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



Posts: 5786
Joined: Mar. 2005

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

Quote (dogdidit @ Sep. 12 2008,05:54)
BTW Henry J is right, we shouldn't be ignoring gravity; why, it's the strongest force in the universe doncha know!  :p

Yeah, ignoring gravity can sometimes have sidewalk effects.

  
Tracy P. Hamilton



Posts: 1239
Joined: May 2006

(Permalink) Posted: Sep. 12 2008,12:45   

Quote (BWE @ Sep. 12 2008,03:20)
Also, if this turns out to be repeatable:
Quote
Rübhausen says the difference in bond lengths could help explain some surprising results he and his collaborators reported last year. His team was comparing RNA made with ordinary organic molecules to RNA made of those molecules’ mirror images. Their goal was to shed light on why life always uses one type of molecule rather than the other.

Chemically, the molecules and their mirror images should be identical. But the researchers found small differences in the energy it takes to excite electrons in the two types of RNA — but only when the RNA molecules were suspended in ordinary water. When the researchers repeated the experiment in heavy water, the differences disappeared.


It will quite possibly be very important.

Betcha it won't be replicated.  Pun intended.

--------------
"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



Posts: 1239
Joined: May 2006

(Permalink) Posted: Sep. 12 2008,13:02   

Quote (dogdidit @ Sep. 12 2008,06:54)
Quote (Louis @ Sep. 12 2008,03:10)
   
Quote (Henry J @ Sep. 12 2008,05:12)
   
Quote
The extra neutron is electrically neutral, and can interact with the electron cloud only weakly (literally),


Is it that it interacts weakly with the electrons, or simply that it doubles the inertia of the atom it's in, making it more resistant to getting shoved around by outside forces? (Also heavier gravitationally, of course.)

Henry

The second one.

Louis

Ah, hadn't considered momentum. I heard hoofbeats and thought of zebras. Great discussion, Louis and BWE! Though it's more science than I can handle right now (7:30 am and in a seriously un-caffeinated state). I'll flatter myself by pretending I'll read up and understand it later.

BTW Henry J is right, we shouldn't be ignoring gravity; why, it's the strongest force in the universe doncha know!  :p

The following may take a bit of work, but it will be worth it for those who really want to understand the PRIMARY kinetic isotope effect.  Here is a wikipedia article with a picture that may illustrate why H and D have different bond properties.  http://en.wikipedia.org/wiki/Morse_potential

See those green horizontal lines?  They denote harmonic vibration energy of (v+0.5) times Planck's constant times frequency.  
Frequency is sqrt(k/mass), where k is the curvature of the parabola.  
E=1/2 k (r-re)^2, the second derivative of E with respect to r is k.  
Force is -dE/dr, or -k (r-re).  
F = -k (r-re) is Hooke's Law.

H is lighter than D, so the frequency is higher for H than D, and the green lines are higher for H than for D.  This analysis carries over to the blue curve, and blue horizontal lines, just more complicated.  However, you can't get out of the green well, which is infinite (i.e. harmonic oscillator breaks down), so in real life you have the blue curve.

The lowest energy any molecule can have is with v=0.  The v=0 level is lower for D, so the D0 is larger for D.  D0 is the bond energy.  So R-D bonds are stronger than R-H bonds.

What about bond distance?  The bond vibrates back and forth, but one can see from the blue curve that for a particular energy, the amount of stretch exceeds the amount of compression, so that the average distance is greater than re.  Since the energy level for D is lower than H, the stretching and compression are both smaller, but the stretch more so, so that re is shorter for R-D.  

R is boring organic stuff of interest only to Louis.

--------------
"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

  
BWE



Posts: 1902
Joined: Jan. 2006

(Permalink) Posted: Sep. 12 2008,13:35   

Tracy,
I wrote down the equations from the Wiki page and tried to figure it out but I'm sadly lacking.

I'm reading "A Stubbornly Persistent Illusion: The Essential Scientific Works of Albert Einstein" right now because I told myself I'm going to understand relativity thoroughly before I die. Halfway through the general theory I figured out the equation in the special theory that explains why mass has a discrete energy value.

In QM I've figured out some of it, like I can calculate the Hamiltonian sometimes, given enough info (I understand that doesn't make sense too :) ). And I can follow the examples for Schrodinger's equations. But the second I put away my notes and books, I can't do shit with it.

And now, even though there's a new LGH powered up, and we can build computers and nanomaterials and cosmology and all that, I have a sneaky suspicion that no one really gets relativity. Or at least not most people who ought to. Is there any justification to my suspicion?

--------------
Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

The Daily Wingnut

   
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Sep. 12 2008,14:12   

Quote (Tracy P. Hamilton @ Sep. 12 2008,19:02)
[SNIP]

R is boring organic stuff of interest only to Louis.

LOL This is undoubtedly true.

That reminds me of the comedy banter I've had with those of an inorganic/physical bent.

Louis

--------------
Bye.

  
Tracy P. Hamilton



Posts: 1239
Joined: May 2006

(Permalink) Posted: Sep. 12 2008,15:08   

Quote (BWE @ Sep. 12 2008,13:35)
Tracy,
I wrote down the equations from the Wiki page and tried to figure it out but I'm sadly lacking.

I'm reading "A Stubbornly Persistent Illusion: The Essential Scientific Works of Albert Einstein" right now because I told myself I'm going to understand relativity thoroughly before I die. Halfway through the general theory I figured out the equation in the special theory that explains why mass has a discrete energy value.

In QM I've figured out some of it, like I can calculate the Hamiltonian sometimes, given enough info (I understand that doesn't make sense too :) ). And I can follow the examples for Schrodinger's equations. But the second I put away my notes and books, I can't do shit with it.

And now, even though there's a new LGH powered up, and we can build computers and nanomaterials and cosmology and all that, I have a sneaky suspicion that no one really gets relativity. Or at least not most people who ought to. Is there any justification to my suspicion?

Just use my equations, and the picture from wiki.  It will be much easier.

--------------
"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

  
BWE



Posts: 1902
Joined: Jan. 2006

(Permalink) Posted: Sep. 12 2008,15:18   

Have you seen my avatar? I think they might be testing the wrong thing..

Thanks. Now I'm reading the paper I linked earlier.

--------------
Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

The Daily Wingnut

   
Lou FCD



Posts: 5455
Joined: Jan. 2006

(Permalink) Posted: Sep. 12 2008,15:33   



My notes and thoughts from Biology 111, for Friday, September 5, 2008. The entire series can be found here.

On this day, Tropical Storm Hannah was expected to hit, so the college closed at 1 PM. Although that was well after the end of our scheduled lecture, Doc (if I recall correctly) cut the class a bit short to give folks headed home a little extra time.

So in the previous lecture, we had left off discussing Cohesion and Adhesion, the first of the emergent properties of water on the table for discussion. With this lecture, we picked up with the next emergent property on the list.

2. Moderation of Temperature

Water has a relatively high specific heat, which means that water can absorb and release large amounts of heat with little change in temperature.

To discuss this topic, it helps to first have an understanding of the difference between heat and temperature.

Heat is the total amount of kinetic energy in a body.

Temperature is the average kinetic energy of the particles in a body.

To illustrate this, we discussed the comparison of a hot cup of coffee to the Arctic Ocean.

While the temperature of the cup of coffee is higher, there are many fewer molecules in that cup than there are in the Arctic Ocean. The Arctic Ocean's greater number of molecules each have lower amounts of kinetic energy (hence the lower temperature) but the sum, the aggregate, the total amount of heat is higher, simply because a lot of little bits of heat add up.



It takes much change in energy to change the temperature of water due to Hydrogen bonding and the crystalline structure of water (even as a liquid, as hydrogen bonds are formed and broken, water has a basically crystalline structure).

The Hydrogen bonds are strong enough that each of them takes a certain amount of energy to break, so much of the heat coming onto the surface of the ocean from the sun is used in breaking those bonds, leaving less energy to impart to the water molecules directly. This energy absorption helps to keep the sun from baking the planet.

Reformation of the hydrogen bonds in the cold winter releases that heat back into the atmosphere, keeping the planet from freezing over.

This ties into the next part of temperature moderation.

Water has a relatively high heat of vaporization

Heat of vaporization is the amount of energy needed to go from a liquid to a gas. This is also due to Hydrogen bonding.

Water's State of Matter


Solid ---------> Liquid ---------> Gas
0°      HEAT                HEAT      100°


Evaporation lowers the average temperature of the water left behind.

Evaporative cooling ---> We use this technique as sweating. Plants use this in the leaves, which then draws water up through the plant from the ground (remember the Hydrogen bonding thing from the last lecture?).

Rain forests are so rainy because of the vast amount of evaporative cooling, which saturates the local atmosphere. All that water vapor then cools, condenses, and falls as rain because it's now heavier than the surrounding air.

The ocean temperature close to our shore varies between the low single digits in the winter to the upper twenties in the summer, so that's a thirty degree temperature difference over the course of the year.

In the desert, the temperature ranges from around zero at night to 50° or more during the day.

Water is a great temperature regulator.

We closed out the lecture with a short discussion of the gulf stream, and how that moderates the climate of the British Islands despite their high latitude. We compared Ireland specifically to the city of Moscow, Russia, which is at about the same latitude.

The one is nicknamed the Emerald Isle because it's lush and green. The other, not so much.

   
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.


--------------
“Why do creationists have such a hard time with commas?

Linky“. ~ Steve Story, Legend

   
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Sep. 12 2008,17:50   

I think this might be the most useful thread ever created at AtBC.

   
simmi



Posts: 38
Joined: Aug. 2007

(Permalink) Posted: Sep. 12 2008,18:51   

Quote (stevestory @ Sep. 12 2008,18:50)
I think this might be the most useful thread ever created at AtBC.

I agree wholeheartedly.  And to be honest, Lou, I totally didn't know that you didn't do any college biology.  Your posts fisking teh tard were so good I assumed you had advanced training in bio.  Please keep the updates coming! (without sacrificing your work, of course)

This thread also inspired me to join in with my own stories of new beginnings (I'm just starting my PhD), but then I remembered I have my own blog which I've been neglecting.  Off to write some posts...

  
Lou FCD



Posts: 5455
Joined: Jan. 2006

(Permalink) Posted: Sep. 12 2008,19:22   

Quote (stevestory @ Sep. 12 2008,18:50)
I think this might be the most useful thread ever created at AtBC.

Thank you Steve. That's some pretty high praise.

 
Quote (simmi @ Sep. 12 2008,19:51)
 
Quote (stevestory @ Sep. 12 2008,18:50)
I think this might be the most useful thread ever created at AtBC.

I agree wholeheartedly.  And to be honest, Lou, I totally didn't know that you didn't do any college biology.  Your posts fisking teh tard were so good I assumed you had advanced training in bio.  Please keep the updates coming! (without sacrificing your work, of course)


:)

Actually, my last biology class was a 9th or 10th grade Microbiology class that bored me to tears. The teacher was dry as a bone as I recall, and I think I squeaked by with a C. That would have been 1983ish?

Whipping up on TARD sometimes takes little more than clear thinking. It doesn't take a biologist to know that "Evilution sucks, therefore the Bible is true" isn't the greatest of arguments. Most of the time, in fact, one need only observe the TARDic tendency towards self-inflicted gunshot wounds to the feet to get a good laugh.

 
Quote (simmi @ Sep. 12 2008,19:51)
This thread also inspired me to join in with my own stories of new beginnings (I'm just starting my PhD), but then I remembered I have my own blog which I've been neglecting.  Off to write some posts...


Some linkage, please? I mean, if my little thread here is going to be someone's inspiration, I should at least get to see the fruits of my labor.

:)

--------------
“Why do creationists have such a hard time with commas?

Linky“. ~ Steve Story, Legend

   
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Sep. 12 2008,19:32   

Quote (Lou FCD @ Sep. 12 2008,20:22)
Quote (stevestory @ Sep. 12 2008,18:50)
I think this might be the most useful thread ever created at AtBC.

Thank you Steve. That's some pretty high praise.

All the praise belongs to you. While lots of us have scientific knowledge, you're the only one bringing it here on a regular basis so that others might learn.

   
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: Sep. 12 2008,21:02   

Quote
It doesn't take a biologist to know that "Evilution sucks, therefore the Bible is true" isn't the greatest of arguments.


Yeah, if the argument consists of some equivalent to "biologists have as a group continuously overlooked such and such basic thing that would totally change their minds if they'd only pay attention to their critics", well, that hardly takes expertise to recognize the illogic.

Henry

  
Lou FCD



Posts: 5455
Joined: Jan. 2006

(Permalink) Posted: Sep. 17 2008,09:30   

First Biology exam was this morning at 8. I think I did pretty well, and none of the questions seemed very difficult, frankly.

So, either I know the material very well and I did well, or I'm talking out my ass and I blew out badly.

Tomorrow I should be able to get back to posting up notes, and hopefully I can get close to caught up on them by the weekend.

--------------
“Why do creationists have such a hard time with commas?

Linky“. ~ Steve Story, Legend

   
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: Sep. 17 2008,13:47   

Quote (Lou FCD @ Sep. 17 2008,08:30)
or I'm talking out my ass and I blew out badly.

That could depend on what you had for lunch... :p

  
Stephen Elliott



Posts: 1776
Joined: Oct. 2005

(Permalink) Posted: Sep. 17 2008,14:49   

Quote (Lou FCD @ Sep. 17 2008,09:30)
First Biology exam was this morning at 8. I think I did pretty well, and none of the questions seemed very difficult, frankly.

So, either I know the material very well and I did well, or I'm talking out my ass and I blew out badly.

Tomorrow I should be able to get back to posting up notes, and hopefully I can get close to caught up on them by the weekend.

Why don't you use this site to help on all your courses? Rather than rewrite your notes to paper do it to here.

You will still get the initial benefit of rewriting and also the secondary benefit of people here who are experts on the subject correcting you sometimes.

It is not asking people to do your work for you if you respond with your own thinking. It would just be even more interesting discussions. Provided that is that you made a new thread for each subject.

It would be like having many instructors/profs and make interesting reading. IMO. Pretty sure I would also learn a few things. Just a thought.

  
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: Sep. 17 2008,22:32   

Is the course still on chemistry, or is it getting into actual biology?

Henry

  
Lou FCD



Posts: 5455
Joined: Jan. 2006

(Permalink) Posted: Sep. 18 2008,05:50   

Quote (Stephen Elliott @ Sep. 17 2008,15:49)
Why don't you use this site to help on all your courses? Rather than rewrite your notes to paper do it to here.

You will still get the initial benefit of rewriting and also the secondary benefit of people here who are experts on the subject correcting you sometimes.

It is not asking people to do your work for you if you respond with your own thinking. It would just be even more interesting discussions. Provided that is that you made a new thread for each subject.

It would be like having many instructors/profs and make interesting reading. IMO. Pretty sure I would also learn a few things. Just a thought.

Stephen, while in principle that is a great thought, I'm finding I barely have time to copy my Biology notes. As it stands, I'm somewhere around four lectures and a pair of labs behind now. (Though the labs will require only a little time to write up.)

Yesterday I had the exam, then a second essay to turn in for English, and a ton of precalc homework and labs to finish up, and a quiz in precalc last night.

The issue really with Biology is that for the notes to make sense (at least to me), I need to draw pictures, and that takes a little time.

For Spanish, there's the special characters, though I've switched to the international keyboard and that would speed things up.

With precalc, there's fractions and radicals and graphs, etc., that just don't translate well to the web without a lot of time consumption.

The English stuff would be easy though, as I'm writing on the computer anyway and the lectures are pretty much note free. The instructor usually takes a point about the upcoming essay and meanders through analogy after analogy. I posted my first essay on my blog after I got it back, and will probably continue to do that as they are returned to me.

 
Quote (Henry J @ Sep. 17 2008,23:32)
Is the course still on chemistry, or is it getting into actual biology?

Henry


Henry, we're currently hitting the chemical structures of functional groups, so we're sort of making the transition now.

Monday's lecture for instance, was on amino acids, peptide bonds, polypeptides, proteins, and we closed out with a first look at nucleic acids.

--------------
“Why do creationists have such a hard time with commas?

Linky“. ~ Steve Story, Legend

   
Lou FCD



Posts: 5455
Joined: Jan. 2006

(Permalink) Posted: Sep. 19 2008,17:30   



My notes and thoughts from Biology 111, for Monday, September 8, 2008. The entire series can be found here.

We left off on Friday discussing the second important emergent property of water, the property of temperature moderation.

On Friday, we began with the third emergent property of water that is critical to biology.

3. Solid form of water is less dense than the liquid form

In other words, ice floats. First we took a quick look at what generally defines each state of matter at room temperatures (we didn't delve into plasmas etc)
States of Matter
Solid
Constant Shape, Constant Volume
Liquid
Constant Volume, Changing Shape
Gas
Changing Volume, Changing Shape

So we can say that generally speaking, the state of matter is dependent on its density and the fixity of its bonding. Ordinarily, the solid state of matter is more dense than the liquid state, and this unusual property of water has a very important consequence for life.



Water is its most dense at 4°.

Because ice floats, the top of a body of water will freeze first in the winter. Because of the moderation of temperature, water (in this case, ice) is a good insulator from heat. What this means is that the floating ice on a body of water hinders the escape of heat from below the ice, and the ice then acts as a thermal blanket, preventing the underlying water from freezing solid. This gives life below the ice a place to continue living, even in the coldest of arctic winters.

4. Solvent Ability

Before we can discuss water's ability to act as a solvent, we need to define some terms.

Solution - A homogeneous mixture of 2 or more different substances

Solvent---> The dissolving agent.

Solute---> The substance that dissolves

So when you salt a pot of water on the stove, the water is the solvent, the salt the solute, and the mixture is a solution.

Water has the ability  to dissolve more different substances and in greater quantity than any other solvent. (It's not universal however, or it would dissolve the container that holds it, etc.)

Salinity

Solution    Seawater         Blood
H2O         96.5%        99.1%
Salt          3.5%         0.9%

The difference in salinity between the body and the seawater is why salt water tastes so salty to us, despite the fact that the salt concentration is only 3.5%.



Salt is an ionic compound, and water dissolves it because of the charges of each of the ions involved. Water's polarity is attracted by its slightly charged poles to the charges of the ions. Because the Sodium is positively charged (a cation), the slight negativity at the Oxygen end of a water molecule is attracted to the Sodium. Conversely, the Chlorine ion is negatively charged (an anion), so the slightly positively charged hydrogen end of the water molecule is attracted to the Chlorine. The water sort of forces the salt ions apart through hydrogen bonding, and so the Sodium is separated from the Chlorine.

The solubility of sugars (for instance) works a little differently, and we cover that a bit later on.

Polarity and electrical charge are the keys to water solubility, and water's polarity and hydrogen bonding are what make it such and excellent solvent.


Oils on the other hand, are non polar molecules. That's why oil will separate from water.

Oil doesn't repel water so much as it just doesn't dissolve in water.

We say that Oils are hydrophobic.

Hydrophilic --->Attractive to water (NOT interchangeable with water soluble, though! ---> Cotton is hydrophilic but not water soluble. Cotton and starch are entirely made of cellulose (a sugar). It's components are water soluble. So we can say that being non-water-soluble is an emergent property of cellulose.

Hydrophobic ---> Not attractive to water.

At this point we moved on to pH.



pH ---> A measure of the concentration of Hydrogen ions in a solution.

H+ is a Hydrogen atom that has lost an e-, and what remains is just a p+

We denote H+ concentration thus: [H+] (where the brackets mean "concentration of" whatever is between them, in this case Hydrogen ions).

Some notes about the scale:

The pH scale is a negative logarithmic scale, meaning that each increase of 1 unit on the scale is a decrease of H+ concentration by a factor of 10. So a solution with a pH of 8 has ten times less [H+] relative to [OH-] than distilled water. A solution with a pH of 9 has ten times less [H+] relative to [OH-] than the previous solution, and 100 times less than distilled water.

A small change in the pH number can mean a big change in the balance of [H+] to [OH-]. At 7, [H+] = [OH-], and the solution is said to be neutral. I find it helpful to think of the pH scale as a balance type of scale. When a solution is neutral, it balances evenly between the [H+] and the [OH-].

Thinking about it, this makes sense, as ideally all the H+ and OH- in water should be joined together as H2O.

Also note that the body needs to be regulated relatively closely. Normally, the pH of human blood is between 7.35 and 7.45. A few tenths of a unit of pH one way or the other is fatal. Too many H+ or OH- floating around would make for a very bad day.

One last note: [H+] in distilled water is 10 to the -7 mols/L. This is where the 7 comes from in the pH of water, and the scale is based on that.

1 mole = 6.02 x 10 to the 23. This number is known as Avogadro's number, and is a handy little number to keep in your back pocket.

The lecture ended there, and we picked it up on Wednesday.
     
Quote

From whence came the art:

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

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


--------------
“Why do creationists have such a hard time with commas?

Linky“. ~ Steve Story, Legend

   
Lou FCD



Posts: 5455
Joined: Jan. 2006

(Permalink) Posted: Sep. 19 2008,19:52   

Got the exam results back today, and was a bit disappointed. Made some dumb mistakes and wound up with an 88. The highest score in all the sections was a 91, so I know I shouldn't feel too damned bad, but damn it.

Most of the 8 that I missed, I looked at the answer I gave and thought, "What the hell was I thinking????"

One of them was "Which of these is the molecular formula for Maltose?" I forgot to drop the two Hydrogens and the Oxygen from the dehydration synthesis, and answered C12H24O12.

What's worse, the very next question was something like "How does Maltose form from Glucose?", and I answered the question correctly.

Damnit. Some days I want to beat my head on a wall and hope some sense gets osmosified in there.

I did help out in the Science Garden later this morning, though. That was some pleasant down time.

Edited by Lou FCD on Sep. 19 2008,20:53

--------------
“Why do creationists have such a hard time with commas?

Linky“. ~ Steve Story, Legend

   
Lou FCD



Posts: 5455
Joined: Jan. 2006

(Permalink) Posted: Sep. 19 2008,20:25   



My notes and thoughts from Biology 111 Lab, for Monday, September 8, 2008. The entire series can be found here.

In this lab we mostly talked about metric system measurements, then went about taking measurements of various things. Honestly, it was pretty mundane stuff for the most part, and I didn't enjoy this lab nearly as much as the first two, though I understand the necessity of it.

We used rulers, calipers, and a scale to take measurements of wooden blocks, dowels, and plastic balls, then calculated their volume and surface area.

We measured the room temperature and the temperature of cold tap water and ice water, and water on a boiling plate, as well as skin temperature.

Then, in the most interesting part of the lab, we measured each other's tibias, and then each other's heights (as well as a real dead guy's tibia). We recorded the tibia length and height of everyone in the lab, and for homework we created scatter plots and trend lines with those numbers.

It was pretty straightforward stuff, really, and well... kinda boring except for the dead guy's bone that Squicky Britches refused to touch. That was a source of mild humor.
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.


--------------
“Why do creationists have such a hard time with commas?

Linky“. ~ Steve Story, Legend

   
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: Sep. 19 2008,21:16   

And here I thought a mole was a small burrowing mammal... :)

Henry

  
Texas Teach



Posts: 2084
Joined: April 2007

(Permalink) Posted: Sep. 19 2008,21:35   

Quote (Henry J @ Sep. 19 2008,21:16)
And here I thought a mole was a small burrowing mammal... :)

Henry

I had a professor for freshmen chem that had actually gotten someone to make him a pair of plush moles to use in class.  They had Velcro in the middle that held the front and back ends together.  After using them for quite some while to make points about moles and half moles, he dropped the back ends of both into a beaker and asked the class what he was holding.

The answer:  500 mL of mole-asses.

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

"I suspect that the English grammar books where you live are outdated" --G. Gaulin

  
Lou FCD



Posts: 5455
Joined: Jan. 2006

(Permalink) Posted: Sep. 19 2008,22:01   

Quote (Doc @ today in class)
Hydrogen ion runs into the police station. "Help, help!"

Policeman: "What's wrong?"

Hydrogen ion: "Someone stole my electron!"

Policeman: "Are you sure?"

Hydrogen ion: "Yeah, I'm positive."


--------------
“Why do creationists have such a hard time with commas?

Linky“. ~ Steve Story, Legend

   
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: Sep. 19 2008,22:06   

man, that's one of my 3 horrible physics jokes. The only good one is

Cop: "You know how fast you were going?"
Driver: "Not a clue! But I know exactly where I am!"

   
Lou FCD



Posts: 5455
Joined: Jan. 2006

(Permalink) Posted: Sep. 20 2008,13:18   



My notes and thoughts from Biology 111, for Wednesday, September 10, 2008. The entire series can be found here.

In the last lecture, we had left off with a discussion of pH and [H+]. We started this lecture by finishing up with pH.

Remember that pH is a negative log scale, so as [H+] goes up, pH goes down.

We came to definitions right off the bat.

Acid --> Any substance that increases [H+] of a solution. This is accomplished by donation of H+ ions (p+, since a Hydrogen without an e- is just a p+)

HCl ---> H+ + Cl-

Hydrochloric acid will break down in solution into its constituent parts, thus directly increasing the [H+] and lowering the pH of the solution.

Base --> Any substance that decreases [H+] of a solution. This can be accomplished in one of two ways:

Donation of OH- to combine with H+ already in the solution

NaOH ---> Na+ + OH- ---> OH- + H+ ---> H2O

Oven or drain cleaner, Sodium Hydroxide, will break down in solution into its constituent parts, one of which is a hydroxide ion. The hydroxide ion combines with H+ in the solution to make water, thus lowering [H+] and raising the pH of the solution.

Sucking up of H+

NH3 + H+ ---> NH4+

Ammonia, NH3, will pick up an H+ and become NH4+, thus directly decreasing [H+], and raising the pH of the solution.

Then we moved on to Chapter 4: Carbon and the Molecular Diversity of Life



Organic Compounds ---> Carbon based compounds

Hydrocarbons ---> Hydrogen and Carbon, joined together in non polar covalent bonds. There is a lot of potential energy in these bonds due to the maximum distance from the nucleus of the shared valence e- pairs. These bonds also make for hydrophobic molecules, due to the non-polarity.



Hydrocarbons are built on a skeleton of these Hydrogen and Carbon bonds, with other stuff added on. Remember that Carbon has four unpaired valence electrons, so it can form four covalent bonds. Hydrogen has one unpaired valence electron, so it can form one covalent bond.

This makes for a very nice set-up between Carbon and Hydrogen, where the carbon atom can form bonds with four Hydrogens, or three Hydrogens and another carbon, or two Hydrogens and two other Carbon atoms. Using this technique, nature can and does form chains of Carbon atoms surrounded by Hydrogens. These are called hydrocarbons, and form a skeleton upon which nature can build almost infinitely complex molecules. We can even think of the surrounding Hydrogens as plug covers for interchangeable parts.



Hydrocarbons form non-polar covalent bonds, and since the shared e- are equally far from each of the nuclei of the two atoms, that gives the bond its high potential energy. That's why Hydrocarbons are so attractive as fuels. There's lots of bang for the buck.

Of course, the big problem is that it takes about 300,000,000 years to make Hydrocarbons, due to the fact that they're made from decayed organic material (i.e. dead plants and animals). As a species, we're using the planet's available Hydrocarbons much faster than they are being made. It doesn't take a genius to work out the math here.

There are four main classes of organic compounds in living things that Bio 111 is going to cover.

Carbohydrates ---> C, H, O
Lipids ---> C, H, O (sometimes N & P)

Proteins ---> C, H, O, N, S

Nucleic Acids ---> C, H, O, N, P

Functional Groups

1. Hydroxyl Group

A Hydroxyl Group, is just an OH- that replaces a Hydrogen atom as in this Hydrocarbon.



Ethane is a Hydrocarbon molecule, and by exchanging one Hydrogen for an OH-, we change it to ethanol. Ethanol is better known as "grain alcohol" or "ethyl alcohol". Note that the ending "ol" always denotes an alchol. Note too that we keep the Hydrogen in the OH- portion of the molecule separate from the other Hydrogens in the molecular formula, to point out that it's not just another Hydrogen hanging off the main skeleton, but is associated with the Oxygen.

2. Carboxyl Group



A Carboxyl Group is made up of a Carbon, two Oxygens, and a Hydrogen, in the form COOH.

When latching onto a Hydrocarbon skeleton, it will ditch the H+, leaving it with a Carbon single bonded to a negatively charged Oxygen, and double bonded to another Oxygen. Because it donates that H+, it is an acid (lowers pH of a solution), and the negative charge makes it very attractive to water (hydrophilic).

3. Amino Group



An amino group is NH2, a Nitrogen and two Hydrogens. It will pick up an H+ from a solution, making it a base, and also hydrophilic.

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 PO42- or sometimes OPO32-, 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.

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.


Edited by Lou FCD on Sep. 21 2008,17:58

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“Why do creationists have such a hard time with commas?

Linky“. ~ Steve Story, Legend

   
Texas Teach



Posts: 2084
Joined: April 2007

(Permalink) Posted: Sep. 20 2008,14:08   

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

This is close to what I tell the introductory students in my physical science class.  For the more clever ones, I also point out that Lewis' dot diagrams are a lovely model, especially for electron bookkeeping, but the real world doesn't care whether our little models work out neatly.  (The patch on his model is to have the one extra bond spread around each of the positions, which lowers the energy.)

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

"I suspect that the English grammar books where you live are outdated" --G. Gaulin

  
Lou FCD



Posts: 5455
Joined: Jan. 2006

(Permalink) Posted: Sep. 20 2008,18:10   

Quote (Texas Teach @ Sep. 20 2008,15:08)
Quote (Lou FCD @ Sep. 20 2008,13:18)
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.

This is close to what I tell the introductory students in my physical science class.  For the more clever ones, I also point out that Lewis' dot diagrams are a lovely model, especially for electron bookkeeping, but the real world doesn't care whether our little models work out neatly.  (The patch on his model is to have the one extra bond spread around each of the positions, which lowers the energy.)

The Intelligent Designer is Microsoft?

Geez, that explains a lot!

--------------
“Why do creationists have such a hard time with commas?

Linky“. ~ Steve Story, Legend

   
Lou FCD



Posts: 5455
Joined: Jan. 2006

(Permalink) Posted: Sep. 21 2008,00:21   



My notes and thoughts from Biology 111, for Monday, September 8, 2008. The entire series can be found here.


There are four main classes of organic compounds in living things that Bio 111 is going to cover.

Carbohydrates* —> C, H, O
Lipids —> C, H, O (sometimes N & P)
Proteins* —> C, H, O, N, S
Nucleic Acids* —> C, H, O, N, P


* Carbohydrates, Proteins, and Nucleic Acids are Macromolecules, meaning "really honkin' big".

1. Carbohydrates - Sugars - all "ose" endings mean "sugar".

"Carbon Water"

They have a C:H:O ratio of 1:2:1, so the basic carbohydrate formula would be CH2O

a) monosaccharides --> "one sugar" - these are the simple sugars, and contain between 3 - 7 C atoms in them.

A Few Simple Sugars

C Atoms     Molecular Formula     Group Name
3               C3H6O3                       triose
5               C5H10O5                     pentose
6               C6H12O6                     hexose



We're going to stick with the hexose group for a bit, because it's pretty common, and useful to illustrate several things in biology.



Because of the interchangeability of parts, a compound with the formula C6H12O6 (for instance) can actually wind up being arranged in more than one way. When compounds are arranged differently but share a molecular formula, they are called isomers ("same part"). Glucose, Fructose, and Galactose are three simple sugars, all hexose sugars, but have their atoms arranged differently. They are isomers that organisms use for energy.

Each of these hexose isomers have 7 C-H bonds (they are hydrocarbons, and remember that C-H bonds are nonpolar covalent bonds, having a great deal of potential energy)

Monosaccharides often rearrange themselves a little bit from the structural diagrams to the right, and fold in on themselves to make a hexagonal shape. There are illustrations of the process in the textbook.

b) Disaccharides --> "two sugars" - these are simply two sugars linked by a covalent bond.

Since all the bonding places are taken up by atoms in the monosaccarides, a place needs to be make for the link between the two simple sugars. This is accomplished by a dehydration synthesis, also known as a condensation reaction.

The OH- at a place on one sugar will be attracted to the H+ on another sugar. They will each leave their parent sugar molecule and combine to form a water molecule, leaving an unpaired electron in the valence shell of one Carbon in each of the sugar molecules.



This is where the hook-up occurs.

When a galactose and a glucose combine, the resulting disaccharide is called lactose and is found in milk.

When two glucose molecules combine, the resulting disaccharide is called maltose, and is used in brewing.

We can't use disaccharides for energy, so our bodies add water back into the disaccharide, in a reverse process known as hydrolysis. This breaks the disaccharide back into two monosaccharides, something our body can use for energy.

c) Polysaccharides --> "many sugars" - many monosaccharides linked by covalent bonds. These are macromolecules, and can be hundreds to thousands of monosaccharides linked together.

Polymer --> "many parts" --> large molecule made of many small and similar molecules.

Monomer --> "one part" --> one of the small molecules.

Some polymers of glucose are used by organisms to store energy, some to do other things, like build structure.

Plants use starch for energy storage.

Animals use glycogen for energy storage.

Plants use cellulose for structure.

An emergent property of these polymers is that they are not water soluble. This is the means by which they store the energy inside cells (otherwise they would just dissolve inside the cell which is mostly water).

They are stuck inside the cell until needed, much like a school bus brought in pieces into a classroom and then assembled. In order for the organism to use the energy stored therein, the polymer must first be broken down by hydrolysis.

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.

Breakdown of any -ose (sugar) is facilitated by a corresponding -ase. Breakdown of lactose needs lactase, etc.

2. Lipids --> Of our four classes with which we began this lecture, lipids are the only ones that are not macromolecules.

It's a diverse class that includes fats and oils, steroids, and phospholipids. Fats and oils are long chains, while steroids are ring structured.

This class is made of mostly C and H, with just a little O. Fats and oils are nonpolar molecules, and so are not water soluble.

Fats and oils = triglyceride --> 1 glycol + 3 fatty acids. The difference between fats and oils is density, and I'll have lovely little drawings of them for you in the next lecture.

Edited to correct the ate/ase mistake pointed out by keiths
           
Quote

From whence came the art:

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

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


Edited by Lou FCD on Sep. 21 2008,17:48

--------------
“Why do creationists have such a hard time with commas?

Linky“. ~ Steve Story, Legend

   
keiths



Posts: 2195
Joined: Jan. 2006

(Permalink) Posted: Sep. 21 2008,01:45   

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.

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And the set of natural numbers is also the set that starts at 0 and goes to the largest number. -- Joe G

Please stop putting words into my mouth that don't belong there and thoughts into my mind that don't belong there. -- KF

  
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