Chapter 2-3 Chemistry & Biochemistry of Life
Chapter 2-3
Chemistry &
Biochemistry of
Life
Composition of Matter
Matter: anything that occupies
space & has mass
Mass: quantity of matter an object
has; not the same as weight
- All matter made of elements
Sect 1
Elements
-Substances that cannot be broken
down chemically into simpler
substances
- 90% of mass of living things made of
4 elements: C, H, O, N
Atom: simplest particle of an element
that retains properties of that element
-Nucleus contains most mass of an
atom
Proton: positive charge
Neutron: no charge
- # of protons = atomic #
- # of protons + # of neutrons
= mass number
Electrons: negatively
charged particles outside
nucleus
-Have virtually
no mass
Orbital: 3-D region around a nucleus
that indicates the probable location of
an e-
-If # of protons doesn’t = # of e-,
charged atom (ion)
-Sometimes # of protons doesn’t = # of
neutrons, isotopes
-will change atomic mass, but not
identity of element
Compounds
1. A group of atoms in a fixed ratio.
a. Held together by chemical bonds.
b. Represented by formulas:
e.g. - H20, NaCl, C6H12O6 c. Three types of bonds
in biology:
1). Covalent bond - 2
atoms share e- (e.g. -
H2O)
molecule: 2 or more
atoms covalently bonded.
2)Ionic bond - 2 atoms of opposite charge join. The e- are transferred from one (+ ion) to another (- ion).
3) Hydrogen bonds - force of
attraction between a hydrogen molecule w/ a partial positive charge & another atom or molecule w/ a partial or full negative charge
Energy & Matter
Energy: ability to do work
-Chemical E, light E, thermal E, etc
-E is absorbed or released when
chemical bonds are formed or broken
Chemical reaction: 1 or more
substances change to produce 1 or
more different substances
Sect 2
Reactants: substances reacting
together; starting substances in a
chemical rxn
Products: new
compounds/substances formed in
chem. rxn
Metabolism: all chem. rxn’s that
take place in an organism
-E usually has to be
added to reactants to
get a rxn to begin
Activation E: E
needed to start a rxn
Catalyst: chemical substance that
lowers the amount of activation E
necessary
Activation E
Enzyme: protein
or RNA molecule
that catalyzes
chemical rxn’s
w/o being
changed or
destroyed
Oxidation Reduction Reactions
*Oxidation is the loss of electrons.
*Reduction is the gain of electrons.
- Reactions in which e-’s are
transferred; redox reactions
Na + Cl Na+ + Cl-
LEO goes GER
--lose electrons = oxidation
--gain electrons = reduction
- Charge on atoms in H2O is
unequally distributed even though
overall charge is neutral
Sect 3
Water & Solutions
Polarity: describes a molecule
with opposite charges on opposite
ends
O
H H
δ- δ-
δ+ δ+
-polarity allows water to dissolve
polar substances
--accounts for many of
H2O’s properties
Hydrogen bond: force of attraction
between a hydrogen molecule with
a partial or full negative charge
1.Cohesion:
attractive force
that holds
molecules of a
single substance
together (H2O
attracted to H2O)
- gives H2O
surface tension
2. Adhesion: attractive force between
2 particles of different substances
-These forces are strong enough so
H2O clings to other surfaces
3. Capillarity:
attraction between
molecules that
results in the rise of
the surface of a
liquid when in
contact with a solid
- H2O can rise
against gravity up a
narrow tube
4. High Heat Capacity (specific heat):
H2O can absorb or release large
amounts of heat w/ only a slight temp
change
- Breaking H-bonds takes lots of E, & E
is released when they are formed
- Why water takes a long time to boil
-In summer, H2O absorbs heat, releases it
at night
--why is it cold in a desert at night?
- helps keep cells at a constant temp
-When H2O evaporates from surface, takes
heat with it = evaporative cooling (sweating)
5. Ice Floats: ice is less dense than
liquid water
- Due to shape of molecule at 4oC,
large amounts of open space form
when H2O freezes
-allows aquatic organisms to survive on
the bottom of bodies of water
Solutions -Mixture in which one
or more substances
are uniformly
distributed in another
substance
Solute: substance
being dissolved
Solvent: substance in
which solute is
dissolving
2016
Concentration [ ]: amount of
solute dissolved in a fixed
amount of the solution
-the more a solute is
dissolved, the higher the [ ]
Saturated soln: no more
solute can be dissolved
Aqueous soln: H2O is
solvent; where most bodily
rxns occur
This is
sweet tea,
bless your
heart!
Acids & Bases
- Acidity & alkalinity are measures
of amounts of hydronium ions
(H3O+) & hydroxide ions (OH-)
-these form randomly in water due
to collisions of molecules
pH = potential hydrogen
- More H3O+ ions than
OH-; 1-6.9 on pH scale
- H3O+ ions = OH-
ions; 7 on pH scale
- More OH- ions than
H3O+; 7.1-14 on pH
scale
pH scale:
scale for
measuring
the amt of
H3O+ ions &
OH- ions in
soln.
• pH or
litmus paper
Buffers
-Chemical substances
that neutralize small
amounts of either an
acid or a base
--buffering systems
maintain pH values in
healthy bodies
Chapter 3
Biochemistry
Organic compounds:
compounds made primarily of
Carbon atoms
-most matter in living organisms
Inorganic compounds: don’t
contain C (w/ a few exceptions)
Sect 1
Functional Groups
-clusters of atoms that influence the
characteristics of the molecules
they compose & the chemical rxns
they undergo
1.Hydroxyl = -OH
- form alcohols
2.Carboxyl
- form carboxylic acids
O
C OH
3.Amino
- form amines
H
N H
4. Phosphate
O
P
OH
O OH
Large Carbon Molecules
Monomer: small, simple molecule
Polymer: repeated, linked
monomers
Macromolecules: large polymers
*carbohydrates, lipids, proteins, &
nucleic acids
Condensation rxn (dehydration synthesis): - chemical rxn that links monomers together
-H2O formed as a byproduct
-H from 1 monomer & OH from 1 monomer
Hydrolysis rxn:
- H2O is used to
break polymers
into monomers
- reverse of
condensation rxn p. 53
Energy Currency
-Life processes require constant
supply of energy
ATP: adenosine triphosphate
-covalent bonds between
phosphate groups are unstable &
easy to break
- This releases energy used to drive
chemical reactions in organisms
4 Molecules of Life
1.Carbohydrates: Source of energy or
are structural materials in cells
a.Monosaccharide:
- monomer of a carbs simple sugar
- organic compounds made of C, H, & O in ratio of 1:2:1
ie: glucose, fructose, galactose
Sect 2
b. Disaccharide: double sugar
- monosaccharides combine
- Fructose + glucose = sucrose
(table sugar)
c. Polysaccharide: complex
molecule composed of 3 or more
monosaccharides
2 types:
1.Storage:
- animals store glucose as
glycogen in liver or muscle
- plants store glucose as starch
2. Structural
- plants have cellulose (gives
strength & rigidity to plant
cells; makes up 50% of wood)
- arthropods have chitin
2.Proteins: organic compounds made mostly of C, H, O, & N
- Macromolecules made of amino acids
- 20 diff aa’s; differ at their R group (side chains) & give proteins different shapes
- Different shapes = different functions
-aa’s form peptide bonds (covalent
bond formed by condensation rxn)
Polypeptide: long chain of aa’s
-1 or more polypeptide chains make up
proteins
-These long chains bend on
themselves, interact w/ themselves thru
H-bonds to create 3-D shapes
(conformation)
*shape of protein is very important
to its function!!!
Enzymes: RNA or protein
molecules that act as catalysts;
most are proteins
Substrate: reactant being
catalyzed; binds to enzyme at a
specific place called active site
-Has a shape that allows only that substrate to fit
--when substrate binds, there’s a slight change in shape of enzyme
--this lowers EA of rxn by weakening bonds in substrate
-- after rxn, products are released, enzyme is unchanged (can be used again)
Factors that Affect Enzymes
- Enzyme activity is directly related to its shape
- If shape changes (denaturation), so does function
1.Temperature
2.pH
3.Salt concentration
3.Lipids
-large, nonpolar, organic molecules;
don’t dissolve in H2O
- triglycerides, phospholipids, steroids,
waxes, & pigments
- Have large # of carbon-hydrogen
bonds = store lots of energy
Fatty acids:
unbranched carbon
chains that make up
most lipids
Hydrophilic region
(carboxylic acid): will
be attracted to water
Hydrophobic region
(hydrogen carbon
chain): is repelled by
water
a. Triglyceride (fats): composed of
3 molecules of fatty acid joined to 1
molecule of the alcohol glycerol
Saturated fatty acid: each C atom is covalently bonded to 4 other atoms
- Single bonds between carbons
- Each C atom is “full” or saturated
- Solid at room temperature
Unsaturated fatty acid:
C atoms are not
bonded to maximum #
of atoms they can be
-Have double bonds
w/in carbon chain
- Liquid at room
temperature
b. Phospholipids: 2 (not 3) fatty
acids attached to molecule of
glycerol, which has a phosphate
group attached
-make up phospholipid bilayer of
cell membranes due to their ability
to form a barrier between outside &
inside cell
c. Waxes: type of structural lipid
consisting of a long fatty-acid chain
joined to a long alcohol chain; are
waterproof
-form protective coatings on outside
of plants & inside animals
d. Steroids: composed of 4 fused
carbon rings w/ various functional
groups attached
ie: cholesterol as precursor for
testosterone
4.Nucleic Acids: large
& complex organic
molecules that store &
transfer important info
in the cell
Made of nucleotides:
phosphate group, 5-C
sugar & a ring-shaped
nitrogenous base
RNA = ribonucleic acid; stores & transfers
info from DNA for making proteins
-DNA = deoxyribonucleic acid;
determines characteristics of an
organism & directs cell activities