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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
Groups for Acid Rain Lab
• Joshua
• Karina
• Jenilee
Che
Mikense
Darling
Kristen
Aneres
Donald
Juan
Christian
Destiny
• Giovani
Justin
Chris
Nicolas
Vashae
Franklin
Jearais
Alayah
Samantha Fady
Amber
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?
Condensation /Dehydration
Synthesis
• Combining simple molecules to form a more
complex one with the removal of water
– ex. monosaccharide + monosaccharide ---->
disaccharide + water
• Polysaccharides are formed from repeated
dehydration syntheses of water
– They are the stored extra sugars known as starch
https://smartsite.ucdavis.edu/access/content/user/050/bis10v/media/ch02/reaction_types.html
Hydrolysis
• Addition of WATER to a compound to
SPLIT it into smaller subunits
– (also called chemical digestion)
– ex. disaccharide + H2O --->
monosaccharide + monosaccharide
https://smartsite.ucdavis.e
du/access/content/user/0
0002950/bis10v/media/ch
02/reaction_types.html
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
• lipids are formed from the union of one glycerol
molecule and 3 fatty acids
• 3 fatty acids + glycerol ----> 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.
Major Protein Functions
•
•
•
•
Growth and repair
Enzymes – speed up chemical reactions by
reducing the amount of energy needed
Energy
Buffer -- helps keep body pH constant
Enzymes are Proteins
• Changes the rate of a chemical reaction
• Involved in all metabolic reactions
• Only works with reactions that normally would happen
• (enzymes speed up the reaction)
Draw graph of enzyme rate
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)
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.