Organic chemistry:Organic chemistry:The Chemistry of CarbonThe Chemistry of Carbon

• Carbontetravalencetetrahedron shape determines function

Hydrocarbons and IsomersHydrocarbons and Isomers

• Hydrocarbons– Only carbon & hydrogen

(petroleum; lipid ‘tails’)– Covalent bonding; nonpolar– High energy storage

• Isomers (same molecular formula, but different structure & properties)– structural~differing covalent

bonding arrangement

– geometric~differing spatial arrangement around a double bond

– enantiomers~mirror images pharmacological industry (thalidomide)

Functional Groups, IFunctional Groups, I

• Attachments that replace one or more of the hydrogen(s) bonded to the carbon skeleton of the hydrocarbon

• These regions are commonly reactive.

• Each has a unique property and behave consistently from one organic molecule to another.

• Hydroxyl Group H bonded to O

• Very polar (oxygen is much more electronegative than hydrogen);

• soluble in water• The main functional group of

ALCOHOLS

• Carbonyl Group• C double bonded to O• Also very polar/soluble• Main functional group of

SUGARS• At end : aldehyde

• Otherwise: ketone

Functional Groups, IIFunctional Groups, II• Carboxyl Group • O double bonded to C to hydroxyl• Main functional group of carboxylic acids• H in the OH extremely polar dissociates to form H ion

• Amino Group N to 2 H atoms;• amines • acts as base (accepts H+)

• Converts to NH3 as it accepts protons

Isomers! (Link)

Functional Groups, IIIFunctional Groups, III

• Sulfhydral Group • sulfur bonded to H• Attract each other to help stabilize

proteins• (disulfide bridges) • thiols

• Phosphate Group phosphate ion

• covalently attached:• 1 of its O to the C skeleton• Polar/hydrophilic• Important in cellular energy &

transfer

PolymersPolymers• Most Macromolecules are

POLYMERS:• Large molecules consisting of

many identical or similar subunits called:

• Monomers (different kinds of monomers for different kinds of polymers)

• Condensation reaction (dehydration reaction):One monomer provides a hydroxyl group while the other provides a hydrogen to form a water molecule

• Hydrolysis: bonds between monomers are broken by adding water (digestion)

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Carbohydrates (Sugars, etc…)Carbohydrates (Sugars, etc…)

Monomer = “monosaccharide”

Used for energy & structure

“-ose” ending!

-OH attached to all carbons except 1which has a carbonyl (C=O) group

Monosaccharides are 3-7 carbons in size:Most common: Triose-3 ; Ribose-5 ; Hexose-6

Form rings in aqueous solutions

Monosaccharides link to form….

DisaccharidesDisaccharides

• Disaccharides • glycosidic linkage:• (covalentbond) between 2

monosaccharides• covalent bond by dehydration reaction

• Sucrose (table sugar) most common disaccharide

• There are also “Trisaccharides”, and even “Oligosaccharides”

• Once you get more than a couple dozen in a row, you then call them…..

Polysaccharides:Polysaccharides: 100s to 1000s of linked Monosaccharides100s to 1000s of linked Monosaccharides

• Polysaccharides Storage: • Plants: Starch

– can be used for energy by animals– Straight chains of glucose

• Animals: Glycogen– Highly branched chains of glucose

• Polysaccharides Structural:

• Cellulose~ what plants are mostly made of…– Earth’s most abundant organic

compound!

• Chitin~ exoskeletons; cell walls of fungi; surgical thread

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LipidsLipids• No long chain polymers; glycerol and fatty acid

• Fats, phospholipids, steroids

• Hydrophobic; H bonds in water exclude fats

• Carboxyl group = fatty acid

• Non-polar C-H bonds in fatty acid ‘tails’

• Ester linkage: 3 fatty acids to 1 glycerol (dehydration formation)

• Triacyglycerol (triglyceride)

• Saturated vs. unsaturated fats; single vs. double bonds

Lipids, IILipids, II

PhospholipidsPhospholipids

• 2 fatty acids instead of 3 (phosphate group)

• ‘Tails’ hydrophobic; ‘heads’ hydrophilic

• Micelle (phospholipid droplet in water)

• Bilayer (double layer);cell membranes

Considered “Amphipathic”:One part hydrophobic, one part Hydrophilic

Hydrophilic head

Hydrophobic Tail

SteroidsSteroids

• Lipids with 4 fused carbon rings

• Ex: cholesterol:cell membranes;precursor for other steroids (sex hormones); atherosclerosis

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ProteinsProteins

• Importance: instrumental in nearly everything organisms do; 50% dry weight of cells; most structurally sophisticated molecules known

• Monomer: amino acids (there are 20) ~ • carboxyl (-COOH) group, amino group (NH2), H atom, variable group (R)….

• Variable group characteristics: polar (hydrophilic), nonpolar (hydrophobic), acid or base

• hyperlink• Three-dimensional shape (conformation)• Polypeptides (dehydration reaction): peptide

bonds~ covalent bond; carboxyl group to amino group (polar)

Primary StructurePrimary Structure

• Conformation: Linear structure

• Molecular Biology: each type of protein has a unique primary structure of amino acids

• Amino acid substitution:hemoglobin; sickle-cell anemia

Secondary StructureSecondary Structure

• Conformation:

• coils & folds (hydrogen bonds)

• 2 main types of 2ndary structures:

• Alpha Helix: coiling; keratin

• Pleated Sheet: parallel; silk

Tertiary StructureTertiary Structure

• Conformation: irregular contortions from R group bonding√hydrophobic √disulfide bridges√hydrogen bonds

√ionic bonds

Quaternary StructureQuaternary Structure

• Conformation: • 2 or more polypeptide chains

aggregated into macromolecule√collagen (connective tissue)

√hemoglobin

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Nucleic Acids, INucleic Acids, I

• Deoxyribonucleic acid (DNA)

• Ribonucleic acid (RNA)

• DNA RNA protein• Polymers of nucleotides

(polynucleotide):nitrogenous basepentose sugarphosphate group

• Nitrogenous bases:

pyrimidines~cytosine, thymine, uracil purines~adenine, guanine

Nucleic Acids, IINucleic Acids, II

• Pentoses:√ribose (RNA)√deoxyribose (DNA)√nucleoside (base + sugar)

• Polynucleotide:√phosphodiester linkages (covalent); phosphate + sugar

Nucleic Acids, IIINucleic Acids, III

• Inheritance based on DNA replication

• Double helix (Watson & Crick - 1953) H bonds~ between paired bases van der Waals~ between stacked bases

• A to T; C to G pairing

• Complementary

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