What is pKa? pKa 2-3 and 9-10BIOSC 1000 Lecture 3Outline of Last Lecture1. Biochemistry of Water2. The pH scale3. Acid StrengthOutline of Current Lecture1. Amino Acids2. Peptides3. Characteristics of Primary Structures of Proteins Current Lecture1. Amino Acids- Large biomolecules (macromolecules) and bioassemblies are built from much smaller building blocks (monomers)- Amino acid  protein- Nucleotide  nucleic acid- Lipid  lipid bilayer- Protein structure and function determined by amino acid sequence- One amino acid substitution can change the color of the GFP protein- Nutritional View of Amino Acidso Non-essential amino acids can be synthesized by mammals Alanine Asparagine Aspartate Glutamate Serineo Conditionally-essential amino acids needed for rapid growth Arginine Cysteine Glutamine Glycine Proline Tyrosineo Essential amino acids are only obtained through our diet Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine- -Amino Acids – general structureαo R group defines the type of amino acid (basic or acidic)o Glycine is non-chiral (2 H’s)o Both amino and carboxyl ionized around ph = 7 o Alpha amino acids where functional groups covalently attachedo Amino group, Carboxyl group, H atom, 20 types of R groups (side chains) ALWAYS L-amino acids (glycine is not chiral)- Amino acids can act as acids or as baseso Free amino acids in aqueous medium may exist as dipolar ions or zwitterionso May act as acids (proton donors) or bases (proton acceptors)o Compounds that can be zwitterions not necessarily exactly electrically neutral under all circumstances o AA charge= 0 at some point pH = pI (isoelectric point)- 19 amino acids have chiral carbon (not glycine)o caution – L form is not always S formo mirror image isomers cannot be superimposed  enantiomerso identical physical and chemical properties except their rotation of polarized lighto but very different biological properties- L-alpha-AA are predominant form in biologyo Side chain atoms are labeled after the alpha carbon (greek alphabet)o But are sometimes numbered- Small Non-polar Aliphatic R-groupso Glycine – Gly – G Achiral, small side chain, flexible Spacecraft “stardust” detected and collected glycine from comet wild2 in ‘06o Proline – Pro – P Cyclic side chain, only imino acid, conformationally inflexible, makes cis-peptide bond, rigid Less conformational entropy lost during folding becauseit is so rigid Blocks secondary structure elements Prevalent in thermophilic organismso Alanine – Ala – A Large hydrophobic effect D-alanine found in bacterial cell walls and used by somefungi in antibiotic compoundso Valine –Val – V Large hydrophobic effect Often buried beneath protein surface Essential – comes from your diet Glutamic acid  Valine (E6V) mutation in hemoglobin results in sickle cell condition- Large non-polar Aliphatic R-groupo Leucine –Leu –L & Isoleucine –Ile –I: Large hydrophobic effect, often buried beneath protein surface Same masso Methionine –Met – M: Sulfur containing thio-ether is NON-POLAR Initiator from protein synthesis also incorporated within proteinso Branched chain aliphatic R-groups; catabolism poses special metabolic challenges  Maple syrup Urine Disease (branched-chain ketoaciduria)- Defect in an enzyme that breaks down branched chain AA (I,L, V)- Results in toxic buildup of these AA- Rare (1:180,000)- Aromatic R-Groupso Large molecular volumeo Can stack on DNA baseso Phenylalanine –Phe –F (precursor to Y) Phenyl side chaino Tyrosine – Tyr – Y Can be converted to Dopamine, Norepinephrine, epinephrine Phenol side chaino Trptophan –Trp –W Indole side chain (fused rings, heterocyclic) Precursor to serotonino Y &W more polar than Fo Y & W can Hydrogen bondo Phenylketonuria (PKU) Defect in the metabolism of phenylalanine leads to buildup of metabolites  Extremely painful condition Severe sequelae are like MSUD Can be controlled by dietary restrictions More common in Turkey, Ireland, Norway Patients are extremely sensitive to artificial peptide sweeteners (Equal or Nutrasweet) that are quickly converted into Phe after consumption o Aromatic side groups absorb UV light W>Y>>F Lambert-Beer Law Allows biochemists to measure concentration of protein Larger side chain = larger UV absorbance per mole- Polar Uncharged R-groupso Soluble in water, can form H-bonds, often exposed on protein surfaceo Serine – Ser- So Threonine – Thr – To Cysteine – Cys – Co S-H weak acid, ionizes to S-, fair H-bond donor, very poor acceptor, only cysteines form disulfides (cysteine) nonpolar, stabilized some structureso Disulfide bond – nonpolar, hydrophobic, stabilizing Can occur on neighboring proteins if Cys is on surfaceo S& T often modified by phosphorylation- Amides sensitive to acid or base hydrolysiso Asparagine –Asn – N Can interact by sharing H – bondso Glutamine – Gln – Q - Negatively charged R-groupso Polar, water soluble, ionizable side chain carboxylic acidso Acidic side-chains often form stabilizing ionic interactions with positively charged side-chainso R-Group at pH has net charge of -1o Aspartate – Asp – Do Glutamate – Glu – E- Positively Charged R-groupso Polar, water soluble and ionizable “amine” goups o Lysine – Lys – Ko Arginine – Arg – Ro Histidine – His – H May be charged at pH 7 and facilitates many enzymatic reactions, actins as general acid or as general baseo K & R also have significant hydrophobic character ( high pKa)- Characteristic titration curveso Example: Glycine R group is not ionizable (H) pI is the isoelectric point (pH of zero net charge) pI = ½ (pK1 + pK2) pH 0.5 charge = +1 pH 1 charge = 0 pH 1.5 charge = -1 What is pKa? pKa 2-3 and 9-10 Around what pH might glycine be useful as a buffer? pH = 0.5, 1.5 - Know pKR (only 7 – for charged AA)o Be able to calculate pI from a pKao2. Peptides -Simply chains of AA residues linked by amide bonds formed by condensation reactions between the carboxylic acid and amino groups of amino acids. Bonds = peptide bonds- Peptide bonds are polar, not charged. In effect, the charged groups have disappeared except on the very first, and very last amino acids- Write sequence from