.
Composed of C,O,H,N,P
Structural units of nucleic
acids
3 parts: nitrogenous base,
pentose sugar and a
phosphate group.

Five nitrogenous bases (memorize

these, name and structure)
Adenine (A)
Guanine (G)
Cytosine (C)
Uracil (U)
Thymine (T)
http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/words/purine.htm

purines

pyrimidines

Deoxyribonucleic acid: DNA

The genetic material of the cell.
DNA replicates itself before cell
division, sends out instructions for
making proteins.
Double stranded helical structure
defined by its sugar and the specific
bonding of its complementary bases.
A-T, G-C

Ribonucleic acid: RNA

Generally single stranded containing
bases G,C,U,A
The rule A+C=U+G CAN'T BE
APPLIED THERE
because most RNA is single
stranded and does not form a double
helix
Note that some viruses genomes are
made of double stranded RNA.

ATP: Adenosine Triphosphate

The energy currency of the cell.
The adenine-containing RNA nucleotide
has 2 additional phosphate groups
connected by high energy bonds.
Breaking these bonds releases energy the
cell can use to do work