Lecture 6 Biochemistry And Biomaterials For Bioengineers PDF

BN2301: Biochemistry and Biomaterials for Bioengineers Amino Acids and Proteins Lecture 6 Dr. Shao Huilin 1 Welcome to Proteins! https://www.youtube.com/watch?v=wJyUtbn0O5Y 2 ...

BN2301: Biochemistry and Biomaterials for Bioengineers Amino Acids and Proteins Lecture 6 Dr. Shao Huilin 1 Welcome to Proteins! https://www.youtube.com/watch?v=wJyUtbn0O5Y 2  Welcome to Proteins! Proteins mediate nearly every process that takes place inside a cell Most abundant biological macromolecules in cells Greek word “proteios” = the most important compound All proteins are composed of amino acids (monomers) 3 3  Today’s outline Amino acids (building blocks) Protein structures (primary, secondary, tertiary and quaternary) 4 Amino acids 5  Amino acid structure Amino acid structure acid R * depending on environment;the amino acid All amino acids have common structural features can have varying charges - show diff characteristics weakbase weak acid Fixed: amino group (-NH2), a carboxylic acid (-COOH) group and a hydrogen bonded to the same carbon atom - amino acids are weak acids and weak bases Variable: unique side chain (R group) distinguishes each amino acid 6  Amino acid structure: ionization neutral state -> ionized state R R Under physiological pH conditions, amino acids are ionized Amino (base) group can be protonated (receiving a proton) => positively charged FOUMS an NH3 I definition of + -> acid bases from organicchem. Carboxylic (acid) group can be de-protonated (giving up a proton) => negatively charged Forms a COO- - Protonation and de-pronation depend on the pH of the environment (how?) 7  Let’s try to recall from Organic Chemistry Dependence of protonation on pH pH is a measurement of proton (H+) concentration in the environment cazidics - The lower the pH, the more concentrated the protons pKa is an index to express acid characteristic - It is a material property (constant) and indicates the ability to release protons A specific tendency to giveaway a proton - The lower the pKa, the stronger the acid => can easily release protons 8  Let’s try to recall from Organic Chemistry Dependence of protonation on pH Amino acid * on surrounding pH is dependent "friendly molecule"will moderate to environment Always compare pH (environment) vs. pKa (of the acid) If pH < pKa NMS Forms Will take in protons from environment - plenty of protons in the environment (pH), protonated form predominates If pH > pKa pKa - lack of protons in the environment (pH), amino acid is in its de-protonated form 11  Let’s see from this example: ~MD: the lower pka is the Question 1: ⑰ acidic more The amino acid has pKa = 2.3 and 9.7 What is the overall charge of the amino acid at pH 5? note:there can be 3pKa When the R group also protonated or gets - R3 deprotonated + CH3 CH3 + CH H3N CO2H H3N CO2 H2N CO2 H pKa1 H pKa2 H low pH (2.3) (9.7) high pH 12  Question 1: The amino acid has pKa = 2.3 and 9.7 What is the overall charge of the amino acid at pH 5? + CH3 R3 + CH -more the lower pla CH acidic: 3 value H3N Amino CO 2H group H3N CO2 CarboxylicHacid 2N CO2 H pKa = 9.7 pKa1 H pKa = 2.3 pKa H 2 low pH (2.3) (9.7) high pH Every amino acid should have at least two pKa pKa of the carboxylic acid group is low (carboxylic acid is an acid) pKa of the amino group is high (amino group is a base) When considering protonation status, consider each pKa independently with respect to the pH 13  Question 1: The amino acid has pKa = 2.3 and 9.7 What is the overall charge of the amino acid at pH 5? [DE-PROTONATED] or [BASE FORM] [PROTONATED] [ACID FORM] negatively charged art to the denominator X charge 5 = 2.3 + log ([COO-]/[COOH]) log ([COO-]/[COOH]) = 5 – 2.3 = 2.7 [COO-]/[COOH] = 501.19 - - x - G I - a a 5 = 9.7 + log ([NH2]/[NH3+]) log ([NH2]/[NH3+]) = 5 – 9.7 = -4.7 - [NH2]/[NH3+] = 1.995 x 10-5 NHst 5 = -- 2x c05+1 X d ↑ [NH3+] predominates, overall positively charged 14  H I - #N #c = NH2 +NH3 =COOH + C08- -  Amino acids: R groups Amino acid structure R R group varies in - size - structure - chemical properties (e.g., solubility in water, interactions with other molecules) 20 naturally occurring amino acids => 20 R groups 15  Amino acids: R groups naturally occuring amino acids Amino acid structure R Based on the 20 R groups, amino acids can be classified into major categories In almost all introductory Biochemistry classes, we have to memorize these 20 structures; the truth is… 16  Nonpolar R groups R groups are nonpolar, cannot waring hydrogen bond with water chydrophobic protein structure will interiorly strated aqueous environ. Due to this hydrophobicity (hate water), they tend to very bulky cluster together within the interior of proteins through ring structure hydrophobic interactions (away from aqueous environment) Glycine has the simplest amino acid structure 17 Aromatic R groups R groups contain aromatic (ring) structures Bulky Generally nonpolar and all can participate in hydrophobic interactions in aqueous solution Tyrosine:can interact forms hydrogen bond ↓ ↳participate in hydrophobic activities chydrophilic compared to Phe & Tr structures but where havering are hydrophobic 18 Polar, uncharged R groups Polar and can form hydrogen bond with water Hydrophilic (love water) and soluble in water 19 Charged R groups R groups are charged at neutral pH 7 Note that this charge is dependent on pH (another pKa, protonation and de- protonation again!) have a 3rd pla * same equ applies have to but Acidic: negatively charged independently Basic: positive charged CAICUAte When they are charged, they are more soluble in water move soluble in water higherorder structure for protein structure 20  In summary Generally water hating Generally water loving Disclaimer: 21 Biology is a science of exceptions  Some exceptions to be asked in this mod vie by chemistry standard base grploups back Proline: not really a amino acid… Cysteine: the only amino acid that can form other Wit covalent bond (S-S) cysteine - conditions use extreme ↳ must to breakbonds much Tyrosine: polar even move t effort though it is aromatic break bonds ginProtein T as bonds Disclaimer: 22 Biology is a science of exceptions  Zwitterions (hybrid ions) Amino acids can carry multiple charges (on amino group, carboxyl group, R group) R Amino acids can exist as zwitterions (overall neutral, all charges cancel, net charge = 0) only pH value where the twitterion exists The pH at which the net charge of the molecule is zero is called the isoelectric point this ph, the potential benefits are neutralised at Amino acids are less soluble in water in this neutral zwitterionic state Increasing or decreasing pH from the isoelectric Examples of amino acids as zwitterions point can improve solubility * zwitterion so that state does not exist 23  Question 2: The amino acid has pKa = 5.1 and 8.5 (R group is not ionizable) Calculate the percentage of zwitterionic form at pH 7.0 + CH3 R3 + CH CH3 H3N CO2H pKa 8.5 = H3N CO2 pKa 5.) = H2N CO2 H pKa1 H pKa2 H low pH (2.3) (9.7) high pH 24  Question 2: The amino acid has pKa = 5.1 and 8.5 (R group is not ionizable) Calculate the percentage of zwitterionic form at pH 7.0 + CH3 R3 + CH CH3 H3N Amino CO 2H group H3N CO2 Carboxylic Hacid 2N CO2 H pKa = 8.5 pKa1 H pKa2 = 5.1 pKa H low pH (2.3) (9.7) high pH 7.0 = 5.1+ log ([COO-]/[COOH]) log ([COO-]/[COOH]) = 7.0 – 5.1 = 1.9 [COO-]/[COOH] = 79.43 = 79.43/1 Charges must co-exist 7.0 = 8.5 + log ([NH2]/[NH3+]) log ([NH2]/[NH3+]) = 7.0 – 8.5 = -1.5 [NH2]/[NH3+] = 0.03162 = 0.03162/ 1 conditional probability 3.Tra carry both COO- & cance to iOns Simultaneous 1y NAst Zwitterionic form = [COO-]/[total] X [NH3+]/[total] in zwitterions, = 79.43/(79.43+1) X 1/(0.03162+1) probability calculation with assumption = 95.73 % Ar 25 COONd of NMs+ of (Onc. 1.00 of ions are in zwitterionform (percentages Let’s take a break for 5 min 26 Protein structures 27  Peptide (amide) bond formed by carboxylic acid ofRe ofRe I am inobase Amino acid structure readfromtheN terminus to (terminus G specific directionality R (like DNA 5'+03'C R1 R2 R1 R2 Amino acids are linked by covalent peptide (amide) bond, through a condensation reaction involving loss of a water molecule A polypeptide is a chain of amino acids linked by multiple peptide bonds 28  Protein: primary structure As the polypeptide grows Amino Amino Amino Amino acid 1 acid 2 acid 3 acid 4 Directionality: N terminus (amino group) and C terminus (carboxyl group) R groups: the identities of the amino acids * growing at the terminus New amino acids are added to an elongating chain at the C terminus Sequence defined from N terminus to C terminus: 1->2->3->4 This linear sequence of amino acids is the primary structure of protein of identity 29 dong the chain-R groups as the amino grp.  Question 3: Let’s determine the primary protein structure TY · read from left to right ↓ N ↓ reU ser Gly Ald Determine directionality of the peptide Identify the peptide bonds to demarcate where the R groups are Identify the R groups (refer to your table on slide 16) 30 Let’s determine the primary protein structure R groups Polypeptide backbone Differentiate between the polypeptide backbone and the R groups - e the group that amide bonds inthe backbone distinguishes ↓ the type of regular repeats of the amino acid a -I bonds 31  Protein: secondary structure R1 R2 R1 R2 Peptide bond cannot rotate - any how cannot is rigid and X turn around planar The peptide bond is rigid and planar behaves like are seudo-double adouble bond -> ↳ bond The peptide bond can form hydrogen bond ↳ With itself The polypeptide backbone can form recurrent local arrangements due to hydrogen bond of peptide bond This is the secondary structure of protein Carbon, oxygen and nitrogen p orbitals overlap only if the 6 Most common types of secondary structures: α-helix and β- atoms are in a plane pleated sheet 32  Secondary structure: α-helix driven by hydrogenbonding within the polypeptide chai repetitive amide bond a its elf forms hydrogen bond among I In some proteins, regions of the polypeptide chains are coiled into a spiral structure called α-helix * due to hydrogen bonding within the peptide Hydrogen bonding of the chain polypeptide backbone atoms Through components of the peptide bonds = H of amino group (N) = O of carboxyl group (C) R groups are pointing outward very orderly - always the 4th bond down the chain to form 33 bond with 1st pep'de bond with 4th pep'de bond (AA #1 with AA #5)  Secondary structure: β-sheet FOlIOWS A ribbon structure polypeptide chains joined together by distant like the way far ahead still same chain just - In some proteins, regions of the polypeptide chains are arranged side by side to form a planar sheet (resemble ones a piece of paper folded into many pleats) Hydrogen bonding between the peptide bonds in the backbone Hydrogen bonding between the chains, with regions far away 3 chains will linked together outwards from surface of R groups point above and below the plane of the sheet R- -> group points the joined together chains (gives the folded paper shapes 34 Better representations driven by polypeptide backbone ~due to ability to form hydrogen bonding with nearby-neighbouring N or with distantamide bonds C Parallel β sheet in Function 42  Can we predict protein folding? If we have the amino acid sequence of the protein (primary structure), can we predict its final native 3D structure (tertiary or quaternary structure)? Protein folding problem: 50-year old problem and not yet solved Why is it so hard? Too many possibilities; need for a massive library of peptide fragments Compare sequences with data bank of structures with known sequences, and look for partial mismatches ….. Supercomputers and beyond! 43 Can we predict protein folding? The protein folding problem https://www.youtube.com/watch?v=cAJQbSLlonI 44 Thank you! 45