BIO 2133 Lecture Notes - Lecture 2: Central Dogma Of Molecular Biology, Reverse Genetics, Ribosomal Rna

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26 Nov 2015

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Topic 2: molecular anatomy of chromosomes, genes, and genomes. There are 2 main ways to find out if traits have a genetic basis. We always start off with a research question. In reverse genetics, it is very directive to begin with and we know something about the gene to start off with; in forward genetics, we know nothing about the gene. Must be relevant, have definable and measurable components / variables, be specific and have parameters, show cause and effect. Everything about genetic investigations revolves around the central dogma of genetics. Hereditary information is stored in the dna and is propagated through the generations. Is the dna being expressed? (i. e. : are we seeing phenotypes of this expression?) There are many ways to test if we have a genetic basis to a system and it always revolves around the central dogma of genetics.

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2.)

a.) Are viruses that infect Archaea different from other bacterial viruses?

Yes, they do not have protein coats because of the extreme conditions where they live.

No, they consist of nucleic acid and protein just like other bacterial viruses.

Yes, the structure of archaeal viruses is always completely different from other bacterial viruses.

Yes, they have only DNA genomes.

b.) Of the following examples, which is not a common part of many viral life cycles?

The pox virus genome is replicated by DNA polymerase.

Adenoviruses attach to the cell and the nucleocapsid is taken up by the cell.

Pox viruses replicate in the cytoplasm of the cell.

Once an adenovirus virion is inside a cell, host RNA polymerases transcribe early genes

c.) Some viruses are associated with cancer. There are a variety of ways in which viruses may affect a cell in a way that may lead to cancer. Based on your knowledge of the life cycles of viruses and of molecular genetics, what is one way that this might happen?

Viral genetic material inserts into a host genome close to the termination sequence, far downstream of the promoter, and causes a silent mutation.

Viral genetic material inserts into a host genome in a repetitive noncoding region.

Viral genetic material inserts into a host genome, placing a promoter in a new location and turning on a gene that had previously been turned off.

Viral genetic material inserts into a host genome and causes a mutation in a promoter, turning off a gene that had previously been turned on.

d.) Which statement describes the difference between the normal neuron protein PrP^C and the pathogenic version PrP^Sc?

PrP^C is just a protein and the PrP^Sc is a protein with nucleic acid inside.

The PrP^C protein contains more beta sheets while the PrP^Sc protein contains more alpha helices.

The three-dimensional conformation is identical, but the amino acid sequence is different.

The amino acid sequence is identical, but the three-dimensional conformation is different.

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.

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Part III â Just How âIdenticalâ Are We?

Elise had been home from college for a week, and she was still preoccupied with Shannonâs diagnosis and her own potential risk for mental illness. Elise expressed her anxiety and concerns to her mother one night after dinner. âElise,â her mother said, âyour concerns are perfectly valid, and you have every reason to want to get more information. Why donât we make you an appointment to consult with a psychiatrist?â Elise decided to make the appointment the next day. * * * * * Elise left Dr. OâBrienâs offi ce feeling that some of the weight had been lifted from her shoulders. On the car ride home, she thought about the things that Dr. OâBrien had said to her during their consultation. âIt was good of you to come in to see me, Elise. You are absolutely right to have concerns for yourself when your identical twin has been diagnosed with schizophrenia. Research shows that schizophrenia is almost 50% heritable, and since you share nearly identical DNA with your sister, that puts you at a higher risk for developing this disease as well.â âFifty percent may sound like a scary number, but remember that schizophrenia is a very complex disease, and 50% of what causes schizophrenia is due to things other than your DNA.â âWell, like what? What else could be contributing to Shannonâs schizophrenia that wouldnât necessarily aff ect me?â Elise asked. Dr. OâBrien replied, âTh ere are many, many environmental infl uences that seem to play a role in the development of this disease, such as increased stresses and anxiety, or diffi cult relationships with other people. Interestingly, there is some groundbreaking research that is going on that suggests that the environment itself might even play a role at infl uencing oneâs DNA at the molecular level. Th is concept is called epigenetics. An example of epigenetics in nature is the calico cat. Each calico cat has a unique orange and black fur color pattern because of alterations, called epigenetic changes, which occur within the cells that produce coat color during the catâs development. Research in the fi eld of epigenetics suggests that individuals with schizophrenia appear to have some of these epigenetic changes to their DNA that are due to environmental infl uences, and that these alterations could be contributing to their development of mental illness.â âBut wouldnât I also have these âepigenetic alterationsâ in my DNA?â Elise asked. âNot necessarily, because you and Shannon have not experienced completely identical environments throughout your lives. For example, you and Shannon have had diff erent teachers and jobs throughout high school. And I also understand that you spent many childhood summers with a friend and her family out in the Grand Canyon, while your sister was off at swim camps. If you are interested, I can give you some literature to read about this subject.â Elise was defi nitely interested. She took the articles and headed home.

1. Briefly describe what you know about the structure of DNA and how DNA is packaged in a cell.

2. At the molecular level, speculate on some ways that the environment might have an infl uence on DNA and its packaging

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BIO 2133 Lecture Notes - Lecture 2: Central Dogma Of Molecular Biology, Reverse Genetics, Ribosomal Rna

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