Biochemistry 2000 - Amino Acids & Protein Biochemistry Questions

Sep 30, 2026

Practice and assessment material covering core biochemistry concepts centered on amino acids, peptides, and proteins. Tasks include defining key terms, identifying amino-acid properties at specific pH values, drawing chemical structures, determining charges and pKa values, and calculating isoelectric point. The set also addresses peptide bond topology, residue chirality, methods supporting protein subunit composition, and chromatographic and electrophoresis behavior.

LanguageEnglish

CategoryExam

FormatPDF

Pages11

Reading Time28 min

AccessFree to download

Questions

Definitions and amino-acid properties

Peptides and charge/isoelectric point

Protein experiments and separation methods

Answers

(1)Give brief definitions or unique descriptions of the following terms: (b)stationary phase (a)oligopeptide (c)neutral drift (d)quatemary structure (e)zwitterion (f)salting out (2)Consider the 20 amino acids that commonly occur in proteins.Draw a stick diagram ofeach of the following: (a)a non-polar residue at pH 7.0 (b)a polar,uncharged residue at pH 4.0 (c)a polar,charged residue at pH 10.0 (3)What are the names and 3-letter abbreviations of the three aromatic amino acids?Drawtheir structures. (4)Which amino acid is not chiral?Draw the structure. (5)Show the difference between the two negatively charged amino acids by drawing theirstructures. (6)What is the difference between glutamate and glutamine?Show by drawing the structure. (7)Which amino acid has a thiol group?Provide the full name,the 3-letter abbreviation andthe structure. (8)Describe in words and with structures the difference between Leucine and Isoleucine. (9)What is special about proline?Explain and draw the structure. (10)Which amino acid has a side chain which is able to accept or donate a proton close tothe physiological pH?Provide the name,3-letter abbreviation,structure and pKa of the sidechain. (11)Which amino acid has an amine group in its side chain?Provide the name,3-letterabbreviation,structure at physiological pH and pKa of the side chain. (12)Draw the structures of the following amino acids at physiological pH and classify them aspolar,aromatic,nonpolar,positively or negatively charged.(a)Arginine(b)Tyrosine(c)Valine(d)Asparagine (13)For the following forms of amino acids,provide the name,the 3-letter abbreviation andindicate in which pH range this would be the predominant form and justify your choice. (b) (c) (a) ## (14)Give the full name and the 3-letter abbreviation of the following tripeptide.Indicate the N- and the C-terminus of the structure. (15)Draw the structure of alanylseryltryptophan at physiological pH. (16)The Lys-Asp-Gly sequence is a characteristic feature of SH3 domains involved in protein-protein interactions.Calculate the charge associated with a sythentic Lys-Asp-Gly tripeptidesequence under the following conditions:(Note:show your work)(a)pH 2.2(b)pH 6.0(c)pH 11.0 (17)You have titrated the free amino acid Glu with strong acid: (a)Draw a reasonable titration curve,label the axis and significant transitions(b)Calculate the isoelectric point (18)Draw the Lys-Asp-Gly tripeptide at pH 7.0 and draw a box around the peptide bonds. (19)What is the net charge of the following amino acid?Draw the corresponding structure.(a)Glutamate at pH 10(b)Lysine at pH 1.5(c)Serine at pH 5.8(d)Isoleucine at pH 1.0 (20)Show the complete reaction equation for formation of Ala-Arg from the individual aminoacids at physiological pH(use complete structures). Biochemistry 2000 (21)Draw the structures of the two amino acids containing sulfur and name these with boththe full name and the 3-letter abbreviation. (22)Consider all possible tripeptides made of the amino acids tyrosine,histidine and proline.Answer the following questions. (a)Give the names of each possible tripeptide using 3-letter code. (b)Of the tripeptide in question(a),draw the structure of the tripeptide which has a C- terminal proline and a N-terminal tyrosine at pH 1.0 (c)What charge will this tripeptide have at pH 12?Explain. (23)A mixture of the following dipeptides was applied to a cation exchange column.Ala-CysHis-Asp Tyr-GluLeu-ArgVal-Lys (a)Which dipeptide(s)would bind at pH 8.0 (b)Would the result differ at pH 4.5?Explain your reasoning. (24)What is the role of 2-mercaptoethanol(b-mercaptoethanol)in SDS-PAGE? (25)Vibrio cholera (causitive agent of “cholera”)secretes a protein toxin with an AB₅quaternary structure.The single “A”subunit has a molecular mass near 22 kDa and each “B”subunit has a mass of near 12 kDa. (a)Sketch and label a figure of the result of an SDS-PAGE experiment. (b)Sketch a

FAQs

What topics do the questions cover?

They cover definitions of biochemical terms, amino-acid properties across pH ranges, peptide/structure drawing, charge calculations and isoelectric point, and protein behavior in chromatography and SDS-PAGE.

How are pH values used in the material?

Many items ask for predominant amino-acid forms, charge, and pKa-related reasoning at specified pH values such as 1.0, 2.2, 4.0, 6.0, 7.0, 10.0, 11.0, and 12.

What experimental techniques are referenced?

The document references SDS-PAGE (including the role of 2-mercaptoethanol), cation exchange chromatography, size exclusion chromatography, and experimental approaches to test whether a protein has more than one subunit.

Sep 30, 2026

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