BIO 201: LEC11 - LEC20
BIO 201: LEC11 - LEC20 BIO 201
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Date Created: 03/19/16
Lecture 11 - Multicellularity 02/22/2016 ▯ Overview Evolution of multicellularity Cellular structures associated with multicellularity o Cell adhesions o Extracellular matrix Integrins: ECM Receptors ▯ ▯ Multicellularity Advantages o Specialization: able to perform functions more efficiently o Smaller cell size: larger surface area – absorb more nutrients o Cellular redundancy: cells could die but the organism doesn’t o Size: bigger Challenges o Coordination/communication: how do you coordinate the activity of all those cells – requires some sort of communication o Reproduction is much harder – unicellular organisms just divide o Growth – need to regulate growth some how o Cell adhesion – holding it all together so it stays together but can still be penetrated ▯ ▯ Evolution of Multicellularity 1. Adhesion of cells (cell adhesions and extracellular matrix) i. Choanoflagellates: multicellular organism that evolved from a unicellular organism – of all the protists/eukaryotes – it’s the most related to animals – multilcellularity has evolved at LEAST 46 times in evolution 2. Diversification (developmental biology) i. Example of this: dictyostelium, volvox 3. Communication (signaling and extracellular matrix) i. In order to achieve diversification, needs to have some sort of intercellular communication ii. Important for coordination 4. Reproduction (developmental biology) i. Important: have to decide which cell types to reproduce etc. 5. A way to absorb nutrients, H2O, gases, and to transport hormones, waste (GI, respiratory, lympathic, renal, genitourinary system: epithelial cells) 6. Protective barriers – protection and prevention of cell mixing (cell adhesions and extracellular matrix) ▯ ▯ Cell Adhesions Mediated by plasma membrane proteins – anchored inside cells (adhesion molecules) Hold cells together Provide protective boundary – important in epithelial cells Prevent cell mixing of different cell types ▯ ▯ Types of Cell Adhesions Tight Junctions*** o Strongest and tightest type of adhesion o Forms a nearly impermeable seal between epithelial cells Desmosomes o Similar to tight junction but allow some things to pass through Gap Junctions (mainly communication) o Protein bridge between cells o Direct electrical communication (e.g. heart) Adhesion mediated by proteins (cell adhesion molecules) anchored in the plasma membrane ▯ ▯ Tight Junctions Epithelial cells are specialized, polar cells that form the boundary between organism (bloodstream) and environment (lumen) -> selective absorption and excretion Skin, lungs, gut – boundary between organism and environment “gate keepers of the body” – decides what goes in and what goes out ▯ ▯ Cell Adhesions in Epithelial Cells Image shows 3 epithelial cells – lumen on top blood stream on the bottom Tight junctions are shown here (4 types in the image) Green things are tight junctions that hold cells together – impenetrable – goes through every single cell Desmosomes are most similar to tight junctions but notice that they don’t surround the cells entirely Tight junctions are the most significant type of cell junction ▯ ▯ Overhead view of tight junctions We can actually use proteins of the immune system to identify proteins in tissues ▯ ▯ Extracellular Matrix (ECM) Many different secreted proteins (constitutive) Anchors cells and holds them together Structural support and cushioning Signaling and communication Prevents cell mixing ▯ ECM is everything inside the body outside of the cell – loaded with proteins Forms all of the connective tissue in the body – ligaments, tissues, bones Forms basil lamina – tough tissue in between organs, one of the most important There exist 3 different types of ECM proteins ▯ ▯ Collagens 1. Most abundant proteins in mammals (25 – 35% of protein) 2. Fibrous protein 3. Precursors to bone and other connective tissues 4. 28 different collagens ▯ cartilage, bone 3 sets of alpha helical peptides that braid with each other – form bundles there are mutations in collagens that cause disease ▯ ▯ Proteoglycans Based in proteins, glycan – sugars that get added on to them Heavily glycosylated – more glycosylation than there are proteins When proteins are glycosylated, enzymes actually add polysaccharides onto them – covalently bond them to certain side chains GLUCOSAMINE gets added on CHONDROITIN SULFATE – common polysaccharide that gets added on as well Both of these are very important for cushioning between joints/cartilage – the reason it’s so good is that these molecules, especially chondroitin sulfate, are very polar Heavily glycosylated -> large polar surface area -> attracts water and other molecules -> cushionin ▯ ▯ Laminins 1. Heteromultimers 2. Diverse functions: i. Stabilizes ECM ii. Boundary between tissues – basal lamina iii. Promotes cell migration iv. Signal for growth and differentiation ▯ ECM receptors: Integrins “hand on the subway” 1. Plasma membrane receptors for ECM proteins 2. A-B heterodimers 3. Different ECM proteins bind to different a-B integrin combinations 4. Cytoplasmic domain of integrins anchored to cytoskeleton ->anchoring and/or cell migration ▯ There are 18 known alpha subunits 8 different beta integrins 24 known heterodimers different integrins expressed in different cells combo determines which ECM protein that integrin will bind too triggers actin polymerization and other things ▯ ▯ Integrins and cancer metastasis Cancer doesn’t kill you, it’s usually the fact that it metastasizes to other organs For those integrin combinations, they’re responsible for mediating cell migration – want to block this activity some how Many cancer tissues will send out signaling molecules that attract the blood vessels to grow into them – ingrowth of blood vessels which do 2 things: o 1. Brings nutrients and oxygen into the tumor so the tumor can grow even faster – so this is very important in the inhibition of cancer o 2. Cancer cells now have access to the bloodstream and if it’s expressing the right kind of combination integrins – which generally they are – they can now migrate by virtue of the correct ECM molecules and will invade and migrate the bloodstream which is how they become metastatic – potentially kill you RGD – arginine-glycine-aspartic acid – hypothetical , however all promote migration – 3 amino acid sequence Can we prevent metastasis by interfering with integrin binding to ECM? o treat with artificial RGD containing peptides o competition: RGD binds to integrin, preventing ECM binding o inhibition of migration ▯ The Plasma Membrane Compartmentalization o All cells and all domains of life have plasma membranes o Structurally and virtually the same o Make sure biological molecules of life is concentrated enough Scaffolding o Interactions with molecules – sometimes these molecules never find each other o Plasma membranes can hold cells/proteins that need to find each other Selective barrier to diffusion o Maintains appropriate number of ions o Prevents toxins from diffusing in o Selectively permeable Active transport o Proteins for active transport & ions Signaling o Cell has to maintain a certain network of proteins in the plasma membrane o These signals come in the form of molecules o Proteins/peptides/neurotransmitters – none of these can diffuse in plasma membrane o If cell needs to respond, we need to communicate this signal from outside the cell inside the cell Intercellular junctions o Proteins – cell adhesins and integrins hold cells together o Important for multicellular organisms o “gap junctions” (with or without signaling) – useful in heart cells Energy/Metabolism o Membranes contain important proteins for aerobic metabolism and photosynthesis in the case of plants o These proteins are concentrated and held together in these membranes o Talking about inner mitochondrial or chloroplast membrane Electrical transduction o Electrical communication is possible due to plasma membrane and selectively of membrane for ions ▯ ▯ Membrane Structure Bilayer – train track appearance with two dark bands next to each other ▯ ▯ Fatty acids & membrane fluidity Saturated – low in fluidity, high Tm Unsaturated – high in fluidity, low in Tm What we see when we incorporate these into phospholipids in membranes Changing fatty acids – ways that organisms adapt to temperature change ▯ ▯ Cholesterol: membrane antifreeze Large and unusual lipid that’s comproised of lots of carbohydrates Non fatty acid derived lipid Found in membranes Cholesterol by itself has a high Tm, low fluidity Different effect with phospholipid due to antifreeze If you have a membrane at a very high temperature and could potentially melt apart – cholesterol fills in the gaps and makes sure holes don’t appear in membrane and increases van der walls Buffers membrane from very high and very low temperatures Works effectively when it’s at 25% membrane ▯ ▯ Estimated % content of different biological membranes RBC: 50/50 lipid and proteins Myelin: part of nervous systems – not neurons – wrap the axon with lots of membranes serving as an insulin which promotes conductivity – reflected in lipid and protein content Mitochondria/chloroplast: has more proteins – in the business of metabolism ▯ ▯ Membrane structure & proteins Hypothetical model of plasma membrane Lots of proteins and cholesterol There are proteins that go into the fatty acid tails – non polar AA – hydrophobic – integral membrane proteins – span through membrane or insert through parts of membrane Peripheral membrane proteins: sit on membrane and stay on membrane & don’t integrate in layer of membrane Sugars from glycosylation: surfaces exposed to outside of cell – analogous to disulfide bonds o Takes place in golgi complex o These proteins were made in RER ▯ ▯ Fluid mosaic model Membrane amphipathy – phospholipids are amphipathic – interior is hydrophobic and exterior is polar Asymmetric – integral proteins – some proteins inserted on the inside not inserted on the outside – lipids aren’t randomly incorporated into the membrane Fluidity ▯ ▯ Measuring membrane fluidity: (FRAP) Illustrates how proteins might move in the membranes – fluorescent covered proteins Lipids that are in that spot never recover Able to plot the rate of recovery ▯ ▯ Incomplete recovery during FRAP Some cells in some cases showed a very low membrane fluidity – unpredictable Initially steep curve (fluid) – but never got complete recovery ever Little patches of bleached area – remained unfluorescent forever – little holes LIPID RAFTS Lipid Rafts Low fluidity – anchored in place within the membrane – more saturated phospholipids and phospholipids with longer chains Large amounts of cholesterol – too much can increase Tm and decrease fluidity Certain proteins anchored here – integral proteins ▯ ▯ Plasma Membrane permeability Osmosis in RBCs Cells shrink when places in hypertonic solution ▯ ▯ Cells swell or shrink due to osmosis Hypertonic concentration – water concentration is the same on both sides Entropy wants to equalize concentration Membrane isn’t permeable to ions Water flows from inside to outside in an effort to dilute out the solute in order to equalize the concentration Result: lose water and die Determine if ions are the only things that the membrane isn’t permeable too ▯ ▯ Plasma membrane is selectively permeable ▯ ▯ Summer of membrane permeability High to low permeability from top to bottom O, C, N – gases are permeable ▯ Overview Review membrane selective permeability Transmembrane transport o Simple diffusion o Facilitated diffusion o Active transport Summary of Membrane Permeability Larger uncharged polar molecules – amino acids, glucose, nucleotides – too big to cross membrane Ions – least likely to get through the membranes because they’re charged, they’re so polar they can never penetrate the hydrophobic layer Small uncharged polar molecules – water, glycerol, ethanol – ethanol is somewhat rather quick because it’s hydrophobic, water diffuses very slowly – goes through aquaporins – only true during certain conditions and in certain cells where the rate of diffusion can be increased Small hydrophobic molecules – O2, CO2, N2, benzene – as long as they’re not charged they can get through Large hydrophobic molecules are a special category – CHOLESTEROL – the membrane is also permeable to large hydrophobic molecules, but because they’re so hydrophobic they tend to stay embedded in the membrane unless bound to a “carrier” protein ▯ ▯ Membrane properties and permeability Protocells: artificial protocells were able to absorb nucleotides – passed through cell membrane – in the case of the protocells, the membranes were not made of phospholipids but were made/derived from highly fatty acids o so a smaller head group COOH (acidic) with a single tail – form lipid bilayers – very permeable – as long as its not too big or not too charged Modern cells: are made up of phospholipids with a much more polar head group (Phosphate is more polar than carboxylate) – large, very polar, squashed together, longer DOUBLE tails that are hydrophobic = NOT SO PERMEABLE o This is why we see the selective permeable membranes today – no entry of large polar molecules ▯ ▯ Things that increase fluidity also increase permeability The properties that make membranes more fluid also make them more permeable Image shows a membrane containing phospholipids made up of entirely fatty acids – lots of van der waals interactions – very solid, not very fluid = not so permeable On the other hand, if you incorporate unsaturated fatty acids into the lipids you have a lot more bent chains = more fluid = more permeable One of the reasons that organisms do adapt is by changing the composition of their fatty acids at different temperatures – to maintain proper fluidity and proper selective permeability Membranes made entirely from unsaturated phospholipids are still less permeable than those made from fatty acids ▯ ▯ Transmembrane Transport Simple diffusion: diffusion of molecules across membrane down their concentration gradient o Not active – simply just what can come through the membrane because of entropy – high concentration to low concentration – NOT THE REVERSE Facilitated diffusion: diffusion down concentration gradient through protein transporter o also involves high concentration to low Active Transport: up their concentration gradient using active transport proteins o Low to high – entropically unfavorable which is why it requires energy ▯ ▯ Gas exchange in lungs is simple diffusion O2 and CO2 diffuse down their concentration gradients What happens continuously especially in aerobic organisms and mammals is that we need to absorb oxygen in order to maintain efficient metabolism We absorb oxygen in the lungs because capillaries that flow through our alveoli (air sacs) allow for very close contact between the cells of the blood vessels and the cells of the alveoli 2 layers thick – oxygen can diffuse from high concentration (breathing O2 in) to low concentration and eventually to the blood stream and into the red blood cells – so it’s very quickly diffusing down its gradient when the RBCs go they send oxygen to other parts of the body – meanwhile you’re body is constantly producing CO2 ends up back in the blood stream and ends up getting sent back to the lungs – so it’s coming from the tissues has a higher concentration than it does outside – flows through the membranes through simple diffusion – aka exhaling larger concentrations of CO2 than inhale ▯ ▯ Facilitated Diffusion Molecules diffuses through a carrier protein down its concentration gradient – 2 types of facilitated diffusion There are large polar molecules that can’t diffuse through the membrane – uses carrier proteins Glucose can’t diffuse through the membrane – if concentration high in the blood stream and low inside of the cell – glucose goes inside using glucose carrier protein – look like pores but they’re not open, always closed In a resting state these proteins are open to the outside of the cell (not open completely) and they have a glucose binding site where glucose binds – which induces a conformational change in the protein IMPORTANT PRINCIPLE Binding of a molecule induces a conformational change that allows for glucose to be released inside of the cell Glucose is an example of carrier proteins: slower – specialized carriers that provide a pathway for larger molecules – specific Another type is ion channels: faster – “pores that open to allow ions to pass through – specific or general; usually open only in response to a signal e.g. hormone or voltage change o some ion channels have open selectively – allowing for cations or only doubly charged cations o some ion channels are very specific and only allow an ion of a specific size shape and charge through Example: just sodium ions ▯ ▯ Carrier protein – glucose transporter 1. Extracellular glucose binds to glucose transporter GluT1 2. Conformation change -> GluT1 opens to interior of cell 3. Glucose dissociates into cytoplasm 4. GluT1 conformation reverts -> open to outside Bidirectional: if [glucose] is very low in bloodstream, glucose can diffuse out through GluT1 ▯ ▯ Kinetics of Diffusion Ion channels and carrier proteins differ mainly only through kinetics Rate (v) vs. solute concentration The rate of simple diffusion depends on the type of molecule Facilitated diffusion is much faster Ion channels tend to be faster than facilitated diffusion – allowing for things like electrical impulses ▯ ▯ Ion concentration gradients ion concentrations are critical for electrical impusles important ions that regulate cellular activity ▯ ▯ Active transport Molecule transported up its concentration gradient Requires energy! Those concentration gradients maintained through active transport (Na/K) This requires a protein – pretty much always involves things that can’t permeate through the cell ▯ ▯ Classes of Active transport 1. Different sources of energy: i. Direct – energy from ATP hydrolysis – convert chemical energy into mechanical energy – gets converted into potential energy ii. Indirect – energy from diffusion of another molecule down its concentration gradient – uses the energy stored in the concentration gradient of another molecule to transport something else up its concentration gradient – this involves diffusion of one molecule down its gradient – the PE is harnessed as mechanical energy to store another molecule at a bigger concentration gradient 1. Is called Indirect Active Transport – because without ATP, this molecule whose diffusion is down its concentration gradient – requires ATP for that initial formation of concentration gradient 2. Transport with or without other molecules i. Uniport - one molecule ii. Symport – two or more molecules in the same direction – one molecule is diffusing down its concentration gradient and the energy is being used to move the other molecule up its concentration gradient iii. Antiport - two molecules in the opposite directions – again one is diffusing down its concentration gradient and energy used to transport other molecule up its concentration gradient 3. Sodium Potassium pump – HIGH outside for Na HIGH inside for K – need to know ▯ ▯ Direct Active Transport: Na/K ATPase Main pump that transport sodium inside cell and potassium outside cell Based on the name – involves Na and K and also is active transport because it involves ATPase (enzyme that catalyzes the hydrolysis of ATP) Another name: Na/K Antiporter or Na/K Antiport ATPase Na/K pump consumes up to a third or more of all the ATP a cell uses in its lifetime – without it we die Pumps sodium out of the cell and pumps potassium into the cell it hydrolyzes ATP and uses the energy from this to do the pumping 3 Na ions pumped out 2 K ions pumped in sodium gradient underlies electrical transport in case of neurons and muscles (so we’re losing Na all the time and its coming back into the cell); also underlies almost all indirect active transport mechanisms – so we need to get as much Na out as possible, K is secondary ▯ ▯ Summary of Na/K ATPase Direct active transport: energy from ATP hydrolysis used to transport Na and K up their concentration gradients Antiport: Na and K transported in opposite directions Responsible for maintaining K and Na concentration gradients used for nerve conduction and many other things ▯ ▯ How does glucose get into cells when blood [glucose] is very low? Cells are incredibly efficient in taking up glucose even when there’s a very low concentration of glucose – the concentration of glucose may be low but they’re even lower in the bloodstream Indirect active transport: Na/glucose symporter it transports Na & glucose and both are transported in the same direction this uses the energy released when Na goes down its concentration gradient – energy is harnessed (mechanical energy) – brings glucose into cells even when glucose concentration in the bloodstream is very high – glucose coming up its concentration gradient indirect because this pump can’t work without ATP ▯ ▯ Summary of Na/glucose symporter Indirect active transport: energy from diffusion of Na down its concentration gradient used to transport glucose up its concentration gradient Symport: Na and glucose co transport in the same direction The Na gradient is the most common driver of indirect active transport Transport mechanism depends on type of molecule and direction of transport relative to concentration gradient Depends on the molecule and depends if you’re going from high to low diffusion or low to high (active transport) Goes down concentration gradient (releases energy) – simple diffusion - Small hydrophobic molecules Up concentration gradient (requires energy) – active transport – small uncharged polar molecules Goes down concentration gradient (releases energy) – facilitated diffusion - larger and ions Up concentration gradient (requires energy) – active transport – ions ▯ ▯ Summary Simple diffusion: down concentration gradient, does not require carrier protein Facilitated diffusion: down concentration gradient, requires carrier protein o Channels – nAChR o Facilitated diffusion, transport proteins – GluT1 Active transport: up concentration gradient, requires carrier protein o Direct active transport – Na/K ATPase o Indirect active transport – Na/glucose symporter ▯ Overview Review transport Signaling modes Types of cell responses o Ion channels o Production of second messengers ▯ Transporters and the cell ATP binding and hydrolysis results in conformational changes of the protein Na/K Pump – Chemical ATP converted to mechanical energy/movement (KE) which then, as it bounces back to its resting orientation is translated to PE (potential energy) stored in the gradients of K and Na Dozens of other transporters in the cell o Nutrient transporters Na/glucose transporter Lysosome – important for breaking down macromolecules to monomers – those monomers have to be used by the cell – one of the ways they do so is by transporting the contents out of the lysosome once its done digesting – contents can’t just diffuse out of the membrane, which is very similar to the plasma membrane o Ion transporters Na/K pump Ca+ - Calcium must maintain an extremely low concentration in the cytoplasm – in order to establish that we have to use some form of active transport to get the calcium outside of the cytoplasm – calcium stored in smooth ER; there are calcium pumps that pump Ca into SER also Ca pumps in plasma membrane that help pump Ca out of the cell just an effort to maintain low [Ca] in cytoplasm o Proton pumps H+ – In addition to producing CO2, metabolism acidifies the cell – so anytime your cells are alive its undergoing metabolism and producing CO2 (aerobic) no matter what it’s also producing protons, which eventually acidify the cell – cells don’t like acid so it needs to pump the protons out of the cell – pumps are on membrane (these can be active transport or facilitated diffusion depending on the contents) Lysosome – in addition the lysosome doesn’t function to digests things unless it’s acidic, it becomes acidic through the pumping of protons into the lysosome when it fuses with an endosome (active transporters – making lysosome more acidic than the cytoplasm) o Ligand-gated ion channels Ion channels are facilitated diffusion mediators – so when they open they’re not pumping ions they’re just allowing ions to flow down their concentration gradients Perfect example: action potential involving Na+ There’s lots of different types of ion channels, some are mediated by binding of protein or small molecule TO that ion channel itself aka some ion channels are actually receptors for signaling molecules many of these include Na+ and also Ca+ Na+ –action potential transduction of a neuron is mediated through the openings of an ion channels – the first ion channel that opens is the Na+ ion channel that causes Na+ to flow rapidly down its gradient INTO the cell which triggers depolarization and initiates the transduction of the electrical impulse Ca++ – signals from outside of the cell or in a neuron – the electrical impulse coming down – triggers the opening of Ca channels – those Ca channels are in the plasma membrane but in many cases are on the SER that allow Ca to diffuse out of the cytoplasm which triggers exocytosis ▯ ▯ Cell Signaling Sometimes called signal transduction is how information from outside of the cell gets transduced to a behavioral response Cells must be able to respond to signals from both outside and inside the organism AND their response should BENEFIT the organism or the population ▯ ▯ The signal itself ( aka ligand ) is produced by a “sender” and received by a “recipient”. Signaling modes are defined by distance between sender and recipient. Signals come in the form of substances – chemicals derived from AA, small peptides, large proteins, lipids, gases Signals are called LIGANDS Signal or ligand is usually/often secreted by sender cell and often/usually diffuses to recipient cell Distance between sender and recipient cells are categorized – mechanisms underlies the distances o Autocrine o Juxtacrine o Paracrine o Endocrine/hormonal Autocrine Sender and recipient are the SAME CELL or GROUP OF CELLS Single signaling cell receives a weak autocrine signal In a group of identical signaling cells, each cell receives a strong autocrine signal – reflects a homogenous population of cells Cancer cells famously secrete signals that promote their own growth that bind to their own receptors to enhance their growth Advantages: very specific responding population, fast Disadvantages: limited utility, very short range ▯ ▯ Juxtacrine Signaling molecule is attached to sender cell or is part of ECM, does not diffuse Contact dependent Involved two different cells – membrane bound signaling so it’s not actually secreted – binds to receptor on immediately adjacent cell(s) It can also involve a signaling molecule that’s secreted but sticks very tightly to the ECM matrix and doesn’t diffuse away at all – lack of diffusion means only can send info to immediately adjacent cells Advantages: precise & immediate Disadvantages: adjacent cells only; very short range Paracrine Signaling molecule can diffuse one or several cell diameters away to nearby recipient cells The most common mechanism during organism development and doesn’t involve secretion of a signal but the protein or small molecule can’t diffuse very far but one or a few diameters away Signaling cell – diffuses to a slightly larger population of cells Advantages: communication with more cells than juxtacrine – moderately fast Disadvantages: not as precise as juxtacrine – still fairly short range ▯ ▯ Endocrine Signaling molecule (hormone) is secreted into the bloodstream allowing it to diffuse throughout the body Advantages: coordinates behavior of all tissues in the body Disadvantages: imprecise, slow ▯ ▯ Types of cell responses Channel opening Production of second messenger Direct activation of receptor enzymatic activity Steroid hormones: gene transcription ▯ ▯ Ligand gated ion channel (channel opening) – nicotinic acetylcholine receptor Classic example: neuromuscular junctions where the neurons signal to the muscles to contract Signal coming from neuron comes in the form of a neurotransmitter In this case – the neurotransmitter is acetylcholine (ACh), a small molecule Neuron secrets ACh into the synapse and it binds to a channel – the channel is the receptor in the membrane – when it binds to the channel, it induces a conformational change and it opens up This particular channel is specific for Na+ (high concentration outside the cell low concentration inside the cell) where the Na+ ion can now diffuse down that channel into the muscle cell which causes the cell to depolarize This triggers downstream events that trigger Ca+ release which triggers muscle contractions o Summary Neuron releases ACh (neurotransmitter) – binds to nACh receptor on muscle Na+ diffuses down concentration gradient into cytoplasm Na+ triggers downstream events that lead to muscle contraction ▯ ▯ Adrenal medulla secretes epinephrine in response to fearful stimuli (production of 2 ndmessenger) Adrenal gland sits on top of kidneys Some of the cells in adrenal medulla (interior of adrenal gland) secretes epinephrine (adrenaline – a hormone) into the bloodstream and circulates throughout the body – this is what mediates all the feelings you have when you’re terrified/stressed – fight or flight response Different cells respond to this in different ways o Liver cells respond to epinephrine by activating the enzyme glycogen phosphorylase liver is an important source for glycogen (glucose polymer, one of the primary storage forms of glucose) major response is to break down glycogen what happens is glycogen phosphorylase (enzyme) phosphorylates glycogen – triggers the output to glucose monomers – glucose gets secreted back into the bloodstream where it can go to your muscles and brain which they can use to produce ATP – use this energy for whatever “fear” causes you to do ▯ What happens in between? o Epinephrine is a very small polar molecule – can’t diffuse through cell membranes so there needs to be a mechanism as to how it gets isto the cell o Epinephrine – 1 messenger in pathway What’s the 2 nd messenger? o Centrifuge to separate cytoplasm and membranes o Add epinephrine to membranes + small molecules (but no soluble proteins) o Centrifuge membranes and keep supernatant o Add supernatant (“activated” cytoplasm) to “inactivated” cytoplasm (inactive glycogen phosphorylase) o Assay glycogen phosphorylase activity o Tells us something is produced when epinephrine binds to the membrane – it’s soluble What’s in the activated cytoplasm from step 3 that causes glycogen phosphorylase to become active? o cAMP – cyclic AMP (amp is adenosine monophosphate) gets made from ATP o ATP – 3 phosphates , there’s an enzyme that causes the removal of 2 phosphate groups from ATP and conversion of one of the O that’s left on AMP gets added to the 3’ carbon of the ribose ▯ ▯ Second Messengers Defined Soluble molecule Not present in absence of 1 messenger st Producted when 1 messenger (signal or ligand) binds to receptor on cell membrane Activates cellular response ▯ ▯ Summary Different modes of signaling based on distance between cells Epinephrine signaling leads to glycogen ndeakdown in liver cells Receptor activation can produce 2 messengers cAMP is 2 ndmessenger for epinephrine signaling in liver ▯ Overview G protein coupled receptors (GPCRs) – epinephrine GPCR signal transduction o Amplification o Adaptation o Turning off the response Receptor tyrosine kinases and Ras Hormone receptors ▯ ▯ Epinephrine binds to a G-protein coupled receptor Every GPCR has 7 transmembrane domains aka the 7 transmembrane domain receptor family – NEED TO KNOW parts of the protein are outside/inside the cell st part of the extracellular domain is responsible for binding to the 1 messenger – the signaling molecule/hormone/neurotransmitter/peptide – LIGAND for the receptor “epinephrine” epinephrine binds to the extracellular domain because epinephrine can’t transfer through the membrane – too polar GPCRs bind to htereotrimeric Gproteins st Unstimulated Ga bstds to GDP as long as there is no 1 messenger present – the 1 messenger binding is what triggers a change in the binding of the alpha subunit to GDP Epinephrine binding leads to activation of G protein Epinephrine binds to receptor Receptor conformational change Ga conformational change GDP falls off Ga GTP binds to Ga o THIS IS NOT A CHEMICAL reaction – this is an exchange reaction ▯ ▯ Ga activates enzyme Adenylate Cyclase Ga binds to adenylate cyclase Adenylate cyclase undergoes conformational change as soon as the alpha subunit binds to it (leads to increase in its activity) Adenylate cyclase catalyzes ATP -> cAMP + PPi nd cAMP our 2 messenger ▯ ▯ How does cAMP activate glycogen phosphorylase? Indirectly activates – so what directly activates this process? ▯ ▯ Glycogen phosphorylase itself is activated by phosphorylation 1. Glycogen phosphorylase itself gets phosphorylated in response to epinephrine (followed by adding radioactively labeled phosphate) 2. Phosphorylation requires ATP 3. The phosphorylated form of Glycogen phosphorylase is active Kinases catalyze ATP dependent phosphorylation You have the inactive enzyme (in this case glycogen phosphorylase) – it’s being phosphorylated by an addition of a phosphate from ATP on to the site on cell enzyme – this results in activation The enzymes that catalyze this process is called protein kinases Covalent attachment – it’s reversible, can only be altered by another enzyme Phosphatases catalyze dephosphorylation – they remove phosphate groups from phosphorylated proteins leaving it to float free Phosphorylation reversibly alters conformation and is the most common way to regulate protein activity ▯ ▯ Protein phosphorylation Any amino acid side chain containing an OH group can be phosphorylated When it’s phosphorylated by kinase, it uses a phosphate group from ATP Kinase is a type of enzyme that catalyzes conversion – moving a phosphate group from ATP onto that amino acid side chain leaving ADP The consequence of this is you go from this tiny polar group a gigantic highly charged group – this has major consequences to protein structure (tertiary structure) – can cause steric changes, chemical changes because this is now repelling any other negatively charged side chain or maybe becoming attracting to a positively charged side chain ▯ ▯ cAMP binds to regulatory subunits of protein kinase A how do we get from cAMP to glycogen phosphorylase? enzyme protein kinase A (PKA) is a heterotetramer with 2 catalytic and 2 regulatory subunits regulatory subunits inhibit catalytic subunits – meaning that when they’re bound to catalytic subunits they’re off cAMP binds to regulatory subunits at those binding sites when this happens, the regulatory subunits undergo a conformational change which kicks off the catalytic subunits – cAMP binding causes regulatory subunits o release from catalytic subunits o notice that that release there’s a cleft to where a substrate will bind catalytic subunits ACTIVE phosphorylation of other proteins ▯ ▯ What does PKA phosphorylate and how does this lead to activation of glycogen phosphorylase? PKA catalyzes the phosphorylation of phosphorylation kinase – becomes active It’s not phosphorylation kinase that catalyzes the phosphorylation of glycogen phosphorylase Name of the enzyme phosphorylase kinase is to refer to the fact that it is a kinase that catalyzes the phosphorylation of phosphorylase (aka glycogen phosphorylase) So now glycogen phosphorylase – now phosphorylated – is now active Having this pathway is very important in the endocrine system ▯ ▯ This “Enzyme cascade” amplifies the signal When you have multiple enzymes in a pathway – Enzyme Cascade A given cell can respond strongly to a single molecule of epinephrine o A single molecule of epinephrine binds to a single epinephrine receptor – which activates a single G protein – G protein activates a single protein adenylate cyclase, the enzyme o Enzymes, when they’re on, can catalyze many rounds of their reactions , a typical response to a single molecule of epinephrine – adenylate cyclase catalyzes conversion of 20 molecules of ATP to 20 molecules of cAMP – 1 epi = 20 cAMP o cAMP activates protein kinase A (PKA) – no amplification here since it’s not a chemical or enzyme catalase reaction o active PKA can catalyze phosphorylation of many molecules of phosphorylate kinase Signal amplification they each catalyze 5 molecules of glycogen phosphorylase – we now have 100 active phosphorylase kinase 1 single molecule of epinephrine – 10,000 molecules of glucose ▯ ▯ Desensitization Cells often desensitize to ligand with continuous exposure. Receptor mediated endocytosis is just one mechanism for desensitization. Cellular consequences of receptor mediated endocytosis If the levels of epinephrine persist for too long, it could kill the cell With receptor mediated endocytosis, some of these receptors ligand complexes will get endocytosed mainly inside of the cell as long as epinephrine levels are high You can shut it down completely ▯ ▯ Turning off the response – 3 ways One of the ways is seen through activation of phosphatases – aka dephosphorylation There are protein phosphatases in the cell that are activated during signal transduction with a delay – catalyzes the dephosphorylation – turns it off However, even if you turn off those enzymes, if there’s cAMP around it will turn everything back on again If G protein is still active it will turn on adenylate cyclase back on again and produce more cAMP and so on Need to actively turn everything off o Mechanism for G protein: activation of GTP hydrolysis Alpha subunit binds to GDP, receptor binding catalyzes this exchange reaction, GTP now activates adenylate cyclase Ga has intrinsic enzymatic activity just like actin/tubulin G protein catalyzes the hydrolysis of GTP & release of organic phosphate – now is GDP and inactive o Mechanism for cAMP: cAMP hydrolysis cAMP gets converted to AMP phosphodiesterase responsible for this process ▯ ▯ Direct activation of receptor enzymatic activity ▯ ▯ Receptor Tyrosine Kinases (RTKs) Classical example – growth factors – involves receptor dimerization The GFs (small proteins) bind to their receptor – symmetric, dimers – as dimers they bring together two different GF receptors called RTKs (enzyme) Receptors catalyze autophosphorylation – requires dimerization to happen Now have a phosphorylated intracellular domain that interacts with G protein called RAS (must know) o Ras is not heterotrimeric it’s a monomertrimeric o GTP GDP exchange – GTP ras causes an enzyme cascade aka SIGNAL amplication Activation of kinase cascade Gene transcription Long term changes including proliferation ▯ ▯ Ras and Cancer Ras is a mutated gene found in cancer Mutation inactives or decrease GTPas activity ->uncontrolled proliferation Discovered as cause of rat sarcoma Monomeric G protein – aka small GTPase Steroid hormone receptors Steroids are lipids – cortisol – lipid soluble molecule, must transport itself through the bloodstream bound to some type of protein carrier o Because it’s a lipid it does transfer through the plasma membrane without binding to a plasma binding receptor o Enters the cell by binding directly to it’s receptor o Carrier picks up steroid right in plasma membrane – receptor moves into the nucleus binding to DNA Usually have intracellular receptors Regulate gene transcription through direct DNA binding Can either stimulate or suppress gene transcription Gene transcription = slow but long lasting ▯ Cortisol mediates our stress response – long term, more permanent responses Epinephrine mediates our responses to fear ▯ Overview Energy conversion Laws of thermodynamics Free energy Activation energy Energy may be converted from one form to another ATP hydrolysis: o a lot of the reasons that ATP can provide energy is bond energy – ATP has a high energy bond and it stores energy in a way that’s like PE – holding energy, holding it against its will o when bond gets broken, it’s a down hill reaction o energy gets converted to/released as KE – energy goes into its surroundings in the cell – mostly water – it increases their KE o what happens when water’s KE increases? HEAT – it gets warmer o bond energy -> heat Indirect active transport: o Potential energy (concentration gradient) -> ME/WORK -> Potential energy Flaming gummy bear o Potential energy in the bonds -> Heat + entropy increase ▯ ▯ Basic thermodynamics for biologists st 1 Law of Thermodynamics: the energy of a closed system is conserved o energy can neither be created or destroyed o but energy can be converted between different forms nd 2 Law of Thermodynamics: the entropy (disorder) of a closed system tends to increase o anytime energy is interconverted, entropy must increase ▯ ▯ What does this mean for us? In the absence of added energy, entropy always increases Increasing entropy -> loss of cellular integrity -> death ▯ ▯ Gibbs free energy (G) is the total energy of the system ΔG (change in free energy) = G productsG reactants If ΔG is < 0, the total energy of the system decreases and the reaction is exergonic or spontaneous – FAVORABLE – sends energy out If ΔG is > 0, the total energy of the system increases and the reaction is endergonic or non spontaneous – requires energy – UNFAVORABLE ▯ Exergonic reaction o If it’s downhill, ΔG < 0 Endergonic reaction o If it’s uphill, ΔG > 0 ▯ ▯ Gibbs free energy (continued) ΔG = ΔH – TΔS o encompasses everything that contributes to the system o ΔH is change in enthalpy – chemical bond energy o ΔS is change in entropy o T is temperature o in a closed system, ΔG = 0, so ΔH and T ΔS are balanced during energy conversions o can measure ΔG indirectly ▯ ▯ Calculating ΔG: A + B < = > C + D Vast majority of chemical reactions in cells are in equilibrium 1. Start with 1M (mol/L) of all reactants and products 2. Let reaction reach equilibrium 3. Measure [reactants] and [products] 4. Calculate equilibrium constant K eq i. K eq= [C][D]/[A][B] If the reaction goes to the right, the reaction is written as exrgonic, and Keq > 1 If the reaction goes to the left, the reaction is written as endergonic, and Keq < 1 ▯ ΔG = -RT ln Keq ( or -2.303 RT log Keq) o If log Keq = 1 -> 0 o If Keq > 1: ΔG < 0 o If Keq < 1: ΔG > 0 ▯ Gibbs free energy and standard conditions * (used to compare relative ΔG’s for different reactions) ΔG’ = -RTlnKeq’ o T = 25 C o P = 1 atm o All starting concentrations = 1M o pH = 7 ▯ ▯ ATP ATP fuels lots of other chemical reactions – this is due to the PE stored in the bonds – aka Phosphodiester linkages: high energy bonds They are high energy bonds primarily because they are phosphate groups linked together ▯ ▯ ATP hydrolysis is highly exergonic Involves converting ATP to ADP ΔG’ = 7.3kcal/mol Can also involve ADP to AMP or ATP to AMP ATP hydrolysis results in a relief of the phosphate group getting away from these other negative repellent charges and formation of ADP and inorganic phosphate Highly favorable So how do we use that hydrolysis to fuel other reactions? ▯ ▯ Energy coupling Physical coupling of two reactions together, particularly when it involves one exergonic reaction and one endergonic reaction ATP hydrolysis doesn’t result in organic phosphate, but actually that phosphate group gets moved over to one of the reactants, directly physically and covalently onto A o Creation of a new high energy bond by phosphorylation of reactant o Dephosphorylation of A is exergonic o ▯ Overview does spontaneous really mean spontaneous activation energy catalysts enzymes o induced fit o mechanisms o factors that affect activity ▯ ▯ Are all spontaneous reactions really spontaneous? ΔG << 0 Spontaneous reactions are rarely truly spontaneous – need a trigger ▯ ▯ Why not? The activation energy reflects that fact that the reactants actually have to undergo a transformation (physical and/or chemical) before they can become products And that physical transformation – intermediate state – has a higher free energy than the reactants Activation energy Ea: energy needed to bring reactants to transition state And only then is when the forward reaction is spontaneous Catalyst: something that alters the transition state of a reaction, which lowers its activation energy -> increased reaction rate ▯ ▯ Properties of a catalyst Lowers the activation energy by altering the path of a reaction, i.e. changes the intermediate (e.g. A-P) Does not alter reactants or products Does not alter ΔG of reaction Is not itself altered by reaction Enzymes are biological catalysts Most enzymes are proteins ( a few are RNAs: ribozymes) A substrate is a reactant that binds to the enzyme active site Enzyme active site conformation and chemistry make them specific for one or a very small number of substrates ▯ ▯ Induced fit Binding of substrate to active site triggers conformational change in enzyme -> activity o “baseball glove” o isn’t the chemical reaction o only in response to this does the chemical reaction take place ▯ ▯ Enzyme Mechanisms Proximity and orientation o Binding sites for two substrates may be near each other and oriented so that they can interact o Reducing entropy Strain o Important in catabolism o Because of induced fit, enzyme may impart force on substrate, straining chemical bonds and increasing likelihood of breakage Chemistry o Most important o Enzymes may interact chemically with substrate, making conversion to product more favorable o Usually the side chains of AAs predict the ability to bind to substrates and the side chains in AAs must be complementary to whatever substrate the chemistry is ▯ ▯ Factors that affect activity Enzymes are sensitive to temperature o Heat denatures proteins – tertiary structure – activity is more sensitive Enzymes are sensitive to pH o same as heat o pepsin: extracellular protease in stomach, optimal pH is 2 o chymotrypsin: extracellular protease in duodenum optimal pH is a little over 7 o arginase: catalyzes final step of the breakdown of ammonia into urea in liver cells (NH3), optimal pH is 9.5 Enzymes are sensitive to changes in 1 structure o Sir Archibald garrod in 1902: mutations in enzyme homogentisic aicd 1,2-dioxygenase (HGD) cause alkaptonuria (black urine disease) ▯ ▯ HGD catalyzes one reaction in the pathway to break down phenylalanine Phenylalanine is an AA and build up of this is toxic HGD catalyze one reaction in the breakdown of phenylalanine and the mutation inactivates it When you inactivate an enzyme that catalyzes a reaction, the amount of the compound is going to build up Loss of HGD leads to accumulation of HGS which makes urine black ▯ ▯ HGD enzyme and mutations Disease is caused by single AA changes Enzymes are extremely sensitive to anything that directly or indirectly alters the conformation of the active site ▯ Overview Mechanisms of regulation o competitive inhibition & feedback inhibition o allosteric regulation & feedback inhibition o covalent modification o zymogen activation principles of regulation ▯ ▯ Regulation of enzymes ensures that: Enough product is made Only enough product is made Reactants are available for other processes toxic compounds don’t accumulate ▯ ▯ Mechanisms of regulation Cells are regulated by these mechanisms or more Types of regulation o Competitive inhibition: - only, usually reversible o Allosteric regulation: +/-, reversible can be either activation or inhibition – more common o Covalent modification: +/-, usually reversible phosphorylation of enzymes o Zymogen activation: + only, irreversible don’t confuse with ribosymes ▯ ▯ Competitive Inhibition Inhibitor binds at active site, preventing substrate binding – it “competes” for that active site Not extremely common mechanism for cells themselves Critically important in the pharmaceutical industry Chemical weapons and pesticides are competitive inhibitors ▯ Many chemical weapons and insecticides: irreversible competitive inhibition of Acetylcholinesterase (AChE) Covalent attachment to a residue in active site Extremely toxic There are enzymes in the synapse that break down ACh to prevent you from constantly contracting – allows you to have a strong muscle contraction but relax afterwards because AChE breaks down any ACh in the synapse Because these reactions are irreversible – it’s toxic ▯ ▯ Alloesteric (“other shape”) regulation Activator/inhibitor binds to any location other than the active site Leads to conformational change of active site Can be activating or inhibitory (allosteric inhibition often called non competitive inhibition) ▯ ▯ Allosteric activation Allosteric activator binds to allosteric site resulting in a conformational change in the active site – allows substrate binding. This means that enzyme is only active in presence of activator Allosteric inhibitor binds somewhere other than active site, causing a conformational change in active site – prevents substrate binding ▯ Allosteric inhibition: isoleucine inhibits one of the first enzymes in the pathway for its own synthesis #1 way in which metabolic pathways are regulated what cells have evolved to do is calibrate isoleucine levels, depending on the needs of the cell when isoleucine lstels reach a certain point, isoleucine itself binds to one of the 1 enzyme
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