BIOL 112 Lecture Notes - Lecture 10: Tata-Binding Protein, Tata Box, Caat Box

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BIOL 112 Full Course Notes

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Almost all of the cells in your body have the same genes because they were generated from a single cell by mitosis, which of course produces cells that are clones. Yet the cells in different tissues are very different. The reason is that different types of cells express different genes. Your blood cells make hemoglobin which makes them red. Your skin cells don"t, so your skin is not red. Some skin cells produce melanin, the pigment that gives your skin color. However, very few other tissues do, hence the observation that we are all the same color on the inside. Of course, there are genes that all cells must express that are necessary for basic functions of metabolism, transcription etc. These are often referred to as housekeeping genes. In addition to these are the genes that must be expressed to make a liver cell a liver cell, blood cells blood cells etc.

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5. Alpha amanitin is a drug that binds RNA polymerase andprevents it from functioning in the cell (this is the compound thatis found in poison mushrooms). The reason people die when theyconsume alpha amanitin is:

a) Alpha amanitin prevents gene expression from occurring in thecell

b) DNA replication is directly inhibited by alpha amantin

c) Alpha amanitin binds tightly to the messenger RNAs that aremade in the cell, preventing translation

d) Alpha amanitin binds to nuclear pores preventing thetransport of messenger RNA into the cytoplasm

6. In order for transcriptional initiation to begin in E. colithe following elements are needed:

a) an origin and RNA polymerase

b) initiator protein and a promoter

c) the sigma subunit of RNA polymerase and an RNA template

d) RNA polymerase and a promoter

e) helicase and primase

Questions 7 and 8. You are studying two species of closelyrelated snakes, one species lives in sandy desert area and has paletan skin and the species lives in a volcanic rock area and has darkbrown skin. You a sequence the DNA from each type of snake anddiscover a gene encoding a protein that transports pigment into theskin cells. The pigment transporter protein is responsible for skincolor. When you analyze the DNA coding sequence of the pigmenttransporter from each snake you find these two DNA sequences (hashmarks have been added to indicate the reading frame):

pale tan snake: GCG/TTG/GAC/TGC/ACC (DNA template strand)CGC/AAC/CTG/ACG/TGG (complementary strand) dark brown snake:ACG/TTG/GAC/TGC/ACC (DNA template strand) TGC/AAC/CTG/ACG/TGG(complementary strand)

7. From these sequences you conclude:

a) that the amino acid sequence of the pigment transporters forthe two proteins are almost identical

b) that the amino acid sequence of the pigment transporters forthe two proteins are very dissimilar

c) that the amino acid sequence of the pigment transporters forthe two proteins are identical

8. Since the skin color is different in each snake, you concludefrom the sequence data above that:

a) the genetic code in the skin cells in each of these snakes isdifferent

b) the DNA sequence encoding the entire gene for pigmenttransporters in these two snakes is different

c) that one of the codons in the gene for the pigmenttransporter in these two snakes is different

9. You are analyzing eukaryotic cells that have been exposed tothe radioactive uracil. In most cells the radioactive uracil isinitially localized in the nucleus and then moves from the nucleusto the cytoplasm. However, you observe that in some cells theradioactive molecules stay in the nucleus and never arrive in thecytoplasm. This is most likely a defect in:

a) the transcription of the DNA

b) the processing of the mRNA

c) the translation of the RNA

d) the labeling of the RNA

e) the replication of the DNA

10. Which of the following is true of both eukaryotic andbacterial transcription? (select all that are true)
a) Transcription factors must bind the promoter before RNApolymerase initiates transcription

b) Messenger RNAs must be spliced before translation begins inorder to produce the appropriate gene product

c) During transcription only one DNA strand is used as atemplate to make the messenger RNA

d) Termination of transcription occurs when the RNA polymerasetranscribes a hairpin structure in the RNA followed by a string ofU

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Question: Think about these questions, and post your thoughts on the use of cloning. Specifically, think the about the use of human cloning and discuss the potential impact on society.

Background Discussion: The scientific research terms, cloning means making exact copies of genes, a cell, or an organism. Therefore, cloning has been around for a long time. Identical twins are clones of a single zygote. When a single bacterium reproduces asexually on a petri dish, a colony of cells results, and each member of the colony is a clone of the original cell. Through biotechnology, bacteria now produce clone copies of human genes.

Through recent advances in science, it is possible to produce a clone of a mammal- and perhaps even one day, a human. The parent need not contribute sperm or egg to the process. During the so-called reproductive cloning, a nucleus (which contains the genetic material of a person) from one adult cell is placed in an enucleated egg. That egg is then allowed to develop. The developing embryo is placed in the uterus of a surrogate mother, and when birth occurs, the clone is an exact genetic copy of the original parent (of course the clone is younger). The process of cloning whole animals, and certainly humans, has not been perfected. Until it is, therapeutic cloning is more likely to become widespread.

Suppose it were possible to put the nucleus from a cell of a burn victim into an enucleated egg that is forced to become skin cells in the laboratory. These cells could be used to provide grafts of new skin that would not be rejected by the recipient. Would this be a proper use of cloning in humans?

Now, suppose parents want to produce a child free of genetic diseases. Scientists produce an embryo though in vitro fertilization, and then they clone the embryo to produce several embryos. Genetic engineering is then used to remove the genetic defect, and the defect free embryos are implanted into the uterus of a surrogate where they are allowed to grow to term. Would this be proper use of cloning in humans?

What if later scientists were able to produce children with increased intelligence or athletic abilities using the same technique? Would this be an acceptable use of cloning in humans?

Immunology worksheet help?

In people infected with human cytomegalovirus, class I MHC andb2-microglobulin are produced, but very little mature class I MHCis found at the cell surface. Inhibition of which of the followingmolecules by human cytomegalovirus may account for thisphenomenon?

A.	TAP
B.	Ii
C.	TCR
D.	CLIP
E.	RAG

Your chances of having the same MHC haplotype as your siblingare:

A.	1:2.
B.	1:4.
C.	1:16.
D.	1:8.
E.	1:1.

Which of the following is the BEST example of self-MHCrestriction of T cells?

A.	A T-cell clone is deleted when it binds too tightly to selfMHC.
B.	A T-cell clone responds more vigorously to a self-peptide thana foreign peptide.
C.	A T-cell clone recognizes foreign MHC.
D.	A T-cell clone only recognizes foreign peptides when presentedby self MHC.
E.	All of the above

MHC molecules:

A.	are conserved between individuals.
B.	bind repeating patterns found on pathogens.
C.	are recognized by T cells.
D.	are membrane-bound molecules found exclusively on T cells.
E.	are secreted by T cells and bind and neutralize antigen in theserum.

Tasmanian devils are a largely inbred population with littlediversity in the MHC. Which of the following would be a likelyoutcome of this?

A.	They would compensate for low diversity in the MHC with highdiversity in the TCR.
B.	They would compensate for low diversity in the MHC with highdiversity in the BCR.
C.	They would rely only on innate immune responses.
D.	They would be at higher risk of infection.
E.	All of the above

How many different MHC classical class I proteins does eachnucleated cell in a human heterozygous at the MHC locusexpress?

A.	Six
B.	Two
C.	Three
D.	One
E.	None. Only APC express class I.

MHC polymorphisms tend to cluster:

A.	in the peptide-binding groove.
B.	in the transmembrane domain.
C.	in the coreceptor contact residues.
D.	in the framework region.
E.	All of the above

A mutation that renders the MHC class II molecule DMnonfunctional would likely lead to:

A.	cells with no class II MHC.
B.	a deficiency in CD8⁺ T cells.
C.	cells with class II MHC only bound with CLIP.
D.	cells with class II MHC bound with a variety ofself-antigens.
E.	cells with no DO.

The human MHC locus is one of the most polymorphic regions ofthe genome. What does this mean?

A.	This region is regulated by many different mechanisms.
B.	Sequence variability is low in this region.
C.	There are many introns in this region.
D.	There are many different alleles of these genes.
E.	It has the most different genes.

10.

Which of the following is an example ofcross-presentation?

A.	An exogenous peptide being presented on MHC class II
B.	A B-cell antigen being presented to a T cell
C.	An endogenous peptide being presented on MHC class I
D.	An endogenous peptide being presented on MHC class II
E.	An exogenous peptide being presented on MHC class I

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BIOL 112 Lecture Notes - Lecture 10: Tata-Binding Protein, Tata Box, Caat Box

BIOL 112 Full Course Notes

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