• Chapter 4~Carbon & The Molecular Diversity of Life

• Chapter 5~ The Structure & Function of

Macromolecules

Organic chemistryOrganic chemistry

• Biological thought:

• Vitalism (life force outside physical & chemical laws) – organic compounds can only arise in living organisms - Berzelius

• Mechanism (all natural phenomena are governed by physical & chemical laws) – organic compounds may be produced in lab - Miller

• Carbon

– Ability to branch in 4 directions allows large molecules possible

– Tetravalence, tetrahedron

– Shape determines function

HydrocarbonsHydrocarbons

• Only carbon & hydrogen (petroleum; lipid ‘tails’)

• Covalent bonding; nonpolar

• High energy storage

• Isomers (same molecular formula, but different structure & properties)

– 1. Structural~differing covalent bonding arrangement

– 2. Geometric~differing spatial arrangement

– 3. Enantiomers~mirror images pharmacological industry (thalidomide)

Functional Groups, IFunctional Groups, I

• Attachments that replace one or more of the hydrogens bonded to the carbon skeleton of the hydrocarbon

• Each has a unique property from one organic to another

• 1. Hydroxyl Group– H bonded to O (-OH);

alcohols; polar (oxygen);solubility in water

• 2. Carbonyl Group– C double bond to O– At end of C skeleton -

aldehyde - ex. proponal– Within C skeleton – ketone –

ex. acetone

Functional Groups, IIFunctional Groups, II

• 3. Carboxyl Group– O double bonded to C to hydroxyl– carboxylic acids, organic acids– covalent bond between

O and H is very polar leads to dissociation,

H ion

• 4. Amino Group – N to 2 H atoms (-NH2)– Amines– acts as a base

• 5. Sulfhydral Group– sulfur bonded to H

– thiols

• 6. Phosphate Group– phosphate ion covalently

attached by 1 of its O to the C skeleton

– transfer energy

PolymersPolymers

• Macromolecules – may have thousands of linked molecules

• Poly = many; mers = parts• Covalent monomers link to form

polymers• Condensation reaction (dehydration

reaction):– One monomer provides a

hydroxyl group while the other provides a hydrogen to form a water molecule

– Forms polymers• Hydrolysis: bonds between

monomers are broken by adding water (digestion) – aided by enzymes

Carbohydrates, ICarbohydrates, I

• Monosaccharides – CH2O (1:2:1) formula – Multiple hydroxyl (-OH) groups

and 1 carbonyl (C=O) group– Location determines if aldehyde

(aldose) sugar or ketone (ketose) sugar

– Cellular respiration breaks them down

– Raw material for amino acids and fatty acids

– Ex. Glucose, fructose

Carbohydrates, IICarbohydrates, II

• Disaccharides

– Glycosidic linkage (covalent bond) between 2 monosaccharides

– No longer have 1:2:1 multiples – water is pulled out (condensation/ dehydration reaction)

– Sucrose (table sugar) -most common disaccharide

Carbohydrates, IIICarbohydrates, III

• Polysaccharides Storage: Starch~ glucose monomers Plants: plastids Animals: glycogen

• Polysaccharides Structural: Cellulose~ most abundant

organic compound; Chitin~ exoskeletons; cell walls of fungi; surgical thread

Lipids, ILipids, I• Fats, phospholipids, steroids

• No polymers; glycerol and fatty acid

• Glycerol – alcohol w/ 3C each w/ hydroxyl group

• Fatty acid – long C chain w/ carboxyl group

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

• Cause to be hydrophobic

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

• Triacyglycerol (triglyceride)

• Saturated (solid) vs. unsaturated (liquid) fats; single vs. double bonds

Lipids, IILipids, II

• Phospholipids – 2 fatty acids instead of

3 – replaced by a phosphate group

– ‘Tails’ hydrophobic; ‘heads’ hydrophilic

– Micelle (phospholipid droplet in water)

– Form a bilayer (double layer) - cell membranes

Lipids, IIILipids, III

• Steroids

– Lipids with 4 fused carbon rings

– Ex: cholesterol:

• Cell membranes

• Precursor for other steroids (sex hormones – estrogen, testosterone)

• Too mcuh = atherosclerosis – narrowing of vessel walls

Proteins, IProteins, I

• Importance - instrumental in nearly everything organisms do; 50% dry weight of cells; most structurally sophisticated molecules known – enzymes, insulin, antibodies

• Monomer: amino acids (there are 20) – Contain a carboxyl (-COOH) group, amino group (NH2), H atom, variable

group (R – aka side chain – gives each its identity and properties)• Variable group characteristics: polar

(hydrophilic), nonpolar (hydrophobic), acid or base• Three-dimensional shape – conformation – determines function• Polypeptides (dehydration reaction)

– Joined by peptide bonds (covalent bond); carboxyl group to amino group (polar)

Proteins, IIProteins, II

• Primary Structure

– Conformation: Linear structure

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

– Ex: lysozyme

– Amino acid substitution: hemoglobin; sickle-cell anemia

Proteins, IIIProteins, III

• Secondary Structure– Conformation: coils &

folds (hydrogen bonds)– Alpha Helix: coiling;

keratin– Beta Pleated Sheet:

parallel; silk

Proteins, IVProteins, IV

• Tertiary Structure

– Conformation: irregular contortions from R group bonding

• hydrophobic

• disulfide bridges

• hydrogen bond

• ionic bonds

Proteins, VProteins, V

• Quaternary Structure

– Conformation: 2 or more polypeptide chains aggregated into 1 macromolecule

• collagen (connective tissue)

• hemoglobin

– Heat, pH, other body disturbances may denature protein (becomes inactive) – loses conformation

Nucleic Acids, INucleic Acids, I

• Deoxyribonucleic acid (DNA)

• Ribonucleic acid (RNA)

• DNA>RNA>protein

• Polymers of nucleotides (polynucleotide):

– nitrogenous base

– pentose – 5 carbon sugar

– phosphate group

• Nitrogenous bases:

– Pyrimidines – single ring ~cytosine, thymine (DNA), uracil (RNA)

– Purines – double ring~adenine, guanine

Nucleic Acids, IINucleic Acids, II

• Pentoses:– ribose (RNA)

– deoxyribose (DNA)

– nucleoside (base + sugar)

• Polynucleotide:– phosphodiester linkages (covalent) –

btw 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