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Bundle Notes- Study guide

by: Rachael Couch

Bundle Notes- Study guide biol 3361

Marketplace > University of Texas at Dallas > biol 3361 > Bundle Notes Study guide
Rachael Couch
GPA 3.9
Biochemistry 1
Dr. Lee

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All notes needed to feel prepared for the upcoming exam! Updated to include extra Exam 2 Review notes and Chapter 31!
Biochemistry 1
Dr. Lee
Study Guide
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This 20 page Study Guide was uploaded by Rachael Couch on Thursday October 8, 2015. The Study Guide belongs to biol 3361 at University of Texas at Dallas taught by Dr. Lee in Summer 2015. Since its upload, it has received 63 views.


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Date Created: 10/08/15
Chapter 6 Protein Structure Primary Structure 0 Amino acid sequence amino acids connected by covalent bonds 0 The primary structure sequence governs O The final folded 3D structure 0 Position of disulfide bonds and posttranslation modifications 0 Localization location of the protein Noncovalent interactions stabilize higher levels of protein structure 0 Hydrogen bonds 0 Interaction between NH and CO of the peptide bond 0 Leads to alpha helices or beta sheets secondary structure 0 Ionic electrostatic interactions 0 Longrange interactions between permanently charged groups 0 Ex Salt bridges buried in hydrophobic environment stabilize protein 0 Van der Waals O Mediumrange weak attraction between all atoms 0 Contributes to stability of interior of protein 0 Hydrophobic interaction 0 Release of water molecules as the protein folds increases the net entropy O Drives protein folding Secondary Structure 0 Stabilized by hydrogen bonds between backbone peptide bond amino hydrogen and carbonyl oxygen 0 Two degrees of freedom per residue 0 Phi Angle about CorN bond 0 Psi Angle about CorC bond 0 Many possible conformations about the alpha carbon will not occur because of steric hindrance 0 The sterically favorable conformations of phi and psi are the basis for preferred secondary structures 0 Ramachandran Plot 0 Shows the sterically reasonable values of phi and psi 0 Secondary structures Ot helix Bsheet Bturns Bhairpin random coil Alpha helix 0 1951 proposed by Pauling and Corey 0 Identified in keratin by Perutz 0 Stabilized by hydrogen bonds between i and i4 residue 0 Can be righthanded follow the coil it runs clockwise or lefthanded CCW 0 Side chains point out and are roughly perpendicular with the helical axis 0 Residues per turn 36 0 Rise per tum 54 A 0 Four NH groups at the N terminal and four CO groups at the Cterminal lack partners for Hbond formation 0 The formation of H bonds with other nearby donor and acceptor groups is called helix capping 0 The peptide bond has a strong dipole moment carbonyl O is negative amide H is positive 0 The x helix has a large macroscopic dipole moment 0 Negatively charged residues often occur near the positive end of the helix dipole Nterminus 0 The x helix can be stabilized by salt bridges 0 Amino acids can be helixformers or helix breakers 0 Strong helix formers Ala and Leu smallhydrophobic 0 Strong helix breakers Pro can t rotate and Gly small R group better for other structures BSheet 0 1951 Proposed by Pauling and Corey 0 Composed of B strands O Strands can be parallel or antiparallel 0 Arrangement held together by hydrogen bonds between more distal backbone amides 0 Side chains protrude from the sheet alternating up and down BTurn Structure 0 Requires 4 residues to form 0 Allow the peptide chain to reverse direction 0 Carbonyl O of one residue is hydrogen bonded to the amide H of the residue 3 away i and i3 0 Often proline and glycine 0 2 forms Trans and cis 0 Trans Usually peptide bonds not involving proline O Cis Can be peptide bonds involving proline I Proline isomerases catalyze proline changing configurations BHairpin Structure 0 2 antiparallel beta strands that look like a hairpin that are linked by 25 amino acids including a B turn structure Tertiary structure I Overall spatial arrangement 3D structure of atoms in a polypeptide chain of protein 0 2 major classes of proteins fibrous and globular 0 Fold to form the most stable structure I Stability comes from 0 Formation of many intramolecular H bonds change in enthalpy 0 Reduction in surface area change in entropy O Hydrophobic interactions hydrophobic groups cluster in the interior Protein Classification I 3 types Fibrous globular and membrane 0 Classified by shape and solubility 0 Fibrous O Insoluble O Mechanically strong I Usually play a structural role 0 Polypeptide chain organized parallel to a single axis 0 3 important fibrous proteins xKeratin 5 Keratin Fibroin collagen 0 Membrane O Hydrophobic AA on inside I Globular 0 Water soluble Mediate cellular function Usually made of helices and sheets Polar residues face outside and interact With solvent Hydrophobic nonpolar residues face interior and interact With each other Packed closely empty space is small cavities that provide exibility for proteins Protein Core I Mostly xhelices and Bsheets because there are lots of hydrogen bonds 0 These hydrogen bonds help to neutralize the highly polar backbone NH and CO in the hydrophobic core I Usually conserved in sequence and structure 0 Protein surface I Not as conserved I Mostly loops and tight turns that connect the helices and sheets of the core I Complex landscape of different structural elements I Can interact With other molecules basis for enzymesubstrate interactions cellsignaling and immune responses I Surface includes water molecules that stabilize the structure I Water molecules are connected by hydrogen bonds With polar backbone and side chain groups OOOOOO I Ot helices on a protein surface are usually amphiphilic polarcharged residues facing out nonpolar residues facing in 0 Amphiphilic a molecule that has both hydrophobic and hydrophilic areas FoldingUnfolding Average stability of a small protein is 510kcalmolecule 0 This means the ration of foldedunfolded at RT is 1x1071 K equilibrium constant is the ratio of the forward folded to reverse unfolded 0 K kf 1ltu Denaturation unfolding leads to loss of structure and function Cellular environment promotes the maintenance of weak forces that preserve the folded state External conditions can disrupt these force and lead to denaturation 0 Thermal denaturation causes disruption of hydrogen bonding and increased hydrophobicity 0 High and low pH denature many but not all proteins 0 Denaturants chemicals such as Urea or GuHCl at high concentration can denature proteins Refolding 0 Anfinsen s Experiment First proof of sequence determines structure because after removing denaturants the protein ribonuclease refolded the same way I The experiment showed that the native form of a protein is the most thermodynamically stable structure 0 Levinthal Paradox Shows that there must be a mechanism of protein folding because there are too many possible protein folding conformations for the protein to randomly go back to the same conformation every time Mechanisms of refolding 0 Secondary structures form first 0 Nonpolar residues coalesce in a process called hydrophobic collapse 0 May involve intermediate states including transition states and molten globules Entropy change from the interaction of nonpolar residues with the solvent is the thermodynamic driving force for the folding of globular proteins Most proteins are only marginally stable because it provides exibility 0 This exibility is essential for ligand binding and enzyme catalysis and regulation Diseases can be caused by loss of protein function due to misfolding 0 Protein can t fold correctly cystic fibrosis Marfan syndrome ALS 0 Protein is not stable enough cancer 0 Protein can t be correctly trafficked 0 Protein forms insoluble aggregates that become toxic neurodegenerative disorders Intrinsically Unstructured Proteins I Can form larger intermolecular interfaces to which ligands could bind I Have more exibility which may reduce protein genome and cell sizes Quaternary Interactions I Subunit organization by more than two polypeptides intermolecular I Weak forces stabilize quaternary structure I Entropy loss due to association is unfavorable but entropy gain due to burying hydrophobic groups is very favorable I Quaternary association increases stability by reducing surface area promotes genetic efficiency less DNA is required to code for a monomer that forms a heterodimer brings catalytic sites together and promotes cooperation I Stable quaternary structures are formed because 0 AH subunits I Enhanced polar interactions between subunits I Increased Van der Waals interactions between subunits 0 AS solvent I Increase in entropy force water molecules released from subunit interface Chapter 14 Mechanisms of Enzyme Action 0 Enzymes have to bind the transition state of the reaction more tightly than the substrate 0 Must stabilize transition state more than substrate for there to be a decrease in activation energy 0 If ES has too high affinity Km too low there is no benefit of the catalyzed reactlon Destabilization of ES 0 If ES too favorable Ea is higher 0 Raising the energy of ES raises the rate 0 Catalysis Will not occur is ES and transition state X are equally stabilized 0 Can destabilize ES destabilize compared to super stable 0 Entropy loss due to formation of ES Decrease in entropy of overall system and of substrate 0 StrainDistortion in ES 0 Desolvation substrate loses favorable interactions With water 0 Electrostatic destabilization Preferential binding of the transition state 0 2 more H bonds to transition state than substrate large increase in rate 0 Transition state analogs TSAs stable molecules similar to transition state 0 TSAs are great inhibitors 0 K1 Binding affinity to the TSA transition state 0 Enzyme binds better to TS than substrate so most inhibitors resemble the TS Covalent Catalysis 0 Nucleophilic centers in enzymes attacked by electrophilic centers of substrates to make covalent ES complex 0 Covalent intermediate can be attacked in a second step by water or by a second substrate General AcidBase Catalysis 0 Noncovalent bonds 0 Specific acidbase catalysis involves H or OH 0 General acidbase catalysis doesn t directly involve HOH ex basic AA histidine 0 These facilitate the transfer of H in the transition state 0 LP electrons in base attack hydrogen Hydrogen polarizes the bond in water oxygen in water can then attach carbonyl Metal Ion Catalysis 0 13 of enzymes require metal ions for catalysis 0 Some play structural rather than catalytic role 0 Bind to substrate to orient it properly for the reaction 0 Mediate redox reactions through reversible changes in metal ion oxidation states 0 Electrostatically stabilizing negative charges 0 Metal ion can polarize to generate OH Proximity and Orientation 0 Bring substrates close to catalytic residues 0 Bind substrate in proper orientation nearattack conformation O NAC Precursors to transition states specific conformationarrangement for reaction to happen Stabilize transition state by electrostatic interaction Reduce overall loss of entropy Intramolecular is significantly faster 0 Intermolecular I loss in entropy Protein motions 0 Proteins under constant motion 0 Natural active site conformations can 0 Assist substrate binding 0 Bring catalytic groups into position 0 Induce formation of NACs 0 Assist in bond makingbreaking O Facilitate product formation Readingwriting mechanisms Curved arrow movement of electron pair Full arrowhead electron pair Half arrowhead single electron Consider protonation states to predict whether a residue will act as an acid or a base Active site residues 0 Polar residues engage directly in catalytic effects 0 Act as nucleophiles 0 Facilitate substrate binding 0 Stabilize transition states 0 Catalytic capacities are in uenced by O Raisinglowering pKa values through weak forces 0 Changing orientation 0 Charge stabilization LowB arrier Hydrogen Bonds LBHBs 0 Hydrogen bonds are equally shared between proton donor and acceptor when pKa values are nearly equal 0 Leads to stability of bond 0 Energy released in forming an LBHB can assist catalysis Serine Proteases Class of proteolytic enzymes 0 Each serine protease has binding pockets that bind specificdifferent substrates which means that they cleave after different AA 0 Chyotrypsin Prefers cleaves after Phe Trp or Tyr deep hydrophobic O Trypsin Cleaves after Lys or Arg deep ion pairs 0 Elastase Cleaves after Ala Gly or Val shallowsmall side chains Cleave peptide bond between alpha C and N 0 Active site reactive Ser195 residue Substrate becomes linked in a covalent bond at one or more points in the pathway 0 Ping pong mechanism Serine proteases employ acidbase catalysis as well as covalent catalysis Catalytic triad Ser195 His57 Asp102 O Asp102 works only to orient His57 O His57 acts as a general acidbase depending on the protonation state of His I Side chain pKa 67 so at physiological pH both the acid and base forms are present 0 Ser195 forms a covalent bond with peptide to be cleaved 0 Each catalytic residue is changed and then restored to initial state I Asp102 1 Ser195 His57 Neutral 0 Acylenzyme intermediate pNitrophenylacetate ester instead of amide used as evidence of intermediate 0 Can monitor products pNitrophenolate and acetate 0 Fast step Burst phase 0 Slow step All enzymes are acetylated waiting for water to release them 0 Involves two tetrahedral oxyanion transition states that are stabilized by amide groups 0 oxyanion hole conformation in which Ser195 and G1y193 NH bonds are stabilizing O 0 The preferential binding of TS over ES complex is responsible for much of the catalytic efficiency of serine proteases Aspartic Proteases 0 EX Pepsin HIV1 protease 0 2 Asp residues at the active site work in acidbase catalysis 0 LBHBs between Asp residues Chapter 45 part 2 Peptide Bond NchCo Formation causes release of water Usually found in the trans conformation Partial 40 double bond character 0 Resonance hybrid with partial DB between Co and O and between Co and N Proteins Monomeric one polypeptide chain Multimeric more than one chain Homomultimer one kind of chain Heteromultimer multiple kinds of chains Size small ex insulin MW 6000 to large ex glutamine synthetase MW 600000 Amino Acid Analysis Protein D mixture of amino acids not all some destroyed in process High temp boil extreme pH HCl Chromatographic methods to separate Only gives composition not sequence Step 1 Separating and purifying the chains Dissolve weak forces that hold the subunits together using extreme pH high concentration urea or guanidine HCl or high salt concentration usually ammonium sulfate Step 2 Cleave disul de bridges Performic acid oxidation HCOOOH Reducing agent causes formation of ZSH have to follow up with an alkylating agent to prevent recombination Step 3 Identify Nterminal and Cterminal residues Nterminal l Edman39s reagent phenylisothiocyanate product is PTHAA Cterminal D Carboxypeptidase Step 4 Cleave chain into smaller fragments using multiple procedures 0 Enzymatic o Trypsin After Lys and Arg 0 Chymotrypsin After Phe Tyr Trp Chemical 0 Cyanogen bromide CNBr After Met Chapter 13 Enzyme Kinetics 1 Substrate binds to active site of enzyme 0 Substrate specifically fits enzyme 2 Enzymesubstrate complex 2l3 Reaction occurs ex cleavage of substrate 3 Enzymeproducts complex 4 Products leavereleased from active site Enzymes lower the free energy of activation for a reaction 0 Decreasing AG Ea increases the reaction rate 0 The activation energy is related to the rate constant 0 No change in AG or Keq Gibbs free energy equation gives no information on rate Characteristics of Enzymes 0 Catalytic Power ratio of catalyzed rateuncatalyzed rate 0 Specificity term used to define the selectivity of enzymes for their substrates 0 Specificity is controlled by structure 0 Induced fit Induced fit binding of a substrate to an enzyme alters the confirmation of both the protein and the substrate I Structural changes may help to stabilize the transition state structure and position catalytic groups in the binding pocket to optimize catalysis steps I Ex Hexokinase closes around glucose 0 Regulation Enzyme activity is regulated to ensure an appropriate metabolic rate for cell requirements 0 Coenzymes and cofactors nonprotein components essential to enzyme activity Enzyme Kinetics study of the rates of enzymecatalyzed reactions 0 Seeks to determine max reaction velocity for enzymes and binding affinities for substrates and inhibitors 0 I insights into enzyme specificities and mechanisms MichaelisMenten kinetics MM Assumptions 0 No enzymeproduct complex 0 Prod I substrate is negligible 0 Catalytic step is the ratelimiting step 0 ES is constant 0 Substrate is in excess Measurements and calculations 0 Initial velocity Measured at the beginning of a reaction very little product 0 initial slope 0 Maximum velocity Theoretical maximum velocity at excess substrate 0 Constant for a given enzyme 0 Never actually reached 0 Km Measurement of binding affinity O S at 12 Vmax 0 Measure of S required for effective catalysis to occur Constant derived from rate constants 0 Under true MM conditions Km is an estimate of the dissociation constant of E from S 0 Small Km means tight binding high Km means weak binding 0 kcat Measurement of catalytic activity 0 Referred to as the molecular activity of the enzyme 0 kcat the turnover number is the number of substrate molecules converted to product per enzyme molecule per unit of time when enzyme is saturated with substrate 0 K2 0 In MM conditions kcat VmX t V At low S v increases linearly with S firstorder kinetics At high S v does not increase with increasing S zeroorder kinetics saturation effect Catalytic Efficiency kmKm An estimate of how perfect the enzyme is Measures how well the enzyme performs when S is low 0 More realistic measure because in the body the substrate will not be saturated kcmKm value allows for direct comparison of the effectiveness of an enzyme toward different substrates Diffusion limit the upper limit for kmKm the rate at which E and S diffuse together perfect enzyme LineweaverBurk doublereciprocal plot Linear plot 1S vs 1v yintercept 1Vm1X Xintercept 1Km Inhibitors Different molecules can inhibit one enzyme Inhibitors can be irreversible or reversible competitive noncompetitive or uncompetitive Competitive Inhibitors Competes with the substrate for the active site looks like substrate 0 Causes decreased affinity of S for E more substrate needed to replace I from E Increased Km 0 No change on VmX can still reach same velocities just need more substrate 0 Ex SDH succinate dehydrogenase competes With malonate inhibitor Pure Noncompetitive Inhibitor 0 Inhibitor binds at remote not active site 0 Km unchanged binding OH to E has no effect on binding of S 0 Vmax decreases because ESI complex is catalytically inactive Uncompetitive Inhibitors 0 Inhibitor binds at remote site but only after S binds to E 0 Vmax decreases because the ES is decreasing and increasing S doesn t prevent I from binding 0 Km decreases because ES is lowered as ESI is formed so more ES is formed S has more binding affinity 0 Slope unchanged Irreversible suicide mechanismbased inhibitors 0 Inhibitor binds covalently to E and both I and E deactivated are changed 0 Km unchanged because binding can still occur to free E 0 Vmax decreased because ES decreased 0 EX Penicillin has reactive peptide bond reactive because of 4membered ring strain Bimolecular Reactions 0 Enzymes can catalyze reactions involving 2 substrates 0 Random sequential random singledisplacement 0 Either substrate can bind first either product can leave first 0 Conversion of SES I PEP is the ratelimiting step 0 Ordered sequential ordered singledisplacement O A specific substrate must bind first followed by the other substrate 0 Usually followed by ordered release of products 0 PingPong DoubleDisplacement Reaction 0 Proceed via formation of a covalently modified enzyme intermediate 0 Modified enzyme is released to react with other substrate 0 Enzyme alternates between 2 types of reactions 0 Ex Glutamatezaspartate Aminotransferase Nonprotein Enzymes 0 Ribozymes RNA segment with enzyme properties 0 EX RNase P peptidyl transferase 0 Catalytic antibodies Abzymes Antibodies raised to bind the transition state of a reaction of interest 0 In many general reactions cannot isolate the transition state unstable 0 Create an antibody that resembles the proposed transition state structure 0 If protein binds to this analog it can be predicted that the protein would bind to the reallife transition state and thus act like a catalyst in the reaction Enzyme Activity is pH and temperaturedependent 0 pH changes ionizable groups which change secondary and tertiary structure 0 pH can change Km and VmX 0 At higher temperatures the protein becomes unstable and denatures Chapter 311 Protein Folding Newly synthesized proteins from the ribosomes have to fold Proteins that have become misfolded or denatured can refold In cells macromolecules including proteins are very crowded and contact each other May be more stable forms than the native structure ex Amyloid fibrils Stability of native state comes from intramolecular contacts Other stable structures amyloid fibrils comes from intermolecular stability States unfolded partially folded aggregates native structure etc 0 Aggregates accumulation of misfolded proteins often toxicdiseasecausing O Equilibrium between unfolded partially folded and native structures Chaperone proteins Assist changes tofrom native state to closest conformations 0 New conformation may be higher or lower in energy Found in all cells Hsp70 Hsp60 and Hsp90 Hsp heat shock protein named because they handle misfolded proteins that occur in extreme heat heat I denaturation Three pathways of folding O Chaperoneindependent folding O Hsp70assisted protein folding 0 Folding assisted by Hsp70 and chaperonin Hsp60 GroELGroES 15 Hsp70Assisted Protein Folding Bind to of polypeptides that are exposed in unfolded or misfolded proteins Hsp70 protein has an and a 0 ATPase domain generates energy by hydrolyzing ATPADP that provides mechanical force to enable peptidebinding domain 0 Bind to polypeptides while they are still on the ribosomes 0 Because Hsp70 is bound to hydrophobic residues it can keep the protein unfolded until productive folding can occur 0 When ATP is bound the chaperone has an open substratebinding pocket loses affinity for unfolded protein 0 If unfolded protein and chaperone protein are bound hydrolysis is triggered O This changes the conformation to a closed conformation that has high affinity for unfolded protein EX DnaK in E coli Hsp 70 Hsp60 Chaperonin Hsp chaperones chaperonins Assist proteins to complete folding after release from ribosomes Assist in an enclosed space called Anfinsen cage Substrate undergoes forced unfolding and refolding Driven by ATP Polypeptide is released from ribosome into Hsp70 ADP complex which delivers it to GroEL complex 0 Can t recognize native protein ATP binds GroES binds and encloses substrate Hydrophobic patches of substrate are buried ADP and GroES trans dissociate allowing the releasing old substrate New substrate remains encapsulated to fold while ATP is hydrolyzed ATP and GroES trans bind which causes cis to open and release substrate 0 When cis binds trans is released 0 When trans side binds cis is released Exam 2 Additional information Chapter 5 0 Carboxypeptidase A Cleaves C term AA all but ArgLysPro 0 Carboxypeptidase B Cleaves C term ArgLys 0 Carboxypeptidase CY Cleaves any C term AA 0 Clostripain Cleaves after Arg Chapter 13 0 MM equations 8 vs v 0 Km S at 12 Vmax 0 v VmaxS Km S O kcat VmaxEt 0 Catalytic efficiency kcatKm 0 LB equations 1S vs UV 0 X intercept 1Km 0 Yintercept 1V max 0 Slope KmV max 0 LB plot change 0 Competitive Same Yintercept increased slope O Noncompetitive Same Xintercept increased slope O Uncompetitive Same slope shifted left Chapter 14 0 Nucleophile base donates an electron pair usually 0 N or S 0 Base can handle losing an electron pair becoming positive 0 Electrophile acid accepts electron pair usually alkenes 0 Acid can handle losing an H can handle negative charge 0 Covalent catalysis O Nucleophilic Amines NR3 carboxylates RCOO hydroxyls OH imidazole N ring structure in histidine thiol SH I Nucleophilic residues mainly serine histidine cysteine andlysine O Electrophilic targets on substrate phosphoryl acyl CO 0 Mechanisms in actual enzymes 0 Serine proteases Ping pong mechanism covalent catalysis general acidbase catalysis 39 Chymotrypin Oxyanion hole transition state stabilization O Aspartic proteases general acidbase catalysis 0 pnitrophenylacetate hydrolysis 0 Example of specific acid or general base catalysis 0 Example of transition state analog that proves burst phase kinetics I Reaction changes to a slower rate after all enzymes are acetylated waiting for water to release them in the rate limiting step 0 Carbonic anhydrase 0 Example of metal ion catalysis 0 Has Zn2 which polarizes water 0 OH39 then attacks C02 0 Prolyl isomerase specifically human cyclophilin A 0 Example of protein motion catalysis O Catalyzes interconversion between trans and cis conformations in peptides 0 Polarcharged and polaruncharged amino acids engage directly in catalytic effects in enzyme active sites by acting as nucleophiles facilitating substrate binding and stabilizing transition states 0 pH in uence on aspartic protease 0 Have a pH optimum significantly impaired function outside of pH optimal range 39 Acidic 245ish 0 Cysteine protease O Degrade proteins hydrolysis of peptide bonds Nucleophilic cysteine Basic amino acid histidine deprotonates cysteine s thiol SH S Deprotonated cysteine attacks sulfur on substrate carbonyl carbon Release N term deprotonates histidine O Creates thioester intermediate that is hydrolyzed to generate a carboxylic acid 0 O O O 0 Lysozymes O Damage bacterial cell walls 0 Active site Gly and Asp 0 General acid catalysis Chapter 6 0 Alpha helix length 015nmresidue 0 Beta turn Hydrogen bonds between i and i3 residues 0 Proline is the least common in alpha helices because proline cannot function as a hydrogen bond donor but the most common in beta turns because it stabilizes the vis bond that beta turns require 0 More glycine in proteins than any other amino acid because it has a small side chain that can be accommodated in smalltight bends that are required in the compact proteins 0 H bond donors Have an H Lysine arginine tryptophan 0 H bond acceptors Lone pair of electrons aspartic acid glutamic acid 0 Donors and acceptors Asparagine glutamine serine threonine histidine tyrosine 0 All have a heteroatom with a hydrogen connected OH NH SH 0 Not threonine because N is in ring 0 Proteins in their native structure are dynamic 0 Have different conformations and can change 0 Changes tofrom different conformations occur by transient H bondlocalized not global changes that pass through the unfolded state


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