EcoRI (pronounced "eco R one") is a restriction endonuclease enzyme isolated from species E. coli. The Eco part of the enzyme's name originates from the species from which it was isolated, while the R represents the particular strain, in this case RY13.In EcoRI, "E" denotes generic name which is "Escherichia" and "co" denotes species name which is "coli" The last part of its name, the I, denotes that it was the first enzyme isolated from this strain. EcoRI is a restriction enzyme that cleaves DNA double helices into fragments at specific sites. It is also a part of the restriction modification system.

In molecular biology it is used as a restriction enzyme. EcoRI creates 4 nucleotide sticky ends with 5' end overhangs of AATT. The nucleic acid recognition sequence where the enzyme cuts is G/AATTC, which has a palindromic, complementary sequence of CTTAA/G. The / in the sequence indicates which phosphodiester bond the enzyme will break in the DNA molecule. Other restriction enzymes, depending on their cut sites, can also leave 3' overhangs or blunt ends with no overhangs. (W)

EcoRI dimer (biological unit) bound to DNA. PDB file 2ckq.

EcoRI recognition site with cutting pattern indicated by a green line.

In biochemistry, an effector molecule is usually a small molecule that selectively binds to a protein and regulates its biological activity. In this manner, effector molecules act as ligands that can increase or decrease enzyme activity, gene expression, or cell signaling. Effector molecules can also directly regulate the activity of some mRNA molecules (riboswitches).

In some cases, proteins can be considered to function as effector molecules, especially in cellular signal transduction cascades.

The term effector is used in other fields of biology. For instance, the effector end of a neuron is the terminus where an axon makes contact with the muscle or organ that it stimulates or suppresses.

• Enzyme activator
• Enzyme inhibitor

(W)

In atomic physics and quantum chemistry, the electron configuration is the distribution of electrons of an atom or molecule (or other physical structure) in atomic or molecular orbitals. For example, the electron configuration of the neon atom is 1s² 2s² 2p⁶, using the notation explained below.

Electronic configurations describe each electron as moving independently in an orbital, in an average field created by all other orbitals. Mathematically, configurations are described by Slater determinants or configuration state functions.

According to the laws of quantum mechanics, for systems with only one electron, a level of energy is associated with each electron configuration and in certain conditions, electrons are able to move from one configuration to another by the emission or absorption of a quantum of energy, in the form of a photon.

Knowledge of the electron configuration of different atoms is useful in understanding the structure of the periodic table of elements. This is also useful for describing the chemical bonds that hold atoms together. In bulk materials, this same idea helps explain the peculiar properties of lasers and semiconductors. (W)

Electron atomic and molecular orbitals.

electron transport chain

The electron transport chain (ETC) is a series of complexes that transfer electrons from electron donors to electron acceptors via redox (both reduction and oxidation occurring simultaneously) reactions, and couples this electron transfer with the transfer of protons (H⁺ ions) across a membrane. The electron transport chain is built up of peptides, enzymes, and other molecules.

The flow of electrons through the electron transport chain an exergonic process. The energy from the redox reactions create an electrochemical proton gradient that drives the synthesis of adenosine triphosphate (ATP). In aerobic respiration, the flow of electrons terminates with molecular oxygen being the final electron acceptor. In anaerobic respiration, other electron acceptors are used, such as sulfate.

In the electron transport chain, the redox reactions are driven by the Gibbs free energy state of the components. Gibbs free energy is related to a quantity called the redox potential. The complexes in the electron transport chain harvest the energy of the redox reactions that occur when transferring electrons from a low redox potential to a higher redox potential, creating an electrochemical gradient. It is the electrochemical gradient created that drives the synthesis of ATP via coupling with oxidative phosphorylation with ATP synthase. (W)

The electron transport chain in the mitochondrion is the site of oxidative phosphorylation in eukaryotes. The NADH and succinate generated in the citric acid cycle are oxidized, providing energy to power ATP synthase.

Photosynthetic electron transport chain of the thylakoid membrane

Depiction of ATP synthase, the site of oxidative phosphorylation to generate ATP.

Electrophoresis (from the Greek "ηλεκτροφόρηση" meaning "to bear electrons") is the motion of dispersed particles relative to a fluid under the influence of a spatially uniform electric field. Electrophoresis of positively charged particles (cations) is sometimes called cataphoresis, while electrophoresis of negatively charged particles (anions) is sometimes called anaphoresis.

The electrokinetic phenomenon of electrophoresis was observed for the first time in 1807 by Russian professors Peter Ivanovich Strakhov and Ferdinand Frederic Reuss at Moscow University, who noticed that the application of a constant electric field caused clay particles dispersed in water to migrate. It is ultimately caused by the presence of a charged interface between the particle surface and the surrounding fluid. It is the basis for analytical techniques used in chemistry for separating molecules by size, charge, or binding affinity.

Electrophoresis is used in laboratories to separate macromolecules based on size. The technique applies a negative charge so proteins move towards a positive charge. Electrophoresis is used extensively in DNA, RNA and protein analysis. (W)

Illustration of electrophoresis. Rappresentazione del trasporto di uno ione in un elettrolita attraverso meccanismo viscoso e sotto l'influsso di un campo elettrico esterno.

Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as deoxyribonuclease I, cut DNA relatively nonspecifically (without regard to sequence), while many, typically called restriction endonucleases or restriction enzymes, cleave only at very specific nucleotide sequences. Endonucleases differ from exonucleases, which cleave the ends of recognition sequences instead of the middle (endo) portion. Some enzymes known as "exo-endonucleases", however, are not limited to either nuclease function, displaying qualities that are both endo- and exo-like. Evidence suggests that endonuclease activity experiences a lag compared to exonuclease activity.

Restriction enzymes are endonucleases from eubacteria and archaea that recognize a specific DNA sequence. The nucleotide sequence recognized for cleavage by a restriction enzyme is called the restriction site. Typically, a restriction site will be a palindromic sequence about four to six nucleotides long. Most restriction endonucleases cleave the DNA strand unevenly, leaving complementary single-stranded ends. These ends can reconnect through hybridization and are termed "sticky ends". Once paired, the phosphodiester bonds of the fragments can be joined by DNA ligase. There are hundreds of restriction endonucleases known, each attacking a different restriction site. The DNA fragments cleaved by the same endonuclease can be joined together regardless of the origin of the DNA. Such DNA is called recombinant DNA; DNA formed by the joining of genes into new combinations. Restriction endonucleases (restriction enzymes) are divided into three categories, Type I, Type II, and Type III, according to their mechanism of action. These enzymes are often used in genetic engineering to make recombinant DNA for introduction into bacterial, plant, or animal cells, as well as in synthetic biology. One of the more famous endonucleases is Cas9. (W)

Restriction enzyme Eco RI.

APEndonucleasecartoon. Endonucleases play a role in DNA repair. AP endonuclease, specifically, catalyzes the incision of DNA exclusively at AP sites, and therefore prepares DNA for subsequent excision, repair synthesis and DNA ligation. For example, when depurination occurs, this lesion leaves a deoxyribose sugar with a missing base. The AP endonuclease recognizes this sugar and essentially cuts the DNA at this site and then allows for DNA repair to continue. E. coli cells contain two AP endonucleases: endonuclease IV (endoIV) and exonuclease III (exoIII) while in eukaryotes, there is only one AP endonuclease.

endorphins

Endorphins (contracted from "endogenous morphine") are endogenous opioid neuropeptides and peptide hormones in humans and other animals. They are produced and stored in the pituitary gland. The classification of molecules as endorphins is based on their pharmacological activity, as opposed to a specific chemical formulation.

The endorphin class consists of α-endorphin, β-endorphin, and γ-endorphin. All three preferentially bind to μ-opioid receptors. The principal function of endorphins is to inhibit the communication of pain signals. Endorphins may also produce a feeling of euphoria very similar to that produced by other opioids. (W)

List of Enzymes (W)

Enzymes are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called enzymology and a new field of pseudoenzyme analysis has recently grown up, recognising that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties.

Enzymes are known to catalyze more than 5,000 biochemical reaction types. Other biocatalysts are catalytic RNA molecules, called ribozymes. Enzymes' specificity comes from their unique three-dimensional structures.(W)

The enzyme glucosidase converts the sugar maltose into two glucose sugars. Active site residues in red, maltose substrate in black, and NAD cofactor in yellow. (PDB: 1OBB​).

Organisation of enzyme structure and lysozyme example. Binding sites in blue, catalytic site in red and peptidoglycan substrate in black. (PDB: 9LYZ​).

Enzyme changes shape by induced fit upon substrate binding to form enzyme-substrate complex. Hexokinase has a large induced fit motion that closes over the substrates adenosine triphosphate and xylose. Binding sites in blue, substrates in black and Mg2+ cofactor in yellow. (PDB: 2E2N​, 2E2Q​).

Chemical structure for thiamine pyrophosphate and protein structure of transketolase. Thiamine pyrophosphate cofactor in yellow and xylulose 5-phosphate substrate in black. (PDB: 4KXV​).

The metabolic pathway of glycolysis releases energy by converting glucose to pyruvate via a series of intermediate metabolites. Each chemical modification (red box) is performed by a different enzyme.

enzyme assay

Enzyme assays are laboratory methods for measuring enzymatic activity. They are vital for the study of enzyme kinetics and enzyme inhibition. (W)

Beckman DU640 UV/Vis spectrophotometer.

Enzyme catalysis is the increase in the rate of a process by a biological molecule, an "enzyme". Most enzymes are proteins, and most such processes are chemical reactions. Within the enzyme, generally catalysis occurs at a localized site, called the active site.

Most enzymes are made predominantly of proteins, either a single protein chain or many such chains in a multi-subunit complex. Enzymes often also incorporate non-protein components, such as metal ions or specialized organic molecules known as cofactor (e.g. adenosine triphosphate). Many cofactors are vitamins, and their role as vitamins is directly linked to their use in the catalysis of biological process within metabolism. Catalysis of biochemical reactions in the cell is vital since many but not all metabolically essential reactions have very low rates when uncatalysed. One driver of protein evolution is the optimization of such catalytic activities, although only the most crucial enzymes operate near catalytic efficiency limits, and many enzymes are far from optimal. Important factors in enzyme catalysis include general acid and base catalysis, orbital steering, entropic restriction, orientation effects (i.e. lock and key catalysis), as well as motional effects involving protein dynamics.

Mechanisms of enzyme catalysis vary, but are all similar in principle to other types of chemical catalysis in that the crucial factor is a reduction of energy barrier(s) separating the reactants from the products. The reduction of activation energy (Ea) increases the fraction of reactant molecules that can overcome this barrier and form the product. An important principle is that since they only reduce energy barriers between products and reactants, enzymes always catalyze reactions in both directions, and cannot drive a reaction forward or affect the equilibrium position - only the speed with which is it achieved. As with other catalysts, the enzyme is not consumed or changed by the reaction (as a substrate is) but is recycled such that a single enzyme performs many rounds of catalysis. (W)

Enzyme changes shape by induced fit upon substrate binding to form enzyme-substrate complex. Hexokinase has a large induced fit motion that closes over the substrates adenosine triphosphate and xylose. Binding sites in blue, substrates in black and Mg2+ cofactor in yellow. (PDB: 2E2N​, 2E2Q).

The different mechanisms of substrate binding.

enzyme kinetics

Enzyme kinetics is the study of the chemical reactions that are catalysed by enzymes. In enzyme kinetics, the reaction rate is measured and the effects of varying the conditions of the reaction are investigated. Studying an enzyme's kinetics in this way can reveal the catalytic mechanism of this enzyme, its role in metabolism, how its activity is controlled, and how a drug or an agonist might inhibit the enzyme.

Enzymes are usually protein molecules that manipulate other molecules—the enzymes' substrates. These target molecules bind to an enzyme's active site and are transformed into products through a series of steps known as the enzymatic mechanism

E + S ⇄ ES ⇄ ES* ⇄ EP ⇄ E + P

These mechanisms can be divided into single-substrate and multiple-substrate mechanisms. Kinetic studies on enzymes that only bind one substrate, such as triosephosphate isomerase, aim to measure the affinity with which the enzyme binds this substrate and the turnover rate. Some other examples of enzymes are phosphofructokinase and hexokinase, both of which are important for cellular respiration (glycolysis). (W)

Dihydrofolate reductase from E. coli with its two substrates dihydrofolate (right) and NADPH (left), bound in the active site. The protein is shown as a ribbon diagram, with alpha helices in red, beta sheathes in yellow and loops in blue. Generated from 7DFR.

As larger amounts of substrate are added to a reaction, the available enzyme binding sites become filled to the limit of Vmax. Beyond this limit the enzyme is saturated with substrate and the reaction rate ceases to increase..

An epigenome consists of a record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an organism's offspring via transgenerational stranded epigenetic inheritance. Changes to the epigenome can result in changes to the structure of chromatin and changes to the function of the genome.

The epigenome is involved in regulating gene expression, development, tissue differentiation, and suppression of transposable elements. Unlike the underlying genome, which remains largely static within an individual, the epigenome can be dynamically altered by environmental conditions. (W)

Epigenome.

Epigenome editing or Epigenome engineering is a type of genetic engineering in which the epigenome is modified at specific sites using engineered molecules targeted to those sites (as opposed to whole-genome modifications). Whereas gene editing involves changing the actual DNA sequence itself, epigenetic editing involves modifying and presenting DNA sequences to proteins and other DNA binding factors that influence DNA function. By "editing” epigenomic features in this manner, researchers can determine the exact biological role of an epigenetic modification at the site in question.

The engineered proteins used for epigenome editing are composed of a DNA binding domain that target specific sequences and an effector domain that modifies epigenomic features. Currently, three major groups of DNA binding proteins have been predominantly used for epigenome editing: Zinc finger proteins, Transcription Activator-Like Effectors (TALEs) and nuclease deficient Cas9 fusions (CRISPR). (W)

A visual overview of how TALE proteins are used for epigenome editing.

The apical membranes of many tight epithelia contain sodium channels that are characterized primarily by their high affinity for the diuretic blocker amiloride. These channels mediate the first step of active sodium reabsorption essential for the maintenance of body salt and water homeostasis. In vertebrates, the channels control reabsorption of sodium in kidney, colon, lung and sweat glands; they also play a role in taste perception.

The epithelial sodium channels are structurally and probably evolutionary related to P2X purinoreceptors, pain receptors that activate when they detect ATP. (W)

ENaC with subunits colored (alpha blue, beta red, gamma magenta). Produced using PyMol from PDB entry 6BQN.

A diagram demonstrating the arrangement of the subunits.

In chemistry, an ester is a chemical compound derived from an acid (organic or inorganic) in which at least one –OH (hydroxyl) group is replaced by an –O–alkyl (alkoxy) group. Usually, esters are derived from a carboxylic acid and an alcohol. Glycerides, which are fatty acid esters of glycerol, are important esters in biology, being one of the main classes of lipids, and making up the bulk of animal fats and vegetable oils. Esters with low molecular weight are commonly used as fragrances and found in essential oils and pheromones. Phosphoesters form the backbone of DNA molecules. Nitrate esters, such as nitroglycerin, are known for their explosive properties, while polyesters are important plastics, with monomers linked by ester moieties. Esters usually have a sweet smell and are considered high-quality solvents for a broad array of plastics, plasticizers, resins, and lacquers. They are also one of the largest classes of synthetic lubricants on the commercial market. (W)

A carboxylate ester. R′ denotes any alkyl or aryl group.

Eukaryotic DNA replication is a conserved mechanism that restricts DNA replication to once per cell cycle. Eukaryotic DNA replication of chromosomal DNA is central for the duplication of a cell and is necessary for the maintenance of the eukaryotic genome.

DNA replication is the action of DNA polymerases synthesizing a DNA strand complementary to the original template strand. To synthesize DNA, the double-stranded DNA is unwound by DNA helicases ahead of polymerases, forming a replication fork containing two single-stranded templates. Replication processes permit the copying of a single DNA double helix into two DNA helices, which are divided into the daughter cells at mitosis. The major enzymatic functions carried out at the replication fork are well conserved from prokaryotes to eukaryotes, but the replication machinery in eukaryotic DNA replication is a much larger complex, coordinating many proteins at the site of replication, forming the replisome.

The replisome is responsible for copying the entirety of genomic DNA in each proliferative cell. This process allows for the high-fidelity passage of hereditary/genetic information from parental cell to daughter cell and is thus essential to all organisms. Much of the cell cycle is built around ensuring that DNA replication occurs without errors.

In G1 phase of the cell cycle, many of the DNA replication regulatory processes are initiated. In eukaryotes, the vast majority of DNA synthesis occurs during S phase of the cell cycle, and the entire genome must be unwound and duplicated to form two daughter copies. During G2, any damaged DNA or replication errors are corrected. Finally, one copy of the genomes is segregated to each daughter cell at mitosis or M phase. These daughter copies each contain one strand from the parental duplex DNA and one nascent antiparallel strand.

This mechanism is conserved from prokaryotes to eukaryotes and is known as semiconservative DNA replication. The process of semiconservative replication for the site of DNA replication is a fork-like DNA structure, the replication fork, where the DNA helix is open, or unwound, exposing unpaired DNA nucleotides for recognition and base pairing for the incorporation of free nucleotides into double-stranded DNA. (W)

Eukaryotic DNA replication.

Exocytosis is a form of active transport and bulk transport in which a cell transports molecules (e.g., neurotransmitters and proteins) out of the cell (exo- + cytosis) by secreting them through an energy-dependent process. Exocytosis and its counterpart, endocytosis, are used by all cells because most chemical substances important to them are large polar molecules that cannot pass through the hydrophobic portion of the cell membrane by passive means. Exocytosis is the process by which a large amount of molecules are released; thus it is a form of bulk transport.

In exocytosis, membrane-bound secretory vesicles are carried to the cell membrane, and their contents (i.e., water-soluble molecules) are secreted into the extracellular environment. This secretion is possible because the vesicle transiently fuses with the plasma membrane. In the context of neurotransmission, neurotransmitters are typically released from synaptic vesicles into the synaptic cleft via exocytosis; however, neurotransmitters can also be released via reverse transport through membrane transport proteins.

Exocytosis is also a mechanism by which cells are able to insert membrane proteins (such as ion channels and cell surface receptors), lipids, and other components into the cell membrane. Vesicles containing these membrane components fully fuse with and become part of the outer cell membrane. (W)

Neuron A (transmitting) to neuron B (receiving) 1. Mitochondrion 2 Synaptic vesicle with neurotransmitters 3. Autoreceptor 4. Synapse with neurotransmitter released (serotonin) 5. Postsynaptic receptors activated by neurotransmitter (induction of a postsynaptic potential) 6. Calcium channel 7. Exocytosis of a vesicle 8. Recaptured neurotransmitter

Phagocytosis versus exocytosis. Phagocytosis and exocytosis can play an important role in nonspecific immune response. In phagocytosis, involving the destruction of pathogens, the pathogens are surrounded and then engulfed through endocytosis. The vacuole then forms and closes around the pathogens. In exocytosis, the lysosome and vacuole fuse together which allows enzymes to destroy pathogens. Debris from the pathogens is then released from the cell..

Exome sequencing, also known as whole exome sequencing (WES), is a genomic technique for sequencing all of the protein-coding regions of genes in a genome (known as the exome). It consists of two steps: the first step is to select only the subset of DNA that encodes proteins. These regions are known as exons – humans have about 180,000 exons, constituting about 1% of the human genome, or approximately 30 million base pairs. The second step is to sequence the exonic DNA using any high-throughput DNA sequencing technology.

The goal of this approach is to identify genetic variants that alter protein sequences, and to do this at a much lower cost than whole-genome sequencing. Since these variants can be responsible for both Mendelian and common polygenic diseases, such as Alzheimer's disease, whole exome sequencing has been applied both in academic research and as a clinical diagnostic. (W)

Exome sequencing workflow: part 1. Exome sequencing workflow: Part 1. Double-stranded genomic DNA is fragmented by sonication. Linkers are then attached to the DNA fragments, which are then hybridized to a capture microarray designed to target only the exons.

Exome sequencing workflow: part 2. Exome sequencing workflow: Part 2. Target exons are enriched, eluted and then amplified by ligation-mediated PCR. Amplified target DNA is then ready for high-throughput sequencing.

In-solution capture.

exon

An exon is any part of a gene that will encode a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term exon refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts. In RNA splicing, introns are removed and exons are covalently joined to one another as part of generating the mature messenger RNA. Just as the entire set of genes for a species constitutes the genome, the entire set of exons constitutes the exome. (W)

Introns are removed and exons joined together in the process of RNA splicing.

Exons in a messenger RNA precursor (pre-mRNA). Exons can include both sequences that code for amino acids (red) and untranslated sequences (grey). Introns — those parts of the pre-mRNA that are not in the mRNA — (blue) are removed, and the exons are joined together (spliced) to form the final functional mRNA. The 5′ and 3′ ends of the mRNA are marked to differentiate the two untranslated regions (grey).

Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3′ or the 5′ end occurs. Its close relative is the endonuclease, which cleaves phosphodiester bonds in the middle (endo) of a polynucleotide chain. Eukaryotes and prokaryotes have three types of exonucleases involved in the normal turnover of mRNA: 5′ to 3′ exonuclease (Xrn1), which is a dependent decapping protein; 3′ to 5′ exonuclease, an independent protein; and poly(A)-specific 3′ to 5′ exonuclease.

In both archaea and eukaryotes, one of the main routes of RNA degradation is performed by the multi-protein exosome complex, which consists largely of 3′ to 5′ exoribonucleases. (W)

3′ to 5′ Exonuclease associated with Pol I.

An exotoxin is a toxin secreted by bacteria. An exotoxin can cause damage to the host by destroying cells or disrupting normal cellular metabolism. They are highly potent and can cause major damage to the host. Exotoxins may be secreted, or, similar to endotoxins, may be released during lysis of the cell. Gram negative pathogens may secrete outer membrane vesicles containing lipopolysaccharide endotoxin and some virulence proteins in the bounding membrane along with some other toxins as intra-vesicular contents, thus adding a previously unforeseen dimension to the well-known eukaryote process of membrane vesicle trafficking, which is quite active at the host-pathogen interface.

They may exert their effect locally or produce systemic effects. Well-known exotoxins include: botulinum toxin produced by Clostridium botulinum; Corynebacterium diphtheriae toxin, produced during life-threatening symptoms of diphtheria; tetanospasmin produced by Clostridium tetani. The toxic properties of most exotoxins can be inactivated by heat or chemical treatment to produce a toxoid. These retain their antigenic specificity and can be used to produce antitoxins and, in the case of diphtheria and tetanus toxoids, are used as vaccines.

Exotoxins are susceptible to antibodies produced by the immune system, but many exotoxins are so toxic that they may be fatal to the host before the immune system has a chance to mount defenses against them. For this reason antitoxin, anti-serum containing antibodies, is injected to provide passive immunity. (W)

This figure shows that exotoxins are secreted by bacterial cells, Clostridium botulinum for example, and are toxic to somatic cells. Somatic cells have antibodies on the cell surface to target exotoxins and bind to them, preventing the invasion of somatic cells. The binding of the exotoxin and antibody forms an antigen-antibody interaction and the exotoxins are targeted for destruction by the immune system. If this interaction does not happen, the exotoxins bind to the exotoxin receptors that are on the cell surface and causes death of the host cell by inhibiting protein synthesis. This figure also shows that the application of heat or chemicals to exotoxins can result in the deactivation of exotoxins. The deactivated exotoxins are called toxoids and they are not harmful to somatic cells.

The exosome complex (or PM/Scl complex, often just called the exosome) is a multi-protein intracellular complex capable of degrading various types of RNA (ribonucleic acid) molecules. Exosome complexes are found in both eukaryotic cells and archaea, while in bacteria a simpler complex called the degradosome carries out similar functions.

The core of the exosome contains a six-membered ring structure to which other proteins are attached. In eukaryotic cells, the exosome complex is present in the cytoplasm, nucleus, and especially the nucleolus, although different proteins interact with the exosome complex in these compartments regulating the RNA degradation activity of the complex to substrates specific to these cell compartments. Substrates of the exosome include messenger RNA, ribosomal RNA, and many species of small RNAs. The exosome has an exoribonucleolytic function, meaning it degrades RNA starting at one end (the 3′ end in this case), and in eukaryotes also an endoribonucleolytic function, meaning it cleaves RNA at sites within the molecule.

Several proteins in the exosome are the target of autoantibodies in patients with specific autoimmune diseases (especially the PM/Scl overlap syndrome) and some antimetabolic chemotherapies for cancer function by blocking the activity of the exosome. In addition, mutations in exosome component 3 cause pontocerebellar hypoplasia and spinal motor neuron disease. (W)

"Ribbon view" of the human exosome complex. PDB 2NN6 See the legend below. The channel through which RNA passes during degradation is visible at the center of the protein complex.

Subunits and organisation of the archaeal (left) and eukaryotic (right) exosome complexes. Different proteins are numbered, showing that the archaeal exosome contains 4 different proteins, but the eukaryotic exosome contains nine different proteins. Schematic drawing of the Exosome complex, a multiprotein complex involved in RNA degradation. The drawing on the left is a schematic of the Archaebacterial exosome, the drawing on the right is of the eukaryotic exosome complex.

Schematic view of the archaeal (left) and eukaryotic (right) exosome complexes with the most common associated proteins. In color and marked with a star are the subunits of each complex that have catalytic activity. Archaeal (left), and eukaryotic (right) exosome complexes, with the catalytically active subunites marked in color and with a star.

An expression vector, otherwise known as an expression construct, is usually a plasmid or virus designed for gene expression in cells. The vector is used to introduce a specific gene into a target cell, and can commandeer the cell's mechanism for protein synthesis to produce the protein encoded by the gene. Expression vectors are the basic tools in biotechnology for the production of proteins.

The vector is engineered to contain regulatory sequences that act as enhancer and promoter regions and lead to efficient transcription of the gene carried on the expression vector. The goal of a well-designed expression vector is the efficient production of protein, and this may be achieved by the production of significant amount of stable messenger RNA, which can then be translated into protein. The expression of a protein may be tightly controlled, and the protein is only produced in significant quantity when necessary through the use of an inducer, in some systems however the protein may be expressed constitutively. Escherichia coli is commonly used as the host for protein production, but other cell types may also be used. An example of the use of expression vector is the production of insulin, which is used for medical treatments of diabetes. (W)

An example of a bacterial expression vector is the pGEX-3x plasmid.

In biology, the extracellular matrix (ECM) is a three-dimensional network of extracellular macromolecules, such as collagen, enzymes, and glycoproteins, that provide structural and biochemical support to surrounding cells. Because multicellularity evolved independently in different multicellular lineages, the composition of ECM varies between multicellular structures; however, cell adhesion, cell-to-cell communication and differentiation are common functions of the ECM.

The animal extracellular matrix includes the interstitial matrix and the basement membrane. Interstitial matrix is present between various animal cells (i.e., in the intercellular spaces). Gels of polysaccharides and fibrous proteins fill the interstitial space and act as a compression buffer against the stress placed on the ECM. Basement membranes are sheet-like depositions of ECM on which various epithelial cells rest. Each type of connective tissue in animals has a type of ECM: collagen fibers and bone mineral comprise the ECM of bone tissue; reticular fibers and ground substance comprise the ECM of loose connective tissue; and blood plasma is the ECM of blood.

The plant ECM includes cell wall components, like cellulose, in addition to more complex signaling molecules. Some single-celled organisms adopt multicellular biofilms in which the cells are embedded in an ECM composed primarily of extracellular polymeric substances (EPS). (W)

Schema de la Matrice Extracellulaire.

1: Microfilaments 2: Phospholipid Bilayer 3: Integrin 4: Proteoglycan 5: Fibronectin 6: Collagen 7: Elastin. The extracellular matrix of a cell, showing how the collagen is connected to the cytoskeleton.

Fats are one of the three main macronutrients, along with carbohydrates and proteins. Fat molecules consist of primarily carbon and hydrogen atoms and are therefore hydrophobic and are soluble in organic solvents and insoluble in water. Examples include cholesterol, phospholipids, and triglycerides.

The terms lipid, oil, and fat are often confused. Lipid is the general term, though a lipid is not necessarily a triglyceride. Oil normally refers to a lipid with short or unsaturated fatty acid chains that is liquid at room temperature, while fat (in the strict sense) specifically refers to lipids that are solids at room temperature – however, fat (in the broad sense) may be used in food science as a synonym for lipid. (W)

A fat, or triglyceride, molecule. Note the three fatty acid chains attached to the central glycerol portion of the molecule.

Ball-and-stick model of the elaidic acid molecule, the trans isomer of oleic acid and the major trans fat found in hydrogenated vegetable oils. Elaidic acid is the principal trans unsaturated fatty acid often found in partially hydrogenated vegetable oils.

Oleic-acid-3D-ball-&-stick. Oleic acid is a cis unsaturated fatty acid making up 55–80% of olive oil.

Ball-and-stick model of the stearic acid molecule (also known as octadecanoic acid), a saturated fatty acid with 18 carbon atoms. Stearic acid is a saturated fatty acid found in animal fats and is the intended product in full hydrogenation. Stearic acid is neither cis nor trans because it has no carbon-carbon double bonds.

Fatty acid metabolism consists of various metabolic processes involving or closely related to fatty acids, a family of molecules classified within the lipid macronutrient category. These processes can mainly be divided into catabolic processes that generate energy, and anabolic processes that create biologically important molecules such as triglycerides, phospholipids, second messengers, local hormones and ketone bodies.

One role of fatty acids in animal metabolism is energy production, captured in the form of adenosine triphosphate (ATP). When compared to other macronutrient classes (carbohydrates and protein), fatty acids yield the most ATP on an energy per gram basis, when they are completely oxidized to CO₂ and water by beta oxidation and the citric acid cycle. Fatty acids (mainly in the form of triglycerides) are therefore the foremost storage form of fuel in most animals, and to a lesser extent in plants.

In addition, fatty acids are important components of the phospholipids that form the phospholipid bilayers out of which all the membranes of the cell are constructed (the plasma membrane and other membranes that enclose all the organelles within the cells, such as the nucleus, the mitochondria, endoplasmic reticulum, and the Golgi apparatus).

Fatty acids can also be cleaved, or partially cleaved, from their chemical attachments in the cell membrane to form second messengers within the cell, and local hormones in the immediate vicinity of the cell. The prostaglandins made from arachidonic acid stored in the cell membrane, are probably the most well known group of these local hormones. (W)

A diagrammatic illustration of the process of lipolysis (in a fat cell) induced by high epinephrine and low insulin levels in the blood. Epinephrine binds to a beta-adrenergic receptor in the cell membrane of the adipocyte, which causes cAMP to be generated inside the cell. The cAMP activates a protein kinase, which phosphorylates and thus, in turn, activates a hormone-sensitive lipase in the fat cell. This lipase cleaves free fatty acids from their attachment to glycerol in the fat stored in the fat droplet of the adipocyte. The free fatty acids and glycerol are then released into the blood. However more recent studies have shown that adipose triglyceride lipase has to first convert triacylglycerides to diacylglycerides, and that hormone-sensitive lipase converts the diacylglycerides to monoglycerides and free fatty acids. Monoglycerides are hydrolyzed by monoglyceride lipase. The activity of hormone sensitive lipase is regulated by the circulation hormones insulin, glucagon, norepinephrine, and epinephrine, as shown in the diagram. (W)

fatty acid synthesis

Fatty acid synthesis is the creation of fatty acids from acetyl-CoA and NADPH through the action of enzymes called fatty acid synthases. This process takes place in the cytoplasm of the cell. Most of the acetyl-CoA which is converted into fatty acids is derived from carbohydrates via the glycolytic pathway. The glycolytic pathway also provides the glycerol with which three fatty acids can combine (by means of ester bonds) to form triglycerides (also known as "triacylglycerols" – to distinguish them from fatty "acids" – or simply as "fat"), the final product of the lipogenic process. When only two fatty acids combine with glycerol and the third alcohol group is phosphorylated with a group such as phosphatidylcholine, a phospholipid is formed. Phospholipids form the bulk of the lipid bilayers that make up cell membranes and surround the organelles within the cells (e.g. the cell nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus etc.) (W)

Synthesis of saturated fatty acids via fatty acid synthase II in E. coli.

The 5′ untranslated region (5′ UTR) (also known as a leader sequence or leader RNA) is the region of an mRNA that is directly upstream from the initiation codon. This region is important for the regulation of translation of a transcript by differing mechanisms in viruses, prokaryotes and eukaryotes. While called untranslated, the 5′ UTR or a portion of it is sometimes translated into a protein product. This product can then regulate the translation of the main coding sequence of the mRNA. In many organisms, however, the 5′ UTR is completely untranslated, instead forming complex secondary structure to regulate translation.

The 5′ UTR has been found to interact with proteins relating to metabolism, and proteins translate sequences within the 5′ UTR. In addition, this region has been involved in transcription regulation, such as the sex-lethal gene in Drosophila. Regulatory elements within 5′ UTRs have also been linked to mRNA export. (W)

This image depicts the general structure of a mRNA molecule.

The binding of an IRP (iron regulatory protein) to and IRE (iron response element), which are hairpin loops, regulate translation.

The process of translation in bacteria.

The process of translation in eukaryotes (By Richard Wheeler (Zephyris) 2005; The process of initiation of translation in eukaryotes).

The various forms of mRNA and how each affects translational regulation.

Interactions between proteins bound to the 3′ UTR and 5′ UTR causing a circularization that regulates translation.

An example IRES in the 5′ UTR of the Poliovirus genome. Genomic structure of poliovirus type 1 (Mahoney) [PV1(M)] The PV genome consists of a single-stranded, positive-sense polarity RNA molecule, which encodes a single polyprotein. The 5' non-translated region (NTR) harbors two functional domains, the cloverleaf and the internal ribosome entry site (IRES), and is covalently linked to the viral protein VPg. The 3'NTR is poly-adenylated. (W)

flavin adenine dinucleotide (FAD)

In biochemistry, flavin adenine dinucleotide (FAD) is a redox-active coenzyme associated with various proteins, which is involved with several enzymatic reactions in metabolism. A flavoprotein is a protein that contains a flavin group, which may be in the form of FAD or flavin mononucleotide (FMN). Many flavoproteins are known: components of the succinate dehydrogenase complex, α-ketoglutarate dehydrogenase, and a component of the pyruvate dehydrogenase complex.

FAD can exist in four redox states, which are the flavin-N(5)-oxide, quinone, semiquinone, and hydroquinone. FAD is converted between these states by accepting or donating electrons. FAD, in its fully oxidized form, or quinone form, accepts two electrons and two protons to become FADH₂ (hydroquinone form). The semiquinone (FADH·) can be formed by either reduction of FAD or oxidation of FADH₂ by accepting or donating one electron and one proton, respectively. Some proteins, however, generate and maintain a superoxidized form of the flavin cofactor, the flavin-N(5)-oxide. (W)

Stereo, Kekulé, skeletal formula of FAD.

Spacefill model of FAD.

folding (chemistry)

In chemistry, folding is the process by which a molecule assumes its shape or conformation. The process can also be described as intramolecular self-assembly, a type of molecular self-assembly, where the molecule is directed to form a specific shape through noncovalent interactions, such as hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi-pi interactions, and/or electrostatic effects.

The most active area of interest in the folding of molecules is the process of protein folding, which is the shape that is assumed by a specific sequence of amino acids in a protein. The shape of the folded protein can be used to understand its function and design drugs to influence the processes that it is involved in.

There is also a great deal of interest in the construction of artificial folding molecules or foldamers. They are studied as models of biological molecules and potential application to the development of new functional materials. (W)

a picture generated from crystal structure data reported by Jean-Louis Schmitt, Adrian-Mihail Stadler, Nathalie Kyritsakas, Jean-Marie Lehn in Helvetica Chimica Acta, 1598-1624, 2003. It shows a helical foldamer. (W)

In population genetics, the founder effect is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. It was first fully outlined by Ernst Mayr in 1942, using existing theoretical work by those such as Sewall Wright. As a result of the loss of genetic variation, the new population may be distinctively different, both genotypically and phenotypically, from the parent population from which it is derived. In extreme cases, the founder effect is thought to lead to the speciation and subsequent evolution of new species.

In the figure shown, the original population has nearly equal numbers of blue and red individuals. The three smaller founder populations show that one or the other color may predominate (founder effect), due to random sampling of the original population. A population bottleneck may also cause a founder effect, though it is not strictly a new population.

The founder effect occurs when a small group of migrants that is not genetically representative of the population from which they came establish in a new area. In addition to founder effects, the new population is often a very small population, so shows increased sensitivity to genetic drift, an increase in inbreeding, and relatively low genetic variation. (W)

Founder effect: The original population (left) could give rise to different founder populations (right).

G protein

G proteins, also known as guanine nucleotide-binding proteins, are a family of proteins that act as molecular switches inside cells, and are involved in transmitting signals from a variety of stimuli outside a cell to its interior. Their activity is regulated by factors that control their ability to bind to and hydrolyze guanosine triphosphate (GTP) to guanosine diphosphate (GDP). When they are bound to GTP, they are 'on', and, when they are bound to GDP, they are 'off'. G proteins belong to the larger group of enzymes called GTPases. (W)

Phosducin- transducin beta-gamma complex. Beta and gamma subunits of G-protein are shown by blue and red, respectively.

Activation cycle of G-proteins (purple) by a G-protein-coupled receptor (GPCR, light blue) receiving a ligand (red). Ligand binding to GPCRs (2) induces a conformation change that facilitates the exchange of GDP for GTP on the α subunit of the heterotrimeric complex (3-4). Both GTP-bound Gα in the active form and the released Gβγ dimer can then go on to stimulate a number of downstream effectors (5). When the GTP on Gα is hydrolyzed to GDP (6) the original receptor is restored (1).

Galactolipids are a type of glycolipid whose sugar group is galactose. They differ from glycosphingolipids in that they do not have nitrogen in their composition.

They are the main part of plant membrane lipids where they substitute phospholipids to conserve phosphate for other essential processes. These chloroplast membranes contain a high quantity of monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG).

General chemical structure of a monogalactosyl diacylglycerol (MGDG), a prevalent type of galactolipid. R1 and R2 are fatty chains..

Gap junctions are a specialized intercellular connection between a multitude of animal cell-types. They directly connect the cytoplasm of two cells, which allows various molecules, ions and electrical impulses to directly pass through a regulated gate between cells.

One gap junction channel is composed of two connexons (or hemichannels), which connect across the intercellular space. Gap junctions are analogous to the plasmodesmata that join plant cells.

Gap junctions occur in virtually all tissues of the body, with the exception of adult fully developed skeletal muscle and mobile cell types such as sperm or erythrocytes. Gap junctions, however, are not found in simpler organisms such as sponges and slime molds.

A gap junction may also be called a nexus or macula communicans. While an ephapse has some similarities to a gap junction, by modern definition the two are different. (W)

The diagram shows a cell union called Gap junction.

Light microscope images do not allow us to see connexons themselves but do let us see the fluorescing dye injected into one cell moving into neighboring cells when gap junctions are known to be present. A–D: Dye diffusion patterns after PI was injected into a single cell in various locations in the cochlea. The type of the cells that was injected is given at lower right corner of each panel. E–F: Diffusion patterns of four different fluorescent dyes after injecting into a single Claudius cell. Name of the dye is given in the lower right corner of each panel. Panels B), C), D), F) & H) were photographed with unfixed fresh samples. Panels A), E), G) were results obtained from fixed samples after the experiments were done. They were labeled with fluorescent phalloidin (red in E, green in A&G) to outline the cell border. Scale bar on the top left of each panel represents approximately 100 µm.

Annular gap junction cross section in TEM thin section. Gap junctions are usually linear rather than annular in TEM thin sections. It is thought that annular gap junctions result from engulfment by one of the two cells of the membrane plaque to form a vesicle within the cell. This example shows three layers to the junction structure. The membrane from each cell is the dark line with the whiter narrow gap between the two darkly stained membranes. In such electron micrographs there may appear to be up to 7 layers. Two lipid mono-layers in each membrane can stain as 3 layers plus one layer from the gap between them, similar to two stacked bread sandwiches with space between them.

Gel electrophoresis is a method for separation and analysis of macromolecules (DNA, RNA and proteins)and their fragments, based on their size and charge. It is used in clinical chemistry to separate proteins by charge or size (IEF agarose, essentially size independent) and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge.

Nucleic acid molecules are separated by applying an electric field to move the negatively charged molecules through a matrix of agarose or other substances. Shorter molecules move faster and migrate farther than longer ones because shorter molecules migrate more easily through the pores of the gel. This phenomenon is called sieving. Proteins are separated by the charge in agarose because the pores of the gel are too small to sieve proteins. Gel electrophoresis can also be used for the separation of nanoparticles. (W)

This liquid-filled box and attached power supply are used for gel electrophoresis.

Overview of Gel Electrophoresis.

The image above shows how small DNA fragments will migrate through agarose gel farther than large DNA fragments during electrophoresis. The graph to the right shows the nonlinear relationship between the size of the DNA fragment and the distance migrated. The image above shows a typical result of DNA electrophoresis in regards to the size of DNA fragments and the distance migrated through the agarose gel. On the left, there is a marker sample that can be used as a control and as a reference for the length of the DNA (in base pairs). To the right of the marker, there are three examples of different DNA samples: Sample A, Sample B and Sample C. The image displays how smaller DNA fragments move farther throughout the agarose gel than the larger fragments of DNA. These distances can be used to identify or match specific DNA sequences. The graph to the right of the image shows the nonlinear, relationship between the size of the DNA fragments and the distance migrated. It is a negative curve because as DNA fragments get larger, they migrate less distance through the gel. (W)

Gel Electrophoresis is a process where an electric current is applied to DNA samples creating fragments that can be used for comparison between DNA samples. 1) DNA is extracted. 2) Isolation and amplification of DNA. 3) DNA added to the gel wells. 4) Electric current applied to the gel. 5) DNA bands are separated by size. 6) DNA bands are stained. This is a diagram that illustrates the process of Gel electrophoresis. Gel electrophoresis is used for DNA fingerprinting, and is very useful in crime investigation since every individual has different DNA patterns. DNA can be extracted from any sample of body fluid(i.e. blood, semen, or saliva). DNA is mixed with restriction enzyme and amplified with PCR. The mixture of DNA fragment plus restriction enzyme is added into the wells of the agarose gel, which leads to a physical change instead of a chemical one. An electric current is applied to the gel from a power source. Negatively charged DNA moves toward the positive side. Larger fragments move slower and are located near the top whereas smaller fragments move faster and are near the bottom. Bands are stained but different shades indicate the amount of DNA each band contains. http://www.yourgenome.org/facts/what-is-gel-electrophoresis. (W)

In molecular biology, gel extraction or gel isolation is a technique used to isolate a desired fragment of intact DNA from an agarose gel following agarose gel electrophoresis. After extraction, fragments of interest can be mixed, precipitated, and enzymatically ligated together in several simple steps. This process, usually performed on plasmids, is the basis for rudimentary genetic engineering.

After DNA samples are run on an agarose gel, extraction involves four basic steps: identifying the fragments of interest, isolating the corresponding bands, isolating the DNA from those bands, and removing the accompanying salts and stain.

To begin, UV light is shone on the gel in order to illuminate all the ethidium bromide-stained DNA. Care must be taken to avoid exposing the DNA to mutagenic radiation for longer than absolutely necessary. The desired band is identified and physically removed with a cover slip or razor blade. The removed slice of gel should contain the desired DNA inside. An alternative method, utilizing SYBR Safe DNA gel stain and blue-light illumination, avoids the DNA damage associated with ethidium bromide and UV light.

Several strategies for isolating and cleaning the DNA fragment of interest exist. (W)

In biology, a gene is a sequence of nucleotides in DNA or RNA that encodes the synthesis of a gene product, either RNA or protein.

During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic trait. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes (many different genes) as well as gene–environment interactions. Some genetic traits are instantly visible, such as eye color or the number of limbs, and some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that constitute life. (W)

A gene is a region of DNA that encodes function. A chromosome consists of a long strand of DNA containing many genes. A human chromosome can have up to 500 million base pairs of DNA with thousands of genes.

Fluorescent microscopy image of a human female karyotype, showing 23 pairs of chromosomes . The DNA is stained red, with regions rich in housekeeping genes further stained in green. The largest chromosomes are around 10 times the size of the smallest.

gene cloning → molecular cloning

Gene delivery is the process of introducing foreign genetic material, such as DNA or RNA, into host cells. Genetic material must reach the genome of the host cell to induce gene expression. Successful gene delivery requires the foreign genetic material to remain stable within the host cell and can either integrate into the genome or replicate independently of it. This requires foreign DNA to be synthesized as part of a vector, which is designed to enter the desired host cell and deliver the transgene to that cell's genome. Vectors utilized as the method for gene delivery can be divided into two categories, recombinant viruses and synthetic vectors (viral and non-viral).

In complex multicellular eukaryotes (more specifically Weissmanists), if the transgene is incorporated into the host's germline cells, the resulting host cell can pass the transgene to its progeny. If the transgene is incorporated into somatic cells, the transgene will stay with the somatic cell line, and thus its host organism.

Gene delivery is a necessary step in gene therapy for the introduction or silencing of a gene to promote a therapeutic outcome in patients and also has applications in the genetic modification of crops. There are many different methods of gene delivery for various types of cells and tissues. (W)

Bacterial transformation involves moving a gene from one bacteria to another. It is integrated into the recipients plasmid. and can then be expressed by the new host. Bacterial Transformation In this diagram, a gene from bacterial cell 1 is moved from bacterial cell 1 to bacterial cell 2. This process of bacterial cell 2 taking up new genetic material is called transformation. Step I: The DNA of a bacterial cell is located in the cytoplasm (1), but also in the plasmid, an independent, circular loop of DNA. The gene to be transferred (4) is located on the plasmid of cell 1 (3), but not on the plasmid of bacterial cell 2 (2). In order to remove the gene from the plasmid of bacterial cell 1, a restriction enzyme (5) is used. The restriction enzyme binds to a specific site on the DNA and “cuts” it, releasing the satisfactory gene. Genes are naturally removed and released into the environment usually after a cell dies and disintegrates. Step II: Bacterial cell 2 takes up the gene. This integration of genetic material from the environment is an evolutionary tool and is common in bacterial cells. Step III: The enzyme DNA ligase (6) adds the gene to the plasmid of bacterial cell 2 by forming chemical bonds between the two segments which join them together. Step IV: The plasmid of bacterial cell 2 now contains the gene from bacterial cell 1 (7). The gene has been transferred from one bacterial cell to another, and transformation is complete..

Electroporators can be used to make the cell membrane permeable to DNA. Electroporator with square wave and exponential decay waveforms for in vitro, in vivo, adherent cell and 96 well electroporation applications. Manufactured by BTX Harvard Apparatus, Holliston MA USA..

Foreign DNA being transduced into the host cell through an adenovirus vector.

A gene drive is a genetic engineering technology that propagates a particular suite of genes throughout a population by altering the probability that a specific allele will be transmitted to offspring from the natural 50% probability. Gene drives can arise through a variety of mechanisms. They have been proposed to provide an effective means of genetically modifying specific populations and entire species.

The technique can employ adding, deleting, disrupting, or modifying genes.

Proposed applications include exterminating insects that carry pathogens (notably mosquitoes that transmit malaria, dengue, and zika pathogens), controlling invasive species or eliminating herbicide or pesticide resistance.

As with any potentially powerful technique, gene drives can be misused in a variety of ways or induce unintended consequences. For example, a gene drive intended to affect only a local population might spread across an entire species. Gene drives used to eradicate populations of invasive species in their non-native habitats may have consequences for the population of the species as a whole, even in its native habitat. Any accidental return of individuals of the species to its original habitats, through natural migration, environmental disruption (storms, floods, etc.), accidental human transportation, or purposeful relocation, could unintentionally drive the species to extinction if the relocated individuals carried harmful gene drives.

Gene drives can be built from many naturally occurring selfish genetic elements that use a variety of molecular mechanisms. These naturally occurring mechanisms induce similar segregation distortion in the wild, arising when alleles evolve molecular mechanisms that give them a transmission chance greater than the normal 50%.

Most gene drives have been developed in insects, and notably mosquitoes, as a way to control insects-borne pathogens. Recent developments however designed gene drives directly in viruses, and notably herpesviruses. These viral gene drives can propagate a modification into the population of viruses, and aim to reduce the infectivity of the virus. (W)

Description of gene-drive in flies.

Molecular mechanism of gene drive.

gene duplication

Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage. (W)

Schematic of a region of a chromosome before and after a duplication event.

Evolutionary fate of duplicate genes.

gene expression

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA. Gene expression is summarized in the central dogma of molecular biology first formulated by Francis Crick in 1958, further developed in his 1970 article, and expanded by the subsequent discoveries of reverse transcription and RNA replication.

The process of gene expression is used by all known life—eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and utilized by viruses—to generate the macromolecular machinery for life.

In genetics, gene expression is the most fundamental level at which the genotype gives rise to the phenotype, i.e. observable trait. The genetic information stored in DNA represents the genotype, whereas the phenotype results from the "interpretation" of that information. Such phenotypes are often expressed by the synthesis of proteins that control the organism's structure and development, or that act as enzymes catalyzing specific metabolic pathways.

All steps in the gene expression process may be modulated (regulated), including the transcription, RNA splicing, translation, and post-translational modification of a protein. Regulation of gene expression gives control over the timing, location, and amount of a given gene product (protein or ncRNA) present in a cell and can have a profound effect on the cellular structure and function. Regulation of gene expression is the basis for cellular differentiation, development, morphogenesis and the versatility and adaptability of any organism. Gene regulation may therefore serve as a substrate for evolutionary change. (W)

The extended central dogma of molecular biology includes all the cellular processes involved in the flow of genetic information.

Simple transcription elongation. The process of transcription is carried out by RNA polymerase (RNAP), which uses DNA (black) as a template and produces RNA (blue).

Illustration of exons and introns in pre-mRNA and the formation of mature mRNA by splicing. The UTRs (in green) are non-coding parts of exons at the ends of the mRNA.

During the translation, tRNA charged with amino acid enters the ribosome and aligns with the correct mRNA triplet. Ribosome then adds amino acid to growing protein chain. Translation: Illustrates how a robosome a mRNA and lots of tRNA molecules work together to produce peptides or proteins.

The lambda repressor transcription factor (green) binds as a dimer to major groove of DNA target (red and blue) and disables initiation of transcription. From PDB: 1LM.

A gene family is a set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions. One such family are the genes for human hemoglobin subunits; the ten genes are in two clusters on different chromosomes, called the α-globin and β-globin loci. These two gene clusters are thought to have arisen as a result of a precursor gene being duplicated approximately 500 million years ago.

Genes are categorized into families based on shared nucleotide or protein sequences. Phylogenetic techniques can be used as a more rigorous test. The positions of exons within the coding sequence can be used to infer common ancestry. Knowing the sequence of the protein encoded by a gene can allow researchers to apply methods that find similarities among protein sequences that provide more information than similarities or differences among DNA sequences.

If the genes of a gene family encode proteins, the term protein family is often used in an analogous manner to gene family.

The expansion or contraction of gene families along a specific lineage can be due to chance, or can be the result of natural selection. To distinguish between these two cases is often difficult in practice. Recent work uses a combination of statistical models and algorithmic techniques to detect gene families that are under the effect of natural selection.

The HUGO Gene Nomenclature Committee (HGNC) creates nomenclature schemes using a "stem" (or "root") symbol for members of a gene family, with a hierarchical numbering system to distinguish the individual members. For example, for the peroxiredoxin family, PRDX is the root symbol, and the family members are PRDX1, PRDX2, PRDX3, PRDX4, PRDX5, and PRDX6. (W)

Gene phylogeny as lines within grey species phylogeny. Top: An ancestral gene duplication produces two paralogs (histone H1.1 and 1.2). A speciation event produces orthologs in the two daughter species (human and chimpanzee). Bottom: in a separate species (E. coli), an gene has a similar function (histone-like nucleoid-structuring protein) but has a separate evolutionary origin and so is an analog..

If a DNA of an organism is genetically modified, the resulting organism is called a "knockdown organism." If the change in gene expression is caused by an oligonucleotide binding to an mRNA or temporarily binding to a gene, this leads to a temporary change in gene expression that does not modify the chromosomal DNA, and the result is referred to as a "transient knockdown"

RNA interference (RNAi) is a means of silencing genes by way of mRNA degradation. Gene knockdown by this method is achieved by introducing small double-stranded interfering RNAs (siRNA) into the cytoplasm.

Another technology made possible by prokaryotic genome manipulation is the use of transcription activator-like effector nucleases (TALENs) to target specific genes TALENs are nucleases that have two important functional components: a DNA binding domain and a DNA cleaving domain.

A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins. These play a central role in morphogenesis, the creation of body structures, which in turn is central to evolutionary developmental biology (evo-devo).

The regulator can be DNA, RNA, protein and complexes of these. The interaction can be direct or indirect (through transcribed RNA or translated protein). In general, each mRNA molecule goes on to make a specific protein (or set of proteins). In some cases this protein will be structural, and will accumulate at the cell membrane or within the cell to give it particular structural properties. In other cases the protein will be an enzyme, i.e., a micro-machine that catalyses a certain reaction, such as the breakdown of a food source or toxin. Some proteins though serve only to activate other genes, and these are the transcription factors that are the main players in regulatory networks or cascades. By binding to the promoter region at the start of other genes they turn them on, initiating the production of another protein, and so on. Some transcription factors are inhibitory. (W)

Structure of a gene regulatory network.

Control process of a gene regulatory network.

Gene silencing is the regulation of gene expression in a cell to prevent the expression of a certain gene. Gene silencing can occur during either transcription or translation and is often used in research. In particular, methods used to silence genes are being increasingly used to produce therapeutics to combat cancer and other diseases, such as infectious diseases and neurodegenerative disorders.

Gene silencing is often considered the same as gene knockdown. When genes are silenced, their expression is reduced. In contrast, when genes are knocked out, they are completely erased from the organism's genome and, thus, have no expression. Gene silencing is considered a gene knockdown mechanism since the methods used to silence genes, such as RNAi, CRISPR, or siRNA, generally reduce the expression of a gene by at least 70% but do not completely eliminate it. Methods using gene silencing are often considered better than gene knockouts since they allow researchers to study essential genes that are required for the animal models to survive and cannot be removed. In addition, they provide a more complete view on the development of diseases since diseases are generally associated with genes that have a reduced expression. (W)

General mechanism utilized by ribozymes to cleave RNA molecules.

Overview of RNA interference. The dicer enzymes produce siRNA from double-stranded RNA and mature miRNA from precursor miRNA. miRNA or siRNA is bound to an argonaute enzyme and an effector complex is formed, either a RISC (RNA-induced silencing complex) or RITS (RNA-induced transcriptional silencing) complex. RITS affects the rate of transcription by histone and DNA methylation, whereas RISC degrades mRNA to prevent it from being translated.

Basic mechanism used by viral vectors to deliver genes to target cells. Example shown is a lentiviral vector.

Gene structure is the organisation of specialised sequence elements within a gene. Genes contain the information necessary for living cells to survive and reproduce. In most organisms, genes are made of DNA, where the particular DNA sequence determines the function of the gene. A gene is transcribed (copied) from DNA into RNA, which can either be non-coding (ncRNA) with a direct function, or an intermediate messenger (mRNA) that is then translated into protein. Each of these steps is controlled by specific sequence elements, or regions, within the gene. Every gene, therefore, requires multiple sequence elements to be functional. This includes the sequence that actually encodes the functional protein or ncRNA, as well as multiple regulatory sequence regions. These regions may be as short as a few base pairs, up to many thousands of base pairs long.

Much of gene structure is broadly similar between eukaryotes and prokaryotes. These common elements largely result from the shared ancestry of cellular life in organisms over 2 billion years ago. Key differences in gene structure between eukaryotes and prokaryotes reflect their divergent transcription and translation machinery. Understanding gene structure is the foundation of understanding gene annotation, expression, and function. (W)

The structure of a eukaryotic protein-coding gene. Regulatory sequence controls when and where expression occurs for the protein coding region (red). Promoter and enhancer regions (yellow) regulate the transcription of the gene into a pre-mRNA which is modified to add a 5' cap and poly-A tail (grey) and remove introns. The mRNA 5' and 3' untranslated regions (blue) regulate translation into the final protein product..

The structure of a eukaryotic protein-coding gene. Regulatory sequence controls when and where expression occurs for the protein coding region (red). Promoter and enhancer regions (yellow) regulate the transcription of the gene into a pre-mRNA which is modified to add a 5' cap and poly-A tail (grey) and remove introns. The mRNA 5' and 3' untranslated regions (blue) regulate translation into the final protein product.

genetic code

The genetic code is the set of rules used by living cells to translate information encoded within genetic material (DNA or mRNA sequences of nucleotide triplets, or codons) into proteins. Translation is accomplished by the ribosome, which links amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.

The code defines how codons specify which amino acid will be added next during protein synthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of genes are encoded with a single scheme (see the RNA codon table). That scheme is often referred to as the canonical or standard genetic code, or simply the genetic code, though variant codes (such as in human mitochondria) exist.

While the "genetic code" is what determines a protein's amino acid sequence, other genomic regions determine when and where these proteins are produced according to various "gene regulatory codes". (W)

A series of codons in part of a messenger RNA (mRNA) molecule. Each codon consists of three nucleotides, usually corresponding to a single amino acid. The nucleotides are abbreviated with the letters A, U, G and C. This is mRNA, which uses U (uracil). DNA uses T (thymine) instead. This mRNA molecule will instruct a ribosome to synthesize a protein according to this code..

Reading frames in the DNA sequence of a region of the human mitochondrial genome coding for the genes MT-ATP8 and MT-ATP6 (in black: positions 8,525 to 8,580 in the sequence accession NC_012920). There are three possible reading frames in the 5' → 3' forward direction, starting on the first (+1), second (+2) and third position (+3). For each codon (square brackets), the amino acid is given by the vertebrate mitochondrial code, either in the +1 frame for MT-ATP8 (in red) or in the +3 frame for MT-ATP6 (in blue). The MT-ATP8 genes terminates with the TAG stop codon (red dot) in the +1 frame. The MT-ATP6 gene starts with the ATG codon (blue circle for the M amino acid) in the +3 frame..

Genetic drift may cause gene variants to disappear completely and thereby reduce genetic variation. It can also cause initially rare alleles to become much more frequent and even fixed.

When there are few copies of an allele, the effect of genetic drift is larger, and when there are many copies the effect is smaller. In the middle of the 20th century, vigorous debates occurred over the relative importance of natural selection versus neutral processes, including genetic drift. Ronald Fisher, who explained natural selection using Mendelian genetics, held the view that genetic drift plays at the most a minor role in evolution, and this remained the dominant view for several decades. In 1968, population geneticist Motoo Kimura rekindled the debate with his neutral theory of molecular evolution, which claims that most instances where a genetic change spreads across a population (although not necessarily changes in phenotypes) are caused by genetic drift acting on neutral mutations (W)

In this simulation each black dot on a marble signifies that it has been chosen for copying (reproduction) one time. There is fixation in the blue "allele" within five generations. Simulation of a common example used describing the effect random sampling has in genetic drift. Dots indicate samples from each generation that are transferred to the next generation. In this population of 20, there is a shift from an allele frequency of 50% for the blue allele to 100% for the blue allele in just 5 generations.

Ten simulations of random genetic drift of a single given allele with an initial frequency distribution 0.5 measured over the course of 50 generations, repeated in three reproductively synchronous populations of different sizes. In these simulations, alleles drift to loss or fixation (frequency of 0.0 or 1.0) only in the smallest population. Effect of population size on genetic drift: Ten simulations each of random change in the frequency distribution of a single hypothetical allele over 50 generations for different sized populations; first population size n=20, second population n=200, and third population n=2000. Based on concept found in Figure 3.1 of "Darwinian Detectives", Norman A. Johnson, 2007, Oxford publishers, p48.

Changes in a population's allele frequency following a population bottleneck: the rapid and radical decline in population size has reduced the population's genetic variation.. Representation of a population bottleneck. Colored balls represent the alleles present in the population. The population numbers 500 initially, but within five years the size of the population has dwindled to 50, and within ten years to just ten. As a consequence of the population bottleneck, there has been a random drift in the allele frequency distribution, and a loss of two of the original five alleles

When very few members of a population migrate to form a separate new population, the founder effect occurs. For a period after the foundation, the small population experiences intensive drift. In the figure this results in fixation of the red allele. Representation of the founder effect: the colored balls represent the two alleles for a specific locus which are present in a hypothetical population; once a random subgroup of a population becomes separated from its ancestral population, the allele frequencies in the two groups' subsequent generations can diverge widely within a relatively short period of time as a consequence of a purely random selection of alleles for reproduction.

Genetic recombination (also known as genetic reshuffling) is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes, genetic recombination during meiosis can lead to a novel set of genetic information that can be passed on from the parents to the offspring. Most recombination is naturally occurring.

During meiosis in eukaryotes, genetic recombination involves the pairing of homologous chromosomes. This may be followed by information transfer between the chromosomes. The information transfer may occur without physical exchange (a section of genetic material is copied from one chromosome to another, without the donating chromosome being changed) (see SDSA pathway in Figure); or by the breaking and rejoining of DNA strands, which forms new molecules of DNA (see DHJ pathway in Figure).

Recombination may also occur during mitosis in eukaryotes where it ordinarily involves the two sister chromosomes formed after chromosomal replication. In this case, new combinations of alleles are not produced since the sister chromosomes are usually identical. In meiosis and mitosis, recombination occurs between similar molecules of DNA (homologous sequences). In meiosis, non-sister homologous chromosomes pair with each other so that recombination characteristically occurs between non-sister homologues. In both meiotic and mitotic cells, recombination between homologous chromosomes is a common mechanism used in DNA repair.

Gene conversion - the process during which homologous sequences are made identical also falls under genetic recombination.

Genetic recombination and recombinational DNA repair also occurs in bacteria and archaea, which use asexual reproduction.

Recombination can be artificially induced in laboratory (in vitro) settings, producing recombinant DNA for purposes including vaccine development.

V(D)J recombination in organisms with an adaptive immune system is a type of site-specific genetic recombination that helps immune cells rapidly diversify to recognize and adapt to new pathogens. (W)

A current model of meiotic recombination, initiated by a double-strand break or gap, followed by pairing with an homologous chromosome and strand invasion to initiate the recombinational repair process. Repair of the gap can lead to crossover (CO) or non-crossover (NCO) of the flanking regions. CO recombination is thought to occur by the Double Holliday Junction (DHJ) model, illustrated on the right, above. NCO recombinants are thought to occur primarily by the Synthesis Dependent Strand Annealing (SDSA) model, illustrated on the left, above. Most recombination events appear to be the SDSA type.

Thomas Hunt Morgan's illustration of crossing over (1916).

In the fields of molecular biology and genetics, a genome is the genetic material of an organism. It consists of DNA (or RNA in RNA viruses) . The genome includes both the genes (the coding regions) and the noncoding DNA, as well as mitochondrial DNA and chloroplast DNA. The study of the genome is called genomics. (W)

📂 A table of some significant or representative genomes A table of some significant or representative genomes (W) Organism type Organism Genome size (base pairs) Approx. no. of genes Note Virus Porcine circovirus type 1 1,759 1.8kb Smallest viruses replicating autonomously in eukaryotic cells. Virus Bacteriophage MS2 3,569 3.5kb First sequenced RNA-genome Virus SV40 5,224 5.2kb   Virus Phage Φ-X174 5,386 5.4kb First sequenced DNA-genome Virus HIV 9,749 9.7kb   Virus Phage λ 48,502 48.5kb Often used as a vector for the cloning of recombinant DNA. Virus Megavirus 1,259,197 1.3Mb Until 2013 the largest known viral genome. Virus Pandoravirus salinus 2,470,000 2.47Mb Largest known viral genome. Bacterium Nasuia deltocephalinicola (strain NAS-ALF) 112,091 112kb Smallest non-viral genome. Bacterium Carsonella ruddii 159,662 160kb Bacterium Buchnera aphidicola 600,000 600kb   Bacterium Wigglesworthia glossinidia 700,000 700Kb Bacterium Haemophilus influenzae 1,830,000 1.8Mb First genome of a living organism sequenced, July 1995 Bacterium Escherichia coli 4,600,000 4.6Mb 4,288   Bacterium Solibacter usitatus (strain Ellin 6076) 9,970,000 10Mb   Bacterium – cyanobacterium Prochlorococcus spp. (1.7 Mb) 1,700,000 1.7Mb 1,884 Smallest known cyanobacterium genome Bacterium – cyanobacterium Nostoc punctiforme 9,000,000 9Mb 7,432 7432 open reading frames Amoeboid Polychaos dubium ("Amoeba" dubia) 670,000,000,000 670Gb Largest known genome. (Disputed) Eukaryotic organelle Human mitochondrion 16,569 16.6kb   Plant Genlisea tuberosa 61,000,000 61Mb Smallest recorded flowering plant genome, 2014. Plant Arabidopsis thaliana 135,000,000 135 Mb 27,655 First plant genome sequenced, December 2000. Plant Populus trichocarpa 480,000,000 480Mb 73,013 First tree genome sequenced, September 2006 Plant Fritillaria assyriaca 130,000,000,000 130Gb Plant Paris japonica (Japanese-native, pale-petal) 150,000,000,000 150Gb Largest plant genome known Plant – moss Physcomitrella patens 480,000,000 480Mb First genome of a bryophyte sequenced, January 2008. Fungus – yeast Saccharomyces cerevisiae 12,100,000 12.1Mb 6,294 First eukaryotic genome sequenced, 1996 Fungus Aspergillus nidulans 30,000,000 30Mb 9,541   Nematode Pratylenchus coffeae 20,000,000 20Mb Smallest animal genome known Nematode Caenorhabditis elegans 100,300,000 100Mb 19,000 First multicellular animal genome sequenced, December 1998 Insect Drosophila melanogaster (fruit fly) 175,000,000 175Mb 13,600 Size variation based on strain (175-180Mb; standard y w strain is 175Mb) Insect Apis mellifera (honey bee) 236,000,000 236Mb 10,157   Insect Bombyx mori (silk moth) 432,000,000 432Mb 14,623 14,623 predicted genes Insect Solenopsis invicta (fire ant) 480,000,000 480Mb 16,569   Mammal Mus musculus 2,700,000,000 2.7Gb 20,210   Mammal Homo sapiens 3,289,000,000 3.3Gb 20,000 Homo sapiens estimated genome size 3.2 billion bp Initial sequencing and analysis of the human genome Mammal Pan paniscus 3,286,640,000 3.3Gb 20,000 Bonobo - estimated genome size 3.29 billion bp Bird Gallus gallus 1,043,000,000 1.0Gb 20,000   Fish Tetraodon nigroviridis (type of puffer fish) 385,000,000 390Mb Smallest vertebrate genome known estimated to be 340 Mb – 385 Mb. Fish Protopterus aethiopicus (marbled lungfish) 130,000,000,000 130Gb Largest vertebrate genome known

An image of the 46 chromosomes making up the diploid genome of a human male. (The mitochondrial chromosome is not shown.)

Composition of the human genome.

Genome instability (also genetic instability or genomic instability) refers to a high frequency of mutations within the genome of a cellular lineage. These mutations can include changes in nucleic acid sequences, chromosomal rearrangements or aneuploidy. Genome instability does occur in bacteria. In multicellular organisms genome instability is central to carcinogenesis, and in humans it is also a factor in some neurodegenerative diseases such as amyotrophic lateral sclerosis or the neuromuscular disease myotonic dystrophy.

The sources of genome instability have only recently begun to be elucidated. A high frequency of externally caused DNA damage can be one source of genome instability since DNA damages can cause inaccurate translesion synthesis past the damages or errors in repair, leading to mutation. Another source of genome instability may be epigenetic or mutational reductions in expression of DNA repair genes. Because endogenous (metabolically-caused) DNA damage is very frequent, occurring on average more than 60,000 times a day in the genomes of human cells, any reduced DNA repair is likely an important source of genome instability. (W)

Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus) and to annotate protein-coding genes and other important genome-encoded features. The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. For the human species, whose genome includes 22 pairs of autosomes and 2 sex chromosomes, a complete genome sequence will involve 46 separate chromosome sequences.

The Human Genome Project was a landmark genome project that is already having a major impact on research across the life sciences, with potential for spurring numerous medical and commercial developments. (W)

When printed, the human genome sequence fills around 100 huge books of close print.

Genomic imprinting is an epigenetic phenomenon that causes genes to be expressed in a parent-of-origin-specific manner. Genes however, can also be partially imprinted. Partial imprinting happens when alleles from both parents are differently expressed rather than complete expression and complete suppression of one parents allele. Forms of genomic imprinting have been demonstrated in fungi, plants and animals. As of 2014, there are about 150 imprinted genes known in the mouse and about half that in humans. In 2019, 260 imprinted genes have been reported in mice and 228 in humans.

Genomic imprinting is an inheritance process independent of the classical Mendelian inheritance. It is an epigenetic process that involves DNA methylation and histone methylation without altering the genetic sequence. These epigenetic marks are established ("imprinted") in the germline (sperm or egg cells) of the parents and are maintained through mitotic cell divisions in the somatic cells of an organism.

Appropriate imprinting of certain genes is important for normal development. Human diseases involving genomic imprinting include Angelman syndrome, Prader–Willi syndrome and male infertility. (W)

A glucogenic amino acid is an amino acid that can be converted into glucose through gluconeogenesis. This is in contrast to the ketogenic amino acids, which are converted into ketone bodies.

The production of glucose from glucogenic amino acids involves these amino acids being converted to alpha keto acids and then to glucose, with both processes occurring in the liver. This mechanism predominates during catabolysis, rising as fasting and starvation increase in severity.

In humans, the glucogenic amino acids are:

• Alanine
• Arginine
• Asparagine
• Aspartic acid
• Cysteine
• Glutamic acid
• Glutamine
• Glycine
• Histidine
• Methionine
• Proline
• Serine
• Valine

Amino acids that are both glucogenic and ketogenic (mnemonic "PITTT"):

• Phenylalanine
• Isoleucine
• Threonine
• Tryptophan
• Tyrosine

Only leucine and lysine are not glucogenic (they are only ketogenic). (W)

Summary of amino acid catabolism, Lippincott's Illustrated Reviews: Biochemistry. The Lippincott's text and the original diagram contained several discrepancies when compared with 5 other prominent biochemistry textbooks. This revised diagram represents consensus information from these 5 texts (see References below). Specific updates: -There is a lack of agreement among textbooks about which amino acids enter at acetoacetate, which enter at acetoacetyl CoA, and which enter directly at acetyl CoA. However, the key point is that there are 7 amino acids that enter the TCA at acetyl CoA, and the diagram has been revised to reflect this. -Threonine was previously listed as glucogenic only, but it is both glucogenic and ketogenic (enters at acetyl CoA) and has been updated accordingly. -Tryptophan was listed as both glucogenic and ketogenic, yet the old version of the diagram did not have it entering at any glucogenic substrate. Diagram has been updated to show it enters at pyruvate. -Only Phenylalanine and Tyrosine were listed as entering at Fumarate, but Aspartate also does. The diagram has been updated accordingly. References: ↑ Chapter 20 (Amino Acid Degradation and Synthesis) in: Denise R., PhD. Ferrier Lippincott's Illustrated Reviews: Biochemistry (Lippincott's Illustrated Reviews), Hagerstwon, MD: Lippincott Williams & Wilkins ISBN: 0-7817-2265-9. Garrett, R. H., & Grisham, C. M. (2008). Biochemistry (5 ed.): Brooks Cole. See p. 805. Gropper, S. S., Smith, J. L., & Groff, J. L. (2009). Advanced Nutrition and Human Metabolism (5 ed.). Belmont, CA: Wadsworth Publishing Company, Inc. See p. 212. Murray, R. K., Bender, D., Rodwell, V. W., Botham, K. M., Kennelly, P. J., & Weil, P. A. (2009). Harper's Illustrated Biochemistry (28 ed.): McGraw-Hill Medical. See p. 505. Nelson, D. L., & Cox, M. M. (2009). Lehninger Principles of Biochemistry (5 ed.): W.H. Freeman and Company. See p. 688. Stipanuk, M. H. (2006). Biochemical, physiological, & molecular aspects of human nutrition (2 ed.): Saunders Elsevier. See p. 369. (W)

Glycine (symbol Gly or G) is an amino acid that has a single hydrogen atom as its side chain. It is the simplest amino acid (since carbamic acid is unstable), with the chemical formula NH₂‐CH₂‐COOH. Glycine is one of the proteinogenic amino acids. It is encoded by all the codons starting with GG (GGU, GGC, GGA, GGG). Glycine is integral to the formation of alpha-helices in secondary protein structure due to its compact form. For the same reason, it is the most abundant amino acid in collagen triple-helices. Glycine is also an inhibitory neurotransmitter — interference with its release within the spinal cord (such as during a Clostridium tetani infection) can cause spastic paralysis due to uninhibited muscle contraction.

Glycine is a colorless, sweet-tasting crystalline solid. It is the only achiral proteinogenic amino acid. It can fit into hydrophilic or hydrophobic environments, due to its minimal side chain of only one hydrogen atom. The acyl radical is glycyl. (W)

Glycolysis (from glycose, an older term for glucose + -lysis degradation) is the metabolic pathway that converts glucose C₆H₁₂O₆, into pyruvate, CH₃COCOO^- (pyruvic acid), and a hydrogen ion, H⁺. The free energy released in this process is used to form the high-energy molecules ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide). Glycolysis is a sequence of ten enzyme-catalyzed reactions. Most monosaccharides, such as fructose and galactose, can be converted to one of these intermediates. The intermediates may also be directly useful rather than just utilized as steps in the overall reaction. For example, the intermediate dihydroxyacetone phosphate (DHAP) is a source of the glycerol that combines with fatty acids to form fat.

Glycolysis is an oxygen-independent metabolic pathway. The wide occurrence of glycolysis indicates that it is an ancient metabolic pathway. Indeed, the reactions that constitute glycolysis and its parallel pathway, the pentose phosphate pathway, occur metal-catalyzed under the oxygen-free conditions of the Archean oceans, also in the absence of enzymes.(W)

The metabolic pathway of glycolysis converts glucose to pyruvate via a series of intermediate metabolites. Each chemical modification (red box) is performed by a different enzyme. Steps 1 and 3 consume ATP (blue) and steps 7 and 10 produce ATP (yellow). Since steps 6-10 occur twice per glucose molecule, this leads to a net production of energy.

Summary of aerobic respiration.

The overall reaction of glycolysis. (W)

Glycolysis pathway overview.

he glycome is the entire complement of sugars, whether free or present in more complex molecules, of an organism. An alternative definition is the entirety of carbohydrates in a cell. The glycome may in fact be one of the most complex entities in nature. "Glycomics, analogous to genomics and proteomics, is the systematic study of all glycan structures of a given cell type or organism" and is a subset of glycobiology.

"Carbohydrate", "glycan", "saccharide", and "sugar" are generic terms used interchangeably in this context and includes monosaccharides, oligosaccharides, polysaccharides, and derivatives of these compounds. Carbohydrates consist of “hydrated carbon”, i.e. [CH₂O]_n. Monosaccharides are a carbohydrate that cannot be hydrolyzed into a simpler carbohydrate and are the building blocks of oligosaccharides and polysaccharides. Oligosaccharides are linear or branched chains of monosaccharides attached to one another via glycosidic linkages. The number of monosaccharide units can vary. Polysaccharides are glycans composed of repeating monosaccharides, generally greater than ten monosaccharide units in length.

The glycome exceeds the complexity of the proteome as a result of the even greater diversity of the glycome's constituent carbohydrates and is further complicated by the sheer multiplicity of possibilities in the combination and interaction of the carbohydrates with each other and with proteins. "The spectrum of all glycan structures — the glycome — is immense. In humans, its size is orders of magnitude greater than the number of proteins that are encoded by the genome, one percent of which encodes proteins that make, modify, localize or bind sugar chains, which are known as glycans."

The outer surface of the cell is a sea of lipids with a fleet of sugar molecules, many of which are attached to proteins, fats or both, that interact with molecules outside the cell and are critical for the communication between cells and the stickiness of a cell. "Glycans are nature's biologic modifiers," says Jamey Marth, a Howard Hughes Medical Institute investigator at the University of California San Diego."Glycans generally don't turn physiologic processes on and off, rather they modify the behavior of the cell by responding to external stimuli." (W)

The glycome is composed of glycoproteins and glycolipids.

Glycopeptides are peptides that contain carbohydrate moieties (glycans) covalently attached to the side chains of the amino acid residues that constitute the peptide.

Over the past few decades it has been recognised that glycans on cell surface (attached to membrane proteins or lipids) and those bound to proteins (glycoproteins) play a critical role in biology. For example, these constructs have been shown to play important roles in fertilization, the immune system, brain development, the endocrine system, and inflammation.

The synthesis of glycopeptides provides biological probes for researchers to elucidate glycan function in nature and products that have useful therapeutic and biotechnological applications. (W)

• Follicle-stimulating hormone
• Luteinizing hormone
• Thyroid-stimulating hormone
• Human chorionic gonadotropin
• Alpha-fetoprotein
• Erythropoietin (EPO)

N-linked protein glycosylation (N-glycosylation of N-glycans) at Asn residues (Asn-x-Ser/Thr motifs) in glycoproteins..

Guanine (or G, Gua) is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine (uracil in RNA). In DNA, guanine is paired with cytosine. The guanine nucleoside is called guanosine.

With the formula C₅H₅N₅O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with conjugated double bonds. This unsaturated arrangement means the bicyclic molecule is planar. (W)

Structure of guanine.

3D balls - Guanine.

3D vdW - Guanine.