does anyone here know a good way of remembering/ explaining 3' and 5' strands like i relearned it a hundred times but i keep mixing them up. which way is downstream? do i even need to know?
Is there anything specific you are having problems with? Transcription, translation or replication etc???
As you know, the DNA strands run anti-parallel to each other.
DNA replication always results in daughter strand synthesis in the 5' - 3' direction. The lagging strand is also synthesized discontinuously as it is formed away from the replication fork.
5' AAATTTCCC 3' (leading strand)
<---------- 5'
5' ----> 5' ---->
3' TTTAAAGGG 5' (lagging strand)
Transcription by RNA pol will also occur in the 5' - 3' direction.
5' AAATTTCCC 3' (coding strand)
5' -------------> (mRNA)
3' TTTAAAGGG 5' (template strand)
mRNA is then read by the ribosome from the 5' to the 3'.
Regarding upstream and downstream, this usually refers to where a point in the sequence is relative to a gene on the coding strand. I don't think you need to know this for VCE though.
5' AA
ATTTCCC 3' (coding strand)
3' TTTAAAGGG 5' (template strand)
For example, let's say our gene sequence is ATTTC (bold). Then we can say that the AA towards the 5' end is upstream of the gene and the CC towards the 3' end is downstream of the gene. You will often hear promotors referred to as upstream, as they are located before the coding sequences towards the 5' end of the coding strand.