BIOC 385
Excess exposure to ultraviolet light can cause DNA damage because of
produces photoproducts
On exposure to insulin, the liver responds by upregulating __________, which in turn causes the upregulation of __________.
protein phosphatase 2A; acetyl-CoA carboxylase
A Holliday junction can best be defined as a region of
quadruplex DNA
Inhibition of the COX-1 enzyme results in ______________ .
reduced mucin secretion in the stomach
The spliceosome ___________.
resembles group 2 introns in its mechanism and product
What is the function of telomerase in termination of DNA synthesis?
reverse transcription of the telomeres
The lipase-mediated release of fatty acids can always be expected to occur when a person is ___________ and ___________. (Choose the best two answers)
running from a bear and hungry after school
In comparison with glycerophospholipids, the structure of cerebrosides contains ________ .
sphingosine
Order the following lipids, from highest to lowest, in terms of melting point.
stearate 18:0 palmitate 16:0 myristate 14:0 linoleate (cis) 18:2 arachidonate (cis) 20:4
Glucagon-like peptide-1 (GLP-1) is a hormone secreted by intestinal cells in response to nutrient detection in the small intestine. The resulting physiological response is the lowering of blood glucose levels. Which of the following is a potential mechanism for how GLP-1 signaling leads to lower blood glucose?
stimulation of insulin release by pancreatic beta cells
Glucagon-like peptide-1 (GLP-1) is a hormone peptide secreted by intestinal L cells. It is secreted in response to the nutrient detection in the small intestine. The resulting physiological response is the lowering of blood glucose levels. Which of the following is a potential mechanism for how GLP-1 causes this physiological response?
stimulation of insulin release by pancreatic-beta cells
Unlike most eukaryotes, prokaryotes make polycistronic mRNAs. These polycistronic mRNAs encode more than one protein. In order to properly synthesize all of the encoded proteins, these prokaryotic polycistronic mRNAs must duplicate which mRNA components?
stop codon and the Shine-Dalgarno sequence
What molecule is the odd chain fatty acid product propionyl-CoA converted into?
succinylcholine-CoA
In the figure below of the E. coli ribonucleotide reductase enzyme, which amino acid is important in the R2 subunit?
tyrosine
Which of the following are common posttranslational modifications of proteins in cells?
ubiquitination methylation acetylation palmitoylation phosphorylation
Plants assimilate nitrogen and synthesize all 20 amino acids, whereas animals only synthesize about 10 amino acids and obtain the other 10 from their diet. Farmers can use an herbicide to kill weeds that is based on inhibiting a pathway in all plants that is required for the synthesis of several essential amino acids. Importantly, this same pathway is not present in animals. Would it be a good idea to use this herbicide to kill weeds (a) in a botanical garden containing prized orchids?, (b) inside a horse corral containing poisonous milkweed plant?, and (c) in a garden pond containing frogs and turtles that depend on fish that feed on plants? Answer yes or no to each question.
No, Yes, No
What are four key biochemical characteristics that differentiate the fatty acid oxidation pathway from the fatty acid synthesis pathway?
(1) Subcellular location of the pathways, (2) distinct enzymes in each pathway, (3) use of NADH or NADPH, (4) reduction versus oxidation reactions
How would you describe your liver glycogen synthase after 24 hours without food with regard to: a) its R/T conformational equilibrium, b) its enzymatic activity, and c) its phosphorylation state?
(a) Mostly in the T state, (b) inactive, (c) phosphorylated
The spliceosome is composed of five ribonucleoproteins, each of which has a specific role in the splicing process. Different combinations of these proteins are associated with different stages of the splicing reaction. Place the snRNP complexes listed into their appropriate stage in the splicing reaction. Each stage should contain only a single combination of proteins.
- Pre-spliceosome: U1 and U2 - precatalytic: U1, U2, U4, U5 and U6 -Active spliceosome: U2, U5, and U6
Bacterial promoters contain two conserved promoter elements. The -35 box (5'-TTGACA-3') is located 15-17 bp upstream of the -10 box (5'-TATAAT-3'). Consider two housekeeping genes in E. coli. The table below lists the sequences found at the -35 and -10 positions in the promoter regions of these two genes. What conclusions can be drawn from this information?
-Gene A has a weaker promoter than Gene B. -Gene A will have a lower rate of transcription initiation than Gene B.
How does depletion of liver glycogen stores during starvation lead to a shift from glucose utilization to fatty acid oxidation as an energy source for most tissues?
-Glucagon activates hormone-sensitive lipase. -Lack of liver glycogen stores results in a drop in serum glucose concentration. -Lack of insulin signaling reduces GLUT4 translocation.
Undiagnosed phenylketonuria (PKU) can lead to severe neuronal damage and mental incapacity, which is avoidable if the disease is diagnosed at birth. In contrast, albinism is easly diagnosed at birth, but there is no treatment, which leads to an increased risk of skin cancer in these patients. Choose the three statements that BEST explain the reasons for these differences.
-PKU is the result of substrate accumulation, which can be avoided using a restricted diet. However, albinism is due to a missing product, which cannot be replaced through injections or dietary regimens. -Defects in the enzyme tyrosinase occur in every cell of the body and there is no way to replace this enzyme without embryonic human gene therapy. In contrast, defects in the enzyme phenylalanine hydroxylase can be ameliorated by restricting certain amino acids in the diet. -Phenylalanine is found in many types of food, including aspartame, and therefore by avoiding foods with high amounts of phenylalanine, the build-up pyruvate metabolites can be controlled. In contrast, skin pigments must be made from tyrosine and there is no way to do this if tyrosine metabolism is compromised.
Sort the descriptions below to indicate whether they describe β oxidation of stearoyl-CoA, oleoyl-CoA, or both.
-Stearoyl-CoA: 8 FAD reduced -Oleoyl-CoA: 7 FAD reduced; requires enol-CoA -Both: 8 NAD+ reduced; beta-oxidation completed in 8 rounds; 9 acetyl-CoA produced
How does the cell regulate the substrate specificity of ribonucleotide reductase to maintain equal amounts of all four deoxynucleoside triphosphates (dNTPs)?
-When dTTP is bound to the specificity site, more dGDP is produced. -When dGTP is bound to the specificity site, more dADP is produced.
Which of the following are regulatory mechanisms that exist to prevent futile cycling in lipid metabolism?
-citrate activation of acetyl-CoA carboxylase -malonyl-CoA inhibition of CPT1 -AMPK phosphorylation of acetyl-CoA carboxylase -fatty acyl-CoA inhibition of acetyl-CoA carboxylase
Sort the amino acids as to whether they are considered essential or nonessential amino acids in humans. Drag the amino acid name into the appropriate bin.
-essential: valine, threonine, lysine -nonessential: glycine, cysteine
Which two statements below accurately describe the roles of insulin and glucagon in maintaining metabolic homeostasis?
-insulin stimulates glucose uptake in muscle cells -glucagon increases blood glucose levels in between meals
What two nucleic acid bases are represented by the structures (1) and (2) shown below?
1 - cytosine 2 - uracil
A variety of energy stores are available for ATP production during exercise. Rank these fuel sources in the order that they would be used in the muscle during a long run (i.e., 10 K or more).
1 - muscle ATP 2 - muscle phosphocreatine 3 - muscle glycogen 4 - fatty acids from adipose tissue
Based on the figure below, cleavage followed by rejoining at which sites would lead to no recombination or loss of genetic information? (Holliday junction)
1 and 3 ( horizontal ones)
Phenylketonuria is caused by a defect in the enzyme phenylalanine hydroxylase (1) / phenylalanine aminotransferase (2). The symptoms of the disorder are caused by substrate accumulation (3) / lack of product (4) and can be treated by diet which limits phenylalanine (5) / tyrosine (6). Albinism is characterized by white skin and hair due to a defect in the enzyme arginase (7) / tyrosinase (8) and is characterized by a substrate accumulation (9) / lack of product (10) mechanism.
1, 3, 5, 8, 10
Which FIVE of the following gene variants are good candidates to function as Thrifty Genes? 1) Acetyl-CoA carboxylase with high affinity for citrate 2) Glucokinase with increased affinity for glucose 3) Decreased catalytic activity of fatty acyl-CoA synthetase 4) Fructokinase with increased affinity for fructose 5) Acetyl-CoA carboxylase with low affinity for palmitoyl-CoA 6) Gherlin mutant with a low affinity for the ghrelin receptor 7) Decreased catalytic activity of fatty acid synthase 8) High basal level expression of Uncoupling Protein 1 9) Low activity lipoprotein lipase on the membrane of adipocytes
1, 4, 2, 5, 3
Glycogen metabolism is regulated by both allosteric control and covalent modification. Circle the best underlined words describing glycogen regulation and record the number. (Muscle glycogen phosphorylase is allosterically (1) activated / (2) inactivated by low energy charge in the cell and is also (3) inhibited / (4) activated by AMP binding. Moreover, binding of glucose-6P (5) inhibits / (6) activates muscle glycogen phosphorylase activity. Liver glycogen phosphorylase activity is (7) decreased / (8) increased by glucose binding, thereby shifting the phosphorylated form of the enzyme into the (9) T state / (10) R state until the enzyme can be (11) dephosphorylated / (12) phosphorylated by insulin signaling.)
1, 4, 5, 7, 9, 11
1. Lynch syndrome is due to an inherited autosomal dominant mutation of one of a handful of genes, including the human mismatch repair gene hMLH1. What is the probability that a man with this mutation and Lynch syndrome and a woman without Lynch syndrome will have two Lynch syndrome children? (The man's mother did not have Lynch syndrome.) 2. Individuals with this mutation have a(n) ---- risk of cancer at some point in their lives compared to individuals with two normal hMLH1 genes.
1. 25% 2. greater
1. Observe the molecular structure of resolvase. Remove the nucleic acid component by clicking the black-outlined boxes for "c (nucl)," "d (nucl)," and "f (nucl)" at the bottom of the player screen under the molecule.Which of the following best describe(s) this enzyme? 2. Restore the molecule to its original view (dropdown menu → Reload Project). Consider the active site of resolvase by observing the interaction between resolvase and DNA.The resolvase active site contains an amino acid with which of the following? 3. Resolvase activity will act upon --- and will generate which of the following? 4.
1. Resolvase is considered to be a homodimer.; Resolvase contains α helices and antiparallel β sheets. 2. side-chain hydroxyl that reacts with a phosphate group of the substrate 3. Holiday 4. either recombinant or nonrecombinant nucleic acid
How many ATPs are obtained from the complete -oxidation of one mole of stearoyl-CoA (18Cs) compared with three molecules of glucose (3 6C = 18Cs)?
120 vs 90
What is the correct order of the following steps to synthesize new DNA?
1. conversion of dsDNA to ssDNA 2. addition of an RNA primer 3. extension of the RNA primer 4. synthesize new DNA
The thymidylate synthase reaction is a linear pathway in E. coli that leads to dTTP production. Rank the following in order of enzymatic activity from earlier to later in the linear pathway of dUTP conversion to dTTP.
1. dUTP diphosphohydrolase 2. Thymidylate synthase 3. thymidylate kinase 4. nucleoside diphosphate kinase
1. BRCA1 and BRCA2 genes have been linked to a series of cancers. The gene product of BRCA1 and BRCA2 is involved in which of the following? 2. Which of the following statements best associates the BRCA genes, protein products, and their involvement in cancer?
1. double-strand DNA break repair 2. The BRCA proteins are found within the nucleoplasm and are encoded by tumor suppressor genes.
1. Examine the ribbon structure of the TATA binding protein without DNA ligand. To do this, isolate just the protein by clicking the black-outlined boxes next to "b (nucl)" and "c (nucl)" to remove them from display. Which of the following are consistent with the secondary structures that are observed? 2. What four amino acid side chains are integral to the DNA binding function of the TATA binding protein? 3. This DNA binding protein associates with --- DNA sequence --- a protein-coding sequence of DNA. If the TATAAA sequence were altered to AGGCTA, then that change would likely result in --- in the rate of transcription at this gene locus
1. one large β sheet and four α helices 2. four phenylalanine residue side chains 3. eukaryotic; upstream of; a decrease
1. Lynch syndrome is caused by inherited autosomal dominant mutation in one of several human mismatch repair genes, such as hMLH1. Which of the following best describes these patients and the condition(s) that they most likely experience? 2. For patients with Lynch syndrome, why might some cancers, like colon cancer, be more prevalent than others, like brain cancer?
1. significantly elevated levels of colon, stomach, ovarian, and uterine cancer 2. Cells of the epithelia replicate at a faster rate than neurons and that correlates with these cancers.
The conversion of 7-dehydrocholesterol to 1,25-hydroxyvitamin D3 involves all of the following EXCEPT
11β-hydroxylase
How many acetyl-CoAs per ketone body are delivered to cells in need of energy?
2
How many ATP are required to incorporate a dietary glucose molecule into liver glycogen?
2 ATP; 1 ATP to generate glucose-6-P, and 1 ATP to regenerate UTP for glycogen synthesis
How many total NADH + FADH2s are made in the -oxidation pathway from the breakdown of the following fatty acid to all acetyl-CoAs?
4
Two reduced plastoquinol molecules (PQBH2) are oxidized in the PQ cycle for every 2 H2O that are oxidized by the oxygen evolving complex (OEC). How many protons are translocated into the thylakoid lumen by the PQ cycle?
4 protons
In an iteration of the Nirenberg-Leder experiment to assign triplet codons to specific amino acids, radioactively labeled aminoacyl-tRNA with the anticodon of 3'-CUG-5' was retained on the filter at the end of the experiment. Which mRNA was used in this iteration of the experiment?
5'-GAC-3'
Put the correct steps required for absorption of dietary fats into order from a à f. a. Step ___ Export of lipoprotein particle b. Step ___ Emulsification of fats c. Step ___ Entry into the circulatory system d. Step ___ Intracellular synthesis of triacylglycerols e. Step ___ Lipase cleavage f. Step ___ Chylomicron assembly
5, 1, 6, 3, 2, 4
How many passes through the fatty acid oxidation pathway are required to degrade palmitic acid?
7
How many moles of acetyl-CoA, FADH2 and NADH are generated by beta-oxidation of one mole of the fatty acid myristate?
7 acetyl-CoA and 6 FADH2/NADH
Considering that 1 mol of H2O is generated in each round of fatty acid synthesis during step 3 (dehydration), and that 1 mol of H2O is required for the thiolase reaction to release the fatty acid, how many net moles of H2O are generated in the synthesis of 1 mole of stearate (C18)?
7 moles of H2O
What are the total number of moles of Acetyl CoA, NADH, and FADH2 resulting from the complete oxidation of one mole of a fatty acid with the molecular formula C18H35O2 , and what is its common name?
9 Acetyl CoA, 8 NADH, 8 FADH2; stearate
The net fatty acid synthesis reaction for stearate (C18) is (fill in the blanks): ___Acetyl CoA + ___ATP + ___NADPH + ___ H+ à stearate + ___ CoA + ___ ADP + ___ Pi + ___ NADP+ + 7 H2O
9, 8, 16, 16, 9, 8, 8, 16
A continual supply of reduced glutathione is required to protect red blood cells against the toxic effects of vicine, which is found at high levels in fava beans. Why would individuals with a defect in the enzyme glucose 6-phosphate dehydrogenase (G6PDH) be susceptible to vicine-induced hemolytic anemia?
A G6PDH deficiency leads to insufficient NADPH to protect against vicine-induced anemia.
A)How many NAD+ and FAD are reduced in each round of mitochondrial fatty acid β oxidation? B)How many NADH and FADH2 would be produced from β oxidation of a 20C saturated fatty acid to acetyl-CoA?
A) 1 NAD+ and 1 FAD are reduced to 1 NADH and 1 FADH2, respectively. B) 9 NADH, 9 FADH2
A) Put the following intermediates in the order they appear in the production of the biologically active form of vitamin D. B) In skin cells, what is necessary for the conversion of 7-dehydrocholesterol to vitamin D3?
A) 7-dehydrocholesterol --> vitamin D3 --> 25-hydroxyvitamin D3 --> 1,25-hydroxyvitamin D3 B) ultra-violet light
A) Which of the following does NOT correctly describe the differences found when comparing the pathways of fatty acid degradation and synthesis? B) The condensation reaction in the fatty acid synthesis pathway requires which domains of fatty acid synthase? C) After the condensation reaction, the acyl chain contacts several other domains in the fatty acid synthase complex. In which order do these domains interact with the acyl chain during reactions 2-4 of each round of fatty acid synthesis?
A) Each pathway involves a unique set of 2-carbon molecules. B) KS and ACP C) KR→DH→ER
A) Which of the following is correct and most accurately describes the complete urea cycle of the eukaryotic cell? B) Which cellular change(s) would not encourage the Krebs bicycle and thus the probability of the urea cycle taking place to completion?
A) The urea cycle occurs between the mitochondrial matrix and the cytoplasm of the eukaryotic cell. B) increased conversion of oxaloacetate into citrate; increased aspartate charging to mitochondrial tRNAs
A) Within the image, identify the components of proteasomal degradation of a biomolecule. Drag the names of the components and/or features to their appropriate targets. B) Other than the proteasome, there is a second organelle mechanism of protein degradation within the eukaryotic cell. Which of the following organelles is also involved in protein degradation?
A) Ub. tag --> condemned protein --> gated pore --> protease active site B) lysosome
A) Upon deamination of an amino acid, which component becomes substrate for the urea cycle? B) In a eukaryotic cell, deamination of amino acids takes place most extensively in the C) Within the urea cycle, citrulline is produced by ornithine transcarbamylase in the___ and is consumed in the ___ .
A) ammonia B) mitochondrial matrix C) mitochondria; cytoplasm
A) In this molecular structure, thymidylate synthase is shown associating with which of the following? B) There are ___ α helices that comprise the secondary structures of thymidylate synthase, and ___ of these α helices comprise the active site of thymidylate synthase. C) Considering the physiology of thymidylate synthase, why is Tomudex an effective anticancer drug?
A) dUMP and raltitrexed B) eight; some C) The drug is a noncompetitive inhibitor that binds to thymidylate synthase and decreases enzymatic activity. This causes an imbalance in the quantities of dNTPs that are available for DNA replication.
A) Which catecholamine is made by the action of tyrosine hydroxylase and aromatic amino acid decarboxylase? (Assume that a biologically relevant molarity of all substrates for both tyrosine hydroxylase and aromatic amino acid decarboxylase are available.) B) Consider the following scenario. Dopamine ß-hydroxylase and phenylethanolamine N-methyltransferase participate in a linear biochemical cascade. Sort the following chemicals into their appropriate bins in terms of their relevance to the reaction cascade that involves dopamine ß-hydroxylase and phenylethanolamine N-methyltransferase enzymatic activity.
A) dopamine B) reactant = dopamine; intermediate = norepinephrine; product = epinephrine; n/a = dopaquinone
A) There is/are ___ subunit(s) in nitrogenase; as a result, this protein ___ exhibit quaternary structure. B) Within one of the homodimeric Fe protein components, shown in green, which ligand has a binding site within each part of the dimer? C) Which of the following best explains why nitrogenase can only catalyze nitrogen fixation in a completely anoxic environment?
A) eight; does B) ADP C) O2 would preferentially oxidize the MoFe protein, so N2 would not become reduced.
The enzyme ___________ primes fatty acids in the cytosol so they can be degraded in the mitochondrial matrix. The enzyme ____________ catalyzes the modification of fatty acyl-CoA derivatives so they can be transported into the mitochondrial matrix. The enzyme _________ generates palmitate from malonyl-CoA. Choose the best answer below.
A) fatty acyl-CoA synthetase B)carnitine acyltransferase 1 C)fatty acid synthase
A) What is found at the core of a glycogen particle? B) Which of the following are roles of glycogenin in formation of the glycogen particle?
A) glycogenin B) acts as anchor for glycogen particle and is a priming enzyme to form the initial α-1,4 glycosidic bonds
A) Consider the mammalian fatty acid synthase that is shown in this molecular structure. Which of the following describes the three-dimensional structure of this enzyme? B) The amino terminal domain of one fatty acid synthase subunit is involved in β-ketoacyl-ACP synthase (KS) activity. Which of the following is consistent with the primary and secondary structures that are observed for the KS domain? C) Mammalian fatty acid synthase is composed of approximately 2,500 residues. This corresponds to approximately __ kDa.
A) homodimer B) The first amino acid of this domain has a side chain with a thioether functional group and the first type of secondary structure within this domain is a β sheet. C) 275 kDa
A) Hepatitis C is a viral infection that is well known for causing ___ damage. Preliminary diagnosis involves recognition of elevated levels of alanine aminotransferase in blood circulation. B) If you needed to design another way to search for elevated alanine aminotransferase levels in blood without actually identifying the enzyme itself, you could add your blood sample to a tube containing equal molarities of alanine and α-ketoglutarate and measure for which of the following?
A) liver B) increasing levels of both glutamate and pyruvate
A) Serum albumin is composed of which of the following? B) Observe only the seven fatty acid ligands of serum albumin. Which of the following is correct for this specific example? C) Which of the following best describes the interaction between serum albumin and its ligands? Once folded, serum albumin contains which of the following?
A) one polypeptide subunit that contains only α helices and no β sheets B) All seven of these ligands contain an unsaturated hydrocarbon chain. C) hydrophobic pockets where oleic acid and arachidonic acid can associate with Y and F residues
Shown here is glycogen phosphorylase. Consider its molecular structure and manipulate the molecule according to the instructions below to answer the following questions. A) Within the molecular structure, identify the ligands of glycogen phosphorylase. Which one(s), if any, would be considered to be a coenzyme? B) What is the closest distance between pyridoxal phosphate and glucose-1-phosphate when interacting with glycogen phosphorylase in this molecular structure? C) How would you best describe the enzymatic catalysis of glycogen phosphorylase?
A) only pyridoxal phosphate B) 3.67 angstroms C) The phosphate groups of pyridoxal phosphate and the glucose-1-phosphate are nearby in the active site, allowing proton transfer to occur between these groups. Within the cell, this reaction is favorable due to the concentration of Pi relative to glucose-1-phosphate.
A) What role does carnitine play in fatty acid degradation? B) Myristoyl-CoA (14:0) would require __ rounds of β oxidation to be completely oxidized. A total of ___ ATP would be produced if all products of β oxidation were completely oxidized. C) If the electron transport chain were inhibited, what would be the overall effect(s) on the ATP yield from fatty acid degradation?
A)It allows the fatty acid to be transported from the cytosol to the mitochondrion. B) 6; 94 C) -ATP yield would be reduced as the production of NADH and FADH2 would be inhibited. -ATP yield would be reduced as oxidation of NADH and FADH2 would be inhibited. -ATP yield would be reduced as the oxidation of acetyl-CoA would be inhibited.
A) Isolate one polypeptide subunit of the ubiquitin structure by clicking the black-outlined box for "a (amino)" or "b (amino)" on the bottom of the player screen. This will either display or remove them from view. Observe the ribbon structure. B) When observing both ubiquitin polypeptides in this molecular structure that are covalently bonded together, the covalent bond that leads to polyubiquitination is a bond between which two residues? C) After covalent modification of a target protein with the ubiquitin that is shown in the molecular structure, what is the most likely fate of the ubiquitin chain?
A)parallel β sheets B) lysine and glycine C) The target protein, without the polyubiquitin attachment, will be accepted into the proteasome and digested; ATP will be consumed during this process. The ubiquitin concentration in the cytoplasm will remain stable.
A) The effect of cholesterol on membrane fluidity at physiological temperatures is to B) The effect of cholesterol on membrane fluidity at low temperatures is to
A)prevent lateral movement of phospholipids and thereby decrease membrane fluidity in that region. B)maintain membrane fluidity through its disruption of fatty acid packing.
A) What purine metabolite is the likely cause of gout? B) Why was gout associated with ethanol and meat consumption? C) In humans, allopurinol can be used as treatment for gout because this drug is a competitive inhibitor of
A)uric acid B)ethanol interferes with excretion of purine breakdown chemicals and some foods contain high levels of purines C) xanthine oxidase
Name the three membrane lipids in the order of A --> B --> C
A; sphingoglycolipid, B; glycerophospholipid, C; sphingophospholipid
Which of the following regulatory mechanisms is NOT used to prevent futile cycling in fatty acid metabolism?
AMP binding regulates AMPK activity. (While AMP plays a regulatory role for many enzymes, including AMPK, it is not a mechanism used to prevent futile cycling in fatty acid metabolism. Allosteric control of key enzymes by metabolites involved in these pathways provides the necessary regulation.)
Individuals with type 2 diabetes are often prescribed the drug, Metformin, which activates AMPK signaling. Why would Metformin be an effective treatment for obese individuals with type 2 diabetes?
AMPK increases glycolytic flux and increases fatty acid oxidation, resulting in burning of fat stores as well as increased cellular glucose uptake.
What precursors are required for the beta-oxidation of palmitate?
ATP and CoA
ADA-SCID is caused by mutations in the enzyme adenosine deaminase leading to accumulation of deoxyadenosine (dA). Excess dA increases production of dATP and inhibition of DNA replication in developing immune cells, causing the SCID immunodeficiency phenotype. Which combination of allosteric effectors bound to the specificity site and the activity site of ribonucleotide reductase provides the BEST biochemical explanation for the ADA-SCID phenotype?
ATP bound to the specificity site; dATP bound to the activity site of ribonucleotide reductase.
Which of the following statements is FALSE concerning translation initiation in prokaryotes?
ATP hydrolysis provides energy necessary for formation of the initiation complex.
Regulation of aspartate transcarbamoylase (ATCase) by nucleotides controls flux through the pyrimidine biosynthetic pathway in bacteria. Choose the two true statements below that describe this regulation.
ATP is an allosteric activator of ATCase activity; CTP is an allosteric inhibitor of ATCase activity
Explain why 8 photons need to be absorbed by photosynthetic eukaryotic plants in order to transfer 4 electrons obtained from the oxidation of H2O through the photosynthetic Z scheme.
Absorption of 4 photons by PSII leads to 4 e- being transferred from 2 H2O through the Z scheme to plastocyanin; 4 more photons need to be absorbed by PSI in order to generate 2 NADPH from 2 NADP+
Why does it makes sense that beta-oxidation reactions take place in the mitochondrial matrix?
Acetyl-CoA is metabolized by the citrate cycle, which is a pathway inside the mitochondrial matrix.
Sort the following into activators or inhibitors of glycogen synthase.
Activates: Insulin and protein phosphatase 1 Inhibits: Glucagon, PKA, epinephrine, and glycogen synthase kinase 3
Leptin secretion from adipocytes is associated with too much stored fat. Leptin binding to POMC neurons causes which of the following effects?
Activation of anorexigenic neurons, resulting in decreased appetite and increased energy expenditure. Fat storage is inhibited.
What accounts for the high fidelity of DNA polymerization? Choose the ONE best answer.
Active site geometry ensures that only correct sized nucleotide base pairs are formed, and 3' to 5' proofreading removes incorrect nucleotides.
What is the biochemical explanation for why rapid weight loss is reported with protein-rich diets?
Amino acid degradation results in urea production to remove excess NH4+, so mostly water weight loss.
Q4.2 - Explain the molecular basis for animal fat being solid at room temperature but vegetable oil being liquid are room temperature.
Animal fat contains a large percentage of full reduced fatty acids, which are able to pack closed together because of their linear structure; close packing increased the melting temperature to disrupt the crystalline lattice. Vegetable oil contains a high mixture of polyunsaturated fats, which do not pack very well because of their irregular structures owing to cis double bonds. Because of this loose packing, the melting temperature is much lower. (See pages 732-734)
Which of the following combinations can be used by farmers to ensure robust nitrogen assimilation by actively growing crops?
Applying cow manure to the fields as a source of fertilizer and always rotating in leguminous plants.
Why is ingesting large amounts of L-arginine a viable treatment for argininosuccinase deficiency?
Arginine is converted to ornithine, which provides urea cycle intermediates needed for nitrogen removal.
Aminoacyl-tRNA synthetases carry out editing _______________.
At a site that is distinct from the active site
What type of antibody or antibodies is/are found in the plasma of a person with type A blood?
B antibodies
Why does it makes sense that ghrelin stimulates orexigenic neurons (eat more/metabolize less)?
Because ghrelin is released from stomach cells when your stomach is empty.
Which statement below best describes the reason why the Cori Cycle has a net cost of 4 ATP for each glucose that is regenerated?
Because it requires an investment of 6 ATP equivalents to generate glucose from lactate in the liver but the recovery of ATP in conversion of glucose to lactate in muscle is only 2 ATP.
Statin drugs can cause severe side effects in some individuals (debilitating muscle pain) and alternative treatments need to be used to lower their serum cholesterol levels. Name the two most common treatments and describe how they lower cholesterol levels
Bile acid resins reduce cholesterol via higher bile acid synthesis; ezetimibe to block dietary cholesterol
Which of the following does NOT occur during starvation?
Brain cells begin using fatty acids as an energy source.
Aspartate transcarbamoylase (ACTase) is a ratelimiting enzyme in the pyrimidine biosynthetic pathway of bacteria. How is ACTase allosterically-regulated in bacterial cells?
CTP shifts ATCase to the T state
Why is it a bad idea to eat a Fun Size bag of Skittles (205 grams) 10 minutes before a half marathon (13.1 miles)? Note the ingredients in a bag of Skittles shown in the box to the right:
Carbohydrate will cause an increase in insulin and inhibit fatty acid oxidation later in the race, which will decrease available metabolic energy.
Nucleotides such as ATP shown at the right have four key roles in biochemical processes. Name TWO of the possible four.
Coenzyme-dependent reactions and energy conversion.
Which of the following is true concerning cholesterol and plasma membranes?
Cholesterol inserts into the membrane via its non-polar planar rings.
Which base location in the figure below (A, B, C, D) explains the wobble hypothesis?
D (5' end)
Which of the following is a coenzyme that is derived from ATP?
FAD
What is the energy source for sustaining the electrochemical proton gradient in chloroplasts; what is the biochemical function of this gradient?
D. Photon absorption; production of ATP via chloroplast ATP synthase complex
What is a Benefit, and what is a Risk, of using a COX-2 selective inhibitor to treat inflammation?
D. Benefit: decreased inflammation; Risk: increased cardiovascular problems
Calculate the DG value (actual change in free energy) at 37 .C for the aldolase reaction, which converts fructose-1,6-bisphosphate (F-1,6-BP) to glyceraldehyde-3-phosphate (GAP) and dihydroxyacetone-phosphate (DHAP), given the DG.' value for this reaction of +23.8 kJ/mol and the concentrations of these metabolites at steady state; F-1,6-BP = 10 mM, GAP = 0.02 mM, DHAP = 0.02 mM.
DG = +23.8 kJ/mol + (8.315 x 10-3 kJ/mol•K) • (310K) • ln (2 x 10-5M) (2 x 10-5M) 1 x 10-2M DG = +23.8 kJ/mol + (8.315 x 10-3 kJ/mol•K) • (310K) • (-17.73) DG = +23.8 kJ/mol + (-43.9 kJ/mol)) DG = - 20.1 kJ/mol
Explain how a deficiency in the enzyme dihydropyrimidine dehydrogenase (DPD) could lead to severe side effects in cancer treatments using 5-fluorouracil (5-FU) as a chemotherapeutic agent.
DPD degrades 5-FU so high doses need to be given, if DPD is deficient, then high 5-FU doses are toxic.
Which of these three diets below is the most incomplete with regard to nutrition and why? Diet 1: carbohydrate + lipid Diet 2: protein + carbohydrates Diet 3: amino acids + fatty acids
Diet 1; because it lacks protein, which provides 10 essential amino acids required for protein synthesis
Why is it necessary for σ factor to dissociate from the RNA polymerase in order for elongation to occur efficiently
Dissociation of σ factor increases the affinity of RNA polymerase for general DNA.
Which of the following proteins is responsible for binding to oriC to initiate replication in E. coli?
DnaA
Which of the three proteins in the ubiquination pathway is the most responsible for recognizing the ubiquintated target protein?
E3
Calculate the Energy Charge of a cell when the levels of ATP, ADP, and AMP are all equal to 1 mM; is this value for the Energy Charge within the physiological range?
EC= 0.5; no, the cell's energy charge does not fall within physiological range.
Metabolic diseases caused by defective enzymes can be caused by decreased amount of product or buildup of substrate. Choose the most correct statement below regarding metabolic diseases:
Favism is caused by decreased NADPH production; Tay Sachs is caused by buildup of GM2 ganglioside
The mitochondrial electron transport system and the photosynthetic electron transport system are different in many ways. In what way are they similar?
Electrons are transferred from one electron carrier to the other by redox reactions in both systems
Sort the following lipids by their major role in the cell.
Energy Storage: triacylglycerols and fatty acids Cell Membrane: glycerolphospholipids and sphingolipids Endocrine Signaling: eicosanoids and steroids
Which of the following statements is correct concerning eukaryotic mRNA?
Eukaryotic mRNA is monocistronic.
In humans and many other animals, triacylglycerols are the major form of stored energy. Which of the following statements describe the differences between triacylglycerols and glucose?
Fatty acids yield more energy than glucose for the same number of carbons upon oxidation. Fatty acids are at a higher reduction state than glucose.
In the Krebs bicycle, which of the following citrate cycle intermediates links to the urea cycle via argininosuccinate?
Fumarate (Explanation: The Krebs bicycle allows for fumarate from the citrate cycle to be used to make aspartate, which is then combined with citrulline to make argininosuccinate, a substrate in the urea cycle. Argininosuccinate is broken down into arginine, which continues in the urea cycle, and fumarate, which is converted back into malate for transport and use in the citrate cycle.)
Q4.1 - Describe in biochemical terms how glucagon and insulin regulate glycogen metabolism. Be specific.
Glucagon stimulates a phosphorylation cascade through the glucagon receptor and protein kinase A that phosphorylates glycogen phosphorylase to activate the enzyme and glycogen synthase to inactivate the enzyme. Insulin stimulates a dephosphorylation cascade through the insulin receptor and protein phosphatase 1 that dephosphorylates glycogen synthase to activate the enzyme and glycogen phosphorylase to inactivate the enzyme. (see pgs 716-718)
Insulin signals for an increase in glucose uptake in both skeletal muscle and adipose tissue. Which of the following correctly describes how these organs use this glucose?
Glucose in muscle cells is completely oxidized or stored as glycogen, depending on the ATP demand. In adipose tissue, glucose is used to synthesize fatty acids and glycerol.
Choose the statement that correctly describes a nitrogen metabolizing enzyme and its function.
Glutamine synthetase incorporates ammonium ion into glutamate to form glutamine.
Choose the best statement below that accurately describes O-linked glycan to a protein.
Glycan forms an O-glycosidic bond involving the anomeric carbon of the oligosaccharide and a Ser or Thr residue on the protein.
How is glycogen phosphorylase allosterically activated in muscle cells?
Glycogen phosphorylase is shifted to R state by binding of AMP
AMP-dependent protein kinase (AMPK) is activated by low energy charge (higher AMP) and phosphorylates downstream target proteins, some of which are inhibited by phosphorylation. Inhibition of which two enzymes by AMPK phosphorylation will result in an increased energy charge (higher ATP)?
Glycogen synthase and acetyl-CoA carboxylase
Which of the following statements correctly describes an interaction between the ATP and GTP biosynthetic pathways?
Greater ATP production will positively regulate GTP synthesis because ATP is involved in the conversion of xanthosine-5'-monophosphate into guanosine-5'-monophosphate.
Which one of the following lipoproteins functions to transport cholesterol from the peripheral tissues to the liver?
HDL
The __________ gene does NOT have a binding site for sterol regulatory element binding proteins (SREBPs).
HDL receptor
Why is de novo biosynthesis of purines markedly elevated in patients with a deficiency in hypoxanthine-guanine phosphoribosyl transferase (HGPRT)?
HGPRT deficiency prevents purine salvage, leading to increased purine biosynthesis to make up for it.
Which enzyme catalyzes the rate-limiting step of cholesterol synthesis?
HMG-CoA Reductase
Why does it make sense that citrate stimulates acetyl-CoA carboxylase activity?
High energy charge leads to export of citrate to the cytosol where it activates acetyl-CoA carboxylase
A common feature of protein synthesis in both eukaryotes and prokaryotes is _____________.
Hydrolysis of GTP to facilitate binding of the AA-tRNAAA
How does the herbicide, glyphosate, work?
It inhibits the shikimate pathway, preventing production of phenylalanine, tyrosine, and tryptophan.
Which of the following causes inhibition of fatty acid synthesis?
Increased AMP-activated protein kinase activity
How do statin drugs function to reduce the risk of cardiovascular disease?
Inhibit HMG-CoA reductase to reduce cholesterol synthesis and increase LDL receptor synthesis
Why does inhibiting 5a-reductase activity block prostate cell growth and induce hair growth?
Inhibiting 5a-reductase activity decreases dihydrotestosterone production, which treats both conditions
What explains the smell of acetone on the breath of dieters following the Atkins diet?
Insufficient carbohydrates to maintain flux through the citrate cycle leads to increased ketogenesis.
Fructose-2,6-bisphosphate (F-2,6-BP) is an allosteric regulator that controls flux through the glycolytic and gluconeogenic pathways. Levels of F-2,6-BP increase in the cell in response to insulin and decrease in response to glucagon. Choose the number corresponding to the correct underlined answer.
Insulin (1) / Glucagon (2) signaling in liver cells leads to the phosphorylation of PFK-2/FBPase-2, which activates PFK-2 (3) / FBPase-2 (4) activity of the enzyme and dephosphorylation (5) / phosphorylation (6) of fructose-2,6-BP. The net result of increased (7) / decreased (8) levels of F-2,6-BP in liver cells is to stimulate flux through the gluconeogenic pathway by lowering the levels of this allosteric inhibitor of the enzyme FBPase-1 (9) / phosphofructokinase-1 (10). Glucagon (11) / insulin (12) signaling stimulates protein phosphatase-1 in liver cells leading to the activation of the PFK-2 (13) / FBPase-2 (14) domain (Answer: 2, 4, 5, 8, 9, 12, 13)
How do liver and skeletal muscle cells utilize ketone bodies?
Liver cells do not have B-ketoacyl-CoA transferase, but muscle cells do
How high should the concentration of aminoacyl-tRNA synthetases be, compared to the concentration of tRNAs in a cell?
Low, because a single aminoacyl-tRNA synthetase can catalyze many reactions.
What is the advantage of using methicillin compared to using penicillin as an antibiotic?
Methicillin is resistant to beta-lactamase activity.
How are plants able to stay alive in the absence of light?
Mitochondria use carbohydrates as an energy source for cellular respiration
Why does glucagon signaling stimulate glucose and fatty acid release from liver and adipose tissue, but has no effect on muscle cells even though muscle cells contain glycogen?
Muscle lacks glucose-6-phosphatase, contains insulin receptors, and lacks glucagon receptors
Which of the following is the net reaction of the urea cycle?
NH+ + HCO3 + aspartate + 3ATP urea + fumerate + 2 ADP + 2Pi + AMP + PPi
Nitric Oxide (NO) is a soluble gas and regulator of intracellular pathways causing vasodilation. What is the mechanism by which NO reduces blood pressure by stimulating vasodilation?
NO binds to guanylate cyclase to stimulate cyclic GMP production, which leads to vasodilation.
Which of the following statements is a correct comparison of patients with type 1 versus patients with type 2 diabetes?
Patients with Type 1 diabetes are generally of normal weight whereas patients with type 2 diabetes are often obese
Which statement below best describes the glycoconjugate structure of bacterial cell walls?
Peptidoglycans with multiple strands of hexosamine polysaccharide chains linked together.
Using the DG.' values for the reactions shown below, what is the DG.' value for the conversion of phosphoenolpyruvate to 3-phosphoglycerate in the gluconeogenesis?
Phosphoenolpyruvate <--> 2 Phosphoglycerate DG.' = -1.7 kJ/mol 3-Phosphoglycerate <--> 2-Phosphoglycerate DG.' = +4.6 kJ/mol 2-Phosphoglycerate <--> 3-Phosphoglycerate DG.' = -4.6 kJ/mol Phosphoenolpyruvate <--> 2-Phosphoglycerate DGº' = -6.3 kJ/mol
Given that ΔG°´ for the glycogen phosphorylase reaction is +3.1 kJ/mol, what factors in the cell make the actual free energy change (ΔΔΔG) favorable?
Pi being much greater than glucose-1-P
Why can puromycin block translation in both prokaryotes and eukaryotes, while many other antibiotics only affect prokaryotic translation?
Puromycin is structurally similar to part of a charged tRNA, which has the same structure in prokaryotes and eukaryotes.
How are RNA tertiary structures different from protein tertiary structures?
RNA adopts multiple structures, whereas protein structures are restricted
Why is photorespiration a bigger problem for plants at high temperatures, and which enzyme is responsible for this wasteful process?
Ratio of soluble O2 : CO2 is increased; Rubisco
The Light Harvesting Complex (LHC) molecules are arranged to facilitate
Resonance energy transfer to the reaction center
Which of the following is correct concerning ribonucleotide reductase?
Ribonucleotide reductase in most eukaryotes contains a dinuclear Fe3+ center in the R2 subunit.
Why do plant root nodules in leguminous plants contain high levels of glutamine synthetase?
Root nodules assimilate NH4 + into glutamine
Identify one way in which RNA splicing can give rise to multiple mRNA transcripts from a gene containing 3 exons and 2 introns.
Splicing between the 3' end of exon 1 and 5' end of exon 3
Which of the following best explains why the ATP yield from complete oxidation of stearoyl-CoA is greater than that of oleoyl-CoA?
Stearoyl-CoA is more reduced than oleoyl-CoA.
Which symptom is the best indication of Phenylketonuria disease in a patient
elevated phenylpyruvate
Ambiguous gender is a genetic condition that often arises from defects in the steroidogenesis pathway. Which enzyme is most likely responsible for an XY chromosome male developing as mostly female and lacking fully developed male genitalia? There is ONE correct asnwer.
Steroid-5-alpha-reductase
Acetyl-CoA carboxylase (ACC) is a key regulated enzyme in fatty acid synthesis. Refer to the figure to the right and choose T (true) or F (false) for each statement below. (T F Phosphorylation inhibits ACC activity. T F Insulin inhibits ACC activity. T F Citrate activates ACC activity. T F Glucagon activates ACC activity)
T, F, T, F
Given the regulatory role of TSIX, what would be the expression pattern of XIST and TSIX in a female with two X chromosomes?
TSIX would be expressed on the active X chromosome and XIST would be expressed on the inactive X chromosome.
What are the different roles played the acyl carrier protein (ACP) and the ketoacyl synthase (KS) domain during fatty acid synthesis?
The ACP carries the growing fatty acid chain more than the KS domain
Q6.2: Describe the TWO major discoveries from the Goldstein and Brown research groups that elucidated the relationship between liver cholesterol biosynthesis and cardiovascular disease - be specific.
The Goldstein and Brown research groups discovered the role of HMGCoA reductase in controlling de novo cholesterol biosynthesis in the liver, which led to the development of statin drugs. The mechanism of statin drugs is to lower cholesterol levels in liver cells and stimulate LDL receptor expression to endocytose more LDL from the serum. Their second discovery was how SREBP transcription factors are activate by protease cleavage in response to low cholesterol and in turn upregulate LDL receptor expression (see pgs 816- 822)
What must be the chemical property of the electron acceptor molecule that is reduced by electron transfer when chlorophyll photooxidized? Choose the one best answer.
The acceptor molecule must have a higher reduction potential than chlorophyll (more positive).
Q6.3: Describe the two enzymatic processes by which NH4 + can be assimilated into glutamate using alphaketoglutarate; which of these two is the most common route and which one requires special conditions - describe those special conditions.
The assimilation of NH4 + into glutamate is most commonly accomplished by combining the reactions catalyzed by glutamine synthetase, an ATP dependent reaction, and glutamate synthase. The ATP-coupled reaction with glutamine synthetase drives the reaction forward. A less common process is NH4 + assimilation by the enzyme glutamate dehydrogenase, which is energetically unfavorable unless NH4 + concentrations are extremely high. One special condition where this occurs is in agricultural use of fertilizers. (see pgs 843-844)
Uric acid is derived from both purine biosynthesis and by diet. What accounts for high levels of 15N in excreted urine after feeding a patient 15N-glycine to diagnose the cause of gout? Explain.
The cause of the gout is excess production of uric acid because glycine is a precursor to purines.
Choose the statement that describes what the actual change in free energy (DG) tells you about an enzymatic reaction, which cannot be determined by the standard free energy (DG.') change.
The direction of the reaction under steady state conditions
Starting with the same number of moles of dehydrated glucose and palmitate, why are less ATP obtained from the breakdown of glucose compared to the breakdown of palmitate?
The glucose carbons are mostly oxidized, whereas the palmitate carbons are mostly reduced.
Q5.2: The lipids 7-dehydrocholesterol and arachidonate are precursors to specific lipid signaling molecules, respectively. Name the active signaling molecule for each and describe a corresponding cellular response.
The lipid 7-dehydrocholesterol is a precursor to the active form of vitamin D called 1, 25-hydroxyvitamin D3, which is required for normal bone growth. Arachidonate is the precursor steroid to prostaglandin H2, which is involved in regulating blood flow and muscle contraction/relaxation (See pages 762-765)
Heparin has one of the highest negative charge densities ever found in a biomolecule and is used commercially to prevent blood clotting. Heparin binds to and activates antithrombin, thereby inhibiting the blood clotting cascade. An accidental heparin overdose can be fatal. How does infusion with protamine sulfate, a cationic protein, counteract the effects of a heparin overdose?
The positively charged protamine sulfate binds to the negatively charged heparin and inactivates it
Which of the following is consistent with the data presented in the feedback inhibition figure?
The product of the guanylate kinase reaction will inhibit the activity of PRPP synthetase.
Which of the following statements is most consistent with all information contained within the figure?
The production of glutamate only occurs when there is significant concentration of NH4+.
Q6.1: Under what metabolic conditions are excess carbohydrates converted to stored tricylglycerols in adipose tissue? List the six steps required.
The six steps are 1) glucose import, 2) glucose metabolism by the glycolytic pathway, 3) export of citrate to the cytosol by the citrate shuttle, 4) conversion of acetyl-CoA to palmitate by fatty acid synthesis, 5) export of triacylglycerol as VLDL particle from the liver, and 6) uptake of fatty acids transported to adipose cells by albumin protein (See pages 746-747 and 791-792)
Insulin-stimulated glucose uptake and utilization by skeletal muscle and liver cells results in a reduction in the blood glucose level. Which organ is primarily responsible for the decrease in serum glucose, and why?
The skeletal muscle is responsible for the majority of glucose uptake, as the total mass of skeletal muscle is greater than the mass of liver cells.
Q5.1: Name the three major types of membrane lipids in animal cells and provide a specific example of "everyday biochemistry" illustrating the function of each type of membrane lipid
The three major types of membrane lipids are glycerophospholipids, sphingolipids, and cholesterol. Many types of snake venoms contain active phospholipase enzymes that cleave glycerophospholipids and destroy cell membranes. There are many human genetic diseases caused by defects in enzymes that modify sphingolipids, e.g., Tay-Sachs disease. Stigmasterol is a plant lipid that is converted into cholesterol by enzymes in the tobacco hornworm (see pgs 753-757)
Q4.3 - Describe the three sources of triacylglycerols in humans and how each is transported through the blood
The three sources of triacylglycerols in humans are dietary triacylglycerols; transported by chylomicrons, newly synthesized liver triacylglycerols; transported by VLDL particles, and triacylglycerols released from adipose tissue; transported by albumin protein. (See pages 742-743)
Long noncoding RNA (lncRNA) is generated from _____________.
The transcription of genomic DNA
What physiological condition is most often associated with increased ketogenesis?
When there are high levels of acetyl-CoA in liver mitochondria and oxaloacetate levels are low.
Calculate net number of moles of ATP generated from the oxidation of 1 mole of the fatty acid shown to the right if all of the NADH, FADH2, and acetyl-CoA is metabolized by citrate cycle and oxidative phosphorylation.
There are 106 net number of moles of ATP generated. (C16 compound)
Cells cannot store excess amino acids such as aspartate and glutamate, which accumulate as a result of protein degradation. Once the nitrogen is removed from aspartate and glutamate, what happens to the alpha-keto acids oxaloacetate and alpha-ketoglutarate, respectively?
These two alpha-keto acids are metabolized in the citrate cycle.
How can DNA strands be synthesized using bidirectional replication?
They are synthesized through Okazaki fragments.
Why are C4 plants better adapted to hot climates than C3 plants?
They can capture CO2 and store it during times that O2 levels are high and minimize photorespiration.
Match the general type of carbohydrate in the first column (a-f) with the best specific example of that carbohydrate in the second column (1-6). Record your answer in the order from a through f.
Type of carbohydrate Specific example ____ a. Disaccharide 1. Fructose ____ b. Disaccharide heteropolymer 2. Raffinose ____ c. Monosaccharide 3. Syndecan ____ d. Oligosaccharide 4. Lactose ____ e. Proteoglycan 5. Chitin ____ f. Glycoprotein 6. Lectin (Answer: 4, 5, 1, 2, 3, 6)
Tyrosine can be encoded by both UAU and UAC. Imagine that these codons are recognized by different tRNAs, and that the UAU tRNA is expressed at five times the level of the UAC tRNA. What would be the consequence of this expression difference?
UAU-containing mRNAs would be translated faster than UAC-containing mRNAs.
Which molecule is attached to the C-1 position of glucose to initiate glycogen synthesis?
UDP
Why is it essential to vigorously agitate dirty clothes with liquid soap in water, why not just let the soap soak into the dirt and then rinse it off?
Vigorous agitation breaks up the fatty acids into micelles that are then rinsed away with the dirt inside
Which of the following is a common breakdown product between AMP and GMP degradation to uric acid?
Xanthine
Do PPARα-specific agonists theoretically offer more advantages for lowering cholesterol as compared to traditional statin drugs?
Yes, treatment with PPARα-specific agonists affects cholesterol transport and uptake as well as synthesis, whereas statins affect synthesis only.
A Holliday junction can best be defined as a region of
a quadraplex DNA structure
The figure at the right shows the cellular processes that synthesize, secrete, and recognize glycoconjugates in eukaryotic cells. Correctly Identify these three types of proteins, a) a lectin protein, b) hexose transport protein, c) a glycoprotein.
a) 4; b) 1; c) 3
Soap: a) When mixed with water, the fatty acids in soap function as amphipathic molecules forming what? b) Free fatty acids inside cells would also act like soap and disrupt biological membranes, except that fatty acids inside cells are chemically neutralized by covalent linkage to what small molecule for energy storage?
a) micelles b) glycerol
Which of the following is the correct net reaction for the combined reaction of glutamine synthetase and glutamate synthase?
a-ketoglutarate + NH4+ --> glutamate
When AMPK is bound by AMP and is phosphorylated at Thr172, _________ activity will _________.
acetyl-CoA carboxylase; decrease
What molecule signals the endothelial cell to produce nitric oxide, and what is the enzymatic reaction?
acetylcholine;
Assuming the enzymes are not currently at their most active state, an increase in which of the following peroxisomal enzymes would result in a corresponding increase in catalase activity?
acyl-CoA dehydrogenase
Which of the following is secreted by visceral fat?
adipokines
Which of the following is directly affected by thiazolidinediones?
adipose tissue
A patient is having problems regulating blood pressure and has poor kidney function. Which steroid could be responsible for this?
aldosterone
What nitrogen source is used to produce carbamoyl phosphate?
ammonia
Sort the phrases to correctly describe the role of anorexigenic and orexigenic neurons in regulating appetite and energy expenditure.
anorexigenic: signals for an increase in energy expenditure, activation initiated by leptin, signals adipocytes to store less fat orexigenic: signals for a decrease in energy expenditure, activation initiated by gherlin, signals adipocytes to store more fat
What is the regulatory mechanism by which arginine stimulates flux through the urea cycle?
arginine stimulates the production of the allosteric activator N-acetylglutamate
What role do BRCA1 and BRCA2 play in DNA repair?
assist with strand invasion
What is the mechanism by which replication errors are fixed in E. coli?
base excision
Thrifty genes are ________ during times of starvation and ________ when physical activity is low.
beneficial; detrimental
Which of the following is the product of uracil degradation?
beta-alanine
The uptake of LDLs by cells is triggered by the
binding of the apoB-100 lipoprotein on LDL to the LDL receptor.
What coenzyme shown at the right is required for reactions catalyzed by the enzyme acetyl-CoA carboxylase?
biotin
What cofactor, common to carboxylase enzymes, is used by acetyl-CoA carboxylase?
biotin
The Tus-Ter complex terminates E. coli DNA synthesis by ____________.
blocking the opening of the DNA helix at the fork by helicase
15N-labeled aspartate is provided to bacteria during the biosynthesis of pyrimidine trinucleotides. The radiolabeled nitrogen would ultimately be found in
both UTP and CTP
Which enzyme catalyzes the formation of alpha(1,6) linkages during glycogen synthesis?
branching enzyme
What is the effect of deficient activity of glucose-6-phosphatase, known as von Gierke's disease?
buildup of glycogen in the liver
Which metabolite is an intermediate in both pyrimidine biosynthesis and the urea cycle?
carbamoyl phosphate
Photons first enter the Z scheme via which molecule?
chlorophyll P680
Which of the following is labeled 3 in the figure below?
citrulline
In the duodenum, enteropeptidase _______________.
cleaves trypsinogen to form trypsin
There are many diseases collectively called porphyrias that are characterized by the accumulation of heme precursors in the blood and liver. Which type of porphyria is characterized by low uroporphyrinogen III synthesis?
congenital erythropoietic porphyria
Glycogen phosphorylase is an enzyme that catalyzes the rate-limiting step in glycogen degradation. The catalytic activity of this enzyme is stimulated by phosphorylation. What is the best description of this type of enzyme regulation?
covalent modification
In the ER, prenylation can occur. Prenylation is the attachment of an isoprenoid group to a _____________ residue via a(n) _____________.
cysteine and thioester
Which types of posttranslational modifications can be attached to which amino acids on proteins?
cysteine: farnesyl, geranylgeranyl, palmitoylate asparagine: N-linked glycan glycine: myristoylate
Individuals with mutations of BRCA have increased incidence of cancer because of their
decreased ability to repair double-strand DNA breaks.
Individuals with mutations of BRCA have increased incidence of cancer because of their___________.
decreased ability to repair dsDNA breaks
Tay-Sachs disease, Fabry disease, and Niemann-Pick disease are all symptomatic because of ___________ .
defects in sphingolipid metabolism
The enzyme responsible for generating siRNA from double strand RNA is ____________.
dicer
In triacylglycerol synthesis, from where is the glycerol backbone derived?
dihydroxyacetone phosphate
Homologous recombination repairs what kind of DNA damage?
double strand break
What is the necessary nucleic acid input for the RNAi pathway to degrade mRNA?Choose one:
ds-RNA
Tobacco smoking, which is associated with a high risk of lung cancer, is described as:
environment
Glucose-6P is a central metabolite in human physiology and functions as a substrate or product in at least six metabolic pathways. What biochemical mechanisms determine glucose-6P flux through these pathways? Choose the THREE BEST answers below.
enzyme levels, allosteric control, and substrate availability
Because muscles lack receptors for glucagon, what hormone activates muscle glycogen phosphorylase?
epinephrine
Tyr122 is important in the mechanism of the E. coli ribonucleotide reductase. The function of this amino acid in the mechanism is to ________________.
generate the Cys439 radical species
A deficiency in the enzyme dihydropyrimidine dehydrogenase (DPD) is best described as:
genes --> environment
In the figure show below of an E. coli replication fork, which protein is responsible for relieving torsional stress?
gyrase
If the efficiency of the urea cycle decreased, there would be a buildup of which amino acid?
glutamine
Which of the following amino acids are required in the first step of heme biosynthesis?
glycine
What is the mechanism by which glyphosate, the active ingredient in Roundup, kills plants?
glyphosate is a competitive inhibitor of plant EPSP synthase
If 15N DNA (heavy) replicated using conservative replication in 14N (light) media, the outcome would be different than semi-conservative replication, and in this case, the two daughter DNA double strands would be ______________after one generation.
heavy for one and light for the other daughter
Why do helicase and gyrase need to work together to keep the replication fork moving forward?
helices unwinds DNA and gyrase relieves the torsional strain created by unwinding
A tyrosine deficiency leads to muscle wasting and Kwashiorkor disease. What is the treatment?
high protein diet
Which fatty acids do you predict have the (a) highest and (b) lowest melting points (MP)? 1. Oleate; cis 18:1(D9) 3. Stearate; 18:0 5. Palmitate; 16:0 2. Myristate; 14:0 4. Arachidonate; cis 20:4(D5,8,11,14) 6. Linoleaete; cis 18:2(D9,12)
high; 3, low; 4
Alkaptonuria is easily diagnosed by the presence black urine. What causes the black color?
homogentisate oxidation
Raffinose-series oligosaccharides are hard for humans to digest because:
humans do not have the enzyme a-1,6-glycosidase necessary to hydrolyze the glycosidic bonds
Which is found in the ketone body pathway?
hydroxybutyrate
Which of the following are ketone bodies?
hydroxybutyrate and acetoacetate
The activation of glycogen phosphorylase will lead to a(n) ____ in blood glucose concentrations and is stimulated by the hormone _____.
increase; glucagon
Orlistat and olestra can both lead to undigested lipids in the colon, yet they do so by contrasting mechanisms. Orlistat ________, whereas olestra ________.
inhibits pancreatic lipase; is a fat substitute that is not a substrate for pancreatic lipase
Which one of the following is involved in the breakdown of glycogen?
inorganic phosphate
Lysogeny by bacteriophages causes what result to the host DNA?
integration of virus DNA into host DNA
Dihydropyrimidine dehydrogenase deficiencies can lead to toxic side effects from high doses of 5-fluorouracil because 5-fluorouracil __________ dihydropyrimidine dehydrogenase.
is degraded by
The lack of an immune systems in patients born a defect in the enzyme adenosine deaminase of ADA-SCID is caused by _________ than normal activity of _________.
lower; ribonucleotide reductase
In order for a cancer cell to be resistant to the drug methotrexate, a mutation in the dihydrofolate reductase enzyme must be able to _____________.
maintain enzyme activity without being inhibited by methotrexate
Which symptom is the best indication of Lesch-Nyhan disease in a patient?
male infant with gout
Which of the following is NOT a cellular role for nucleotides?
membrane formation
A common chemical modification found in RNA is __________________.
methylation of the nucleotide bases in tRNA
What elements are indispensible metal ion cofactors of the active nitrogenase enzyme complex?
molybdenum and iron
Glycogen can provide fuel for both a short race (e.g., 200 m) and a long race (i.e., 10 K or more). Which of the following best describe(s) the use of muscle and liver glycogen during short and long races?
muscle glycogen can be used to fuel short AND long runs but liver glycogen can only be used to fuel long runs
What are the four key enzymes in nitrogen fixation and assimilation in plants and bacteria?
nitrogenase complex, glutamine synthetase, glutamate synthase, and glutamate dehydrogenase
Aspartate is a(n) ________ amino acid, so if a person had a diet that contained no aspartate then ________.
nonessential; aspartate could be synthesized from other intermediates
What is the explanation for why leptin injections cause weight loss in the strain of ob/ob mutant mice, but leptin injections has no effect in the majority of people?
ob/ob mutant mice lack leptin, and by providing it through injection, they are able to better maintain energy balance and metabolic homeostasis. In contrast, obese humans have chronically high leptin levels and are often leptin-insensitive.
Leptin is an adipocyte hormone that send signals to the brain to "eat less" and "metabolize more." What is the explanation for why leptin injections cause weight loss in the strain of ob/ob mutant mice, but leptin injections has no effect in the majority of people?
ob/ob mutant mice lack leptin, and by providing it through injection, they are able to better maintain energy balance and metabolic homeostasis. In contrast, obese humans have chronically high leptin levels and are in fact leptin-insensitive.
What is the specific site on the E. coli genome where DNA replication can initiate?
oriC
The biosynthesis of triacylglycerols in animals uses which citrate cycle intermediate in the liver?
oxaloacetate
A person who has alkaptonuria is easily diagnosed from their black urine. What causes the black color?
oxidation of homogentisate
What two pathways provide the ATP needed to phosphorylate creatine during muscle contraction?
oxidative phosphorylation and glycolysis
Which of these enzymes function in the human small intestine?
pancreatic lipase
Which step is required for the synthesis of phosphatidylethanolamine?
phosphatidylserine is decarboxylated
Chylomicrons contain a monolayer on the outside of the particle consisting of ___________.
phospholipids and chlosterol
The conversion of ribose-1-phosphate to guanosine-5'-triphosphate via the salvage pathway would require the activity of several enzymes. Choose the answer that lists them in the order that they would act in this pathway.
phosphopentomutase --> PRPP synthetase --> phosphoribosyl transferase --> kinase --> kinase
The conversion of ribose-1-phosphate to ATP via the salvage pathway would require the activity of several enzymes. Choose the answer that lists them in the order that they would act in this pathway.
phosphopentomutase; PRPP synthetase; phosphoriboxyl transferase; kinase; kinase
Elevated serum levels of free fatty acids prevents the
phosphorylation of tyrosine in insulin receptor substrate 1 protein.
Diseases affecting heme biosynthesis as a result of deficiencies in the heme biosynthetic pathway are called _________.
porphyria
Ubiquitination is most often regulated by biochemical modifications to which two types of proteins (choices at the right):
target proteins and E3 ligases
Prokaryotic and eukaryotic DNA polymerases rarely make mismatched base pairs because ____________
the active site does not fit well with mismatches
The Ames test is designed to identify mutation rates using a strategy based on ___________.
the frequency of new mutations that compensate for an existing mutation
In which direction is mRNA synthesized by prokaryotic and eukaryotic RNA polymerases?
the mRNA is synthesized in the 5' to 3' directional with phosphodiester linkages
What would happen if purified leptin protein were injected daily into the db/db (diabetes) mouse as compared to a littermate db/db mouse that did not get leptin injections?
the mouse with leptin would be as fat as the mouse without leptin
Which of the structures above is a component of a glycerophospholipid? Choose the one best answer.
the one with NH3+ only (not the one with two Nitrogens)
Which of the following do -oxidation and fatty acid synthesis have in common?
the presence of an oxidized fatty acyl -carbon with a hydroxyl or carbonyl group as a pathway intermediate
T is the less active form of an allosteric enzyme and R is the more active form of enzyme. What happens to the value for the ratio of [inactive enzyme]/[active enzyme] when the substrate concentration decreases relative to high substrate levels?
the ratio is increased
The term greenhouse effect refers to the idea that
the temperature of the earth is increasing because of heat trapped by gases such as CO2.
How does biological fixation convert nitrogen to ammonia?
through the ATP-dependent process catalyzed by nitrogenase complex
Q5.3: What is the total yield of NADH, FADH2, and acetyl-CoA from the complete oxidation of myristate? Assuming all of these metabolites are oxidized by the citrate cycle and oxidative phosphorylation, what is the net yield of ATP?
the total yield for this C14 fully saturated fatty acid is 6 NADH, 6 FADH2, and 7 acetyl-CoA. Using the ATP currency exchange of 2.5 ATP/NADH and 1.5 ATP/FADH2, the total yield of ATP from the complete oxidation of myristate is 94 ATP, but with 2 ATP required in the charging reaction, the net yield is 92 ATP (see pgs 782-783)
Long noncoding RNA (lncRNA) is generated from
the transcription of genomic DNA
How do bacterial sigma factor proteins promote RNA synthesis?
they recruit RNA polymerase to specific sequences of the 5' of the gene
The two key elements of the oriC include
three 13-bp repeats and four 9-bp repeats with enriched A-T pairs
What is the role of most chlorophyll molecules in a photosynthetic membrane?
to serve as light-harvesting antennae
Partial hydrogenation can result in the formation of
trans double bonds
What step in the process of translation of a nascent protein into the lumen of the ER requires hydrolysis of GTP?
transfer of the signal peptide sequence into the transloson
Which pathway does NOT provide metabolic precursors for amino acid synthesis?
urea cycle (pentose phosphate pathway, citrate cycle, and glycolysis are precursors)
Which of the following is NOT a major type of plasma membrane lipid?
wax
If an alteration occurred in the activity site of the R1 subunit of E. coliribonucleotide reductase that allowed dATP to bind but precluded ATP binding to the site, a possible result would be that ribonucleotide reductase
would be decreased when dATP bound both the activity and specificity sites.
What are biochemical properties of enzyme active sites? Choose the TWO best answers.
~ Enzyme active sites provide optimal orientation ~ Enzyme active sites exclude excess solvent.
