Biology Midterm 1

A disulfide bond is formed between _______ residues.

cysteine; most cysteine residues are covalently bonded to other cysteine residues to form disulfide bonds which play an important role in the folding and stability of some proteins, usually the ones that are secreted to the extracellular medium. since most cellular compartments are reducing environments, disulfide bonds are generally unstable in the cytosol with some exceptions. Methionine contains a sulfur atom but does not form disulfide bonds and tyrosine and glycine do not contain sulfur atoms.

The function of telomeres is to

ensure chromosome replication and maintenance.

Cholesterol, a membrane lipid in animals, has a chemical structure similar to ...

estradiol because it is a steroid and cholesterol is a precursor to steroids, cholesterol is found in low density proteins but does not share a chemical structure with it

T/F Since RNA contains ribose, a five carbon sugar, it can make glycosidic bonds and is considered a polysaccharide.

false because RNA contains ribose but does not make glycosidic bonds and is not a polysaccharide, Like DNA, RNA can only make phospodiester bonds between 3' hydroxyl groups and 5' phosphate group of another nucleotide.

T/F: The SDS in SDS-PAGE helps proteins fold in to their native conformation.

false because SDS is negatively charged detergent used to denature proteins and give them an overall negative charge

Which statement about the glucose transporter is false?

flow is unidirectional; true statements -- flow is two directional, it transports glucose across the plasma membrane via a mechanism called facilitated diffusion, it has 12 a-helical transmembrane segments, a conformational change in the transporter is involved in the transport process

A pseudogene is a ...

gene that arose through gene duplication, but after acquiring mutations became nonfunctional.

Phospholipids consist of a 3-carbon core to which fatty acids and a phosphate group are linked. The most common 3-carbon core is ...

glycerol

Which one of the sets of terms below BEST completes the following sentence? Monosaccharides are to ________ as _________ are to DNA.

glycogen and nucleotides because they are both the building blocks

Two examples of membrane lipids that are present in small amounts are

glycolipids and phosphatidylinositol.

The two strands of DNA in the double helix are held together by

hydrogen bonds between the bases of each strand.

Membrane proteins are able to move

laterally within the plane of a membrane.

What technique would you use to determine if the level of a specific mRNA had been increased in response to an inducer?

northern blotting

Which of the following is not a common lipid modification to proteins?

phosphorylation; although phosphorylation is a common post-translational modification of proteins, adding small phosphate group is not sufficient to add lipid portion. prenylation, palmitoylation and myristoylation are all lipid anchors which direct proteins to the inner leaflet of a plasma membrane, while GPI anchors help proteins to outer leaflet of plasma membranes.

A centromere is a region of the chromosome that

plays a critical role in ensuring the correct distribution of duplicated chromosomes to daughter cells during mitosis.

The enzyme that synthesizes DNA using RNA templates is called

reverse transcriptase

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

size

A PCR reaction does not require

sodium dodecyl sulfate; it DOES require: a heat stable DNA polymerase, DNA containing the sequence to be amplified, short single stranded DNA primers complementary to each end of the target sequence

Which molecule serves as an adaptor between amino acids and mRNA during translation?

tRNA

Which statement about ion channels is true?

they are opened either by the binding of ligands or b changes in electrical potential across the membrane... the following are false: --they require ATP, they are open most of the time, the rate of transport is slow compared to the rate of transport via carrier proteins.

The process by which proteins are made from RNA templates is called

translation

T/F: 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

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

true

The human genome is distributed among _______ pairs of chromosomes.

23

Even though its complete genome is significantly smaller than that of humans, the flowering plant Arabidopsis thaliana has about _______ genes, which is about the same number as humans have.

26,000

Which of the following correctly describes a cDNA molecule?

A DNA copy of an RNA sequence synthesized by the enzyme reverse transcriptase; cDNA is synthesized from a single stranded RNA template (mRNA or microRNA) in a reaction catalyzed by the enzyme reverse transcriptase

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.

Why can't a digest of human genomic DNA be resolved by gel electrophoresis?

A typical digest of the human genome produces too many fragments to resolve

The human genome contains only 20,000 to 25,000 actual gene sequences, yet the human genome can produce up to 100,000 gene products. Which of the following processes accounts for this difference?

Alternative splicing

Which of the following statements about exons is false?

An exon may contain sequences for small nucleolar RNAs; the following are FALSE: An exon may contain a 5' untranslated region, An exon may contain a 3' untranslated region, Exons are separated by introns.

What are antibodies?

Antibodies are proteins produced by the immune system that bind a specific antigen.

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.

Which of the following lipids are distinctly enriched in lipid rafts?

Cholesterol and sphingolipids

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.

Which sequence correctly outlines the process of RNA interference, beginning with a double-stranded RNA molecule?

Cleavage by Dicer; association with RISC; unwinding of siRNA; pairing with target mRNA; mRNA cleavage

The characterization of restriction endonucleases was a key step in the development of recombinant DNA technology. What is the function of these enzymes?

Cleavage of DNA at specific sequences

A cDNA molecule is

DNA synthesized from an RNA template using the enzyme reverse transcriptase.

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.

Which of the following statements about ABC transporters is false?

Each member of the family is a Cl- channel; ABC transporters are members of a transport system superfamily that is one of the largest and oldest families with representatives in all extant phyla from prokaryotes to humans. ABC transporters use ATP binding and hydrolysis to energize the translocation of substrates across a plasma membrane, either for uptake or for export of the substrate. Most members of the family share structural domains and features necessary to ove substrate in or out of the cell. Some members of the family include channel to transport chloride ions, however there are many more transporters in the family which transport a variety of substrates. ABC uptake porters take up a large variety of primary and secondary metabolites.

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.

Facilitated diffusion is a lipid-mediated process.

False.

Which of the following are integral membrane proteins that do not contain a transmembrane a helix?

Glycosylphosphatidylinositol (GPI)-anchored proteins

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.

The resting plasma membrane potential as described by the Nernst equation is the sum of the movement of many ions. However, in practice, the movement of _______, a single ion, is the major component determining membrane potential.

K+

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.

The ENCODE project revealed that as much as 75% of the genome in humans is actually transcribed into RNA. Most of this is non‒protein-coding RNA. Which of the following include two new classes of noncoding RNA discovered by the ENCODE project?

MicroRNA and lncRNA

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.

The CRISPR/Cas system is a fast and powerful method to introduce specific mutations into cellular genomes via homologous recombination to study the function of genes and the proteins they encode. Which reagents are necessary for CRISPR/Cas?

Mutant copy of target gene, guide RNA, and Cas9

Transport of glucose into the intestinal epithelium is driven by ion gradients established by the

Na+-K+ pump.

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.

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

Nonpolar amino acids are hydrophobic and are in the interior of proteins

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

Northern, Southern, Western blotting

Extensive digestion of chromatin with micrococcal nuclease was found to yield particles called nucleosome core particles that appear as beads when viewed by electron microscopy. Which of the following is not found in the nucleosome core particle?

One molecule of H1 protein; the following ARE found in the nucleosome core particle: two molecules of H3 protein, the H2A protein, and the H4 protein

Imagine you are a student trying to decode the genetic code. An artificial mRNA molecule consisting of poly-CA (5ʹ... CACACACACACACAC..3ʹ) yields a polypeptide consisting solely of histidines and threonine, and another artificial mRNA consisting of poly-CAA (5ʹ...CAACAACAACAACAA...3ʹ) yields three different polypeptides: polythreonine, polyglutamine, and polyasparagine. On the basis of this information, which codons can you assign to which amino acids?

Poly-CA contains two alternating codons, CAC and ACA, one of which codes for histidine and the other for threonine. Depending on where translation begins, poly-CAA can be read as repeating CAA, repeating AAC, or repeating ACA. The common amino acid is threonine, and the common codon is ACA. Thus ACA codes for threonine and CAC must therefore code for histidine. That leaves CAA and AAC, one of which codes for glutamine and the other for asparagine. More data are needed to determine which codes for which.

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.

Which of the following is not involved in receptor-mediated endocytosis?

Pseudopodia

What is unique about RNA tumor viruses (retroviruses) that allows their RNA genome to be replicated and inserted as DNA into host cells?

Retroviruses encode a very unique enzyme, called reverse transcriptase, that uses an RNA template to synthesize DNA copies. This is widespread knowledge now, but at the time it was controversial because it flew in the face of the then accepted model of the "central dogma" in which the flow of information in genetic material is from DNA to RNA to protein.

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.

Which statement best describes the mechanism of action of miRNAs in blocking expression of proteins?

Single-stranded miRNA, in association with the RISC complex, binds to the complementary sequence in the 3ʹ UTR of mRNAs, blocking translation and inducing degradation of the mRNA.

Which characteristic is NOT necessary in a plasmid vector in order to facilitate successful cloning?

Strong bacterial promoter; the following is REQUIRED: origin of replication, restriction sites, gene conferring resistance to antibiotic

In dogs, the Fgf4 gene encodes a protein that regulates bone growth, and in its normal chromosomal location, Fgf4 yields dogs with long legs. Which statement best explains the mechanism leading to a short-legged phenotype in dogs?

The Fgf4 gene is retrotransposed into the middle of a LINE that contains mutated regulatory sequences that give abnormal expression of Fgf4.

Addition or deletion of one or two nucleotides in the coding part of a gene produces a nonfunctional protein, whereas addition or deletion of three nucleotides often results in a protein with nearly normal function. Explain.

The addition or deletion of one or two nucleotides would alter the reading frame, resulting in a completely different amino acid sequence, whereas a change of three nucleotides affects only one amino acid, and this frequently yields a protein that functions normally.

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.

Which statement about the relative concentrations of Na+ and K+ inside and outside of a typical mammalian cell is true?

The concentration of Na+ outside the cell is about 30 times higher than inside the cell, and the concentration of K+ inside the cell is 10 to 30 times higher than outside the cell.

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

The correct answer is C, 8 unique nucleotides. Combine the three components of a nucleotide: the base, the sugar and the phosphate, and realize that although we abbreviate the A, C and G in DNA and RNA the same way, they are in fact not identical molecules (HINT: the sugars are different).

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

The double bond introduces a kink in the hydrocarbon chain.

The genetic code is said to be degenerate. What does "degenerate" mean in this context?

The genetic code is based on multiples of three nucleotides, and it is a triplet code. In other words, once initiated, every three RNA bases encode a different amino acid or stop codon. There are four possible bases: A, U, G, and C. Therefore, the maximum number of possible codon sequences of three bases would be 43, or 64 possible triplets. Three codons that are referred to as "stop codons" signal termination of the growing polypeptide strand, leaving a possible 61 codons that can encode amino acids. Since there are only 20 amino acids, most are specified in the genetic code by more than one codon. For example, CGU, CGC, CGA, and CGG all encode the amino acid arginine. This property of multiple codons per amino acid is what is meant by "degenerate."

Which statement correctly represents the distinction between the terms "genotype" and "phenotype"?

The genotype is the genetic composition of an organism, and the phenotype is its physical appearance.

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.

According to the "central dogma" of molecular biology, information flows from DNA to RNA to protein. In its original version, the dogma stated that information does not flow in the reverse direction. To what extent is this true?

The reproductive cycle of retroviruses includes a step, catalyzed by reverse transcriptase, in which a DNA copy of the viral RNA genome is synthesized. Thus, DNA is made from an RNA template, contradicting the original version of the dogma. However, it has not yet been found that a nucleic acid can be made using a protein template, so it appears that information does not flow backward from proteins.

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.

If a human gene is found to contain five introns, the mature mRNA encoded by that gene would have how many exons?

There could be multiple mRNAs that contain between one and six exons.

Partial digestion of chromatin with micrococcal nuclease was found to yield DNA fragments approximately 200 base pairs long. What accounts for this phenomenon?

This result suggests that the binding of proteins to DNA in chromatin protects regions of DNA from nuclease digestion; The DNA helix wraps itself around an octamer histone complex that gives chromatin fibers a beaded appearance, with beads spaced at intervals of approximately 200 base pairs.

Which class of molecule accelerates transport across biological membranes?

Transporters in membranes are proteins of either the channel or carrier protein class.

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

True.

The pH of endosomes and lysosomes is

acidic

Active transport differs from facilitated diffusion in that

active transport involves the transport of molecules up their concentration gradient.

Mutations in the internalization signal of endocytic receptors prevent their interaction with

adaptor proteins.

Transgenic mice carry a foreign gene in

all their cells

For many enzymes that are activated by phosphorylation of a serine residue, the substitution of serine with aspartic acid results in continual unregulated activity (or in other words, constitutively active). What features of serine, phosphoserine and aspartic acid account for this phenomenon?

aspartic acid resembles phosphoserine, leading to constitutive activation; since it resembles phosphoserine, the aspartic acid mimics the activity of serine in enzymatic assays. aspartic acid cannot be phosphorylated, acidic nature and hydrophilicty of aspartic acid do not determine if it is more active, phosphoserine is an ester of serine and phosphoric acid, while serine and aspartic acids are polar amino acids