Bio 230 Exam 1

Use your knowledge of amino acid characteristics to order the peptides below according to the net charge contributed by their side chains at physiological pH (~pH 7). Each peptide contains eight amino acids. Use the single-letter amino acid designations to generate your list, placing the most negatively charged peptide on the left and the most positively charged peptide on the right. In addition, for each peptide, list the total number of positive and negative charges. Remember that, at neutral pH, the amino terminus carries a positive charge and the carboxyl terminus carries a negative charge. A. YGAKKRA B. ARRKSTRK C. DERKQNST D. DDAEIYSA E. NQSTYEEG

(D) This peptide has 4 negative charges and one positive charge. The peptide in (E) has 3 negative charges and one positive charge. The peptide in (C) has 3 negative charges and 3 positive charges. The peptide in (A) has 4 positive charges and one negative charge. The peptide in (B) has 6 positive charges and one negative charge.

2.28.b. if .5 kilocalories of energy are required to break 6x10^23 bonds of a particular type, what is the strength of this bond?

.5 kcal/mole

16. what is the smallest distance two points can be separated and still resolved using light microscopy?

0.2 um

47. On average, eukaryotic cells are BLANK times longer and have BLANK times more volume than prokaryotic cells

10, 1000

2.14. you have a concentrated stock solution of 10M NaOH and want to use it to produce a 150mL solution of 3 M NaOH. what volume of water and stock solutions will you measure out to make this new solution?

105mL water 45 mL NaOH stock

2.38.b. what concentration of hydronium ions does a solution of pH 8 contain?

10^-8 M

2.8. if the isotope 32S has 16 protons and 16 neutrons, how many protons, neutrons, and electrons will the isotope 35S have, respectively?

16,19,16

2.9a. if .5 mole of glucose weighs 90g, what is the molecular mass of glucose?

180 daltons. a mole of a substance has a mass equivalent to its molecular weight

2.50.a. how many carbon atoms does the molecule represented in figure q2-50

20 carbon atoms

2.13. the first task you are assigned in your summer laboratory job is to prepare a concentrated NaOH stock solution. the molecular weight of NaOH is 40. how many grams of solid NaOH will you need to weigh out to obtain a 500mL solution that has a concentation of 10 M?

200g

2.51. most types of molecules in the cell have asymmetric (chiral) carbons. consequently there is the potential to have to different molecules that look much the same but are mirror images of each other and therefore not equivalent. these special types of isomers are called sterioisomers. which of the four carbons circles is the assymmetric carbon that determines whether the amino acid is a d or l stereoisomer?

3

2.12. avogadro's number, calculated from the atomic weight of hydrogen, tells us how many atoms or molecules are in a mole.The resulting base for all calculations of moles and molarity (how many molecules are present when you weigh out a substance or measure from a stock solution) is the following: 1 g of hydrogen atoms = 6 × 1023 hydrogen atoms = 1 mole of hydrogen Sulfur has a molecular weight of 32. How many moles and atoms are there in 120 grams of sulfur? (a) 3.75 and 6 × 1023 (b) 32 and 6 × 1023 (c) 1.75 and 1.05 ×1024 (d) 3.75 and 2.25 × 1024

3.75 and 2.25x10^24

2.50.b. how many hydrogens does figure q2-50 have?

31 hydrogen atoms

2.9.b. what is the concentration, in grams per liter, of a .25M solution of glucose?

45g/L

2.36. how many bonds can urea form if dissolved in water?

6

2.9.c. how many molecules are there in 1 mole of glucose?

6x10^23 molecules

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Van der Waals interactions and hydrophobic interactions are two ways to describe the same type of weak forces that help proteins fold.

A. False. Van der Waals attractions are weakly attractive forces that occur between all atoms. Hydrophobic interactions are only observed between nonpolar molecules in the context of an aqueous solution.

The sequences for three different tripeptides are written out below. Indicate whether you expect to find them in the inner core or on the surface of a cytosolic protein, and explain your answer. A. Serine-Threonine-Tyrosine B. Alanine-Glycine-Leucine C. Proline-Serine-Alanine

A. This tripeptide is made up of entirely polar amino acids, which means it will most likely be found on the surface of the protein, interacting with the aqueous environment of the cytosol. B. This peptide is made up of nonpolar amino acids. The side chains are most likely buried in the interior of the protein, which would promote interactions with other hydrophobic side chains and avoid unfavorable interactions with the aqueous environment of the cytosol. C. This peptide is made up of both polar and nonpolar amino acids, and one of the nonpolar amino acids is proline. Proline residues have a restricted degree of conformational freedom because the side chain is covalently linked to the backbone nitrogen as well as the α-carbon. So, a likely scenario is that the proline is at the surface of the protein, providing a structural turn between two secondary structure elements (β strands or α helices), the serine is still close enough to the surface to interact with water, and the alanine is close enough to the interior of the protein to interact with other hydrophobic side chains.

Match the basic protein functions in the left column with a specific example of that type of protein in the column on the right. gene regulatory

A. insulin

64. Genomic sequences are now available for an increasing number of species, and scientists studying evolutionary processes can take advantage of this enormous amount of data to bring evolution into the arena of molecular studies. By aligning the sequences of homologous genes and looking for regions of similarity and where changes have occurred, it is possible to infer the sequence of the ancestral gene. b. It is possible to express an ancestral gene sequence in modern organisms and subsequently compare the function of its product with that of the modern protein. Why might this approach give misleading conclusions?

Although an inferred ancestral sequence can be reconstructed and the protein expressed, you would be placing an inferred, ancient protein in the context of a modern cell. If there are important interacting partners for the modern protein, there is a chance they may not recognize the ancestral protein, and therefore any information about its function may be inaccurate.

2.11. you explain to a friend what you have learned about avogadro's number. your friend thinks the number is so large that he doubts there is even a mole of living cells on the earth.You have recently heard that there are about 50 trillion (5 × 1013) human cells in each adult human body and that each human contains more bacterial cells (in the digestive system) than human cells, so you bet your friend $5 that there is more than a mole of cells on Earth. The human population is approximately 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 × 109) × (1 × 1014) = 7 × 1023. Thus, even when only considering the human population and the associated microbial populations, you can estimate more than a mole of living cells on Earth. You win $5.

2.72.b.Eukaryotic cells have their DNA molecules inside their nuclei. However, to package all the DNA into such a small volume requires the cell to use specialized proteins called histones. Histones have amino acid sequences enriched for lysines and arginines.B. Lysine side chains are substrates for enzymes called acetylases. A diagram of an acetylated lysine side chain is shown in Figure Q2-72. How do you think the acetylation of lysines in histone proteins will affect the ability of a histone to perform its role (refer to your answer in part A)?

B. A histone with acetylated lysine residues will not be as good at packaging the DNA. The addition of the acetyl group to the terminal amino on the lysine side chain lowers the histone's net positive charge, which makes it less effective at buffering the negative charges on the DNA backbone.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. B. A large number of noncovalent interactions is required to hold two regions of a polypeptide chain together in a stable conformation.

B. True.

65. The antibiotic streptomycin inhibits protein synthesis in bacteria. If this antibiotic is added to a culture of animal cells, protein synthesis in the cytosol continues normally. However, over time, the population of mitochondria in the cell becomes depleted. Specifically, it is observed that the protein-synthesis machinery inside the mitochondria is inhibited.B. What do you expect to observe if, in a new experiment, animal cells are treated with diphtheria toxin, a compound that is known to block cytosolic protein synthesis but does not have any impact on bacterial growth?

B. We would expect that although cytosolic protein synthesis would stop, mitochondrial protein synthesis should still occur normally (at least for a little while). This result would lend further support to the idea that mitochondria are derived from a noneukaryotic organism. If this were not the case, these compounds would be expected to affect protein synthesis at both locations.

Match the basic protein functions in the left column with a specific example of that type of protein in the column on the right. ___ motor

B. carboxylase

The biosynthetic pathway for the two amino acids E and H is shown systematically in figure Q4-60. You are able to show that E inhibits enzyme V, and H inhibits enzyme X. Enzyme T is most likely to be subject to feedback inhibition by ____________ alone. a) H b) B c) C d) E

C

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. C. A single polypeptide tends to adopt 3-4 different conformations, which all have equivalent free-energy values (G).

C. False. There is a single, final fold for every polypeptide. The fold adopted is the "best" conformation, for which the free energy (G) of the molecule is at a minimum.

54.a. what would be the best model organism to use for the investigation of the process of: programmed cell death

C. elegans

Match the basic protein functions in the left column with a specific example of that type of protein in the column on the right. ___ storage

C. rhodopsin

2.38.c. completer the following reaction: CH3COOH + H2O <-> BLANK

CH3COO- + H30+

22. some prokaryotes can live by utilizing entirely inorganic materials. which of the following inorganic molecules would you predict to be the predominant building block for fats, sugars, and proteins? a. O2 b. N2 c. CO2 d. H2

CO2

64. Genomic sequences are now available for an increasing number of species, and scientists studying evolutionary processes can take advantage of this enormous amount of data to bring evolution into the arena of molecular studies. By aligning the sequences of homologous genes and looking for regions of similarity and where changes have occurred, it is possible to infer the sequence of the ancestral gene. a. What term is used to describe the changes in gene sequences that have occurred? How can we use what we know about this process to construct a time line showing when various sequence changes occurred and when they led to the modern sequences that we know today?

Changes in gene sequence occur through mutation. Mutations accumulate over time, occuring independently and at different sites in each gene lineage. homologous gens that diverted recently will differ only slightly; genes that diverged long ago will differ more. Knowing the average mutation rate, you can estimate the time that has elapsed since the different versions of the gene diverged. By seeing how closely the various members of the family of the homologous genes resemble one another, you can draw up a family tree, showing the sequence of lineage splits that lead from the ancestral gene to its many modern descendants. Suppose this family tree shows that family members A and B diverged from one another long ago, but that C diverged from B more recently; and suppose that at a certain site in the gene, A and B have the same sequence but C is different. Then, it is likely that the sequence of A and B is ancestral, while that of C reflects a recent mutation that has occurred in the lineage of C alone.

Match the basic protein functions in the left column with a specific example of that type of protein in the column on the right. ___ enzyme

D. hemoglobin

3.c. Similarly, the genetic information of all cells is stored in their BLANK.

DNA

2.72.a.Eukaryotic cells have their DNA molecules inside their nuclei. However, to package all the DNA into such a small volume requires the cell to use specialized proteins called histones. Histones have amino acid sequences enriched for lysines and arginines. A. What problem might a cell face in trying to package DNA into a small volume without histones, and how do these special packaging proteins alleviate the problem?

DNA is a nucleic acid polymer in which each monomer has a negatively charged phosphate group. The negative charges will naturally repel each other, so in order to wrap the high density of negative charges into a small space, positively charged molecules must be present. Histones accomplish this because they are rich in lysines and arginines, which are positively charged in solution at pH 7.

Use your knowledge of amino acid characteristics to order the peptides below by their degree of polarity. Each peptide contains eight amino acids. Use the single-letter amino acid designations to generate your list, placing the most polar peptide on the left and the most nonpolar peptide on the right. A. SGAKKRAH B. CATWNGQV C. FWGTSILA D. DDAEIHWA E. SSTAMYRK

E, A, D, B, C

Match the basic protein functions in the left column with a specific example of that type of protein in the column on the right. __ transport

E. ferritin

4. How does cellular specialization serve multicellular organisms and how might a high degree of specialization be detrimental?

Each type of cells in a multicellular organism, relies on the other cells types for survival, which is the specialization component of cells that creates the division of labor between cells. This specialization of cells is essential for the organism as a whole, because if one type of specialized cells were to be removed, then that lack of capabilities would discontinue the ability to generate offspring and would not live very long.

Match the basic protein functions in the left column with a specific example of that type of protein in the column on the right. ___ structural

F. myosin

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. B. The "polypeptide backbone" refers to all atoms in a polypeptide chain, except for those that form the peptide bonds.

False. Peptide bonds are planar amide bonds that are central to the polypeptide backbone formation. The atoms in the amino acid side chains are not considered to be part of the backbone.

2.2.c. true or false: The chemical reactions in living systems are loosely regulated, allowing for a wide range of products and more rapid evolution.

False. The chemical reactions in living systems are very tightly controlled, ensuring that events occur at the proper time and at the proper location inside the cell.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Generally, the total number of nonpolar amino acids has a greater effect on protein structure than the exact order of amino acids in a polypeptide chain.

False. The order in which amino acids are linked unique for each the most important factor in determining overall protein structure.

19.a. true or false: the terms "prokaryote" and "bacterium" are synonyms

False. archaea are significantly different from bacteria

66. You have been following the recent presidential elections and have heard some candidates disparaging excessive and "unnecessary" federal expenditures.One particular candidate asks: "Why are we spending millions of dollars studying fruit flies? How can that possibly help us find a cure for cancer?" Use your knowledge of model organisms to explain why studies in D. melanogaster (the fruit fly) areactually an excellent use of research funding.

Fundingresearch on D. melanogaster is a worthwhile investment for several reasons: (1) working with insect animal models is relatively inexpensive; (2) fruit flies have historically proven useful in helping understand eukaryotic chromosome behavior; and (3) many of the genes in Drosophila are highly similar in sequence to the homologous human genes, and thus can be used to study human diseases.

Match the basic protein functions in the left column with a specific example of that type of protein in the column on the right. __ special purpose

G. green fluorescent protein

Match the basic protein functions in the left column with a specific example of that type of protein in the column on the right. __ receptor

H. tubulin

Match: __ removes a phosphate group from a molecule __ hydrolyzes ATP __ hydrolyzes bonds between molecules __ adds phosphate groups to molecules __ catalyzes reactions in which one molecule is oxidized and another is reduced __ hydrolyses peptide bonds __ joins 2 ends of DNA together __ catalyses the synthesis of polymers such as RNA and DNA __ rearranges bonds within a single molecule a. ATPase b. polymerase c. ligase d. kinase e. isomerase f. nuclease g. oxido-reductase h. protease i. phosphatase

I A F D G H C B E

Match the basic protein functions in the left column with a specific example of that type of protein in the column on the right. ___ signal

I. homeodomain proteins

65. The antibiotic streptomycin inhibits protein synthesis in bacteria. If this antibiotic is added to a culture of animal cells, protein synthesis in the cytosol continues normally. However, over time, the population of mitochondria in the cell becomes depleted. Specifically, it is observed that the protein-synthesis machinery inside the mitochondria is inhibited. a.Explain this observation based on what you know about the origins of the modern eukaryote.

If the mitochondria originated from an ancient aerobic bacterium that was engulfed by an ancient eukaryote, as postulated, it is possible that an antibiotic that inhibits protein synthesis in bacteria could also block that process in mitochondria.

59. you wish to explore how mutations in specific genes affecting sugar metabolism might alter tooth development. which organism is likely to provide the best model system for your studies, and why?

Mice, because they have teeth and have been used as a model organism for a long time. They can reproduce relatively rapidly and the extensive scientific community that works with mice has developed techniques to facilitate genetic manipulations. E. coli and arabidopsis do not have teeth. horse like sugar and have big teeth.

67. Cellular processes are often regulated by unknown mechanisms. In many cases, biologists work backward in an attempt to understand a process in which they are interested.This was the case when Nurse and Hartwell were trying to understand how cell division is controlled in yeast. Describe the process by which they "broke" the system and then supplied the "missing parts" to get the cell cycle running again. What further evidence did they collect to show that human cells and yeast cells regulate the cell cycle using a similar mechanism?

Nurse and Hartwell first treated yeast cells with a chemical mutagen. The mutated population of cells was then grown and observed. Cells that demonstrated defects in cell-cycle regulation (characterized by cell-cycle arrest, larger-than-normal cells, and smaller-than-normal cells) were then isolated. The use of a library of plasmids that each express a normal gene from yeast cells allowed the scientists to identify exactly which gene could be used to "rescue" the mutant, because when the normal gene is expressed again, the cells return to a normal cell cycle. After this big result, the scientists went on to show that the homologous gene from other organisms could also rescue the mutant phenotype. The most exciting result was obtained with the human version of the cdc2 gene, which demonstrated that there are common principles underlying cell-cycle regulation across a large range of eukaryotic organisms.

2.59.b.peptide: Pro-Val-Thr-Gly-Lys-Cys-Glu write the single-letter code for amino acids

PVTGKCE

63. employ the principles of evolution discussed in this chapter to explain how the specific features of predatory behaviors of some primitive eukaryotes may have given them a selective advantage over others 1.5 billion years ago.

The Earth's atmosphere became oxygen-rich roughly 1.5 billion years ago. If some primitive predatory eukaryotic cells were similar to modern-day protozoans, they may have been mobile and able to engulf other cells. These characteristics would have been advantageous in the face of a changing atmosphere, and the establishment of a symbiotic relationship with an engulfed aerobe would have been selected for in the eukaryotic cell populations.

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. C. The chemical properties of amino acid side chains include charged, uncharged polar, and nonpolar.

True

Indicate whether the following statements are true or false. If a statement is false, explain why it is false. D. The relative distribution of polar and nonpolar amino acids in a folded protein is determined largely by hydrophobic interactions, which favor the clustering of nonpolar side chains in the interior.

True

2.34. the relative strengths of a covalent bonds and van der Waals interactions remain the same when tested in a vacuum or in water.However, this is not true of hydrogen bonds or ionic bonds, whose bond strengths are lowered considerably in the presence of water. Explain these observations.

We estimate bond strengths by measuring the amount of energy needed to break them. As explained in Panel 2-7 (p.78-79), in an aqueous solution, water can form hydrogen bonds with any polar molecules that are capably of forming hydrogen bonds with each other. This formation of bonds with water takes away from the net energy that would be gained from the molecules forming hydrogen bonds with each other, as they would in a vacuum. Similarly, water forms favorable electrostatic interactions with ions, thereby greatly weakening the ionic bonds that form between positive and negative ions in a vacuum (see Panel 2-7). Thus, for example, solid table salt (NaCl) readily dissociates in water, producing separate Na+ and Cl- ions as it dissolves. In contrast, covalent bonds and van der Waals attractions have an intrinsic bond strength that is independent of the aqueous environment, because changes in water molecule associations are not involved in the formation of these two types of bonds.

68. Your friend has just returned from a deep-sea mission and claims to have found a single-celled life-form. He believes this new life-form may not have descended from the common ancestor that all types of life on Earth share. You are convinced that he must be wrong, and you mange to extract DNA from the cells he has discovered. He says that the mere presence of DNA is not enough to prove the point: his cells might have adopted DNA as a useful molecule quite independently of all other known life-forms. What could you do to provide additional evidence to support our argument?

You could use modern technology to discover the sequence of the DNA. if you are right, you would expect to find parts of this sequence that are unmistakably similar to corresponding sequences in other, familiar, living organisms; it would be highly improbably that such similar sequences would have evolved independently. You could, of course, also analyze other feature of the chemistry of his cells; for examples, do they contain proteins made of the same set of 20 amino acids? This could all be supporting evidence that this newly discovered species arose from the same common ancestral cells as all other life on earth.

2.62. each nucleotid in DNA and RNA has an aromatic base. what is the principal force that keeps the bases in a polymer from interacting with water? a. hydrophobic interactions b. hydrogen bonds c. covalent bonds d. van der waal interactions

a

2.64. there are 20^100 different possible sequence combinations for a protein chain with 100 amino acids. in addition to the amino acid sequence of a protein, what other factors increase the potential for diversity in these macromolecules? a. free rotation around single bonds during synthesis b. noncovalent interactions sampled as protein folds c. the directionality of amino acids being added d. the planar nature of the peptide bond

a

31.

a

10. select the option that correctly finishes the following statement: "a cell's genome contains all of ...."

a cell's dna

Of the choices below, which alteration of Ras activity is most likely to contribute to the uncontrolled growth of cancer cells? a) a change that prevents Ras from being made b) a change that increases the affinity of Ras for GDP c) a change that decreases the affinity of Ras for GTP d) a change that decreases the rate of hydrolysis of GTP by Ras

a change that decreases the rate of hydrolysis of GTP by Ras

Motor proteins use the energy in ATP to transport organelles, rearrange elements of the cytoskeleton during cell migration, and move chromosomes during cell division. Which of the following mechanisms is sufficient to ensure the unidirectional movement of a motor protein along its substrate? (a) A conformational change is coupled to the release of a phosphate (Pi). Which of the following mechanisms is sufficient to ensure the unidirectional movement of a motor protein along its substrate? a) a conformational change is coupled to the release of a phosphate b) the substrate on which the motor moves has a conformational polarity c) a conformational change is coupled to the binding of ADP d) a conformational change is linked to ATP hydrolysis

a conformational change is linked to ATP hydrolysis

2.50.c. what type of molecule is figure q2-50

a fatty acid

18. although there are many distinct prokaryotic species, most have a small range of shapes, sizes, and growth rates. Which of the following characteristics are NOT observed in prokaryotes? a. a highly structured cytoplasm b. endoplasmic reticulum c. the ability to divide rapidly d. a cell wall

a highly structured cytoplasm endoplasmic reticulum

Fully folded proteins typically have polar side chains on their surfaces, where electrostatic attractions and hydrogen bonds can form between the polar group on the amino acid and the polar molecules in the solvent. In contrast, some proteins have a polar side chain in their hydrophobic interior. Which of the following would not occur to help accommodate an internal, polar side chain? a) a hydrogen bond forms between two polar side chains b) a hydrogen bond forms between a polar side chain and a protein backbone c) a hydrogen bond forms between a polar side chain and an aromatic side chain d) hydrogen bonds form between polar side chains and a buried water molecule

a hydrogen bond forms between a polar side chain and an aromatic side chain

Protein structures have several different levels of organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. Consider the definitions below and select the one that best fits the term "protein domain". a) a small cluster of alpha helices and beta sheets b) the tertiary structure of a substrate-binding pocket c) a complex of more than one polypeptide chain d) a protein segment that folds independently

a protein segment that folds independently

The condensation reaction between the growing polypeptide chain and the next amino acid to be added involves the loss of _____________. a) a water molecule b) an amino group c) a carbon atom d) a carboxylic acid group

a water molecule

Studies conducted with a lysozyme mutant that contains an Asp>Asn change at position 52 and a Glu>Gln change at position 35 exhibited almost a complete loss in enzymatic activity. What is the most likely explanation for the decrease in enzyme activity in the mutant? a) increased affinity for substrate b) absence of negative charges in the active site c) change in the active site scaffold d) larger amino acids in the active site decreases the affinity for substrate

absence of negative charges in the active site

The process of generating monoclonal antibodies is labor-intensive and expensive. An alternative is to use polyclonal antibodies. A subpopulation of purified polyclonal antibodies that recognize a particular antigen can be isolated by chromatography. Which type of chromatography is used for this purpose? a) affinity b) ion-exchange c) gel-filtration d) any of the above

affinity

61. genes that have homologs in a variety of species have been discovered through the analysis of genome sequences. in fact, it is not uncommon to find a family of homologous genes encoding proteins that are unmistakably similar in amino acid sequence in organisms as diverse as budding yeast, archaea, plants, and humans. even more remarkably, many of these proteins can substitute functionally for their homologs in other organisms. explain what it is about the origins of cells that makes it possible for proteins expressed by homologous genes to be functionally interchangeable in different organisms.

all living beings on Earth (and thus, all cells) are thought to be derived from a common ancestor. solutions to many of the essential challenges that face a cell (such as the synthesis of proteins, lipids, and DNA) seem to have been achieved in this ancient common ancestor. the ancestral cell therefore possessed sets of proteins to carry out these essential functions. many of the essential challenges facing modern-day cells are the same as those facing the ancestral cell, and the ancient solutions are often still effective. thus, it is not uncommon for organisms to use proteins usually show some species-specific diversification they still retain the basic biochemical characteristics of the ancestral protein. for example, homologous proteins often retain their ability to interact with a specific protein target, even in cells of diverse species. because the basic biochemical characteristics are retained, homologous proteins are often capable of functionally substituting for one another.

51. biologist cannot possibly study all living species. instead they try to understand cell behavior by studying a select subset of them. which of the following characteristics are useful in an organism chosen for use as a model in laboratory studies? a. amenability to genetic manipulation b. ability to grow under controlled conditions c. rapid rate of reproduction d. all of the above

all of the above

Energy required by the cell is generated in the form of ATP. ATP is hydrolyzed to power many of the cellular processes, increasing the pool of ADP. As the relative amount of ADP molecules increases, they can bind to glycolytic enzymes, which will lead to the production of more ATP. The best way to describe this mechanism of regulation is _________. a) feedback inhibition b) oxidative phosphorylation c) allosteric activation d) substrate-level phosphorylation

allosteric activation

Which of the following statements about allostery is true? a) allosteric regulators are often products of other chemical reactions in the same biochemical pathway b) allosteric regulation is always used for negative regulation of enzyme activity c) enzymes are the only types of proteins that are subject to allosteric regulation d) binding of allosteric molecules usually locks an enzyme in its current conformation, such that the enzyme cannot adopt a different conformation

allosteric regulators are often products of other chemical reactions in the same biological pathway

3.b. Despite the diversity, cells resemble each other to an astonishing degree in their chemistry. For example, the same 20 BLANK are used to make proteins.

amino acids

6. Proteins are important architectural and catalytic components within the cell, helping to determine its chemistry, its shape, and its ability to respond to changes in the environment. Remarkably, all of the different proteins in a cell are made from the same 20 BLANK. By linking them in different sequences, the cell can make protein molecules with different conformations and surface chemistries and therefore different functions.

amino acids

2.55. cholesterol is an essential component of biological membranes. although it is much smaller than the typical phospholipids and glycolipids in the membrane, it is a BLANK molecule, having both hydrophilic and hydrophobic regions

amphipathic

36.b. what cell type has a nucleus?

animal, plant

36.f. what cell type has lysosomes?

animal, plant

36.g. what cell type has mitochondrion?

animal, plant

36.h. what cell type has Golgi apparatus?

animal, plant

36.a. what cell type has DNA?

animal, plant, bacterial

36.c. what cell type has plasma membrane?

animal, plant, bacterial

2.1. chemical reactions in living systems occur in an BLANK environment, within a narrow range of temperatures

aqueous

54.b.what would be the best model organism to use for the investigation of the process of: chloroplast function

arabidopsis

2.68. you are trying to make a synthetic copy of a particular protein but accidentally join the amino acids together in exactly the reverse order. one of your classmattes says the two proteins must be identical, and bets you $20 that your synthetic protein will have exactly the same biological activity as the original. after having read this chapter, you have no hesitation in staking your $20 that it won't. what particular feature of a polypeptide chain makes you sure your $20 is safe and that project must be done again.

as a peptide bond has a distinct chemical polarity, a polypeptide chain also has a distinct polarity. the reversed protein chain cannot make the same noncovalent inerations during folding and thus will not adopt the same three-dimensional structure as the original protein. the activities of these two proteins will definitely be different, because the activity of a protein depends on its 3d structure. it is unlikely that the reverse chain will fold into any well-defined, and hence functionally useful, structure at all, because it has not passed the stringent selective pressures imposed during evolution.

2.40. the amino acid histidine is often found in enzymes. depending on the pH of its environment, sometimes histidine is neutral and at other times it acquires a proton and becomes positively charged. consider an enzyme with a histidine side chain that is known to have an important role in the function of the enzyme. it is not clear whether this histidine is required in its protonated or its unprotonated state. which form of histidine is necessary for the active enzyme?

assuming that the change in enzyme activity is due to the change in the protonantion state of histidine, the enzyme must require histidine in the protonated, charged state. the enzyme is active only at low, acidic pH, where the proton (or hydronium ion) concentration is high; thus, the loss of a proton from histidine will be disfavored so that histidine is likely to be protonated

2.6. atomic number and weight of carbon

atomic number=6 atomic weight=12

2.63. because there are four different monomer building blocks that can be used to assemble RNA polymers, the number of possible sequence combinations that can be created for an RNA molecule made of 100 nucleotides is... a. 100^4 b. 4^100 c. 4*100 d. 100/4

b

37. which of the following choices best describes the role of the lysosome? a. transport of material to the golgi b. clean-up, recycling, and disposal of macromolecules d. the storage of excess macromolecules

b

11. which statement is NOT true about the events/conclusions from studies during the mid- 1800s surrounding the discovery of the cells? a. cells came to be known as the smallest universal building block of living organisms b. scientists came to the conclusion that new cels can form spontaneously from the remnants of ruptured cells. c. light microscopy was essential in demonstrating the commonalities between plan and animal tissues. d. new cells arise from the growth and division of previously existing cells.

b. scientists came to the conclusion that new cells can form spontaneously from the remnants of ruptured cells.

49. a. good or bad to study in the model organism E. coli: formation of endoplasmic reticulum

bad

49.c. good or bad to study in the model organism E. coli: how the actin cytoskeleton contributes to cell shape

bad

49.e. good or bad to study in the model organism E. coli: how mitochondria get distributed to cells during cell division

bad

2.58.c. the nitrogen-containing aromatic ring is called

base

2.69.a. choose the class of amino acids most important for the interaction: forming ionic bonds with negatively charged DNA

basic

Beta sheets can participate in the formation of amyloid fibers, which are insoluble protein aggregates. What drives the formation of amyloid fibers? a) denaturation of proteins containing beta sheets b) extension of beta sheets into much longer beta strands c) formation of biofilms by infectious bacteria d) beta-sheet stabilization of abnormally folded proteins

beta-sheet stabilization of abnormally folded proteins

The human immune system produces ________ of different immunoglobulins, also called __________, which enable the immune system to recognize and fight germs by specifically binding one or a few related ______________. The hyper variable structural element that forms the ligand-building site is comprised of several _____________. Purified antibodies are useful for a variety of experimental purposes, including protein purification using _________ chromatography.

billions, antibodies, antigens, loops, affinity

13. f.employs a light microscope and requires that samples be fixed and stained in order to reveal cellular details

bright-field

Which of the following mechanisms best describes the manner in which lysozyme lowers the energy required for its substrate to reach its transition-state conformation? a) by binding 2 molecules and orienting them in a way that favors a reaction between them b) by altering the shape of the substrate to mimic the conformation of the transition state c) by speeding up the rate at which water molecules collide with the substrate d) by binding irreversibly to the substrate so that it cannot dissociate

by speeding up the rate at which water molecules collide with the substrate

2.59.c.peptide: Pro-Val-Thr-Gly-Lys-Cys-Glu according to the conventional way of writing the sequence of a peptide or a protein, identify the c-terminal and n-terminal acids

c-terminal is glutamic acid n-terminal is proline

7. Which statement is NOT true about mutations? a. A mutation is a change in the dna that can generate offspring less fit for survival than their parents b. A mutation can be a result of imperfect dna duplication. c. A mutation is a result of sexual reproduction d. A mutation is a change in the dna that can generate offspring that are less fit for survival as their parents are.

c. A mutation is a result of sexual reproduction

45. Microtubules BLANK and are required to pull duplicated chromosomes to opposite poles of dividing cells

can rapidly organize

1. living systems are incredibly diverse in size, shape, environment, and behavior. It is estimated that there are between 10 million and 100 million different species. Despite this wide variety of organisms, it remains difficult to define what is alive. Which of the following can be described as the smallest living unit?

cell

43. despite the differences between eukaryotic and prokaryotic cells, prokaryotes have proteins that are distantly related to eukaryotic actin filaments and microtubules. what is likely to be the most ancient function of the cytoskeleton?

cell division

62.c.match the following biological process with the model organism that is best suited or most specifically useful for its study: s. pombe

cell division

62.e.match the following biological process with the model organism that is best suited or most specifically useful for its study: s. cerevisae

cell division

53. brewer's yeast, apart from being an irreplaceable asset in the brewery and in the bakery, is an experimental organism used to study eukaryotic cells. however, it does have some limitations. which of the processes below cannot be studied in yeast? a. dna replication b. cell motility c. exocytosis d. cell division

cell motility

24.c. In contrast, the BLANK is a type of organelle found only in the cells of plants and algae, and performs photosynthesis.

chloroplasts

26. the nucleus, an organelle found in eukaryotic cell, confines the BLANK, keeping them separated from other components of the cell.

chromosomes

Which of the following is not a feature commonly observed in beta sheets? a) antiparallel regions b) coiled-coil patterns c) extended polypeptide backbone d) parallel regions

coiled-coil patterns

Coiled-coils are typically found in proteins that require an elongated structural framework. Which of the following proteins do you expect to have a coiled-coil domain? (a) insulin (b) collagen (c) myoglobin (d) porin

collagen

13. a. a BLANK scans the specimen with a focused laser beam to obtain a series of two-dimensional optical sections, which can be used to reconstruct an image of the specimen in three dimensions the laser excites a fluorescent dye molecule, and the emitted light from each illuminated point is captured through a pinhole and recorded by a detector

confocal

2.57. dna and rna are different types of nucleic acid polymer. which of the following is true of dna but not true of rna? a. contains uracil b. contains thymine c. is single stranded d. it has 5' to 3' directionality

contains thymine

24.d. If we were to strip away the plasma membrane from a eukaryotic cell and remove all of its membrane-enclosed organelles, we would be left with the BLANK, which contains many long, fine filaments of protein that are responsible for cell shape and structure and thereby form the cell's BLANK.

cytosol cytoskeleton

2.66. macromolecules in the cell can often interact transiently as a result of noncovalent interactions. these weak interactions also produce stable, highly specific interactsion between molecules. which of the factors below is the most significant in determining whether the interaction will be transient or stable? a. the size of each molecule b. the concentration of each molecule c. the rate of synthesis d. surface complementarity between molecules

d

2.58.d. five-carbon sugar found in DNA is called

deoxyribose

62.f.match the following biological process with the model organism that is best suited or most specifically useful for its study: d. rerio (zebrafish)

development

62.g.match the following biological process with the model organism that is best suited or most specifically useful for its study: d. melongaster

development

62.b. match the following biological process with the model organism that is best suited or most specifically useful for its study: m. musculus (mouse)

development immunology

62.a. match the following biological process with the model organism that is best suited or most specifically useful for its study: a. thaliana (arabidopsis)

development photosynthesis

2.37.

diagram

38.

didinium engulfs prey by changing its shape, and for this it uses its cytoskeleton. bacteria have no cytoskeleton and cannot easily change their shape because they are generally surrounded by a tough cell wall.

Which of the following statements is true? a) disulfide bonds are formed by the cross-linking of methionine residues b) disulfide bonds are formed mainly in proteins that are retained within the cytosol c) disulfide bonds stabilize but do not change a protein's final conformation d) agents such as mercaptoethanol can break disulfide bonds through oxidation

disulfide bonds stabilize but do not change a protein's final conformation

54.d.what would be the best model organism to use for the investigation of the process of: development of a multicellular tissue

drosophila

52. many of the mechanisms that cells use for maintenance and reprodution were first studied at the molecular level in bacteria. which bacterial species had a central role in advancing the field of molecular biology?

e. coli

Globular proteins fold up into compact, spherical structures that have uneven surfaces. They tend to form multisubunit complexes, which also have a rounded shape. Fibrous proteins span relatively large distances within the cell and in the extracellular space. Which of the proteins below is not classified as a fibrous protein? a) elastase b) collagen c) keratin d) elastin

elastase

2.31. although covalent bonds are 10-100 times stronger than noncovalent interactions, many biological processes depend upon the number and type of noncovalent interactions between molecules. what noncovalent bond interaction will contribute most to the strong and specific binding of two molecules, such as a pair of proteins?

electrostatic attractions

39. the cell constantly exchanges materials by bringing nutrients in from the external environment and shuttling unwanted by-products back out. which term describes the process by which external materials are captured inside vesicles and brought into the cell?

endocytosis

30. mitochondia contain their own genome, are able to duplicate, and actually divide on a different time line from the rest of the cell. nevertheless, mitochondia cannot funcition for long when isolated from the cell because they are...

endosymbionts

8. Changes in dna sequence from one generation to the next may result in offspring that are altered in fitness compared with their parents. the process of change and selection over the course of many generations is the basis of BLANK.

evolution

2.19.c. true or falseL atoms with unfilled outer electron shells are especially stable and are therefore less reactive

false, atoms that have their outer electron shells filled are the most stable and least reactive. atoms with unfilled outer shells are more reactive because they tend to share or transfer electrons.

2.35.a. true or false: any covalently bonded H atom can participate in a hydrogen bond if it comes in close proximity with an oxygen atom that forms part of a water molecule

false, hydrogen atoms that are covalently bonded to carbon atoms do not participate in hydrogran bonds because these hydrogens have almost no net postive charge

60.c. true or false: the vast majority of our genome encodes functional RNA molecules or proteins and most of the intervening DNA is nonfunctional

false, it is a relatively small proportion of our DNA that encodes RNA and protein molecules. the majority of nonencoding sequences is probably involved in critical regulatory processes

2.19.b. true or false: there is no limit to the number of electrons that can occupy the fourth electron shell

false, the fourth electron shell has the capacity to hold 18 electrons

2.65.a. true or false: "nonpolar interactions" is simply another way of saying "van der Waals attractions"

false, van der waals attractions describe the general attractive forces between all atoms. the contact distance between any two nonbonded atoms is the sum of van der waals radii. nonpolar interactions are based on the exclusion of hydrophobic molecules from a hydrophilic environment

2.52.a. true or false: a disaccharide consists of a sugar covalently linked to another molecule such as an amino acid or nucleotide.

false. a disaccharide consists of two sugar molecules that undergo a condensation reaction to form a covalent bond

46. a.true or false: plants do not require a cytoskeleton because they have a cell wall that lend structure and support to the cell

false. although plant cells do have a cell wall that lends structure and support, they still need a cytoskeleton, which also helps with connections between cells and the transport of vesicles inside the cell

2.2.a. true or false:The chemistry of life is carried out and coordinated primarily by the action of small molecules.

false. although small molecules are important in many processes, the chemical reactions in living systems are regulated by the coordinated action of large polymeric molecules

2.24.b. true or false: copper, zinc, and manganese are among 11 nonessential trace elements that contribute less than 0.1% of all the atoms in the human body

false. cu, zn, and mn are essential trace elements in the body.

2.15.b. true or false: H,C,O,N are the most common elements in biological molecules because they are most stable

false. h,c,n,o are the most common elements in biological molecules because their outer shells are unfilled, making them highly reactive

32.a. true or false: the number of mitochondria inside a cell remains constant over the life of the cell.

false. in plants, only mitochondria perform cellular respiration (using oxygen to break down organic molecules to produce carbon dioxide) just as in animal cells. Chloroplasts perform photosynthesis in which water molecules are split to generate oxygen and fix carbon dioxide molecules.

2.a. True or False: the paramecium is a multicellular microorganism covered with hairlike cilia

false. it is a single-celled organism

35.c. true or false: lysosomes are small organelles where fatty acid synthesis occurs.

false. lysosomes house enzymes that break down nutrients for use by the cell and help recycle materials that cannot be used, which will later be excreted from the cell

32.b. the number of mitochondria inside a cell remains constant over the life of the cell

false. mitochondria have their own division cycle and their numbers change based on the rate of division

21.b. true or false: mitochondria are thought to have evolved from anaerobic bacteria

false. mitochondria use oxygen to generate energy and are thought to have evolved from aerobic bacteria

2.24.c. true or false: approximately .9% of the atoms in the human body come from seven essential elements- Na, Mg, K, Ca, P, S, and Cl- all of which form stable ions in aqueous solution.

false. na, mg, k, ca, and cl form ions in aqeuous solution, but P and S form covalent bonds in order to fill their outer shells

21.c. true or false: photosynthetic bacteria contain chloroplasts

false. photosynthetic bacteria have enzyme systems similar to those found in chloroplasts, which allow them to harvest light energy to fix carbon dioxide

14.c. the cytosol is fairly empty, containing a limited number of organelles, which allows room for rapid movement via fusion.

false. the cytosol is actually brimming with individual proteins, protein fibers, membrane systems, transport vesicles, and small molecules. The rate of movement is limited by the space available.

48.c. true or false: the first eukaryotic cells on earth must have been aerobic; otherwise, they would not have been able to survive when the planet's atmosphere became oxygen-rich

false. the first eukaryotic cells likely contained a nucleus but no mitochondria. these ancestral eukaryotes subsequently adapted to survive in a world filled with oxygen by engulfing primitive aerobic prokaryotic cells

48.a. true or false: primitive plant, animal, and fungal cells probably acquired mitochondria after they diverged from a common ancestor.

false. the mitochondria in modern plant, animal and fungal cells are very similar, implying that these lines diverted after the mitochondrion was acquired by the ancestral eukaryote

14.a. true or false: the nucleus of an animal cell is round, small, and difficult to distinguish using light microscopy

false. the nucleus is one of the largest organelles and the easiest to discern within a typical cell

2.52.c. true or falseL the presence of double bonds in the hydrocarbon tail of a fatty acid does not greatly influence its structure

false. the presence of a double bond in the hydrocarbon chain of a fatty acid causes a kink in the chain, decreasing its felxibility and packing with neighboring hydrocarbon chains

2.44. what monomer building block is necessary to assemble selectively permeable boundaries around and inside cells?

fatty acis

13. c.requires the use of two sets of filters. the first filter narrows the wavelength range that reaches the specimen and the second blocks out all wavelengths that pass back up to the eyepiece except for those emitted by the dye in the sample

fluorescence

Which of the following methods would be the most suitable to asses the relative purity of a protein in a sample you have prepared? a) gel-filtration chromatography b) gel electrophoresis c) western blot analysis d) ion-exchange chromatography

gel electrophoresis

Which of the following methods would be the most suitable to asses whether your protein exists as a monomer or in a complex? a) gel-filtration chromatography b) gel electrophoresis c) western blot analysis d) ion-exchange chromatography

gel-filtration chromatography

2.49. which of the following are examples of isomers? a. glucose and galactose b. alanine and glycine c. adenine and guanine d. glycogen and cellulose

glucose and galactose

2.53.3.

glycerol

2.58.f. linkage between the sugar and the base is called

glycosidic bond

4.b. good or bad to study in the model organism E. coli: DNA replication

good

49.d. good or bad to study in the model organism E. coli: how cells decode their genetic instructions to make proteins

good

2.20. on the basis of the information in the chart and what you know about atomic surfaces, which elements are chemically inert?

helium, neon

40. eukaryotic cells are able to trigger the release of material from secretory vesicles to the extracellular space using a process called exocytosis. an example of materials commonly released this way is...

hormones

2.61. both DNA and RNA are synthesized by covalently linking a nucleoside triphosphate to the previous nucleotide, constantly adding to a growing chain. in the case of DNA, the new strand becomes part of a stable helix. the two stands are complementary in sequence and antiparallel in directionality. what is the principal force that holds these two strands together?

hydrogen bonds

Cyclic AMP (cAMP) is a small molecule that associates with its binding site with a high degree of specificity. Which types of non covalent interactions are the most important for providing the 'hand in the glove' binding of cAMP? a) hydrogen bonds b) electrostatic interactions c) van der Waals interactions d) hydrophobic interactions

hydrogen bonds

Although all protein structures are unique, there are common structural building blocks that are referred to as regular secondary structures. Some proteins have α helices, some have β sheets, and still others have a combination of both. What makes it possible for proteins to have these common structural elements? a) specific amino acid sequences b) side-chain interactions c) the hydrophobic-core interactions d) hydrogen bonds along the protein backbone

hydrogen bonds along the protein backbone

Lysozyme is an enzyme that specifically recognizes bacterial polysaccharides, which renders it an effective antibacterial agent. Into what classification of enzymes does lysozyme fall? a) isomerase b) protease c) nuclease d) hydrolase

hydrolase

2.33. the pH of an aqueous solution is an indication of the concentration of available protons. however, you should not expect to find lone protons in solution; rather, the proton is added to a water molecule to form a BLANK ion.

hydronium

2.53.5.

hydrophilic region

2 or 3 alpha helices can sometimes wrap around each other to form coiled-coils. The stable wrapping of one helix around another is typically driven by __________________ interactions. a) hydrophilic b) hydrophobic c) van der Waals d) ionic

hydrophobic

2.53.6.

hydrophobic region

2.43.c. inorganic or organice: sodium chloride

i

2.43.d. inorganic or organice: water

i

2.43.g. inorganic or organice: calcium

i

2.43.i. inorganic or organice: oxygen

i

2.43.j. inorganic or organice: iron

i

33. chloroplasts are found only in eukaryotic cells that carry out photosynthesis: plants and algae. plants and algae appear green as a result of the presence of chlorophyll. where is chlorophyll located in the chloroplast?

in the third, innermost membrane

56. drosophila melanogaster is a BLANK. this type of animal is the most abundant of all animal species, making it an appropriate choice as an experimental model.

insect

Proteins bind selectively to small-molecule targets called ligands. The selection of one ligand out of a mixture of possible ligands depends on the number of weak, noncovalent interactions in the protein's ligand-binding site. Where is the binding site typically located in the protein structure? a) on the surface of the protein b) inside a cavity on the protein surface c) buried in the interior of the protein d) forms on the surface of the protein in the presence of the ligand

inside a cavity on the protein surface

2.46. diagram

ionic bonds

2.30. when atoms are held together by BLANK, they are typically referred to as BLANK. a. hydrogen bonds, molecules b. ionic interactions, salts. c. ionic interactions, molecules

ionic interactions, salts

2.56.c. in solutions of neutral pH, amino acids are BLANK, carrying both a positive and negative charge.

ionized

55. A. thaliana or Arabidopsis, is a common weed. biologists have selected it over hundreds or thousands of other flowering plant species to serve as an experimental model organism because BLANK

it can reproduce in 8-10 weeks

2.28.a. in which scientific unit is the strength of a chemical bond usually expressed?

kilocalories per mole

20. prokarytic cells are able to evolve very fast, which helps them to rapidly adapt to new food sources and develop resistance to antibiotics. what are the three main characteristics that support the rapid evolution of prokaryotic populations?

large population rapid growth can exchange DNA

Which of the following is not a feature commonly observed in alpha helices? a) left-handedness b) one helical turn every 3.6 amino acids c) cylindrical shape d) amino acid side chains that point outward

left-handedness

2.18.b. these covalent bonds have characteristic bond BLANK and become stronger and more rigid when two electrons are shared in a BLANK.

length; double bond

Any substance that will bind to a protein is known as its ___________. Enzymes bind their ___________ at the ___________. The enzyme hexokinsae is so specific that it reacts with only one or 2 __________ of glucose. Enzymes catalyze a chemical reaction by lowering the ________, because they provide conditions favorable for the formation of a ___________ intermediate called the ____________. Once the reaction is completed, the enzyme releases the __________ of the reaction.

ligands, substrates, active site, isomers, activation energy, high energy, transition state, products

2.26. double covalent bonds are both shorter and stronger than single covalent bonds, but they also limit the geometry of the molecule because they....

limit the rotation of the bonded atoms

2.22.on the basis of the information in the chart and what you know about atomic surfaces, which elements will form ions with a net charge of +2 in solution?

magnesium, calcium

12. what unit of length would you generally use to measure a typical plant or animal cell?

micrometers

3.a. Cells can be very diverse: superficially, they come in various sizes, ranging from bacterial cells such as lactobacillus, which is a few BLANK in length, to larger cells such as frog's egg, which has a diameter of about one BLANK.

micrometers; millimeter

42. the cytoskeleton provides support, structure, motility, and organization, and it forms tracks to direct organelle and vesicle transport. which of the cytoskeletal elements listed below is the thickest? a. actin filaments b. microtubules c. intermediate filaments

microtubules

24.b. Another organelle found in essentially all eukaryotic cells is the BLANK, which generates the chemical energy for the cell.

mitochondrion

27. what organelle has both an outer and inner membrane?

mitochondrion

2.29.

model

54.c.what would be the best model organism to use for the investigation of the process of: immunology

mouse

9. select the option that best finishes the following statement: "evolution is a process that can be bst understood on the based principles of...."

mutation and selection

2.5. what subatomic particles can vary between isotopes of the same element, without changing the observed chemical properties?

neutrons

2.7. carbon 14 is an unstable isotope of carbon that decays very slowly. compared to the common, stable carbon 12 isotope, carbon 14 has two additional...

neutrons

2.23.on the basis of the information in the chart and what you know about atomic surfaces, which elements form stable but reactive diatomic gases?

nitrogen, oxygen

Which of the following statements is true? a) peptide bonds are the only covalent bonds that can link together two amino acids in proteins b) the polypeptide backbone is free to rotate about each peptide bond c) non polar amino acids tend to be found in the interior of proteins d) the sequence of the atoms in the polypeptide backbone varies between different proteins

non polar amino acids tend to be found in the interior of proteins

2.18.c. equal sharing of electrons yields a BLANK covalent bond.

nonpolar

2.69.d. choose the class of amino acids most important for the interaction: localizing an "integral membrane" protein that spans a lipid bilayer

nonpolar

2.69.e. choose the class of amino acids most important for the interaction: tightly packing the hydrophobic interior core of a globular protein

nonpolar

2.71.b.Your lab director requests that you add new growth medium to the mammalian cell cultures before heading home from the lab on a Friday night. Unfortunately, you need to make fresh medium because all the premixed bottles of medium have been used. One of the ingredients you know you need to add is a mix of the essential amino acids (those that cannot be made by the cells, but are needed in proteins). On the shelf of dry chemicals you find the amino acids you need, and you mix them into your medium, along with all the other necessary nutrients, and replace the old medium with your new medium. On Sunday, you come in to the lab just to check on your cells and find that the cells have not grown. You are sure you made the medium correctly, but on checking you see that somebody wrote a note on the dry mixture of amino acids you used: "Note: this mixture contains only ᴅ-amino acids." Are there any organisms that could grow using this mixture? Justify your answer.

not unless l-amino acids were also mixed in. certain types of bacteria use d-amino acids to product their cell walls, but they would still require l-amino acids for the rest of the proteins they make.

Which of the following methods used to study proteins is limited to proteins with a molecular mass of 50 kD or less? a) X-ray crystallography b) fingerprinting c) nuclear magnetic resonance d) mass spectroscopy

nucelar magnetic resonance

2.58.e. sugar unit linked to a base is called

nucleoside

2.58.h. sugar linked to a base and a phosphate

nucleotide

2.58.h. sugar linked to a base and a phosphate is called

nucleotide

2.70. it is now a routine task to determine the exact order in which individual subunits have been linked together in polynucleotides (DNA) and polypeptides (proteins). however, it remains difficult to determine the arrangement of monomers in a polysaccharide. explain why this is the case.

nucleotides and amino acids have an intrinsic directionality, and the mechanism by which monomers are added into a growing polymer is always the same. this yields a linear polymer with the same directionality as the monomers. polysaccharides are produced by linking monosaccharides together. the monosaccharides can be either added directly or modified to produce various derivatives before addition. beyond this, there are multiples sites on each monosaccharide where addition can occur, producing highly complex, branched polymers.

17. by definition, prokaryotic cells do not possess a...

nucleus

24. a. Eukaryotic cells are bigger and more elaborate than prokaryotic cells. By definition, all eukaryotic cells have a BLANK, usually the most prominent organelle.

nucleus

2.43.a. inorganic or organice: glucose

o

2.43.b. inorganic or organice: ethanol

o

2.43.e. inorganic or organice: cholesterol

o

2.43.f. inorganic or organice: adenosine

o

2.43.h. inorganic or organice: glycine

o

2.43.k. inorganic or organice: phospholipid

o

2.67. As a protein is made, the polypeptide is in an extended conformation, with every amino acid exposed to the aqueous environment. Although both polar and charged side chains can mix readily with water, this is not the case for nonpolar side chains. Explain how hydrophobic interactions may play a role in the early stages of protein folding, and have an influence on the final protein conformation.

one reason that nonpolar groups are excluded from an aqueous environment is that hydrophobic surface would organize water into a highly structured network of hydrogen bonds, which is energetically unfavorable.So, you would expect that nonpolar amino acids would group together early, forming "hydrophobic pockets," while the polar and charged side chains remain at the interface of the surrounding solution. In the final, folded protein, most of the nonpolar amino acids will remain buried inside the protein. This fold is more stable because nonpolar atoms are prevented from contact with water and remain in contact with each other.

2.38.a. what is the pH of pure water?

pH 7

2.32. what describes the calculation of pH?

pH=-log10[H+]

2.56.d. when a protein is made, amino acids are linked together through BLANK, which are formed by condensation reactions between the carboxyl end of the last amino acid and the BLANK end of the next amino acid to be added to the growing chain

peptide bonds amino

41. BLANK are fairly small organelles that provide a safe place within the cell to carry out certain biochemical reactions that generate harmful, highly reactive oxygen species. these chemicals are both generated and broken down in the same location

perioxisomes

13. d.uses a light microscope with an optical component to take advantage of the different refractive indices of light passing through different regions of the cell

phase contrast

2.53.2.

phosphate

2.58.g. linkage between phosphate groups is called

phosphoanhydride bond

2.58.a. the linkage between two nucleotides is called

phosphodiester bond

2.58.b. the linkage between the 5' sugar hydroxyl and a phosphate group is called

phosphoester bond

2.45. diagram

phosphoryl

36.d. what cell type has chloroplasts?

plant, bacterial

36.e. what cell type has cell walls?

plant, bacterial

25. The BLANK is made up of two concentric membranes and is continuous with the membrane of the endoplasmic reticulum

plasma membrane

2.18.d. these BLANK covalent bonds should not be confused with the weaker BLANK bonds that are critical for the 3d structure of biological molecules and for the interactions between these molecules

polar noncovalent

2.53.1.

polar head group

2.56.a. proteins are BLANK built from amino acids, which each have an amino group and a BLANK group attached to the central BLANK.

polypeptides carboxyl a-carbon

57. caenorhabditis elegans is a nematode. during its development, it produces more than 1000 cells. however, the adult worm has only 959 somatic cells. the process by which 131 cells are specifically arget for destruction is called BLANK

programmed cell death

62.d.match the following biological process with the model organism that is best suited or most specifically useful for its study: c. elegans

programmed cell death

2.59.a. peptide: Pro-Val-Thr-Gly-Lys-Cys-Glu write out the sequence of amino acids.

proline valine threonine glycine lysine cysteine glutamic acid

The activity, the phosphorylation of a protein is typically associated with a change in assembly of a protein complex, or the triggering of a downstream signaling cascade. The addition of ubiquitin, a small polypeptide, is another type of covalent modification that can affect the protein function. Ubiquitylation often results in _______________. a) membrane association b) protein degradation c) protein secretion d) nuclear translocation

protein degradation

Instead of studying one or two proteins or protein complexes present in the cell at any given time, we can now look at a snapshot of all proteins being expressed in cells being grown in specific conditions. This large-scale, systematic approach to the study of proteins is called _______________. (a) proteomics. (b) structural biology. (c) systems biology. (d) genomics.

proteomics

2.3. which subatomic particles contribute to the atomic number for any given element?

protons

2.4. which subatomic particles contribute to atomic mass for any given element

protons and neutrons

5. The flow of genetic information is controlled by a series of biochemical reactions that result in the production of proteins, each with its own specific order of amino acids. Choose the correct series of biochemical reactions from the options presented here:

replication, transcription, translation

2.39. aromatic carbon compounds such as benzene are planar and very stable. double bond character extends around the entire ring, which is why it is often drawn as a hexagon with a circle inside. this characteristic is caused by election...

resonance

For some proteins, small molecules are integral to their structure and function. Enzymes can synthesize some of these small molecules, whereas others, called vitamins, must be ingested in the food we eat. Which of the following molecules is not classified as a vitamin but does require the ingestion of a vitamin for its production? a) retinal b) biotin c) zinc d) heme

retinal

The three-dimensional coordinates of atoms within a folded protein are determined experimentally. After researchers obtain a protein's structural details, they can use different techniques to highlight particular aspects of the structure. Which visual model best displays a protein's secondary structures (alpha helices and beta sheets)? a) ribbon b) space-filling c) backbone d) wire

ribbon

2.47. cells requir one particular monosaccharide as a starting material to synthesize nucleotide building blocks. which of these fills this important role: glucose, fructose, ribulose, ribose

ribose

2.58.i. five-carbon sugar found in rna is called

ribose

44. which of the following characteristics would not support the idea that the ancestral eukaryote was a predator cell that captured and consumed other cells? a. dynamic cytoskeleton b. large cell size c. ability to move d. rigid membrane

rigid membrane

2.18. whereas ionic bonds for a BLANK, covalent bonds between atoms form a BLANK.

salt molecule

2.53.7.

saturated fatty acid

13. e. requires coating the sample with a thin layer of a heavy metal to produce three dimensional images of the surface of the sample

scanning electron

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. The alpha helices and beta sheets are examples of protein __________ structure. A protein such as hemoglobin, which is composed of more than one protein _________, has ____________ structure. A protein's amino acid sequence is known as its __________ structure. A protein __________ is the modular unit from which many larger single-chain proteins are constructed. The 3-D conformation of a protein is its _____________ structure.

secondary, subunit, quaternary, primary, domain, tertiary

The variations in the physical characteristics between different proteins are influenced by the overall amino acid compositions, but even more important is the unique amino acid ___________. a) number b) sequence c) bond d) orientation

sequence

2.48. oligosaccharides are short sugar polymers that can become covalently linked to proteins and lipids though condensation reactions. these modified proteins and lipids are called glycoproteins and glycolipids, respectively. within a protein, which of the amino acids is the most probable target for this type of modification?

serine

2.16. a covalent bond between two atoms is formed as a result of the BLANK

sharing of electrons

2.56.b. there are twenty possible BLANK that differ in structure and are generally referred to as "R."

side chains

2.41. silicon is n element, like carbon, has four vacancies in its outer electron shell and therefore has the same bonding chemistry as carbon. silicon is not found to any significant degree in the molecules found in living systems, however. does this difference arise because elemental carbon is more abundant than silicon? what other explanations are there for the preferential selection of carbon over silicon as the basis for the molecules of life?

silicon is actually more abundant in the earths crust than carbon, so this is not likely to be the reason that carbon was used preferentially. carbon might have been the element of choice in living systems because it is lighter than silicon and forms shorter covalent bonds with other elements. shorter bonds are typically stronger and more stable

2.21.on the basis of the information in the chart and what you know about atomic surfaces, which elements will form ions with a net charge of +1 in solution?

sodium, potassium

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. A newly synthesized protein generally folds up into a ____________ conformation. All the info required to determine a protein's conformation is contained in its amino acid ________. On being heated, a protein molecule will become _________ as a result of breakage of ___________ bonds. On removal of urea, an unfolded protein can become __________. The final folded conformation adopted by a protein is that of __________ energy.

stable, sequence, denatured, non covalent, renatured, lowest

34. photosynthesis enables plants to capture the energy from sunlight. in this essential process, plants incorporate the carbon from CO2 into high-energy BLANK molecules, which the plant cell mitochondria use to produce ATP.

sugar

28. mitochondria perform cellular respiration, a process that uses oxygen, generates carbon dioxide, and produces chemical energy for the cell. Which answer below indicates a correct pairing of material "burned" and the form of energy produced during cellular respiration? a. fat, ADP b. sugar, fat c. sugar, ATP d. fat, protein

sugar, ATP

2.10. which of the following elements is least abundant in living organisms? a. sulfur b. carbon c. oxygen d. nitrogen

sulfur

2.42. selenium (se) is an element required in the human body in trace amounts. selenium is obtained through the diet and levels of selenium found in food depend greatly on the soil where it is grown. once ingested and absorbed as selenate, it can become incorporated into a small number of polypeptides. these selenoproteins are formed when selenium replaces an element that is found in two of the twenty "standard" amino acids. using your knowledge of atomic structure, the periodic table, and structure of amino acids, deduce which 2 amino acids may be converted to "seleno" amino acids and used to make selenoproteins.

sulfur is the only element found exclusively in two of the twenty amino acids. this element is located directly above selenium in the periodic table, indicating that these elements have the same number of electrons in their outer shell and both prefer to form bonds with other atoms to fill their outer orbital. if selenium instead of sulfur is incorporated into cysteine or methionine, the alteres "seleno" amino acids will be produced. we can expect that this substitution will alter the nature of the proteins in which these amino acids are incorporated because selenium is a large atom than sulfur

Antibody production is an indispensible part of our immune response, but it is not the only defense our bodies have. Which of the following is observed during an infection that is not a result of antibody-antigen interactions? a) B cell proliferation b) aggregation of viral particles c) systemic temperature increase d) antibody secretion

systemic temperature increase

50. scientists learned that cell death is a normal and even import part of life by studying the development of the nematode worm C. elegans. What was the most important feature of C. elgans for the study of programmed cell death?

the developmental pathway of each cell in the adult worm was known

You have two purified samples of protein Y: the wild-type (nonmutated) protein and a mutant version with a single amino acid substitution. When washed through the same gel-filtration column, mutant protein Y runs through the column more slowly than the normal protein. Which of the following changes in the mutant protein is most likely to explain this result? (a) the loss of a binding site on the mutant-protein surface through which protein Y normally forms dimers (b) a change that results in the mutant protein acquiring an overall positive instead of a negative charge (c) a change that results in the mutant protein being larger than the wild-type protein (d) a change that results in the mutant protein having a slightly different shape from the wild-type protein

the loss of a binding site on the mutant-protein surface through which protein Y normally forms dimers

2.71.a. Your lab director requests that you add new growth medium to the mammalian cell cultures before heading home from the lab on a Friday night. Unfortunately, you need to make fresh medium because all the premixed bottles of medium have been used. One of the ingredients you know you need to add is a mix of the essential amino acids (those that cannot be made by the cells, but are needed in proteins). On the shelf of dry chemicals you find the amino acids you need, and you mix them into your medium, along with all the other necessary nutrients, and replace the old medium with your new medium. On Sunday, you come in to the lab just to check on your cells and find that the cells have not grown. You are sure you made the medium correctly, but on checking you see that somebody wrote a note on the dry mixture of amino acids you used: "Note: this mixture contains only ᴅ-amino acids." What is the meaning of the note and how does it explain the lack of cell growth in your culture?

the note indicates that the mixture contains only one of the two possible stereoisomers (l or d). because mammalian cells use only the l stereoisomer, the d-amino acid mixture could not be used and therefore it is as though no amino acids were added at all.

Protein folding can be studied using a solution of purified protein and a denaturant (urea), a solvent that interferes with noncovalent interactions. Which of the following is observed after the denaturant is removed from the protein solution? a) the polypeptide returns to its original conformation b) the polypeptide remains denatured c) the polypeptide forms solid aggregates and precipitates out of solution d) the polypeptide adopts a new, stable conformation

the polypeptide returns to its original conformation

To study how proteins fold, scientists must be able to purify the protein of interest, use solvents to denature the folded protein, and observe the process of refolding at successive time points. What is the effect of the solvents used in the denaturation process? (a) The solvents break all covalent interactions. (b) The solvents break all noncovalent interactions. (c) The solvents break some of the noncovalent interactions, resulting in a misfolded protein. (d) The solvents create a new protein conformation.

the solvents break all non covalent interactions

2.25. what does not influence the length of a covalent bond?

the tendency of atoms to fill the outer electron shells

2.60. the cell is able to harvest energy from various processes in order to generate ATP molecules. these ATPs represent a form of store energy that can be used later to drive other important processes. explain how the cell can convert the chemical energy store in ATP to generate mechanical energy, for example changing the shape of a protein

the terminal phosphate group is typically hydrolyzed and the energy released from this chemical bond is often "reinvested" to generate a new bond that links the phosphate group to a protein. this addition of a phosphate group can cause a change in the protein's conformation. this conformational change is usually associated with change in function of transient interactions with other macromolecules, generating a domino effect within the cell.

Which of the following is not true of molecular chaperones? a) they assist polypeptide folding by helping the folding process follow the most energetically favorable pathway b) they can isolate proteins from other components of the cells until folding is complete c) they can interact with unfolded polypeptides in a way that changes the final fold of the protein d) they help streamline the protein-folding process by making it a more efficient and reliable process inside the cell

they can interact with unfolded polypeptides in a way that changes the final fold of the protein

The correct folding of proteins is necessary to maintain healthy cells and tissues. Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer's, Huntington's, and Creutzfeld-Jacob disease (the specific faulty protein is different for each disease). What is the ultimate fate of these disease-causing, unfolded proteins? a) they are degraded b) they bind a different target protein c) they form structured filaments d) they form protein aggregates

they form protein aggregates

Molecular chaperones can work by creating an 'isolation chamber'. What is the purpose of this chamber? a) the chamber acts as a garbage disposal, degrading improperly folded proteins so that they don't interact with properly folded proteins b) this chamber is used to increase the local protein concentration, which will help speed up the folding process c) this chamber serves to transport unfolded proteins out of the cell d) this chamber serves to protect unfolded proteins from interacting with other proteins in the cytosol, until protein folding is completed

this chamber serves to protect unfolded proteins from interacting with other proteins in the cytosol, until protein folding is completed

2.17. an ionic bond between two atoms is formed as a result of the BLANK

transfer of electrons from one atom to another

Proteins can assemble to form large complexes that work coordinately, like moving parts inside a single machine. Which of the following steps in modulating the activity of a complex protein machine is least likely to be directly affected by ATP or GTP hydrolysis? a) translation of protein components b) conformational change of protein components c) complex assembly d) complex disassembly

translation of protein components

13. b. has the ability to resolve cellular components as small as 2nm

transmission electron

58. zebrafrish (danio rerio) are especially useful in the study of early development because their embryos are BLANK

transparents

2.54. many types of cells have stores of lipids in their cytoplasm, usually seen as fat droplets. what is the lipid most commonly found in these droplets?

triacylglycerol

14.b. true or false: the presence of the plasma membrane can be inferred by the well-defined boundary of the cell

true

19.b. true or false: prokaryotes can adopt several different basic shapes, including spherical, rod-shaped, and sprial

true

19.c. some prokaryotes have cell walls surrounding the plasma membrane

true

2.15.a. true or false: electron shells fill discrete regions around the nucleus of the atom and limit the number of electrons that can occupy a specific orbit

true

2.15.c. true or false: some atoms are more stable when they lose one or two elections, even though this means they will have a net positive charge.

true

2.19.a. true or false: electrons are constantly moving around the nucleus of the atom, but they can move only in discrete regions

true

2.2.b. true or false:Carbon-based compounds make up the vast majority of molecules found in cells.

true

2.24.a. true or false: there are 4 elements that constitute 99% of all the atoms found in the human body.

true

2.35.b. true or false: protons are constantly moving between water molecules, which means there is an overall equilibrium between hydroxyl ions and hydronium ions in aqueous solutions

true

2.35.c. true or false: a strong base is defined as a molecule that can readily remove protons from water

true

2.52.b. true or false: the hydroxyl groups on monosaccharides are reaction hot spots and can be replaced by other functional groups to produce derivatives of the original sugar

true

2.65.b. true or false: "nonpolar interactions" is simply another way of saying "van der waals attractions"

true

2.65.c. true or false: all proteins and RNAs pass through many unstable conformations as they are folded, finally settling on one single, preferred conformation.

true

2.b. true or false: cells of different types can have different chemical requirements

true

2.c. true or false: the branchlike extensions that sprout from a single nerve cell in a mammalian brain can extend over several hundred micrometers

true

21.a. true or false: oxygen is toxic to certain prokaryotic organisms

true

35.a. true or false: membrane components in the cell are made in the endoplasmic reticulum.

true

35.b. true or false: the Golgi apparatus is made up of a series of membrane-enclosed compartments through which material destined for secretion must pass.

true

46.b. true or false: the cytoskeleton is used as a transportation grid for the efficient, directional movement of cytosolic components

true

46.c. true or false: thermal energy promotes random movement of proteins, vesicles, and small molecules in the cytosol

true

48.b. true or false: protozoans are single-celled eukaryotes with cell morphologies and behaviors that can be as complex as those of some multicellular

true

60.a. true or false: the human genome is roughly 30 times larger than the arabidopsis genome, but contains approximately the same number of protein-coding genes

true

60.b.true or false: the variation in genome size among protozoans is larger than that observed across all species of mammals, birds, and reptiles

true

Which of the following globular proteins is used to form filaments as an intermediate step to step hollow tubes? a) tubulin b) actin c) keratin d) collagen

tubulin

2.69.b. choose the class of amino acids most important for the interaction: forming hydrogen bonds to aid solubility in water

uncharged polar

2.69.c. choose the class of amino acids most important for the interaction: binding to another water-soluble protein

uncharged polar, basic, and acidic

2.53.4.

unsaturated fatty acid

3.d. Although BLANK contain the same types of molecules as cells, their inability to reproduce themselves by their own efforts means that they are not considered living matter.

viruses

2.27. polar covalent bonds are formed when the electrons in the bond are not shared equally between the two nuclei. which one of these molecules contain polar bonds: molecular oxygen, methane, propane, water

water

15. cell biologists employ targeted fluorescent dyes or modified fluorescent proteins in both standard fluorescence microscopy and confocal microscopy to observe specific details in the cell. even though fluorescence permits better visualization, the resolving power is essentially the same as that of a standard light microscope because the resolving power of a microscope is limited by the BLANK of light.

wavelength

Which of the following methods would be most suitable to asses levels of expression of your target protein in different cell types? a) gel-filtration chromatography b) gel electrophoresis c) western blot analysis d) ion-exchange chromatography

western blot analysis

2.38.d. will the reaction in C occur more readily (be driven to the right) if the pH of the solution is high?

yes. if the pH is high, then the concentration of hydronium ions will be low. therefore the rightward reaction, which produces hydronium ions, will be favored.

29. You fertilize egg cells from a healthy plant with pollen (which contains the male germ cells) that has been treated with DNA-damaging agents. You find that some of the offspring have defective chloroplasts, and that this characteristic can be passed on to future generations. This surprises you at first because you happen to know that the male germ cell in the pollen grain contributes no chloroplasts to the fertilized egg cell and thus to the offspring. What can you deduce from these results?

your results show that not all of the information required for making a chloroplast is encoded in the chloroplasts own DNA; some, at least, must be encoded in the DNA carried in the nucleus. The reasoning is as follows: genetic info is carried only in DNA, so the defect in the chloroplasts must be due to a mutation in DNA. But all of those chlorplasts in the offspring (and thus all of the chloroplast DNA) must derive from those in the female egg cell, since chloroplasts only arise from other chloroplasts. Hence, all of the chloroplasts contain undamaged DNA from the female parent's chloroplasts. In all the cells of the offspring, however, half of the nuclear DNA will have come from the male germ-cell nucleus, which combined with the female egg nucleus at fertilization. Since this DNA has been treated with DNA-damaging agents, it must be the source of the heritable chloroplast defect. Thus, some of the info required for make a chloroplast is encoded by the nuclear DNA.