AP BIOLOGY 12

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BIOLOGY 12
Chemistry of Life
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• INTRODUCTION TO Chemistry

All living things are made up of protoplasm,
which is the material that links living and
non-living things. Our bodies are primarily made
up of WATER H2O. We use O2 to produce energy in
the form of ATP and use amino acids as the
building blocks of life. 96 of our bodies are
made up only 4 elements C, H, O, and N.
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Chemical Elements

• There are 92 naturally occurring elements in the
  universe.
• Most of these are not used by life.
• All elements are made of atoms of the same type.
• Compounds are matter made of units of atoms
  chemically bonded together, the first level above
  the atom.

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The Elements of Life

• Life uses only about 25 of the 92 naturally
  occurring elements.
• Of these 25, four elements alone make up 96 of
  cytoplasm on average.
• Carbon - 18.5
• Hydrogen - 9.5
• Oxygen - 65
• Nitrogen - 3.3

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• ELEMENTS in the human body
• Nitrogen N found in all proteins, ATP, and
  nucleic acids DNA
• OXYGEN O necessary for burning glucose and
  making ATP
• CARBON C found in all organic compounds
• HYDROGEN H found in all organic compounds and
  water
• SODIUM Na nerve conduction, muscle
  contractdion and is essential for osmotic
  pressure (water balance in body, positive bathing
  ion in our body fluids)
• CALCIUM Ca bones, teeth, muscle contraction,
  nerve conduction and blood clotting
• POTASSIUM K nerve conduction and muscle
  contraction

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• ELEMENTS in the human body
• PHOSPHORUS P ATP, DNA, RNA and cell membrance
• IODINE I used by the thyroid gland to produce
  thyroxin which controls your metabolism
• IRON Fe necessary for the production of
  hemoglobin in blood which is used to transport
  oxygen
• SULFUR S sulphide bonds, holds proteins
  together
• MAGNESIUM Mg production of some vital hormones
  
• ZINC Zn necessary for some enzymes and sperm
  production
• CHLORINE Cl part of salt and is necessary for
  water balance (negative bathing ion in our
  fluids)

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Chemical Elements

• POLYMERS are large MACRO MOLECULES which are
  broken down or synthesized by the body
• MONOMERS are smaller MOLECULES or sub units like
  (sugars, amino acids, and fatty acids ) which
  are used to synthesize larger molecules (COMPLEX
  CARBS, PROTEINS, FATS)
• DEHYDRATION SYNTHESIS is building new larger
  compounds (PROTEIN SYNTHESIS)
• HYDROLYSIS is breaking down large polymers into
  monomers (DIGESTION)

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Chemical Elements

• The universe is, at its most fundamental levels,
  made of two things
• A. Matter anything which has mass and occupies
  space. Mass is a measure of the amount of
  matter.
• B. Energy The ability to do work.

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Atomic Structure

• Electron Orbitals or Shells
• Electrons orbit the atomic nucleus but not like
  planets orbit the sun.
• They are located at any point in time somewhere
  inside their orbital.
• In biology, the first three orbital levels are of
  most significance.

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Chemical Reactions

• To achieve closed shell, elements can either
• a) gain electrons (reduction),
• b) lose electrons (oxidation), or
• c) share electrons
• All chemical reactions involve energy as
  electrons must move between energy levels.

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Basic chemistry

• Atom the smallest unit of matter that retains
  the physical and chemical properties of the
  element. (H, Fe, Ca, K )
• NITROGEN
• CARBON

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Basic chemistry

• Molecule chemical made up of two or more of the
  same atoms chemically combined (F2, O3, N2, H2 )

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Basic chemistry

• Compound chemical made up of 2 or more
  different atoms chemically combined.
• METHANE GAS

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The Elements of Life

• CHNOPS 98.3
• Phosphorus - 1 Sulfur - .3
• Calcium - 1.5 Potassium - .4
• Sodium - .2 Chlorine - .2
• Magnesium - .1 Iron - .01
• Iodine - .01
• Trace boron, copper, fluorine, zinc

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The Elements of Life
COVALENT BONDS (sharing of electrons)
IONIC BONDING (losing or gaining of electrons)
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Atomic Structure

• Any atom can vary in its normal number of
  electrons or neutrons, but never in its protons.
• Ion an atom with more or less than the neutral
  number of electrons.
• Isotope an atom with more or less than the
  typical number of neutrons.

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Atomic Structure

• Many isotopes are unstable and eject subatomic
  particles from their nucleus at high speeds.
• These are Radioisotopes and have many uses in
  biology, specifically medicine.
• Ions are highly reactive and are responsible for
  much of the chemistry of life.

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Nuclear Medicine
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Ionic Bonds

• Atoms which have few, or atoms which have many
  valence electrons, tend to react by giving away
  or taking valence electrons during the reaction.
• This results in the formation of Ions.
• Ionic bonds form between ions of opposite charges
  due to electrical attractions.

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Ionic Reaction
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Ionic Bonds

• Individually, ionic bonds are fairly weak but due
  to the large number of them in an ionic compound,
  they can collectively be strong.
• A lot of this strength comes from their tendency
  to form lattice structures.
• Ionic compounds are therefore polar in nature,
  and as a result, can readily dissolve in water to
  form solutions.
• When dissolved in water, they dissociate into
  free ions.

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Ionic Bonds

• In their solid form, ionic compounds have a high
  melting point.
• They are composed of a metal and a non metal (or
  polyatomic ions).
• They can conduct a current of electricity.
• They tend to form crystals.
• They can be highly reactive.

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Ionic Bonds

• Ionic compounds can be divided into three groups
• 1. Acids any ionic compound which when dissolved
  in water releases H.
• 2. Bases any ionic compound which when dissolved
  in water removes H.
• 3. Salts any ionic compound which neither adds
  or releases H.

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Covalent Compounds

• Atoms in covalent compounds complete their octet
  by more or less equally sharing pairs of valence
  electrons.
• This creates very strong bonds.
• Typically, covalent compounds are formed between
  non metals.
• In biology, covalent compounds are used to make
  structures.

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Covalent Compounds

• If the elements involved are equally
  electronegative (equal pull on electrons) the
  result will be a Non Polar covalent bond.
• These compounds do not dissolve in water and are
  said to be Hydrophobic.
• Non polar covalent bonds can be single, double or
  triple.

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Fats and oils which are made up of long chains of
carbon and hydrogen, are non-polar and are
considered hydrophobic. These fatty acids do
not dissolve in water.
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Other Types of Bonds

• While ionic and covalent bonds form the bulk of
  biological molecules, two other types of weak
  bonds are also important.
• 1. Hydrogen Bonds
• Water is a polar covalent compound.
• As a result, the partial negative oxygen and
  partial negative hydrogens attract.

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• Water and Living Things
• Water is the basis of life on Earth.
• No other substance has such unique chemical
  properties that are critical as a medium for
  life.

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The Water Molecule

• The polar nature of the water molecule is what
  determines all of its properties.
• Water is a tetrahydral shaped molecule with the
  oxygen end more negative than the hydrogen end
  (which is slightly positive).
• Therefore, water readily forms hydrogen bonds.

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HYDROGEN BONDS will form between the partial
positive charge of the hydrogen and the partial
negative charge of the oxygen. This bond is very
weak.
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• Water is a liquid at room temperature.
• Liquids are vital to all living things
• Lubricates
• Allows for the transport of molecules
• Protects vital organs (cerebral spinal fluid)

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• 2. Solvent Properties
• Water is close to being a universal solvent.
• It cant dissolve non polar compounds, but can
  dissolve most other polar and ionic compounds.

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• 3. Water molecules are cohesive
• Water molecules readily stick to each other.
• One water molecule could be hydrogen bonded
  to as many as
• 4 other water molecules
• This creates surface tension and capillary
  action, necessary for living things.

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• 4. Moderating Effect of Water
• Water takes a long time to heat up but holds
  the heat for a long period of time. Very little
  fluxuations in the temperature of water. Very
  important for aquatic life as well as warm
  blooded animals like ourselves to hold heat.

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• 5. Heat of Vaporization
• Water exists in all three phases on Earth.
• It takes a lot of energy to cause water to change
  phase - due to hydrogen bonding.
• This is due to waters very high specific heat.
• Its also key in many aspects of animal
  physiology, such as sweating.
• Also, organisms are mostly water, so are less
  effected by wide temperature fluctuations.
• This has a great moderating effect upon the
  Earths climate.

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• 6. Solid Water is Less Dense than Liquid
• As water freezes, the hydrogen bonds become less
  moveable which actually moves them farther apart
  than in a liquid - therefore the density
  decreases.
• This allows solid water, ice, to float on top of
  liquid water - thus lakes and even oceans can
  never freeze solid.

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Dissociation of Water

• The polarity of the water molecule results in
  another important property of water - it can
  dissociate into ions.
• It does this by a hydrogen from one molecule
  being stripped off it and added to another water
  molecule.
• This creates a hydroxide ion and a hydronium ion

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Dissociation of Water

• 2 H2O -----gt OH- H3O
• In practice, we ignore the hydronium ion and just
  call it a hydrogen ion.
• Therefore, the ionization of water is typically
  written as
• H2O ------gt H OH-
• This dissociation of a water molecule does not
  occur very often, but often enough.

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IMPORTANCE OF WATER TO HUMANS

• 1. allows molecules to be transported between
  cells
• 2. dissolves molecules (sugars and salts)
• 3. lubricates joints (sinovial fluid found in
  bursa sacs)
• 4. protects vital organs (pericardial fluid
  around heart)
• 5. temperature control (blood and sweating)
• 6. chemical reactions in the body (synthesis and
  hydrolysis)

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• ORGANIC
• COMPOUNDS
• LARGER with MANY atoms
• associated with living
• things
• covalent bonding (sharing of
• electrons)
• examples are
• ( glucose, fats, proteins,
• and nucleic acids )

• INORGANIC
• COMPOUNDS
• SMALL with few atoms
• associated with non-
• living things
• Ionic bonding (form ions)
• examples are
• (salts, carbon dioxide,
• oxygen, water )

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pH Scale

• Note that the magnitude of the pH scale goes up
  by 10 for each unit (logarithmic).
• By definition, pH 7 is pure water, therefore
  neutral.
• pH 0 - 6.999.. are acids with the acid strength
  increasing as the number decreases.
• pH 7.0001 are bases with the base strength
  increasing as the number increases.

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pH scale
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Buffers

• Buffers are substances that resist changes in the
  pH of a solution.
• Buffers work by donating H when the solution
  H is too low, or by accepting H if the H
  is too high.
• Most buffers are weak acids or bases that can
  shift their ionization equilibrium to maintain a
  constant H .

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Buffers

• H2CO3 lt---gtHCO3- H lt---gt CO3-2 2H
• Buffers can become overloaded when they have
  released or absorbed all their H .
• Buffers are critical to biological systems
  because virtually all chemistry of cells occur in
  an aqueous environment which are highly sensitive
  to the very reactive hydrogen and hydroxide ions.

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• Most biological molecules are polymers.
• They are made of sub molecules called
• monomers.
• The monomers are joined together by a
• covalent bond.
• The reaction that joins them together is called
  Dehydration Synthesis because a water molecule
  is split out in the reaction.

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• A polymer is broken apart into monomers by
  another reaction called Hydrolysis in which a
  water molecule is added.
• These form two very basic reaction types in
  biology.
• In cells, these reactions require
• 1. Enzymes
• 2. Water
• 3. ATP Energy

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POLYMERS polysaccharides
(starch, glycogen) Polypeptides (proteins)
Triglycerides Nucleic Acids (DNA and RNA)

HYDROLYSIS Breaking down larger complex
compounds into smaller molecules (monomers)
Photosynthesis and protein synthesis are examples
Anabolic reaction

• ALL CHEMICAL REACTIONS REQUIRE
• ENERGY (ATP)
• WATER H OH-
• ENZYMES (catalysts)

Water used
Water lost
DEHYDRATION SYNTHESIS building larger compounds
using smaller sub units (monomers
Digesting food is an example Catabolic
reaction
MONOMERS Mono / disaccharides (glucose,
maltose) Amino acids / dipeptides glycerol
and fatty acids nucleotides
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The Importance of Carbon

• Compounds which contain carbon are called
  Organic.
• Organic chemistry is the branch of chemistry that
  deals with organic compounds.
• Inorganic chemistry deals with the all the other
  elements and their compounds.
• Central to understanding organic chemistry is an
  understanding of the chemistry of carbon.

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• Carbon is one of only two elements which is
  common and tetravalent.
• Having 4 electrons in its valence shell, carbon
  has no tendency to either gain or lose electrons.
• Therefore, carbon forms mostly covalent compounds
  by electron sharing.

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• With its four valence electrons, it can bond to
  four other atoms.
• This enables carbon to be central to the
  formation of an endless array of molecules

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Isomers

• 1. Structural Isomers differ in the arrangement
  of the atoms within the molecule. Ex butane and
  isobutane.
• 2. Geometric Isomers have the same atoms in the
  same place but arranged differently in three
  dimensional space.
• Many organic compounds can exist in different
  configurations while having the same molecular
  formula.

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Isomers

• 3. Enantiomers These are the most difficult to
  visualize. They have the same elements in the
  same 3D space, but the isomers are mirror images
  of each other.
• Ex. Your two hands are enantiomers of each other.

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Hydrocarbons

• Carbon can bond to other carbons or to other
  elements.
• The base of most organic compounds are the
  hydrocarbons made of only carbon and hydrogen.
• Chains of carbons bonded together form the carbon
  backbone upon which all complex organic and
  biological molecules are built.

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Hydrocarbons

• Carbon can also form double and triple bonds
  with other carbons as well as with other non
  metals such as oxygen and nitrogen.
• Hydrocarbon chains can become very long and
  branch many times.

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Functional Groups

• Functional groups behave consistently from one
  organic compound to another.
• Organic chemistry depends not only upon the
  configuration of the carbon skeleton but also the
  attachment of specific and reactive functional
  groups.
• There are 7 basic groups that you need to learn.

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Functional Groups

• 1. Methyl Group CH3
• fillsspace in many compounds.
• Is non polar, generally quite unreactive.
• Found in lipids.

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Functional Groups

• 2. Hydroxyl Group -OH
• These are polar groups.
• Organic compounds that contain one or more
  hydroxyl groups are called alcohols.

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Functional Groups

• 3. Carbonyl Group is an oxygen doubly bonded to
  a carbon.
• Two types
• a) Aldehydes b) Ketones

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Functional Groups

• 4. Carboxyl Group -COOH
• Contains doubly bonded oxygen and hydroxyl group.
• Has limited ability to ionize and lose its
  hydroxyl hydrogen as H.
• - COOH lt----gt COO- H.
• This results in a resonant sharing of the double
  bond between the two oxygens. They are also very
  weak and are very important to biological
  molecules.

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Functional Groups

• 5. Amino Group -NH2
• This group tends to
• attract H and can act as a base.
• NH2 H lt-----gt NH3

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Functional Groups

• 6. Sulfhydryl Group -SH
• Sulfur is also strongly electronegative so this
  group, like the hydroxyl group, is polar.

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Functional Groups

• 7. Phosphate Group -PO4-2
• These groups can be highly reactive.
• They are involved in energy transfer in organisms
  (ATP), and in making nucleic acids.

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Carbohydrates

• There are four basic groups of biological
  molecules.
• These are the matter that forms life.
• 1. Carbohydrates
• These hydrates of carbon are derivatives of the
  basic empirical formula (CH2O)
• They contain only carbon, oxygen, and
• hydrogen.

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Carbohydrates

• Functions of Carbohydrates
• 1. Energy primary energy molecules of life
• 2. Structures in some organisms, notably plants,
  carbohydrates form structures the cell wall.
• A) Monosaccharides single sugars
• There are no subunits composing them.

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Carbohydrates

• There are two groups
• Most common are
• 6 carbon (hexoses)
• and 5 carbon (pentoses).
• Most sugars end in ose
• Monosaccharides like
• glucose are the primary
• energy source in
• living things.

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GLUCOSEchain ring
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Dehydration synthesis of MALTOSE
GLUCOSE
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• Disaccharides 2 sugars
• Made of two monosaccharides covalently bonded by
  dehydration synthesis.
• This is a relatively weak bond called a
  glycosidic or ester linkage.
• These are broken without using too much energy.
• This reflects their primary function energy.

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• However, only monosaccharides can be directly
  used by organisms for energy disaccharides must
  first be broken back down to their monomers
  before they can be used for energy by a cell.
• Common examples are
• Sucrose
• Lactose
• Maltose
• Dextrose

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Carbohydrates

• Polysaccharharides many sugars
• Considered to be macromolecules
• Composed of monomers of glucose.
• 4 types
• 1. Starch (amylose)
• made by plants of multiple glucose units linked
  by glycocidic bonds.
• Weaker bonds my be branched
• Made by plants for storage of glucose

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Carbohydrates

• 2. Glycogen animal starch
• Chemically similar to starch but produced by
  animals.
• Stored in muscles and liver.

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Carbohydrates

• 3. Cellulose structural polysaccharide.
• produced by plants for cell walls.
• Is most commonly produced polysaccharide on
  Earth fixes most carbon.
• Made of strong glycocidic covalent bonds.
• Never branched straight chains form cellulose
  fibers.
• Use to make paper and paper products

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Carbohydrates

• 4. Chitin Animal cellulose
• Used to make exoskeletons in arthropods and cell
  wall in fungi.
• Structured similar to cellulose.
• Combines with calcium carbonate to form strong
  structural compound.

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Lipids

• Contain C, H, and O, but in no set ratio.
• Are all water insoluble (hydrophobic).
• Contain large numbers of C - C covalent bonds
  lots of energy.
• Four types of lipids
• Triglycerides
• Soaps
• Phopholipids
• Steroids

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• 1. Triglycerides (neutral fats)
• Composed of one molecule of glycerol and
  three fatty acids.
• Joined by weaker covalent bonds.
• Two types
• A). Saturated Fats
• no double bonds in fatty acid chains.
• B) Unsaturated Fats
• double bonds in the fatty acid chains.

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• 2. Soaps one fatty acid substituted for a sodium
  ion.
• Made by hydrolyzing animal fat (pig) with lye
  (NaOH) soaponification.
• Produces molecule that one end is water soluble
  (hydrophilic) and the other end lipid soluble
  (hydrophobic).
• Therefore dissolves grease in water.

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• 3. Phospholipids.
• One of three fatty acids is replaced by a
  phosphate, therefore this end is hydrophilic.
• The fatty acid tails are hydrophobic.
• In water, they form micelles or spheres with
  phosphates out and fatty acid tails in
• This also is arrangement in cell membranes which
  are primarily composed of them.

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• 4. Steroids
• Difficult to classify but placed in lipids
  because are made of C,H,O and insoluble in water.
• Formed by 4 fused rings with different functional
  groups attached.
• Form hormones
• and cholesterol

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• Roles of FATS in our diets
• Cushion and protect organs
• Surrounds all cells and speeds up nerve impulses
• Inuslates our bodies and energy storage
• Necessary for androgens (sex hormones)

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Proteins

• If you remove the water from animals, 50 of what
  is left is protein.
• Proteins have two primary functions
• 1. Structures especially in animals
• 2. Function by forming enzymes
• Proteins are polymers of monomers called amino
  acids.

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• Structure of Amino Acids
• There are about 20 different kinds of amino
  acids all have the same basic structure
• The carboxylic acid this resonates with the
  acetate configuration, releasing a H.
• The amine group this also resonates accepting
  the H from the carboxylic acid.
• The central carbon attaches the carboxylic acid,
  the amine group, a hydrogen, and the R group.
• The R group this is the variable portion of the
  molecule which determines its specific chemistry
  and reactivities. R groups can be non polar,
  polar, or charged (ionic).

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PROTEINS COME IN MANY SHAPES, SIZES AND FUNCTIONS

• STRUCTURAL PROTEINS collagen(skin) fibrin
  (clots) elastin (ligaments) actin and mysoin
  (muscles)
• TRANSPORT PROTEINS hemoglobin
• HORMONAL PROTEINS insulin adrenalin thyoxin
• MESSENGER PROTEINS dopamine seretonin
• DEFENSIVE PROTEINS immunoglobulins (antibodies)
  
• ENZYMATIC PROTEINS amylase lipase pepsin

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Some example of AMINO ACIDS Protein structure
is determined by the number and different kinds
of amino acids in sequence. This sequence is
determined by the genetic makeup of each
individual through DNA expression.
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• Peptide Bonds
• Amino acids join together by dehydration
• synthesis forming a special type of covalent
• bond called a Peptide Bond.
• The result is a polypeptide.
• If the chain becomes long enough (over 100
  minimum) it may be considered a protein.

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• Levels of Protein Structure
• In the formation of a protein, up to 4 levels of
  structural configurations may be seen.
• 1. Primary Structure
• This is the type and order of the amino acids in
  the chain.
• 2. Secondary Structure
• Hydrogen bonding between the double bonded oxygen
  of the carboxylic acid and the hydrogens of the
  amine group result in two shape changes an
  alpha helix or a beta pleated sheet.
• Alpha helix is typical of proteins destined to be
  enzymes, pleated sheets of structural proteins.

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• 3. Tertiary Structure
• Due to interactions (attractions or repulsions)
  between the R groups, the protein folds over into
  a highly specific 3 dimensional shape.
• This specific shape was pre determined by the
  amino acid sequence.
• This shape is most significant in enzymes as it
  results in very specifically shaped Active
  Sites which gives the enzyme their catalytic
  abilities.
• 4. Quaternary Structure
• Sometimes, two or more polypeptide chains will
  combine to form one large, stable protein ex.
  Hemoglobin.

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Proteins

• The reactivity of a protein is entirely dependent
  upon its ultimate 3D shape.
• Anything which alters this shape AFTER the
  formation, is said to denature it.
• Denaturation can be temporary or permanent
  depending upon the severity of the denaturing
  agent acting upon it.

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• Denaturing Agents
• 1. Heat speeds up molecular speed thus breaking
  weak H bonds.
• 2. pH action of positive hydrogen ion can change
  attraction of R groups.
• 3. Heavy metals are so massive that when they
  attach to a protein they simply distort the
  entire molecular shape.

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Nucleic Acids

• These contain the largest molecules on Earth.
• They are the molecules of life!
• DNA deoxyribonuclesic acid
• RNA ribonucleic acid
• Nucleic acids code for all the information
  necessary to make any organism of any
  specification - including you!
• They also direct all of a cells activity and all
  the biochemistry of life.
• Nucleic acids are polymers of the monomers called
  Nucleotides

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• Structure of Nucleotides
• 1. Sugar
• ribose or deoxyribose
• 2. Phosphate molecule
• 3. Nitrogen base
• (purine or pyrimidine).

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• These monomers are connected by Phosphate Bonds
  (covalent).
• The variable portion is in the nitrogen bases -
  there are 5 types
• Purines adenine and guanine (DNA, RNA).
• Pyrimidines Thymine (DNA), cytosine (DNA, RNA),
  and Uracil (RNA).

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• The information of nucleic acids is stored in the
  sequence of the bases in the linear sequence of
  the molecule.
• DNA is a double stranded molecule that forms a
  double helix.
• RNA is a single stranded molecule that takes on
  various shapes and occurs in three forms.
• Much more on nucleic acids later.

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