chapter 20

Where in a DNA strand do restriction enzymes cut the strand? (A) At symmetrical sequences of bases (B) At methylated sections of the DNA molecule (C) Only at the 3ꞌ end of a DNA molecule (D) At the sticky ends (D) At asymmetrical sequences of bases (E) Only at the 5ꞌ end of a DNA molecule

(A) At symmetrical sequences of bases. Restriction sites are symmetrical sequences of bases. Restriction enzymes cut them into "asymmetrical" shapes to form sticky ends.

The efficiency of cloning, and the ability to generate healthy cloned animals, has been largely hampered by the difficulty of __________. (A) completely reversing epigenetic alterations in donor cell nuclei such as DNA methylation and chromatin packing (B) transforming donor cells with genes encoding proteins required for normal embryonic development (C) inducing recombination in differentiated donor cells in order to restore the full genomic complement (D) physically removing the nucleus from the egg cell that will ultimately receive the donor cell nucleus (E) implanting the clone into the surrogate mother

(A) completely reversing epigenetic alterations in donor cell nuclei such as DNA methylation and chromatin packing Because DNA methylation helps regulate gene expression, misplaced methyl groups in the DNA of donor nuclei may interfere with the pattern of gene expression necessary for normal embryonic development.

Expression of a cloned eukaryotic gene in a bacterial cell involves many challenges. The use of mRNA and reverse transcriptase is part of a strategy to solve the problem of (A) post-transcriptional processing. (B) post-translational processing. (C) nucleic acid hybridization. (D) restriction fragment ligation

(A) post-transcriptional processing. After transcription, it can process mRNA (instead of something like mDNA...)

Which arrangement of the following four enzymes represents the order in which they would be used in a typical gene-cloning experiment resulting in the insertion of a cDNA into a bacterial plasmid? Begin with the gene's mRNA transcript. (A) reverse transcriptase, DNA polymerase, restriction enzyme, DNA ligase (B) restriction enzyme, reverse transcriptase, DNA polymerase, DNA ligase (C) restriction enzyme, DNA ligase, reverse transcriptase, DNA polymerase (D) reverse transcriptase, restriction enzyme, DNA polymerase, DNA ligase (E) reverse transcriptase, DNA ligase, DNA polymerase, restriction enzyme

(A) reverse transcriptase, DNA polymerase, restriction enzyme, DNA ligase Reverse transcriptase is the enzyme used in a gene-cloning experiment (reverse transcription). DNA polymerase immediately follows after to make a second strand. The restriction enzyme then cuts the restriction site and the ligase binds it together.

Because eukaryotic genes contain introns, they cannot be translated by bacteria, which lack RNA-splicing machinery. But if you want to engineer a bacterium to produce a eukaryotic protein, you can synthesize a gene without introns. A good way to do this is to __________. (A) work backward from mRNA to make a version of the gene without introns (B) use a phage to insert the desired gene into a bacterium (C) use a nucleic acid probe to find a gene without introns (D) use a restriction enzyme to remove introns from the gene (E) alter the bacteria so that they can splice RNA

(A) work backward from mRNA to make a version of the gene without introns f you want to engineer a bacterium to produce a eukaryotic protein, you can synthesize a gene without introns through reverse transcription (mRNA => DNA).

Which of the following tools of DNA technology is incorrectly paired with its use? (A) electrophoresis—separation of DNA fragments (B) DNA ligase—cutting DNA, creating sticky ends of restriction fragments (C) DNA polymerase—polymerase chain reaction to amplify sections of DNA (D) reverse transcriptase—production of cDNA from mRNA

(B) DNA ligase—cutting DNA, creating sticky ends DNA ligase seals sticky ends together.

Which of the following sequences in double-stranded DNA is most likely to be recognized as a cutting site for a restriction enzyme? (A) AAGG TTCC (B) GGCC CCGG (C) ACCA TGGT (D) AAAA TTTT

(B) GGCC CCGG Cutting site for restriction enzymes are palindromic (same back and forth).

6. Which of the following is not true of cDNA produced using human brain tissue as the starting material? (A) It can be amplified by the polymerase chain reaction. (B) It was produced from pre-mRNA using reverse transcriptase. (C) It can be labeled and used as a probe to detect genes expressed in the brain. (D) It lacks the introns of the pre-mRNA.

(B) It was produced from pre-mRNA using reverse transcriptase. Reverse transcriptase uses mRNA to produce DNA. 1. cDNA lacks introns because of splicing. 2. Probes are used to detect genes in brain through dyes. 3. It can be amplified by PCR.

Which of the following would be considered a transgenic organism? (A) a fern grown in cell culture from a single fern root cell (B) a rat with rabbit hemoglobin genes (C) a human treated with insulin produced by E. coli bacteria (D) a bacterium that has been treated with a compound that affects the expression of many of its genes (E) All of the listed responses are correct.

(B) a rat with rabbit hemoglobin genes Transgenic organisms contain genes from other species.

All of the following are true regarding induced pluripotent stem (iPS) cells EXCEPT __________. (A) iPS cells are formed by added genes to the genome of differentiated skin cells (B) iPS cells have been demonstrated to function identically to embryonic stems cells (C) iPS cell technology may provide a more morally acceptable approach to therapeutic cloning (D) iPS cell technology could offer the potential to regenerate nonfunctional or diseased tissues and avoid the risk of transplant rejection in the diseased patient (E) the reprogramming of diseased cells in humans to form iPS cells could provide model systems for studying the origins of the disease

(B) iPS cells have been demonstrated to function identically to embryonic stems cells. iPS stem cells CANNOT do everything that ES cells can do.

A paleontologist has recovered a bit of tissue from the 400-year old preserved skin of an extinct dodo (a bird). To compare a specific region of the DNA from a sample with DNA from living birds, which of the following would be most useful for increasing the amount of dodo DNA available for testing? (A) SNP analysis (B) polymerase chain reaction (PCR) (C) electroporation (D) gel electrophoresi

(B) polymerase chain reaction (PCR) PCR amplifies DNA in order to get a large "amount" of the DNA for sequencing.

Which of the following statements best describes the process of in vitro mutagenesis? None of the listed responses is correct. (A) Primers, nucleotides, and polymerases are added to a solution of DNA fragments to make copies of the fragments. (B) Synthetic double-stranded RNA molecules matching the sequence of a particular gene are used to trigger breakdown of the gene's messenger RNA or to block its translation. (C) Specific mutations are introduced into a cloned gene, and the mutated gene is returned to the cell in such a way that it disables ("knocks out") the normal cellular copies of the same gene. (D) A solution of nucleic acid probes is added to animal embryos in order to analyze gene expression. (E) A solution of DNA fragments is placed inside a gel to separate the fragments based on size.

(C) Specific mutations are introduced into a cloned gene, and the mutated gene is returned to the cell in such a way that it disables ("knocks out") the normal cellular copies of the same gene. "in vitro" = in the cell. In in vitro mutagenesis, mutations are introduced in a cloned gene => placed "in cell" to see phenotype. Genes can be disabled in this way. (A) PCR (B) RNAi (D) DNA Microarray (E) Gel electrophoresis

In the polymerase chain reaction (PCR) technique, a heating phase and a cooling phase alternate. An original sample of DNA would have to pass through how many total rounds of heating and cooling before a sample is increased eight times in quantity? (A) Six (B) Four (C) Three (D) Eight (E) Two

(C) Three The amount of DNA doubles with each round. After one round, there is twice as much as was originally present. After two rounds, four times as much. After three rounds, eight times as much would be present.

Plants are more readily manipulated by genetic engineering than are animals because (A) plant genes do not contain introns. (B) more vectors are available for transferring recombinant DNA into plant cells. (C) a somatic plant cell can often give rise to a complete plant. (D) plant cells have larger nuclei.

(C) a somatic plant cell can often give rise to a complete plant. It is easier to manipulate a plant than an animal because a plant can de-differentiate and give rise to different types of plant.

DNA technology has many medical applications. Which of the following is not done routinely at present? (A) production of hormones for treating diabetes and dwarfism (B) analysis of gene expression for more informed cancer treatments (C) gene editing by the CRISPR-Cas9 system in viable human embryos to correct genetic diseases (D) prenatal identification of genetic disease alleles

(C) gene editing by the CRISPR-Cas9 system in viable human embryos to correct genetic diseases ???

In genetic engineering, the highly active plasmid from Agrobacterium tumefaciens is used to __________. (A) locate specific genes on animal chromosomes (B) detect and correct mistakes in DNA replication (C) insert genes of interest into plant chromosomes (D) cut DNA at a specific base sequence (E) All of the listed responses are correct.

(C) insert genes of interest into plant chromosomes Bacterial plasmids for usually vectors for moving genes into plants.

DNA fingerprints used as evidence in a murder trial look something like supermarket bar codes. The pattern of bars in a DNA fingerprint shows __________. (A) the presence of dominant or recessive alleles for particular traits (B) the order of bases in a particular gene (C) the presence of various-sized fragments of DNA (D) the order of genes along particular chromosomes (E) the exact location of a specific gene in a genomic library

(C) the presence of various-sized fragments of DNA All humans have the same genome, but individuals have varying genetic markers that can be visually recognizable (like the size of fragment in DNA).

Therapeutic cloning refers to __________. (A) cloning animals to obtain organs that could be used for transplantation into humans (B) All of the listed responses are correct. (C) the use of cloned embryos as a source of stem cells that could be used to treat disease (D) treating a genetic disease by obtaining cells from an individual with the disease, introducing genes into the cells in order to repair the genetic defect, and then reintroducing the cells back into the individual (E) treating patients with therapeutic proteins made using recombinant DNA technology

(C) the use of cloned embryos as a source of stem cells that could be used to treat disease

Human nerve cells differ from human muscle cells because different sets of genes are expressed; in each type of cell, different genes are transcribed into mRNA and translated into protein. Which of the following techniques would be the most efficient way to identify the genes that these cells express? (A) gel electrophoresis of DNA fragments (B) production of expression vectors (C) PCR (D) DNA microarray assay (E) isolating and analyzing all the proteins from each type of tissue

(D) DNA microarray assay DNA microarray assays allow all different kinds of mRNA tested for specific genes.

In DNA technology, the term vector can refer to (A) the enzyme that cuts DNA into restriction fragments. (B) the sticky end of a DNA fragment. (C) a SNP marker. (D) a plasmid used to transfer DNA into a living cell

(D) a plasmid used to transfer DNA into a living cell A bacterial plasmid is used as a cloning vector because it is easy to manipulate and reproduces quickly.

What two enzymes are needed to produce recombinant DNA? (A) a restriction enzyme and a polymerase (B) a polymerase and a topoisomerase (C) a polymerase and a ligase (D) a restriction enzyme and a ligase (E) a restriction enzyme and a topoisomerase

(D) a restriction enzyme and a ligase The restriction enzyme will cut the foreign DNA at the restriction sites, and use DNA ligase to seal the ends together. Polymerase is not used in synthesizing a new second strand.

Gene cloning is crucial to any application involving one gene because __________. (A) genes occupy only a small proportion of the chromosomal DNA in eukaryotes, the rest being noncoding nucleotide sequences (B) it provides a means to produce large quantities of its protein product (C) naturally occurring DNA molecules are very long and contain many genes (D) it provides a means to produce many copies of a gene in a short period of time (E) All of the listed responses are correct.

(E) All of the listed response are correct. Since a typical gene is usually a very small part of the total DNA, scientists use "gene cloning" to AMPLIFY specific genes, for recombinant applications, and as a mean to generate large quantities of protein products.

The process that uses nucleic acid probes to study gene expression in intact organisms is called __________. (A) DNA cloning (B) PCR (C) DNA microarray assay (D) reverse transcriptase-polymerase chain (E) dideoxy chain termination method (F) in situ hybridization

(F) in situ hybridization Probes are attached to fluorescent dyes => when binded to complementary mRNA in tissue, research can identify location of specific gene.

single nucleotide polymorphisms (SNPs)

- small nucleotide differences among indiv. located in coding and nc sequences - are single base-pair variations in genomes - are genetic markets used to study genetic basis for disease - can be the molecular basis for diff. alleles

restriction sites

Specific site where a restriction enzyme cuts the DNA

gene of interest

a gene for a desired trait; the one being added to a plasmid.

genetic marker

a particular nucleotide sequence at a particular locus whose inheritance can be followed

polymerase chain reaction (PCR)

a technique for amplifying DNA in vitro by incubating with special primers, DNA polymerase molecules, and nucleotides

CRISPR-Cas9 system

a technique for editing genes in living cells, involving a bacterial protein called Cas9 associated with a guide RNA complementary to a gene sequence of interest

nuclear transplantation

a technique in which the nucleus of one cell is placed into another cell that already has a nucleus or in which the nucleus has been previously destroyed can support normal development of the egg

in situ hybridization

a technique where nucleic acid probes are attached to fluorescent light when probes bind to complementary mRNA => research can identify which sp. gene

iPS cells

a type of pluripotent stem cell that can treat differentiated cells to act like ES cells

progenitor cells

adult tissue specific stem cells

genetic profile

an individual's unique set of genetic markers

transgenic

animals are made by introducing genes from one species into the genome of another animal expresses a foreign gene that was added to the zygote

nuclear acid hybridization

base pairing between gene and complementary sequence

pluripotent

cell that can become many types of cells

totipotent

cells that can generate a complete new organism

expression vectors

cloning vector that contains a highly active bacterial promoter

cDNA

complementary DNA

cDNAs

complementary DNA; double-stranded DNA copies of all the mRNAs in a cell reverse transcriptase from retroviruses can be used to make cDNA out of mRNA

bioinformatics

computer and math models to integrated large data sets

induced pluripotent

differentiated adult stem cells that have been reprogrammed to act pluripotent

electroporation

electrical pulse to create temporary holes in plasma membranes

restriction enzymes

enzymes that cut DNA at specific sequences

restriction fragments

fragments of DNA that result from the cuts made by restriction enzymes contains sticky ends that other base pairs can bind to

microinjection

injects DNA into cells using microscopically thin needles

DNA technology

methods used to study and/or manipulate DNA, including recombinant DNA technology

recombinant DNA molecules

molecule that contains DNA with 2 different sources

in vitro mutagenesis

mutations are introduced in cloned gene => placed into cell to study changes in phenotype

short tandem repeats (STRs)

occurs when a pattern of two or more nucleotides are repeated and the repeated sequences

nanopore sequencing

passing a single strand of DNA through an electrically charged pore

cloning vectors

plasmids used to clone a foreign gene

genetic engineering

process of making changes in the DNA code of living organisms can be done by bacterial restriction enzymes

organismal cloning

produces organisms that are genetically identical to parent donor cell

RT-PCR

reverse transcriptase polymerase chain reaction a technique in which RNA is first converted to cDNA by the use of the enzyme reverse transcriptase, then the cDNA is amplified by the polymerase chain reaction

RNA interference (RNai)

synthetic ds RNA molecules match mRNA sequence of interest breaks down or block gene's mRNA

genome-wide association studies

test that tracks SNP patterns among individuals who share a particular trait or disorder

nucleic acid probe

the complementary molecule ( a short, single-stranded nucleic acid) that can be either RNA or DNA

DNA sequencing

the process of determining the precise order of nucleotides within a DNA molecule can search for disease-causing mutation

gene cloning

the production of multiple identical copies of a gene-carrying piece of DNA

gel electrophoresis

the separation of nucleic acids or proteins on size or other physical properties measures their rate of movement through an electrical field in a gel

sticky ends

the uneven ends of a double-stranded DNA molecule that has been cut with a restriction enzyme used to complementary bind to other sequences

gene therapy

transplantation of normal genes into cells in place of missing or defective ones in order to correct genetic disorders

stem cells

unspecialized cell that can reproduce itself indefinitely in certain conditions, it can differentiate to specialized cells

RNA sequencing (RNA-seq)

used to determine gene expression in different samples can screen all genes at once, not just GOI => is the entire sequence of protein producing section of genome

chemical poration

uses a chemical that weakens plasma membrane

DNA microarrays

wells that contain identical copies of DNA fragments that carry a specific gene; compares patterns of gene expression in thousands of genes in different tissues/times under diff. conditions