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 …hybridization of s and p orbitals.)
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
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)
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
Isomers - see pages 61 and 62
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
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
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
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
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
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
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
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
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
FUNCTION definition examples Structural support silk, collagen, 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 chemical reactions digestive enzymes
Functions of proteins - again
FUNCTION definition examples Structural support silk, collagen, keratin
collagen is the protein that holds skin to muscles Storage amino acids albumin, milk, seeds milk is full of albumin so babies have a.a. to build with Transport transport hemoglobin, CM
hemoglobin contains Fe and bonds to O2 for transport 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
Receptor respond neurotransmitters Contractile movement actin, myosin, flagella actin and myosin are proteins that are the cytoskeleton fibers that cause muscle cells to contract Defensive protection antibodies Enzymatic chemical reactions digestive enzymes
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)
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
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.