BIO 111 Exam 2 book questions

WHAT IF? Which type of microscope would you use to study(a) the changes in shape of a living white blood cell? (b) the details of surface texture of a hair?

(a) Light microscope, (b) scanning electron microscope.

DRAW IT A region along one DNA strand has this sequence of nitrogenous bases: 5′-TAGGCCT-3′. Write down its complementary strand, labeling the 5′ and 3′ ends.

5'-TAGGCCT-3' 3'-ATCCGGA-5'

The enzyme amylase can break glycosidic linkages between glucose monomers only if the monomers are in the αα form. Which of the following could amylase break down? (A) glycogen, starch, and amylopectin (B) glycogen and cellulose (C) cellulose and chitin (D) starch, chitin, and cellulose

A

The structural level of a protein least affected by a disruption in hydrogen bonding is the (A) primary level. (B) secondary level. (C) tertiary level. (D) quaternary level.

A

Describe the structure of a nucleosome, the basic unit of DNA packing in eukaryotic cells.

A nucleosome is made up of eight histone proteins, two each of four different types, around which DNA is wound. Linker DNA runs from one nucleosome to the next.

Compare the structure and functions of a plant cell wall and the extracellular matrix of an animal cell.

A plant cell wall is primarily composed of microfibrils of cellulose embedded in other polysaccharides and proteins. The ECM of animal cells is primarily composed of collagen and other protein fibers, such as fibronectin and other glycoproteins. These fibers are embedded in a network of carbohydrate-rich proteoglycans. A plant cell wall provides structural support for the cell and, collectively, for the plant body. In addition to giving support, the ECM of an animal cell allows for communication of environmental changes into the cell.

Explain the basis for the great diversity of proteins.

A polypeptide, which may consist of hundreds of amino acids in a specific sequence (primary structure),has regions of coils and pleats (secondary structure), which are then folded into irregular contortions (tertiary structure) and may be non covalently associated with other polypeptides (quaternary structure). The linear order of amino acids, with the varying properties of their side chains (R groups), determines what secondary and tertiary structures will form to produce a protein.The resulting unique three-dimensional shapes of proteins are key to their specific and diverse functions.

What does the endosymbiont theory propose as the origin for mitochondria and chloroplasts? Explain.

According to the endosymbiont theory, mitochondria originated from an oxygen-using prokaryotic cell that was engulfed by a cell that was ancestral to eukaryotic cells. Over time, the host and endosymbiont evolved into a single unicellular organism containing a mitochondrion. Chloroplasts originated when at least one of these eukaryotic cells containing mitochondria engulfed and then retained a photosynthetic prokaryote, which eventually evolved into a chloroplast.

Find another myosin motor protein walking on a microfilament in this figure. What organelle is being moved by that myosin protein?

Amitochondrion.

DRAW IT After you have read the section on ribosomes, circle a ribosome in the micrograph that might be making a protein that will be secreted.

Any of the bound ribosomes (attached to the endoplasmic reticulum) could be circled, because any could be making a protein that will be secreted.

Considering the structures of a nucleosome and of RNA polymerase, speculate about what must happen before RNA polymerase can transcribe the DNA that is wrapped around the histone proteins of a nucleosome.

As shown in the figure, the enzyme RNA polymerase moves along the DNA, transcribing the genetic information into an mRNA molecule. Given that RNA polymerase is somewhat larger than a nucleosome, the enzyme would not be able to fit between the histone proteins of the nucleosome and the DNA itself. Thus, the group of histone proteins must be separated from or moved along the DNA somehow in order for the RNA polymerase enzyme to access the DNA.

Enzymes that break down DNA catalyze the hydrolysis of the covalent bonds that join nucleotides together. What would happen to DNA molecules treated with these enzymes? (A) The two strands of the double helix would separate. (B) The phosphodiester linkages of the polynucleotide backbone would be broken. (C) The pyrimidines would be separated from the deoxyribose sugars. (D) All bases would be separated from the deoxyribose sugars.

B

The molecular formula for glucose is C6H12O6C6H12O6. What would be the molecular formula for a polymer made by linking ten glucose molecules together by dehydration reactions? (A) C60H120O60C60H120O60 (B) C60H102O51C60H102O51 (C) C60H100O50C60H100O50 (D) C60H111O51

B

Which statement about unsaturated fats is true? (A) They are more common in animals than in plants. (B) They have double bonds in their fatty acid chains. (C) They generally solidify at room temperature. (D) They contain more hydrogen than do saturated fats having the same number of carbon atoms.

B

Describe two characteristics shared by chloroplasts and mitochondria. Consider both function and membrane structure.

Both organelles are involved in energy transformation, mitochondria in cellular respiration and chloroplasts in photosynthesis. They both have multiple membranes that separate their interiors into compartments. In both organelles, the inner most membranes—cristae, or infoldings of the inner membrane, in mitochondria and the thylakoid membranes in chloroplasts—have large surface areas with embedded enzymes that carry out their main functions.

Compare starch and cellulose. What role does each play in the human body?

Both starch and cellulose are polymers of glucose, but the glucose monomers are in the αα configuration in starch and the ββ configuration in cellulose. The glycosidic linkages thus have different geometries, giving the polymers different shapes and thus different properties. Starch is an energy-storage compound in plants; cellulose is a structural component of plant cell walls. Humans can hydrolyze starch to provide energy but cannot hydrolyze cellulose. Cellulose aids in the passage of food through the digestive tract.

Which of the following pairs of base sequences could form a short stretch of a normal double helix of DNA? (A) 5′-AGCT-3′ with 5′-TCGA-3′ (B) 5′-GCGC-3′ with 5′-TATA-3′ (C) 5′-ATGC-3′ with 5′-GCAT-3′ (D) All of these pairs are correct.

C

Colpidium colpoda is a unicellular protist that lives in freshwater, eats bacteria, and moves by cilia (see Figure 6.23b). Describe how the parts of this cell work together in the functioning of C. colpoda, including as many organelles and other cell structures as you can.

Colpidium colpoda moves around in freshwater using cilia, projections from the plasma membrane that enclose microtubules in a "9 + 2" arrangement. The interactions between motor proteins and microtubules cause the cilia to bend synchronously, propelling the cell through the water. This is powered by ATP, obtained via breaking down sugars from food in a process that occurs in mitochondria. C. colpoda obtains bacteria as their food source, maybe via the same process (involving filopodia) the macrophage uses in Figure 6.31. This process uses actin filaments and other elements of the cytoskeleton to ingest the bacteria. Once ingested, the bacteria are broken down by enzymes in lysosomes. The proteins involved in all of these processes are encoded by genes on DNA in the nucleus of the C. colpoda.

Which of the following categories includes all others in the list? (A) disaccharide (B) polysaccharide (C) starch (D) carbohydrate

D

Describe how cilia and flagella bend.

Dynein arms, powered by ATP, move neighboring doublets of microtubules relative to each other. Because they are anchored within the flagellum or cilium and with respect to one another, the doublets bend instead of sliding past each other. Synchronized bending of the nine microtubule doublets brings about bending of both cilia and flagella.

WHAT IF? As a cell begins the process of dividing, its chromosomes become shorter, thicker, and individually visible in an LM (light micrograph). Explain what is happening at the molecular level.

Each chromosome consists of one long DNA molecule attached to numerous protein molecules, a combination called chromatin. As a cell begins division, each chromosome becomes "condensed" as its diffuse mass of chromatin coils up.

VISUAL SKILLS While trying to develop a vaccine for S. pneumonia, Griffith was surprised to discover the phenomenon of bacterial transformation. Based on the results in the second and third panels of Figure 16.2, what result was he expecting in the fourth panel? Explain.

Griffith expected that the mouse injected with the mixture of heat-killed S cells and living R cells would survive, since neither type of cell alone would kill the mouse.

Given a polynucleotide sequence such as GAATTC, explain what further information you would need in order to identify which is the 5' end. (See Figure 16.5.)

In order to tell which end is the 5' end, you need to know which end has a phosphate group on the 5' carbon (the 5' end) and/or which end has an —OH group on the 3' carbon (the 3 end).

Describe the role of motor proteins inside the eukaryotic cell and in whole-cell movement.

Inside the cell, motor proteins interact with components of the cytoskeleton to move cellular parts. Motor proteins "walk" vesicles along microtubules. The movement of cytoplasm within a cell involves interactions of the motor protein myosin and microfilaments (actin filaments). Whole cells can be moved by the rapid bending of flagella or cilia, which is caused by the motor protein-powered sliding of microtubules within these structures. Cell movement can also occur when pseudopodia form at one end of a cell (caused by actin polymerization into a filamentous network), followed by contraction of the cell toward that end; this amoeboid movement is powered by interactions of microfilaments with myosin. Interactions of motor proteins and microfilaments in muscle cells causes muscle contraction that can propel whole organisms (for example, by walking or swimming).

Why are lipids not considered to be polymers or macromolecules?

Lipids are not polymers because they do not exist as a chain of linked monomers. They are not considered macromolecules because they do not reach the giant size of many polysaccharides, proteins, and nucleic acids.

WHAT IF? A classmate proposes that mitochondria and chloroplasts should be classified in the endomembrane system. Argue against the proposal.

Mitochondria and chloroplasts are not derived from the ER, nor are they connected physically or via transport vesicles to organelles of the endo-membrane system. Mitochondria and chloroplasts are structurally quite different from vesicles derived from the ER, which are bounded by a single membrane.

Describe the molecular composition of nucleoli and explain their function.

Nucleoli consist of DNA and the ribosomal RNAs (rRNAs) made according to its genes in the DNA, as well as proteins imported from the cytoplasm. Together, the rRNAs and proteins are assembled into large and small ribosomal subunits. (These are exported through nuclear pores to the cytoplasm, where they will participate in polypeptide synthesis.)

How do the two ends of a DNA strand differ in structure?

One end, the 5'' end, has a phosphate group, which is attached to the 5'' carbon of the sugar, the one that is not in the ring. The other end, the 3'' end, has an —OH group attached to the 3'' carbon of the sugar; this carbon is in the ring.

What role do ribosomes play in carrying out genetic instructions?

Ribosomes in the cytoplasm translate the genetic message, carried from the DNA in the nucleus by mRNA, into a polypeptide chain.

Briefly describe the structure and function of the nucleus, the mitochondrion, the chloroplast, and the endoplasmic reticulum.

See Figure 6.8.

How do stains used for light microscopy compare with those used for electron microscopy?

Stains used for light microscopy are colored molecules that bind to cell components, affecting the light passing through, while stains used for electron microscopy involve heavy metals that affect the beams of electrons.

WHAT IF? Males afflicted with Kartagener's syndrome are sterile because of immotile sperm, and they tend to suffer from lung infections. This disorder has a genetic basis. Suggest what the underlying defect might be

Such individuals have defects in the microtubule-based movement of cilia and flagella. Thus, the sperm can't move because of malfunctioning or nonexistent flagella, and the airways are compromised because cilia that line the trachea malfunction or don't exist, and so mucus cannot be cleared from the lungs.

How does euchromatin differ from heterochromatin in structure and function?

The 10-nm fiber of euchromatin is less compacted during interphase than in mitosis and is accessible to the cellular proteins responsible for gene expression. In contrast, the 10-nm fiber of heterochromatin is relatively compacted (densely arranged) during interphase, and genes in heterochromatin are largely inaccessible to proteins necessary for gene expression.

MAKE CONNECTIONS Chromosomes contain the genetic material and reside in the nucleus. How does the rest of the cell get access to the information they carry? (See Figure 5.22.)

The DNA in a chromosome dictates synthesis of a messenger RNA (mRNA) molecule, which then moves out to the cytoplasm. There, the information is used for the production, on ribosomes, of proteins that carry out cellular functions.

How would sequencing the entire genome of an organism help scientists to understand how that organism functioned?

The DNA of an organism encodes all of its proteins, and proteins are the molecules that carry out the work of cells, whether an organism is unicellular or multicellular. By knowing the DNA sequence of an organism, scientists would be able to catalog the protein sequences as well.

WHAT IF? If the plant cell wall or the animal extracellular matrix were impermeable, what effect would this have on cell function?

The cell would not be able to function properly and would probably soon die, as the cell wall or ECM must be permeable to allow the exchange of matter between the cell and its external environment. Molecules involved in energy production and use must be allowed entry, as well as those that provide information about the cell's environment. Other molecules, such as products synthesized by the cell for export and the by-products of cellular respiration, must be allowed to exit.

VISUAL SKILLS When the tissue was sliced, what was the orientation of the cilia in the lower portion of the TEM? The upper portion? Explain how the orientation of the cilia determined the type of sections we see

The cilia in the lower portion of the TEM were oriented lengthwise in the plane of the slice, while those in the upper portion of the TEM were oriented perpendicular to the plane of the slice. Therefore, the cilia in the lower portion were cut in longitudinal section, and the cilia in the upper portion were cut in cross section.

What role does complementary base pairing play in nucleic acids?

The complementary base pairing of the two strands of DNA makes possible the precise replication of DNA every time a cell divides, ensuring that genetic information is faithfully transmitted. In some types of RNA, complementary base pairing enables RNA molecules to assume specific three-dimensional shapes that facilitate diverse functions.

VISUAL SKILLS What parts of the membrane diagram in (b) correspond to the dark bands in the TEM in (a)? What parts correspond to the gold band? (Review Figure 5.11.)

The dark bands in the TEM correspond to the hydrophilic heads of the phospholipids, while the light band corresponds to the hydrophobic fatty acid tails of the phospholipids.

Compare the information conveyed in the three ladder diagrams.

The left diagram shows the most detail. It shows that each sugar-phosphate backbone is made up of sugars (blue pentagons) and phosphates (yellow circles) joined by covalent bonds (black lines). The middle diagram doesn't show any detail in the backbone. Both the left and middle diagrams label the bases and represent their complementarity by the complementary shapes at the ends of the bases (curves/indents for G/C or V's/notches for T/A). The diagram on the right is the least detailed, implying that the base pairs pair up, but showing all bases as the same shape so not including the information about specificity and complementarity visible in the other two diagrams. The left and right diagrams show that the strand on the left was synthesized most recently, as indicated by the light blue color. All three diagrams show the 5'' and 3'' ends of the strands.

WHAT IF? Imagine a protein that functions in the ER but requires modification in the Golgi apparatus before it can achieve that function. Describe the protein's path through the cell, starting with the mRNA molecule that specifies the protein.

The mRNA is synthesized in the nucleus and then passes out through a nuclear pore to the cytoplasm, where it is translated on a bound ribosome, attached to the rough ER. The protein is synthesized into the lumen of the ER and may be modified there. A transport vesicle carries the protein to the Golgi apparatus. After further modification in the Golgi, another transport vesicle carries it back to the ER, where it will perform its cellular function.

In what way are the cells of plants and animals structurally different from single-celled eukaryotes?

The most obvious difference is the presence of direct cytoplasmic connections between cells of plants (plasmodesmata) and animals (gap junctions). These connections result in the cytoplasm being continuous between adjacent cells.

MAKE CONNECTIONS Interphase chromosomes appear to be attached to the nuclear lamina and perhaps also the nuclear matrix. Describe these two structures. See Figure 6.9 and the associated text.

The nuclear lamina is a netlike array of protein filaments that provides mechanical support just inside the nuclear envelope and thus maintains the shape of the nucleus. Considerable evidence also supports the existence of a nuclear matrix, a framework of protein fibers extending throughout the nuclear interior.

Describe the bonds that hold together the nucleotides in one DNA strand. Then compare them with the bonds that hold the two DNA strands together.

The nucleotides in a single DNA strand are held together by covalent bonds between an oxygen on the 3 carbon of one nucleotide and the phosphate group on the 5 carbon of the next nucleotide in the chain. Instead of covalent bonds, the bonds that hold the two strands together are hydrogen bonds between a nitrogenous base on one strand and the complementary nitrogenous base on the other strand. (Hydrogen bonds are weaker than covalent bonds, but there are so many hydrogen bonds in a DNA double helix that, together, they are enough to hold the two strands together.)

When a cell ingests a bacterium, what role does the nucleus play?

The nucleus houses the chromosomes; each is made up of proteins and a single DNA molecule. The genes that exist along the DNA carry the genetic information necessary to make the proteins involved in ingesting a bacterial cell, such as the actin of microfilaments that form pseudopodia(filopodia), the proteins in the mitochondria responsible for providing the necessary ATP, and the enzymes present in the lysosomes that will digest the bacterial cell.

MAKE CONNECTIONS The polypeptide chain that makes up a tight junction weaves back and forth through the membrane four times, with two extracellular loops and one loop plus short C-terminal and N-terminal tails in the cytoplasm. Looking at Figure 5.14, what would you predict about the amino acid sequence of the tight junction protein?

The parts of the protein that face aqueous regions would be expected to have polar or charged (hydrophilic) amino acids, while the parts that go through the membrane would be expected to have nonpolar (hydrophobic) amino acids. You would predict polar or charged amino acids at each end (tail), in the region of the cytoplasmic loop, and in the regions of the two extracellular loops. You would predict nonpolar amino acids in the four regions that go through the membrane between the tails and loops.

What is the fundamental basis for the differences between large carbohydrates, proteins, and nucleic acids?

The polymers of large carbohydrates (polysaccharides), proteins, and nucleic acids are built from three different types of monomers (monosaccharides, amino acids, and nucleotides, respectively).

Describe the structural and functional distinctions between rough and smooth ER.

The primary distinction between rough and smooth ER is the presence of bound ribosomes on the rough ER. Both types of ER make phospholipids, but membrane proteins and secretory proteins are all produced by the ribosomes on the rough ER. The smooth ER also functions in detoxification, carbohydrate metabolism, and storage of calcium ions.

MAKE CONNECTIONS If you arrested a human cell in metaphase I of meiosis and applied this technique, what would you observe? How would this differ from what you would see in metaphase of mitosis? Review Figure 13.8 and Figure 12.7

The two members of a homologous pair (which would be the same color) would be associated tightly together at the metaphase plate during metaphase I of meiosis I. In metaphase of mitosis, however, each chromosome would be lined up individually, so the two chromosomes of the same color would be in different places at the metaphase plate.

VISUAL SKILLS How many tubulin dimers are in the boxed row?

Three dimers

Describe how transport vesicles integrate the endomembrane system.

Transport vesicles move membranes and the substances they enclose between other components of the endomembrane system.

Given the function of DNA, why would you expect two species with very similar traits to also have very similar genomes?

Ultimately, the DNA sequence carries the information necessary to make the proteins that determine the traits of a particular species. Because the traits of the two species are similar, you would expect the proteins to be similar as well, and therefore the gene sequences should also have a high degree of similarity.

MAKE CONNECTIONS Considering the examples provided here, describe how the approaches of genomics and proteomics help us to address a variety of biological questions.

Using a genomics approach allows us to use gene sequences to identify species and to learn about evolutionary relationships among any two species. This is because all species are related by their evolutionary history, and the evidence is in the DNA sequences. Proteomics—looking at proteins that are expressed—allows us to learn about how organisms or cells are functioning at a given time or in an association with another species.

Do plant cells have mitochondria? Explain.

Yes. Plant cells are able to make their own sugar by photosynthesis, but mitochondria in plant cells (which are, of course, eukaryotic) are the organelles that are able to generate ATP molecules to be used for energy generation from sugars, a function required in all cells.

Given the sequences of a particular gene in fruit flies, fish, mice, and humans, predict the relative similarity of the human sequence to that of each of the other species.

You would expect the human gene sequence to be most similar to that of the mouse (another mammal), then to that of the fish (another vertebrate), and least similar to that of the fruit fly (an invertebrate).

MAKE CONNECTIONS If you wanted to study the process of translation of proteins from mRNA, which part of which fraction would you use? (See Figure 5.22.)

You would use the pellet from the final fraction, which is rich in ribosomes. These are the sites of protein translation.

DRAW IT Draw a simplified elongated cell that measures 125×1×1125×1×1 arbitrary units. A nerve cell would be roughly this shape. Predict how its surface-to-volume ratio would compare with those in Figure 6.7. Then calculate the ratio and check your prediction.

https://cite-media.pearson.com/legacy_paths/1f410ca4-47a8-4402-bdb3-7b1a2b4d5e63/1887406132.png This cell would have the same volume as the cells in columns 2 and 3 in Figure 6.7 but proportionally more surface area than that in column 2 and less than that in column 3. Thus the surface-to-volume ratio, should be greater than 1.2 but less than 6. To obtain the surface area, you would add the area of the six sides (the top, bottom, sides, and ends): 125+125+125+125+1+1=502125+125+125+125+1+1=502. The surface-to-volume ratio equals 502 divided by a volume of 125, or roughly 4.0.

DRAW IT Copy the polynucleotide strand in Figure 5.23a and label the bases G, T, C, and T, starting from the 5′ end. Assuming this is a DNA polynucleotide, now draw the complementary strand, using the same symbols for phosphates (circles), sugars (pentagons), and bases. Label the bases. Draw arrows showing the 5′ →→ 3′ direction of each strand. Use the arrows to make sure the second strand is antiparallel to the first. Hint: After you draw the first strand vertically, turn the paper upside down; it is easier to draw the second strand from the 5′ toward the 3′ direction as you go from top to bottom.

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DRAW IT In Figure 5.23a, number all the carbons of the top three nucleotides (use primes), circle the nitrogenous bases, and star the phosphates.

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Figure 11.12: Figure Question DRAW IT The bacterium that causes the disease cholera produces a toxin that locks the G protein in its activated state. Review Figure 11.8, then draw this figure as it would be if cholera toxin were present. (You do not need to draw the cholera toxin molecule.)

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Construct a table that organizes the following terms and label the columns and rows. Monosaccharides Fatty acids Amino acids Nucleotides Polypeptides Triacylglycerols Polynucleotides Polysaccharides Phosphodiester linkages Peptide bonds Glycosidic linkages Ester linkages

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List the following structures from largest to smallest: proton pump, nuclear pore, cyt c, ribosome.

nuclear pore, ribosome, proton pump, cyt c.