Organic ChemistryMs. NapolitanoHonors Biology

Introduction to Orgo Organic chem – the study of C based

compounds (must have both C & H)

Why Carbon? It’s versatile! 4 valence electrons (4 covalent bonds) Form simple or complex compounds C chains form backbone of most biological

molecules (straight, bent, double bond, rings)

Hydrocarbons Hydrocarbons

ONLY consist of C & H

Importance – store energy

Hydrophobic

Organic Shorthand

Isomers Isomers – same number of

atoms per element, different arrangement

3 types: Structural – differ in covalent

partners Geometric – differ in

arrangement around a double bond

Enantiomers – mirror images of each other

Different structure means different function!

Isomers

Structural Isomers

Geometric Isomers

Enantiomers

cis trans

Functional Groups Functional groups – parts of organic molecules

that are most commonly involved in chemical reactions

replace H in hydrocarbons

Most are hydrophilic

Variation of life is due to molecular variation

Functional Groups

Macromolecules Huge biological

molecules!

4 classes: Carbohydrates Lipids Proteins Nucleic Acids

Polymers – long molecule made of monomers

Polymerization

Building dimers or polymers Condensation rxn AKA dehydration

synthesis: Monomer-OH + monomer-H dimer + H2O

Breaking down dimers or polymers Reverse rxn called hydrolysis Dimer + H2O monomer-OH + monomer-H

Carbohydrates Cells get most of their energy from carbs

Carbs are sugars, most end in “-ose”

Multiple of molecular formula: CH2O Glucose: C6H12O6

Carbonyl group

Multiple hydroxyl groups

Carbohydrates Monosaccharides

Monomers: simple sugars w/ 3-7 carbons Ex. (C6H12O6): Glucose, Fructose, Galactose

Disaccharide – formed by 2 monosaccharides forming a glycosidic linkage by dehydration synthesis

Ex: glucose + glucose maltose + H2O glucose + fructose sucrose + H2O glucose + galactose lactose + H2O

Carbohydrates

Carbohydrates Polysaccharides: 100’s – 1000’s of monosaccharides

joined by glycosidic linkages

Storage polysaccharides Starch

Plants – stored in plastids Made entirely of glucose - helical

Glycogen Animals – stored in liver & muscle (in vertebrates) Made entirely of glucose - branched

Structural polysaccharides Cellulose – plant cell walls

Made of glucose – linear Chitin

Exoskeleton of arthropods & fungi cell walls

Lipids No polymers!

Hydrophobic (mostly hydrocarbons)

Store energy efficiently (2x more than carbs!)

Types : Fats & oils Phospholipids Steroids Waxes

Fats & Oils Fat = dehydration synthesis of:

Glycerol C3H5(OH)3

Fatty acid: 16 or 18 carbon hydrocarbon chain w/ carboxyl group

Glycerol + 3 fatty acid chains = triglyceride + 3 H2O

Function: Energy storage Insulation Protective cushioning around organs

Saturated Fats No double bonds between carbons

Saturated with hydrogens

Solid at room temperature

Mostly animal fat

Ex: butter, lard, adipose

Unsaturated Fats 1 or more double bonds between carbons

Bent or kinked chains

Liquid at room temperature

Mostly plant or fish fat

Ex: olive oil, cod liver oil, corn oil

Phospholipids Glycerol + 2 fatty acids + phosphate

Phosphate head = hydrophilic

Fatty acid tails = hydrophobic

Form a bilayer in water

Makes up cell membranes

Phospholipids

Steroids 4 fused carbon rings

with various functional groups

Ex: cholesterol Component of cell

membrane & many hormones

Proteins Functions: enzymes, structural support, storage,

transport, cellular communication, movement, defense

Monomer = amino acid Short C chain Amino group Carboxylic acid group “R” group determines type

Cells use 20 different amino acids to build 1000’s of different proteins

Amino acids linked by peptide bonds via dehydration synthesis to form polymers – polypeptides

Chaperonins assist in protein folding

Protein Structure 10 Structure

- Sequence of amino acids (length vary)- Determined by genes

20 Structure How polypeptide folds or coils Α helix β pleats

30 Structure - 3D (fold onto itself) H bonds Hydrophobic interaction Disulfide bridges

40 Structure – bonds to other polypeptides 2 or more polypeptide chains bonded together

Protein Conformation Structure of a protein is directly related to function

Protein conformation is determined when it is synthesized, and it is maintained by chemical interactions

Protein conformation also depends on environmental factors: pH, salt concentration, temp…etc

Protein can be denatured – unravel and lose conformation, therefore biologically inactive. When conditions change again, protein can be renatured

(restored to normal)

Nucleic Acids 2 types:

DNA (deoxyribonucleic acid) Found in nucleus of eukarya Double stranded helix Provides directions for its own replication Also directs RNA synthesis

Though RNA controls 10 structure of proteins

RNA (ribonucleic acid) Single stranded, variety of shapes Transfers information from nucleus to cytoplasm (where

proteins are made)

DNA RNA Proteins

Structure of Nucleic Acids

Monomers – nucleotides composed of 3 parts: Pentose (ribose or deoxyribose) Phosphate group Nitrogenous base

Pyrimidines – 6 membered rings of C & N Cytosine (C) Thymine (T)….DNA only Uracil (U)… RNA only

Purines – 6 membered ring fused to 5 membered ring of C & N Adenine (A) Guanine (G)

Nucleotide Structure

Bonding of Nucleotides

ATP Not a macromolecule, but still important

for life!

Adenosine Triphosphate (ATP) – primary energy transferring molecule in the cell

ATP ADP + Pi + Energy