CH.4: CARBON CHEMISTRY

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CH.4 CARBON CHEMISTRY

• Water required for life as the MEDIUM for all the
  reactions
• Actual chemistry of living organisms is CARBON-
  BASED.
• Organic compounds are those built around long
  chains or rings of carbons.
• Carbon is elementally unique. ( almost as unique
  as the water molecule is .)

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Carbon

• 6 protons, 6 neutrons (8), 6 electrons.
• 2,4 configuration
• sp hybridization
• 4 unshared electrons
• Forms 4 bonds.
• Bonds readily to other carbons - creating chains
  (and rings in aqueous solution)
• Also bonds to CHNOPS

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A little philosophy..

• Historically interested in synthesis of compounds
• Mechanism vs. vitalism
• Mechanism all natural phenomenon are governed
  by laws of chemistry and physics.
• Vitalism belief in a life force outside the
  jurisdiction of chemistry and physics.
• Berzelius (organic cpds), Wohler / Kolbe (make
  organic cpds), Miller (spontaneous)

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Bonding

• Carbon chemistry is that of COVALENT BONDING.
  Usually nonpolar.
• Single bond
• Double bond
• C-C, C-N, C-S, C-O.? S-S
• Because S is the closest in chemical structure to
  C its possible their would be unique compounds
  with sulfur and in areas with lots of sulfur
  (ocean vents) their would be S-S life forms
  (instead of C based life forms
• Hydrogen bonding and sulfur bonds are also
  important to emerging properties of organic
  molecules.the folding of proteins, so C-N or C-C
  makes the structure but the 3D shape depends on S
  attractions and H bonding in various
  regions/zones
• Hydrocarbons.lots of variety

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Isomers

• Vary in architecture, not empirical formula
• Structural isomers butane and isobutane on pg
  61. 18 versions of C8H18
• Geometric isomers same covalent partnerships
  but different spatial arrangement. (often double
  bond)
• Enantiomers (stereo isomers) mirror images
  around a central carbon.
• Enantiomers are important pharmaceutically

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Functional Groups

• Common grouping that occur on C chains.
• Give distinct properties to molecules.
• Difference between estrogen and testosterone is
  one functional group
• (actually just a H)
• See next slide

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Functional groups

• Hydroxyl OH, alcohols, solubility
• Carbonyl -CO, -COH, double bonds, aldehydes and
  ketones,
• Carboxyl -COOH, carboxylic acids, sour taste,
  good source of H ions,
• Amino -NH2, basic
• Sulfhydryl -SH, thiols, stability
• Phosphate -PO4, negativity, energy transfer
• Methyl CH3, expression of genes

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Structure and Function of Organic Macromolecules

• Hierarchy
• Structure and function
• Emergent properties
• Highly organized
• Many organic macromolecules are very large and
  very complex, but are made from smaller,
  repeating subunits liked in a specific way.
  letters of alphabet

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Polymerization

• Monomer small piece, building block
• Dimer
• Polymer long chain made from many repeating
  pieces. Variety and specificity
• Polymerization is the process of constructing
  large molecules from smaller pieces.
• Dehydration (condensation) reactions remove
  waters and create covalent bonds between
  monomers.
• Hydrolysis reactions are used to split polymers
  into monomers.

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Organic macromolecules

• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids

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Carbohydrates Lipids Proteins Nucleic Acids
Saccharides sugars and starches Glucose, fructose, maltose, lactose -sucrose Amylose and pectin Cellulose Glycerol and fatty acids Saturated and unsaturated Amino acid based Found in DNA and ATP
Fuel immediate use and transport short term storage Fuel storage ! Insulation Messengers 8 functions Information storage and transmission
Plants/photo-synthesis and animal tissue like liver and muscle Plant oils (liquid) and waxes Animal more solid Muscle, tendon, ligament, egg white and seeds All cells anything with a nucleus
Fruits, vegetables, grains Butter, milk, egg yolk, olive oil, fat Soy, peanuts, meat, cheese, etc Unprocessed/ fresh fruits, vegetables
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Carbohydrates

• C and H, some oxygen
• Ratio is CH2O
• Sugars , carbohydrates and starches
• Monosaccharides (glucose C6H12O6) are for energy
  in cells
• Disaccharides (like sucrose) are for transport in
  plants after photosynthesis (sap and fruit)
• Polysaccharides (starches) are for storage in
  plants. Also found in animal liver.
• Carbs can also be structural - cellulose

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Lipids

• Hydrophobic
• Glycerol and 3 fatty acids
• Fatty acids are hydrocarbon chains of 12 24
  carbons.
• saturated fats have no double bonds and are
  solid ( animal )
• unsaturated fats have double bonds are more
  fluid.
• Fats are for energy storage ( fat, oils, waxes,
  seeds, nuts )
• They are also for insulation heat and
  electrical
• Lipids are also used for protection/ cushion
• Some lipids ( cholesterol ) are important as
  components of chemical messengers in the body
  (hormones)
• They are a MAJOR component of the phospholipid
  bilayer of cell membranes

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Proteins

• Proteios means of first importance
• 50 of dry weight (just chemicals no water,
  ashes)
• Variety of structures and shapes
• Variety of functions
• UNIQUE 3-D SHAPE known as the proteins
  CONFORMATION
• Based on amino acid sequence
• Peptide bonds are between C and N

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Functions of proteins everything IS protein or
is REGULATED by a protein

• FUNCTION definition examples
• Structural support silk, collagan, keratin
• Storage amino acids albumin, milk, seeds
• Transport transport hemoglobin, CM
• Hormonal coordinate insulin
• Receptor respond neurotransmitters
• Contractile movement actin, myosin, flagella
• Defensive protection antibodies
• Enzymatic chem. rxns. digestive enzymes

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Specific Conformation of Proteins

• Primary structure sequence of amino acids
• Linear structure determined by mRNA code from
  the DNA infinite sequences from the 20 amino
  acids arranged in rows of 200-300
• Secondary structure twisting, H bonds
• Coils start of 3D
• Globins (glob shaped hemoglobin, myoglobin)
• And sheets (flat, sheet like pieces actin,
  collagen)
• Tertiary structure cross link, S bonds
• coils coil twisted rope that twists again to
  make a loop very 3D form fits function
  things like enzymes have very specific shapes and
  active zones
• Quaternary structure multiple pieces
• Some proteins are made and transported in pieces
  and assembled later from subunits. (enzymes and
  hemoglobin)

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Nucleic Acids

• Nucleic acids store INFORMATION
• Deoxyribonucleic acid (DNA)
• Ribonucleic acid (RNA)
• Groups of 3 bases codon amino acid
• 5 nitrogenous bases
• Adenine A
• Cytosine C
• Guanine G
• Thymine T
• Uracil U

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ATP
ADP P makes ATP which stores energy needs
ATPase enzymes to direct ATP H2O yields ADP
and P and releases energy
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Phospholipid Bilayers