BIOCHEMISTRY

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BIOCHEMISTRY
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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

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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 -
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• 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
PROTONS
-
ATOMIC 2 (PROTONS) ATOMIC MASS 4 (PROTONS
NEUTRONS)


ELECTRONS
-
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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
• CARBON DATING
• TRACERS
• KILL BACTERIA / CANCER CELLS

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COMPOUNDS

• a substance formed by the chemical combination of
  2 or more elements in definite proportions
• Ex water, salt, glucose, carbon dioxide

H20
CO2
NaCl
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• 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

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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)

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CHEMICAL BONDS

• Chemical bonds hold the atoms in a molecule
  together.
• There are 2 types of chemical bonds IONIC and
  COVALENT

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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)

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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!
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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

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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.

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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
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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)

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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.

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Neutralization Reactions

• When an acid reacts with a base to produce a salt
  and water.

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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

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• 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

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And now for the Biochemistry portion of things.
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ORGANIC COMPOUNDS
LIPIDS
PROTEINS
NUCLEIC ACIDS
CARBOHYDRATES
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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 21 ratio to oxygen)

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Monosaccharides (simple sugars)

• all have the formula C6 H12 O6
• all have a single ring structure
• (glucose is an example)

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Disaccharides (double sugars)

• all have the formula C12 H22 O11
• sucrose (table sugar) is an example

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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

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How are complex carbohydrates formed and broken
down?
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Dehydration Synthesis

• Combining simple molecules to form a more complex
  one with the removal of water
• ex. monosaccharide monosaccharide ----gt
  disaccharide water
• (C6H12O6 C6H12O6 ----gt C12H22O11 H2O
• Polysaccharides are formed from repeated
  dehydration syntheses of water
• They are the stored extra sugars known as starch

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Hydrolysis

• Addition of WATER to a compound to SPLIT it into
  smaller subunits
• (also called chemical digestion)
• ex. disaccharide H2O ---gt monosaccharide
  monosaccharide
• C12 H22 O11 H2 O ---gt C6 H12 O6 C6 H12 O6

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Lipids (Fats)

• Fats, oils, waxes, steroids
• Chiefly function in energy storage, protection,
  and insulation
• Contain carbon, hydrogen, and oxygen but the HO
  is not in a 21 ratio
• Tend to be large molecules -- an example of a
  neutral lipid is below

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• Neutral lipids are formed from the union of one
  glycerol molecule and 3 fatty acids
• 3 fatty acids glycerol ----gt 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

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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.

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AN R GROUP IS ANY GROUP OF ATOMS THIS CHANGES
THE PROPERTIES OF THE PROTEIN!
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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.

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Major Protein Functions

• Growth and repair
• Energy
• Buffer -- helps keep body pH constant

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Dipeptide

• formed from two amino acid subunits
• Formed by the process of Dehydration Synthesis
• amino acid amino acid ----- dipeptide water

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Hydrolysis of a dipeptide

• Breaking down of a dipeptide into amino acids
• dipeptide H2O ---gt aminoacid amino acid

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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

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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

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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)

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RNA (ribonucleic acid)

• directs cellular protein synthesis
• found in ribosomes nucleoli

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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.

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• 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?

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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)

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• It is thought that, in order for an enzyme to
  affect the rate of a reaction, the following
  events must take place.
• The enzyme must form a temporary association with
  the substance or substances whose reaction rate
  it affects. These substances are known as
  substrates.
• The association between enzyme and substrate is
  thought to form a close physical association
  between the molecules and is called the
  enzyme-substrate complex.
• While the enzyme-substrate complex is formed,
  enzyme action takes place.
• Upon completion of the reaction, the enzyme and
  product(s) separate. The enzyme molecule is now
  available to form additional complexes.

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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 -------------gt product

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"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

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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

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• 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)

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• 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.