Dory's Biology Questions Thread

[Dory]

More of biochemistry here but here's the question:

Would elevation in body temperature effect lipids in the same way as denaturation? Why or why not?

[Dory]

Another question.

I keep hearing that the indians got to America via land bridge. But I've looked at the map of planet earth even 60 million years ago when primates got their start and I see no land bridge. According to what I hear they did it 20000 years ago! The land was far similar to what it is today then.

[Feck]

Another question.

I keep hearing that the indians got to America via land bridge. But I've looked at the map of planet earth even 60 million years ago when primates got their start and I see no land bridge. According to what I hear they did it 20000 years ago! The land was far similar to what it is today then.

Ice ages Dory ?

[Dory]

Another question.

I keep hearing that the indians got to America via land bridge. But I've looked at the map of planet earth even 60 million years ago when primates got their start and I see no land bridge. According to what I hear they did it 20000 years ago! The land was far similar to what it is today then.

Ice ages Dory ?

makes sense!

[GenesForLife]

More of biochemistry here but here's the question:

Would elevation in body temperature effect lipids in the same way as denaturation? Why or why not?

Firstly, Dory, denaturation is the loss of secondary structure, lipids don't usually have a secondary structure, the self organizing nature of lipid bilayers is governed by hydrophobicity and hydrophily, for one thing, and I don't think this changes wrt body temperature, proteins and nucleic acids, though, have a secondary structure and tertiatry structures governed by hydrogen bonds between amino acids in the primary amino acid chain, and these can be broken down by temperature. Then again there are very heat resistant proteins too, for instance the Taq polymerase used in PCR, which can withstand temperatures of up to 110'C.

So to answer your question... Denaturation is an exclusive property of the secondary/tertiary structures of proteins or nucleic acid, and lipids don't have such a secondary structure driven by chemical bonding, so it is very unlikely that they'd be affected by changes in body temperature in the same way as proteins or nucleic acids might.

[Dory]

More of biochemistry here but here's the question:

Would elevation in body temperature effect lipids in the same way as denaturation? Why or why not?

Firstly, Dory, denaturation is the loss of secondary structure, lipids don't usually have a secondary structure, the self organizing nature of lipid bilayers is governed by hydrophobicity and hydrophily, for one thing, and I don't think this changes wrt body temperature, proteins and nucleic acids, though, have a secondary structure and tertiatry structures governed by hydrogen bonds between amino acids in the primary amino acid chain, and these can be broken down by temperature. Then again there are very heat resistant proteins too, for instance the Taq polymerase used in PCR, which can withstand temperatures of up to 110'C.

So to answer your question... Denaturation is an exclusive property of the secondary/tertiary structures of proteins or nucleic acid, and lipids don't have such a secondary structure driven by chemical bonding, so it is very unlikely that they'd be affected by changes in body temperature in the same way as proteins or nucleic acids might.

I understand your point, but you've said that nucleic acids have a secondary and tertiary structures? Do they? It's just a strand, it doesn't create bonds that are not A = T G= C ...right? DNA/RNA don't "fold" in anyway as far as I know.

for instance the Taq polymerase used in PCR, which can withstand temperatures of up to 110'C.

Neat fact.

[mistermack]

Another question.

I keep hearing that the indians got to America via land bridge. But I've looked at the map of planet earth even 60 million years ago when primates got their start and I see no land bridge. According to what I hear they did it 20000 years ago! The land was far similar to what it is today then.

Ice ages Dory ?

makes sense!

There's a fairly strong theory that people 20,000 years ago could make crude dugout canoes, or even some kind of skin kayak.
They would live like eskimos, and travel along the edge of the ice sheet, hunting fish, seals and walrus etc.
As well as that, the ice age dropped the sea levels by drastic amounts, so the land stretched out farther than today.
Some make a pretty good case for humans reaching america from France in this way, as well as from Asia.
The american Clovis point stone technology is almost identical that found in France dating from a similar time.
.

[Dory]

Another question.

I keep hearing that the indians got to America via land bridge. But I've looked at the map of planet earth even 60 million years ago when primates got their start and I see no land bridge. According to what I hear they did it 20000 years ago! The land was far similar to what it is today then.

Ice ages Dory ?

makes sense!

There's a fairly strong theory that people 20,000 years ago could make crude dugout canoes, or even some kind of skin kayak.
They would live like eskimos, and travel along the edge of the ice sheet, hunting fish, seals and walrus etc.
As well as that, the ice age dropped the sea levels by drastic amounts, so the land stretched out farther than today.
Some make a pretty good case for humans reaching america from France in this way, as well as from Asia.
The american Clovis point stone technology is almost identical that found in France dating from a similar time.
.

I see...cool info mist!

[GenesForLife]

The primary structure of DNA is a strand of nucleotides, Dory, when it binds to a complementary strand, it constitutes the secondary structure, to quote wikipedia...

* Primary structure—the raw sequence of nucleobases of each of the component DNA strands;
* Secondary structure—the set of interactions between bases, i.e., which parts of which strands are bound to each other;
* Tertiary structure—the locations of the atoms in three-dimensional space, taking into consideration geometrical and steric constraints; and
* Quaternary structure—the higher-level organization of DNA in chromatin, or to the interactions between separate RNA units in the ribosome or spliceosome.

http://en.wikipedia.org/wiki/Nucleic_acid_structure

And as far as RNA is concerned, you may want to remember that the termination of transcription by Rho independent mechanisms involves auto-looping.

tRNA too is a fine example of the initial RNA strand folding into a myriad of shapes based on self-pairing and looping.



The sequence of bases, read from 5' -> 3' is the primary structure, what you see with all those loops and arms is the secondary structure stemming from the relevant molecular interactions within and amongst the constituents of the primary structure.

So, nucleic acids have a secondary structure...

For further reading, Dory, try reading about Ribozymes as well as shRNA (short hairpin RNA) , also try to read about splicing interactions, where autolooping intermediates may mark the excision point for intragenic introns, which plays a major role in post-transcriptional modification.

[Dory]

The primary structure of DNA is a strand of nucleotides, Dory, when it binds to a complementary strand, it constitutes the secondary structure, to quote wikipedia...

* Primary structure—the raw sequence of nucleobases of each of the component DNA strands;
* Secondary structure—the set of interactions between bases, i.e., which parts of which strands are bound to each other;
* Tertiary structure—the locations of the atoms in three-dimensional space, taking into consideration geometrical and steric constraints; and
* Quaternary structure—the higher-level organization of DNA in chromatin, or to the interactions between separate RNA units in the ribosome or spliceosome.

http://en.wikipedia.org/wiki/Nucleic_acid_structure

And as far as RNA is concerned, you may want to remember that the termination of transcription by Rho independent mechanisms involves auto-looping.

tRNA too is a fine example of the initial RNA strand folding into a myriad of shapes based on self-pairing and looping.



The sequence of bases, read from 5' -> 3' is the primary structure, what you see with all those loops and arms is the secondary structure stemming from the relevant molecular interactions within and amongst the constituents of the primary structure.

So, nucleic acids have a secondary structure...

Neat explanation!

For further reading, Dory, try reading about Ribozymes as well as shRNA (short hairpin RNA) , also try to read about splicing interactions, where autolooping intermediates may mark the excision point for intragenic introns, which plays a major role in post-transcriptional modification.

Ohhhhhhhhhhhhhhhhhh! I remember ribozymes from the RNA world hypothesis! Awesome... they have tertiary structure! An RNA with a tertiary structure! How sci-fi!

The shRNA were a bit difficult to understand, hairpin turns....vectors... RNA interference...U6 or H1 promoter... I'm getting a bit tangled with the terms. But, I won't have you explain me that...I think I got some knowledge holes as far as deep-insight knowledge about RNA functionality.

Not sure how splicing interaction is related to our subject but I couldn't find a decent article anyway. Though I do know about splicing, and alternative splicing, which are a part of gene regulation.

[GenesForLife]

Ohhhhhhhhhhhhhhhhhh! I remember ribozymes from the RNA world hypothesis! Awesome... they have tertiary structure! An RNA with a tertiary structure! How sci-fi!

<pedant> They're real , so they're more sci than sci-fi </pedant>

The shRNA were a bit difficult to understand, hairpin turns....vectors... RNA interference...U6 or H1 promoter... I'm getting a bit tangled with the terms. But, I won't have you explain me that...I think I got some knowledge holes as far as deep-insight knowledge about RNA functionality.

Holes in knowledge are always dangerous, so I am going to explain anyway

Hairpin turns are when you have a sequence like this.... bbbbbbbbbxxxxxxxb'b'b'b'b'b'b'b'b'b' where b and b' are complementary bases in the same order, which leads to complementary base pairing, while x , or the linker section, doesn't do that, the following diagram should make it clearer, what they show here is a construct to induce RNA Interference, which is a way of turning genes off by degrading mRNA. The promoters themselves are used to get the cell to produce shRNA...



This is RNAi made easy for you...

Not sure how splicing interaction is related to our subject but I couldn't find a decent article anyway. Though I do know about splicing, and alternative splicing, which are a part of gene regulation.

http://mcb.asm.org/cgi/content/full/24/24/10505

[Dory]

http://mcb.asm.org/cgi/content/full/24/24/10505

Right, splicosome, that RNA proteins. There aren't many of them are there?

Hairpin turns are when you have a sequence like this.... bbbbbbbbbxxxxxxxb'b'b'b'b'b'b'b'b'b' where b and b' are complementary bases in the same order, which leads to complementary base pairing, while x , or the linker section, doesn't do that, the following diagram should make it clearer, what they show here is a construct to induce RNA Interference, which is a way of turning genes off by degrading mRNA. The promoters themselves are used to get the cell to produce shRNA...

Problem is some terms I hear in that video clip are difficult to find info about... like "endogenous transposition". You could start by explaining that before moving to fancy stuff like the weird variations of RNA that certainly aren't covered in general biology.

[GenesForLife]

http://mcb.asm.org/cgi/content/full/24/24/10505

Right, splicosome, that RNA proteins. There aren't many of them are there?

Hairpin turns are when you have a sequence like this.... bbbbbbbbbxxxxxxxb'b'b'b'b'b'b'b'b'b' where b and b' are complementary bases in the same order, which leads to complementary base pairing, while x , or the linker section, doesn't do that, the following diagram should make it clearer, what they show here is a construct to induce RNA Interference, which is a way of turning genes off by degrading mRNA. The promoters themselves are used to get the cell to produce shRNA...

Problem is some terms I hear in that video clip are difficult to find info about... like "endogenous transposition". You could start by explaining that before moving to fancy stuff like the weird variations of RNA that certainly aren't covered in general biology.

Endo = inside , genous = originating, transposition = or genetic transposition, a mutation in which a chromosomal segment is transferred to a new position on the same or another chromosome.

Basically Dory, RNAi goes like this, say you introduce double stranded RNA into the cell, an enzyme called Dicer slices it up into shorter fragments, this then binds to an enzyme complex called the RNA Induced Silencing Complex, or RISC, which then separates the fragments into a single stranded, bound version, the complex can then bind to complementary mRNA and cleave it, thus blocking expression of the gene which produced the mRNA.



You're right they don't teach these in General Biology, Dory, but this is where some of the coolest molecular biology is.

[Dory]

Endo = inside , genous = originating, transposition = or genetic transposition, a mutation in which a chromosomal segment is transferred to a new position on the same or another chromosome.

Oh right, old Barbaria Mcklinglock (sp?) figured that shit up with corn, IIRC. Something with their melanin, or colour. I don't remember exactly how she did it. I just remember it being termed "transposable elements". Not "endegonous transposition"...kinda confused me.

Basically Dory, RNAi goes like this, say you introduce double stranded RNA into the cell

wtf, RNA can be double-stranded? Since when???

an enzyme called Dicer slices it up into shorter fragments, this then binds to an enzyme complex called the RNA Induced Silencing Complex, or RISC, which then separates the fragments into a single stranded, bound version, the complex can then bind to complementary mRNA and cleave it, thus blocking expression of the gene which produced the mRNA.

So it has to go through all this complex stages to become a sort of molecular knife that cleaves mRNA's?

[Dory]

Okay, I reread how Barbra McClintock (now got her name right) did it, or what did she figure out exactly anyway. How she did it was probably complex...I assume she used some radioactive elements or looked at some cytological markers on the chromosomes to find out about it. Yes, it had to do with corn's pigmentation. She somehow tracked down its mutation to understand exactly what mutated where. So yea, I remembered that!