Amino Acids and the Primary Structures of Proteins

Firefly Luciferase and Luciferin

Hemoglobin in erythrocytes

Keratin

Chemical structure of an amino acid R = side chain C = alpha carbon Amino terminus Carboxyl terminus

The alpha  carbon of amino acids is chiral (except glycine). There are two stereoisomers of amino acids (L and D). Proteins contain L-amino acids

L-amino acid at neutral pH Figure 3.1

Amino acids with aliphatic R groups

The amino acid proline is a cyclic molecule

Amino acids with aromatic R groups

Amino acids with sulfur-containing R groups

Oxidation can form cystine from two cysteines Figure 3.4

Side chains with alcohol groups

Amino acids with basic R groups

Amino acids with acidic R groups

Amide derivatives of acidic R groups

Other amino acids and amino acid derivatives Figure 3.5

Selenocysteine is the 21 st amino acid

Ionization of amino acids Pages 60 – 64 pH ?

Ionization of amino acids Pages 60 – 64 pH 1pH 7

pH ? pH 7 Ionization of amino acids Pages 60 – 64

pH 12 pH 7 Ionization of amino acids Pages 60 – 64

Ionization of histidine Figure 3.7

Ionization of histidine Figure 3.7

Ionization of glutamate Figure 3.8

Ionization of arginine Figure 3.8

Peptide bonds link amino acids in proteins Figure 3.9

Peptide bonds link amino acids in proteins Figure 3.9 Alanine Ala (A)Serine Ser (S) Dipeptide Ala – Ser or AS

Practice Problem Draw the chemical structure of the tripeptide Ala – Thr– Cys at pH 7. Answer the following with regard to this tripeptide: 1. Indicate the charge present on any ionizable group(s). 2. Indicate, using an arrow, which covalent bond is the peptide bond. 3. What is the net, overall charge of this tripeptide at pH 7? __________ 4. What is this peptide called using the one-letter code system for amino acids? ______

Proteins can be very large, hundreds of amino acids long The enzyme HMG-CoA reductase MLSRLFRMHGLFVASHPWEVIVGTVTLTICMMSMNMFTGNNKICGWNYECPK FEEDVLSSDIIILTITRCIAILYIYFQFQNLRQLGSKYILGIAGLFTIFSSFVFSTVVIH FLDKELTGLNEALPFFLLLIDLSRASTLAKFALSSNSQDEVRENIARGMAILGPTF TLDALVECLVIGVGTMSGVRQLEIMCCFGCMSVLANYFVFMTFFPACVSLVLEL SRESREGRPIWQLSHFARVLEEEENKPNPVTQRVKMIMSLGLVLVHAHSRWIAD PSPQNSTADTSKVSLGLDENVSKRIEPSVSLWQFYLSKMISMDIEQVITLSLALL LAVKYIFFEQTETESTLSLKNPITSPVVTQKKVPDNCCRREPMLVRNNQKCDSV EEETGINRERKVEVIKPLVAETDTPNRATFVVGNSSLLDTSSVLVTQEPEIELPRE PRPNEECLQILGNAEKGAKFLSDAEIIQLVNAKHIPAYKLETLMETHERGVSIRR QLLSKKLSEPSSLQYLPYRDYNYSLVMGACCENVIGYMPIPVGVAGPLCLDEKE FQVPMATTEGCLVASTNRGCRAIGLGGGASSRVLADGMTRGPVVRLPRACDSA EVKAWLETSEGFAVIKEAFDSTSRFARLQKLHTSIAGRNLYIRFQSRSGDAMGM NMISKGTEKALSKLHEYFPEMQILAVSGNYCTDKKPAAINWIEGRGKSVVCEA VIPAKVVREVLKTTTEAMIEVNINKNLVGSAMAGSIGGYNAHAANIVTAIYIAC GQDAAQNVGSSNCITLMEASGPTNEDLYISCTMPSIEIGTVGGGTNLLPQQACL QMLGVQGACKDNPGENARQLARIVCGTVMAGELSLMAALAAGHLVKSHMIH NRSKINLQDLQGACTKKTA

Next: Chapter 4 Proteins: Three-Dimensional Structure and Function