Why Carbon? AP Bio – Campbell Ch. 4 2007-2008

Why study Carbon? All of life is built on carbon Cells ~72% H2O ~25% carbon compounds carbohydrates lipids proteins nucleic acids ~3% salts Na, Cl, K… Why do we study carbon -- is it the most abundant element in living organisms? H & O most abundant C is the next most abundant

No…Not organic like THIS… We’re talking organic CHEMISTRY! Why Study Carbon? Carbon is the centerpiece of all organic compounds Organic vs. Inorganic? No…Not organic like THIS… We’re talking organic CHEMISTRY!

Organic vs. Inorganic Organic compounds Inorganic compounds Contain carbon With hydrogen Large in size Complex in structure Inorganic compounds No carbon Or just an atom or two with NO hydrogen Example CO2 Small simple Water

C atoms are GREAT TINKERTOYS Okay…so carbon is important…but WHY CARBON?? Why not some other element?? C atoms are GREAT TINKERTOYS Carbon chemistry = organic chemistry Why is it a foundational atom? What makes it so important? Can’t be a good building block if you only form 1 or 2 bonds. H C H H H

C atoms are great tinkertoys??!! What the heck does THAT mean? It means they are GREAT BUILDING BLOCKS for LARGER, more COMPLEX molecules Ok…WHY? It all has to do with those ALL important VALENCE electrons!!

Carbon’s Valence Electrons Atomic # = 6 6 protons and 6 electrons in neutral atom 2 electrons in first shell 4 electrons in outer shell Half way to being full; Half way to being empty… Not particularly eager to either gain or lose electrons Readily forms very nice, strong covalent bonds with UP TO 4 other atoms Carbon has 4 “hands to hold” 4 valence electrons that readily engage in covalent bonds

Carbon Chains Carbon can “hold hands” with other carbons to make long chains Called Carbon Skeletons or Backbones. These chains often act as the “scaffolding” on which complex organic molecules are made.

Complex molecules assembled like TinkerToys Like sugars: C6H12O6 But can be arranged in different ways -glucose -galactose -dextrose

Carbon Chains These chains can be Straight Branched ringed Variety!

These carbon chains are called Hydrocarbons methane (simplest HC) Combinations of C & H C & H share electrons very “nicely” and equally Both their outer shells are only “half full” Results in non-polar covalent bonds not soluble in H2O (water likes to bond with polar things) Thus hydrocarbons are hydrophobic stable very little attraction between molecules a gas at room temperature

Hydrocarbon Chains While these hydrocarbon chains can be almost infinitely long, they are very “boring”… That is, they lack complexity which is a hallmark of organic compounds. How do we achieve complexity with these fairly simple (though perhaps long) carbon skeletons? FUNCTIONAL GROUPS

What are Functional Groups? Groups of atoms that have certain characteristic properties For example: Some may be polar or non polar These properties are retained regardless of where it is “hung” on a carbon skeleton The nature of the functional groups and their particular placement on a carbon skeleton can cause the molecule to fold and react with other molecules in MANY different ways. VARIETY!! Accessorize, Accessorize…

Functional Groups Create Diversity of Molecules Substitute other atoms or groups of atoms around the carbon (in place of a boring old hydrogen) ethane vs. ethanol H replaced by an hydroxyl group (–OH) nonpolar vs. polar gas vs. liquid biological effects! ethane (C2H6) ethanol (C2H5OH)

Functional groups Parts of organic molecules that are involved in chemical reactions give organic molecules distinctive properties  hydroxyl  amino  carbonyl  sulfhydryl  carboxyl  phosphate Affect reactivity – For example… Can make hydrocarbons hydrophilic Can increase hydrocarbon solubility in water

Viva la difference! Basic structure of male & female hormones is identical identical carbon skeleton attachment of different functional groups interact with different targets in the body different effects For example the male and female hormones, testosterone and estradiol, differ from each other only by the attachment of different functional groups to an identical carbon skeleton.

Hydroxyl –OH organic compounds with OH = alcohols names typically end in -ol ethanol

Carbonyl C=O O double bonded to C if C=O at end molecule = aldehyde if C=O in middle of molecule = ketone

Carboxyl –COOH C double bonded to O & single bonded to OH group compounds with COOH = acids fatty acids amino acids

Amino -NH2 N attached to 2 H compounds with NH2 = amines amino acids NH2 acts as base ammonia picks up H+ from solution

Sulfhydryl –SH S bonded to H compounds with SH = thiols SH groups stabilize the structure of proteins

Phosphate –PO4 P bound to 4 O connects to C through an O lots of O = lots of negative charge highly reactive transfers energy between organic molecules ATP, GTP, etc.

Functional Groups

Isomers Molecules with same molecular formula but different structures (shapes) different chemical properties different biological functions Same formula but different structurally & therefore different functionally. Molecular shape determines biological properties. Ex. Isomers may be ineffective as medicines 6 carbons 6 carbons 6 carbons

Form affects function Structural differences create important functional significance amino acid alanine L-alanine used in proteins but not D-alanine medicines L-version active but not D-version sometimes with tragic results… stereoisomers

Form affects function Thalidomide prescribed to pregnant women in 50s & 60s reduced morning sickness, but… stereoisomer caused severe birth defects

Building Blocks of Life Macromolecules Building Blocks of Life 2007-2008

Macromolecules Enormous molecules(as molecules go) Extremely complex Some composed of 1000s of atoms Extremely complex Shape is often CRITICAL to function Most biological molecules are MACROmolecules This does NOT mean that smaller and/or inorganic molecules are unimportant. Think WATER!

Making Macromolecules… Smaller organic molecules join together to form larger molecules Polymerization

Polymers Covalent Bonds monomers Polymer Long molecules built by linking repeating building blocks in a chain = polymerization monomers building blocks small units Linked by covalent bonds Covalent Bonds monomers H2O HO H • great variety of polymers can be built from a small set of monomers • monomers can be connected in many combinations like the 26 letters in the alphabet can be used to create a great diversity of words • each cell has millions of different macromolecules Polymer

How to build a polymer Dehydration Synthesis joins monomers by taking H2O out one monomer loses OH– other monomer loses H+ together these form H2O requires energy & enzymes H2O HO H enzyme Dehydration synthesis Condensation reaction

How to break down a polymer Hydrolysis use H2O to breakdown polymers reverse of dehydration synthesis (“put the water back”) cleave off one monomer at a time H2O is split into H+ and OH– H+ & OH– attach to ends requires enzymes releases energy H2O HO H enzyme Most macromolecules are polymers • build: condensation (dehydration) reaction • breakdown: hydrolysis An immense variety of polymers can be built from a small set of monomers Hydrolysis Digestion

There are 4 major classes of organic macromolecules: Carbohydrates Lipids Proteins nucleic acids

Any Questions?? 2007-2008