genetics test study guide

Which of the following statements regarding Nucleotide Excision Repair (NER) and Base Excision Repair (BER) is true?

Both NER and BER involve the removal of one or more damaged bases by a nuclease

f a segment of DNA were replicated without any errors, the replicated strand would have the following sequence of nucleotides: 5' - ACTACGTGA - 3' Sort the following replicated DNA sequences by the type of point mutation each contains (frameshift, base substitution, or neither), as compared to the correct sequence shown above. Sort the items into the appropriate bins.

frameshift mutation 5'-ACTCGTGA-3' 5'-ACTTACGTGA-3' base substitution mutation 5'-ACTACGTGT-3' 5'-ACTAAGTGA-3'

Huntington's disease occurs when a CAG repeat expansion in the coding region of the HTT gene becomes too long. The CAG repeat is also in frame.(... | CAG | CAG | CAG | ...) Which amino acid is coded for in this repeat?

glutamine CAG codes for glutamine. Normal individuals typically have 10-34 CAG. Individuals affected by Huntington's disease have 40-200 CAG repeats; therefore they have a longer polyglutamine tract than normal individuals.

Which bacteria grow on the agar plate if the Ames test is positive?

his + prototrophs The bacteria used in the Ames test to evaluate mutagenicity are his− auxotrophs. If the Ames test is positive, these bacteria have reverted back to wild type and are his + prototrophs

Contrast the role of the repressor in an inducible system and in a repressible system.

in an inducible system , the repressor that normally interacts with the operator to inhibit transcription is inactivated by an inducer, thus permitting transcription. in a repressible system a normally inactive repressor is activated by a corepressor, thus enabling it (the activated repressor) to bind to the operator to inhibit transcription.

repressor

is a protein that inhibits gene transcription. In prokaryotes, this protein binds to the DNA in or near the promoter.

inducer

is a specific small molecule that binds to a bacterial regulatory protein and changes its shape so that it cannot bind to an operator, thus switching an operon on.

operon

is a stretch of DNA consisting of an operator, a promoter, and genes for a related set of proteins, usually making up an entire metabolic pathway.

The codon?

mRNA

During translation, what molecule bears the anticodon?

tRNA

In positive control of gene expression,

the regulatory molecule stimulates transcription.

Each transfer RNA requires at least four specific recognition sites that must be inherent in its tertiary structure in order for it to carry out its role. What are these sites? Select the four sites.

the site for interaction with the ribosome the site for interaction with the aminoacyl tRNA synthetasethe site for attachment of a specific amino acid the site for interaction with the codon (anticodon)

Which of the following best describes the biological role of the lac operon?

It ensures that a cell dedicates resources to the production of enzymes involved in lactose metabolism only when lactose is available in the environment.

What properties demonstrate that the laclac repressor is a protein? What are the evidences that it indeed serves as a repressor within the operon system? Drag the terms on the left to the appropriate blanks on the right to complete the sentences. Not all terms will be used.

Mutations could be isolated, so these mutations functioned in cis positions. This aspect strengthened the thought that a protein was involved. There are some evidences that lac repressor indeed serves as a repressor. First, a component in extracts from lacIq cells could bind to labeled IPTG, whereas this component was missing in extracts from lacI- cells. Second, radioactive IPTG-binding protein was found to bind to dna from lambda phage that contained only the lacO+ region, indicating that the binding was specific.Third, experiments showed that the protein did not bind to DNADNA with the lac Oc mutation

operator

Regulatory proteins bind to the______ to control expression of the operon.

What led researchers to conclude that a repressor molecule regulates the lac operon?

Scientists identified constitutive mutants that produced lactose-metabolizing enzymes in the absence of lactose. the first such mutant gene mapped close to the lac structural genes. since the operon was active in the absence of the gene product and repressed when the gene was wild type it was concluded that the gene encoded a repressor

The placement of the operator sequence between the promotor and the structural genes is critical to the proper function of the lac operon.

true

promoter

a specific nucleotide sequence in DNA that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place.

To ensure that a human gene is translated properly in a bacterial cell, you should clone the________ for the gene instead of the genomic DNA fragment that contains the gene.

cDNA Bacteria are able to translate eukaryotic processed mRNAs and produce normal, functioning eukaryotic proteins. cDNAs are complementary copies of mRNAs--processed pre-mRNAs-- and these cDNAs can be cloned into bacterial vectors and expressed in bacteria.

In maize, a DsDs or AcAc transposon can alter the function of genes at or near the site of transposon insertion. It is possible for these elements to transpose away from their original insertion site, causing a reversion of the mutant phenotype. In some cases, however, even more severe phenotypes appear, due to events at or near the mutant allele. What might be happening to the transposon or the nearby gene to create more severe mutations? Select all that apply.

chromosome breakage deletions in the nearby gene

regulatory gene

codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes.

For the lac genotypes shown below, predict whether the structural genes (ZZ) are constitutive, permanently repressed, or inducible in the presence of lactose. Sort the genotypes into the appropriate categories.

constitutive I−O+Z+ I+OCZ+ /F′O+ I−OCZ+/ F′O+ I−OCZ+ permanently repressed ISO+Z+ / F′I+ ISO+Z+ inducible I+O+Z+

The role of transposase activity in IS element transposition includes _______.

cutting DNA at the target sequence

What genetic defects result in the disorder xeroderma pigmentosum (XP) in humans?

defects in the DNA repair system

In their first round of screening, Beadle and Tatum plated spores on minimal medium. The purpose of this screen was to

determine whether any auxotrophic mutants had been generated

In Part C you identified the portion of the mRNA sequence (5'...AGGAGG...3') that base pairs with the 16S rRNA. Where do you expect to find the start codon in relation to this sequence?

downstream The 16S rRNA makes contact with the Shine-Dalgarno mRNA sequence near the exit site (E Site) of the 30S subunit of the ribosome. This positions the downstream start codon into the peptidyl site (P Site) in order for the initiator tRNA to base pair with the start codon. Once the initiator tRNA is bound, the 50S subunit binds the 30S subunit.

Host cells

express foreign genes introduced in the recombinant DNA.

DNA fragments that are 600 bp long will migrate more quickly through a sequencing gel than fragments that are 150 bp long

false

Attenuator systems such as the one described for regulation of tryptophan synthesis would be just as likely to occur in eukaryotes as in prokaryotes.

false Regulation by attenuation requires that translation of a given transcript can begin before transcription is completed. This is not possible in eukaryotes, as the two processes are spatially separated by the nuclear membrane.

How do we know that the trp operon is a repressible control system, in contrast to the lac operon, which is an inducible control system?

for the lac system, addition of lactose to the medium causes the synthesis of utilizing structural proteins. for the trp system, when tryptophan is added to the medium, no biosynthetic enzymes are produced.

It has been observed that diseases caused by repeat expansions are the result of trinucleotide repeats rather than smaller or larger repeat lengths. If non-trinucleotide repeat expansions were present in the coding region of a gene, which type of mutation would you expect to be the most likely?

frameshift

Order the following events from first to last in initiation of translation in eukaryotes.

1.40S subunit binds the 5'-cap region of the mRNA 2.40S subunit scans the mRNA for the Kozak sequence 3.60S subunit binds the 40S subunit

In bacteria, a 70S initiation complex is assembled from the two ribosomal subunits, mRNA, and initiator tRNA with the assistance of three initiation factors and energy from GTP. Drag the labels into the flowchart to show the order of events as they are thought to occur during bacterial translation initiation.

1.IF3 binds to the 30S subunit and prevents its association with the 50S subunit. 2.The 16S rRNA base-pairs with the Shine-Dalgarno sequence. 3.tRNAfMet, with IF2 and GTP bound, binds to the start codon. IF1 then binds to the A site of the 30S subunit. 4.The 50S subunit joins the complex. 5.Initiation factors are released from the complex. 6.A 70S initiation complex is formed.

The first base at the 5' end of the anticodon has relaxed base-pairing rules allowing some tRNAs to bind multiple codon sequences. This is called the third base "wobble" hypothesis. How many codons could a tRNA with the anticodon 5'-GAA-3' recognize?

2

The DNA sequence is repeated here:5'...Exon 1...AGCTTGGGAGCGGCG GTGAGGCGGGAGGCG...Intron 1...TCCTCTCTCCCCCAG GGCCCACCAGCTCTG...Exon 2...3'Recall that the DNA sequence that corresponds to intron 1 is underlined and bolded.You are now interested in using FISH to visualize the pattern of expression of this gene during mouse embryo development. This time you need to design a probe that will only bind the mature mRNA and not genomic DNA. Note that often DNA probes are used to hybridize to RNA sequences. Which of the following DNA probes could you use to detect mature mRNA from this gene?

3' GCCGCCCGGG 5' The RNA transcribed from this gene will have the same sense as the coding/nontemplate strand, except that U's will replace T's. Therefore the initial RNA will be:5'...Exon 1...AGCUUGGGAGCGGCG GUGAGGCGGGAGGCG...Intron 1...UCCUCUCUCCCCCAG GGCCCACCAGCUCUG...Exon 2...3'Following RNA processing, introns will be removed The bolded bases represent the regions of exons 1 and 2 that are spliced together.5'...Exon 1...AGCUUGGGAGCGGCG GGCCCACCAGCUCUG...Exon 2...3'The splicing together of exon 1 and 2 provides a unique target sequence that is not present in the original genomic sequence. 3' GCCGCCCGGG 5' is the only probe listed that will bind this sequence that is unique to the mRNA.

What is the difference between a knockout animal and a transgenic animal?

A knockout animal has a piece of DNA missing, whereas a transgenic animal usually has a piece of DNA added.

What is the difference between a silent mutation and a neutral mutation? Drag the terms on the left to the appropriate blanks on the right to complete the sentences. ResetHelp

A neutral mutation is a mutation that occurs in noncoding D N A and does not affect gene products or gene expression A silent mutation is a point mutation in an open reading frame that does not alter the amino acid encoded, due to degeneracy of the genetic code.

What is a single guide RNARNA, and what role does it play in CRISPR-Cas genome editing in eukaryotic cells?

A single guide RNARNA is a short RNARNA molecule that mediates sequence specificity for the Cas9 nuclease. The sgRNAsgRNA guides Cas9 to the appropriate genomic DNADNA sequence by binding to a complementary site that is near a PAM sequence.

Consider the predominant types of alternative splicing events that occur in mammals. Which of the following choices represent mRNA molecules that could be produced from the primary RNA transcript by alternative RNA splicing? (In each choice, the yellow part on the left represents the 5' cap, and the yellow part on the right represents the poly-A tail.)

ACEI ACGI ACEGI Alternative RNA splicing produces different mRNA molecules from the same primary RNA transcript. During alternative RNA splicing, introns are removed, and some exons may also be removed. The removal of different exons produces different mRNA molecules, which are then translated into different proteins. While intron retention is the most common type of alternative splicing event in plants, fungi, and protozoa, recall that it is a rare event in mammals. Alternative RNA splicing can greatly expand the number of proteins produced from the same gene.

Describe the manner in which activators and repressors influence the rate of transcription initiation.

Activators and repressors change the relationship of RNAP II to the transcription complex.

Most mutations are thought to be deleterious. Why, then, is it reasonable to state that mutations are essential to the evolutionary process?

All mutations may not be deleterious. Few beneficial mutations will provide a basis for possible differential propagation of the variation, and so of the evolutionary process.

What advantages do BACs and YACs provide over plasmids as cloning vectors?

BACs and YACs: DNA inserts from 100 kb to 1000 kb can be cloned Plasmids: can only accept DNA pieces up to 25 kb easy to separate from the host bacterial chromosome can use only bacteria as hosts

Refer to the figure below, what enzymes would be able to cut at this sequence?

BamHI Sau3AI

What role does DNA ligase perform in a DNA cloning experiment? How does the action of DNA ligase differ from the function of restriction enzymes?

DNA ligase generates the covalent bonds of the phosphodiester backbone, while restriction enzymes break those bonds.

How might chromatin structure be involved in such regulation?

DNA loops are thought to bring distant enhancer or silencer elements into proximity with promoter regions of the genes under their regulation

Which enzyme is responsible for proofreading during replication?

DNA polymerase

The regulation of mRNAmRNA decay relies heavily upon deadenylases and decapping enzymes. Explain how these classes of enzymes are critical to initiating mRNAmRNA decay. Select the two correct statements.

Deadenylases, which function in deadenylation-dependent decay, shorten the 3′3′-poly-AA tail and lead to the recruitment of either a degradative exosome complex or decapping enzymes. Decapping enzymes function in both deadenylation-dependent and -independent decay, by removing the 5′5′ cap and allowing XRN1 exonuclease degradation.

All compounds that have been found to be mutagenic in the Ames test are also carcinogenic.

False

Bacteria can distinguish between a newly replicated DNA strand and the original template strand because the newly replicated strand is methylated, whereas the original template strand is not.

False

In the mid-1960s, George Streisinger proposed that strand slippage during DNA replication (shown in the figure) altered the number of DNA repeats found in trinucleotide repeat disorders. Formation of a hairpin structure in the region of repeated DNA during strand slippage could facilitate this process. Which trinucleotide repeat disorder would not be consistent with the hairpin formation part of this model?

Friedreich ataxia (GAA repeat)

Using DNADNA sequencing on a cloned DNADNA segment, you recover the nucleotide sequence shown below. CAGTATGGATCCCAT Does this segment contain a palindromic recognition sequence for a restriction enzyme? If so, what is the double-stranded sequence of the palindrome?

GGATCCGGATCC CCTAGG

Sort the statements below according to whether they are true for a genomic library, a cDNA library, or both types of genetic libraries. Drag each statement into the correct bin.

Genomic library only can be used to study promoter regions of genes can be used to study splice sites and introns is the same regardless of which cell type is used to make the library cDNA library only can be used to study the genes expressed at different developmental stages Both genomic and cDNA libraries can be used to study coding regions of genes

92−−95∘C

Heating to 92−−95∘C∘C denatures the double-stranded DNADNA so that it dissociates into single strands.

What are the two different types of histone modifications and how do they impact transcription? Drag the terms on the left to the appropriate blanks on the right to complete the sentences. Not all terms will be used.

Histone modification involves two main enzymes: histone acetyltransferase, which adds groups to (a) histone tails, and histone deacetylase, which removes groups. Acetylation creates more "open" chromatin, which allows transcription, whereas deacetylation restores chromatin to a more "closed" state.

Which of the following transposition events is most likely to result in a loss of function mutation?

Insertion of an IS element within the coding region of a gene Insertions of DNA elements within coding regions have the greatest potential for altering amino acid sequence and/or causing truncation of a polypeptide due to frameshift.

What are the advantages of CRISPR-Cas over traditional methods for creating knockout or transgenic animals?

It can be very precise. It is both rapid and efficient.

Which of the following molecules is not required for a PCR reaction?

Ligase

Why are liver extracts used in the Ames test?

Liver enzymes may activate some innocuous compounds, making them mutagenic.

45−−65∘C

Lowering the temperature to 45−−65∘C∘C allows the primers to bind to the denatured DNADNA.

What is a spontaneous mutation?

Mutations that occur as a result of natural biological and/or chemical processes are considered spontaneous.

A 1.5‑kb fragment of DNA is cloned into a plasmid vector that is 5.5 kb long at the EcoRI site, and the plasmid vector is then used to transform bacteria. If the plasmid DNA is then extracted from a single bacterial colony and digested with EcoRI, what digestion products will be produced if the plasmid contains the fragment?

One 1.5‑kb fragment and one 5.5‑kb fragment

Which amino acid does this tRNA carry?

Phenylalanine

In 1998, future Nobel laureates Andrew Fire and Craig Mello, and colleagues, published an article in Nature entitled, "Potent and Specific Genetic Interference by Double-Stranded RNARNA in Caenorhabditis elegans." Explain how RNAiRNAi is both "potent and specific."

RNAi is considered potent because only a few molecules are needed to degrade large amounts of mRNA Gene silencing occurs in a sequence-specific manner since RNAi depends on complementary base pairing.

Which repair system uses the RecA and LexA proteins?

SOS repair

RNAiRNAi may be directed by small interfering RNARNAs (siRNAsiRNAs) or microRNAmicroRNAs (miRNAmiRNAs); how are these similar, and how are they different? Drag the appropriate items to their respective bins.

Similarities association with RISC the result of cleavage the source are double-stranded sncRNA Differences processing of longer RNAs the source of dsRNA secondary structure mechanism of silencing

Although many cloning applications involve introducing recombinant DNA into bacterial host cells, many other cell types are also used as hosts for recombinant DNA. why?

Some studies are carried out to research a specific DNA segment in a specific host environment Bacteria do not process transcripts as do eukaryotes.

It is estimated that about 0.2 percent of human mutations are due to TE insertions, and a much higher degree of mutational damage is known to occur in some other organisms. In what way might a TE insertion contribute positively to evolution?

Sometimes the new genetic variation confers a selective advantage.

Which of the following statements about manual Sanger sequencing is true?

The DNA sequence obtained is complementary to the template strand.

Digestion of a 1.1‑kb fragment of DNA with BamHI produces two fragments of 700 bp and 400 bp. Digestion of the same 1.1‑kb fragment with XhoI produces two fragments of 300 bp and 800 bp. Digestion with both enzymes produces three fragments of 100 bp, 300 bp, and 700 bp. Which of the following statements is true about the DNA fragment?

The XhoI site is located within the BamHI 400‑bp fragment

Suppose that you would like to make a human protein in bacteria. You clone a fragment of genomic DNA that contains the human gene into a plasmid, transform the plasmid into the bacteria, and isolate colonies containing the recombinant plasmid. Which of the following results would you expect from this experiment?

The bacteria could produce a much longer protein with an incorrect amino acid sequence. The bacteria could produce a truncated, nonfunctional human protein. Human genes contain introns that are spliced out before the gene is translated. Because bacteria are not able to process eukaryotic genes, the bacteria would not splice out the introns, and would instead translate them. If an intron contained a stop codon, this would lead to a truncated protein. If an intron did not contain a stop codon, the translated protein would be longer than normal and contain an incorrect amino acid sequence as a result of translating the intron.

The diagram below shows two stretches of DNA in the genome of an imaginary eukaryotic cell. The top stretch of DNA includes the fantasin gene, along with its promoter and one of its enhancers. The bottom stretch of DNA includes the imaginin gene, its promoter, and one of its enhancers. The slash marks (//) indicate that more than 1,000 nucleotides separate the promoter and enhancer of each gene. Which statements about the regulation of transcription initiation in these genes are true? Select all that apply.

The fantasin gene will be transcribed at a high level when activators specific for control elements A, B, and C are present in the cell. Both the fantasin gene and the imaginin gene will be transcribed at high levels when activators specific for control elements A, B, C, D, and E are present in the cell. Control elements C, D, and E are distal control elements for the imaginin gene.

When disrupting a mouse gene by knockout, why is it desirable to breed mice until offspring homozygous (-/-) for the knockout target gene are obtained?

The knockout gene cannot be faithfully transmitted at high frequency

How may the covalent modification of a protein with a phosphate group alter its function?

There is no general "rule" describing the absolute effect of phosphorylation on the function of the protein.

What are the consequences of having pyrimidine dimers in DNA?

These dimers distort the DNA structure and result in errors during DNA replication.

Why are spontaneous mutations rare?

They are relatively rare in comparison to induced mutations that are more directed to the physical or chemical properties of DNA.

Which of the following statements about ddNTPs is true

They have a hydrogen at the 3′ carbon of the sugar.

This sequence represents a single mutation.Mutation #1: 5' - | GGC | GCG | GTA | TTA | GCG | - 3' Complete these sentences about this mutated DNA sequence.

This mutant DNA sequence is the result of a transition (transition or transversion?) mutation. The effect of this base substitution on the amino acid sequence results in a missense mutation.

This sequence represents a single mutation.Mutation #2: 5' - | GGC | GTG | GTA | TAA | GCG | - 3' Complete these sentences about this mutated DNA sequence.

This mutant DNA sequence is the result of a transversion (transition or transversion?) mutation. The effect of this base substitution on the amino acid sequence results in a nonsense mutation.

This sequence represents a single mutation.Mutation #3: 5' - | GGC | GTG | GTC | TTA | GCG | - 3' Complete these sentences about this mutated DNA sequence

This mutant DNA sequence is the result of a transversion (transition or transversion?) mutation. The effect of this base substitution on the amino acid sequence results in a silent mutation.

What is the purpose of raising the temperature to 90-95°C at the beginning of each cycle of PCR?

To separate the double‑stranded DNA

Many chemicals are more mutagenic after being processed in the liver.

True

Why would a mutation in a somatic cell of a multicellular organism not necessarily result in a detectable phenotype?

When conducting genetic screens, it is assumed that all the cells are genetically identical. Since a somatic mutation first appears in a single cell, it is highly unlikely that the organism will be sufficiently altered to respond to a screen because none of the other cells will have the mutation.

Why are X rays more potent mutagens than UV radiation?

X rays are of higher energy and shorter wavelength than UV light. They have greater penetrating ability and can create more disruption of DNA.

What advantages do cDNAcDNA libraries provide over genomic DNADNA libraries? Describe cloning applications where the use of either a genomic library or a cDNAcDNA library is necessary to provide information. Drag the terms on the left to the appropriate blanks on the right to complete the sentences. Not all terms will be used.

a cDNA library provides DNAs from mRNA transcripts and is useful in identifying what are likely to be functional DNAs. if one desires to examine noncoding as well as coding DNAs, a genomic library would be more useful.

All of the following are characteristics of insertion sequences elements except _______.

a copy of the insertion sequence becomes integrated at a new location

How does the silencing process begin, and what major components participate? Drag the terms on the left to the appropriate blanks on the right to complete the sentences. Terms can be used once, more than once, or not at all.

a cytoplasmic protein, dicer, processes double-stranded noncoding RNA (sncRNA) molecules to produce shorter dsRNAs These associate with RISC where an Argonaute family protein cleaves and discards one of the two strands. The retained strand guides RISC to the complementary target message, where the complex acts to prevent expression.

Generally speaking, which of the following mutations would most severely affect the protein coded for by a gene?

a frameshift deletion at the beginning of the gen A frameshift mutation at the beginning of a gene would affect every codon after the point where the mutation occurred. During protein synthesis, incorrect amino acids would be inserted from the point where the frameshift mutation occurred on; the resulting protein would most probably be nonfunctional. For this reason, a frameshift mutation at the beginning of a gene is generally the most severe type of mutation.

Vectors

are plasmids, bacteriophages, or cosmids that receive, through ligation, a piece or pieces of foreign DNA.

X-Gal is included in the growth medium on which cells transformed with bacterial plasmids are grown. The reason X-Gal is included is to

identify bacteria that contain a recombinant plasmid

How and why are eukaryotic mRNAs transported and localized to discrete regions of the cell? Select the three correct answers.

mRNA transport is dependent on motor proteins, which "walk" along microtubules of the cytoskeleton. Because of mRNA transportation each component of a cell is unique. mRNA localization is dependent on the binding with RBPs.

What features of eukaryotes provide additional opportunities for the regulation of gene expression compared to bacteria? Select all that apply.

presence of chromatin opportunity for posttranscriptional and pre-translational regulation separated processes of transcription and translation

In the Ames Test, the appearance of his+ revertants in the presence of a non-mutagenic control compound indicates that _______.

some of the reversion mutations are not caused by the mutagen being tested

The purpose of the Ames Test is to _______.

test the mutagenic effects of chemicals

Although the process of translation is similar in bacteria and eukaryotes, there are some important differences. Drag each item into the appropriate bin based on whether it is involved in translation in bacteria only, eukaryotes only, both, or neither.

translation in bacteria: Shine-Dalgarno sequence tRNAfMet translation in eukaryotes: Kozak sequence translation in both: GTP hydrolysis release factor UAA codon mRNA tRNASer not part of translation: promoter RNA polymerase

The products of restriction digestion can be visualized by gel electrophoresis, which separates fragments based on their size.

true

Trinucleotide repeat disorders are hereditary diseases caused by mutant genes containing an increased number of repeats of a DNA trinucleotide sequence. Which sequence(s) contain a trinucleotide repeat? Select all that apply.

...AGCGACAGCAGCAGCAGCAGCAAGT...... CACGGAAGAAGAAGAAGAAATAGAC...... CACGGCGGCGGCGGCGGCATCGC...

Which of the following DNA sequences is one strand of a restriction enzyme recognition sequence?

5' GGATCC 3' The 5' →→ 3' sequence of the complementary strand would be the same as the 5' →→ 3' sequence of this strand; i.e., this sequence is symmetrical about the midpoint.

A tRNA anticodon is 5' GAA 3'. Answer the following questions. Which one of the following codons is recognized by this tRNA?

5' UUC 3'

Restriction enzymes

cut DNA at specific sites.

The thermostability of Taq polymerase is required during the annealing phase of PCR.

false

The following portion of the 16S rRNA base pairs with the Shine-Dalgarno sequence found in mRNA.5'...CCUCCU...3'Which mRNA sequence would have perfect complementarity with this rRNA?

5'...AGGAGG...3'

A typical cloning plasmid includes these elements:

a multiple cloning site, which is a region that contains multiple restriction enzyme cut sites that are used to clone the DNA of interest sequencing primer sites, which allow for the cloned DNA to be sequenced and identified the origin of replication, which allows for the plasmid to be replicated in bacteria the ampR gene, which allows for selection of cells that contain the plasmid the lacZ gene, which allows for selection of cells that contain a cloned DNA fragment

Thymine dimers can be repaired by Photoreactivation Repair or Nucleotide Excision Repair.

true

Within a six-base DNA recognition sequence, an enzyme that cuts between the 3rd and 4th bases from the 5' end will generate blunt ends.

true

What techniques can scientists use to determine if a particular transgene has been integrated into the genome of an organism?

use of reporter genes

How do we know that the lac repressor is a protein?

The lac repressor was shown to be a protein with using radioactive labeling of sulfur amino acids.

How does an enzyme function?

Enzymes lower the energy of activation, allowing chemical reactions to occur under conditions that are compatible with living systems.

why?

All higher levels are dependent on the sequence of amino acids.

Order the following events from first to last in initiation of translation in prokaryotes.

1.30S subunit binds near 5' end of mRNA 2.16S rRNA base pairs with the Shine-Dalgarno sequence 3.initiator tRNA charged with fMet binds the P site on the 30S 4.50S subunit binds the 30S subunit

The DNA sequence is repeated here:5'...Exon 1...AGCTTGGGAGCGGCG GTGAGGCGGGAGGCG...Intron 1...TCCTCTCTCCCCCAG GGCCCACCAGCTCTG...Exon 2...3'Recall that the DNA sequence that corresponds to intron 1 is underlined and bolded. Which of the following DNA probes could you also use to detect this gene in mice? Select all that apply.

5' CGGCGGTGAG 3' 3' GCCGCCACTC 5' 5' TCCTCTCTCC 3' The genomic sequence contains introns, therefore these sequences can be used to design probes that hybridize to genomic DNA.

You have identified a partial genomic sequence for a gene in mice and would like to use fluorescent in situ hybridization (FISH) to study this gene. Below is a partial DNA sequence (coding/nontemplate strand). The DNA sequence that corresponds to intron 1 is underlined and bolded.5'...Exon 1...AGCTTGGGAGCGGCG GTG AGGCGGGAGGCG...Intron 1...TCCTCTCTCCCCCAG GGCCCACCAGCTCTG...Exon 2...3'Use this sequence to answer the following questions. First, you would like to use FISH to confirm the position of the gene on chromosome 7 as well as the location of this part of the chromosome in an interphase nucleus. You decide to design a probe to hybridize to the genomic DNA containing this gene. Which of the following DNA probes could you use to detect this gene in mice? Select all that apply.

5' TTGGGAGCGG 3' 3' AACCCTCGCC 5' Although only the coding/nontemplate strand is given, the gene is present in the genome as double-stranded DNA. Therefore a probe can be made to hybridize to either strand. The probe must be complementary and antiparallel.

Which of the following mutations could lead to constitutive expression of the genes of the lac operon?

A mutation in the operator sequence

In principle, RNAi may be used to fight viral infection. How might this work? Drag the terms on the left to the appropriate blanks on the right to complete the sentences.

A number of viruses use RNARNA as their genome rather than DNADNA. If the genome consists of dsRNA, siRNA molecules could be generated directly from this genomic RNA using the cellular enzyme dicer. If the genome consists of ssRNA, virally encoded replicase could synthesize a complementary RNA strand, thus making the viral genome available for degradation

Predict the effect on the inducibility of the lac operon of a mutation that disrupts the function of: The crp gene, which encodes the CAP protein

Absence of a functional crp would compromise the positive control exhibited by CAP.

Which statements about the modification of chromatin structure in eukaryotes are true?

Acetylation of histone tails in chromatin allows access to DNA for transcription. DNA is not transcribed when chromatin is packaged tightly in a condensed form. Some forms of chromatin modification can be passed on to future generations of cells. Acetylation of histone tails is a reversible process. Methylation of histone tails in chromatin can promote condensation of the chromatin.

Choose the types of alternative splicing patterns with the correct description of how they lead to the production of different protein isoforms. Select the three correct statements.

Alternative polyadenylation−−produces messages with different 3′3′ coding sequences as well as different 3′3′ untranslated regions, which can be important in regulatory events. Alternative promoters−−produce messages with different 5′5′ exons and proteins with different NN-terminal ends. Cassette exons−−whole exons are excluded from the mature message, resulting in a protein that is missing certain sequences (perhaps an entire protein domain).

Complete a regulatory model to account for the regulation of erythritol catabolism in such bacterial strains. Does this system appear to be under inducible or repressible control?

As long as the four genes are closely spaced and appear to be under coordinate control, a(n) operon is likely to be involved. he product of the eryD gene is involved in repressing a promoter site. The system is induced when erythritol interrupts the action of the eryD repressor. These data are consistent with a(n) inducible system of regulation

Describe the role of attenuation in the regulation of tryptophan biosynthesis.

Attenuation functions to reduce the synthesis of tryptophan when it is in full supply. it does so by reducing transcription of the tryptophan operon. The same phenomenon is observed when tryptophan activates he repressor to shut off transcription of the tryptophan operon.

65−−75∘C∘C

Bringing the temperature to 65−−75∘C∘C allows the heat stable DNADNA polymerase an opportunity to extend the primers by adding nucleotides to the 3′3′ ends of each growing strand.

Present an overview of the manner in which chromatin can be remodeled. Describe the manner in which these remodeling processes influence transcription. Drag the terms on the left to the appropriate blanks on the right to complete the sentences. Terms can be used once, more than once, or not at all.

DNA methylation has been linked to a decrease(s) in gene expression. It most often occurs at position 5 of cytosine. Histone acetylation decrease(s) the positive charge on histones, resulting in a reduced affinity of the histone for DNA. The process is catalyzed by HATs and results in forming "open" chromatin. Chromatin remodeling leaves DNA open to associate with transcription factors and RNA polymerase by repositioning or removing nucleosomes using large, energy dependent multi-subunit complexes. One way in which nucleosomes can be modified is by changing their composition. Histone variants, like H2A.Z affect nucleosome mobility and positioning on DNA.

Many promoter regions contain CAATCAAT boxes containing consensus sequences CAATCAAT or CCAATCCAAT approximately 70 to 80 bases upstream from the transcription start site. How might one determine the influence of CAATCAAT boxes on the transcription rate of a given gene?

Delete the CAATCAAT box sequence and measure the transcription rate. Introduce extra CAATCAAT box sequences and measure the transcription rate. Make mutations in the CAATCAAT box sequence and measure the transcription rate. All of the above would be good ways to determine the influence of CAATCAAT boxes on transcription rate.

Wild-type strains of E. coli have a tRNA with a 5′-GUA-3′ anticodon that recognizes the UAC codon for tyrosine. We can represent this tRNA as GUA-tRNATyr.Suppose you isolated a strain of E. coli in which a mutation changed the anticodon in this tRNA to 5′-CUA-3′ (creating CUA-tRNATyr). Answer the following questions about translation elongation in each strain. Drag the correct label to each target in the table. Labels can be used more than once.

During translation elongation, a peptide bond is formed between the amino acid (or polypeptide) covalently attached to the tRNA in the P site and the amino acid on the tRNA in the A site. This process continues until a stop codon is presented in the A site.In wild-type strains of E. coli, there are no tRNAs with anticodons complementary to stop codons. Instead, release factors recognize the stop codons, bind in the A site, and cause the polypeptide to be released from the ribosome, terminating translation.In a mutant strain that has charged tRNAs with the anticodon 5′-CUA-3′, those tRNAs will bind to the stop codon 5′-UAG-3′. As a result, translation will continue beyond the stop codon, producing an abnormal polypeptide that is longer than its wild-type equivalent. Such strains are called suppressor strains because they suppress translation termination.

Why are enzymes essential for living organisms?

Enzymes catalyze all essential biochemical reactions

Which of the following can be inferred from the Beadle and Tatum experiments?

For a mutation resulting in the production of a defective enzyme involved in a biosynthetic pathway, the compound preceding the corresponding step will accumulate

What is the major difference between the mechanism involved in attenuation and riboswitches and the mechanism involved in the regulation of the lactose operon?

For both attenuation and riboswitches, the regulation is mediated by the RNA secondary structure, whereas the regulation of the lac operon is mediated by a repressor protein.

Part complete For the following genotypes and conditions (lactose present or absent), predict whether functional enzymes, nonfunctional enzymes, or no enzymes are made. Drag the appropriate items to their respective bins.

Functional enzyme made I+OCZ+I/ F′O+(Lactose) I+OCZ+(Lactose) I+OCZ+/ F′O+Z+(Lactose) Non-functional enzyme made I−O+Z−(Lactose) I−O+Z−(No lactose) Both types made I+O+Z−/ F′I+O+Z+(Lactose) No enzyme made I−O+Z+/ F′I+(No lactose) I+O+Z+I(No lactose) I−O+Z−/ F′I+O+Z+(No lactose) ISO+Z+/ F′O+(No lactose)

Place the steps involved in making a genomic library and a cDNA library in their correct order in the flow charts below. Drag the labels onto these two flow charts in the correct order.

Genomic library: 1. isolate genomic dna from an organism 2.partially digest genomic dna with a restriction enzyme 3.ligate pieces of genomic dna into a cloning vector cDNA library: 1.isolate mRNA from a specific cell or tissue using an oligo-dT primer that hybridizes to the mRNA poly-A tail 2.create a single-stranded dna molecule complementary to the mrna using reverse transcriptase 3.partially degrade the mrna with rnase H 4.synthesize a strand of cDNA using DNA polymerase with mRNA fragments as primers 5.ligate cDNAs into a cloning vector

Which of the following occurs as a result of an abundance of tryptophan in E. coli?

The 5 trp genes (TrpA - TrpE) are not transcribed.

Review the concept of colinearity and consider the following question: Certain mutations called amber in bacteria and viruses result in premature termination of polypeptide chains during translation. Many amber mutations have been detected at different points along the gene that codes for a head protein in phage T4. How might this system be further investigated to demonstrate and support the concept of colinearity

The nearer to the 5′end of mRNAmRNA the amber mutation occurs, the shorter the resulting polypeptide.

Which of the following features of the trp operon is likely least essential to the process of attenuation?

The order of the structural genes, E, D, C, B, A

How do we know that bacteria regulate the expression of certain genes in response to the environment?

When certain additives are supplied to growth media, organisms respond with the production of certain enzymes.

What evidence established that lactose serves as the inducer of a gene whose product is related to lactose metabolism?

When lactose is added to the medium, E. coli respond with the production of enzymes involved in lactose metabolism. When lactose was removed, such enzymes decreased in concentration.

Predict the effect on the inducibility of the lac operon of a mutation that disrupts the function of: The CAP-binding site within the promoter.

Without a CAP binding site there would be a reduction in the inducibility of the lac operon.

The Beadle and Tatum experiments were based on all of the following assumptions except that

answer: two strains of auxotrophic Neurospora that grow on minimal medium supplemented with biotin have mutations in the same gene these are all true: auxotrophs fail to grow on minimal media X-irradiation can induce mutations. supplemented media permit growth of auxotrophic strains of Neurospora

genes of an operon

are arranged sequentially after the promoter.

Why are frameshift mutations likely to be more detrimental than point mutations, in which a single pyrimidine or purine has been substituted?

because they are likely to change more than one amino acid

How do these defects create the phenotypes associated with the disorder?

by decreasing the rate of DNA mutation repair in skin cells

How is fluorescent in situ hybridization (FISH) used to produce a spectral karyotype?

by using probes that fluoresce at different wavelengths

The trp and lac operons are regulated in various ways. How do bacteria regulate transcription of these operons? Sort the statements into the appropriate bins depending on whether or not each operon would be transcribed under the stated conditions.

operon is not transcribed lac operon: lactose absent trp operon: tryptophan present operon is transcibed, but not sped up through positive control lac operon: lactose present,glucose present trp operon: tryptophan absent operon is transcribed quickly through positive control lac operon: lactose present, glucose absent

Which of the four levels of protein organization is the most critical to a protein's function?

primary

Explain how the use of alternative promoters and alternative polyadenylation signals produces mRNAmRNAs with different 5′5′ and 3′3′ ends. Drag the terms on the left to the appropriate blanks on the right to complete the sentences.

promoters mark transcriptional start sites, which exist at the 5' end of the transcript. a gene with multiple alternative promoters would produce transcripts with different 5' ends. On the other hand, polyadenylation signals On the other hand, polyadenylation signals mark transcriptional polyadenylation signals sites at the polyadenylation signals ends of genes. Once such a signal is encountered, transcription is terminated and downstream exons are not included in the message. When alternative polyadenylation signals are used, the exon containing the first signal is skipped, allowing previously excluded exons to be transcribed and resulting in a message with a different polyadenylation signals end. mark transcriptional stop On the other hand, polyadenylation signals mark transcriptional polyadenylation signals sites at the polyadenylation signals ends of genes. Once such a signal is encountered, transcription is terminated and downstream exons are not included in the message. When alternative polyadenylation signals are used, the exon containing the first signal is skipped, allowing previously excluded exons to be transcribed and resulting in a message with a different polyadenylation signals end. sites at the 3′3′ On the other hand, polyadenylation signals mark transcriptional stop sites at the 3' ends of genes. Once such a signal is encountered, transcription is terminated and downstream exons are not included in the message. When alternative polyadenylation signals are used, the exon containing the first signal is skipped, allowing previously excluded exons to be transcribed and resulting in a message with a different 3' end.

In negative control of gene expression,

removal of the regulatory molecule from DNA stimulates transcription.