MBS-02 Amino acids Petides and Proteins.pdf

Amino Acids, Peptides and Proteins Kassim, PhD Smith Hall 433 [email protected] 412-396-5717  Learning Objectives: o Identify the common chemical structure of amino acids and their nomenclature o Describe which group (nonpolar, polar-u...

Amino Acids, Peptides and Proteins Kassim, PhD Smith Hall 433 [email protected] 412-396-5717  Learning Objectives: o Identify the common chemical structure of amino acids and their nomenclature o Describe which group (nonpolar, polar-uncharged, polar-basic, polar-acidic) each of the 20 amino acids belongs to. o Recognize the sidechain structures for D,E,K,R,H,C,S,Y and memorize their sidechain pKa values o Discuss the ionization state of selected amino acids base on pH and determine the zwitterion form of amino acids o Determine total charges on polypeptides based on amino acid contain at specific pH o Determine the isoelectric point PI of polyampholyte (form of the molecule with net charge of zero)  A living cell A “miniature world” encapsulated by a cell wall: players (proteins, mostly)  Amino Acids and Peptides and Proteins o Amino acids (AA) are biochemical building blocks of proteins. o AA form short polymer chains called peptides or polypeptides which in turn form structures called proteins. o There are twenty natural occurring amino acids found in proteins called standard amino acids. o Rarer, more complicated ones are produced by the body and are called nonstandard. o Other amino acids contained in proteins are usually formed by post-translational modification,  Chemical Nature of the Amino Acids o Each amino acid has a central carbon, called the α-carbon, to which four different groups are attached A basic amino group (–NH3+ ) An acidic carboxyl group (–COOH) A hydrogen atom (–H) A distinctive side chain (– R)  Amino Acids Share Common Structural Features chiral “alpha” (a) carbon pK a= 9.5 pK a= 2 “L” vs. “D” R = variable “side chain” (20 different types) A.A. are optically active – that is, they rotate plane-polarized light “L” vs. “D” amino acids are “ampholytes”: they have acidic and basic groups  Amino acids Classification o The "R" represents a side chain specific to each amino acid. o Amino acids are usually classified by properties of the side chain into four groups: 1. Nonpolar, Aliphatic R groups (hydrophobic) 2. Aromatic R Groups: 3. Polar R groups (Hydrophilic) a. Uncharged R group b. Acidic R group c. Basic R group  Amino acids Classification 1. Nonpolar, Aliphatic R groups (hydrophobic) -Alanine -Valine -Leucine -Isoleucine -Glycine -Methionine -Proline  Amino acids Classification 1. Nonpolar, Aliphatic R groups (hydrophobic) “b-branched” glycine (G) alanine (A) valine (V) leucine (L) proline (P) isoleucine (I) methionine (M) o These are “hydrophobic” amino acids They have an hydrophobic side chain No side chain pKa value  Amino acids Classification 2. Aromatic amino acids pK a= 10 phenylalanine (F) tryptophan (W) tyrosine (Y) these are also hydrophobic!  Amino acids Classification 3a. Polar Uncharged R groups (hydrophilic) hydroxy or pKa=8.3 sulfur-containing amino acids serine (S) cysteine (C) threonine (T) and their amides….. asparagine (N) glutamine (Q) hydrogen bonding capability!  Amino acids Classification 3b. Polar charged R groups (hydrophilic) Negatively charged (R) Positively charged (R) (Acidic) (Basic) - Lysine - Aspartate - Arginine - Glutamate - Histidine  Amino acids Classification 3b. Polar charged R groups (hydrophilic) “Acidic” amino acids pK a=3.9 pK a=4.2 aspartic acid (D) glutamic acid (E)  Amino acids Classification 3b. Polar charged R groups (hydrophilic) “Basic” amino acids pK a= 10.0 pKa= 12.5 lysine (K) arginine (R) pK a= 6.1 histidine (H)  Amino acids Classification o Dietary protein provides amino acids not made in our systems. these are called essential amino acids Essential Amino Acids Non essential Amino Acids Glycine histidine alanine lysine cysteine isoleucine aspartic acid leucine glutamic acid valine asparagine threonine glutamine methionine proline phenylalanine Arginine tryptophan serine  Biological Importance: Example Tyrosine: Tyr is the precursor for the synthesis of catecholamines including: dopamine epinephrine norepinephrine Dopamine & norepinephrine function as neurotransmitters in the brain Epinephrine and norepinephrine function as hormones that regulate carbohydrate and lipid metabolism  Biological Importance: Example Histidine: the precursor for the synthesis of histamine histamine is a chemical messenger that mediates a wide variety of cellular responses such as: - gastric acid secretion - allergic & inflammatory reactions  Ionization State of Amino Acids Amino acids are polyprotic, they all contain two or three dissociable protons. H+ In addition of OH-  Ionization of Alanine Net Charge +1 0 -1 pKa1 = 2.19 pKa3 = 9.67 PI = pKa1 + pKa2 2 zwitterion  Ionization of Glutamic acid Net Charge +1 0 -1 -2 pKa1 = 2.19 pKa2 = 4.25 pKa3 = 9.67 PI = pKa1 + pKa2 2 PI = 2.19 + 2.45 = 2.4 2  Ionization of Lysine Net Charge +2 +1 0 -1 pKa1 = 2.18 pKa2 = 8.95 pKa3 = 10.53 PI = pKa2 + pKa3 2  Polymerization of amino acids Amino acid “residues” can polymerize one after another in a linear chain. (“beads on a chain”) amino acid structure N-terminus C-terminus “amino” end aa 1 aa 2 aa 3 ….. “carboxy” end peptide bonds When polymerized, amino acids lose their zwitterions  Peptides and Proteins o Peptides and Proteins are polymers of amino acids (residues), with each of the amino acids joined to its neighbor by specific type of bond (a.k.a. peptide bond) amino terminus carboxy terminus “N” “C” “N” globular fold “C” Peptides and Protein sequences are given as linear sequences of their one-letter amino acids code: Example: MAKRNIVTATTSKGEFTMLGVHDNVAILPTHASPGESIVIDGKE- VEILDAKALEDQAGTNLEITIITLKRNEKFRDIRPHIPTQITETNDG- VLIVNTSKYPNMYVPVGAVTEQGYLNLGGRQTARTLMYNFPTRAGQ….  The peptide bond o The peptide bond is one of the strongest and most durable of covalent bonds.  Peptides and Polypeptides - Dipeptide = Two amino acids joined. - Tripeptide = Three AAs joined. - Oligopeptide a few AAs joined - Polypeptide Many AAs joined =. - Polypeptide " refers to the structure of a single chain. Every polypeptide has one free amino group (called the "N-terminus") and one free carboxyl group(called the "C-terminus").  Example problem 1: pK a=9 M-S-A-L-I-G pK a=4 - COOH -- pKa =4 - NH3 + -- pKa =9 a) What is the average charge of this peptide at pH 8.0? Answer is “ 0” b) What is the pI? Answer is “ 6.5”  Proteins are polyampholytes (i.e. they have many pKa’s that titrate) - + + - + + + - - + - N C pI = isoelectric point The isoelectric point is the pH at which the polyampholyte has a net charge of zero.  Thank You! https://unsplash.com/s/photos/natural