Login

Join for Free!
117036 members


Virology - Calculations

Debate and discussion of any biological questions not pertaining to a particular topic.

Moderator: BioTeam

Virology - Calculations

Postby mkay28 » Mon Sep 16, 2013 1:05 am

I'm needing some help understanding where to go on sample problems. I haven't had any success finding tutorials or anything online to explain how to complete problems such as:

**A virus has a genome of 1.184 MB (1184 kb) of double stranded DNA. 90.5% is coded into 1262 ORFs. What would be the average size of a coded protein in kiloDaltons?
-1184 kb is 1184000 bases times the 660 Da per base pair gives 7.8144x10^8Daltons... Not sure where to go to further this. Somehow, I think a codon of 3 nucleotides (990 Da) factors in to this??

**What is the molecular weight of single-stranded RNA needed to code for a capsid protein of 60 kilodaltons and how many nucleotide bases does this represent?
-I believe I'd take the 60kd and turn it into 60,000daltons and then multiply the 60000 by 330Da/nucleotide to get 1.98x10^7 bases or 1.98x10^4 kilobases. How do I calculate the molecular weight?

**How many kilobase pairs in a single double-stranded DNA 9345 nucleotide base pairs long?
-9345 base pairs /660(Da/base pr) = 14.16 Daltons... Where else do I take this??

**A double-stranded viral genome is 240 kilobases. What is a reasonable estimate of how many genes could be present and what are three variables that effect the exact number of genes present?

For these problems, I'm using an average of 330 as the weight of one nucleotide. Any tips on how to solve these problems or a tutorial I can find to solve them? My book and google searches have been unsuccessful in helping me. Thanks in advance.
mkay28
Garter
Garter
 
Posts: 3
Joined: Tue Sep 10, 2013 8:43 pm

Re: Virology - Calculations

Postby JackBean » Tue Sep 17, 2013 3:58 pm

mkay28 wrote:**A virus has a genome of 1.184 MB (1184 kb) of double stranded DNA. 90.5% is coded into 1262 ORFs. What would be the average size of a coded protein in kiloDaltons?
-1184 kb is 1184000 bases times the 660 Da per base pair gives 7.8144x10^8Daltons... Not sure where to go to further this. Somehow, I think a codon of 3 nucleotides (990 Da) factors in to this??

ahh... no!
So, the size of genome is 1184 kbp (whether you express it in kbp, Mbp or bp really doesn't matter, just the result will be shifted).
90.5% of the genome, that is 1071.52 kbp, are ORF. And you know that there are 1262 ORFs, so you just calculate the average length of one ORF as 1071.52 kbp/1262 ORFs = 849 bp per ORF. Of course this is only average length and there will be longer and shorter ORFs.
I notice they ask also about the protein size. So 849 bp produce 283 AAs long protein, which weight about 31.13 kDa.

mkay28 wrote:**What is the molecular weight of single-stranded RNA needed to code for a capsid protein of 60 kilodaltons and how many nucleotide bases does this represent?
-I believe I'd take the 60kd and turn it into 60,000daltons and then multiply the 60000 by 330Da/nucleotide to get 1.98x10^7 bases or 1.98x10^4 kilobases. How do I calculate the molecular weight?

those 60 kDa or weight of the protein, so you must take the average amino acid weight, which should be 110 Da ( http://www.nordicbiosite.com/ViewPage.aspx?PageID=33 ), those it will be composed of 60 000 Da/110 Da = 545.4 AAs (i.e. 545 AAs).
For each amino acids you need three bases in RNA (codon is triplet, right?), thus you'll need 1635 bp long RNA. And the weight is 1635 bp × 340 Da = 555.9 kDa

What about if you tried the rest and showed us how you're doing?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
User avatar
JackBean
Inland Taipan
Inland Taipan
 
Posts: 5667
Joined: Mon Sep 14, 2009 7:12 pm


Return to General Discussion

Who is online

Users browsing this forum: No registered users and 6 guests

cron