Biochemistry J.A.L Midterm PDF

BIOCHEMISTRY J.A.L | 3PsyC | Midterm Peptide (peptide bond): Amide linkage formed by the reaction between α-carboxyl Quaternary Structure group of one amino acid and α-amino group ➔ Many proteins however consist of of another amino acid with the elimination of several polypept...

BIOCHEMISTRY J.A.L | 3PsyC | Midterm Peptide (peptide bond): Amide linkage formed by the reaction between α-carboxyl Quaternary Structure group of one amino acid and α-amino group ➔ Many proteins however consist of of another amino acid with the elimination of several polypeptide chains, also water molecule. known as subunits. ➔ Example is hemoglobin Dipeptide - two amino acids are combined ➔ Same types of interactions that lead to tertiary structure (mostly weak Oligopeptide – 3 to 10 amino acids interactions, such as hydrogen bonding and dispersion forces in Polypeptide - >10 amino acids London) also hold the subunits together to give quaternary Proteins – 300-1000 amino acids structure. There are four levels of protein structure: Denaturation ➔ Any disruption in the secondary, 1. Primary - linear sequence of amino acids tertiary and quaternary levels of protein structure. 2. Secondary - regular patterns formed by ➔ It does not cleave the peptide bonds, primary structure folding therefore the primary level of structure is not altered. 3. Tertiary - completely folded polypeptide ➔ Physical signs of protein with one or more domains denaturation are precipitation and coagulation, but the most 4. Quaternary - association of multiple significant consequence of polypeptides; not found in all proteins denaturation is the loss of biological activity. Primary Structure ➔ The simplest level of protein Renaturation structure, the primary structure, is ➔ Happens in many cases when simply the amino acid sequence denatured protein goes back to its within a polypeptide chain. native biologically active form. Secondary Structure The common agents of denaturation are ➔ Local interactions between stretches the following: of a polypeptide chain and includes α-helix and β-pleated sheets 1. Heat and UV radiation – this breaks the structures. H-bonds causing the folded structures of protein to uncoil or unwind into random Tertiary Structure loops ➔ A polypeptide 's overall, three-dimensional structure. 2. Organic solvents form intermolecular H- ➔ Interactions between the R groups bonds with the protein of amino acid which make up the protein. 3. Acids and bases break salt linkages by altering the pH causing a change in the R group interactions ionization pf -COOH and -NH2 groups. hydrogen bonding Prolonged contact with acids and bases will ionic bonding also cleave peptide bonds dipole-dipole interactions London dispersion forces 4. Heavy metals like Hg+2, Ag+, Pb2+ and their salts form stronger bonds with Hydrophobic Interactions: Which amino carboxylate ions of acidic amino acids. It acids with non-polar, hydrophobic R groups also cleaves the -SH bonds cluster together within the protein, leaving hydrophilic amino acids outside to interact with surrounding water molecules. BIOCHEMISTRY J.A.L | 3PsyC | Midterm 5. Alkaloid reagents like picric acid and tannic acid precipitate proteins by Enzymes can be divided into two general combining with positively charged groups structural classes: and disrupting salt linkages Simple enzyme – An enzyme composed Catalyst: A substance that speeds up a only of protein (amino acid chains) chemical reaction without being a reactant. Conjugated enzyme – An enzyme that Enzymes: The catalysts for biochemical has a nonprotein part in addition to a protein reactions that happen in living organisms part. Substrate: The reactant in an Apoenzyme – The protein part of a enzyme-catalyzed reaction. conjugated enzyme Active Site: The small portion of the Cofactor -The non-protein part of a molecule that is responsible for the catalytic conjugated enzyme action of the enzyme. Holoenzyme – A biologically active conjugated enzyme produced from an Enzymes perform the critical task of lowering a reaction's activation apoenzyme and a cofactor energy—that is, the amount of energy that must be put in for the reaction to Apoenzyme + Cofactor = Holoenzyme begin. Two broad categories of cofactors: Enzymes work by binding to reactant - Simple metal ions – Zn, Mg, Fe Cu molecules and holding them in such a way that the chemical bond-breaking - Small organic molecules – and bond-forming processes take coenzyme (FAD, NAD, Vitamins) place more readily. Coenzymes can be classified by their source: Enzymes are superior to other catalysts in several ways: 1. Metabolite Coenzymes ➔ Most abundant is ATP, but also 1. They have a much greater catalytic include uridine diphosphate glucose power. (UDP-glucose) and S- adenosylmethionine 2. The activity of enzymes is closely ➔ ATP can donate all of its three regulated, whereas the catalyst is difficult to phosphoryl groups in group-transfer control. reactions ➔ S-adenosylmethionine can donate 3. Enzymes are highly specific with varying its methyl group in biosynthetic degrees of specificity reactions. ➔ UDP-glucose is a source of glucose Absolute specificity – They act on one for synthesis of glycogen in animals substrate and only on that substrate. and starch in plants. Stereospecificity – Such enzymes that Vitamin-derived Coenzymes can detect the difference between optical ➔ Vitamins are required for coenzyme isomers (mirror images) and select only one synthesis and must be supplied in of such isomers; the diet. ➔ Lack of particular vitamins causes Reaction specificity – Enzymes that disease catalyze certain types of reactions; no waste or side reactions Group specificity – Enzymes that catalyze a group of substances that contain specific compounds. BIOCHEMISTRY J.A.L | 3PsyC | Midterm There are two categories of vitamins: Effect of Concentration ➔ Speed is increased with an increase 1. Water-soluble - B vitamins and vit. in concentration of reacctants. C required daily in diet; excess ➔ With an increased concentration of excreted in the urine substrate, the rate of the reaction will increase until available enzyme 2. Lipid-soluble - vitamins A, D, E, K becomes saturated with substrate. intake must be limited stored in fat ➔ With an increase in the amount of enzyme, the rate of reaction will IUBMB classifies enzymes based upon the increase, assuming an unlimited class of organic chemical reaction supply of substrate. catalyzed: Inhibitors: Any substance that will make 1. Oxidoreductases - catalyze redox the reactions dehydrogenases, enzyme less active or render it inactive. oxidases, peroxidases, reductases Enzyme inhibition may be of two main 2. Transferases - catalyze group types: transfer reactions; often require coenzymes 1. Irreversible Inhibition - bind tightly to the enzyme and 3. Hydrolases - catalyze hydrolysis inactivate it. reactions - often form a covalent bond to an amino acid residue at or near the 4. Lyases - lysis of substrate; produce active site, and permanently contains double bond inactivate the enzyme. 5. Isomerases - catalyze structural 2. Reversible Inhibition changes; isomerization - can be overcome by removing the inhibitor from the enzyme. 6. Ligases - ligation or joining of two - can be classified as either substrates with input of energy, competitive or noncompetitive usually from ATP hydrolysis; often called synthetases or synthases. To catalyze a reaction: an enzyme will grab on (bind) to one or more reactant molecules. These molecules are the enzyme's substrates. Enzymes can be coagulated by heat, alcohol, strong acids, and alkaloidal reagents. Optimum Temperature: The temperature at which the rate of a reaction involving an 1. Regulation of rate of synthesis or enzyme is the greatest. degradation - Is fairly slow (several hours), so is Role of pH really too slow to be effective in ➔ Optimun pH range: Each enzyme eucaryotic cells. has a pH range within which it can - Usually done through regulatory best function. enzymesNand occur in metabolic ➔ If the pH of a substrate is too far pathways early or at first committed from the optimum pH required by the step: enzyme, that enzyme cannot function at all. BIOCHEMISTRY J.A.L | 3PsyC | Midterm 2.Allosteric Regulation Energy Currency of the Cell - Done through allosteric sites or regulatory sites on enzymes - site ATP is the primary and universal carrier of other than active site where inhibitor chemical energy in the cell or activator can bind. - Terminal (alpha) phosphate group of ATP on hydrolysis yields -7.3 Properties of allosteric enzymes: kcal/mol Sensitive to metabolic inhibitors and activators High energy phosphates Binding is noncovalent; not chemically - The phosphate compounds whose altered by enzyme △G values higher than that of ATP, they are called high energy Bioenergetics phosphates. ➔ The study of the transformation of energy in living organisms. Cellular Respiration ➔ It helps to explain how living ➔ Glucose and other molecules from organisms are obtaining energy and food are broken down to release using it for biological work. energy in a complex series of ➔ Adenosine triphosphate (ATP) is the chemical reactions that together main "energy currency" for ➔ Set of metabolic reactions and organisms. processes that take place in the cells ➔ Living organisms generate ATP by of organisms to convert biochemical way of oxidative phosphorylation energy from nutrients into ATP, and from energy sources. then release waste products. Laws of Thermodynamics Aerobic Respiration ➔ Requires oxygen- this is the reason FIRST LAW why we breathe oxygen in from the ▪ The total energy of a system is constant, air. including its surroundings ➔ Releases a large amount of energy from glucose that can be stored as SECOND LAW ATP. ▪ Total entropy of a system must increase ➔ Happens all the time in animals and for a spontaneous reaction to occur plants, where most of the reactions occur in the mitochondria. Free Energy Change (Useful Energy) ➔ This process has an overall release ▪ △G = △H -T △S of energy which is captured and ▪ Useful energy = change in Enthalpy- stored in 38 molecules of ATP. change in entropy ➔ glycolysis, the citric acid cycle, and ▪ Enthalpy – energy content oxidative phosphorylation. ▪ Entropy – randomness of the system C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + Types of Reactions ATP EXERGONIC Anaerobic Respiration ➔ Is a spontaneous reaction that ➔ It occurs in the absence of oxygen. releases energy. If the free energy ➔ It does not release enough energy to change is negative, this reaction is power human cells for long. due to loss of energy form reactants ➔ Occurs in muscle cells during hard ➔ Example: Catabolic Reactions exercise (after the oxygen has been used up). It also occurs in yeast ▪ ENDERGONIC when brewing beer. Many ➔ Is an anabolic reaction that prokaryotes perform anaerobic consumes energy. If the free energy respiration. change is positive, the reaction. ➔ Involve glycolysis, and none of them ➔ Example: Anabolic Reactions go through the citric acid cycle or oxidative phosphorylation. BIOCHEMISTRY J.A.L | 3PsyC | Midterm 2. consumes 2H+ when oxygen is reduced to H2O -- -> lowers [H+]matrix C6H12O6 + NAD+ → various waste products + NADH + 2 ATP Carbon monoxide (CO) and cyanide (HCN) bind Complex IV Chemiosmosis - In oxidative phosphorylation, the V - ATP synthase hydrogen ion gradient formed by the ➔ Does not contribute to H+ gradient, electron transport chain is used by but helps relieve it. ATP synthase to form ATP ➔ Also called FOF1 ATP synthase. ➔ F1 component contains catalytic ATP Synthase subunits. - ATP synthase is a complex, ➔ FO component is proton channel molecular machine that uses a that istransmembrane. proton (H+) gradient to form ATP ➔ Per ATP synthesized, 3H+ move from ADP and inorganic phosphate through ATP synthase. (Pi) Oligomycin - antibiotic that binds to Components of Electron Transport channel and prevents proton entry --> no System ATP synthesized. I - NADH-ubiquinone oxidoreductase OXIDATIVE PHOSPHORYLATION Transfers 2e- from NADH to Q as ▪ Oxidative phosphorylation - process in hydrideion (H-) which NADH and QH2 are oxidized and First electron transferred to FMN → ATP is produced. FMNH2---> Fe-S cluster ---> Q. Also pumps 4H+/2e- into ▪ Enzymes are found in inner intermembrane space mitochondrial membrane in eukaryotes. II Succinate-Ubiquinone Oxidoreductase ▪ In prokaryotes, enzymes are found in cell membrane. Transfers e- from succinate to Q First transferred to FAD ---> FADH2 1) respiratory electron-transport chain --->3 Fe-S clusters ---> Q. Responsible for NADH and QH2 Not enough energy to contribute to oxidation proton gradient via proton pumping Final e- acceptor is molecular oxygen III- Ubiquinol-Cytochrome c ATP SYNTHESIS Oxidoreductase Transfers e- from QH2 to ▪ Proton concentration gradients cytochrome c facing intermembrane represents stored energy space. Composed of 9-10 subunits ▪ When H+ are moved back across inner including 2 Fe-S clusters mitochondrial membrane through ATP cytochrome b560, cytochrome b566, synthase ---> ADP is phosphorylated to form ATP. and cytochrome c1. Transports 2H+ from matrix into intermembrane space Carbohydrates Uses: IV - Cytochrome c Oxidase Contains cytochromes a and a3 Yield energy (ATP) to drive metabolic Contributes to proton gradient in two processes ways: Energy-storage molecules (i.e. glycogen, starch) 1. pumps 2H+ for each pair of e-transferred (per O2 reduced) Structural – cell walls and exoskeletons of some organisms BIOCHEMISTRY J.A.L | 3PsyC | Midterm Example: Carbohydrate derivatives found in coenzymes (FAD) and nucleic acids Maltose - 2 glucose molecules joined by α- glycosidic bond. Classifications - C1 of one residue and C4 of second residue. Monosaccharides - Also known as α-D-glucopyranosyl- ➔ Also known as polyhydroxy (1,4)-β-D-glucopyranose aldehydes or ketones ➔ Classified based upon the type of Cellobiose carbonyl group - 2 glucose units joined by - Aldose- sugar with aldehyde group β-glycosidic bond - Ketose - sugar with ketone group - Plant polysaccharide ➔ Both aldoses and ketoses are engaged in intramolecular Lactose cyclization - Galactose and glucose in β- - Hemiacetal- alcohol + aldehyde glycosidic bond - Hemiketal – alcohol + ketone - Major carbohydrate in milk ➔ Both 5 and 6 carbon monosaccharides can form Sucrose hemiacetals - Glucose and fructose in 1-2 linkage - Furanose – 5 membered - Table sugar - Pyranose – 6 membered Polysaccharides two classes: MONOSACCHARIDES CAN FORM STRUCTURES Homoglycans: Composed of one monosaccharide Heteroglycans: Made of more than one type of monosaccharide Starch: Mixture of amylose and amylopectin Amylose: Unbranched polymer of 100-1000D-glucose in α 1-4 glycosidic bond Amylopectin: Branched polymer of α 1-4 and α 1-6 glycosidic bond α-amylase: An endoglycosidase found in human saliva but also in plants that randomly hydrolyzes the α 1-4 bond of amylose and amylopectin Metabolism: Sum total of all chemical reactions in living cells (carbohydrates, lipids, amino acids, nucleotides) Catabolic Reactions: Degrade macromolecules and other molecules to Disaccharides release energy ➔ Two monosaccharides joined by covalent bond called a glycosidic Anabolic Reactions: Used to synthesize linkage via a condensation reaction macromolecules for cell growth, repair, and ➔ Bond is created between C1 of one reproduction sugar and –OH of another carbon BIOCHEMISTRY J.A.L | 3PsyC | Midterm Pathways can take different forms: Catabolism yields 3 possible compounds: 1. Linear - product of one reaction is substrate for another (e.g. glycolysis) 1. acetyl CoA 2. nucleoside triphosphates 2. Cyclic - regeneration of 3. reduced coenzymes intermediates (e.g. Krebs cycle) There are several types of group transfer 3. Spiral - same set of enzymes is reactions that involve ATP: used repeatedly (e.g. fatty acid synthesis, beta-oxidation) 1) Phosphoryl Group Transfer Some metabolites have high phosphoryl Reasons why metabolic reactions have group transfer potential (ability to transfer many steps: phosphoryl groups) 1) energy input and output can be e.g. phosphoenolpyruvate transfer controlled Ø energy transfer occurs in of phosphoryl group to ADP to discrete steps as it it transferred to form pyruvate; reaction is acceptors a little at a time metabolically irreversible. e.g. phosphagens, such as 2) enzymes can catalyze only a single phosphocreatine and step of a pathway phosphoarginine - found in animal muscle cells. 3) provides opportunities to establish phosphocreatine acts as storage control points, which are essential for cell of phosphoryl group by the function following reaction: creatine kinase Major Catabolic Pathways phosphocreatine + ADP -------------> creatine + ATP Begins with extracellular digestion of polymers (exogenous). 2) Nucleotidyl-Group Transfer Amylase in mouth and intestine work on e.g. synthesis of acetyl CoA - AMP starch. is transferred to nucleophilic carboxylate group of acetate --> Protein digestion starts in stomach and acetyl group is transferred to sulfur finished via pancreatic proteases and atom of CoA intestinal peptidases. acetyl CoA synthetase Lipid digestion - triacylglycerols ATP + acetate + CoA -----------> AMP + hydrolyzed to fatty acids by acetyl CoA phospholipases. Absorption occurs in intestine ---> blood 3) Thioesters ---> body. usually make ATP equivalents Can also have endogenous sources, such succinyl CoA + GDP + Pi -----> succinate as glycogen and triacylglycerols. + GTP + HS-CoA Starts with glycolysis (glucose Reduced Coenzymes catabolism), citric acid cycle, polysaccharide mobilization, oxidative ➔ Another class of energy-rich phosphorylation molecules. ➔ Energy can be donated in Nucleotides are metabolized for oxidation-reduction reactions excretion, not energy production. Ared + Box -----> Aox + Bred BIOCHEMISTRY J.A.L | 3PsyC | Midterm CATABOLIC PATHWAYS 4 Fructose-1,6-bisphos aldolase phate → 1. GLYCOLYSIS Dihydroxyacetone Purpose: catabolism of glucose to provide phosphate + ATPs and NADH molecules Glyceraldehyde-3-ph - Also provides building blocks for osphate anabolic pathways. - Sequence of 10 enzyme-catalyzed 5 Dihydroxyacetone triose reactions: phosphate → phosphate Electrons are transferred to oxidizing agents Glyceraldehyde-3-ph isomerase NAD+ or FAD. osphate 6 Glyceraldehyde-3-ph glyceraldeh NADH ---> NAD+ ATP production in osphate + Pi + NAD+ yde mitochondria →1,3-Bisphosphogly 3-phosphate cerate + NADH + H+ dehydrogen NADP+ -----> NADPH Pentose phosphate ase pathway 7 1,3-Bisphosphoglycer Phosphogly FMNH2 -----> FMN ETS electron carrier ate + ADP3− → cerate 3-Phosphoglycerate kinase FADH2 -----> FAD + ATP 8 3-Phosphoglycerate phosphogly Glycolysis: All enzymes (and reactions) are →2-Phosphoglycerat cerate cytosolic. e mutase 9 2-Phosphoglycerate enolase glucose —> pyruvate 2 ATPs and 2 →Phosphoenolpyruv NADH produced. ate + H2O Net reaction: 10 Phosphoenolpyruvate Pyruvate glucose + 2ADP + 2NAD+ +2Pi —> 2 + ADP + H → kinase pyruvate + 2ATP + 2NADH +2H+ +2H2O Pyruvate− + ATP Can catabolize sugars other than Fate of Pyruvate glucose: —> Under anaerobic conditions, cells must e.g. fructose ----> 2 glyceraldehyde be able to regenerate NAD+ or glycolysis 3-phosphate. will stop. e.g. lactose --> glucose + galactose —> Usually regenerated by oxidative galactose --> glucose 1-phosphate phosphorylation, but that requires O2. --> glucose 6-phosphate. e.g. mannose ---> mannose There are 2 anaerobic pathways that use 6-phosphate → fructose NADH and regenerate NAD+. 6-phosphate 1) alcoholic fermentation: Conversion of 10 Steps of Glycolysis pyruvate to ethanol. Step Reaction Enzymes 1 Glucose + ATP → Hexokinas Glucose-6-phosphate e + ADP + H+ 2 Glucose-6-phosphate glucose 2− → 6-phosph 2) lactate fermentation Fructose-6-phosphate ate 2− isomerase 3 Fructose-6-phosphate phosphofr + ATP. → uctokinas Fructose-1,6-bisphos e-1 phate4− + ADP + H+ (PFK-1) BIOCHEMISTRY J.A.L | 3PsyC | Midterm Kreb Cycle: Aerobic process that Glycogenolysis comprises eight definite steps. In order to The primary carbohydrate stored in the enter the Kreb 's Cycle, pyruvate must first liver and muscle cells of animals, is be transformed by pyruvate dehydrogenase broken down into glucose to provide complex located in the mitochondria into immediate energy and to maintain blood acetyl-coA. glucose levels during fasting Occurs primarily in the liver and is Net reaction for Kreb Cycle: stimulated by the hormones glucagon and epinephrine (adrenaline). The vast majority of glucose that is released from glycogen comes from glucose 1-phosphate. Regulation of Kreb Cycle In the liver, kidneys, and intestines, glucose-1-phosphate is converted 1) isocitrate dehydrogenase (reversibly) to glucose 6-phosphate by - allosterically activated by high the enzyme phosphoglucomutase. [Ca2+] and high [ADP] Those tissues also house the enzyme - allosterically inhibited by high glucose-6-phosphatase, which converts [NADH] glucose-6-phosphate into free glucose that is secreted into the blood, thereby 2) a-ketoglutarate dehydrogenase restoring blood glucose levels to normal. - allosterically activated by high Glucose-6-phosphate is also taken up by [Ca2+] allosterically inhibited by high muscle cells, where it enters glycolysis [NADH] and high [succinyl CoA] (the set of reactions that breaks down glucose to capture and store energy in Pentose Phosphate Pathway the form of adenosine triphosphate, or Provides NADPH (serves as e- ATP). donor) and forms ribose Small amounts of free glucose also are 5-phosphate (nucleotide synthesis). produced during glycogenolysis through Pathway active is tissues that the activity of glycogen debranching synthesize fatty acids or sterols enzyme. because large amounts of NADPH are needed. The pentose phosphate pathway can be thought of as two separate pathways: The first is the oxidative phase, in which NADPH is generated glucose 6-phosphate +2 NADP+ + H2O --> ribulose 5-phosphate + 2 NADPH + CO2 + 2H+ The second is non-oxidative synthesis of 5-carbon sugars.