9/6/2011. Amino Acids. C α. Nonpolar, aliphatic R groups
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1 Amino Acids Side chains (R groups) vary in: size shape charge hydrogen-bonding capacity hydrophobic character chemical reactivity C α Nonpolar, aliphatic R groups Glycine (Gly, G) Alanine (Ala, A) Valine (Val, V) Simplest amino acid (achiral) other amino acids built by adding side chain complexity 1
2 Leucine (Leu, L) Isoleucine (Ile, I) Methionine (Met, M) Proline also has an aliphatic side chain The side chain is bonded to both the nitrogen and the a-carbon atom. It influences protein architecture because its ring structure gives it a more restricted conformation than other amino acids. Proline (Pro, P) 2
3 Phenylalanine phenyl ring (purely hydrophobic) Tyrosine contains a hydroxyl group (reactive in contrast to the rather inert side chains of other amino acids (less hydrophobic because of OH) Phenylalanine (Phe, F) Aromatic R groups Tyrosine (Tyr, Y) Tryptophan (Trp,W) Tryptophan indole ring joined to (-CH 2 -) group (less hydrophobic because of NH 2 ) Polar, uncharged R groups Serine is a hydroxylated version of alanine. Threonine is a hydroxylated version of valine. Serine (Ser, S) Threonine Thr, T) The OH is hydrophilic (water loving) and reactive. 3
4 Similar to serine but OH is replaced by SH -SH is very reactive pairs of cysteines may react forming disulfide bonds which are important for stabilizing protein structure Cysteine (Cys, C) Contain terminal carboxamide in place of carboxylic acid Asparagine (Asn, N) Glutamine (Gln, Q) Derivatives of glutamate and aspartate. 4
5 Basic amino acids (positively charged) Lysine (Lys, K) Arginine (Arg, R) Histidine (His, H) Histidine pka 6, imidazole can be uncharged or positively charged near neutral ph, often found in the active site of enzymes. 5
6 Aspartate (Asp, D) Glutamate (Glu, E) Acidic amino acids (negatively charged) Aspartate and Glutamate -COO - can be protonated Typical pka s 6
7 Carbohydrates Earth s most abundant biomolecule Roles Serve as energy, fuels, and metabolic intermediates Structural framework of DNA and RNA Structural elements in cell walls of bacteria and plants Lubricate joints Linked to proteins and lipids Mediators of cellular interactions Monosaccharides small 3-9 carbon molecules that vary in size and stereochemical configuration Oligosaccharides monosaccharides linked together Monosaccharides aldehydes or ketones with 2 or more OH s aldose ketose Most monosaccharides have asymmetric (chiral) carbon atoms glyceraldehyde dihydroxyacetone The simplest monosaccharides are three carbon sugars, trioses 7
8 Enantiomers optical isomers D isomer and the L isomer A molecule with n chiral carbons can have 2 n stereoisomers. Reference carbon the most distant chiral carbon from the carbonyl. This defines configurations of the carbohydrate. -OH on the left L isomer -OH on the right D isomer * * * * *Atoms joined to the asymmetric carbon *Reference carbon How many chiral carbons does this molecule have? 8
9 Structure and Nomenclature Monosaccharides Many have the empircal formula (CH 2 O) n n = 3, trioses n = 4, tetroses n = 5, pentoses n = 6, hexoses Aldose series Ketose series Assymetric centers - 2 n stereoisomers aldohexoses: 2 4 = 16 8 will be D configuration ketohexoses: 2 3 = 8 4 will be D configuration Multiple asymmetric carbons Enantiomer isomers that are mirror images Diastereomers isomers that are not mirror images Epimers sugars differing in configuration at a single asymmetric center D and L designate the absolute configuration of the asymmetric carbon farthest from the aldehyde or keto group 9
10 Epimers D-glucose and D-mannose differ in configuration only at C-2 and therefore are epimeric at C-2. Are D-Mannose and D-Galactose isomers of glucose? If so what kind? 10
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