DENF 1521 Biochemistry
Glossary for Lessons on Intermediary Metabolism
This glossary is not meant to be all-inclusive. It is meant to further define the terms in the context of Intermediary Metabolism. Use the back button on the browser to return to the lesson. Please let me know if there are other terms that you feel should be included. If you need a more extensive glossary of terms not included in this one try the "Glossary of Biochemistry and Molecular Biology" by David M. Glick.
Absolute configuration The configuration of 4 different substituents on an asymmetric carbon. The configuration is expressed relative to D- or L-glyceraldehyde.
Acyl phosphate A molecule containing a phosphate group attached to a carbonyl carbon. Such a compound has the general formula:
Adrenal medulla The adrenal medulla and the adrenal cortex are the two main divisions of the adrenal gland which is located just above the kidneys. The adrenal medulla is responsible for the secretion of the catecholamines epinephrine, norepinephrine, and dopamine. Most of the epinephrine in the body is found here. The adrenal cortex produces cortisone.
Adrenocorticotropin hormone ACTH (also called Corticotropin) is secreted by the anterior pituitary and acts on the adrenal gland. The major action of ATCH is to stimulate growth and secretion of the cells of the adrenal cortex. More information.
Aerobic conditions This refers to conditions when oxygen is present. For example, oxidative phosphorylation occurs under aerobic conditions. Glycolysis does not require oxygen and therefore, can take place under anaerobic conditions.
Allosteric regulation Allosteric regulation of an enzyme occurs when a compound binds to the enzyme in a non-covalent manner and alters the activity of the enzyme. This may either increase or decrease the activity of the enzyme. Enzymes that are regulated in this manner are called allosteric enzymes. Therefore, compounds can be referred to as allosteric activators or allosteric inhibitors of a specific enzyme. An enzyme may be effected by both types of compounds. An example of an allosteric inhibitor is the inactivation of glycogen phosphorylase by high concentrations of glucose.
See also: Covalent modificationAnaphalactic shock A severe allergic reaction that affects the whole body and can lead to death.
Anaerobic conditions Reactions occurring in the absence of oxygen. Glycolysis does not require oxygen and therefore, can take place under anaerobic conditions. In contrast, oxidative phosphorylation requires oxygen and therefore, occurs under aerobic conditions.
Antibodies A protein synthesized by the immune system as part of a defensive mechanism. Immunoglobulins are antibody proteins generated against and capable of binding to an antigen.
Asymmetric carbon A carbon atom that has 4 different substituents bound to it. For example, the alpha-carbon of an amino acid or the carbon atoms in glucose. An asymmetric carbon can exist in 2 different tetrahedral configurations.
ATP Adenosine triphosphate (ATP) is the energy currency for the cell. It consists of an adenine base, ribose sugar, and three phosphates. Two of these are anhydride, "high energy", bonds, each having a
of -7.3 kcal/mol. Thus, the coupling of ATP hydrolysis to a reaction which has a positive
Autoimmune disease A disease in which the immune system mistakenly attacks self, targeting the cells, tissues, and organs of a person's own body. Examples include Type I diabetes, Myasthenia gravis, Systemic lupus erythematosus, Scleroderma, and Sjogren's syndrome.
Bond energy The energy required to break a bond.
Cartilage A specialized type of dense connective tissue consisting of cells embedded in a matrix. It is a translucent elastic tissue that is capable of withstanding considerable pressure or tension.
Catecholamine The catecholamines are epinephrine, norepinephrine, and dopamine. All 3 are synthesized from the amino acid tyrosine in the adrenal medulla. They are also stored in sympathetic neural endings.
Citric acid cycle The citric acid cycle, also known as the tricarboxylic acid (TCA) cycle or the Kreb's cycle is the pathway responsible for the breakdown of Acetyl CoA. Acetyl CoA enters the cycle by condensing with oxaloacetate to for citrate. In the cycle, 2 molecules of carbon dioxide are released and NADH and FADH2 are produced. These nucleotide coenzymes enter the electron transport chain where ATP is produced. See lesson 4.
See also: ATP; Electron transportCommitted step The committed step of a pathway is the rate-limiting step which commits a reactant to a specific pathway. This step is usually the key regulated reaction in the pathway.
Covalent modification After synthesis, proteins can be modified covalently in several ways. These include proteolytic cleavage or glycosylation. Covalent modification of proteins is also a means to alter the protein's activity. In metabolism, a commonly used covalent modification involves phosphorylation/dephosphorylation. A phosphate group is covalently linked to a serine residue in the protein. This can either activate or inactivate the protein's activity.
Cytoplasm The cytoplasm of the cell is the contents of the cell that are within the plasma membrane but outside the nucleus.
See also: Plasma membrane; Glycogen phosphorylase
Diabetes mellitus Diabetes mellitus is a metabolic disorder which is characterized by alterations in glucose metabolism. Insulin-dependent type I diabetes is characterized by the lack of insulin production due to the loss of the insulin-producing cells of the pancreas. In non-insulin dependent type II diabetes insulin is produced but is not effective in regulating glucose metabolism. In both cases the blood glucose levels are elevated above normal. The glucose is not taken up and utilized by the cells and there is a shift to the utilization of fats as an energy source.
See also: Insulin; Low blood sugar
Electrostatic repulsion Repulsion between like charges. In ATP, the negative charges on the oxygens repulse each other. This repulsion is relieved by charge separation that occurs upon the hydrolysis of ATP. Electrostatic repulsion contributes to the large free energy change associated with ATP hydrolysis.
Energy charge The measure of the relative amounts of ATP, ADP, and AMP in the cell. It is the degree to which the system is filled with high-energy phosphate groups. If all of the nucleotide was in the form of ATP, the energy charge of the cell would be 1.0. If everything was in the form of AMP, the energy charge would be 0. Most cells have an energy charge between 0.85 and 0.95.
See also: ATPEpinephrine Epinephrine is a hormone and neurotransmitter and is referred to as a catecholamine. It is synthesized from the amino acid tyrosine. Epinephrine triggers the breakdown of glycogen by activating adenylate cyclase and increasing the cellular levels of cAMP. This in turn activates a phosphorylation cascade leading to the activation of glycogen phosphorylase and the inhibition of glycogen synthase. The structure of epinephrine is shown below.
Glycogen phosphorylase Glycogen phosphorylase is the enzyme responsible for the breakdown of glycogen. This enzyme cleaves the alpha 1,4-linkages between glucose residues. This is a phosphorolysis reaction which utilizes inorganic phosphate as a substrate. Glucose 1-phosphate is released by this reaction. This enzyme can be regulated allosterically and covalently.
Glycolysis Glycolysis is the metabolic pathway responsible for the breakdown of glucose to 2 molecules of pyruvate. The pyruvate can be converted to acetyl CoA to enter the citric acid cycle. This pathway is described in lesson 3.
Glycosidic bond A bond between a sugar and another molecule such as another sugar, a purine or pyrimidine, or an akcohol. It can occur between an oxygen (O-glycosidic) or nitrogen (N-glycosidic).
Hexokinase An enzyme which catalyzes the formation of glucose 6-phosphate from glucose as part of glycolysis. It is an isozyme of glucokinase.
High energy phosphate bond The phosphoanhydride bond found in such molecules as ATP is considered a high energy phosphate bond. It has a
See also: ATPHydride ion A hydrogen nucleus with 2 electrons. Represented as :H-. NAD+ accepts a hydride ion to form NADH.
See also: NADHHydrophilic Polar or charged. Association with water.
Hydrophobic Nonpolar. Hydrophobic interactions (or bonds) are the association of nonploar groups with the exclusion of water.
Insulin Insulin is a polypeptide hormone secreted by the
-cells of the pancreas. It has a molecular weight of 6,000 and is synthesized as an inactive precursor, proinsulin. The secretion of insulin is stimulated by glucose and the parasympathetic nervous system. Insulin signals the fed state (high blood glucose levels) and stimulates the storage of fuels and the synthesis of proteins.
See also: Epinephrine; Low blood sugar; Diabetes mellitusIntegral membrane proteins Integral membrane proteins are a class of proteins found in the plasma membrane of cells. These proteins are tightly bound to the membrane. Also called intrinsic proteins. Harsh conditions such as the use of detergents, denaturants, or organic solvents are needed to remove integral proteins from the membrane lipid component.
Lectin A protein which specifically binds a carbohydrate moiety. For example, peanut lectin binds specifically to GalNAc-Gal.
Low blood sugar Blood sugar levels refer to the concentration of glucose in the bloodstream. Normal blood sugars are in the range of 80-120 mg/100ml. The levels of blood sugar are tightly controlled in the normal individual.
See also: Epinephrine; InsulinLysosome A membrane-bound organelle containing enzymes involved in degrading many cellular components such as protiens.
Myelin A layer composed of protein and lipid that surrounds most nerves. The myelin sheath speeds the transmission of impulses along nerves.
Multienzyme complex A goupr of enzymes which are associated and participate in a given metabolic pathway or process.
Nitrogenous bases Bases containing nitrogen. The nitrogenous bases found in the body are adenine, guanine, cytosine, thymine, and uracil.
Non-reducing end When an anomeric carbon is linked in a glycosidic bond, the sugar is considered non-reducing. In glycogen, for example, the non-reducing residue at the end of each branch is the non-reducing end.
Nucleotide coenzyme The nucleotide coenzymes NAD, FAD, etc. carry electron within the cell
Peripheral membrane protein Peripheral membrane proteins are a class of proteins found loosely associated with the plasma membrane of cells. Also called extrinsic proteins. Mild conditions such as high salt are needed to remove peripheral proteins from the membrane lipid component. Once released form the membrane peripheral proteins are often water soluble.
Pernicious anemia A form of anemia ( the decreased ability of red blood cells to provide adequate oxygen to body tissues) caused by the lack of a protein called intrinsic factor which is necessary for the absoption of vitamin B12 from the gastrointestinal track. More information.
Phosphorolysis Phosphorolysis is the process by which a bond is split using inorganic phosphate as a substrate instead of water. An example of phosphorolysis is the release of glucose 1-phosphate from glycogen by the enzyme glycogen phosphorylase
Phosphoryl group transfer reactions The transfer of a phosphate group usually from ATP to another molecule.
Plasma membrane All cells are surrounded by a plasma membrane surrounding the cytoplasm. The plasma membrane is composed of a lipid bilayer in which proteins are imbedded.
Primer Small building blocks used to begin the synthesis of larger macromolecules
Prosthetic group A metal ion or organic molecule (such as a vitamin derivative) that is bound to a protein and is essential for its activity.
Pyridoxal phosphate PLP. A coenzyme formed from Vitamin B6 pyridoxine. Involved in enzyme reactions involving the transfer of amino groups.
R and T conformation Relaxed (R) and tight (T) conformations refer to different conformations of a given enzyme or protein. Often used in the context of allosteric activations.
Receptor tyrosine kinase Receptor tyrosine kinases are proteins found in the plasma membrane of the cell. These receptors possess intrinsic tyrosine kinase activity, which is the ability to phosphorylate on a tyrosine residue in a protein. The kinase activity is activated by ligand binding which initiates a signal cascade ultimately leading to alteration in gene expression.
Reconstitution experiment An experiment in which isolated parts are mixed back together and an ectivity examined. For example, mixing an enzyme (ATPase) into an artificial membrane is a reconstitution experiment. Also recombining separated proteins or enzymes is another example. These experiments are often done to confirm that certain components are necessary to carry out a chemical or biological process.
Resonance stabilization The sharing of a charge over several atoms. In inorganic phosphate, the negative charge is distributed over the 4 oxygen atoms. This stabilizes the molecule by introducing a partial double-bond character to the molecule. This stabilization makes it favorable for the formation of inorganic phosphate after ATP hydrolysis.
Secreted proteins Secreted proteins are a class of proteins transported out of the cell. They are targeted during translation to the endoplasmic reticulum by their signal sequence. Once synthesized these proteins are transported to the Golgi, incorporated into secretory granules, which fuse with the plasma membrane dumping their contents (the secretory proteins) outside of the cell.
Schiff base A Schiff base is an organic compound in which the nitrogen atom of an amino group is double bonded to a carbon atom. Important in many reactions including those involving pyridoxal phosphate.
Substrate level phosphorylation The phosphorylation of ADP to form ATP independent of electron transport. In substrate level phosphorylation, the phosphorylation of ADP is coupled to the dehydration of a substrate (for example, 1,3-bisphosphoglycerate or phosphoenolpyruvate in glycolysis).
Transketolase An enzyme which transfers a 2-carbon fragment to another molecule. Thiamine pyrophosphate is a cofactor for this enzyme. Another enzyme transaldolase catalyzes the transfer of a 3-carbon unit. These enzymes are important in the non-oxidative branch of the pentose phosphate pathway.
ATP 
cAMP 
Epinephrine 
