Biochemistry 301 Week 5 Notes
Biochemistry 301 Week 5 Notes BBMB 301
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This 13 page Class Notes was uploaded by Emily on Thursday February 11, 2016. The Class Notes belongs to BBMB 301 at Iowa State University taught by Robert Thornburg in Spring 2016. Since its upload, it has received 23 views. For similar materials see Survey of Biochemistry in General Science at Iowa State University.
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Date Created: 02/11/16
Biochemistry 301 – Survey of Biochemistry Professor Robert Thornburg LECTURE 11 – CHAPTER 11 – LIPID STRUCTURE AND FUNCTION By: Emily Settle Functions of lipids o Passive functions Storage of chemical energy Fats, oils, and waxes serve as fuel Highly reduced, more energy rich than carbohydrates o Carbohydrates – 4 cal/gm o Lipids – 9 cal/gm Structural functions in membrane Lipid bilayer o Active functions Signaling Hormones and second messenger molecules Steroids and phospholipids can control and change cell behavior Prosthetic groups – non-amino acid components of holoenzymes Ex lipoic acid Required for certain enzyme activities Pigments Light absorption Carotene Digestive functions Bile acids Oxidation states of carbon o Oxidation – loss of electrons o Reduction – gain of electrons o Reduced carbon Higher electron density around carbon nucleus More bonds to hydrogen or carbon Fewer bonds to oxygen o Oxidized carbon Less electron density around carbon nucleus Fewer bonds to hydrogen or carbon More bonds to oxygen o Reduced carbon possesses more chemical energy than oxidized carbon. Fatty Acids o Hydrocarbon chains with a terminal carboxylic acid Amphiphilic: polar and non-polar components Usually even number of carbon atoms o Saturated fatty acids No double bonds o Unsaturated fatty acids One or more double bonds Mono-unsaturated or polyunsaturated Usually cis configuration o Nonessential fatty acids Synthesized by mammals o Essential fatty acids Essential = required for biological processes Not produced by mammals Must be obtained in diet Fatty acid nomenclature o Identifying each carbon Numerals: carboxylic acid carbon is number 1 Greek letters: α is C-2, β is C-3, etc. Alternate system o ω is the carbon furthest away from the carboxylic acid o ω is number 1, then counts towards the carboxylic acid o Numerical abbreviation Number of carbons, then number of double bonds 16:0 means sixteen carbons, saturated. Position of double bonds noted by “Δ” Numbered from the carboxylate carbon (C-1) 18:1^ Δ9 one double bond between C-9 and C-10 o Common and systematic names as well as numerical names Memorization assignment o Be able to draw the structure of any fatty acid given the numerical abbreviation o “ate” indicates the carboxylic acid group is ionized Completely ionized at physiological pH Properties of Fatty Acids o Solubility decreases with increasing chain length o Melting point increases with increasing chain length Stronger packing owing to van der Waals bonds o Melting point decreases with unsaturation Kinks decrease packing efficiency o Fewer double bonds result in higher melting point Essential ω Fatty Acids o Omega-3 fatty acids 18:3ω-3 (α linolenic acid) 20:5ω-3 (eicosapentanoic acid – EPA) 22:6 ω-3 (docosahexaenoic acid – DHA) o Health benefits in diet Precursors of hormones Other health benefits not yet understood Fatty Acid Derivatives o Produced from arachidonic acid (ω-6) or EPA (ω-3) o Many biological signaling functions in mammals Local responses, occur in cells where compounds produced Important in many diseases or physiological responses Prostaglandins o Inflammation, pain, ovulation signals, uterine contractions o Synthesis disruption is the target of aspirin, other pain meds Thromboxanes o Blood clotting and vasoconstriction in response to injury Leukotrienes o Anaphalactic shock Fats and Oils o Energy storage Synthesized when calories in excess Oxidized to produce ATP when chemical energy is required o Fats High frequency of saturated FAs High melting points solid at room temperature o Oils High percentage of unsaturated FAs Low melting points Liquid at room temperature Non-polar lipids o Storage lipids Glycerol with three FA chains attached Polar lipids o Membrane lipids Phosphoglycerides Sphingolipids Sphingosine Backbone – long chain, hydroxylated, secondary amine Amino group of backbone joined to a fatty acid by amide linkage C-1 hydroxyl phosphorylated o Can have a head group attached Galactolipids Prevalent in plant membranes A galactose is linked to glycerol by a glycoside bond o Can by monogalactosyl- or digalactosyldiacylglycerol Chloroplast membranes o Total phospholipid: 8% o Total galactolipid: 92% Lipids of Archaeabacteria o Archaeabacterial prokaryotes live in extreme environments High temperature and pressure, high salt conditions Altered lipid structures Ether linkages between alkane chains and glycerol backbone Ether resistant to hydrolysis reaction Lack of double bonds resistant to oxidation reactions Terpenes (Isoprenoids) o Built from isoprene units o Linear terpene chains of 10, 15, 20, etc. carbon subsequently modified by oxidation, ring formation, etc. Referred to as terpenoids in plants Secondary metabolites o Not part of the metabolic pathways found in other organisms More than 50,000 different terpenoids known in plant species o Terpenoid Functions Colors and odors used in plant reproduction Signaling molecules exhormones Photon absorption in photosynthesis Antioxidants Protect from excess light Neutralize free radicals before they propagate Protective function Secreted tree resins o Time, temperature, and pressure convert terpenoids into amber Protein modification Terpenoid tails on proteins causes membrane localization o Anticancer target Steroids o Terpenoid derivatives: 30 carbons Four fusing rings Different steroids vary by modifications to rings o Functions Structural Membrane structure, affects fluidity Signaling molecules A wide variety of steroid hormones Hydrophobic nature allows steroids to pass through membranes o Move to nucleus, bind proteins as allosteric effectors o Bind DNA to regulate gene expression Precursors to bile salts Aid digestion of fats by dissolving them in the intestine Terpenoids in Protein/Lipid Conjugates o Terpenoids can be attached to proteins as membrane anchors Farnesyl groups: 15 carbons Geranylgeranyl groups: 20 carbons Thioether linkage (Cys residue at C terminus) C terminal carboxylic acid group converted to methyl ester o Fatty acids can also be attached to proteins by thioester Internal Cys residues o These modifications are anticancer targets GPI Anchors – Protein/Lipid Conjugates o Phosphoglyceride is part of compound molecules Function is to anchor protein to membrane Phosphatidylinositol anchored in membrane Oligosaccharide liked to inositol Phosphoethanolamine linked to carbohydrate Protein linked to phosphoethanolamine o Amide bond with C terminal carboxyl group Triacylglycerols – neutral lipids o Most common lipids: fats and oils o Structure (MEMORIZE) Glycerol with 3 fatty acids attached by ester bonds Each fatty acid is an acyl group o Simple Same acyl group at all 3 positions o Mixed Two or three types of acyl group Phospholipids: polar lipids o Phosphoglycerides Glycerol backbone Two acyl groups, ester linked Polar head group linked to backbone by a phosphoryl group Phosphodiester linkage o Sphingomeylins Sphingosine backbone One acyl group, amide linked Polar head group linked by phosphodiester bond Amphipathic Nature of Polar Lipids o Non-polar parts associate with each other Subject to hydrophobic effect o Polar or charged head group in aqueous phase Soaps o Ester linkages cleaved by acid or base Heat fats/oils in the presence of KOH or NaOH (lye) Products are: Glycerol K+ or Na+ salts of the fatty acids (strong acid) Detergents o Salts of the weak acids o Detergents are more gentle than soaps o Amphipathic fatty acids dissolve non-polar compounds Biochemistry 301 – Survey of Biochemistry Professor Robert Thornburg LECTURE 12 – CHAPTER 12 – MEMBRANE AND TRANSPORT By: Emily Settle Functions of membranes o Boundaries between aqueous compartments The cell and its external environment Compartments within cells (organelles) o Cellular recognition Contacts between cells occur at plasma membranes o Signal transduction Information flow from cell surface to the interior o Transport Selective passage of small molecules across membranes Channels and pumps o Energy conservation systems Production of ATP, using either chemical or electromagnetic energy Components of membranes o Lipids Recall the structures of phosphoglycerides, sphingolipids Polar headgroups exposed to water on the outsider of lipid bilayers Aliphatic regions of the fatty acids align with each other in the interior of the bilayer Hydrophobic effect o Proteins Free or attached to lipids Integral or peripheral with respect to the lipid bilayer o Carbohydrates Always attached to a lipid or a protein, not free in the membrane Lipid bilayers o Lipids in each type of membrane are specific o Different membranes in the same cell have specific compositions o Sheet like structure with outer and inner “leaflets” o Inner and outer leaflets have different compositions Lipid Vesicles – artificial membranes o Artificial membranes created in vitro by vigorous shaking of lipid:water mixtures Can be made to include particular molecules Measure rate of leakage from inside to outside of the vesicle Permeability o Not absolute Molecules can diffuse through lipid bilayer at different rates Membranes are effectively impermeable to ions Higher solubility in water correlates with slower rate of diffusion across membranes Membrane Fluidity o Molecular motion within the non-polar interior of membranes reflects melting points of the fatty acids present Longer FAs less fluid Fewer double bonds less fluid o Solid character imparted by Van der Waals contacts Modulation of Fluidity by Cholesterol o Cholesterol present in animal cell membranes Hydroxyl group H-bonds to phosphate group of lipid Increases fluidity by preventing close packing of acyl groups o Concentration in different membranes varies 3% in mitochondrial membranes 38% in plasma membranes o Can isolate certain regions into “rafts” Diffusion limited so molecules within remain associated Classes of Membrane Proteins o Membranes vary from 80% lipid:20% protein to 25% lipid:75% protein o Integral membrane proteins (A&B) All or part located within the hydrophobic core of the membrane o Peripheral membrane proteins (C&D) Located on outer surface Weak bonds to lipid head groups or other proteins Small hydrophobic regions of the protein insert into hydrophobic interior o Anchored (E) Terpenoid or fatty acid tails GPI anchors Serpentine Transmembrane Protein o Ex bacteriohodopsin Yellow cylinders are α-helices Hydrophobic amino acids located within the membrane spanning helices Charged amino acids located in loops on the outside of the membrane o Proteins fold “inside out” compared to water-soluble type Hydrophilic residues on the inside instead of outside β-barrel transmembrane protein o β sheet wraps into a barrel shape alternating R groups on opposite sides of sheet hydrophobic residues outside hydrophilic residues inside Peripheral Membrane Proteins o Attached relatively loosely to one side of the bilayer Can be removed without disrupting the bilayer o Enzymes that use hydrophobic molecules as substrates are often peripheral membrane proteins Carbohydrate Components o Attached to lipids Gangliosides, a type of sphingolipid Oligosaccharide built onto the head group o Attached to proteins Integral membrane glycoproteins o Can account for up to 5% of the mass of the membrane o Frequently on the exterior surface of plasma membranes Contacted first in interactions between the cell surface and any external molecule The Fluid-Mosaic Model o Lipids within a membrane can diffuse laterally in one leaflet of the bilayer o Proteins can also diffuse Can be thought of as “floating” in the organic layer o Membrane is a dynamic environment where different molecular contacts are continuously made and broken Fluorescence recovery after photobleaching – how we know proteins can migrate in membranes Overview of Transport Across Membranes o Hydrophilic molecules must pass through hydrophobic environment of the membrane Water, gases, some small non-polar molecules pass freely Cell membranes are selective for large molecules, polar molecules, ions o Types of transport Passive transport – diffusion, movement from region of high concentration to region of low concentration Chemical energy from the cell not required, energy that is used is already stored in the concentration gradient Second law of thermodynamics explains movement without energy input – spontaneous Simple diffusion – molecules that pass directly through the bilayer Facilitated diffusion – protein provided a pore through the bilayer, specific molecules can fit through pore, regulated by signals, allosteric protein movements. Active transport – movement against a concentration gradient (low to high) requires energy! Gated Facilitated Transport o Activation of a facilitated transporter by a molecular signal Channel normally closed, then opens in response to signal o Ligand gated: binding of an effector molecule causes allosteric change in conformation that opens the channel o Voltage-gated: another channel in the membrane opened in response ΔV Responsible for transmission of signal over the length of the neuron Active Transport Sources of Energy o ATP hydrolysis o Photons o Secondary transport Energy stored in concentration gradient of one molecule Used to pump different molecule against gradient Na+/K+ ATPase – pumps both Na+ and K+ against concentration gradient o Keeps [Na+] outside the cell higher than inside o Keeps [K+] outside the cell lower than inside o 30% of our ATP supply is spent doing this in the brain o Establishes the membrane potential of neurons Toxins that interfere with the pump quickly kill animals Antifreeze – mammals Grapes – dogs Lilies – cats Se toxicity – horse and cattle ABC Transporter Family o Human genome codes for 140 proteins of this structure o ATP-binding cassette Gives name to the family ATP hydrolysis provides energy to pump against concentration gradient o Multi-drug resistance (MDR) Pumps a wide variety of “foreign” organic molecules out of the cell o CFTR – Cystic Fibrosis Transmembrane conductance Receptor Pumps calcium ions out of cell Mutations cause osmotic imbalance Mucous in lungs causes death typically by age 30 Ion Channel Selectivity o Na+ smaller K+ but cannot passes the K+ channel Solvated ions, K+ or Na+, enter water filled cavity in membrane Ions must mose contact with water molecules to fit into the narrow channel K+ replaces bonds to water molecules with bonds to partial negative charges on amide oxygens in peptide bonds Na+ cannot bond to amide oxygens as effectively as K+ Smaller radius Thus, the transition state is higher energy for Na+ compared to K+ This provides a selectivity filter for the channel Biochemistry 301 – Survey of Biochemistry Professor Robert Thornburg LECTURE 13 – CHAPTER 13 – MOLECULAR SIGNALING ACROSS MEMBRANES By: Emily Settle General Outline of Signal Transduction o Information from outside the cell causes internal response Sent as a primary messenger signal o Receptor is a transmembrane protein Binds primary messenger Enzyme activity changes inside cell o Enzyme produces many second messenger molecules Amplification – one signaling molecule, many second messenger molecules o Cell is in a new state (signal has been transduced) o Cellular change to changed internal state Ex 7-transmembrane helix proteins (7TM) o β-adrenergic receptor adrenaline fight or flight o vasopressin receptor retention of water by kidney Ex Receptor Tyrosine Kinases o Activity of tyrosine kinase domain requires binding of ligand on extracellular domain o Transfers phosphate group of ATP to hydroxyl group of tyrosine side chain o Epidermal growth factor receptor EGF stimulates cell growth and division in gut-lining epidermal cells o Insulin receptor Regulates body’s response to glucose Β-adrenergic Receptor o Ex 7TM receptor protein - G protein coupled receptors o Signal is epinephrine (adrenaline) Produced by adrenal gland, circulates in bloodstream Response is metabolic change that stimulates ATP production o Cytoplasmic domain regulates activity of GTPase – G protein 7TM Receptors as a Class o 100s – 1000s of these proteins encoded in mammalian genomes o Similar structures, from evolutionarily conserved module o Respond to many different ligands Odorants Taste molecules Hormones Light – not a molecular ligand, but still an external signal All regulate activity of G proteins G proteins o Internal domain of 7TM receptor interacts with trimeric G protein Only when receptor is bound to ligand G αβΥ– three subunits G α bound to GDP o Interaction with ligand-bound 7TM causes allosteric change in G α structure Causes GDP to dissociate from binding site GTP binds to free site βΥ dissociates from quaternary structure, leaving G -GαP free one ligand-bound 7TM receptor causes generates many G -GTP α Effects of Gα-GTP o After the βΥ subunits disassociate from the G -GαP complex, adenylate cyclase binds to the covered face that is covered by βΥ subunits o G αGTP complex binds to adenylate cyclase and stimulates its activity Adenylate Cyclase reaction: ATP cAMP(second messenger) + PPi Protein Kinase A - PKA is a kinase regulated by cAMP o PKA catalyzes transfer of phosphate groups from ATP to specific target proteins o Ser, Thr residues o Activities of target enzymes changed by covalent modification (phosphorylation) o Multiple targets including: Enzymes that release glucose from glycogen are activated Enzymes that store glucose in glycogen are inhibited Hydrolysis of fatty acids from triacylgylcerols stimulates Result is increased fuel for energy production cAMP Activation of PKA o cAMP bind to negative regulatory subunit active catalytic subunit is released Turning the signal off o G αGTP hydrolyzes GTP to GDP + Pi at a set rate o G αGTP can’t bind adenylate cyclase Adenylate cyclase no longer active, cAMP no longer made o cAMP is eliminated by hydrolysis of phosphodiester bond cAMP + H2O AMP The “Off” Signal o Receptor protein dissociates from its ligand (epinephrine) – any molecule that gets bound by a receptor Equilibrium between bound and unbound Free epinephrine is removed (degradation) As concentration of epinephrine decreases, the receptor returns to the unbound, off state Another 7TM Receptor o Different 7TM receptors work with different versions of G α Different Gα-GTP complexes have distinct target enzymes Vasopressin receptor activates a G protein that activates phospholipase C Two second messengers: diacylglycerol (DAG) and inositol-1,4,5-triphosphate (IP3) Concerted Effects of PIP3 and DAG nd o Two 2 messengers cooperate, activate protein kinase C PIP3 opens a gated facilitated transporter for Ca2+, which is released from internal membrane compartments DAG moves through membrane to activate PKC Increased Ca2+ also is a signal for activation of PKC Ca2+ binding changes protein folding Calcium Signaling o Ca2+ ions bind to calmodulin and cause a change its tertiary structure Activated calmodulin binds to other proteins to regulate their activity Calmodulin-dependent protein kinase Ca2+-ATPase pump o So high calcium concentration stimulates the pump that evicts calcium from the cell Single-Pass Receptors o Signal molecule binding causes dimerization Mobility of proteins within membrane Dimers form both in extracellular and intracellular domain Intracellular domain dimerization activates a protein kinase Usually a tyrosine kinase o Distinct class from Ser-Thr kinases Referred to as “receptor tyrosine kinases” (RTK) Cross-Phosphorylation o RTK internal domains phosphorylate each other Specific amino acid in each subunit is the substrate for the catalytic domain in the other substrate After phosphorylation each RTK subunit becomes accessible to other substrates Regulated by phosphorylation RTK Ex Epidermal Growth Factor (EGF) Receptor o 53 amino acids; signals cell division in epidermal ells; functions in healing stomach ulcers o Family of similar signaling molecules stimulate division of different cell types Cross-phosphorylation of EGFR o EGFR tail phosphorylated by opposite subunit Causes assembly of an extended quaternary structure Grb-2 is adaptor protein Binds pTyr by SH2 domain, proline rich regions by SH3 domain These domains shared by many protein Downstream Signaling from EGFR o Grb-2 bound to EGFR recruits Sos and brings it to Ras Ras located in membrane through attached isoprenoid, fatty acid Ras is a small G protein Similar GDP/GTP binding site to G α Sos causes GDP to leave, GTP binds, Ras activates Activated Ras starts a protein kinase cascade cell division o Hyperactive Ras present in 40% of human tumors Off-mechanism compromised GTPase activity reduced Participates in uncontrolled cell division RTK Ex Insulin Receptor o Insulin signals the well-fed state, adjusts metabolism 51 amino acids – made in pancreas Signal transduction cascade o Receptor is tetramer, already assembled o Insulin binding activates tyrosine kinase o These phosphorylate insulin receptor substrates on Tyr o SH2 domain of phosphoinositide-3-kinase This is a kinase that transfers phosphate group to a lipid head group o PIP3 moves in membrane to PIP3-dependent protein kinase (PDK) PDK phosphorylates Akt o Activated Akt causes glucose transporters to move to membrane o Glucose from the meal taken up into cells (objective) Signal Transduction and Cancer o Oncogenes are viral genes that cause cancer These are mutant derivatives of normal cellular genes that function in signaling pathways o Signaling pathways are hyperactive in cancer cells Targeting these molecules with drugs is a new way of treating cancer Ex monoclonal antibody to EGFR external domain Ex drugs that interfere with transfer of isoprenoid lipid to Ras C terminus
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