This is absolutely fantastic. I am preparing a Neuromuscular Disorders lecture for med students. Do you have any great pictures (biochem, physiology, etc..) that describe the action potential or excitation-contraction coupling?

Hi DG,

Thanks again for this series of lectures, I am slowly but surely making my way through them.  On this one, I am up to the point where you start writing about how food molecules are broken down to provide energy.

As per usual, I have a few questions about the things that I've read up until this point, and again if you could correct them, or me, when you get a chance, that would be much appreciated:

You said "The group just discussed above is called the alkenes. But a similar pattern exists for a group discussed last lecture, the alkenes:"

should be "The group just discussed above is called the ALKANES..." ?

You didn't finish this sentence: "These are examples of homologous series, series of organic molecules which get larger in succession based on a simple formula. There are many such series, such as the aldehydes, the alcohols, the"

Regarding branching.  Figure 1.14 you have shown 2-methylbutane, and in figure 1.17 you have shown "a branched butane isomer".  Would it be correct to say that 2-methylbutane is a branched pentane isomer, and that the "branched butane isomer" depicted in figure 1.17 is 2-methlpropane?

You said "If they were double covalent, they would be indicated by a double line, like this skeletal drawing of butene:"

But is figure 1.19 not, in fact, a skeletal drawing of hexene?  ch3-ch2-ch-ch-ch2-ch3 ?

You've shown the numbering system for indicating where things like the methyl group are in a particular molecule, is there also a way of indicating where the double bond is in the alkene group?

You said: "Carbon is the structural framework for everything. Proteins, nucleic acids, fatty acids, hydrocarbons, sugars etc. It must have hydrogen in it by definition."

I can see that hydrocarbons must have hydrogen in them by definition, but is that what you were referring to?  Or were you saying that organic molecules must have hydrogen in them by definition?  I was just a bit confused as it seems that carbon as the structural framework for everything rather than hydrocarbons was the subject of the previous sentence.  Or I could be completely mistaken of course!  But would say O=C=C=O, or O=C=C=C=O be considered organic?

You said : "In cyclic molecules, the labeling is always done clockwise."

and then : "As a cyclic molecule, the carbon vertices will be numerically denoted counterclockwise."

I'm confused!

Regarding figure 1.23, glucose.  You said "the ketone group (=C=O)" I took this to mean that the ketone group is a carbon that has a double covalent bond to the 'main body' and another double covalent bond to an oxygen.  Then you said "glucose has a ketone group and is hence a ketose, as opposed to an aldose" but I can't see the ketone group on that picture, have I misunderstood something?

You said: "There are other common properties of sugars. Although biological sugars tend to be cyclic, they can usually take many isomers. For example, glucose can adopt an unbranched conformation like this:"

Was there supposed to be a picture after that paragraph?

"large ring shaped structure containing nitrong"

Should be nitrogen?

You said: "Those with only a large six-carbon ring are called pyrimidines, while those with an additional five-carbon ring are called purines."

But in the pictures none of them have six carbons in their ring, and of those with an additional ring, none of them have five carbons.  Did you mean 6-sided ring and additional 5 sided ring?  Or 6-verticied ring and 5 verticied ring?

Very nice.

*bump*

I'm with phooney. *bump*

2.5 hours. Going to re-read

Thank you so much for this.

Well, enzymes are composed of polypeptide chains, they are formed by means of polymerizing amino acids. All enzymes are constructed in the cytosol. Some enzymes are partially modified later in the Endoplasmic Recticulum. All enzymes, indeed, all proteins that the mitochondria needs, will be imported into the mitochondria from the cytosol through a process called endoplasmic translocation.

I am unsure what precisely is meant by the latter part of your question. The reaction that constructs proteins by linking amino acids is called petidyl transferase. The reactive bond in question is donated by ATP hydrolysis into AMP and pyrophosphate, which links a tRNA with an amino acid via an enzyme called amino acyl synthetase. The reactive thioester bond is later transferred to the nascent polypeptide chain as the protein is being constructed inside a machine called a ribosome. Take note that the ribosome is unusual. Virtually all catalysis is carried out by proteins, but the catalytic sites of ribosomes are formed by structural RNA. Any RNA catalytic molecule is called a ribozyme. The ribosome is one of the most abundant supramolecular structures within the cell. It is formed by four large ribosomal RNAs and at least 50 smaller proteins.

Ribosomes are free in the cytosol and will construct proteins, of which enzymes  are hence a subset, in the cytosol. Hence any mitochondrial proteins will be delivered to the mitochondria by virtue of endoplasmic translocation through its bilayer. The only exception the protein translation always occuring in the cytosol is the rough endoplasmic recticulum, a large convluted organelle in Eukaryotic cells which junctions against the nucleus, and against which numerous ribosomes studd the lumen through which proteins are translated then translocated into the recticulum. Numerous cytosolic proteins are modified within the ER for re-export back into the cytosol, or for retainment in the ER depending on the signal sequence attached to it.

Hi DG,

Any comment on my last read-through?

This paragraph caused me to question about the bonds of the cytosolic membrane. In your answer, you said all enzymes are constructed in the cytosol so that cleared it up some.

The battery analogy didn't really work for me because I envision the mitochondrion as taking in-processing-releasing and not really being a piece of a circuit because it is powering its own 'internal' reactions by the oxidative phosphorylation.

For me, I think coupling the enzyme lecture with this will click.

Absolutely, I like difficult concepts. I'm reading and learning. I expect the curve to be high, but later I'll have a better grasp on what 'hyper-specialized' field fascinates me the most.

I know that I am fascinated by stem cell research and I understand the concepts behind cell differentiation. A better understanding on the molecular level will make me a much more powerful advocate.

Knowing more than Bush shouldn't be enough for anyone. lol.

This is puzzling. A membrane is a distinct structural unit in biology. A membrane is not composed of polymerization of small molecules. Enzymes are a class of proteins, and therefore are polymers of amino acids linked together. The membrane and the membrane proteins are structurally distinct. A protein is formed from polypeptides, which are the polymers of amino acids. Polypeptides are therefore very large single molecules. The membrane is also composed of many repeating small molecules however these are not held together by covalent bonds hence it is NOT a polymer because it is not a single molecule. It is many small molecules held together by non-covalent interactions to form a lipid bilayer. This lipid bilayer is formed from small lipid molecules which are held together noncovalently. Within this are proteins, which are made from polypeptides which ARE held together covalently, and proteins that transverse the membrane constitute a completely distinct structural entity than does a cell membrane. You should avoid called it the cytosilic membrane, since every organelle has a cytosilic membrane. It should be called the outer mitochondrial membrane. 

OK. I gotta go back.