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  Topic: Biology @ Coastal Carolina & UNCW, Lou FCD Goes to School< Next Oldest | Next Newest >  
keiths



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(Permalink) Posted: Sep. 21 2008,01:49   

Quote (Lou FCD @ Sep. 20 2008,22:21)

This is where the hook-up occurs.


Dig the dehydration sex.  But why does she get to have an orgasm while he doesn't?

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Lou FCD



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(Permalink) Posted: Sep. 21 2008,06:12   

Quote (keiths @ Sep. 21 2008,02:45)
Quote (Lou FCD @ Sep. 20 2008,22:21)
In order to digest cellulose, water and cellulate are needed. Animals don't make cellulate in their bodies, and so can't digest cellulose.

Lou, I think you mean "cellulase" rather than "cellulate".
 
Quote
Breakdown of any -ose (sugar) is facilitated by a corresponding -ate. Breakdown of lactose needs lactate, etc.

Ditto here.  You really want to say
 
Quote
Breakdown of any -ose (sugar) is facilitated by a corresponding -ase. Breakdown of lactose needs lactase, etc.

The distinction is important.  A lactate is completely different from a lactase, for example.

You're right. It was late.

Thanks for the correction.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Lou FCD



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(Permalink) Posted: Sep. 21 2008,06:23   

Quote (keiths @ Sep. 21 2008,02:49)
Dig the dehydration sex.  But why does she get to have an orgasm while he doesn't?

Because I ran out of gas and the artistic editing ended prematurely.

XVIVO better look out. There's a new animator in town.

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Texas Teach



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(Permalink) Posted: Sep. 21 2008,08:09   

Quote (Lou FCD @ Sep. 21 2008,06:23)
XVIVO better look out. There's a new animator in town.

Better tell ERV to keep an eye on it for you, or it might appear in one of the Dr Dr's talks.  Something about how materialist biochemistry leads to corruption of our youth.

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"Creationists think everything Genesis says is true. I don't even think Phil Collins is a good drummer." --J. Carr

  
Lou FCD



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(Permalink) Posted: Sep. 21 2008,11:39   

Quote (Texas Teach @ Sep. 21 2008,09:09)
Quote (Lou FCD @ Sep. 21 2008,06:23)
XVIVO better look out. There's a new animator in town.

Better tell ERV to keep an eye on it for you, or it might appear in one of the Dr Dr's talks.  Something about how materialist biochemistry leads to corruption of our youth.

Well, it is licensed under the CC, so as long as they abode by the terms of that...

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Spottedwind



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(Permalink) Posted: Sep. 22 2008,08:05   

I'm so glad you are continuing these...except that this is the area of biology that I was always weakest. :)  So it's probably actually a good thing to go over these basics again.

I admit, I'm an organism (and above) level person.  I just understand that more and it fascinates me more.  Not that the chemical, cellular, etc level isn't amazing...I just don't follow it as well.

Also, to all those adding in the discussion...thanks to you too.  The extra info and clarification is great.

  
Lou FCD



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(Permalink) Posted: Sep. 23 2008,06:36   

I'm trying to get them caught up, Spottedwind.

I noticed that on my exam, there was a significant cluster to the questions I missed, and that cluster was in the area of notes I hadn't put online yet.

Copying the notes really does seem to help.

I was disappointed: I got an 88. The highest score in all three sections was a 91, and the median score was in the 60s. One of the questions I missed was the molecular formula of maltose. What did I do wrong? I forgot to take out the water molecule from the dehydration synthesis.

Hence the graphic above that will ensure that I never ever repeat that mistake. The sugar porn has a purpose, and was not at all gratuitous.

At the moment, we're actually doing the tour of the cell, and as I sat through the lecture taking notes, I couldn't help but be reminded of The Inner Life of the Cell, and as Doc explained the different functions of different parts, I could visualize parts of the animation. I kept thinking, "Oh! so THAT'S what that thingy was that did thus and so".

The images were especially strong in my mind when we started talking about the Endoplasmic Reticulum, the Transport Vesicles, and the Golgi Apparatus. In a way, it was kind of odd to have a picture in my mind of what was going on before I could name the parts, rather than the usual way of naming things and then seeing pictures of them.

I <3 XVIVO.

Lab yesterday was kind of cool, in that it was the first time we got to use microscopes. (We have monocular compound light microscopes, fyi.) It was sort of a let-down when I was looking at my cheek cells, though. I guess I was expecting to see all the cool stuff we had been discussing in lecture yesterday morning. I saw a circle with a blob in it.

:(

WE NEED MORE POWER SCOTTY! REVERSE THE DAMNED POLARITY OR SOMETHIN', WILL YA'?

Edit to add: On the upside, I also got my second English essay back yesterday - I got an A+

Edited by Lou FCD on Sep. 23 2008,07:38

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Lou FCD



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(Permalink) Posted: Sep. 23 2008,20:16   



My notes and thoughts from Biology 111, for Monday, September 15, 2008. The entire series can be found here.

The class started with a reminder that the next class period (Wednesday the 17<sup>th</sup>) would be our first exam.

Then there was a short review of Hydrocarbons generally, and carbohydrates specifically, just to get us back to the place where we had left off.

We picked up this lecture with our discussion of Lipids.

2. Lipids

Triglycerides ---> Fats &amp; Oils



Glycerol + 3 Fatty Acids

When a glycerol molecule, C<sub>3</sub>H<sub>5</sub>(OH)<sub>3</sub> (the vertical part on the left of the image), picks up three fatty acids (the long strings of C and H on the right), they combine to form a triglyceride.

Triglycerides are fats and oils. If the long fatty acid chains all remain straight, each carbon bonding with two Hydrogen atoms and its two neighbor Carbon atoms, the triglyceride can pack densely, and thus becomes a solid at room temperature. This is a saturated fat.



If one or more of the long fatty acids develops a "kink", ie two Carbons double bond and dump a Hydrogen, the stack can not pack as densely, and thus becomes a liquid at room temperature. This is an unsaturated oil. If there is one kink, it's a monounsaturated oil, and if more than one, it's a polyunsaturated oil.

Ta-da. It was kind of cool to suddenly understand the difference between them after having heard the terms for so long in reference to food labels.

We can measure energy in units called calories.

Because of fat's high percentage of hydrocarbons (all along those fatty acid chains), it has a high caloric content. For comparison, a gram of fat contains 9 calories, while a gram of carbohydrates contains 4 calories. Remember that those Hydrogen - Carbon bonds are high energy content because of the non-polar covalent bond.

Some properties of solid fats:

They are good insulators. (whales, walrus, Rush Limbaugh, etc. are good examples.)

They also make good shock absorbers. Vital organs are wrapped in fat, especially where not protected by bone.

3. Proteins

Life on earth is protein based.



Proteins are macromolecules. They are polymers of amino acids.

On the left of this structural diagram of an amino acid is the amino functional group, and on the right, the carboxyl functional group. Note the Oxygen and the Hydroxide dangling off the end there. Those two really make an amino acid hydrophillic.

Note the big R in a circle. Checking the Periodic Table, you'll note that R is not an element. R is used as a place holder for whatever plug and play molecule might go there in any given amino acid. There are hundreds of different amino acids, depending on what gets plugged in there. Living things use twenty different amino acids to make proteins.

The R is what makes each of them different.

Amino Acids

There are three groups of amino acids.

Nine of them are nonpolar ---> They are made almost entirely of C and H

Six of them are polar.

Five of them are electrically charged  ---> two are negatively charged, and three positively charged.

There's a nice amino acid chart on page 79 of our text book that shows these amino acids in their groups, and it will be important all semester. I won't bother to reproduce it here, though.



When two amino acids hook up, it's by a dehydration synthesis, similar to what we saw before in sugars. In this case though, we call it a peptide bond.

When two amino acids form a peptide bond, it's called a dipeptide. three is a tripeptide, and more than three is a polypeptide.

Long chains of amino acids, about when they reach 100 or so in a chain (not a hard and fast number), are called proteins. The average length of a protein in the human body is about 400 amino acids long.

There are three levels of protein structure that we looked at:

A) Primary Structure ---> proteins are a sequence of amino acids. A dipeptide can have 400 different possible primary structures (20 possible amino acids in the first position, 20 in the second = 20 X 20 = 400). A tripeptide can have 8,000 (20 X 20 X 20), a polypeptide of four amino acids 160,000 (20 X 20 X 20 X 20), etc. Remember, with proteins we're talking about at least about 100 amino acids long. The sequence of amino acids is critical at each and every location.

B) Secondary Structure ---> Hydrogen Bonding causes kinking, curling, twisting, etc, causing a protein to look like a twisted or knotted slinky.

C) Tertiary Structure ---> Complex 3D shape caused by the R groups interacting with each other and with the water solution in which they reside. The long molecules are electrically charged in places, polar in places and nonpolar in other places. The nonpolar parts are hydrophobic, the polar parts hydrophilic. So the nonpolar parts tend to wind up in the middle, while the polar parts and the fully charged parts tend to wind up around the outside, close to the water.

The end shape of a protein is determined by its primary structure and the Hydrogen Bonds, and the shape determines its function, much like the shape of a key determines which lock it will open.

Denaturation, the unwinding of the protein, is a result of broken Hydrogen bonds. Extreme heat or pH will denature a protein, and since shape determines function, a denatured protein will cease to function properly (or at all). High fever for instance (body temp of 42 or 43°) will denature the body's proteins and cause death. Death is bad.

Functions of Proteins

Body structure ---> Much of the body's structure is formed by proteins.

Contraction ---> Contraction of muscles (how you move) is a function of proteins

Enzymes ---> are proteins

Transport of molecules through the body

Hormones ---> insulin, growth hormone

Receptors ---> I apparently forgot to write down what Doc said about this.

These are just a few of the many functions of proteins.

4. Nucleic Acids

Macromolecules ---> Biggest of organic molecules

Polymers of nucleotides

pentose, phosphate group, nitrogenous base

Two types of Nucleic Acids ----> Ribonucleic Acid (RNA) and Deoxyribonucleic Acid (DNA)

We'll discuss these more later on, but here's where the lecture ended.

The following class period was our first exam, so there were no lecture notes for Wednesday, September 17<sup>th</sup>. We picked it up on Friday, September 19<sup>th</sup>.

Quote
From whence came the art:

The first image is of our textbook, Biology, Eighth Edition, by Campbell &amp; Reese et al.

Other images by me and are licensed under the Creative Commons Attribution- NonCommercial- Share Alike 3.0 License.


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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Henry J



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(Permalink) Posted: Sep. 23 2008,23:25   

Quote
Some properties of solid fats:

They are good insulators. (whales, walrus, Rush Limbaugh, etc. are good examples.)


You came close to owing me a new keyboard with that one. :p

Quote
A dipeptide can have 400 different possible primary structures (20 possible amino acids in the first position, 20 in the second = 20 X 20 = 400). A tripeptide can have 8,000 (20 X 20 X 20), a polypeptide of four amino acids 160,000 (20 X 20 X 20 X 20), etc.


What if one protein is identical to another one flipped around? Seems like that formula would double count the ones that aren't their own inverse. (e.g., ABCAB and BACBA, where the letters are arbitrary amino acid units, are really the same polypeptide.)

Henry

  
Lou FCD



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(Permalink) Posted: Sep. 24 2008,05:36   

Quote (Henry J @ Sep. 24 2008,00:25)
Quote
Some properties of solid fats:

They are good insulators. (whales, walrus, Rush Limbaugh, etc. are good examples.)


You came close to owing me a new keyboard with that one. :p

Quote
A dipeptide can have 400 different possible primary structures (20 possible amino acids in the first position, 20 in the second = 20 X 20 = 400). A tripeptide can have 8,000 (20 X 20 X 20), a polypeptide of four amino acids 160,000 (20 X 20 X 20 X 20), etc.


What if one protein is identical to another one flipped around? Seems like that formula would double count the ones that aren't their own inverse. (e.g., ABCAB and BACBA, where the letters are arbitrary amino acid units, are really the same polypeptide.)

Henry

I had the same thought, Henry. I don't think the point was a specific number, but rather a simplified illustration of just how important and varied the sequence is when dealing with proteins. We certainly weren't tested on the exact number of possible sequences of amino acids in a dipeptide.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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fusilier



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(Permalink) Posted: Sep. 24 2008,07:13   

Quote (Henry J @ Sep. 24 2008,00:25)
{snip}


What if one protein is identical to another one flipped around? Seems like that formula would double count the ones that aren't their own inverse. (e.g., ABCAB and BACBA, where the letters are arbitrary amino acid units, are really the same polypeptide.)

Henry

Close, but not quite.

If a polypeptide is a real palindrome - abcdeedcba, for example - then, yeah, you just have the same compound.  Your example, however, is of two entirely different compounds, because you must read from only one direction.

I like to use the example of the elephant parade in Disney's "Dumbo."  Amino acids have a trunk, the -COOH end, and a tail, the HHN- end.  A peptide bond is solely a trunk-to-tail arrangement, and you must read the parade starting with the first elephant - the one whose trunk is not connected to another elephant's tail.  (It's perfectly OK to call the amino end the trunk and the acid end the tail, I'm just giving an illustration.)

"Nutrasweet" brand artificial sweetener is a dipeptide called aspartame, see http://www.chm.bris.ac.uk/motm/aspartame/aspartameh.html . If you reverse the order of the amino acids, then you have an entirely different compound which does not have the same chemical properties.

Just like at the end of "Dumbo," when the original boss-lady elephant is at the rear end of the parade and Dumbo's Mom is now the leader.

Same elephants, but a different parade.

ETA:  hunh, I can't get a "subscript" tag to work.  Oh well.

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fusilier
James 2:24

  
Wesley R. Elsberry



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(Permalink) Posted: Sep. 24 2008,07:19   

Why not?

Use square instead of angle brackets...

Wh<sub>y</sub> no<sup>t</sup>?

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
Lou FCD



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(Permalink) Posted: Sep. 24 2008,09:09   

Quote (fusilier @ Sep. 24 2008,08:13)
I like to use the example of the elephant parade in Disney's "Dumbo."  Amino acids have a trunk, the -COOH end, and a tail, the HHN- end.  A peptide bond is solely a trunk-to-tail arrangement, and you must read the parade starting with the first elephant - the one whose trunk is not connected to another elephant's tail.  (It's perfectly OK to call the amino end the trunk and the acid end the tail, I'm just giving an illustration.)

Oh, right, because



would not be the same as



because the R1 in the first image would be close to the acid end, while in the second it would be close to the amino end of the dipeptide, giving the two completely different shapes, and thus functions.

Edited by Lou FCD on Sep. 24 2008,10:09

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Lou FCD



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(Permalink) Posted: Sep. 24 2008,09:10   

Quote (Wesley R. Elsberry @ Sep. 24 2008,08:19)
Wh<sub>y</sub> no<sup>t</sup>?

Use square instead of angle brackets...

Wh<sub>y</sub> no<sup>t</sup>?

When you hit the preview button, the bbcode has been changed to html code, Wesley. Same when you hit submit, then try to go back and edit.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Tracy P. Hamilton



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(Permalink) Posted: Sep. 24 2008,10:08   

Quote (Lou FCD @ Sep. 23 2008,20:16)


If one or more of the long fatty acids develops a "kink", ie two Carbons double bond and dump a Hydrogen, the stack can not pack as densely, and thus becomes a liquid at room temperature. This is an unsaturated oil. If there is one kink, it's a monounsaturated oil, and if more than one, it's a polyunsaturated oil.



Trans fats are like the unsaturated one you mention, except that the double bond does not introduce a kink, so trans fat does not lower lipid density like the good unsaturated oils.  The health risk of trans fat is actually higher than saturated fat.

Quote



Denaturation, the unwinding of the protein, is a result of broken Hydrogen bonds. Extreme heat or pH will denature a protein, and since shape determines function, a denatured protein will cease to function properly (or at all). High fever for instance (body temp of 42 or 43°) will denature the body's proteins and cause death. Death is bad.



I find denaturing of protein at 42 hard to believe! It is possible I suppose.

 
Quote


Functions of Proteins

Receptors ---> I apparently forgot to write down what Doc said about this.



Receptors are proteins that "receive" ligand molecules and in turn produce a change in the receptor that produces a signal of some sort.  Regulation is done via the production of these molecules.  

An example is G-protein coupled receptors.

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"Following what I just wrote about fitness, you’re taking refuge in what we see in the world."  PaV

"The simple equation F = MA leads to the concept of four-dimensional space." GilDodgen

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Tracy P. Hamilton



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(Permalink) Posted: Sep. 24 2008,10:19   

Quote (Lou FCD @ Sep. 20 2008,13:18)
4. Phospate Group



A Phosphate Group is a Phosphorus bonded with two negatively charged Oxygen atoms, one regular Oxygen atom, and double bonded with one Oxygen atom. It's molecular formula is PO<sub>4</sub><sup>2-</sup> or sometimes OPO<sub>3</sub><sup>2-</sup>, to separate the double bonded Oxygen.

Here is where the lecture ended. Although I asked in a later lecture about the odd bondings here that seem to break the rules that we earlier set forth, Doc basically said, "It's complicated, and you don't need to know that for this class, though you'll learn about it in a Chemistry class if you take one." Ok, fair enough.


Chemical education discourages the use of the double bond in phosphate, and in sulfate groups as well.  As you noticed, it violates the octet rule, and does so unnecessarily!  There are some molecules where we chemists violate the rule out of necessity, such as having five atoms bonded to P, which requires 5 bonds.

The double bonds in phosphate and sulfate are historical, hence the biologists still use it a lot because that is how they learned it.  :O

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"Following what I just wrote about fitness, you’re taking refuge in what we see in the world."  PaV

"The simple equation F = MA leads to the concept of four-dimensional space." GilDodgen

"We have no brain, I don't, for thinking." Robert Byers

  
Tracy P. Hamilton



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(Permalink) Posted: Sep. 24 2008,10:28   

Quote (Lou FCD @ Sep. 21 2008,00:21)
In order to digest cellulose, water and cellulase are needed. Animals don't make cellulase in their bodies, and so can't digest cellulose. Hearkening back to the termite lab, remember that termites subsist on a diet of wood. Wood is made of cellulose. How do they do that? They depend on little microorganisms to digest the cellulose for them.

Some animals do produce cellulase!  Termites are an example.

 
Quote

Scientific Correspondence

Nature 394, 330-331 (23 July 1998) | doi:10.1038/28527
A cellulase gene of termite origin

Hirofumi Watanabe1, Hiroaki Noda1, Gaku Tokuda2 and Nathan Lo3

The traditional view of cellulose digestion in animals is that they cannot produce their own cellulase, and so rely on gut microorganisms to hydrolyse cellulose. A classic example of this symbiosis is that between phylogenetically lower termites and the unicellular organisms (protists) that colonize their hindguts: cellulose fermented to acetate by the protists can be used as an energy source by the termite1. There is evidence for the production of endogenous cellulase components by termites and other wood-feeding insects2; however, an unambiguous origin for such enzymes1 has not been established, to our knowledge, until now. Here we describe the first insect cellulase-endoding gene to be identified, RsEG, which encodes an endo-beta-1,4-glucanase (EC 3.2.1.4) in the termite Reticulitermes speratus


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"Following what I just wrote about fitness, you’re taking refuge in what we see in the world."  PaV

"The simple equation F = MA leads to the concept of four-dimensional space." GilDodgen

"We have no brain, I don't, for thinking." Robert Byers

  
Henry J



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(Permalink) Posted: Sep. 24 2008,11:04   

Quote (Tracy P. Hamilton @ Sep. 24 2008,09:19)
Quote (Lou FCD @ Sep. 20 2008,13:18)
4. Phospate Group



A Phosphate Group is a Phosphorus bonded with two negatively charged Oxygen atoms, one regular Oxygen atom, and double bonded with one Oxygen atom. It's molecular formula is PO<sub>4</sub><sup>2-</sup> or sometimes OPO<sub>3</sub><sup>2-</sup>, to separate the double bonded Oxygen.

Here is where the lecture ended. Although I asked in a later lecture about the odd bondings here that seem to break the rules that we earlier set forth, Doc basically said, "It's complicated, and you don't need to know that for this class, though you'll learn about it in a Chemistry class if you take one." Ok, fair enough.


Chemical education discourages the use of the double bond in phosphate, and in sulfate groups as well.  As you noticed, it violates the octet rule, and does so unnecessarily!  There are some molecules where we chemists violate the rule out of necessity, such as having five atoms bonded to P, which requires 5 bonds.

The double bonds in phosphate and sulfate are historical, hence the biologists still use it a lot because that is how they learned it.  :O

So is the proper way to do it to put a - sign on three of the O's and a + sign on the P?

  
Louis



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(Permalink) Posted: Sep. 24 2008,11:20   

Quote (Tracy P. Hamilton @ Sep. 24 2008,16:19)
Quote (Lou FCD @ Sep. 20 2008,13:18)
4. Phospate Group



A Phosphate Group is a Phosphorus bonded with two negatively charged Oxygen atoms, one regular Oxygen atom, and double bonded with one Oxygen atom. It's molecular formula is PO<sub>4</sub><sup>2-</sup> or sometimes OPO<sub>3</sub><sup>2-</sup>, to separate the double bonded Oxygen.

Here is where the lecture ended. Although I asked in a later lecture about the odd bondings here that seem to break the rules that we earlier set forth, Doc basically said, "It's complicated, and you don't need to know that for this class, though you'll learn about it in a Chemistry class if you take one." Ok, fair enough.


Chemical education discourages the use of the double bond in phosphate, and in sulfate groups as well.  As you noticed, it violates the octet rule, and does so unnecessarily!  There are some molecules where we chemists violate the rule out of necessity, such as having five atoms bonded to P, which requires 5 bonds.

The double bonds in phosphate and sulfate are historical, hence the biologists still use it a lot because that is how they learned it.  :O

So are you saying there's no pi character to the sulfur-oxygen or phosphorous-oxygen "double" bond?

If so I beg to differ!

The bond lengths alone demonstrate p pi-d pi bonding.

And now a brief diversion:

For those not of the Secret Chemist Club, here's a brief and very simplified explanation:

The chemical drawings we use are simplified pictures of what's really going on, and we tend to use one resonance canonical as opposed to a matrix containing all of them, but as with so many things that's a convenient shorthand. Lou's prof was right, in a chemistry class you'd learn a LOT more about it.

Here's a very simple reason why these things can get complicated(ish): resonance.

If you look at the picture below and imagine that the red oxygen is an isotopically labelled atom (i.e. 18O instead of "normal" 16O) you can see that the label is scrambled by the resonance of the double bond in the phosphate. The blue arrows denote movement of electrons, for the uninitiated! (Even this is a gross oversimplification)



The reason this works is, simply put, because not all of the bonds are going to the outer (valence) orbitals of phosphorous. The similarity in energy between the full p orbitals oxygen and the large and available empty d orbitals on phosphorus/sulfur allow a "double" bond to form.

Another classic example of this is in phosphorous/sulfur double bonds to carbon. There is, to some extent, restricted rotation about the "double" bond, indicating it's pi character. Granted this pi character is a lot less than a carbon-carbon double bond, but it is sufficient to noticeably (i.e. chemically and spectroscopically) restrict rotation about the bond.

Also because pi bonds tend to be shorter than the corresponding sigma bond, the multiplicity of the bond (i.e. single, double etc) and thus to some degree the nature (sigma, pi) of the bond can be spectroscopically determined. Obviously this also has implications for bond strength, i.e. multiple bonds tend to be stronger than the corresponding single bond. This is because you have a sigma and a pi bond forming your double bond, as opposed to just a sigma bond forming your single bond.

And look I did that almost without referring to orbitals or hybridisation or overlap or electronegativity or...... oh dear! I get a prize for that surely?

Wikipedia on sigma and pi bonding. Not brilliant explanations actually, but enough to get an idea. The diagrams suck mighty big IMO. Almost worth me registering to edit them.......hmmmm that way madness and no job lies!

If absolutely necessary I'll explain bonding in a bit more detail. Be warned: I'll even use maths if necessary, and the word "quantum" may feature.

Shock, horror!

Louis

Edited to fix my pi

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Louis



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(Permalink) Posted: Sep. 24 2008,11:22   

Quote (Henry J @ Sep. 24 2008,17:04)
Quote (Tracy P. Hamilton @ Sep. 24 2008,09:19)
 
Quote (Lou FCD @ Sep. 20 2008,13:18)
4. Phospate Group



A Phosphate Group is a Phosphorus bonded with two negatively charged Oxygen atoms, one regular Oxygen atom, and double bonded with one Oxygen atom. It's molecular formula is PO<sub>4</sub><sup>2-</sup> or sometimes OPO<sub>3</sub><sup>2-</sup>, to separate the double bonded Oxygen.

Here is where the lecture ended. Although I asked in a later lecture about the odd bondings here that seem to break the rules that we earlier set forth, Doc basically said, "It's complicated, and you don't need to know that for this class, though you'll learn about it in a Chemistry class if you take one." Ok, fair enough.


Chemical education discourages the use of the double bond in phosphate, and in sulfate groups as well.  As you noticed, it violates the octet rule, and does so unnecessarily!  There are some molecules where we chemists violate the rule out of necessity, such as having five atoms bonded to P, which requires 5 bonds.

The double bonds in phosphate and sulfate are historical, hence the biologists still use it a lot because that is how they learned it.  :O

So is the proper way to do it to put a - sign on three of the O's and a + sign on the P?

NOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO!

Well, yes-ish. Well, no. Maybe. Ylides!

The best approach is to realise that chemical drawing are massive oversimplifications.

Louis

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Lou FCD



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(Permalink) Posted: Sep. 24 2008,11:50   

Quote (Tracy P. Hamilton @ Sep. 24 2008,11:28)
Quote (Lou FCD @ Sep. 21 2008,00:21)
In order to digest cellulose, water and cellulase are needed. Animals don't make cellulase in their bodies, and so can't digest cellulose. Hearkening back to the termite lab, remember that termites subsist on a diet of wood. Wood is made of cellulose. How do they do that? They depend on little microorganisms to digest the cellulose for them.

Some animals do produce cellulase!  Termites are an example.

 
Quote

Scientific Correspondence

Nature 394, 330-331 (23 July 1998) | doi:10.1038/28527
A cellulase gene of termite origin

Hirofumi Watanabe1, Hiroaki Noda1, Gaku Tokuda2 and Nathan Lo3

The traditional view of cellulose digestion in animals is that they cannot produce their own cellulase, and so rely on gut microorganisms to hydrolyse cellulose. A classic example of this symbiosis is that between phylogenetically lower termites and the unicellular organisms (protists) that colonize their hindguts: cellulose fermented to acetate by the protists can be used as an energy source by the termite1. There is evidence for the production of endogenous cellulase components by termites and other wood-feeding insects2; however, an unambiguous origin for such enzymes1 has not been established, to our knowledge, until now. Here we describe the first insect cellulase-endoding gene to be identified, RsEG, which encodes an endo-beta-1,4-glucanase (EC 3.2.1.4) in the termite Reticulitermes speratus

See, Doc specifically talked about the microcritters producing the cellulase for the termites. I'll have to point him to that.

Thanks for your input here, by the way. I appreciate the assists.

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Lou FCD



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(Permalink) Posted: Sep. 24 2008,11:57   

Louis,

When you have time, I'd appreciate a bit more on that. Obviously not a rush as it's not for Bio class, but for my personal edification.

Thanks

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Louis



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(Permalink) Posted: Sep. 24 2008,12:05   

Quote (Lou FCD @ Sep. 24 2008,17:57)
Louis,

When you have time, I'd appreciate a bit more on that. Obviously not a rush as it's not for Bio class, but for my personal edification.

Thanks

No worries. Anything specific? Or just "general principles of chemical bonding"?

Louis

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Lou FCD



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(Permalink) Posted: Sep. 24 2008,12:16   

Quote (Louis @ Sep. 24 2008,13:05)
Quote (Lou FCD @ Sep. 24 2008,17:57)
Louis,

When you have time, I'd appreciate a bit more on that. Obviously not a rush as it's not for Bio class, but for my personal edification.

Thanks

No worries. Anything specific? Or just "general principles of chemical bonding"?

Louis

General principles in general, and the specific case above re: P specifically, would be grand.

I'm not getting what you're saying, perhaps because I don't understand p and s orbitals, etc.

I had a Chem class back in the dark ages (95ish), but that's a long time gone, frankly.

ETA: In other words, I can't understand the sentences because I don't know all the words, if that helps.

Edited by Lou FCD on Sep. 24 2008,13:17

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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midwifetoad



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(Permalink) Posted: Sep. 24 2008,12:53   

Quote
In other words, I can't understand the sentences because I don't know all the words, if that helps.

Life would be so much more enjoyable if we could hear this said more often. Whenever it's true, for instance.

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Henry J



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(Permalink) Posted: Sep. 24 2008,13:07   

Quote
I'm not getting what you're saying, perhaps because I don't understand p and s orbitals, etc.


An orbital can have 1 or 2 electrons.
The 1st shell of an atom has only an s orbital.
That's all H and He (1-2) have.
The 2nd shell has an s and three p orbitals.
Li and Be (3-4) use only the s orbital of their 2nd shell.
B through Ne (5-10) add electrons to their 2nd shell p orbitals.
IIRC, B, C, and N (5-7) add 1 electron to each p orbital,
and O, F and Ne (8-10) add the 2nd electron to each of those p's.
Na through Ar (11-18) do the same for the third shell.
K and Ca (19-20) add electrons to the 4th shell s orbital.
Then it gets interesting: Sc through Zn (21-30) add electrons to the d orbital of their 3rd shell, even though they're in the 4th period.

The 1st shell has only the s orbital.
The 2nd shell has s and three p's.
The 3rd has s, p, and d.
The 4th has s, p, d, and f.

The one s orbital of a shell can hold up to 2 electrons.
The three p orbitals of a shell can hold up to 6.
The five d orbitals of a shell, up to 10.
The seven f orbitals of a shell, up to 14.
I wonder if they've picked a letter for the next type of orbital, which I presume would appear in elements 121 and up.

http://www.webelements.com/

  
stevestory



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(Permalink) Posted: Sep. 24 2008,13:16   

Quote (Lou FCD @ Sep. 24 2008,13:16)
I'm not getting what you're saying, perhaps because I don't understand p and s orbitals, etc.

The bond shapes are kinda cool. s is like a basketball, p is like a dumbell, sigma, pi, hybrids like sp3 etc. It's usually somewhere around chapter 1 or 2 of an Organic Chem textbook. Not necessary for your bio class, but kinda interesting if you have a free afternoon.

   
Louis



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(Permalink) Posted: Sep. 24 2008,14:00   

Quote (Lou FCD @ Sep. 24 2008,18:16)
Quote (Louis @ Sep. 24 2008,13:05)
 
Quote (Lou FCD @ Sep. 24 2008,17:57)
Louis,

When you have time, I'd appreciate a bit more on that. Obviously not a rush as it's not for Bio class, but for my personal edification.

Thanks

No worries. Anything specific? Or just "general principles of chemical bonding"?

Louis

General principles in general, and the specific case above re: P specifically, would be grand.

I'm not getting what you're saying, perhaps because I don't understand p and s orbitals, etc.

I had a Chem class back in the dark ages (95ish), but that's a long time gone, frankly.

ETA: In other words, I can't understand the sentences because I don't know all the words, if that helps.

It makes perfect sense, and I was knocking a post together when something came up.

Anyway, I have to get home at some point today, so I'm off. I see that Henry and Steve have kicked proceedings off, so I'll expand tomorrow or Friday if and when I get a minute. Sound fair?

Louis

ETA: The Wikipedia articles on atomic orbitals and Electron configuration are a good place to start.

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Lou FCD



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(Permalink) Posted: Sep. 24 2008,14:01   

Midwife, it seems the only route to go, if one wants to understand the sentences.

Thanks for the enumeration, Henry. But what makes an s orbital different from a p orbital? Why is it different?

Is this what you were touching on, Steve? Shape? If so, why is the shape of one orbital different from the shape of another in the same orbital (or even in different orbitals, for that matter)? Why does the second shell have one s and three p orbitals? Why not two and two or all of one or the other, for instance?

And what makes a d or f orbital different from s or p orbitals?

Does the p stand for pi and the s for sigma, as in Louis' previous explanation, or is that a whole 'nuther thing?

I think I'd have to get all that before I could even begin to understand resonance and continue with his explanation.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Lou FCD



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(Permalink) Posted: Sep. 24 2008,14:03   

Quote (Louis @ Sep. 24 2008,15:00)
Anyway, I have to get home at some point today, so I'm off. I see that Henry and Steve have kicked proceedings off, so I'll expand tomorrow or Friday if and when I get a minute. Sound fair?

Louis

ETA: The Wikipedia articles on atomic orbitals and Electron configuration are a good place to start.

Awesome. As I said, no rush, this is to satisfy my own personal curiosity.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

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