The Chemical Level of Organization

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• The Chemical Level of Organization

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The Chemical Level of Organization

• Matter
• elements
• atoms and molecules
• Chemical bonds
• Chemical energy
• Chemical reactions
• Inorganic compounds
• Organic compounds

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How Matter is Organized

• Chemistry is the science of the structure and
  interactions of matter.
• all living things consist of matter.
• Matter is anything that occupies space.
• mass is the amount of matter in any object.
• weight is the force of gravity acting on matter.

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Chemical Elements

• Elements are substances that can not be split
  into simpler substances by ordinary means.
• 112 elements ( 92 occur naturally )
• 26 of naturally occurring elements are in the
  body
• represented by chemical symbols ( first 1-2
  letters of name )
• 4 elements form 96 of the bodys mass
• hydrogen, oxygen, carbon and nitrogen
• Trace elements are present in tiny amounts
• such as copper, tin, selenium zinc

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Structure of Atoms

• Atoms are the smallest units of matter that
  retain the properties of an element
• Atoms consist of 3 types of subatomic particles
• protons, neutrons and electrons
• Nucleus contains protons (p) neutrons (neutral
  charge)
• Electrons (e-) surround the nucleus as a cloud
  (electron shells are designated regions of the
  cloud)

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Electron Shells

• Most likely region of the electroncloud in which
  to find electrons
• Each electron shell can hold onlya limited
  number of electrons
• first shell can hold only 2 electrons
• 2nd shell can hold 8 electrons
• 3rd shell can hold 18 electrons
• higher shells (up to 7) hold many more electrons
• Number of electrons number of protons
• Each atom is electrically neutral charge 0

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Atomic Number Mass Number

• Atomic number is number of protons in the
  nucleus. .
• Mass number is the sum of its protons and
  neutrons.

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Isotopes

• Atoms of an element with different numbers of
  neutrons different mass numbers . Ex. Hydrogen,
  Deuterium, Tritium
• All isotopes of an element have same properties
• have same number of electrons (which determine
  its chemical properties)

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Isotopes
Figure 2.1
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Molecule, Element, compound

• Molecule more than one atom existing in union
• Element Molecule contains identical atoms
• Compound Molecule contains different atoms

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IONS Charged particles

• When an atom gains or loses electros ions are
  formed
• Positively charged cation
• Negatively charged anion

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Free Radicals

• Atom with an unpaired electron in its outmost
  shell
• Unstable and highly reactive
• Can become stable
• by giving up electron
• taking one off another molecule (breaking apart
  important body molecules)

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Free Radicals Your Health

• Produced in your body by absorption of energy in
  ultraviolet light in sunlight, x-rays, by
  breakdown of harmful substances, during normal
  metabolic reactions
• Linked to many diseases -- cancer, diabetes,
  Alzheimer, atherosclerosis and arthritis
• Damage may be slowed with antioxidants such as
  vitamins C and E, selenium beta-carotene
  (precursor to vitamin A)

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Chemical Bonds

• Bonds hold together the atoms in molecules and
  compounds
• An atom with a full outer electron shell is
  stable and unlikely to form a bond with another
  atom
• Octet rule states that biologically important
  elements interact to produce chemically stable
  arrangements of 8 electrons in the valence shell.
• Whether electrons are shared, donated or acquired
  determines the types of bonds formed

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Covalent Bonds

• Atoms share electrons to form covalent bonds
• Electrons spend most of the time between the 2
  atomic nuclei
• single bond share 1pair
• double bond share 2 pair
• triple bond share 3 pair

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Polar Covalent Bonds

• Unequal sharing of electrons between atoms.
• In a water molecule, oxygen attracts the hydrogen
  electrons more strongly
• Oxygen has greater electronegativity as indicated
  by the negative Greek delta sign.

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Ionic Bonds

• Positively and negatively charged ions attract
  each other to form an ionic bond
• In the body, ionic bonds are found mainly in
  teeth and bones
• An ionic compound that dissociates in water into
  and - ions is called an electrolyte

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The Ionic Bond in Sodium Chloride

• Sodium loses an electron to become Na (cation)
• Chlorine gains an electron to become Cl- (anion)
• Na and Cl- are attracted to each other to form
  the compound sodium chloride (NaCl) -- table salt
• Ionic compounds generally exist as solids

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Hydrogen bonds

• Hydrogen bonds are the most important inter
  molecular force of attraction .
• Formed by the attraction between slightly
  positive Hydrogen atom and a slightly negative
  atom of another element.
• Too weak to create molecules but creates shapes
  and stabilizes large molecules like proteins or
  nucleic acids

Water_Polarity QT Mov
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Chemical Reactions

• When new bonds form or old bonds are broken
• Metabolism is all the chemical reactions in the
  body

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Energy and Chemical Reactions

• Chemical reactions involve energy changes
• Law of conservation of energy
• energy can neither be created nor destroyed--just
  converted from one form to another
• Reactions that yield energy Exergonic reactions
  (Larger to smaller mols.)
• AB ? A B
• Reactions that require energy to occur
  Endergonic reactions (smaller to larger mols )
• A B ?AB

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Energy Transfer in Chemical Reactions

• Chemical reactions usually involve both
• Human metabolism couples exergonic and endergonic
  reactions, so that the energy released from one
  reaction will drive the other.
• Glucose breakdown releases energy used to build
  ATP molecules that store that energy for later
  use in other reactions

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Activation Energy

• Atoms, ions moleculesare continuously moving
  colliding
• Activation energy is the collision energy needed
  to break bonds begin a reaction
• Increases in concentration temperature,
  increase the probability of 2 particles colliding
• more particles in a given space as concentration
  is raised
• particles move more rapidly when temperature is
  raised

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Catalysts or Enzymes

• Normal body temperatures and concentrations are
  too low to cause chemical reactions to occur
• Catalysts speed up chemical reactions by lowering
  the activation energy needed to get it started
• Catalysts orient the colliding particles properly
  so that they touch at the spots that make the
  reaction happen
• Catalyst molecules are unchanged and can be used
  repeatedly to speed up similar reactions.

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Effectiveness of Catalysts

• Catalysts speed up chemical reactions by lowering
  the activation energy.

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Synthesis Reactions--Anabolism

• Two or more atoms, ions or molecules combine to
  form new larger molecules
• All the synthesis reactions in the body together
  are called anabolism
• Usually are endergonic because they absorb more
  energy than they release
• Example
• combining amino acids to form a protein molecule

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Decomposition Reactions--Catabolism

• Large molecules are split into smaller atoms,
  ions or molecules
• All decomposition reactions occurring together in
  the body are known as catabolism
• Usually are exergonic since they release more
  energy than they absorb

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Exchange Reactions

• Substances exchange atoms
• consist of both synthesis and decomposition
  reactions
• Example
• HCl NaHCO3 gives rise to H2CO3 NaCl
• ions have been exchanged between substances

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Reversible Reactions

• Chemical reactions can be reversible.
• Reactants can become products or products can
  revert to the original reactants
• Indicated by the 2 arrows pointing in opposite
  directions between the reactants and the products
• AB A B

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Inorganic Compounds Solvents

• Most of the chemicals in the body are compounds
• Inorganic compounds
• usually lack carbon are structurally simple
• water, salts, acids and bases
• Organic compounds
• contain carbon usually hydrogen
• always have covalent bonds

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Dissociation

• pH - measure or acidity/alkalinity pH - log
  H
• acidic lt 7 lt basic
• Acids-raise H content
• Bases-lower H content
• release OH- or accepts H (alkaline)
•  
• 1pH unit 10x difference
• 1000 as many H in a pH of 5 as there are in 8
•  
• Buffer-takes up or releases H or OH- to prevent
  changes in pH. In the bicarbonate system,
  H2CO3 H base acceptor, HCO3- acid acceptor

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Concept of pH

• pH scale runs from 0 to 14 (concentration of H
  in soln.)
• pH of 7 is neutral (distilled water)
• pH below 7 is acidic and above 7 is alkaline

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Inorganic Acids, Bases Salts

• Acids, bases and salts always dissociate into
  ions if they are dissolved in water
• acids dissociate into Hand one or more anions
• bases dissociate into OH-and one or more
  cations
• salts dissociate into anions and cations, none
  of whichare either H or OH-
• Acid bases react in the body to form salts
• Electrolytes are important salts in the body that
  carry electric current (in nerve or muscle)

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Water Its Properties

• Most important inorganic compound in living
  systems
• Medium of nearly all chemical reactions
• Polarity
• uneven sharing of electrons
• partial negative charge near oxygen atom and
  partial positive charge near hydrogen atoms
• makes it an excellent solvent for ionic or polar
  substances
• gives water molecules cohesion
• allows water to moderate temperature changes

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Water has a high surface tension

• Water is wet
• Water is attracted to itself, and this
  attraction, due to H bonds is stronger than the
  attraction to the air above
• Adhesion and cohesion allow for capillary action
  water transport in plants

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Water as a Solvent

• Most versatile solvent known
• polar covalent bonds (hydrophilic versus
  hydrophobic)
• its shape allows each watermolecule to interact
  withneighboring ions/molecules
• oxygen attracts sodium
• hydrogen attracts chloride
• sodium chloride separate as ionicbonds are
  broken
• hydration spheres surround each ion and
• decrease possibility of bonds being reformed
• Water dissolves many substances

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Water molecules and solutions
Dissolving_Salt QT Mov
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Water in Chemical Reactions

• Participates as a product or reactant in certain
  reactions in the body
• hydrolysis reactions
• water is added to a large molecule to separate it
  into two smaller molecules
• digestion of food
• dehydration synthesis reaction
• two small molecules are joined to form a larger
  molecule releasing a water molecule

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Heat Capacity of Water

• Heat capacity is high
• can absorb a large amount of heat with only a
  small increase in its own temperature
• large number of hydrogen bonds in water
• bonds are broken as heat is absorbed instead of
  increasing temperature of water
• large amount of water in body helps lessen the
  impact of environmental changes in temperature

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Water is a good evaporative coolant

• Heat of vaporization is also high
• amount of heat needed to change from liquid to
  gas
• evaporation of water from the skin removes large
  amount of heat
• B/c it takes a lot of energy to change water from
  a liquid to a gas, it takes energy with it

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Water as a Lubricant

• Major component of lubricating fluids within the
  body
• mucus in respiratory and digestive systems
• synovial fluid in joints
• serous fluids in chest and abdominal cavities
• organs slide past one another

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Ice floats

• Water has a high freezing point and lower density
  as a solid than a liquid

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Chemical Reactions

• energy causes rearrangement of e-'s and new
  bonds, new compounds are formed, E can be force
  of collision, heat, electricity etc.
• reactants yield product(s)
• Balanced equations (energy cannot be created or
  destroyed). Balance the following equations
• CH4 O2 CO2 H2O
• CuO NH3 Cu H2O N2
• NH3 O2 NO H2O

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• CH4 2O2 CO2 2H2O
• 3CuO 2NH3 3Cu 3H2O N2
• 4NH3 5O2 4NO 6H2O

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• Mixtures-- combination of substances in which the
  individual components retain their own properties
• solutions-- or more substances is distributed
  evenly in another substance
• solution solvent(H2O)solute(dissolved
  particles)
• suspension-- particles of materials are
  temporarily mixed together
• colloid-- particles larger than solution,
  smaller than suspension

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Chemistry Tutorial

• http//www.biology.arizona.edu/biochemistry/tutori
  als/chemistry/main.html

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Organic Compounds

• Always contain carbon and hydrogen
• Usually contain covalent bonds
• Usually large, unique molecules with complex
  functions

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Carbon Its Functional Groups

• Properties of carbon atoms
• forms bonds with other carbon atoms produce
  large, stable molecules
• with many different shapes (rings, straight or
  branched chains)
• Many functional groups can attach to carbon
  skeleton
• esters, amino, carboxyl, phosphate groups (Table
  2.5)
• Very large molecules called macromolecules
  (polymers if all monomer subunits are similar)

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• The properties of different biological molecules
  depend on certain characteristic groupings of
  atoms called functional groups.
• If you know the properties of some of the
  functional groups, you will be able to quickly
  look at many simple biological molecules and get
  some idea of their solubility and possible
  identity. The names of the six most important
  functional groups are
• Hydroxyl Carbonyl Carboxyl Amino
  Sulfhydryl Phosphate

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Hydroxyl

• Two functional groups containing oxygen, the
  hydroxyl and carbonyl groups, contribute to water
  solubility.
• Hydroxyl groups have one hydrogen paired with
  one oxygen atom (symbolized as -OH). Hydroxyl
  groups are not highly reactive, but they readily
  form hydrogen bonds and contribute to making
  molecules soluble in water. Alcohols and sugars
  are "loaded" with hydroxyl groups.

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• Genistein and daidzein, two phytoestrogens from
  legumes
• Notice that the only difference between these two
  molecules is the additional hydroxyl (-OH)  group
  on genistein. Both are typical isoflavones.
  Genistein, however, is considerably more
  estrogenic than daidzein chemists attribute this
  to the influence of the additional hydroxyl
  group. The hydroxyl groups are important for
  binding to estrogen receptors.

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Carbonyl

• Carbonyl groups have one oxygen atom
  double-bonded to a carbon atom (symbolized as
  -CO). Like hydroxyl groups, carbonyl groups
  contribute to making molecules water-soluble. All
  sugar molecules have one carbonyl group, in
  addition to hydroxyl groups on the other carbon
  atoms.
• Aldehyde groups, where the CO group is at the
  end of an organic molecule. A hydrogen atom is
  also located on the same carbon atom.
• Keto groups, where the CO group is located
  within an organic molecule. All sugars have
  either a keto or an aldehyde group.

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• Carbonyl -COH C3H6O aldehydeend
  (propanol) ketone inside (acetone)

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Carboxylic Acids

• Carboxyl groups are weak acids, dissociating
  partially to release hydrogen ions.The carboxyl
  group (symbolized as COOH) has both a carbonyl
  and a hydroxyl group attached to the same carbon
  atom, resulting in new properties. Carboxyl
  groups frequently ionize, releasing the H from
  the hydroxyl group as a free proton (H), with
  the remaining O carrying a negative charge.
  Molecules containing carboxyl groups are called
  carboxylic acids and dissociate partially into H
  and COO. Carboxyl groups are common in many
  biological molecules, including amino acids and
  fatty acids.

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Amino Group

• Nitrogen in biological molecules usually occurs
  in the form of basic amino groups.Nitrogen is
  another abundant element in biological molecules.
  Having a valence of 3, nitrogen normally forms
  three covalent bonds, either single, double, or
  triple bonds. Amino groups (-NH2) are common
  functional groups containing nitrogen. Amino
  groups are basic, and often become ionized by the
  addition of a hydrogen ion (H), forming
  positively charged amino groups (-NH3).

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Sulfhydryl

• Sulfur is found mainly in proteins in the form of
  sulfhydryl groups or disulfide groups.Like
  oxygen, sulfur typically has a valence of 2,
  although it can also have a valence of 6, as in
  sulfuric acid. Sulfur is found in certain amino
  acids and proteins in the form of sulfhydryl
  groups (symbolized as -SH). Two sulfhydryl groups
  can interact to form a disulfide group
  (symbolized as -S-S-).

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Phosphate Groups

• In biological molecules, phosphorus occurs mainly
  in the form of acidic phosphate groups.
• Phosphorus normally has a valence of 5. Its most
  common functional group in organic molecules is
  as a phosphate group (symbolized as OPO32-).
  Phosphorus is covalently paired to 4 oxygen atoms
  in phosphate groups one PO bond and three P-O-
  bonds.

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Function Groups Practice
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Types of Organic compounds

• Four major groups of organic compounds,
  necessary for life are
• polymers monomers
• Carbohydrates monosacchrides
• Lipids fatty acids
• Proteins amino acids
• Nucleic acids nucleotides

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Resources

• Bare Bones Chemistry www.hcs.ohio-state.edu/hcs30
  0/chem.htm
• BioTopics Contents http//www.biotopics.co.uk/con
  ten.html