Transcript CH.4: CARBON CHEMISTRY

CH.4: CARBON CHEMISTRY
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Water required for life as the MEDIUM for all the
reactions
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Actual chemistry of living organisms is CARBON- BASED.
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Organic compounds are those built around long chains
or rings of carbons.
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Carbon is elementally unique. ( almost as unique as the
water molecule is ….)
Carbon
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6 protons, 6 neutrons (8), 6 electrons.
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2,4 configuration
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sp hybridization
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4 unshared electrons
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Forms 4 bonds.
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Bonds readily to other carbons - creating chains (and
rings in aqueous solution)
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Also bonds to CHNOPS
A little philosophy…..
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Historically interested in synthesis of compounds
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Mechanism vs. vitalism
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Mechanism = all natural phenomenon are governed by laws of chemistry
and physics.
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Vitalism = belief in a life force outside the jurisdiction of chemistry and
physics.
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Berzelius (organic cpds), Wohler / Kolbe (make organic cpds), Miller
(spontaneous)
Bonding
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Carbon chemistry is that of COVALENT BONDING. Usually nonpolar.
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Single bond
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Double bond
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C-C, C-N, C-S, C-O….? S-S
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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……
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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
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Hydrocarbons….lots of variety
Isomers
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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
Functional Groups
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Common grouping that occur on C chains.
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Give distinct properties to molecules.
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Difference between estrogen and testosterone is one
functional group
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(actually just a H)
See next slide
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
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Hierarchy
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Structure and function
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Emergent properties
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Highly organized
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Many organic macromolecules are very large and very
complex, but are made from smaller, repeating subunits
liked in a specific way. ‘letters of alphabet’
Polymerization
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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.
Organic macromolecules
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Carbohydrates
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Lipids
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Proteins
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Nucleic Acids
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/photosynthesis and
animal tissue like
liver and muscle
Plant oils (liquid)
Muscle, tendon,
All cells –
and waxes
ligament, egg white anything with a
nucleus
Animal – more solid and seeds
Fruits, vegetables,
grains
Butter, milk, egg
yolk, olive oil, ‘fat’
Soy, peanuts,
meat, cheese, etc
Unprocessed/
fresh fruits,
vegetables
Carbohydrates
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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
Lipids
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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
Proteins
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Proteios means ‘of first importance’
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50 % of dry weight (just chemicals; no water,
“ashes”)
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Variety of structures and shapes
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Variety of functions
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UNIQUE 3-D SHAPE known as the proteins
‘CONFORMATION’
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Based on amino acid sequence
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Peptide bonds are between C and N
Functions of proteins
** everything IS protein or
is REGULATED by a protein
FUNCTION
definition
examples
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Structural
support
silk, collagan, keratin
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Storage
amino acids
albumin, milk, seeds
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Transport
transport
hemoglobin, CM
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Hormonal
coordinate
insulin
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Receptor
respond
neurotransmitters
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Contractile movement
actin, myosin, flagella
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Defensive
protection
antibodies
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Enzymatic
chem. rxns.
digestive enzymes
Specific Conformation of
Proteins
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Primary structure – sequence of amino acids
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Secondary structure – twisting, H bonds
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Coils; start of 3D
Globins (glob shaped; hemoglobin, myoglobin)
And sheets (flat, sheet like pieces; actin, collagen)
Tertiary structure – cross link, S bonds
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Linear structure; determined by mRNA code from the
DNA; infinite sequences from the 20+ amino acids
arranged in rows of 200-300
‘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
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Some proteins are made and transported in pieces and
assembled later from subunits. (enzymes and
hemoglobin)
Nucleic Acids
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Nucleic acids store INFORMATION
Deoxyribonucleic acid (DNA)
Ribonucleic acid
(RNA)
Groups of 3 bases = codon = amino acid
5 nitrogenous bases
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Adenine A
Cytosine C
Guanine G
Thymine T
Uracil U
ATP
ADP + P makes ATP which stores energy;
needs ATPase enzymes to direct
ATP + H2O yields ADP and P and releases
energy
Phospholipid Bilayers