Chapter%203:%20The%20Chemistry%20of%20Organic%20Molecules

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Chapter 3 The Chemistry of Organic Molecules
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3.1 Organic Molecules

• Organic Molecule A molecule that contains carbon
  and hydrogen it may also have O, N, P, or S.

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Carbon

• Has four electrons in outer shell, therefore make
  up to four covalent bonds with four other atoms.
• It can also bond itself to form both chains and
  rings. Carbon chains make up the skeleton or
  backbone of organic molecules.

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Functional Groups

• Functional groups clusters of certain atoms,
  attached to the carbon back bone (see figure 3.2).

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• Differences in the carbon backbone and attached
  functional groups cause an organic molecule to
  have different chemical properties.
• (ex) molecules composed of only carbon and
  hydrogen are hydrophobic (not attracted to
  water). But the addition of a functional group
  like OH makes the molecule polar, or hydrophilic
  (attracted to water).

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• 4 classes of organic molecules carbohydrates,
  lipids, proteins, and nucleic acids.
• Each of these 4 types of macromolecules is a
  polymer, which is a long chain of covalently
  bonded unit molecules called monomers.

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Monomers and Polymers

• Carbohydrates polymer polysaccharide monomer
  monosaccharide
• Proteins polymer polypeptide
• monomer amino acid
• Nucleic acids polymer nucleic acid
• Monomer nucleotide

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• Condensation synthesis when a water molecule is
  removed in order to form a bond between two
  monomers. (an OH group is removed from one
  molecule and a hydrogen (H) is removed from the
  other.)
• Hyrdolysis The means by which polymers are
  broken down. A water molecule is added to break
  the bond between monomers.

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3.2 Carbohydrates

• Energy storage compounds building materials.
• Monosaccharides simple sugars, carbon back has
  3-7 atoms.
• Glucose (C6H12O6) and fructose are both hexoses
  6-carbon sugars glucose found in blood of
  animals, fructose found in fruits. (isomers)
• Ribose and deoxyribose are both pentoses
  5-carbon sugars found in DNA and RNA.

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Disaccharides

• Two monosaccharides joined by condensation.
• Lactose contains galactose and glucose found in
  milk.
• Maltose two glucose molecules result in starch
  digestion.

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Polysaccharides

• Long polymers of monosaccharides
• Glycogen- have many branches of Glucose. Storage
  vessel for animals. Liver and Muscles. Allows for
  breakdown to happen at many points.
• Starch- have many branches of glucose. Storage
  vessel of carbohydrates for plants. Seeds and
  roots. Allows for breakdown to happen at many
  points.

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Polysaccharides

• Cellulose Straight and Fibrous (structure
  support) glucose.
• Hydrogen bonds.
• Plant cell walls (cotton) (wood)

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Polysaccharides Contd

• Chitin Exoskeletons, amino group attached to
  each glucose.
• Sutures

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3.2 Lipids

• Lipids organic molecules that are generally
  insoluble in water used as long-term energy
  storage compounds in plants and animals.

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Fats and Oils

• Glycerol compound with 3 hydroxyl groups (-OH)
  hydroxyl groups are polar which makes glycerol
  soluble in water.
• Fatty Acids Long hydrocarbon chain with carboxyl
  group (-COOH)at one end
• Formation of a fat/oil Condensation synthesis
  involving 3 fatty acids and one glycerol, forming
  a triglyceride.

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• Fatty acids carboxyl group is polar which makes
  fatty acid soluble in water.
• Types
• Saturated no double bonds between carbon atoms,
  causes molecule to be more rigid.
• Unsaturated have double bonds in carbon chain,
  causes molecule to be more fluid.

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Waxes

• Waxes are long-chain fatty acid bonded to a
  long-chain alcohol.
• Solid at room temp., hydrophobic, usually act as
  a protective coating in plants and animals. (ex.
  ear wax in humans for trapping dirt and dust
  particles, preventing them from reaching the
  eardrum.)

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Phospholipids

• Soluble in water contains a glycerol molecule, 2
  fatty acids, and one phosphate group.
• Phosphate group is the polar head of molecule.
• Fatty acid chains are nonpolar tails of
  molecule.
• Plasma membrane in eukaryotic cells is a
  phospholipid bilayer.

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The Phopholipid Bilayer of Plasma Membranes
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Steriods

• Backbone of 4 fused carbon rings, vary according
  to the types of functional groups bonded to the
  rings.
• Cholesterol- component of animal cell membrane,
  precursor for other types of steroids (estrogen,
  testosterone).

Cholesterol is the molecule from which other
steroids, including the sex hormones, are
synthesized.
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3.4 Proteins

• Polymers of amino acids
• Functions
• Support / structure Keratin in hair and nails,
  collagen in ligaments, skin, tendons.
• Regulation Enzymes that speed up reactions
  (catalyze), Hormones like insulin regulates
  levels of glucose in blood

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Protein Functions contd

• Defense Antibodies, and antigens
• Motion contractile proteins (actin and Myosin)
  in muscles.
• Transport Channel and carrier proteins in plasma
  membrane, hemoglobin (O2)

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Monomers Of Proteins

• Amino Acids Carbon Atom bonded to 3 functional
  groups.
• Animo group (-NH2)
• Carboxyl group (-COOH) (acidic)
• R group remainder of molecule determines the
  20 different amino acids found in life unique
  properties.

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Polymers of proteins

• Polypeptides two or more amino joined by
  condensation
• Peptide bond between Carbon of one amino acid
  and the nitrogen of another.
• Most proteins are at least 150 A.A. long.
• Some proteins can contain more than one
  polypeptide chain

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Protein Structure

• Primary Structure The sequence of amino acids
  joined by peptide bonds.
• Secondary Structure Coiling or folding of
  polypeptide chain due to properties of A.A. w/in
  primary structure. (H-bonds b/w different A.A.)
• Beta sheets
• Alpha helix

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Protein Structure Contd

• Tertiary Structure The folding and twisting that
  results in the 3-D shape of polypeptide.
• H-bonds, disulfide links (fxnl group?), Ionic
  bonds, and other molecular interactions between R
  groups.
• Quaternary Structure arrangement of more than
  one polypeptide chain
• Hemoglobin globular protein with 4 peptide
  chains
• Some proteins

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Protein Structure 2 models
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Denaturation

• When a protein loses its 40/30/20 structure.
• Renders a protein inactive.
• Caused when the environment that protein is in
  changes (temperature, pH)
• Causes interactions/bonds to break
• Proteins have optimal environments.
• Renaturation when protein is place back into
  optimal environment it will reform into proper
  structure.

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High temperatures or various chemical treatments
will denature a protein, causing it to lose its
conformation and hence its ability to function.
If the denatured protein remains dissolved, it
can often renature when the chemical and physical
aspects of its environment are restored to
normal.
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Importance of Denaturation / Renaturation

• Regulation This is a way for cells to regulate
  which chemical reactions will happen and when
  they will occur.
• Not very efficient if cells are undergoing all
  reaction all at once.

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Nucleic Acids

• Three types of nucleic acids

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1) DNA

• DNA (deoxyribonucleic acid) the genetic
  material that store information for replicating
  itself and the sequence of amino acids to make
  all of an organisms proteins
• Monomers nucleotide
• There are three molecules that make up a
  nucleotide
• Phosphate functional group
• Nitrogen containing base
• Pentose monosaccharide deoxyribose
• There are four types of nucleotides that are
  determined by the type of base each has
  Cytosine, Thymine, Adenine, and Guanine

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DNA Continued

• The different nucleotides are joined together by
  a bond between the phosphate of one nucleotide
  and the sugar of another. (SugarPhosphate
  Backbone) Process?
• DNA has two strands of nucleotides that are
  joined together by hydrogen bond between
  different bases (A-T, T-A, C-G, G-C)
• This results in the double-helix

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2) RNA

• RNA (ribonucleic acid) involved in the process
  of making proteins form DNA.
• Similar to DNA except
• Single Stranded
• Ribose instead of Deoxyribose
• Uracil instead of Thymine

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3) ATP

• ATP (Adenosine Triphosphate) supplies energy
  for synthetic reactions and for all energy
  requiring processes in cells. (a cells energy
  currency)
• Adenosine ribose adenine
• Triphosphate three phosphates bonded together

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ATP Contd

• High energy molecule due to the instability of
  phosphates.
• ATP ? ADP P H20 (energy) Reversible reaction
  constantly recycled in cells