MMSC 491/691 Exam 1 Qs

polymorphism

A DNA variant in the ALX gene is observed at a frequency of 0.012 %, how would this variant be described? a. polymorphism b. rare varient c. mutation d. transgene

The three phases of a PCR reaction are the lag phase, the exponential phase, and the saturation phase. The lag phase is where there is a slow increase in product, in the first few cycles. The exponential phase is where the amount of PCR product is proportional to the amount of DNA input into the process. The saturation phase is where the reaction's efficiency declines as the products compete for hybridization with the DNA template with the leftover primer.

Describe the three recognized phases of a PCR reaction.

The three stages of PCR are denaturation, annealing, and extension. It begins with denaturation where the DNA is heated to break up the hydrogen bonds so that the strands can be separated. Then annealing occurs, this is where the primer binds to the target sequence of the DNA. Finally, extension is where the oligonucleotides begin the synthesis of the new DNA strands. The two types of enzymes necessary for cell-based DNA cloning are restriction endonucleases and DNA ligase. The Class II restriction endonuclease recognizes certain specified sequences of DNA, and cut the DNA to fit that region. This makes the DNA sequence a more reasonable size and is specific to the DNA needed. DNA ligase covalently joins the cut fragments of DNA (from the restriction endonuclease).

During PCR, each cycle has three defined steps. What are they, and what is involved?In cell-based DNA cloning two types of enzyme are critical for making recombinant DNA. What are they, and what roles do they carry out?

messenger; noncoding; introns; exons; GU; AG; genomic; DNA

During gene expression, the initial RNA transcript needs to undergo processing to make a mature RNA, either a ____ ____ RNA or a ____ ___ RNA. For many of our genes, the initial RNA transcript needs to be cleaved into pieces. Some of the pieces, called ____ ____, are discarded, but other alternating pieces called ___ ____ are retained and fused in the same linear order as their order when transcribed. The junctions between ___[4]____ and ____[3]____ contain some highly conserved nucleotides, notably a ____ ____ dinucleotide at the beginning of ___[3]____ and an ___ ____ dinucleotide at the ends of ____[3]____. For ____[4]_____ and _____[3]_____ the original definitions have been broadened to include the corresponding segments of _____ _____ ____ ______.

2n chromosomes, DNA content of 2C in G1; 2n chromosomes, DNA content of 4C in G2.

If we take the number of chromosomes in a haploid sperm cell or egg cell to be n and the total content of genomic DNA to be C, what is the number of chromosomes and the total genomic DNA content of a diploid G1 phase cell and in a diploid G2 phase cell from the same organism. a. n chromosomes, DNA content of 2C in G1; 2n chromosomes, DNA content of 4C in G2. b. 2n chromosomes, DNA content of 2C in G1; 4n chromosomes, DNA content of 4C in G2. c. 2n chromosomes, DNA content of 2C in G1; 4n chromosomes, DNA content of 2C in G2. d. 2n chromosomes, DNA content of 2C in G1; 2n chromosomes, DNA content of 4C in G2.

guanine and uracil

In a DNA double helix each type of base forms a stable base pair with only one type of base. When bases on an RNA strand are involved in base pairing, which bases can form stable base pairs with more than one type of base? a. adenine and uracil b. cytosine and uracil c. guanine and uracil d. uracil

4%

In addition to coding sequence, which is generally very highly conserved, what additional percentage of our genome is highly to moderately conserved? a. 0.4% b. 4% c. 14% d. 24%

Four parameters that affect the stability of a heteroduplex are the temperature, salt concentration, base composition, and the length of the region of base matching. The temperature affects the stability because heat/high temperatures will break down H bonds and cause instability. The salt concentration is considered a parameter because low salt levels can increase instability for the heteroduplex. The base composition affects the stability because GC bonds have more structure than the AT bonds because they have more H bonds, so more GC pairs would add stability to the heteroduplex. Finally, the length of the region of base matching plays in because longer regions have more hydrogen bonds and therefore more stability than a shorter area.

List four parameters that affect the stability of a heteroduplex and describe how they have an effect.

Copy number

Microsatellite DNA is expected to show variation with respect to.... a. DNA sequence b. Chromosome location c. Copy number d. Replication efficiency

Four additional key requirements for the reaction to be successful are (1) a DNA polymerase that is heat-stable, (2) oligonucleotide primers that flank the desired target DNA sequence, (3) an adequate supply of the deoxynucleoside triphosphates, and (4) a thermal cylinder so that the successive cycles may continue from denaturation to annealing to extension.

Most PCR reactions are intended to amplify a specific DNA sequence of interest from within a complex starting DNA, often a genomic DNA sample. In addition to a sample of starting DNA of this type in an appropriate buffer with the correct ions to sustain the reaction, list four additional key requirements of the reaction to be successful.

both a and c.

Nucleic acid hybridization assays are normally carried out under relaxed hybridization stringency (to maximize the chances of heteroduplex formation) but afterwards, washes are carried out that can be designed to favor perfectly matched sequences only by changing some parameter. Which, if any, of the following changes would be consistent with that aim? Note more than one response may be correct. a. An increase in temperature. b. An increase in salt concentration. c. An increase in the concentration of a polar molecule, such as urea or formamide. d. both a and c. e. a, b, and c.

The goal of the hybridization assay is to form and detect artificial heteroduplexes composed of single nucleic acid strands from the probe and the test sample. Therefore one of the populations needs to be labeled so that the artificial heteroduplexes can be identified or detected against strands that did not form heteroduplexes (formed homoduplexes). The nucleic acid is labeled using a respective DNA or RNA polymerase in a synthesis reaction where the deoxyribonucleotides/ribonucleotides carry a distinct group that can identify the specific strand, like fluorescence.

Nucleic acid hybridization assays require one of the interacting nucleic acid populations to be labelled in some way. Why is that required and what does it involve?

Nucleotide excision repair

Patients with Xeroderma Pigmentosum have defects in which DNA repair system? a. Mismatch repair b. Nucleotide excision repair c. Single strand break repair d. Homologous recombination

Cytogenetic methods (chromosome analysis)

Patients with disorders of the mismatched repair system can be easily diagnosed using which type of laboratory analysis? a. Next generation DNA sequencing b. PCR c. Cytogenetic methods (chromosome analysis) d. Biochemical assays

A DNA polymerase always requires a DNA template to synthesize a complementary DNA.

Regarding DNA replication and DNA synthesis, which, if any, of the following statements is incorrect? a. The leading strand is replicated continuously. b. The lagging strand is replicated discontinuously: the new DNA is synthesized as short pieces of DNA that must be ligated together. c. A DNA polymerase always requires a DNA template to synthesize a complementary DNA. d. A DNA polymerase requires a short RNA primer when synthesizing new DNA strands using a DNA template.

DNA replication is said to be semi-conservative because for each DNA helix only one strand serves as a template for new DNA synthesis.

Regarding DNA replication, which, if any, of the following statements is incorrect? a. DNA replication is said to be semi-conservative because for each DNA helix only one strand serves as a template for new DNA synthesis. b. The two DNA strands of the parental DNA helix are unwound using a DNA helicase. c. The replication fork marks the point at which DNA is actively being replicated from a single DNA duplex to form new DNA strands. d. The synthesis of new DNA strands always proceeds in the 5' --> 3' direction.

Some exons in protein-coding genes consist of noncoding DNA.

Regarding exons, which, if any, of the following statements is correct? a. Some exons in protein-coding genes consist of noncoding DNA. b. The first exon of a protein-coding gene always contains the translational start site. c. A coding exon is always translated in just one of the three possible forward reading frames. d. The last exon of a protein-coding gene always contains the normal termination codon.

A polypeptide normally adopts a rod-like conformation, with the side chains orientated in the same direction relative to the polypeptide backbone.

Regarding polypeptide structure, which, if any of the following statements is incorrect. a. A polypeptide is a polymer composed of a linear sequence of amino acids. b. A polypeptide normally adopts a rod-like conformation, with the side chains orientated in the same direction relative to the polypeptide backbone. c. The amino acids within a polypeptide are joined by a covalent bond known as a peptide bond. d. Peptide bonds form by a condensation reaction between the amino group of an amino acid and the carboxyl group of its neighbor.

The M phase is the only phase in the cell cycle when chromosomes stained with chemical dyes are visible under the light microscope.

Regarding the cell cycle, which, if any, of the following statements is correct? a. The M phase and the S phase are the critically important phases of the cell cycle; according to circumstance, the G2 phase and the G1 phase are dispensable. b. The M phase is the only phase in the cell cycle when chromosomes stained with chemical dyes are visible under the light microscope. c. The G0 phase is a specialized phase that allows terminally differentiated cells to irretrievably exit the cell cycle and become post-mitotic cells. d. The G0 phase is a modified version of the G2 phase.

Purines carry an amino group, unlike pyrimidines

Regarding the structure of bases in nucleic acids, which, if any, of the following statements is incorrect? a. Pyrimidines have a single heterocylic ring consisting of four carbon atoms plus two nitrogen atoms that are linked to the same carbonyl (-C=O) group b. Purines have two heterocyclic rings, each with two nitrogen atoms c. Thymine = 5-methyluracil d. Purines carry an amino group, unlike pyrimidines

The side chain of an amino acid is based on a branch that contains one or more carbon atoms

Regarding the structures of amino acids, which, if any, of the following statements is incorrect? a. The general formula for a nonionised amino acid is H2N-CH(R)-COOH, that is, a central carbon atom is linked to an amino group, a carboxyl group, a hydrogen atom, and a side chain, R. b. The identity of the amino acid is determined by the side chain that is connected to the central carbon atom. c. The side chain of an amino acid is based on a branch that contains one or more carbon atoms d. Proline is unique in having a side chain that is connected to both the central carbon and also to the nitrogen atom of the amino group.

The internal sugar residues in a DNA strand normally have free hydroxyl groups, unlike those in an RNA strand.

Regarding the sugar residues in nucleic acids, which, if any, of the following statements is incorrect? a. The sugar is always based on a heterocyclic ring that consists of one oxygen atom and four carbon atoms, one of which is connected to a fifth carbon atom, the 5? carbon atom. b. The internal sugar residues in a DNA strand normally have free hydroxyl groups, unlike those in an RNA strand. c. Bases are covalently linked to the carbon 1? atoms of the sugars. d. Neighboring sugar residues are linked to each other by a phosphodiester bond that connects the 3' carbon atom on one sugar to the 5' carbon atom of its neighbor.

1%

Roughly what percentage of our genome is made up of coding sequence? a. 1% b. 5% c. 10% d. 25%

7%

Roughly what percentage of our genome is made up of constitutive heterochromatin? a. 0.7% b. 7% c. 27% d. 57%

45%

Roughly what percentage of our genome is made up of transposon repeats? a. 0.45% b. 4.5% c. 25% d. 45%

C>T

The most frequent type of single-nucleotide substitution is? a. G>T b. C>T c. A>T d. G>C

The essential difference between the Sanger dideoxynucleotide sequencing method and the massively parallel (next generation) DNA sequencing is the quantity and efficiency of producing the product. The dideoxynucleotide makes labeled copies of a single DNA template and requires gel electrophoresis. The next generation sequencing can simultaneously sequence millions of DNA fragments (exponentially more than the Sanger method) and it does not require gel electrophoresis, so it is faster and it allows for a large amount of DNA to sequence DNA.

What is the essential difference between the Sanger dideoxynucleotide sequencing method and massively parallel (= next generation) DNA sequencing?

1%

What, approximately, is the fraction of genetic variation in the nuclear genome is that is expected to have a harmful effect on gene function? a. 50% b. 25% c. 10% d. 1%

transcriptional; template; primary; sense; anti-sense; anti-sense; unit

When a gene is expressed, the two DNA strands are locally unwound to allow access by the ____ ____ machinery. One of the DNA strands serves as a ____ ____ for an RNA polymerase to synthesize a complementary RNA. The initial transcript, often called the ____ ____ transcript, is identical in base sequence (except that U replaces T) to the sequence of the other DNA strand, which is known as the ____ ____ strand (and so the opposing strand that serves as the ___[2]____ is also known as the ____ ____ strand). The segment of genomic DNA that corresponds to the ____[3]____ transcript is known as the ___ ___ ___ ____.

A functional RNA that is not translated to make a protein.

Which is the best definition of noncoding RNA? a. A mutant mRNA that is not capable of making a protein. b. Any RNA sequence that is not translated to make a protein c. Any RNA sequence in an mRNA, or in the primary transcript used to make the mRNA, that is not translated to make a protein. d. A functional RNA that is not translated to make a protein.

Because centromeres and telomeres are critically important for chromosome function their DNA has been very highly conserved during evolution.

Which of the following statements is incorrect? a. Because centromeres and telomeres are critically important for chromosome function their DNA has been very highly conserved during evolution. b. Centromeres are important for correct segregation of chromosomes during cell division. c. The DNA of both centromeres and telomeres consist of repetitive DNA sequences. d. The DNA of our chromosomes may have multiple replication origins but their sequences are not very well conserved.

The only structural difference between DNA and RNA strands is that they have different sugars, respectively deoxyribose and ribose.

Which of the following statements is incorrect? a. Nucleic acids are always negatively charged. b. Cellular DNAs are structured as a double helix. c. The only structural difference between DNA and RNA strands is that they have different sugars, respectively deoxyribose and ribose. d. Cellular RNAs are single-stranded.

A-T base pairs are stronger than G-C base pairs.

Which of the following statements is incorrect? a. Purines are nitrogenous bases with a double ring structure. b. Base pairs may form between bases on a single nucleic acid strand. c. Two types of stable base pairing occur in DNA but a third type of base pairing is common in RNA-RNA and RNA-DNA base pairing. d. A-T base pairs are stronger than G-C base pairs.

Segregation of mtDNA molecules into daughter cells needs to be equal.

Which of the following statements is incorrect? a. Segregation of mtDNA molecules into daughter cells needs to be equal. b. The copy number of nuclear DNA molecules is tightly controlled. c. Hundreds or thousands of mtDNA molecules are found in human cells. d. The replication of nuclear DNA and mtDNA molecules is not coordinated.

Amplifying DNA must be carried out in bacterial or yeast cells.

Which of the following statements, if any, is false? a. Amplifying DNA always requires a DNA polymerase. b. Amplifying DNA must be carried out in bacterial or yeast cells. c. DNA cloning in cells involves attaching the DNA to be cloned to a vector DNA to form a recombinant DNA that may be circular or linear. d. Vector molecules in DNA cloning must have a replication origin that confers the ability to replicate extrachromosomally.

PCR is superior to cell-based DNA cloning for two major reasons: it is much quicker and it allows much greater DNA amplification.

Which of the following statements, if any, is false? a. PCR requires the use of a heat-stable DNA polymerase to make copies of the template DNA. b. PCR is usually used to amplify a specific DNA sequence of interest using. c. oligonucleotide primers that bind to closely flanking sequences. d. PCR is superior to cell-based DNA cloning for two major reasons: it is much quicker and it allows much greater DNA amplification.

All of the statements are true.

Which, if any, of the following statements are false? a. Constitutive heterochromatin remains highly condensed throughout the cell cycle. b. Unlike constitutive heterochromatin, facultative heterochromatin describes chromatin that can de-condense and behave as euchromatin under certain circumstances. c. Most of the long arm of the Y chromatin is made up of constitutive heterochromatin. d. In women one of the two X chromosomes in each diploid cell is heterochromatinised. e. All of the statements are true.

All of the statements are true.

Which, if any, of the following statements are false? a. During translation, the individual codons of an mRNA are "read" by transient hydrogen bonding to a complementary anticodon sequence on a transfer RNA. b. According to their anticodon, transfer RNAs usually have a specific amino acid attached to their 3' end. c. When the anticodon of a tRNA binds to a codon with a suitably complementary sequence, the amino acid is released and becomes part of a polypeptide. d. All of the statements are true.

The broadest definition of a pseudogene is any gene that has received inactivating mutations and can no longer make a functional product.

Which, if any, of the following statements are false? a. The broadest definition of a pseudogene is any gene that has received inactivating mutations and can no longer make a functional product. b. A retropseudogene is a non-functional cDNA copy of a processed RNA that has integrated elsewhere into the genome. c. A non-processed pseudogene is an inactive copy of a gene that has arisen by some type of gene duplication. d. An estimated 14,000 pseudogenes are found in the human genome.

Most of the inherited changes in our DNA arise because of exposure to extracellular mutagens, including radiation sources and chemical mutagens.

Which, if any, of the following statements is false, regarding the sources of genetic variation? a. Most of the inherited changes in our DNA arise because of exposure to extracellular mutagens, including radiation sources and chemical mutagens. b. Most of the inherited changes in our DNA arise because of unavoidable endogenous errors in cellular mechanisms and harmful effects of certain natural molecules and atoms within our cells. c. Errors in DNA replication and DNA repair are a major source of mutations in our cells. d. Significant chemical damage is sustained by DNA because of its proximity to water molecules in our cells.

Unlike DNA, RNAs are unmethylated, and only the four standard bases - A, C, G and U - are found in RNAs.

Which, if any, of the following statements is false? a. Unlike DNA, RNAs are unmethylated, and only the four standard bases - A, C, G and U - are found in RNAs. b. The primary structure of an RNA is the linear sequence of nucleotides. c. The secondary structure of an RNA is dominated by hydrogen bonding between bases on the same strand. d. Stem-loop structures are common in RNA and consist of complementary sequences that form stable base pairs, separated by a short sequence of unpaired bases.

Repair of double stranded DNA breaks is easier in cells prior to DNA replication than after DNA replication has occurred.

With reference to DNA repair, which of the following statements, if any, is false? a. Crosslinking of bases on opposing DNA strands is especially problematic for cells because it presents an obstacle to DNA replication (the replication fork stalls). b. Crosslinking of bases on opposing DNA strands can be problematic for cells because it may present an obstacle to transcription (the RNA polymerase stalls). c. Double strand DNA breaks are a challenge for cells because if repair is not affected immediately the ends can drift apart quickly making correct repair impossible. d. Repair of double stranded DNA breaks is easier in cells prior to DNA replication than after DNA replication has occurred.

Guanine is occasionally methylated to give O-6-methylguanine which base pairs with adenine rather than with cytidine.

With reference to aberrant methylation of bases which of the following statements, if any, is false? a. S-adenosylmethionine donates methyl groups to a range of different molecules in cells and frequently inappropriately methylates bases in DNA. b. Guanine is occasionally methylated to give O-6-methylguanine which base pairs with adenine rather than with cytidine. c. In each nucleated cell, about 300-600 adenines are converted to 3-methyladenine per day. d. 3-methyladenine can be a cytotoxic base: it distorts the double helix and that can disrupt crucial DNA-protein interactions.

The cross-linked bases are on opposing DNA strands.

With reference to base cross-linking, which, if any, of the following statements, is false? a. Base cross-linking means that covalent bonds form between two bases. b. The cross-linked bases are on opposing DNA strands. c. The anti-cancer agent cisplatin causes a type of cross-linking between two guanine residues. d. Pyrimidine dimers are a type of base cross-linking that is commonly induced by excess exposure to sunlight.

Regulatory antisense RNAs sometimes undergo splicing

With respect to expression of an RNA gene, which, if any, of the following statements are false? a. RNA processing sometimes includes RNA splicing b. Regulatory antisense RNAs sometimes undergo splicing c. Ribosomal RNAs and transfer RNAs are formed by cleavage of RNA precursors. d. Ribosomal RNAs and transfer RNAs undergo base modification.

To identify a target sequence that is distantly related to the probe, high stringency hybridization needs to be used.

With respect to nucleic acid hybridization, which, if any, of the following statements is false? a. The strength of base pairing between a probe and a complementary target sequence depends on the number of stable base pairs that are formed. b. Among other parameters, the hybridization stringency depends on the salt concentration and temperature of the hybridization reaction. c. To identify a target sequence that is distantly related to the probe, high stringency hybridization needs to be used. d. Under conditions that favor low hybridization stringency long heteroduplexes with significant base mismatching may be stable.