INFORMATION FLOW WITHIN CELLS

Information flow within a cell is generally referred to as the central dogma of biology (see Figure 2.1). It is a complex system in which one

cellular component (or stock) influences the next. Typically speaking, the process is unidirectional—proteins do not become RNA and RNA does not become DNA. The arrows in Figure 2.1 represent flows within the system. The flow from DNA to RNA is called transcription. The flow from RNA to protein is called translation. The following subsections detail the key biological parts and processes involved in each.6

Briefly, DNA is transcribed into RNA. Some RNA belongs to a class called messenger RNA (mRNA). mRNA is translated into proteins. Various factors influence the rate of transcription and translation. Some are shown in Figure 2.1.

Central dogma of biology as a stock/flow system diagram

Figure 2.1. Central dogma of biology as a stock/flow system diagram.

Central Dogma and Biological Exceptions

All cells contain nucleic acids, of which there are two varieties—commonly referred to as DNA and RNA. Subunits of both DNA and RNA are comprised of a five-carbon ringed sugar (i.e., deoxyribose or ribose), a phosphate group, and a series of sequence-defining nitrogenase bases. Collectively, these sugar—phosphate—base structures are called nucleotides (nt) (see Figure 2.2). Nucleotides are covalently linked together by their phosphate groups (connected to the 5’ carbon within the respective sugar) and hydroxyl functional groups (connected to the 3’ carbon within the respective sugar). A chain of linked nucleotides is called a strand. Together, the alternating phosphate/sugar groups are referred to as the “backbone” of the nucleic acid, and form a structure similar to a supportive vertical component of a ladder. Continuing with this analogy, the nitro- genase bases, extending from the 1’ carbon of each sugar, make up the many rungs of the ladder. The bases come in four varieties—A, T, G, and C within DNA and A, U, G, and C within RNA. The bases in nucleic acids are described in a conventional 5’ ^ 3’ orientation, a naming scheme that represents the location of terminal 5’ or 3’ carbons at the end of a strand.7

Nucleotides of DNA and RNA contain a phosphate group (P), five-carbon sugar, and nitrogenase base (i.e., A, C, G, T/U). Nitrogenase bases have the propensity to hydrogen bond to complementary bases on antiparallel strands. The carbons within the sugar molecule are numbered 1-5, in a clockwise fashion. Ribose contains an hydroxyl (-OH) group on the 2’ carbon, where deoxyribose does not. New nts are added to the growing nucleic acid chain by DNA or RNA Pol. This occurs at the hydroxyl group on the 3’ carbon.

Three-component nucleotide structure

Figure 2.2. Three-component nucleotide structure.

In a typical cell, DNA is primarily double-stranded (i.e., “ds”) in its resting state. Relatively weak hydrogen bonds between the bases of two strands link them together. These hydrogen bonds can be broken with heat or enzymatic activity, causing the strands to separate to create two single stranded (i.e., “ss”) DNA molecules. Such a process is called denaturation. Unzipping is a colloquial term for the same process. When denaturation occurs, it is important to note that the covalent bonds contained within each strand of the backbone remain intact. As such, when conditions allow, the two strands of the DNA are able to come back together to reform the double-stranded molecule by H-bonding between the bases. This process is called base pairing, annealing, or hybridization of the two DNA strands.

Not just any two strands of DNA can come together to form a double-stranded molecule—the bases within the two strands must be antiparallel and complementary. That is, the strands must run in opposite directions (i.e., 5’^3’and 3’^ 5’) and the chemical structure of the bases must match up in space such that hydrogen bonds can form. Generally speaking, Gs only bond with Cs, and As only bond with Ts (in DNA) or Us (in RNA). For example, a 5’—GATC—3’ strand is complementary to a 3’—CTAG—5’ strand, but not another 5’—GATC—3’, a 3’—GATC—5’,

or any other strand with an alternative combination of bases. These DNA base pairing rules are critical for cellular and artificial mechanisms of DNA replication (i.e., copying or amplifying) and transcription.

While the structures of DNA and RNA are relatively similar—and both can contain information about how to build protein machines—each molecule performs a distinct role within cells and the central dogma. DNA serves as the complete and relatively unchanging permanent record of all the genetic material within a cell. The complete set of DNA within a cell is called the genome. Genomes are often broken down into multiple physical structures, called chromosomes. Bacteria typically have 1-2 circular chromosomes while eukaryotic cells have numerous linear chromosomes. Genes—DNA sequences that encode the instructions for the production of proteins—are found scattered along the length of a chromosome. Versions of a gene are called alleles. Genotype describes the combination of alleles within a cell or organism. The characteristics that an allele, or combination of alleles, produce is the phenotype. The DNA sequences that occur between genes are called intergenic regions. Intergenic regions contain critical information about when a gene should be used to create an associated protein. Regulatory regions called promoters occur immediately before—i.e., upstream—of genes. Transcriptional terminators occur downstream of genes, and help to stop transcription. There is also what was once referred to as non-coding “junk” DNA8 within intergenic regions.

Transcription and translation are terms to describe the cellular processes used to extract encoded genetic information to produce a protein. Transcription is the process of copying a single strand of DNA to produce a complementary single strand of RNA, called a transcript. When the RNA is destined to be read to produce a protein, it is called messenger RNA (mRNA). Some other forms of RNA include transfer (tRNA), ribosomal (rRNA), and micro (miRNA) RNA. The complex process of transcription is performed by RNA polymerase (RNA Pol)—a massive molecular machine comprised of numerous protein components—and fine-tuned/enhanced by additional transcription factor proteins. When it is appropriate for a cell to produce a given transcript, transcription factors and RNA Pol bind to an associated promoter sequence upstream of the coding region. The DNA template locally denatures, via enzymatic activity of the complex. RNA Pol links free RNA nucleotides together to create a new strand of mRNA to match the DNA template. For example, if the DNA template sequence is 3’—ATGGATCGTG—5’, the complementary mRNA that is produced by RNA Pol is 5’—CACGAUCCAU—3’. Note that mRNA nucleotides are added in a complementary fashion and that Us take the place of Ts in the transcribed RNA. The polymerase can only add new nucleotides onto the hydroxyl group attached to the RNA molecule’s 3’ carbon of the ribose sugar (i.e., in the 5’^3’ direction).9 When the RNA Pol complex arrives at a terminator (downstream of a coding region), it disassociates from the DNA template and transcription is complete.

Translation is the process of reading an mRNA molecule—in consecutive groupings of three nucleotides, called codons—to construct a chain of amino acids. Amino acids, for which there are 20 naturally occurring varieties, are the building blocks of proteins. Ribosomes, another kind of massive molecular machine, link amino acids together in an order defined by the mRNA sequence. Ribosomes are comprised of two distinct subunits (small and large), which differ slightly between prokaryotic and eukaryotic cells. A special type of RNA, called ribosomal RNA (rRNA),10 is part of the ribosomal complex.

The small ribosomal subunit binds to ribosome binding sites (RBS) located at the 5’ end of single-stranded mRNA transcripts. From there, the ribosomal subunit scans the RNA sequence until it identifies a triplicate start codon. The canonical start codon is 5’—AUG—3’, but alternative start codons (e.g., GUG) may be used in some cells. When the small subunit identifies a start codon, the large ribosomal subunit on the other side of the strand, creates a complete (or holo-) enzyme. From there, the frame is set, and the ribosome will begin to translate each mRNA codon into the specific amino acid it encodes. This process is accomplished through the use of transfer RNA (tRNA) molecules, which are hybrid molecules that contain RNA-based triplicate anti-codons attached to specific amino acids. For example, an AUG start codon matches with a UAC-Methi- one-tRNA. Translation ceases when a stop codon is encountered in the mRNA. Stop codons pair with tRNAs that lack amino acids. When this happens, the translational complex disassociates, leaving an amino acid chain that will fold to produce a functional protein. Proteins are transported to the appropriate place within a cell (e.g., the cell membrane, cytoplasm, or an organelle) to perform their function. The transport of proteins is called protein trafficking.

 
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