Question on biochemistry

[gluadys]

Here are some excerpts from a conversation I am having with Geobubs:

Yet every living thing has DNA and a limited set of environmental
variables. DNA is only composed of amino acids and proteins not other elements.
Therefore, DNA bahaves in a specific manner consistent with amino acids and
proteins.
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I challenged his assertion that DNA is made of amino acids and proteins.

Here is his reply:

GeoBubs: Here is biology 101. The build blocks of life are amino acids and
protiens. Amino acids make protiens. The process of making proteins is called
translation and involves the step-by-step addition of amino acids to a growing
protein chain called a ribosome. The order in which the amino acids are added is
read through the genetic code from an mRNA template. There are 22 amino acids of
which 21 are in DNA. Nucleic Acids is in the amino acid group. Three nucleotides
usually represent one amino acids. The base components of these complex
molecules are hydrogen-carbon chains, sugars. There are other elements involved
that all center on the hydrogen-carbon chains. Nucleotides are composed of
hydrogen, nitrogen, and oxygen principally. Phosphates are hydrogen, potassium
and oxygen. Please note the presence of hydrogen. All of these contribute
towards the amino acids and protiens.

I encourage to research the structure of DNA a little more intensely.
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It seems to me that he has confused the fact that DNA codes for amino acids with DNA being composed of amino acids.

However, I am unsure of his claim that nucleic acids are part of the amino acid group. Is he right or wrong on that?


Hmmm, just noted that he doesn't know what a ribosome is either.

 

[Mallon]

DNA and RNA are nucleic acids. So, no, they are not a sub-category of amino acid. Your friend is terribly confused.

 

[shernren]

Nucleic acids:

Amino acids:

 

[Jimlarmore]

One of the most interesting aspects of biochemistry is the stereochemistry involved. In living systems the amino acids are levo or left handed. No dextro amino acid will work in living systems at all. If things had "evolved" randomly we should have had both levo and dextro chirality in amino acids,,,,, we don't. DNA uses dextro or right handed molecular stero orientation. It is almost as if God did this on purpose to let us at some point see His handiwork and design
God Bless
Jim Larmore

 

[gluadys]

Nucleic acids:


Amino acids:

Thanks, shernren. That really does the trick.

 

[Mallon]

One of the most interesting aspects of biochemistry is the stereochemistry involved. In living systems the amino acids are levo or left handed. No dextro amino acid will work in living systems at all. If things had "evolved" randomly we should have had both levo and dextro chirality in amino acids,,,,, we don't. DNA uses dextro or right handed molecular stero orientation. It is almost as if God did this on purpose to let us at some point see His handiwork and design
God Bless
Jim Larmore

CB040: Left-handed amino acids

 

[lucaspa]

It seems to me that he has confused the fact that DNA codes for amino acids with DNA being composed of amino acids.

However, I am unsure of his claim that nucleic acids are part of the amino acid group. Is he right or wrong on that?


Hmmm, just noted that he doesn't know what a ribosome is either.

Yes, he is confusing DNA with proteins. Amino acids have the basic structure H2N-CHR-COOH. R stands for any group attached.

Nucleic acids have the structure base-sugar-phosphate.

The only similarity is that they all have C, N, O, and H.

 

[lucaspa]

One of the most interesting aspects of biochemistry is the stereochemistry involved. In living systems the amino acids are levo or left handed. No dextro amino acid will work in living systems at all. If things had "evolved" randomly we should have had both levo and dextro chirality in amino acids,,,,, we don't. DNA uses dextro or right handed molecular stero orientation. It is almost as if God did this on purpose to let us at some point see His handiwork and design

1. There are dextro amino acids in living organisms that do function. In addition to the examples given by Mallon, consider this paper:
configuration determination methods for D-amino acid-containing peptides in living organisms. Iida T, Santa T, Toriba A, Imai K.

Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, Japan.

"D-amino acid-containing peptides with biological activities have been isolated from invertebrates and amphibians, and partial racemization of amino acid residues in mammalian peptides associated with aging and diseases have been discussed. Here, we review the amino acid configuration determination methods in these peptides and recent progress of simultaneous determination method for sequence and configuration of amino acid residues. The applicability of C-terminus sequence analysis and mass spectrometry to configuration determination of amino acids is also discussed. "

2. You can make living cells with a mixture fo dextro and levo amino acids:
Saunders MA and Rohlfing DL, Inclusion of nonproteinous amino acids in thermally prepared models for prebiotic protein. Biosystems 6. 81-92, 1974.

3. There are at least 2 ways that homochirality can be selected for from a set of proteins that have both D and L amino acids. IOW, you can start out with a mixture and evolve to homochirality. Here is one way:

Nature 2001 Feb 15;409(6822):797-801
NAI: News Stories

Comment in:
Nature. 2001 Feb 15;409(6822):777-8.
A chiroselective peptide replicator.

Saghatelian A, Yokobayashi Y, Soltani K, Ghadiri MR.

Department of Chemistry, and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

The origin of homochirality in living systems is often attributed to the generation of enantiomeric differences in a pool of chiral prebiotic molecules, but none of the possible physiochemical processes considered can produce the significant imbalance required if homochiral biopolymers are to result from simple coupling of suitable precursor molecules. This implies a central role either for additional processes that can selectively amplify an initially minute enantiomeric difference in the starting material, or for a nonenzymatic process by which biopolymers undergo chiroselective molecular replication. Given that molecular self-replication and the capacity for selection are necessary conditions for the emergence of life, chiroselective replication of biopolymers seems a particularly attractive process for explaining homochirality in nature. Here we report that a 32-residue peptide replicator, designed according to our earlier principles, is capable of efficiently amplifying homochiral products from a racemic mixture of peptide fragments through a chiroselective autocatalytic cycle. The chiroselective amplification process discriminates between structures possessing even single stereochemical mutations within otherwise homochiral sequences. Moreover, the system exhibits a dynamic stereochemical 'editing' function; in contrast to the previously observed error correction, it makes use of heterochiral sequences that arise through uncatalysed background reactions to catalyse the production of the homochiral product. These results support the idea that self-replicating polypeptides could have played a key role in the origin of homochirality on Earth"

By the way, that "designed according to our earlier principles" means startiing with a random production of proteins and then uses natural selection to find a replicator. So, "they" didn't design it at all.