DNA and RNA

Post Reply
User avatar
Tero
Just saying
Posts: 34244
Joined: Sun Jul 04, 2010 9:50 pm
About me: Something something birds
Location: USA
Contact:

DNA and RNA

Post by Tero » Tue Aug 18, 2020 11:20 am

I gave a class in the early spring on humans and DNA, and most of it went on the big scheme of things, taking the terms and connecting them to human populations, diseases etc.

I had really poor biology in college in the early 70s. I picked up a bit more at work after 1980. I worked with many biochemists, and did get Lehninger's Biochemistry at the time to see what we were working on. Generally I just had to work with papers on a single enzyme, so DNA was not important. But we did make some antivirals, so at least nucleosides were familiar. The little bits DNA is made of.

Just collecting a few concepts I have learned lately.

Sense and antisense. Only one strand has info for any particular section. You read from one "end" and there are start and stop codes that are easy to find.
Sense and antisense

A DNA sequence is called a "sense" sequence if it is the same as that of a messenger RNA copy that is translated into protein.[32] The sequence on the opposite strand is called the "antisense" sequence. Both sense and antisense sequences can exist on different parts of the same strand of DNA (i.e. both strands can contain both sense and antisense sequences). In both prokaryotes and eukaryotes, antisense RNA sequences are produced, but the functions of these RNAs are not entirely clear.[33] One proposal is that antisense RNAs are involved in regulating gene expression through RNA-RNA base pairing.[34]

A few DNA sequences in prokaryotes and eukaryotes, and more in plasmids and viruses, blur the distinction between sense and antisense strands by having overlapping genes.[35] In these cases, some DNA sequences do double duty, encoding one protein when read along one strand, and a second protein when read in the opposite direction along the other strand. In bacteria, this overlap may be involved in the regulation of gene transcription,[36] while in viruses, overlapping genes increase the amount of information that can be encoded within the small viral genome.[37]
https://en.wikipedia.org/wiki/DNA#Sense_and_antisense

Gene mapping: from 5' to 3' /3' to 5'
https://biolympiads.com/principles-of-g ... -problems/
Last edited by Tero on Tue Aug 18, 2020 11:35 am, edited 1 time in total.

User avatar
Tero
Just saying
Posts: 34244
Joined: Sun Jul 04, 2010 9:50 pm
About me: Something something birds
Location: USA
Contact:

Re: DNA and RNA

Post by Tero » Tue Aug 18, 2020 11:28 am

Viruses, bacteria etc can have double stranded DNA where there is info on both strands:
But keep in mind that sometimes, such as in prokaryotes, overlapping genes on opposite strands means the sense for one mRNA can be the antisense for another mRNA[2].
https://en.wikipedia.org/wiki/Sense_strand

User avatar
Tero
Just saying
Posts: 34244
Joined: Sun Jul 04, 2010 9:50 pm
About me: Something something birds
Location: USA
Contact:

Re: DNA and RNA

Post by Tero » Tue Aug 18, 2020 11:37 am

A bit of confusion in the coding and template strands:
https://upload.wikimedia.org/wikipedia/ ... b/MRNA.svg

User avatar
Tero
Just saying
Posts: 34244
Joined: Sun Jul 04, 2010 9:50 pm
About me: Something something birds
Location: USA
Contact:

Re: DNA and RNA

Post by Tero » Tue Aug 18, 2020 11:43 am

More on the confusion of sense and antisense. It seems to be a local convention, dealing with only the gene at hand:

Juan Pablo Matte Risopatron
Pontificia Universidad Católica de Chile
Sense and anti-sense is used as reference in regard to a specific gene. The name is used only locally in a segment of the whole DNA. For example an specific gene in the genome which coding region start from the 5’ to 3’, is called “sense”, the strand that goes in the “opposite” direction (which is also from 5’ to 3’) is called “anti-sense”. Moreover, genes are spread in the genome in both strand, and the direction of the genome is arbitrary to have a consensus of the localization of the genes. The important is that genes orientation is always the same (5’ to 3’), and in coding DNA, start codon (5’-ATG-3’) is located in the sense strand, where the complementary sequence is situated in the antisense strand (3’-TAC-5’). Nevertheless, the antisense strand is the one that is transcribed to give a sense mRNA with the start codon 5’-AUG-3’.

https://www.researchgate.net/post/If_I_ ... _antisense

User avatar
Tero
Just saying
Posts: 34244
Joined: Sun Jul 04, 2010 9:50 pm
About me: Something something birds
Location: USA
Contact:

Re: DNA and RNA

Post by Tero » Wed Aug 19, 2020 1:16 am

Genes for most important proteins have been mapped. The documents and wikipedia draw a continuous chromosome with bands (these are from staining experiments). Insulin is found on chromosome 11 in the "reverse strand"
http://may2017.archive.ensembl.org/Homo ... 79-2161341
https://en.wikipedia.org/wiki/Insulin

the convention is to read DNA 5' top 3' end. This seems to indicate that you number the residues 5' to 3', but this protein is in the complementary band. To make it, you read again from 5' to 3', but now toward the "tip" of the chromosome.

Another example:
https://en.wikipedia.org/wiki/Angiotens ... ing_enzyme

http://may2017.archive.ensembl.org/Homo ... 1-63498380

this one is in the "forward strand"

User avatar
Tero
Just saying
Posts: 34244
Joined: Sun Jul 04, 2010 9:50 pm
About me: Something something birds
Location: USA
Contact:

Re: DNA and RNA

Post by Tero » Sun Aug 30, 2020 2:12 pm

Imprinted genes: favoring either the gene from male or female parent

The majority of imprinted genes in mammals have been found to have roles in the control of embryonic growth and development, including development of the placenta.[23][47] Other imprinted genes are involved in post-natal development, with roles affecting suckling and metabolism.Another hypothesis proposed is that some imprinted genes act coadaptively to improve both fetal development and maternal provisioning for nutrition and care.[9][55][56] In it, a subset of paternally expressed genes are co-expressed in both the placenta and the mother's hypothalamus. This would come about through selective pressure from parent-infant coadaptation to improve infant survival. Paternally expressed 3 (PEG3) is a gene for which this hypothesis may apply.

23
https://www.sciencedirect.com/science/a ... via%3Dihub

wiki
https://en.wikipedia.org/wiki/Genomic_imprinting

User avatar
Tero
Just saying
Posts: 34244
Joined: Sun Jul 04, 2010 9:50 pm
About me: Something something birds
Location: USA
Contact:

Re: DNA and RNA

Post by Tero » Sun Aug 30, 2020 2:44 pm

The imprinting example related to placenta in humans and horses:
https://news.cornell.edu/stories/2013/0 ... tudy-shows

DNA is silenced
https://en.m.wikipedia.org/wiki/Gene_silencing

User avatar
Tero
Just saying
Posts: 34244
Joined: Sun Jul 04, 2010 9:50 pm
About me: Something something birds
Location: USA
Contact:

Re: DNA and RNA

Post by Tero » Wed Oct 14, 2020 5:39 pm

when you discover a tool in science, you publish it, it gets wide use immeadiately (socialism!) instead of patenting it (for a limited number of uses)
Then you get a Nobel
https://cen.acs.org/biological-chemistr ... mpaign=CEN
I think the video is playable to all

Post Reply

Who is online

Users browsing this forum: No registered users and 13 guests