Download 1. PROTEIN MODIFICATION 1.1 What are posttranslational

1. PROTEIN MODIFICATION
1.1
What are posttranslational modifications?
1.2
Describe the synthesis of Selenocysteine and Pyrrolysin.
1.3
Describe proteolytic cleavage as posttranslational modification with the example of insulin.
1.4
What is the carrier of a methyl group for example for the methylation of lysine?
1.5
How do proteins get phosphorylated? Which amino acids can carry a phosphate group? How
does this modification change the protein properties in general?
1.6
Describe the chemical phosphorylation of a peptide within the Solid Phase Peptide Synthesis.
1.7
Draw the following mechanisms of protein modification. Indicate the electrophile and
nucleophile in each case. SAM (below)-mediated methylation of lysine. ATP (below)-mediated
phosphorylation of serine.
1.8
Name three types of cotranslational or posttranslational protein modification that are found in
nature. Why are proteins modified?
1.9
Name the two classes of glycoproteins and the three amino acid side chains in proteins that
are used to attach glycosyl groups.
2. PROTEIN FUNCTION AND FOLDING
2.1
Describe the function of: structure-, motor-, defence-, storage-, transport-, and regulatory
proteins and enzymes in general. Know one example for each protein class.
2.2
What types of interactions contribute to protein folding?
2.3
Explain the Levinthal paradox.
2.4
What are molten globules? Describe the differences between an unfolded state, a molten
globule and a folded state of protein.
2.5
What is the key event in protein folding?
2.6
What are multiple folding pathways?
2.7
What are folding helpers and how do they assist protein folding?
2.8
How do chaperones work?
2.9
Name and briefly describe (with a cartoon) the third thermodynamic state of a protein that is
observed upon folding or unfolding, the intermediate between random coil and native state.
3. PROTEIN STRUCTURE
3.1
Describe the structural hierarchy of proteins. What is the purpose of forming highly complex
structures?
3.2
How are protein structures being classified? Know and be able to draw schematically one
typical example for each of the 3 classes.
3.3
The Leucine-zipper fold and the TIM-barrel are two of the 10 most abundant protein folds.
Draw both folds schematically and specify to which class of protein folds they belong to.
3.4
How is the solubility of proteins in aqueous environment being realized?
3.5
Briefly describe with a scheme the Protein universe map by S.-H. Kim.
3.6
Sketch an isolated α-helix and an isolated β-strand (with R for side chains) and indicate the
following features. For the α-helix: Where are the main chain hydrogen bonds? In which direction are
the side chains oriented? For the β-strand: In which direction would hydrogen bonds be formed with
additional β-strands (to form β-sheets)? In which direction(s) are the side chains oriented?
4. DIRECTED EVOLUTION OF PROTEINS
4.1
Describe the purpose of protein evolution approaches. What can be achieved?
4.2
Briefly describe, with pictures, the principles of phage display, Ribosome display and mRNA
display. Specify where the protein of interest is displayed.
4.3
Many methods for generating diversity in directed evolution experiments exist. Briefly
describe, with a picture where necessary, the conditions and products of the following two strategies:
1) error-prone PCR and 2) random oligonucleotide mutagenesis / overlap extension PCR. What is the
main difference between the two approaches, in terms of the type of library that is produced?
4.4
Describe, with pictures, the process of DNA shuffling and discuss its importance in generating
DNA libraries.
4.5
To evolve the property of interest, it is extremely important that the appropriate selection or
screen be used in conjunction with large libraries of mutant sequences. Define positive selection and
negative selection.
4.6
Protein evolution is accomplished by first generating an appropriate library of mutants, then
subjecting the library to a selection or screen, then isolating and characterizing the individual mutants
that have the desired new property. We discussed three methods by which the genotype and
phenotype of the library members can be linked during the selection or screen: phage display, mRNA
display, and ribosome display. Choose one method and describe with words or pictures where the
protein of interest and the DNA that codes for it are located.
4.7
Protein evolution is accomplished by first generating an appropriate library of mutants, then
subjecting the library to a selection or screen, then isolating and characterizing the individual mutants
that have the desired new property. Describe one way in which a library can be constructed. Why
might it be beneficial to use DNA shuffling in this process?
4.8
Many methods for generating diversity in directed evolution experiments exist. Briefly
describe, with a picture where necessary, the conditions and products of the following two strategies:
1) error-prone PCR and 2) random oligonucleotide mutagenesis / overlap extension PCR. What is the
main difference between the two approaches, in terms of the type of library that is produced?
4.9
Describe, with pictures, the process of DNA shuffling and discuss its importance in generating
DNA libraries.
4.10
To evolve the property of interest, it is extremely important that the appropriate selection or
screen be used in conjunction with large libraries of mutant sequences. Define positive selection and
negative selection.
5. NONRIBOSOMAL PEPTIDE SYNTHETASES
5.1
What are the characteristic features of nonribosomally synthesized peptides? Know one
example with its structure.
5.2
Describe the steps of the synthesis catalyzed by NRPSs.
5.3
What is the role of Coenzyme A?
5.4
At what step of the synthesis and how is the peptide cyclization carried out?
5.5
Based on the following drawing of a hypothetical three-module nonribosomal peptide synthase
that synthesizes the acyclic peptide Ala-Ala-Ala, answer the following questions. Hint: A is the amino
acid activation domain; T the thiolation domain; C the condensation domain; and Te the thioesterase
domain. Draw the cofactor that is required for the activation of the amino acid in the A domain. To
what molecule is the sulfur atom of the thioesters (drawn above) attached? Draw the first two alanines
with all atoms and show how the first peptide bond is formed (indicate the electrophile and the
nucleophile).
5.6
Nonribosomal peptide synthases are large and complex molecular machinery that
biosynthesize peptides in the absence of a ribosome and mRNA template. In this context, define the
terms “module” and “domain” using words or pictures. Name two common stereochemical or structural
features of peptides produced by these assemblies.
5.7
Outline the key steps in the biosynthesis of the glycopeptide antibiotic vancomycin, and draw
the final product.
6. CARBOHYDRATES
6.1
Describe the steps of the glucose catabolism. What is the detailed mechanism of the ring
cleavage?
6.2
Describe the steps of the citric acid cycle (without detailed mechanisms).
6.3
How are the syntheses paths of purine and pyrimidine nucleotides, fatty acids and steroids
connected to the carbohydrate metabolism?
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6.4
Why can
F-fluorodeoxyglucose be applied in PET imaging?
6.5
What is the mechanism of the CO2 fixation catalyzed by RUBISCO?
6.6
How is glucose stored in the body?
6.7
Glycosyltransferases catalyze the glycosidic linkage completely stereo- and regioselective.
What are the limitations that prevent application for tailor-made molecules in the chemistry lab?
6.8
Suggest a synthesis of a disaccharide with selective cis- and trans- linkage of the glycosidic
bond. Specify the protecting group strategy and the activation method.
6.9
What are reducing and nonreducing ends of complex carbohydrates?
6.10
Why does nature combine several biopolymers (e.g. carbohydrates and proteins) to form more
complex molecules?
6.11
Describe briefly with a picture how glycoproteins are biosynthesized.
6.12
Know four examples (with structure) of monosaccharide building blocks which form the glycan
part of glycoproteins in mammals.
6.13
Based on the Fischer projections given below, show the mechanism of the cleavage of
fructose-1,6-bisphosphate to glycerinaldehyde-3-phosphate (GAP) and dihydroxyacetone phosphate
(DHAP). What is the general chemical term for this reaction?
6.14
Suggest a synthesis of a disaccharide with selective cis (alpha) and trans (beta) linkage of the
glycosidic bond. Specify the protecting group strategy and the activation method.
6.15
Based on the first coupling step of a one-pot oligosaccharide synthetic scheme shown below
(Wong et al., Angew. Chem. Intl. Ed. 2006, 45(17), 2753-2757), draw the product (all atoms, chair
conformation, correct stereochemistry) and indicate which atom is the electrophile and which atom is
the nucleophile in the bond-forming reaction.
6.16
Nucleoside diphosphate monosaccharides are nature’s version of activated glycosylating
agents (sugar donors). Draw the detailed chemical structure of uridine diphosphate glucose, which is
biosynthesized by a glycosyl-1-phosphate nucleotide transferase from the starting materials glucose1-phosphate and UTP.
6.17
Draw the mechanism of the phosphoglucose isomerase‐catalyzed isomerization of
glucose‐6‐phosphate to fructose‐6‐phosphate in the glycolysis pathway of glucose breakdown. Why
is the PET imaging agent 2‐fluoro‐2‐deoxy‐D‐glucose (FDG) unable to undergo isomerization?
6.18
Draw the mechanism of the class‐I aldolase‐catalyzed decomposition of
fructose‐1,6‐bisphosphate to glycerinaldehyde‐3‐phosphate (GAP) and dihydroxyacetone
phosphate (DHAP), and the subsequent tautomerization of DHAP to GAP, steps 4 and 5 of the
glycolysis pathway.
6.19
Nucleoside diphosphate monosaccharides are nature’s version of activated glycosylating
agents (sugar donors), and they are produced by enzymes called glycosyl-1-phosphate nucleotide
transferases from the starting materials monosaccharide-1-phosphate and NTP. Draw the detailed
chemical structures of the starting materials glucose-1-phosphate and UTP and the products UDPglucose and pyrophosphate. What is the driving force for the biosynthesis of the activated sugar? Hint:
think about pyrophosphatases.
6.20
Shown here is a one-pot synthetic strategy used by Wong et al. in a recent paper to produce a
biologically interesting octasaccharide (Angew. Chem Intl. Ed. 2006, 45(17) 2753-2757). Brifely sketch
the retrosynthetic analysis of the product based on their approach.
7. AMINO ACID METABOLISM
7.1
Why are proteins degraded?
7.2
What is specific about lysosomal degradation?
7.3
Describe protein degradation by ubiquitinylation. How is ubiquitin connected to a protein?
7.4
Describe briefly with a picture how proteasomes work. Mark all important subunits.
7.5
How is the transfer of an amino group from an amino acid to alpha-ketoglutarate realized in
the cell? What is the function of PLP in this process? Describe the mechanism of transamination in
detail.
7.6
Why are transaminases being used as biomarkers in clinical diagnosis?
7.7
How does ammonia enter the urea cycle? Describe this reaction with a detailed mechanism.
7.8
Which molecule delivers the second nitrogen atom for urea formation?
7.9
What is the role of arginine?
7.10
How are amino acids classified based on their catabolic pathway?
7.11
How does PLP assist in the dehydration of serine?
7.12
Why is threonine both a glucogenic and ketogenic amino acid? (know reactions and
intermediates)
7.13
Describe the mechanism of the rearrangement of (R)-Methylmalonyl-CoA to Succinyl-CoA.
Which coenzyme is necessary for this reaction?
7.14
Describe the part of the mechanism of the tryptophan-ring cleavage that corresponds to a
Bayer-Villiger-Oxidation.
7.15
Describe the generation of SAM.
7.16
Describe the mechanism of the NIH shift in the formation of tyrosine from phenylalanine.
7.17
Describe the mechanism of aromatic ring cleavage starting from homogentisate to
maleylacetoacetate.
7.18
What is the molecular basis for the metabolic diseases phenylketonuria and alkaptonuria?
7.19
What is the common precursor for arginine and proline?
7.20
Amino acid catabolism is complex because the carbon backbones of the 20 proteinogenic
amino acids are broken down via different pathways and mechanisms. However, the first step in the
catabolism of all 20 amino acids is the same: deamination that is catalyzed by an aminotransferase,
which is dependent upon the cofactor pyridoxalphosphate (PLP). In the first part of the deamination
reaction, pyridoxamine (PMP) and an α-ketoacid are formed from the PLP-Ezyme imine and an amino
acid. Using the figures of the PLP-Enzyme imine and the amino acid alanine (below), draw the
products PMP and the α-ketoacid pyruvate. In the second part of the deamination reaction, PMP must
be restored to the PLP-Enzyme imine for future catalysis of amino acid deamination. If α-ketoglutarate
(shown below) is the α-ketoacid that accepts the amine group of PMP, draw and name the amino acid
that is produced.
7.21
Discuss the mechanism of the NIH-shift with the example of Phenylalanine hydroxylation and
the consecutive steps by which the breakdown of the aromatic ring of Tyrosine is performed.
7.22
Production of the enzymes that catalyze the reactions of the urea cycle can increase or
decrease according to the metabolic needs of the organism. High levels of these enzymes are
associated with high-protein diets as well as starvation. Explain this apparent paradox.
7.23
Draw the amino acid-Schiff base that is formed during the breakdown of 3-hydroxkynurenine
to produce 3-hydroxyanthranilate in the Tryptophan degradation pathway and indicate which bond is
to be cleaved.
8. UNNATURAL NUCLEIC ACIDS, APTAMERS, AND RIBOZYMES
8.1
Explain the concept of LNA-Bases. Draw a structure and specify the structural consequences
of this type of modification. What can be achieved by introducing these derivatives into natural DNA
structures?
8.2
What is the structure of a TNA-Base? Why are they discussed to be the ancestors of RNA?
8.3
What are PNSs and how can they get synthesized in the lab? Explain how these molecules
can be active in antisense strategies.
8.4
Explain the concept of GNAs and draw a general structure. How can you synthesize such
molecules?
8.5
Describe the concept of aptamers. How would you proceed to select an aptamer that binds to
a target of interest?
8.6
What are ribozymes?
8.7
Define the term “RNA aptamer”. Briefly describe in words or pictures how you would proceed
to identify an RNA aptamer that binds to a target of interest.
9. NUCLEIC ACID METABOLISM
9.1
Describe the general catabolic pathway of pyrimidines. What are the intermediates that
connect pyrimidine catabolism with the citric acid cycle and fatty acid biosynthesis?
9.2
How is the reduction of the uridine ring double bond carried out?
9.3
How is the transamination reaction accomplished in the cell? Explain with the example of the
mechanism of the conversion of beta-alanine to malonic acid semialdehyde.
9.4
Describe the general catabolic pathway of purines (no mechanisms). What is the final
molecule that is excreted by mammals?
9.5
What is the main difference between the anabolic pathways of nucleotides?
9.6
Describe with structures what the sources of the ring atoms of purines and pyrimidines are.
9.7
Give the mechanism of the fixation of ammonia by reaction with hydrogencarbonate
(pyrimidine synthesis).
9.8
How is the cyclization to dihydroorotate performed?
9.9
At what step and how is cytidine synthesized from uridine?
9.10
What is the initial step in purine nucleotide biosynthesis?
9.11
Describe the mechanism of the biotin-independent carboxylation step of purine biosynthesis.
9.12
Describe the final cyclization step in purine biosynthesis.
9.13
How are the amino groups transferred to IMP to produce AMP and GMP?
9.14
CDP.
Describe the mechanism of the synthesis of deoxyribonucleotides from ADP, GDP, UDP, and
9.15
Describe briefly how dTDP is synthesized (no mechanism).
9.16
The pyrimidines cytidine, thymidine, and uridine share a common catabolic pathway. Draw the
mechanism of the water-mediated (acidic conditions) deamination of cytidine (shown below) to uridine.
Draw the mechanism of the first step of uridine catabolism, which yields β-ribose-1-phosphate and
uracil, based on the following scheme.
9.17
All deoxyribonucleoside diphosphates (dNDPs) are biosynthesized from the corresponding
ribonucleoside diphosphates (NDPs) by ribonucleotide reductases. Complete the scheme for the thiyl
radical based mechanism of a ribonucleotide reductase, given below (A is acid and B is base), by
drawing all of the necessary arrows that show the movement of single electrons (half-headed arrows)
or pairs of electrons (full-headed arrows).
9.18
Suggest a mechanism for the oxidation of malonic acid semialdehyde to malonyl-CoA, the
final step of uracil catabolism.
9.19
Suggest a mechanism for the biosynthesis of nicotinate mononucleotide from quinolinate.
9.20
Suggest a mechanism for the formylation of glycinamide ribonucleotide, the third step of
inosine biosynthesis.
10. DNA DAMAGE AND REPAIR
10.1
At what positions can DNA be damaged?
10.2
By what mechanisms can DNA molecules be damaged spontaneously?
10.3
Which environmental factors contribute to DNA damage?
10.4
Describe the mechanism for deamination of C to U and describe the consequences of such
change with a picture.
10.5
Describe how strand breakage can occur.
10.6
Which reactive species contribute to oxidative damage?
10.7
Know one example (mechanism) for an oxidative damage process. Know one example of the
tools that have been evolved by organisms to prevent oxidative damage. Which chemicals (structures)
can inhibit oxidative damage processes in the organism?
10.8
What process causes pyrimidine dimer formation?
10.9
Where can alkylating reagents attack DNA? Know one example.
10.10
What is the molecular foundation of cancer treatment using cisplatin?
10.11
Describe the detailed mechanism of the photoreactivation of DNA by photolyase.
10.12
Be able to describe the principle of one of the repair mechanisms BER or NER.
10.13
Mutations in some cases are beneficial for an organism. Explain why.
10.14 Sketch the process of Base Excision Repair of a damaged DNA nucleobase including the
roles of glycosylase, lyase, polymerase, and ligase.
10.15 Various types of DNA damage were discussed in the course. Choose one of the following
products of DNA damage, draw its detailed structure and mechanism of formation, and briefly state
what effects it can have in terms of DNA replication or mutagenesis. Choose one: 1) hypoxanthine
(deamination of adenine), 2) an abasic site leading to strand breakage via β-elimination, or 3) cis-syn
cyclobutadipyrimidine (T-T dimer).
10.16 The first step of Base Excision Repair (BER) is the cleavage of the N-glycosidic bond of the
damaged nucleotide. This reaction is catalyzed by a DNA Glycosylase and is depicted below. Draw
the mechanism (SN1) and the transition state (TS), and explain why the following molecules are good
inhibitors of DNA Glycosylases (three different reasons).
10.17 The subsequent steps of BER (short patch) are as listed below. In each case, please draw the
substrate and the product of the enzyme-catalyzed reaction.
- AP Endonuclease-catalyzed hydrolysis of the phosphodiester bond 5’ to the abasic site (generated
by the DNA Glycosylase in the first step of repair) to produce a nick in the DNA strand.
- DNA Polymerase-catalyzed (template-directed) incorporation of a single nucleotide triphosphate
(what is the nucleophile? what is the electrophile?)
- AP Lyase-catalyzed hydrolysis of the phosphodiester bond 3’ to the abasic site
- DNA Ligase-catalyzed sealing of the nick in the DNA strand
11. EXPANSION OF THE GENETIC ALPHABET AND CODE
11.1
Know structures and Watson-Crick base pairing of natural base pairs.
11.2
What are the requirements for the development of artificial nucleobases? What forces are
usually responsible for forming tight base pairs?
11.3
Describe, with a picture if necessary, how you can determine the properties of a new base
pair. What would be desirable properties and which challenge has not been solved yet in this
technology?
11.4
What are motivations for the incorporation of nonproteinogenic amino acids into proteins?
11.5
Describe the principles of the two strategies (residue-specific and site-specific via cell-free
systems).
11.6
Analogues of nucleobases have been developed that enable stable DNA double helices to
form. The nucleobases F (2,4-difluorotoluene) and Z (4-methylbenzimidazole) form a pair within
double stranded DNA oligonucleotides that has the same shape as an A:T base pair. Draw the A:T
base pair. Draw the F:Z base pair. What intermolecular interactions are responsible for forming a
stable natural base pair? List them and explain the main difference between A:T and F:Z. Why is the
F:Z base pair able to stabilize a DNA duplex?
11.7
In the context of expanding the genetic alphabet, we discussed the importance of
SELECTIVITY of the unnatural nucleobase analogues. SELECTIVITY is the property that enables 1)
the unnatural nucleotide triphosphate dXTP to be incorporated opposite its unnatural partner, dY, in
the DNA template strand by a DNA polymerase more efficiently than opposite all of the natural
nucleotides dN, and 2) more efficiently than all of the natural nucleotide triphosphates, dNTP, against
dY in the template. The same must also be true for dYTP and dX in order for the additional genetic
information to be passed down over generations. Consider a novel unnatural base pair X:X, in which
one novel nucleobase pairs with itself. It was observed that X has a “selectivity problem” in which the
natural nucleotide triphosphate dATP is incorporated opposite dX in the template by a DNA
polymerase as efficiently as is dXTP. It was also observed that dXTP is not readily incorporated
opposite dA in the template. Assume that a double-stranded closed circular sequence of DNA
containing the unnatural X:X pair is introduced into cells, along with the unnatural dXTP. Draw the
consequences of normal DNA replication over two doubling events, and explain why the new genetic
information will be lost over time.
12. STRATEGIES FOR PROTEIN SYNTHESIS (LIGATION, COVALENT MODIFICATION,
LABELING)
12.1
Why is chemical ligation necessary in the laboratory synthesis of large proteins?
12.2
Name two ways in which the smaller fragments of a large protein can be obtained (in vitro and
in vivo).
12.3
Draw the mechanism of the native chemical ligation (thioester can be indicated with SR),
which results in a native peptide bond.
12.4
If the protein of interest does not contain cystein residues, but contains an alanine near the
middle of the sequence, how can one make use of mutagenesis, the native chemical ligation, and a
desulfurization protocol to synthesize the protein? On the other hand, if a new peptide bond is to be
introduced between a Gly residue and a Gln residue, what approach would be necessary?
12.5
Name two types of modifications that can be chemically introduced into proteins, and why they
would be interesting to synthesize and study further.
12.6
The Staudinger reaction has been a very useful tool in the chemoselective modification of
azido-proteins. Based on the structures of given starting materials, be prepared to draw the
mechanism of the Staudinger ligation with phosphine and the Staudinger ligation with phosphite.
12.7
Be prepared to draw a brief mechanism of a copper-free Click reaction between an azide and
an alkyne (starting materials will be given). How can this reaction be used to image living cells (no
chemical structures must be drawn)?
12.8
The SNAP-Tag is a useful strategy for introducing nonnatural functional groups into proteins.
Briefly describe what this concept is based on (mention fusion protein and enzyme activity in your
description).
12.9
Briefly describe (in words) how the GFP chromophore is formed (in nature).
12.10 “Caging” and “uncaging” is a method for “inactivating” and “activating”, respectively, a
biologically active molecule by means of a photocleavable group, commonly an o-nitrobenzyl moiety
attached to a heteroatom of the molecule of interest. Draw the o-nitrobenzyl caged molecule XR
(where X is any heteroatom and the R represents the rest of the biomolecule) and the products of
photolysis (hint: nitroso aldehyde).
12.11 One strategy for covalently coupling two peptide or protein fragments is the Native Chemical
Ligation (NCL) using an N-terminal thioester and a C-terminal cystein. If the protein of interest does
not contain cystein residues, name or draw a picture of one alternative strategy that can be used to
join two fragments of this protein, and whether the strategy will work with any C-terminal and Nterminal amino acid or is restricted to a specific subset of amino acids.
12.12 Some current topics in bioorganic chemistry relate to new methods for labeling proteins with
fluorophores or small molecules, like biotin, in vitro or in vivo. Write a brief description OR draw a
cartoon that shows how either the ”SNAP-tag” or “proximity biotinylation” can be used to label a
protein (choose one).
12.13 Below is a scheme from a recent paper from the Bertozzi lab (PNAS 2010, 107(5), 18211826). An azido derivative of mannose was injected into mice, followed by a FLAG tag-labelled
cyclooctyne. Briefly respond to the following points.
A) Where does the mannose derivative end up in the cell?
B) Draw the copper-free click chemistry reaction between the azide group and the cyclooctyne.
C) Why is this reaction thermodynamically favorable (enough to proceed in the absence of copper)?
13. TRIGLYCERIDE METABOLISM AND FATTY ACID BIOSYNTHESIS
13.1
Draw an example of a triglyceride and label the glycerin and fatty acid components.
13.2
What is the first step of triglyceride catabolism?
13.3
How are triglycerides “packaged” as they travel through the bloodstream on their way to
muscle or fat tissues? Why is this necessary?
13.4
Given the structure of myristoyl-CoA, indicate in what order (1 being the first, 6 and 7 being
the last two) the C2 units are removed, as acetyl-CoA molecules, over six rounds of β-oxidation.
13.5
Name the four chemical transformations that a fatty acid-CoA undergoes in one round of βoxidation.
13.6
Draw the product of the Claisen condensation between the following two thioesters (given).
13.7
Draw the products of the retro-Claisen condensation of the following β-ketothioester (given).
13.8
Draw a cartoon of the multienzyme complex that synthesizes fatty acids in mammals, and
draw an acetyl group attached to a synthase and a malonyl group attached to acyl carrier protein.
13.9
By which type of chemical bond are both groups anchored to the complex? Which group is
linked via a cystein side chain, and which via a “prosthetic” group? What is the “prosthetic” group
called (abbreviation OK)?
13.10 Assume that acetyl-synthase and malonyl-ACP have reacted to yield acetoacetyl-ACP. Which
carbon atoms in the product come from acetyl, and which from malonyl? What happened to the fifth
carbon atom (counting carbon atoms in the starting materials)?
13.11 Name the three chemical transformations that acetoacetyl-ACP undergoes in the biosynthesis
of butyryl-ACP.
13.12 Once butyryl-ACP has been formed, it must undergo additional rounds of chain elongation. To
what part of the multienzyme complex is the butyryl acid bound as it reacts with malonyl-ACP to yield
a C6 fatty acid product?
13.13 The key step in fatty acid biosynthesis is the Claisen condensation between a synthase-bound
electrophilic acceptor and an acyl-carrier protein-bound nucleophilic donor. Complete the following
biosynthetic scheme by drawing all necessary arrows that show electron movement, indicating what
byproduct is evolved, and drawing the tetrahedral intermediate.
13.14 The key transformations in the catabolism (β-oxidation) and biosynthesis of fatty acids are a
retro-Claisen condensation and a Claisen condensation, respectively, by which C2 units are separated
or joined. Starting from the following drawing, complete the mechanism of the retro-Claisen
condensation.
13.15 Regarding the Claisen condensation in fatty acid biosynthesis, briefly sketch the mechanism
by which acetyl-Synthase and malonyl-ACP react to yield free synthase and acetoacetyl-ACP. How is
the decarboxylation like a retro-Aldol reaction? What feature of the malonyl group facilitates
decarboxylation?
13.16 Draw the following transthioesterifications:
a) acetyl-CoA to acetyl-ACP
b) acetyl-ACP to acetyl-Synthase
14. TERPENES AND STEROIDS
14.1
Draw isopentenyldiphosphate (IPP).
14.2
What are the four chemical transformations in the biosynthesis of IPP (mevalonate pathway)?
How many molecules of acetyl-CoA are needed? How is the formation of acetoacetyl-CoA different in
this pathway than in the fatty acid synthesis pathway? Why are only five carbon atoms present in IPP
when six carbon atoms are provided by acetyl-CoA (what happens to the sixth carbon atom)?
14.3
Draw the mechanism of the isomerization of IPP to dimethylallyldiphosphate (DMAPP,
structure will be given).
14.4
Assume IPP and DMAPP have reacted to yield geranyldiphosphate (GPP, given). Which
carbon atoms in the product come from IPP, and which from DMAPP? Does the diphosphate in the
product come from IPP or DMAPP?
14.5
Draw the reaction (no detailed mechanism) by which GPP is extended to farnesyldiphosphate
(FPP).
14.6
Two molecules of FPP dimerize to yield squalene (C30) via a cyclopropane intermediate
called presqualenediphosphate.
14.7
Squalene must first undergo what chemical transformation to yield lanosterol, the precursor
from which all steroids are synthesized.
14.8
Sketch the molecular scaffold of all steroids (line structure, no hydrogens or methyls must be
drawn) and label rings A, B, C, and D.
15. LIPIDATED PROTEINS
15.1
Consider a living cell. Where are lipoproteins found? Name one biological process in which
lipoproteins are involved.
15.2
One type of posttranslational modification of proteins is lipidation. Draw the starting molecule
from which fatty acids are synthesized in living cells. Draw the starting molecule from which terpenoids
are synthesized in living cells. Why must strong acid- and H2-labile protecting groups be avoided in
lipopeptide synthesis in the lab? To what part of the cell are lipoproteins localized? Briefly state why.
16. GENERAL CONCEPTS
16.1
By means of what molecule does the cell produce and consume energy?
16.2
Enzymes use amino acid side chains, cofactors, and coenzymes to carry out chemical
transformations. Which amino acid side chains can act as a general base? Which can act as a general
acid? Name and draw one example for each.
16.3
How can mutation be beneficial to an organism?
16.4
How do enzymes accelerate reaction rates?
16.5
Why is a transition state analogue often a good inhibitor of an enzyme?
16.6
Name two distinct ways in which metal ions participate in enzyme-catalyzed reactions.
16.7
Name the coenzyme that typically participates in the reduction of an alcohol to an aldehyde or
ketone, and one coenzyme that can donate a single carbon building block (methyl, methylene, or
formyl group) to its substrate.