Synthesis[Edit]
Despite each cell in the body possessing an identical DNA sequence, they will differ in their function. For example, islet cells in the pancreas exclusively synthesize insulin, while hepatocytes, which are found in the liver, produce serum proteins such as albumin or clotting factors. These differences in function are often reflected in a cell’s physical attributes, which can also be highly variable. For example, leukocytes have an irregular shape, are highly motile and generally short-lived, contrary to osteocytes, which are immobile, develop long processes and are extremely long-lived.
The cellular response to stimuli may be manifested in an observable movement or change in state and may trigger various signaling pathways. Integral to each response is the cell's ability to synthesize biomolecules like proteins and lipids. It is these biomolecules that eventually produce changes in cellular morphology and control cellular function.
Unlike DNA, of which there is only a single type in each cell, there are three types of RNA (ribonucleic acid); namely rRNA (ribosomal RNA), mRNA (messenger RNA) and tRNA (transfer RNA). Each is synthesized from DNA via a process known as ‘transcription’. In this process, RNA polymerase synthesizes an RNA molecule that is complementary to the coding strand of DNA. Of the three types, only mRNA serves as template for protein synthesis. Since each mRNA molecule is used for the synthesis of only a few proteins, errors in mRNA are not necessarily detrimental to the cell and hence RNA polymerase has a higher error rate of 1 in 105 bases.
Proteins, which make up the majority of the structural and functional components of a cell, are synthesized via the process of translation. During this process, an mRNA strand is read, and an amino acid sequence is produced based on the mRNA sequence. This usually takes place within the cytoplasm, and is carried out by ribosomes, and tRNA.
In eukaryotes, synthesis of DNA, RNA, proteins and lipids is performed in a spatiotemporal manner. Each molecule is produced within specialized organelles or compartments with strict regulatory mechanisms existing to control the timing and rate of synthesis. These regulatory mechanisms are complicated, and may involve feedback loops, external stimuli and a multitude of signaling pathways.
DNA and RNA are both produced within the nucleus. DNA is entirely replicated during the s-phase of the cell cycle. One copy is then passed to each of the daughter cells. During other phases of the cell cycle a minimal amount of DNA is synthesized, primarily for the repair of the genetic material. Although a basal rate of RNA synthesis maintains mRNA synthesis throughout the life of the cell, the mRNA for specific genes may only be expressed, or may be up-regulated or down-regulated, following the detection of certain mechanical or chemical signals. As a result, different cells have different mRNA profiles, and this is often observed through the use of microarray technologies that screen the genetic profiles of cells.
After being processed and modified in the nucleus, transcribed mRNA is delivered to the cytosol for translation, or protein synthesis. Similar to RNA synthesis, a basic level of protein synthesis is maintained throughout the cell’s life, however this may also be altered when particular stimuli induces the production of specific proteins, or when regulatory mechanisms reduce the production of others. For example, protein synthesis is up-regulated during the G1 phase of the cell cycle, just prior to S-phase. This is to ensure the cell has a sufficient concentration of the protein machinery required to carry out DNA replication and cell division.
In prokaryotes, where there are no separate compartments, both transcription and translation occur simultaneously.
Lipids, which are synthesized in the endoplasmic reticulum (ER) or Golgi, are transported to other organelles in the form of vesicles which fuse with the acceptor organelle. Some cells may also use carrier proteins to ferry lipids from one location to another. Lipid synthesis is also dynamic, and may be up-regulated during cell proliferation or during processes involving plasma membrane extension, when new membranes are required.
Stem cells, or undifferentiated cells, have the capacity to replicate whilst maintaining their undifferentiated state and expressing all genes at low levels. With certain stimulation however, large-scale changes in gene and protein expression will occur, leading to cell differentiation or specialization. Once differentiated, a cell will maintain its gene expression profile to ensure it meets the functional requirements of the differentiated population. This will give rise to tissues such as epithelial tissue, muscle tissue or nervous tissue. This is particularly relevant in the field of mechanobiology, where mechanical signals have been found to direct the stem cell differentiation. For instance, mesenchymal stem cells can differentiate into chondrogenic or smooth muscle cells depending on the stiffness of their substrate [1, 2]. In this case, the two lineages were associated with different gene expression profiles.
Importantly, differentiated cells can still modulate the expression of certain genes in response to external stimuli. Mechanical signals have, for example, been shown to regulate the activation of several transcription factors including NF-ƙB and MKL, as well as modulate the accessibility of genes and the assembly of transcription foci in the nucleus [3]. Furthermore, several studies have depicted the influence of mechanical stimulation on fibroblast cells. In these cases, stretch mediated induction of matrix proteins like tenascin, elastin, collagen, MMP, were reported [4, 5, 6].
Even with proofreading capabilities and numerous regulatory mechanisms in place, errors can still be introduced into DNA, and proteins may be overexpressed to a level that is detrimental to the cell. Such imbalances can be induced by dysfunctional proteins, especially those that function as machinery in the synthesis of DNA, RNA or proteins [7]. Mutations in transcription factors, elongation factors, and in the regulatory sequences of genes are often responsible for perturbations in RNA synthesis. Likewise, mutations in ribosomal proteins and translational elongation factors such as tRNA, are often responsible for perturbations in protein synthesis.
As a result, protein levels may be higher or lower than the cell requires and this may be detrimental to the cell. For example, excessive protein levels have been linked with inclusion body formation in neurological disorders like Parkinson’s disease and Huntington disease [8, 9]. Reduced protein production on the other hand is associated with type I diabetes. In this case Islet cells fail to adequately produce insulin, which results in an increase in blood glucose levels [10, 11].
Errors in DNA synthesis are also associated with the process of aging, and linked to many age related diseases. The shortening of telomeres and the lack of proper segregation of chromosomes in the daughter cells are commonly seen in aged cells [12, 13, 14, 15].
Of all the diseases associated with DNA mutations, or dysfunctional regulation of gene or protein expression, is cancer. Although this broadly groups together a wide range of distinct diseases, in the majority of cases it is the presence of DNA mutations, and the modulation RNA or protein synthesis that promotes a metastatic phenotype in cells.
One of the most prominent examples of this is in breast cancer, where a small percentage of patients will have inherited mutations in the BRCA1 and BRCA2 genes. The products of these genes, known as ‘breast cancer type susceptibility protein’ would normally function in the repair of double-stranded DNA breaks, and in mismatch repair, thus serving as tumour suppressors. When mutated however, these proteins do not function correctly and promote the incorporation of additional mutations to subsequently produce a type of cancer with a particularly poor prognosis.
In some cases, genetic mutations may also lead to proteins being over or under-expressed. Two common examples of this include the growth controlling transcription factor c-Myc, which is often under-expressed, and p53, which is known to be over-expressed and mutated in a large number of tumor types [16, 17, 18].
Significant differences occur in the synthesis machinery in eukaryotes and prokaryotes and bacteria take ample advantage of this during by secreting toxins that selectively inhibit eukaryotic protein synthesis. For instance, Corynebacterium diptheriae is the agent that causes diphtheria, an upper respiratory tract infection. It carries a lysogenic phage coding for diphtheria toxin that post-translationally modifies EF2, the elongation factor for eukaryotic protein synthesis and thus inhibiting protein synthesis [19]. This toxin is extremely potent and even a few micrograms are sufficient to kill humans. The differences in prokaryotic translation machinery have also been exploited in the generation of antibiotics against bacteria. Chloramphenicol is one such drug that inhibits bacterial protein elongation by specifically interacting with the prokaryotic ribosomal subunit.
How do cells achieve this specialization?
Protein production is, in part, indicative of a cell’s ‘specialization’, however it also reveals how this differentiated state is possible in the first place - cells are able to synthesize different biomolecules, or varying quantities of a given protein, at different stages of their life, and in response to specific mechanical, chemical or electrical stimuli. Just as leukocytes and osteocytes have vastly different physical properties, so too do they possess significant differences in their rates of synthesis. Osteocytes may be long lived, however they are associated with a reduced synthetic activity and do not divide as other cells do. In contrast, the synthesis machinery of leukocytes is highly dynamic and results in cell division every few days to weeks.The cellular response to stimuli may be manifested in an observable movement or change in state and may trigger various signaling pathways. Integral to each response is the cell's ability to synthesize biomolecules like proteins and lipids. It is these biomolecules that eventually produce changes in cellular morphology and control cellular function.
What do cells synthesize?
Cells synthesize a large number of proteins, lipids and molecules throughout their lifetime. Specialized cellular machinery carries out these tasks, using information encoded within DNA to guide the process.Genetic material: DNA and RNA
Every cellular component stems from the genetic information stored within DNA (deoxyribonucleic acid). It is therefore imperative that cells synthesize this molecule during cell division, faithfully replicating the DNA of one cell, and passing it on to both daughter cells. Accurate replication of the molecule is essential as it contains the core genetic sequence of the cell. Any mutation that is introduced into the molecule, be it substitution, addition or deletion of one or more bases, may prove harmful not only for the daughter cells, but also for the organism.
For this reason DNA synthesis can be described as involving two key processes: the generation of a new DNA molecule and DNA proofreading and repair. Generation of the new molecule is carried out by a class of proteins known as DNA polymerases which add nucleotides to the 3’ end of the growing DNA strand. Although these proteins have one of the highest fidelity rates, with an error rate of around 1 in 109 bases, mutations, in the form of base mismatches, can still be introduced into the new DNA strand. For this reason some DNA polymerases have a proofreading capacity and this is usually supplemented by additional proteins that specifically check for errors in the DNA and initiate repair mechanisms to remove any mutations.
Unlike DNA, of which there is only a single type in each cell, there are three types of RNA (ribonucleic acid); namely rRNA (ribosomal RNA), mRNA (messenger RNA) and tRNA (transfer RNA). Each is synthesized from DNA via a process known as ‘transcription’. In this process, RNA polymerase synthesizes an RNA molecule that is complementary to the coding strand of DNA. Of the three types, only mRNA serves as template for protein synthesis. Since each mRNA molecule is used for the synthesis of only a few proteins, errors in mRNA are not necessarily detrimental to the cell and hence RNA polymerase has a higher error rate of 1 in 105 bases.
Proteins, which make up the majority of the structural and functional components of a cell, are synthesized via the process of translation. During this process, an mRNA strand is read, and an amino acid sequence is produced based on the mRNA sequence. This usually takes place within the cytoplasm, and is carried out by ribosomes, and tRNA.
Lipids must also be synthesized by the cell. These represent the basic component of the cellular membrane and the many vesicles and vacuoles that are found throughout the cell.
Spatiotemporal control of synthesis
DNA and RNA are both produced within the nucleus. DNA is entirely replicated during the s-phase of the cell cycle. One copy is then passed to each of the daughter cells. During other phases of the cell cycle a minimal amount of DNA is synthesized, primarily for the repair of the genetic material. Although a basal rate of RNA synthesis maintains mRNA synthesis throughout the life of the cell, the mRNA for specific genes may only be expressed, or may be up-regulated or down-regulated, following the detection of certain mechanical or chemical signals. As a result, different cells have different mRNA profiles, and this is often observed through the use of microarray technologies that screen the genetic profiles of cells.
After being processed and modified in the nucleus, transcribed mRNA is delivered to the cytosol for translation, or protein synthesis. Similar to RNA synthesis, a basic level of protein synthesis is maintained throughout the cell’s life, however this may also be altered when particular stimuli induces the production of specific proteins, or when regulatory mechanisms reduce the production of others. For example, protein synthesis is up-regulated during the G1 phase of the cell cycle, just prior to S-phase. This is to ensure the cell has a sufficient concentration of the protein machinery required to carry out DNA replication and cell division.
In prokaryotes, where there are no separate compartments, both transcription and translation occur simultaneously.
Lipids, which are synthesized in the endoplasmic reticulum (ER) or Golgi, are transported to other organelles in the form of vesicles which fuse with the acceptor organelle. Some cells may also use carrier proteins to ferry lipids from one location to another. Lipid synthesis is also dynamic, and may be up-regulated during cell proliferation or during processes involving plasma membrane extension, when new membranes are required.
The Dynamic Nature of Synthesis
The ability of cells to express genes and synthesize proteins at varying levels enables them to specialize in a particular role or function. This is crucial in the development of every organism, and has, in recent years, been exploited in laboratories that aim to grow mammalian tissues or organs from stem cells.Stem cells, or undifferentiated cells, have the capacity to replicate whilst maintaining their undifferentiated state and expressing all genes at low levels. With certain stimulation however, large-scale changes in gene and protein expression will occur, leading to cell differentiation or specialization. Once differentiated, a cell will maintain its gene expression profile to ensure it meets the functional requirements of the differentiated population. This will give rise to tissues such as epithelial tissue, muscle tissue or nervous tissue. This is particularly relevant in the field of mechanobiology, where mechanical signals have been found to direct the stem cell differentiation. For instance, mesenchymal stem cells can differentiate into chondrogenic or smooth muscle cells depending on the stiffness of their substrate [1, 2]. In this case, the two lineages were associated with different gene expression profiles.
Importantly, differentiated cells can still modulate the expression of certain genes in response to external stimuli. Mechanical signals have, for example, been shown to regulate the activation of several transcription factors including NF-ƙB and MKL, as well as modulate the accessibility of genes and the assembly of transcription foci in the nucleus [3]. Furthermore, several studies have depicted the influence of mechanical stimulation on fibroblast cells. In these cases, stretch mediated induction of matrix proteins like tenascin, elastin, collagen, MMP, were reported [4, 5, 6].
Altered Synthesis and Disease
Although it is sometimes difficult to determine whether it is the cause or effect of a given disease, in many cases associations between disease states and altered gene expression profiles and protein levels are evident.Even with proofreading capabilities and numerous regulatory mechanisms in place, errors can still be introduced into DNA, and proteins may be overexpressed to a level that is detrimental to the cell. Such imbalances can be induced by dysfunctional proteins, especially those that function as machinery in the synthesis of DNA, RNA or proteins [7]. Mutations in transcription factors, elongation factors, and in the regulatory sequences of genes are often responsible for perturbations in RNA synthesis. Likewise, mutations in ribosomal proteins and translational elongation factors such as tRNA, are often responsible for perturbations in protein synthesis.
As a result, protein levels may be higher or lower than the cell requires and this may be detrimental to the cell. For example, excessive protein levels have been linked with inclusion body formation in neurological disorders like Parkinson’s disease and Huntington disease [8, 9]. Reduced protein production on the other hand is associated with type I diabetes. In this case Islet cells fail to adequately produce insulin, which results in an increase in blood glucose levels [10, 11].
Errors in DNA synthesis are also associated with the process of aging, and linked to many age related diseases. The shortening of telomeres and the lack of proper segregation of chromosomes in the daughter cells are commonly seen in aged cells [12, 13, 14, 15].
Of all the diseases associated with DNA mutations, or dysfunctional regulation of gene or protein expression, is cancer. Although this broadly groups together a wide range of distinct diseases, in the majority of cases it is the presence of DNA mutations, and the modulation RNA or protein synthesis that promotes a metastatic phenotype in cells.
One of the most prominent examples of this is in breast cancer, where a small percentage of patients will have inherited mutations in the BRCA1 and BRCA2 genes. The products of these genes, known as ‘breast cancer type susceptibility protein’ would normally function in the repair of double-stranded DNA breaks, and in mismatch repair, thus serving as tumour suppressors. When mutated however, these proteins do not function correctly and promote the incorporation of additional mutations to subsequently produce a type of cancer with a particularly poor prognosis.
In some cases, genetic mutations may also lead to proteins being over or under-expressed. Two common examples of this include the growth controlling transcription factor c-Myc, which is often under-expressed, and p53, which is known to be over-expressed and mutated in a large number of tumor types [16, 17, 18].
Significant differences occur in the synthesis machinery in eukaryotes and prokaryotes and bacteria take ample advantage of this during by secreting toxins that selectively inhibit eukaryotic protein synthesis. For instance, Corynebacterium diptheriae is the agent that causes diphtheria, an upper respiratory tract infection. It carries a lysogenic phage coding for diphtheria toxin that post-translationally modifies EF2, the elongation factor for eukaryotic protein synthesis and thus inhibiting protein synthesis [19]. This toxin is extremely potent and even a few micrograms are sufficient to kill humans. The differences in prokaryotic translation machinery have also been exploited in the generation of antibiotics against bacteria. Chloramphenicol is one such drug that inhibits bacterial protein elongation by specifically interacting with the prokaryotic ribosomal subunit.