Amino Acid & Peptide CENTRAL DOGMA

Glycine simplest form of amino acid H CH COONH3

Replication DNA Transcription RNA Translation Protein Polymers- connection of repeating subunits Proteins polymers of amino acid Amino Acid building blocks of macromolecules - most basic form of proteins a. nucleatic acids b. fatty acids c. carbohydrates Peptides single linear molecule - 2 or more amino acids linked by peptide bonds Proteins 1 or more polypeptides - folded and hung properly - biologically functional 20 amino acids for genetic materials a. non essential not synthesized by the body b. essential can not be synthesized by the body - needed in the diet MNEMONICS: essential amino acids PVT TIM HALL P V T T IM HALL Phe Try Trp H CH COOR- group Carboxyl NH3 Amine group Amino Acids: Chiral mirror symmetry - type of molecule that lacks internal plane of symmetry and has superimposable mirror image L-a molecules dextrorotation and levorotaion refers to the properties of rotating plane polarized light clockwise (dextrorotation) / counter clockwise (levorotation) Zwitterions no net charge - has equal number of ionization group of opposite charge has 2 dissociating group: -COOH and NH3 - has 2 pKa values pI is the isoelectric pH, a value midwayof the pKa values acidic dissociates a -carbon = Chiral

pKa = dependent on a medium water soluble charged functional group

insoluble to non-polar solvents: Benzene and Hexane

Sulfur active in forming bonds with other sulfur group. Aromatic Ring electrons are moved around the double bonds Amino Acid R group specific properties of each amino acid Free Functional = Chemical reaction a. carboxylic anhydridation b. amino groups acylation c. hydroxyl / sulfhydryl oxidation Peptide Bond Formation - carboxyl group an amino acid combines with amino group of another amino acid ex. O O HCHC NH3 HCHCO NH H2O Peptide Bond *always write the amino acid chain as: - amino group - carboxyl group left most right most

3. tertiary conformation of secondary structure into a 3d structure 4. quadrnary assembly of tertiary proteins; 1 or more polypeptide chain Secondary structure held by hydrogen bonds a. a - helix b. related sheet c. loops, bends Tertiary structure produce scientific domains - different domain = different functions - Domains binds substances - Anchors proteins - Localize target - Regulates function Quarternary structure - monomeric, dimeric, trimeric, tetrameric, etc - homodinamers, heterodinamers, homotetramers, etc. Tertiary and Quarternary high order proteins are stabilized by non covalent interactions Protein folding 1. thermodynamics most energetic favored 2. stepwise assortment primary secondary etc 3. assistants prevents formation of insoluble aggregates breaksdisulfide bonds chaperones glutathione clumps at H2O

Protein Structure 4 orders of protein structure: 1. primary amino acid sequence 2. secondary infolding of 1 polypeptide chain into its 2D structure

Protein folding is disturbed - Soluble a helix becomes insoluble sheet Abnormal protein aggregates Seen in: 1. Alzheimers ( amyloid) 2. thalassemia (a hemoglobin units) 3. Prion diseases: CJD, scrapie (PrP) and Mad cow dse.

Protein Purification principle of separation of proteins a. pH b. polarity c. salt / ionic concentration Chromatography separates protein by: 1. stationary phase 2. mobile phase liquid form Seuence Determination - Edman reaction use of phenylisothiocyanate to label the amino - Mass spectrometry use of magnets / time of light which detects genetic disorders. Essential Amino Acids 3 letter 1 letter Name name name Glycine Gly G Alanine Ala A Valine Val V Leucine Leu L Isoleucine Ile I Serine Ser S Threonine Thr T Tyrosine Tyr Y Cysteine Cys C Methionine Met M Aspartic Acid Asp D Asparagines Asn N Glutamic Acid Glu E Glutamine Gln Q Arginine Arg R Lysine Lys K Histidine His H Phenylalanine Phe F Tryptophan Trp W Praline Pro P

Influences protein folding Protein denaturation destruction of higher structures of particular protein - unfolding of proteins caused by : oxidizing agents, heat, chemicals Post translational modification Translation synthesizing of proteins - collagen - 3 helix Primary : Gly X-Y series Secondary: left handed helix Tertiary: continous helix Quarternary: right handed 3 helix Collagen Life Cycle (Translation Protien Synthesis) Collagen Disease: - Menkes Syndrome - Ehlers Danlos Syndrome - Osteogenesis imperfecta - Vitamin C deficiency Protein Function - catalyzing reaction - cellular motion - provide structural support Steps in Analyzing Protiens: 1. protein collection 2. purification 3. protein purity determination 4. sequencing order