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Does DNA contain information beyond protein synthesis?

Does DNA contain information beyond protein synthesis?


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It's well known that genetic information is stored in DNA. As far as I know, DNA only has information at the protein level. What about higher levels, such as organelles, cells, tissue, organs? Is there any known carrier of information at that level? If not, what guides those levels of structure?

Hypothesis: Above the protein level, there is no real genotype/phenotype. Instead, it's all done through cell division. So, there is no split between information and embodiment. Instead, it's through a prototype-duplication model: cells grow and split, creating more cells. As for differentation into different types of cells, and organization into tissue and organs: the information and control systems for that are currently unknown.


What a timely question.

Does DNA contain information beyond protein synthesis?

Yes. In fact, protein-coding genes only constitute a tiny part - less than 2% - of the whole DNA. There are of course many other genes which aren't protein coding: there are genes for ribosomal RNA and we find more and more genes which code for small RNAs, such as tRNA. But even if we count all those genes we won't come above maybe 10% of the total DNA.

Most of the DNA is instead devoted to the regulation of gene expression, most importantly via the binding of transcription factors (but the picture is much more complex than that). With the conclusion of the ENCODE project, a whole slew of papers were published which show that in fact most of the DNA is actively implicated in the binding of various factors (although it's not known how much of that actually contributed to the cell's fitness).

But I've hijacked your question a bit here. So let's come back to what you're actually interested in:

What about higher levels, such as organelles, cells, tissue, organs?

There is no known mechanism (beyond the already mentioned regulation) which would encode such information in the DNA. Excluding its existence categorically may be hard but given that we haven't found any machinery which would be necessary to read such information, we can be pretty confident that it doesn't exist.

If not, what guides those levels of structure?

The higher levels of organisation are to all appearances emergent. That is, they are a consequence of the lower level organisation. For instance, take the cytoskeleton which carries much of the cell's physical structure. It is composed of different protein complexes which form spontaneously through assembly of globular proteins (such as actin). The are several ways in which the process can be guided but strikingly it's largely stochastic - i.e. mostly unguided, and it still succeeds in building a stable skeleton, simply by virtue of molecular properties encoded in the proteins.

I think this is a common theme of cell organisation: the elementary building blocks are encoded by the DNA, and their abundance is tightly regulated. Everything else, i.e. higher-level organisation - follows from that: abundance and localisation of the right proteins.

As for differentation into different types of cells, and organization into tissue and organs: the information and control systems for that are currently unknown.

In fact, much is known here, and it goes back to regulation on the level of DNA: we know that genes are differentially expressed depending on the cell type and stage of development (and the stage in the cell cycle). This regulation is highly complex and decoding it is a slow process. Nevertheless, the factors involved here are decoded one by one. This is the domain of developmental biology.


15.4: Protein Synthesis

  • Contributed by Suzanne Wakim & Mandeep Grewal
  • Professors (Cell Molecular Biology & Plant Science) at Butte College

The Central Dogma of Biology

Your DNA, or deoxyribonucleic acid, contains the genes that determine who you are. How can this organic molecule control your characteristics? DNA contains instructions for all the proteins your body makes. Proteins, in turn, determine the structure and function of all your cells. What determines a protein&rsquos structure? It begins with the sequence of amino acids that make up the protein. Instructions for making proteins with the correct sequence of amino acids are encoded in DNA.

Figure (PageIndex<1>): Transcription and translation (Protein synthesis) in a cell.

DNA is found in chromosomes. In eukaryotic cells, chromosomes always remain in the nucleus, but proteins are made at ribosomes in the cytoplasm or on the rough endoplasmic reticulum (RER). How do the instructions in DNA get to the site of protein synthesis outside the nucleus? Another type of nucleic acid is responsible. This nucleic acid is RNA or ribonucleic acid. RNA is a small molecule that can squeeze through pores in the nuclear membrane. It carries the information from DNA in the nucleus to a ribosome in the cytoplasm and then helps assemble the protein. In short:

DNA &rarr RNA &rarr Protein

Discovering this sequence of events was a major milestone in molecular biology. It is called the central dogma of biology. The two processes involved in the central dogma are transcription and translation.

Figure (PageIndex<2>): An overview of transcription and translation. The top panel shows a gene. A gene is composed of the open reading frame (aka coding sequence) that is flanked by regulatory sequences. At the beginning of the gene, the regulatory sequence contains a promoter where RNA polymerase attaches and starts transcription. At the end of the open reading frame, the regulatory sequence contains a terminator (not shown.)The middle panel shows a pre mRNA which is modified by excising introns and keeping exons. This is called post transcription modification. A mature mRNA contains a 5' cap and poly-A tail. The bottom panel shows a synthesis of protein via translation.


What Is the Role of DNA in Protein Synthesis? (with pictures)

The role of deoxyribonucleic acid or DNA in protein synthesis is that of a blueprint. It is a guide to the structure of the proteins being produced. Without DNA, the ribosomes in any given cell would not know what order to put amino acids in. DNA has the same function in both prokaryotic and eukaryotic cells, although there are subtle differences.

DNA is a chain of nucleic acids arranged into two polymers or strands. Each strand has one set of amino acids that connects to an opposite amino acid on the other polymer to produce a structure that looks like a window cleaner’s ladder. The order of amino acids is a genetic map of information that tells the cell how it is to be structured and tells the cells how to combine to form a larger organism. The information is used directly to build cell components such as ribonucleic acid (RNA) and protein.

The presence of DNA in protein synthesis is vital. Protein synthesis is the act of creating a new protein within a cell. The entire process takes place within a ribosome, a kind of protein factory, within a cell. Free ribosomes in eukaryotic cells and all ribosomes in prokaryotic cells synthesize proteins in the cytoplasm.

There are many steps to the protein synthesis process. The use of DNA during protein synthesis takes place in the first stage called amino acid synthesis. The second stage is called transcription, and the final phase is where the ribosome translates the information into protein.

A protein called helicase splits apart both polymers of DNA in protein synthesis. One of the strands will contain the protein blueprint the cell requires. This strand will be copied into messenger RNA (mRNA) when the mRNA is organized so that it is made up of the opposite amino acids to those present in the DNA section being copied.

The mRNA then takes the information to the ribosome. The ribosome will process the mRNA so that it translates the amino acid code using the opposites of those in the mRNA, therefore returning the chain back to its original form. From this, the ribosome makes proteins.

Organisms are not capable of synthesizing all amino acids. There are around 20 known amino acids in the world, and humans can synthesize around 12 of them. The rest are ingested through food and sometimes drink.

The prokaryotic cell will convert DNA in protein synthesis directly into mRNA. Eukaryotic cells, however, first transcribe the DNA into heterophil nuclear RNA (hnRNA). This hnRNA is created when the polymer section is capped with 7-methyl-guanosine and a poly A tail. The cell then converts hnRNA into mRNA.


From RNA to Protein: Translation

Like translating a book from one language into another, the codons on a strand of mRNA must be translated into the amino acid alphabet of proteins. Translation is the process of synthesizing a chain of amino acids called a polypeptide. Translation requires two major aids: first, a &ldquotranslator,&rdquo the molecule that will conduct the translation, and second, a substrate on which the mRNA strand is translated into a new protein, like the translator&rsquos &ldquodesk.&rdquo Both of these requirements are fulfilled by other types of RNA. The substrate on which translation takes place is the ribosome. Remember that many of a cell&rsquos ribosomes are found associated with the rough ER, and carry out the synthesis of proteins destined for the Golgi apparatus.

Ribosomal RNA (rRNA) is a type of RNA that, together with proteins, composes the structure of the ribosome. Ribosomes exist in the cytoplasm as two distinct components, a small and a large subunit. When an mRNA molecule is ready to be translated, the two subunits come together and attach to the mRNA. The ribosome provides a substrate for translation, bringing together and aligning the mRNA molecule with the molecular &ldquotranslators&rdquo that must decipher its code. The other major requirement for protein synthesis is the translator molecules that physically &ldquoread&rdquo the mRNA codons.

Transfer RNA (tRNA) is a type of RNA that ferries the appropriate corresponding amino acids to the ribosome, and attaches each new amino acid to the last, building the polypeptide chain one-by-one. Thus tRNA transfers specific amino acids from the cytoplasm to a growing polypeptide. The tRNA molecules must be able to recognize the codons on mRNA and match them with the correct amino acid. The tRNA is modified for this function. On one end of its structure is a binding site for a specific amino acid. On the other end is a base sequence that matches the codon specifying its particular amino acid. This sequence of three bases on the tRNA molecule is called an anticodon. For example, a tRNA responsible for shuttling the amino acid glycine contains a binding site for glycine on one end. On the other end it contains an anticodon that complements the glycine codon (GGA is a codon for glycine, and so the tRNAs anticodon would read CCU). Equipped with its particular cargo and matching anticodon, a tRNA molecule can read its recognized mRNA codon and bring the corresponding amino acid to the growing chain (Figure 4).

Figure 5. From DNA to Protein: Transcription through Translation. Transcription within the cell nucleus produces an mRNA molecule, which is modified and then sent into the cytoplasm for translation. The transcript is decoded into a protein with the help of a ribosome and tRNA molecules.

Much like the processes of DNA replication and transcription, translation consists of three main stages: initiation, elongation, and termination. Initiation takes place with the binding of a ribosome to an mRNA transcript. The elongation stage involves the recognition of a tRNA anticodon with the next mRNA codon in the sequence. Once the anticodon and codon sequences are bound (remember, they are complementary base pairs), the tRNA presents its amino acid cargo and the growing polypeptide strand is attached to this next amino acid. This attachment takes place with the assistance of various enzymes and requires energy. The tRNA molecule then releases the mRNA strand, the mRNA strand shifts one codon over in the ribosome, and the next appropriate tRNA arrives with its matching anticodon. This process continues until the final codon on the mRNA is reached which provides a &ldquostop&rdquo message that signals termination of translation and triggers the release of the complete, newly synthesized protein. Thus, a gene within the DNA molecule is transcribed into mRNA, which is then translated into a protein product (Figure 5).

Commonly, an mRNA transcription will be translated simultaneously by several adjacent ribosomes. This increases the efficiency of protein synthesis. A single ribosome might translate an mRNA molecule in approximately one minute so multiple ribosomes aboard a single transcript could produce multiple times the number of the same protein in the same minute. A polyribosome is a string of ribosomes translating a single mRNA strand.

Watch this video to learn about ribosomes. The ribosome binds to the mRNA molecule to start translation of its code into a protein. What happens to the small and large ribosomal subunits at the end of translation?


Structure of DNA

The building blocks of DNA are nucleotides. The important components of each nucleotide are a nitrogenous base, deoxyribose (5-carbon sugar), and a phosphate group (see Figure 2). Each nucleotide is named depending on its nitrogenous base. The nitrogenous base can be a purine, such as adenine (A) and guanine (G), or a pyrimidine, such as cytosine (C) and thymine (T). Uracil (U) is also a pyrimidine (as seen in Figure 2), but it only occurs in RNA, which we will talk more about later.

Figure 2. Each nucleotide is made up of a sugar, a phosphate group, and a nitrogenous base. The sugar is deoxyribose in DNA and ribose in RNA.

The nucleotides combine with each other by covalent bonds known as phosphodiester bonds or linkages. The phosphate residue is attached to the hydroxyl group of the 5′ carbon of one sugar of one nucleotide and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, thereby forming a 5′-3′ phosphodiester bond.

In the 1950s, Francis Crick and James Watson worked together to determine the structure of DNA at the University of Cambridge, England. Other scientists like Linus Pauling and Maurice Wilkins were also actively exploring this field. Pauling had discovered the secondary structure of proteins using X-ray crystallography. In Wilkins’ lab, researcher Rosalind Franklin was using X-ray diffraction methods to understand the structure of DNA. Watson and Crick were able to piece together the puzzle of the DNA molecule on the basis of Franklin’s data because Crick had also studied X-ray diffraction (Figure 3). In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine. Unfortunately, by then Franklin had died, and Nobel prizes are not awarded posthumously.

Figure 3. The work of pioneering scientists (a) James Watson, Francis Crick, and Maclyn McCarty led to our present day understanding of DNA. Scientist Rosalind Franklin discovered (b) the X-ray diffraction pattern of DNA, which helped to elucidate its double helix structure. (credit a: modification of work by Marjorie McCarty, Public Library of Science)

Watson and Crick proposed that DNA is made up of two strands that are twisted around each other to form a right-handed helix. Base pairing takes place between a purine and pyrimidine namely, A pairs with T and G pairs with C. Adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. The base pairs are stabilized by hydrogen bonds adenine and thymine form two hydrogen bonds and cytosine and guanine form three hydrogen bonds. The two strands are anti-parallel in nature that is, the 3′ end of one strand faces the 5′ end of the other strand. The sugar and phosphate of the nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside. Each base pair is separated from the other base pair by a distance of 0.34 nm, and each turn of the helix measures 3.4 nm. Therefore, ten base pairs are present per turn of the helix. The diameter of the DNA double helix is 2 nm, and it is uniform throughout. Only the pairing between a purine and pyrimidine can explain the uniform diameter. The twisting of the two strands around each other results in the formation of uniformly spaced major and minor grooves (Figure 4).

Figure 4. DNA has (a) a double helix structure and (b) phosphodiester bonds. The (c) major and minor grooves are binding sites for DNA binding proteins during processes such as transcription (the copying of RNA from DNA) and replication.


Difference Between Protein Synthesis and DNA Replication

Definition

Protein Synthesis: Protein synthesis refers to a process by which a linear chain of amino acids is produced based on the information stored on a gene.

DNA Replication: DNA replication refers to a process of producing an identical copy of a double-stranded DNA molecule.

Mechanism

Protein Synthesis: Transcription and translation are the two processes involved in the protein synthesis.

DNA Replication: The production of an exact replica of an existing DNA molecule occurs in the DNA replication.

Occur in

Protein Synthesis: Protein synthesis occurs inside the nucleus as well as in the cytoplasm.

DNA Replication: DNA replication occurs inside the nucleus in eukaryotes and in the cytoplasm of prokaryotes.

Protein Synthesis: mRNA molecules are involved in protein synthesis apart from DNA.

DNA Replication: No RNA molecules are involved in DNA replication.

Enzymes

Protein Synthesis: The enzyme involved in the protein synthesis is RNA polymerase.

DNA Replication: Helicase, RNA primase, and DNA polymerase are the enzymes in DNA replication.

Final Product

Protein Synthesis: The final product of the protein synthesis is a protein molecule.

DNA Replication: The final product of the DNA replication is an exact replica of an existing DNA molecule.

Conclusion

Protein synthesis and DNA replication are two mechanisms where double-stranded DNA molecules are involved in the initial template. Protein synthesis is the synthesis of an amino acid sequence of a protein. DNA replication is the synthesis of a new DNA molecule from an existing DNA molecule. The main difference between protein synthesis and DNA replication is the mechanism and the final product of the two processes.

References:

1. Bailey, Regina. “Steps of DNA Replication.” ThoughtCo, Available here.
2. “Protein Synthesis.” SparkNotes, Available here.

Image Courtesy:

1. “Bacterial Protein synthesis” By Joan L. Slonczewski, John W. Foster – Microbiology: An Evolving Science (CC BY-SA 3.0) via Commons Wikimedia
2. � DNA Replication” By OpenStax (CC BY 4.0) via Commons Wikimedia

About the Author: Lakna

Lakna, a graduate in Molecular Biology & Biochemistry, is a Molecular Biologist and has a broad and keen interest in the discovery of nature related things


Which describes the flow of information in protein synthesis? A. RNA to DNA to protein B. DNA to RNA to protein C. Protein to DNA to RNA D. Protein to RNA to DNA

DNA is the central archive containing all the genetic info a living organism needs. This info is divided into Genes.

In a process called Transcription, the info contained in a Gene is copied into a short strand of a slightly different nucleic acid: RNA . This short strand called messenger RNA ( mRNA ) is then "Translated" into Protein.

Therefore, the answer is B.

Note: "The Central Dogma" was severely shaken when a viral enzyme was discovered that was able to copy RNA back into DNA:
Aptly named Reverse Transcriptase, it doesn't invalidate the "dogma": it doesn't produce proteins itself. Moreover, the DNA synthesised by RT will still be transcribed (into mRNA) by the host cell. This mRNA will then be used for the production of proteins.

Here is a video which summarizes the central dogma of molecular biology using DNA Workshop from PBS.


DNA to Protein

This online interactive module of 10 pages or frames integrates textual information, 3D molecular models, interactive molecular simulations, and embedded assessment items to guide students in understanding the copying of DNA base sequences from translation to transcription into proteins within each cell. The module divides the exercises in to Day 1 and Day 2 time frames. Teachers can view student assessment responses by assigning the module within a class created within the Molecular Workbench application. This Java-based module must be downloaded to each computer. An important note is that user data is not saved unless students and teachers sign up through an available project portal called &ldquoInnovative Technology in Science Inquiry&rdquo: http://itsi.portal.concord.org/home

Performance Expectations

HS-LS1-1 Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins which carry out the essential functions of life through systems of specialized cells.

Clarification Statement: none

Assessment Boundary: Assessment does not include identification of specific cell or tissue types, whole body systems, specific protein structures and functions, or the biochemistry of protein synthesis.

This resource is explicitly designed to build towards this performance expectation.

Comments about Including the Performance Expectation
The module explicitly addresses the Performance Expectation as students analyze models of the molecular structure of DNA and the processes involved with DNA serving as the template for transcription and translation of DNA to RNA to proteins. The module begins by having students explore DNA’s double helix structure in an interactive 3D model. Subsequent animations of 2D molecular models of transcription and translation and interactive simulations take students through the process to the formation of segments of proteins. Teachers may want to help students connect 3D models to 2D models by showing both types of model of the same molecule and asking students to identify the same parts of the molecule in both models. Simulations and models describing mutations in a similar format are provided. Students also work with frameshift and silent mutations and substitutions, deletions and insertions. While the concept of mutations and their effects is not directly addressed in the performance expectation, engaging students in this portion of the model may help students better understand the connections between DNA, transcription, translation, and proteins, and how these processes can be affected by mutations. Throughout the module students are asked to construct explanations of various processes using the information they have gathered from the models they have examined.

Science and Engineering Practices

This resource is explicitly designed to build towards this science and engineering practice.

Comments about Including the Science and Engineering Practice
The module explicitly engages students in using 2D molecular representations, 3D interactive molecular models, and interactive simulations to answer questions to illustrate interactions among the components of the cell to make a protein. It should be noted that students do not generate the models but use the models that are provided. The functions of the nucleus and ribosomes are included and illustrated. The module asks students to snapshot/capture their answers to specific questions throughout. This is done for students to show their understanding of the different steps in this process and the relationship between the steps. Students are also asked to answer explicit questions about what they have captured as evidence of their understanding of protein synthesis from the DNA template. A thirteen page teacher guide is included and provides thoughts on possible student misconceptions, discussion questions emphasizing main concepts and extension ideas. An example of a question provided in the teacher guide that expands the information, “Where does transcription take place in an eukaryotic cell? Where does translation take place in a eukaryotic cell? What would be an advantage of this arrangement?" Teachers can combine/modify some of the final questions, so that the questions are asking students to construct explanations of the processes, based on what they learned from analyzing the models throughout the activity. Several of the extension ideas could also be utilized to make this module suitable for an honors or a more advanced high school biology class.

Disciplinary Core Ideas

This resource appears to be designed to build towards this disciplinary core idea, though the resource developer has not explicitly stated so.

Comments about Including the Disciplinary Core Idea
The module implicitly addresses the Disciplinary Core Idea by providing students the opportunity to work through the steps of protein synthesis. The teacher will have to support students in making the connection between a gene as a specific region of DNA for coding of a protein.

Crosscutting Concepts

This resource appears to be designed to build towards this crosscutting concept, though the resource developer has not explicitly stated so.

Comments about Including the Crosscutting Concept
A large part of this module focuses on what happens to the structure of proteins when different types of mutations occur, and students have the opportunity to practice working with each of the different types of mutations described. Changes in nucleotides, codons, and anticodons as a result of mutations are included and the effects of these changes on the resulting amino acid sequence are illustrated. By analyzing the effects of changes in the DNA sequence on the RNA and proteins coded by the DNA, students can develop an understanding of how the structure of DNA allows it to carry out its function in the cell.


Transcription: RNA made according to base sequence in DNA

30 base pairs (10 triplets) shown for example - actual genes are usually hundreds or thousands of base pairs in length

The two strands of DNA - shown here in black and grey - separate (under the influence of the enzyme RNA polymerase). Messenger RNA - here red - forms on one - black - strand of DNA. The other strand - grey - does not take part in the process.

The strand of messenger RNA (mRNA) formed then leaves the nucleus and passes into the cytoplasm. The opened-up section of DNA re-forms into a double helix, as before.


Making RNA (Transcription)

The coded instructions for producing a specific protein or RNA molecule are contained in sections of the DNA called genes.

An enzyme unwinds the section of DNA to form RNA. Here the RNA nucleotides line up with their complementary bases transcribing the information from the DNA to RNA. The RNA is made up of ribonucleotides, which are matched to their compliments in the DNA.

A pairs with T
C pairs with G
G pairs with C
U pairs with A

RNA contains the base uracil (U) instead of thymine (T).

RNA Splicing

Segments of the RNA molecule not required for coding of the protein are removed and the remaining section reconnected. This process is called splicing and results in a messenger RNA (mRNA) ready to be used as a template for protein synthesis.

The mRNA leaves the nucleus via the nuclear pores.

Making Proteins (Translation)

The mRNA is translated into a protein in the cytoplasm of the cell. This is done by transfer RNA (tRNA). There are different tRNAs for each of the twenty amino acids that make up proteins. One end of the tRNA molecule holds 3 bases called an anti-codon and these pair with the complimentary bases on the mRNA. On the other end of the tRNA is a specific amino acid.

The tRNA docks onto the mRNA with the help of ribosomes. The ribosomes have sites on which the tRNA molecules can bind. The ribosomes help the amino acid from the first tRNA bond to the amino acid of the second tRNA. On forming the bond the first tRNA molecules leaves and the process is repeated till the ribosome reaches a part of the mRNA that does not code for an amino acid. The ribosome dissociates from the mRNA and the protein is released. The resulting chain of amino acids then folds into a complex three-dimensional shape to form a functional protein.


Watch the video: DNA Replication 3D Animation (May 2022).