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53 Cards in this Set
- Front
- Back
What are the non-polar (hydrophobic) amino acids?
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Luecine, Proline, Mehionine, Tryptophan, Alanine, Valine, Phenylalanine, Isoleucine
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What are the polar (hydrophilic) uncharged amino acids?
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Glycine, Serine, Threonine, Cysteine, Asparagine, Glutamine, Tyrosine, Histidine
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What are the acidic amino acids?
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Aspartic, Glutamic
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What are the basic amino acids?
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Lysine, Arginine
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What amino acids is not an alpha-amino acid?
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proline
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Which two groups of an amino acid react to form a peptide bond?
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the alpha-amino gropu and the alpha-carboxyl group
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Understanding the unique characteristic behaviour of amino acid side-chains is important because:
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1) chemical reactivity of some can be used ot modify proteins in specific ways
2) chemical and physical propreties of some allow detections and quantification 3) chemical and physical properties of some bestow propteins with specific biological functions |
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Ninhydrin is used to detect and quantify a-amino acids. Reactions with ninhydrin results in:
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deamination and decarboxylation
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Which amino acid lacks a chiral center?
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glycine
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Which amino acids absorb light at 250-280 nm?
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arginine, lysine & histidine
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Which amino acid has two chiral centers?
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L-Threonine
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For all amino acids except one, the L-configuration corresponds to the S-configuration. Which one has the R-configuration?
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L-Cysteine
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amino acids are always what configuration
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L-amino acids
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Amino acids join via
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peptide bonds which release water
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What contributes to protein folding?
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aliphatic and aromatic R-group containing amino acids
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At neutral pH, amino acids are
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zwitterions - bipolar ions
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What is the pH of a glutamic acid solution if the α p g
carboxyl is 1/4 dissociated? |
pH = 2 + log10 [1]/[3]
pH = 2 + (-0.477) pH = 1.523 |
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What is the pH of a lysine solution if the side p y
chain amino group is 3/4 dissociated? |
pH = 10.5 + log [3]/[1]
pH = 10.5 + (0.477) pH = 10 977 = 11 |
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The first amino acid that is eluted is
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the lowest postitive charge; the higher the charge the greater affinity and the slower the elution
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What must the elution tube contain for the elution to work?
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salt
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Which pairs of amino acid side chains might you expect to find in a salt bridge in a protein at pH 7.0?
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Aspartate & Arginine
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The 20 common amino acids found in proteins are usually the L enantiomers. The exception is:
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Glycine
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At pH 7.0 which of the following amino acid side chains would you expect to be protonated?
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Arginine
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The pKa of the side chain of histidine is 6.0. At pH 7.0 what is the ratio of positively charged histidine side chains to neutral side chains?
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1:10
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Which of the following amino acid side chains reacts chemically with DTNB and p-HydroxyMercuriBenzoate
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Cysteine
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If a mixture of Glutamic acid (side chain pKa = 4.3) and Aspartic acid (side chain pKa = 3.9), at pH 4.0 are separated by using anion exchange chromatography at pH 4.0, what will happen?
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Both will stick but using a salt gradient will elute the glutamate before the aspartate
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In water the pKa of the side chain of glutamic acid is 4.3. If the local dielectric constant of the medium was changed to that of hexane (dielectric constant 1.9) the pKa would
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Increase
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Which of the following amino acids has two chiral centers?
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Isoleucine
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Which of the following amino acids is not found occasionally in proteins?
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Ornithine
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The green fluorescent properties of GFP (green Fluorescent Protein) result from:
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A chromophore formed autocatalytically involving a particular sequence of amino acids in the protein
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The color formed when ninhydrin is used to detect and quantitate amino acids
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Is a derivative containing two ninhydrin moieties formed by reaction with released ammonia during the reaction
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Peptide bond formation is
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a dehydration reaction
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In a peptide bond
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-the C-Co-N-C configuration is trans; the six atoms are co-planar; there is rotation about C-R, C-Co and C-N bonds; rotation about Co-N is restricted; there is a distinct polarity
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As a first approximation proteins can be assigned to one of three classes on the basis of shape and solubility. These are:
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fibrous, globular, membrane
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Through H-bond interactions between adjacent amino acids residues the polypeptide chain can arrange itself into characteristic helical or pleated segments. This is a definition of the
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secondary structure
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The secondary, tertiary and quaternary structures of proteins are stabilized principally by
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H-bonds; electrostatic interactions; van der Waals forces; hydrophobic interactions
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In general protein solubility is influenced by:
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pH; amino acid sequence; polarity of solvent
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The effect of ionic strength on protein solubility is attributed to:
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the decrease in electrostatic interactions between protein molecules; The increase in charge-counter ion interactions; competition between the protein and the salt ions for water of solution
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The first step in determining the amino acid composition of a protein involves hydrolyzing the protein in 6NHCl at 110C for 24, 48 and 72 h. This procedure:
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slowly destroys Ser and Thr, but their original concentration is estimated by extrapolation to zero time from their concentrations at 24, 48 and 72 h.
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The complex amino acid mixture in a protein hydrolysate is separated using:
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ion-exchange chromatography
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Comparing the amino acid composition of different proteins allows the following generalizations:
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each of the 20 naturally occurring amino acids is usually represented at least once.
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Determining the amino acid sequence of a protein (its primary structure) involves both chemical and enzymatic strategies. A procedure for the cleavage of disulfide bonds is:
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reduction with 2-mercaptoethanol or dithiothreitol (DTT) followed by alkylation with iodoacetate.
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Determining the amino acid sequence of a protein (its primary structure) involves both chemical and enzymatic strategies in seven basic steps. A procedure for determining the N-terminal amino acid is:
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specific hydrolysis with cyanogen bromide (CNBr) to yield a sulfonium ion that undergoes rapid intramolecular rearrangement to form the iminolactone
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Determining the amino acid sequence of a protein (its primary structure) involves both chemical and enzymatic strategies in seven basic steps. A procedure for determining the C-terminal amino acid is:
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specific hydrolysis with carboxypeptidase using an automated protocol
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Determining the amino acid sequence of a protein (its primary structure) involves both chemical and enzymatic strategies in seven basic steps. A chemical procedure for specifically cleaving next to Met residues is:
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specific hydrolysis with cyanogen bromide (CNBr) to yield a sulfonium ion that undergoes rapid intramolecular rearrangement to form the iminolactone
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What is the order of procedures for determining the position of disulfide bonds?
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hydrolysis with enzymes such as trypsin; electrophoresis; oxidation with performic acid; electrophoresis; sequencing with phenylisothiocyanate (Edman degradation)
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Homologous proteins are those with:
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the same function in different organisms; different functions but similarities in sequence and tertiary structures; the same function and a high degree of sequence similarity; positions in the primary sequence where the same amino acid always occurs; positions in the primary sequence where the same type of amino acid always occurs
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Procedure/s used for the separation of proteins based on solubility is/are:
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ammonium sulfate precipitation
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Procedure/s used for the separation of proteins based on activity or function is/are:
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affinity chromatography
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Procedure/s used for the separation of proteins based on net charge is/are:
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isoelectric focusing
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Procedure/s used for the separation of proteins based on mass is/are:
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size exclusion chromatography; sodium dodecylsulfate-polyacrylamide gel electrophoresis
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Procedure/s used for the separation of proteins based on charge and mass is/are:
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electrophoresis
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Procedure/s used for the separation of proteins based on mass and/or density is/are:
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ultracentrifugation
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