Glucuronic Acid
Heme Degradation - Erythrocytes have a lifetime of about 120 days. Aged erythrocytes are destroyed upon passage through the spleen or liver Figure 21.31 . The basic pathway of heme breakdown is Heme - gt Biliverdin - gt Bilirubin - gt passage through blood to liver as bilirubin-albumin complex - gt Bilirubin diglucuronide - gt excretion. Bilirubin is insoluble in aqueous solutions, so complexing with albumin and gluruonic acid is essential for passage through the body. Accumulation of bilirubin...
INTERNET LINK Metalloprotein Database
Some kinds of biological processes require catalytic functions beyond those built into protein molecules alone. In such cases, a protein may require the help of some other small molecule or ion to carry out the reaction. Molecules bound to enzymes for this purpose are called coenzymes. The water soluble vitamin B complexes are metabolic precursors of a number of coenzymes. Table 11.5 lists several important coenzymes together with their related vitamins. NAD - Nicotinamide adenine dinucleotide...
Fumarate Hydratase Fumarase
m Fumarase is an enzyme of the citric acid cycle, glyoxylate cycle, and urea cycle that catalyzes addition of water to the double bond of fumarate to form L-malate. Fumarate H20 lt gt L-Malate AG' -3.8 kj mol . The enzyme is stereospecific, working only on the trans isomer. Next enzyme of citric acid cycle Previous enzyme of cycle See also Enzymes of the citric acid cycle, Intermediates of the Citric Acid Cycle, Pathway of the Citric Acid Cycle, Table 14.1
See also Oxygen Binding by Heme Proteins Oxygen Binding by Myoglobin Oxygen
Figure 7.3 Comparison of myoglobin and hemoglobin. Li Figure 7.3 Comparison of myoglobin and hemoglobin. Li Figure 6.1 Three-dimensional folding of the protein myoglobin. Figure 6.1 Three-dimensional folding of the protein myoglobin. Myoglobin Hemoglobin Structure - The myoglobin-hemoglobin family of proteins employs Fe II for O2 binding. Throughout the myoglobin-hemoglobin family, the iron is chelated by a tetrapyrrole ring system called protoporphyrin IX, one of a large class of porphyrin...
Eukaryotic Promoter Database
Figure 28.31 Structure of a small nuclear RNA snRNA . Li Figure 28.31 Structure of a small nuclear RNA snRNA . Li Figure 28.24 A model for the formation of the minimal preinitiation complex PIC for pol II on a TATA promoter. Li Figure 28.24 A model for the formation of the minimal preinitiation complex PIC for pol II on a TATA promoter. Li Fte aid Lid I proriiole i ornp lex E Ion gal io n ori ipl x Courtesy of R. G. Roeder, Trends Biochem. Sci. 1996 21 327-335. 1996 with permission of Elsevier...
See also Monosaccharide Nomenclature Derivatives of Monosaccharides
Figure 9.9a Stereochemical relationships of the D-aldoses. Figure 9.9a Stereochemical relationships of the D-aldoses. Figure 9.9b Stereochemical relationships of the D-ketoses. Figure 9.9b Stereochemical relationships of the D-ketoses.
Xanthosine Monophosphate
Inosine Monophosphate IMP NAD H2O lt gt Xanthosine Monophosphate XMP NADH Subsequently, XMP is converted to GMP by the enzyme XMP aminase Figure 22.6 . See also De Novo Biosynthesis of Purine Nucleotides AMP Deaminase is an enzyme in purine catabolism that deaminates AMP to form IMP and ammonia, as follows See also Figure 22.7, Purine Degradation Figure 22.7 Catabolism of purine nucleotides to uric acid. Figure 22.7 Catabolism of purine nucleotides to uric acid. Figure 22.7 shows pathways of...
INTERNET LINKS Rod Photoreceptor
Figure 19.26 Schematic drawing of a rod cell. Li Figure 19.26 Schematic drawing of a rod cell. Li Figure 19.27 The chemical changes in photoreception. Li Figure 19.27 The chemical changes in photoreception. Li
Glutamine HCO3 2ATP H2O Carbamoyl Phosphate 2 ADP Pi Glutamate
A bacterial reaction catalyzes both reactions. In eukaryotes, two forms of the enzyme one in mitochondria and one in cytoplasm are found. The enzyme is inhibited by UTP, consistent with the involvement of carbamoyl phosphate in pyrimidine nucleotide synthesis. See also Metabolic Nitrogen Balance, Transamination in Amino Acid Metabolism, Amino Acid Degradation, Urea Cycle, Ammonia Transport in the Body, De Novo Pyrimidine Nucleotide Metabolism from Chapter 22 . Figure 20.7 Reactions in...
tRNA Sequence Database
Figure 27.7 A sampling of the modified and unusual bases found in tRNAs. Li Figure 27.7 A sampling of the modified and unusual bases found in tRNAs. Li The hydrogen bond is an interaction between a covalently bonded hydrogen atom on a donor group i. e., -OH or -NH and a pair of nonbonded electrons on an acceptor group i.e., Q or N as shown in Figure 2.7. The atom to which hydrogen is covalently bonded is called the hydrogen bond donor and the atom with the nonbonded electron pair is called the...
Allolactose
S Allolactose Gal i l-- gt 6 Glc is a molecule that HO is the inducer of the lactose operon in E. coli. CHi See also Lactose Operon Regulation, IPTG IPTG is an artificial inducer of the Lac operon. It is used in laboratories to induce the lac operon because, in contrast to to allolactose, which is the natural inducer of the operon, IPTG cannot be hydrolyzed and broken down by the cell. Hence, its concentration does not change during an experiment.
Gluconeogenesis
Iii Li Gluconeogenesis is a central metabolic pathway involving biosynthesis of the sugar glucose. Figure 16.6 shows an overview of the process. With the exception of the enzymes shown in red on the right hand side of the figure, the enzymes of gluconeogenesis and glycolysis are the same. One starting point for gluconeogenesis is two molecules of pyruvate and the process ends with formation of one glucose molecule. See also Gluconeogenesis Enzymatic Reactions, Gluconeogenesis Molecular...
INTERNET LINK Fatty Acid Metabolism
3-Ketoacyl-CoA is an intermediate in the oxidation of fatty acids. It is the last acyl moiety made prior to cleavage of the acetyl group by thiolase. 3-Ketoacyl-CoA is produced and used respectively in the reactions that follow Figure 18.16 1. L-3-Hydroxyacyl-S-CoA NAD lt gt 3-Ketoacyl-S-CoA NADH H catalyzed by 3-Hydroxyacyl-CoA Dehydrogenase 2. 3-Ketoacyl-CoA CoASH lt gt Acyl-CoA less 2 carbons Acetyl-CoA catalyzed by Thiolase . See also Oxidation of Saturated Fatty Acids, Unsaturated Fatty...
See also Glycogen Synthase Glycogen Biosynthesis Glycogen Synthase D
Glycogen synthesis and breakdown are controlled tightly by hormonal action. These involve regulatory kinase cascades, as depicted in Figure 13.18 for glycogen breakdown. Like gluconeogenesis glycolysis, glycogen synthesis breakdown is reciprocally regulated. For example, epinephrine inhibits glycogen synthesis at the same time as it promotes glycogen breakdown. Glycogen synthase is the primary regulatory enzyme in glycogen synthesis. Like glycogen phosphorylase, the enzyme that breaks down...
See also Mitochondrial Structure and Function from Chapter 15 Basic Processes
Figure 1.13 Distribution of biomolecules in a cell. Figure 1.13 Distribution of biomolecules in a cell. From Neil Campbell, Jane Reece, and Larry Mitchell, Biology, 5th ed. Menlo Park, CA Addison Wesley Longman, 1999 Addison Wesley Longman, Inc. Metabolic oxidations generate reduced electron carriers, such as NADH and FADH2. Oxidation of these electron carriers in the mitochondrion generates most of the energy needed for ATP synthesis. Most vertebrate cells contain several hundred mitochondria,...
Figure 56 Absorption spectra of the aromatic amino acids in the nearultraviolet
Li From D. Wetlaufer, Adv. Protein Chem. 1962 17 303-390. 1962 Academic Press. Iii Li Tyrosine is an ot amino acid found in proteins. In mammals, tyrosine is an nonessential amino acid, meaning it does not need to be present in the diet. Tyrosine's hydroxyl group is a target for phosphorylation in some proteins. Tyrosine's benzene-ring side chain classifies it as an aromatic amino acid. The aromatic amino acids, like most compounds carrying conjugated rings, exhibit strong absorption of light...
DNA Replication Overview
i i . DNA replication is an essential aspect of cellular and viral reproduction. Replication of a double-stranded DNA results in two double-stranded DNAs as products. Some important general points about DNA replication are as follows The mechanism of replication is semi-conservative--each newly made strand is copied from one of the parental strands and the products of replication are two molecules, each containing one parental strand and one newly synthesized strand see here . DNA replication...
Figure 1519 F1 ATP synthase as a rotary engine driving the synthesis of ATP
Li From Y. Zhou, T. M. Duncan, and R. L. Cross, Proc. Natl. Acad. Sci. USA 1997 94 10583. Reprinted with permission of the PNAS. Complex V also called ATP synthase or the F0F1 complex is a multi-protein structure with three-fold symmetry, resembling a mushroom Figure 15.14 . It consists of a top knob called F1 and a stalk, which joins the knob to the base called F0 in the inner mitochondrial membrane. The F1 knob projects into the mitochondrial matrix and contains three Qt i dimers arranged...
Nadh
m NADH is a carrier of electrons produced in biological oxidations. The molecule exists in two forms that vary in whether or not they are carrying electrons. NADH is the reduced form of the molecule carries electrons and NAD is the oxidized form of the molecule lacks electrons . NADH is produced from NAD in reactions such as conversion of acetaldehyde to ethanol by alcohol dehydrogenase Figure . NADH is converted back to NAD by donating electrons such as in the conversion of pyruvate to...
FCCP is a chemical uncoupler of electron transport and oxidative phosphorylation
FCCP permeabilizes the inner mitochondrial membrane to protons, destroying the proton gradient and, in doing so, uncouples the electron transport system from the oxidative phosphorylation system. In this situation, electrons continue to pass through the electron transport system and reduce oxygen to water, but ATP is not synthesized in the process. FCCP acts similar to 2,4-dinitrophenol DNP in uncoupling electron transport and oxidative phosphorylation.
Chorismic Acid Chorismate
tan Chorismic acid is a metabolic intermediate that is the branch point in the synthesis of coenzyme Q and the aromatic amino acids, phenylalanine, tyrosine, and tryptophan Figure 21.12 . Chorismate is formed from 5-enoylpyruvylshikimic acid 3-phosphate Figure 21.13 . Conversion of chorismate to p-hydroxybenzoic acid leads to synthesis of coenzyme Q. Conversion of chorismate to anthranilate leads to biosynthesis of tryptophan Figure 21.14 . See also Metabolism of Aromatic Amino Acids and...
Pyruvate HCO3 ATP Oxaloacetate ADP Pi H
Pyruvate carboxylase is activated allosterically by acetyl-CoA. The enzyme is a tetrameric protein carrying four molecules of biotin, each bound covalently through an amide bond involving the -amino group of a lysine residue. In animals the reaction catalyzed by pyruvate carboxylase is the most important anaplerotic reaction, particularly in liver and kidney. Pyruvate carboxylase is the only enzyme of gluconeogenesis in the mitochondria, requiring pyruvate and oxaloacetate to be transported...
DIsocitrate
S D-Isocitrate is a citric acid cycle and glyoxylate cycle intermediate produced as a result of action of the enzyme aconitase on citrate. Isocitrate is converted to oi-ketoglutarate by action of the enzyme isocitrate dehydrogenase See also Glyoxylate Cycle, Aconitase, Citrate, Isocitrate Dehydrogenase, ot-Ketoglutarate, Fluorocitrate, Citric Acid Cycle Intermediates, Figure 14.3, Table 14.1
Vitamin Kl Phylloquinone
m Vitamin K is found in plants as phylloquinone vitamin K1 and in animals as menaquinone vitamin K2 . Vitamin K2 is essential for the carboxylation of glutamate residues in certain proteins, to give - carboxyglutamate. This modification allows the protein to bind calcium, an essential event in the blood clotting cascade. Carboxylation of glutamate is also important in other proteins involved in the mobilization or transport of calcium.
Ribonucleotide Reductase and Deoxyribonucleotide Biosynthesis
Li Most of the carbon that flows through nucleotide synthetic pathways goes into ribonucleotide triphosphates rNTPs - ATP, CTP, GTP, and UTP . A relatively small fraction is diverted to the synthesis of deoxyribonucleoside triphosphates dNTPs . rNTPs are synthesized in excess of dNTPs because most cells contain 5-10 times as much RNA as DNA and because rNTPs have multiple metabolic roles, whereas dNTPs are used only to make DNA. As seen in Figure 22.12, rNDPs D here refers to di- are all...
INTERNET LINK Gly Ser Thr Metabolism
Cysteine is an ot amino acid found in proteins. In mammals, cysteine is a non- c essential amino acid, meaning it does not need to be present in the diet. The hydroxy and sulfur-containing amino acids are generally more hydrophilic than their aliphatic analogs, although methionine is fairly hydrophobic. Cysteine can ionize at high pH see here Cysteine, together with another cysteine in a protein, can form disulfide bonds see here . Disulfide bonds help to stabilize the structure of some...
Triacylglycerol Lipase HormoneSensitive Lipase
Triacylglycerol lipase is a hormonally regulated enzyme Figure 18.11 that catalyzes the hydrolytic release of fatty acid from carbon 1 or 3 of the glycerol moiety. The fatty acid release is followed by the action of a diacylglycerol lipase and a monoacylglycerol lipase, in turn. Together these three enzymes degrade the original molecule to glycerol and three unesterified fatty acids. In adipose tissue, the primary hormonal effects are mediated by epinephrine in stress situations and by glucagon...
Phospholipid Catabolism
Figure 19.4 Synthesis of polar head groups of bacterial phospholipids. CH. 0 P 0 P 0 Cytidine I I 0 c CH. 0 P O CH CH CH 0 P 0 Ph os p h a l i dylg lycerol-3- phos phaie CH., 0 P C CH., CH., NH CH 0 P 0 CH2 CH CH., Oh 0-P 0 CH , CH CH O P 0 This is an Image Map of Glycerophospholipid Synthesis from Figure 19.2. Click on a Box to Link to the Molecule.
See also Covalent Bonds vs NonCovalent Forces DNA Secondary Structure from
Figure 2.2 Types of noncovalent interactions. i - Figure 2.2 Types of noncovalent interactions. i -
Argininosuccinate
Argininosuccinate is an intermediate in the urea cycle. It participates in the reactions below. 1. Citrulline ATP Aspartate lt gt Argininosuccinate AMP PPi catalyzed by Argininosuccinate Synthetase 2. Argininosuccinate lt gt Arginine Fumarate catalyzed by Argninosuccinase . See also Urea Cycle Description, Urea Cycle Reactions, Figure 20.13 INTERNET LINK Urea Cycle and Metabolism of Amino Groups
See also Monoacylglycerol Lipase Diacylglycerol Triacylglycerol Lipase Fat
A monoacylglycerol is a glycerol with only one fatty acid esterified to it. Monoacylglycerol can be produced by digestion of a diacylglycerol by diacylglycerol lipase. Hydrolysis of the monoacylglycerol, catalyzed by monoacylglycerol lipase, yields glycerol and a free fatty acid, as follows Monoacylglycerol lt gt Glycerol Fatty Acid Monoacylglycerol lipase is an enzyme that hydrolyzes a fatty acid from a monoacylglycerol glycerol with one fatty acid esterified to it to yield glycerol and a free...
See also Reciprocal Regulation of Glycogen Biosynthesis and Mobilization
Figure 16.8 Pathway for conversion of glucose monomers to polymeric Li Figure 16.10 The branching process in glycogen synthesis. - o XIXo XlyL oXlA oXIyU gt XIXo -X yL oXIyL o- Gj i j t O j j J i j Glycogen synthase I, like the other form of the enzyme glycogen synthase D , catalyzes the addition of a glucose molecule from UDP-glucose in an ot 1,4 linkage to a growing glycogen chain. The two enzymes are identical except that glycogen synthase D arises from phosphorylation of glycogen synthase I...
INTERNET LINK Pentose Phosphate Pathway
The enzymes of the pentose phosphate pathway are listed below 6-Phosphogluconate Dehydrogenase Phosphopentose Isomerase Phosphopentose Epimerase Transketolase Transaldolase See also Pentose Phosphate Pathway, Intermediates of the Pentose Phosphate Pathway, Calvin Cycle from Chapter 17 INTERNET LINK Pentose Phosphate Cycle Lactonase is an enzyme of the pentose phosphate pathway that catalyzes the reaction below 6-Phosphogluconolactone H2O lt gt 6-Phosphogluconate H See also Pentose Phosphate...
Hjj C Coo H
Tryptophan's side chain classifies it as an aromatic amino acid. The aromatic amino acids, like most compounds carrying conjugated rings, exhibit strong absorption of light in the near-ultraviolet region of the spectrum Figure 5.6 . This absorption is frequently used for the analytical detection of proteins. Tyrosine and tryptophan have some hydrophobic character, but it is tempered by the polar groups in their side chains. In addition, tyrosine can ionize at high pH. Tryptophan is an...
See also Figure 174c Figure 1716 Thylakoid Lumen Chloroplast Anatomy Stroma
Figure 17.15 Summary view of the light reactions as they occur in the thylakoid. i Figure 17.15 Summary view of the light reactions as they occur in the thylakoid. i Figure 17.4c Chloroplasts, the photosynthetic organelles of green plants and algae. lumen surround rjr naj lisme-lla lumen surround rjr naj lisme-lla From Neil Campbell, Jane Reece, and Larry Mitchell, Biology, 5th ed. Menlo Park, CA Addison Wesley Longman, 1999 . Addison Wesley Longman, Inc. Figure 17.16 Arrangement of components...
Fluoroacetate
S Metabolism of fluoroacetate produces an inhibitor of the citric acid cycle enzyme, aconitase. Fluoroacetate is known as a suicide substrate because by itself it is not toxic to cells, but it kills cells by being made into a toxic substance. For fluoroacetate, this occurs as follows
See also Figure 43 DNA Acyclovir Ganciclovir De Novo Biosynthesis of Purine
Deoxyribose more accuratey named 2-deoxyribose is a five carbon sugar contained in deoxyribonucleosides, deoxyribonucleotides, and their derivatives. Deoxyribose differs from ribose in lacking a hydroxyl at position 2. Deoxyribonucleotides are the monomeric units building blocks of DNA. See also Ribonucleotide Reductase and Deoxyribonucleotide Biosynthesis
See also Calmodulin Mechanism of Activating Glycogen Breakdown Glycogen
Regulation, Glycogen Breakdown, Kinase Cascade in Fat Mobilization from Chapter 18 , Second Messenger Systems Figure 16.11 Regulatory cascades affecting glycogen synthesis and mobilization. Li Figure 16.11 Regulatory cascades affecting glycogen synthesis and mobilization. Li Figure 16.12 Regulation of glycogen synthase activity through cAMP mediated control of phosphoprotein phosphatase PP-1 activity. Li Figure 16.12 Regulation of glycogen synthase activity through cAMP mediated control of...
See also Citrate Shuttle
Malic Enzyme officially named malate dehydrogenase-decarboxylating NADP catalyzes the reaction below. Pyruvate HCO3- NADPH H lt gt L-Malatt NAD H2O This important anaplerotic reaction provides a means of replenishing L-malate in the citric acid cycle Figure 14.18 and it also plays an important role in the citrate shuttle Figure 18.31 . See also Citric Acid Cycle, Anaplerotic Reaction, Citrate Shuttle Figure 14.18 Major biosynthetic roles of some citric acid cycle intermediates. Li Figure 14.18...
Fatty Acid Synthase
Li Fatty acid synthase is the name of the complex of six enzymatic activities that performs biosynthesis of fatty acids in cells. The enzyme is composed of two multifunctional polypeptide chains, which contain the enzymatic activities below -Ketoacyl-ACP Synthase Malonyl-CoA-ACP Transacylase -Ketoacyl-ACP Reductase 3-Hydroxylacyl-ACP Dehydrogenase Enoyl-ACP Reductase See also Palmitate Biosynthesis from Acetyl-CoA, Fatty Acid Biosynthesis Strategy, Synthesis of Long Chain Fatty Acids, Figure...
Glyceraldehyde3Phosphate Dehydrogenase G3PDH
Li G3PDH catalyzes the oxidation reduction of D-glyceraldehyde-3-phosphate G3P and 1,3-bisphosphoglycerate 1,3BPG . G3P NAD Pi lt gt 1,3BPG NADH H AG' 6.3 kj mol The AG ' of the enzymatic reaction is sufficiently low for it to be used in lycolysi , gt luconeogenesis, and the Calvin cycle. The reaction involves a two-electron oxidation of the carbonyl carbon of G3P to the carboxyl level, a reaction that is normally quite exergonic. However, the overall reaction is slightly endergonic under...
See also Fischer Projection Diastereomers Sugar Ring Structures
Chiral carbons carbons covalently linked to 4 different entities give rise to stereoisomers. Molecules that are stereoisomers have the same formula and the same structure, but have their atoms arranged in different ways in 3D space. For example, compare the structures of D-glyceraldehyde and L-glyceraldehyde in Figure 9.5. Notice that they are nonsuperimposable. Common sugars typically have not one, but multiple chiral carbons. Glucose, for example, contains four chiral carbons. For a carbon...
See also Phosphorolysis Glycogen phosphorylase Figure 1318 Kinase Cascade
Glycosidic bonds between monosaccharides give rise to oligosaccharides and polysaccharides. The simplest oligosaccharides, the disaccharides, include compounds such as sucrose and lactose, which are referred to as sugars like the monosaccharides . Other common disaccharides include trehalose, maltose, gentiobiose, and cellobiose. Four features distinguish disaccharides from each other 1. The two specific sugar monomers and their stereoconfigurations 2. The carbons involved in the linkage 3. The...
Glutamine formation Glutamine synthetase catalyzes the following reaction
The E. coli glutamine synthetase is a dodecamer, with 12 identical subunits and the complex has a molecular weight of about 600,000 Daltons. The amide nitrogen of glutamate is used for the synthesis of several amino acids, purine and pyrimidine nucleotides, and amino sugars, so glutamine synthetase plays a central role in nitrogen metabolism. In animals, the enzyme is a key participant in detoxifying ammonia, particularly in the brain, and in ammonia excretion in the kidney. Accumulation of...
Calcium in Contraction Troponins
Figure 8.14 The regulation of muscle contraction by calcium. Figure 8.14 The regulation of muscle contraction by calcium. From W. M. Becker, L.J. Kleinsmith, and J. Hardin, The World of the Cell, 4th ed. San Francisco, CA Addison Wesley Longman, 2000 Addison Wesley Longman, Inc. Tropomyosin is a fibrous protein that exists as elongated dimers lying along, or close to, the groove in the F-actin helix. Bound to each tropomyosin molecule are three small proteins called troponins I, C, and T. The...
Phosphribosyl Pyrophosphate Synthetase PRPP Synthetase
Li PRPP synthetase is an enzyme that catalyzes there reaction below see here also ATP Ribose-5-Phosphate lt gt PRPP AMP PRPP is an important intermediate in the de novo synthesis of purines pathway Figure 22.4 . Defects in PRPP synthetase may render it insensitive to feedback inhibition by purine nucleotides. Thus, purine nucleotides are overproduced, leading to excessive uric acid synthesis and gout Figure 22.9 . See also The Importance of PRPP, De Novo Biosynthesis of Purine Nucleotides,...