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Course: HS biology (archived) > Unit 34
Lesson 1: Ask a biologist!Ask a biologist (archived questions)
This video was open for questions from July 28-August 2, 2015, and is now CLOSED (archived). Look below to browse the questions, or ask your own question in the comments section of another video or article!
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Hello, my name is Justin Joo, student in South Korea. How does methanogens produce methane, and why are they anaerobic? Where do methanogens exist, and how can individuals (students) collect samples and culture them?(31 votes)
Methane can be found in the outer planets, most animals digestive systems (farts) and other chemicals.(4 votes)
At7:24PM,
Hi, my name is Akeel Howell and I'm a high school student in New York.
1. What exactly occurs when proteins fold and unfold? How does understanding the folding and unfolding of proteins relate to treatment for diseases such as Huntington's, Alzheimer's and cancer? What causes protein to misfold and what connection could be made between this (the cause of protein misfolding) and cancer?
2. How could studies in the field of genetics help to improve human resilience to diseases? How could an understanding of the human genome lead to more effective treatments for genetic disorders such as breast and colon cancer and cystic fibrosis? What effect does altered genes have on human beings? Could excessive consumption of Genetically Modified Organisms (GMOs) essentially lead to the acquisition of genetic diseases?(17 votes)
Hi Akeel,
Thanks for your very thoughtful questions! For your first question, concerning the folding of proteins, you may want to look at the below videos and articles to get a general sense of how proteins fold and what kind of molecular interactions influence their structure:
Overview of protein structure: https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-acids/v/overview-of-protein-structure
Tertiary structure of proteins: https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-acids/v/tertiary-structure-of-proteins
Orders of protein structure: https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-acids/a/orders-of-protein-structure
As for your specific questions about disease, you are absolutely correct that Huntington's, Alzheimer's, and many types of cancer are related to problems in protein folding.
- In the case of Huntington's disease, the folding problems relate to a change in the primary sequence of the protein Huntingtin. People with Huntington's disease have an alteration in the amino acid sequence of this protein, such that it has a longer-than-usual chain of glutamines in a region of the protein called the polyglutamine tract. Mutant Huntingtin proteins with larger polyglutamine tracts will stick to each other through hydrogen bonds, forming large clumps of protein called aggregates rather than folding into their normal, functional form. The clumps of protein appear to mechanically block neurotransmission in neurons, causing the neurological symptoms characteristic of Huntington's.
- In the case of Alzheimer’s disease, it is a little less clear exactly what causes the disease. However, two different hypotheses for the cause of Alzheimer’s relate to problems in protein folding. One, the “amyloid hypothesis,” suggests that the neurodegenerative features of Alzheimer’s are due to large protein aggregates called plaques, made up of a protein called beta-amyloid. Beta-amyloid is found in healthy people too, but it’s thought to misfold in people with Alzheimer’s, such that the hydrophobic (water-hating) amino acids are no longer on the inside of the protein where they’re supposed to be. The misfolded beta-amyloid protein will then cluster together to shield the hydrophobic amino acids from the watery environment of the cell, resulting in plaque formation. (It’s actually thought that smaller accumulations of beta-amyloid, called oligomers, may be the disease-causing form rather than the large plaques.) Another hypothesis for the cause of Alzheimer’s revolves around another protein, called tau. It’s thought that tau proteins are hyperphosphorylated in Alzheimer’s (too many phosphate groups are attached to them), and this causes them to bind to other tau proteins, resulting in the formation of large “neurofibrillary tangles” of tau inside of neurons. Tau proteins normally organize the microtubules of the cytoskeleton, so the loss of tau to these tangles results in instability and disintegration of the microtubule cytoskeleton and problems in transport and communication within the neuron.
- Cancer is a very diverse disease (can have many different underlying causes), so not all cases of cancer are related to protein folding problems. However, many cases of cancer involve problems with a protein called p53, often described as the “guardian of the genome.” p53 is responsible for maintaining genome integrity, ensuring that DNA is not mutated or damaged. If damage is present, p53 is activated and triggers pathways to make sure the damage is repaired (if possible) or that the cell is destroyed (if repair is impossible). When p53 is defective or missing, mutation can accumulate in the genome unchecked, leading to cancer. Some cases of cancer are associated with mutations in the p53 protein that cause it to fold incorrectly, such that it cannot do its job of genome surveillance correctly.
You may find it interesting to read more about protein folding and disease in this article: http://www.nature.com/horizon/proteinfolding/background/disease.html.
As for your second question, this is a great (but also very big!) question. I guess the short answer is that the more we know about the human genome and its diversity, the better we will be able to understand the causes of genetic (and genetically influenced) diseases. For instance, if we sequence the genomes of many people who have breast cancer and many people who are healthy, we can use statistical techniques to identify sequence differences between these groups that are correlated with diseases. Once we’ve found these differences, we can look at what genes they are in or near; these genes are candidates for playing a role in the development of breast cancer. Knowing what genes are related to breast cancer risk could help people be more aware of their own likely disease risk (e.g., encouraging them to make lifestyle changes to prevent disease), and could also guide efforts to develop new therapeutics such as drugs.
As for what effect an altered gene will have on a human being, it depends a great deal on the specific gene and the particular alteration we’re discussing. In some cases, an alteration does little or nothing. For instance, “silent mutations” are mutations in which the nucleotide sequence of a gene is changed, but the amino acid sequence remains the same (because the same amino acid can be encoded by more than one codon, or triplet sequence, of nucleotides). In most cases, silent mutations don’t have any effect on the functionality of the gene or the health of the person carrying them. On the other hand, even just a tiny change in the nucleotide sequence of a gene can sometimes have very serious consequences. For instance, a friend of mine growing up was diagnosed with Lafora progressive myoclonus epilepsy, a severe and incurable neurodegenerative genetic disorder. This disorder can be caused by a change of just one base pair change in the gene encoding a protein called laforin, which regulates the production of a storage form of sugar called glycogen. This may seem like a very tiny change, yet it caused my childhood friend to progressively lose her speech ability, motor skills, and ability to communicate, and eventually claimed her life when she was in her mid-twenties.
As for whether excessive consumption of GMOs could lead to the acquisition of genetic diseases, my answer would be, probably not directly. The fact that an organism is genetically modified means that its genome contains a small quantity of extra genetic material, but doesn’t mean it’s able to transfer that genetic material to you. Every kind of food you eat (including the most organic, all-natural tomato) contains genes and genetic material, but this genetic material doesn’t generally modify your genome. Instead, your body breaks down the DNA of what you eat and reuses its building blocks (nucleotides) to replicate and maintain its own normal DNA.
However, you may notice that I said “not directly.” The fact that an organism is genetically modified doesn’t mean that it’s likely to affect your genome, but certain types of genetic modifications may be associated with an elevated risk of genetic disease in the bigger picture. For instance, some crop plants are genetically modified by the introduction of a gene that allows them to resist the herbicide Roundup (glyphosate). This allows farmers to use Roundup to kill the weeds in their fields without killing the crops. However, there is some evidence that glyphosate may damage DNA and be carcinogenic (cancer-causing). In that case, glyphosate residues remaining on genetically modified crops could be a risk factor for DNA damage and related diseases such as cancer. This is a controversial topic, so I encourage you to do your own research if you are interested.
References for protein folding:
Alzhemer's disease. Retrieved from Wikipedia: https://en.wikipedia.org/wiki/Alzheimer's_disease.
Huntington's disease. Retrieved from Wikipedia: https://en.wikipedia.org/wiki/Huntington's_disease.
Protein folding diseases. Retrieved from Nature.com: http://www.nature.com/horizon/proteinfolding/background/disease.html
References for genetic disease and GMOs:
Lafora progressive myoclonus epilepsy. Retrieved from Genetics Home Reference: http://ghr.nlm.nih.gov/condition/lafora-progressive-myoclonus-epilepsy.
Widely used herbicide linked to cancer. Retrieved from Scientific American: http://www.scientificamerican.com/article/widely-used-herbicide-linked-to-cancer/.
Marques et al. (2014). Progression of DNA damage induced by a glyphosate-based herbicide in fish. http://doi.org/10.1016/j.cbpc.2014.07.009.(7 votes)
Hello, I'm a student, from Brazil and I have a question. The chemical formula of the nucleotide with adenine looks like the chemical formula of the ATP (or even the ADP)and the difference are the phosphates, rigth? If I'm right, is it possible to turn nucleotides to ATP at sometime?(7 votes)- Hi Guilherme, thanks for your question. You are right, ATP is simply a nucleotide (specifically, an RNA nucleotide) with adenine as a base and a chain of three phosphates attached to it. And yes, it is possible to turn the single-phosphate nucleotide (adenosine monophosphate, or AMP) into ATP. This can happen in a two-step process, where AMP first combines with ATP to make two ADP, and the two ADPs each combine with a phosphate to make ATPs. Hope that helps!
References:
Adenosine monophosphate. (2015, 30 July). Retrieved July 31, 2015 from Wikipedia: https://en.wikipedia.org/wiki/Adenosine_monophosphate.(6 votes)
I was wondering about marine animals and how dolphins can use echolocation. Could you go into more detail about echolocation and maybe if humans had it, could it help us in the future?
thank you(4 votes)- Thanks for your question! Echolocation is a very cool phenomenon that allows dolphins to form a picture of their surroundings by sending out sound waves and collecting the echoes that bounce back. The sounds that dolphins use in echolocation consist of series of very short clicks, each click lasting less than a fifth of a second. The sounds are thought to originate in the nasal passage (nose) of the dolphin, and then pass through a special anatomical structure on its head, called the melon, which focuses the clicks into a beam in front of the dolphin. The sound waves will travel through the water, bounce off objects in the surroundings (such as prey, predators, obstacles, or other dolphins), and be reflected back to the dolphin. They are detected in fat-filled cavities in the dolphin's jaw, transmitted through the ear, and relayed to the hearing centers of the brain in the form of nerve signals. The dolphin's brain can then construct a picture based on these nerve signals, complete with information about the distance, size, shape, and sometimes even internal structure of objects.
Echolocation is something that works very well in the watery environment where dolphins live, as sound waves travel over four times faster in the water than in the air, making echolocation a fast way for a dolphin to scan its surroundings. (Some land animals, such as bats, do use echolocation as well, though.) Humans don't have echolocation mechanisms built into their bodies the way dolphins do, but human-built sonar equipment essentially mimics echolocation, bouncing sound waves off of objects to sense their distance (typically, in an underwater context, such as docking a boat or navigating a submarine).
Hope that helps! You can learn more about the details of echolocation by exploring some of the articles in the references below.
Bottlenose dolphins. Retrieved from Seaworld: http://seaworld.org/en/animal-info/animal-infobooks/bottlenose-dolphins/communication-and-echolocation/.
How can dolphins disarm sea mines? Retrieved from Howstuffworks: http://animals.howstuffworks.com/mammals/dolphin-disarm-sea-mine1.htm.
Melon (cetacean). Retrieved from Wikipedia: https://en.wikipedia.org/wiki/Melon_(cetacean).(4 votes)
What is the difference between homologs, paralogs, and orthologs?(3 votes)- Hi Kendall, that's a good question!
The term "orthologs" refers to genes that evolved from a common ancestral gene through speciation. For example, the beta-hemoglobin gene in humans and the beta-hemoglobin gene in chimpanzees are orthologs of one another. Orthologs often have the same function, and orthology (based on sequence) can be used to predict function for genes in newly sequenced genomes.
The term "paralogs" refers to genes that share a common evolutionary origin through a genetic duplication event (gene, chromosomal, or genome-scale duplication). For instance, the alpha-hemoglobin and beta-hemoglobin genes of humans are paralogs. Paralogs often have similar functions, but in some cases, their functions may diverge after duplication (i.e., one or both of them may acquire new functions, or lose function altogether).
Finally, "homologs" is a more general term that refers to any genes descended from a common ancestral DNA sequence. These genes could have been split into separate lineages by a speciation event, as in the case of orthologs, or by a duplication event, as in the case of paralogs.
Hope that helps! If you want more detailed information about these definitions, you may want to look at the Wikipedia article in the references below.
References:
Lewis, Christopher, Definition of homolog, ortholog, and paralog. Retrieved from http://homepage.usask.ca/~ctl271/857/def_homolog.shtml.
Homology (biology). Retrieved from Wikipedia: https://en.wikipedia.org/wiki/Homology_(biology)#Sequence_homology.(3 votes)
Why is there a possibility of silicon based life?(4 votes)
Silicon based life actually refers to the possibility that Silicon chemistry could replace carbon chemistry, the reason being that silicon also has four valence electrons (ie. It can bond four times, like carbon). In addition, Silicon is relatively abundant in the universe, at 650ppm by mass. For camparison, carbon is 4500ppm by mass. However there are drawbacks. Silicon does not form double bonds as readily, does not readily bond to as many elements that carbon does, and in often trapped in unreactive silicon oxides. In addition, silanes (compounds of Silicon and Hydrogen) react violently with water. However stability of silicon compounds does make them advantageous in high temperature environments, and Polysilanols (Silicon based sugars) are soluble in nitrogen, making them potentially useful in colder climates.(1 vote)
Hi, this is Mitchell Lee. I like in Dallas Texas. I've heard that new technological advances have made it possible to recreate human stem cells. If this is true, would that mean you would be able to remove a cancerous organ, then grow it back? This has stumped me for a long time and I need help. Thanks!(2 votes)- Hi Mitchell, that's a good question. The concept you've described - growing new organs to replace old, damaged, or diseased ones - is a central goal of the field of regenerative medicine. Stem cells, with their ability to give rise to many different types of mature cells, are central to scientists' current thinking on how best to regenerate organs. However, to my knowledge, researchers have not yet managed to regrow fully functional versions of most types of organs from stem cells (though steps have certainly been made in this direction, such as a Japanese group's production of miniature "liver buds" from stem cells). This is a complex problem because, during development, organs are not developing in the isolation of a test tube; instead, they are receiving many chemical and mechanical signals and cues from the surrounding tissue that tell them how to grow, what shape to take on, what genes to express, and so forth. To re-grow functional organs, we not only need to "reprogram" some of a patient's own cells into the right type of stem cells to produce the organ of interest, be we also need to provide the appropriate chemical and mechanical cues to instruct the organ's growth and development in vitro (outside the living body). This is a big challenge, but there are many dedicated researchers in the fields of materials science, stem cell biology, and developmental biology who are working to understand the many interacting factors needed to re-grow a human organ. Hope that answer you question, at least somewhat!
McGowan, Kat. (2014). Scientists make progress in growing organs from stem cells. In Discover. Retrieved from http://discovermagazine.com/2014/jan-feb/05-stem-cell-future.(5 votes)
why is mitochondria known as a semi autonomous organelle??(2 votes)- Mitochondria is considered as autonomous cell organelle due to the following counts :
Mitochondria have their own DNA which can replicate independently. The mitochondrial DNA produces its own mRNA, tRNA and rRNA.
The organelles posses their own ribosomes, called mitoribosomes.
Mitochondria synthesize some of their own structural proteins. However, most of the mitochondrial proteins are synthesized under instructions from cell nucleus.
The organelles synthesize some of the enzymes required for their functioning. e.g. succinate dehydrogenase.
They show hypertrophy .i.e. internal growth.(3 votes)
- Hello, this is Saravanan from India doing my class 11.
Eventhough erythrocytes do not have a nucleus how do they survive and is nucleus a significant feature to distinguish a living system dead or alive?
How are the roots of aquatic plants somewhat unique comparitively with terrestrial plants? what are their unique features?
.................thank you for considering my question.(3 votes) 
In a adolescent period why the skin become oily and why pimple start growing?
what are the tips to avoid it can you please suggest it?(3 votes)
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