I understand that mass spec is widely used to study PTMs likeglycosylation of proteins, but how can mass spec determine correctPTM structure of say glycosylation if two glycan structures havethe same mass but different arrangement (i.e. isobaric)? Also, howcan mass spec determine the difference between structuralisomers?

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Beverley SmithLv2

7 Aug 2019

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Examine the following proteins and determine how many domains each polypeptide has. (If there is more than one chain or model, only examine one.) List the residues in each domain (e.g. 17-98, 141-169), and classify each domain (as in part 1).

1. One subunit of human branched chain aminotransferase (4HBA)

2. Escherichia carbenicillin-binding protein (5ECB)

3. One subunit of the enterobacterial ligand-gated ion channel (6ELC)

C. Examine the following multimeric proteins and classify the symmetrical arrangement of the subunits (e.g. C2, C3, D2, helical, icosahedral). If the program asks you to âLoad __ modelsâ, just hit OK with whatever number it has by default. (Note that each model will load as a different layer.)

1. Nitrosomonas hydroxylamine oxidoreductase (7NHO)

2. Enterobacterial lectin (8EBL)

3. Enterobacterial ligand-gated ion channel (6ELC)

D. Examine the 2 pairs of proteins below. In each case, these are enzymes that catalyze the same reaction in different species. The question is: are they related or not? i.e. Are the structures essentially the same? Often you can get similar reactions from proteins that evolved from a common ancestor (e.g. trypsin and chymotrypsin). Sometimes the same reaction can be catalyzed by proteins with very different evolutionary origins and with very different structures (e.g. trypsin and subtilisin). Your job is to decide if these proteins have fundamentally different folds or if they have basically the same fold. Briefly justify your answer (â¤3 sentences).

Aldolase from an Archaea and a Bacillus (PR1A & PR1B)

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I am trying to understand the Y2H screening method. I canunderstand how we can check if two specific proteins interact witheach other. For example, if we want to check whether protein A andprotein B interact, we fuse A with the Activation Domain (AD) of atranscription factor and B with the Binding Domain (BD) of anothertranscription factor. When the two fusion proteins are transfectedinto a yeast cell, the reporter gene is expressed only if the ADand the BD get together and form a complete transcription factorand that happens only if proteins A and B interact with eachother.

However, I have seen claims that Y2H is a high throughputsystem, i.e., it can be used to detect several interactions atonce. But most articles online that attempt to describe it, seemvague to me.

For example, suppose I fuse the "bait" protein to the BD andseveral different cDNA's to the AD and let the yeast grow. Next, Iobserve that the reporter gene is expressed. Doesn't thisobservation only imply that there exists some protein from the cDNAlibrary that interacts with our bait protein? How do we knowexactly which of the target proteins have interacted with the baitand resulted in the expression of the reporter gene?

1. Which of the follow are traits that can be used to make a phylogenetic tree?

a)The bone structure differences between species

b)Similarities in how organs develop between species

c) Based on the differences of the organs found in each species

d)All of the above

E) None of the above

2. Two traits are homologous if:

a)They are what is used to differentiate two population

b)Required for random mating

Any feature that is shared by two or more species

d)All of the above

3. When looking at essential proteins that are conserved amongst different species

a)The only thing to look at is DNA sequence
		b)The only thing to look at is a protein sequence
	c)	Often the sequences are different but the structures are very similar
	4	d)Sequence alignments will tell you very little