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Biochem Metabolism Exam 3 Studyguide

by: Madeline Abuelafiya

Biochem Metabolism Exam 3 Studyguide BIOL 5311

Marketplace > Southern Methodist University > Biology > BIOL 5311 > Biochem Metabolism Exam 3 Studyguide
Madeline Abuelafiya

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Biochem Metabolism Exam 3 Studyguide
Biochemistry: Metabolism
Dr. Vogel
Study Guide
Biochem Metabolism Exam 3 Studyguide
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This 174 page Study Guide was uploaded by Madeline Abuelafiya on Wednesday April 6, 2016. The Study Guide belongs to BIOL 5311 at Southern Methodist University taught by Dr. Vogel in Winter 2016. Since its upload, it has received 31 views. For similar materials see Biochemistry: Metabolism in Biology at Southern Methodist University.


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Date Created: 04/06/16
Review Lipids • Chapter 10.1 and 10.2 • Fatty acids • Triacylglycerols • Phospholipids • Sphingolipids • Cholesterol • Lipid bilayer Fatty acids • Hydrocarbon chains of various length (14 to 20 carbon atoms most common) and degrees of unsaturation, terminated with a carboxylic acid group. • Named after the parent hydrocarbon, ionized at physiological pH, therefore named as carboxylate. • Usually cis-configuration at double bond Nomenclature of fatty acids Solubility and Melting Point of Saturated Fatty Acids • Solubility decreases as the chain length increases • Melting point increases as the chain length increases Conformation of Fatty Acids • The saturated chain tends to adopt extended conformations • The double bonds in natural unsaturated fatty acids are commonly in cis configuration • This introduces a kink in the chain Trans Fatty Acids • Trans fatty acids form by partial dehydrogenation of unsaturated fatty acids • A trans double bond allows a given fatty acid to adopt an extended conformation. • Trans fatty acids can pack more regularly, and show higher melting points than cis forms • Consuming trans fats increases risk of cardiovascular disease – Avoid deep-frying partially hydrogenated vegetable oils – Current trend: reduce trans fats in foods (Wendy’s, KFC) Triacylglycerols: Fatty acid esters of glycerol, fat storage Glycerophospholipids Glycerophospholipids, phosphoglycerides Cardiolipin: two lipids hooked together Other membrane lipids Sphingolipids: derivatives of sphingosine Cerebrosides: glycosphingolipids Gangliosides: glycosphingolipids with oligosaccharide attached, including at least one sialic acid. Glycosphingolipids: determinants of blood types Cholesterol Melting, fluidity of membranes Fatty acid catabolism- β oxidation Chapter 17 Three stages of fatty acid oxidation 1- β-oxidation breaks down the fatty acid chain from the carboxylic acid end to make acetyl-CoA 2- Acetyl-CoA enters the citric acid cycle to be fully oxidized to CO 2hile generating NADH reducing equivalents 3- NADH is used in respiratory chain to reduce O2to H 2 and ATP is generated Oxidation of unsaturated fatty acids Vitamin B12, X-ray structure solved by Dorothy Hodgkin Recap of β-Oxidation Ketone bodies: The alternative fate of Acetyl CoA Adipose tissue to store fatty acids and in thermogenesis Endocrine function of adipose tissue Left: mouse with defective leptin gene Right: same mouse as left but after daily Injections with leptin Oxidative Phosphorylation CHAPTER 19.1 – 19.5 © 2013 W. H. Freeman and Company Life is driven by nothing else but electrons, by the energy given off by these electrons while cascading down from the high level to which they have been boosted up by photons. An electron going around is a little current. What drives life is thus a little electric current, kept up by the sunshine. All the complexities of intermediary metabolism are but lacework around this basic fact. -Albert Szent-Gyögyi- battle hymn of the aerobes: Left: heart mitochondria: Cristae bring large area of inner membrane for high density of electron transport systems and ATP generation. Right: liver mitos, About 1-2 µm, mitos from different organisms differ in size and shape Common Redox partners: NAD(P) /NAD(P)H H + Common Redox partner: Flavin nucleotides as stepwise e- acceptors Reducing equivalents produced in: How are e transported? One solution is coenzyme Q = ubiquinone Cytochromes with porphyrin or heme systems - FeS cluster in e transport Methods for determining sequence of electron transport: Studying effects of inhibitors on the redox states of e- carriers Electron transport through multi enzyme complexes: Where is the error in this slide? Complex II or succinate dehydrogenase Electron transport complexes assemble into supercomplexes of 2 or more of the complexes X-ray structures of complex III (red) and IV (green) overlaid over image from electron microscopy O2 consumption andATP synthesis are strictly coupled DNP is chemical uncoupler -At least 8 different subunits: α 3 3δ in F 1 and abc in mitochondrial F . 10 o -Three catalytic sites, three noncatalytic sites on αand β subunits. - O exchange experiments: ADP+Pi ↔ATP + H O are 2lose to unity. -Binding change mechanism: catalytic sites exist three different conformations that are Interchangeable. Energy is needed to release product. X-ray structural model indicates catalytic sites in three different Conformations. AMPPNP: non-hydrolysable ATP analog ATP -synthesis through rotational catalysis Visualizing Rotation of subunit g: ATP ADP + Pi Rotary Motion: ReconstitutedATPase-Actin Noji et al., Nature 1997 Features of the ATPase motor: ▯ Three ATP are hydrolyzed per 360 o revolution ▯ Hydrolysis of one ATP results in rotation of 120 o ▯ Actin filaments of up to 4 mm are rotated at 1 revolution per sec (ATPase:15 nm) ▯ The torque generated is larger than 40 pNnm . o ▯ The energy needed to generate the torque per 120 rotation is 8x10-20J ▯ The energy per ATP hydrolyzed is 9x10 -20J ▯ Energy efficiency > 90 % Asp (-) and Arg H interact in hydrophilic half-channel. Upon entering of H+, Asp(-) can take on H fromArg H+ and become protonated/neutral to circle into the membrane. Continuous influx of H+ brings the protons to the exit site where pK ofAsp decreases in hydrophilic environment And H+ is released into matrix. Other processes powered by electrochemical gradient and proton motive force: ATPsynthasome complex provides substrates for ATP synthesis Shuttle systems: malate-aspartate shuttle in kidney, liver and heart Shuttle systems: glycerol- 3-phosphate shuttle in skeletal muscle and brain Photosynthesis Compounds that absorb light Lipid Biosynthesis Cholesterol metabolism CHAPTER 21 Fatty acid synthesis starts with malonyl-CoA Malonyl-CoA is formed through carboxylation of acetyl-CoA. The reaction uses biotin as a co-enzyme and is similar to the carboxylation of pyruvate to oxaloacetate in gluconeogenesis Acetyl-CoA carboxylase with distinct catalytic activities: • Biotin carrier protein has biotin attached to a lysine residue. • In an ATP-powered reaction, biotin is carboxylated and serves as transient carrier of the carboxylate group. • The carboxylate is then transferred onto acetyl-CoA to make malonyl-CoA Fatty acid synthase: • Asequence of transesterifications and reduction reactions. Followed by • Decarboxylation provides energy for C-C bond formation. • NADPH is needed for the reduction events. • Synthase continues until C 16tty acid is generated. Fatty acid synthase: Sequence of transesterifications and reduction reactions. Followed by Decarboxylation provides energy for C-C bond formation. NADPH is needed for the reduction events. Synthase continues until C fatty acid 16 is generated. For synthesis of palmitate: 8 acetyl-CoA 7ATP - 7 CO (2CO ) 3 14 NADPH/ H + Expensive! NADPH is mainly produced in pentose-phosphate pathway, some by malic enzyme oxidative decarboxylation of malate to pyruvate Specialized enzymes needed to elongate beyond C16 and to desaturate to introduce double bonds Introducing double bonds involves O and t2e production of H O 2 catalyzed by mixed function oxidases: in the end, O 2s reduced and NADPH is oxidized Essential fatty acids are produced in plants as PC lipids containing linoleate (18:2 or 18:3 fatty acids). Once ingested, linoleate may be converted into longer f.a. like arachidonic acid = arachidonate, a 20:4 f.a. that is precursor to other eicosanoides: Family of potent signaling molecules like • prostaglandins • thromboxanes • leukotrienes Eicosanoids: short range messengers Prostaglandins (cyclic) Auto- or paracrine, can have Two derivatives: different effect depending on receptors. Prostacyclin: Strong vasodilator, inhibit aggregation of blood platelets. Thromboxane: Strong vasoconstrictor, causes aggregation of blood platelets. Leukotrienes (linear) Inflammatory mediators produces by immune cells Eicosanoides, prostaglandines, thromboxanes are potent signaling molecules Stimuli cause phospholipase2A to cleave off arachidonate COX converts into prostaglandines and thromboxanes, important messengers of inflammation and pain, Thromboxans involved in blood clotting COX inhibitors: i.e. aspirin, ibuprofen, others. anti-inflammatory, analgesic, anticoagulants by reducing thromboxane production Aleve Leukotriene synthesis is not inhibited by NSAID Biosynthesis of T riacylglycerols Chapter 21.2 Biosynthesis of triacylglycerols starts with generating phosphatidic acid Depending on metabolic resources: glycerophospholipids or triacylglycerols are made Rate of triacylglycerol synthesis altered by hormones • In severe diabetes mellitus (failure of insulin secretion or action), inability to metabolize glucose as well as to synthesize fatty acids from carbohydrates or amino acids. • If untreated, individuals have increased fatty acid oxidation and ketone body formation and lose weight. Two strategies to attach phospholipid head groups Activation of diacylglycerol with CTP both in eukaryotes and bacteria Formation of phosphatidylglycerol and phosphatidylserine. Dimerization of phosphatidylglycerol-3 phosphate leads to cardiolipin Decarboxylation of phosphatidylserine results in phosphatidylethanolamine Summary: Depending on metabolic resources: glycerophospholipids or triacylglycerols are made Example of strategy 2: PC-synthesis through activating cholin with CMP. Also used in PE synthesis Sphingosine biosynthesis Disease relevance Cholesterol “The most highly decorated small molecule in biology” (Brown and Goldstein, Nobel lecture 1985) with 13 Nobel Prizes associated • Importance in maintaining fluidity and plasticity of biological membranes • Derivatives as bile salts, steroid hormone • Synthesized from acetyl-CoA Overview: Nobel prize 1985


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