h i j k l

📌 H—L

hedgehog signaling pathway helicase helix-turn-helix hemolysin hemolysis heterochromatin HindIII histone histone: H1/H5, H2A, H2B, H3, and H4 histone methylation homologous recombination homology directed repair horizontal gene transfer human mitochondrial genetics huntingtin hybridization hybridization probe hydrate hydrocarbon hydrogen bond hydrogen bonds in polymers hydrolysis hydroxy group hydroxide hydroxyl radical

immunoelectrophoresis immunoglobulin (lg) = antibody (Ab) indirect DNA damage induction innexin insertion (genetics) integral membrane protein integral monotopic protein intercalation (biochemistry) interferon intergenic region internal transcribed spacer intrinsically disordered proteins intron ion channel ionic bonding insulin insulin receptor integrin iron response element iron-responsive element-binding protein

jumping library juxtacrine signalling

karyopherin ketone ketone bodies ketogenesis ketosis kinase kinesin kinome

lac operon lactose Lewis structure ligand (biochemistry) ligand-gated ion channel light-dependent reactions lignin lipid lipid metabolism lipidome lipidomics lipopolysaccharide lipoprotein liposome lysis lysogenic cycle lytic cycle


hedgehog signaling pathway

The Hedgehog signaling pathway is a signaling pathway that transmits information to embryonic cells required for proper cell differentiation. Different parts of the embryo have different concentrations of hedgehog signaling proteins. The pathway also has roles in the adult. Diseases associated with the malfunction of this pathway include basal cell carcinoma.

The Hedgehog signaling pathway is one of the key regulators of animal development and is present in all bilaterians. The pathway takes its name from its polypeptide ligand, an intracellular signaling molecule called Hedgehog (Hh) found in fruit flies of the genus Drosophila; fruit fly larva lacking the Hh gene are said to resemble hedgehogs. Hh is one of Drosophila's segment polarity gene products, involved in establishing the basis of the fly body plan. Larvae without Hh are short and spiny, resembling the hedgehog animal. The molecule remains important during later stages of embryogenesis and metamorphosis.

Mammals have three Hedgehog homologues, Desert (DHH), Indian (IHH), and Sonic (SHH), of which Sonic is the best studied. The pathway is equally important during vertebrate embryonic development and is therefore of interest in evolutionary developmental biology. In knockout mice lacking components of the pathway, the brain, skeleton, musculature, gastrointestinal tract and lungs fail to develop correctly. Recent studies point to the role of Hedgehog signaling in regulating adult stem cells involved in maintenance and regeneration of adult tissues. The pathway has also been implicated in the development of some cancers. Drugs that specifically target Hedgehog signaling to fight this disease are being actively developed by a number of pharmaceutical companies. (W)

Helicases are a class of enzymes vital to all organisms. Their main function is to unpack an organism's genes. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands such as DNA and RNA (hence helic- + -ase), using energy from ATP hydrolysis. There are many helicases, representing the great variety of processes in which strand separation must be catalyzed. Approximately 1% of eukaryotic genes code for helicases. The human genome codes for 95 non-redundant helicases: 64 RNA helicases and 31 DNA helicases. Many cellular processes, such as DNA replication, transcription, translation, recombination, DNA repair, and ribosome biogenesis involve the separation of nucleic acid strands that necessitates the use of helicases. (W)

Structure of E. coli helicase RuvA.

Helicase action in DNA replication.

DNA replication or DNA synthesis is the process of copying a double-stranded DNA molecule. This process is paramount to all life as we know it.


In proteins, the helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix-loop-helix motif. (W)

The λ repressor of bacteriophage lambda employs two helix-turn-helix motifs (left; green) to bind DNA (right; blue and red). The λ repressor protein in this image is a dimer.

Hemolysins or haemolysins are lipids and proteins that cause lysis of red blood cells by disrupting the cell membrane. Although the lytic activity of some microbe-derived hemolysins on red blood cells may be of great importance for nutrient acquisition, many hemolysins produced by pathogens do not cause significant destruction of red blood cells during infection. However, hemolysins are often capable of lysing red blood cells in vitro.

While most hemolysins are protein compounds, some are lipid biosurfactants. (W)

Representation of Alpha Haemloysin from Staph Aureus, created from PDB file 7AHL, using PyMol. Created by me for wikipedia use.

The process of hemolysis in blood cells.
Hemolysis by Streptococcus seen on a plate.

Hemolysis or haemolysis (also known by several other names, is the rupturing (lysis) of red blood cells (erythrocytes) and the release of their contents (cytoplasm) into surrounding fluid (e.g. blood plasma). Hemolysis may occur in vivo or in vitro (inside or outside the body).

One cause of hemolysis is the action of hemolysins, toxins that are produced by certain pathogenic bacteria or fungi. Another cause is intense physical exercise. Hemolysins damage the red blood cell's cytoplasmic membrane, causing lysis and eventually cell death. (W)

These tubes illustrate different grades of hemolysis, as assessed visually and by our chemistry analyzer, which provides a quantification of the amount of hemoglobin in the sample as a hemolysis index. The hemolysis index (HI) value was determined on the AU5800 analyzer (Beckman Coulter, Brea, CA). The relationship between HI value and concentration of free hemoglobin on the Beckman Coulter analyzers was classified as follows: HI 0: <0,5 g/L, HI 1: 0,5–0,99 g/L, HI 2: 1–1,99 g/L, HI 3: 2–2,99 g/L, HI 4: 3–4,99 g/L

Hemolysis from streptococcus. Examples of the blood culture patterns created by (from left) alpha-, beta- and gamma-hemolytic streptococci.

Heterochromatin is a tightly packed form of DNA or condensed DNA, which comes in multiple varieties. These varieties lie on a continuum between the two extremes of constitutive heterochromatin and facultative heterochromatin. Both play a role in the expression of genes. Because it is tightly packed, it was thought to be inaccessible to polymerases and therefore not transcribed, however according to Volpe et al. (2002), and many other papers since, much of this DNA is in fact transcribed, but it is continuously turned over via RNA-induced transcriptional silencing (RITS). Recent studies with electron microscopy and OsO4 staining reveal that the dense packing is not due to the chromatin.

Constitutive heterochromatin can affect the genes near itself (e.g. position-effect variegation). It is usually repetitive and forms structural functions such as centromeres or telomeres, in addition to acting as an attractor for other gene-expression or repression signals.

Facultative heterochromatin is the result of genes that are silenced through a mechanism such as histone deacetylation or Piwi-interacting RNA (piRNA) through RNAi. It is not repetitive and shares the compact structure of constitutive heterochromatin. However, under specific developmental or environmental signaling cues, it can lose its condensed structure and become transcriptionally active.

Heterochromatin has been associated with the di- and tri-methylation of H3K9 in certain portions of the genome. H3K9me3-related methyltransferases appear to have a pivotal role in modifying heterochromatin during lineage commitment at the onset of organogenesis and in maintaining lineage fidelity.

Note that the informal diagram shown here may be in error as to the location of heterochromatin. An inactivated X-chromosome (a.k.a. Barr body) migrates to the nuclear membrane alone, leaving the active X and other chromosomes within the nucleoplasm (away from the membrane in general). Other heterochromatin appear as particles separate from the membrane, "Heterochromatin appears as small, darkly staining, irregular particles scattered throughout the nucleus ...".(7) (W)

The nucleus of a human cell showing the location of heterochromatin.

Heterochromatin vs. euchromatin.
Heterochromatin contains specialized proteins (red) that bind to histone H3 or H4 subunits that have been marked by a specific modification (green). The enzyme that performs this modification is also present in heterochromatin (blue), ensuring that the modification is maintained.

General model for duplication of heterochromatin during cell division.

Heterochromatin contains specialized proteins (red) that bind to histone H3 or H4 subunits that have been marked by a specific modification (green). The enzyme that performs this modification is also present in heterochromatin (blue), ensuring that the modification is maintained. When the chromosome is duplicated, the marked histone H3–H4 tetramers of the parent chromosome are distributed randomly to the two daughter strands, resulting in a mixture of old (light grey) and new (dark grey) nucleosomes. In heterochromatin, new nucleosomes are rapidly marked by the histone-modifying enzymes bound to old nucleosomes. This provides new binding sites for heterochromatin proteins. These proteins (such as the Sir complex or HP1) also have the ability to bind to each other, further promoting the assembly of a protein polymer along the chromosome. It can also be seen in this diagram that the boundary between heterochromatin and euchromatin is not rigidly fixed, because small local changes in the extent of histone modification could cause shifts in its position.

HindIII (pronounced "Hin D Three") is a type II site-specific deoxyribonuclease restriction enzyme isolated from Haemophilus influenzae that cleaves the DNA palindromic sequence AAGCTT in the presence of the cofactor Mg2+ via hydrolysis.

The cleavage of this sequence between the AA's results in 5' overhangs on the DNA called sticky ends:

5'-A |A G C T T-3'

3'-T T C G A| A-5'

Restriction endonucleases are used as defense mechanisms in prokaryotic organisms in the restriction modification system. Their primary function is to protect the host genome against invasion by foreign DNA, primarily bacteriophage DNA. There is also evidence that suggests the restriction enzymes may act alongside modification enzymes as selfish elements, or may be involved in genetic recombination and transposition. (W)

Crystallographic structure of the HindIII restriction endonuclease dimer (cyan and green) complexed with double helical DNA (brown) based on the PDB: 2E52​ coordinates.

HindIII restrictions process results in formation of overhanging palindromic sticky ends.

BglII catalytic site, showing the coordination of Asp 84 and Mg2+ with water.
In biology, histones are highly basic proteins found in eukaryotic cell nuclei that pack and order the DNA into structural units called nucleosomes. Histones are abundant in lysine and arginine. Histones are the chief protein components of chromatin, acting as spools around which DNA winds, and playing a role in gene regulation. Without histones, the unwound DNA in chromosomes would be very long (a length to width ratio of more than 10 million to 1 in human DNA). For example, each human diploid cell (containing 23 pairs of chromosomes) has about 1.8 meters of DNA; wound on the histones, the diploid cell has about 90 micrometers (0.09 mm) of chromatin. When the diploid cells are duplicated and condensed during mitosis, the result is about 120 micrometers of chromosomes

Classes and histone variants
Five major families of histones exist: H1/H5, H2A, H2B, H3, and H4. Histones H2A, H2B, H3 and H4 are known as the core histones, while histones H1/H5 are known as the linker histones. (W)

Schematic representation of the assembly of the core histones into the nucleosome.

Structure of the H2AFJ protein. Based on PyMOL rendering of PDB 1aoi.

linker histone H1 and H5 family. PDB rendering of HIST1H1B based on 1ghc.

Steps in nucleosome assembly.

Basic units of chromatin structure.

Scheme of nucleosome organization.

Histone tails and their function in chromatin formation.

Functions of histone modifications (L)

Schematic representation of histone modifications. Based on Rodriguez-Paredes and Esteller, Nature, 2011

A huge catalogue of histone modifications have been described, but a functional understanding of most is still lacking. Collectively, it is thought that histone modifications may underlie a histone code, whereby combinations of histone modifications have specific meanings. However, most functional data concerns individual prominent histone modifications that are biochemically amenable to detailed study.

histone: H1/H5, H2A, H2B, H3, and H4

A diagram showing where H1 can be found in the nucleosome.

Histone H1 is one of the five main histone protein families which are components of chromatin in eukaryotic cells. Though highly conserved, it is nevertheless the most variable histone in sequence across species. (W)

Structure of the H2AFJ protein.

Histone H2A is one of the five main histone proteins involved in the structure of chromatin in eukaryotic cells.highly conserved, it is nevertheless the most variable histone in sequence across species. (W)

Histone tails and their function in chromatin formation.

Histone H2B is one of the 4 main histone proteins involved in the structure of chromatin in eukaryotic cells. Featuring a main globular domain and long N-terminal and C-terminal tails, H2B is involved with the structure of the nucleosomes. (W)

Histone H3 is one of the five main histones involved in the structure of chromatin in eukaryotic cells. Featuring a main globular domain and a long N-terminal tail, H3 is involved with the structure of the nucleosomes of the 'beads on a string' structure. Histone proteins are highly post-translationally modified however Histone H3 is the most extensively modified of the five histones. The term "Histone H3" alone is purposely ambiguous in that it does not distinguish between sequence variants or modification state. Histone H3 is an important protein in the emerging field of epigenetics, where its sequence variants and variable modification states are thought to play a role in the dynamic and long term regulation of genes.

Histone H4 is one of the five main histone proteins involved in the structure of chromatin in eukaryotic cells. Featuring a main globular domain and a long N-terminal tail, H4 is involved with the structure of the nucleosome of the 'beads on a string' organization. Histone proteins are highly post-translationally modified. Covalently bonded modifications include acetylation and methylation of the N-terminal tails. These modifications may alter expression of genes located on DNA associated with its parent histone octamer. Histone H4 is an important protein in the structure and function of chromatin, where its sequence variants and variable modification states are thought to play a role in the dynamic and long term regulation of genes. (W)
histone methylation
Histone methylation is a process by which methyl groups are transferred to amino acids of histone proteins that make up nucleosomes, which the DNA double helix wraps around to form chromosomes. Methylation of histones can either increase or decrease transcription of genes, depending on which amino acids in the histones are methylated, and how many methyl groups are attached. Methylation events that weaken chemical attractions between histone tails and DNA increase transcription because they enable the DNA to uncoil from nucleosomes so that transcription factor proteins and RNA polymerase can access the DNA. This process is critical for the regulation of gene expression that allows different cells to express different genes. (W)

Epigenetic mechanisms.

Epigenetic mechanisms are affected by several factors and processes including development in utero and in childhood, environmental chemicals, drugs and pharmaceuticals, aging, and diet. DNA methylation is what occurs when methyl groups, an epigenetic factor found in some dietary sources, can tag DNA and activate or repress genes. Histones are proteins around which DNA can wind for compaction and gene regulation. Histone modification occurs when the binding of epigenetic factors to histone “tails” alters the extent to which DNA is wrapped around histones and the availability of genes in the DNA to be activated. All of these factors and processes can have an effect on people’s health and influence their health possibly resulting in cancer, autoimmune disease, mental disorders, or diabetes among other illnesses. National Institutes of Health
homologous recombination
Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in cellular organisms but may be also RNA in viruses). It is widely used by cells to accurately repair harmful breaks that occur on both strands of DNA, known as double-strand breaks (DSB), in a process called homologous recombinational repair (HRR). Homologous recombination also produces new combinations of DNA sequences during meiosis, the process by which eukaryotes make gamete cells, like sperm and egg cells in animals. These new combinations of DNA represent genetic variation in offspring, which in turn enables populations to adapt during the course of evolution. Homologous recombination is also used in horizontal gene transfer to exchange genetic material between different strains and species of bacteria and viruses. (W)

Figure 1. During meiosis, homologous recombination can produce new combinations of genes as shown here between similar but not identical copies of human chromosome 1.

Figure 2. An early illustration of crossing over from Thomas Hunt Morgan.

Figure 3. Homologous recombination repairs DNA before the cell enters mitosis (M phase). It occurs only during and shortly after DNA replication, during the S and G2 phases of the cell cycle.

Figure 4. Double-strand break repair models that act via homologous recombination.

Left panel: Gene conversion. After resection, the single-stranded 3' tail invades a homologous, intact double-stranded DNA, forming a D-loop (displacement loop). This process tolerates a limited number of imperfect sequence homologies, thus creating heteroduplex intermediates bearing mismatches (yellow circles). The invading 3'-end primes DNA synthesis, which then fills in the gaps. The cruciform junctions (Holliday junctions, HJ) migrate. Resolution (or dissolution) of HJs occurs in two different orientations (orange or red triangles), resulting in gene conversion either with or without crossing over. Middle panel: Break-induced replication (BIR). The initiation is similar to that of the previous models, but the synthesis continues over longer distances on the chromosome arms, even reaching the end of the chromosome. Here, there is neither resolution of the HR nor crossover. Right panel: Synthesis-dependent strand annealing (SDSA). Initiation is similar to that of the previous model, but the invading strand de-hybridizes and re-anneals at the other end of the injured molecule; no HJ is formed. (W)

Figure 5. The DSBR and SDSA pathways follow the same initial steps, but diverge thereafter. The DSBR pathway most often results in chromosomal crossover (bottom left), while SDSA always ends with non-crossover products (bottom right).

Figure 6. Recombination via the SSA pathway occurs between two repeat elements (purple) on the same DNA duplex, and results in deletions of genetic material. (Click here to view animated diagram in Firefox, Chrome, Safari, or Opera web browsers.)
homology directed repair
Homology directed repair (HDR) is a mechanism in cells to repair double-strand DNA lesions. The most common form of HDR is homologous recombination. The HDR mechanism can only be used by the cell when there is a homologous piece of DNA present in the nucleus, mostly in G2 and S phase of the cell cycle. Other examples of homology-directed repair include single-strand annealing and breakage-induced replication. When the homologous DNA is absent, another process called non-homologous end joining (NHEJ) takes place instead. (W)

Double-strand break repair models that act via homologous recombination.

Left panel: Gene conversion. After resection, the single-stranded 3' tail invades a homologous, intact double-stranded DNA, forming a D-loop (displacement loop). This process tolerates a limited number of imperfect sequence homologies, thus creating heteroduplex intermediates bearing mismatches (yellow circles). The invading 3'-end primes DNA synthesis, which then fills in the gaps. The cruciform junctions (Holliday junctions, HJ) migrate. Resolution (or dissolution) of HJs occurs in two different orientations (orange or red triangles), resulting in gene conversion either with or without crossing over. Middle panel: Break-induced replication (BIR). The initiation is similar to that of the previous models, but the synthesis continues over longer distances on the chromosome arms, even reaching the end of the chromosome. Here, there is neither resolution of the HR nor crossover. Right panel: Synthesis-dependent strand annealing (SDSA). Initiation is similar to that of the previous model, but the invading strand de-hybridizes and re-anneals at the other end of the injured molecule; no HJ is formed.

horizontal gene transfer

Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the evolution of many organisms.

Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria, and plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created pesticides and in the evolution, maintenance, and transmission of virulence. It often involves temperate bacteriophages and plasmids. Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various mechanisms of HGT such as transformation, transduction and conjugation, subsequently arming the antibiotic resistant genes' recipient against antibiotics. The rapid spread of antibiotic resistance genes in this manner is becoming medically challenging to deal with. Ecological factors may also play a role in the LGT of antibiotic resistant genes. It is also postulated that HGT promotes the maintenance of a universal life biochemistry and, subsequently, the universality of the genetic code.

Most thinking in genetics has focused upon vertical transfer, but the importance of horizontal gene transfer among single-cell organisms is beginning to be acknowledged.

Gene delivery
can be seen as an artificial horizontal gene transfer, and is a form of genetic engineering. (W)

Horizontal gene transfer.
human mitochondrial genetics

Human mitochondrial genetics is the study of the genetics of human mitochondrial DNA (the DNA contained in human mitochondria). The human mitochondrial genome is the entirety of hereditary information contained in human mitochondria. Mitochondria are small structures in cells that generate energy for the cell to use, and are hence referred to as the "powerhouses" of the cell.

Mitochondrial DNA
(mtDNA) is not transmitted through nuclear DNA (nDNA). In humans, as in most multicellular organisms, mitochondrial DNA is inherited only from the mother's ovum. There are theories, however, that paternal mtDNA transmission in humans can occur under certain circumstances.

Mitochondrial inheritance is therefore non-Mendelian, as Mendelian inheritance presumes that half the genetic material of a fertilized egg (zygote) derives from each parent.

Eighty percent of mitochondrial DNA codes for mitochondrial RNA, and therefore most mitochondrial DNA mutations lead to functional problems, which may be manifested as muscle disorders (myopathies).

Because they provide 30 molecules of ATP per glucose molecule in contrast to the 2 ATP molecules produced by glycolysis, mitochondria are essential to all higher organisms for sustaining life. The mitochondrial diseases are genetic disorders carried in mitochondrial DNA, or nuclear DNA coding for mitochondrial components. Slight problems with any one of the numerous enzymes used by the mitochondria can be devastating to the cell, and in turn, to the organism. (W)

Map of the human mitochondrial DNA genome (16569 bp, NCBI sequence accession NC_012920Anderson et al. 1981). The H (heavy, outer circle) and L (light, inner circle) strands are given with their corresponding genes. There are 22 transfer RNA (TRN) genes for the following amino acids: F, V, L1 (codon UUA/G), I, Q, M, W, A, N, C, Y, S1 (UCN), D, K, G, R, H, S2 (AGC/U), L2 (CUN), E, T and P (white boxes). There are 2 ribosomal RNA (RRN) genes: S (small subunit, or 12S) and L (large subunit, or 16S) (blue boxes). There are 13 protein-coding genes: 7 for NADH dehydrogenase subunits (ND, yellow boxes), 3 for cytochrome c oxidase subunits (COX, orange boxes), 2 for ATPase subunits (ATP, red boxes), and one for cytochrome b (CYTB, coral box). Two gene overlaps are indicated (ATP8-ATP6, and ND4L-ND4, black boxes). The control region (CR) is the longest non-coding sequence (grey box). Its three hyper-variable regions are indicated (HV, green boxes).

Mitochondrial inheritance patterns.

The reason for maternal inheritance in mitochondrial DNA is that when the sperm enters the egg cell, it discards its middle part, which contains its mitochondria, so that only its head with the nucleus penetrates the egg cell.
Clinical significance
Main article: Huntington's disease

The huntingtin gene, also called the HTT or HD (Huntington disease) gene, is the IT15 ("interesting transcript 15") gene, which codes for a protein called the huntingtin protein. The gene and its product are under heavy investigation as part of Huntington's disease clinical research and the suggested role for huntingtin in long-term memory storage.

It is variable in its structure, as the many polymorphisms of the gene can lead to variable numbers of glutamine residues present in the protein. In its wild-type (normal) form, it contains 6-35 glutamine residues. However, in individuals affected by Huntington's disease (an autosomal dominant genetic disorder), it contains more than 36 glutamine residues (highest reported repeat length is about 250). Its commonly used name is derived from this disease; previously, the IT15 label was commonly used. (W)

hybridization → nucleic acid hybridization
hybridization probe

In molecular biology, a hybridization probe is a fragment of DNA or RNA of variable length (usually 100–10000 bases long) which can be radioactively or fluorescently labeled. It can then be used in DNA or RNA samples to detect the presence of nucleotide substances (the RNA target) that are complementary to the sequence in the probe. The probe thereby hybridizes to single-stranded nucleic acid (DNA or RNA) whose base sequence allows probe–target base pairing due to complementarity between the probe and target. The labeled probe is first denatured (by heating or under alkaline conditions such as exposure to sodium hydroxide) into single stranded DNA (ssDNA) and then hybridized to the target ssDNA (Southern blotting) or RNA (northern blotting) immobilized on a membrane or in situ. To detect hybridization of the probe to its target sequence, the probe is tagged (or "labeled") with a molecular marker of either radioactive or (more recently) fluorescent molecules; commonly used markers are 32P (a radioactive isotope of phosphorus incorporated into the phosphodiester bond in the probe DNA) or digoxigenin, which is a non-radioactive, antibody-based marker. DNA sequences or RNA transcripts that have moderate to high sequence similarity to the probe are then detected by visualizing the hybridized probe via autoradiography or other imaging techniques. Normally, either X-ray pictures are taken of the filter, or the filter is placed under UV light. Detection of sequences with moderate or high similarity depends on how stringent the hybridization conditions were applied—high stringency, such as high hybridization temperature and low salt in hybridization buffers, permits only hybridization between nucleic acid sequences that are highly similar, whereas low stringency, such as lower temperature and high salt, allows hybridization when the sequences are less similar. Hybridization probes used in DNA microarrays refer to DNA covalently attached to an inert surface, such as coated glass slides or gene chips, to which a mobile cDNA target is hybridized.

Depending on the method, the probe may be synthesized using the phosphoramidite method, or it can be generated and labeled by PCR amplification or cloning (both are older methods). In order to increase the in vivo stability of the probe RNA is not used. Instead, RNA analogues may be used, in particular morpholino- derivatives. Molecular DNA- or RNA-based probes are now routinely used in screening gene libraries, detecting nucleotide sequences with blotting methods, and in other gene technologies, such as nucleic acid and tissue microarrays. (W)

Fluorescence Microscope and Pipettes.

A technician viewing a blot on a fluorescence microscope while another technician is using a pipette at the Advanced Technology Research Facility (ATRF), Frederick National Laboratory for Cancer Research, National Cancer Institute. (L)
In chemistry, a hydrate is a substance that contains water or its constituent elements. The chemical state of the water varies widely between different classes of hydrates, some of which were so labeled before their chemical structure was understood. (W)
In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. 620 Hydrocarbons are examples of group 14 hydrides. Hydrocarbons from which one hydrogen atom has been removed are functional groups called hydrocarbyls. Hydrocarbons are generally colorless and hydrophobic with only weak odors. Because of their diverse molecular structures, it is difficult to generalize further. (W)

Ball-and-stick model of the methane molecule, CH4. Methane is part of a homologous series known as the alkanes, which contain single bonds only.

hydrogen bond

A hydrogen bond (often informally abbreviated H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative atom or group, particularly the second-row elements nitrogen (N), oxygen (O), or fluorine (F)—the hydrogen bond donor (Dn)—and another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac). Such an interacting system is generally denoted Dn–H···Ac, where the solid line denotes a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond. The use of three centered dots for the hydrogen bond is specifically recommended by the IUPAC. While hydrogen bonding has both covalent and electrostatic contributions, and the degrees to which they contribute are currently debated, the present evidence strongly implies that the primary contribution is covalent.

Hydrogen bonds can be intermolecular (occurring between separate molecules) or intramolecular (occurring among parts of the same molecule). Depending on the nature of the donor and acceptor atoms which constitute the bond, their geometry, and environment, the energy of a hydrogen bond can vary between 1 and 40 kcal/mol. This makes them somewhat stronger than a van der Waals interaction, and weaker than fully covalent or ionic bonds. This type of bond can occur in inorganic molecules such as water and in organic molecules like DNA and proteins. (W)

Model of hydrogen bonds (1) between molecules of water.

An example of intermolecular hydrogen bonding in a self-assembled dimer complex. The hydrogen bonds are represented by dotted lines.

Crystal structure of hexagonal ice. Gray dashed lines indicate hydrogen bonds.

hydrogen bonds in polymers

Hydrogen bonding plays an important role in determining the three-dimensional structures and the properties adopted by many synthetic and natural proteins. Compared to the C-C, C-O, and C-N bonds that comprise most polymers, hydrogen bonds are far weaker, perhaps 5%. Thus, hydrogen bonds can be broken by chemical or mechanical means while retaining the basic structure of the polymer backbone. This hierarchy of bond strengths (covalent bonds being stronger than hydrogen-bonds being stronger than van der Waals forces) is key to understanding the properties of many materials. (W)

Hydrogen bonding between guanine and cytosine, one of two types of base pairs in DNA.


Hydrolysis (from Ancient Greek hydro- 'water', and lysis 'to unbind') is any chemical reaction in which a molecule of water ruptures one or more chemical bonds. The term is used broadly for substitution, elimination, and solvation reactions in which water is the nucleophile.

Biological hydrolysis is the cleavage of biomolecules where a water molecule is consumed to effect the separation of a larger molecule into component parts. When a carbohydrate is broken into its component sugar molecules by hydrolysis (e.g., sucrose being broken down into glucose and fructose), this is recognized as saccharification.

Hydrolysis reactions can be the reverse of a condensation reaction in which two molecules join together into a larger one and eject a water molecule. Thus hydrolysis adds water to break down, whereas condensation builds up by removing water and any other solvents. Some hydration reactions are hydrolyses. (W)

Generic mechanism for a hydrolysis reaction. (The 2-way yield symbol indicates an equilibrium in which hydrolysis and condensation can go both ways.).
hydroxy group

A hydroxy or hydroxyl group is the entity with the formula OH. It contains oxygen bonded to hydrogen. In organic chemistry, alcohols and carboxylic acids contain hydroxy groups. Both the negatively charged anion OH, called hydroxide, and the neutral radical ·OH, known as the hydroxyl radical, consist of an unbounded hydroxyl group.

According to IUPAC rules, the term hydroxyl refers to the hydroxyl radical (·OH) only, while the functional group −OH is called hydroxy group. (W)

Representation of an organic hydroxy group, where R represents a hydrocarbon or other organic moiety, the red and grey spheres represent oxygen and hydrogen atoms respectively, and the rod-like connections between these, covalent chemical bonds.

Sulfuric acid contains two hydroxyl groups.

Hydroxide is a diatomic anion with chemical formula OH. It consists of an oxygen and hydrogen atom held together by a covalent bond, and carries a negative electric charge. It is an important but usually minor constituent of water. It functions as a base, a ligand, a nucleophile, and a catalyst. The hydroxide ion forms salts, some of which dissociate in aqueous solution, liberating solvated hydroxide ions. Sodium hydroxide is a multi-million-ton per annum commodity chemical. A hydroxide attached to a strongly electropositive center may itself ionize, liberating a hydrogen cation (H+), making the parent compound an acid.

The corresponding electrically neutral compound HO• is the hydroxyl radical. The corresponding covalently bound group –OH of atoms is the hydroxy group. Hydroxide ion and hydroxy group are nucleophiles and can act as a catalysts in organic chemistry.

Many inorganic substances which bear the word hydroxide in their names are not ionic compounds of the hydroxide ion, but covalent compounds which contain hydroxy groups. (W)

Lewis structure of the hydroxide ion showing three lone pairs on the oxygen atom.

Space-filling representation of the hydroxide ion.

Ball-and-stick model of the hydroxide ion.
hydroxyl radical

The hydroxyl radical, •OH, is the neutral form of the hydroxide ion (OH). Hydroxyl radicals are highly reactive (easily becoming hydroxy groups) and consequently short-lived; however, they form an important part of radical chemistry. Most notably hydroxyl radicals are produced from the decomposition of hydroperoxides (ROOH) or, in atmospheric chemistry, by the reaction of excited atomic oxygen with water. It is also an important radical formed in radiation chemistry, since it leads to the formation of hydrogen peroxide and oxygen, which can enhance corrosion and SCC in coolant systems subjected to radioactive environments. Hydroxyl radicals are also produced during UV-light dissociation of H2O2 (suggested in 1879) and likely in Fenton chemistry, where trace amounts of reduced transition metals catalyze peroxide-mediated oxidations of organic compounds. (W)

Stick model of the hydroxyl radical with molecular orbitals.

Comparison of a hydroxide ion and a hydroxyl radical.

📂Biological significance

Biological significance (W)

Hydroxyl radicals can occasionally be produced as a byproduct of immune action. Macrophages and microglia most frequently generate this compound when exposed to very specific pathogens, such as certain bacteria. The destructive action of hydroxyl radicals has been implicated in several neurological autoimmune diseases such as HAND when immune cells become over-activated and toxic to neighboring healthy cells.

The hydroxyl radical can damage virtually all types of macromolecules: carbohydrates, nucleic acids (mutations), lipids (lipid peroxidation), and amino acids (e.g. conversion of Phe to m-Tyrosine and o-Tyrosine). The hydroxyl radical has a very short in vivo half-life of approximately 10−9 seconds and a high reactivity. This makes it a very dangerous compound to the organism.

Unlike superoxide, which can be detoxified by superoxide dismutase, the hydroxyl radical cannot be eliminated by an enzymatic reaction.


Immunoelectrophoresis is a general name for a number of biochemical methods for separation and characterization of proteins based on electrophoresis and reaction with antibodies.All variants of immunoelectrophoresis require immunoglobulins, also known as antibodies, reacting with the proteins to be separated or characterized. The methods were developed and used extensively during the second half of the 20th century. In somewhat chronological order: Immunoelectrophoretic analysis (one-dimensional immunoelectrophoresis ad modum Grabar), crossed immunoelectrophoresis (two-dimensional quantitative immunoelectrophoresis ad modum Clarke and Freeman or ad modum Laurell), rocket-immunoelectrophoresis (one-dimensional quantitative immunoelectrophoresis ad modum Laurell), fused rocket immunoelectrophoresis ad modum Svendsen and Harboe, affinity immunoelectrophoresis ad modum Bøg-Hansen. (W)

Crossed immunoelectrophoresis of 2 microLitre of normal human serum. The electrophoresis was performed in thin layers of agarose, the pictured gel is about 7x7 cm. The lower part is the first dimension gel without antibodies, where the serum was applied into the slot at the lower left. The upper part is the second dimension gel with Dako antibodies against human serum proteins. More than 50 major serum proteins can be named.

immunoglobulin (Ig) → antibody (Ab)
indirect DNA damage
Indirect DNA damage occurs when a UV-photon is absorbed in the human skin by a chromophore that does not have the ability to convert the energy into harmless heat very quickly. Molecules that do not have this ability have a long-lived excited state. This long lifetime leads to a high probability for reactions with other molecules—so-called bimolecular reactions. Melanin and DNA have extremely short excited state lifetimes in the range of a few femtoseconds (10−15s). The excited state lifetime of compounds used in sunscreens such as menthyl anthranilate, avobenzone or padimate O is 1,000 to 1,000,000 times longer than that of melanin, and therefore they may cause damage to living cells that come in contact with them. (W)

Indirect DNA damage: The chromophore absorbs UV-light (* denotes an excited state), and the energy of the excited state is creating singlet oxygen (1O2) or a hydroxyl radical (•OH), which then damages DNA through oxidation.
induction → redox

Innexins are transmembrane proteins that form gap junctions in invertebrates. Gap junctions are composed of membrane proteins that form a channel permeable to ions and small molecules connecting the cytoplasm of adjacent cells. Although gap junctions provide similar functions in all multicellular organisms, it was not known what proteins invertebrates used for this purpose until the late 1990s. While the connexin family of gap junction proteins was well-characterized in vertebrates, no homologues were found in non-chordates.

Innexins or related proteins are widespread among Eumetazoa, with the exception of echinoderms. (W)

insertion (genetics)

In genetics, an insertion (also called an insertion mutation) is the addition of one or more nucleotide base pairs into a DNA sequence. This can often happen in microsatellite regions due to the DNA polymerase slipping. Insertions can be anywhere in size from one base pair incorrectly inserted into a DNA sequence to a section of one chromosome inserted into another. The mechanism of the smallest single base insertion mutations is believed to be through base-pair separation between the template and primer strands followed by non-neighbor base stacking, which can occur locally within the DNA polymerase active site. On a chromosome level, an insertion refers to the insertion of a larger sequence into a chromosome. This can happen due to unequal crossover during meiosis.

N region addition
is the addition of non-coded nucleotides during recombination by terminal deoxynucleotidyl transferase.

P nucleotide insertion
is the insertion of palindromic sequences encoded by the ends of the recombining gene segments.

Trinucleotide repeats
are classified as insertion mutations and sometimes as a separate class of mutations. (W)

An illustration of an insertion at chromosome level.
Insulin (from Latin insula, 'island') is a peptide hormone produced by beta cells of the pancreatic islets; it is considered to be the main anabolic hormone of the body. It regulates the metabolism of carbohydrates, fats and protein by promoting the absorption of glucose from the blood into liver, fat and skeletal muscle cells. In these tissues the absorbed glucose is converted into either glycogen via glycogenesis or fats (triglycerides) via lipogenesis, or, in the case of the liver, into both. Glucose production and secretion by the liver is strongly inhibited by high concentrations of insulin in the blood. Circulating insulin also affects the synthesis of proteins in a wide variety of tissues. It is therefore an anabolic hormone, promoting the conversion of small molecules in the blood into large molecules inside the cells. Low insulin levels in the blood have the opposite effect by promoting widespread catabolism, especially of reserve body fat. (W)

Insulin is a peptide hormone containing two chains cross-linked by disulfide bridges.

Chain A in green, chain B in orange, disulfide bridges in yellow.

INS Gene location (Human).
Chromosome 11 (human).

Ideogram of human chromosome. Chromosome 11 highlighted. G-band, 850 bphs (bands per haploid set). Black and gray: Giemsa positive. Red: Centromere. Light blue: Variable region. Dark blue: Stalk.

Diagram of insulin regulation upon high blood glucose.

In the pancreatic β cells, glucose is the primary physiological stimulus for the regulation of insulin synthesis. Insulin is mainly regulated through the transcription factors PDX1, NeuroD1, and MafA.

The structure of insulin. The left side is a space-filling model of the insulin monomer, believed to be biologically active. Carbon is green, hydrogen white, oxygen red, and nitrogen blue. On the right side is a ribbon diagram of the insulin hexamer, believed to be the stored form. A monomer unit is highlighted with the A chain in blue and the B chain in cyan. Yellow denotes disulfide bonds, and magenta spheres are zinc ions.

Insulin undergoes extensive posttranslational modification along the production pathway. Production and secretion are largely independent; prepared insulin is stored awaiting secretion. Both C-peptide and mature insulin are biologically active. Cell components and proteins in this image are not to scale.

Insulin release from pancreas oscillates with a period of 3–6 minutes.

📹 Diabetes / blausen (LINK)


During the digestive process, the foods that we eat are converted into glucose, commonly known as blood sugar. Glucose circulates in the bloodstream and is used as food for the body's cells. But the cells cannot absorb glucose alone. A hormone called insulin, which is produced in the pancreas, must first bind to the cell surface. When this occurs, cells of the body are activated and are able to absorb the glucose. This process returns the body's blood sugar to a normal level. Diabetes mellitus is a disorder that affects the body's ability to efficiently utilize blood glucose. In type 1 diabetes, the pancreas does not produce enough insulin, so glucose cannot be absorbed to refuel the cells. In type 2 diabetes, insulin is produced, but it does not work properly and the glucose is not absorbed consistently by the cells. Both types of diabetes have the same results: glucose is not absorbed by the cells. That is why people with diabetes have high blood sugar levels. Without proper absorption of glucose from the bloodstream, the cells are starving for food. Regardless of which type of diabetes a person may have, people with diabetes must monitor their blood sugar levels. Depending on the type and severity of the disease, diabetes can be managed with diet or with medication.
insulin receptor
The insulin receptor (IR) is a transmembrane receptor that is activated by insulin, IGF-I, IGF-II and belongs to the large class of tyrosine kinase receptors. Metabolically, the insulin receptor plays a key role in the regulation of glucose homeostasis, a functional process that under degenerate conditions may result in a range of clinical manifestations including diabetes and cancer. Insulin signalling controls access to blood glucose in body cells. When insulin falls, especially in those with high insulin sensitivity, body cells begin only to have access to lipids that do not require transport across the membrane. So, in this way, insulin is the key regulator of fat metabolism as well. Biochemically, the insulin receptor is encoded by a single gene INSR, from which alternate splicing during transcription results in either IR-A or IR-B isoforms. Downstream post-translational events of either isoform result in the formation of a proteolytically cleaved α and β subunit, which upon combination are ultimately capable of homo or hetero-dimerisation to produce the ≈320 kDa disulfide-linked transmembrane insulin receptor. (W)

The dimeric Insulin Receptor ectodomain colourised to demonstrate L1 (blue), CR (cyan), L2 (green), FnIII-1 (yellow), FnIII-2 (orange), FnIII-3 (red) domains with foreground and background monomers represented as cartoon and sphere projections respectively. Image generated by Pymol, derived from structure PDB:3LOH.

INSR Gene location (Human).
Ideogram of human chromosome. Chromosome 19 highlighted. G-band, 850 bphs (bands per haploid set). Black and gray: Giemsa positive. Red: Centromere. Light blue: Variable region. Dark blue: Stalk.

Colour coded Schematic of the Insulin Receptor featuring each domain with black lines representing disulphide linkages.

Effect of insulin on glucose uptake and metabolism. Insulin binds to its receptor (1) which in turn starts many protein activation cascades (2). These include: translocation of Glut-4 transporter to the plasma membrane and influx of glucose (3), glycogen synthesis (4), glycolysis (5) and fatty acid synthesis (6).

Signal transduction of Insulin: At the end of the transduction process, the activated protein binds to the PIP2 proteins embedded in the membrane.

Mechanism of action of Insulin: Excreted from the pancreas, insulin circulates through the blood (λ=30min) before binding to an insulin receptor (IR) expressed on the surface of myocytes, adipocytes and hepatocytes. Once insulin binds to the receptor, phosphorylation takes place and attaches to the beta-subunit, thus initiating the transduction process. A protein binds to the phosphorylated receptor protein, becoming phosphorylated as well. Once the protein detaches from the receptor protein, the signal has successfully been transported from the receptor to the newly active protein. Through a series of kinase proteins, the proteins are constantly being phosphorylated and activated. At the end of the transduction process, the activated protein binds to the PIP2 proteins embedded in the membrane. By doing so, the initial signal has successfully transmitted the extracellular signal. As a result, another protein is activated, later activating the storage vesicles found within the cell. Upon activation, the vesicle is transported to the membrane, where its membrane becomes integrated within the cellular membrane under a process known as phagocytosis. The Glucose transporter type 4 (GLUT4) protein channels that were once embedded in the storage vesicles are now embedded in the cellular membrane. Much more (×100,000?) Glucose can now flow into the cell through these glucose transport channels. Source information: http://vcell.ndsu.nodak.edu/animations/insulinsignaling/movie-flash.htm
integral membrane protein
An integral membrane protein (IMP) is a type of membrane protein that is permanently attached to the biological membrane. All transmembrane proteins are IMPs, but not all IMPs are transmembrane proteins. IMPs comprise a significant fraction of the proteins encoded in an organism's genome. Proteins that cross the membrane are surrounded by annular lipids, which are defined as lipids that are in direct contact with a membrane protein. Such proteins can only be separated from the membranes by using detergents, nonpolar solvents, or sometimes denaturing agents. (W)

Group I and II transmembrane proteins have opposite orientations. Group I proteins have the N terminus on the far side and C terminus on the cytosolic side. Group II proteins have the C terminus on the far side and N terminus in the cytosol..
integral monotopic protein

Integral monotopic proteins, are permanently attached to the membrane from one side.

Three-dimensional structures of the following integral monotopic proteins have been determined:

There are also structures of integral monotopic domains of transmembrane proteins:


Schematic representation of the different types of interaction between monotopic membrane proteins and the cell membrane: 1. interaction by an amphipathic α-helix parallel to the membrane plane (in-plane membrane helix) 2. interaction by a hydrophobic loop 3. interaction by a covalently bound membrane lipid (lipidation) 4. electrostatic or ionic interactions with membrane lipids (e.g. through a calcium ion).


Integrins are transmembrane receptors that facilitate cell-extracellular matrix (ECM) adhesion. Upon ligand binding, integrins activate signal transduction pathways that mediate cellular signals such as regulation of the cell cycle, organization of the intracellular cytoskeleton, and movement of new receptors to the cell membrane. The presence of integrins allows rapid and flexible responses to events at the cell surface (e.g. signal platelets to initiate an interaction with coagulation factors).

Several types of integrins exist, and one cell may have multiple different types on its surface. Integrins are found in all animals while integrin-like receptors are found in plant cells.

Integrins work alongside other proteins such as cadherins, the immunoglobulin superfamily cell adhesion molecules, selectins and syndecans, to mediate cell–cell and cell–matrix interaction. Ligands for integrins include fibronectin, vitronectin, collagen and laminin.


Integrins have two main functions, attachment of the cells to the ECM and signal transduction from the ECM to the cells. They are also involved in a wide range of other biological activities, including extravasation, cell-to-cell adhesion, cell migration, and as receptors for certain viruses, such as adenovirus, echovirus, hantavirus, and foot-and-mouth disease, polio virus and other viruses.

A prominent function of the integrins is seen in the molecule GpIIb/IIIa, an integrin on the surface of blood platelets (thrombocytes) responsible for attachment to fibrin within a developing blood clot. This molecule dramatically increases its binding affinity for fibrin/fibrinogen through association of platelets with exposed collagens in the wound site. Upon association of platelets with collagen, GPIIb/IIIa changes shape, allowing it to bind to fibrin and other blood components to form the clot matrix and stop blood loss. (W)

Structure of the extracellular segment of integrin alpha Vbeta3.

Cartoon representation of the molecular structure of protein registered with 1jv2 code.

Integrins are localised at the growth cone of regenerating neurons.

Integrins are localised at the growth cone of regenerating neurons. © Nieuwenhuis, B., Haenzi, B., Andrews, M. R., Verhaagen, J. and Fawcett, J. W. (2018), Integrins promote axonal regeneration after injury of the nervous system. Biol Rev. doi:10.1111/brv.12398.
intercalation (biochemistry)

In biochemistry, intercalation is the insertion of molecules between the planar bases of deoxyribonucleic acid (DNA). This process is used as a method for analyzing DNA and it is also the basis of certain kinds of poisoning.

There are several ways molecules (in this case, also known as ligands) can interact with DNA. Ligands may interact with DNA by covalently binding, electrostatically binding, or intercalating. Intercalation occurs when ligands of an appropriate size and chemical nature fit themselves in between base pairs of DNA. These ligands are mostly polycyclic, aromatic, and planar, and therefore often make good nucleic acid stains. Intensively studied DNA intercalators include berberine, ethidium bromide, proflavine, daunomycin, doxorubicin, and thalidomide. DNA intercalators are used in chemotherapeutic treatment to inhibit DNA replication in rapidly growing cancer cells. Examples include doxorubicin (adriamycin) and daunorubicin (both of which are used in treatment of Hodgkin's lymphoma), and dactinomycin (used in Wilm's tumour, Ewing's Sarcoma, rhabdomyosarcoma).

Metallointercalators are complexes of a metal cation with polycyclic aromatic ligands. The most commonly used metal ion is ruthenium(II), because its complexes are very slow to decompose in the biological environment. Other metallic cations that have been used include rhodium(III) and iridium(III). Typical ligands attached to the metal ion are dipyridine and terpyridine whose planar structure is ideal for intercalation. (W)

Intercalation induces structural distortions. Left: unchanged DNA strand. Right: DNA strand intercalated at three locations (black areas).

Ethidium intercalated between two adenine-thymine base pairs.

Interferons (IFNs) are a group of signaling proteins made and released by host cells in response to the presence of several viruses. In a typical scenario, a virus-infected cell will release interferons causing nearby cells to heighten their anti-viral defenses.

IFNs belong to the large class of proteins known as cytokines, molecules used for communication between cells to trigger the protective defenses of the immune system that help eradicate pathogens. Interferons are named for their ability to "interfere" with viral replication by protecting cells from virus infections. IFNs also have various other functions: they activate immune cells, such as natural killer cells and macrophages; they increase host defenses by up-regulating antigen presentation by virtue of increasing the expression of major histocompatibility complex (MHC) antigens. Certain symptoms of infections, such as fever, muscle pain and "flu-like symptoms", are also caused by the production of IFNs and other cytokines.

More than twenty distinct IFN genes and proteins have been identified in animals, including humans. They are typically divided among three classes: Type I IFN, Type II IFN, and Type III IFN. IFNs belonging to all three classes are important for fighting viral infections and for the regulation of the immune system. (W)

Interferon type I (α/β/δ…).
1RH2 Recombinant Human Interferon Alpha 2b.

The molecular structure of human interferon-alpha (PDB: 1RH2​)

Interferon type II (γ).
The three-dimensional structure of human interferon gamma (PDB: 1HIG​).
intergenic region
An Intergenic region (IGR) is a stretch of DNA sequences located between genes. Intergenic regions are a subset of noncoding DNA. Occasionally some intergenic DNA acts to control genes nearby, but most of it has no currently known function. It is one of the DNA sequences sometimes referred to as junk DNA, though it is only one phenomenon labeled such and in scientific studies today, the term is less used. Recently transcribed RNA from the DNA fragments in intergenic regions were known as "dark matter" or "dark matter transcripts". (W)

Illustration of intergenic DNA.

internal transcribed spacer
Internal transcribed spacer (ITS) is the spacer DNA situated between the small-subunit ribosomal RNA (rRNA) and large-subunit rRNA genes in the chromosome or the corresponding transcribed region in the polycistronic rRNA precursor transcript. (W)

Organization of the eukaryotic nuclear ribosomal DNA tandem repeats.
intrinsically disordered proteins
An intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure. IDPs range from fully unstructured to partially structured and include random coils, (pre-)molten globules, and large multi-domain proteins connected by flexible linkers. They are one of the main types of protein along with globular, fibrous and membrane proteins. (W)

Conformational flexibility in SUMO-1 protein (PDB:1a5r). The central part shows relatively ordered structure. Conversely, the N- and C-terminal regions (left and right, respectively) show ‘intrinsic disorder’, although a short helical region persists in the N-terminal tail. Ten alternative NMR models were morphed. Secondary structure elements: α-helices (red), β-strands (blue arrows).

SUMO-1 morphing based on NMR structure 1a5r. Ten alternative NMR models were morphed. Secondary structure elements: α-helices (red), β-strands (blue arrows). Interactive version of figure from: Majorek, Karolina; Kozlowski, Lukasz; Jakalski, Marcin; Bujnicki Janusz M. (2008) First Steps of Protein Structure Prediction. In: Prediction of Protein Structures, Functions, and Interactions Pages: 39-62. DOI: 10.1002/9780470741894.ch2. (W)

An ensemble of NMR structures of the Thylakoid soluble phosphoprotein TSP9, which shows a largely flexible protein chain.
Cartoon representation of the molecular structure of protein registered with 2fft code.

REMARK465 - missing electron densities in X-ray structure representing protein disorder (PDB: 1a22​, human growth hormone bound to receptor). Compilation of screenshots from PDB database and molecule representation via VMD. Blue and red arrows point to missing residues on receptor and growth hormone, respectively.


An intron (for intragenic region) is any nucleotide sequence within a gene that is removed by RNA splicing during maturation of the final RNA product. In other words, introns are non-coding regions of an RNA transcript, or the DNA encoding it, that are eliminated by splicing before translation. The word intron is derived from the term intragenic region, i.e. a region inside a gene. The term intron refers to both the DNA sequence within a gene and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final mature RNA after RNA splicing are exons.

Introns are found in the genes of most organisms and many viruses and can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA) and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA splicing takes place as part of the RNA processing pathway that follows transcription and precedes translation. (W)

Simple illustration of an unspliced mRNA precursor, with two introns and three exons (top). After the introns have been removed via splicing, the mature mRNA sequence is ready for translation (bottom).
ion channel

Ion channels are pore-forming membrane proteins that allow ions to pass through the channel pore. Their functions include establishing a resting membrane potential, shaping action potentials and other electrical signals by gating the flow of ions across the cell membrane, controlling the flow of ions across secretory and epithelial cells, and regulating cell volume. Ion channels are present in the membranes of all cells. Ion channels are one of the two classes of ionophoric proteins, the other being ion transporters.

The study of ion channels often involves biophysics, electrophysiology, and pharmacology, while using techniques including voltage clamp, patch clamp, immunohistochemistry, X-ray crystallography, fluoroscopy, and RT-PCR. Their classification as molecules is referred to as channelomics.

Basic features

There are two distinctive features of ion channels that differentiate them from other types of ion transporter proteins:

  1. The rate of ion transport through the channel is very high (often 106 ions per second or greater).
  2. Ions pass through channels down their electrochemical gradient, which is a function of ion concentration and membrane potential, "downhill", without the input (or help) of metabolic energy (e.g. ATP, co-transport mechanisms, or active transport mechanisms).


Schematic diagram of an ion channel. 1 - channel domains (typically four per channel), 2 - outer vestibule, 3 - selectivity filter, 4 - diameter of selectivity filter, 5 - phosphorylation site, 6 - cell membrane.

Selectivity filter allowing only potassium ions through the potassium channel (PDB: 1K4C).
ionic bonding
Ionic bonding is a type of chemical bonding that involves the electrostatic attraction between oppositely charged ions, and is the primary interaction occurring in ionic compounds. (W)

Sodium and fluorine atoms undergoing a redox reaction to form sodium fluoride. Sodium loses its outer electron to give it a stable electron configuration, and this electron enters the fluorine atom exothermically. The oppositely charged ions – typically a great many of them – are then attracted to each other to form a solid.

Ionic Bonding (a) Sodium readily donates the solitary electron in its valence shell to chlorine, which needs only one electron to have a full valence shell. (b) The opposite electrical charges of the resulting sodium cation and chloride anion result in the formation of a bond of attraction called an ionic bond. (c) The attraction of many sodium and chloride ions results in the formation of large groupings called crystals.
iron response element
In molecular biology, the iron response element or iron-responsive element (IRE) is a short conserved stem-loop which is bound by iron response proteins (IRPs, also named IRE-BP or IRBP). The IRE is found in UTRs (untranslated regions) of various mRNAs whose products are involved in iron metabolism. For example, the mRNA of ferritin (an iron storage protein) contains one IRE in its 5' UTR. When iron concentration is low, IRPs bind the IRE in the ferritin mRNA and cause reduced translation rates. In contrast, binding to multiple IREs in the 3' UTR of the transferrin receptor (involved in iron acquisition) leads to increased mRNA stability. (W)

Iron response element.
Predicted secondary structure and sequence conservation of Iron response element (IRE).
iron-responsive element-binding protein
The iron-responsive element-binding proteins, also known as IRE-BP, IRBP, IRP and IFR , bind to iron-responsive elements (IREs) in the regulation of human iron metabolism. (W)

Iron Regulatory Protein.

jumping library
Jumping libraries or junction-fragment libraries are collections of genomic DNA fragments generated by chromosome jumping. These libraries allow us to analyze large areas of the genome and overcome distance limitations in common cloning techniques. A jumping library clone is composed of two stretches of DNA that are usually located many kilobases away from each other. The stretch of DNA located between these two “ends” is deleted by a series of biochemical manipulations carried out at the start of this cloning technique. (W)

This figure illustrates the basic principle behind jumping libraries.The arrows represent two physically distant sequences which are brought closer together using this method.

This figure is a schematic representation of the method used for creating jumping libraries when it was originally developed in the 80s.

This figure is schematic representation of one of the most recently used methods for creating jumping libraries.
juxtacrine signalling

In biology, juxtacrine signalling (or contact-dependent signalling) is a type of cell–cell or cell–extracellular matrix signalling in multicellular organisms that requires close contact. Hence, this stands in contrast to releasing a signaling molecule by diffusion into extracellular space, the use of long-range conduits like membrane nanotubes and cytonemes (akin to 'bridges') or the use of extracellular vesicles like exosomes or microvesicles (akin to 'boats'). There are three types of juxtacrine signaling:

  1. A membrane ligand (proteinoligosaccharidelipid) and a membrane protein of two adjacent cells interact.
  2. A communicating junction links the intracellular compartments of two adjacent cells, allowing transit of relatively small molecules.
  3. An extracellular matrix glycoprotein and a membrane protein interact.

Additionally, in unicellular organisms such as bacteria, juxtacrine signaling refers to interactions by membrane contact.

Juxtacrine signaling has been observed for some growth factorscytokine and chemokine cellular signals, playing an important role in the immune response. It has a critical role in development, particularly of cardiac and neural function. Other types of cell signaling include paracrine signalling and autocrine signalling.

The term "juxtacrine" was originally introduced by Anklesaria et al. (1990) to describe a possible way of signal transduction between TGF alpha and EGFR.(W)

Notch-mediated juxtacrine signal between adjacent cells.


Karyopherins are a group of proteins involved in transporting molecules between the cytoplasm and the nucleus of a eukaryotic cell. The inside of the nucleus is called the karyoplasm (or nucleoplasm). Generally, karyopherin-mediated transport occurs through the nuclear pore, which acts as a gateway into and out of the nucleus. Most proteins require karyopherins to traverse the nuclear pore.

Karyopherins can act as importins (i.e. helping proteins get into the nucleus) or exportins (i.e. helping proteins get out of the nucleus). They belong to The Nuclear Pore Complex Family in the transporter classification database (TCDB).

Energy for transport is derived from the Ran gradient. See Ran for further details.

Upon stress, several karyopherins stop shuttling between the nucleus and the cytoplasm and are sequestered in stress granules, cytoplasmic aggregates of ribonucleoprotein complexes. (W)

The Ran-GTP cycle.


Ketogenesis is the biochemical process through which organisms produce ketone bodies through breakdown of fatty acids and ketogenic amino acids. This process supplies energy under circumstances such as fasting or caloric restriction to certain organs, particularly the brain, heart and skeletal muscle. Insufficient gluconeogenesis can cause hypoglycemia and excessive production of ketone bodies, ultimately leading to a life-threatening condition known as non-diabetic ketoacidosis.

Ketone bodies are not obligately produced from fatty acids, but rather any meaningful amount of them is synthesized only in a situation of carbohydrate and protein insufficiency, where fatty acids are the only readily available fuel for their production. (W)

Ketogenesis pathway. The three ketone bodies (acetoacetate, acetone, and beta-hydroxy-butyrate) are marked within an orange box.

Ketogenesis pathway. The enzymes are coloured red, the substrates/products are coloured blue. The three ketone bodies (acetoacetate, acetone and beta-hydroxy-butyrate) are marked within an orange box. (W)


Ketone group.

In chemistry, a ketone is a functional group with the structure RC(=O)R', where R and R' can be a variety of carbon-containing substituents. Ketones contain a carbonyl group (a carbon-oxygen double bond). The simplest ketone is acetone (R = R' = methyl), with the formula CH3C(O)CH3. Many ketones are of great importance in industry and in biology. Examples include many sugars (ketoses), many steroids (e.g., testosterone), and the solvent acetone. (W)

Representative ketones, from the left: acetone, a common solvent; oxaloacetate, an intermediate in the metabolism of sugars; acetylacetone in its (mono) enol form (the enol highlighted in blue); cyclohexanone, precursor to nylon; muscone, an animal scent; and tetracycline, an antibiotic.
ketone bodies

Ketone bodies are the water-soluble molecules (acetoacetate, beta-hydroxybutyrate, and the spontaneous breakdown product of acetoacetate, acetone) containing the ketone group that are produced by the liver from fatty acids during periods of low food intake (fasting), carbohydrate restrictive diets, starvation, prolonged intense exercise, alcoholism, or in untreated (or inadequately treated) type 1 diabetes mellitus. Ketone bodies are readily transported into tissues outside the liver and converted into acetyl-CoA, which then enters the citric acid cycle and is oxidized in the mitochondria for energy. In the brain, ketone bodies are also used to make acetyl-CoA into long-chain fatty acids.

Ketone bodies are produced by the liver under the circumstances listed above, resultant of intense gluconeogenesis, which is the production of glucose from non-carbohydrate sources (including fatty acids). They are therefore always released into the blood by the liver together with newly produced glucose after the liver glycogen stores have been depleted (these glycogen stores are depleted within the first 24 hours of fasting). (W)

Ketosis is a metabolic state characterized by elevated levels of ketone bodies in the blood or urine. Physiologic ketosis is a normal response to low glucose availability, such as low-carbohydrate diets or fasting, that provides an additional energy source for the brain in the form of ketones. In physiologic ketosis, ketones in the blood are elevated above baseline levels, but the body's acid-base homeostasis is maintained. This contrasts with ketoacidosis, an uncontrolled production of ketones that occurs in pathologic states and causes a metabolic acidosis, which is a medical emergency. Ketoacidosis is most commonly the result of complete insulin deficiency in type 1 diabetes or late-stage type 2 diabetes. Ketone levels can be measured in blood, urine or breath and are generally between 0.5 and 3.0 millimolar (mM) in physiologic ketosis, while ketoacidosis may cause blood concentrations greater than 10 mM. (W)

Biochemical pathway of ketone synthesis in the liver and utilization by organs.

In biochemistry, a kinase is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the substrate gains a phosphate group and the high-energy ATP molecule donates a phosphate group. This transesterification produces a phosphorylated substrate and ADP. Conversely, it is referred to as dephosphorylation when the phosphorylated substrate donates a phosphate group and ADP gains a phosphate group (producing a dephosphorylated substrate and the high energy molecule of ATP). These two processes, phosphorylation and dephosphorylation, occur four times during glycolysis.

Kinases are part of the larger family of phosphotransferases. Kinases should not be confused with phosphorylases, which catalyze the addition of inorganic phosphate groups to an acceptor, nor with phosphatases, which remove phosphate groups (dephosphorylation). The phosphorylation state of a molecule, whether it be a protein, lipid or carbohydrate, can affect its activity, reactivity and its ability to bind other molecules. Therefore, kinases are critical in metabolism, cell signalling, protein regulation, cellular transport, secretory processes and many other cellular pathways, which makes them very important to human physiology. (W)

Dihydroxyacetone kinase in complex with a non-hydrolyzable ATP analog (AMP-PNP). Coordinates from PDB ID:1UN9.

General reaction that is catalyzed by kinases.

Overview of signal transduction pathways. Many of the proteins involved are kinases, including protein kinases (such as MAPK and JAK) and lipid kinases (such as PI3K).

A variety of mitogenic signals engage the MAPK pathway and promote cell growth and differentiation through a kinase cascade.

Glycolysis includes four phosphorylations, two that create ATP from ADP and two that use ATP and converting it into ADP. Glycolysis is the first step of metabolism and includes ten reaction ultimately resulting in one glucose molecule producing two pyruvate molecules.

The active site of riboflavin kinase bound to its products--FMN (on left) and ADP (on right). Coordinates from PDB ID: 1N07.


A kinesin is a protein belonging to a class of motor proteins found in eukaryotic cells.

Kinesins move along microtubule (MT) filaments, and are powered by the hydrolysis of adenosine triphosphate (ATP) (thus kinesins are ATPases), a type of enzyme. The active movement of kinesins supports several cellular functions including mitosis, meiosis and transport of cellular cargo, such as in axonal transport. Most kinesins walk towards the plus end of a microtubule, which, in most cells, entails transporting cargo such as protein and membrane components from the center of the cell towards the periphery . This form of transport is known as anterograde transport. In contrast, dyneins are motor proteins that move toward the minus end of a microtubule in retrograde transport. (W)

The kinesin dimer (red) attaches to, and moves along, microtubules (blue and green).

Mobile and self-inhibited conformations of kinesin-1. Self-inhibited conformation:IAK region of the tail (green) binds to motor domains (yellow and orange) to inhibit the enzymatic cycle of kinesin-1.Mobile conformation: Absent the tail binding, kinesin-1 motor domains (yellow and orange) can move freely along the microtubule(MT). PDB 2Y65; PDB 2Y5W.

Detailed view of kinesin-1 self-inhibition (one of two possible conformations shown). Highlight: positively charged residues (blue) of the IAK region interact at multiple locations with negatively charged residues (red) of the motor domains PDB 2Y65.

Animation of kinesin "walking" on a microtubule

Diagram illustrating motility of kinesin.
In molecular biology, biochemistry and cell signaling the kinome of an organism is the complete set of protein kinases encoded in its genome. Kinases are usually enzymes that catalyze phosphorylation reactions (of amino acids) and fall into several groups and families, e.g., those that phosphorylate the amino acids serine and threonine, those that phosphorylate tyrosine and some that can phosphorylate both, such as the MAP2K and GSK families. The term was first used in 2002 by Gerard Manning and colleagues in twin papers analyzing the 518 human protein kinases, and refers to both protein kinases and protein pseudokinases and their evolution of protein kinases throughout the eukaryotes. Other kinomes have been determined for rice, several fungi, nematodes, and insects, sea urchins, Dictyostelium discoideum, and the process of infection by Mycobacterium tuberculosis. Although the primary sequence of protein kinases shows substantial divergence between unrelated eukaryotes, and amino acid differences in catalytic motifs have permitted their separation of kinomes into canonical and pseudokinase subtypes, the variation found in the amino acid motifs adjacent to the site of actual phosphorylation of substrates by eukaryotic kinases is much smaller. (W)


lac operon

The lactose operon (lac operon) is an operon required for the transport and metabolism of lactose in E.coli and many other enteric bacteria. Although glucose is the preferred carbon source for most bacteria, the lac operon allows for the effective digestion of lactose when glucose is not available through the activity of beta-galactosidase. Gene regulation of the lac operon was the first genetic regulatory mechanism to be understood clearly, so it has become a foremost example of prokaryotic gene regulation. It is often discussed in introductory molecular and cellular biology classes for this reason. This lactose metabolism system was used by François Jacob and Jacques Monod to determine how a biological cell knows which enzyme to synthesize. Their work on the lac operon won them the Nobel Prize in Physiology in 1965.

Bacterial operons are polycistronic transcripts that are able to produce multiple proteins from one mRNA transcript. In this case, when lactose is required as a sugar source for the bacterium, the three genes of the lac operon can be expressed and their subsequent proteins translated: lacZ, lacY, and lacA. The gene product of lacZ is β-galactosidase which cleaves lactose, a disaccharide, into glucose and galactose. lacY encodes Beta-galactoside permease, a membrane protein which becomes embedded in the cytoplasmic membrane to enable the cellular transport of lactose into the cell. Finally, lacA encodes Galactoside acetyltransferase. (W)

Layout of the lac operon.

The lac operon. Top: Repressed, Bottom: Active. 1: RNA polymerase, 2: Repressor, 3: Promoter, 4: Operator, 5: Lactose, 6: lacZ, 7: lacY, 8: lacA.

1: RNA Polymerase, 2: Repressor, 3: Promoter, 4: Operator, 5: Lactose, 6: lacZ, 7: lacY, 8: lacA. Top: The gene is essentially turned off. There is no lactose to inhibit the repressor, so the repressor binds to the operator, which obstructs the RNA polymerase from binding to the promoter and making lactase. Bottom: The gene is turned on. Lactose is inhibiting the repressor, allowing the RNA polymerase to bind with the promoter, and express the genes, which synthesize lactase. Eventually, the lactase will digest all of the lactose, until there is none to bind to the repressor. The repressor will then bind to the operator, stopping the manufacture of lactase. (W)

Structure of lactose and the products of its cleavage.


Lactose is a disaccharide. It is a sugar composed of galactose and glucose subunits and has the molecular formula C12H22O11. Lactose makes up around 2–8% of milk (by weight). The name comes from lac (gen. lactis), the Latin word for milk, plus the suffix -ose used to name sugars. The compound is a white, water-soluble, non-hygroscopic solid with a mildly sweet taste. It is used in the food industry (W)

Structure of beta-D-Lactose.

The molecular structure of α-lactose, as determined by X-ray crystallography.
Lewis structure
Lewis structures, also known as Lewis dot diagrams, Lewis dot formulas, Lewis dot structures, electron dot structures, or Lewis electron dot structures (LEDS), are diagrams that show the bonding between atoms of a molecule and the lone pairs of electrons that may exist in the molecule. (W)

Two lewis structures of the canonical structures of the nitrite ion, NO2−.

ligand (biochemistry)

In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. The binding typically results in a change of conformational isomerism (conformation) of the target protein. In DNA-ligand binding studies, the ligand can be a small molecule, ion, or protein which binds to the DNA double helix. The relationship between ligand and binding partner is a function of charge, hydrophobicity, and molecular structure. The instance of binding occurs over an infinitesimal range of time and space, so the rate constant is usually a very small number. (W)

Myoglobin (blue) with its ligand heme (orange) bound. Based on PDB: 1MBO.
ligand-gated ion channel

Ligand-gated ion channels (LICs, LGIC), also commonly referred to as ionotropic receptors, are a group of transmembrane ion-channel proteins which open to allow ions such as Na+, K+, Ca2+, and/or Cl- to pass through the membrane in response to the binding of a chemical messenger (i.e. a ligand), such as a neurotransmitter.

When a presynaptic neuron is excited, it releases a neurotransmitter from vesicles into the synaptic cleft. The neurotransmitter then binds to receptors located on the postsynaptic neuron. If these receptors are ligand-gated ion channels, a resulting conformational change opens the ion channels, which leads to a flow of ions across the cell membrane. This, in turn, results in either a depolarization, for an excitatory receptor response, or a hyperpolarization, for an inhibitory response.

These receptor proteins are typically composed of at least two different domains: a transmembrane domain which includes the ion pore, and an extracellular domain which includes the ligand binding location (an allosteric binding site). This modularity has enabled a 'divide and conquer' approach to finding the structure of the proteins (crystallising each domain separately). The function of such receptors located at synapses is to convert the chemical signal of presynaptically released neurotransmitter directly and very quickly into a postsynaptic electrical signal. Many LICs are additionally modulated by allosteric ligands, by channel blockers, ions, or the membrane potential. LICs are classified into three superfamilies which lack evolutionary relationship: cys-loop receptors, ionotropic glutamate receptors and ATP-gated channels. (W)

Ligand-gated ion channel.

Neurotransmitter-gated ion-channel transmembrane region.

Ion-channel-linked receptor Ions Ligand (such as acetylcholine) When ligands bind to the receptor, the ion channel portion of the receptor opens, allowing ions to pass across the cell membrane.

Ion Channel Receptor Ions Ligand (such as acetylcholine) This is an example of an ion channel-receptor. On the left, the channel is closed, because the ligand (dark purple triangle) has not binded to the receptor. When the ligand binds to the receptor, the channel opens, and the ions (orange circles) can freely flow through the membrane. In a neuromuscular junction, these are used to transfer the action potential from the neuron to the muscle. The ligand is acetylcholine, and when it binds to the ion channel receptor on the membrane of the muscle, the channel opens and allows sodium ions to flow into the muscle..

Nicotinic acetylcholine receptor in closed state with predicted membrane boundaries shown, PDB 2BG9.

Regulation of AMPAR trafficking to the postsynaptic density in response to LTP-inducing stimuli.

Figure 1. Schematic representation showing the membrane topology of a typical P2X receptor subunit. First and second transmembrane domains are labeled TM1 and TM2.

light-dependent reactions

In photosynthesis, the light-dependent reactions take place on the thylakoid membranes. The inside of the thylakoid membrane is called the lumen, and outside the thylakoid membrane is the stroma, where the light-independent reactions take place. The thylakoid membrane contains some integral membrane protein complexes that catalyze the light reactions. There are four major protein complexes in the thylakoid membrane: Photosystem II (PSII), Cytochrome b6f complex, Photosystem I (PSI), and ATP synthase. These four complexes work together to ultimately create the products ATP and NADPH. (W)

Light-dependent reactions of photosynthesis at the thylakoid membrane.

Lignin is a class of complex organic polymers that form key structural materials in the support tissues of vascular plants and some algae. Lignins are particularly important in the formation of cell walls, especially in wood and bark, because they lend rigidity and do not rot easily. Chemically, lignins are cross-linked phenolic polymers. (W)

An example of a possible lignin structure. The portion shown here (not counting the side chain denoted "Carbohydrate") has 28 monomers (mostly coniferyl alcohol), 278 carbon atoms, 407 hydrogen atoms, and 94 oxygen atoms (64% carbon, 8% hydrogen, and 29% oxygen by weight) which seems to be too high in hydrogen.

In biology and biochemistry, a lipid is a macrobiomolecule that is soluble in nonpolar solvents. Non-polar solvents are typically hydrocarbons used to dissolve other naturally occurring hydrocarbon lipid molecules that do not (or do not easily) dissolve in water, including fatty acids, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E, and K), monoglycerides, diglycerides, triglycerides, and phospholipids.

The functions of lipids include storing energy, signaling, and acting as structural components of cell membranes. Lipids have applications in the cosmetic and food industries as well as in nanotechnology. (W)

Structures of some common lipids. At the top are cholesterol and oleic acid. The middle structure is a triglyceride composed of oleoyl, stearoyl, and palmitoyl chains attached to a glycerol backbone. At the bottom is the common phospholipid phosphatidylcholine.

Structure of the saccharolipid Kdo2-lipid A. Glucosamine residues in blue, Kdo residues in red, acyl chains in black and phosphate groups in green.

Self-organization of phospholipids: a spherical liposome, a micelle, and a lipid bilayer.

Structure of a triacylglycerol lipid.

lipid metabolism
Lipid metabolism is the synthesis and degradation of lipids in cells, involving the breakdown or storage of fats for energy and the synthesis of structural and functional lipids, such as those involved in the construction of cell membranes. In animals, these fats are obtained from food or are synthesized by the liver. Lipogenesis is the process of synthesizing these fats. The majority of lipids found in the human body from ingesting food are triglycerides and cholesterol. Other types of lipids found in the body are fatty acids and membrane lipids. Lipid metabolism is often considered as the digestion and absorption process of dietary fat; however, there are two sources of fats that organisms can use to obtain energy: from consumed dietary fats and from stored fat. Vertebrates (including humans) use both sources of fat to produce energy for organs such as the heart to function. Since lipids are hydrophobic molecules, they need to be solubilized before their metabolism can begin. Lipid metabolism often begins with hydrolysis, which occurs with the help of various enzymes in the digestive system. Lipid metabolism also occurs in plants, though the processes differ in some ways when compared to animals. The second step after the hydrolysis is the absorption of the fatty acids into the epithelial cells of the intestinal wall. In the epithelial cells, fatty acids are packaged and transported to the rest of the body. (W)

Breakdown of fatty acids by beta oxidation.
Beta oxidation of palmitic acid.


The lipidome refers to the totality of lipids in cells. Lipids are one of the four major molecular components of biological organisms, along with proteins, sugars and nucleic acids. Lipidome is a term coined in the context of omics in modern biology, within the field of lipidomics. It can be studied using mass spectrometry and bioinformatics as well as traditional lab-based methods. The lipidome of a cell can be subdivided into the membrane-lipidome and mediator-lipidome.

The first cell lipidome to be published was that of a mouse macrophage in 2010. The lipidome of the yeast Saccharomyces cerevisiae has been characterised with an estimated 95% coverage; studies of the human lipidome are ongoing. For example, the human plasma lipidome consist of almost 600 distinct molecular species. Research suggests that the lipidome of an individual may be able to indicate cancer risks associated with dietary fats, particularly breast cancer. (W)

The lipodome in connection with the total interactome of a cell.

The quantitative lipidome (on the level of lipid classes) of yeast Saccharomyces cerevisiae in different phases of growth.

Lipidomics of yeast in different growth phases. Yeast cells were grown in SCglc at 30°C and harvested in early logarithmic (OD1), middle logarithmic (OD3.5) and early stationary (OD6) phase as well as after overnight growth (ODstat). Lipid class composition in mol% of total lipids in the sample. LysoPS and ceramides as minor constituents are not shown. Inset: Growth curve with data points indicated by arrowheads. All data were calculated from n=3 independent samples ± SD. (W)
Lipidomics is the large-scale study of pathways and networks of cellular lipids in biological systems. The word "lipidome" is used to describe the complete lipid profile within a cell, tissue, organism, or ecosystem and is a subset of the "metabolome" which also includes the three other major classes of biological molecules: proteins/amino-acids, sugars and nucleic acids. Lipidomics is a relatively recent research field that has been driven by rapid advances in technologies such as mass spectrometry (MS), nuclear magnetic resonance (NMR) spectroscopy, fluorescence spectroscopy, dual polarisation interferometry and computational methods, coupled with the recognition of the role of lipids in many metabolic diseases such as obesity, atherosclerosis, stroke, hypertension and diabetes. This rapidly expanding field complements the huge progress made in genomics and proteomics, all of which constitute the family of systems biology. (W)

General schema showing the relationships of the lipidome to the genome, transcriptome, proteome and metabolome. Lipids also regulate protein function and gene transcription as part of a dynamic "interactome" within the cell.

Schema showing detection of a fatty acid by LC-MS/MS using a linear ion-trap instrument and an electrospray (ESI) ion source.

Quantitative lipid profiles (lipidomes) of yeast Saccharomyces cerevisiae grown in different temperatures.

Lipidomics of yeast grown in different temperatures. Yeast cells were grown in SCglc at 15°C (T15), 24°C (T24) 30°C (T30) and 37°C (T37). A) Lipid class composition in mol% of total lipids in the sample. LysoPS and ceramides as minor constituents are not shown. B) Total double bonds of glycerophospholipids (CL omitted for clarity), given as sum of double bounds in fatty acids, in mol% of category. C) Total length of glycerophospholipids, given as sum of fatty acids, in mol% of category. Lysospecies and cardiolipin lengths are omitted for clarity. D) Phosphatidylcholine (PC) species profile in mol% of class. The least abundant species are not shown. E) Sphingolipid species profile in mol% of category. All data were calculated from n=3 independent samples ± SD. .

Lipopolysaccharides (LPS), also known as endotoxins, are large molecules consisting of a lipid and a polysaccharide composed of O-antigen, outer core and inner core joined by a covalent bond; they are found in the outer membrane of Gram-negative bacteria.

The term lipooligosaccharide ("LOS") is used to refer to a low-molecular-weight form of bacterial lipopolysaccharides. (W)

Structure of a lipopolysaccharide.

The saccharolipid Kdo2-Lipid A. Kdo residues in red (core), glucosamine residues in blue, acyl chains in black and phosphate groups in green.

A lipoprotein is a biochemical assembly whose primary purpose is to transport hydrophobic lipid (also known as fat) molecules in water, as in blood plasma or other extracellular fluids. They consist of a Triglyceride and Cholesterol center, surrounded by a phospholipid outer shell, with the hydrophilic portions oriented outward toward the surrounding water and lipophilic portions oriented inward toward the lipid center. A special kind of protein, called apolipoprotein, is embedded in the outer shell, both stabilising the complex and giving it a functional identity that determines its fate.

Many enzymes, transporters, structural proteins, antigens, adhesins, and toxins are lipoproteins. Examples include plasma lipoprotein particles (HDL, LDL, IDL, VLDL and chylomicrons). Subgroups of these plasma particles are primary drivers or modulators of atherosclerosis.


Structure of a chylomicron. ApoA, ApoB, ApoC, ApoE are apolipoproteins; green particles are phospholipids; T is triacylglycerol; C is cholesterol ester.

Chylomicron structure ApoA, ApoB, ApoC, ApoE (apolipoproteins); T (triacylglycerol); C (cholesterol); green (phospholipids).

Simplified flowchart showing the essentials of lipoprotein metabolism.

A diagram to the endogenous and exogenous pathways of lipoprotein metabolism.

📹 Lipoproteins / blausen (LINK)


Lipoproteins are defined as protein-bound lipids that are transported to cells. The phospholipid and protein surface makes these lipids soluble in the bloodstream. The five major groups of lipoproteins include chylomicron, VLDL, IDL, LDL, and HDL.

A liposome is a spherical vesicle having at least one lipid bilayer. The liposome can be used as a vehicle for administration of nutrients and pharmaceutical drugs. Liposomes can be prepared by disrupting biological membranes (such as by sonication).

Liposomes are most often composed of phospholipids, especially phosphatidylcholine, but may also include other lipids, such as egg phosphatidylethanolamine, so long as they are compatible with lipid bilayer structure. A liposome design may employ surface ligands for attaching to unhealthy tissue.

The major types of liposomes are the multilamellar vesicle (MLV, with several lamellar phase lipid bilayers), the small unilamellar liposome vesicle (SUV, with one lipid bilayer), the large unilamellar vesicle (LUV), and the cochleate vesicle. A less desirable form are multivesicular liposomes in which one vesicle contains one or more smaller vesicles.

Liposomes should not be confused with lysosomes, or with micelles and reverse micelles composed of monolayers (W)

Scheme of a liposome formed by phospholipids in an aqueous solution.
Schema of a liposome showing phospholipid bilayer surrounding an aqueous interior and excluding an aqueous exterior environment .

Liposomes are composite structures made of phospholipids and may contain small amounts of other molecules. Though liposomes can vary in size from low micrometer range to tens of micrometers, unilamellar liposomes, as pictured here, are typically in the lower size range with various targeting ligands attached to their surface allowing for their surface-attachment and accumulation in pathological areas for treatment of disease.

Lysis (Greek λύσις lýsis, "a loosing" from λύειν lýein, "to unbind") is the breaking down of the membrane of a cell, often by viralenzymic, or osmotic (that is, "lytic") mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a lysate. In molecular biologybiochemistry, and cell biology laboratories, cell cultures may be subjected to lysis in the process of purifying their components, as in protein purificationDNA extractionRNA extraction, or in purifying organelles.

Many species of bacteria are subject to lysis by the enzyme lysozyme, found in animal salivaegg white, and other secretions. Phage lytic enzymes (lysins) produced during bacteriophage infection are responsible for the ability of these viruses to lyse bacterial cells. Penicillin and related β-lactam antibiotics cause the death of bacteria through enzyme-mediated lysis that occurs after the drug causes the bacterium to form a defective cell wall. If the cell wall is completely lost and the penicillin was used on gram-positive bacteria, then the bacterium is referred to as a protoplast, but if penicillin was used on gram-negative bacteria, then it is called a spheroplast. (W)

Epidermis cells of Rhoeo Discolor (Tradescantia) after plasmolysis. The vacuoles (pink) have shrunk. Size: Field of view ca. 450 µm.
lysogenic cycle
Lysogeny, or the lysogenic cycle, is one of two cycles of viral reproduction (the lytic cycle being the other). Lysogeny is characterized by integration of the bacteriophage nucleic acid into the host bacterium's genome or formation of a circular replicon in the bacterial cytoplasm. In this condition the bacterium continues to live and reproduce normally. The genetic material of the bacteriophage, called a prophage, can be transmitted to daughter cells at each subsequent cell division, and at later events (such as UV radiation or the presence of certain chemicals) can release it, causing proliferation of new phages via the lytic cycle. Lysogenic cycles can also occur in eukaryotes, although the method of DNA incorporation is not fully understood. (W)

Lysogenic cycle, compared to lytic cycle.

Lysogenic Cycle:1. The prokaryotic cell is shown with its DNA, in green. 2. The bacteriophage attaches and releases its DNA, shown in red, into the prokaryotic cell. 3. The phage DNA then moves through the cell to the host’s DNA. 4. The phage DNA integrates itself into the host cell's DNA, creating prophage. 5. The prophage then remains dormant until the host cell divides. 6. After the host cell has divided, the phage DNA in the daughter cells activate, and the phage DNA begins to express itself. Some of the cells containing the prophage go on to create new phages which will move on to infect other cells.
lytic cycle

The lytic cycle  is one of the two cycles of viral reproduction (referring to bacterial viruses or bacteriophages), the other being the lysogenic cycle. The lytic cycle results in the destruction of the infected cell and its membrane. Bacteriophages that only use the lytic cycle are called virulent phages (in contrast to temperate phages).

In the lytic cycle, the viral DNA exist separate free floating molecule within the bacterial cell, and replicates separately from the host bacterial DNA, whereas in the lysogenic cycle, the viral DNA is located within the host DNA. This is the key difference between the lytic and lysogenic (bacterio)phage cycles. However, in both cases the virus/phage replicates using the host DNA machinery. (W)

Lytic cycle, compared to lysogenic cycle.