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CH.4: CARBON CHEMISTRY
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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 …hybridization of s and p orbitals.)
Carbon
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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
A little philosophy…..
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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)
Bonding
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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
Isomers - see pages 61 and 62
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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.
Give distinct properties to molecules.
Difference between estrogen and
testosterone is one functional group
–
(actually just a H)
See next slide
Functional groups
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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
Ch. 5: Structure and Function of
Organic Macromolecules
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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’
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
Lipids
Proteins
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/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
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’
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
Functions of proteins
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FUNCTION
Structural
Storage
Transport
Hormonal
Receptor
Contractile
Defensive
Enzymatic
definition
support
amino acids
transport
coordinate
respond
movement
protection
chemical reactions
examples
silk, collagen, keratin
albumin, milk, seeds
hemoglobin, CM
insulin
neurotransmitters
actin, myosin, flagella
antibodies
digestive enzymes
Functions of proteins - again
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FUNCTION
Structural
definition
support
examples
silk, collagen, keratin
collagen is the protein that holds skin to muscles
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Storage
amino acids
albumin, milk, seeds
milk is full of albumin so babies have a.a. to build with
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Transport
transport
hemoglobin, CM
hemoglobin contains Fe and bonds to O2 for transport
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Hormonal
coordinate
insulin
insulin is a hormone produced by pancreas that causes muscles and liver to change the
response of their cell membranes to glucose
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Receptor
Contractile
respond
movement
neurotransmitters
actin, myosin, flagella
actin and myosin are proteins that are the cytoskeleton fibers that cause muscle cells to contract
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Defensive
Enzymatic
protection
chemical reactions
antibodies
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
Review:
Table on pg. 90
and
Hand out over types of
organic macromolecules.