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 ….)

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

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

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** 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

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