Chapter 13 Biotechnology and Genomics

Noncoding DNA

(about 98% of genome)

Can GM foods make people sick?

Food and Drug Administration (FDA) must approve for human consumption

modify plants

Frost-minus bacteria can help crops to resist frost GM Bacteria endowed with genes that code for an insect toxin

__________ examines how genes are transcribed, translated, and regulated to produce a protein product. __________ compares the human genome to that of other organisms.

Functional genomics; Comparative genomics

Host is genetically engineered and is a genetically modified organism (GMO)

Can make a product it could not make before (e.g., insulin or GFP)

Genetic modification of animals could one day lead to

All of these answers correctly complete this statement.

which of these are desired ends of GM Plants

All of these are correct

Number of proteins far outnumbers the coding genes:

Alternative pre-mRNA splicing in the nucleus Posttranslational modification in the cytoplasm

Utilized polymerase chain reaction (PCR) and high-speed DNA sequencing machines.

Automation increased the speed during the project. Now modern instruments can automatically analyze up to 3 billion base pairs of DNA in a 24-hour period. Sperm DNA or white blood cells. DNA donors were of European, African, American (North and South), and Asian ancestry.

we are closely related to chimpanzees

Chimpanzees have 48 chromosomes and we have 46. In 1991, investigators showed that human chromosome 2 is a fusion of two chimpanzee chromosomes.Humans and chimpanzees have similar patterns of transposons in their genomes. The pseudogene pattern in humans is most similar to that in chimpanzees.

Genetically modified bacteria can be used to:

Clone a gene that can be isolated and used in basic research

Many other applications of PCR

Confirm a viral infection, a genetic disorder, or cancer. Screen suspects, convicted criminals and exonerate those wrongly convicted. Identify the victims of natural disasters. Identify relatives and paternity suits Useful for evolutionary studies.

Requires recombinant DNA (rDNA)

Contains DNA from 2 or more different sources

Use of GM animals in basic research

Identify SRY (sex-determining region of the Y chromosome) DNA for maleness Study human disease such as cystic fibrosis Beneficial for drug tests

Coding DNA

In protein-coding genes, only the exons are incorporated into mRNA. Only 2% of our genome consists of protein-coding exons. We have 23,000 protein-coding genes. A pseudogene is a copy of a gene that is nonfunctional because of a mutation.

gene therapy

Insertion of a foreign gene into human cells for the treatment of a disorder Ex vivo gene therapy - gene inserted into cells that have been removed and then returned to the body

Produce commercial products

Insulin, vaccine, enzyme, dye... Antifreeze protein (for making ice cream) Chymosin (rennet) from calf cells (for making cheese)

DNA Microarray Technology

It is now possible to place the entire human genome onto a single microarray

DNA Microarray Technology

It is now possible to place the entire human genome onto a single microarray.

Differences include:

Missing DNA stretches Certain genes are not expressed in chimps to the same degree in humans Genes controlling brain development

Prevent environmental pollution

Natural oil-eating bacteria clean up beaches after oil spills Remove sulfur from coal "suicide" gene self-destruction

Vector introduces genes of interest into host

Plasmid - accessory ring of DNA Restriction enzyme - cleaves the DNA DNA ligase - used to seal foreign DNA into opening created in plasmid

Unique noncoding DNA

Possible that this region codes for the regulatory small RNAs

Corn, potato, soybean, and cotton plants have been engineered to be resistant to either insect predation or widely used herbicides.

Potato plants resistant to the Colorado potato beetles Potato plants that are invulnerable to a range of blight strains.

Proteomics analyzes the proteins in human cells

Proteins have a particular structure that is suitable to their function in the cell. Each type of cell has its own mix of proteins. Use a variety of techniques including X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy to collect data Z-corporation printer builds a 3D model

which of the following is not required for the polymerase chain reaction

RNA Polymerase

Short tandem repeat (STR) profiling is now preferred for DNA fingerprinting.

STRs - DNA sequences that contain a number of base repeats, such as TCG"TCG"TCG"TCG The number of repeats is inherited and unique to the individual PCR can make copies of targeted DNA sequences that have STR repeats. STR repeats from PCR can be labeled with fluorescent color After being separated by gel electrophoresis, the fluorescent STR repeats can be detected by a detector.

Crops with other improved agricultural and food-quality traits are desirable.

Salt- , drought-, and cold-tolerant crops Na+ channel gene salt-tolerant crops Soybeans that produce mainly monounsaturated fatty acid Golden rice containing beta-carotene

Human Genome Project (HGP) (1990-2003)

Sequencing the bases in the human genome. Human genome has approximately 3.2 billion base pairs It would take you 60 years to read all the bases out loud, reading 5 bases a second for 8 hours a day!

Are GM crops environmentally safe?

Studies support safety Concerns about insecticide resistance

Proteomics

Study of the structure, function, and interaction of cellular proteins

Which of these is a true statement

The complexity of an organism does not necessarily correlate with the number of coding genes

Animals can be cloned using surrogate mothers

The desired end of reproductive cloning is an individual that is exactly like the original. Any 2n nucleus contains all the genes necessary to produce an organism. But the genes must be turned on in order for an adult cell to "start over" and overcome its present specialization.

Techniques have been developed to insert genes into the eggs of animals

Through microinjection of foreign genes into eggs or using vortex mixing Resulting offspring are GM animals

Use of GM animals in Xenotransplantation

Use of animal organs, instead of human organs, in transplant patients Pigs are being genetically modified to make their organs less likely to be rejected by the human body.

Use of GM animals in Gene pharming

Use of transgenic animals to produce pharmaceuticals Genes that code for therapeutic and diagnostic proteins are incorporated into an animal's DNA, and the proteins appear in the animal's milk

polymerase chain reaction (PCR) is used to create copies of DNA segments quickly in a test tube.

Use primers to mark the location of a DNA sequence The enzyme DNA polymerase amplifies (makes copies of) only the targeted segment. PCR is a chain reaction because the targeted DNA is repeatedly replicated as long as the process continues.

Analyzing DNA: Before the advent of PCR:

Use restriction enzymes to chop up all of an individual's DNA from one cell Each person has their own set of restriction enzyme sites, resulting a distinctive set of fragments Gel electrophoresis allows DNA fragments to move through a gel in an electric field, becoming separated according to size.

DNA microarray

Used to monitor the expression of thousands of genes simultaneously Can be used to create genetic profile

The vector most commonly used to transfer recombinant DNA into a new organism is

a plasmid

The sequence of the human genome, resulting from the 13-year efforts of the Human Genome Project, was determined using

a thermocycler for PCR and automated DNA sequencing machines.

Modern cheese production is dependent upon __________, which can be produced by transformed bacteria in lieu of being extracted from a substance found in calves' liver

chymosin

BLAST (Basic Local Alignment Search Tool)

computer program that can identify homologous genes/proteins among the sequences of various organisms Can help trace evolutionary history

Reproductive cloning requires a cell from the animal to be cloned, which is the source of a __________ nucleus, an egg with its own nucleus removed, and __________.

diploid; a surrogate mother

Proteome

entire collection of a species' proteins

during reproductive cloning a _____ is placed into a ______

enucleated egg cell , adult cell nucleus

True or False: The presence of mRNA for a protein, detected by microarray, is a quick and easy way to determine what proteins are present in a cell.

false

Gene pharming can be defined as the use of

genetically modified animals to produce pharmaceuticals.

Which choice does not correctly complete this statement: Plants have been genetically modified to

produce insecticide proteins, which increases human exposure to pesticides.

genes that code for proteins that stimulate the mitotic cell cycle

proto oncogenes

In the process of creating recombinant DNA, __________ are used to cleave DNA at specific sites to create an opening into which a piece of foreign DNA can be placed.

restriction enzymes

In order to clone a gene, __________ are used to cleave DNA and __________ is used to seal foreign DNA into the newly created opening.

restriction enzymes; DNA ligase

Proteins function in metabolism, signaling, movement, support, transport, defense, osmolarity, and regulation of gene expression, to name a few. Silk, keratin, and collagen are proteins that function in

support

Proteomics is defined as

the study of the structure and function of proteins.

"Sticky ends" are important in the gene cloning process because

they facilitate insertion of new DNA into a plasmid.

Interspersed repeats -

thought to play role in evolution of new genes

restriction enzymes found in bacterial cells are ordinarily used

to degrade viral DNA that enters the cell

True or False: Ex vivo gene therapy means that a gene is inserted into cells that have been temporarily removed from the body of the patient.

true

True or False: Proteomics is a challenging field of study because there are even more proteins than genes in the proteome in order to include protein variants with different functions.

true

The polymerase chain reaction (PCR) is

used to create copies of DNA segments quickly in a test tube.

Bioinformatics applies computer technology and statistics to the wealth of biological information stored in several online databases. What does a BLAST search look for in a database?

homologous genes, which code for the same proteins despite differences in base sequences

Introns (~ 24% of the noncoding DNA)

intervening sequences regulators of gene expression Source of small RNAs

which of these pairs is mismatched

introns --- same as eons

Gene cloning

is done to produce many identical copies of the same gene.

Bioinformatics

is the application of computer technologies to the study of biological information.

a farmer decides to clone a GM goat that produces GM product because

its more likely to produce GM goats than by breeding them

The first step in transforming an animal to make a human protein, like human growth hormone, is

microinjection of a human gene into the donor animal's egg.

A cell contains __________ because __________.

more proteins than there are protein-coding genes; of alternative pre-mRNA splicing and posttranslational modification.

The textbook includes several examples of ex vivo and in vivo gene therapy. Which of the following disorders might be treated using a gene therapy that injects a virus containing VEGF into the heart? What kind of gene therapy is this?

poor coronary circulation; in vivo

Tandem repeats

- STRs used in DNA fingerprinting

Database

- data stored in a single location and organized for easy accessibility Protein Data Bank, GenBank

in vivo gene therapy

- gene is delivered directly into the body Cystic fibrosis deliver needed gene by spraying into the nose or to the lower respiratory tract by a virus or liposomes Poor coronary circulation Genes coding for VEGF can be injected into the heart to stimulate branching of coronary blood vessels. Cancer therapy Genes are used to make healthy cells more tolerant of chemotherapy and to make tumor cells more vulnerable to chemotherapy The gene p53 brings about apoptosis

Transposons

- have ability to move within and between chromosomes

Repetitive DNA may not be just "junk".

...

What percentage of the human genome consists of protein-coding DNA, the exons left behind after mRNA is processed?

2%

Dolly the sheep

A cloned Dorset sheep, Dolly, was born in March 1997 The necessary steps to clone an animal After choosing an animal to be cloned, remove a cell to serve as the source for a 2n nucleus. Place this nucleus in an egg after its own nucleus has been removed. After development begins, place the embryo in the uterus of a surrogate mother so development will continue to term. The newborn animal will be a clone of the animal that donated the 2n nucleus.

All but one of the following examples is a beneficial application of DNA fingerprinting. Select the example that is not a beneficial application of DNA fingerprinting.

A viral infection or cancer can be treated.

Comparative genomics

Aim to compare the human genome to the genome of other organisms Offers a way to study changes in a genome over time Helps to understand evolutionary relationships

Functional genomics

Aim to understand the exact role of the genome in cells or organisms

Are GM crops really needed?

Do not result in increased yield when compared with traditional crops Prevent a loss of yield to pests during storage Allow use of less pesticides and herbicides; permit no-till farming

can be used to

Determine the difference in gene expression between different cell types Generate a person's genetic profile Identify genes associated with diseased tissues Identify links between disease and chromosome mutations Distinguish species based on genetic differences Detect cell responses to the environment

Restriction enzymes

act as molecular scissors to cleave any piece of DNA at a specific site.

repetitive DNA could

all of these are correct

What does DNA fingerprinting detect? How?

an individual's profile of STRs; using PCR, gel electrophoresis, and a fluorescence detector

Genetically modified animals with the gene for bovine growth hormone

are larger than unmodified animals.

which of these pairs is mismatched

bioinformatics-- all the genetic information present in the rganism

the use of both ex vivo and in vivo gene therapy shows that

both B AND C are correct

recombinant DNA technology is used

both b and c are correct

put the lettered phases in the correct order to form a plasmid carrying recombinant DNA

cabd