Download Amino Acids - Biochemistry - Lecture Slides and more Slides Biochemistry in PDF only on Docsity! Amino Acids Docsity.com Amino Acids: The building blocks of proteins a amino acids because of the a carboxylic and a amino groups pK1 and pK2 respectively pKR is for R group pK’s pK1 2.2 while pK2 9.4 pK1 pK2 In the physiological pH range, both carboxylic and amino groups are completely ionized Docsity.com Linear arrays of amino acids can make a huge number of molecules Consider a peptide with two amino acids AA1 AA2 20 x 20 = 400 different molecules AA1 AA2 AA3 20 x 20 x 20 = 8000 different molecules For 100 amino acid protein the # of possibilities are: 130100 1027.120 x The total number of atoms in the universe is estimated at 78109x Docsity.com Characteristics of Amino Acids There are three main physical categories to describe amino acids: 1) Non polar “hydrophobic” nine in all Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline, Phenylalanine and Tryptophan 2) Uncharged polar, six in all Serine, Threonine, Asparagine, Glutamine Tyrosine, Cysteine 3) Charged polar, five in all Lysine, Arginine, Glutamic acid, Aspartic acid, and Histidine Docsity.com Amino Acids You must know: Their names Their structure Their three letter code Their one letter code H2N CH C CH2 OH O OH Tyrosine, Tyr, Y, aromatic, hydroxyl Docsity.com
Cystine consists of two disulfide-linked
cysteine residues
| |
oe ne
ea ea + ee
i nah
Cysteine [0] Cysteine
residue residue
H,O
| |
oe gs
ee ae p= S-- ne ee
: =
Cystine residue
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Acid - Base properties of amino acids [HA] ][A log pK pH - ji pKpK 2 1 pI Isoelectric point: the pH where a protein carries no net electrical charge For a mono amino-mono carboxylic residue pKi = pK1 and pKj = pK2 ; for D and E, pKi = pK1 and pKj - pKR ; For R, H and K, pKi = KR and pKj = pK2 Docsity.com The tetra peptide Ala-Tyr-Asp-Gly or AYDG Greek lettering used to identify atoms in lysine or glutamate Docsity.com The Fischer Convention Absolute configuration about an asymmetric carbon related to glyceraldehyde (+) = D-Glyceraldehyde (-) = L-Glyceraldehyde Docsity.com In the Fischer projection all bonds in the horizontal direction is coming out of the plane if the paper, while the vertical bonds project behind the plane of the paper All naturally occurring amino acids that make up proteins are in the L conformation The CORN method for L isomers: put the hydrogen towards you and read off CO R N clockwise around the Ca This works for all amino acids. Docsity.com An example of an amino acid with two asymmetric carbons Docsity.com The major advantage of the CIP or RS system is that the chiralities of compounds with multiple asymmetric centers can be unambiguously described Docsity.com Prochiral substituents are distinguishable Two chemically identical substituents to an otherwise chiral tetrahedral center are geometrically distinct. Docsity.com Planar objects with no rotational symmetry also have prochariality Flat trigonal molecules such as aldehydes can be prochiral With the flat side facing the viewer if the priority is clockwise it is called the (a) re face (rectus) else it is the (b) si face (sinistrus). Docsity.com
