Exam 2 study guide
Exam 2 study guide 4115
Popular in General Biochemistry
verified elite notetaker
Popular in Biochemistry
This 8 page Study Guide was uploaded by Thomas Salazar on Sunday October 16, 2016. The Study Guide belongs to 4115 at Virginia Polytechnic Institute and State University taught by Dr. Richard Helm in Fall 2016. Since its upload, it has received 15 views. For similar materials see General Biochemistry in Biochemistry at Virginia Polytechnic Institute and State University.
Reviews for Exam 2 study guide
Report this Material
What is Karma?
Karma is the currency of StudySoup.
You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!
Date Created: 10/16/16
Exam 2 Study Guide General Biochemistry CARBOHYDRATES Carbohydrate sugars are typically “D” form o In Fischer projections, if the –OH group closest to the bottom is on the right, it is a D-sugar, on the left is an L-sugar e.g. sucrose is made up of D-glucose + D-fructose D and L forms of a sugar are enantiomers of each other, and are mirror images, with all –OH groups mirrored Changing just one H/OH pair forms epimers o the general formula for carbohydrates C +n(H O2 n RING STRUCTURES o Closing the ring of an aldose sugar hemiacetal, a ketose sugar hemiketal o If a ring has its C1 –OH group facing down in a Haworth projection, it is α; if the –OH group is facing up, it is β o Chair conformers should be drawn with the C6 facing up in D-sugars, facing down in L-sugars, and the C5 hydroxyl oxygen binding C5 and C1 depending on the stereochemistry of this bond’s formation, the sugar will either be α or β. CYCLIC SACCHARIDES o The Anomeric Position: the carbon that originally carried the carbonyl functional group o Furanoses: 5-membered rings from sugars that bond C5 hydroxyls to C2, where C2 was the anomeric carbon D-form still has C6 up, and C1 position depends on the stereochemistry of the bond formation o Variants: Uronic acid: C6 hydroxyl is oxidized to COOH detoxification Aldonic Acid: C1 hydroxyl oxidized to COOH blood monitoring Sugar alcohols: a carbonyl C=O bond is reduced to hydroxyl –OH Deoxy sugars: C2 has no hydroxyl group, or C6 becomes CH 3 Amino sugars: C2 hydroxyl is removed, then adds amido group Sugar phosphates: conversion of hydroxyls to phosphate groups GLYCOSYDIC BONDING o Accomplished organically by enzymatic processes can either retain or invert the α / β stereochemistry o Adds monosaccharides to the non-reducing end of sugars, and once it is bonded the ring cannot open again In sucrose, both anomeric positions of glucose and fructose are bonded to each other In starches, carbohydrates form branching bonds off C6 positions as well OLIGOSACCHARIDES AND POLYSACCHARIDES Exam 2 Study Guide General Biochemistry o Reducing ends of sugars can form O-linked bonds Serine, and Threonine, or N-linked bonds Asparagine o Glycoproteins: slippery Oligosaccharides are typically found at random coil regions in proteins Can act as cellular markers or identifiers o Proteoglycans: carbohydrates bound to membrane proteins Bound within cell membranes Highly hydrated Usually form part of the structural aspect of a cell o ABO blood scheme The essential “O” antigen is present in everyone, various glycan chains added by certain enzymes will convert this to either an A or B antigen o O-GlcNAc signaling UDP-GlcNAc is synthesized as a “byproduct” of a large number of metabolic pathways that produce energy in cells By analyzing the levels of UDP-GlcNAc and its subsequent forms, one can measure the energy output of a cell LIPIDS o Humans cannot oxidize single bonds to double bonds past C9 on fatty acids o Fatty acids are generally made of chains of equal lengths Nomenclature o Built in units of 2, based on Acetyl-CoA o Unsaturated fatty acids Named as: (Acid Name) C(#of carbons): (# of double bonds) (Δ a,b,c,d,e,f) (cis or trans) e.g. An acid with a 22 carbon chain with 6 double bonds at 4,7,10,13,16, and 19 that are all cis-configuration would have the name: Acid C22: 6 Δ4, 7, 10, 13, 16, 19 cis trans fats are “bad,” but trans-conjugated fatty acids are found to be the most effective anti-carcinogenic found to date Fatty Acids (FA) characteristics o Amphipathic, with non-polar and polar regions (tail and head) o Removing one of the non-polar tails forms a detergent, very hazardous to organic systems o Low solubility in water, blood density of FA’s is very low They must be moved by carrier proteins through the blood stream o Stored typically as triglycerides tri-glycerol base that is modified through esterification reactions to form many different chains and variations R 1OO-CH -CH2CH -OOCR2 3 (COOR ) 2 If all three R groups are the same it is considered simple. If they are different, it is complex Deposited in adipose tissue Exam 2 Study Guide General Biochemistry White adipose tissue has fewer mitochondria Brown adipose tissue has more, burns more energy Adipose tissues can cleave fatty acids as signaling to other cell types (muscles, neurons, etc.…) and responds to extracellular signals; we have very little control over how adipose tissue acts Membranes: o Lipid bilayers contain lipophilic substances and proteins o The lipids on the inside of a membrane are different from the ones on the outside layer o The head-group typically has a phosphate ***by convention, the phosphatized group is considered C3 of the triglyceride structure*** o The other two chains, C1 and C2 contain various fatty acids, which lends to a plethora of possible different lipids. C2 chains are typically unsaturated, while C3 chains are typically saturated Phosphatidyl-X C3 phosphate group forms bonds with an R1 group, either choline, ethanolamine, serine, or glycerol Ether glycerophospholipids: present in extremely small quantities, formed during allergic reactions. If concentration >10e-12 M, leads to anaphylactic shock Plasmologens: cis-vinyl ethers Sphingolipids: modified version of the central triglyceride molecule C18 molecule o The central –OH group is converted to a primary amine, reacts o 2° hydroxyl typically not modified, but C3 o 1° hydroxyl reacts 1. Ceramides: acylated at 1° amine 2. Sphingomyelin: acylated at 1° amine + 1° OH converted to phosphorylcholine or phosphorylethanolamine 3. Cerebrosides: acylated at 1° amine + 1° OH converted to β-D-glucopyranosyl or β- D-galactopyranosyl 4. Sulfatides: 1° OH converted to β-D-Galp-3-O STEROIDS Basic form is the cholesterol “fused ring” structure o Modifying and substituting on the rings form different products o Makes up the precursor for androgens, progestin, glucocorticoids, bile acids, and plant steroids as well Biosynthesis o Isopentyl diphosphate + dimethylallyl diphosphate C5 terpenes Energetically favored due to phosphate cleavage Adds another IPP to form farnesyl diphosphate Exam 2 Study Guide General Biochemistry One enzyme does both rxns., occurs in hydrophobic environments Ultimately forms squalene which is the precursor to all steroids LIPIDS o Peroxidation of key lipids can trigger autoimmune response, other “disease states” o Membranes Fluid mosaic, diff. proteins in diff. leaflets Peripheral: associates “loosely” with membrane outer leaflet Intrinsic: bound within membrane to maintain its structure Lipid rafts: many associated lipids and proteins as a system on membrane Curvature comes from differing lipids in leaflets, cytoskeletal interactions, and protein structural influence o Organisms seek homeostasis to maintain membrane fluidity Lateral movement: diffusion along membrane face Transverse: moving from outside inside or reverse (COSTS ATP) Hotter environment chain lengthening, less desaturation Colder environment chain shortening, more desaturation o Membrane proteins α helix takes ~ 25 AA to pass perpendicularly through a membrane B sheets take ~8 AA Proline disrupts helices Arg and Lys do outward “snorkeling” – Phe does inward “snorkeling” Lipid anchored proteins: fatty acid or cholesterol precursor inserted in membrane linked to a protein Amide linked, thio-ester linked, thio-ether linked, GPI proteins Vesicle insertion: SNARE proteins ”molecular twist ties” to bond vesicles to membranes Botulin Toxin: inhibits SNARE process, cause “flaccid” paralysis Tetanus: constantly exhibits SNARE process rigid paralysis o Membrane transport Passive diffusion Facilitated transport: has selective filters/conduit proteins Active: transporting against a concentration gradient (COSTS ATP) Secondary active transport: uses the gradient created by active transport to accomplish an alternate transportation process Symporters/antiporters Usually use Sodium or Proton gradients to do work Move glucose or AAs through membranes ABD proteins: get rid of waste, bring in nutrients; induced in most organisms Remove toxins, transport ions Has gates regulated by ATP ????2 Eqn. for passive diffusion: ΔG = RTln ( ) for neutral molecules ????1 Exam 2 Study Guide General Biochemistry ????2 Eqn. of charged passive diffusion: ΔG = RTln ( ) + zFΔΨ for charged molecules ????1 Where z is the charge of a molecule, F is Faraday constant, and ΔΨ is difference in voltage Na , K - ATPase o Active transporter for functioning neuron and muscle cells + E-ATP binds 3 Na in cytosol P is transferred to protein (Asp-P bond) and ADP leaves + + Protein gate opens, releases 3 Na to outside of cell, picks up 2 K Asp-P bond hydrolyzes, P leaies + ATP binds, opens protein gates and releases 2 K into cell ENZYMOLOGY Hexokinase o Coupled reaction, kinase transfers Phosphates o Humans have 4 different kinds o Have regulatory elements, and Catalytic sites [e.g. Glc-6-P kinase] Determining kinetics 1. Get a pure sample (SDS-PAGE) 2. Put enzyme in buffer with [E] known 3. Make sure [P] = 0 4. Add substrate S, make [S] >> [E] 5. Monitor change in [P] or [S] by the assay over a period of time Absorbance can usually be a surrogate for concentration “Units” are define @ specific conditions (pH, temp., etc.) and are the amount of enzyme that converts 1 µmol substrate into 1 µmol product in 1 min. o Enzymatic activity: µmoles min mL -1 -1 -1 -1 o Specific activity: µmoles min mg Directed evolution o Assumes an enzyme is not optimized o Follows the process of Diversification, Selection, Amplification, and Repetition to modify enzymes genetically and discovery more optimalforms and mutations ENZYME KINETICS CONTINUED E + S ↔ES ↔ EP ↔ E + P 1 order rxns: ???????? o one substrate goes to one product: A ↔ P and ln ???? = -Kt nd ???? 2 order rxns: o 2 [1 order substrate] goes to two products: 2A ↔ P + Q r = K[A] or, nd o Two 2 order substrates go to two products: A + B ↔ P + Q r = K[A][B] Where “r” is the reaction rate, and “K” is the reaction rate constant Exam 2 Study Guide General Biochemistry Formulas for Enzyme Kinetics: o V =0 ????????????????[????], where K m [S] when V = ½ V max ????????+[????] Low K mhigh affinity for ES complex, high K lom affinity for ES o K cat= turnover rate constant ???????????????? K cat [???? ], where [E]tis total enzyme concentration *organic systems do not operate at max; but usually closer to maxin order to allow for easier adjustment of the enzymatic rate in either direction* Lineweaver-Burke (LB) Equation: a plot of 1/V vs. 1/[S] 1 ???? 1 1 = ???? ( ) + y = mx + b ???? ???????????? [????] ???????????????? o The y-intercept of this graph is 1/V max o The x-intercept is 1/K m o The term ???????? is equal to the slope of the line ???????????????? Enzyme Inhibition: o Irreversible: covalently bonded to enzyme until it is degraded, very difficult to dose properly in drug applications o Reversible: Competitive: binds active site of E, inhibits the formation of ES complex In an LB plot, the apparent V maxis unchanged, but the apparent K m does change This causes the slope of the line to increase with [I], but the y-intercept remains unchanged [????] The slope is modified by a value, α = (1+ ???????? Non-competitive (mixed): binds active site of E and/or binds ES complex In LB plot, the apparent V maxchanges, and depending on the rxn, the apparent K may or may not change This causes both the slope and the y-intercept to change with [I] [????] The slope is modified by the value α = (1+ ), and the y-int. is modified ???? ???? [????] by the value α’ = (1+???????? Uncompetitive: binds ES complex only In LB plot, the apparent Vmax is changed, and the apparent K amso changes This causes the slope to remain the same, but the y-int. increases with [I] [????] The y-int. is modified by the value α = (1+????) ???? Kinetics with Two Substrates: o Single Displacement: one substrate binds the E, followed by a second. The substrates are modified, then released. Exam 2 Study Guide General Biochemistry Ordered sequential – one substrate must bind first for the rxn to occur, this substrate binds first, and is released last E + A EA + B EAB ↔ EPQ – P EQ – Q E , has rate constant K 1 Random sequential – either substrate can bind first and be released o Double displacement/ping-pong: a covalent intermediate from initial substrate remains and modifies the enzyme for following substrate Substrate A binds enzyme E, a covalent intermediate from A binds E to form EA. EA forms enzyme-product complex FP. As P is released, F binds substrate B to form FB. FB forms enzyme-product complex EQ. As Q is released, the original enzyme E remains. E + A EA ↔ FP – P F + B FB ↔ EQ – Q E , has rate constants K 1 and 2 Transition State Theory: o Enzymes optimize for transition state o Must bind in proper orientation to the catalytic site o Molecular environment geometrically forces substrate to adopt transition state o All components, amino acids, cofactors, must be present for rxn to proceed Moonlighting – one protein fills multiple functions and roles in an organic system Fructose-1,6-biphosphate aldolase o Central enzyme in glycolysis o Class I: mammals/plants – covalent catalysis o Class II: microbes *Know the mechanisms of zinc as an electron acceptor, and 1, 2-hydride shifts!* ENZYME REGULATION Phosphorylation o Kinase: puts P on o Phosphatase: takes P off This modification is either on or off However, phosphorylation cascades (an initial phosphorylation event triggering another and so on,) can produce and modulate many types of cell responses Uncontrolled activity of phosphorylation is indicative of cancer cells Regulatory proteins: block access to the catalytic site of kinases; released by cAMP o Auto-regulation: a “pseudo-substrate sequence” in the kinase acts as its own inhibitor and blocks cat. Site. An activator molecule alters the kinase structure and releases the cat. Site Zymogens: inactive forms of proteases, cleavage at specific sites activates them o Proteases do not inactivate until they are degraded by the cell, must be carefully regulated Acetylation o Modulates enzyme function, some activate, some inhibit Exam 2 Study Guide General Biochemistry Allosteric regulation o Allosteric activator and inhibitors (often used in negative feedback cycles) o If [A] is relatively constant, then activators and inhibitors can drastically change the reaction rate o Symmetry Without substrate, all enzyme subunits are T-state Adding S, all units become R-state Allosteric activators favor R-state, called positive heterotrophic reactors Allosteric inhibitors favor T-state, called negative heterotrophic reactors Conversion of one subunit to R-state favors the addition conversion of other units to R-state, such that once one is R, all other subunits become R as well Glycogen Phosphatase: homodimer; (glycogen) + P (nlycoien) n-1+ Glucose-1- phosphate o Has two forms, A and B A: phosphorylated, R-state is much more reactive than R-state of B form B: un-phosphorylated, can be regulated more easily by allosteric regulators, while A is typically unaffected by allosteric AMP upregulates activity ATP downregulates activity o Conversion from form B to A is done by phosphorylase kinase, in a series of phosphorylation cascades. G coupled protein receptors o Membrane associated protein systems, 7 membered receptors o Transfer cellular signal from the outside-in; signal ligands don’t enter the cell o Agonists: increase signal strength; Antagonists: decrease signal strength o Inverse agonists: requires a base signal level, turns off signals.
Are you sure you want to buy this material for
You're already Subscribed!
Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'