Amino Acid Nomenclature and Properties, Exams of Biochemistry

Download Amino Acid Nomenclature and Properties and more Exams Biochemistry in PDF only on Docsity! Biochemistry ACS Final Exam (100 Questions with SOLUTION)2024 GUARANTEE PASS BEST GRADED A+ Biochemistry I What is the difference between an apo and holoprotein - SOLUTION Apo = 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? - SOLUTION L Most alpha amino acids are _____, expect for glycine. All amino acids have ______ unique to itself. - SOLUTION Chiral, R-group/4th substituent When naming an amino acid using biochemical designation, what carbon do you start numbering at? - SOLUTION At the alpha carbon (one after the COO- group) What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Glycine? - SOLUTION Glycine: G, Gly What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Alanine? - SOLUTION Alanine: A, Ala What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Proline? - SOLUTION Proline: P, Pro What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Valine? - SOLUTION Valine: V, Val What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Leucine? - SOLUTION Leucine: L, Leu What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Isoleucine? - SOLUTION Isoleucine: I, Ile What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Methionine? - SOLUTION Methionine: M, Met What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Serine? - SOLUTION Serine: S, Ser What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Threonine? - SOLUTION Threonine: T, Thr What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Cysteine? - SOLUTION Cysteine: C, Cys What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Asparagine? - SOLUTION Asparagine: N, Asn What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Glutamine? - SOLUTION Glutamine: Q, Gln What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Phenylalanine? - SOLUTION Phenylalanine: F, Phe What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Tyrosine? - SOLUTION Tyrosine: Y, Tyr What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Tryptophan? - SOLUTION Tryptophan: W, Trp What amino acids can absorub UV light at 270-290 nm? - SOLUTION Phenylalanine, Tyrosine, Tryptophan What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Lysine? - SOLUTION Lysine: K, Lys What is the structure, 1 letter abbreviation, and 3 letter abbreviation for: Arginine? - SOLUTION Arginine: R, Arg What bonds can be rotated? What are the names of the specific bonds? - SOLUTION Rotation around bonds connected to the alpha carbon 1. Phi: angle around the C alpha-amide N bond 2. Psi: angle around the C alpha-carbonyl bond What plots show the distribution of allowable Phi and Psi angles? What are the axes? - SOLUTION Ramachandran plot 1. y axis = psi 2. x axis = phi Unfavorable combinations of psi and phi angles are due to what? What is favorable interactions due to? - SOLUTION Unfavorable = steric crowding of backbone atoms with other atoms in the backbone or side chains Favorable = favorable H-bonding interactions along the backbone What quadrants of a Ramachandran plot relate to the secondary structures? - SOLUTION Hydrogen bonds in the backbone are between what residues? - SOLUTION i and i+4 of the amides Peptide bonds in a right handed helix has peptide bonds alighed where? What bout the side chains? - SOLUTION Peptide bonds: roughly parallel with the helical axis Side chains: point out of the backbone and are roughly perpendicular with the helical axis What type of reisues are strong helix fomers? - SOLUTION Hydrophobic residues The backbone in a beta sheet is held together by what? - SOLUTION Hydrogen bonds between the backbone amides in different strands How are side chains siutated in a beta sheet? - SOLUTION Alternating 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? - SOLUTION Antiparallel since the bonds are linear What connects beta sheets together? - SOLUTION H bond between NH and CO groups of resides on adjacent strands What is tertiary structure? - SOLUTION Spatial arrangement of atoms in a protein Tertiary structure is stablized by what? - SOLUTION Weak 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? - SOLUTION 1. 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? - SOLUTION Assembly of indivudal polypeptidues into a larger functional cluster How do proteins know how to told into the correct conformation? - SOLUTION Primary sequence What is beta-mercaptoethanol (BME)? - SOLUTION Protein degrading agent - reduces cystines or disulfide bonds Why do proteins fold so fast? - SOLUTION Direction toward native structure is thermodynamically most favorable Explain the nucleation-condensation model. - SOLUTION Explains the many paths that lead to the same energy minimum of the native structure. Max entropy is at the top What is proteostatsis? - SOLUTION Cellular protein activity maintained by coordination of many different pathways. Chapter 3: Protein Techniques - SOLUTION Differential centriguation pellets what materials at the bottom? - SOLUTION Denser material What is zonal centrifugaiton? - SOLUTION Uses ultracentrifugation for a sample to reach equilibrium at its buoyant density of the density gradient Dialysis removes what? - SOLUTION Salt or other solutes after precipitation or change of buffers Explain column chromatography - SOLUTION Has a mobile (solute) and stationary phase (resin) where samples are separated based on polarity or hydrophobicity of resin and solute. Explain separation by charge. - SOLUTION Column 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. - SOLUTION Size 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. - SOLUTION Resin has a specific ligand that binds the protein of interest. How can specific activity be determined? - SOLUTION Activity/total protein A gel matrix hinders protein mobility according to what? - SOLUTION Protein size and shape