Fact 5

DNA Transcription, Translation and Replication requires hundreds of complex proteins and protein machines to function.

Transcription requires a complex protein RNA Polymerase Enzyme that reads the DNA section and copies certain sections and transmits this RNA strand to a ribosome for protein production. The proteins needed to translate the data are themselves created by the DNA protein production. This circular system cannot be created randomly.

Chicken or the egg.

Translation requires converting RNA information to build a protein. This process uses over 100 complex proteins and protein machines to build the proteins. Complex DNA Polymerase and other proteins read and replicate the entire DNA section. The proteins needed to replicate the data are themselves created by the DNA protein production. These proteins had to be present for the system to work and they are only produced by the system.

Transcription-from pages 65-67 Signature in the Cell by Stephen Meyer

During transcription, a copy, or transcript, of the DNA text is made by a large protein complex, known as RNA polymerase, that moves down the DNA chain and "reads" the original DNA text. As RNA polymerase pro-ceeds, it makes an identical copy of the DNA transcript in an RNA format, (Like DNA, RNA contains four chemical bases, called nucleotide bases.

These bases are the same as those in DNA with one exception: RNA uses a base called uracil instead of thymine.) The resulting single-stranded RNA copy, or transcript, then moves from the chromosomes to the ribosome in the outer cytoplasm to begin translation, the next step in the processing of genetic information.22 (See Fig. 5.4.)

Transcription can be thus described in a few simple sentences. Yet any such description conceals an impressive complexity. In the first place RNA polymerase is an extraordinarily complex protein machine of great specificity. The RNA polymerases present in the simplest bacteria Mycoplasma) comprise several separate protein subunits with (collective-ly) thousands of specifically sequenced amino acids.23

RNA polymerase performs several discrete functions in the process of transcription. First, it recognizes (and binds to) specific regions of the DNA that mark the beginning of genes. Second, it unwinds (or helps unwind) the DNA text, exposing the strand that will serve as the template for making the RNA copy. Third, it sequesters and positions RNA bases (A, U, G, C) with their complementary partners on the DNA template (T, A, C, G, respectively). Fourth, it polymerizes or links together the separate RNA nucleotides, thus forming a long message-bearing ribbon of mRNA.24 As molecular biologist Stephen Wolfe explains: "The structure of the RNA polymerases reflects the complexity of their activities in RNA transcription. The enzymes have sites that recognize promoters, react with initiation, elongation and termination factors, recognize DNA bases for correct pairing, bind and hydrolyze RNA nucleotides, form phospho-diester linkages, terminate transcription and perhaps unwind and rewind DNA."25

Yet for all its complexity and specificity, RNA polymerase alone does not ensure accurate transcription. The process involves several other complex and functionally integrated parts and steps. For example, for RNA polymerase to access the genetic text, the DNA double helix must unwind and expose the nucleotide bases. Further, to initiate transcrip-tion, the RNA polymerase must bind to the correct part of the DNA sequence in order to begin transcribing at the beginning of a genetic message, rather than in the middle or at the end. For its part, the DNA text provides a promoter sequence or signal upstream of the actual coding sequence to facilitate recognition of the correct location by the Transcription is a highly regulated process. By binding to specific sites on the DNA, various proteins will either inhibit or promote the transcription of particular genes in response to the varying needs of the cell.

By regulating transcription, repressor and activator proteins ensure that the cell maintains appropriate levels of proteins. Thus, even in prokaryotic organisms many separate proteins are necessary to facilitate-and regulate—tran-scription.

Transcription - RNA Polymerase

RNA polymerase is an enzyme responsible for synthesizing RNA from a DNA template in a process called transcription. It plays a key role in gene expression by copying genetic information from DNA into messenger RNA (mRNA), which is later translated into proteins.

Functions of RNA Polymerase

1. Transcription

Synthesizes RNA by adding ribonucleotides (A, U, C, G) in a 5’ to 3’ direction.

2. Initiation

Binds to DNA at the promoter region and starts RNA synthesis.

3. Elongation

Moves along the DNA, adding ribonucleotides to the growing RNA strand.

4. Termination

Stops transcription at specific sequences and releases the RNA molecule.
Eukaryotic RNA polymerases are much more complex, consisting of multiple subunits:
- RNA Polymerase I – 14 subunits
- RNA Polymerase II – 12 subunits
- RNA Polymerase III – 17 subunits

DNA Transcription (Basic)

Translation- from pages 68-69 Signature in the Cell

The next step in gene expression, called translation, exhibits even greater integrated complexity. Whereas transcription makes a single-stranded copy—a transcript—of DNA in an RNA format, translation uses that information to build a protein. Since many biologists think of protein molecules themselves as information-rich molecules constructed from a twenty-character amino-acid alphabet, they think of the process of protein synthesis as a process of translating information from the four-char-acter alphabets of DNA and RNA into the twenty-character amino-acid alphabet; hence the name "translation."

The process of translation begins as the ribosome subunits dissociate and the messenger RNA (mRNA) binds to the smaller of the two subunits (see Fig. 5.7). Auxiliary proteins known as initiation factors catalyze this disassociation and temporarily stabilize the second subunit in its disassociated state.

At each step in the translation process, specialized proteins perform crucial functions. For example, the initial coupling of specific amino acids to their specific tRNA molecules (Crick's adapters) depends upon the cat-alytic action of twenty specific enzymes, one for each tRNA-amino acid pair. The integrity of the genetic code depends upon the specific properties of these enzymes, known as aminoacyl-tRNA synthetases, 36

DNA Polymerase components

DNA Polymerase is a multi-domain enzyme with several functional components that allow it to synthesize, proofread, and repair DNA. Here’s a breakdown of its key components (domains and subunits):

Core Domains (Common to Most DNA Polymerases)

1. Palm Domain (Catalytic Site)

Contains the active site for nucleotide addition.
Coordinates metal ions (Mg²⁺ or Mn²⁺) for catalysis.
Responsible for the 5’ to 3’ polymerization activity.

2. Finger Domain

Helps position the incoming nucleotide.
Assists in the correct alignment of the template strand and nucleotide.

3. Thumb Domain

Holds the DNA substrate in place.
Ensures stability and processivity of the enzyme.

4. Exonuclease Domain (Proofreading)

Provides 3’ to 5’ exonuclease activity to correct mismatched bases.
Reduces errors during replication.

DNA Polymerase Amino Acid Profiles: Prokaryotes vs. Eukaryotes

The total number of amino acids in DNA polymerase varies depending on the organism and type of DNA polymerase. Here’s a breakdown:

Prokaryotic DNA Polymerase (E. coli)

1. DNA Polymerase I: ~928 amino acids

Functions in replication, proofreading, and DNA repair.

2. DNA Polymerase III (α subunit): ~1,160 amino acids

The main enzyme responsible for replicating the bacterial genome.
Other subunits (ε, θ, etc.) add around 600–700 more amino acids.
Total for DNA Polymerase III Holoenzyme: ~2,000+ amino acids

Eukaryotic DNA Polymerase (Human)

1. DNA Polymerase α (Catalytic Subunit): ~1,460 amino acids

2. DNA Polymerase δ (Catalytic Subunit): ~1,100 amino acids

3. DNA Polymerase ε (Catalytic Subunit): ~2,300 amino acids

4. DNA Polymerase γ (Mitochondrial): ~1,250 amino acids

mRNA Translation (Advanced)

Credit: VWALevi2020

Replication page 70-71 Signature in the cell Stephen Meyer Replication Making Copies

Besides transcribing and translating, the cell's information-processing system also replicates DNA. This happens whenever cells divide and copy themselves. As with the processes of transcription and translation, the process of DNA replication depends on many separate protein catalysts to unwind, stabilize, copy, edit, and rewind the original DNA message. In prokaryotic cells, DNA replication involves more than thirty specialized proteins to perform tasks necessary for building and accurately copying the genetic molecule. These specialized proteins include DNA polymeras-es, primases, helicases, topoisomerases, DNA-binding proteins, DNA lig-ases, and editing enzymes,38 DNA needs these proteins to copy the genetic information contained in DNA. But the proteins that copy the genetic information in DNA are themselves built from that information.

This again poses what is, at the very least, a curiosity: the production of proteins requires DNA, but the production of DNA requires proteins. To complicate matters further, proteins must catalyze formation of the basic building blocks of cellular life such as sugars, lipids, glycolipids, nucleotides, and ATP (adenosine triphosphate, the main energy molecule of the cell). Yet each of these materials is also constructed with the help of specific enzymes. For example, each of the systems involved in the processing of genetic information requires energy at many discrete steps. In the cell, ATP (adenosine triphosphate) or a similar molecule (GTP, guanosine triphosphate) supplies this energy whenever one of its three phosphates are cleaved during a reaction known as "hydrolysis." The cell manufactures ATP from glucose by a process known as glycolysis. Yet glycolysis involves ten discrete steps each catalyzed by a specific protein.

These proteins (e.g., hexokinase, aldolase, enolase, pyruvate kinase) are, in turn, produced from genetic information on DNA via the processes of transcription and translation. Thus, the information-processing system of the cell requires ATP, but ATP production (via glycolysis) requires the cell's information-processing system, again forming a "closed loop."

Indeed, it even takes ATP to make ATP during glycolysis. 39 integrated Complexity and the Origin of Life Following the elucidation of the structure and function of DNA during the 1950s and early 1960s, a radically new conception of life began to emerge.

Not only did molecular biologists discover that DNA carried information; they soon began to suspect that living organisms must contain systems for processing genetic information. Just as the digital information stored on a disc is useless without a device for reading the disc, so too is the information on DNA useless without the cell's information-processing system. As Richard Lewontin notes, "No living molecule [i.e., biomole-cule] is self-reproducing. Only whole cells may contain all the necessary machinery for self-reproduction.... Not only is DNA incapable of making copies of itself, aided or unaided, but it is incapable of 'making' anything else... The proteins of the cell are made from other proteins, and without that protein-forming machinery nothing can be made."40

Biochemist David Goodsell describes the problem, "The key molecular process that makes modern life possible is protein synthesis, since proteins are used in nearly every aspect of living. The synthesis of proteins requires a tightly integrated sequence of reactions, most of which are themselves performed by proteins."41 Or as Jacques Monod noted in 1971:

"The code is meaningless unless translated. The modern cell's translating machinery consists of at least fifty macromolecular components which are themselves coded in DNA: the code cannot be translated otherwise than by products of translation."42 (Scientists now know that translation actually requires more than a hundred proteins.

Credit: Christinelmiller

DNA Polymerase

DNA polymerase is an essential enzyme responsible for DNA replication and repair, ensuring genetic information is accurately copied and passed on to daughter cells. It synthesizes new DNA strands by adding nucleotides to a pre-existing strand (template).

Functions of DNA Polymerase

1. DNA Replication

Adds nucleotides to the growing DNA strand in a 5’ to 3’ direction.

2. Proofreading and Error Correction

Detects and removes mismatched bases using 3’ to 5’ exonuclease activity to maintain high fidelity during replication.