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From Wikipedia

Transcription factor

In molecular biology and genetics, a transcription factor (sometimes called a sequence-specific DNA-binding factor) is a protein that binds to specific DNA sequences, thereby controlling the movement (or transcription) of genetic information from DNA to mRNA. Transcription factors perform this function alone or with other proteins in a complex, by promoting (as an activator), or blocking (as a repressor) the recruitment of RNA polymerase (the enzyme that performs the transcription of genetic information from DNA to RNA) to specific genes.

A defining feature of transcription factors is that they contain one or more DNA-binding domains (DBDs), which attach to specific sequences of DNA adjacent to the genes that they regulate. Additional proteins such as coactivators, chromatin remodelers, histone acetylases, deacetylases, kinases, and methylases, while also playing crucial roles in gene regulation, lack DNA-binding domains, and, therefore, are not classified as transcription factors.

Conservation in different organisms

Transcription factors are essential for the regulation of gene expression and are, as a consequence, found in all living organisms. The number of transcription factors found within an organism increases with genome size, and larger genomes tend to have more transcription factors per gene.

There are approximately 2600 proteins in the human genome that contain DNA-binding domains, and most of these are presumed to function as transcription factors. Therefore, approximately 10% of genes in the genome code for transcription factors, which makes this family the single largest family of human proteins. Furthermore, genes are often flanked by several binding sites for distinct transcription factors, and efficient expression of each of these genes requires the cooperative action of several different transcription factors (see, for example, hepatocyte nuclear factors). Hence, the combinatorial use of a subset of the approximately 2000 human transcription factors easily accounts for the unique regulation of each gene in the human genome during development.

Mechanism

Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the genes that they regulate. Depending on the transcription factor, the transcription of the adjacent gene is either up- or down-regulated. Transcription factors use a variety of mechanisms for the regulation of gene expression. These mechanisms include:

  • stabilize or block the binding of RNA polymerase to DNA
  • catalyze the acetylation or deacetylation of histone proteins. The transcription factor can either do this directly or recruit other proteins with this catalytic activity. Many transcription factors use one or the other of two opposing mechanisms to regulate transcription:
    • histone acetyltransferase (HAT) activity – acetylates histone proteins, which weakens the association of DNA with histones, which make the DNA more accessible to transcription, thereby up-regulating transcription
    • histone deacetylase (HDAC) activity – deacetylates histone proteins, which strengthens the association of DNA with histones, which make the DNA less accessible to transcription, thereby down-regulating transcription
    • recruit coactivator or corepressor proteins to the transcription factor DNA complex

Function

Transcription factors are one of the groups of proteins that read and interpret the genetic "blueprint" in the DNA. They bind DNA and help initiate a program of increased or decreased gene transcription. As such, they are vital for many important cellular processes. Below are some of the important functions and biological roles transcription factors are involved in:

Basal transcription regulation

In eukaryotes, an important class of transcription factors called general transcription factors (GTFs) are necessary for transcription to occur. Many of these GTFs don't actually bind DNA but are part of the large transcription preinitiation complex that interacts with RNA polymerase directly. The most common GTFs are TFIIA, TFIIB, TFIID (see also TATA binding protein), TFIIE, TFIIF, and TFIIH. The preinitiation complex binds to promoter regions of DNA upstream to the gene that they regulate.

Differential enhancement of transcription

Other transcription factors differentially regulate the expression of various genes by binding to damping in any oscillatory system or in numerical algorithms.

In audio system terminology, the damping factor gives the ratio of the rated impedance of the loudspeaker to the source impedance. Only the resistive part of the loudspeaker impedance is used. The amplifier output impedance is also assumed to be totally resistive. The source impedance (that seen by the loudspeaker) includes the connecting cable impedance. The load impedance Z_\mathrm{load} (input impedance) and the source impedance Z_\mathrm{source} (output impedance) are shown in the diagram.

The damping factor DF is:

DF = \frac{Z_\mathrm{load}}{Z_\mathrm{source}} \,

Solving for Z_\mathrm{source}:

Z_\mathrm{source} = \frac{Z_\mathrm{load}}{DF} \,

Explanation

In loudspeaker systems, the value of the damping factor between a particular loudspeaker and a particular amplifier describes the ability of the amplifier to control undesirable movement of the speaker cone near the resonant frequency of the speaker system. It is usually used in the context of low-frequency driver behavior, and especially so in the case of electrodynamic drivers, which use a magnetic motor to generate the forces which move the diaphragm.

Speaker diaphragms have mass, and their surrounds have stiffness. Together, these form a resonant system, and the mechanical cone resonance may be excited by electrical signals (e.g., pulses) at audio frequencies. But a driver with a voice coil is also a current generator, since it has a coil attached to the cone and suspension, and that coil is immersed in a magnetic field. For every motion the coil makes, it will generate a current that will be seen by any electrically attached equipment, such as an amplifier. In fact, the amp's output circuitry will be the main electrical load on the "voice coil current generator". If that load has low resistance, the current will be larger and the voice coil will be more strongly forced to decelerate. A high damping factor (which requires low output impedance at the amplifier output) very rapidly damps unwanted cone movements induced by the mechanical resonance of the speaker, acting as the equivalent of a "brake" on the voice coil motion (just as a short circuit across the terminals of a rotary electrical generator will make it very hard to turn). It is generally (though not universally) thought that tighter control of voice coil motion is desirable, as it is believed to contribute to better-quality sound.

A high damping factor indicates that an amplifier will have greater control over the movement of the speaker cone, particularly in the bass region near the resonant frequency of the driver's mechanical resonance. However, the damping factor at any particular frequency will vary, since driver voice coils are complex impedances whose values vary with frequency. In addition, the electrical characteristics of every voice coil will change with temperature; high power levels will increase coil temperature, and thus resistance. And finally, passive crossovers (made of relatively large inductors, capacitors, and resistors) are between the amplifier and speaker drivers and also affect the damping factor, again in a way that varies with frequency.

For audio power amplifiers, this source impedance Z_\mathrm{source} (also: output impedance) is generally smaller than 0.1 ohm (Ω), and from the point of view of the driver voice coil, is a near short-circuit.

The loudspeaker's load impedance (input impedance) of Z_\mathrm{load} is usually around 4 to 8Ω, although other impedance speakers are available, sometimes as low as 1Ω.

The damping circuit

The voltage generated by the moving voice coil forces current through three resistances:

  • the resistance of the voice coil itself;
  • the resistance of the interconnecting cable; and
  • the output resistance of the amplifier.

Effect of voice coil resistance

This is the major factor in limiting the amount of damping that can be achieved electrically, because its value is larger (say between 4 and 8Ω, typically) than any other resistance in the output circuitry of an Output TransformerLess amplifier.

Effect of cable resistance

The damping factor is affected to some extent by the resistance of the speaker cables. The higher the resistance of the speaker cables, the lower the damping factor. When the effect is small, it is called voltage bridging. Z_\mathrm{load} >> Z_\mathrm{source}.

Amplifier output impedance

Modern solid state amplifiers, which use relatively high levels of negative feedback to control distortion, have extremely low output impedances—one of the many consequences of using feedback—and small changes in an already low value change overall damping factor by only a small, and therefore negligible, amount.

Thus, high damping factor values do not, by themselves, say very much about the quality of a system; most modern amplifiers have them, but vary in quality nonetheless. Given the controversy that has long surrounded the use of feedback, some extend their distaste for negative feedback amplifier designs (and so a high damping factor) as a mark of poor quality. For them, such high values imply a high level of NFB in the amplifier.

Tube amplifiers typically have much lower feedback ratios, and in any case almost always have output transformers that limit how low the output impedance can be. Their lower damping factors are one of the reasons many audiophiles prefer tube amplifiers. Taken even further, some tube amplifiers are designed to have no negative feedback at all.

In practice

Transient oscillations in electric circuits are normally reduced (damped) by inserting resistance into the circuit, or reactance (which increases resistance in the frequency region requiring damping).

This technique cannot be used with loudspeakers, because increasing the mechanical resistance to cone movement would make the speaker less efficient, requiring larger amplifiers. For high fidelity use, such speakers would be less capable of responding properly to musical or speech transients. Instead, the generator effect in voice coil drivers is used

Abiotic component

In biology, abiotic components are non-living chemical and physical factors in the environment. Abiotic phenomena underlie all of biology. Abiotic factors, while generally downplayed, can have enormous impact on evolution. Abiotic components are aspects of geodiversity.They can also be recognised as "abiotic pathogens"

From the viewpoint of biology, abiotic influences may be classified as light or more generally radiation, temperature, water, the chemical surrounding composed of the terrestrial atmospheric gases, as well as soil. The macroscopic climate often influences each of the above. Not to mention pressure and even sound waves if working with marine, or deep underground, biome.

Those underlying factors affect different plants, animals and fungi to different extents. Some plants are mostly water starved, so humidity plays a larger role in their biology. Many archaebacteria require very high temperatures, or pressures, or unusual concentrations of chemical substances such as sulfur, because of their specialization into extreme conditions. Certain fungi have evolved to survive mostly at the temperature, the humidity, and stability.

For example, there is a significant difference in access to water as well as humidity between temperate rainforests and deserts. This difference in water access causes a diversity in the types of plans and animals that grow in these areas.


Chelation

Chelation is the formation or presence of two or more separate bindings between a polydentate (multiple bonded) ligand and a single central atom. Usually these ligands are organic compounds, and are called chelants, chelators, chelating agents, or sequestering agents.

The ligand forms a chelate complex with the substrate. Chelate complexes are contrasted with coordination complexes composed of monodentate ligands, which form only one bond with the central atom.

Chelants, according to ASTM-A-380, are "chemicals that form soluble, complex molecules with certain metal ions, inactivating the ions so that they cannot normally react with other elements or ions to produce precipitates or scale."

The word chelation is derived from Greekχηλή, chelè, meaning claw; the ligands lie around the central atom like the claws of a lobster.

The chelate effect

The chelate effect describes the enhanced affinity of chelating ligands for a metal ion compared to the affinity of a collection of similar nonchelating (monodentate) ligands for the same metal.

Consider the two equilibria, in aqueous solution, between the copper(II) ion, Cu2+ and ethylenediamine (en) on the one hand and methylamine, MeNH2 on the other.

Cu2+ + en [Cu(en)]2+ (1)
Cu2+ + 2 MeNH2 [Cu(MeNH2)2]2+ (2)

In (1) the bidentate ligand ethylene diamine forms a chelate complex with the copper ion. Chelation results in the formation of a five–membered ring. In (2) the bidentate ligand is replaced by two monodentate methylamine ligands of approximately the same donor power, meaning that the enthalpy of formation of Cu—N bonds is approximately the same in the two reactions. Under conditions of equal copper concentrations and when the concentration of methylamine is twice the concentration of ethylenediamine, the concentration of the complex (1) will be greater than the concentration of the complex (2). The effect increases with the number of chelate rings so the concentration of the EDTA complex, which has six chelate rings, is much much higher than a corresponding complex with two monodentate nitrogen donor ligands and four monodentate carboxylate ligands. Thus, the phenomenon of the chelate effect is a firmly established empirical fact.

The thermodynamic approach to explaining the chelate effect considers the equilibrium constant for the reaction: the larger the equilibrium constant, the higher the concentration of the complex.

[Cu(en)] =β11[Cu][en]
[Cu(MeNH2)2]= β12[Cu][MeNH2]2

Electrical charges have been omitted for simplicity of notation. The square brackets indicate concentration, and the subscripts to the stability constants, β, indicate the stoichiometry of the complex. When the analytical concentration of methylamine is twice that of ethylenediamine and the concentration of copper is the same in both reactions, the concentration [Cu(en)] is much higher than the concentration [Cu(MeNH2)2] because β11>> β12.

An equilibrium constant, K, is related to the standard Gibbs free energy, ΔG by

ΔG = −RT ln K = ΔH− TΔS

where R is the gas constant and T is the temperature in kelvins. ΔH is the standard enthalpy change of the reaction and ΔS is the standard entropy change. It has already been posited that the enthalpy term should be approximately the same for the two reactions. Therefore the difference between the two stability constants is due to the entropy term. In equation (1) there are two particles on the left and one on the right, whereas in equation (2) there are three particles on the left and one on the right. This means that less entropy of disorder is lost when the chelate complex is formed than when the complex with monodentate ligands is formed. This is one of the factors contributing to the entropy difference. Other factors include solvation changes and ring formation. Some experimental data to illustrate the effect are shown in the following table.

These data show that the standard enthalpy changes are indeed approximately equal for the two reactions and that the main reason why the chelate complex is so much more stable is that the standard entropy term is much less unfavourable, indeed, it is favourable in this instance. In general it is difficult to account precisely for thermodynamic values in terms of changes in solution at the molecular level, but it is clear that the chelate effect is predominantly an effect of entropy.

Other explanations, Including that of Schwarzenbach, are discussed in Greenwood and Earnshaw (loc.cit).

In nature

Virtually all biochemicals exhibit the ability to dissolve certain metal cations. Thus, proteins, polysaccharides, and polynucleic acids are excellent polydentate ligands for many metal ions. In addition to these adventitious chelators, several biomolecules are produced to specifically bind certain metals (see next section). Histidine, malate and phytochelatin are typical chelators used by plants.

In biochemistry and microbiology

Virtually all metalloenzymes feature metals that are chelated, usually to peptides or cofactors and prosthetic groups. Such chelating agents include the porphyrin rings in


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Question:What factors in the external environment will most likely affect Human Resource Management?

Answers:individual participative goal setting (PGS) is placed within the theoretical foundation of social cognitive theory (SCT). Based on this foundation, a cognitive-based self-leadership approach is suggested as a mechanism to enhance the PGS process and to achieve effective participation behavior. Propositions are described to serve as catalysts for empirically testing the applicability of self-leadership to goal-setting process a basic starting framework for a strategic human resource planning system. The framework involves several complex subsystems which require sustained effort and persistence in developing a workable model. The incomplete practices often used by organizations run the risk of reducing human resource planning to an unproductive management activity, instead of recognizing it as an important component in the total strategic planning process of a business.

Question:Question 11 Choose the correct factor affecting the rate of a reaction. What factor would this be? Hydrogen peroxide decomposes into water and oxygen gas quickly when solid MnO2 is added. Atemperature Bsurface area Ccatalyst Dnature of reactants Question 12 Choose the correct factor affecting the rate of a reaction. What factor would this be? Two reactive gases are mixed together, and a large amount of pressure is put on the container. They react more rapidly because of the increase in pressure. If the pressure increases so does the _____. Atemperature Bsurface area Ca catalyst Dconcentration Question 1 Fill in the blanks using one of the following words: dynamiceffective collisionexothermicendothermictemperature smallernature of reactantselectrolyteslargeractivation energy collisionintermediatekineticscatalystactivated complex _____ is the study of reaction rates. Question 14 Fill in the blanks using one of the following words: dynamiceffective collisionexothermicendothermictemperature smallernature of reactantselectrolyteslargeractivation energy collisionintermediatekineticscatalystactivated complex _____ is the minimum amount of energy required to get a reaction going. Question 15 Fill in the blanks using one of the following words: dynamiceffective collisionexothermicendothermictemperature smallernature of reactantselectrolyteslargeractivation energy collisionintermediatekineticscatalystactivated complex A/An _____ reaction gives off energy. Question 16 Fill in the blanks using one of the following words: dynamiceffective collisionexothermicendothermictemperature smallernature of reactantselectrolyteslargeractivation energy collisionintermediatekineticscatalystactivated complex _____ theory states that in order for reactants to form products, they need two things: sufficient kinetic energy and proper orientation. Question 17 Fill in the blanks using one of the following words: dynamiceffective collisionexothermicendothermictemperature smallernature of reactantselectrolyteslargeractivation energy collisionintermediatekineticscatalystactivated complex A/An _____ speeds up a reaction without being used up in that reaction. Question 18 Fill in the blanks using one of the following words: dynamiceffective collisionexothermicendothermictemperature smallernature of reactantselectrolyteslargeractivation energy collisionintermediatekineticscatalystactivated complex When reactants have sufficient kinetic energy and are oriented in the proper direction to form products, a/an _____ has taken place. Question 19 Fill in the blanks using one of the following words: dynamiceffective collisionexothermicendothermictemperature smallernature of reactantselectrolyteslargeractivation energy collisionintermediatekineticscatalystactivated complex The _____ is the high-energy particle produced when reactants collide. It is highly unstable. Question 20 Fill in the blanks using one of the following words: dynamiceffective collisionexothermicendothermictemperature smallernature of reactantselectrolyteslargeractivation energy collisionintermediatekineticscatalystactivated complex A/An _____ reaction absorbs energy.

Answers:11. D as MnO2 is a catalyst 12. D id pressure increases concentration increases 1. Kinetics 14.activation energy 15. exothermic 16.nature of reactants 17.catalyst 18.effective collision 19.collision intermediate 20. endothermic

Question:I thought maybe stability of substrate strength of base nature of leaving group solvent in which the reaction is run

Answers:1. Solvent: You need a polar, protic solvent for an E1 reaction to take place. Protic just means that it can form hydrogen bonds. The leaving group does not just fall off as some books leave you to believe, it is technically ripped off by the solvent so you need strong bonds to form and then stabilize. 2. Heat: As you increase temperature, you also increase the rate of the reaction, whether it be Sn1 or E1. Increase the temp enough though and you will break a threshold to favor E1 over Sn1 because it will cause the beta hydrogen to be ripped off more easily. 3. Substrate substitution: In order to form the most stable carbocation intermediate, once the leaving group is ripped off, tertiary substrates are more stable than secondary substrates. Primary and methyl substrates generally do not allow an E1 reaction to occur because they are so unstable. 4. Base: Although the base technically does not affect the rate of the reaction, it can affect whether the reaction actually occurs. A weak base will favor an E1 reaction because it allows time for the leaving group to come off instead of being substituted. 5. Leaving group: The ability of the leaving group is affected by its basicity, and definitely affects how fast the reaction will take place. A good leaving group is really just the conjugate base of a strong acid. Meaning, it is a weak and stable base. This makes it more likely to depart. Thus, I- > Br- > Cl- > F-

Question:How do biotic and abiotic factors affect the health and carrying capacity of an ecosystem?

Answers:Carrying capacity is the maximum population of a given species that a particular habitat can sustain indefinitely without degrading the habitat. Keep in mind that no population can increase its size indefinitely. Populations grow rapidly with ample resources, but as resources become limited, its growth rate slows and levels off and the population size stabilizes at or near the carrying capacity. Why? Environmental resistance. Depending on resource availability, the size of a population often fluctuates around its carrying capacity, although a population may temporarily exceed its carrying capacity and suffer a sharp decline or crash in its numbers.

From Youtube

Arecor: Factors affecting protein stability :One of a series of short videos produce by iemedia solutions ( www.iemedia.co.uk ) for Arecor Ltd ( http ) to help explain the scientific principles behind their protein stabilisation technologies. This video sumarises the various factors affecting protein stability, namely: amino acid side-chain damage by free radicals, proton exchange between amino acid side-chains and other molecules leading to changes in charge distribution, disruption of protein-metal interactions, hydrophobic interactions between proteins, and sugar side-chain cleavage by free radicals.

Arecor: Summary of factors affecting protein stability (with explanatory text) :One of a series of short videos produce by iemedia solutions ( www.iemedia.co.uk ) for Arecor Ltd ( http ) to help explain the scientific principles behind their protein stabilisation technologies. This video sumarises the various factors affecting protein stability, namely: amino acid side-chain damage by free radicals, proton exchange between amino acid side-chains and other molecules leading to changes in charge distribution, disruption of protein-metal interactions, hydrophobic interactions between proteins, and sugar side-chain cleavage by free radicals.