Upstream / Downstream / Anti-sense / sense DNA... what?

[pm1]

I am a little confused on the terminology of upstream versus downstream.

If I understood it correctly upstream is towards the 5' end and downstream towards the 3', right?

But I get confused when the statement is referring to the sense or anti-sense strand.

For example, I read that the lac operon is regulated by a promoter (P) and lac operator (O) upstream. However, TPR shows a figure where the P and O are towards the 3' end of the anti-sense strand.
So, when they say that P and O are upstream are they referring to the sense strand, even though this is not the strand being transcribed?
Also, I've noticed the interchanging of terms, which gets quite confusing as it is in the sentence:
"It is customary to say that transcription starts at a point and proceeds DOWNSTREAM, which means toward the 3' end of the coding strand and transcript."
So should I have as a reference the coding strand even though it is not the strand being transcribed?

---

Members don't see this ad.

 

[pfaction]

It's screwed up, I know.

Anti-sense = noncoding = transcribed = template: this is the thing getting acted on by RNA polymerase.

Sense = coding = nontranscribed = complementary: this is the thing that is NOT getting acted on by RNA polymerase.

Helicase moves downstream (+) towards the 5'end of the transcribed DNA strand as the RNA is made 5'-3'. meaning that the upstream (-) is towards the 3' end.

 

[pm1]

It's screwed up, I know.

Anti-sense = noncoding = transcribed = template: this is the thing getting acted on by RNA polymerase.

Sense = coding = nontranscribed = complementary: this is the thing that is NOT getting acted on by RNA polymerase.

Helicase moves downstream (+) towards the 5'end of the transcribed DNA strand as the RNA is made 5'-3'. meaning that the upstream (-) is towards the 3' end.

but isn't downstream towards the 3' end? do we just always go by the non transcribed strand?

thank you!

 

[MedPR]

Read upstream (from 3' to 5') and write downstream (from 5' to 3').

So when transcription starts at a point and proceeds downstream, it is writing downstream (making the transcript from 5' to 3') but it is reading the template upstream (from 3' to 5').

 

[HollowSuperet36]

Yeah, think in terms of the compliment being transcribed. Antiparallel strands. If you are reading in one direction, then you have to be writing in the opposite.

EK uses the analogy of thinking about a photographer paddeling up river to take a photo of a landscape directly off the river to them. They paddle upstream to see what they are going to take a photo of (Read 3-5) then take photos of the landscape as the current carries them down stream (Write 5-3).

Maybe this makes it worse, but it makes sense to me.

 

[Class1P]

You always "write" 5'-3'

If you look at the structure of your NTP's the high energy weak phosphate bond is on Carbon #5 of the ribose sugar. This phosphate reacts with the hydroxyl group on another NTP at carbon #3.

Once you have 2 NTPs hooked together, you'll notice that one end has a phosphate still attached at the 5' end and one has a hydroxyl at the 3'. This is why it is called 3' to 5'. The polymerase can only add new triple phosphorylated nucleotides because it holds onto the chain of growing DNA and uses the hydroxyl group as the active site for attachment of a new NTP.

If it worked the other way your polymerase would hold onto the phosphorylated 5' end and wait until a suitable hydroxyl group of a NTP would float into the active site. The polymerase might not know whether it is a partial unphosphorylated nucleotide, at which point your elongation would stop and your cell would be screwed.