Molecular biology (II)

Below I have added some more quotes and links related to the book’s coverage:

“[P]roteins are the most abundant molecules in the body except for water. […] Proteins make up half the dry weight of a cell whereas DNA and RNA make up only 3 per cent and 20 per cent respectively. […] The approximately 20,000 protein-coding genes in the human genome can, by alternative splicing, multiple translation starts, and post-translational modifications, produce over 1,000,000 different proteins, collectively called ‘the proteome‘. It is the size of the proteome and not the genome that defines the complexity of an organism. […] For simple organisms, such as viruses, all the proteins coded by their genome can be deduced from its sequence and these comprise the viral proteome. However for higher organisms the complete proteome is far larger than the genome […] For these organisms not all the proteins coded by the genome are found in any one tissue at any one time and therefore a partial proteome is usually studied. What are of interest are those proteins that are expressed in specific cell types under defined conditions.”

“Enzymes are proteins that catalyze or alter the rate of chemical reactions […] Enzymes can speed up reactions […] but they can also slow some reactions down. Proteins play a number of other critical roles. They are involved in maintaining cell shape and providing structural support to connective tissues like cartilage and bone. Specialized proteins such as actin and myosin are required [for] muscular movement. Other proteins act as ‘messengers’ relaying signals to regulate and coordinate various cell processes, e.g. the hormone insulin. Yet another class of protein is the antibodies, produced in response to foreign agents such as bacteria, fungi, and viruses.”

“Proteins are composed of amino acids. Amino acids are organic compounds with […] an amino group […] and a carboxyl group […] In addition, amino acids carry various side chains that give them their individual functions. The twenty-two amino acids found in proteins are called proteinogenic […] but other amino acids exist that are non-protein functioning. […] A peptide bond is formed between two amino acids by the removal of a water molecule. […] each individual unit in a peptide or protein is known as an amino acid residue. […] Chains of less than 50-70 amino acid residues are known as peptides or polypeptides and >50-70 as proteins, although many proteins are composed of more than one polypeptide chain. […] Proteins are macromolecules consisting of one or more strings of amino acids folded into highly specific 3D-structures. Each amino acid has a different size and carries a different side group. It is the nature of the different side groups that facilitates the correct folding of a polypeptide chain into a functional tertiary protein structure.”

“Atoms scatter the waves of X-rays mainly through their electrons, thus forming secondary or reflected waves. The pattern of X-rays diffracted by the atoms in the protein can be captured on a photographic plate or an image sensor such as a charge coupled device placed behind the crystal. The pattern and relative intensity of the spots on the diffraction image are then used to calculate the arrangement of atoms in the original protein. Complex data processing is required to convert the series of 2D diffraction or scatter patterns into a 3D image of the protein. […] The continued success and significance of this technique for molecular biology is witnessed by the fact that almost 100,000 structures of biological molecules have been determined this way, of which most are proteins.”

“The number of proteins in higher organisms far exceeds the number of known coding genes. The fact that many proteins carry out multiple functions but in a regulated manner is one way a complex proteome arises without increasing the number of genes. Proteins that performed a single role in the ancestral organism have acquired extra and often disparate functions through evolution. […] The active site of an enzyme employed in catalysis is only a small part of the protein, leaving spare capacity for acquiring a second function. […] The glycolytic pathway is involved in the breakdown of sugars such as glucose to release energy. Many of the highly conserved and ancient enzymes from this pathway have developed secondary or ‘moonlighting’ functions. Proteins often change their location in the cell in order to perform a ‘second job’. […] The limited size of the genome may not be the only evolutionary pressure for proteins to moonlight. Combining two functions in one protein can have the advantage of coordinating multiple activities in a cell, enabling it to respond quickly to changes in the environment without the need for lengthy transcription and translational processes.”

Post-translational modifications (PTMs) […] is [a] process that can modify the role of a protein by addition of chemical groups to amino acids in the peptide chain after translation. Addition of phosphate groups (phosphorylation), for example, is a common mechanism for activating or deactivating an enzyme. Other common PTMs include addition of acetyl groups (acetylation), glucose (glucosylation), or methyl groups (methylation). […] Some additions are reversible, facilitating the switching between active and inactive states, and others are irreversible such as marking a protein for destruction by ubiquitin. [The difference between reversible and irreversible modifications can be quite important in pharmacology, and if you’re curious to know more about these topics Coleman’s drug metabolism text provide great coverage of related topics – US.] Diseases caused by malfunction of these modifications highlight the importance of PTMs. […] in diabetes [h]igh blood glucose lead to unwanted glocosylation of proteins. At the high glucose concentrations associated with diabetes, an unwanted irreversible chemical reaction binds the gllucose to amino acid residues such as lysines exposed on the protein surface. The glucosylated proteins then behave badly, cross-linking themselves to the extracellular matrix. This is particularly dangerous in the kidney where it decreases function and can lead to renal failure.”

“Twenty thousand protein-coding genes make up the human genome but for any given cell only about half of these are expressed. […] Many genes get switched off during differentiation and a major mechanism for this is epigenetics. […] an epigenetic trait […] is ‘a stably heritable phenotype resulting from changes in the chromosome without alterations in the DNA sequence’. Epigenetics involves the chemical alteration of DNA by methyl or other small molecular groups to affect the accessibility of a gene by the transcription machinery […] Epigenetics can […] act on gene expression without affecting the stability of the genetic code by modifying the DNA, the histones in chromatin, or a whole chromosome. […] Epigenetic signatures are not only passed on to somatic daughter cells but they can also be transferred through the germline to the offspring. […] At first the evidence appeared circumstantial but more recent studies have provided direct proof of epigenetic changes involving gene methylation being inherited. Rodent models have provided mechanistic evidence. […] the importance of epigenetics in development is highlighted by the fact that low dietary folate, a nutrient essential for methylation, has been linked to higher risk of birth defects in the offspring.” […on the other hand, well…]

The cell cycle is divided into phases […] Transition from G1 into S phase commits the cell to division and is therefore a very tightly controlled restriction point. Withdrawal of growth factors, insufficient nucleotides, or energy to complete DNA replication, or even a damaged template DNA, would compromise the process. Problems are therefore detected and the cell cycle halted by cell cycle inhibitors before the cell has committed to DNA duplication. […] The cell cycle inhibitors inactive the kinases that promote transition through the phases, thus halting the cell cycle. […] The cell cycle can also be paused in S phase to allow time for DNA repairs to be carried out before cell division. The consequences of uncontrolled cell division are so catastrophic that evolution has provided complex checks and balances to maintain fidelity. The price of failure is apoptosis […] 50 to 70 billion cells die every day in a human adult by the controlled molecular process of apoptosis.”

“There are many diseases that arise because a particular protein is either absent or a faulty protein is produced. Administering a correct version of that protein can treat these patients. The first commercially available recombinant protein to be produced for medical use was human insulin to treat diabetes mellitus. […] (FDA) approved the recombinant insulin for clinical use in 1982. Since then over 300 protein-based recombinant pharmaceuticals have been licensed by the FDA and the European Medicines Agency (EMA) […], and many more are undergoing clinical trials. Therapeutic proteins can be produced in bacterial cells but more often mammalian cells such as the Chinese hamster ovary cell line and human fibroblasts are used as these hosts are better able to produce fully functional human protein. However, using mammalian cells is extremely expensive and an alternative is to use live animals or plants. This is called molecular pharming and is an innovative way of producing large amounts of protein relatively cheaply. […] In plant pharming, tobacco, rice, maize, potato, carrots, and tomatoes have all been used to produce therapeutic proteins. […] [One] class of proteins that can be engineered using gene-cloning technology is therapeutic antibodies. […] Therapeutic antibodies are designed to be monoclonal, that is, they are engineered so that they are specific for a particular antigen to which they bind, to block the antigen’s harmful effects. […] Monoclonal antibodies are at the forefront of biological therapeutics as they are highly specific and tend not to induce major side effects.”

“In gene therapy the aim is to restore the function of a faulty gene by introducing a correct version of that gene. […] a cloned gene is transferred into the cells of a patient. Once inside the cell, the protein encoded by the gene is produced and the defect is corrected. […] there are major hurdles to be overcome for gene therapy to be effective. One is the gene construct has to be delivered to the diseased cells or tissues. This can often be difficult […] Mammalian cells […] have complex mechanisms that have evolved to prevent unwanted material such as foreign DNA getting in. Second, introduction of any genetic construct is likely to trigger the patient’s immune response, which can be fatal […] once delivered, expression of the gene product has to be sustained to be effective. One approach to delivering genes to the cells is to use genetically engineered viruses constructed so that most of the viral genome is deleted […] Once inside the cell, some viral vectors such as the retroviruses integrate into the host genome […]. This is an advantage as it provides long-lasting expression of the gene product. However, it also poses a safety risk, as there is little control over where the viral vector will insert into the patient’s genome. If the insertion occurs within a coding gene, this may inactivate gene function. If it integrates close to transcriptional start sites, where promoters and enhancer sequences are located, inappropriate gene expression can occur. This was observed in early gene therapy trials [where some patients who got this type of treatment developed cancer as a result of it. A few more details hereUS] […] Adeno-associated viruses (AAVs) […] are often used in gene therapy applications as they are non-infectious, induce only a minimal immune response, and can be engineered to integrate into the host genome […] However, AAVs can only carry a small gene insert and so are limited to use with genes that are of a small size. […] An alternative delivery system to viruses is to package the DNA into liposomes that are then taken up by the cells. This is safer than using viruses as liposomes do not integrate into the host genome and are not very immunogenic. However, liposome uptake by the cells can be less efficient, resulting in lower expression of the gene.”


One gene–one enzyme hypothesis.
Molecular chaperone.
Protein turnover.
Isoelectric point.
Gel electrophoresis. Polyacrylamide.
Two-dimensional gel electrophoresis.
Mass spectrometry.
Peptide mass fingerprinting.
Worldwide Protein Data Bank.
Nuclear magnetic resonance spectroscopy of proteins.
Immunoglobulins. Epitope.
Western blot.
Crystallin. β-catenin.
Protein isoform.
Gene expression. Transcriptional regulation. Chromatin. Transcription factor. Gene silencing. Histone. NF-κB. Chromatin immunoprecipitation.
The agouti mouse model.
X-inactive specific transcript (Xist).
Cell cycle. Cyclin. Cyclin-dependent kinase.
Retinoblastoma protein pRb.
Cytochrome c. CaspaseBcl-2 family. Bcl-2-associated X protein.
Hybridoma technology. Muromonab-CD3.
Recombinant vaccines and the development of new vaccine strategies.
Knockout mouse.
Adenovirus Vectors for Gene Therapy, Vaccination and Cancer Gene Therapy.
Genetically modified food. Bacillus thuringiensis. Golden rice.


May 29, 2018 - Posted by | Biology, Books, Chemistry, Diabetes, Engineering, Genetics, Immunology, Medicine, Molecular biology, Pharmacology

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