active site

Examples of active site in the following topics:

• Enzyme Active Site and Substrate Specificity

  • The enzyme's active site binds to the substrate.
  • The positions, sequences, structures, and properties of these residues create a very specific chemical environment within the active site.
  • Environmental conditions can affect an enzyme's active site and, therefore, the rate at which a chemical reaction can proceed.
  • If the enzyme changes shape, the active site may no longer bind to the appropriate substrate and the rate of reaction will decrease.
  • The active site of an enzyme also creates an ideal environment, such as a slightly acidic or non-polar environment, for the reaction to occur.

• Control of Metabolism Through Enzyme Regulation

  • In noncompetitive inhibition, an inhibitor molecule binds to the enzyme at a location other than the active site (an allosteric site).
  • Their binding induces a conformational change that reduces the affinity of the enzyme's active site for its substrate. 
  • They bind to an allosteric site which induces a conformational change that increases the affinity of the enzyme's active site for its substrate.
  • Allosteric inhibitors modify the active site of the enzyme so that substrate binding is reduced or prevented.
  • In contrast, allosteric activators modify the active site of the enzyme so that the affinity for the substrate increases.

• ATP and Muscle Contraction

  • The energy released during ATP hydrolysis changes the angle of the myosin head into a "cocked" position, ready to bind to actin if the sites are available.
  • The muscle contraction cycle is triggered by calcium ions binding to the protein complex troponin, exposing the active-binding sites on the actin.
  • As soon as the actin-binding sites are uncovered, the high-energy myosin head bridges the gap, forming a cross-bridge.
  • ATP then binds to myosin, moving the myosin to its high-energy state, releasing the myosin head from the actin active site.
  • The cross-bridge muscle contraction cycle, which is triggered by Ca2+ binding to the actin active site, is shown.

• Regulatory Mechanisms for Cellular Respiration

  • A number of enzymes involved in each of the pathways (in particular, the enzyme catalyzing the first committed reaction of the pathway) are controlled by attachment of a molecule to an allosteric (non-active) site on the protein.
  • This site has an effect on the enzyme's activity, often by changing the conformation of the protein.
  • These regulators, known as allosteric effectors, may increase or decrease enzyme activity, depending on the prevailing conditions, altering the steric structure of the enzyme, usually affecting the configuration of the active site.
  • The attachment of a molecule to the allosteric site serves to send a signal to the enzyme, providing feedback.

• Regulatory Proteins

  • To keep actin from binding to the active site on myosin, regulatory proteins block the molecular binding sites.
  • Troponin, which regulates the tropomyosin, is activated by calcium, which is kept at extremely low concentrations in the sarcoplasm.
  • A change in the receptor conformation causes an action potential, activating voltage-gated L-type calcium channels, which are present in the plasma membrane.
  • The inward flow of calcium from the L-type calcium channels activates ryanodine receptors to release calcium ions from the sarcoplasmic reticulum.
  • Calcium then binds to troponin, causing the troponin to change shape and remove the tropomyosin from the binding sites.

• Platelets and Coagulation Factors

  • When the endothelial layer is injured, collagen is exposed, releasing other factors to the bloodstream which attracts platelets to the wound site.
  • When the platelets are activated, they clump together to form a platelet plug (fibrin clot) ( b), releasing their contents.
  • The released contents of the platelets activate other platelets and also interact with other coagulation factors.
  • Outside of the body, platelets can also be activated by a negatively-charged surface, such as glass.
  • The platelets collect at a wound site in conjunction with other clotting factors, such as fibrinogen, to form a fibrin clot that prevents blood loss and allows the wound to heal.

• Cancer and Transcriptional Control

  • Mutations that activate transcription factors, such as increased phosphorylation, can increase the binding of a transcription factor to its binding site in a promoter.
  • This could lead to increased transcriptional activation of that gene that results in modified cell growth.
  • Researchers have been investigating how to control the transcriptional activation of gene expression in cancer.
  • The EGFR pathway activates many protein kinases that, in turn, activate many transcription factors that control genes involved in cell growth.
  • New drugs that prevent the activation of EGFR have been developed and are used to treat these cancers.

• The trp Operon: A Repressor Operon

  • The trp operon is a repressor operon that is either activated or repressed based on the levels of tryptophan in the environment.
  • Just before the coding region is the transcriptional start site.
  • The promoter sequence is upstream of the transcriptional start site.
  • Each operon has a sequence within or near the promoter to which proteins (activators or repressors) can bind and regulate transcription.
  • When tryptophan is not present in the cell, the repressor by itself does not bind to the operator; therefore, the operon is active and tryptophan is synthesized.

• Altered Gene Expression in Cancer

  • There are many proteins that are turned on or off (gene activation or gene silencing) that dramatically alter the overall activity of the cell.
  • While these changes do not occur simultaneously in one cancer, changes at each of these levels can be detected when observing cancer at different sites in different individuals.
  • These are tumor suppressor genes, which are active in normal cells to prevent uncontrolled cell growth.
  • It can bind to sites in the promoters of genes to initiate transcription.
  • Myc is a transcription factor that is aberrantly activated in Burkett's Lymphoma, a cancer of the lymph system.

• Catabolite Activator Protein (CAP): An Activator Regulator

  • When glucose levels decline in E. coli, catabolite activator protein (CAP) is bound by cAMP to promote transcription of the lac operon.
  • Just as the trp operon is negatively regulated by tryptophan molecules, there are proteins that bind to the operator sequences that act as a positive regulator to turn genes on and activate them.
  • When glucose levels decline in the cell, accumulating cAMP binds to the positive regulator catabolite activator protein (CAP), a protein that binds to the promoters of operons that control the processing of alternative sugars, such as the lac operon.
  • In these operons, a CAP-binding site is located upstream of the RNA-polymerase-binding site in the promoter.
  • Explain how an activator works to increase transcription of a gene