Relation between Mendelian genes and bases?

[jonjacson]

Hi folks,

When you study Mendelian laws you learn about dominant alleles of a gene, A, or recessive alleles of a gene.

My question is, What is its relation to DNA?

-So in terms of bases we have A, T, C and G. And I know a gene may be in a chromosome and it may contain several million of these bases.

What do we mean in terms of bases that a gene is recessive or dominant? Does that mean there are only two versions of that gene? I mean two different sequences of bases, one is the dominant and the other is the recessive.

I am confused too with homozygous and heterozygous. In terms of bases what is an homozygous gene? DNA is a double stranded molecule of complementary bases, I don't see what could be a heterozygous gene.

Thanks!

 

[jim mcnamara]

Try to use this concise oversimplified model:

What is a gene? It is a chunk of DNA strand. It is "marked" with "start" and "stop" signs. A "sign" is a special sequence of bases, like AAT, or TAT. These 3 base special sequences are called codons. Like the alphabet and punctuation we use to write English words. Some sequences are start, some stop, but most represent the position of an amino acid in the protein molecule (long chain of amino acids) the gene is "in charge of mapping" during protein synthesis.

A chromosome is a long "wound up" strand of DNA. So. There are many genes on a given chromosome. Each gene has its own parking spot on the chromosome.

So when we look at a normal body cell in humans, we find that the chromosomes occur in pairs. Kind of like not perfectly duplicated twins. This is because the gene at position 13 (locus) on one chromosome in a pair has a few different codons, maybe. Reality check: chromosomes may or may not have lots of these mismatches. If you go to locus 17, you may find that the genes there are identical twins on your chromosome pair, all sequences are the same. Homozygous==identical twins. heterozygous==not quite identical twins at a given locus.

Allele means one of the possible genes that live at that locus. Several possible genes at one locus are common, not just 1 or 2. So human blood types have multiple alleles, for example. A, B, and O(recessive).

Since we can have genes that code for slightly different proteins at position 13, maybe one of the genes codes for a do-nothing protein. The gene got damaged somehow so part of the codon sequence got scrambled into nonsense. The other gene works perfectly. (This is for understanding on your part only.) Dominant==gene always "rules" the protein sequence, recessive==gene only rules when is it lives on BOTH chromosomes at position 13. In this pretend case, no real protein ever gets synthesized when the gene is homozygous and recessive.

Now we have several terms defined: gene, chromosome, codon, DNA base sequences, locus, pairs of chromosomes.
So using these we can now look at what happens if an organism goes through some parts of the life cycle (humans do this) with only a single set of chromosomes? The cells in your thumb all have pairs (2's) of each chromosome. n is the number of kinds of chromsomes, not how many total. Humans have 46 total, and n==23 since 46/2 = 23. 2n==diploid, 1n==haploid. So when do humans "spend time" as 1n cells. In sperm cells for about 45 days in males, and in cells in the female ovary from 4 months (fetus) in the womb. So, humans go 1n->2n->1n->2n ... forever. So do almost all eukaryotic (cells with organelles) livings thing. Going 1n->2n->1n->2n is called 'alternation of generations'

Since life is REALLY diverse there are some livings things that sort of bend the rules. Plants are bad for this. The strawberries you eat are 8n. That means they have 8 pairs of chromosomes, 8 of each and every type of chromosome. Strawberries are just fine with this. So, naturally there are terms for all of the varying numbers of "n", polyploid is more than 2n ... 3n, 4n, ... (LOTS)n. 3n is triploid, 4n tetraploid, 8n octaploid. Some ferns and grasses carry this to an extreme.

Last term: aneuploid. This means that a chomosome count is not right in the part of the lifecycle that is supposed to be be even, usually diploid (2n). It is not an even number. A missing chromosome or an extra one, so in humans the count might be 47 or 45, but not 46 which is the correct even number. This often spells trouble for the individual, especially in humans. Also true in most organisms.

 

[Ygggdrasil]

Here's a site with some useful information on the subject:

http://www.thetech.org/genetics/ask.php?id=227
[edit: updated link http://genetics.thetech.org/ask/ask227]

Here's a previous PF threads discussing the issue further:
https://www.physicsforums.com/showthread.php?p=3744324#post3744324

Basically, whether an allele is dominant or recessive depends on the particular biochemical function of the gene involved. In general, this is not something straightforward to predict from the DNA sequence alone.

Let us know if you have any more questions after you read through these links.

 

[jonjacson]

Here's a site with some useful information on the subject:

http://www.thetech.org/genetics/ask.php?id=227

Here's a previous PF threads discussing the issue further:
https://www.physicsforums.com/showthread.php?p=3744324#post3744324

Basically, whether an allele is dominant or recessive depends on the particular biochemical function of the gene involved. In general, this is not something straightforward to predict from the DNA sequence alone.

Let us know if you have any more questions after you read through these links.

Thanks for both answers.

The first link doesn't work.

Try to use this concise oversimplified model:

What is a gene? It is a chunk of DNA strand. It is "marked" with "start" and "stop" signs. A "sign" is a special sequence of bases, like AAT, or TAT. These 3 base special sequences are called codons. Like the alphabet and punctuation we use to write English words. Some sequences are start, some stop, but most represent the position of an amino acid in the protein molecule (long chain of amino acids) the gene is "in charge of mapping" during protein synthesis.

A chromosome is a long "wound up" strand of DNA. So. There are many genes on a given chromosome. Each gene has its own parking spot on the chromosome.

So when we look at a normal body cell in humans, we find that the chromosomes occur in pairs. Kind of like not perfectly duplicated twins. This is because the gene at position 13 (locus) on one chromosome in a pair has a few different codons, maybe. Reality check: chromosomes may or may not have lots of these mismatches. If you go to locus 17, you may find that the genes there are identical twins on your chromosome pair, all sequences are the same. Homozygous==identical twins. heterozygous==not quite identical twins at a given locus.

Allele means one of the possible genes that live at that locus. Several possible genes at one locus are common, not just 1 or 2. So human blood types have multiple alleles, for example. A, B, and O(recessive).

Since we can have genes that code for slightly different proteins at position 13, maybe one of the genes codes for a do-nothing protein. The gene got damaged somehow so part of the codon sequence got scrambled into nonsense. The other gene works perfectly. (This is for understanding on your part only.) Dominant==gene always "rules" the protein sequence, recessive==gene only rules when is it lives on BOTH chromosomes at position 13. In this pretend case, no real protein ever gets synthesized when the gene is homozygous and recessive.

Now we have several terms defined: gene, chromosome, codon, DNA base sequences, locus, pairs of chromosomes.
So using these we can now look at what happens if an organism goes through some parts of the life cycle (humans do this) with only a single set of chromosomes? The cells in your thumb all have pairs (2's) of each chromosome. n is the number of kinds of chromsomes, not how many total. Humans have 46 total, and n==23 since 46/2 = 23. 2n==diploid, 1n==haploid. So when do humans "spend time" as 1n cells. In sperm cells for about 45 days in males, and in cells in the female ovary from 4 months (fetus) in the womb. So, humans go 1n->2n->1n->2n ... forever. So do almost all eukaryotic (cells with organelles) livings thing. Going 1n->2n->1n->2n is called 'alternation of generations'

Since life is REALLY diverse there are some livings things that sort of bend the rules. Plants are bad for this. The strawberries you eat are 8n. That means they have 8 pairs of chromosomes, 8 of each and every type of chromosome. Strawberries are just fine with this. So, naturally there are terms for all of the varying numbers of "n", polyploid is more than 2n ... 3n, 4n, ... (LOTS)n. 3n is triploid, 4n tetraploid, 8n octaploid. Some ferns and grasses carry this to an extreme.

Last term: aneuploid. This means that a chomosome count is not right in the part of the lifecycle that is supposed to be be even, usually diploid (2n). It is not an even number. A missing chromosome or an extra one, so in humans the count might be 47 or 45, but not 46 which is the correct even number. This often spells trouble for the individual, especially in humans. Also true in most organisms.

Ok, I understand it.

Just another question, I read that DNA only wraps into chromosomes when the cell is going to divide by mitosis, that means normally we don't have chromosomes in the cells, just DNA wraped around histones right? Does that matter?

 

[Ygggdrasil]

Thanks for both answers.

The first link doesn't work.

Thanks for pointing that out. Here's an updated link: http://genetics.thetech.org/ask/ask227

Just another question, I read that DNA only wraps into chromosomes when the cell is going to divide by mitosis, that means normally we don't have chromosomes in the cells, just DNA wraped around histones right? Does that matter?

While DNA does not exist as condensed chromosomes during interphase, the DNA from each chromosome still occupies a distinct and somewhat separate space inside the nucleus called a chromosome territory. Chromosomes do not stay as condensed, mitotic chromosomes throughout interphase because the DNA is very tightly packed in these structures, which prevents proteins such as transcription factors and RNA polymerase from accessing the DNA to transcribe mRNA. The more loosely packed interphase chromatin, on the other hand, allows access of these factors to the DNA in certain regions (called euchromatin). Other regions (called heterochromatin) still remain somewhat highly packaged which impedes the access of many factors to the DNA, leaving these regions transcriptionally silent.

 

[jim mcnamara]

Just another question, I read that DNA only wraps into chromosomes when the cell is going to divide by mitosis, that means normally we don't have chromosomes in the cells, just DNA wraped around histones right? Does that matter?

Well yes, when DNA is transcribed to RNA then proteins are assembled based on the sequence of the bases RNA has copied. This could not happen when DNA is in a chromatid (chromosome "arm").
Edit:
@Ygggdrasil answer is far more detailed. And much better in that regard. I am trying more for the 10000 foot view(Biology for poets) because the whole subject is anything but simple.

But.

Histones and methylation of DNA can alter the places where transcription can occur. So some individual genes can be inactivated even though they are perfectly okay. Then there are Barr bodies - "extranuclear " chromosomes in human females - the result of one of X chromosome pair has been "evicted" (lyonization) from the nucleus so that only the genes on the other remaining X chromosome are expressed in that particular cell.

Aren't you glad you asked?
Please see: https://en.wikipedia.org/wiki/Epigenetics - the methylation and histone bit above
https://en.wikipedia.org/wiki/Barr_body - You will see W chromosome mentioned, follow the link there if you like. Sex chromosome in birds and reptiles, some fish.

 

[jonjacson]

Great answers folks, now I understand it.