Cell and Molec Exam 1

What cellular feature distinguishes prokaryotic cells from eukaryotic cells?

eukaryotes have a membrane bound nucleus

Monomeric proteins do not contain

quaternary structure

Steps 6 and 7 of glycolysis are catalyzed by the enzymes glyceraldehyde 3-phosphate dehydrogenase and phosphoglycerate kinase, respectively. Together, they ...

result in the oxidation of an aldehyde to a carboxylic acid. B. produce both ATP and NADH. C. couple the oxidation of a C-H bond to the activation of carrier molecules. D. catalyze the only glycolytic reactions that create a high-energy phosphate linkage directly from inorganic phosphate.

The two chromosomes in each of the 22 homologous pairs in our cells ...

show identical banding patterns after Giemsa staining.

You have two tubes. Tube 1 contains the DNA encoding the genome of a human being and tube 2 contains the DNA encoding the genome of a lithotrophic archaean that lives adjacent to a deep-sea hydrothermal vent that has an average temperature of 115°C (note that normal human body temperature is 37°C). You lend your tubes to a chemist friend, who loses the label on your tubes. However, he was able to determine the percentage molar ratios of As and Ts in these tubes, and finds that the DNA in tube 1 is composed of 59% As and Ts while the DNA in tube 2 is composed of 48% As and Ts. Which tube contains the human DNA and which tube contains the archaean DNA? Explain

tube 1 human, tube 2 archea, tube 2 has higher GC content and higher melting temperature needed in a high temp environment

Dephosphorylation, mutation, or deletion of a particular tyrosine residue in the C-terminal tail of the protein leads to increased activity of the kinase and promotes cancerous transformation of cells. Do you expect the proteolytic fragment containing the kinase domain to be regulated strongly by phosphorylation of the key tyrosine in the C-terminal tail? Explain.

No regulation because c-terminal tail binds to the SH2 domain which isn't present In the kinase domain

Which of the following statements is true?

Nonpolar amino acids tend to be found in the interior of proteins

Which of the following statements is true?

Nonpolar amino acids tend to be found in the interior of proteins.

The free-energy change (ΔG) for a simple reaction, A → B, is 0 kJ/mole at 37°C when the concentrations of A and B are 10 M and 0.1 M, respectively. What is the free-energy change for the reaction when the concentrations of A and B are instead 0.01 M and 1 M, respectively? Recall that ΔG° = -5.9 × log(Keq). Write down your answer as a number with the appropriate sign (+ or -) and in kJ/mole, e.g. +11.8 kJ/mole

+23.6kJ/mole

At physiological pH, what is the approximate net che of a hexapeptide with the following amino acid sequence? Asp-Val-Ile-Glu-Arg-Ser

-1

The folding of proteins can be considered a simple conversion from the unfolded to the natively folded state. At about 27°C (or 300 K), the free-energy change of folding for a particular protein is measured to be -40 kJ/mole. If the enthalpy change (ΔH) of folding is -640 kJ/mole, what is the entropy change (ΔS) of folding for this protein? Write down your answer with the appropriate sign (+ or -) and in kJ/mole/K, e.g. -1000 kJ/mole/K.

-2Kj/mole/K Feedback: For the folding reaction, the free-energy change can be written as: ΔG = ΔH - TΔS ΔS = (ΔH - ΔG)/T = (-640 kJ/mole + 40 kJ/mole) / (300 K) = -2 kJ/mole/K The negative value of ΔS means a decrease in entropy. This is not unexpected since folding results in the formation of a single conformation (or a limited set of conformations) out of an enormous number of possible coils

In the first reaction of the glycolytic pathway, the enzyme hexokinase uses ATP to catalyze the phosphorylation of glucose, yielding glucose 6-phosphate and ADP. The ΔG° value for this reaction is -17 kJ/mole. The enzyme glucose 6-phosphatase catalyzes a "reverse" reaction, in which glucose 6-phosphate is converted back to glucose, and a phosphate is released. The ΔG° value for this reaction is -14 kJ/mole. What is the ΔG° value for the following reaction? ATP + H2O → ADP + Pi

-31 kJ/mole

What interactions hold the heme group in place in the hemoglobin monomer

-Hydrophobic interactions hold the heme group in place -Anchoring of the heme---> histidine nitrogen that binds to iron

Explain what causes red blood cells to sickle in a patient that has sickle cell anemia on a molecular level

-Mutation in the beta globin gene in hemoglobin. Amino acid change from GLU to VAL causing clumped hemoglobin molecules

Which amino acids stabilize the Iron atom in the heme group.

-histidine amino acid and imidazole ring

Which of the following is true regarding Escherichia coli?

. E. coli strain K-12 encodes about 4300 proteins.

In the following schematic diagram of a simple signaling pathway, protein Z regulates the activity of protein X, which is an upstream protein kinase, through a negative feedback loop. Which of the following better describes protein Z?

. It is a protein phosphatase that is activated by phosphorylation.

This model organism is particularly well suited for studying developmental processes in higher animals. It develops from a fertilized egg to an adult in only two to three months, and its body is transparent for the first two weeks, making it easy to observe cell behavior during development. Which of the following describes this organism?

. It is a vertebrate. B. It is well suited for genetic analysis. C. Its early stages of development occur outside of the mother's body. D. Its genome size is almost half that of humans.

The substrate for the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase is glyceraldehyde 3-phosphate (with one phosphate group) while its product is 1,3- bisphosphoglycerate (with two phosphate groups). Where does the extra phosphate group come from? A

. Pi

The enzyme phosphoglucose isomerase converts glucose 6-phosphate to its isomer fructose 6-phosphate in the second step of glycolysis. The equilibrium constant for the reaction is 0.36. Evaluating the ΔG° of the reaction (ΔG° = -5.9 × log Keq), decide which of the following conclusions is true.

. The ΔG° is positive, but in a cell that is active in glycolysis, the reaction can still proceed in the forward direction.

Evolutionary tracing has identified clusters of the most invariant amino acids in the SH2 domain family. Which of the following is true regarding these sites?

. These sites correspond to the binding site for peptides containing phosphorylated tyrosine.

Mitochondria and chloroplasts are thought to have evolved from free-living aerobic bacteria that were engulfed by an ancestral anaerobic cell and established a mutually beneficial (symbiotic) relationship with it. Which of the following statements is NOT true about these organelles?

. They are found in all eukaryotes.

In terms of molecular function, what do Ras and myosin have in common?

. They couple the hydrolysis of a bound nucleoside triphosphate to protein movements.

A hydrophobic molecule is typically ...

. incapable of interacting favorably with water.

A polyubiquitin chain has been attached to a protein. The ubiquitin molecules are linked together via isopeptide bonds between Lys48 of one molecule and the carboxyl end of the next one. This protein is expected to ...

. undergo proteasomal degradation

The equilibrium constant for the reaction that breaks down each molecule of substrate A to one molecule of B and one molecule of C is equal to 0.5. Starting with a mixture containing only molecules A at 1 M concentration, what will be the concentration of molecule A after reaching equilibrium under these conditions?

0.5M

A protein X that is known to exist in two slightly different conformations, called X1 and X2. Proteins A, B, and C are ligands that can bind to protein X. The sites on X required for binding to A, B, and C are located in different regions of the protein. On the basis of experimental evidence of protein-protein complexes, you devise the hypothetical binding reaction scheme shown in Figure Q9. According to the hypothesis, which pairs of binding sites on X exhibit negative coupling (negative linkage)? Which pairs exhibit positive coupling (positive linkage)? Does the addition of a high concentration of protein A increase or decrease the affinity of X for B? Of X for C?

1) negative cooperativity a/c & b/c if A or B binds C cant if C binds A&B are blocked 2) positive cooperativity A+B, bind a or b first allows the other B or A to bind 3) high concentration of A increase affinity for B

The electron carriers NADH and FADH2 donate their electrons to the electron-transport chain in the inner mitochondrial membrane, leading to ATP synthesis powered by an H+ gradient across the membrane. If, on average, the oxidation of each NADH or FADH2 molecule in this pathway results in the production of 2.5 and 1.5 molecules of ATP, respectively, how many ATP (and GTP) molecules are produced on average as a result of the complete oxidation of one molecule of acetyl CoA in the mitochondrion? Consider only the citric acid cycle and oxidative phosphorylation.

10

The turnover number for an enzyme is equivalent to the number of substrate molecules processed per second per enzyme molecule. To a test tube containing a 100 mM concentration of its substrate, you have added an enzyme at a final concentration of 10 µM, and have measured the rate of the reaction to be approximately 500 µM/sec. If the Km for the binding of the enzyme to this substrate is about 100 mM, what is the turnover number?

100 Feedback: Under these conditions, we have: [S] = Km = 100 mM. This means the rate of reaction is: V = ½ × Vmax. Thus, Vmax = 2 × 500 µM/sec = 1000 µM/sec. Finally, turnover number is equal to this rate divided by the enzyme concentration; that is: kcat = (1000 µM/sec) / (10 µM) = 100 per second.

Findings from a number of experiments on human chromatin have suggested that the DNA in our chromosomes is organized into loops of various lengths. Approximately how long is a typical loop (in nucleotide pairs of DNA)?

100,000

Assume two isolated human communities with 500 individuals in each. If the same neutral mutation happens at the same time in two individuals, one from each community, what is the probability that it will be eventually fixed in both of the populations? How would the result change if the two communities fully interbreed? Write down the numbers in scientific notation and separate the two answers with a comma:

10^-6, 10^-3

In assembling a nucleosome, normally the ...(1) histone dimers first combine to form a tetramer, which then further combines with two ... (2) histone dimers to form the octamer.

1: H3-H4; 2: H2A-H2B

In each of the following comparisons, indicate whether the molecular clock is expected to tick faster on average in the first (1) or the second (2) case. ( ) 1: The exons, or 2: the introns of a gene ( ) 1: The mitochondrial, or 2: the nuclear DNA of vertebrates ( ) 1: The first, or 2: the third position in synonymous codons ( ) 1: A gene, or 2: its pseudogene counterpart

2122

For each of the following classifications, indicate whether you would expect to find an actively transcribed gene in the first category (1) or the second (2) ( ) 1: Heterochromatin, or 2: euchromatin ( ) 1: Chromosome puffs, or 2: condensed chromosome bands ( ) 1: Nuclear periphery, or 2: the center of the nucleus ( ) 1: Within the chromosome territory, or 2: extended out of the territory ( ) 1: Apart from, or 2: close to actively transcribed genes within the nucleus ( ) 1: 11-nm "beads-on-a-string" fibers, or 2: 30-nm fibers

212221

Indicate if each of the following descriptions matches lipids (1), nucleic acids (2), polysaccharides (3), or proteins (4). Your answer would be a four-digit number composed of digits 1 to 4 only, e.g. 1332. Their monomers contain phosphorus and nitrogen. ( ) They constitute almost half of the cell's dry mass. ( ) They are the main constituent of all cellular membranes. ( ) They are largely hydrophobic and can store energy.

2411

Indicate which feature (1 to 4) in the schematic drawing below of a chromatin fiber corresponds to each of the following. Your answer would be a four-digit number composed of digits 1 to 4 only

2431

If the genetic code consisted of four bases per codon rather than three, the maximum number of unique amino acids that could be encoded would be

256

Imagine a protein that can be independently phosphorylated on any of its 10 tyrosine residues and acetylated on either of its 2 lysine residues. In principle, how many different combinations of these modifications are possible for this protein?

2^12

In the citric acid cycle shown above, which steps produce CO2 as a by-product? List all such steps by their number, from the smallest number to the largest. Your answer would be a number composed of digits 1 to 8 only, e.g. 258

34 Feedback: Steps 3 and 4 are catalyzed by isocitrate dehydrogenase and the α-ketoglutarate dehydrogenase complex, respectively, and involve decarboxylation of the substrates and the release of carbon dioxide.

In the citric acid cycle shown above, which steps produce either NADH or FADH2? List all such steps by their number, from the smallest number to the largest.

3468

Indicate which numbered feature (1 to 5) in the schematic drawing below of the DNA double helix corresponds to each of the following. Your answer would be a five-digit number composed of digits 1 to 5 only

43215

Which of the regulatory interactions 1 to 5 depicted in the following diagram is NOT an example of a negative feedback regulation? P Q T R S 1

5

Imagine a human protein containing 33 repeats of a simple domain arranged in tandem. In contrast, a homolog found in bacteria contains only one domain. What is the minimum number of duplication events that can account for the evolution of this protein since our divergence from bacteria?

6

The cell can change the pH of its internal compartments using membrane transport proteins that pump protons into or out of a compartment. How many protons should be pumped into an endocytic vesicle that is 10-15 liters in volume and has a neutral pH in order to change the pH to 5? Avogadro's number is 6 × 1023 . Omit complications such as the membrane potential, buffers, and other cellular components.

6000

If the genetic code consisted of 5 bases per codon instead of three, then it would be possible to encode ______ unique amino acids

625

What is the pH of a 10-8 M solution of hydrochloric acid? Round the pH value to the nearest integer, e.g. 10

7

Your friend learns about Avogadro's number and thinks it is so huge that there may not even be a mole of living cells on Earth. You have recently heard that there are about 50 trillion (50 ´ 1012) human cells in each adult human body, so you bet your friend $5 that there is more than a mole of cells on Earth. Once you learn that each human contains more bacterial cells (in the digestive system) than human cells, you are sure that you have won the bet. In the year 2011, the human population surpassed 7 billion (7 ´ 109). What calculation can you show your friend to convince him you are right?

7 x 10^23

A DNA nucleotide pair has an average mass of approximately 660 daltons. Knowing the number of nucleotides in the human genome, how many picograms of DNA are there in a diploid human nucleus? Avogadro's number is 6 × 1023 . Write down the picogram amount without decimals (round the number to the closest integer)

7PG

Chromosome 3 contains nearly 200 million nucleotide pairs of our genome. If this DNA molecule could be laid end to end, how long would it be? The distance between neighboring base pairs in DNA is typically around 0.34 nm.

7cm

The position effect variegation (PEV) phenotype described in this chapter can be used to identify new genes that regulate heterochromatin formation. For instance, strains of Drosophila melanogaster with the White variegation phenotype have been subjected to mutagenesis to screen for dominant mutations (in other genes) that either enhance or suppress PEV, meaning the mutations result in either lower or higher red pigment production, respectively. Which of the following mutations is expected to be an enhancer of variegation?

A gain-of-function mutation in a gene encoding a histone methyl transferase that trimethylates lysine 9 on histone H3, resulting in a hyperactive form of the enzyme.

In an enzymatic reaction involving NADH or NADPH, reduction of a substrate accompanies the oxidation of these carrier molecules to NAD+ or NADP+ , respectively. What else typically happens in such a reaction?

A proton is taken up by the substrate that is being reduced.

Which of the following stretches of amino acid residues would you expect to find in the interior of protein molecules?

A. Ala-Asp-Asp-Tyr-Arg B. Gly-Lys-Ser-Pro-Thr C. Phe-Glu-Gln-Glu-Asn D. Ala-Val-Leu-Ile-Trp E. Gly-Tyr-His-Arg-His Feedback: Hydrophobic side chains in a protein—belonging to amino acids such as phenylalanine, leucine, isoleucine, valine, and tryptophan—tend to be buried in the interior of the molecule to avoid the unfavorable contact with water. D

Many viruses have large capsids in the form of a hollow sphere, made of hundreds of identical protein subunits. What are the advantages of having coats made of several copies of only a few subunits?

A. Assembly can be readily regulated. B. Disassembly can be readily regulated. C. It requires a smaller amount of genetic information. D. The effect of mistakes in protein synthesis on the overall assembly is minimized. E. All of the above. Feedback: Especially for some viruses, small genome sizes confer high evolutionary fitness.

Which of the following pairs of amino acid residues would you expect to form ionic bonds?

A. Glutamic acid and glutamine B. Arginine and lysine C. Lysine and glutamic acid-------- D. Tryptophan and tyrosine E. Tyrosine and glutamine Feedback: Electrostatic attractions can hold together amino acid residues of opposite charge, i.e. an acidic and a basic residue.

Which of the following can be a function for intrinsically disordered protein sequences?

A. High-specificity binding to other proteins B. Cell signaling through covalent modification of the protein sequence C. Tethering to hold interacting proteins in close proximity D. Formation of a diffusion barrier from a dense network of such sequences E. All of the above Feedback: Intrinsically disordered protein sequences are frequent in nature, and many of them are involved in one or more of these four important functions.

Which of the following is NOT the role of molecular chaperones in the folding of cellular proteins?

A. They assist proteins in folding into their correct conformations. B. They help prevent formation of protein aggregates. C. They specify the final three-dimensional shape of proteins. D. They catalyze the folding of proteins in the crowded environment of the cell. E. They make the protein-folding process in the cell more reliable. Feedback: The molecular chaperones assist a protein in adopting its correct conformation, which is specified by the protein's amino acid sequence. C

An amino acid residue that is not part of the active site of an enzyme and does not interact with the ligand is nevertheless critical for ligand binding and is highly conserved. How can this be explained?

A. This residue is critical for the correct folding and the placement of ligand-binding site residues. B. The residue helps with restricting the access of water to the ligand-binding site. C. This residue can affect the chemical properties of the residues in the ligand-binding site. D. All of the above. Feedback: Residues that are far from the binding site can still influence ligand binding by affecting global or local folding of the protein, by controlling the access of water to the binding site, or by changing the chemical properties of other residues. D

The SCF ubiquitin ligase can recognize and mark various target proteins at different stages of the cell cycle. In this complex, ...

A. different F-box subunits recognize different target proteins. B. the F-box subunit and the E2 ubiquitin-conjugating enzyme are at the opposite ends of the C-shaped molecule. C. a scaffold protein arranges the other subunits such that the two ends of the complex are separated by a gap. D. the use of interchangeable parts such as the F-box subunits makes economical use of the genetic information and allows for rapid evolution of new functions.

The observation that proteins often renature into their original conformations after they have been unfolded by denaturing solvents implies that ...

A. the information needed to specify the three-dimensional shape of a protein is encoded in its amino acid sequence

In the following paragraph, fill in the blanks (indicated by numbers) with either Archaea (A), Bacteria (B), or Eukaryotes (E). Your answer would be a three-letter string composed of letters A, B, and E only, e.g. ABE. "Methanococcus jannaschii is an anaerobic thermophilic microbe that belongs to the domain ... (1) and is found in extreme environments such as hydrothermal vents. It lives at temperatures near the boiling point of water and at pressures over 200 times higher than at sea level. Its genome sequence, identified in 1996, revealed that most of its metabolic processes are similar to those in ... (2), while its genetic machinery is more similar to that of ... (3)."

ABE Feedback: Archaea usually live in extreme environments, and resemble eukaryotes more in their genetic machinery, and bacteria more in their metabolic machinery.

Gene duplication can give rise to homologous genes that are part of gene families. For example, there are six actin genes in the genome of most mammalian species. In humans, the ACTB gene, which encodes a cytoskeletal actin, is expressed ubiquitously, while ACTC1 is expressed mainly in cardiac cells. Although bacteria lack the eukaryotic cytoskeletal organization, the bacterial MreB gene bears recognizable sequence similarity to mammalian actin genes and codes for a protein that is similar to actin in structure and function. Which of the following statements is true about these genes?

ACTB is paralogous to ACTC1 but not to MreB

The phosphofructokinase (PFK) enzyme is one of the key players in the glycolytic pathway in which glucose eventually breaks down into pyruvate, some ATP is generated, and some NAD+ is reduced. PFK catalyzes the committed step in the pathway and is under extensive regulation. Which of the following compounds would you expect to activate PFK?

ADP

The human estrogen receptor is a symmetrical dimeric nuclear protein that can regulate gene expression by binding to a DNA sequence called an estrogen response element (ERE) near the promoter of its target genes. Each subunit of the receptor binds to about six base pairs of DNA. Which of the following sequences is a likely candidate for the ERE? The sequences are written in the 5′-to-3′ direction. The letter N represents any of the four DNA bases.

AGGTCANNNTGACCT

The investigators examined the behavior of the ATCase enzyme in the presence of CTP, and in the presence of both CTP and ATP. The concentration of CTP is 0.1 mM and the concentration of ATP is 2 mM. The results are shown in Figure 16.3. What is the significance of these observations?

ATCase is Asparatate trans-carbamoylase enzyme, and is allosterically regulated. The effector molecule binds to an enzyme to enhance/activate activity. ATP, in this case, is the regulator of ATCase -- there are sites on the enzyme where both can bind. ATCase has only 2 subsites (A and B); for A, ATP or CTP bind competitively. For B, UTP and ATP bind competitively. In this case, UTP is not present, so ATP binds to subsite B without competition as CTP binds to subsite A.

Which of the following would you NOT expect to find in a bacterial cell?

ATP production in mitochondria

What are the molecules that normally supply carbon and oxygen atoms, respectively, for the citric acid cycle?

Acetyl CoA, H2O

Aconitase catalyzes an isomerization reaction in the citric acid cycle shown above, in which H2O is first removed and then added back to the substrate. Which step is catalyzed by this enzyme?

Aconitase converts citrate to isocitrate through an aconitate intermediate created by dehydration of the substrate.

Switch proteins that bind and hydrolyze GTP are ubiquitous cell regulators in a wide variety of molecular processes. Which of the following statements is NOT true regarding these proteins?

Activation of the GTPase involves addition of a phosphate group to its bound guanine nucleotide.

The kinetics of the ATCase reaction were examined using increasing concentrations of aspartate, in the presence and absence of CTP and ATP as shown in Figure 16.2. a. What information can you obtain by looking at the shapes of the curves in this figure?

Allosteric interaction; allows enzyme to report efficiently in quick time, as the concentration changes, a sigmoidal shape forms, and a slight change can have a dramatic effect on the pathway. A combination of cooperative and allosteric binding that makes the process effective. What kinetic parameter(s) change in the presence of CTP? What parameter(s) do not change? What is the significance of these observations? If CTP is present, ATCase is inhibited and does not work to build CTP. Therefore synthesis of pyrimidines would not occur and purines would be favorable. Answer question 2b for ATP. ATP is still needed in the cell, however a large amount of ATP is not necessary to generate CTP using ATCase because the cell is inhibited by the already present CTP.

Which of the following is NOT true regarding the tree of life?

Archaeal species were thought to belong to the eukaryotic world before sequence analysis placed them in a separate domain of life

Your friend learns about Avogadro's number and thinks it is so huge that there may not even be a mole of living cells on Earth. You have recently heard that there ar about 50 trillion (50 ́ 1012) human cells in each adult human body, so you bet your friend $5 that there is more than a mole of cells on Earth. Once you learn that each human contains more bacterial cells (in the digestive system) than human cells, you are sure that you have won the bet. In the year 2011, the human population surpassed 7 billion (7 ́ 109). What calculation can you show your friend to convince him you are right?

Avogadro's number, or 6 × 1023, is the number of atoms (or units) in a mole. If you multiply the number of people on Earth by the number of cells in the human body, then double it to account for the bacteria, you will calculate: (7 × 10^9)persons × (50 × 10^12)cells × 2 = 7 x10^23

The number of ways in which protein domains fold in nature is limited. Which of the following is a better estimate of this number?

B. 2000

Which of the following chemicals do you NOT expect to be readily dissolved in water?

B. Hexane

Indicate whether each of the following histone modifications adds a negative charge to the histone (A), removes a positive charge from the histone (B), or does neither of these (C). ( ) H3 lysine 9 acetylation ( ) H3 serine 10 phosphorylation ( ) H3 lysine 4 trimethylation ( ) H3 lysine 9 trimethylation

BACC

The regions of synteny between the chromosomes of two species can be visualized in dot plots. In the example shown in the following graph, a chromosome of a hypothetical species A has been aligned with the related chromosome in species B. Each dot in the plot represents the observation of high sequence identity between the two aligned chromosomes in a window located at the two corresponding chromosome positions. A series of close dots can make a continuous line. Choosing a sufficiently large window size allows a "clean" dot plot with solid lines that show only the long stretches of identity, allowing ancient large-scale rearrangements to be identified. Several chromosomal events can be detected in such dot plots. Indicate which feature (a to g) in the dot plot is best explained by each of the following events. Your answer would be a seven-letter string composed of letters a to g only, e.g. cdbagef. Each letter should be used only once ( ) A duplication that exists in both species ( ) A duplication in species A only ( ) A triplication in species B only ( ) An inversion without relocation ( ) An inversion combined with relocation ( ) A deletion in species A ( ) A translocation in species A from a different chromosome

BCFEDAG

If species A in the distance matrix represents human, indicate which of the other species (B to D) represents chimpanzee, gorilla, and orangutan, respectively

BDC

The following tree can be constructed from these distances assuming a constant molecular clock, meaning that the length of each horizontal branch corresponds to evolutionary time as well as to the relative genetic distance from the common ancestor that gave rise to that branch. Indicate which one of the species in the matrix (B to D) corresponds to branches 1 to 3, respectively.

BDC

Sort the following from a low to a high contribution to the total mass of an E. coli bacterium. Your answer would be a four-letter string composed of letters A to D only (A)Water (B) Sugars (C) Proteins (D)Nucleic acids

BDCA

Two ligands, A and B, bind to two different conformations of the enzyme X. The ligand A is the enzyme's substrate, whereas ligand B binds to a remote allosteric site. Which of the following is a consequence of this arrangement?

Binding of B to X decreases the affinity of X for A.

How do multi-enzyme complexes in the cell, such as the fatty acid synthase, enhance reaction rates?

By allowing the channeling of pathway intermediates from one enzyme to the next

Which of the following elements is not normally found in cells?

C. Silver

Imagine a cellular protein composed of 3000 amino acid residues in one continuous polypeptide chain. This protein is almost certainly ...

C. multidomain.

Sort the following molecules from a low to high rate of diffusion inside the cytosol. Your answer would be a four-letter string composed of letters A to D only, e.g. ADCB. A)Myoglobin (a protein) (B) Glycine (an amino acid) (C) Ribosome (a protein-RNA complex) (D)CO2

CABD

Which of the following correctly summarizes the overall process of photosynthesis?

CO2 + H2O → O2 + sugars

Many years later, in 1989, Wild, et al. revisited the idea of allosteric control of ATCase by CTP. They noted that CTP did indeed inhibit ATCase, but that the inhibition was always incomplete, even at high concentrations of CTP. They hypothesized that perhaps CTP did not act alone, but in combination with some other nucleotide. They tested the activity of ATCase in the presence of several nucleotide combinations. The results are shown in Table 16.3. a. What combination gives the most effective inhibition?

CTP/ UTP Things that are similar to CTP would also inhibit ATCase→ other pyrimidines like cytosine, uracil, thymine that create CTP, UTP, TTP b. What is the physiological significance of this combination? ATCase inhibited by CTP (final product of ATCase pathway). When CTP is absent, ATCase reaction is quick. The rate of the reaction decreases as CTP concentration increases. CTP is synthesized from UTP. When UTP levels rise, both UTP and CTP can inhibit ATCase.

In interactions between proteins, each hydrogen bond contributes to the free energy of binding by about -4 kJ/mole. If two proteins bind to each other through nine hydrogen bonds, six of which are eliminated when one of these proteins is mutated, how much would you expect the equilibrium constant for their binding to change as a result of the mutation? (ΔG° = -5.9 × log Keq

Decrease by four orders of magnitude

Protein secondary structure elements such as α helices and β sheets constitute the major regular folding patterns in proteins. With regard to these elements, ...

D. the folding patterns result from hydrogen-bonding between the N-H and C=O groups in the polypeptide backbone.

The molecules inside the cell constantly collide with other molecules and diffuse through the cytoplasm in a random walk. The average net distance traveled by such a molecule after a certain time period t is proportional to the square root of t, i.e. (t) 0.5 , as well as to its diffusion coefficient. If, on average, it takes a molecule 100 milliseconds to travel a net distance of 0.5 µm from its starting point, how long would it normally take for the same molecule to travel a net distance of 5 µm from the same starting point?

D. 10 seconds

What is the order of the following evolutionary landmarks (A to D), from the oldest to the most recent? A. Divergence of human and bird lineages B. Divergence of human and chimpanzee lineages C. Divergence of A. thaliana lineage from the conifers lineage D. Divergence of fish and insect lineages

DACB

Sort the following molecules (A to E) based on the oxidation of the carbon atom, from higher to lower oxidation states. Your answer would be a five-letter string composed of letters A to E only, e.g. ADCBE. Put the letter corresponding to the highest oxidation level on the left.

DAECB

Sort the following molecules based on the amount of energy that is released when their phosphate bond is hydrolyzed as indicated. Your answer would be a four-letter string composed of letters A to D only, e.g. ADCB. Put the molecule with the highest amount of hydrolysis energy on the left. (A)ATP when hydrolyzed to ADP (B) Glucose 6-phosphate when hydrolyzed to glucose (C) 1,3-bisphosphoglycerate when hydrolyzed to 3-phosphoglycerate (D)Phosphoenolpyruvate when hydrolyzed to pyruvate

DCAB

The centromeric regions in the fission yeast Schizosaccharomyces pombe are wrapped by nucleosomes containing the CENP-A histone H3 variant, and are flanked by clusters of tRNA genes that separate them from the surrounding pericentric heterochromatin. If the tRNA clusters are removed from this region, the HP1-bound heterochromatin spreads further to cover the centromeric regions. The tRNA genes are transcribed by strong RNA polymerase III promoters, which can associate with transcription factors and recruit chromatin-modifying enzymes. Based on these observations, indicate which blanks (A to E) in the paragraph below correspond to each of the following phrases. "The ...(A) are not sufficient to prevent heterochromatin expansion to the centromeric regions. Instead, the ...(B) are acting as ...(C) in S. pombe, similar to the role of the ...(D) in the β-globin locus in chickens and humans. Likely candidates for the histone-modifying enzymes recruited by the RNA polymerase III complexes are ...(E)." ( ) HS4 element ( ) chromatin boundaries ( ) histone acetyl transferases ( ) tRNA genes ( ) CENP-A-containing histones

DCEBA

Indicate if each of the following descriptions matches RNA (R) or DNA (D). Your answer would be a five-letter string composed of letters R and D only ( ) It is mainly found as a long, double-stranded molecule. ( ) It contains the sugar ribose. ( ) It normally contains the bases thymine, cytosine, adenine, and guanine. ( ) It can normally adopt distinctive folded shapes. ( ) It can be used as the template for protein synthesis.

DRDRR

You have purified a multisubunit extracellular protein that has several interchain disulfide bonds. Which of the following chemicals would you add to your purified protein mixture if you wanted to eliminate the disulfide bonds?

DTT, a reducing agent

Which of the following processes that happens inside a cell DOES NOT normally require consumption of free energy by the cell?

Diffusion of small molecules within the cell

Which of the following processes that happens inside a cell DOES NOT normally require consumption of free energy by the cell?

Diffusion of small molecules within the cell

Protein A can bind to each of the proteins B or C. The association rate constants are the same for forming the AB and the AC complexes. However, the dissociation rate constant for AB is 100 times higher than that for AC. Given that every tenfold increase in the equilibrium constant (of the association reaction) corresponds to about -5.9 kJ/mole difference in the standard free-energy change for the reaction (ΔG°), what is the value of (ΔG°AB - ΔG°AC) in kJ/mole?

E. +11.8 Feedback: The equilibrium constant for complex formation is equal to the ratio of association and dissociation rate constants; thus, it is 100 times higher for AC compared to AB. This makes ΔG°AB more positive than ΔG°AC by a 11.8 kJ/mole difference.

Based on the variation of genome size and gene number in the organisms presented in the following graph, which organism has

E. coli

The three families of cellular macromolecules are polymerized and depolymerized by a general mechanism involving water. Each of them has a set of monomers whose polymerization changes the total free energy of the system. Which of the following statements is true regarding these macromolecules?

Each polymerization step requires free-energy input and proceeds by the release of one water molecule.

Fill in the blank in the following paragraph. "During intense 'anaerobic' physical exercise, the high energy demand in the muscle cells leads to an accumulation of lactic acid in these cells and their surrounding tissues. Similarly, the yeast Saccharomyces cerevisiae can produce ethanol when grown anaerobically. The lactate or ethanol production takes place in a process called ..."

FERMENTATION

Weak noncovalent attractions in the cell can be very strong in a nonaqueous environment. Some of these attractions are as strong as covalent interactions in a vacuum (their bond energy is approximately 340 kJ/mole), but become more than twenty-five times weaker (their bond energy becomes approximately 13 kJ/mole) in water. What type of attraction shows this phenomenon?

Electrostatic interactions

Enzymes are the cell's catalyst crew. They make the life of the cell possible by carrying out various reactions with astounding performance. Which of the following is NOT true regarding cellular enzymes?

Enzymes can change the equilibrium point for reactions that they catalyze.

Indicate true (T) and false (F) statements below regarding a genome and its evolution. Your answer would be a four-letter string composed of letters T and F only ( ) The genome of the last common ancestor of mammals can be investigated only if a DNA sample of the ancestor can be obtained. ( ) All of the "ultraconserved" elements found in the human genome have been shown to encode long noncoding RNAs. ( ) If a mouse carrying a homozygous deletion of a highly conserved genomic sequence survives and shows no noticeable defect, the highly conserved sequence has to be functionally unimportant. ( ) The "human accelerated regions" are genomic regions that are found in humans with no homologs in chimpanzees or other animals.

FFFF

Indicate true (T) and false (F) statements below regarding the cellular metabolism of nucleotides and amino acids. Your answer would be a four-letter string composed of letters T and F only, ( ) Nitrogen fixation occurs in the mitochondria in most animal cells to generate amino acids. ( ) All 20 natural amino acids must be provided in our diet and are therefore "essential." ( ) There are NO essential nucleotides that must be provided in the diet. ( ) Catabolism of amino acids in our body leads to the production of urea which is excreted

FFTT

As each cell in our body prepares for mitosis, its chromosomes start to look different. What are the changes in chromosome appearance that accompany the entry into M phase? Indicate true (T) and false (F) descriptions below. ( ) The chromosomes become readily visible by the naked eye. ( ) The chromosomes coil up further to become about 10 times shorter. ( ) Each chromosome is condensed and then replicated to form two sister chromatids. ( ) The typical diameter of a mitotic chromosome arm is about 70 nm. ( ) The two sister chromatids are disentangled from each other by the time chromosome condensation is complete

FTFFT

Indicate true (T) and false (F) statements below regarding glycolysis. Your answer would be a four-letter string composed of letters T and F only Molecular oxygen is used in glycolysis to oxidize glucose. ( ) Along the glycolytic pathway, ATP is both consumed and generated. ( ) In the course of glycolysis, one molecule of NADH is formed per molecule of glucose. ( ) Following the production of one molecule of fructose 1,6-bisphosphate, the rest of the glycolytic pathway generates four molecules of ATP.

FTFT

Indicate true (T) and false (F) statements below regarding human genetic variations ( ) The genomes of two randomly chosen humans are expected to be identical with respect to at least 99.99% of the nucleotides. ( ) Copy number variations can contain genes. ( ) If the frequency of a point mutation in a population is only 0.1%, with no mutation at this site in the rest of the population, then the variation is NOT considered to constitute a single-nucleotide polymorphism. ( ) Most of the common genetic variants in the current human population could have

FTTT

Indicate true (T) and false (F) statements below about the human genome. Your answer would be a six-letter string composed of letters T and F only ( ) Only about 1.5% of the human genome is highly conserved. ( ) Almost half of our genome is composed of repetitive sequences. ( ) Genes occupy almost a quarter of the genome. ( ) There are roughly as many pseudogenes in the human genome as functional genes. ( ) Transposable elements occupy almost 10% of our genome. ( ) On average, exons comprise 1.5% of our genes.

FTTTFF

It is a model organism used to study various cell processes such as regulation of the eukaryotic cell cycle. Mutants are available for every gene in its exceptionally small genome. It can live indefinitely in either a haploid or a diploid state. Which of the following describes this organism?

FUNGUS

To discover genes that have undergone accelerated evolution in the human lineage, you compared the amino acid sequences of dozens of proteins from orthologous protein-coding genes in humans, chimpanzees, and mice. For each gene, you build an unrooted phylogenetic tree in which the branch lengths (a, b, or c) correspond to the number of amino acid substitutions in that branch, as depicted below. Primates and rodents diverged ~90 million years ago, and humans and chimpanzees diverged ~5.5 million years ago. For each individual gene shared by the three species, you therefore define the "normalized substitution rate" parameters h and k as h = (a/5.5)/[c/([2 × 90] - 5.5)], and k = (b/5.5)/[c/([2 × 90] - 5.5)]. Based on these definitions, which genes are more likely to be responsible for "uniquely human" traits?

Genes with very high h values but not very high k values

In step 1 of the citric acid cycle drawn above, what is the molecule indicated with a question mark?

H20

Laboratory strains of the model organism Escherichia coli that are resistant to antibiotics are very often used in research laboratories as well as in the biotechnology industry. If cultures of such bacteria were allowed to contaminate the environment uncontrollably, it is possible that at some point, pathogenic bacteria such as Neisseria meningitidis (which causes meningitis and can cause death, especially in children) could acquire the same antibiotic-resistance gene, causing a meningitis outbreak that is difficult to treat. In this scenario, which of the following mechanisms is a more likely source of the antibiotic-resistance gene in N. meningitidis?

HORIZONTAL GENE TRANSFER

What features do Cajal bodies, interchromatin granule clusters, and nucleoli have in common?

High permeability to the surrounding nucleoplasm

For each of the following pairs, indicate whether they interact via hydrogen bonds (H) or ionic bonds (I), or do not favorably interact (N). Your answer would be a four-letter string composed of letters H, I, and N only, e.g. HNNI ATP and Mg2+ ( ) Urea and water ( ) Glucose and the enzyme hexokinase (which uses glucose as a substrate) ( ) A phospholipid tail and inorganic phosphate

IHHN

Five major types of chromatin were identified in studies performed on Drosophila melanogaster cells, although much more remains to be learned about chromatin diversity and dynamics. Which of the following is correct regarding these findings in Drosophila?

In addition to these five major types of chromatin, there seem to be additional minor types as well.

Despite their overall similarity, NADH and NADPH are not used indiscriminately by the cell. What are the distinctive features of these two carrier molecules?

In the cell, NADH is found mostly in the form that acts as an oxidizing agent, whereas NADPH is found mostly in the form that acts as a reducing agent.

The enzyme lysozyme catalyzes the cutting of a polysaccharide chain through hydrolysis. Which of the following is NOT true regarding the catalytic cycle for this enzyme?

It involves metal ion catalysis. Lysozyme uses several mechanisms to accelerate the reaction by several orders of magnitude. The process involves using amino acid side chains that act as acids (donate protons) or bases (accept protons) during the catalytic cycle, straining the substrate to expose the target bonds, and even forming a temporary covalent linkage with one half of the substrate. However, metal ions are not used by this enzyme for catalysis.

Imagine the reaction A → B with a negative ΔG value under experimental conditions. Which of the following statements is true about this reaction?

Increasing the concentration of B molecules would increase the ΔG value (toward more positive values).

Which of the following is true regarding a fatty acid molecule in water?

It is negatively charged at physiological pH, but can become neutral when the pH is low enough.

Nucleosomes that are positioned like beads on a string over a region of DNA can interact to form higher orders of chromatin structure. Which of the following factors can contribute to the formation of the 30-nm chromatin fiber from these nucleosomes?

Interactions that involve the histone tails of neighboring nucleosomes B. Interaction of the linker histone H1 with each nucleosome C. Binding of proteins to DNA or the histones D. ATP-dependent function of chromatin remodeling complexes

It is a model organism used to study various cell and developmental processes such as the growth of developing body parts in the right place and with the correct shape. It develops from a fertilized egg to an adult in a little over a week, and has been a favorite of geneticists for almost a century. Some of its cells have giant chromosomes whose banding patterns have been extremely helpful in classical genetic studies. Which of the following describes this organism?

It normally only reproduces sexually.

Arsenate is a toxic ion that can interfere with both glycolysis and oxidative phosphorylation. Arsenate resembles Pi (inorganic phosphate) and can replace it in many enzymatic reactions. One such reaction is catalyzed by glyceraldehyde 3-phosphate dehydrogenase in step 6 of glycolysis. Upon completion of the reaction, instead of the normal product, 1,3-bisphosphoglycerate, the mixed anhydride 1-arsenato-3-phosphoglycerate is formed; this undergoes rapid spontaneous hydrolysis into arsenate plus 3-phosphoglycerate, the latter being a normal product of step 7 in glycolysis. What would be the effect of arsenate poisoning in glycolysis?

It results in fewer ATP molecules generated per glucose molecule, but NADH generation is not directly affected

ATP is the main energy currency in cells, and it can especially be used to drive condensation reactions that produce macromolecular polymers. How does ATP normally catalyze the condensation reaction, which by itself is energetically unfavorable?

It transfers either one or two terminal phosphate(s) to one of the substrates and is released as either ADP or AMP.

Indicate whether each of the following descriptions matches glycolysis (G) or the Krebs cycle (K). It oxidizes acetyl CoA to CO2. ( ) In eukaryotic cells, it is carried out in the cytosol. ( ) It produces FADH2. ( ) α-Ketoglutarate, one of its intermediates, is used to synthesize the amino acid glutamic acid.

KGKK

Which of the following structures is exclusively found in eukaryotic cells?

LYSOSOME

Indicate if each of the following descriptions matches messenger RNAs (M), ribosomal RNAs (R), or transfer RNAs (T). Your answer would be a four-letter string composed of letters M, R, and T only, ( ) They contain codons. ( ) They contain anticodons. ( ) They are (covalently) attached to amino acids. ( ) They are at the core of a complex that carries out protein synthesis.

MTTR

Most fish genomes are at least 1 billion nucleotide pairs long. However, the genome of the puffer fish Fugu rubripes is quite small at only about 0.4 billion nucleotide pairs, even though the number of Fugu genes is estimated to be comparable to that of its relatives which have larger genomes. What do you think mainly accounts for the Fugu genome being this small?

Low relative rate of DNA addition compared to DNA loss in the Fugu lineage

Indicate whether each of the following descriptions better matches the major histones (M) or the histone variants (V). Your answer would be a six-letter string composed of letters M and V only, e.g. VVMVMV ( ) They are more highly conserved over long evolutionary time scales. ( ) They are present in much smaller amounts in the cell. ( ) They are synthesized primarily during the S phase of the cell cycle. ( ) Their incorporation often requires histone exchange. ( ) They are often inserted into already-formed chromatin. ( ) They are assembled into nucleosomes just behind the replication fork.

MVMVVM

The bond energies associated with noncovalent attractions in the cell are too weak to resist disruption by thermal motion. However, cellular macromolecules can interact specifically AND strongly with each other (or fold by themselves) merely via such interactions. How is this possible?

Many weak bonds together in a complementary geometry can afford a strong binding

A gene that had been turned off in a liver cell has just been induced to be highly expressed as the cell responds to a new metabolic load. What observations do you expect to accompany this change?

More than 100 proteins would become associated with the gene for its transcription. B. The nuclear position of the gene would change to place it in a "transcription factory." C. Chromatin modifications associated with the gene would change in favor of higher expression

Which of the following would most reliably suggest that a genomic sequence is functionally important?

Multispecies conservation of the sequenc

Which of the following represents an "activated" carrier molecule?

NADH

A protein X that is known to exist in two slightly different conformations, called X1 and X2. Proteins A, B, and C are ligands that can bind to protein X. The sites on X required for binding to A, B, and C are located in different regions of the protein. On the basis of experimental evidence of protein-protein complexes, you devise the hypothetical binding reaction scheme shown in Figure Q9. According to the hypothesis, which pairs of binding sites on X exhibit negative coupling (negative linkage)? Which pairs exhibit positive coupling (positive linkage)? Does the addition of a high concentration of protein A increase or decrease the affinity of X for B? Of X for C?

Negative coopertivity a/c & b/c. If a or b binds c cant — if c binds a & b are blocked ~positive copertivity a&b bind, a or b first allow the other to bind ~high a increase affinity for b

Indicate if each of the following descriptions matches lithotrophic (L), organotrophic (O), or phototrophic (P) organisms. Your answer would be a four-letter string composed of letters L, O, and P only, e.g. LLPP. ( ) They feed on other living organisms or their organic products. ( ) They are responsible for the current oxygen-rich atmosphere of the Earth. ( ) They are all known to be prokaryotic. ( ) They are the primary energy converters in hydrothermal vents in the ocean floor.

OPLL

Didinium nasutum is a single-celled eukaryote that can hunt and feed on other living cells. It has an elaborate anatomy with beating cilia, a "mouth opening," an "anal aperture," and a set of contractile bundles; it can also shoot "darts" to paralyze its prey. What group of living cells does D. nasutum represent?

PROTOZOA

Which of the following groups of living organisms has the highest variation in haploid genome size?

PROTOZOA

Which of the following is true regarding energy production and storage in plants and animals?

Plant seeds often contain large amounts of fats and starch

In the formation of the earliest cells, which of the following components most likely arose first?

Plasma membrane cell surface

Fill in the blanks in the following paragraph regarding genome evolution "Conservation of genomic sequences between humans and chickens is mainly due to ... selection, whereas the conservation observed between humans and chimpanzees is mostly due to the short time available for mutations to accumulate. Even the DNA sequences at the ... position of synonymous codons are nearly identical between humans and chimpanzees."

Purifying, third

What is the end product of glycolysis in the cytoplasm of eukaryotic cells? How many carbon atoms does the molecule have?

Pyruvate; it has three carbon atoms

Most GTPases are present inside the cell at a much higher concentration than their upstream GAP and GEF proteins. Imagine a mutation in a certain GTPase, such as a Rab protein, resulting in an extremely tight binding between the GTPase and its GEF, and a very slow dissociation. What would you expect to happen in the cell as a result?

Rab proteins will be inactivated, because the tightly bound GEFs will be unavailable.

To study the chromatin remodeling complex SWR1, a researcher has prepared arrays of nucleosomes on long DNA strands that have been immobilized on magnetic beads. These nucleosomes are then incubated with an excess of the H2AZ-H2B dimer (which contains the histone variant H2AZ) in the presence or absence of SWR1 with or without ATP. She then separates the bead-bound nucleosomes (bound fraction) from the rest of the mix (unbound fraction) using a magnet, elutes the bound fraction from the beads, and performs SDS-PAGE on the samples. This is followed by a Western blot using an antibody specific to the H2AZ protein used in this experiment. The results are shown below, with the presence (+) or absence (-) of ATP, SWR1, or the H2AZ-H2B dimer in each incubation reaction indicated at the top of the corresponding lane. Which of the following statements is confirmed by the Western blot shown?

SWR1 deposits H2AZ histones into the nucleosome arrays

Imagine a chromosome translocation event that brings a gene encoding a histone acetyl transferase enzyme from its original chromosomal location to a new one near heterochromatin. Which of the following scenarios is definitely NOT going to happen?

Since the gene encodes a histone acetyl transferase, it resists heterochromatin expansion by acetylating its own histones.

Complete the DNA sequence below such that the final sequence is identical to that of the complementary strand. Your answer would be a seven-letter string composed of letters A, C, T, and G only, e.g. TTCTCAG

TCTAAAG

Indicate if each of the following statements is true (T) or false (F). Your answer would be a five-letter string composed of letters T and F only ( ) Animals ultimately depend on bacteria for fixation of the atmospheric nitrogen. ( ) If one finds animals in an isolated ecosystem, there should be photosynthetic organisms in that ecosystem as well. ( ) Carbon fixation can be carried out by bacteria only. ( ) All eukaryotes are organotrophs. ( ) Compared to eukaryotic cells, prokaryotes show greater biochemical diversity

TFFFT

Indicate true (T) and false (F) statements below regarding fatty acid metabolism. Your answer would be a four-letter string composed of letters T and F Most animals derive their energy from fatty acids between meals. ( ) Fatty acids are converted to acetyl CoA in the cytosol, which is then transported into mitochondria for further oxidation. ( ) Fatty acids are stored in fat droplets in the form of triacylglycerols. ( ) The breakdown of fatty acids into each acetyl CoA unit requires the hydrolysis of two ATP molecules.

TFTF

In a double-stranded DNA molecule, one of the chains has the sequence CCCATTCTA when read from the 5′ to the 3′ end. Indicate true (T) and false (F) statements below regarding this chain ( ) The other chain is heavier, i.e. it has a greater mass. ( ) There are no C residues in the other chain. ( ) The 5′-terminal residue of the other chain is G. ( ) The other chain is pyrimidine-rich.

TTFF

You have performed a chromosome conformation capture (3C) experiment to study chromatin looping at a mouse gene cluster that contains genes A, B, and C, as well as a regulatory region R. In this experiment, you performed in situ chemical cross-linking of chromatin, followed by cleavage of DNA in the nuclear extract with a restriction enzyme, intramolecular ligation, and cross-link removal. Finally, a polymerase chain reaction (PCR) was carried out using a forward primer that hybridizes to a region in the active B gene, and one of several reverse primers, each of which hybridizes to a different location in the locus. The amounts of the PCR products were quantified and normalized to represent the relative crosslinking efficiency in each analyzed sample. You have plotted the results in the graph below. The same experiment has been done on two tissue samples: fetal liver (represented by red lines) and fetal muscle (blue lines). Interaction of the A, B, and C genes with the regulatory R region is known to enhance expression of these genes. Indicate true (T) and false (F) statements below based on the results. Your answer would be a four-letter string composed of letters T and F only ( ) The B gene would be predicted to have higher expression in the fetal liver compared to the fetal muscle tissue. ( ) Interaction between the R region and the B gene involves the A gene looping out. ( ) Interaction between the R region and the B gene involves the C gene looping out. ( ) In fetal muscle, the B gene definitely does not engage in looping interactions with any other elements in the cluster

TTFF

Indicate whether each of the following molecules is an intermediate in glycolysis (G) or in the tricarboxylic acid cycle (T). Your answer would be a four-letter string composed of letters G and T onlY Fumarate ( ) Malate ( ) Phosphoenolpyruvate ( ) Succinate

TTGT

Indicate whether each of the following descriptions better applies to a centromere (C), a telomere (T), or an origin of replication (O). ( ) It contains repeated sequences at the ends of the chromosomes. ( ) It is NOT generally longer in higher organisms compared to yeast. ( ) Each eukaryotic chromosome has many such sequences. ( ) There are normally two such sequences in each eukaryotic chromosomal DNA molecule. ( ) There is normally one such sequence per eukaryotic chromosomal DNA molecule. ( ) It is where DNA duplication starts in S phase. ( ) It attaches the chromosome to the mitotic spindle via the kinetochore structure

TTOTCOC

Macromolecules in the cell can be made from their monomers using one of two polymerization schemes. One is called head polymerization, in which the reactive bond required for polymerization is carried on the end of the growing polymer. In contrast, in tail polymerization, the reactive bond is carried by each monomer for its own incorporation. In the figure, indicate the polymerization scheme and the type of macromolecule.

Tail polymerization of a nucleic acid

What are the consequences for the cell of the "fractal globule" arrangement of chromosome segments?

The ability of the chromatin fiber to fold and unfold efficiently is maintained.

Which of the following does NOT typically involve horizontal gene transfer?

The accidental duplication of a small region of a bacterial chromosome followed by cell division

In terms of cellular lifestyle, different kingdoms of life can be likened to hunters, farmers, and scavengers. Which of the following is true in this scheme?

The ancestral eukaryotic cell was a hunter, but upon acquiring chloroplasts it made the transition into farming.

Which of the following statements is true regarding reactions involving oxidation and reduction?

The carbon atom is more oxidized in formaldehyde (CH2O) than in methanol (CH3OH).

Which of the following features of DNA underlies its simple replication procedure?

The complementary relationship in the double helix

Which of the following is true regarding heterochromatin in a typical mammalian cell?

The different types of heterochromatin share an especially high degree of compaction.

All cells in a multicellular organism have normally developed from a single cell and share the same genome, but can nevertheless be wildly different in their shape and function. What in the eukaryotic genome is responsible for this cell-type diversity?

The genes that encode transcription regulatory proteins B. The regulatory sequences that control the expression of genes C. The genes that code for molecules involved in receiving cellular signals D. The genes that code for molecules involved in sending cellular signals to other cells

Judged by the average number of nucleotide-pair differences per 1000 nucleotide pairs, which of the following pairs show the highest difference?

The genomes of S. cerevisiae and M. musculus

Which of the following statements is true regarding cellular metabolism?

The heat released by an animal cell as part of its metabolic processes comes from the bond energies in the foodstuffs that are consumed by the animal.

How does the KM of the nucleotide combination compare with the values for the nucleotides alone?

The new graph will show a sigmoidal curve shifted to the right indicating . Km will decrease for UTP/ CTP production less than CTP alone.

Back in 1962, Gerhart and Pardee developed a model for the regulation of the activity of the ATCase enzyme by CTP and ATP, using the pathway given in Figure 16.1. Describe that model, using information presented here as well as what you have learned about allosteric enzymes. Be sure to include a sentence explaining the physiological significance of your model

The pathway shows the pyrimidine synthesis regulated by allosteric enzymes at ATCase. ATCase in inhibited by CTP, while ATP is an allosteric activator. They both compete for the site of the enzyme. The steps take place as follows: Carbamoyl phosphate synthesis: this is synthesised from glutamine and carbonic acid in presence of enzyme arbamoyl phosphate synthatase-II which consumes 2 ATP molecules Synthesis of carbamoyl aspartate : Carbamoyl phosphate condensed with aspartic acid with aspartate transcarbamoylase (ATCase) to form carbamoyl aspartate. UMP formation of decarboxylation: Carbamoyl aspartate formation happened after formation of dihydroorotate. Orotidine-5-monophosphate (OMP) added on reaction of PRPP transfered the release of pyrophosphate. Finally, decarboxylation of OMP by OMP decarboxylase does not need co-factors. Synthesis of UTO and CTP: CTP formed by animation of UTP with CTP synthase. Phosphate exchanges from UMP forms UTP ALLOSTERIC ENZYMES: Enzymes which when binds to an effector causes conformational changes resulting in change in binding affinity at different ligand binding site. PHysiological significance of model: rate of reaction in presence of ATCase increases when CTP is absent but decreases when CTP concentration increases. More molecules are being sent in pathway to form new pyrimidines.

A mutation in the cdc28 gene in the budding yeast Saccharomyces cerevisiae causes cellcycle arrest, giving rise to unbudded cells that look like "dumbbells." Treatment of wild-type cells with nocodazole, a drug that destabilizes some cytoskeletal polymers, leads to a similar phenotype. Based only on these observations, which statement is true regarding cdc28?

The product of the cdc28 gene is involved in cell cycle regulation.

A simple protein interaction map is shown below for human cytochrome c (Cyt), a hemecontaining protein that is normally found inside the mitochondria and is associated with the electron-transport chain (ETC) of the inner mitochondrial membrane. Under special emergency conditions, this protein can also moonlight as a signal transducer for the onset of a pathway leading to programmed cell death (PCD). As shown in the map, it also interacts with a group of phosphoprotein phosphatases (PPP) involved in cell signaling pathways. Assuming that the functions of the proteins labeled as X, Y, and Z are unknown, which of the following points can be reasonably argued from this interaction map?

The protein labeled Y probably has a role in PCD, especially if its orthologs in other organisms have such a role and show a similar pattern of interactions.

Comparing the genomes of present-day mitochondria or chloroplasts with the genomes of their corresponding bacteria reveals that these organelles do not have many of the genes that are essential for their function. For instance, they lack the many genes that are required for DNA replication. What has happened to these genes?

The required genes are kept in the nucleus, but many have evolved by gene transfer from the organelle.

Which of the following is NOT true about the nuclear subcompartments?

The subcompartments are constitutively present in a cell except during nuclear divisions

A cellular enzyme catalyzes the catabolic reaction shown below. Its coenzyme is shown in the box. Which of the following is correct regarding this reaction?

The substrate is oxidized in this reaction and the coenzyme is converted from state 1 to state 2.

The eukaryotic chromosomes are organized inside the nucleus with a huge compaction ratio of several-thousand-fold. What is responsible for such a tight packaging?

The various chromatin proteins that wrap and fold the DNA

Imagine two spherical cells, one of which is 5000 times larger in volume than the other. The smaller is a prokaryote, and the larger cell is a eukaryote with 20% of its volume confined in a spherical nucleus. If the diameter of the prokaryotic cell is 0.7 micrometers, what is the diameter of the nucleus in the eukaryotic cell in micrometers? Write down your answer as a number only.

The volume of the nucleus is 1000 times that of the prokaryotic cell in this example (that is, 20% × 5000), which means its diameter should be 10 times larger.

Enzymes can catalyze cellular reactions through various mechanisms. Which of the following statements is NOT true regarding enzymes?

They accelerate a cellular reaction by destabilizing the transition state

Many macromolecular complexes in the cell contain scaffold proteins. What do these proteins do that benefits the cell?

They can enhance the rate of critical cellular reactions. B. They can hold the many subunits of a large complex together. C. They can confine and concentrate a specific set of interacting proteins to a particular cellular location. D. They can provide a large macromolecular complex with either flexibility or rigidity.

Which of the following is NOT true regarding the members of a protein family in general?

They can functionally replace each other.

Stable β-sheet aggregates can form from many proteins, forming intertwined cross-beta strands that have the potential to kill cells or damage tissues. Which of the following is NOT true regarding these aggregates?

They form almost exclusively in the cells of the nervous system.

Scientists discover more than ten thousand new species of living organisms every year. What is shared between all of these organisms?

They produce and use adenosine triphosphate (ATP).

What is the reaction performed on the molecule labeled as substrate in the following diagram? What is the name of the activated carrier?

This is a carboxylation reaction and the activated carrier is carboxylated biotin

The main reason that proteins adopt secondary structure (alpha helices & beta sheets) is

To neutralize the partial charge on amino and carboxyl groups

You have two tubes. Tube 1 contains the DNA encoding the genome of a human being and tube 2 contains the DNA encoding the genome of a lithotrophic archaean that lives adjacent to a deep sea hydrothermal vent that has an average temperature of 115°C (note that normal human body temperature is 37°C). You lend your tubes to a chemist friend, who loses the label on your tubes. However, he was able to determine the percentage molar ratios of As and Ts in these tubes, and finds that the DNA in tube 1 is composed of 59% As and Ts while the DNA in tube 2 is composed of 48% As and Ts. Which tube contains the human DNA and which tube contains the archaean DNA? Explain.

Tube 1 probably contains the human genomic DNA, and tube 2 contains the DNA from the deep sea lithotropic archaea. The DNA in tube 1 has a greater AT content than the DNA in tube 2. Because a CG base pair is stronger than an AT base pair, the melting temperature of the DNA in tube 1 will be lower than that for the DNA in tube 2. Because humans exist at lower temperatures than temperatures at the deep sea hydrothermal vents, it is likely that human genomic DNA will have a lower melting temperature than the genomic DNA of organisms that live at high temperatures

Gerhart and Pardee measured ATCase activity in the presence of a variety of purine and pyrimidine derivatives. Their results are presented in Table 16.2. What compound(s) were the most effective inhibitors? activators? Explain the significance of the metabolites that served as inhibitors or activators in the context of the biosynthetic pathway presented in Figure 16.1.

With CTP, CMP, and CDP, there is an increasing amount of inhibition. Therefore, inhibition is facilitated as phosphate groups increase. Cytosine cannot inhibit by itself -- cytidine and deoxycytidine containing sugar show slight inhibition. UTP couldn't inhibit the enzyme which shows that the amino group may be required for the function. ATP and dATP function as stimulators of the enzyme CTP is the product of the pathway, and high concentrations signal the enzyme that CTP is no longer needed -- it is the inhibitor, therefore. ATP stimulates the pathway due to a high amount of purines, which must be matched with pyrimidines for efficiency in DNA and RNA synthesis.

Under anaerobic conditions, glycolysis provides most of the ATP that the cell needs. In animal cells, pyruvate, the end product of glycolysis, is converted to lactic acid by lactate dehydrogenase, as shown below: CH3(CO)COO- + X →CH3(CHOH)COO-+ Y What is the correct carrier pair (in place of X and Y) in this reaction?

X is (NADH + H+), and Y is (NAD+)

~Which fragment contains the kinase domain? On the basis of the regulation of Src explained in the textbook, would you have expected this fragment to be active as a kinase, as observed? If so, do you expect the kinase activity be greater than, the same as, or less than that of the intact protein? Explain. PIC:

Yes, with greater activity without regulatory domain which inhibits kinase

The compound GDPNP is a GTP analog that can bind to GTPases in the same way as GTP. However, unlike GTP, it cannot undergo the hydrolysis reaction that normally releases Pi. Therefore, ...

a GDPNP-bound Ras is constitutively active.

An enzyme acts on a tyrosine residue in a target protein to create a binding site for the SH2 domain. This enzyme is most specifically ...

a kinase.

Src protein kinase is composed of several domains that interact to control the behavior of the protein. Figure Q8 (A and B) shows the structure of the repressed conformation of Src. In 1979, long before the x-ray crystal structure of Src was known, scientists used a technique called partial proteolysis to explore the structure of Src. Treatment with small amounts of the V8 protease cleaved Src at a single location to generate two protein fragments. The addition of more V8 protease caused further cleavage of one of the fragments, but in both cases kinase activity was maintained. Figure Q8C shows a protein gel from this experiment. The proteolytic fragments are detected by their radioactivity because the Src protein contained radioactive atoms; in some reactions Src was radiolabelled throughout its length ("all") and in others the radiolabel was only at the N-terminal end ("end"). A. Indicate on the ribbon diagram where you think cleavage first occurs to generate the 34 kD and 26 kD fragments. Circle and label the regions corresponding to each fragment. B. Which fragment contains the kinase domain? On the basis of the regulation of Src explained in the textbook, would you have expected this fragment to be active as a kinase, as observed? If so, do you expect the kinase activity be greater than, the same as, or less than that of the intact protein? Explain. C. Dephosphorylation, mutation, or deletion of a particular tyrosine residue in the C-terminal tail of the protein leads to increased activity of the kinase and promotes cancerous transformation of cells. Do you expect the proteolytic fragment containing the kinase domain to be regulated strongly by phosphorylation of the key tyrosine in the C-terminal tail? Explain.

a) 1st cleavage long skinny line b) yes, with greater activity without regulatory domains which inhibits kinase c) no regulation because C-terminal tail binds SH2 domain which is not present in the fragment (kinase domain)

In the following diagram showing the reaction pathway for a simple single-substrate enzymatic reaction, which of the quantities corresponds to the activation energy of the forward reaction?

a-b

Indicate whether each of the following histone modifications is generally associated with active genes (A) or silenced genes (S). ( ) H3 lysine 9 acetylation ( ) H3 serine 10 phosphorylation ( ) H3 lysine 4 trimethylation ( ) H3 lysine 9 trimethylation

aaas

In the following diagram showing the distribution of thermal energy in a population of substrate molecules, the energy thresholds indicated by numbers represent ...

activation energy with and without an enzyme

Scientists believe that all living cells are related because

all use DNA to store genetic information all use L-isomers of amino acids to synthesize proteins

Consider the proteins Ras, Src, kinesin, and the ATP synthase pump. All of them ...

are allosteric proteins. B. can have two or more distinct conformations. C. can bind to ATP (or GTP). D. can hydrolyze ATP to ADP (or GTP to GDP).

Lampbrush chromosomes ...

are thought to have a structure that is relevant to mammalian chromosomes in interphase.

The copy number of some human genes, such as the salivary amylase gene AMY1, varies greatly between different individuals. The salivary amylase breaks down some of the dietary starch into smaller sugars. In the case of AMY1, a positive correlation has been observed between the copy number and the amount of amylase in the saliva. Gene copy number per diploid genome can be estimated by performing a quantitative polymerase chain reaction (PCR) using primers specific to the gene of interest. You have performed such PCR experiments on samples from two human populations that have traditional diets with low and high starch levels, respectively, and have plotted the data in the histogram below. Which population (A or B) in the histogram is likely to be the one with traditionally higher dietary starch?

b

Arginine (ARG, R) and Lysine (Lys, K) are examples of

basic amino acids positively charged amino acids

A chromatin "reader complex" ...

binds tightly to the chromatin only when a specific set of histone marks is present.

The globin gene family in mammals, birds, and reptiles is organized into α- and β-globin gene clusters that are located on two different chromosomes. In most fish and amphibians, however, the globin genes are close to each other on one chromosome. At which point (A to E) in the following simplified phylogenetic tree is a chromosomal translocation likely to have happened that placed the α- and β-globin genes on two separate chromosomes?

c

A virus ...

can act as a vector for gene transfer.

The acetylation of lysines on the histone tails ...

can be performed on methylated lysines only after they are first demethylated.

In human cells, the alpha satellite DNA repeats ...

can be seen to be packaged into alternating blocks of chromatin, one of which contains the histone H3 variant CENP-A.

The chromatin remodeling complexes play an important role in chromatin regulation in the nucleus. They ...

can slide nucleosomes on DNA. B. have ATPase activity. C. interact with histone chaperones. D. can remove or exchange core histone subunits.

For the Human Genome Project, cloning of large segments of our genome was first made possible by the development of yeast artificial chromosomes, which are capable of propagating in the yeast Saccharomyces cerevisiae just like any of the organism's 16 natural chromosomes. In addition to the cloned human DNA, these artificial vectors were made to contain three elements that are necessary for them to function as a chromosome. What are these elements? Write down the names of the elements in alphabetical order, and separate them with commas, e.g. gene, histone, nucleosome

centromere, origin of replication, telomere

Phosphorylation of a protein by a protein kinase ...

create binding site for other proteins

Natural amino acids are found in the "D" isomer configuration.

false

Fill in the blank in the following paragraph regarding chromatin organization. Do not use abbreviations.

fractal globules

Indicate true (T) and false (F) statements below regarding histones. Your answer would be a six-letter string composed of letters T and F only ( ) The histones are highly acidic proteins. ( ) The histone fold consists of three α helices. ( ) The core histones are much more conserved than the H1 histone. ( ) The N-terminal tails of the core histones undergo a variety of reversible posttranslational modifications. ( ) Every nucleosome core is made up of three polypeptide chains. ( ) The H1 histone is absent in the 30-nm fibers.

ftttff

Polytene chromosomes are useful for studying chromatin because they ...

have distinct visible banding patterns.

All cells ...

have membrane transport proteins. B. synthesize proteins on the ribosome. C. replicate their genome by DNA polymerization. D. transcribe their genetic information by RNA polymerization

Compared to the human genome, the genome of yeast typically has ...

higher fraction of coding DNA

A hydrophobic molecule is typically ...

incapable of interacting favorably with water.

The marking of a protein by polyubiquitylation to signify degradation ...

involves the recognition of the target protein by an E2-E3 ligase

It has been shown that inhibition of a key chromatin remodeling complex known as NuRD, by deleting one of its subunits, can result in a significant increase in the efficiency of reprogramming of somatic cells into pluripotent stem cells. The reprogramming is normally done by the induced expression of a battery of transcription factors in the somatic cells, but is typically not very efficient. Such an observation suggests that the NuRD complex is normally involved in

maintaining the epigenetic memory in somatic cells.

Out of nearly 5000 protein-coding gene families, there is a set of nearly 300 conserved gene families that are found in species from all domains of life. When one looks at the general functions assigned to these gene families, it is found that ...

more than one-third of them are involved in translation or amino acid transport and metabolism.

Why does hemoglobin form a tetramer, instead of remaining as a monomer

tetramer/ dimer equilibrium.. Oxygen transport ability= better, more binding to oxygen, best binding capacity, extracellular oxygen carrier.

For b-sheets, the terms 'parallel' and 'anti-parallel' refer to

the 'direction' of the associated peptide strands

Imagine a segment of DNA (within a gene) encoding a certain amount of information in its nucleotide sequence. When this segment is fully transcribed into mRNA and then translated into protein, in general, ...

the protein sequence would carry less information compared to the DNA and mRNA sequences, because several codons can correspond to one amino acid.

Cells are limited in size because:

they require adequate concentrations of nutrients

The genetic information carried by a cell is passed on, generation after generation, with astonishing fidelity. However, genomes are still altered over evolutionary time scales, and even their overall size can change significantly. Which of the following genome-altering events has increased the size of the mammalian genome the most?

transposition

A viral version of the Src kinase called v-Src is found in some retroviruses. Unlike the cellular Src, the v-Src kinase is constitutively active, and can drive the cell into uncontrolled growth and tumor formation. Which of the following molecular differences between the two versions of Src is more likely to be responsible for this?

v-Src lacks the C-terminal tail that can bind to Src's SH2 domain.

To trace family relationships between distantly related organisms such as humans, algae, bacteria, and archaea, one should compare their genomes in regions ...

where mutations are hardly tolerated