Question 10

Which of the following is not in common to both prokaryotic and eukaryotic promoters?

A.

They have consensus sequences that proteins bind in order to help RNA polymerase assemble in a transcriptional complex.

B.

They bind proteins that assist RNA polymerase assembly into the transcriptional complex.

Question 12

In the process of intrinsic transcription termination, what RNA structural features are important to the process?

A.
The stem loop that forms because of complementarity between bases making up two inverted repeat sequences in the termination sequence.

B.
The C terminal domain of RNA pol II serves as a scaffold upon which the cleavage and polyadenylation complex resides, therefore enabling efficient transcription termination.

C.
A specific sequence of bases at the 3' end of an mRNA is able to catalyze its own excision, thereby terminating transcription.

D.
The rut sequence in the mRNA that forms a structure that binds Rho protein, which causes mRNA release and transcription termination.

2 points  

Question 13

Imagine that you do this experiment: you create a synthetic gene, based on what you know about the insulin gene in humans (that is, what you know about the nature of genes in humans, i.e. eukaryotes). You create a strain of E. coli in which this synthetic gene has been inserted into the bacterial chromosome. After checking for expression of your synthetic gene, you discover that no mRNA is produced. Which of the following is a possible explanation for this observation?

A.
The gene is lacking the Shine-Delgarno sequence, therefore RNA polymerase won't be able to assemble on the promoter with any of the sigma subunits.

B.
The synthetic gene has a eukaryotic promoter that will not be recognized by any of the E. coli sigma-70 subunits, thus RNA polymerase will not bind to the promoter.

C.
The synthetic gene has a prokaryotic promoter that is missing the TATA box or GC box, thus no sigma subunit can bind and recruit RNA polymerase.

D.
TFIID and the other general transcription factors are not able to recognize a prokaryotic promoter, therefore they cannot assemble on the promoter of the synthetic gene in a bacterial cell.

2 points  

Question 14

You are studying the expression of a gene in a certain type of eukaryotic cell. Under normal conditions, you measure that the gene is expressed at a certain value. You are able to experimentally alter a nucleotide pair at position -75 relative to the transcription start site. In the altered cells, you now measure a reduced rate of gene expression, 50% the value that you measured from normal cells. What is a reasonable interpretation or hypothesis to explain this observation?

A.
You likely altered a base located in a consensus sequence of the promoter, and the general transcription factors have a lower affinity for the mutated sequence, therefore transcription initiation complexes form at a reduced rate.

B.
The mutation most likely altered a consensus sequence for sigma subunit binding, therefore the appropriate sigma subunit is less likely to bind to the sequence in the promoter to recruit RNA polII.

C.
The mutation likely created an improved binding site for TFIID and the other general transcription factors, thus they are less likely to disassemble to form a new pre-initiation complex.

D.
You likely altered a base in a sequence that RNA polymerase II requires for binding, therefore it is less able to recruit general transcription factors to the promoter to assemble the pre-initiation complex.

1. Why are clades “supported” by one or more synapomorphy? We expect the synapomorphy to be present in all the members of the clade defined by the trait – but the character might be highly modified, or present only a brief developmental stage. [Sometimes the trait is lost altogether, a situation we call being “secondarily lost”]

4. Explain the statement “all clades are subsets of larger clades”. What is the largest clade?

Which genotype will allow the bacteria to make ß-galactosidase (lacZ) in the absence of lactose? (superscripts don't work in this panopto quiz, so check the lecture slide itself)

1) O+Z+/F’O+Z+

2) O+Z-/F’OCZ+

3) O+Z+/F’OCZ-

B) 1Which genotype will allow the bacteria to make ß-galactosidase (lacZ) in the absence of lactose?

1) I+O+Z+/F’I+O+Z+

2)I-O+Z-/F’I+O+Z+

3) I+O+Z-/F’I-O+Z+

4) I-O+Z+/F’I-O+Z+

Bacterial Identification by Molecular Methods

Type your responses in blue.

Go to the Howard Hughes Medical Institute educational website and open the “Bacterial Identification Lab” (http://www.hhmi.org/biointeractive/bacterial-identification-virtual-lab). Click on "Launch Interactive." Perform the entire simulated lab exercise. Be sure to read all of the instructions and background information provided along the way. Type your answers in blue and include with your Cloning Lab Write-Up.

1. Which specific gene is used to identify the unknown bacteria?

2. How is the bacterial DNA extracted from the cells? How is the DNA separated from the cellular debris?

3. What is PCR? What is the source of the special DNA polymerase that is used in PCR (name the organism (genus and species) and its natural habitat)?

4. What is contained in the PCR Master Mix? What should happen at each of the 3 temperatures cycled: 95^o C, 60^o C and 72^o C?

5. About how many total copies of the bacterial gene should there be at the end of the 30 cycles? About how long (in base pairs) should the PCR product be?

6. Why are the fluorescent dideoxynucleotides called terminators? Why were 12 primers used in the sequencing step?

7. What is the purpose of the gel electrophoresis performed in the sequencer machine? What does BLAST stand for?

8. Use the NCBI site to compare the gene sequences and identify the genus and species of each sample. Write the organisms' names below (should be 6 different species):

Sample A (lymph aspirate)

Sample B (stool sample)

Sample C (urine sample)

Sample D (blood sample)

Sample E (sputum sample)

Sample F (stool sample)

The histone proteins of nucelosomes are often abnormally modified in cancer cells, leading to _____.

Pick blood OR lymph to fill in the following blanks. (1 point) Once T and B cells mature they circulate through the body in (a)_____________ vessels. Dendritic cells that encounter a pathogen in the tissue and became activated traffic to the draining lymph node via a (b)_____________ vessel. Once a T cell is activated in the lymph node it enters a (c)____________ vessel to travel and migrate into the infected tissue.

2. True or False: Tertiary lymphoid organs can form at mucosal sites that have a high exposure to microbes and can activate adaptive immunity. (1 point) a. True b. False

3. Macrophagesanddendriticcellsareinthetissueandnotcirculatingintheblood stream; what cell present in the blood migrates into the tissue to differentiate into macrophages and dendritic cells? (1 point) a. Basophils b. Monocytes c. Lymphocytes d. Eosinophils

4. ShortAnswer:Name and describe the shared mechanism that increases the diversity of the BCR, antibody and TCR repertoire. Outline the general sequence of events in this mechanism in either the development of antibody producing B cells or T cells that allows for the diversification of the antigen binding receptors in lymphocytes. (2 points)

5. ShortAnswer:What is the affinity hypothesis for T cell development?Briefly describe 3-4 main outcomes for T cells proposed by this model. (1 point)

6. ShortAnswer:Define central tolerance and peripheral tolerance of B cells to antigen (include location and the overall outcome of tolerance) (2 points).

7. ShortAnswer:Describe two mechanisms of B cell tolerance( include antigen type). Why are these important processes in the development of B cells? (2 points)

Genetically modified organisms are not new. According to the USDA, in 2009, 93 percent of soy, 93 percent of cotton and 86 perfect of corn grown in the United States was GMO. However, in 2010, life on earth as we currently understand it, changed. By inserting computer-designed genetic material into a bacterial cell, scientist created an entirely new strain of bacteria, a new life form, the world's first synthetic cell. In annoucing his creation, scientist Craig Venter called if the first life on earth "whose parent was a computer."

1. Do you favor the creation of GMO crops? Defend your answer.

2. Do all GMO products need to be labeled as such?

3. Are we really ready for a life form whose parent is a computer?

4. What precautions would you like to see put in place-perhaps a suicide gene implanted in these new life forms to assure us that they cannot survive outside the lab?

Scientists have been making discoveries regarding inheritance, and how that information is expressed, for almost 200 years now. Please pick 10 key individuals that have made major contributions to our understanding of the genetic basis of inheritance, and write a short summary connecting these contributions. Once you have your 10 individuals in mind, focus on how the process of science involves building on the discoveries of others

Draw the phylogenetic tree that shows that understanding of the evolutionary relationships of all invertebrates among the major phyla of metazoans. What are the major clades shown on the tree? Why are the phyla grouped together in the specific clades that you have drawn? What are the synapomorphies that define each of the clades and the different phyla within them? What sources of evidence were used to reconstruct the phylogeny that you have drawn? Are certain sources of evidence more reliable than others? Explain and provide examples. Do you think that there are someareas of the tree that seem uncertain and are likely to be revised by additional study?

In which direction do you think the pK_a of aspartate would shift when it is buried in the hydrophobic interior of a protein, and does not form an ion pair with a positively charged group? Explain in 1-2 sentences.

You notice that many Alaskan foxes and Himalayan rabbits are darker in color at the ears, nose, paws, and tail. What is most likely causing this pattern?

a) genetic patterns of inheritance b) environmental influences c) polygenic inheritance d) an autosomal disorder e) the law of segregation

Pick one of these topics related to biology, animals, environmental issues, disease, exercise or nutrition, and search the internet, finding an interesting website related to the topic.

After looking over the websites, write a summary, 200-300 words, related to the topic.

Calico cats have two genes that govern their coat color. One gene codes for the white undercoat and the other codes for the fur colors black and orange and this gene is X-linked. We will look at the gene for black and orange fur color only. In this situation, both black and orange are codominant, so that heterozygous individuals are a different phenotype.

Based on this information, what would black, orange and calico female cats' genotypes be?

What would be the genotypes for males of the same colors?

What would the male and female offspring of a male black cat and a female calico cat look like?

Is it possible for a male cat to have the calico coat pattern? Explain.

1. Cholesterol is a membrane plasticizer or a membrane buffer. Explain what are the effects of cholesterol at high and low temperatures.

2. What is the difference between integral and peripheral proteins?

3. Membrane lipids are distributed asymmetrically. Explain the concept and the reason behind this asymmetrical distribution