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BIOCHEMISTRY
CHEMISTRY OF LIFE
• Elements: simplest form of a
substance - cannot be broken down
any further without changing what it is
• Atom: the actual basic unit composed of protons, neutrons, and
electrons
THE ATOM
• Just like cells are the basic unit of life, the
ATOM is the basic unit of matter.
• They are very small. If placed side by side
one million would stretch a distance of 1cm.
• The atom is made up of 3 particles.
Particle
Charge
PROTON
+
NEUTRON
NEUTRAL
ELECTRON
-
• Electrons are not present within the atom,
instead THEY REVOLVE AROUND THE
NUCELUS OF THE ATOM & FORM THE
ELECTRON CLOUD
• Draw a helium atom. Indicate where the
protons, neutrons and electrons are.
NEUTRONS
-
ELECTRONS
PROTONS
+
ATOMIC # = 2 (PROTONS)
+
-
ATOMIC MASS = 4
(PROTONS &
NEUTRONS)
ISOTOPES
•
•
•
atoms of the same element that HAVE A
DIFFERENT NUMBER OF NEUTRONS
Some isotopes are radioactive. This means
that their nuclei is unstable and will break
down at a CONSTANT RATE over time.
There are several practical uses for
radioactive isotopes:
1. CARBON DATING
2. TRACERS
3. KILL BACTERIA / CANCER CELLS
COMPOUNDS
• a substance formed by the chemical
combination of 2 or more elements in definite
proportions
– Ex: water, salt, glucose, carbon dioxide
• The cell is a COMPLEX CHEMICAL
FACTORY containing some of the same
elements found in the nonliving
environment.
• carbon (C), hydrogen (H), oxygen (O), and
nitrogen (N) are present in the greatest
percentages
TWO TYPES OF COMPOUNDS
•
Organic - Contain C, H, and O in some
ratio (usually referred to as chemicals of
life)
–
•
Carbohydrates, Proteins, Lipids, Nucleic Acids
Inorganic - usually "support" life - no
specific ratio of C, H, and O
–
Water (H2O), Carbon Dioxide (CO2)
CHEMICAL BONDS
• Chemical bonds hold the atoms in a
molecule together.
• There are 2 types of chemical bonds
IONIC and COVALENT
IONIC BONDS
• Occur when 1 or more electrons are
TRANSFERRED from one atom to another.
• When an atom loses an electron it is a
POSITIVE charge.
• When an atom gains an electron it is a
NEGATIVE charge
• These newly charged atoms are now called
IONS
– Example: NaCl (SALT)
COVALENT BONDS
• Occur when electrons are SHARED by atoms.
• These new structures that result from covalent
bonds are called MOLECULES
• ** In general, the more chemical bonds a
molecule has the more energy it contains
SHARING IS CARING!
MIXTURES
• Water is not always pure. It is often found as
part of a mixture.
• A mixture is a material composed of TWO OR
MORE ELEMENTS OR COMPOUNDS THAT
ARE PHYSICALLY MIXED
– Ex: salt & pepper mixed, sugar and sand – can be
easily separated
SOLUTION
Two parts:
• SOLUTE – SUBSTANCE THAT IS BEING
DISSOLVED (SUGAR / SALT)
• SOLVENT - the substance in which the solute
dissolves
• Materials that do not dissolve are known as
SUSPENSIONS.
– Blood is the most common example of a
suspension.
– Cells & other particles remain in suspension.
FORMULA
•
•
•
The chemical symbols and numbers that
compose a compound ("recipe")
Structural Formula – Line drawings of the
compound that shows the elements in
proportion and how they are bonded
Molecular Formula – the ACTUAL
formula for a compound
C2H6O
ACIDS & BASES
•
Acids: always (almost) begin with "H" because
of the excess of H+ ions (hydrogen)
–
Ex: lemon juice (6), stomach acid (1.5), acid rain
(4.5), normal rain (6)
Facts about Acids
• Acids turn litmus paper BLUE and usually
taste SOUR.
• You eat acids daily (coffee, vinegar, soda,
spicy foods, etc…)
ACIDS & BASES
• Bases: always (almost) end with -OH because
of the excess of hydroxide ions (Oxygen &
Hydrogen)
– EX: oven cleaner, bleach, ammonia, sea water,
blood, pure water
Facts about Bases
• Bases turn litmus BLUE.
• Bases usually feel SLIPPERY to touch and taste
BITTER.
Neutralization Reactions
• When an acid reacts with a base to produce a
salt and water.
pH SCALE
• measures degree of
substance alkalinity or
acidity
• Ranges from 0 to 14
• 0 – 5 strong acid
• 6-7 neutral
• 8-14 strong base
• The goal of the body is to maintain
HOMEOSTASIS (neutrality) – to do this when
pH is concerned, we add weak acids & bases to
prevent sharp changes in pH.
• These are called BUFFERS
And now for the
Biochemistry portion of
things….
CARBOHYDRATES
• Living things use carbohydrates as a key source
of ENERGY!
• Plants use carbohydrates for structure
(CELLULOSE)
– include sugars and complex carbohydrates
(starches)
– contain the elements carbon, hydrogen, and oxygen
(the hydrogen is in a 2:1 ratio to oxygen)
Monosaccharides (simple sugars)
• all have the formula C6 H12 O6
• all have a single ring structure
– (glucose is an example)
Disaccharides (double sugars)
• all have the formula C12 H22 O11
• sucrose (table sugar) is an example
Polysaccharides
•
•
•
•
Formed of three or more simple sugar units
Glycogen - animal starch stored in liver & muscles
Cellulose - indigestible in humans - forms cell walls
Starches - used as energy storage
How are complex
carbohydrates formed
and broken down?
Dehydration Synthesis
• Combining simple molecules to form a more
complex one with the removal of water
– ex. monosaccharide + monosaccharide ---->
disaccharide + water
– (C6H12O6 + C6H12O6 ----> C12H22O11 + H2O
• Polysaccharides are formed from repeated
dehydration syntheses of water
– They are the stored extra sugars known as starch
Hydrolysis
• Addition of WATER to a compound to
SPLIT it into smaller subunits
– (also called chemical digestion)
– ex. disaccharide + H2O --->
monosaccharide + monosaccharide
C12 H22 O11 + H2 O ---> C6 H12 O6 + C6 H12 O6
Lipids (Fats)
• Fats, oils, waxes, steroids
• Chiefly function in energy storage, protection,
and insulation
• Contain carbon, hydrogen, and oxygen but the
H:O is not in a 2:1 ratio
• Tend to be large molecules -- an example of a
neutral lipid is below
• Neutral lipids are formed from the union of one
glycerol molecule and 3 fatty acids
• 3 fatty acids + glycerol ----> neutral fat (lipid)
• Fats -- found chiefly in animals
• Oils and waxes -- found chiefly in plants
• Oils are liquid at room temperature, waxes are
solids
• Lipids along with proteins are key components of
cell membranes
• Steroids are special lipids used to build many
reproductive hormones and cholesterol
PROTEINS
• contain the elements carbon, hydrogen, oxygen,
and nitrogen
• composed of MANY amino acid subunits
• It is the arrangement of the amino acid that
forms the primary structure of proteins.
• The basic amino acid form has a carboxyl
group on one end, a methyl group that only
has one hydrogen in the middle, and a amino
group on the other end.
• Attached to the methyl group is a R group.
AN R GROUP IS ANY GROUP
OF ATOMS – THIS CHANGES
THE PROPERTIES OF THE
PROTEIN!
FUNCTIONAL GROUPS
• There are certain groups of atoms that are
frequently attached to the organic molecules we
will be studying, and these are called functional
groups.
• These are things like hydroxyl groups which
form alcohols, carbonyl groups which form
aldehydes or ketones, carboxyl groups which
form carboxylic acids, and amino groups
which form amines.
Major Protein Functions
•
•
•
Growth and repair
Energy
Buffer -- helps keep body pH constant
Dipeptide
• formed from two amino acid subunits
• Formed by the process of Dehydration Synthesis
• amino acid + amino acid ----- dipeptide + water
Hydrolysis of a dipeptide
• Breaking down of a dipeptide into amino acids
• dipeptide + H2O ---> aminoacid + amino acid
Polypeptide (protein)
• composed of three or more amino acids linked
by synthesis reactions
• Examples of proteins include insulin,
hemoglobin, and enzymes.
• ** There are an extremely large number of
different proteins.
• The bases for variability include differences in
the number, kinds and sequences of amino
acids in the proteins
NUCLEIC ACIDS
•
•
•
•
•
•
•
in all cells
composed of NUCLEOTIDES
store & transmit heredity/genetic information
Nucleotides consist of 3 parts:
1. 5-Carbon Sugar
2. Phosphate Group
3. Nitrogenous Base
DNA (deoxyribonucleic acid)
• contains the genetic code of instructions that direct a
cell's behavior through the synthesis of proteins
• found in the chromosomes of the nucleus (and a few
other organelles)
RNA (ribonucleic acid)
• directs cellular protein synthesis
• found in ribosomes & nucleoli
CHEMICAL REACTIONS
• a process that changes one set of chemicals into
another set of chemicals
• REACTANTS – elements or compounds that
enter into a chemical reaction
• PRODUCTS – elements or compounds that are
produced in a chemical reaction
• Chemical reactions always involve the breaking of
bonds in reactants and the formation of new
bonds in products.
• In a reaction, energy is either TAKEN IN
(ENDOTHERMIC) or GIVEN OFF
(EXOTHERMIC)
• Can you think of an everyday example of
each type of reaction?
Enzymes and Enzyme Action
• catalyst: inorganic or organic substance which
speeds up the rate of a chemical reaction without
entering the reaction itself
• enzymes: organic catalysts made of protein
• most enzyme names end in -ase
• enzymes lower the energy needed to start a
chemical reaction. (activation energy)
• begin to be destroyed above 45øC. (above this
temperature all proteins begin to be destroyed)
It is thought that, in order for an enzyme to affect the rate of a
reaction, the following events must take place.
1. The enzyme must form a temporary association with the
substance or substances whose reaction rate it affects.
These substances are known as substrates.
2. The association between enzyme and substrate is thought to
form a close physical association between the molecules and
is called the enzyme-substrate complex.
3. While the enzyme-substrate complex is formed, enzyme
action takes place.
4. Upon completion of the reaction, the enzyme and product(s)
separate. The enzyme molecule is now available to form
additional complexes.
How do enzymes work?
• substrate: molecules upon which an enzyme acts
• the enzyme is shaped so that it can only lock up
with a specific substrate molecule
enzyme
substrate -------------> product
"Lock and Key Theory"
• each enzyme is specific for one and ONLY one
substrate (one lock - one key)
• this theory has many weaknesses, but it
explains some basic things about enzyme
function
Factors Influencing Rate of
Enzyme Action
1. pH - the optimum (best) in most living things is
close to 7 (neutral)
• high or low pH levels usually slow enzyme activity
• A few enzymes (such as gastric protease) work
best at a pH of about 2.0
2. Temperature - strongly influences enzyme
activity
• optimum temperature for maximum enzyme
function is usually about 35-40 C.
• reactions proceed slowly below optimal
temperatures
• above 45 C most enzymes are denatured
(change in their shape so the enzyme active site
no longer fits with the substrate and the enzyme
can't function)
3. Concentrations of Enzyme and Substrate
• ** When there is a fixed amount of enzyme and
an excess of substrate molecules -- the rate of
reaction will increase to a point and then level
off.