Biology Lecture Questions

Introducing a double bond into a fatty acid puts a(n) _______ into the conformation of the molecule.

kink

Which of the following classes of amino acids is buried within the folded structure of the protein?

non polar

Which class of molecule accelerates transport across biological membranes?

proteins

SDS-polyacrylamide gel electrophoresis (SDS-PAGE) separates proteins by .

. size

Taken together, what is the total number of unique nucleotides in DNA and RNA?

8; A phosphate group, deoxyribose, and G, C, T, A for DNA and a phosphate group, ribose, and G, C, U, A for RNA

The drug ouabain inhibits the plasma membrane Na+-K+ pump. Why does it also inhibit glucose transport across the intestinal epithelial layer?

A Na+-glucose co-transporter is responsible for the transport of glucose into intestinal epithelial cells. Two Na+ ions are transported inward with each glucose molecule. The Na+ moves down both a concentration and voltage gradient, and the glucose moves up a concentration gradient. For glucose, there is no charge consideration. The overall transport is energetically favorable because of the energy gain from Na+. If the Na+-K+pump that generates the favorable Na+ gradient is inhibited, then the energetics are no longer favorable for Na+-glucose transport. The ouabain effect on the co-transporter is indirect. The direct effect is on the pump.

How does the structure of a transport protein such as a glucose transporter create an aqueous environment in which glucose may be transported across the plasma membrane?

A glucose transporter has multiple transmembrane domains. These α-helical segments cluster together to surround an aqueous environment through which the glucose may bind and pass.

Because telomeres are longer in the cells of infants than they are in older people, it has been hypothesized that telomere length determines a cell's life expectancy. Thus, some believe that finding a way to extend the length of telomeres in older people would extend their life expectancy. What is a possible problem with this approach?

As cells age, the lengths of their telomeres gradually decrease until the chromosomes, and subsequently the cells themselves, are destroyed. In some cancer cells, however, this process reverses itself and the telomeres start to extend again. If telomere length really does extend a cell's life span, there is a danger that cells will start dividing uncontrollably, as in cancer, and kill the organism.

What is one function of cell-surface carbohydrates?

Cell-surface carbohydrates serve as markers for cell-cell recognition, protect the cell surface from ionic and mechanical stress, and form a barrier to invading microorganisms.

In their acceptance speech for the Nobel Prize in 1985, Michael Brown and Joseph Goldstein said, "Cholesterol is a Janus-faced molecule. The very property that makes it useful in cell membranes, namely its absolute insolubility in water, also makes it lethal." Explain this remark.

Cholesterol in the plasma membranes maintains their fluidity at a fairly constant level, preventing them from becoming overly rigid at low temperatures or overly fluid at high temperatures. However, its hydrophobicity, which is the very property that makes cholesterol useful in plasma membranes fluidity, can cause it to aggregate on arterial walls when present in high concentrations in the blood stream. Aggregations result in the narrowing of blood vessels, which can cause a heart attack or a stroke.

Why are dideoxynucleotides used in DNA sequencing?

Deoxyribonucleotides have hydrogen at the 2ʹ position and a hydroxyl group on the 3ʹ position of the ribose sugar. The hydroxyl group is absolutely required to form the covalent bond with the incoming nucleotide. With the dideoxy, there is no 3ʹ hydroxyl, so the growth of the chain is terminated.

Detergents are used to solubilize membranes because they are dual molecules possessing both hydrophobic and hydrophilic portions. Why are they also used as cleaning reagents (to clean, for example, clothes and dishes)?

Detergents are used as cleansers because the hydrophobic portions of the molecules bind to hydrophobic substances, such as an oil stain, while the hydrophilic portions bind to water, and the detergent/dirt complex is subsequently washed away in the rinse. Simply trying to remove the stain with water doesn't work because the hydrophilic water molecules do not interact with the lipid molecules in the oil stain.

Why are E. coli DNA polymerases not used in the polymerase chain reaction (PCR)?

E. coli DNA polymerases cannot be used in PCR because they are not stable at the temperatures required to denature the DNA strands in the first step of each PCR cycle—the enzyme would rapidly be inactivated, and polymerization would cease. Instead, polymerases from bacteria that have evolved to live at high temperatures (such as Thermus aquaticus) are used, since they are stable at high temperatures.

EcoRI restriction mapping on a sample of a large piece of DNA resulted in six distinct bands following agarose gel electrophoresis. Similar mapping on an identical sample that was subjected to high intensity ultraviolet light resulted in only four distinct bands. What might best explain the reduction in the number of detectable bands in the UV light-treated sample?

EcoRI specifically cleaves DNA at GAATTC sequences. In the first experiment, there must have been five EcoRI sites. Following UV treatment, in which only four bands were detectable, there were only three EcoRI sites. Therefore, the most likely explanation is that the UV light causes mutations in at least two of the GAATTC EcoRI sites. If any one of the six nucleotides in the recognition sequence becomes mutated, that site will not be recognized by the restriction enzyme.

A "complete" sequence of the Drosophila genome has recently been obtained; that is, the part of the genome that lies within euchromatin (and only that part) has been sequenced. Why would sequencing be focused on euchromatin, and why is the acquisition of the Drosophila genome sequence now considered to be virtually complete?

Euchromatin is the part of the genome that consists of relatively decondensed chromatin, and active genes are located within it. Researchers focused on euchromatin because knowledge of the genes encoded by a genome yields the most information about the cell biology of an organism. In contrast, the useful contribution from heterochromatin, with its noncoding repetitive sequences, would most likely be very small. Hence, the sequencing of the genome is considered virtually complete.

True or false: Facilitated diffusion is a lipid-mediated process.

False

If adenine makes up 22% of the bases in a given double-stranded DNA molecule, what percentage is made up of guanines?

If adenine makes up 22%, then thymine would also make up 22% because of complementary base pairing. That would leave 56% of the DNA to cytosines and guanines, which must be present in equal amounts, again due to the complementarity between them. Thus, the percentage of guanines would be 56/2, or 28%.

In experiments using polymerase chain reactions (PCR), it is often more difficult to amplify through regions of DNA that are high in GC content versus those regions that are either lower in GC content or are AT-rich. Based on your knowledge of DNA structure, explain why.

In base pairing between strands of DNA, there are three hydrogen bonds between each G-C base pair and only two hydrogen bonds between A-T base pairs. In PCR, heat is used to denature the hydrogen bonds between strands of DNA. The energy required to denature regions of DNA high in GC are significantly higher than those that are either less so or are AT-rich.

Suppose you are working on a set of experiments using Western blotting. Using an antibody that recognizes amino sequences encoded by exon 3 of a five-exon gene, you have demonstrated that a protein is highly expressed in a particular cell line. To assess the mRNA, you design reverse transcriptase polymerase chain reaction (rtPCR) primers to exons 2 and 4, which flank exon 3. Despite all your efforts, you cannot amplify an mRNA. You know that it is indeed expressed, since the protein is detectable. You also know that your controls are working and your experimental procedure is sound, because you are able to detect an mRNA for the other cell lines. Given what you know about the "central dogma" and gene structure, how might you explain this inability to identify the mRNA encoding this exon 3 protein?

It is likely that of the five exons, the experimental cell line does not express exons 2 and/or 4; if even one of the exons is missing in the mRNA, there will be no PCR amplification. For example, the cell line may only express an mRNA which, by alternative splicing, uses exons 1, 3, and 5. In this case the protein would be detected by Western blot analysis because the antibody recognizes protein sequences in exon 3, but the primers designed to hybridize to exons 2 and 4 have no target to which they could anneal.

Suppose you are studying a mammalian transcription factor that you would like to express in bacteria so that you can purify large quantities of it to use in biochemical studies. You introduce the cDNA encoding the transcription factor into an expression plasmid and transform E. coli with the new recombinant vector. You find no expression. What might be occurring?

Lack of expression could result from a number of factors. The plasmid must have appropriate unique restriction sites, an origin of replication, and a selective antibiotic resistance marker. If any of these are perturbed during cloning, there will be no expression of the gene of interest.

Why are most ion channels gated?

Most ion channels are ligand- or voltage-gated. This means that their opening and closing, and thus the flow of ions, is regulated, which is essential to the regulation of other cell processes, such as the production of an action potential, which results from reversible changes in Na+ and K+ currents. If channels were not gated most of the time (i.e., open), then the plasma membrane would be much more likely to leak water and other substances, and it could not produce action potentials.

Which genes are actively undergoing transcription during mitosis?

None. There are essentially no active transcriptional processes occurring during mitosis because as cells enter mitosis, the chromosomes become highly condensed so they can be distributed to daughter cells. In mitotic cells at metaphase, the DNA will have been condensed approximately ten-thousand-fold. This highly condensed DNA can no longer serve as a template for RNA synthesis. and transcription ceases during mitosis.

To detect RNA, DNA and proteins respectively, you would you which technique?

Northern, Southern, Western blotting

Processed pseudogenes do not have introns. Why not?

Processed pseudogenes are cDNA that come from the reverse transcription of mRNAs. Since the mRNA templates have no introns, there are no intronic sequences available to be reverse transcribed.

A gene containing three exons would have how many introns?

Since exons are distinctly separated by introns, a three-exon gene would have to contain at least two introns

Cystic fibrosis (CF) is the most common inherited disease of Caucasians. It is due to mutations in an ABC transporter, the cystic fibrosis transmembrane conductance regulator (CFTR), which is a Cl- and bicarbonate channel. Why have efforts at gene therapy to correct CF concentrated on the lungs when CF affects other tissues as well?

The cells lining the surface of the lungs are readily accessible to aerosols carrying plasmids that express wild-type CFTR. Moreover, the immediate cause of death from CF is typically from bacterial infections of the lung trapped in CF-induced mucus accumulation. Therefore, introducing wild-type CFTR into the lung is an attractive approach to treating many of the symptoms and averting the most common cause of death associated with CF. This approach does nothing to cure mucus accumulation in pancreatic ducts or problems in other tissues. Unfortunately, to date, this approach has had only short-term success in the lungs.

How is rapid transport of water across the plasma membrane achieved?

The presence of aquaporin in the plasma membrane provides water-specific channels for the rapid flow of water across this membrane.

Consider this statement: An increase in the levels of a protein within a cell indicates that expression of the gene encoding it was also increased. Why is the statement not necessarily true?

The statement may be true, but a number of factors can give rise to an increase in the level of a protein. For example, as stated, the expression of the gene could be responsible, but stabilization of the mRNA could increase the protein as well. Reduced degradation may be another. Think about the central dogma and other factors that can increase protein levels.

Suppose you have a cell line that expresses a protein whose structure you know but not the function. Describe an experiment that would help you determine the protein's function.

There are several possible experiments. For example, you could use antisense RNA or RNA interference to block expression of the protein from the mRNA encoding the protein and observe changes.

Why is it thought that the DNA sequences of centromeres are not critical to their function, whereas the chromatin structure is?

There are two primary reasons: The first is that the sequences of centromeres among species are incredibly variable and share virtually no sequence identity. The other reason is that the substitution of histone H3 with CENP-A in nucleosome around centromeric regions occurs in all species in which it has been studied, and these unique nucleosomes are required for the assembly of kinetochore proteins, suggesting it is the chromatin structure, and not the DNA sequence, that is important.

How many possible mRNAs could be derived from a gene with three exons (exon 1, exon 2, and exon 3)?

Three mRNAs could be produced through alternative splicing with exons 1‒2, 1‒3, and 2‒3

Embryonic stem cells introduced into early mouse embryos can give rise to cells in all of the tissues of the mouse, including germ cells.

True

The major ATPase maintaining the plasma membrane potential is the Na+-K+ pump.

True

Vectors usually contain an antibiotic-resistance gene so that cells that incorporate the vector can be selected by their resistance to the antibiotic.

True