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4.1: Introduction to Functional Groups - Biology

4.1: Introduction to Functional Groups - Biology


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Categorize molecules according to their functional group

In this outcome, we’ll learn about functional groups and the effects they have on the molecules they are bonded to.

What You’ll Learn to Do

  • Identify the attributes of molecules with hydroxyl groups
  • Identify the attributes of molecules with carboxyl groups
  • Identify the attributes of molecules with amino groups
  • Identify the attributes of molecules with phosphate groups
  • Identify the attributes of molecules with methyl groups
  • Identify the attributes of molecules with carbonyl groups
  • Identify the attributes of molecules with sulfhydryl groups

Learning Activities

The learning activities for this section include the following:

  • Functional Groups
  • Self Check: Functional Groups

Consequences of the introduction of exotic and translocated species and future extirpations on the functional diversity of freshwater fish assemblages

Correspondence: Shin-ichiro S. Matsuzaki, Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba-shi, Ibaraki 305-8506, Japan.

Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8653 Japan

Department of Ecoregion Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509 Japan

Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba-shi, Ibaraki, 305-8506 Japan

Correspondence: Shin-ichiro S. Matsuzaki, Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba-shi, Ibaraki 305-8506, Japan.

Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8653 Japan

Department of Ecoregion Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509 Japan

Abstract

To explore the effects of the introduction of exotic and translocated species and possible future extirpation of native species on the functional diversity (FD) of freshwater fish assemblages.

Location

Methods

We examined spatio-temporal changes in species richness, FD, functional richness (the number of trait-based functional groups), and the functional group composition between historical and current fish assemblages for 27 eco-regions, and compared the relative effects of the introduction of exotic and translocated species on FD. We also used a null model approach to determine the assembly patterns and the extent of functional redundancy. Finally, we determined the effect of the loss of endangered species on FD by comparing the observed losses with simulated random loss.

Results

Through the introductions of non-native species, the species richness, FD and functional richness of the fish assemblages increased 2.4-, 1.6- and 2.1-fold, respectively. The functional group composition also changed largely through the additions of new functional groups. Exotic species had a significantly greater effect size than translocated species, but there were no differences in the overall net effects of exotic and translocated species. Null modelling approaches showed that the observed FD was higher than expected by chance (i.e. trait divergent) in both historical and current assemblages. There was also low functional redundancy. In our simulation, FD decreased in proportion to the loss of species, independent of whether the species were endangered.

Main conclusions

We demonstrated that both exotic and translocated species may change FD and functional group composition, which might have dramatic consequences for ecosystem processes. We suggest that the future extirpation of even a few native species can cause a substantial loss of FD. Our findings emphasize the need to improve conservation strategies based on species richness and conservation status, and to incorporate translocated species into targets of the management of non-native species.

Figure S1 Functional relationships among 110 freshwater fish species in Japan including native and exotic species. The numbers correspond to fish ID in Table S1 (black in bold: exotic species grey in bold: translocated species grey: native species). The vertical line indicates the partitioning level defining 17 functional groups (see also text).

Figure S2 Relationship between the cophenetic (or ultrametric) distance matrix derived from the dendrogram and the original distance matrix based on the Gower distance.

Table S1 Freshwater fish species evaluated in the study, including status, biogeographical realm, and historical and current distributions.

Table S2 Summary of functional groups constructed based on the dendrogram produced by UPGMA of the distance matrix calculated from the functional traits of species.

Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.


1.2 What is a wound?

A wound is described as a break or a defect in the skin, which can result from thermal or physical damage or in the presence of an underlying physiological or medical condition (5). It is a disruption of normal anatomic structure and function (6). Acute wounds normally progress through a systematic and timely reparative process that results in continual restoration of anatomic and functional integrity. Chronic wounds have failed to proceed through an orderly and timely process to produce anatomic and functional integrity, or proceeded through the repair process without establishing a sustained anatomic and functional result (6).


Fungi: Meaning, Characteristics and Occurrence | Botany

Fungi (singular fungus — mushroom, from Greek) are chlorophyll-less thallophytic plant. Due to absence of chlorophyll, they are heterophytes i.e., depend on others for food. They grow in various habitats and show much diversity in their structure, physiology and reproduction. They developed long back in the geological time scale.

Their existence was found from fossil records of Pre-Cambrian period. Information from ancient literature indicates that the fungi were used as food by human beings. At present, the fungi are used in medicine and also as food in addition to other aspects. The fungi cause diseases of crops (spots, rusts and smuts etc.) and on human beings (Aspergillosis, Blastomycosis etc.).

Some of the plant diseases like late blight of potato (c.o. Phytophthora infestans) and brown spot of rice (c.o. Helminthosporium oryzae) caused famine in Ireland (1845) and in West Bengal (India) (1943), respectively.

More than 5,000 genera and 50,000 species of fungi have been recorded, but their number may be much more than the actual record. The subject which deals with fungi is known as Mycology (mykes — mushroom logos— study) and the concerned scientist is called mycologist.

The various definitions of fungi as proposed by mycologists are:

1. Alexopoulos (1962):

Alexopoulos (1962) defined fungi as “nucleated, spore-bearing, achlorophyllous organisms which generally reproduce sexu­ally and asexually and whose usually fila­mentous, branched somatic structures are typically surrounded by cell walls contai­ning cellulose or chitin or both”.

2. Alexopoulos and Mims (1979):

Alexopoulos and Mims (1979) defined fungi as eukaryotic spore bearing, achlorophyl­lous organisms that generally reproduce sexually and asexually, and whose usually filamentous, branched somatic structures are typically surrounded by cell walls con­taining chitin or cellulose, or both of these substances, together with many other com­plex organic molecules”.

Characteristics of Fungi:

1. Fungi are cosmopolitan in distribution i.e., they can grow in any place where life is possible.

2. They are heterotrophic in nature due to the absence of chlorophyll. On the basis of their mode of nutrition, they may be parasite, saprophyte or symbionts.

3. The plant body may be unicellular (Synchytrium, Saccharomyces) or filamen­tous (Mucor, Aspergillus). The filament is known as hypha (plural, hyphae) and its entangled mass is known as mycelium.

4. The hypha may be aseptate i.e., coenocytic (without septa and containing many nuclei) or septate. The septate mycelium in its cell may contain only one (monokaryotic), two (dikaryotic) or more nuclei.

5. The septa between the cell may have different types of pores: micropore (Geotri- chum), simple pore (most of the Ascomycotina and Deuteromycotina) or dolipore (Basidiomycotina, except rusts and smuts).

6. The cells are surrounded by distinct cell wall (except slime molds), composed of fungal cellulose i.e., chitin but in some lower fungi (members of Oomycetes), the cell wall is composed of cellulose or glucan.

7. The cells generally contain colourless proto­plasm due to absence of chlorophyll, contai­ning nucleus, mitochondria, endoplasmic reti­culum, ribosomes, vesicle, microbodies, etc.

8. The cells are haploid, dikaryotic or diploid. The diploid phase is ephemeral (short-lived).

9. In lower fungi like Mastigomycotina, the reproductive cells (zoospores and gametes) may be uni- or biflagellate, having whiplash and/or tinsel type of flagella. But in higher fungi like Zygomycotina, Ascomycotina, Basidiomycotina and Deuteromycotina, motile cells never form at any stage.

10. In response to functional need, the fungal mycelia are modified into different types such as: Plectenchyma, Stroma, Rhizo- morph, Sclerotium, Hyphal trap, Appreso- rium, Haustorium, etc.

11. The unicellular fungi, where entire plant body becomes converted into reproductive unit, are known as holocarpic fungi (e.g., Synchytrium). However, in many others, only a part of the mycelial plant body is con­verted into reproductive unit, thus they are called eucarpic fungi (e.g., Pythium, Phytophthora).

12. They reproduce by three means: Vegetative, asexual and sexual.

(a) Vegetative reproduction takes place by fragmentation (Mucor, Penicillium, Fusarium), budding (Saccharomyces, Ustilago) and fission (Saccharomyces).

(b) Asexual reproduction takes place by different types of spores. These are zoospores (Synchytrium), conidia (Pythium, Aspergillus), oidia (Rhizo- pus), chlamydospore (Fusarium), etc. The spores may be unicellular (Asper­gillus) or multicellular (Alternaria).

(c) With the Exception of Deuteromycotina, Sexual Reproduction takes Place by the following Five Processes:

Gametic copulation (Synchytrium), Gametangial contact (Pythium, Phytophthora), Game­tangial copulation (Rhizopus, Mucor), Spermatization (Puccinia, Podospora) and Somatogamy (Polyporus, Agaricus).

General Account:

The fungi are chlorophyll-less thallophytes or achlorophyllous non-vascular plants.

Occurrence of Fungi:

The fungi are cosmopolitan in distribution and occur in all possible habitats. Due to absence of chlorophyll, they depend on other for food, that is why they may be saprophytes, parasites or symbionts.

Most of the fungi are ter­restrial which grow in soil, on dead and decay­ing organic material. Some grow on both plants and animals. They can grow on foods like jam, bread, fruits etc. Some members are also found in water — aquatic fungi. They are also present in the air. Thus the fungi are universal in their distribution.

Vegetative Structure of Fungi:

Except certain unicellular forms (Fig. 4.1 A) like Synchytrium, Saccharomyces the fungi are generally thalloid and filamentous type. The fila­ments are known as the hyphae (sing, hapha). The tangled mass of these hyphae is the myceli­um. The hypha may be aseptate which contains many nuclei and vacuolated cytoplasm. The multinucleate tubular aseptate hypha is called coenocyte (Fig. 4.1 C).

On the other hand, hypha that has partition walls dividing the hypha into many cells is called septate (Fig. 4.1 D-F). The septate mycelium in its cell may contain only one (monokaryotic), two (dikaryotic) or many nuclei (multinucleate) with vacuolated protoplasm.

The septa between the cells may have different types of pores. In Geotrichum, small pores are present on the wall, called micropore (Fig. 4.2A), when only one bigger sized pore is present on the wall, it is called simple pore (Fig. 4.2B), found in most of the Ascomycotina and Deuteromycotina.

In Trichomycetes and Mucorales, the pore is sur­rounded by an overarching bifurcation of the margin of partition wall which looks like a bor­dered pit of tracheid. A biumbonate, electron dense plug of material is present between the two bifurcations (Fig. 4.2C).

But in Basidiomycotina, except rust and smuts, the complicated type of pore with single opening is called dolipore (dolium, a large Jar or cash, i.e., barrel) septum (Fig. 4.2D).

Lastly in lower fungi, the older part and the basal region of reproductive part forming partition wall, without any pore, is called solid septum (Fig. 4.2E).

The cells have distinct cell wall (except slime molds), made up of fungal cellulose i.e., chitin along with other substances. Fungal cells have chlorophyll-less vacuolated protoplasm, which contains nuclei/nucleus, mitochondria, endoplasmic reticulum, ribosomes, microbodies, vesicles, etc. (Fig. 4.3). The chief reserve foods are glycogen and oil.

Mycelium that contains only one nucleus (n) in each cell is called monokaryotic mycelium or primary mycelium. Whereas, in many cases, cells of mycelium contain two nuclei i.e., binucleate (n + n), formed due to transfer of nuclei from one monokaryotic mycelium to the other and ini­tially form dikaryotic cell and then to dikaryotic mycelium or secondary mycelium by growth with the help of clamp connection.

The cell may contain diploid nucleus (2n), formed by the fusion of two haploid nuclei (n) of opposite strain. But this stage is ephimeral (Fig. 4.1 E, F).

In lower fungi i.e., members of sub-division Mastigomycotina, the reproductive cells (zoos­pores or gametes) may be uni- or biflagellate with (9 + 2) organisation having either whiplash (acronematic type) i.e., smooth-walled flagella and/or tinsel (pantonematic type) i.e., flagella covered with many minute hair-like mastigonemes or flimers, those originate from the axile filament (Fig. 4.4, 4.5).

The tinsel type gives for­ward movement and the whiplash type gives beating movement. But, in all other fungi placed under subdivisions Zygomycotina, Ascomycotina, Basidiomycotina and Deuteromycotina, motile cell does not occur at any stage.

Composition of Cell Wall:

The cells are surrounded by outer rigid struc­ture, the cell wall. Its composition varies in different groups of fungi. According to Aronson (1965) and Bartnicki-Garcia (1970), the cell wall consists of about 80-90% polysaccharides along with proteins (1-15%) and lipids (2-10%).

The most common cell wall material is chitin. But in some other fungi, cellulose or other glucans are present. The chemical structure of cellulose and chitin is given below. Bartnicki-Garcia (1968) reported that the composition of cell wall varies in different groups of fungi.

These are cellulose- glycogen (Acrasiomycetes), cellulose-glucan (Oomycetes), cellulose-chitin (Hyphochytridiomycetes), chitin-chitosan (Zygomycetes), chitin- glucan (Chitridiomycetes, Asco-, Basidio- and Duteromycotina), mannan-glucan (Saccharo- mycetaceae and Cryptococcaceae), mannan- chitin (Sporobolomycetaceae), Polygalacto- samine-galactan (Trichomycetaceae).

Hyphal Forms:

In response to functional need, the fungal mycelia are modified into different types of struc­ture:

When the component hyphae completely interwoven to form a compact thick tissue, it is called plecten­chyma.

Prosenchyma or prosoplectenchyma, where the hyphae remain more or less parallel to each other, retain their individuality and do not fuse (Fig. 4.6B) and pseudoparenchyma or para- plectenchyma, where the hyphae are com­pletely fused to each other, form a compact mass and lose their individuality. In cross- section the whole mass looks like paren­chyma of angiospermic plant (Fig. 4.6B).

2. Sclerotia (sing. Sclerotium):

It is a compact structure of different shapes and sizes, formed by the aggregation of mycelia. It may be round to elongated pod-like, very minute dots to large ball-like structure weighing approximately 14 kg (30 lbs). It may survive for many years as resting stage (Fig. 4.6A).

In this case, hyphae are aggre­gated longitudinally in varying degree of complexity, where the hyphae lose their indi­viduality and the whole structure behaves as an organised unit. They can withstand adverse environmental conditions and after few years, they can start growing (Fig. 4.6E).

4. Haustoria (sing. Haustorium):

These are intracellular outgrowth of the mycelium that grows intercellularly for absorption of nutri­ent from host cells. They are of various shapes and sizes, like simple, knob-like, coiled, branched, etc. They penetrate the cell wall and generally do not rupture the cell membrane during absorption (Fig. 4.6F, G).

5. Appresoria (sing. Appresorium):

It is the swollen tip of germ tube or mycelium of plant pathogenic fungi which helps the myce­lium to adhere to the surface of the host and also helps in penetration (Fig. 4.6H).

Certain fungi develop sticky hypha or hyphal loops to catch predators like nematode, protozoa, small animals etc., known as hyphal trap. The fungi of this kind is known as Predaceous fungi (Fig. 4.61).

It is a solid body of various shapes and sizes, formed by the compact aggrega­tion of mycelium. Reproductive structures and fruit bodies are developed inside the stroma (Fig. 4.6D).

Reproduction in Fungi:

In unicellular fungi (Synchitrium, Saccharo­myces), entire vegetative cell is transformed into a reproductive unit, called Holocarpic. However, in others (Pythium, Penicillium, Helmintho- sporium), only a part of the vegetative body forms reproductive unit and the rest portion remains as vegetative, called Eucarpic.

The fungi reproduces by all the three means:

Vegetative, Asexual and Sexual.

1. Vegetative Reproduction:

It takes place by the following ways:

It is common in filamen­tous fungi (Rhizopus, Alternaria, Fusarium) where the hyphae break up into two or more fragments due to some external force and each one develops into a new individual (Fig. 4.7A, B).

It takes place in unicellular fungi (Saccharomyces, Schizosaccharo- myces). A small outgrowth, the bud emerges out from the parent cell. Nucleus divides into two and one pass­es to the bud. The bud is then separated by partition wall, but continues its growth.

Later on, it breaks off from the mother and grows individually. Some­times, the process repeats very fast and the buds remain attached with the mother in chain, that looks like myce­lium, called pseudomycelium (Gr. pseu- do, false + mycelium). This process takes place in ascospores and basiclio- spores of some fungi (Fig. 4.7C, 4.1 B).

Normally unicellular fungi (Saccharomyces, Schizosaccharomyces) reproduce by this method, where the vegetative cell elongates, and divides into two daughter cells of equal size by simple constriction in the middle with simultaneous nuclear division (Fig. 4.7D).

2. Asexual Reproduction:

It takes place by means of several types of spore generally form during favourable condition. The spores may be unicellular (Penicillium, Aspergillus) or multicellular (Fusarium, Helminthosporium). They may be exoge­nous, developed on conidiophore (Penicillium) (Fig. 4.8C) or endogenous, developed in sporangium (Mucor) (Fig. 4.8L) or pycnidium (Ascochyta pisi).

Some of the spores are:

The zoospores may be uni- or biflagellate, generally pear-shaped, produced in sporangium, e.g., Synchy­trium, Phytophthora (Fig. 4.8J).

These are exogenously pro­duced non-motile spores develop by constriction at the end of specialised hyphal branches, called conidiophores. They may produce singly (Phytoph­thora, Pythium) or in chain (Penicillium, Aspergillus) (Fig. 4.8A, B, C).

In some fungi (Mucor mucedo), the hyphal tips often divide by trans­verse wall into large number of small segments, may remain in chain or becomes free from each other, these are known as oidia. The oidia on germina­tion develop into new plants (Fig. 4.8D).

The chlamydospores are thick walled round to oval in outline, coloured brown or black. They produce either terminally or in intercalary at some intervals throughout the length of hyphae, e.g., Fusarium (Fig. 4.8E, F, G).

These are globose, multinucleate, non-motile aplanospores, formed inside the sporangium. The sporangiospore germinates by producing germ tube. Later on, it develops pro­fusely branched mycelium (Fig. 4.8K, L).

It is the process of union between two compatible nuclei. The nuclei in some members are contributed by two well-organized gametes.

The whole pro­cess of sexual reproduction consists of three phases, in the sequence of plasmogamy, karyogany and meosis:

It involves the union of two protoplasts, brings two haploid nuclei close together in the same cell.

It involves the fusion of two haploid nuclei brought together during plasmogamy. This results in the forma­tion of diploid nucleus i.e., zygote, which is ephemeral (short-lived).

It follows karyogamy and reduce the number of chromosome from diploid zygote nucleus to original haploid number in the daughter nuclei.

The plasmogamy i.e., the first phase of sexual reproduction, differs in different fungi.

The different methods of plasmogamy are:

(a) Planogametic Copulation:

Planogametes are motile gametes. This process involves the fusion of two gametes, where either one or both are motile.

Depending on the structure and nature of gametes, it is of three types:

Isogamy, Anisogamy and Oogamy:

The uniting gametes are morphologically similar, but physio­logically different. This process is common in primitive unicellular fungi, e.g., Synchytrium (Fig. 4.9A).

Both the uniting gametes are morphologically simi­lar, but different physiologically and in size. The smaller one is more active, considered as male and the larger less active one as female, e.g., Allomyces (Fig. 4.9B).

Both the uniting gametes are morphologically and physio­logically different. The male gamate is smaller and motile, and the female gamete is larger and non-motile, e.g., Monoblepharis (Fig. 4.9C).

(b) Gametangial Contact:

The uniting gametes are present in different gametangium, thus the male and female gametangia are known as antheridium and Oogonium (Ascogonium in Asco­mycotina), respectively. The gametes are never released from gametangium. Both the gametangia come in close contact and transfer male gamete to the egg through fertilization tube. The gametangia do not lose their identity, e.g., Ascobolus, Pythium (Fig. 4.9D, E).

(c) Gametangial Copulation:

The process involves the fusion of the entire content of the uniting gametangia.


Alcohols

The alcohol functional group involves an oxygen atom that is bonded to one hydrogen atom and one carbon atom. The carbon atom will be part of a larger organic structure. One way to indicate a generic alcohol would be with the formula (ce). (ce) represents any organic fragment in which a carbon atom is directly bonded to the explicitly indicated functional group (in this case, (ce)). The (ce) group is typically a chain of carbon atoms.

Figure (PageIndex<3>): Primary, secondary, and tertiary alcohols.

Alcohols can be classified as primary, secondary, or tertiary based on the characteristics of the carbon to which it is attached. In a primary alcohol, the carbon bonded directly to the oxygen atom is also bonded to exactly one carbon atom, with the other bonds generally going to hydrogen atoms. In a secondary alcohol, the carbon is attached to two other carbon atoms, and in a tertiary alcohol, the carbon is bonded to three other carbon atoms. The type of alcohol being used will determine the product of certain reactions. Note the naming of alcohols as illustrated in the figure above. The location of the (ce<-OH>) group is indicated with the number of the carbon to which it is attached.

We are already familiar with several common alcohols. For example, ethanol (left( ce ight)) is the alcohol present in alcoholic beverages. It is also widely used in the industrial manufacture of other chemicals. Methanol (left( ce ight)) is used as a gasoline additive or alternative. Additionally, methanol can be used to manufacture formaldehyde, which is employed in the production of plastics, paints, and other useful substances. Isopropanol is commonly known as rubbing alcohol. In addition to its industrial uses, isopropanol is used to clean various surfaces, including computer monitors, whiteboards, and even skin (e.g., before getting blood drawn).


Contents

Before the 18th century, chemists generally believed that compounds obtained from living organisms were endowed with a vital force that distinguished them from inorganic compounds. According to the concept of vitalism (vital force theory), organic matter was endowed with a "vital force". [4] During the first half of the nineteenth century, some of the first systematic studies of organic compounds were reported. Around 1816 Michel Chevreul started a study of soaps made from various fats and alkalis. He separated the acids that, in combination with the alkali, produced the soap. Since these were all individual compounds, he demonstrated that it was possible to make a chemical change in various fats (which traditionally come from organic sources), producing new compounds, without "vital force". In 1828 Friedrich Wöhler produced the organic chemical urea (carbamide), a constituent of urine, from inorganic starting materials (the salts potassium cyanate and ammonium sulfate), in what is now called the Wöhler synthesis. Although Wöhler himself was cautious about claiming he had disproved vitalism, this was the first time a substance thought to be organic was synthesized in the laboratory without biological (organic) starting materials. The event is now generally accepted as indeed disproving the doctrine of vitalism. [5]

In 1856 William Henry Perkin, while trying to manufacture quinine accidentally produced the organic dye now known as Perkin's mauve. His discovery, made widely known through its financial success, greatly increased interest in organic chemistry. [6]

A crucial breakthrough for organic chemistry was the concept of chemical structure, developed independently in 1858 by both Friedrich August Kekulé and Archibald Scott Couper. [7] Both researchers suggested that tetravalent carbon atoms could link to each other to form a carbon lattice, and that the detailed patterns of atomic bonding could be discerned by skillful interpretations of appropriate chemical reactions. [8]

The era of the pharmaceutical industry began in the last decade of the 19th century when the manufacturing of acetylsalicylic acid—more commonly referred to as aspirin—in Germany was started by Bayer. [9] By 1910 Paul Ehrlich and his laboratory group began developing arsenic-based arsphenamine, (Salvarsan), as the first effective medicinal treatment of syphilis, and thereby initiated the medical practice of chemotherapy. Ehrlich popularized the concepts of "magic bullet" drugs and of systematically improving drug therapies. [10] [11] His laboratory made decisive contributions to developing antiserum for diphtheria and standardizing therapeutic serums. [12]

Early examples of organic reactions and applications were often found because of a combination of luck and preparation for unexpected observations. The latter half of the 19th century however witnessed systematic studies of organic compounds. The development of synthetic indigo is illustrative. The production of indigo from plant sources dropped from 19,000 tons in 1897 to 1,000 tons by 1914 thanks to the synthetic methods developed by Adolf von Baeyer. In 2002, 17,000 tons of synthetic indigo were produced from petrochemicals. [14]

In the early part of the 20th century, polymers and enzymes were shown to be large organic molecules, and petroleum was shown to be of biological origin.

The multiple-step synthesis of complex organic compounds is called total synthesis. Total synthesis of complex natural compounds increased in complexity to glucose and terpineol. For example, cholesterol-related compounds have opened ways to synthesize complex human hormones and their modified derivatives. Since the start of the 20th century, complexity of total syntheses has been increased to include molecules of high complexity such as lysergic acid and vitamin B12. [15]

The discovery of petroleum and the development of the petrochemical industry spurred the development of organic chemistry. Converting individual petroleum compounds into types of compounds by various chemical processes led to organic reactions enabling a broad range of industrial and commercial products including, among (many) others: plastics, synthetic rubber, organic adhesives, and various property-modifying petroleum additives and catalysts.

The majority of chemical compounds occurring in biological organisms are carbon compounds, so the association between organic chemistry and biochemistry is so close that biochemistry might be regarded as in essence a branch of organic chemistry. Although the history of biochemistry might be taken to span some four centuries, fundamental understanding of the field only began to develop in the late 19th century and the actual term biochemistry was coined around the start of 20th century. Research in the field increased throughout the twentieth century, without any indication of slackening in the rate of increase, as may be verified by inspection of abstraction and indexing services such as BIOSIS Previews and Biological Abstracts, which began in the 1920s as a single annual volume, but has grown so drastically that by the end of the 20th century it was only available to the everyday user as an online electronic database. [16]

Since organic compounds often exist as mixtures, a variety of techniques have also been developed to assess purity chromatography techniques are especially important for this application, and include HPLC and gas chromatography. Traditional methods of separation include distillation, crystallization, evaporation, magnetic separation and solvent extraction.

Organic compounds were traditionally characterized by a variety of chemical tests, called "wet methods", but such tests have been largely displaced by spectroscopic or other computer-intensive methods of analysis. [17] Listed in approximate order of utility, the chief analytical methods are:

    is the most commonly used technique, often permitting the complete assignment of atom connectivity and even stereochemistry using correlation spectroscopy. The principal constituent atoms of organic chemistry – hydrogen and carbon – exist naturally with NMR-responsive isotopes, respectively 1 H and 13 C. : A destructive method used to determine the elemental composition of a molecule. See also mass spectrometry, below. indicates the molecular weight of a compound and, from the fragmentation patterns, its structure. High-resolution mass spectrometry can usually identify the exact formula of a compound and is used in place of elemental analysis. In former times, mass spectrometry was restricted to neutral molecules exhibiting some volatility, but advanced ionization techniques allow one to obtain the "mass spec" of virtually any organic compound. can be useful for determining molecular geometry when a single crystal of the material is available. Highly efficient hardware and software allows a structure to be determined within hours of obtaining a suitable crystal.

Traditional spectroscopic methods such as infrared spectroscopy, optical rotation, and UV/VIS spectroscopy provide relatively nonspecific structural information but remain in use for specific applications. Refractive index and density can also be important for substance identification.

The physical properties of organic compounds typically of interest include both quantitative and qualitative features. Quantitative information includes a melting point, boiling point, and index of refraction. Qualitative properties include odor, consistency, solubility, and color.

Melting and boiling properties Edit

Organic compounds typically melt and many boil. In contrast, while inorganic materials generally can be melted, many do not boil, and instead tend to degrade. In earlier times, the melting point (m.p.) and boiling point (b.p.) provided crucial information on the purity and identity of organic compounds. The melting and boiling points correlate with the polarity of the molecules and their molecular weight. Some organic compounds, especially symmetrical ones, sublime. A well-known example of a sublimable organic compound is para-dichlorobenzene, the odiferous constituent of modern mothballs. Organic compounds are usually not very stable at temperatures above 300 °C, although some exceptions exist.

Solubility Edit

Neutral organic compounds tend to be hydrophobic that is, they are less soluble in water than in organic solvents. Exceptions include organic compounds that contain ionizable groups as well as low molecular weight alcohols, amines, and carboxylic acids where hydrogen bonding occurs. Otherwise, organic compounds tend to dissolve in organic solvents. Solubility varies widely with the organic solute and with the organic solvent.

Solid state properties Edit

Various specialized properties of molecular crystals and organic polymers with conjugated systems are of interest depending on applications, e.g. thermo-mechanical and electro-mechanical such as piezoelectricity, electrical conductivity (see conductive polymers and organic semiconductors), and electro-optical (e.g. non-linear optics) properties. For historical reasons, such properties are mainly the subjects of the areas of polymer science and materials science.

The names of organic compounds are either systematic, following logically from a set of rules, or nonsystematic, following various traditions. Systematic nomenclature is stipulated by specifications from IUPAC. Systematic nomenclature starts with the name for a parent structure within the molecule of interest. This parent name is then modified by prefixes, suffixes, and numbers to unambiguously convey the structure. Given that millions of organic compounds are known, rigorous use of systematic names can be cumbersome. Thus, IUPAC recommendations are more closely followed for simple compounds, but not complex molecules. To use the systematic naming, one must know the structures and names of the parent structures. Parent structures include unsubstituted hydrocarbons, heterocycles, and mono functionalized derivatives thereof.

Nonsystematic nomenclature is simpler and unambiguous, at least to organic chemists. Nonsystematic names do not indicate the structure of the compound. They are common for complex molecules, which include most natural products. Thus, the informally named lysergic acid diethylamide is systematically named (6aR,9R)-N,N-diethyl-7-methyl-4,6,6a,7,8,9-hexahydroindolo-[4,3-fg] quinoline-9-carboxamide.

With the increased use of computing, other naming methods have evolved that are intended to be interpreted by machines. Two popular formats are SMILES and InChI.

Structural drawings Edit

Organic molecules are described more commonly by drawings or structural formulas, combinations of drawings and chemical symbols. The line-angle formula is simple and unambiguous. In this system, the endpoints and intersections of each line represent one carbon, and hydrogen atoms can either be notated explicitly or assumed to be present as implied by tetravalent carbon.

History Edit

By 1880 an explosion in the number of chemical compounds being discovered occurred assisted by new synthetic and analytical techniques. Grignard described the situation as "chaos le plus complet" (complete chaos) due to the lack of convention it was possible to have multiple names for the same compound. This led to the creation of the Geneva rules in 1892. [18]

Functional groups Edit

The concept of functional groups is central in organic chemistry, both as a means to classify structures and for predicting properties. A functional group is a molecular module, and the reactivity of that functional group is assumed, within limits, to be the same in a variety of molecules. Functional groups can have a decisive influence on the chemical and physical properties of organic compounds. Molecules are classified based on their functional groups. Alcohols, for example, all have the subunit C-O-H. All alcohols tend to be somewhat hydrophilic, usually form esters, and usually can be converted to the corresponding halides. Most functional groups feature heteroatoms (atoms other than C and H). Organic compounds are classified according to functional groups, alcohols, carboxylic acids, amines, etc. [19] Functional groups make the molecule more acidic or basic due to their electronegative influence on surrounding parts of the molecule.

As the pka (aka basicity) of the molecular addition/functional group increases, there is a corresponding dipole, when measured, increases in strength. A dipole directed towards the functional group (higher pka therefore basic nature of group) points towards it and decreases in strength with increasing distance. Dipole distance (measured in Angstroms) and steric hindrance towards the functional group have an intermolecular and intramolecular effect on the surrounding environment and pH level.

Different functional groups have different pka values and bond strengths (single, double, triple) leading to increased electrophilicity with lower pka and increased nucleophile strength with higher pka. More basic/nucleophilic functional groups desire to attack an electrophilic functional group with a lower pka on another molecule (intermolecular) or within the same molecule (intramolecular). Any group with a net acidic pka that gets within range, such as an acyl or carbonyl group is fair game. Since the likelihood of being attacked decreases with an increase in pka, acyl chloride components with the lowest measured pka values are most likely to be attacked, followed by carboxylic acids (pka =4), thiols (13), malonates (13), alcohols (17), aldehydes (20), nitriles (25), esters (25), then amines (35). [20] Amines are very basic, and are great nucleophiles/attackers.

Aliphatic compounds Edit

The aliphatic hydrocarbons are subdivided into three groups of homologous series according to their state of saturation:

  • alkanes (paraffins): aliphatic hydrocarbons without any double or triple bonds, i.e. just C-C, C-H single bonds
  • alkenes (olefins): aliphatic hydrocarbons that contain one or more double bonds, i.e. di-olefins (dienes) or poly-olefins.
  • alkynes (acetylenes): aliphatic hydrocarbons which have one or more triple bonds.

The rest of the group is classed according to the functional groups present. Such compounds can be "straight-chain", branched-chain or cyclic. The degree of branching affects characteristics, such as the octane number or cetane number in petroleum chemistry.

Both saturated (alicyclic) compounds and unsaturated compounds exist as cyclic derivatives. The most stable rings contain five or six carbon atoms, but large rings (macrocycles) and smaller rings are common. The smallest cycloalkane family is the three-membered cyclopropane ((CH2)3). Saturated cyclic compounds contain single bonds only, whereas aromatic rings have an alternating (or conjugated) double bond. Cycloalkanes do not contain multiple bonds, whereas the cycloalkenes and the cycloalkynes do.

Aromatic compounds Edit

Aromatic hydrocarbons contain conjugated double bonds. This means that every carbon atom in the ring is sp2 hybridized, allowing for added stability. The most important example is benzene, the structure of which was formulated by Kekulé who first proposed the delocalization or resonance principle for explaining its structure. For "conventional" cyclic compounds, aromaticity is conferred by the presence of 4n + 2 delocalized pi electrons, where n is an integer. Particular instability (antiaromaticity) is conferred by the presence of 4n conjugated pi electrons.

Heterocyclic compounds Edit

The characteristics of the cyclic hydrocarbons are again altered if heteroatoms are present, which can exist as either substituents attached externally to the ring (exocyclic) or as a member of the ring itself (endocyclic). In the case of the latter, the ring is termed a heterocycle. Pyridine and furan are examples of aromatic heterocycles while piperidine and tetrahydrofuran are the corresponding alicyclic heterocycles. The heteroatom of heterocyclic molecules is generally oxygen, sulfur, or nitrogen, with the latter being particularly common in biochemical systems.

Heterocycles are commonly found in a wide range of products including aniline dyes and medicines. Additionally, they are prevalent in a wide range of biochemical compounds such as alkaloids, vitamins, steroids, and nucleic acids (e.g. DNA, RNA).

Rings can fuse with other rings on an edge to give polycyclic compounds. The purine nucleoside bases are notable polycyclic aromatic heterocycles. Rings can also fuse on a "corner" such that one atom (almost always carbon) has two bonds going to one ring and two to another. Such compounds are termed spiro and are important in several natural products.

Polymers Edit

One important property of carbon is that it readily forms chains, or networks, that are linked by carbon-carbon (carbon-to-carbon) bonds. The linking process is called polymerization, while the chains, or networks, are called polymers. The source compound is called a monomer.

Two main groups of polymers exist synthetic polymers and biopolymers. Synthetic polymers are artificially manufactured, and are commonly referred to as industrial polymers. [21] Biopolymers occur within a respectfully natural environment, or without human intervention.

Biomolecules Edit

Biomolecular chemistry is a major category within organic chemistry which is frequently studied by biochemists. Many complex multi-functional group molecules are important in living organisms. Some are long-chain biopolymers, and these include peptides, DNA, RNA and the polysaccharides such as starches in animals and celluloses in plants. The other main classes are amino acids (monomer building blocks of peptides and proteins), carbohydrates (which includes the polysaccharides), the nucleic acids (which include DNA and RNA as polymers), and the lipids. Besides, animal biochemistry contains many small molecule intermediates which assist in energy production through the Krebs cycle, and produces isoprene, the most common hydrocarbon in animals. Isoprenes in animals form the important steroid structural (cholesterol) and steroid hormone compounds and in plants form terpenes, terpenoids, some alkaloids, and a class of hydrocarbons called biopolymer polyisoprenoids present in the latex of various species of plants, which is the basis for making rubber.

Small molecules Edit

In pharmacology, an important group of organic compounds is small molecules, also referred to as 'small organic compounds'. In this context, a small molecule is a small organic compound that is biologically active but is not a polymer. In practice, small molecules have a molar mass less than approximately 1000 g/mol.

Fullerenes Edit

Fullerenes and carbon nanotubes, carbon compounds with spheroidal and tubular structures, have stimulated much research into the related field of materials science. The first fullerene was discovered in 1985 by Sir Harold W. Kroto of the United Kingdom and by Richard E. Smalley and Robert F. Curl, Jr., of the United States. Using a laser to vaporize graphite rods in an atmosphere of helium gas, these chemists and their assistants obtained cagelike molecules composed of 60 carbon atoms (C60) joined together by single and double bonds to form a hollow sphere with 12 pentagonal and 20 hexagonal faces—a design that resembles a football, or soccer ball. In 1996 the trio was awarded the Nobel Prize for their pioneering efforts. The C60 molecule was named buckminsterfullerene (or, more simply, the buckyball) after the American architect R. Buckminster Fuller, whose geodesic dome is constructed on the same structural principles.

Others Edit

Organic compounds containing bonds of carbon to nitrogen, oxygen and the halogens are not normally grouped separately. Others are sometimes put into major groups within organic chemistry and discussed under titles such as organosulfur chemistry, organometallic chemistry, organophosphorus chemistry and organosilicon chemistry.

Organic reactions are chemical reactions involving organic compounds. Many of these reactions are associated with functional groups. The general theory of these reactions involves careful analysis of such properties as the electron affinity of key atoms, bond strengths and steric hindrance. These factors can determine the relative stability of short-lived reactive intermediates, which usually directly determine the path of the reaction.

The basic reaction types are: addition reactions, elimination reactions, substitution reactions, pericyclic reactions, rearrangement reactions and redox reactions. An example of a common reaction is a substitution reaction written as:

where X is some functional group and Nu is a nucleophile.

The number of possible organic reactions is infinite. However, certain general patterns are observed that can be used to describe many common or useful reactions. Each reaction has a stepwise reaction mechanism that explains how it happens in sequence—although the detailed description of steps is not always clear from a list of reactants alone.

The stepwise course of any given reaction mechanism can be represented using arrow pushing techniques in which curved arrows are used to track the movement of electrons as starting materials transition through intermediates to final products.

Synthetic organic chemistry is an applied science as it borders engineering, the "design, analysis, and/or construction of works for practical purposes". Organic synthesis of a novel compound is a problem-solving task, where a synthesis is designed for a target molecule by selecting optimal reactions from optimal starting materials. Complex compounds can have tens of reaction steps that sequentially build the desired molecule. The synthesis proceeds by utilizing the reactivity of the functional groups in the molecule. For example, a carbonyl compound can be used as a nucleophile by converting it into an enolate, or as an electrophile the combination of the two is called the aldol reaction. Designing practically useful syntheses always requires conducting the actual synthesis in the laboratory. The scientific practice of creating novel synthetic routes for complex molecules is called total synthesis.


Organs: Made of Tissues

An organ is a structure that is composed of at least two or more tissue types and performs a specific set of functions for the body. The liver, stomach, brain, and blood are all different organs and perform different functions. Each organ is a specialized functional center responsible for a specific function of the body.

At the organ level, complex functions become possible because of the specialized activities of various tissues. Most organs contain more than one tissue type. For example, the stomach consists of smooth muscle tissue for churning movement while it is innervated, but it is also supplied by blood, which is a connective tissue.

The next level is the organ system level. Many organs working together to accomplish a common purpose create an organ system. For example, the heart and the blood vessels of the cardiovascular system circulate blood and transport oxygen and nutrients to all the body cells.

Levels of Organization: Molecules form cells. Cells form tissues, and tissues form organs. Organs that fulfill related functions are called organ systems. An organism is made up of interconnected organ systems.


Lesson 4.1 - Introduction to Cellular Respiration and Fermentation Flashcards Preview

Define Aerobic Cellular Respiration

A process that uses oxygen to harvest energy from organic compounds.

What is a process that uses oxygen to harvest energy from organic compounds known as?

Aerobic Cellular Respiration

An organism that cannot live without oxygen.

What is an organism that cannot live without oxygen known as?

Define Substrate-Level Phosphorylation

The formation of ATP by the direct transfer of a phosphate group from a substrate to ADP.

What is the formation of ATP by the direct transfer of a phosphate group from a substrate to ADP known as?

Define Oxidative Phosphorylation

A process that forms ATP using energy transferred indirectly from a series of redox reactions.

What is a process that forms ATP using energy transferred indirectly from a series of redox reactions known as?

A series of reactions in which a glucose molecule is broken into two pyruvate molecules and energy is released.

What is a series of reactions in which a glucose molecule is broken into two pyruvate molecules and energy is released known as?

Define Pyruvate Oxidation

A reaction in which pyruvate is oxidized by NAD + and CO2 is removed, forming an acetyl group and releasing NADH.

What is a reaction in which pyruvate is oxidized by NAD + and CO2 is removed, forming an acetyl group and releasing NADH known as?

A cyclic series of reactions that transfers energy from organic molecules to ATP, NADH, and FADH2 and releases carbon atoms as CO2.

What is a cyclic series of reactions that transfers energy from organic molecules to ATP, NADH, and FADH2 and releases carbon atoms as CO2​ known as?

Define Anaerobic Respiration

A process that uses a final inorganic oxidizing agent, other than oxygen, to produce energy.

What is a process that uses a final inorganic oxidizing agent, other than oxygen, to produce energy known as?

A process that uses an organic compound as the final oxidizing agent to produce energy.

What is a process that uses an organic compound as the final oxidizing agent to produce energy known as?

An organism that cannot survive in the presence of oxygen.

What is an organism that cannot survive in the presence of oxygen known as?

Define Facultative Anaerobe

An organism that can live with or without oxygen.

What is an organism that can live with or without oxygen known as?

There are three main types of energy pathways: _____ respiration, _____ respiration, and _____. They all produce ATP.

There are three main types of energy pathways: aerobic respiration, anaerobic respiration, and fermentation. They all produce ATP.

The four stages of aerobic cellular respiration are _____, _____ oxidation, the _____ acid cycle, and the electron _____ chain.

The four stages of aerobic cellular respiration are glycolysis, pyruvate oxidation, the citric acid cycle, and the electron transport chain.

Mitochondria generate most of the ATP that is used in _____ cells.

Mitochondria generate most of the ATP that is used in eukaryotic cells.

Respiration pathways use _____ transport systems to generate ATP by _____ phosphorylation. Fermentation pathways lack such transport systems.

Respiration pathways use electron transport systems to generate ATP by oxidative phosphorylation. Fermentation pathways lack such transport systems.

_____ respiration uses an inorganic substance other than oxygen as the final oxidizing agent. Fermentation relies on an organic compound.

Anaerobic respiration uses an inorganic substance other than oxygen as the final oxidizing agent. Fermentation relies on an organic compound.


Contents

In order to understand functional genomics it is important to first define function. In their paper [1] Graur et al. define function in two possible ways. These are "Selected effect" and "Causal Role". The "Selected Effect" function refers to the function for which a trait (DNA, RNA, protein etc.) is selected for. The "Causal role" function refers to the function that a trait is sufficient and necessary for. Functional genomics usually tests the "Causal role" definition of function.

The goal of functional genomics is to understand the function of genes or proteins, eventually all components of a genome. The term functional genomics is often used to refer to the many technical approaches to study an organism's genes and proteins, including the "biochemical, cellular, and/or physiological properties of each and every gene product" [2] while some authors include the study of nongenic elements in their definition. [3] Functional genomics may also include studies of natural genetic variation over time (such as an organism's development) or space (such as its body regions), as well as functional disruptions such as mutations.

The promise of functional genomics is to generate and synthesize genomic and proteomic knowledge into an understanding of the dynamic properties of an organism. This could potentially provide a more complete picture of how the genome specifies function compared to studies of single genes. Integration of functional genomics data is often a part of systems biology approaches.

Functional genomics includes function-related aspects of the genome itself such as mutation and polymorphism (such as single nucleotide polymorphism (SNP) analysis), as well as the measurement of molecular activities. The latter comprise a number of "-omics" such as transcriptomics (gene expression), proteomics (protein production), and metabolomics. Functional genomics uses mostly multiplex techniques to measure the abundance of many or all gene products such as mRNAs or proteins within a biological sample. A more focused functional genomics approach might test the function of all variants of one gene and quantify the effects of mutants by using sequencing as a readout of activity. Together these measurement modalities endeavor to quantitate the various biological processes and improve our understanding of gene and protein functions and interactions.

At the DNA level Edit

Genetic interaction mapping Edit

Systematic pairwise deletion of genes or inhibition of gene expression can be used to identify genes with related function, even if they do not interact physically. Epistasis refers to the fact that effects for two different gene knockouts may not be additive that is, the phenotype that results when two genes are inhibited may be different from the sum of the effects of single knockouts.

DNA/Protein interactions Edit

Proteins formed by the translation of the mRNA (messenger RNA, a coded information from DNA for protein synthesis) play a major role in regulating gene expression. To understand how they regulate gene expression it is necessary to identify DNA sequences that they interact with. Techniques have been developed to identify sites of DNA-protein interactions. These include ChIP-sequencing, CUT&RUN sequencing and Calling Cards. [4]

DNA accessibility assays Edit

Assays have been developed to identify regions of the genome that are accessible. These regions of open chromatin are candidate regulatory regions. These assays include ATAC-seq, DNase-Seq and FAIRE-Seq.

At the RNA level Edit

Microarrays Edit

Microarrays measure the amount of mRNA in a sample that corresponds to a given gene or probe DNA sequence. Probe sequences are immobilized on a solid surface and allowed to hybridize with fluorescently labeled “target” mRNA. The intensity of fluorescence of a spot is proportional to the amount of target sequence that has hybridized to that spot, and therefore to the abundance of that mRNA sequence in the sample. Microarrays allow for identification of candidate genes involved in a given process based on variation between transcript levels for different conditions and shared expression patterns with genes of known function.

SAGE Edit

Serial analysis of gene expression (SAGE) is an alternate method of analysis based on RNA sequencing rather than hybridization. SAGE relies on the sequencing of 10–17 base pair tags which are unique to each gene. These tags are produced from poly-A mRNA and ligated end-to-end before sequencing. SAGE gives an unbiased measurement of the number of transcripts per cell, since it does not depend on prior knowledge of what transcripts to study (as microarrays do).

RNA sequencing Edit

RNA sequencing has taken over microarray and SAGE technology in recent years, as noted in 2016, and has become the most efficient way to study transcription and gene expression. This is typically done by next-generation sequencing. [5]

A subset of sequenced RNAs are small RNAs, a class of non-coding RNA molecules that are key regulators of transcriptional and post-transcriptional gene silencing, or RNA silencing. Next generation sequencing is the gold standard tool for non-coding RNA discovery, profiling and expression analysis.

Massively Parallel Reporter Assays (MPRAs) Edit

Massively parallel reporter assays is a technology to test the cis-regulatory activity of DNA sequences. [6] [7] MPRAs use a plasmid with a synthetic cis-regulatory element upstream of a promoter driving a synthetic gene such as Green Fluorescent Protein. A library of cis-regulatory elements is usually tested using MPRAs, a library can contain from hundreds to thousands of cis-regulatory elements. The cis-regulatory activity of the elements is assayed by using the downstream reporter activity. The activity of all the library members is assayed in parallel using barcodes for each cis-regulatory element. One limitation of MPRAs is that the activity is assayed on a plasmid and may not capture all aspects of gene regulation observed in the genome.

STARR-seq Edit

STARR-seq is a technique similar to MPRAs to assay enhancer activity of randomly sheared genomic fragments. In the original publication, [8] randomly sheared fragments of the Drosophila genome were placed downstream of a minimal promoter. Candidate enhancers amongst the randomly sheared fragments will transcribe themselves using the minimal promoter. By using sequencing as a readout and controlling for input amounts of each sequence the strength of putative enhancers are assayed by this method.

Perturb-seq Edit

Perturb-seq couples CRISPR mediated gene knockdowns with single-cell gene expression. Linear models are used to calculate the effect of the knockdown of a single gene on the expression of multiple genes.

At the protein level Edit

Yeast two-hybrid system Edit

A yeast two-hybrid screening (Y2H) tests a "bait" protein against many potential interacting proteins ("prey") to identify physical protein–protein interactions. This system is based on a transcription factor, originally GAL4, [9] whose separate DNA-binding and transcription activation domains are both required in order for the protein to cause transcription of a reporter gene. In a Y2H screen, the "bait" protein is fused to the binding domain of GAL4, and a library of potential "prey" (interacting) proteins is recombinantly expressed in a vector with the activation domain. In vivo interaction of bait and prey proteins in a yeast cell brings the activation and binding domains of GAL4 close enough together to result in expression of a reporter gene. It is also possible to systematically test a library of bait proteins against a library of prey proteins to identify all possible interactions in a cell.

AP/MS Edit

Affinity purification and mass spectrometry (AP/MS) is able to identify proteins that interact with one another in complexes. Complexes of proteins are allowed to form around a particular “bait” protein. The bait protein is identified using an antibody or a recombinant tag which allows it to be extracted along with any proteins that have formed a complex with it. The proteins are then digested into short peptide fragments and mass spectrometry is used to identify the proteins based on the mass-to-charge ratios of those fragments.

Deep mutational scanning Edit

In deep mutational scanning every possible amino acid change in a given protein is first synthesized. The activity of each of these protein variants is assayed in parallel using barcodes for each variant. By comparing the activity to the wild-type protein, the effect of each mutation is identified. While it is possible to assay every possible single amino-acid change due to combinatorics two or more concurrent mutations are hard to test. Deep mutational scanning experiments have also been used to infer protein structure and protein-protein interactions.

Loss-of-function techniques Edit

Mutagenesis Edit

Gene function can be investigated by systematically “knocking out” genes one by one. This is done by either deletion or disruption of function (such as by insertional mutagenesis) and the resulting organisms are screened for phenotypes that provide clues to the function of the disrupted gene*

RNAi Edit

RNA interference (RNAi) methods can be used to transiently silence or knock down gene expression using

20 base-pair double-stranded RNA typically delivered by transfection of synthetic

20-mer short-interfering RNA molecules (siRNAs) or by virally encoded short-hairpin RNAs (shRNAs). RNAi screens, typically performed in cell culture-based assays or experimental organisms (such as C. elegans) can be used to systematically disrupt nearly every gene in a genome or subsets of genes (sub-genomes) possible functions of disrupted genes can be assigned based on observed phenotypes.

CRISPR screens Edit

CRISPR-Cas9 has been used to delete genes in a multiplexed manner in cell-lines. Quantifying the amount of guide-RNAs for each gene before and after the experiment can point towards essential genes. If a guide-RNA disrupts an essential gene it will lead to the loss of that cell and hence there will be a depletion of that particular guide-RNA after the screen. In a recent CRISPR-cas9 experiment in mammalian cell-lines, around 2000 genes were found to be essential in multiple cell-lines. [11] [12] Some of these genes were essential in only one cell-line. Most of genes are part of multi-protein complexes. This approach can be used to identify synthetic lethality by using the appropriate genetic background. CRISPRi and CRISPRa enable loss-of-function and gain-of-function screens in a similar manner. CRISPRi identified

2100 essential genes in the K562 cell-line. [13] [14] CRISPR deletion screens have also been used to identify potential regulatory elements of a gene. For example, a technique called ScanDel was published which attempted this approach. The authors deleted regions outside a gene of interest(HPRT1 involved in a Mendelian disorder) in an attempt to identify regulatory elements of this gene. [15] Gassperini et al. did not identify any distal regulatory elements for HPRT1 using this approach, however such approaches can be extended to other genes of interest.

Functional annotations for genes Edit

Genome annotation Edit

Putative genes can be identified by scanning a genome for regions likely to encode proteins, based on characteristics such as long open reading frames, transcriptional initiation sequences, and polyadenylation sites. A sequence identified as a putative gene must be confirmed by further evidence, such as similarity to cDNA or EST sequences from the same organism, similarity of the predicted protein sequence to known proteins, association with promoter sequences, or evidence that mutating the sequence produces an observable phenotype.

Rosetta stone approach Edit

The Rosetta stone approach is a computational method for de-novo protein function prediction. It is based on the hypothesis that some proteins involved in a given physiological process may exist as two separate genes in one organism and as a single gene in another. Genomes are scanned for sequences that are independent in one organism and in a single open reading frame in another. If two genes have fused, it is predicted that they have similar biological functions that make such co-regulation advantageous.

Because of the large quantity of data produced by these techniques and the desire to find biologically meaningful patterns, bioinformatics is crucial to analysis of functional genomics data. Examples of techniques in this class are data clustering or principal component analysis for unsupervised machine learning (class detection) as well as artificial neural networks or support vector machines for supervised machine learning (class prediction, classification). Functional enrichment analysis is used to determine the extent of over- or under-expression (positive- or negative- regulators in case of RNAi screens) of functional categories relative to a background sets. Gene ontology based enrichment analysis are provided by DAVID and gene set enrichment analysis (GSEA), [16] pathway based analysis by Ingenuity [17] and Pathway studio [18] and protein complex based analysis by COMPLEAT. [19]

New computational methods have been developed for understanding the results of a deep mutational scanning experiment. 'phydms' compares the result of a deep mutational scanning experiment to a phylogenetic tree. [20] This allows the user to infer if the selection process in nature applies similar constraints on a protein as the results of the deep mutational scan indicate. This may allow an experimenter to choose between different experimental conditions based on how well they reflect nature. Deep mutational scanning has also been used to infer protein-protein interactions. [21] The authors used a thermodynamic model to predict the effects of mutations in different parts of a dimer. Deep mutational structure can also be used to infer protein structure. Strong positive epistasis between two mutations in a deep mutational scan can be indicative of two parts of the protein that are close to each other in 3-D space. This information can then be used to infer protein structure. A proof of principle of this approach was shown by two groups using the protein GB1. [22] [23]

Results from MPRA experiments have required machine learning approaches to interpret the data. A gapped k-mer SVM model has been used to infer the kmers that are enriched within cis-regulatory sequences with high activity compared to sequences with lower activity. [24] These models provide high predictive power. Deep learning and random forest approaches have also been used to interpret the results of these high-dimensional experiments. [25] These models are beginning to help develop a better understanding of non-coding DNA function towards gene-regulation.

The ENCODE project Edit

The ENCODE (Encyclopedia of DNA elements) project is an in-depth analysis of the human genome whose goal is to identify all the functional elements of genomic DNA, in both coding and noncoding regions. Important results include evidence from genomic tiling arrays that most nucleotides are transcribed as coding transcripts, noncoding RNAs, or random transcripts, the discovery of additional transcriptional regulatory sites, further elucidation of chromatin-modifying mechanisms.

The Genotype-Tissue Expression (GTEx) project Edit

The GTEx project is a human genetics project aimed at understanding the role of genetic variation in shaping variation in the transcriptome across tissues. The project has collected a variety of tissue samples (> 50 different tissues) from more than 700 post-mortem donors. This has resulted in the collection of >11,000 samples. GTEx has helped understand the tissue-sharing and tissue-specificity of EQTLs. [26]


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