BCMB20002 question thread

[ChickenCh0wM1en]

Hey guys,

Since I and other people I have talked to are finding BCMB20002 to be really difficult, I wanted to start a thread where people can post questions and get them answered!

I'll start it off:

I'm not totally confident with the whole concept of DNA major grooves and minor grooves. Esp in the A-type and B-type helix.
Attached here are two diagrams with the grooves.
1) http://classconnection.s3.amazonaws.com/308/flashcards/1147308/png/figure_8-131330574242091.png
2) http://www.math.andyou.com/content/07/ec/images/mu_pe_07_re_025.png

The 1st picture points to the grooves as part of the bp/nucleotides of the helix while the 2nd picture implies that the grooves are the gaps? Which one would the grooves actually be? (Sorry if this makes no sense)

Also where would the major and minor grooves be in A-DNA? I know from the lecture recently that the major groove is narrow + deep while the minor groove is wide + shallow but where along the helix would it be?

Thanks so much!

[simpak]

The grooves are the gaps, the first picture is just misrepresented because it's difficult to indicate a 3D property on a 2D picture I think.  A-DNA is wound just like B-DNA so the grooves would be around the outside of the helix much like in B-DNA (aka 'the gaps'), just of a different shape.  Does that make sense?

[MelonBar]

hey dud,

in the first picture, the first bit of space is a major groove, in the middle is a minor groove and the third gap at the bottom represents another major groove.

in the other pic, the face drawn in yellow pertains to the helix's major groove, and the other side (blue) would be the minor groove. we know this because the a-type helix has a particular deep major groove but its minor groove is shallow and close to the outer rim (written on the slide)

[MelonBar]

nah dude, you can see 'grooves' as gaps in between the sugar phosphate backbone which are drawn in white ie what you are pointing to in red. from this perspective we can see 4 belts of this backbone. in between the first and second little belts is the major groove. in between the second and third belts of the backbone is a narrow space, the minor groove.

you were probz confused when i said the orange face is the major groove. What we actually see in the orange and blue there are the base pairs. the 'major' groove refers to the distance from the outer rim at 8oclock to that side of the base pairs highlighted in orange. The minor groove is the distance from the outer rim to the side of the base pairs highlighted in blue - as you can see there is virtually no space in the picture, cf with the major groove

btw if someone else can explain better pls do

also wtf happened to the lecture recordings for last friday???
     

[MelonBar]

There is piano playing on one of the friday lecture recordings. I thought that maybe the system screwed up and put a World Music Choir lecture on there or sum chiz, but i figured that there was no lecture friday, due to the MST. and it was a placeholder file

[MelonBar]

Could someone explain underwinding/overwinding/topoisomerase's role in DNA replication and RNA synthesis? (The slide with these two examples are in Lecture 14).

[LeviLamp]

The detail she went into is literally just what's on the slides, it's really simplistic. During prokaryotic DNA synthesis the topoisomerase gyrase moves ahead of the replication fork to relax the double helix by cutting the overwound DNA and relaxing it, then religating it, to prevent an eventual gridlock as the strands unwind with helicase's action (since the underwound replication bubble behind the helicase causes complementary overwinding further down the strand, as well as lots of unwanted positive supercoils). In RNA synthesis, RNA polymerase forms a transcription bubble and then moves down the end, and as the bubble moves with it, the strands need to separate at one end and reanneal at the other. The prokaryotic gyrase here acts to reduce strain in both the underwound and overwound regions at each end of the bubble as it moves. Note that eukaryotic topoisomerases cannot underwind relaxed DNA like gyrase does to form transcription or replication bubbles, so transcription or replication bubbles form from the underwound DNA coiled around the octameric histone cores in the nucleosome when the histones detach from the DNA to free it up for proteins (like polymerases etc.) to bind (via methylation and phosphorylation that makes the histones more negative and so less tightly bound to the negative strand).

It's all sort of weird and confusing to me, but taking the time to nut out what Irene is saying/the slide is saying on the lecture recording will probably help. Anyway, the second MST is only MCQ, so maybe your memory will be triggered just fine anyway

[LeviLamp]

The overwound DNA regions are relaxed by topoisomerase immediately after they unwind to form the replication/transcription bubble, so the entirety of the DNA bar the bubble ends up relaxed, but the underwound region is not completely relaxed. It is constantly relaxed by cutting from topoisomerase as it moves, since underwinding and overwinding have to be met with relaxation (according to Irene) or the process won't be viable energetically or functionally, but it acts as a single point bearing all the energetic strain for the benefit of the rest of the helix, so I doubt it is 100% energetically relaxed. It's definitely being relaxed by topoisomerase the whole time it's moving, though, at both ends.

[MelonBar]

Thanks. Do you know why each helicase travels past each other's termination loci to reach their own traps on the other side of the circle? What's wrong with having the respective loci nearer to their helicase? I don't understand her explanation.

Cheers

[MelonBar]

What was the answer to the question, 'do you think the promoter is a palindrome? Why/Why not?'

[scribble]

has irene said what material we need to learn up to for fridays midsem? cause i know she said only the content before the break, but she kind of started the content from the lecture 19-20 slides, but didnt get very far into it so i wasnt sure if that is going to be assessed or not. :S

[MelonBar]

Lysines and Arginines in the histone tail can be methylated or acetylated, which makes them forfeit their positive charge. It has the same effect of Serines in the histone protein being phosphorylated; causing a change in size/charge of histones and loosening the chromatin which allows regulatory proteins to penetrate the chromosome and to control gene expression. tl dr yes dna binds less strongly

i wrote some extra stuff to help me with revision too

[LeviLamp]

Irene's description of termination made no sense, I'm so confused. Can someone please explain it to me? D; She makes it look like the chromosomes are cut unevenly...

[LeviLamp]

I've only been to one of them, and know literally nothing about them, but I'd assume you need to know everything on the slides.

[LeviLamp]

I still have 14 lectures to summarise, most of which I didn't go to (including this week's three) and I remember zero content from 1-19. I'm going to dieeee D: