Genes and Proteins Intelligent Design by Owen Borville September 5, 2024
The Genetic Code
There are 20 amino acid structures found in proteins.
The Central Dogma: DNA Encodes RNA, RNA Encodes Protein
The central dogma describes the flow of genetic information in cells from DNA to mRNA to proteins and states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins.
Colinear, in terms of RNA and protein, is when three “units” of RNA (nucleotides) specify one “unit” of protein (amino acid) in a consecutive fashion.
Instructions on DNA are transcribed onto messenger RNA. Ribosomes are able to read the genetic information inscribed on a strand of messenger RNA and use this information to string amino acids together into a protein.
The Degeneracy of the Genetic Code describes that a given amino acid can be encoded by more than one nucleotide triplet and the code is degenerate, but not ambiguous.
These nucleotide triplets are called codons, which are three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation. Translation is the process of translating the sequence of a messenger RNA (mRNA) molecule to a sequence of amino acids during protein synthesis.
The reading frame is the sequence of triplet codons in mRNA that specify a particular protein; a ribosome shift of one or two nucleotides in either direction completely abolishes synthesis of that protein.
Scientists carefully solved the genetic code by translating synthetic mRNAs in vitro and sequencing the proteins they specified. The genetic code is translated for each nucleotide triplet in mRNA into an amino acid or a termination signal in a protein.
Nonsense codons (stop codons) are one of three (of 64) mRNA codons that specifies termination of translation, terminates protein synthesis, and releases the polypeptide from the translation machinery.
The reading frame for translation is set by the AUG start codon near the 5' end of the mRNA. Following the start of the codon, the mRNA is read in groups of three until a stop codon is encountered. The arrangement of the coding table reveals the structure of the code.
The specification of a single amino acid by multiple similar codons is called "degeneracy." Degeneracy is believed to be a cellular mechanism to reduce the negative impact of random mutations.
The genetic code is nearly universal and with a few minor exceptions, virtually all species use the same genetic code for protein synthesis.
Prokaryotic Transcription
Prokaryotes are mostly single celled organisms like bacteria and archaea (bacteria) that lack membrane-bound nuclei and other organelles. Prokaryotes commonly have plasmids, which are extrachromosomal, covalently closed, circular DNA molecule that may only contain one or a few genes.
Transcription in prokaryotes (and in eukaryotes) requires the DNA double helix to partially unwind in the region of mRNA synthesis, and this region of unwinding is called a transcription bubble. Transcription always proceeds from the same DNA strand for each gene, which is called the template strand.
The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate strand, or the coding strand. The only nucleotide difference is that in mRNA, all of the T nucleotides are replaced with U nucleotides.
Messenger RNA is a copy of protein-coding information in the coding strand of DNA, with the substitution of U in the RNA for T in the coding sequence. The nucleotide pair in the DNA double helix that corresponds to the site from which the first 5' mRNA nucleotide is transcribed is called the +1 site, or the initiation site.
Nucleotides preceding the initiation site are denoted with a “-” and are designated upstream nucleotides. Conversely, nucleotides following the initiation site are denoted with “+” numbering and are called downstream nucleotides.
The core enzyme is the prokaryotic RNA polymerase consisting of α, α, β, and β' but missing σ; this complex performs elongation. The holoenzyme is the
prokaryotic RNA polymerase consisting of α, α, β, β', and σ; this complex is responsible for transcription initiation.
A promoter is a DNA sequence in prokaryotes that RNA polymerase and associated factors bind and initiate transcription. The transcription elongation phase begins with the release of the σ subunit from the polymerase.
Termination signals for prokaryotic polymerase include: Rho-dependent termination of transcription by an interaction between RNA polymerase and the rho protein at a run of G nucleotides on the DNA template. Rho-independent termination sequence-dependent termination of prokaryotic mRNA synthesis is caused by a stable hairpin formation in the mRNA that stalls the polymerase.
Eukaryotic Transcription is fundamentally the same as in prokaryotes, but with some key differences that are due mainly to the eukaryotic membrane-bound nucleus and organelles. While the prokaryotic polymerase can bind to a DNA template on its own, eukaryotes require several other proteins, called transcription factors, to first bind to the promoter region and then to help recruit the appropriate polymerase.
Eukaryotes have three polymerases each with 10 or more subunits and each eukaryotic polymerase also requires a distinct set of transcription factors to bring it to the DNA template. RNA polymerase I is located in the nucleolus, a specialized nuclear substructure in which ribosomal RNA (rRNA) is transcribed, processed, and assembled into ribosomes. RNA polymerase II is located in the nucleus and synthesizes all protein-coding nuclear pre-mRNAs. RNA polymerase III is also located in the nucleus and this polymerase transcribes a variety of structural RNAs that includes the 5S pre-rRNA, transfer pre-RNAs (pre-tRNAs), and small nuclear pre-RNAs.
Eukaryotic promoters have a sequence called the TATA box (for the TATAAA sequence) on the coding strand. Other eukaryotic promoters are the CAAT box (GGCCAATCT), GC-rich boxes (GGCG), or octamer boxes (ATTTGCAT). Scientists have difficulty explaining the origin or evolution of promoters, strengthening the Intelligent Design argument.
FACT is a complex that “facilitates chromatin transcription” by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by (and moves the histones out of the way and replaces them). The termination of transcription is different for the different polymerases.
RNA Processing in Eukaryotes
The eukaryotic pre-mRNA undergoes extensive processing before it is ready to be translated. Pre-mRNAs are first coated in RNA-stabilizing proteins. The three most important steps of pre-mRNA processing are the addition of stabilizing and signaling factors at the 5' and 3' ends of the molecule, and the removal of the introns.
The 7-methylguanosine cap is added to the 5' end of the growing transcript by a phosphate linkage. An enzyme called poly-A polymerase then adds a string of approximately 200 A residues, called the poly-A tail.
Eukaryotic genes are composed of exons, which correspond to protein-coding sequences (ex-on signifies that they are expressed), and intervening sequences called introns (int-ron denotes their intervening role), which may be involved in gene regulation but are removed from the pre-mRNA during processing. Intron sequences in mRNA do not encode functional proteins.
All of a pre-mRNA’s introns must be completely and precisely removed before protein synthesis. The process of removing introns and reconnecting exons is called splicing.
Anticodons are three-nucleotide sequence in a tRNA molecule that corresponds to an mRNA codon.
Ribosomes and Protein Synthesis
Protein synthesis uses more cell energy than any other metabolic process, and proteins account for more mass than any other component other than water.
A ribosome is a complex macromolecule composed of structural and catalytic rRNAs, and many distinct polypeptides. Ribosomes are located in the cytoplasm and rough endoplasmic reticulum of eukaryotes. A polysome is an mRNA molecule simultaneously being translated by many ribosomes all going in the same direction.
The tRNAs are structural RNA molecules that were transcribed from genes by RNA polymerase III. The tRNAs must interact with three factors: they must be recognized by the correct aminoacyl synthetase; they must be recognized by ribosomes; they must bind to the correct sequence in mRNA.
The aminoacyl tRNA synthetase is an enzyme that “charges” tRNA molecules by catalyzing a bond between the tRNA and a corresponding amino acid.
Protein synthesis can be divided into three phases: initiation, elongation, and termination. The process of translation is similar in prokaryotes and eukaryotes.
Protein synthesis begins with the process of initiation, and formation of an initiation complex, which involves a ribosome, three initiation factors, and a certain initiator tRNA.
The sequence (AGGAGG) interacts with the rRNA molecules that compose the ribosome. The initiator tRNA then interacts with the start codon AUG. According to Kozak’s rules, the nucleotides around the AUG indicate whether it is the correct start codon.
During translation elongation, the mRNA template provides tRNA binding specificity. As the ribosome moves along the mRNA, each mRNA codon comes into register, and specific binding with the corresponding charged tRNA anticodon is ensured.
Elongation proceeds with charged tRNAs sequentially entering and leaving the ribosome as each new amino acid is added to the polypeptide chain. The formation of each peptide bond is catalyzed by peptidyl transferase, an RNA-based enzyme that is integrated into the 50S ribosomal subunit.
Termination of translation occurs when a nonsense codon (UAA, UAG, or UGA) is encountered. Upon aligning with the A site, these nonsense codons are recognized by protein release factors that resemble tRNAs.
During and after translation, individual amino acids may be chemically modified, signal sequences appended, and the new protein “folded” into a distinct three-dimensional structure as a result of intramolecular interactions.
A signal sequence is a short sequence at the amino end of a protein that directs it to a specific cellular compartment. These sequences are the protein’s pathway to its ultimate destination, and are recognized by signal-recognition proteins that act as conductors.
Many proteins fold spontaneously, but some proteins require helper molecules, called chaperones, to prevent them from aggregating during the complicated process of folding.
The Genetic Code
There are 20 amino acid structures found in proteins.
The Central Dogma: DNA Encodes RNA, RNA Encodes Protein
The central dogma describes the flow of genetic information in cells from DNA to mRNA to proteins and states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins.
Colinear, in terms of RNA and protein, is when three “units” of RNA (nucleotides) specify one “unit” of protein (amino acid) in a consecutive fashion.
Instructions on DNA are transcribed onto messenger RNA. Ribosomes are able to read the genetic information inscribed on a strand of messenger RNA and use this information to string amino acids together into a protein.
The Degeneracy of the Genetic Code describes that a given amino acid can be encoded by more than one nucleotide triplet and the code is degenerate, but not ambiguous.
These nucleotide triplets are called codons, which are three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation. Translation is the process of translating the sequence of a messenger RNA (mRNA) molecule to a sequence of amino acids during protein synthesis.
The reading frame is the sequence of triplet codons in mRNA that specify a particular protein; a ribosome shift of one or two nucleotides in either direction completely abolishes synthesis of that protein.
Scientists carefully solved the genetic code by translating synthetic mRNAs in vitro and sequencing the proteins they specified. The genetic code is translated for each nucleotide triplet in mRNA into an amino acid or a termination signal in a protein.
Nonsense codons (stop codons) are one of three (of 64) mRNA codons that specifies termination of translation, terminates protein synthesis, and releases the polypeptide from the translation machinery.
The reading frame for translation is set by the AUG start codon near the 5' end of the mRNA. Following the start of the codon, the mRNA is read in groups of three until a stop codon is encountered. The arrangement of the coding table reveals the structure of the code.
The specification of a single amino acid by multiple similar codons is called "degeneracy." Degeneracy is believed to be a cellular mechanism to reduce the negative impact of random mutations.
The genetic code is nearly universal and with a few minor exceptions, virtually all species use the same genetic code for protein synthesis.
Prokaryotic Transcription
Prokaryotes are mostly single celled organisms like bacteria and archaea (bacteria) that lack membrane-bound nuclei and other organelles. Prokaryotes commonly have plasmids, which are extrachromosomal, covalently closed, circular DNA molecule that may only contain one or a few genes.
Transcription in prokaryotes (and in eukaryotes) requires the DNA double helix to partially unwind in the region of mRNA synthesis, and this region of unwinding is called a transcription bubble. Transcription always proceeds from the same DNA strand for each gene, which is called the template strand.
The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate strand, or the coding strand. The only nucleotide difference is that in mRNA, all of the T nucleotides are replaced with U nucleotides.
Messenger RNA is a copy of protein-coding information in the coding strand of DNA, with the substitution of U in the RNA for T in the coding sequence. The nucleotide pair in the DNA double helix that corresponds to the site from which the first 5' mRNA nucleotide is transcribed is called the +1 site, or the initiation site.
Nucleotides preceding the initiation site are denoted with a “-” and are designated upstream nucleotides. Conversely, nucleotides following the initiation site are denoted with “+” numbering and are called downstream nucleotides.
The core enzyme is the prokaryotic RNA polymerase consisting of α, α, β, and β' but missing σ; this complex performs elongation. The holoenzyme is the
prokaryotic RNA polymerase consisting of α, α, β, β', and σ; this complex is responsible for transcription initiation.
A promoter is a DNA sequence in prokaryotes that RNA polymerase and associated factors bind and initiate transcription. The transcription elongation phase begins with the release of the σ subunit from the polymerase.
Termination signals for prokaryotic polymerase include: Rho-dependent termination of transcription by an interaction between RNA polymerase and the rho protein at a run of G nucleotides on the DNA template. Rho-independent termination sequence-dependent termination of prokaryotic mRNA synthesis is caused by a stable hairpin formation in the mRNA that stalls the polymerase.
Eukaryotic Transcription is fundamentally the same as in prokaryotes, but with some key differences that are due mainly to the eukaryotic membrane-bound nucleus and organelles. While the prokaryotic polymerase can bind to a DNA template on its own, eukaryotes require several other proteins, called transcription factors, to first bind to the promoter region and then to help recruit the appropriate polymerase.
Eukaryotes have three polymerases each with 10 or more subunits and each eukaryotic polymerase also requires a distinct set of transcription factors to bring it to the DNA template. RNA polymerase I is located in the nucleolus, a specialized nuclear substructure in which ribosomal RNA (rRNA) is transcribed, processed, and assembled into ribosomes. RNA polymerase II is located in the nucleus and synthesizes all protein-coding nuclear pre-mRNAs. RNA polymerase III is also located in the nucleus and this polymerase transcribes a variety of structural RNAs that includes the 5S pre-rRNA, transfer pre-RNAs (pre-tRNAs), and small nuclear pre-RNAs.
Eukaryotic promoters have a sequence called the TATA box (for the TATAAA sequence) on the coding strand. Other eukaryotic promoters are the CAAT box (GGCCAATCT), GC-rich boxes (GGCG), or octamer boxes (ATTTGCAT). Scientists have difficulty explaining the origin or evolution of promoters, strengthening the Intelligent Design argument.
FACT is a complex that “facilitates chromatin transcription” by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by (and moves the histones out of the way and replaces them). The termination of transcription is different for the different polymerases.
RNA Processing in Eukaryotes
The eukaryotic pre-mRNA undergoes extensive processing before it is ready to be translated. Pre-mRNAs are first coated in RNA-stabilizing proteins. The three most important steps of pre-mRNA processing are the addition of stabilizing and signaling factors at the 5' and 3' ends of the molecule, and the removal of the introns.
The 7-methylguanosine cap is added to the 5' end of the growing transcript by a phosphate linkage. An enzyme called poly-A polymerase then adds a string of approximately 200 A residues, called the poly-A tail.
Eukaryotic genes are composed of exons, which correspond to protein-coding sequences (ex-on signifies that they are expressed), and intervening sequences called introns (int-ron denotes their intervening role), which may be involved in gene regulation but are removed from the pre-mRNA during processing. Intron sequences in mRNA do not encode functional proteins.
All of a pre-mRNA’s introns must be completely and precisely removed before protein synthesis. The process of removing introns and reconnecting exons is called splicing.
Anticodons are three-nucleotide sequence in a tRNA molecule that corresponds to an mRNA codon.
Ribosomes and Protein Synthesis
Protein synthesis uses more cell energy than any other metabolic process, and proteins account for more mass than any other component other than water.
A ribosome is a complex macromolecule composed of structural and catalytic rRNAs, and many distinct polypeptides. Ribosomes are located in the cytoplasm and rough endoplasmic reticulum of eukaryotes. A polysome is an mRNA molecule simultaneously being translated by many ribosomes all going in the same direction.
The tRNAs are structural RNA molecules that were transcribed from genes by RNA polymerase III. The tRNAs must interact with three factors: they must be recognized by the correct aminoacyl synthetase; they must be recognized by ribosomes; they must bind to the correct sequence in mRNA.
The aminoacyl tRNA synthetase is an enzyme that “charges” tRNA molecules by catalyzing a bond between the tRNA and a corresponding amino acid.
Protein synthesis can be divided into three phases: initiation, elongation, and termination. The process of translation is similar in prokaryotes and eukaryotes.
Protein synthesis begins with the process of initiation, and formation of an initiation complex, which involves a ribosome, three initiation factors, and a certain initiator tRNA.
The sequence (AGGAGG) interacts with the rRNA molecules that compose the ribosome. The initiator tRNA then interacts with the start codon AUG. According to Kozak’s rules, the nucleotides around the AUG indicate whether it is the correct start codon.
During translation elongation, the mRNA template provides tRNA binding specificity. As the ribosome moves along the mRNA, each mRNA codon comes into register, and specific binding with the corresponding charged tRNA anticodon is ensured.
Elongation proceeds with charged tRNAs sequentially entering and leaving the ribosome as each new amino acid is added to the polypeptide chain. The formation of each peptide bond is catalyzed by peptidyl transferase, an RNA-based enzyme that is integrated into the 50S ribosomal subunit.
Termination of translation occurs when a nonsense codon (UAA, UAG, or UGA) is encountered. Upon aligning with the A site, these nonsense codons are recognized by protein release factors that resemble tRNAs.
During and after translation, individual amino acids may be chemically modified, signal sequences appended, and the new protein “folded” into a distinct three-dimensional structure as a result of intramolecular interactions.
A signal sequence is a short sequence at the amino end of a protein that directs it to a specific cellular compartment. These sequences are the protein’s pathway to its ultimate destination, and are recognized by signal-recognition proteins that act as conductors.
Many proteins fold spontaneously, but some proteins require helper molecules, called chaperones, to prevent them from aggregating during the complicated process of folding.