Download Ch. 6 Biochemistry

Ch. 6 Biochemistry
I.
Atoms, Elements and Compounds
Atoms: building blocks of matter
1. matter: anything that has mass and takes up space
2. chemistry: the study of matter’s composition and
properties
3. atoms: building blocks of matter. Made of:
a. protons (p+): positively charged particles
located in nucleus
b. neutrons (n0): particles with no charge
located in nucleus
c. electrons (e-): negatively charged particles
that move around the outside of the nucleus
in energy levels
4. overall charge of atom = p+ + e- = 0
5. nucleus = core of atom = p+ + n0 = mass of atom
B. Elements: a pure substance that cannot be broken down into
other substances by physical or chemical means
1. 92 naturally occurring elements exist
2. C, H, N, O are the elements most abundant in
living things.
What elements are important?
1.
C
7.
S
13. Cu
2.
H
8.
Ca
14. Zn
3.
O
9.
Fe
15. Cl
4.
P
10. Mg
16. Mo
5.
K
11. B
17. I
6.
N
12. Mn
I C HOPKNS CaFe Mg B Mn CuZn Cl Mo
C, H, & O - 96% of Human weight
Water (H2O) - 75 - 85% of cell weight
What makes elements important?
a. Metabolism - photosynthesis, respiration, & other
metabolism
b. Heredity and evolution
c. Growth and development
d. Growth regulation
e. Physiological ecology
3. trace elements = required in very small amounts
(ex: iodine)
4. isotopes: atoms of the same element that have
different numbers of neutrons.
a. Ex : carbon-12 (p + n)
carbon-14
5. radioactive isotopes: unstable isotopes that give
off radiation
a. nucleus becomes unstable due to having
extra neutrons. Nucleus decays or breaks
apart, giving off radiation.
b. Ex: carbon-14 is used in dating remains
while others are used in radiation therapy for
cancer
C. Compounds: a pure substance formed when two or more
different elements combine (ex: water, salt, methane).
1. compounds always form from a specific
combination of elements in a fixed ratio
2. compounds can’t be broken down into simpler
compounds or elements by physical means
3. compounds do not always have the properties of
the elements that make them up (ex: NaCl does not
have the properties of sodium or chlorine)
D. Chemical Bonds
1. covalent: 2 atoms share electrons (ex: water,
sugars, fats, proteins)
a. molecule: a compound in which the atoms
are held together by covalent bonds
b. covalent bonds can be single, double or
triple depending on how many pairs of
electrons are shared
2. ionic bond: transfer of electrons from one atom to
another (ex: NaCl—salt). When atoms lose or gain
electrons they either have a positive or negative
charge.
a. ion = charged atom
b. in living things, ions include Na+, K+, Ca2+,
Cl- and carbonate ions. These ions help
maintain homeostasis and cellular
communication.
c. Electrical attraction between ions holds
atoms together
3. # of electrons each energy level can hold:
1st—2 e2nd—8 e3rd – 18 e4th – 32 ea. atoms are stable if the outermost energy
level is full (8 electrons)
b. some atoms donate or accept electrons more
easily than other atoms.
 Metallic atoms tend to donate electrons
 Nonmetals tend to accept electrons
c. ionic compounds break down into ions when
dissolved in water and can carry an electric
current
E. van der Waals Forces: attractive forces between molecules (ex:
water molecules)
1. caused by temporary areas of slightly positive and
negative charges created by unequal distribution of
the electron cloud around a molecule
2. strength of molecule attraction depends on size and
shape of molecule and its ability to attract
electrons.
3. van der waals forces are not as strong as covalent
or ionic bonds
4. help hold water molecules together to form
droplets and a surface
F. Polar Molecule: molecule with oppositely charged ends (ex:
water)
1. Oxygen end of water is bigger and pulls harder on the
electrons causing the oxygen end to be slightly negative and the
hydrogen ends to be slightly positive. Opposites attract so that
is why water molecules stick together and you can skip a rock
across a pond’s surface.
II. Chemical Reactions: process by which atoms or groups of
atoms in substances are reorganized into different substances
1. in living things, chemical reactions allow growth,
development, reproduction and adaptation.
A. Chemical Equations: chemical reactions are expressed in
equations.
Reactants → Products
C6H12O6 + O2 → CO2 + H2O
(glucose and oxygen react to form carbon dioxide and water)
1. atoms are neither created nor destroyed in a chemical
equation—only rearranged (law of conservation of mass).
C6H12O6 + 6O2 → 6CO2 + 6H2O
B. Activation energy: the minimum amount of energy needed for
reactants to form products in a chemical reaction
1. reactions may be exothermic (release energy like
heat/ light) or endothermic (energy is absorbed
causing cold)
C. catalysts: a substance that lowers the activation energy needed to
start a chemical reaction
1. enzymes: special proteins that act as biological
catalysts in living organisms to speed up the rate of
chemical reactions
a. enzymes may be used again after a reaction
b. ex: amylase found in saliva speeds the
breakdown of starch
2. substrates: the reactants that bind to the enzyme
3. active site: the specific location where a substrate
binds on an enzyme
a. once bonded, the active site changes shape
and forms the enzyme-substrate complex
which helps chemical reactions occur
between substrates to form the new product
which is then released.
III.
Water and Solutions
A. Water’s Polarity
1. polar molecules: molecules that have an unequal
distribution of charges causing oppositely charged
regions.
2. hydrogen bond: the attraction of the positive
hydrogen end of a water molecule to the negative
end of another water molecule in water
a. a strong type of van der Waals force
B. Mixtures with water
1. mixture: a combination of two or more substances in which
each substance retains its individual characteristics
and properties
2. types of mixtures:
a. homogenous mixture (solution): uniform
composition throughout (substances evenly
distributed). Ex: salt water, air, tea, saliva,
gasoline
solute = substance being dissolved
solvent = dissolving medium
water = universal solvent
b. heterogenous mixture: components remain
distinct (you can identify the individual
components)
1.suspension = particles settle out to
bottom (ex: sand/ water)
2. colloid = particles do not settle out
(ex: blood, fog, smoke, milk)
C. Acids and Bases
1. acids: substances that release hydrogen ions (H+)
when dissolved in water; ex: HCl (hydrochloric
acid)
2. bases: substances that release hydroxide ions
(OH-); ex: NaOH (sodium hydroxide)
3. pH: the measure of concentration of H+ in a
solution.
0←--------------------------7--------------------------→14
increasingly acidic neutral
increasingly basic
< 7 = acidic
> 7 = basic (alkaline)
7 = neutral = pure water
Acid = forms hydrogen ions (H+) in water
Ex: HCl (stomach acid)
Base = forms hydroxide ions (OH-) in water
Ex: NaOH (sodium hydroxide)
4. buffers: mixtures that can react with acids or bases
to keep pH within a particular range
a. in living cells, buffers keep the pH within
6.5 to 7.5.
Neutralization Reaction: Acid + Base
Water’s Unique Properties:
 We can only survive a few days w/o water (makes up 70% of cells)
 Because it is polar, water attracts other polar molecules (water, sugar)
and ions (salt). (Universal solvent)
 Polarity allows for cohesion (water molecules stick together) which
creates surface tension (leaves, insects float on surface). Explains
why you can skip a flat rock across a pond.
 Water is adhesive (forms H bonds w/ molecules on other surfaces).
This allows water to creep up tubes (capillary action in plants – water
travels from roots to leaves defying gravity).
 Water resists changes in temp. Water requires more heat to increase
in temp. than most other substances. Likewise, water loses a lot of
heat when it cools – acts as an insulator.
 One of few substances to expand when it freezes. Ice is less dense
than water and floats. Water expands as it freezes inside cracks in
rocks – breaks apart, forming soil over time.
IV. The Building Blocks of Life
Organic Chemistry: the study of compounds containing carbon
which is found in almost all biological molecules.
1. life on earth is considered “carbon-based” and
carbon compounds lead to diversity of life on
Earth.
2. carbon has 4 electrons in its outer energy level so it
can form 4 covalent bonds with other atoms.
3. these compounds can be straight chains, branched
chains, or rings.
B. Macromolecules/ Polymers: large molecules that are formed by
joining smaller organic molecules together.
1. polymers are made from repeating units of identical or nearly
identical compounds called monomers that are linked by
covalent bonds
2. 4 major categories of macromolecules: carbohydrates, lipids,
proteins and nucleic acids.
a.
carbohydrates: main source of energy for plants/animals;
structural support in plant cell walls
(cellulose) and exoskeletons of insects
and crustaceans (chitin); stored in liver
and skeletal muscle (glycogen); plants
store glucose as starch
(CH2O)n
general formula for carbohydrates
n is the number of CH2O units in a chain
3-7 n units = simple sugars
(monosaccharides) ex: glucose
2 monosaccharides = disaccharide (ex:
sucrose, lactose)
polysaccharides = complex (3+) sugars; ex:
starch, glycogen, cellulose, chitin (makes
tough outer shell of shrimp, lobsters and
certain insects)
b. Lipids = secondary energy source (stored energy)
 Lipo = fat
 C, H, O (C:H ratio higher than in carbs)
 Fats, oils, waxes
 Make up cell membrane (phospholipids)
 Insoluble in water (nonpolar)
 Stored under skin and around organs
 Energy storage, insulation, and protective coatings
 Triglycerides: a fat if solid at room temperature, an oil if
liquid at room temperature—stored in fat cells in human
body
 Waxes: protective coating on leaves to prevent water loss
Saturated Fats: carbons in the chain are bonded to the max
number of H atoms
 Stack easily—solids at room temp.
 Ex: animal fat—lard, butter
Unsaturated Fats: double bonds b/w carbon atoms and have less than
the max number of H atoms
 Bent shape—less likely to form solids
 Liquids at room temp.
 Ex: vegetable oils (corn, canola), fish oils (cod liver oils)
Steroids: cholesterol and hormones
 Estrogen and testosterone = sex hormones
 Anabolic steroids = synthetic version of testosterone (male sex
hormone)—muscle, bone mass during puberty, maintaining
masculine characteristics
C. Proteins: build and repair body tissues
 Composes muscle, skin and hair
 C, H, O, N and sometimes S
 Carry out cell metabolism
 Amino acids= building blocks of protein
 20 amino acids make up all proteins
 peptide bonds link amino acids together
1. proteins may have up to four levels of structure:
a. primary: number of amino acids and their
order
b. secondary: 3-d folded shape (helix or
pleat)
c. tertiary: globular
d. 4th: combine with other proteins
D. Nucleic acids:
 Store and transmit genetic information
 DNA (deoxyribonucleic acid): 5 carbon sugar (deoxyribose),
phosphate group, and a N base make up a repeating unit in
DNA called a nucleotide
 RNA (ribonucleic acid): involved in protein synthesis—helps
DNA make protein
 ATP (adenosine triphosphate) = energy molecule used by cells