 Chapter 3~ Carbon and the Molecular Diversity of Life

Functional Groups Groups of atoms acting as a unit, that give organic molecules their physical properties, their chemical reactivity, & solubility in aqueous solutions. Most possess electronegative atoms (N, P, O, S... EASILY ATTRACT PROTONS) Key bonds are : ester (C-O-C) & amide (O=C-N-) are ionizable at physiological pH -NH 2 AMINE= amino acid -C=O x CARBONYL= aldehyde/ketone -COOH x CARBOXYL= acid -OH x HYDROXYL = alcohol -PO 4 PHOSPHORYL= organic phosphate -SH SULFHYDRYL= disulfide -CH 3 METHYL= hydrocarbon

Hydroxyl group  Polar group; the bond between the oxygen and hydrogen is a polar covalent bond.  Makes the molecule to which it is attached water soluble. Polar water molecules are attracted to the polar hydroxyl group which can form hydrogen bonds.  Organic compounds with hydroxyl groups are called alcohols.

Carbonyl Group  Functional group that consists of a carbon atom double-bonded to oxygen (-C=O)  Is a polar group. The oxygen can be involved in hydrogen bonding, and molecules with his functional group are water soluble.  Is a functional group found in sugars.  Aldehyde = carbonyl group on end carbon of chain  Ketone =- carbonyl group attached to internal carbon

Carboxyl group  Functional group that consists of a carbon atom which is both double- bonded to an oxygen and single-bonded to the oxygen of a hydroxyl group (-COOH).  Is a polar group and water soluble. The covalent bond between oxygen and hydrogen is so polar, that the hydrogen reversibly dissociates as H +. This polarity results from the combined effect of the two electronegative oxygen atoms bonded to the same carbon.  Since it donates protons, this group has acidic properties. Compounds with this functional group are called carboxylic acids.

Amino group  Functional group that consists of a nitrogen atom bonded to two hydrogen atoms & to the carbon skeleton (—NH 2 ).  Is a polar group and soluble in water.  Acts as a weak base. The unshared pair of electrons on the nitrogen can accept a proton, giving the amino group a +1 charge.  Organic compounds with this functional group are called amines.

Sulfhydryl group  Functional group which consists of an atom of sulfur bonded to an atom of hydrogen (—SH).  Stabilize the structure of proteins. (Disulfide bridges of proteins)  Organic compounds with this functional group are called thiols.

Phosphate group  Functional group which is the dissociated form of phosphoric acid (H 3 PO 4 ).  Loss of two protons by dissociation leaves the phosphate group with a negative charge.  Has acid properties since it loses protons.  Polar group and soluble in water.  Organic phosphates are important in cellular energy storage and transfer

Methyl group  methyl group (—CH 3 )  Non-polar hydrophobic functional group

Polymers  Covalent monomers  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)

Carbohydrates, I  Monosaccharides √CH 2 O formula; √multiple hydroxyl (-OH) groups and 1 carbonyl (C=O) group: aldehyde (aldoses) sugar ketone sugar  √cellular respiration;  √ raw material for amino acids and fatty acids.

Carbohydrates, II  Disaccharides √ glycosidic linkage (covalent bond) between 2 monosaccharides. √ covalent bond by dehydration reaction.  Sucrose (table sugar) √ most common disaccharide

Carbohydrates, 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  No 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, II

Phospholipids  2 fatty acids instead of 3 (phosphate group)  ‘Tails’ hydrophobic; ‘heads’ hydrophilic  Micelle (phospholipid droplet in water)  Bilayer (double layer);cell membranes

Steroids  Lipids with 4 fused carbon rings  Ex:  cholesterol: cell membranes.  precursor for other steroids (sex hormones).

Proteins  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 (NH 2 ), H atom, variable group (R)….  Variable group characteristics: polar (hydrophilic), nonpolar (hydrophobic), acid or base  Three-dimensional shape  Polypeptides (dehydration reaction): peptide bonds~ covalent bond; carboxyl group to amino group.

Primary Structure  Conformation: Linear structure  Molecular Biology: each type of protein has a unique primary structure of amino acids  Forms a zwitterion  Amino acid substitution: hemoglobin; sickle-cell anemia

Secondary Structure  Conformation: coils & folds (hydrogen bonds)  Alpha Helix:coiling; keratin  Pleated Sheet: parallel; silk

Tertiary Structure  Conformation: irregular contortions from R group bonding √hydrophobic √disulfide bridges √hydrogen bonds √ionic bonds

Quaternary Structure  Conformation: 2 or more polypeptide chains aggregated into 1 macromolecule √collagen (connective tissue) √hemoglobin

Nucleic 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, II  Pentoses: √ ribose (RNA) √deoxyribose (DNA) √nucleoside (base + sugar)  Polynucleotide: √ phosphodiester linkages (covalent); phosphate + sugar

Nucleic Acids, III  Inheritance based on DNA replication  Double helix (Watson & Crick ) H bonds~ between paired bases van der Waals~ between stacked bases  A to T; C to G pairing  Complementary

Nucleic Acids IV