Nucleotide Metabolism II This course is part of a series taught by Kevin Ahern at Oregon State University on General Biochemistry. For more information about online courses go to ecampus.oregonstate.edu 1. Ribonucleotide reductase (RNR) catalyzes the formation of deoxyribonucleotides from ribonucleotides. The substrates are ribonucleoside diphosphates (ADP, GDP, CDP, or UDP) and the products are deoxyribonucleoside diphosphates (dADP, dGDP, dCDP, or dUDP). 2. RNR has two pairs of two identical subunits - R1 (large subunit) and R2 (small subunit). R1 has two allosteric binding sites and the active site of the enzyme. R2 forms a tyrosine radical necessary for the reaction mechanism of the enzyme. 3. Ribonucleotide reductase is allosterically regulated via two binding sites - a specificity () binding site (controls which substrates the enzyme binds and which deoxyribonucleotides are made) and an activity binding site (controls whether or not enzyme is active - ATP activates, dATP inactivates). Specificity sites act in a generally complementary fashion. Binding of deoxypyrimidine triphosphates to the specificity site tends to inhibit binding and reduction of pyrimidine diphosphates at the enzyme's active site and stimulates binding and reduction of purine diphosphates at the active site. Binding of deoxypurine triphosphates tends to inhibit reduction of purine diphosphates and stimulates reduction of pyrimidine diphosphates. Don't confuse the active site with the activity site. The ACTIVE SITE is ...
Fatty Acid Synthesis This course is part of a series taught by Kevin Ahern at Oregon State University on General Biochemistry. For more information about online courses go to ecampus.oregonstate.edu 1. The process occurs similar to beta-oxidation, though in reverse. Important distinctions are noted below in af. * a. Fatty acid synthesis up to palmitate occurs in the cytoplasm, but beta oxidation occurs in mitochondrial matrix. * b. Fatty acids are built using an acyl carrier protein (ACP), but beta oxidation uses CoA. * c. NADPH is used to donate electrons in synthesis, but NAD+ or FAD are used to accept electrons in oxidation in the mitochondrion. * d. A three carbon molecule, malonyl-ACP donates two carbons to the growing fatty acid chain - a carbon dioxide is lost in the process. Beta oxidations yield two carbon acetyl-CoA units. * e. Synthesis of fatty acids longer than 16 carbons occurs in endoplasmic reticulum or mitochondrion. Oxidation of fatty acids longer than 16 carbons begins in peroxisomes. * f. In fatty acid biosynthesis, a D-hydroxyl intermediate is formed at carbon #3. In fatty acid oxidation, an L-hydroxyl intermediate is formed at carbon #3. 2. Acetyl-CoA carboxylase catalyzes the addition of a carboxyl group to acetyl-CoA to form malonyl-CoA. The enzyme is regulated allosterically (inhibited by palmitoyl-CoA and activated by citrate) and by covalent modification (phosphorylation inhibits, dephosphorylation activates). 3. Fatty acid biosynthesis occurs in the cytoplasm and ...
Gluconeogenesis This course is part of a series taught by Kevin Ahern at Oregon State University on General Biochemistry. For more information about online courses go to ecampus.oregonstate.edu 1. Glycerol is a breakdown product of fat metabolism. Glycerol can be metabolized in glycolysis by conversion to glycerol-3-phosphate and then to DHAP, a glycolytic intermediate. 2. Gluconeogenesis accomplishes the reverse of glycolysis - synthesis of glucose from pyruvate using four different enzymes to replace three energetically unfavorable reactions in glycolysis. 3. Gluconeogenesis does not occur in all tissues of the body. The primary gluconeogenic organs of the body are the liver and part of the kidney. 4. The enzymes unique to gluconeogenesis Pyruvate Carboxylase and PEP carboxykinase (PEPCK) instead of Pyruvate Kinase of glycolysis, Fructose 1,6 Bisphosphatase (F1,6BPase) instead of Phosphofructokinase (PFK) from glycolysis, and Glucose-6-phosphatase (G6Pase) instead of Hexokinase from glycolysis. 5. F1,6BPase and G6Pase act by similar mechanisms, clipping a phosphate from their substrates and thus avoiding synthesis of ATP, which is what would be required if the glycolysis reactions were simply reversed. 6. One reaction of gluconeogenesis occurs in the mitochondrion. It is catalyzed by pyruvate carboxylase and yields the four carbon intermediate, oxaloacetate. The carboxyl group is added in forming oxaloacetate thanks to the coenzyme biotin, which carries carbon dioxide for attachment ...
A Quantum of Solace - Molecular Electronics of Benzodiazepines (Google Workshop on Quantum Biology) Google Workshop on Quantum Biology A Quantum of Solace: Molecular Electronics of Benzodiazepines Presented by Luca Turin October 22, 2010 ABSTRACT Benzodiazepines and related drugs modulate the activity of GABA-A receptors, the main inhibitory receptor of the central nervous system. The prevailing view is that these drugs bind at the interface between two receptor subunits and allosterically modulate the response to GABA. In this talk I shall present evidence that benzodiazepines work instead by facilitating electron transport from the cytoplasm to a crucial redox-sensitive group in the gamma subunit. If this idea is correct, benzodiazepines should not only be regarded as keys fitting into a lock, but also as one-electron chemical field-effect transistors fitting into an electronic circuit. About the speaker:
Citric Acid Cycle II This course is part of a series taught by Kevin Ahern at Oregon State University on General Biochemistry. For more information about online courses go to ecampus.oregonstate.edu 1. The citric acid cycle consists of two main parts - release of CO2 (first part) and conversion to oxaloacetate (second part). You are responsible for the structures of molecules in the citric acid cycle and the names of the enzymes. 2. In the "first" reaction of the citric acid cycle, citrate synthase catalyzes the joining of the acetyl group from acetyl-CoA to oxaloacetate to make citrate. This reaction is VERY energetically favorable, due to breaking of the thioester bond in acetyl-CoA. The energetically favorable reaction helps to "pull" the relatively unfavorable reaction preceding it. 3. Aconitase catalyzes the rearrangement of citrate to isocitrate. For your information - Aconitase is inhibited by fluorocitrate. Fluoroacetate is a poison that can be used by citrate synthase to make fluorocitrate. 4. The first decarboxylation of the citric acid cycle is catalyzed by isocitrate dehydrogenase and the reaction is strongly favored to the right. The products of this reaction are NADH and alpha ketoglutarate. 5. Alpha ketoglutarate is an important intermediate for its involvement in anapl*** reactions related to transamination (we'll talk about these later). The mechanism of the enzyme acting on alpha ketoglutarate (alpha ketoglutarate dehydrogenase complex) is virtually identical to the ...
Glycolysis II This course is part of a series taught by Kevin Ahern at Oregon State University on General Biochemistry. For more information about online courses go to ecampus.oregonstate.edu 1. Regulation of glycolysis occurs through 3 enzymes - hexokinase, PFK, and pyruvate kinase. Hexokinase is regulated by substrate-level regulation. PFK is regulated allosterically by ATP (turns off), AMP (turns on), citrate (turns off), and F2,6BP (strongly turns on). Note that ATP and citrate will be present when cells have a lot of energy, so it is logical that they turn off the enzyme. By contrast, AMP is present when cells have little energy and it is logical that it turn on the enzyme under these conditions. F2,6BP can counteract the negative effects of ATP on the enzyme to some extent. 2. Note also that PFK is very unusual in being negatively regulated by a molecule (ATP) that is also a substrate. This is possible because the enzyme has an allosteric binding site for ATP in addition to the substrate binding site and the Km for the allosteric site is higher than the substrate binding site. 3. Pyruvate kinase is regulated both allosterically andby covalent modification (phosphorylation/dephosphorylation). Phosphorylation of the enzyme by a protein kinase turns the enzyme activity down, whereas F1,6BP acts as an allosteric activator. This activation is known as feedforward activation. 4. Feed forward activation is rare in metabolism. It is a term used to describe a metabolic product (such as F1 ...
Hemoglobin Hemoglobin and its role in the circulatory system
Glycolysis Pt 1 Original Composition Glycolysis steps provided: Were here now and we're just getting started, Embden- Meyerhoff- Parnas knew enough to sound retarded=biochemistry scientists who are highly regarded but let's take up the problems here's a story, hear to solve em. IT all goes back to when I stole the cake I didn't mean to take ish but I had to fake-my body into feeling like it made no mistake, here's the glucose now, where's the hexokinase? Enzymes are fluid are not druid are you sure you can handle two if I haven't concluded who you is, if you's not stupid or being ruthless, add a phosphate from ATP we'll call yourself cool kid. glucose right here with a phosphate at the six, can you tell that its the end product of gluconeogenesis? I assume you can, but lets say you cant , what you gotta do is shove this rhyme in your pants. G-6-P isomerase makes the next move faced after the change made earlier by hexokinase. It takes the g-6-p and converts it to fructose, with the phosphate at the six the race becomes too close Hold up now cuz you must consider we deal with glucokinase when we're in the liver. The induced fit enxyme with a Km much quicker hexo- and glucokinases irreversible rivers it's known that only hexokinase can be controlled by G-6P-and so we're told-allosterically hindered and consoled. pancreas matches liver process zis story unfolds The product of the reaction is just a minor faction fructose-6-phosphate becomes the major attraction to phosphofructokinase an unsettling foe who ...
Glycogen Metabolism II This course is part of a series taught by Kevin Ahern at Oregon State University on General Biochemistry. For more information about online courses go to ecampus.oregonstate.edu In the notes below, I refer to Glycogen Phosphorylase a as GPa and Glycogen Phosphorylase b as GPb. I also refer to Glycogen Synthase a as GSa and Glycogen Synthase b as GSb. You are welcome to do the same. 1. Glycogen phosphorylase is present in two forms, GPa and GPb. They differ in phosphorylation. GPa is phosphorylated and GPb is not.1. GPb is converted into GPa by phosphorylation at two sites. Covalent modifications are DIFFERENT from allosteric controls, which interconvert the R and T states of BOTH GPa and GPb. 2. 9. Thus, the binding of epinephrine to the cell surface stimulates the following events in muscle relating to glycogen breakdown A. Epinephrine binds receptor B. Receptor activates a G protein to bind GTP C. Alpha subunit of G protein activates adenylate cyclase D. Adenylate cyclase catalyzes formation of cAMP E. cAMP activates protein kinase A F. Protein kinase A phosphorylates phosphorylase kinase, activating it. G. Phosphorylase kinase phosphorylates GPb, converting it to GPa H. GPa breaks down glycogen to yield G1P 10. Glycogen synthase, like glycogen phosphorylase, is regulated at least partially by phosphorylation. Note that GSa has NO PHOSPHATE whereas GSb HAS PHOSPHATE. You should know the function/activites of the enzymes in glycogen synthesis - phosphoglucomutase ...
Allostery and Regulation I This course is part of a series taught by Kevin Ahern at Oregon State University on General Biochemistry. For more information about online courses go to ecampus.oregonstate.edu 1. Aspartate transcarbamoylase (ATCase) is an enzyme that catalyzes the first step in pyrimidine biosynthesis (aspartate + carbamoyl phosphate N-carbamoylaspartate). This enzyme is allosterically regulated in both a positive and negative fashion and also responds to the binding of the substrate (aspartate) to it. 2. CTP, the end product of pyrimidine biosynthesis, inhibits the enzyme,whereas ATP (a purine and an indicator of high energy) activates the enzyme. This phenomenon - where the end product of a metabolic pathway inhibits the first enzyme in the pathway - is known as feedback inhibition. Feedback inhibtion is mediated allosterically - when a small molecule binds to a protein and affects the protein's activity. 3. ATCase has 12 subunits - 6 catalytic and 6 regulatory. The smaller regulatory subunits bind CTP, but not the catalytic subunits. 4. Binding of CTP to the regulatory subunits of ATCase causes the enzyme to stabilize (lock) in the T state (tight, less reactive state). In the T state, the quaternary structure of the enzyme the enzyme exhibits reduced affinity for substrate. In the opposite state, the R state (relaxed state, more reactive state), the enzyme has increased activity and a higher affinity for substrate. ATP stabilizes the R state of the enzyme. 5. In the absence of ATP ...
Enzymes III This course is part of a series taught by Kevin Ahern at Oregon State University on General Biochemistry. For more information about online courses go to ecampus.oregonstate.edu 1. "Perfect" enzymes are enzymes that have evolved to the point where any additional mutation will reduce their ability to catalyze reactions. They are not common. Perfect enzymes have a very high ratio of Kcat/Km and are such that the only thing that inhibits their ability to function more efficiently is the rate of diffusion of substrate in water. 2. Substrate binding to enzymes is relevant to catalysis that we will consider. The first is the category of Sequential Displacement. It has two subsets. a. Random binding - the order of binding multiple substrates is not rigidly set. b. Ordered binding - Simple ordered binding - one substrate binds first followed by another followed by release of product. 3. Note that the models of substrate binding above are all non-covalent. 4. Allosterism is a phenomenon in which a small molecule interacts with a protein and affects the proteins activity. Such an enzyme is an allosteric enzyme. I pointed out the similarity between the kinetics of allosterically acting enzymes and the coopertivity of binding of oxygen by hemoglobin. 5. Lineweaver-Burk plots are alternative plots of V vs S data obtained by taking the inverse of each and plotting it, thus making a 1/V vs 1/[S] plot (also called a double reciprocal plot). 6. On a Lineweaver-Burk plot, the Y intercept ...
DustDoesntTweet: @Harkatatarley sometimes that substrate even allosterically modifies that enzyme and changes it forever.