Explaining Dragons

Monday, February 8, 2016

Biology Example Question #5 Outline the effects of a base substitution mutation in the case of sickle-cell anaemia

Thank you again to my biology teacher for teaching me everything I know about biology (far too many repeated words in this sentence...).

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DNA is made up of a series of nucleotides. Each nucleotide has a nitrogenous base attached to it, either adenine, guanine, thymine, or cytosine.
Different combinations of these nitrogenous bases code for different proteins
The DNA is transcribed by RNA polymerase, into mRNA (messenger RNA) so it can leave the nucleus
From there mRNA leaves the nucleus and makes it way to a ribosome which can then translate the mRNA strand into a protein
The ribosome "reads" the mRNA three nucleotides at a time, called codons, each codon codes for an amino acid, which is then attached to a growing chain of amino acids, which ultimately make a protein
There are some cases where a codon can be altered due to a base substitution, whereby one of the bases is replaced by one that should not be there, this is the case in sickle-cell anaemia
Usually the DNA codon is CTC, which then gets translated to the mRNA strand as GAG, this codon then codes for the amino acid glutamic acid in the ribosome, which ultimately leads to the formation of haemogloblin which carries oxygen on the red blood cells.
If someone has sickle-cell anemia instead of the DNA codon CTC, it is CAC, which when translated to mRNA, results in a GUG codon. Unfortunately, this does not code for the same amino acid, so instead of glutamic acid, valine is attached.
Because the wrong amino acid is placed haemoglobin is not formed properly, and cannot form its quaternary (globular) structure, this makes is significantly worse at carrying oxygen, and thus sufferers tend to get short-winded. It also results in the characteristic sickle shaped red blood cells, which are less efficient at carrying oxygen.
If two copies of the mutated gene are inherited then all of the red blood cells are sickle shaped
If only one copy of the mutated gene is inherited half of the red blood cells will be sickle shaped, and the others will be normal.
The sickle shaped cells make sufferers resistant to malaria.

CTC

GAG- normal

GUG- not normal

Science

Biology Example Question #4 describe the lock and key model of enzyme activity and how induced fit model extends it

Hakuna Matata 7:05 PM

Enzymes are proteins, which have the specific role of lowering the activation energy of reactions. A key fact about them, is that they are not used up during a reaction, and can thus be reused for multiple reactions. Enzymes have a Quaternary structure, making them globular in shape. Each of them has a so called active site, whereupon a substrate binds to it. The way the enzymes then lower the activation energy of a reaction is by stressing the bonds of the reactants (substrate), thus speeding up the process, and increasing rate of reaction. Though, it is important to note, that an enzyme will not increase the amount of product formed, merely the rate at which it is formed.

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The lock and key model goes by the premise that there is a specific enzyme for each substrate. Which would mean there is an absurd amount of enzymes. Each of the active sites are perfectly shaped to fit the substrate, and thus there is only one enzyme that fits each substrate. It can thus perfectly stress the bonds of its particular substrate. However, the fact that so many enzymes would have to exist led to a revision of this particular model to the induced fit model.
This model takes more of a "glove and hand" approach, whereby the enzyme is roughly shaped like the substrate, and once one enters its active site it will shape itself around it. Making slight modifications in form until its active site fits the substrate. Once this has occurred it can once again stress the bonds of the substrate speeding up the reaction. With this model one enzyme can "fit" multiple substrates, thus reducing the number of enzymes needed.

Thank you again to my biology teacher for teaching me everything I know about this!

Science

Biology example question #3 Explain the processes involved in the Krebs Cycle

Hakuna Matata 6:37 PM

It's back. Yup. Here we go again, cellular respiration is back. For those of you that mix up when it's the Krebs cycle and when it's the Calvin cycle I have a little way that you might be able to remember it a little better. Though, it would involve you learning the meaning of one German word- you guessed it "Krebs". In German this word means crab. A crab is an animal. Animals cannot photosynthesize, but they can undergo cellular respiration, so the Krebs (crab) cycle occurs during cellular respiration.

On to the steps. Sigh.

The Krebs cycle follows the Link reaction and takes place in the matrix of the mitochondria
One of the two, two-carbon Acetyl CoA molecules enter the Krebs cycle
Already in the Krebs cycle is a four carbon molecule called oxaloacetate
One of the Acetyl CoA molecules will bind with oxaloacetate forming a six carbon compound, this compound is called citrate. The CoA (Co enzyme A) will recycled, and return to the link reaction.
Citrate will be oxidized and decarboxylated (lose a carbon), this will result in a five carbon compound, a NADH molecule (which was reduced from NAD+), and one CO2 molecule.
The five carbon compound will again be oxidized and decarboxylated, resulting in a four carbon compound, another NADH molecule, and another CO2 molecule
This four carbon compound will be oxidized again, and undergo further modification. Resulting in another NADH molecule, one FADH2 molecule (reduced FAD), and one ATP molecule.
By the time all of this has occurred the four carbon compound is oxaloacetate again, and the cycle can begin again.
Keep in mind this cycle with occur twice for every molecule of glucose as two Acetyl CoA molecules are produced during the link reaction.

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Products

6 NADH (electron carrier)

2 FADH (electron carrier)

4 CO2

2 ATP

Thank you again to my biology teacher for teaching me everything I know about this!

starchy seed

Biology Example Question #2 Outline the metabolic processes during germination of a starchy seed

Hakuna Matata 5:44 PM

The steps (or so I am led to believe...). On with the germination! Thank you again to my biology teacher for teaching me everything I know about this!

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The first step needed is water. Without out none of the following would occur. Think of it as the activator. So step one, water needs to touch the seed.
This activates a hormone in the cotyledon of the seed (the starchy reserves, used for initial growth), which goes by the fanciful name of gibberrellin. For some reason I always think of the word gerbil...
Gibberrellin activates the production of amylase, which is an enzyme that helps to break down starch.
Amylase causes the hydrolyses of some of the starch reserves into maltose (starch is a polysaccharide and maltose is a disaccharide). Hydrolysis, for those who don't remember is the process whereby macromolecules are broken down into smaller molecules using water. That's why we needed water...
Finally, the maltose is then converted into glucose (hydrolysed again). Maltose is a disaccharide molecule made up of two glucose molecules, which when broken down make two glucose molecules, which are monosaccharides. Glucose can then be used to undergo cellular respiration, allowing the seed to begin growth.

Voila! There we have it, the first steps of germination.

Science

Biology Example Question #1 Distinguish between aerobic and anaerobic respiration

Hakuna Matata 5:29 PM

This is going to be the first post in a series of posts which answers (often short hand) several biology questions, that do well to summarize large sections of a high school level course. Again please be aware that I am no scientist, so take my words with a pinch of salt. Also, I won't be writing these rambling sort of introductions for the next posts, so there's that. Now on to the answer.

Thank you again to my biology teacher for teaching me everything I know about this!

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Cellular respiration is the process whereby glucose is converted into usable energy, in the form of ATP. The amount of ATP produced depends on the whether or not oxygen is present. If oxygen is present aerobic respiration is undertaken, if not then anaerobic respiration is undergone. In aerobic respiration a total of 36 ATP molecules are produced, whereas in aerobic respiration only 2 ATP molecules are produced.

Both processes begin in the cytoplasm of a cell, however, aerobic respiration will continue in the matrix and inner membranes of the mitochondria. Whilst anaerobic respiration only undergoes glycolysis aerobic respiration will also involve the link reaction, the krebs cycle, and the electron transport chain. Aerobic respiration will result in 10 NADH molecules and 2 molecules of FDH2 (electron carriers) whilst anaerobic respiration will only result in 2 NADH molecules.

Both processes undergo glycolysis resulting in two pyruvate molecules, however whilst in aerobic respiration they go on to be modified in the link reaction and so forth, in anaerobic respiration other bi products are formed with no additional ATP formed.

If anaerobic respiration takes place in a yeast cell ethanol and CO2 will be the bi-products, whilst in humans the bi-product is lactate (also known as lactic acid).

I hope this was edumactional. I realize that is not a word.

Sunday, February 7, 2016

time travel

A super brief book recommendation: The Map of Time

Hakuna Matata 4:30 PM

I will keep this brief, mostly because I can barely keep my eyes open. I'm just going to quickly write this before I go take a nap. With that in mind, do forgive me for any absurdly ridiculous spelling errors, grammar mistakes, or just general buffoonery.

Anyway, I read this book a few months ago, so as usual, I don't remember the finer details about it, nonetheless, I do recall enjoying it. Until the end that is... By the time I had about 100 pages left (for perspective the copy I had had 800 pages) I had to force myself to finish it. I'm not entirely certain why that was, but anywho. The book is The Map of Time by Felix J. Palma. It was originally written in Spanish, however, my Spanish is nowhere near good enough to take on the daunting task of 800 pages, so I read it in English.

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Probably the most interesting thing about this novel was the number of plot twists. But not really in the traditional sense, you would understand if you read it. There were at least two occasions at which the book had convinced me of something only to prove otherwise. I think the issue was once the "thing" finally happened, I was just sort of sick of the number of times I hadn't been true, and when it finally did it was somewhat anti-climatic. Nonetheless, I really enjoyed this book and it is certainly unlike anything I have read before. I'm not entirely certain if I would classify this as science fiction or perhaps some sort sub-genre. I should probably have mentioned that this book is primarily about time travel.

I just have a few more points and then I'm done. Number one, this book definitely has some darker undertones and concepts, so be aware of that. Number two, it is very well written, I really like how Palma, or rather the translator, wrote the book. It' somewhat reminiscent of the old classics. Finally, I would have to say though I really enjoyed the story and the concept I think it got a little tedious to read because at the end of the day I didn't really care what happened to the characters. It was written in a believe three (possibly four) parts, each of which focuses on a different character. There are some reoccurring characters, but they are either not pivotal to the story, or I still don't really care about them (I promise I'm not a cold person...). I tend to have issues in general of books that change perspectives within the book, as I find it considerably harder to get invested into the characters. The way that George R.R. Martin did it is somewhat better because they are still all interconnected, but with this novel they are only vaguely connected and are structured more as short stories, a genre which I stay clear of.

If you are looking for a traditional science fiction novel this is probably not for you, nor is it fantasy really. It's sort of a juxtaposition of a number of genres, and in a way pretending to be one genre when in reality most of it does not fit it. If you want an original well-written book, with a really interesting concept, I would say give this a try. Though, I don't imagine you will feel to invested into any of the characters. Nonetheless, I would give it a read just for its fascinating premise.

It ended up being not brief... Sorry...

Science

Mendelson and Stahl Experiment

Hakuna Matata 4:09 PM

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Credit to my biology teacher for teaching me basically all the biology I know, and thus this as well.

I'm back! At least for now. Apologies in advance, the next posts for a while will be primarily scientific concepts...

So let's start off with a bang, shall we? Deoxyribonucleic acid, or rather DNA. Our DNA is essentially in charge of controlling everything a cell does and what it does or does not produce. Every single one of your billions of cells (well nearly every one, red blood cells don't have DNA because they need the space to carry oxygen) has a nucleus. And within that quaint nucleus you house your DNA. All of it that is. The only real difference between DNA in your different cells is the parts which are activated the the parts which are not. Anyway, when you started off, and I mean single cell start off, you had one cell with one copy of your DNA. Now, how are you going to get a copy of this DNA into your other cells. Well, that my friends, is the process of DNA replication (I will get into that in a later post). What I want to get into today is how it was proven that this process is semi-conservative.

Essentially it is semi conservative because in each new cell one old parent strand of DNA is located. Recalling that DNA is a double helix made up of two strands. Because of this process there is always half of a preexisting DNA molecule in each new cell. So how did Methelson and Stahl (I can't recall these distinguished gentlemens' first names) prove that this was true? Let me tell you.

Number one) they took a common bacteria, E. Coli and placed it in nitrogen 15 isotope (which is a heavy isotope- the atomic mass of nitrogen is 14.01). They then let the E. Coli grow in this heavy isotope of nitrogen for four generations.

Numero dos) These cells were taken, and transferred to a new "growing area" (not really sure what you would want to call it...), this time with a lighter isotope of nitrogen, namely nitrogen 14. Now samples were taken from this population periodically.

Numero tres) Once DNA was extracted from the samples they were dissolved int a solution of cesium chloride.

Numero quatro) Solution was centrifuged (the spinny thing), allowing for a concentration gradient to be built up.

Numero cinco) Last one. I promise. The DNA molecules would then move around in the created gradient and would "stop" at the point where the density equaled that of the cesium.

The first sample taken at step one, all DNA was heavy, as they were grown in nitrogen 15, and thus sat at the bottom of the test tube.

Once the solution was transferred into the nitrogen 14 medium and a sample was taken of the first generation, the bacteria had DNA, all of which were located at a density between nitrogen 14 and 15, indicating that each DNA had one strand of the "old" nitrogen 15, and a new strand made when in nitrogen 14.

When a second sample of DNA was taken (from the second generation) from the E. Coli in the nitrogen 14 mixture, there were two areas where "bands" of DNA could be found. One was at higher up in the test tube indicating that both strands of DNA had the lighter nitrogen 14. The second band was once again between nitrogen 15-14, indicating that one strand had nitrogen 14 and the other stand nitrogen 15.

Labelled for reuse https://upload.wikimedia.org/wikipedia/commons/2/2a

Do excuse the Chinese, I believe... But this image is essentially showing what I just wrote. The first generation grown in the heavy nitrogen isotope has all DNA in one band near the bottom. Once the bacteria was then place into the lighter nitrogen isotope solution all of the first generation DNA was located in one band, which was between the band of nitrogen 15 and nitrogen 14. This indicates that one strand of each was nitrogen 14 and the other nitrogen 15. This is due to semi conservative DNA replication! Anyway, hope it makes a little more sense now.