Best of Chapter 12 HW

The sticky end of the DNA restriction fragment shown here will pair with a DNA restriction fragment with the sticky end _____.

-ACGT

Which of the following would be considered a transgenic organism?

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

In gel electrophoresis DNA molecules migrate from _____ to _____ ends of the gel.

negative ... positive (An electrical current is generated across the gel, and DNA molecules migrate from the negative end toward the positive end.)

The production of genetically identical animals that are carrying recombinant human genes for pharmaceutical purposes, for example using goats to produce antithrombin, is called a __________.

pharm (This word is a combination of pharmaceutical and farming, or basically a pharmaceutical factory of "pharm" animals that produce otherwise rare biological substances for medical use)

Bacteria lack RNA-splicing machinery, which means they are unable to splice out introns from eukaryotic genes. To engineer a bacterium to produce a eukaryotic protein, it is necessary to synthesize a gene without introns. If you know the nucleotide sequence, you can _____.

work backward from mRNA to make a version of the gene without introns (Reverse transcriptase can be used to make cDNA copies of mRNA)

DNA fragment A consists of _____ base pairs.

1,268

DNA fragment B consists of _____ base pairs.

1,405

The gene density for each organism is shown in the last column of this data table. Use the table to identify three statements that are true regarding the genomes of organisms. -More complex organisms (e.g., vertebrates) generally have larger genome sizes -An organism's number of genes is not a good predictor of its gene density. -Humans have a smaller genome size than yeast. -More complex organisms (e.g., vertebrates) generally have lower gene densities than less complex organisms (e.g., bacteria). -A genome size of 2 billion base pairs is the same as a genome size of 200 Mb

-An organism's number of genes is not a good predictor of its gene density. -More complex organisms (e.g., vertebrates) generally have larger genome sizes. -More complex organisms (e.g., vertebrates) generally have lower gene densities than less complex organisms (e.g., bacteria). (Less complex organisms typically have smaller, more compact genomes and higher gene densities, whereas more complex organisms tend to have larger, but less compact, genomes and lower gene densities.)

Next, can you identify what the source is trying to accomplish by providing this information? As you read the post, think about what the writer's agenda might be with regard to GMOs. What seems to be the main purpose of the blog post?

to convince the public that genetic engineering is not the solution to citrus greening

Finally, how can you use your assessment of the authority, motivation, and reliability of the information to evaluate this web site relative to other sources? Use the scales below to assign a numerical score to this source. Assign a numerical score for each category. Then add up the total score. (The highest possible score is 6; the lowest is 0.) In what range does this source fall?

2 to 4

Open the site in your browser and skim the article. Think about whether you believe the information presented or whether you have doubts about some of it. On a scale of 0 to 6, where 6 is the most trustworthy, how would you rate this site? (Note that all responses will be marked as "correct" at this point.)

2-4 (somewhat trustworthy; want to check some things)

In this example the marker DNA includes fragments that have 23,130, 9,416, 6,557, 4,361, 2,322, 2,027, and 564 base pairs. Approximately how many base pairs are in the DNA fragment indicated by the letter A?

6,557

When comparing genomes from different species, scientists are often interested in the genome density, or the number of genes per number of nucleotides in the genome. Genome density can be calculated from the size of the genome and the number of genes. What is the gene density of the human genome? Calculate your answer in genes per Mb (mega base pairs, or 1 million base pairs).

7 (To calculate gene density as genes per Mb, convert the human genome size of 3.0 billion base pairs to Mb (3,000). Next, divide the number of human genes (21,000) by the genome size in Mb. Dividing 21,000 by 3,000 reveals the human gene density to be 7 genes per Mb.)

DNA Profiling - Question 4:If I cut a piece of DNA into one long and two short pieces, which of the following gels shows how it would look? A B C D E

A

DNA Profiling - Question 3:I've accidentally hooked up the wires to this gel electrophoresis chamber backwards, with the positive pole at the top and the negative pole at the bottom. If I turn on the power with it hooked up this way, what will happen to the DNA? A. the DNA will move up the gel B. the DNA will move in a circle C. it will move down the gel as normal D. nothing, the DNA will move down the gel but twice as fast

A. the DNA will move up the gel

This is a DNA fingerprint exhibiting samples from a victim, two suspects, and the crime scene. Which of these DNA fragments is common to both the victim and Suspect 1?

B (A visual comparison of the gel electrophoresis results should reveal that Suspect 1 has a DNA fragment that matches victim DNA fragment B.)

DNA Profiling - Question 1:This model represents a DNA nucleotide. Which part of a DNA nucleotide contains a negative charge? A. base B. phosphate C. sugar D. double helix E. polynucleotide

B. phosphate

DNA Profiling - Question 5:In this gel, the DNA from the crime scene is loaded into the left-most lane. The DNA from suspect 1 is loaded into the middle lane. And DNA from suspect 2 is loaded into the right lane. What can you conclude from these DNA profiles? A. the profile from suspect 1 matches the crime scene B. the profile from suspect 2 matches the crime scene C. the profiles from suspects 1 and 2 both match the crime scene D. neither profile matches the crime scene E. you cannot conclude anything

B. the profile from suspect 2 matches the crime scene

This is a DNA fingerprint exhibiting samples from a victim, two suspects, and the crime scene. Which of these DNA fragments is common to both the victim and Suspect 2?

C (A visual comparison of the gel electrophoresis results should reveal that Suspect 2 has a DNA fragment that matches victim DNA fragment C.)

DNA moves through a gel toward the positive electrode when an electric charge is applied. What property of DNA allows this movement or migration to occur?

DNA has a negative charge. (The phosphate groups give DNA a negative charge. Thus, negatively charged molecules flow through the gel toward the positive pole, allowing for separation of the fragments to occur.)

Which of these DNA molecules is the shortest?

E (The shorter the DNA molecule, the farther it moves.)

DNA Profiling - Question 2:This machine is used to create a large sample of DNA for testing from a small sample of DNA. What is that method called? A. DNA fingerprinting B. gel electrophoresis C. RFLP analysis D. DNA profiling E. PCR

E. PCR

Most scientists describe biodiversity in terms of the number of species that have been discovered and described in scientific journals. Roughly 1.8 million species have been described, although most scientists think there could be as many as 50 million species or more currently living on Earth. However, in the video, Craig Venter seems more interested in the total number of discovered genes (he gives a total number of 20 million genes in the video) than the total number of discovered species. Why is that?

For recombinant DNA technology or for the creation of synthetic life, only the gene that produces a particular desired product is needed, and not the entire organism that carried the gene.

If a biochemist were searching for the nucleic acid sequence CTAGTTATG, what sequence would the biochemist use to make a nucleic acid probe?

GATCAATAC (This is the nucleic acid probe sequence that would locate CTAGTTATG.)

Which of these genes codes for a protein that plays a role in growth?

GH1 ("GH" stands for growth hormone.)

Which of the following describes gene cloning?

Gene cloning occurs when a bacterium carrying a recombinant plasmid reproduces, thus allowing for the production of multiple copies of the recombinant plasmid.

The ........................... was a massive scientific undertaking meant to identify and sequence all of the genes found In a human cell. This is just one example of ..................., the branch of biology that studies whole................., which are the complete sets of DNA found within organisms. One of the interesting conclusions from this project was that only about 1.5% of human DNA encodes for ................ Although it was groundbreaking for its time, it is now fairly routine to completely sequence the DNA of an organism using the ...................... In this method, the DNA is chopped up with restriction enzymes, the fragments are sequenced, and then they are reassembled into one continuous sequence. Through such analyses, scientists are learning much about human DNA and its relation to other species.

Human Genome Project, genomics, genomes, proteins, whole-genome shotgun method

Which of these genes codes for a protein that plays a role in white blood cell function?

MPO

How was the hepatitis B vaccine produced?

Microorganisms were genetically engineered to produce hepatitis B proteins. (These proteins were then used as a vaccine.)

Which of the following accurately describes the relationship between modern humans (Homo sapiens) and Neanderthals?

Neanderthals productively interbred with Homo sapiens populations that had left Africa. (Present-day humans of European and Asian descent possess genes derived from Neanderthals.)

Which of the following accurately describes "next generation sequencing" technology?

Numerous short DNA fragments are rapidly and simultaneously sequenced.

How can you know if the information is based on scientifically collected data and if it's corroborated by other sources? Look more closely around the web page. Click the "serious risks" link in the fourth paragraph; then click the "scientific review" link in the sixth paragraph. What do you find when you click these two links?

One links to another page on the CFS web site, and one links to a paper in a peer-reviewed journal.

Now, search for information on GMOs on at least two other web sites, including the United States Department of Agriculture (USDA.gov) and the World Health Organization (WHO.int). Is the information provided by these sites consistent with what you found on the CFS web site?

Other sites discuss both the risks and benefits associated with GMOs.

How can you know if the person or organization providing the information has the credentials and knowledge to speak on this topic? One clue is the type of web site it is--the domain name ".org" tells you that this site is run by a nonprofit organization. Now scan the post to find the name and credentials of the person who wrote it. What is the affiliation of the writer?

She is on staff at the Center for Food Safety (CFS).

Which of the following suspects matches the samples taken from the crime scene?

Suspect 2

Why is Suspect 1 considered more likely to have committed the crime than Suspect 2?

The crime scene sample contains DNA fragments from both the victim and Suspect 1. (Such a good match between crime scene DNA fragments and Suspect 1 DNA fragments strongly suggest that Suspect 1 committed the crime.)

A new treatment for cystic fibrosis (CF) is currently being tested. The treatment is sprayed into the noses of patients with CF. The spray contains a genetically engineered adenovirus that carries a (CFTR) gene, which codes for a normal protein involved in the function of chlorine channels. Cells that harbor the adenovirus express the gene, and patients experience relief from the debilitating respiratory symptoms of CF. What is the significant drawback of this treatment?

The treatment would only last until the epithelial cells lining the nasal cavity and lungs are shed. (Because the gene is being delivered into a somatic cell, it is a transient procedure that produces proteins only until the epithelial cells are replaced by the body.)

Which of the following statements best describes the DNA "watermarks" that Venter suggests adding to all lab-created organisms?

The watermarks can be used for tracing any descendants of the lab-created organisms.

Scientists like Craig Venter could choose to try to make any type of synthetic organism, from a bacterium to a mammal, but there are many things to consider when choosing a type of organism for research. Which of the following is a potential reason for choosing to create a type of organism other than a synthetic bacterium?

There is always a chance that a microscopic bacterium could escape undetected from the lab, and end up in the environment.

Genetically modified organisms include microbes used in biotechnology that possess enzymes promoting antibiotic resistance. This could be a problem given the rise of antibiotic-resistant organisms. However, these engineered microorganisms do not pose a risk to public health. What do you think prevents them from spreading antibiotic resistance to pathogens outside the laboratory?

These microbes have been designed so that conditions outside the laboratory would be unfavorable to their survival. (The microbes used for recombinant DNA technology have been engineered in such a way that they cannot survive outside of the laboratory. This means they are unable to spread antibiotic resistance to other organisms)

In which of the following ways are sticky ends and nucleic acid probes alike?

They both undergo complementary base pairing. (Both have unpaired nucleotides that can bind to their complement.)

In traditional recombinant DNA technology, a desirable gene from one organism is inserted into the DNA of a host organism. However, to create a synthetic life form, Craig Venter's team actually builds the entire DNA molecule from individual DNA nucleotides. Why would it be harder to create a synthetic life form than to use recombinant DNA technology?

To create a synthetic life form, you would need to understand the role of every gene, and make sure all of the genes were included that are necessary for the organism to survive.

What would be an advantage to creating a synthetic organism, as compared to creating a genetically modified organism through recombinant DNA technology?

When creating a synthetic organism, you can more easily control the genes present in that organism, and make sure the organism cannot survive out in the environment.

When is PCR particularly applicable?

When there are small quantities of DNA to analyze (PCR is used to amplify DNA.)

The recombinant molecule below was generated using which two enzymes?

a restriction enzyme and a ligase (Recombinant DNA technology involves combining genes from two sources, such as different species, into a single chromosome or individual. Restriction enzymes cut the segments, and ligase seals the pieces in place.)

In this example the marker DNA includes fragments that have 23,130, 9,416, 6,557, 4,361, 2,322, 2,027, and 564 base pairs. Approximately how many base pairs are in the DNA fragment indicated by the letter B?

between 6,557 and 4,361 base pairs

Sequencing the human genome required a number of steps. Which of the following is the correct sequence of stages for the whole genome shotgun method?

cleavage of DNA into smaller fragments, DNA sequencing, reassembly of complete sequence

Which of the following have NOT already been done by scientists? -genetic engineering to create sheep that produce pharmaceuticals in their milk-fertilization of a human egg in a petri dish, called in vitro fertilization -cloning of a dinosaur from genes found in the blood of a fossil mosquito -gene therapy that uses a virus to deliver healthy genes into the cells of sick patients -cloning of mammals, such as sheep, cows, horses, and dogs

cloning of a dinosaur from genes found in the blood of a fossil mosquito

In the CRISPR-Cas9 system, the Cas9 protein __________.

cuts double-stranded DNA (he Cas9 protein is similar to a restriction enzyme in this regard. However, while a given restriction enzyme recognizes only one particular DNA sequence, the Cas9 protein will cut any sequence to which it is directed by a molecule of RNA.)

Which of these genes are located on the q arm of chromosome 17?

gastrin and GH1 (The q arm is the long arm of a chromosome.)

In a PCR reaction, the strands of DNA are first separated by ___.

heating (Heat separates the DNA strands.)

The RP13 gene of chromosome 17 codes for a protein _____.

involved in eye development (The RP13 gene codes for a protein that plays a role in eye development.)

The TP53 gene of chromosome 17 codes for a protein _____.

involved in the regulation of the cell cycle

To date, the "easy" part of gene therapy has been _____

isolating and cloning the normal gene (Many technical questions are posed by gene therapy, such as how the proper genetic control mechanisms can be made to operate on the transferred gene and how to assess the safety of potential vectors.)

The gene that codes for gastrin is located on the _____ of chromosome 17.

q arm (The gene that codes for gastrin is located on the long arm of chromosome 17.)

What is the correct sequence of events that occur in a PCR reaction?

separation of DNA strands; addition of primers; use of DNA polymerase to produce second strand of DNA

To identify an individual involved in a crime, criminologists analyze DNA from a suspect's blood and compare the __________ to samples found at the crime scene.

short tandem repeat DNA profile (Using a subset or a full set of 13 predetermined short tandem repeat sites (CODIS), criminologists are able to place individuals at crime scenes.)

The unpaired nucleotides produced by the action of restriction enzymes are referred to as _____.

sticky ends (They are called sticky ends since they will "stick" to a complementary single-stranded sequence.)

The science of proteomics __________.

studies when and where proteins are produced in an organism and how the proteins interact (Because proteins, not genes, carry out the activities of a cell, scientists are very interested in when and where proteins are created and their specific functions and interactions.)

DNA polymerase is a heat-sensitive enzyme. What is one thing that would need to be considered concerning the activity of this enzyme in PCR when the temperature is heated during each cycle to separate the DNA strands?

that the DNA polymerase could be denatured

In the video, Craig Venter says, "We are trying to understand basic life, by learning how to now write the genetic code. So we start with the digital code in the computer, and four bottles of chemicals, and we actually build the DNA molecule from scratch." What chemicals are in those four bottles?

the four types of nucleotides (A, T, C, and G) that are the building blocks of DNA