AP Biology : Molecular Genetics

Microarrays use single-stranded pieces of DNA of known genes, which are placed on a slide to determine whether these genes are being expressed in a particular tissue. For example, if the cells come from seedlings that are germinated and kept in the dark, the chlorophyll genes would not be active. Which of the following would you wash across the slide to determine that the chlorophyll genes are active in a plant grown in light?

(A) Single-stranded cDNA made from the mRNA transcribed from the chlorophyll genes. Genes that are active are producing mRNAs. The mRNAs of the active genes are used to make cDNA, which will bind to the single-stranded DNA on the microarray. The DNA on the chip serves as a probe and will bind to a complementary sequence of DNA, so cDNA must be made from the mRNA of the tissue. In the light, the chlorophyll genes are on, producing mRNAs, which are used to produce cDNA and washed across the chip.

In order to match the pilot's remains to the correct family using DNA profiling,

(B) Each of the 13 STR bands must match. These profiles were done using short tandem repeats as genetic markers. All 13 sites must amtch because this shows the highest degree of certainty between the pilot's DNA and the DNA from the three families. In addition, because the DNA for comparison comes from a probable twin of the pilot, it is expected that the bands would be identical for the twins of the same family.

RNA retroviruses such as HIV discharge both strands of RNA and molecules of reverse transcriptase into cells they infect. What is the purpose of the reverse transcriptase?

(B) The host cells lack enzymes that can replicate the viral genome. Reverse transcription is an enzyme that is required to produce DNA from the RNA of a retrovirus.

When a virus infects a bacterium by injecting its DNA and the genome of the virus is incorporated into the host cell, this is ______?

(B) The lysogenic cycle of a phage. In the lysogenic cycle, the phage genome becomes incorporated into the host cell's DNA without destroying the host cell. It then lurks much like a Trojan horse, waiting to receive chemical signals that would trigger its lytic cycle.

Which of the following has a DNA genome surrounded by a protein coat?

(B) Viruses. Viruses have either a DNA genome or an RNA genome surrounded by a protein coat. The answer is not A because retroviruses have an RNA genome. HIV is a retrovirus.

How many sites on DNA were cut by the particular restriction enzyme used in Sample 1 (far left)?

(C) 8. The restriction enzyme used to cut the DNA that was placed into the first well of the gel must have cut the DNA at eight sites because it produced nine DNA fragments. Linear DNA : DNA fragments produced = restriction sites cut + 1

Do the data suggest that any of these possible control elements are actual control elements?

(C) All three appear to be control elements. All three elements appear to be control elements because when they were deleted, the levels of reporter mRNA differed from the level produced by the intact enhancer construct (control). The control established the 100% mark for the experiment. The three elements are all diferent from the 100% expression of the control; therefore, all three must function as control elements.

A bacterium is infected with an experimentally constructed bacteriophage composed of the T2 phage protein coat and T4 phage DNA. The new phages produced by lysis of infected cells would have _____?

(C) T4 protein & T4 DNA. T4 Phage injects its DNA , which is used to assemble new protein coast and viral DNA.

Lateral gene transfer involves the movement of genes between members of a species without sexual reproduction. In bacteria, there are three mechanisms for this: conjugation, transformation, and transduction. Predict how these processes are most likely to affect bacteria.

(C) The bacteria's genetic diversity will be increased. Bacteria do not perform mitosis, meiosis, or sexual reproduction. However, the processes of transformation, transduction, and conjugation are processes that bacteria use to increase their genetic diversity. (review all three)

When the electric field was applied, the fragments of DNA in each of the three samples migrated to different locations along the gel. Which of the following explains the pattern shown here?

(C) The fragments differed in size. The fragments of DNA separated out from one another along the gel once the electric field was applied because they differ in size.

The most likely method by which the mutated CCR5 gene prevents AIDS is by ____?

(D) Coding for a mutant receptor protein on the cell membrane, thus not allowing the entry of the virus. In HIV, the envelope glycoprotein enables the virus to bind to specific receptors on certain white blood cells. After binding, the virus fuses with the cell's plasma membrane, entering the cell. The mutated gene CCR5 prevents binding and subsequenmt entering of the cell by HIV.

The human globin genes are located on two different chromosomes and include variants that are expressed at different times in the life cycle as well as a number of nonfunctional pseudogenes. Which of the following would best describe this gene family?

(D) Identical or similar genes have evolved by gene duplication. This is an example of a multigene family. The alpha-globin gene family is on chromosome 16, whereas the beta-globin gene family is on chromosome 11. The genes arose by duplication and translocation.

PCR allows target segments of DNA to be produced quickly by using heat to denature and separate stands of DNA, then cooling to allow primers to attach to the single strands and DNA polymerase to synthesize new stands of the target DNA by adding nucleotides to the 3; end of each primer on the two stands. Why was this process considered so important that it earned Kary Mullis a Nobel prize?

(D) It can produce multiple copies of even minute samples of DNA. PCR is a technique by which any piece of DNA can be copied many times without the use of cells.

What was the control treatment in this experiment?

(D) The construct that had no DNA deleted from the enhancer. The control treatment was the construct that had no DNA deleted from the enhancer. The top bar on the graph represents this construct. All the other treatment groups were compared to that control group.

If deletion of a control element causes a reduction in gene expression, what must be the normal role of that control element?

(D) To activate gene expression without the control element, activators are not able to bind to the enhancer, and the level of gene expression decreases. This question refers to the bottom bar on the graph, showing a reduction in reporter mRNA of over 50%. If the absence of the control element causes a reduction, its presence must active gene expression by producing activators that normally increase the level of gene expression.

Which of the following is a laboratory application of restriction enzymes?

(D) To cut DNA molecules at specific locations. Restriction enzymes can be used to cut DNA at specific locations and this enables researches to perform recombination DNA techniques.

If deletion of a control element causes an increase in gene expression, what must be the normal role of that control element?

(D) To repress gene expression; without the control element, repressors are not able to bind to the enhancer, and the level of gene expression increases. The question could refer to either the second or third bar on the graph because thye are both over 100% of the control. THe control element in both cases represses gene expression by producing a repressor protein as its normal function,. IT is important to note that control elements do not turn the volume of a gene up as high as possible but turn the volume to the proper level for the cell. Too much gene product can cause just as many problems as too little.

Which of the following shows the steps of a retroviral infection in the proper order?

(D) Virus locates host cell -> penetrates cell membrane -> viral RNA used to make DNA -> host cell produces copies of virus. In HIV infections, recall that the infectious agent is a retrovirus with RNA as the genetic material. In the cytoplasm of the host cell the viral RNA is converted to DNA, then incorporated as a provirus into the host cell's DNA. The provirus can direct the production of new viral particles.

Based on analysis of the STR sites shown, does the missing pilot belong to any of these three families?

(D) Yes, family 3 matches. Family 3 matches in all 13 sites. This is a good time to review the principles of gel electrophoresis, making sure you understand which poles onj the gel are positive and negative, how the bands are arranged by size on the gel, and the role of restriction enzymes in preparing the DNA.

Question refers to an experiment that was performed to separate linear DNA fragments from three samples radioactively labeled with 32P. The fragments were then separated using gel electrophoresis. The visualized bands are depicted as follows:

(model on page 154 of AP test prep book)

In E. colo the DNA is 24% adenine. Based on this information, what percentage of this DNA is guanine?

26%. Adenine binds to thymine, resulting in 52% of the DNA being A or T. This leaves 48% of the DNA to be cytosine or guanine, and since they are in pairs, 48% is divided by 2 to get 24%.

B: 1: - Restriction enzymes could cut out a gene of interest from another organism's DNA, along with a bacterium. - Restriction enzymes could be used to cut a plasmid, forming sticky ends - Due to the gene of interest being removed and the plasmid's now sticky ends, the gene of interest would now bind to the sticky ends, and ligase would join them together. - Researcher exposes bacterium to solution with plasmid, which would then absorb plasmids from the solution via transduction. (results in plasmids being incorperated).

2: -Recombinant bacteria could be identified by testing for phenotype (Gene for ampicillin resistance was present in the bacteria, testing could be done to see what bacteria picked up the plasmid by putting all the bacteria onto a plate with ampicillin and adding genes that produce color or glow. Bacteria that live and reproduce, and/or form colors, display plasmid absorption and inheritance of the gene.) 3: - gene of interest is being expressed the gene of interest can be inserted downstream of a promoter that can be induced when giving certain nutrients such as lactose

A linear strip of DNA has two restriction sites for the restriction enzyme EcoR1 and three restriction sites for the restriction enzyme Hind III. If the strip of DNA were incubated with the restriction enzymes and then the cut DNA were collected and run on an electrophoretic gel, how many bands would be expected on the gel?

6. Check to see if DNA is linear or circular. Draw strip of DNA, then mark cut sites, then simply count.

FRQ Stuff A : Chart : Top of circle = 10KB, Bottom = 20KB, Right = 30KB, Left = 40KB. H is on the top and bottom left, E is on the top and bottom right.

Explanation: 1. Trial and Error (beginning with one restriction point and adding to make progress) 2. Restriction site within larger fragment

(This one is really long, im sorry) The promoter of a gene includes the DNA immediately upstream of the transcription start site, but expression of the gene can also be affected by control elements. These can be thousands of base pairs upstream of the promoter, grouped in an enhancer. Because the distance and spacing of these control elements make them difficult to identify, scientists begin by deleting sections of DNA that contain possible control elements and measuring the effect on gene expression. In this question set, you will analyze data obtained from DNA deletion experiments that tested possible control elements and measuring the effect on gene expression. In this question set, you will analyze data obtained from DNA deletion experiments that tested possible control elements for the human gene mPGES-1. This gene code for an enzyme that synthesizes a type of prostaglandin, a chemical made during inflammation.

The researchers hypothesized that there were three possible control elements in an enhancer region eight to nine kilobases upstream of the mPGES-1 gene. Control elements regulate whatever gene is in the appropriate downstream location. TO test the activity of the possible elements, researchers synthesized four types of DNA molecules ("constructs"). 1. One DNA construct had an intact enhancer region. 2. One DNA construct had possible control element #1 deleted from the enhancer region. 3. One DNA construct had possible control element #2 deleted from the enhancer region. 4. One DNA construct had possible control element 3# deleted from the enhancer region.

In all constructs , the enhancer region was located upstream of a "reporter gene," a gene that would be expressed at the same time as mPGES-1 and whose mRNA product could be easily measured experimentally. The researches then introduced each DNA construct into a separate human cell culture, where the cells took up the artificial DNA molecules. After 48 hours, the amount of reporter gene mRNA made by the cells was measured. Comparing these amounts allowed the researchers to determine if any of the deletions had an effect on expression

of the reporter gene, mimicking the effect that deletions would have had on mPGES-1 gene expression. (THe mPGES-1 mRNA itself couldn't be used to measure expression levels because the cells in culture have their own mPGES-1 gene with an intact enhancer region. Therefore, the cells produced mPGES-1 mRNA regardless of which DNA construct they took up.)

Four decades after the end of the Vietnam War, the remains of an Air Force pilot were discovered and returned to the United States. A search of Air Force records identified three families to which the remains might possibly belong. Each family had a surviving twin of a missing service member. A DNA comparison was done, and the following STR profiles were obtained from the remains of the pilot and the surviving twins from the three families.

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