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Amylase is an enzyme that breaks down starch in the form of amylopectin and amylose. Both amylose and amylopectin are formed by alpha glucose joined together by (1-4) and (1-6) glycosidic bonds. Glycogen is no exception, just that it has more branching. However, why is it that a google search shows that it is hydrolyzed by Glycogen Phosphorylase rather than amylase? Also, how can amylase digest both (1,6) and (1,4) glycosidic bonds?

Any help would be greatly appreciated.

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At an approximation the active sites of enzymes can be considered as having two aspects. The first relates to the catalysis — in this case the breaking of the glycosidic linkage. The second relates to binding the substrate. This review of the α-amylases by MacGregor et al. shows that there is a range of a-amylases, differing in this latter respect — their substrate specificity. In general there are binding sites for a varying numbers of glucose residues at either side of the bond being cleaved. This is shown in Fig. 3 of that review:

Speificity of alpha-amylase

The important difference in the structure of glycogen and starch (amylopectin) — seldom mentioned in general biochemical or biology texts — is their patten of branching:

branching pattern of glycogen and starch

As this previous answer of mine to a different question explains, this results in a globular structure for glycogen granules in which only the ends of the chains are accessible. (The image below, from Protopedia, illustrates this better, especially if you imagine it in three dimensions.)

Glycogenin

Hence the substrate-binding site of α-amylase does not have access to the residues that need to bind for it to perform hydroysis of glycogen, and, indeed, the enzyme that breaks down glycogen — glycogen phosphorylase — is specific for these free ends.

The α-amylases that can hydrolyse both α-1,4 and α-1,6 glycosidic links are quite few compared with those with specificity to one or the other type of linkage (see Table 2 of the MacGregor review, if you can obtain access to it). The impression obtained from following up two of the examples there is that the enzymes involved can exist in alternative conformations, the correct one of which is triggered by the substrate. An example is the glycogen debranching enzyme, the studies of which in Sulfolobus solfataricus and Candida glabrata can be read freely on-line. Although somewhat less directly relevant, the example of a Thermoactinomyces vulgaris neopullulanase is another variation on this theme.

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  • $\begingroup$ So in summary it means that glycogen is arranged like a sphere so that only the ends of the glucose chain is exposed, hence amylase cannot work on it. $\endgroup$ – user35897 Jan 21 '18 at 3:30
  • $\begingroup$ And that some amylase have active site flexible enough to accommodate both sort of linkages? $\endgroup$ – user35897 Jan 21 '18 at 3:31
  • $\begingroup$ @user35897 — As regards the spherical form of glycogen, yes, and I have added another image (referenced). As regards my guess about flexible active sites, no, I was wrong. I seems that it is the enzyme overall that is flexible in being able to adopt alternative conformations. I have altered the last part of my answer with references to examples of studies with crystal structures. Good questions educate us all. $\endgroup$ – David Jan 21 '18 at 10:54
  • $\begingroup$ just a random afterthought but how does glycogen get digested as it goes through the gut to the small intestine, since glycogen phosphorylase is not produced in the stomach or small intestine? Some sources seem to tell me that amylase CAN indeed hydrolyze glycogen. $\endgroup$ – user35897 Jan 27 '18 at 13:05
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    $\begingroup$ @user35897 — You are failing to differentiate between two different situations. One is the mammalian cell (e.g. a liver or muscle cell), from which amylase is absent, and where the breakdown of glycogen can be (and is) controlled by controlling the activity of the only enzyme in that cell able to do so — glycogen phosphorylase. The second is in the digestive system where any glycogen from a meal of meat is digested (or not). There it will presumably be exposed to, and succumb to, the same amylases that break down starch in food. [I mistakenly wrote GS, not GP in previous version of comment.] $\endgroup$ – David Jan 27 '18 at 23:23

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