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medical sciences
biochemistry

Questions and Answers of Biochemistry

Draw the chemical structures for the products of transamination reactions involving α- ketoglutarate and (a) Threonine, (b) Isoleucine, and (c) Glycine?
What is the advantage of channeling? Why is it especially important for indole in the tryptophan synthase reaction?
How many carbons of heme would be labeled with 14C if the starting material included (a) glycine with a 14C-labeled carboxyl group and (b) succinyl-CoA with a 14C-labeled carboxyl group?
In what form is PLP found in aminotransferases prior to reacting with an amino acid? In what form is this coenzyme found after the release of the α-keto acid?
Aminotransferase reactions occur via a Ping Pong mechanism (see p. 367.) Use Cleland notation to describe the reaction shown in Figure 21-8, including substrates, intermediates, and products?
In which direction would you expect flux through the glutamate dehydrogenase reaction in starved individuals? Why?
Write the overall equation for the formation of urea. What is the total free energy cost (in terms of "high-energy" phosphoanhydride bonds) per mole of urea synthesized?
Complete the diagram below, which shows the flux of alanine's amino group from its entry into the liver to its exit as urea.
Helicobacter pylori, the bacterium responsible for gastric ulcers, can survive in the stomach (where the pH is as low as 1.5) in part because it synthesizes large amounts of the enzyme urease. (a)
Which of the 20 "standard" amino acids are (a) Purely glucogenic, (b) Purely ketogenic, and (c) Both glucogenic and ketogenic?
Unlike the other 19 standard amino acids, lysine does not undergo transamination. What is the fate of its α and ε-amino groups when it is catabolized?
Compare the ATP yield for the complete oxidation of glutamate and methionine, both of which contain five carbons atoms, to CO2.
In the degradation pathway for isoleucine, draw the reactions that convert tiglyl-CoA to acetyl-CoA and propionyl-CoA.
Draw the amino acid-Schiff base that forms in the breakdown of 3-hydroxykynurenine to yield 3-hydroxyanthranilate in the tryptophan degradation pathway (Fig. 21-23, Reaction 4) and indicate which
Tyrosine and cysteine are listed as nonessential amino acids, but an inadequate diet may cause tyrosine and/or cysteine insufficiency. Explain.
Compile a list of all the cofactors involved in adding or removing one-carbon groups in carbohydrate, lipid, and amino acid metabolism. Provide an example of a reaction that uses each cofactor.
What are the metabolic consequences of a defective uridylylremoving enzyme in E. coli?
One of the symptoms of kwashiorkor, the dietary protein deficiency disease in children, is the depigmentation of the skin and hair. Explain the biochemical basis of this symptom.
Explain why protein degradation by proteasomes requires ATP even though proteolysis is an exergonic process.
The compound shown here inhibits an archaebacterial proteasome, binding to each of its active sites, which (unlike those of eukaryotic proteasomes) are all identical. What can you conclude about the
Explain why it was advantageous for human ancestors to evolve a taste receptor for glutamate.
Explain why the symptoms of a partial deficiency in a urea cycle enzyme can be attenuated by a low-protein diet.
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
(a) How many ATP equivalents are consumed by the reactions of the urea cycle? (b) Operation of the urea cycle actually generates more ATP than it consumes. Explain.
List the possible products of acetyl-CoA metabolism in animals. Include the pathway involved and, where appropriate, the key regulatory enzyme that commits acetyl-CoA to that pathway.
Which glucose transporter (GLUT2 or GLUT4) would you expect to find in the insulinsecreting β-islet cells of the pancreas? Provide a rationale?
Why does AMPK respond to AMP and ATP instead of ADP and ATP?
Fill in the following table with the effects of AMPK in cardiac muscle, skeletal muscle, liver, and adipose tissue. What general metabolic flux is favored by the activities of AMPK in these
Which hormones regulate the production of the appetite-stimulating hormone neuropeptide Y? Which acts as a long-term regulator? Which is a short-term regulator?
You obtain a liver homogenate from a fasting mouse and "spike" it with a high concentration of glucose. In what form would you expect glycogen phosphorylase?
During a fast to lose weight, is it important to be physically active or might it be better to remain sedentary? Explain.
List the metabolic products of pyruvate metabolism in animals. Include the pathway involved and, where appropriate, the key regulatory enzyme that commits pyruvate to that pathway. Fate Pathway
List the metabolic products of glucose-6-phosphate metabolism. Include the pathway involved and the key regulatory enzymes.Fate Pathway Key Enzyme1.2.3.4.
Match the metabolic pathways below with the cellular compartments in which they occur. A. Cytosol B. Inner mitochondrial membrane C. Mitochondrial matrix D. Mitochondrial intermembrane space E.
Match the metabolic function below with the appropriate pathway(s). A. Glycolysis B. Pentose phosphate pathway C. Gluconeogenesis D. Fatty acid oxidation E. Glycogen synthesis F. Amino acid
What is the significance of high levels of hexokinase activity in the brain?
What similarities are shared by the Cori cycle and the glucose-alanine cycle? What distinguishes them?
Muscle phosphofructokinase is allosterically stimulated by NH4+. What is the physiological function of this stimulation?
How does an increase in blood glucose affect triacylglycerol metabolism in adipocytes?
Why does oxidative metabolism, which generates ATP, cease when a cell's ATP supply is exhausted?
(a) Identify the two reactions that allow the kidney to produce NH4+. (b) Which gluconeogenic precursor is thereby generated? Describe the pathway by which it can be converted to glucose.
Fatty acids appear to stimulate insulin secretion to a much greater extent when glucose is also present. Why is this significant?
Would you expect insulin to increase or decrease the activity of the enzyme ATP-citrate lyase?
Individuals with a deficiency of medium chain acyl-CoA dehydrogenase (MCAD) tend to develop nonketotic hypoglycemia. Explain why this defect makes them unable to undertake (a) Ketogenesisand (b)
Experienced runners know that it is poor practice to ingest large amounts of glucose immediately before running a marathon. What is the metabolic basis for this apparent paradox?
After several days of starvation, the capacity of the liver to metabolize acetyl-CoA via the citric acid cycle is greatly diminished. Explain.
Explain why type 1 diabetics require insulin injections, whereas insulin injections are effective in only a portion of type 2 diabetics.
AMPK activates phosphofructokinase-2. Explain how this would contribute to the antidiabetic effect of stimulating AMPK activity.
Discuss, in molecular terms, how physical inactivity might lead to insulin resistance.
Many cancer cells generate ATP primarily by glycolysis, an anaerobic pathway, even when O2 is available (this phenomenon was first noted by Otto Warburg in 1924). Explain how a high flux of carbon
Adaptation to high altitude includes increases in GLUT1 and phosphofructokinase in muscle. Explain why this would be advantageous.
The heart cannot convert lactate back to glucose, as the liver does, but instead uses it as a fuel. What is the ATP yield from the complete catabolism of one mole of lactate?
The passive glucose transporter, called GLUT1 (Fig. 10-13), is present in the membranes of many cells, but not in the liver. Instead, liver cells express the GLUT2 transporter, which exhibits
Use the results of Problem 7 to explain why a deficiency of GLUT2 produces symptoms resembling those of Type 1 glycogen storage disease (Box 16-2).
The small intestine catabolizes amino acids, producing significant amounts of NH4+. Describe the metabolic fate of the NH4+
Why is 5-fluorouracil a powerful antitumor agent? Why is it considered a suicide substrate?
What is the rationale for administering a high dose of methotrexate followed by a massive amount of N5-formyltetrahydrofolate and thymidine to a cancer patient?
Adenosine deaminase (ADA) catalyzes the first step in the catabolism of adenine nucleotides. Why does an absence of ADA seriously compromise the immune system?
Summarize the metabolic pathway by which 14C initially present at position 5 of uracil could appear in long-chain fatty acids?
Some terrestrial organisms secrete excess nitrogen as uric acid rather than urea. Why is this an advantage?
In most tissues, most purine bases have been salvaged rather than synthesized de novo. What is the advantage of this metabolic strategy?
In what way is UMP synthesis similar to fatty acid synthesis in mammals?
Why is the administration of uridine an effective treatment for human orotic aciduria? Why is it preferable to use uridine instead of UMP?
Mouse embryonic stem cells divide extremely rapidly, about once every 5 hours. These cells require large amounts of threonine in their medium. Explain how threonine catabolism (Fig. 21-14) helps meet
Normal cells die in a nutrient medium containing thymidine and methotrexate, whereas mutant cells defective in thymidylate synthase survive and grow. Explain.
Some microorganisms lack DHFR activity, but their thymidylate synthase has an FAD cofactor. What is the function of the FAD?
Why is it important that muscle cells have low levels of glutamate dehydrogenase?
Why does von Gierke's glycogen storage disease (Box 16-2) cause symptoms of gout?
Describe how the fumarate produced by the purine nucleotide cycle could be catabolized to CO2.
Calculate the ATP yield of converting the carbons of thymine to CO2.
Individuals with a partial deficiency of dihydropyrimidine dehydrogenase experience severe toxic effects when given high doses of the anticancer drug 5-fluorouracil. Explain.
In animals, one pathway for NAD+ synthesis begins with nicotinamide. Draw the structures generated by the reactions shown.
In the synthesis of FAD, riboflavin is phosphorylated by a kinase to form FMN (Fig. 18-10). The FMN then reacts with ATP. How many "high-energy" bonds are broken in this process?
Certain glutamine analogs irreversibly inactivate enzymes that bind glutamine. Identify the nucleotide biosynthetic intermediates that accumulate in the presence of those compounds.
Rats are given cytidine that is 14C-labeled at both its base and ribose components. Their DNA is then extracted and degraded with nucleases. Describe the labeling pattern of the recovered
Why does it make metabolic sense for UTP to inhibit carbamoyl phosphate synthetase II, whereas ATP activates the enzyme?
Why does it make metabolic sense for ADP and GDP to inhibit ribose phosphate pyrophosphokinase?
Explain why hydroxyurea, which destroys tyrosyl radicals, is useful as an antitumor agent.
What form of DNA might you expect to see in desiccated (but viable!) brine shrimp eggs? Why?
Ice-cold ethanol is used to precipitate DNA. What is the significance of the temperature of the ethanol? Is this more important for shorter or longer DNA strands?
Samples of a circular plasmid are incubated with increasing concentrations of ethidium bromide and then analyzed on an agarose gel. Which gel below shows the results of this procedure?
Specific DNA-binding proteins mainly contact DNA through hydrogen bonds in the major groove of B-DNA. (a) Why might sequence-specific binding be more common in the major groove than in the minor
In what ways do HTH proteins and the met repressor represent two general modes of DNA-protein interaction?
Is histone H1 present in the electron micrograph shown in Figure 24-41? What is the relationship of H1 to the nucleosome structure?
Double-stranded DNA is relatively stiff, whereas single-stranded DNA is a flexible coil. What factors influence the structure of single-stranded versus double-stranded DNA?
How does the ribose pucker affect DNA structure?
A sample of a circular plasmid is digested with Type IA topoisomerase and analyzed by agarose gel electrophoresis followed by staining with ethidium bromide. Fifteen bands of DNA are visible. What do
High concentrations of denaturing agents such as urea or formamide (HCONH2) tend to favor a rodlike conformation for single-stranded DNA, rather than a flexible coil. What molecular interactions
Explain how the following affect the Tm of double-stranded DNA: (a) Increasing the monovalent salt concetration. (b) Decreasing the pH. (c) Increasing the pH. (d) Increasing the concentration of
Unusual bases and non-Watson-Crick base pairs frequently appear in tRNA molecules. Which base is most likely to pair with hypoxanthine (Section 23-1)? Draw this base pair.
The asterisk in the structure shown in Problem 9 indicates the site where the base is attached via a two-carbon linker. Compare the overall backbone length for a PNA and a DNA molecule and explain
Which of the DNAs shown in Figure would move fastest during agarose gel electrophoresis?
When the helix axis of a closed circular duplex DNA of 2310 bp is constrained to lie in a plane, the DNA has a twist (T) of 207. When released, the DNA takes up its normal twist of 10.5 bp per turn.
A closed circular duplex DNA has a 100-bp segment of alternating C and G residues. On transfer to a high salt solution, the segment undergoes a transition from the B conformation to the Z
Compare the melting temperature of a 1-kb segment of DNA containing 20% A residues to that of a 1-kb segment containing 30% A residues under the same conditions.
The melting curve for the polyribonucleotide poly(A) is shown below.(a) Explain why absorbance increases with increasing temperature.(b) Why does the shape of the curve differ from the one shown in
Draw the structure of a G ∙ U base pair.
In addition to the standard base-paired helical structures (e.g., Fig. 24-2), DNA can form X-shaped hairpin structures called cruciforms in which most bases are involved in Watson-Crick pairs. Such
E. coli ribosomes contain three RNA molecules named for their sedimentation behavior: 5S, 16S, and 23S. Draw a diagram showing the approximate positions of the three RNA species following
Mouse genomic DNA is treated with a restriction endonuclease and electrophoresed in an agarose gel. A radioactive probe made from the human gene rxr-1 is used to perform a Southern blot. The

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