I.
Section 2-1 The Nature of Matter
-
Life depends on chemistry. Your body uses the food you eat and the
oxygen you breathe in chemical reactions that keep you alive
Living things are made from chemical compounds
A. Atom- the basic unit of matter; "unable to be cut"
1. Placed side by side, 100 million
atoms would make a row one
your
pinkie!
centimeter long-the width of
2. Subatomic particles within an atom: Protons, neutrons and
electrons
a. Proton-positively charged particle
b. Neutron- no charge; both protons and neutrons have about
the same mass
c. Nucleus- strong forces bind protons and neutrons together to
form this, found at the center of an atom
d. Electron- negatively charged particle with 1/1840 the mass of
a proton; electrons are in constant motion around the nucleus
being both attracted to the positive protons in the nucleus yet
remain outside the nucleus due to the energy of their motion
e. OVERALL- the atom is neutral in charge with the number of
protons balanced by the number of electrons (therefore, equal
but opposite charges)
B. Elements and Isotopes
1. Element- a pure substance that consists entirely of one Wpe of
atom; about 241t00 known elements are commonly found in living
organisms.
2. Atomic number- the number of protons in an atom of the
element
3. Isotope- Atoms of the same element that differ in the number of
neutrons; Mass number/atomic mass- the number of protons + the
number of neutrons in the nucleus of one atorn of an element
4. Because they have the same number of electrons, all isotopes of an
element have the same chemical properties
5. Radioactive isotopes- the nuclei are unstable and break down at
a constant rate over time; the radiation given off can be dangerous
yet these isotopes play crucial roles in the study of science
6. Geologists can determine the age of rocks and fossils by analyzing
the isotopes found Within; Radiation from ceftain isotopes used to
treat cancer AND kill bacteria in the food we eat!
T.Inbiology,theseisotopescanbeusedas.'tracers,,tofollowthe
to follow the
|.norem6nt of substances within organisms OR used
rePlication of DNA within cells
chemical combination of
c. chemical compounds- a substance formed by the
proportions
two
-" - or more elements in definite
a
1. Scientists show the chemical composition of these compounds using
chemical formula (HzO or COz or NaCl)
much
2. The pnyircaiand chemical properties of a compound are usually
different from the elements that form it
in compounds
D. Chemical gonJ.-for..t that hold atoms together
1. Bond format'lon involves the electrons that surround each atomic
-
nucleus.Valenceelectrons.thoseelectronsthatareavailableto
form bonds
types of chemical bonds are ionic and covalent
2. The
bonds
from
3. Ionic bond- fOrmed when one or more electrons are transferred
the attraction of
one at;; io anottrer; USUALLY forms due to
,iin
are electrically neutral
oppositeiy inirgeo ions; REMEMBER: atoms
positive charge
tnererore, ir unito* t-cisrs one or more electrons =
negative charge
JUST RS if an atom GAINS electrons =
4. Ion- positively and negatively charged atoml.;.lPilt,1-3
between- atoms;
5. Covaleni UonO- formi when electrons are SHARED
between the atoms
sHARr = moving electrons are located in a region
where the electron orbitals overlap
4
6. Single covalent bond- atoms share two electrons; Double =
shaied electrons; Triple = 6 shared electrons
are joined together
7. Molecule- the structure that results when atomscompounds
unit of most
Oy couJent OonOs, it is the smallest
close together' a
B. Van der waals forces- when molecules are found
charged regions
slight attraction can develop between th.e. oppositely
molecules together
of n.uiO,-roi.cules; thereiore, involved in holding
in large complexes-example = Gecko's feet
II.
A.
Section 2-2 Propefties of Water
Facts about water
l.
of the world is covered by oceans
2. Water is the single most abundant compound in most living things
3. Water is one of the few compounds that is a LIQUID at the temperatures
found over much of the Earth's surface
4. Water expands as it freezes (unlike most other substances); therefore ice
is LESS DENSE than liquid water and floats on the surface of lakes and rivers
5. If ice was MORE DENSE than liquid water, it would sink to the bottom,
being disastrous to life living in the water at cold temperatures!
B. The water molecule
1. It is neutral in charge, like all molecules
2. Polarity-within the covalent bond formed between the oxygen and
hydrogen atoms, the oxygen atom has a much stronger attraction for the
shared electrons; therefore, the oxygen end of the molecule is slightly
negative vs. the hydrogen end is slightly positive
3. Polar molecule- charges are unevenly distributed throughout the
molecule; it is like a magnet with poles of charge
4. Hydrogen bonds- the attraction between the paftial (+) charge of the
hydrogen of one molecule (in this case, water) and the paftial (-) charge
on the atom of a second molecule (in this case oxygen atom in water).
These bonds are the strongest that form between molecules (yet, not as
strong as ionic and covalent bonds forming between atoms)
NOTE: a single water molecule may be involved in as many as
FOUR hydrogen bonds at the same time; the ability of water to
form multiple hydrogen bonds is responsible for many of water's
unique properties
5. Cohesion- attraction between molecules of the same substance; water's
cohesive ability causes molecules on water's surface to be drawn inward
(why drops of water form beads on a smooth surface) as well as
explaining how a spider or insects can walk on a pond's surface
6. Adhesion- attraction between molecules of different substances (for
example, looking at the meniscus of a graduated cylinder). Capillary
action- adhesion between water and glass allows water to rise in a narrow
tube against the force of gravity (responsible for drawing water out of a
plant's roots and into its stems and leaves)
75o/o
C, Solutions and suspensions
1. Mixture- a material composed of two or more elements or compounds
that are physically mixed together but not chemically combined (salt and
pepper mixed together OR sugar and sand OR Earth's atmosphere
Z. 2 ty'pes of mixtuies that can be made with water are solutions and
susPensions:
a. bolution- all of the components are evenly distributed throughout a
solution; Solute- substance that is dissolved vs. Solvent- the substance
in which the solute dissolves within
b. Water's polarity gives it the ability to dissolve both ionic compounds as
well as other polar molecules (such as sugar); WATER IS THE
GREATEST SOLVENT ON EARTH!
c. Suspension- mixtures of water and nondissolved materials; these
materials do not completely dissolve within water but are separated
into pieces so small that they do not settle out (the movement of
water molecules keeps them suspended)
d. Blood is both a solution AND a suspension since it is water-based;
there are both dissolved materials (solution) as well as other
undissolved particles (suspension) as blood moves throughout the
bodY
D. Acids. Based and PH
1. a water rnolecule can react to form ions (H+ and OH-)HzO
2.
<--)
H+ and OH-
pH scale- indicates the concentration of H* ions in solution
pH < 7 is acidic meaning solution conta.ins more H* vs OH- ions
b. pH = 7 means the concentration of both ions is equal OR neutral
;.
pH
c. ph > 7 is basic meaning concentration
ions
NoTE: the pH scale is LoGARITHMIC (based on units of t0)
Buffer- weak acids or bases that can react with a strong acid or base
io prevent sharp, sudden changes in pH. Buffers are used to control
homeostasis (most chemical reactions that take place within a cell only
occur at a PH between 6.5-7'5
d.
3.
of H+ ions is lower than OH-
A. The chemistry of Carbon
1. Organic chemistry- study of all compounds that contain bonds between
B.
carbon atoms
2. WHY is there a whole branch of chemistry devoted to this element?
a. Carbon atoms have 4 valence electrons; therefore each electron can
join with an electron from another atom to form a strong covalent
bond
b. Carbon can bond to other carbon atoms, giving carbon the ability to
form chains almost unlimited in length; these bonds can be single,
double or triple covalent bonds; in fact, these chains of carbon atoms
can close upon themselves forming rings
c. Carbon is the most versatile element on the planet
Macromolecules - "giant molecules" , most of the molecules in living cells
are these large molecules
1. They are formed by polymerization in which small molecules are joined
together to form larger ones; MONOMERS join together to form DIMERS
and, eventually, POLYMERS (each monomer may be the same or different
as they are linked together)-Figure 2-L2
2. There are FOUR groups of orginic compounds found in living things:
c. Nucleic acids
a.
d. Proteins
b.
a. Carbohydrates- compounds made up of carbon, hydrogen and
oxygen atoms in a ratio of 1:2:1
1. Purpos6- main energy source in living things. In addition, some
plants and animals use these for structural purposes
2. The breakdown of sugars supplies immediate energy for all cell
activities; in addition, extra sugar is stored in the form of starch (a
polymer/polysaccharide)-Figure 2- 13
3. Monosaccharide- single sugar molecule (glucose, galactose, and
fructose)
4. Disaccharide- two sugar molecules linked together (sucrose and
maltose)
5. Polysaccharide-large macromolecules formed from many, many
monosaccharides linked together (glycogen = animal starch) vs.
(plant starch)
6. iellulose- plant polysaccharide providing plants with much of their
strength and rigidity; major component of wood and paper
Carbohydrates
Lipids
b. Lipids- insoluble in water, they are made up mostly from carbon and
hydrogen atoms (examples include: fats, oils, waxes, STERIODS)
1. Purpose- Long-term energy storage as well as being important
components of biological membranes and waterproof coverings
2. Formed when a glycerol molecule combines with fatty acid
compounds (Figure 2-L4)
3. Saturated lipid- every carbon atom is joined to another carbon
atom by a single covalent bond (the fatty acids therefore contain
the maximum number of hydrogen atoms)
4. Unsaturated lipid- at least one carbon-carbon double bond in a
fatty acid; more than one double bond = polyunsaturated
5. Olive OlL/cooking oils = unsaturated = liquid at room temperature
C. Nucleic Acids- macromolecules containing hydrogen, oxygen,
nitrogen, carbon and phosphorous
1. tt'lucleotides (monomers) assemble to produce these via covalent
bonds
2. f,f ucieotiae- a S-carbon sugar, a phosphate group and a
nitrogeneous base (Figure 2-15)
3. Purpose: to store and transmit hereditary or genetic information
(DNA and RNA)
D. Proteins- contain nitrogen as well as carbon, hydrogen and oxygen
1. Monomers (amino acids) combine to form proteins; amino acids
are compounds with an amino group 1-NHz) on one end and a
carboxyl group (-COOH) on the other end; there are 20 a.a. found
in nature and they all are identical in the region where they are
joined together by covalent bonds (bonding a carboxyl group to an
amino group); differences lie in their FUNCTIONAL GROUPS or side
chain/R-group
2. R-groupi can be acidic, basic, polar, nonpolar, or contain carbon
rings; the instructions for the arrangement of the a.a. into different
proteins is encoded by DNA
3. EACH PROTEIN HAS A UNIQUE ROLE in living things
a. control rate of reactions and regulate cell processes
b. form bones and muscles
c. transport substances into or out of cells
d. help to fight disease
4.
Four levels of organization in a protein (NOTE: VERY IMPORTANT
TO PROTEIN'S FUNCTION:
a. Primary = a.a. sequence in a protein chain
b. Secondary = twist or fold primary sequence to form an alpha
helix or a beta sheet
c. Teftiary = the secondary sequence/chain is folded onto itself
with the appearance of hydrogen bonding, Van der Waals
forces, disulfide bridges, etc.
d. Quaternaty = more than one secondary/teftiary chain is
bonded to each other (Figure 2-L7 blue and red structures)
IV.
1. Chemical Reactions- a process that changes
one set of chemicals
into another set of chemicals
a. Reactants- the elements or compounds that enter into a chemical
reaction
b. Products- the elements or compounds produced by a chemical
reaction
Chemical reactions always involve the breaking of bonds in
reactants and the forming of new bonds in products
(example is formation of carbonic acid within the bloodstream)
Energy in Reactions
a. As part of the breaking and forming of bonds, changes in energy
occur (energy is released or absorbed whenever the bonding either
forms or is broken, resPectivelY)
b. Chemical reactions that release energy often occur
spontaneouslY
c. chemical reactions that absorb energy will not occur
without a source of energy (the reaction requires an input of
energy in order for the chemical reaction to occur)
c.
.
2.
d.
need to carry out reactions
that require energy; every organism requires an energy source
to carry out chemical reactions
2. Plants obtain their energy via the trapping and storing of
sunlight (energy source) in energy-rich compounds
3. Animals obtain their energy when they consume plants and/or
animals; As humans metabolize (break down their digested
food) energy is released to drive life's processes
4. Activation energy- The energy that is needed to get a
reaction started; it is THE factor that determines whether the
overall chemical reaction releases or absorbs energy (Analyzing
Data example)
1. In order to stay alive, organisms
3.
4.
Enzymes- proteins that act as biological catalysts; they are NOT
"used up" or changed as a result of the chemical reaction
Catalyst- a substance that speeds up the rate of a reaction; they
function by lowering a reaction's activation energy
b. Cells use enzymes to speed up chemical reactions that take
place within cells (Figure 2-20)
Enzymes are very specific; with a one-to one relationship with the
chemical reaction they assist
Enzyme action
a. For a chemical reaction to take place, the reactants must collide
with enough energy so that existing bonds will be broken and new
bonds will form; NOTE: if the reactants DO NOT have enough
energy the bonds will remain unchanged after the collision and no
products will be formed
b. Enzymes provide a'tdocking site" where reactants can be brought
together to react; this site reduces the energy needed for the
reaction
Substrate- the reactants of an enzyme-catalyzed reactions;
therefore, this is referred to as an enzyme-substrate complex
d.
Active site- the actual site on the enzyme where the substrates
bind to each other; the active site and the substrate have
complementary shapes or a "lock and key" approach!
e. Once the reaction is finished, the products of the reaction are
released from the enzyme's active site and the enzyme is free to
start the process again (Figure 2-22)
Regulation of enzyme activity- any variable that impacts a
chemical reaction affects the enzyme directly. These factors
include: pH, temperature, proteins acting to turn on/off key
enzymes at key stages in the cell's life
g. Enzymes play essential roles in regulating chemical pathways,
making materials that cells need, releasing energy and transferring
information