3-7 CHAPTER 3 REVIEW WKST
1. The study of amino acids will help biochemists to further understand the
_______________ and _______________ of proteins.
2. Identify three scientific challenges that may be solved by studying proteins.
3. Identify seven biological functions of proteins.
4. Draw a wedge-and-dash structure for L-isoleucine as it would look in the physiological
pH range. Name it using the IUPAC system of nomenclature. Label the carbons using
the Greek alphabet system.
5. In 19 of the 20 amino acids, the ___-carbon is chiral. What does it mean to be chiral?
Draw the only amino acid that is an exception to this.
6. Why can two stereoisomers not be easily converted from one to the other?
7. Draw the two enantiomers of valine. Identify the one that is biologically favored. This is
proof that all species on Earth are descended from a common _______________. What
would a mixture of these two enantiomers be called? The predominance of the
biologically favored enantiomer is due to the evolution of _______________ pathways
that produce that enantiomer instead of the other.
8. The property that helps to determine how proteins fold is called _______________ hydrophobic side chains will be clustered in the _______________ of a protein where
hydrophilic are usually found on the _______________.
9. The properties of the side chains greatly influence the _______________ of a protein.
10. Draw a Fischer projection of 2-aminopropanoic acid in its L- form and in its biologically
favored form, and identify it by its common name. Replace a hydrogen on the  carbon
with an isopropyl group and identify it by its common name.
11. Which four aliphatic amino acids play important roles in the 3D structures of proteins
because they cluster away from water?
12. Draw and identify the amino acid that has a heterocyclic ring and restricts the
_______________ of polypeptides, which can sometimes cause abrupt changes in the
_______________ of a peptide chain.
13. Draw the amino acid that is the most hydrophobic of the aromatics, and the two that
absorb UV light at 280 nm, which is used in _______________ to estimate the
concentration of proteins in solution.
14. Draw the amino acid that is almost always first in a polypeptide chain, and the amino
acid that forms disulfide bridges between side chains, _______________ the structures of
some proteins by cross-linking their residues.
15. Draw the amino acids that have R groups that can weakly ionize like primary and
secondary alcohols.
16. Draw the amino acid that has an imidazole ring, the one that is a diamino acid, and the
most basic of the 20 amino acids because its _______________ ion side chain is
protonated under all normal cellular conditions.
17. Draw the smallest of the two dicarboxylic acids, the amino acid that is familiar as its
monosodium salt, and the two amino acids that are highly polar and found at the surface
of proteins.
18. How can amino acids other than the 20 common ones form? Some of them are
chemically modified to produce biologically important _______________, and this can
happen _______________ they’ve been incorporated into polypeptides. The 21st and
22nd amino acids (_______________ and _______________) are derivatives of what two
common amino acids?
19. The physical properties of amino acids are influenced by the ionic states of what two (or
three) parts of amino acids? These ionic states influence the __-__ structures of proteins,
and can help understand the mechanisms of _______________.
20. Draw a titration curve for cysteine with OH– equivalents given that it’s carboxyl group
pKa = 1.9, its side chain pKa = 8.4 and its amino group pKa = 10.7. Draw the structure at
each stage of ionization, and label them as cation, zwitterion and anion.
21. Refer to table 3.2 on page 64 to calculate the isoelectric points for the following amino
acids. Also determine the pH ranges in which each amino acid could be an effective
buffer.
a. Thr
b. Val
c. Asn
22. The primary structure of a protein can be described as the linear _______________ of
amino acid residues in a polypeptide chain.
23. Why are the reactions that form peptide bonds not thermodynamically favored in cells?
What helps to overcome this barrier?
24. Write an equation for the formation of a dipeptide from Met and Thr, name the product,
identify the N-terminus and the C-terminus, and explain why residues are numbered from
the N- to the C-terminus.
25. Why is most of the ionic character of a polypeptide from its side chain? What properties
does this affect?
26. (# 15, pg 82) Several common amino acids are modified to produce
biologically important amines like Serotonin shown on the right, which is
an important neurotransmitter synthesized in the brain. Low levels of
serotonin in the brain have been linked to depression, aggression, and
hyperactivity. From what amino acid is serotonin derived?
27. Draw the structure of the sequences of amino acids given.
a. Cytochrome c from alligator (amino acids 41-50)  GQAPGFSYTE
b. Cytochrome c from bullfrog (amino acids 31-40)  NLYGLIGRKT
28. Some concerns with purifying proteins include _______________ it from all other cell
components and other similar proteins, finding a suitable _______________ for the
desired protein, keeping the protein biologically _______________, and doing it between
_____ and _____ to avoid degradation and denaturation.
29. Protein purification uses the differences in _______________, _____ __________,
__________ and _______________ _______________.
30. Protein purification includes…
a.
preparing a _______________ of proteins through dissolving cells into a
_______________, allowing the cell to _______________ and cause proteins to
_______________...
b. separating the mixture of proteins with _______________ _______________ as
the _______________ agent, and then using _______________ to isolate the
fraction containing the desired protein…
c. separating using _______________ by washing the fraction through an
_______________ material (matrix) using a specific solvent, dividing the mixture
into _______________ fractions, which must be _______________.
31. Proteins can be further separated using _______________, which separates proteins on
their migration in an _______________ field. _______________ _____ electrophoresis
(PAGE) uses a basic gel matrix with an electric field passed through it to
_______________ the migration of large molecules, thus fractionating the protein
mixture based on both _______________ and _______________. The fractions of
proteins can be visualized by _______________. _______________ _______________
_______________ (SDS) is sometimes added to overwhelm the native charge on proteins
so they are separated based only on _______________. This helps to assess the
_______________ and the _______________ weight of the protein. The “bands” of
proteins can be cut out of the _____ and isolated for _______________ analysis,
preparation of _______________, or other purposes.
32. The technique known as __________ _______________ determines the __________ of a
molecule by measuring the __________ it takes for a charged gas phase molecule to
travel from the _______________ point to the _______________. The time depends on
the __________ and __________ of the molecule, and the technique was not applicable
to biochemists until _______________ MS was developed which disperses charged
_______________ molecules into a _______________ stream of particles. MS can
determine the mass of a protein from _______________ quantities isolated from SDSPAGE gel, and the correct mass can be determined with an accuracy of less than the mass
of a single _______________!
33. Once a protein is isolated, its amino acid composition is determined by cleaving the
peptide bonds by acid _______________ using 6 M _____, as exemplified below.
Complete the equation where R1 = Met, R2 = Thr and R3 = Asn.
34. Write a mechanism for the use of PITC at pH = 9.0 on Ala to generate
____________________-amino acid derivatives, in this case PTC-Ala. What technique
will separate a PTC-amino acid mixture? What setback may occur using acid hydrolysis?
35. Show how the Edman reagent can remove Gly from Gly-Val-Glu.
36. Show how 2-mercaptoethanol cleaves a generic disulfide bridge and how iodoacetate
prevents the re-formation of the disulfide bond.
37. Edman degradation can approach _____ yield under carefully controlled conditions.
Treatment of proteins with cyanogen bromide, trypsin, S. aureus V8 protease and
chymotrypsin will _______________ proteins that have too many residues to be
completely sequenced by Edman degradation.
38. Who was the first to determine the complete sequence of a protein, what protein did he
use, when did he accomplish this, and what did he earn? Why did he earn two of what he
earned?