Biochem Test 1 Study Guide
Biochem Test 1 Study Guide CHEM 351
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This 6 page Study Guide was uploaded by Kayli Antos on Saturday September 19, 2015. The Study Guide belongs to CHEM 351 at Towson University taught by Ana Soto in Summer 2015. Since its upload, it has received 68 views. For similar materials see Biochemistry in Chemistry at Towson University.
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Date Created: 09/19/15
Biochem Test l G Buffers 0 5 steps for working buffer problems l Write the equilibrium equation 2Calculate the concentrations of acid and conjugate base 3Convert to moles 4Add or subtract the change 5 Plug the numbers into the HH equation and calculate pH 6 Amino Acids 0 20 common amino acids 0 Chiral amino acids are named using L and D to describe the way they rotate polarized light To determine L or D configuration assign priority the amino group will always have the highest priority followed by the carboxyl group having the second highest priority and then the R group If highest to lowest priority is clockwise around the alpha carbon the molecule is in D conformation L is assigned if the priority is counterclockwise 6 Amino Acid Classification 0 The 20 common amino acids can be divided into 5 different groups based on the properties of their R groups 39 Non polar and Aliphatic not in an aromatic ring 39hydrophobic Glycine GlyG Alanine AlaA Proline ProP Valine ValV Leucine LeuL Isoleucine IleI and Methionine MetM I Aromatic 39non polar side chains 39greater hydrophobic interactions in Tyr and Trp than in Phe v39hydroxyls in Tyr and Trp make hydrogen bonds v39nitrogen on indole ring of Trp increases polarity v39Phenylalanine PheF Tyrosine TyrY Tryptophan TrpW I Polar and Uncharged 39hydrophilic Cys is a weak acid Asn and Gln are amides of Asp and Glu Cys can be oxidized to cystine which is two Cys connected by a disulfide bond ThrT Cysteine GinQ SerS Threonine ASHN I Positively Charged 39Serine CysC Asparagine Glutamine His is the only one of the common 20 amino acids whos side chain has a pKa near 7 and therefore can be a proton donor or accepter Lysine LysK Arginine ArgR Histidine HisH I Negatively Charged 39have a second carboxyl group in R group Aspartate AspD Glutamate GluE Amino Acids as Acids and Bases Amino acids are weak acids and bases due to the d amino groups d carboxyl groups and some R groups A simple amino acid with an unionizable R group is a diprotic acid at low pHs When one of these simple amino acids is dissolved in water it exists as a zwitterion with a pH of 7 Amino Acid Titrations 4 steps are 1 Draw the amino acid in its fully protonated form 2 Deprotonate it in pKa order its proton first 3Write pKas on equilibrium rrows 4 Write charged and OH equivalents that correspond with each deprotonation carboxyl group will lose The pH where the net charge is zero is the isoelectric point pl Peptides and Proteins Amino acids are linked with a covalent bond called a peptide bond One amino acid will lose an oxygen and a hydrogen from its carboxyl group and the next amino acid will lose a The peptide bond will form between the carboxylic carbon and amino nitrogen hydrogen from its amino group Column Chromatography The column contains a porous solid that has specific chemical properties it Ion Exchange Chromatography A buffered solution is run through 39 Contains beads with charge opposite that of the protein I The protein will bind to beads and can then be washed out with a salt solution 0 Size Exclusion Chromatography I Contains beads with pores to trap the protein and let the larger molecule elute first I The protein will elute without assistance 0 Affinity Chromatography I Contains beads with ligand which will bind to the protein I Can remove the protein be changing pH and changing its shape or add a solution of abundant ligand to wash out protein Electrophoresis 0 Used for determining if protein was sufficiently purified 0 After the gel has been run use a dye to easily see the proteins Edman Degradation 0 Removes amino terminal amino acid with FTC 0 The derivatized amino acid can be extracted and identified This process can be repeated up to about 40 times Any larger fragments need to be broken down into smaller fragments if they are to be identified by these means Remove Disulfide Bonds 0 There are two ways to remove the disulfide bond from cystine 0 Can oxidize with performic acid to create a sulfur trioxide group 0 Can reduce with DTT which adds a hydrogen to each sulfur Can then carboxymethlyate with iodoacetate to remove hydrogen and add CH2COO Protein Structure 0 4 levels I The primary structure of a protein is the sequence of amino acids I The secondary structure of a protein is the repetitive arrangement of amino acids into reoccurring structural patterns like d helixes and B sheets These structures are stabilized by hydrogen bonds I The tertiary structure of a protein is the 3D folding of polypeptides The quaternary structure of a protein is the arrangement in space of the polypeptide subunits This is only for proteins with multiple subunits Configuration and Conformation Configuration is from chiral centers and double bonds which do not allow for freedom of rotation Conformation is the spatial arrangement of atoms that are free to move and rotate CisTrans Conformation is limited due to sterics Peptide Bond The d carbons of neighboring amino acids have three covalent bonds between them dC C N dC The carbonyl oxygen an amino nitrogen have resonance which leads to a positive partial charge on the nitrogen and a negative partial charge on the oxygen This gives the peptide bond double bond characteristics making it very rigid and unable to rotate The six atoms of the peptide groups will always be in the same plane Carbonyl oxygen and amino nitrogen will be trans There are two kinds of rotation in a peptide N dC and dC C w The conformation of a peptide is defined by the two cp previous angles and angle m which is whether or not the peptide is cis oO which is rare or trans wl80 Dihedral Angles of Secondary Structures 0 Dihedral angles remaining constant through a structure leads to secondary structures like d helices B sheets and B turns Helices Maximized internal hydrogen bonding Polypeptide backbone wound around imaginary axis with R groups on the outside One turn is 54 A and contains 36 amino acids All naturally occurring helices are right handed Hydrogen bonds are between amino acids 4 apart Many helices are amphipathic When determining if a structure is amphipathic or not follow these rules V The highly polar amino acids are all charged amino acids and along with glutamine and asparagine His Lys Arg Glu Asp Asn Gln The highly nonpolar amino acids are all aliphatic amino acids with the exception of glycine alanine and proline and including phenylalanine Leu lle Met Val Phe I Helices have a net dipole partial positive on the N terminal and a partial negative on the 0 terminal I Pro and Gly destabilize a helix because Pro s R group is too rigid and unable to make a hydrogen bond and Gly is too flexible and unstable 0 B Sheets I Backbone in a zigzag I A sheet is several zigzags next to each other hydrogen bonded together I R groups will protrude on opposite sides of the sheet I The sections can be parallel or antiparallel which is more stable I Stability is also increased if they are twisted slightly to the right I Can also be amphipathic 0 B Turns I Amino acid chains make loops or turns when changing direction I Turn connects two neighboring antiparallel sheets I 4 amino acids turn l80 I The first and fourth amino acid are hydrogen bonded I Gly and Pro are very common in turns due to Gly s flexibility and Pro s stability in the cis conformation 6 Some equations to be familiar with 0 Gibbs Free Energy AGAH TAS S Gibbs Free Energy H enthalpy T temperaturein Kelvin S entropy H0H K l8 x lo 16 o HZO H0H39 2 KW 10 14 39Henderson Hasselbalch pH pKa 10g M1 HA 0 Electric Mobility velocityelectrical potential Chargefrictional coefficienty
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