I know i've seen a thread on here about his summer course, but i can't find it. Can anyone tell me what to expect on his exams...degree of difficulty, trick questions, stickler for specificity, etc.?

7/12/2006 9:16:22 AM

it seems like it's pretty cut and dry as far as what he wants us to know. The quiz on amino acids was EXACTLY like the practice quizzes, so I would imagine that the practice tests in the manual would be similar to our actual tests.

7/12/2006 2:45:28 PM

i had him for 452, the lab, he was ok w/ the labs he just talks a lot before the experiments.

7/14/2006 10:26:57 AM

test wasn't too bad...really similar to the practice test in the manual like I said

7/14/2006 11:20:14 AM

I'm pissed, i was hoping there'd be a beta sheet question on there. It was too much like the one in the book. Wasn't there a thread about his summer class on here a couple of months ago?? I can't find it, but i know i remember reading it

7/14/2006 12:34:35 PM

http://www.brentroad.com/message_topic.aspx?topic=394364

found it

7/14/2006 12:40:45 PM

i didnt think it was bad at all...there was 1 questions that i totally was unsure about (one about the name of the protonated species) but other than that...it was pretty straightforward...

7/14/2006 5:33:55 PM

Aight guys I got a question. My quiz tommorow is on the catalytic triad. I have looked thorough the bottom lines but havnt really found much on this. Could someone point me to the right page for this. Thanks

7/19/2006 1:58:25 PM

page 59 in the course pack

good luck interpretting that in order to understand it though.

maybe you can enlighten me after you look at it

[Edited on July 19, 2006 at 2:34 PM. Reason : im in the 8 am problem session]

7/19/2006 2:33:00 PM

you only have to know how to draw the structure at the bottom of page 59 (and maybe the first one at the top of p.60) NOT including glycine.


the one at the bottom of 59: (vague interpretation from problem session)

Aspartate is "pulling" on Histidine which causes Hist to become polarized. This in turn, causes the Hydrogen on Serine to come off.

7/19/2006 2:51:26 PM

so the triad is the relationship between the aspartate, histidine and the hydrogn on the serine?

7/19/2006 2:55:04 PM

I think so...

read the bold part and the paragraph after for a better description of what happens

Serine proteases have independently evolved a similar catalytic device characterized by the Ser, His, Asp triad (Ser-195, His-57, Asp-102 in chymotrypsin, trypsin and elastase; Ser-221, His-64, Asp-32 in the bacterial subtilisin).
The serine in the triad is much more reactive then other serines in the protein. The serine hydroksyl is normally protonated at neutral pH, but in the enzyme Ser-195 (Ser-221) is hydrogen-bonded to His-57 (His-64), which is further hydrogen-bonded to Asp-102 (Asp-32). These three amino acids are often referred to as a catalytic triad.
As the serine oxygen attacks the carbonyl carbon of a peptide bond, the hydrogen-bonded His functions as a general base to abstract the serine proton, and the negatively charged Asp stabilizes the positive charge that forms on the His residue. This prevents the development of a very unstable positive charge on the serine hydroxyl and increase its nucleophilicity. The residues of the catalytic triad form a charge-transfer relay network.

7/19/2006 8:24:09 PM

Quote :

"hydroksyl "

7/19/2006 8:36:47 PM

That's right packman-the whole point of the catalytic triad is to prepare the enzyme to bind with its substrate-it does that by initiating the "charge-relay" among the three amino acids. by creating that charged AA, it can reach out to the available substrate and you have contact

7/20/2006 6:01:07 PM

could someone try to explain to me the charts on pg 55 of the bottom lines? i think all he is trying to show is that enzymes lower activation energy...but there seems to be so much stuff going on...

7/20/2006 8:57:00 PM

oh cool, i am in this class

*add to my topics*

[Edited on July 20, 2006 at 9:07 PM. Reason : grr]

7/20/2006 9:06:56 PM

Quote :

"could someone try to explain to me the charts on pg 55 of the bottom lines? i think all he is trying to show is that enzymes lower activation energy...but there seems to be so much stuff going on..."

there are 5 charts on that page. a set of 3 charts and a set of 2 more below it.

the first 3 charts are labled A, B and C. the y axis in the charts are the free energy required for the reaction. think of the x axis as a position in the reaction. (left to right corresponds to how the reaction progresses from beginning to end.)

the first chart shows a standard reaction without an enzyme. notice the reactants at a low free energry with a high "hump" to get over the activation energy required to move the reactants into products.

the second chart illustrates the concept of proximity (defined at the top of page 55) notice that by bringing the reactants together in the active site of a catalyzed reaction decreases the free energy required to get up to the top of the "hump" and then go into products.

the third chart illustrates the concept of stabilization of the transition state. here the enzymes effect is favored in the transition state of the reaction instead of the reactants side (as in the proximity example) in this case the actual activation energy required to go from reactions to products is lowered.


the two charts on the bottom show the same concepts but in a case where you have a reaction that intermediates are formed.

[Edited on July 21, 2006 at 8:20 AM. Reason : ]

7/21/2006 8:20:14 AM

^^ thanks so much. ...also....for those of you that have looked at the practice exam...there's some questions that ask about drawing structures such as Schiff bases and one of the molecules in the ATCase reaction, but we DONT need to know those, right? I want to make sure I have the correct structures written down to memorize (ATP, NAD+, NADH, Acetylcholine, Pyruvate to acetyl CoA, Glutamate to Asparatate, the Catalytic Triad, and the Aldoses and glucose stuff that he just randomly decided to throw in on Friday....). Am I forgetting anything?

7/23/2006 6:14:48 PM

^ We do need to know the Schiff base, he said as much... don't know why you would think we wouldn't need to. And while he might have said we didn't need to know some of the other structures, I wouldn't be surprised to see them on there

7/23/2006 7:15:57 PM

i swear he didnt say we needed to know its structure...just what it was....but oh well. perhaps ill try to memorize it.

7/23/2006 7:25:09 PM

aside from all the structures we need to memorize what is everyone else focusing on?

7/24/2006 3:24:14 PM

it seemed like he put a lot of emphasis on the catalytic triad mechanism and the acetalcholine esterase mechanism.

it seems like so long ago that we did michaelis menten stuff but im gonna focus on that as well.

i think those are the big things, the rest will prolly be all the little definitions and stuff that will trip you up in the multiple choice section.

i think pages 54 and 55 on factors that control enzyme activities and those charts on modes of catalysis might be short answer questions.

7/24/2006 4:23:57 PM

aight sounds good

I'm gonna study all that and the practice test (since the last one seemed very similar)

7/24/2006 4:33:25 PM

seriously screw this class...I have no problem memorizing tons of structures, it's everything else that annoys me

7/25/2006 8:51:07 AM

^ everything that i mentioned was on the test

7/25/2006 10:57:05 AM

again...wasnt too bad. the Km compared to pKa through me a bit. What did ya'll put for that one?

i was suprised he put the acetylcholine one on there though because it was a quiz question....

[Edited on July 25, 2006 at 12:22 PM. Reason : .]

7/25/2006 12:17:42 PM

Guys just a heads up-considering he writes the lab manual for that class-he loves enzymes and it sounds like you guys had a lot of enzyme related questions-even about acetylcholine (in the manual)- i would focus on stuff he knows-look through the lab manual next time to get some pointers.

[Edited on July 25, 2006 at 12:29 PM. Reason : sp]

7/25/2006 12:28:48 PM

i would think that it would have something to do with redox reactions (oxidoreductase)

A (ox) + B (red) <--> A (red) + B (ox)

km would be basically the overall rate governing constant for the catalysis. if pka is varying (which is related to ph) then you are altering the ability of reactants to become protonated or deprotonated as necessary. it would seem that certain pka values would ultimately favor one side of the general reversible reaction above. if a certain side of the reaction is being favored, then that would ultimately affect the km of the overall reaction by decreasing it or increasing it. (meaning that it could change the concentrations of enzymes or substrates needed to make things work)

thats kind of the general way that i thought about it.

[Edited on July 25, 2006 at 12:35 PM. Reason : ]

[Edited on July 25, 2006 at 12:36 PM. Reason : ]

7/25/2006 12:34:53 PM

again..very similar to the practice test...and yeah, I drew a blank on the KM and pKa question too

7/25/2006 1:02:01 PM

I BS'ed the Km and pka question and got full credit. I pretty much wrote the definitions of what each was, then drew charts Km=[s] v. Vo and then pka=pH v. % deprotonated

[Edited on July 26, 2006 at 6:12 PM. Reason : 'ed]

7/26/2006 6:12:24 PM

ya...i got 1.5pts.....but i havent looked at the key...so im not sure what i left out...it sounds like our answers ^ were similar.

7/26/2006 6:41:19 PM

ok....what page did he say the exam on wednesday would go through? i want to say he said 122, but i wanna be sure....

7/29/2006 6:14:52 PM

He didnt say a page, whatever he makes it through Mon will be on the test. Nothin for tues. So I guess it depends on how fast he goes mon.

7/29/2006 7:05:33 PM

anyone know what is supposed to be on the quiz tomorrow?

7/30/2006 3:49:55 PM

i was told by the girl that sits next to me to know how to draw the stuff on page 81, the nucleic acids on page 99 and the thing we drew on the board on wednesday on page 184

7/30/2006 7:21:54 PM

how far did he go in the notes today, and are there any particular topics he highlighted or said to ignore? thanks

7/31/2006 8:55:13 PM

He went all the way to 128. The test will cover up to 131.

7/31/2006 9:54:05 PM

I thought he said his goal was to go up to 131, but that we would stop at wherever we got to today which was pg. 128

[Edited on July 31, 2006 at 9:58 PM. Reason : ]

7/31/2006 9:57:53 PM

ya....only what we covered today is on it...so 128.

7/31/2006 10:25:22 PM

does anyone have a complete list of the carbs we should know? All I have written down is furanose, pyranose, ketose, aldose...

7/31/2006 10:54:30 PM

hey guys im taking the class next semester and was wondering if anyone had the 4th ed they were willing to sell. I have an offer right now of $55...so let me know what you are willing to sell it for; any note cards etc. would be appreciated as well (Im taking it with sylvia so the tests wouldnt help much)

7/31/2006 11:08:06 PM

GKMatt

You were right on the money last time with what you thought would be on the test. What do you think for this one? (there is a ton of stuff )

8/1/2006 12:05:16 AM

^ the stuff on the practice exam in the back is stuff he skipped over a lot of...and some of the multiple choice are just like wtf?

8/1/2006 6:56:50 AM

so much material!

8/1/2006 7:47:30 AM

Quote :

" so much material! "

this is how I feel...I'm not even really sure where to start

8/1/2006 9:31:30 AM

this one might be a little tougher to guess than the last time.

im pretty sure we will have to draw some sort of lipid. know the chains, the different head groups and the glycerol backbone.

another structure we will have to draw is at least one dealing with a pyrimidine or purine. i doubt we will have to draw a full watson-crick base pair.

i doubt the fluid mosaic model will be on the exam, but it is good to know. i have this suspicion that he will ask us to draw and explain the alkaline hydrolysis of RNA. (page 119) that was on our quiz today, so i think it will show up again tomorrow on the exam.

there will definately be some questions on the differences between forms of DNA.

short answer could be about signal transduction, charge separation, and definately the key pathways/reactions on page 125

---

it all seems like a lot of stuff to know, but it really isnt... for instance
he told us we need to know how to draw glucose, and he told us to know how to draw galactose.
now he also told us that we need to know lactose.
stay with me here, he told us that we also need to know about 1-6 and 1-4 linkages.
that could seem like a lot...

so what does all that mean...
well, 1-6 and 1-4 linkages are how carbohydrates are connected to each other, and with that... the structure of lactose is nothing more than the 1-4 linkage of galactose with glucose

look at the coursepack like sections and just try and conceptualize how things relate to each other within that section and you should be fine.

look at all the structures like building blocks and just become familiar with the names, and all the information might not seem so overwhelming

[Edited on August 1, 2006 at 12:46 PM. Reason : ]

8/1/2006 12:32:46 PM

do you think we'll have to know the structures of NAG and NAM? i have it written in my notes...but he hasnt said anything about them..

8/1/2006 5:49:20 PM

doubt it

8/1/2006 5:52:48 PM

I can't seem to find charge separation...where's it at?

8/1/2006 9:00:15 PM

p. 93, 1st paragraph

8/1/2006 9:32:28 PM