Biochemistry 3382A Lecture Notes - Lecture 1: Grb2, Glycogen, Alpha Helix

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OC389922

11 Jan 2015

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At first, sequencing a human genome cost a lot of money, but now it costs far less. Also, there was only one genome that was sequenced, but now there are thousands of genomes sequenced. As the years increase, the graph predicts that the cost of sequencing will decrease and the number of human genome sequenced will increase. No guess work is needed anymore in dealing with defects and disease that affect the human genome. Biochemical regulation is important to find out what went wrong in human diseases and ways to treat them. This includes the wealth of information about the determinants of disease and the challenge of interpreting the information. There are 100 hundred thousand billion cells in adults. Each cell is a factory with specialized function (blood, muscle, bone, liver, brain, kidney etc. ). Each cell is comprised of many constituents (25,000 genes, >>25,000 proteins, >4,000 known reactions). Regulation is essential for survival and diseases arise from loss of regulation.

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You decide to identify the CFTR mutation by analyzing the genomic DNA of your patients compared to healthy individuals. You specifically are looking to see whether a specific 3' gene truncation has occurred in the patients. You will determine this using hybridization techniques with samples from healthy and CF patients. Which of the following will allow you to accomplish this?

	Using an RNA probe complementary to the region not removed by the truncation.
	Using an RNA probe complementary to the region removed by the truncation.
	Using an DNA probe complementary to the region not removed by the truncation.
	Using an DNA probe complementary to the region removed by the truncation.

To conduct the hybridization experiment, you are trying to decide between using a DNA or RNA probe. Which would be ideal to use and why?

	As both are composed of nucleic acids, using either would result in identical results.
	An RNA probe because RNA has uracil bases.
	An RNA probe because it could also be used in a translation experiment.
	A DNA probe because it is more stable than RNA.
	A DNA probe because RNA cannot bind to DNA.

Imagine Hershey/Chase had used an RNA virus (genome composed of RNA) instead of a DNA virus in their experiment. Would radioactivity still have been found in the pellet?

	No, because only DNA can be labeled with radioactivity.
	No, because the RNA genome would not enter the bacteria upon infection.
	No, because while DNA and RNA nucleotides are similar, they are not identical.
	Yes, because DNA and RNA nucleotides are similar.
	Yes, because genome in any form (DNA, RNA, protein) would be labeled similarly.

The human genome consists mostly of non-coding DNA. Which of the following are benefits of this?

	Random DNA mutations generally won't affect RNA and protein function.
	It is faster to duplicate the genome when these are present.
	The existence of introns can lead to multiple variations of proteins encoded by a single gene.
	It is unlikely transposons would exist in the genome if there was too much protein coding DNA.

You accidentally add a mutant dNTP (which has an H instead of an OH connected to the 3â carbon) to a reaction where DNA is being replicated. Which of the following is true of this mutant dNTP?

	It can be incorporated into DNA strand but cannot form a phosphodiester bond with an incoming wild type dNTP
	It can be incorporated into a DNA strand but cannot base pair with a complementary nucleotide
	It can be incorporated into a DNA strand and can form a phosphodiester bond with an incoming dNTP, but only if it is another mutant dNTP
	It cannot be incorporated into a DNA strand.

Andrew Murray's sister, Andrea, is adding to her brother's work on chromosomes. She is using cells that are unable to synthesize adenine (âade) and histidine (âhis). The plasmid she is currently working with consists of an origin of replication and the Ade gene.

Following her transformation of the plasmid into her yeast, what media will the cells be plated on to select for cells that have picked up the plasmid?

	Media containing histidine
	Media containing adenine
	Media lacking adenine
	Media lacking histidine

She starts by attempting to add the centromere DNA into a plasmid containing the origin of replication. Unfortunately, when adding the centromere sequence, the origin of replication is removed, thus leaving a plasmid with only a centromere and selection marker. Following plasmid transformation, what growth result will she see on her plates?

	No colonies
	Little colonies
	Big colonies

She fixes the mistakes from the previous experiment and now has a complete plasmid (selection marker, origin of replication, centromere). She then inserts telomere sequences into the plasmid. How will this impact her transformation?

	It will not impact her transformation
	Her transformation will no longer work because plasmids donât require telomeres
	She will now see much larger colonies
	She will now see fewer but larger colonies
	She will now see smaller colonies

In the Meselson/Stahl experiment, E. coli were first grown in media containing heavy nitrogen, 15N, and then transferred to light nitrogen, 14N, at the beginning of the experiment.

Imagine that their data showed that replication occurs in a conservative manner instead of semi-conservative. What fraction of the DNA helices will consist of mixed DNA after 4 rounds of replication in this case?

	None
	More than 75%
	25-50%
	51-75%
	Less than 25%

peachmarten804

For years we have been able to analyze the fossils of extincthumans like those of Neanderthals. Their bones gave us clues to howthey looked, how they lived, and how they might be related to us.In the last few years, we have been able to get a better view intothese extinct species and their relationship to our species. Thanksto next generation genomic sequencing technologies, we have beenable to obtain genetic data on Neanderthals, Denisovans and othersthat have allowed us to make direct comparisons between our speciesand theirs. In addition, we have been able to observe the presenceof DNA from these extinct species within our own genomes which tellus that we had kids with these now extinct humans.

If we take Neanderthal DNA as an example, we find that we share99.5 percent of our DNA with them. Which means that we andNeanderthals were separated from each other for more than 500,000years. This also means that we were genetically similar enough tobe able to have offspring with each other. We see evidence of thisgenetic introgression between us and Neanderthals when we look atour DNA. Interestingly, if we obtain one thousand DNA samples fromGrossmont College students, we estimate that we would be able toextract at least 20% of the Neanderthal genome from them. Thismeans that 20% of our collective nucleotide sequences are sharedwith Neanderthals but this doesnât mean that 20% of our genes areNeanderthal specific genes. Of the twenty-one thousand genes thatNeanderthals had, only a few dozen of their genes survive withinour genome. The same holds true for Denisovans. What is moreinteresting is that older versions of ourselves have a tendency tohave higher levels of DNA from extinct humans compared toourselves. In other words, over the course of thousands of years wehave been slowly weeding out the DNA of the other humans from ourgenome in favor of our genes.

One basic question that we might like to ask is why have we beenlosing Neanderthal and Denisovan genes over time? Also, why do westill have a significant amount of DNA segments that donât seem tobe going anywhere? The answer to this has to do with selection.

The answer to the first part of the question has to do with thefact that we were not fully genetically compatible with the otherhuman species to begin with. Basically, to have had Neanderthal orDenisovan genes in the past meant that an individual's level offitness was reduced. To get rid of their genes in favor of our ownwould mean that the relative fitness of individuals would increaseovertime.

The answer to the second question has to do with the fact thatDNA segments from Neanderthals and Denisovans that did not code forproteins remained because there was little selective pressureagainst them. As far as genes are concerned, the only Neanderthaland Denisovan genes that remain only exist because they had aselective advantage or at least have been neutral to ourspecies.

DNA segments that that were neutral or that had a selectiveadvantage, whether genes or not, simply remained because they wereadvantages or there was little selective pressure against them.

Your task for this week is to look for information about oneNeanderthal or Denisovan gene that survive within our species andto tell me what function that gene has and how that gene mayincrease the fitness of modern human populations.

In your post, discussONE Neanderthal orDenisovan gene that is currently found within our species.
- Tell us about the gene and its function. Explain what it doesfor us. (Make sure you give a citation.)
- Explain in your own words any possible advantages that yourNeanderthal or Denisovan gene might have. Make sure you give ininformed opinion that is grounded in your research.

azurecrow764

Read the following passage focusing your attention on the scientific procedures and scientific abilities illustrated in it. Think about what types of experiments (observation, testing or application) are described. Identify the hypothesis, predictions, outcomes of experiments and assumptions that appear in the passage. The standard explanation of how humans originally acquired AIDS is that HIV (human immunodeficiency virus) originally was transmitted to humans from monkeys or apes carrying SIV, simian immunodeficiency virus. How could the transmission have occurred? Several similar hypotheses involve an African hunter coming in contact with monkey blood. For example this could have occurred when a hunter butchering a monkey, got some of its blood in a cut, or when a human ate undercooked monkey meat, or when a monkey bit a human. Depending on one's assessment of the genetic diversity of HIV over time, this transmission might have occurred only a few decades ago or, alternatively, hundreds or thousands of years ago. If the latter is correct then AIDS could have been restricted to remote African villages until recent decades when trade and international travel led to the current pandemic. There are however other alternative explanations for the spread of AIDS. One of them is that AIDS arose from contaminated polio vaccines used in Africa from 1957-59. Why is this a plausible explanation? Polio vaccines are cultured on apesâ kidneys, so contamination of a batch of vaccine by an SIV is a possibility. There is a precedent: in the 1950s and early 1960s millions of doses of polio vaccine were contaminated by another simian virus, SV-40. The vaccine alleged to be the origin of AIDS was given to hundreds of thousands of people in central and west Africa from 1957-1959. These locations later had some of the world's highest levels of HIV infection. The timing is also right, since the earliest known cases of AIDS date from the 1960s; the earliest HIV-positive blood sample was collected in Kinshasa in 1959. At the time, there was no way of testing for the presence of SIVs, which were only discovered in the 1980s. Another factor adds plausibility to the theory: the vaccine was given to many infants less than a month old, in an extra high dose. Since the immune systems of infants are not fully developed, this is an excellent way to help a virus jump the species barrier. Some scientists argue that the above explanation is not necessarily correct but that it is worth taking seriously. There are a number of ways to test it. One is to analyze stocks of polio vaccine; if the explanation is correct, then it is probable that some of the vaccines will carry SIV. Another is to scrutinize records of early polio vaccination campaigns in Africa. If it is true that the immunodeficiency virus passed to humans by way of those vaccines, the areas where the campaigns took place would be the same as those where the initial sprouts of the disease occurred and where the larger number of cases occurred during the early stages of the pandemic. Another is to analyze blood samples in Africa from the 1950s and earlier (pre polio vaccination): if the immunodeficiency virus was transmitted via the polio vaccine, HIV should not be found. Adapted from âPolitical refutation of a scientific theory: the case of polio vaccines and the origin of AIDSâ. Brian Martin, published in Health Care Analysis, Vol. 6, 1998, pp. 175-179. Now reread the passage and answer the following questions.

5. For each experiment, write an outcome that would disprove the hypothesis of AIDS passing from monkeys to humans through polio vaccines.

6. What outcomes of the experiments would fail to disprove the hypothesis of AIDS passing from monkeys to humans through polio vaccines?explain.

7.What outcomes would prove the hypothesis? Hint: This is not the same as question 6. Think about what would you need to do to 100% prove a hypothesis.

8. For what reasons do scientists need to conduct testing experiments?

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Biochemistry 3382A Lecture Notes - Lecture 1: Grb2, Glycogen, Alpha Helix

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