A basic base pair (dna) question

[ardmore]

This question seems to be silly, but my major is not biology. So hopefully somebody can give me a plain explaintion.

We all know a DNA for humanbeing has two chains.
Can we say one chain comes from father, the other one is from mother?


Thanks.

[stefanoberri]

You are mixing two things.

We have 22 pairs of chromosomes + 2 sex chromosomes. For each pair, one comes from the mother, the other from the father.
Each chromosome is made by two long complementary DNA molecules. The famous double helix. However both the strands come from the same parent.
Look up those terms in Wikipedia and follow relevant links for further details. Hope this helps.

[Joann]

Also keep in mind that the message (that results in biological structure) is read from one strand of a double strand "chain" and that in the case when DNA is replicated during cell division in a growing organism, the double stranded chain unwinds to permit complementary duplication of each.

[ardmore]

Thanks for kind help.

[ardmore]

I still have something to ask. Example, suppose in chromsome 12(mother side) bp 50,000,000 to 50,000,004, the sequence data in one strand is "AGCT", so how about the other strand in the same position?

Then how about the sequence in chromsome 12 father side, the same position?

[stefanoberri]

On the other STRAND OF THE SAME CHROMOSOME, it will say 'TCGA'.
On the same (let's say plus) strand of the other chromosome (from the father) it is very likely to say 'AGCT', but it might have a variant allele and be 'ATCT'. If this is the case, the other STRAND of the father chromosome will be 'TAGA'.

The two strand are ALWAYS complementary. if this is not the case, the cell will try to fix one of the two. The two chromosomes, however, can be different. They carry the same information but they might have two different versions (alleles) of a given piece of information.

For instance you might have that your mother's chromosome, somewhere says you should be blood type A, your father's chomosome, in the SAME POSITION, says that you are blood type B and you end up being blood type AB

[ardmore]

So for SNP, does it refer to mother side chromsome or father side chromsome or both?

[stefanoberri]

either

if you find a heterozygous SNP, it means one of the two chromosomes, for that position, had a nucleotide different from the reference genome. If it is a homozigous SNP it means that both are different from the reference genome. You can't tell if it is the mother's or the father's chromosome, uless you have the same information for the two parents as well.

[ardmore]

I found a link at http://seqanswers.com/forums/showthread.php?t=1175

Explanation by example:

SNPs

Heterozygous:

GCTA
GCCA


Homozygous:

GCTA
GCTA

What does it mean? The first line comes from one strand of (mother or father chromsome)? The second line comes from the reference genome?

[stefanoberri]

...

So, that link is right, but inclomplete as it assumes you know DNA is double stranded but just does not write the other strand, because you can get it yourself.
Here how it would look like reporting both strands

Heterozygous:

...GCTA...
...CGAT...


...GCCA...
...CGGT...


Homozygous:

...GCTA...
...CGAT...


...GCTA...
...CGAT...

[ardmore]

Okay, for the safety, let me clarify it. Please correct me if I am wrong.

Heterozygous SNP:

GCTA...strand 1 in mother chromsome
CGAT...strand 2 in mother chromsome


GCCA...strand 1 in father chromsome
CGGT...strand 2 in father chromsome

Homozygous SNP:

GCTA...strand 1 in mother chromsome
CGAT...strand 2 in mother chromsome

GCTA...strand 1 in father chromsome
CGAT...strand 2 in father chromsome

[stefanoberri]

that's right

[ardmore]

One follow up question, I am using Plink software. Please look at http://pngu.mgh.harvard.edu/~purcell...data.shtml#ped

CHR          SNP   A1   A2          MAF       NM
        1         snp1    C    A         0.25        8
       23         snp2    C    A          0.2        5
       24         snp3    C    A            0        1
       25         snp4    C    A         0.25        8
       26         snp5    C    A            0        2

So
A1 comes strand 1, either mother or father chromsome.
A2 comes strand 2, either mother or father chromsome.