Download Review Problems #2 (Enzyme Review, Phosphatases

Review Problems (Amino acid Biosynthesis) Week 10
1) The carbons of phenylalanine and tyrosine are derived from what glucogenic
molecules?
2) The branchpoint for aromatic amino acid biosynthesis is chorismate. What is the
structure of chorismate? What are the three immediate products derived from chorismate
that constitute the first unique steps in the synthesis of the three aromatic amino acids?
3) From where are the two carbons of the five-membered ring of tryptophan derived? Be
specific. (Show the molecule and highlight the carbons that are used.) The carbons that
are not used are converted into what compound?
4) The nonaromatic carbons of tryptophan are derived from what precursor? What
cofactor is involved in this reaction? Show the mechanism of this transformation.
5) Roundup (glyphosate) inhibits biosynthesis of aromatic amino acids. Which step does
it inhibit? Why does this inhibitor have little effect on humans? Considering that
glyphosate is an incredibly effective herbicide, can you give a likely reason for why this
compound is not an effective antibiotic.
6) Which transformation in aromatic amino acid biosynthesis requires NAD+, but does
not yield NADH as a product. Explain the role of this cofactor. (Hint: this is similar to
the reaction catalyzed by S-adenosylhomocysteine hydrolase).
7) What are the carbon-containing precursors used for the synthesis of valine and
isoleucine? What cofactor is common to both these biosynthetic pathways? Explain its
role and draw a mechanism for the transformation.
8) The biosynthesis of valine and isoleucine have a rearrangement step that is very
similar. Draw this rearrangement (curly arrows please).
9) Leucine is derived from the same pathway that generates valine. What additional
carbon source is used in this synthesis? The later stages of leucine’s biosynthetic
pathway are similar to what other pathway?
10) Threonine is derived from what non-proteinacious amino acid? Which common
amino acid is the ultimate source of this molecule?
11) The methyl group of methionine is derived from what common amino acid? What is
the byproduct of this one carbon transfer? What cofactor catalyzes this carbon cleavage?
What is the acceptor of this carbon? The actual agent that ultimately transfers the carbon
is which cofactor?
12) Alpha-ketoglutarate provides the carbon skeleton for which amino acids?
13) Two different amidation methods are used to install side chain amides in amino acids.
Describe these two methods and match them to the relevant amino acid. Why do you
think this difference exists? Where are similar activation strategies employed in
biosynthesis?
14) Which amino acids derive their carbon skeletons completely from oxaloacetate?
15) Which amino acid is derived from oxaloacetate and pyruvate? What carbon piece is
lost in this process? What cofactor plays a role in this process? Draw a general
mechanism for this reaction. What molecule plays a role as a protecting group in this
pathway?
16) Serine is derived from which glucogenic precursor?
17) Inhibition of a key enzyme activity by the end product of a biosynthetic pathway is
known as what?
18) Why is it useful to have multiple isozymes of enzymes that comprise common
pathways to multiple amino acids?
19) What molecules provide the carbon and nitrogen sources for histidine. Please
delineate which atoms in the starting materials wind up in which places in histidine.
20) What enzyme is responsible for the fixation of nitrogen?
21) How many electrons are required to reduce nitrogen gas to ammonia? How many
electrons are required in the biological reduction? If these are not the same, explain why.
22) What are the ultimate biological molecules that act as acceptors of ammonia in higher
organisms? What enzymes mediate this(ese) transformation(s)? What are the energetic
requirements for this(ese) reaction(s)?
23) What nine amino acids cannot be synthesized in humans?
24) Draw the degradative pathways for threonine.
25) What cofactor is used for hydroxylation of phenylalanine. Draw the mechanism of
this reaction.
26) Outline the degradative pathway for phenyalanine.
27) Outline the degradative pathway for lysine.
28) The indole ring of trp is degraded into which molecule? What amino acid is derived
from the first three carbons of trp? How does this explain whether trp is ketogenic or
glucogenic?