Biology Questions

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LemonyCricket
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Biology Questions

Postby LemonyCricket » Thu Jan 14, 2010 5:10 am UTC

I have a few questions for the biology majors out there.

    1. Why did "protoplasm" fall out of technical use? The explanations I have gotten were vague and didn't explain why "cytoplasm" was a seemingly suitable replacement.
      (I know there is a difference between the definitions of the two, but I don't really understand it. ._.; )
    2. How do prokaryotes make their ribosomes?
      This probably sounds like a stupid question, but in my biology textbook it explicitly states that all cells have ribosomes and then it later states that ribosomes are produced in the nucleolus... Which prokaryotes do not have.
    3. What is the "huge" difference between eukaryotic flagella and prokaryotic flagella?
      (Again, my biology book has failed me. All it says is that they are "totally different.")

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Re: Biology Questions

Postby Interactive Civilian » Thu Jan 14, 2010 3:00 pm UTC

LemonyCricket wrote:I have a few questions for the biology majors out there.

    1. Why did "protoplasm" fall out of technical use? The explanations I have gotten were vague and didn't explain why "cytoplasm" was a seemingly suitable replacement.
      (I know there is a difference between the definitions of the two, but I don't really understand it. ._.; )

It seems to me that it is really a semantics thing, but it fell out of use because the word protoplasm (lit. "first created thing") isn't particularly accurate, and with better understanding of the nature of cells (through advances in microscopy) it was shown that thoughts about the differentiation between cytoplasm and nucleoplasm weren't as everyone thought (first thoughts were that the cytoplasm was homogenous and surrounding the nucleas, but later understanding showed it to be full of organelles and endomembranes). Cytoplasm (lit. "cell created thing") became the more accepted term for everything in the cell, though the part inside the nucleus is still the nucleoplasm. For prokaryotes, it's all cytoplasm.

2. How do prokaryotes make their ribosomes?
    This probably sounds like a stupid question, but in my biology textbook it explicitly states that all cells have ribosomes and then it later states that ribosomes are produced in the nucleolus... Which prokaryotes do not have.

In Eukaryotes, ribosomes ARE assembled in the nucleolus. In prokaryotes, they are simply assembled in the cytoplasm. Books don't often bother to point this out, because, for some reason, prokaryotes don't get a lot of love in general biology books.

3. What is the "huge" difference between eukaryotic flagella and prokaryotic flagella?
    (Again, my biology book has failed me. All it says is that they are "totally different.")

The proteins they use, the methods of assembly, and the motor mechanisms are different. Check out the wikipedia article: http://en.wikipedia.org/wiki/Flagellum. It does use a lot of complex terminology, but you can probably get the basic ideas from the pictures if you are not familiar with the different proteins and mechanisms of their action.
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Re: Biology Questions

Postby Admiral Valdemar » Thu Jan 14, 2010 7:00 pm UTC

The one thing I like about certain bacterial flagella is that they are nature's only instance of a motor with a wheel in use. I always found the engineering at that level to be fascinating.

The production of 70S ribosomes in prokaryotes is always in the cytoplasm, and the distinction between this and what eukaryotes do is generally just that eukaryotes have bigger, segmented production areas for their larger ribosomes. A lot of biochemical reactions in eukaryotes goes on within specific organelles, whereas your average bacterium will perform a lot of this in the cytoplasm, almost in a chaotic fashion (after all, DNA synthesis in bacteria is "out in the open", while our cells have the nucleus and its subunit, the nucleolus).

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Re: Biology Questions

Postby Cobramaster » Fri Jan 15, 2010 1:37 am UTC

Prokaryotes are awesome in the fact that all of the genetic processes can and do occur simultaneously, replication, translation and transcription all out in the open where you can watch it all happen. and you can have almost the same thing happen in Mitochondria which are basically the most successful prokaryote species except for the transcription since the cell supplies the ribosome.
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Re: Biology Questions

Postby LemonyCricket » Sat Jan 16, 2010 7:58 am UTC

Image

This is beautiful. :D Thank you so much~! <3

Interactive Civilian wrote:It seems to me that it is really a semantics thing, but it fell out of use because the word protoplasm (lit. "first created thing") isn't particularly accurate, and with better understanding of the nature of cells (through advances in microscopy) it was shown that thoughts about the differentiation between cytoplasm and nucleoplasm weren't as everyone thought (first thoughts were that the cytoplasm was homogenous and surrounding the nucleas, but later understanding showed it to be full of organelles and endomembranes). Cytoplasm (lit. "cell created thing") became the more accepted term for everything in the cell, though the part inside the nucleus is still the nucleoplasm. For prokaryotes, it's all cytoplasm.


Hmm, I still don't really understand it. I understand the root words of "proto" meaning "first" and "cyto" meaning "cell" (or empty chamber, if taken as a literal translation I believe) and "plasm" meaning "molded thing"... But I don't understand why "first created thing" wasn't as accurate and "cell created thing"... Unless it's because the cytoplasm isn't created first when a cell forms? That would make sense. :O I'm guessing it has to do with the fact that the cell has a basic form before the cytoplasm is added, as opposed to the cell being built upon the cytoplasm as some sort of foundation? I definitely need to brush up on my cellular reproduction studies. ._.;

Interactive Civilian wrote:In Eukaryotes, ribosomes ARE assembled in the nucleolus. In prokaryotes, they are simply assembled in the cytoplasm. Books don't often bother to point this out, because, for some reason, prokaryotes don't get a lot of love in general biology books.


The sections on prokaryotes and protists are so paltry! Even fungi is inadequately explained when compared to plants and animals. :( (Especially animals. ._.; ) But yeah, prokaryotes are definitely the most abridged section in any general high school biology book. :(

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Re: Biology Questions

Postby Agent_Irons » Sun Jan 17, 2010 1:25 am UTC

I wish there was more about Fungi in textbooks, at least. Protists are basically miscellaneous, so more of that is probably out of the question. But hyphae! Lichen! Cells with two nuclei! Fungi are weird. Ballistic spores! There's so much cool to know about.

Prokaryotes don't get as much love as eukaryotes because everything happens in one pocket, or on one membrane. Eukaryotes are more complex, I guess?

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Re: Biology Questions

Postby James Scott-Brown » Sun Jan 17, 2010 4:09 pm UTC

Agent_Irons wrote:I wish there was more about Fungi in textbooks, at least. Protists are basically miscellaneous, so more of that is probably out of the question. But hyphae! Lichen! Cells with two nuclei! Fungi are weird. Ballistic spores! There's so much cool to know about.

Prokaryotes don't get as much love as eukaryotes because everything happens in one pocket, or on one membrane. Eukaryotes are more complex, I guess?


The fact that everything can happen in one pocket is itself fascinating.

Unfortunately, enthusing people with the wonders of the natural world, and preparing them to sit standardised examinations are orthogonal aims. Textbooks tend to sacrifice the former (and, at the same time, rigor & accuracy) for the latter.

As an aside, it's not just fungi that have cells containing multiple nuclei: synctia are also found in skeletal muscles, placenta, and Drosophila embryos.

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Re: Biology Questions

Postby Meteorswarm » Mon Jan 18, 2010 5:04 am UTC

James Scott-Brown wrote:As an aside, it's not just fungi that have cells containing multiple nuclei: synctia are also found in skeletal muscles, placenta, and Drosophila embryos.


Not to mention flowering plant megagametophytes - all flowering plants have a 2-nuclei cell that forms the endosperm when the 2nd sperm nucleus fuses with it. In some plants (that under go tetrasporic megagametogenesis) one nucleus is triploid and the other is haploid.

RE wheels: Isn't ATP syntase based on a rotor-stator model, too?
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Re: Biology Questions

Postby Interactive Civilian » Mon Jan 18, 2010 7:26 am UTC

Meteorswarm wrote:RE wheels: Isn't ATP syntase based on a rotor-stator model, too?

Indeed it is. It is essentially a molecular dynamo. This rather in-depth article has some stuff to say about the evolution of ATPases, though it may be difficult to follow for non-specialists. However, the diagrams in the article show the structure of V- and F-type ATPases rather well.

http://www.macromol.uni-osnabrueck.de/paperMulk/Mulkid_Nat_Rev_Micro_2007.pdf

The wikipedia articles on V-ATPase and on ATP Synthase have nice diagrams and ok explanations.
http://en.wikipedia.org/wiki/V-ATPase
http://en.wikipedia.org/wiki/ATP_synthase

These are such awesome little machines. 8)
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Re: Biology Questions

Postby LemonyCricket » Thu Feb 25, 2010 1:44 am UTC

endergonic reactions: An energy-requiring chemical reaction, which yields products with more potential energy than the reactants. The amount of energy stored in the products equals the difference between the potential energy in the reactants and in the products.


Is it just me, or does that definition seem a little confusing? I understand what endergonic reactions are now, but when I first read that definition, it completely threw me off. I read the italicized part as:

"The amount of potential energy in the products equals the amount of potential energy in the products minus the amount of potential energy in the reactants."


Which, y'know, doesn't make sense to me. ._.;

NOTE: I have never taken physics and I am terrible with chemistry, so that might explain why this concept is so foreign and incomprehensible to me. ._.;

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Re: Biology Questions

Postby hawkmp4 » Thu Feb 25, 2010 4:43 am UTC

That is a bit ambiguous. But what I think it means the amount of external energy that is required for (and subsequently stored in the products of) the reaction is the total potential energy of the products minus the total potential energy of the reactants. 'Stored' in this case is a verb, not an adjective...I think...>.> Maybe ignore that part. Just go off my second sentence.
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Re: Biology Questions

Postby PM 2Ring » Fri Feb 26, 2010 4:34 pm UTC

John Baez wrote:In Newtonian mechanics, we can only measure energy differences, not energies themselves. The reason is that we can add any real number to our definition of energy without changing any of the physics. This means it doesn't make much sense to ask what the energy of a system is - we can answer this question only after picking an arbitrary convention about what counts as "zero energy". What makes more sense is to talk about the difference between the energy of a system in one state and the energy of that system in some other state.

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Re: Biology Questions

Postby PossibleSloth » Fri Feb 26, 2010 5:48 pm UTC

Agent_Irons wrote:Prokaryotes don't get as much love as eukaryotes because everything happens in one pocket, or on one membrane. Eukaryotes are more complex, I guess?

There's also an issue of bias, since the majority of biology textbooks are written by eukaryotes.

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Re: Biology Questions

Postby LemonyCricket » Tue Mar 02, 2010 1:17 am UTC

PossibleSloth wrote:
Agent_Irons wrote:Prokaryotes don't get as much love as eukaryotes because everything happens in one pocket, or on one membrane. Eukaryotes are more complex, I guess?

There's also an issue of bias, since the majority of biology textbooks are written by eukaryotes.


XD !!! This made me lol. <3

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Re: Biology Questions

Postby LemonyCricket » Thu Mar 18, 2010 1:44 pm UTC

I'm very confused about entropy and enthalpy now. ._.;

I understand entropy is disorder and random molecular motion, and I understand the equation for enthalpy:

H = U + pV

(Enthalpy being the internal energy plus the product of pressure and volume—and in biological reactions, it's basically the internal energy since pressure and volume are typically constant?)

But then when I begin to look into the free energy equation:

∆G = ∆H – T∆S

I DON'T UNDERSTAND. Because if enthalpy, in biological reactions, is basically internal heat, and entropy, random molecular motion, is most evident in thermal energy (heat), then isn't that like saying:

entropy = disorder; enthalpy = heat; heat = disorder; enthalpy = entropy?
Because, y'know, that totally throws the entire equation off for me. ._.;

(My apologies again. I'm terrible at physics. This is completely new for me. D: )

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Re: Biology Questions

Postby iop » Thu Mar 18, 2010 2:46 pm UTC

LemonyCricket wrote:∆G = ∆H – T∆S


This equation tells you one thing: Among two possible states, which one is thermodynamically favored at the current temperature?

To answer this question you look first at the 'internal' energy of the two states (∆H). If more energy gets released when the bonds in state A are formed than in state B, A is energetically favorable, for example.

Second, you look at the entropy: If the system has more degrees of freedom in state A, for example because state A are more molecules than state B, or because the molecule in state B has lots of interaction surface and thus adsorbs lots of water molecules whose movement is consequently limited, A has higher entropy than B. To get an energy from the entropy, you multiply with the current temperature. This temperature is unaffected by whatever energy is liberated/used from forming the bonds, because what we're doing here is equilibrium thermodynamics, where only the end result counts, and not you get there (or whether you can get there, for example, if the molecules of state A are in different bottles, they can never form B, even though B might be thermodynamically favorable).

The interesting case is if ∆H and ∆S have the same sign, i.e. one is energetically favorable, and the other state is entropically favorable. For example, polymerization of tubulin into microtubules is good for entropy, because the tubulin 'binds' lots of water that gets liberated when the polymer is formed. However the polymer is not very favorable enrgetically. At low temperatures (4C), the T∆S term is comparatively small, and thus, tubulin is in monomer form. The more you raise the temperature, the more microtubules are formed (until you go too high and the proteins fall apart).

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Re: Biology Questions

Postby LemonyCricket » Fri Mar 19, 2010 7:29 pm UTC

OH, BEFORE I FORGET—here is some "art" I made in honor of this thread. <3 It's on my facebook, har har. (Eubacteria?)

Image

Image

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Re: Biology Questions

Postby LemonyCricket » Tue Mar 23, 2010 1:32 pm UTC

Okay, so, the beautiful ATP molecule—I'm trying to draw this to add to my small collection of biology-inspired art work. ._.;

Anyway, here's my problem. I am REALLY confused about the ribose monomer in the ATP molecule. ._.; I spent forever looking for the third hydroxyl group, and then I realized that, at least according to this diagram, the third hydroxyl group is replaced by a nitrogen atom in the purine compound (adenine) of ATP.

How does that work? O_O (I took my one and only chemistry course online. It was awful. I didn't learn anything.)

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Re: Biology Questions

Postby Levi » Tue Mar 23, 2010 8:25 pm UTC

I don't know the answer to you question, but I have to post to say that your handwriting looks amazing.

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Re: Biology Questions

Postby Interactive Civilian » Wed Mar 24, 2010 1:54 am UTC

LemonyCricket wrote:How does that work? O_O (I took my one and only chemistry course online. It was awful. I didn't learn anything.)

Put most simplistically, without talking about how the reaction is catalyzed, look at the ribose and the adenine. On carbon 1 of a ribose, there is an OH hanging off of it. On the corresponding Nitrogen on the Adenine, there is a hydrogen. H + OH = H2O, right?
So, Ribose + Adenine -> Adenosine + H2O .
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Re: Biology Questions

Postby LemonyCricket » Sat Mar 27, 2010 6:59 am UTC

Levi wrote:I don't know the answer to you question, but I have to post to say that your handwriting looks amazing.


Thank you so much. :D ~!

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Re: Biology Questions

Postby LemonyCricket » Thu Sep 16, 2010 10:49 pm UTC

OKAY, I'M BACK WITH MORE ANNOYING QUESTIONS.

I'm reading a summary of the IUPAC's rules for naming organic molecules, specifically alkanes. I understand the concept of combining numerical prefixes with "ane," but only from "pentane" onwards. I don't understand how "meth" is equivalent to "one," "eth" to "two," "prop" to "three," and "but" to "four."

ALSO: Is methanol just methane with a hydroxyl group? Because that would totally blow my mind.

ALSO ALSO: I feel bad for neglecting to read ipo's and Interactive Civilian's responses to my questions on energy and ATP-formation and whatnot. :( Y'know, those questions from... a year ago or something. >_>;;

ALSO ALSO ALSO: Am I breaking some forum rule by having this thread? I feel annoying and ignorant already; I would hate to be burdened with the guilt and paranoia of inappropriate thread posting as well. :<

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Re: Biology Questions

Postby StNowhere » Thu Sep 16, 2010 11:18 pm UTC

Limited chemistry understanding incoming -

LemonyCricket wrote:I'm reading a summary of the IUPAC's rules for naming organic molecules, specifically alkanes. I understand the concept of combining numerical prefixes with "ane," but only from "pentane" onwards. I don't understand how "meth" is equivalent to "one," "eth" to "two," "prop" to "three," and "but" to "four."


As far as I know, all of the lower-weight alkanes were discovered before a systematic knowledge of what an "alkane" is came into being, thus they were named independently, and for varied reasons (methane possibly from methanol, which was intended to be formed from Greek for "wood alcohol"? Propane and butane coming from the fatty acids they form?)

LemonyCricket wrote:ALSO: Is methanol just methane with a hydroxyl group? Because that would totally blow my mind.


Let your mind be blown.

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Re: Biology Questions

Postby Mr_Rose » Fri Sep 17, 2010 8:27 pm UTC

LemonyCricket wrote:ALSO: Is methanol just methane with a hydroxyl group? Because that would totally blow my mind.

Welcome to Organic Chemistry. :wink:
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Re: Biology Questions

Postby PossibleSloth » Fri Sep 17, 2010 9:09 pm UTC

LemonyCricket wrote:ALSO: Is methanol just methane with a hydroxyl group? Because that would totally blow my mind.

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Re: Biology Questions

Postby Tass » Mon Sep 20, 2010 12:18 pm UTC

LemonyCricket wrote:OKAY, I'M BACK WITH MORE ANNOYING QUESTIONS.


There are no stupid questions only stupid answers. People are free to not respond to you. :)

LemonyCricket wrote:I'm reading a summary of the IUPAC's rules for naming organic molecules, specifically alkanes. I understand the concept of combining numerical prefixes with "ane," but only from "pentane" onwards. I don't understand how "meth" is equivalent to "one," "eth" to "two," "prop" to "three," and "but" to "four."


History. That is just the way the names are, accept it. You have them right.

LemonyCricket wrote:ALSO: Is methanol just methane with a hydroxyl group? Because that would totally blow my mind.


Chemistry is wonderful isn't it. By the way ethanol is also just ethane with a hydroxyl group.

LemonyCricket wrote:ALSO ALSO ALSO: Am I breaking some forum rule by having this thread? I feel annoying and ignorant already; I would hate to be burdened with the guilt and paranoia of inappropriate thread posting as well.


Questions from people curious of science are welcome. So are asking for help with homework in a way that leads to learning and understanding. What is not welcome is trying to get ones homework done without working and without learning.

If you were breaking any rules you would have been told by now. Fire away.

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Re: Biology Questions

Postby Jplus » Mon Sep 20, 2010 6:20 pm UTC

I second the above. Also, I might be somewhat more aware of this thread from now on.
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Re: Biology Questions

Postby Coffee » Wed Sep 22, 2010 4:26 pm UTC

Also you guys: sometimes the questions you ask are on the minds of others as well. And anyway, we need more biology discussion on this forum.
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