Carbohydrates

Plans

1. Midterm Review
2. Filling in some gaps from chapters 6 through 8
3. Monosaccharide Structure
4. Glycosides, Polysaccharides, and Glycocongugates

Midterm Review

The key for the exam is found on the web here.

Filling some gaps from chapters 6 through 8

Chapter 6:

• Induced fit
  The conformations of enzymes don't change enormously when they bind substrates, but they do change to some extent. An instance where the changes are fairly substantial is the binding of substrates to kinases. Here the danger is that the enzyme will catalyze the unproductive hydrolysis of ATP in the same site where the kinase reaction might occur; that is, the unwanted reaction reaction
  ATP + H-O-H ⇒ ADP + P_i
  will compete with the desired reaction
  ATP + R-O-H ⇒ ADP + R-O-P
  where the emboldening P indicates a phosphate group that is covalently attached to the organic moeity R-O-. Kinases minimize the likelihood of this unproductive activity by changing conformation upon binding substrate so that hydrolysis of ATP cannot occur until the binding happens.
• Zymogens
  We have already discussed the fact that many proteins are not synthesized in their active form; instead, they undergo covalent modification after synthesis on the ribosome. Zymogens are inactive forms of proteins that have to be shortened by hydrolysis in order for them to assume their active state. A variety of proteins require this kind of activation, but the prototypical zymogens are the precursors to proteases. Here the utility of this form of synthesis is clear: if a molecule of a broad-spectrum protease is synthesized in its active form, it might cleave a neighboring molecule of the same enzyme before the latter ever had a chance to cleave its biologically relevant target, thereby decreasing the availability of the enzyme. So most serine proteases, and some other proteases, are synthesized in a longer form that must be cleaved--by a protease--in order to produce the active form.

Chapter 7:

• tetrahydrofolate
  This is a nitrogen heterocyclic compound (like a nucleic acid base, in that sense) that can undergo oxidation in the ring, but also can act as a donor of one-carbon groups--methyl, methylene, and formyl groups. It is derived from the vitamin folic acid, whose importance as a nutrient is publicized in posters featuring Daisy Fuentes.
• cobalamin
  This is one of the more complex organometallic structures we will encounter in this course. It includes a ring system called corrin, which resembles protoporphyrin apart from a missing carbon between two of the five-membered nitrogenous rings. The corrin system has a cobalt ion in its core, and there is a nucleotide-like 5,6-dimethylbenzimidazole system attached to the ring and to a phosphoribose group. It binds to a glycoprotein, intrinsic factor, found in the stomach mucosa.
• lipoamide
  This is a disulfide-containing, mostly hydrophobic molecule typically complexed to a lysine side chain in a few specific proteins. It is involved in acyl transfers in multienzyme complexes.
• lipid vitamins
  Horton points out that these vitamins are difficult to study, so our understanding of them has progressed slowly. The ones we're familiar with are vitamins A, D, E, and K; all of these are oligomers of a very common hydrophobic building block called isoprene, CH₂=C(CH₃-CH=CH₂; isoprene-based compounds are collectively known as terpenes, and we will encounter many of them as we study steroids and other lipophilic metabolites.
• ubiquinone (coenzyme Q)
  This quinone is involved in one- and two-electron transfers in the inner mitochondrial membrane in the final stages of electron transport reactions (chapter 10). In its diketo form it is a stronger oxidizing agent than either NAD⁺ or FAD; therefore it can be reduced by NADH or FADH₂.
• protein coenzymes: cytochromes The notion that a protein could be considered a coenzyme is a relatively new one. Each of the protein coenzymes that Horton describes is involved in transferring a group or participating in an oxidation-reduction reaction in the vicinity of a true enzyme. These protein coenzymes are typically small (< 20kDa) and soluble. Many of these proteins have ordinary cofactors associated with them, so we're encountering fleas upon fleas.

Monosaccharide Structure

• Ketoses and aldoses: (CH₂O)_n, 3 ≤ n ≤ 9
• Chirality in sugars: enantiomers, epimers, stereoisomers
• Growing the chains: n = 3 up through n = 6
• Conformations and ways of drawing sugars (Fischer, Haworth, ...)
• Pyranose and furanose structures for pentoses and hexoses
• Derivatives of monosaccharides

Glycosides

• Disaccharides: maltose, cellobiose, lactose, sucrose
• Reducing sugars
• Glycosides

Polysaccharides

• starch and glycogen: glucose homoglycans used for storage
• heteroglycans
• structural polysaccharides

Glycocongugates

• proteoglycans and cartilage
• cell walls: peptidoglycans: O-links and N-links