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BIO 201 Cell Biology with Todd Hennessey, Second Week of Notes

by: ChiWai Fan

BIO 201 Cell Biology with Todd Hennessey, Second Week of Notes BIO 201

Marketplace > University at Buffalo > Biology > BIO 201 > BIO 201 Cell Biology with Todd Hennessey Second Week of Notes
ChiWai Fan
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Notes from the second week's lectures. Includes professor's explanation of material as well as the examples.
Class Notes
BIO 201 Cell Biology
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This 29 page Class Notes was uploaded by ChiWai Fan on Saturday February 6, 2016. The Class Notes belongs to BIO 201 at University at Buffalo taught by TODD HENNESSEY in Spring2015. Since its upload, it has received 103 views. For similar materials see CELL BIOLOGY in Biology at University at Buffalo.


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Date Created: 02/06/16
Cell Biology on Feb 1, 3, 5 with Todd Hennessey The four main types of organic macromolecules: 1. Proteins 2. Carbohydrates 3. Lipids 4. Nucleic acids Polymerization- lipids are not polymers Polymerize [CONDENSATION] water is removed so the covalent bond form between monomers-- an monomer and an monomer get together will become a dimer 1. Proteins are polymers of amino acids 2. Polycaccharides are polymers of carbohydrates (sugars)—put together sugars as polymers 3. DNA and RNA are polymers of nucleic acids Depolymerize [HYDROLYSIS] –add water so the covalent bond between monomers is broken Examples of enzymes: (generally ends with –ase) 1. Proteases 2. Glycosidases 3. RNAse, DNAse Terminology  Monomer: One subunit  Dimer: Two subunits  Trimer: Three subunits  Tetramer: Four subunits  Polymer: More than two subunits PROTEINS: 1. Proteins are polymers of amino acids. 2. The amino acids differ in their side chains. 3. Free (unbound) amino acids all have an amino group and a carboxyl group. (amino on one side, carboxyl on the other when unbound) 4. The amino acids are covalently attached by peptide bonds between neighboring amino and carboxyl groups—(one type of covalent bond is called peptide bonds— especially in proteins) 5. The charge on the protein is dependent upon the pH Protein Structure Protein is a linear polymer of amino acid but it can fold back at itself to form certain structures Linear polymer  structure supported by hydrogen bonds folding stabilized by covalent and noncovalent bonds 1. Primary Structure(Linear polymer) (the amino sequence) asks: what is the order of the amino acid sequence? 2. Secondary Structure: supported by hydrogen bonds, fold the protein into its shape 3. Tertiary structure: structure stabilized by covalent and noncovalent bonds 4. Quaternary structure: Two or more proteins together Free amino acid R represents the side chain group. You can tell which amino acid it is if you know what R is. Can’t tell amino acid without knowing what R is. R determines which amino acid it is. At neutral pH (pH=7.0) the amino group is full positive (H3N+) and the carboxyl group (COO-) is full negative on a free amino acid An example of a protein: myoglobin—it has to be folded exactly this way to do its job! This is a linear polymer of amino acids, folded into it native conformation (3D shape). Each number is an amino acid. There are 153 amino acids in this protein. Conformation means its 3-D shape; the folding  Its structure determines its function. A change in conformation can inactivate this protein (mutations can be good, bad, or does not affect) We will group amino acids into 4 general groups, based on their side chains (R groups) A. Polar and fully charged at pH=7.0. These are hydrophilic—ionic bonds B. Polar but uncharged at pH=7.0. (Yes, it is possible to be polar without having a full charge). These are also hydrophilic—hydrogen bonds C. Nonpolar at pH=7.0. These are hydrophobic (but not lipids) not water- soluble D. Miscellaneous  It is important to know what group the amino acid goes into than memorizing the structure of each amino acid. This is to help us find out its functions. What does structure do to the function of the protein? GROUP A: Polar, charged amino acid side chains—full charges; ionic bonds  At pH=7.0, aspartate and glutamate are negative but lysine, arginine and histidine are positive  Water likes hydrophilic (charge compounds) put charged stuff on the outside exposed to water  Any amino acids in this group can do ionic bonds!  In general, charged amino acids on the outside of soluble proteins determine the overall charge (net charge) of the protein in solution and its solubility  Side chains determine what amino acid it is! (The boxed chains are side chains)  Having Charged amino acid on inside are helping to form and stabilize the conformation with ionic bonds What happens to the net charge on a protein if you change the pH? Net charge is overall charge; charge depends on pH It depends on what ionizable groups are exposed and what the pH is. Why is the pH important?  Deprotonate means take away a proton; high pH means low proton concentration in solution  If you want a polar proton, you should go to high pH then it will turn negative Amino acid side chains can have different charges at different pH because of ionization due to deprotonation and protonation Since low pH means high [H+], it is protonated (by adding acid) at low pH because there are more H+(more protons around to protonate) This means you got to know pH to know its charge!! GROUP B: Polar, uncharged amino acid side chains (can have partial charge and can undergo hydrogen bonding) Q. Will a protein with many polar, uncharged side chains be water soluble? Could be, but not always A. It is hard to predict. It depends upon such things as: 1. How many hydrophilic and hydrophobic side chains are exposed to the water? Why? Water solubility depends on relative hydrophobicity and hydrophillicity 2. The pH of the solution. Why? It determines which other side chains are ionized and relative hydrophobicity 3. What else is around for the protein to bind to? Why? It might be bound to something else, like other proteins or the membrane What’s the point?  A change in pH could affect the charge, conformation and function of a protein. It may not. It depends on: 1. How many amino acids in the Charged Polar group are present 2. Their location on the protein (exposed or hidden inside) 3. The direction and extent of the pH change 4. Other things we haven’t even mentioned GROUP C: Nonpolar amino acid side chains In general, nonpolar (hydrophobic) amino acid side chains can be seen in two places on proteins: A. Inside the protein (hidden away from water) B. On the outside of membrane proteins (facing the membrane lipids)—by hydrophobic aggregation Can a water-soluble protein have many nonpolar amino acids on the outside of it? Yes, but it all depends on the relative amount of hydrophobic and hydrophilic groups that are exposed to the water  Polar fully charged: likes ionic bonds but depends on pH  Polar uncharged: can’t do ionic bonds but can do partial hydrogen bonding  Nonpolar: GET OUT OF HERE. DON’T GET NEAR WATER GROUP D: Miscellaneous Cysteine side chains can form disulfide bridges with other cysteines. These are covalent bonds. (Disulfide bond is not peptide bond; these are two covalent bonds we learned so far) What are the most important words on this slide? Feb 3, 2016 Some ways to express concentrations -3  1.0mM = 1.0 millimolar = 10 molar = 0.001M  1.0μM = 1.0 micromolar = 10 molar6 -9  1.0nM = 1.0 nanomolar = 10 molar  1,000uM = 10 x 10 M = 10 M = 1mM  1,000 nM = 1.0 μM Redox Couple Lose electrons oxidize (LEO), gain electrons reduce (GER) If I lose e-, I become oxidized If I gain e-, I become reduced  In a redox couple, one gets oxidized and one gets reduced  If you are an oxidized compound, you want to gain electrons to become reduced  The reduced compounds donate the electrons to oxidized compound so it can become reduced Ex. Once a reduced compounds has given all its electrons to an oxidized compound, now the reduced compound becomes the oxidized compound because it wants to gain back electrons A compound in its oxidized state can be reduced by the appropriate reducing agent A compound in its reduced state can be oxidized by an oxidizing agent A reduced compound causes the oxidized compound to become reduced. (It is like a cycle of giving electrons back and forth) A living cell has to be able to use redox to generate energy Disulfide bridges between cysteines in a protein. Cysteine(special amino acid because it can form disulfide bridges (covalent bonds)) is in miscellaneous group If you have 3D structure and want to stabilize it, put it in more covalent bonds to really stabilize it. Explanation: (The left side is in its reduced form. Left loses electron to the right. Lose one electron means lose one proton. Upon oxidation, this compound loses an electron (a proton). Now it becomes oxidized. And forms disulfide bond, if you want to break that bond, add a reducing agent so you’re back to the reduced compound by adding electrons back to the left.) The reduction state of a protein can affect its conformation—what causes the protein to fold into its appropriate shape?  Not all proteins are affected by redox. Why? Because not all proteins have cysteines that are exposed to the outside. Have to have at least two cysteines to form disulfide bonds.  These disulfide bonds are broken by reduction and can re-form by oxidation  A reducing agent causes an oxidized compound to become reduced  Structure determines function, if you unfold it, you could change its function Extra FYI information  Ammonium thioglycolate is also known as perm salt for its use in permanent waves.  Perm salt is a reducing agent which weakens the hair's cysteine bonds  Afterward, the hair can be “set” in a new conformation when the cysteines are re-oxidized with hydrogen peroxide or sodium bromate Amino acid side chain summary 1. Amino acids in the polar charged group have the capability to form ionic bonds (if the pH is right) and make proteins more hydrophilic 2. Amino acids in the polar uncharged group can form hydrogen bonds and make a protein more hydrophilic (water-loving/water-soluble) 3. Amino acids in the nonpolar group don’t form ionic or hydrogen bonds and can make a protein more hydrophobic 4. Cysteine can form covalent bonds (disulfides) with other cysteines when oxidized What can hold proteins together in their proper conformation? What can hold proteins together in their proper conformation? 1. Vander Waals can help stabilize 3D conformation but they’re distance- depended and very weak individually. But if there are a lot of them, it can help stabilize conformation. 2. Hydrogen bond—if you have side chains in the polar uncharged group, you can have HB between two amino acid side chains to stabilize conformation 3. Ionic bond—if you have side chains from the polar charged group and they’re opposite charges, you can have ionic bond and if the pH is right. 4. Hydrophic aggregations of nonpolar side chains 5. Covalent bonds—(Peptide bonds and Disulfide bonds) All amino acids form peptide bonds. Only amino acids with at least two cysteines can form disulfide bonds Which is more important for this class? A. Memorize the structures of each amino acid. NOPE B. Memorize which amino acids go in each group. NOPE C. Memorize the function of each amino acid. NOPE D. Know why there are 4 groups and understand what an amino acid side chain in each group does for a protein E. Be able to predict the correct structure of a protein by knowing the amino acid sequence. NOPE Peptide bond formation Take out water to make this bond, take away water to break this bond. Putting amino acids together to make a protein  Proteins are held together as linear polymers by special covalent bonds called peptide bonds Is every covalent bond in a protein a peptide bond?  Some of them. Because some are disulfide bonds if you got cysteines. Conformation (shape) changes Shape/structure determines its function What determines structure? –amino acid sequence, pH, oxidizing conditions CARBOHYDRATES I. Carbohydrates (sugars). Usually polar. Some can be charged but most are uncharged. Two main types to focus on in BIO201B: A. Metabolic sugars. Primarily used for energy. Glucose, glycogen, starch (Polymer of glucose) B. Structural carbohydrates. Other polysaccharides, oligosaccharides, complex carbohydrates (Polymer of sugars) 1. Cell walls of plants 2. Sugars on glycoproteins and glycolipids in membranes Two forms of a monosaccharide: Two different ways to see a hexose (a six- carbon sugar) Some common types of carbohydrates Formation of a disaccharide A glycosidase can break (hydrolyze—when you’re breaking down sugar) this glycosidic linkage Sucrose is not glucose, it is a disaccharide of glucose and fructose Two different polysaccharides Feb 5, 2016 Types of lipids in cells I. Metabolic lipids. Usually in fat droplets –stored extra energy—not all lipids are fats A. Triglycerides (fats). Triglycerides are hydrophobic (Not water-soluble)(form clogs in bloodstream) B. Triglycerides are not found in membranes II. Structural lipids. Usually in membranes. Most membrane lipids are amphipathic. Make up structures of the membrane A. Phospholipids B. Sterols (Not only cholesterol) Some Terminology 1. Free fatty acid. A fatty acid that is not covalently attached to anything (monomer) floating around by itself. 2. Fatty acyl side chain (or fatty acid side chain). A fatty acid that is covalently attached to something (like a triglyceride, phospholipid or protein) 3. Saturated fatty acid or saturated fatty acyl side chain. No double bonds 4. Unsaturated. At least one double bond 5. Polyunsaturated. Many double bonds Triglycerides—glycerol covalently bonded with 3 fatty acid molecules. Saturated and unsaturated free fatty acids Palmitic is like uncooked spaghetti. Linoleic has vacancy. An example of a Triglyceride (fat) [Tristerate=beef fat]—completely hydrophobic (clogs arteries)  Three fatty acyl side chains. All are stearic acid (18:0)—saturated at 18 carbon. 0 means no unsaturation  All of the fatty acid side chains are fully saturated. It is solid at room temperature How to make lye soap--Alkaline hydrolysis of lard by lye: You save beef fat to make lye(3Molar KOH) soap by soaking beef fat into lye. It will break into glycerol and three free fatty acids  Which of these compounds are hydrophobic? triglyceride  Which of these compounds are amphipathic? Free fatty acid—cannot be in membrane bilayer because it is detergent and destroys the membrane  Which of these are detergents? Free fatty acids You can turn solid fat into detergent!!! Another Triglyceride. This one is fluid at room temperature The double bonds make it more unsaturated, more disordered and fluid at room temperature Linseed oil (plant’s fat) is more fluid at room temperature because it has lots of double bonds (18:2) (18:1) (18:2) You lower the saturation, you lower the melting point  Double bonds add “kinks” and disorder to the packing of fatty acids and fatty acyl side chains, making them more fluid because there is more room to move.  More double bonds, more fluid (in general).  More double bonds, more fluid, lower Melting Point. Increasing the unsaturation lowers the Melting Point  If a fatty acid is at a temperature above its Melting Point it will be more fluid Artic salmon has lots of poly unsaturated fatty acids can they’re good for you. Why? Because it adds a fluidizing affect to counteract the cold. Membrane fluidity is important. Phospholipids  The head must be polar (NOT NECESSARILY CHARGED), the tails must be hydrophobic. Has to be amphipathic. You are detergent if you are too hydrophilic (number of free fatty side chains and polar head group are significant)  When you take off hydrophobic amino acid side chains, you made it less hydrophobic. Now you put on polar head group, you made it less hydrophobic. You take away some hydrophobic, you add some hydrophilic, you made it more hydrophilic.  If you took triglyceride and turn into a phospholipid, you’re making an insoluble hydrophobic fat and turning it into amphipathic compound.  This is not a detergent even though it is amphipathic, because it’s a matter of how hydrophobic and hydrophilic you are. If you are more hydrophilic than hydrophobic, then you’re a detergent. If the other way around, you’re most likely a phospholipid membrane.  Like triglycerides, the tails are fatty acid side chains Phospholipid head groups Phospholipids can add charge to a membrane. In nature, we assume there’s no positively charged membrane Which membrane could have more peripheral proteins, one that is pure PE or one that is pure  PS (at pH=7)? PE is 0, PS is -1. Will pH affect its ability to form ionic bonds? --yes Some Phospholipid Structures: PE, PC, PS, PI Are these R groups saturated or unsaturated? How much are they going to contribute to membrane fluidity? Lysolipids—to break Phospholipid:Phospholipase breaking down bonds Lysolipids: (detergent) Free fatty acid: (detergent)  PhospholipidLysolipid & Free fatty acid [Like bee sting breaking open the cell]  Taking away necessary structure and adding something that destroys the structure!  Phospholipid is more amphipathic and hydrophobic taking away one of the hydrophobic parts (lysolipid) it becomes more hydrophilic.  This is why cells die when they lose structural lipids  Phospholipids are necessary for membranes and free fatty acids destroy them. Why? Free fatty acids are too polar and too water soluble at high pH. No free fatty acids in the membrane. No triglyceride in the membrane!!!


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