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148 Cards in this Set
- Front
- Back
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Citric acid cycle begins with what intermediate
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Acetyl CoA
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___________ & ________ are the coenzymes that act as electron acceptor during CAC
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NAD+ and FAD+
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Conversion of Citrate to isocitrate is a reversible reaction, but during CAC this reaction is still driven in one direction. Explain.
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Rapid conversion of isocitrate to Alpha-ketoglutarate drives the reversible previous reaction forming isocitrate.
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Which one of the reactions of CAC that generates either ATP or GTP?
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Succinyl-CoA to Succinate
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How many moleculars of NADH are generated during CAC?
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3
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Why is CAC also considered to be an amphibolic pathway? Explain giving two specific examples
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Amphibolic pathways function both in catabolism as well as anabolism. CAC is catabolic since acetyl-CoA is oxides to form CO2 and energy is conserved in the form of NADH and FADH2. It is also anabolic since many of its intermediates serve as precursors for amoco acid synthesis. Acetyl-CoA is a precursor for lipid biosynthesis but in cannot enter inner mitochondrial membrane.
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During Glyoxylate cycle _____ is converted to _____ and ____ to bypass the reactions of CAC
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Isocitrate, Glyoxylate, malate
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CAC is allosterically regulated by regulating the activities of ____, _____, and _____ enzymes.
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Citrate synthesis, isocitrate dehyrdogenase, alpha- ketoglutarate dehydrogenase
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Complex II of ETC accepts electrons from ______ and donates to _____.
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FADH2 and UQ
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In complex I electrons are serially transferred from ________ to _____ to ____ to be finally donated to _____.
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NADH and proton, FMN, 2 FE-Scentsis to UQ.
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Complex IV is also known as ________ activity of which is inhibited by _____, ____, and ____.
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Cytocrome oxidase, CO (carbon Dioxide), N3- (azide), cyanide (CN-)
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Transfer of electrons through ETC generates _____ in the inter membrane or periplasmic space
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Protons
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Passing of ____ through ____ ultimately generate ATPs by phosphorylation of____
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Electrons, Intermediate space, ADP
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Two major components to ATP synthase are ____ and ____, of which ____ is a transmembrane channel.
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F0, F1, F0
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How many molecules of ATP are generated from one molecule of Glucose during CAC
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2, transport price is 1 so apps 1.5
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what is the citric acid cycle?
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citric acid cycle is the series of biochemical reactions which aerobic microorganisms use to release energy stored in Acetyl-CoA. Acetyl-CoA is a product of catabolic reaction of carbohydrate, lipids and amino acid metabolism. The high energy electrons removed from citric acid cycle intermediates are transferred to NAD and FAD to form reduced coenzymes NASH and FADH2.
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The first step of CAC
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The two carbon acetyl-coA condenses with four carbon eoaloaxetate to form six carbon citric acid molecule. The enzyme which catalyzed this reaction is citrate synthase.
Acetyl-CoA + citrate synthase-> Citrate. |
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Second Step CAC
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In the next reaction citrate is reversibly converted to isocitrate by an enzyme 'aconite'. It is an isomerization reaction.
Citrate + Aconitase -> isocitrate. |
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Third Step CAC
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?The isocitrate thus formed is oxidatively decarboxylated by 'Isocitrate dehydrogenase' to alpha- ketoglutarate. This react generates NADH. Rapid conversion of isocitrate to alpha-ketoglutarate drives the reversible previous reaction forming isocitrate.
Isocitrate + Isocitrate dehydrogenase -> alpha ketoglutarate. |
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Fourth step CAC
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The conversion of Alpha-ketoglutarate to succinyl- CoA is catalyzed by alpha-ketglutarate dehyrdogenase complex. This enzyme requires cofactors like CoASH and NAD. This enzyme activity is inhibited by succinyle CoA, NADH, ATP, and GTP.
Alpha-ketoglutarate + alpha-ketoglutarate dehyrdogenase -> Succinyl-CoA |
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Fifth step CAC
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The cleavage of thirster bond of Succinyl CoA to form sucinate is catalyzed by succinate thiokinase. This reaction is coupled with the formation of GTP (in some microorganisms it is ATP.)
Succinyl-CoA +succinate thiokinase -> Succinate. |
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Sixth step CAC
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Succinate dehyrdogenase catalyzes the oxidation of succinate to form fumarate. This enzyme is tightly bound to the mitochondria inner membrane and not present in the matrix with other enzymes. It is activated by high concentration of succinate, Pi, and ADP and inhibited by oxaloacetate. Produces FADH2
Succinate-> Succinate dehydrogenase -> Furmarate. |
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Seventh step CAC
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Fumarate is concerted to L-Malate in reversible sterospecific hydration reaction catalyzed by 'fumarase' 'fumarase hydratase.'
Fumarate + Fumarase -> Malate. |
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Eighth Step CAC
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Finally oxaloacetate is generated by the action of 'malate dehryogen' which oxides malate to oxaloacetate. This reaction also produces on molecule to NADH. It ins an endergonic reaction but its further conversion to citrate drives the reaction.
Malate + malate dehydrogenase -> oxaloacetate. |
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End result of CAC
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Thus during the cycle three molecules of NADH and one molecule of FADH2 are generated which enter into electron transport chain to generate ATPs.
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Glyoxylate Cycle
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Plants, some fungi, algae, protozoans, and bacteria have the ability to grow on two carbon compounds like ethanol, acetate, and acetyl-CoA. The series of biochemical reactions involved in metabolizing these two carbon compouts are the glyoxylate cycle.
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Five steps of Glyoxylate cycle
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Acetyl-CoA + Citrate synthase -> citrate
Citrate + acintase -> isocitrate Isocitrate + isocitrate lyase -> Glyoxylate Glyoxylate + Malate Synthase -> Malate Malate + Malate dehyrdogenase ->oxaloacetate Sometimes isocitrate will form succinate and finish the rest of the cycle. 2 acetyl-CoA will produce one oxaloacetate and 1 succinate. |
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Regulation of citric acid cycle
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In order to meet the constant energy and biosynthetic requirements of a cell, CAC is precisely regulated by modulation of its key enzymes and availability of certain substrates. The Key enzymes are Citrate synthase, isocitrate dehrydogenase, and alpha ketoglutarate dehydrogenase.
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Citrate Synthase
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Stimulated by the substates, acetyl-CoA and oxaloacetate while allosterically.
Inhibited by high concentration of citrate and succinyl-CoA. Other allosteric inhibitors are NADH and ATP whose concentration reflect the cell's energy status. |
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Isocitrate Dehydrogenase
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Stimulated by relatively high concentration of ADP and NAH
Inhibited by ATP and NADH. This is a key enzyme which rapidly converts isocitrate to alpha-ketoglutarate and thereby drives the formation os isocitrate forward. |
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Alpha-ketoglutarate dehyrdogrenase
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Strictly regulated because of its role in several metabolic pathways
Stimulated by low concentration of NADH Inhibited by high concentrations of NADH |
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Electron Transport Chain
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The mictochondrial electron transport chain is a series of electron carriers that transfer the electrons derived from reduced coenzymes to oxygen. The process in which oxygen is use as a final electron acceptor is sometimes referred to as aerobic respiration. The energy released during eTC is couple with ATP synthesis
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Principal sources of electrons
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Reduced coenxymes derived from glycolysis, the citric acid cycle, and fatty acid oxidation.
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The components to ETC
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Located in the mitochondrial inner membranes in eukaryotes and in the inner membrane of the cell in bacteria. These complexes are organized in four complexes which each consist of several proteins and prosthetic groups. Other components include coenzyme Q (ubiquinone, UQ) and cytochrome C (cty c)
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Complex 1
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NADH Dehydrogenase complex
Cataluzed the transfer of electrons from NADH to UQ. It is a huge protein that consists of over two dozen polypeptides, one molecule of FMS, and seven Iron-sulfur centers. Thus electrons are first transferred to FMN to form FMNH@. Electron is then transferred from FMNH2 to an iron-sulfur center one at a time. After the transfer from one iron-sulfur center to another, electrons are eventually donated to UQ. |
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Complex 2
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Succinate dehydrogenase Complex
CAC enzyme that con taints two or three iron-sulfur proteins. It mediates the transfer of electrons from succinate to UQ. This molecule also contains a covalently bond FAD |
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Complex 3
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Cytochrome bc1 complex
This is composed of two b-type cytochromes, one cytochrome C, and one iron-sulfur center. It transfers electrons from reduced coenzyme Q (UQH2) to cytochrome C. Cytochromes are iron-hem proteins like hemoglobin and myoglobin. Electrons are transferred one at a time as each oxidized iron atom (Fe3+) is reversibly reduced to Fe2+. Transfer of electrons from UQH2 to Cyo C is a complex multistep process. |
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Complex 4
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Cytochrome oxidase
Catalyzes the four electron reduction of oxygen to form H20. The membrane-spanning complex in mammals may contain between six and thirteen subunits. It also contains three copper atoms, iron-heme atoms of cytochromes a and a3. The copper atoms alternated between +1 and +2 oxidation state. One Cu referred to as CuB is closely associated with the iron atom of cyt a3 while another cu referred to as CuA is a short distance from the heme of Cyt a. Electrons from Cty C transfer to cyt a and Cua one at a time. These electrons are then donated to cyt a and Cub, which occur on the matrix side of the membrane. This electron shuttle allows four electrons and four protons to be delivered to dioxygen molecule bound to cyt a3-Fe2+. Two water molecules are formed and leave the side. During each sequential redox reaction in the TC, and electron loses energy. This energy is utilized for the synthesis of ATPS. |
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Inhibitors of ETC
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Antimycin A inhibits cyt b (complex 3)
rotenone and amytal inhibit NADH dehrydogenase (complex 1) CO, N3-, CN- inhibit cytochrome oxidase (complex 4) |
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Oxidative phosphorylation
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This is the process by which energy is generated by the ETC is conserved by the phosphorylation of ADP to yield ATP.
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Chemiosmotic Coupling theory
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as electrons pass through the ETC, protons from the matrix are transported into the inter membrane space. This created a proton gradients between the matrix and inter membrane space. The electrochemical proton gradient is sometimes referred to as proton motive force.
Proton, which are present in the inter membrane space in great excess, can then pass through the inner membrane back to the matrix, but only through specific channels. As protons pass through these channels, each of which contains ATP synthase activity. Synthesizing of ATP is linked to the osmotic gradient of protons. |
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ATP synthase
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A large enzyme which studs out in the inner side of the mitochondrial inner membrane. It consist of two major components: F0 and F1.
the current hypothesis says that the protons flow through the channel formed by f0 unit which spins the top. When three proton have gone through it is enough energy to make and release an ATP. |
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F1
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The active ATP synthase consists of five different subunits present in the ratio alpha 3, beta 3, gamma, delta, epsilon. There are three nucleotide binding sites on F1.
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General Characteristics of lipids
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Defined as substances which are soluble in non polar organic solvents such as ether, chloroform, acetone, and sparingly soluble in water.
Differ widely both in structure and function Structural components of cells, serve as rich energy source and also serve as important components of cells such as chemical signals, vitamins, or pigments. They serve as protective and water proof outermost layer in many cells. |
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Lipid classes
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Fatty acids
Triacylglycerols wax esters phospholipids sphinglipids Isoprenoids |
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Fatty Acids
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Monocarboxylic acids with hydrocarbon chairs of variable lengths. React with alcohol to form esters. Most naturally occurring fatty acids have even number of carbon atoms. Can be saturated or unsaturated. Organisms like plants and bacteria synthesize their fatty acids from acetyl-coa while mammals obtain it through dietary sources.
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Saturated Fatty Acids
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All single bonds
High melting point. |
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Unsaturated Fatty Acids
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Have at least one double bond. Are rigid and are either cis or trans. Usually cis. Do not pack well, and have a low melting point.
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Non-essential fatty acids
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Mammals synthesize some saturated and monounsaturated fatty acids.
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Essential fatty acids
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The fatty acids that the body cannot synthesize, and therefore has to be eaten.
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Triacylglycerols
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The esters of glycerol with three fatty acid molecules. The fatty acids can be saturated or unsaturated.
No charge due to the carboxyl group of fatty acids. Depending on their fatty acid composition they can be either fat or oil. Rich in energy source due to fatty acids Poor conductor of heat provides insulation. Digested in small intestine by pancreatic lipase to form fatty acids and monoacylglycerol. Monoacylglycerols are then transported across the llama membrane of intestinal wall cells and converted to tricylglycerols. |
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Fats
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Solid at room temperature
Highly Saturated |
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Oils
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Liquid at room temperature.
Highly unsaturated. |
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Wax Esters
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Complex mixtures of non polar lipids
Due to their hydrophobicity they form a protective layer on leaves, stems, and fruits of plants and the skin and fur of animals. |
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Phospholipids
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Structural components of membranes.
Amphipathic molecules- both hydrophobic and hydrophilic chains. Hydrophobic domain large consist of hydrocarbon chain of fatty acids while the hydrophilic domain consists mainly of polar head group which contains phosphate and other charged polar groups. Will organize so that hydrophobic groups are protected. |
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Phosphoglycerides
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Phosphatidic acid is the precursor for all other phosphoglycerides.
Phosphatidic acid is composed of glycerol-3-phosphate that is esterified with two fatty acids. classified based on the alcohol which is esterfied. c1 of glycerol usually have saturated fatty acids while C2 have unsaturated fatty acids. |
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Sphingolipids
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Structural components of both plant and animal cells. All of them are long chain amino-alcohol
The core is ceramide, which is a fatty acid derivative of sphingosine. In sphingomyelin the 1-hydroxyl group ceramide is esterified with the phosphate group of phosphorylcholine or phosphorylethanolamine. Sphinomyelin is found in animal cell membrane and in nerve cells facilitating rapid transmission of impulses. Cermides are precursors for glycolipids. Hydroxyl group is linked with o-glycosidic linage with mono, di or olgiosaccharides. Many glycolipids serve as receptors for bacterial cellos as well as their toxins such as botulism and tetanus. |
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Isoprenoids
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Wide variety of biomolecules that contain repeating five carbon structural units known as 'isoprene' units.
Precursor of isoprenoids is isopentenyl pyrophosphate which is formed from acetyl-coa. Consist of two groups of compounds terpenes and steroids. |
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Terpenes
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Huge group of molecule that are found largely in essential oils.
Classified according to the numbers of isoprene residues they contain. Monoterpenes contain two units of isoprene. Carotenoid is the orange colored pigments found in plants is the only example of tertaterpenes. Natural rubber is a polyterpene composed of 3000-6000 isoprene's. |
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Mixed terpenoids
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Many important biomolecules consists of nonterpene groups attached to isoprenoid groups.
Important examples are Vitamin E, Ubiquinone, Vitamin K, and sine cytokinins. |
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Steroids
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Derivates of complex hydrocarbon ring systems.
Complex derivates of triterpenes. Found in all eukaryotes and few bacteria. Distinguished on the basis of placement of carbon-carbon double bonds and various substituents like hydroxyl, carbonyl, and alkyl groups. Cholesterol is an example |
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Cholesterol
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Steroid
Component in animal cell member and precursor in the biosynthesis of all steroid hormones, vitamin D and bile salts Precursor for all steroid hormones and bile salts. Synthesis of steroid hormones through cholesterol is very compacted by completely understood. |
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Lipoproteins
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The molecules where protein is covalently linked to lipid groups. The lipid group may be faty acids or prenyl groups.
Many are found in blood plans. They transport lipid molecules from one organ to another. Contain certain types of lipid soluble antioxidants. The protein part of lipoprotein is called apolipoprotein or apoproteins. amount of protein can vary to 2%-55%. Classified according to their density. Chylomicrons with extremely low density VLDL very low density LDL low density formed fro VLDL- carry cholesterol into tissues, import an in plaque formation. HDL- high density important in scavenging excessive cholesterol from cell membrane |
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Membrane
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Lipid bilayer within which proteins float. Proteins determine largely the biological function of the membrane.
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Membrane Structure
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Membrane lipids are amphiphathic molecules when suspended in water they spontaneously rearrange into ordered structure.
Responsible for several important features of biological membranes 1. membrane fluidity 2. Selective permeability 3. Self-sealing capability 4. Asymmetry (each half if different) |
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membrane proteins
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Most functions require proteins. Classified based on their function, structural components, enzymes, hormone receptor, transport proteins, or location as integral or peripheral proteins. The most important functions include transportation of molecules and ions in and out of the cell. organelles and the binding of hormones and other membranes.
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Membrane transport
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Vital to organisms since it provides nutrients and takes care of waste disposal. Classified as passive or active transport.
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Passive transport
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no energy simple diffusion or facilitated diffusion.
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Active Transport
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Requires energy which in most cases is provided by ATP hydrolyses
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What is the difference between saturated and unsaturated fatty acids?
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Saturated fatty acids contain all single bonds, while unsaturated fatty acids have at least one double bond.
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Why do unsaturated fatty acids have lower melting points?
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They require less energy to break the bonds.
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What are nonessential fatty acids?
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Fatty acids that can be synthesized.
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Why is triacylglycerol also referred to as 'neutral fat'?
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The carboxyl groups of the fatty acids are used in covalent bond formation, so there is no charge.
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Oils are rich in _______ type of fatty acids
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unsaturated.
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Why do fatty acids release more energy than glycogen on degradation?
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Because they are less oxidized compared to glycogen.
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Melissyl cerotate is an example of ______
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Wax esters
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Which property of phospholipid is responsible for bilayer formation?
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Amphipathic
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What are the function of glycolipids
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Receptors for bacterial cells as well as their toxins.
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Give two examples of each mixed terpenoids and steroid hormones.
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Mixed terpenoids- vitamin E & K
Steroid Hormones- Vitamin D and bile salt |
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Rubber is an example of _______?
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polyterpene
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What is the function of lipoproteins in blood?
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Transport lipid molecules and cholesterol from one organ to another.
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What is the difference between peripheral and integral membrane proteins?
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Peripheral proteins are bound primarily through non covalent interactions with integral membrane proteins.
Integral proteins are embedded in and/ or extend through a membrane. |
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How does active transport differ from passive transport?
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Active transport requires energy, while passive transport does not.
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Lipogenesis
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Glycerol-3-phosphate or Dihydroxyl acetone phosphate reacts sequentially with three molecules of acyl-coa. Phosphatidic acid is formed by two sequential acylation of glycerol-3-phosphate or by direct acylation of dihydroxy acetone phosphate.
Phosphatidic acid is converted to diaglycerol. Fatty acids are derived from diet and de novo synths are incorporated into triacylglycerol. |
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Lipolysis
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When the body is under low energy conditions stored fat is metabolized.
Occurs during fasting, vigorous exercise, and in response to stress. |
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What happens in lipolysis
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Hormones like glucagon and epinephrine bind to specific adipocyte plasma membrane recpertos and begin the sequential activation of lipase enzyme by activating cAMP synths. Both the products of lipolysis, fatty acids, and glycerols are released into the blood. Glycerol is transported to the liver where it can be used to form either glucose or lipid. Fatty acids bind to albumin and are transported to various tissues where they are oxized to generate energy. Most fatty acids are degraded to from Acetyl-CoA within Mitochondria in a process refried to as beta-oxidation. b-oxidation is also known to occur in peroxisomes. Certain non-standard fatty acids are oxides in different pathways as alpha-oxidation.
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Beta-Oxidaton
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Beta-oxidation primartuly occurs in mitochondria. Before B-oxidation begins, each fatty acid is activated in reaction with ATP and CoASH catalyzed by Acyl-CoA ligase in mitochondrial outer membrane. Mitochondrial inner membrane are impermeable to acyl-CoA therefore they are attached to carrier protein via attachment to a molecule known as 'carnitine' which transport them to matrix of mitochondria. Oce the Acyl-CoA is in the matrix the B-oxidation begins with oxidation-reduction reaction catalyzed by acyl-CoA dehyrdogenase, in which on H atom is removed from alpha and beta carbons to form Enoyl-CoA. This is further oxidized by L-B Hydroxylacyl-CoA Dehrydrogenase to B-ketoacyl-CoA generating NADH. In the final step, by thiolytic cleavage an acetyl-CoA molecule is release with Acyl-CoA as the other product. This cycle continues until the formation of the last two molecule of Acetyl-CoA??
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Ketone Bodies
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Most of the Acetyl-CoA produced during fatty acid oxidation is used by the citric cycle or in isprenoid synthesis. Since fatty cid metabolism is carefully regulated, only small amount of excess Acetyl0CoA is produced in the cell under normal conditions. Acetyl-CoA molecules are converted to acetoacetate, beta-hydroxybutyrate, and acetone a group of molecules called 'ketone bodies' through a process called ketogenesis.
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Ketogensis
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Begins with the condensation of two acetyl-CoA to form acetoacetyl-CoA which condenses with another molecule of acetyl0CoA to form B- hydroxy-B-Methyl-Glutaryl-CoA (HMG-CoA). In the next reaction HMG-CoA is cleaved to form acetyl-CoA and acetoacetate. Acetoacetate is then reduced to form B-hydrobutyrate. Acetone is formed from acetoacetate by spontaneous decarobxylation at high conc. of acetoacetate. Ketosis is observed in uncontrolled diabetic conditions. During prolonged starvation brain cells use ketone bodies as energy sources.
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Why does diabetes result in high acetone?
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Low insulin makes it where you cannot degrade glucose so the body must degrade fatty acids. Ketone bodies is degraded causing an increase in acetone.
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Cholesterol Metabolism
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Cholesterol is derived from diet or synthesized de novo. Cholesterol biosynthesis is stimulated when the diet is low in cholesterol. Although all tissues can make it, the liver cells make the most. Cholesterol synthesis is divided into three stages.
1. Formation of HMG-CoA from Acetyl-CoA. 2. Conversion of HMG-CoA to squalene 3. Conversion of Squalene to Cholesterol. |
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First phase of cholesterol synthesis
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Acetyl-CoA to HMG-CoA.
This is the same as that of ketosis until the formation of HMG-CoA. |
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Second phase of cholesterol synthesis
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HMG-CoA to Squalene.
HMG-CoA is reduced to form mevalonate. NADPH is the reducing agent and the reaction is catalyzed by HMG-CoA reducatase. Series of Cytoplasmic reactions convert mevalonate to farnesylpyrophosphate. Squalene is synthesized when two molecules of farnesylphosphate are condensed by farnesyl transferase of squalene synthase enzyme. This requires NADPH. |
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Third phase of cholesterol synthesis
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Multiple enzymes like squalene monooxygenase and 2,3-osidosqualene lanosterol cyclase convert squalene to lanosterol. In a series of tern formation, lanosterol, NADPH, and oxygen make a conversation to 7-Dehydrocholestrol which is then reduced by NADPH to cholesterol.
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Cholesterol degradtion
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Unlike other biomolecules, cholestrols and steroid cannot be degraded to smaller molecules, but are derivatized to other products. One important derivatives are bile acts, which are formed from cholesterol. Bile acids are synthesized from cholesterol in the liver.
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Bile
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used in the small intestine to enhance the absorption of dietary fat. Bile salts act as an emulsifying agent which break up large droplets into smaller ones. Bile salts are also involved in the formation of biliary micelles which aid in absorbing fat and fat soluble vitamins (A,D,E &K.)
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How does a blood glucose level influence triacylglycerol metabolism?
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If a person has a low glucose level then the body will automatically start to metabolize triacylglycerol to generate energy.
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Triacylglycerol is digested in intestinal cells by pancreatic lipase to
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Fatty acids and monoacylglycerol
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What are the precursors of lipogensis?
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Glyceraldehyde-3-phosphate
Dihydroxyacetone phosphate |
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What is the fate of glycerol produced as the result of lypolysis?
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Transported to the liver to form either glucose to a lipid
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What is the mechanism of signaling to innate lipolysis
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hormones like glucagon and epinephrine bind to specific adipocyte plamsa membrane receptors.
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Degration of fatty acids via Beta-Oxidation is energetically considered to be an important pathway. explain
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Acetyl-CoA molecules go to CAC while NADH and FADH2 are oxidized by ETC
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What is an example of a ketone body?
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Acetoacetate
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HMG CoA is an important intermediate of lipid metabolism-Explain
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In ketone bodies it is cleaved to from acetyl-CoA. It is also an intermediate to form Squalene in cholesterol metabolism
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'Cholesterol can only be obtained from diet' true or false explain
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In some people they will get all the cholesterol they will need from diet, but in people with low cholesterol levels the body will synthesize cholesterol to maintain levels.
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Derivation of cholesterol is a useful reaction for digestion. Explain
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Cholesterol is derived to form bile acid which then goes into the small intestine to help digest foods.
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Nitrogen
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Found in a vast array of biomolecules ranging from amino acids, nitrogenous bases, porphyins and several lipids. In addition there are some biogenic amine and glutathione which are required in small amount also contain nitrogen. Despite the importance of nitrogen as a part of many important biomolecules, its availability in useful form is scare since majority of the nitrogen is present as inert nitrogen gas.
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Nitrogen fixation
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Conversion of inert nitrogen to useful form (NH3) requires a large amount of energy and is carried out by only a few prokaryotic microorganism through the process known as nitrogen fixation.
These species possess the enzyme 'nitrogenase complex.' It consists of two proteins called nitrogenase and nitrogenase reductase. Nitrogenase is a heterodimer that contains two Molybdenum atoms between 28 to 32 iron atoms, and four polypeptide subunits. It catalyzes the reaction N2+6H++6e- -> 2NH3. Nitrogenase reductase is a dimer containing identical subunits. Enzymatic nitrogen fixation requires at least four molecules of ATP and series of electron transfers from NADH/ NADPH to iron-sulfur protein ferredoxin to nitrogenase reductase to nitrogenase to form 2NH3. Both of the components to nitrogenase enzymes are irreversible inactivated by oxygen therefore in aerobic nitrogen fixing bacteria nitrogenase is contained in specialized cells called heterocysts while legumes produce oxygen-binding protein celled leg hemoglobin which traps oxygen before it interacts with nitrogenase complex. |
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Nitrogen facts
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Whatever way the plants obtain their nitrogen it is assimilated to the amide group of glutamine which is used to synthesize other carbon containing nitrogen compounds like amino acids, nucleotides, and nucleic acids.
Many microorganisms can synthesize all the amino acids they need. Animals on the other hand can only synthesize half of the amino acids they require, known as nonessential amino acids (NAA) while the other have they have to obtain from diet- Essential amino acids (EAA) Amino acids provided by diet are often not in the correct proportion required by the body, therefore their concentrations are adjusted by metabolic mechanisms. Excessive amount of all NAA and EAA are degraded. Concentration of certain EAA referred to as branched amino acids (Leu, Ile, Val) remain unchanged. These amino acids are used for the synthesis of many NAA. |
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Nitrogen Cycle
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Nitrogen flows in the ecosystem from nitrogen fixation by bacteria to plants to animals to waste to microorganism again. This is a complex process of nitrogen transformation.
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Transamination
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It is a dominating chemical reaction in amino acid metabolism. This reaction is catalyzed by a group of enzyme referred to as the 'Aminotransferases' or 'Transaminases'
During transamination reaction the alpha-amino group is transferred from alpha-amino acid to a alpha-keto acid. Since these reactions are readily reversible, thy play important roles in both the synthesis and degradation of the amino acids. Eukaryotic cells possess a wide variety of aminotransferase found in both cytoplasm and mitochondria. These enzymes possess two types of specificity: 1. the type of alpha-amino acid that donates alpha-amino group and 2. The type of alpha-keto acid that accepts the alpha-amino group. Most of them use 'Glutamate' as amino group donor. The important pairs: alpha-ketoglutarate/glutamate pair, oxaloacetate/aspartate pair and pyruvate/alanine pair. |
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Amino Acid Biosynthesis
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Plants and microorganisms can synthesize all of the amino acids Required by them, while animals cal synthesize some NAA, but have to obtain EAA from their diet.
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EAA
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Essential amino acids- must be eaten
Isoleucine Leucine Lysine Methionine Phylalnine Theonine Tryptophan Valine ILMF2/3TV |
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NAA
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Synthesized.
Alanine Arginine Asparagine Aspartate Cysteine Clutamate Clutamine Glycine Histidine Proline Serfine Tryosine. |
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Amino Acids
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Serve a number of function besides the building block of proteins. They are the source of nitrogen atoms required in various synthetic reaction pathways. The non nitrogen parts of amino acids serve as energy sources.
The molecules that are immediately available for metabolic processes are referred to as 'amino acid pool' Amino acid pools are derived from both the break down of dietary and tissue proteins. Depending upon the current requirements of the body the amino acids are either synthesized or interconverted and transported to various tissues where they are used. Transport of amino acids into cells is mediated by a specific membrane bound transport proteins transporting specific amino acids. Once amino acids enter cells, the amino groups are available for synthetic reactions. These include: transfer of amino group from alpha-amino acid to an alpha-keto acid (transamination) and direct incorporation of NH4+ group into certain amino acid molecules. |
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Direct incorporation of NH4.
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There are two principal means by which NH4 ions are incorporated into amino acids and eventually other metabolites. 1. Reductive amination of alpha-keto acids and 2. formation of the amides of aspartic and gluatmic acids.
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Synthesis of Amino Acids
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Amino acids are synthesized via unique pathways in animals. Although they still share a common featudyre that all NAA are synthesized either from glycerinate-3-phosphaste, pyruvate, alpha-ketoglutarate, or oxaloacetate. The only except is tyrosine which is synthesized from essential amino acid phenyl alanine. On the basis of similarities in their synthetic pathways they are divided into 6 families. Glutamate, Serine, Aspartate, pyruvate, the aromatics and histidine. The amine acids in each family are ultimately derived from one precursor molecule.
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Glutamate family
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Glutamate family includes glutamate, glutamine, proline, and arginine. Glutamate is formed from alpha-ketoglutarate by reductive amination. Glutamate is very important amino acid since, apart from it being part of a protein, it is also used in the central nervous system as an excitatory neurotransmitter.
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Glutamate to glutamine
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This is catalyzed by glutamine synthase. This is a transamination reaction where branched chain amino acids (BCAA) serve as amino group donor. Glutamine serves as part of protein as well as amino group in many important reactions and also serves as energy source. Proline is a cyclized derivative of glutamate. Formation of proline from glutamate is negative controlled by feedback inhibition by proline of the first enzymes gamma-glutamyl kinase. Arginine synthesis begins with acetylation of alpha-amino group of glutamate. N-acetylglutamate is then converted to Ornithine which is converted to arginine through a part of urea cycle.
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Serine Family
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The members of the serene family include serene, glycine and cysteine. All of them are derived from glycolytic intermediate glycerinate-3-phosphate. Amino acids in this family preform many important functions. Serine is a precursor of ethanol amine and sphingosine. Glycine is used in the purine, porphyrin, and glutathione synthetic pathways. Cysteine plays a significant role in sulfur metabolism.
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Serine Synthesize
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Serine is synthesized directly from glycerinate-3-phosphate via dehydrogenation, transamination, and hydrolysis by a phosphatase. This pathway is controlled by feedback inhibition of phosphatase by cellular concentration of serine. High protein diet can also inhibit serene biosynthesis. Glycine is formed from serene via a single complex reaction catalyzed by an enzyme Serine hydroxymethyltransferase. Serine is the major source of glycine. In cysteine biosynthesis, carbon skeleton is derived from serene while sulfhydryl group is transferred from methionine.
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Neurotransmitters
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More than 30 different substances have been proven or proposed to act as neurotransmitters. Neurotransmitters can be either excitatory or inhibitory in nature. A significant percentage of neurotransmitter molecules are either amino acids or amino acid derivatives. The amino acid derivatives are also referred to as the biogenic amines.
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Histamine
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Histamine is produced in many cells through out the body as a mediator of allergic and inflammatory reactions, a stimulator of gastric acid production and a neurotransmitter in several areas of brain. It is formed by decarboxylation of L-histidine
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Nitric Oxide
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Nitric oxide is formed in many cells and it plays a role in the dilation of blood vessels, inhibition of platelet aggregation and destruction of foreign or damaged cell by macrophages. In the brain it is linked with the neurotransmitter function of glutamate.
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Give a few examples of nitrogen containing compounds found in living cells.
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Amino acids, nitrogenous bases, porphyins, and several lipids.
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Symbiotic nitrogen fixing bacteria belong to the _______ species.
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Rhizobium
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What are the sources of nitrogen for growing plants?
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bacteria and absorption through the ground.
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Unlike plants and bacteria animals need to be supplied with certain amino acids in their diet because?
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They cannot synthesize some amino acids.
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Transamination reaction is catalyzed by an enzyme ________.
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Transaminase.
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Which are the two ways in which nitrogenase is protected from oxygen?
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They are contain in specialized cells & they produce oxygen binding proteins which traps the oxygen before it interacts with nitrogenase.
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What in an amino acid pool
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Amino acids that are immediately available for metabolic processes.
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Which are the two ways in which amino group can be incorporated to form new amino acids?
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Transamination and direct incorporation of NH4+.
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Give the names of the six families of amino acids?
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Glutamate
Serine Aspartate Pyruvate Aromatics Histidine |
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What amino acid acts as a neurotransmitter
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Glutamate.
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Nitrogen Degradation
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Living organisms recycle organic nitrogen into a variety of metabolites before it is reconverted to its inorganic forms. The soil and water inhabiting organisms convert organic nitrogen of all dead organisms into ammonia and then it is oxidized to form nitrate and nitrites.
Ammonia, nitrate, nitrites are absorbed and used by nearby organisms and some organisms covert nitrate to atmospheric nitrogen by the process known as 'denitifaction.' Generally, the nitrogen in amino acids is removed by deamination reactions and converted to ammonia. The ammonia is toxic and should be removed quickly. It is removed by different means in different organisms. Since ammonia is soluble, it is removed directly in aquatic animals while in mammals and birds, reptiles, and insects it is converted to urea and uric acid respectively. |
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Amino Acid Catabolism
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Catabolism of amino acid usually begins by removing the amino group. Amino groups are then disposed of through urea synthesis. The carbon skeleton produced from deamination is further degraded to form acetyl-CoA, Acetoacetyl CoA, pyruvate, fume rate, Alpha-ketoglutarate, succinyl CoA, and Oxaloacetate. Depending on the current metabolic requirements of the animal these products are converted to either fatty acids or glucose. The degradation of amino acids to acetyl CoA and Aceto-acetyl CoA is termed as ketogenic since these products can be either converted to ketone bodies or fatty acids. The carbon skeleton of amino acids are degraded to form pyruvate or CAC intermediate which can be used in 'gluconeogensis'
Thus amino acid catabolism involves 1. Deamination 2. urea Synthese 3. catabolism of carbon skeleton |
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Deamination
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Involves two types of reaches.
1. Transamination. 2. Oxidative deamination. These reactions are reversible and also used in synthetic pathways. Amino acids are degraded when they are in excess and amino groups are available for urea synthesis. Thus urea is synthesized in a large amount when the diet is rich in protein content. In muscles, excess amino groups are transferred to alpha-ketoglutarate to form glutamate. Alpha-ketoglutarate + l-amino acid -> L-glutamate and alpha-ketoacid. The amino groups of glutamate are transferred to the liver by blood through alanine cycle. Pyruvate+l-glutamate -> L-alanine + alpha-Ketoglutarate. In the liver reverse reaction takes place to form glutamate catalyzed by alanine transaminase. The oxidative deamination of glutamate yields alpha-ketoglutarate and NH4+. Ammonia is carried to the lover as an amide group of glutamine formed from glutamate in a reaction catalyzed by glutamine synthase. L-glucamate +NH4+ + ATP-> L Glutamine Glutamine is further hydrolyzed by glutaminase to form glutamate and NH4+ an additional NH4+ is generated as glutamate dehydrogenase which converts glutamate to alpha-ketoglutarate. L-glutamine + h2o -> L-glutamate +NH4 -> L-glutamate + H2O -> NAD+ alpha-ketoglutarate +NADH Additional ammonia is generated in several other reactions catalyzed by various enzymes including, L-amino acid oxidase, Serine throning dehydrates and bacterial urease. Ammonia thus formed through various reactions is disposed off by urea cycle with formation of urea utilizing ammonia. |
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Urea Synthesis
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In ureotelic organisms 90% of the nitrogen is disposed of through urea cycle. Urea is formed from ammonia, CO2, and aspirate in a cylic pathway referred to as urea cycle. It is also referred to as Krebs-Henseleit cycle. Urea synthesis beting in hepatocytes with the formation of carbamoyl phosphate from NH4+ and HCO3- catalyzed by caramel phosphate synthetase I. This is an energy requiring (two ATPS) irreversible reaction. Carbamoyl phosphate subsequently reacts with ornithine to form citrulline. This reaction is catalyzed by ornithine transcarbamoylase and is driven by the release of phosphate. Citrulline is transported to the cytoplasm where after series of reaction urea is formed from arginine along with ornithine which gets back into the matrix to continue the urea cycle with int formation of citrulline using ornithine. Urea is released in the bloodstream from hepatocyte and is ultimately elimated in the urine by the kidneys.
If one of the intermediate steps are needed somewhere else, then no urea will be formed. |
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Control of the urea cycle
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Since urea is toxic to the cell its formation is strictly regulated. The level of all of the five enzymes involved int he urea cycle are altered by the variation in dietary protein content. Several hormones like glucagons and glucocorticoids are believed to be involved in the regulation. The activities of these enzymes are also controlled by the concentration of their substrates.
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Catabolism of amino acid carbon skeletons
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The alpha-amino acids can be grouped into classes according to the end products of their catabolic pathways these include acetyl-CoA, acetoacetyl CoA, pyruvate, and several citric acid cycle intermediates.
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Degradation of Neurotransmitters
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To maintain the precision in the information transfer, neurotransmitters are quickly deranged or removed from the synaptic cleft. The catecholamines epinephrine, norepinephrine and dopamine are inactivated by oxidation reaction catalyzed by monoamine oxidase (MAO) this enzyme is found within the nerve endings. Catecholamines are also inactivated by methaltion reaction catalyzed by catachol-O-methyltransferase production methylated products
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Serotonin degradation
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Serotonin is degraded in a two-step reaction: in the first step serotonin is oxidized by MAO. The product is further oxidized by aldehydge dehydrogenase to form 5-hydroxyindole-3-acetate
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Birds and insects remove ammonia by
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Converting to uric acid
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Ketogenic catabolism converts amino acids into
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Acetyl-CoA and acetoacetyl-CoA
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How are the amino groups from the excess of amino acids in the muscle transported to the lier
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In muscle excess the amino groups are transferred to alpha-ketoglutarate to form glutamate. The amino groups of glutamate are transferred to the liver by blood through alanine cycle
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What are the precursors to Urea
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NH3, CO3, and aspartate
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Urea cycle begins in ______ while ends in _____
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Hepatocyte and urine
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Neurotransmitters are mainly inactivated by ______ catalyzed by the enzyme ______
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Oxidalion reduction & monoamine oxidase.
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