Molecules
What is the molecule at right?
Of course, this is water
H2O
But it is not made up of letters
The view at right is the old, classic "ball and stick" model for molecules. It illustrates that atoms are connected by bonds, but molecules don't really look like this.
Molecules are "fat" (they fill space)
Hold that thought....
They also have bits of charged distributed across the molecule. The red oxygen "takes" more of the shared electrons and becomes partially negative, while the hydrogens are left partially positive. The molecule is "polar"
Note that water is less than 0.2 nm across.
Molecules
What is the molecule below?
CH3CH2OH
This is ethanol. A bit more complicated than water.
Again, it is not a tinkertoy, but rather, each atom occupies significant space. Overlaps between atoms are what form the bonds.
But it's hard to make out who is bonded to whom in this representation.
So we return to the Tinker Toy view because we can see the connections (and the connections tell us about the chemistry!).
Ethanol is about 0.5 nm in its longest dimension.
Sucrose - Table Sugar
Sucrose is a di-saccharide - two simple sugars connected together.
At this point, we can simplify the picture just a bit.
We can always figure out where the hydrogens need to be, so simply turn them off.
The resulting picture is simpler.
The resulting picture is still simpler, and we have lost no information.
Sucrose is about 1 nm in its longest dimension.
Sucralose - Artificial sugar
Sucralose is a di-saccharide - two simple sugars connected together, but with some OH groups replaced by the larger Cl (orange).
At this point, we can simplify the picture just a bit.
We can always figure out where the hydrogens need to be, so simply turn them off.
The resulting picture is simpler.
The resulting picture is still simpler, and we have lost no information.
Sucralose is about 1 nm in its longest dimension.
This family of naturally occuring
cyclic oligosaccharides has a variety of uses, all centered on the fact that the molecules are water soluble, yet can bind insoluble compounds within the ring. They are used to bind pollutants and toxins in environmental remediation.
They also bind cholesterol. and are used industrially to remove cholesterol from food stuffs. They are being explored in the treatment of Niemann Pick Type C disease, a disorder in which young children are unable to normally metabolize cholesterol (recent work of Brown & Goldstein, winners of the Nobel Prize in Physiology or Medicine, 1985).
How does this "really" look?
Or as before, we can simplify the picture just a bit.
Identify a single sugar (saccharide)
Can you see the six-membered ring structure?
Sugars (oligo saccharides) and starches (poly saccharides) come in many forms.
ATP
Plays
essential roles in our cells
Key features
A somewhat nonpolar (and flat) base
A polar sugar (5 membered ring)
A very negatively charged triphosphate (the energetic importance of which was recognized by 1953 Nobel prize winner Fritz Lipmann, who coined the expression "energy-rich phosphate bonds"
Note: the Nobel Prize in Chemistry in 1997 was awarded to Paul D. Boyer, John E. Walker, & Jens C. Skou for contributions to the understanding of ATP synthase, the essential enzyme in our cells that creates ATP from ADP.
What roles does ATP play in the cell?
DNA
DNA is a polymer made up of connected "ATP-like" molecules
Find a single AMP
Why do "strands" of DNA come together?
Remember that ATP had polar (charged) phosphates. DNA strands only come together in water. Why?
And the bases are moderately "oily"
Remember that ATP had polar (charged) and nonpolar (oily) parts. DNA strands only come together in water. Why?
A very small protein
Bovine pancreatic trypsin inhibitor - an example of a polypeptide (polymer of connected amino acids) - about 3.5 nm in size
Problem: this is a single chain polymer, but who can tell?
Now you can trace the "backbone" of the chain, but we can simplify even more.
Follow the path
Look at just the path
Accentuate common structural elements
Remove the path
Put back the "trees"
You can see why we tend to take away the "trees," at least when we want to focus on the big picture "forest"
Let's look a bit more at just a small part of the "trees"
So we remember that the "rocket" is really a helical folding of a part of the protein chain
A moderately big protein
T7 RNA polymerase - a "small" RNA polymerase (the enzyme that makes RNA copies from archival DNA)
A single chain polymer, almost 10 nm across. Let's follow the path
But the path is still hard to follow. Turn off the Tinker Toy view.
OK, but key structural elements are hard to see.
We really don't need the path anymore.
Much easier to see the parts of the protein.
It turns out that this protein binds DNA
Let's see how the DNA binds. Zoom in.
But we've lost the chemical detail. Selectively turn sticks back on.
Zoom in for a better look
Focus on just the interacting DNA(base)-protein(amino acid) pair
"Hammerhead" Ribozyme
We now know that RNA can form protein-like structures
The old view:
In 2D it looks like a hammer. In 3D, no...
It still doesn't look like a hammer
Bases that do not look like they are interacting in the 2D representation are indeed interacting
This is also about 3-4 nm in size
Sidney Altman, Thomas R. Cech
The Ribosome
The next protein in the central dogma, the one that takes information in RNA and converts it into protein,
is really big!
Cartoonify the protein
And it is only part protein -
mostly RNA!
"Cartoonify" the RNA to see it better
The ribosome is over 40 nm in size.
Leave it spinning
In fact, the "active site" of this protein is composed entirely of RNA!
(ask me about the evolutionary implications...)
Venkatraman Ramakrishnan, Thomas A. Steitz, Ada E. Yonath