Carbohydrate Structure and Function

Discovered this interesting flash presentation of carbohydrate structure and function. Thought I'd share it.

http://kisdwebs.katyisd.org/campuses/MRHS/teacherweb/hallk/Teacher%20Documents/AP%20Biology%20Materials/Chemistry%20of%20Life/Carbohydrates/05_A01s.swf

Ionic Bonds - Weak or Strong

This is the much anticipated blog entry regarding the stength of an ionic bond. The following is the best answer I've come across so far regarding the question from a Dartmouth College source. 

In biological terms, ionic bonds, hydrogen bonds and van der Waals interactions are considered weak bonds.

Ionic bonding in a cell is indeed very weak. Here's a statement from Karp's 2nd edition Cell and Molecular Biology text (pp. 34-35):

Ionic bonds within a salt crystal may be quite strong. However, if the crystal of salt is dissolved in water, each of the individual ions becomes surrounded by water molecules, which inhibit oppositely charged ions from approaching one another closely enough to form ionic bonds. Since cells are composed primarily of water, bonds between free ions are of little importance.

So, within an aqueous environment, the interaction between ions of opposite charge is minimal and ionic bonds can be considered weak. To add a little perspective, consider Karp's next statements:

In contrast, weak ionic bonds between oppositely charged groups of large biological molecules are of considerable importance.  For example, when negatively charged phosphate atoms in a DNA molecule are closely associated with positively charged groups on the surface of a protein, ionic bonds between them help hold the complex together.  ...  The strength of ionic bonds in a cell is generally weak (about 3 kcal/mole) due to the presence of water, but deep within the core of a protein, where water is often excluded, such bonds can be influential."

In water, ionic bonds are very weak. (Your bio teacher didn’t lie to you!) However, in an aprotic solvent or in an anhydrous environment, you have a totally different situation. When using LDA as a base, there is no water around. If you form an enolate anion, the O^- will be closely associated with the Li⁺ and will form a strong ionic bond. Ionic bonding in crystals will be even stronger than in solution...but that’s a topic for an inorganic chemistry class!

Biological Molecules Slides

Here are the slides for Chapter 2 - Biological Molecules.

Biological Molecules

View more presentations from Jaya Kumar.

Water

View more presentations from Jaya Kumar.

Identification of Biological Molecules

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Trans fat

Photo taken from: http://stanford.wellsphere.com/healthy-eating-article/disorders-of-lipid-metabolism-trans-fat-facts/8066

Someone asked me what is the difference between trans fat and unsaturated fat. To answer, I decided to post up some links here so everyone can know.

First of all, we will have to remember what we learnt about unsaturated fatty acids. They have double bonds and those double bonds can cause kinks in the molecule. Now the structure of the trans fat is related to your unsaturated fatty acid. However, they don't have kinks. The following website gives us the idea:
http://www.natural-health-information-centre.com/trans-fats.html

Of course, any reference to food related molecules would not be complete without referring to the FDA website. You can find other relevant information about trans fat here:
http://www.fda.gov/Food/LabelingNutrition/ConsumerInformation/ucm109832.htm

Collagen Tutorial

I find the tutorial at the link below very helpful to understand the structure of collagen as a fibrous protein. We can thank Kathleen, Jingyi and E-man for it. I would like to congratulate both groups (Jean, Ying Jee and Adelyn too) for an excellent first effort. Looking forward to the next two groups' presentations:
Group 3 - Jane, Indra and Nigel
Group 4 - Soo Qing, Santhana and Kelly

http://www.messiah.edu/departments/chemistry/molscilab/Jmol/collagen/chapter1.htm

Macromolecules

For the A Level 609 students, I've included the link for the animation we used in class today. This link includes animations for lipids, proteins and nucleic acids as well. I trust this will help you understand especially how the monomers come together to form a macromolecule.

http://bcs.whfreeman.com/thelifewire/content/chp03/0302002.html

Amino anime

I noticed another poor chapter in our syllabus that has not been given any blog space here. So here's a link to some animations on amino acid basics.


http://www.johnkyrk.com/aminoacid.html