COO - l + H 3 N C a H l R 1
Amino acids There are 20 standard amino acids. All proteins are built from the same amino acids. The most important criteria for classification is affinity to water: hydrophilic and hydrophobic. Hydrophilic are aliphatic and aromatic. Hydrophobic are divided into aliphatic and aromatic. 2
AMINO ACIDS Natural (D,L) Synthetic (D, L or DL) Protein (L) Non-protein (D or L) exogenous endogenous 3
glycine alanine valine leucine isoleucine Thiol group proline methionine cysteine 4
phenylalanine tyrosine tryptophan phenol group can participate in creating hydrogen bond 5
Amino acids with hydrophilic charged polar side chains In neutral ph : Cations histidine arginine lysine Anions Aspartic acid Glutamic acid 6
Amino acids with hydrophilic non-charged polar side chains asparagine Amid group can participate in creating hydrogen bond glutamine Polar character serine threonine 7
Cannot be synthesized in human body (exogenous): leucine isoleucine lysine phenyloalanine methionine threonine tryptophan histidine Valine arginine - semiessential, needed for children s growth The highest daily requirement for adults is for leucine, the least for tryptophan. 8
Non-essential (nutritionally) amino acids Can be synthesized in human body (endogenous): glycine alanine proline serine aspartic acid glutamic acid glutamine arginine Amino acids partially nonessential: Tyrosine is synthesized from essential phenylalanine cysteine is synthesized from: Essential methionine Non-essential serine 9
Non-protein amino acids Non-protein amino acids: other important biological role, ex.: b-alanine CH 2 CH 2 COO - l NH 3 + g-aminobutyric acid (GABA) CH 2 CH 2 CH 2 COO - l NH 3 + Is formed during metabolism of pirimidic bases. It is a component of: pantothenic acid coenzyme A carnosine It is synthesized from glutamine in brain (neurotransmitter) 10
Intermediates in metabolism: ornitine and cytruline are involved in biosynthesis of urea NH + 3 CH 2 CH 2 CH 2 CH COOl l l + H 3 N CH 2 CH 2 CH COO - NH NH + 3 l H 2 N C=O homocysteine ( 2-amino-4 mercaptobutyric acid) NH 3 + l HS CH 2 CH 2 CH COO - It is a product of the demethylation of methionine and intermediate metabolite in methionine synthesis 11
Independent risk factor for development of: - heart failure - atherosclerosis - stroke Factors leading to increased level of homocysteine : genetic factors smoking alcohol abuse excessive coffee drinking some drugs defficiency: vitamin B6 vitamin B12 folic acid 12
Amino acids in water solution are in 99.5% in ionic form. Different ph of solution allows for amino acid s separation. COOl + H 3 N C H l R zwitterion +H + -H + COOH l + H 3 N C H l R cation COO - l H 2 N C H l R anion 13
Isoelectric point (pi) of amino acids it s such a value of ph at which amino acids exist as a zwitterion. at ph equal to pi amino acids do not have a net charge and do not migrate in electric field at ph < pi - amino acids are cations at ph > pi amino acids are anions ph value which is equal to pi is an average of pk1 and pk2 14
anion zwitterion cation Equivalents of OH - 15
Stereoisomers of amino acids Except glycine, all amino acids are optically active, they can rotate the plane of polarization of linearly polarized light amino acids can exist as a pair of enantiomers. they have a chiral center water solutions of amino acids: rotate polarised light to the left or to the right exist in two stereoisomeric forms L and D in proteins almost only L- forms can exist D form can exist in bacteria cell wall and some antibiotics. L- alanine D- alanine 16
Amino acids form peptides: oligopeptides up to 25 amino acids polypeptides above 25 amino acids proteins above 100 amino acids 17
Covalent bond formed between a-amine group of one amino acid and a- carboxylic group of another amino acid. free pair of electrons from nitrogen atom in peptide bond is delocalized as a result of orbitals overlapping from carbonyl group peptide bond is stiff and flat atoms forming peptide bond are positioned in one plane hydrogen from amine group almost always is in trans position in respect to oxygen atom from carbonyl group. 18
There is no possibility of free rotation around C N bond. There is possibility of rotation around C a -N and C a -C Rotation angles influences polypeptide chain conformation. The angles allow for predicting shape of polypeptide. 19
1 st : amino acid with a free amine group + -yl ending 2 nd : amino acid with a free carboxylic group (C-end) glycine (Gly) glycylalanine alanine (Ala) peptide name always starts with name of amino acid with free amino group alanine (Ala) glycine (Gly) alanylglycine 20
COOH dicarboxylic amino acids NH 2 diamine amino acids OH tyrosine and threonine SH cysteine imidazol residue of histidine imine residue of arginine 21
glutation g-glutamylcysteinylglycine Angiotensin II : contracts blood vessels (vasoconstrictor) the strongest factor increasing blood pressure stimulates the release of aldosterone (from adrenal cortex) which increases sodium (Na + ) resorption in kidney and counteracts loosing of this ions with urea. Bradykinin, nonapeptide : dilates blood vessels and lowers blood pressure. 22
Oligopeptides glutation g-glutamylcysteinylglycine Vasopressin and oxytocin: nonapeptides with hormone activities produced in hypothalamus and stored in posterior pituitary. Both have very similar structure (only 2 amino acids different). Vasopressin (antidiuretic hormon, ADH) - increases water reabsorption in distal kidney tubules. ADH deficiency leads to diabetes insipidus. Oxytocin stimulates contraction of uterus smooth muscles and mammary gland. 23
Penicillin is created from: D valine and L cysteine It contains a β- lactam ring and thiazolidine ring. Carboxylic group is connected to β- lactam ring by peptide bond. Tiazolidine ring b-lactam ring Penicillin, thanks to the reactive β- lactam ring, inhibits bacterial glycopeptide transpeptidase L-cysteine D-valine 24
Actinomycin D - polypeptide antibiotic; inhibits RNA synthesis Valinomycine - most potent agent against severe acute respiratory syndrome (SARS), caused by coronavirus Gramicidin S - an antibiotic effective against some Gram-positive and Gram-negative bacteria as well as some fungi 25
Primary structure composition and sequence of amino acids in polypeptide chain. It is stabilized by peptide bonds. Secondary structure space conformation of polypeptide chain. is hold by noncovalent bonds such as: hydrogen bonds hydrophobic interaction electrostatic interaction van der Waals forces 26
Tertiary structure spatial connection between structural elements of secondary structure. It shows mutual interaction between domains (cluster units connected by polypeptide skeleton). stabilized by disulfide bonds and electrostatic forces. Quaternary structure proteins consisting of two or more peptide chains connected by noncovalent bonds: electrostatic interaction hydrogen bonds 27
cysteine cystine cysteine 28
Two molecules of cysteine reacting with each other form disulfide bridge (oxidizing of thiol group (-SH)). they can be formed: between amino acids from the same chain between amino acids from different chains disulfide bonds are present often in extracellular peptides and very rarely in intracellular peptides. reduction oxidation disulfide bond disulfide bond 29
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Nonparallel arrangement of peptide chains Parallel arrangement of peptide chains 32
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