Chapter 3 Sapling Learning Curve: Amino Acids, Peptides and proteins, Structure of Proteins

The resin used for cation exchange is _______ charged. If a solution of Val, Lys, and Glu at pH = 7 are loaded onto a column with cation exchange resin, what order would the amino acids elute from the column if eluted with salt?

Cation exchange resin has anionic groups bound to it. negatively; Glu, Val, Lys

Which substance can be used in the determination of the N-terminal amino acid of a protein?

FDNB

A nonapeptide was determined to have the following amino acid composition: two Lys, two Gly, two Phe, one each of His, Leu, and Met. When the native peptide was exposed to cyanogen bromide, a heptapeptide and a dipeptide were recovered. Incubation of the native peptide with trypsin gave a pentapeptide and a tetrapeptide. Cyanogen bromide cleaves at Met (C); whereas trypsin cleaves at Lys and Arg (C). Which sequence is compatible with this data?

Gly-Met-Leu-Lys-His-Phe-Gly-Phe-Lys

What structural feature makes proline unique among the 20 standard amino acids?

It is the only one with a ring linking the α-carbon and the amine group.

What is the role of SDS in gel electrophoresis?

It masks the intrinsic charge of the protein and contributes a large negative charge, giving each protein a similar charge-to-mass ratio. AND It partially unfolds proteins, enabling separation of protein almost exclusively on the basis of mass.

Affinity chromatography can be used to purify proteins such as growth factor receptors. The ligand of the growth factor receptor can be linked to resin, and then an extract containing membrane proteins can be poured over the resin. If a high concentration of free ligand were poured over the resin next, what would you expect to happen?

The excess ligand will compete with the ligand attached to the resin, releasing the growth-factor receptor from the resin.

In an SDS-PAGE experiment, a protein migrates much faster than expected relative to protein standards, based on its known molecular weight. What could cause this?

The protein had a very high intrinsic negative charge.

Which of the following statements is false regarding amino acids? All amino acids have amino groups and carboxyl groups. They can be grouped according to the properties of their R groups. They are found in the D-form in proteins. pH can influence the charge of an amino acid.

They are found in the D-form in proteins.

Which statement is true about the configuration of amino acids in proteins? They are in the L-configuration. They are in the D-configuration. There is usually about an equal mix of the L and D configurations. The amount of each configuration varies widely among proteins.

They are in the L-configuration.

gel of Coomassie-blue stained proteins.

This procedure separates proteins by their isoelectric points.

Consider two weak acids (acid 1 and acid 2) that have pKa values of 4 and 5, respectively. Which statement below is true?

Weak acid 1 has a tendency to donate protons 10-fold that of weak acid 2.

Which amino acid has the one-letter abbreviation and name properly matched?

Y; tyrosine

What generally happens during a successful enzyme purification protocol (comparing crude extract to final product)?

activity decreases and specific activity increases

Why can the pKa value for an ionizable R group change when an amino acid becomes incorporated into a peptide? Environmental factors can influence pKa. Ionizable R groups can interact with other peptide R groups. There can be a loss of charge to alpha-carboxyl and alpha-amino groups. all of the above

all of the above

A substance that can act as either an acid or a base is _______.

amphoteric

In the cation exchange chromatography of amino acids where the elution buffer is applied as a gradient from low pH to high pH, what is the order of elution (first to last) of a mixture of glycine, aspartate and arginine?

aspartate; glycine; arginine

Peptide bond formation is an example of a ______________ reaction.

condensation

Peptide bonds are _______ bonds between the carboxyl group of one amino acid and the amino group of another amino acid and are formed by _______.

covalent; condensation

What effect would decreasing the column length have in column chromatography?

decreased resolution and separation of proteins

Which of the following is a procedure in which small molecules are removed from a solution of a macromolecule by their diffusion through a semipermeable membrane into a suitable buffered solution?

dialysis

desmosine is found in?

elastin

Which of the following can be obtained through the process of SDS gel electrophoresis? estimation of the purity of a protein sample estimation of protein molecular weight protein purification all of the above estimation of the purity and molecular weight of a protein sample

estimation of the purity and molecular weight of a protein sample

Which statement describes the hydrolysis of a peptide bond?

exergonic with a high activation energy

Which amino acid has an amido group in its side chain?

glutamine

A protein that binds to glutathione can be purified using an affinity column where the solid phase is a cellulose matrix covalently attached to the molecule glutathione. What should be included in the elution buffer for this experiment to remove the protein from the column?

glutathione

The configurations of ________ are used as the basis for assigning the L and D configurations.

glyceraldehyde

In what range would you expect the pI to be for Ala-Val-Lys?

greater than 7

Which is the only common amino acid with a side-chain pKa near neutrality?

histidine

You have isolated a crude sample of two related peptides (Peptide A and Peptide B). To separate the two, what protein purification method would be most effective? Peptide A: Ala-Ala-Gly-Glu-Asp-Ser-Glu-Ala Peptide B: Ala-Ala-Gly-Lys-Arg-Ser-His-Ala

ion exchange chromatography

In size-exclusion chromatography _____.

larger protein molecules appear in earlier fractions.

Which amino acid would tend to stabilize a protein through the hydrophobic effect?

leucine

Proteins are _____________ polymers of _____________.

linear; amino acids

If the molecular weight range is not too broad in SDS-PAGE (electrophoresis), which plot will be linear?

log(Mr) versus Relative migration

Which two amino acids contain sulfur?

methionine and cysteine

6-N-methylysine is found in ?

myosin

In an oligomeric protein, how are the subunits associated with each other?

non-covalent interactions

4-hydroxylysine is found in?

plant cell walls

Which level of protein structure describes the covalent backbone of a protein, including the sequence of amino acids?

primary

Paralogs are _____.

proteins from one species with the same function

Which uncommon amino acid is not created through postsynthetic modification of one of the standard 20 amino acids?

selenocysteine

The purpose of adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, is to make it possible to _____.

separate proteins exclusively on the basis of molecular weight

Which of the following groups can ionize and contribute to the total acid-base behavior of a peptide: some R-groups terminal alpha-amino groups alpha-carboxyl groups involved in peptide bonds all of the above some R-groups and terminal alpha-amino groups

some R-groups and terminal alpha-amino groups

Which rare amino acid is mismatched with where it is found?

γ-carboxyglutamate; collagen

If the absorption of a solution at 300 nm is 0.100, what is the absorption if the concentration is doubled?

0.200

Which statement about biologically active peptides is true? Most active peptides are 2-10 amino acids in length. Active peptide lengths vary widely from two to many thousands of amino acids. Active peptides must be at least 50 amino acids in length, but may be much larger as well. Nearly all active peptides are large proteins (>1000 residues).

Active peptide lengths vary widely from two to many thousands of amino acids.

Which type of chromatography has the potential to save many steps in a purification protocol?

Affinity chromatography because of its specificity for a protein.

What information can be gained by comparing the sequences of proteins that have the same or similar function in different species? - to determine sequences that are conserved among species since they are likely to be important to the function and stability of the proteins - to determine evolutionary relationships and relatedness of species -to predict similarity in protein folding -all of the above

All of the above

If a protein is composed of 100 amino acids, what would its approximate molecular weight be?

11 (kilodaltons)

Estimate the number of amino acids in a protein with a molecular weight (Mr) of 43,000 (in daltons)?

391

Imagine a reaction mixture favors only the formation of dipeptides. If the mixture contains ample amounts of glycine and alanine, how many different dipeptides can possibly be formed?

4

At which pH would the net electric charge of tyrosine be zero, given that its -COOH group has a pKa of 2.20, its -NH3+ group has a pKa of 9.11, and its R group has a pKa of 10.07?

5.66