Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438 - Introductory Biochemistry - Spring 2013

Lecture Notes:


Vitamins and Cofactors, cont.

Note the relationships of the various cofactors to their vitamin precursors. Chapter 7 of your text has images of the various cofactors and vitamins, as well as example chemistries. You should keep it in mind to refer back too during our studies.

Nucleotide Functions: Most involve use of the nucleotide as a recognition molecule, e.g. ATP [Figure 7.4]

structural diagram of ATP

Nicotinamide Adenine Dinucleotide (NAD+) uses ADP (bolded) as a recognition "handle." (Note the two nitrogenous bases each attached to a ribose and linked through a phosphoric acid anhydride linkage: [Figure 7.8]

structural diagram of NAD

Similarly adenosine with a modified ribose (reduced to the alcohol - ribitol) is used in Flavin Adenine Dinucleotide = FAD (not truly a dinucleotide since ribitol instead of ribose!): [Figure 7.10B]

structural diagram of FAD

Coenzyme A has an ADP attached to an arm of pantothenic acid, which in turn is attached to beta-mercaptoethylamine. Acetyl groups can be carried on the sulfhydryl group: [Figure 7.12]

structural diagram of Coenzyme A

Three vitamins give cofactors with long "arms" which enable the cofactors to shift an attached substrate between adjacent active sites on a single enzyme.

lipoic acid structure

Note attachment of biotin and lipoate to lysine side-chain to give 10 atom arms. [Figure 7.29]

lipoyllyine structure



  The carbohydrates, or sugars, are our third group of biomolecules. They are characterized by having a carbonyl carbon (aldehyde or ketone) and multiple hydroxyl groups. The smallest sugars are thus the three carbon trioses, glyceraldehyde (aldotriose) and dihydroxyacetone (ketotriose) [Figure 8.1].
Fischer structures of D & L Glyceraldehyde and Dihydroxyacetone
Note that sugars occur in both D and L forms. [Figure 8.2] As we shall see the natural sugars are generally D. [Figure 8.4]

Let's look at the two families, aldoses and ketoses. The important aldoses include the five carbon aldopentose, ribose [Figure 8.3]:

Fischer and Haworth structures of alpha-D-ribose
which commonly occurs in the cyclic furanose form named for furan. [Figure 8.11a, 8.6b] Note that sugars can generally form different isomeric cyclic forms [Figure 8.3]

The six carbon aldohexoses, glucose, mannose, and galactose [Figure 8.3].

Fischer and Haworth structures of alpha-D-glucose & Fischer structures of D-mannose and D-galactose
which commonly occur in the cyclic pyranose form named for pyran (as shown for glucose above; [Figure 8.6a]), and the six carbon ketohexose, fructose [Figure 8.5].
Fischer structure of D-fructose
which commonly occurs in a cyclic furanose form. The important ketoses include dihydroxyacetone, D-Xylulose, D-Ribulose, and D-Fructose [Figure 8.5] Note the relationship between the Fischer projections and the cyclic Haworth projections, using the example of glucose.
diagram showing the relationship of a Fischer structure to a Haworth Structural diagram

The ring is then sealed via a hemiacetal bond. [Figure 8.8] This would normally be quite unstable, however the closeness of the two reacting centers in the same chain makes them poor leaving groups, thus the hemiacetal is in fact the stable form of the six carbon aldoses. Thus the expected aldehyde chemistry for glucose is not seen (glucose is stable to oxygen etc.). Note that if drawn in the proper conformations [Figure 8.12], or if constructed as models it will be seen that the chair conformation should be more stable. In addition, the beta configuration of the hemiacetal -OH will be equatorial and should thus be preferred steriochemically as is in fact the case. Interestingly organisms can generally only use the alpha form, so isomerases are provide to interchange the two.

An important reaction is the Lobry-de-Bruyn-van Ekenstein Transformation. This base catalyzed reaction sequence interconverts three of the major hexoses, and will be used later in understanding some isomerase enzyme mechanisms. The mechanism is symmetrical. You should finish the second half on your own.

Mechanism diagram of the Lobry-de-Bruyn-van Ekenstein Transformation using Fischer structures



Can link sugars via acetal bonds, known as glycosidic bonds. [Figure 8.19]

reaction diagram showing the formation of glycosidic bonds

There are four common disaccharides [Figure 8.20]:

The first three are reducing sugars, that is they have "free" aldehyde groups, whereas sucrose has both carbonyl groups tied up in the relatively stable glycosidic bond. Maltose and fructose are joined in alpha-glycosidic bonds. In general the alpha-glycosidic bond is easily cleaved (it is less stable chemically and organisms have enzymes to cleave it) whereas the beta-glycosidic bond is very difficult to break down.

Thus for cellobiose, and more importantly, cellulose which is also linked by beta-bonds, essentially only bacteria can digest this bond.

So animals can't digest cellulose! You may ask, What about Cows and things? Well they use bacteria. Cows for instance are basically walking fermentation tanks.

Cool biological examples of cellulose use by animals: Desert Iguana consume feces to maintain culture; Rabbits eat and reprocess first pass feces (soft) to take advantage of fermentation; Multiple stomachs in Ruminants; Ultimate symbiosis in some termites: protozoans in gut have bacteria in gut, and use spirochetes as "cilia" (rowers).



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© R. A. Paselk 2010;

Last modified 4 March 2013