BIOCHEMISTRY ACS FINAL (ACTUAL EXAM (100 QUESTIONS WITH CORRECT SOLUTIONS) GRADED A+ 2024, Exams of Biochemistry

Download BIOCHEMISTRY ACS FINAL (ACTUAL EXAM (100 QUESTIONS WITH CORRECT SOLUTIONS) GRADED A+ 2024 and more Exams Biochemistry in PDF only on Docsity! 1 BIOCHEMISTRY ACS FINAL ( ACTUAL EXAM (100 QUESTIONS WITH CORRECT SOLUTIONS) GRADED A+ 2024 UPDATED . Biochemistry I What is the difference between an apo and holoprotein - SOLUTIONApo = protein part of an enzyme without its characteristic prosthetic group (cofactor is not bound) Holo = apoprotein with its prosthetic group (cofactor bound) Many amino acids exist as what isomer? - SOLUTIONL Most alpha amino acids are _____, expect for glycine. All amino acids have ______ unique to itself. - SOLUTIONChiral, R-group/4th substituent When naming an amino acid using biochemical designation, what carbon do you start numbering at? - SOLUTIONAt the alpha carbon (one after the COO- group) What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Glycine? - SOLUTIONGlycine: G, Gly What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Alanine? - SOLUTIONAlanine: A, Ala What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Proline? - SOLUTIONProline: P, Pro What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Valine? - SOLUTIONValine: V, Val What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Leucine? - SOLUTIONLeucine: L, Leu What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Isoleucine? - SOLUTIONIsoleucine: I, Ile What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Methionine? - SOLUTIONMethionine: M, Met What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Serine? - SOLUTIONSerine: S, Ser 2 What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Threonine? - SOLUTIONThreonine: T, Thr What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Cysteine? - SOLUTIONCysteine: C, Cys What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Asparagine? - SOLUTIONAsparagine: N, Asn What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Glutamine? - SOLUTIONGlutamine: Q, Gln What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Phenylalanine? - SOLUTIONPhenylalanine: F, Phe What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Tyrosine? - SOLUTIONTyrosine: Y, Tyr What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Tryptophan? - SOLUTIONTryptophan: W, Trp What amino acids can absorub UV light at 270-290 nm? - SOLUTIONPhenylalanine, Tyrosine, Tryptophan What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Lysine? - SOLUTIONLysine: K, Lys What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Arginine? - SOLUTIONArginine: R, Arg What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Histidine? - SOLUTIONHistidine: H, His What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Aspartate? - SOLUTIONAspartate: D, Asp What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Glutamate? - SOLUTIONGlutamate: E, Glu What is the typical pKa for: terminal alpha-carboxyl group? - SOLUTION3.1 What is the typical pKa for: Aspartic/Glutamic acid? - SOLUTION4.1 What is the typical pKa for: Histidine? - SOLUTION6.0 What is the typical pKa for: terminal alpha amino group? - SOLUTION8.0 5 How are side chains siutated in a beta sheet? - SOLUTIONAlternating up and down in direction Differentiate the difference between parallel and antiparallel beta sheets. - SOLUTION What type of beta sheet results in strong hydrogen bonds? - SOLUTIONAntiparallel since the bonds are linear What connects beta sheets together? - SOLUTIONH bond between NH and CO groups of resides on adjacent strands What is tertiary structure? - SOLUTIONSpatial arrangement of atoms in a protein Tertiary structure is stablized by what? - SOLUTIONWeak interactions between amino acid side changes - hydrophobic and polar interactions can be stabilized by disulfide bonds What are the two main classes of tertiary structures? What id the difference between the two? - SOLUTION1. Fibrous: regular repeating structures; insoluble; does NOT denature easily; play structural or supportive role 2. Globular: compact interior; water soluble; folding driven What is quaternary structure of amino acid? - SOLUTIONAssembly of indivudal polypeptidues into a larger functional cluster How do proteins know how to told into the correct conformation? - SOLUTIONPrimary sequence What is beta-mercaptoethanol (BME)? - SOLUTIONProtein degrading agent - reduces cystines or disulfide bonds Why do proteins fold so fast? - SOLUTIONDirection toward native structure is thermodynamically most favorable Explain the nucleation-condensation model. - SOLUTIONExplains the many paths that lead to the same energy minimum of the native structure. Max entropy is at the top What is proteostatsis? - SOLUTIONCellular protein activity maintained by coordination of many different pathways. Chapter 3: Protein Techniques - SOLUTION Differential centriguation pellets what materials at the bottom? - SOLUTIONDenser material 6 What is zonal centrifugaiton? - SOLUTIONUses ultracentrifugation for a sample to reach equilibrium at its buoyant density of the density gradient Dialysis removes what? - SOLUTIONSalt or other solutes after precipitation or change of buffers Explain column chromatography - SOLUTIONHas a mobile (solute) and stationary phase (resin) where samples are separated based on polarity or hydrophobicity of resin and solute. Explain separation by charge. - SOLUTIONColumn chromatography where resin is charged and binds to the oppositely charged particles better to remove the same charged molecules first. Then a solution can be passed through to unbind the bound particles and elute. Explain seperation by size. - SOLUTIONSize exclusion chromotogrphay - where resin has a molecular weight cut-off and passes larger molecules faster and smaller molecules slower or until a new solute is added to outcomplete the binding. Explain an affinity chromotography. - SOLUTIONResin has a specific ligand that binds the protein of interest. How can specific activity be determined? - SOLUTIONActivity/total protein A gel matrix hinders protein mobility according to what? - SOLUTIONProtein size and shape In gel electrophoresis of proteins what direction is the gel ran? Larger proteins are where? Why? - SOLUTIONRan: cathode to anode (minus lus plus) Larger proteins are towards the top of the gel since they are unable to migrate in the cross- linking of the gel What is SDS? - SOLUTIONSodium dodecyl sulfate - detergent that unfolds or denatures proteins to give a uniformly negative charge. Movement in electric field is only dependent on size then. Reducing gels contain what compared to non-reducing? - SOLUTIONContain BME to reduce cystine disulfide bonds to free thiols Non-reducing gels have no BME and therefore disulfide remain intact What is ioselectric focusing? - SOLUTIONUsed to determine the pI of a protein - by changing the pH gradient so no futher migration is seen Define antigens, haptens, ad epitope. - SOLUTIONAntigens substance that stimulates antibody production 7 Haptens are small mlecules attached to a larger carrier that can elicit an immune response Epitope: antigen recognizing part of an antibody Compare polyclonal to monoclonal antibodies. - SOLUTIONPolyclonal recognize many different epitopes to an antigen with differing affinities, where monoclonal only recognize one epitope with one affinity Describe the lab process for apply antibodies. - SOLUTION1. Coat the surface with your sample/antigen 2. Block unoccupied sites with a nonspecific protein 3. Incubate in primary antibody against specific antigen 4. Incubate with secondary antibody - enzyme complex that binds to the primary antibody 5. Add substarte 6. Formation of colored product indicates presence of specific antigen. What is ELISA? Describe the assay steps. - SOLUTIONEnzyme-linked immunosorbant assay 1. Wells are coated with antigens 2. Antibodies are added to bind to specific antigens 3. Enzyme linked antibodys bink to specific antibody 4. When substrate is added, enzymes are converted to a colored product - color formation is proportional to the amount of a specific antibody Recombination proteins can be easier to purify because what can be added to them? - SOLUTIONTags - useful for affinity resin Explain Edman degradation. - SOLUTIONAmino acids are labeled then released for absorbance deterection then repeated. Easy for SMALL peptides How are Edman degradation products pieced together? - SOLUTIONOverlapping sequences and that is the sequence of the protein How are disulfide bonds reduced? - SOLUTIONDTT or MME What is Maldi-MS? - SOLUTIONMass spectrometry with matrix-assisted laser desoprtion/ionization