Praise God for DNA and Proteins

[womanatwell]

Praise God for His creation! The universe and its contents are amazing and as Catholics we believe the Lord made them. This thread is to praise Him for the life-sustaining molecules of DNA and proteins.

I admire one of His greatest creations, physical life. It is way above genius that He came up with the idea of DNA and proteins and how He got them working together in their extreme complexity. In nature atoms and molecules (collections of atoms) move and react in certain ways, They can combine with each other and interact to carry out chemical reactions, but they can also come apart or clump depending on various factors. God has put together atoms and molecules in a way that biological life can function. This gets down to the cell, the basic unit of life.

Each human has trillions of cells which have different kinds of molecules. Two major molecules are DNA and proteins. These go hand in hand, with DNA used as a code to copy instructions for making proteins which in turn do many different jobs, like using food for energy. DNA and proteins depend on the numbers, properties and arrangements of their atoms for function.

The molecule DNA is not considered a protein but carries our genes, which are used as a code to make the proteins. The DNA double helix structure was discovered in the 1950’s by Franklin, Watson and Crick. It is in almost every living cell from one-celled creatures to the trillions in human beings.

As an aside, it is not necessary to know the what the “DNA” letter abbreviations stand for to appreciate them, but you can go to the first Wikipedia link at the bottom of the post if you want more detail. Though Wikipedia articles are often not considered academically complete, they have much information and many good visuals. Also, they list references and further reading at the bottom which are journal articles, texts and the like.

This unusually detailed image of a section of DNA comes from Wikipedia (below link to “DNA”). The picture is notable for showing the precise placement of atoms, named in the upper right corner, in the DNA structure.

The alignment of atoms is made up of sub-structures (themselves molecules) that are necessary for function. In humans, in almost every cell there are about 3.2 billion links, called base pairs, shown in the bottom right corner in the DNA molecule image. The letters T, A, C, and G stand for the 4 molecules that make up the genetic code by their specific placements within the DNA. The pairs come apart in the middle when the DNA is copied by proteins in order to make other proteins and more DNA. This exposes a single base of the pair for copying and it continues down the line of one side of the strand of DNA for the required length.

DNA - Wikipedia

en.wikipedia.org

Here is a link for the image information (by Zephyris, licensed under Creative Commons Attribution-Share Alike 3.0 Unported license):

https://commons.wikimedia.org/wiki/File:DNA_Structure+Key+Labelled.pn_NoBB.png

 

[womanatwell]

Proteins themselves are needed to copy the DNA code in order to make proteins. Also, proteins are needed for DNA to be replicated for cells in growth and replacement.

Like DNA, proteins are also made up of molecular subunits, but they are different than the DNA. The subunits are called “amino acids,” (pronounced ah-ME-no acids). There are 20 main (and two rare) kinds in natural proteins. One of them, Valine, is pictured here with atoms (represented by letters) and chemical bonds (lines}:

All the amino acids are categorized by a part of them that has the same structure chemically. Then the rest of each of the 20 has variations to give them individual chemical properties.

This image shows DNA (same as in my first post but simply colored orange) being copied by a protein (blue) called RNA Polymerase (pronounced RNA poh-LIM-er-ace) into another type of molecule called messenger RNA (green). Proteins are often depicted in databases by images of ribbons, arrows and strings to represent the various shapes and places the amino acids form in the proteins.

The RNA polymerase protein detects the code in DNA and matches it to pieces in the cell to put into the RNA. This type of RNA then goes to another part of the cell and is “read” by yet other proteins to produce the specific protein product the DNA coded for. The “machine” that reads the RNA, the ribosome, is itself very complex. It is made up of dozens of specific proteins consisting of thousands of amino acids.

For one species of the Fruit Fly, an RNA Polymerase subunit contains 1383 amino acids. Below is a link for more information on this molecule at Uniprot, a protein database supported in part by the National Institutes of Health. The webpage at the link below describes the purpose of RNA polymerase, what species it is from, and various other information. Further down it has the composition of amino acids, given as letters for the abbreviations of each amino acid. Articles from which the information was derived can be found at the “Publications” link on the left column.

Uniprot for RNA Polymerase:

Polr3A - DNA-directed RNA polymerase subunit - Drosophila melanogaster (Fruit fly) - Polr3A gene & protein .

For more information about Uniprot, see this link:

About UniProt .
Genes and proteins are critical instruments of our physical being and their composition and functionality are enormously complex. We humbly praise God the Father, Son and Holy Ghost who has created and given us life.

The picture here, by Thomas Splettstoesser, is from Wikimedia, and licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license. More information about it is at this link:

File:T7 RNA polymerase at work.png - Wikimedia Commons

commons.wikimedia.org

 

[womanatwell]

Now we can look at some of the proteins that DNA codes for and that the first line of proteins working from the DNA template produce.

Whether you know much about chemistry or not, you can appreciate that the cells in plants, animals and even the tiniest of bacteria need to continually carry on reactions. Don’t worry about scientific terms, you can still see what a wonder life is.

One of the most important reactions is called “oxidative phosphorylation” (pronounced, in my unofficial way, ox-ih-date-ihv fos-for-ih-LAY-shun). It is a part of cell respiration.

This image is from KEGG (Kyoto Encyclopedia of Genes and Genomes) website. You can use the link below the image if you would like to see it better. The picture shows a lineup of sets of proteins that function together to produce energy and building blocks for cells. Different colors and shades stand for different proteins. The proteins are labeled and the boxes at the bottom have information about them. When you click the boxes at the website, they give information on the proteins.

https://www.genome.jp/kegg-bin/show_pathway?ko00190

The set of proteins on the far right of this image is known as ATP Synthase. It is found in all levels of known life, from bacteria to humans. The lineup of protein sets to the left of ATP Synthase, sitting in one of the cells’ membranes, use electrons and protons (parts of atoms) among other ingredients to produce an electrochemical gradient which is needed to turn an axle in the ATP Synthase. This action transforms a particular molecule (ADP) from lower to higher energy (becoming ATP) so the ATP can drive metabolism. ATP is needed, for example, in the synthesis of DNA and proteins.

In case you are interested, a link describing oxidative phosphorylation is here:

Oxidative phosphorylation - Wikipedia

en.wikipedia.org

From Home Page for KEGG: “KEGG is a database resource for understanding high-level functions and utilities of the biological system…” at KEGG: Kyoto Encyclopedia of Genes and Genomes .
Citations for KEGG (listed on web page KEGG Database ) :

• Kanehisa, Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K.; KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353-D361 (2017). [pubmed] [doi]
• Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016). [pubmed] [doi]
• Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000). [pubmed] [doi]

 

[womanatwell]

DNA and proteins consist of billions of atoms in almost every cell. Though various combinations of their sub-units may work in different species, they still need to be arranged correctly just as there are various types of buildings and vehicles but all need to be built well.

In cell respiration, there are sets of proteins that are needed to produce a molecule that provides energy for our metabolism. To further appreciate what is involved, we can look at just one protein in one set of the series and see what the protein consists of and what its genetic makeup is. Here is an image from KEGG (also in an earlier post) and its web link:

https://www.genome.jp/kegg-bin/show_pathway?ko00190

One protein of ATP Synthase (the set on the right) is marked beta (ϐ) and is the darker blue on the bottom of the complex. Below it in the boxes marked “F-type ATPase (Eukaryotes)” there is a box marked “beta.” When you click the box at the website, it leads to more information:

https://www.genome.jp/dbget-bin/www_bget?K02133

The box marked “Genes”has HSA: 506. Click for the human version of that protein. At the bottom of that page will be the letter symbols for the 529 amino acids that make up that particular protein in humans. Below that is the DNA code, 1590 base pairs. In the database chart image below, the 20 protein sub-units, known as amino acids, are represented by twenty different capital letters. The DNA bases are described by small letters: a, c, t, and g.

The sequences look like this:

The link for this webpage:

https://www.genome.jp/dbget-bin/www_bget?hsa:506

A link for the PUBMED abstract for the article from which this information was taken:Human F1-ATPase: molecular cloning of cDNA for the beta subunit - PubMed

These letters stand for the groups of atoms which make up the sub-units of the proteins and DNA.

Praise to God the Father, Son and Holy Spirit for His Creation (cf. Ps. 150)!

Home page for KEGG:

https://www.genome.jp/kegg/

Citations for KEGG (listed on web page KEGG Database ) :

• Kanehisa, Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K.; KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353-D361 (2017). [pubmed] [doi]
• Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016). [pubmed] [doi]
• Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000). [pubmed] [doi]

 

[Beryllos]

Wow! That is too much for me to read, but I agree that nature is amazing and reveals its Creator.

 

[Aquinas11]

The fact that only about 20% of our DNA is actually ever used is more evidence that we don’t understand God. Its like having a library full of books where only 20% of the books have letters on the pages. Complete mystery to us which evidences our limited understanding of God.

 

[Francis]

Praise God for His creation! The universe and its contents are amazing and as Catholics we believe the Lord made them.

Thanks for this post .May God (Holy Trinity/Holy Eucharist ) be praised as many times are molecules of DNA proteins,(just adding neutrons ,protons,) as many as trillions of cells in the body,may he be Praised Honor and Glory, be to God in our hearts.nice to meditate each cell in our body worship God ,the heart beat keeps it moving …

 

[womanatwell]

Proteins are amazing in their functions and some are quite stunning when they are depicted in scientific images. I’d like to post a few more examples of proteins that I think you will find worth a look.

Proteins have what are called “folds” which are usable forms to allow them to do many specialized jobs. They are visualized in different ways which you will see below. The spirals (helices), lines, and arrows (sheets) stand for the way the sub-parts, called amino acids, are put together.

Protein complexes are needed to process the other proteins of the cells into the folds. They belong to class called “molecular chaperones.” They are found in all cells. They can be made up of thousands of amino acids which are themselves organized in a way that allows for the right work to be done. Different chaperones are used for different proteins.

I will put 2 images of chaperones here with links to information from Wikipedia at the bottom of this post and more citations below the images. The first image is from an organism called an “archaea” which is one-celled like bacteria are. This chaperone is called a thermosome:

Thermosome hetero16mer + 8 ADP (green-red-blue), Sulfolobus solfataricus.

Deposition authors: Stewart, A.G., Smits, C., Chaston, J.J., Stock, D.;

RCSB PDB - 4XCG: Crystal structure of a hexadecameric TF55 complex from S. solfataricus, crystal form I

Crystal structure of a hexadecameric TF55 complex from S. solfataricus, crystal form I

www.rcsb.org

The above is an example of a ribbon style image from the RCSB Protein Data Bank, one of the most important compilations of protein discoveries. Below is cylinder and plate style of a chaperone from a cow from the National Center for Biotechnology Information:

Information on this one is found at NCBI here:

https://www.ncbi.nlm.nih.gov/Structure/pdb/3IYG

The article it comes from is:

4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement. Cong Y, Baker ML, Jakana J, Woolford D, Miller EJ, Reissmann S, Kumar RN, Redding-Johanson AM, Batth TS, Mukhopadhyay A, Ludtke SJ, Frydman J, Chiu W. Proc. Natl. Acad. Sci. U.S.A. (2010) 107 p.4967-72.

Citing MMDB

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes.Nucleic Acids Res. 2014 Jan; 42(Database issue)297-303

The links to Wikipedia are here:

Chaperonin - Wikipedia

en.wikipedia.org

Visualization author: User:Astrojan -

https://creativecommons.org/licenses/by/4.0/

 

[womanatwell]

Praise him for his mighty acts: praise him according to his excellent greatness.
Let every thing that hath breath praise the LORD. Praise ye the LORD.
Psalm 150: 2,6 (KJV):

Photosynthesis is a necessary chemical process for life as we know it. Plants use carbon dioxide, water and sunlight to make food for our cells and give off oxygen. Below is an image of a molecular machine of photosynthesis called Photosystem I. It captures photons from the sun and uses their energy to move electrons in a cascade of chemical processes.

(Article: Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution, Jordan P, Fromme P, Witt, HT, Klukas O, Saenger W, Krauss N Nature (2001) 411 p.909-917.

The image is from the National Center for Biotechnology Information, 1JB0: 1JB0: Crystal Structure of Photosystem I: a Photosynthetic Reaction Center and Core Antenna System from Cyanobacteria

The Photosystem I complex has more than one type of protein. Different ones are depicted in what is called “cylinder and plate” style in this example.

For perspective, the next image shows further breakdown of the protein makeup. The upper left has the same image as above. The letters in the chart on the right stand for what are called amino acids. Twenty kinds of amino acids make up most natural proteins. Then one of the proteins from the Photosystem I is circled with an arrow pointed to the 755 amino acids that make it up. The amount and arrangements of amino acids in a protein are important in their function.

The chart on the right is from this protein’s Uniprot Database webpage:

https://www.uniprot.org/uniprot/P0A405

I have circled one of the amino acid letter symbols in the chart on the right to show the atomic makeup of just one amino acid. It is a “V” that stands for Valine (rhymes with way lean). The structure of the amino acid valine is pictured on the lower left. The letters here are in a different context than the amino acid symbols and stand for atoms.

Photosystem I is not the only molecular system involved in photosynthesis. If interested, you can learn more:

Photosynthesis - Wikipedia .

Citing MMDB: Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes.Nucleic Acids Res. 2014 Jan; 42(Database issue)297-303

Uniprot is funded in part by the National Institutes of Health. More about Uniprot:

https://www.uniprot.org/help/about

 

[TheHolyTrinity]

The fact that only about 20% of our DNA is actually ever used is more evidence that we don’t understand God. Its like having a library full of books where only 20% of the books have letters on the pages. Complete mystery to us which evidences our limited understanding of God.

1% DNA is made up of protein-coding genes, whilst the remaining 99% is non-coding DNA (has no instructions in making proteins). The non-coding DNA is no longer recognized as junk-DNA rather that they have regulatory sequences as with epigenetics (gene’s turned on/off), transcription factors and many regulatory elements etc

Recent research by jax.org are recognizing non-coding DNA indicate that they are crucial contributers to genetic variation especially in transposons (duplication’s) causing cancerous mutations or serious genetic diseases. I have been monitoring this area as my son has a genetic duplication that has had an impact on him.

The percentage differs slightly to 2% and 98% or greater dependent on the year and the writer.

 

[Sundiver]

I just heard a talk where scientists say human DNA was created instantaneously from a very complex energy pattern. The creator of human DNA was an extremely intelligent being. I love it when scientist admit there is a God or superior being in this case.