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Exam 1 Study Guide BIO201 with Todd Hennessey

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by: ChiWai Fan

Exam 1 Study Guide BIO201 with Todd Hennessey BIO 201

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ChiWai Fan
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Study Guide for Exam 1 Lectures 1-9. Lecture 10 will be on the Exam, but it is not included because I have to upload this a few days prior to the exam. Email me if you have any questions.
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BIO201 Study Guide for Exam 1 Todd Hennessey Cell Biology
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This 38 page Study Guide was uploaded by ChiWai Fan on Saturday February 13, 2016. The Study Guide belongs to BIO 201 at University at Buffalo taught by TODD HENNESSEY in Spring2015. Since its upload, it has received 304 views. For similar materials see CELL BIOLOGY in Biology at University at Buffalo.


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Date Created: 02/13/16
BIO 201 with Todd Hennessey Exam 1 Study Guide for lectures 1-9 —by ChiWai (Information credited to Professor Todd Hennessey, Notes edited by ChiWai Fan) Weak acids and Strong acids—only strong acids dissociate fully into ions + For example: H 2 H + OH- pH tells you how much of the acid has dissociated. It is a way to express the concentration of H+ If you add strong acids, the [H+] will increase and the pH will go down becoming more acidic. [H+] means concentration of hydrogen ions, also called protons pH scale ranges from 1-14 pH 1-6 means acidic. pH 7 means neutral. pH 8-14 means basic pH = -log [H+] (-log is their relationship) pH 7 means neutral -7 Ex: If pH = 7.0, the [H+] = 1.0 x 10 M H+ or 0.0000001M H+ -2 If pH = 2.0, the [H+] = 1.0 x 10 M or 0.01M H+ + As [H ] goes up, the pH goes down As [H ] goes down, the pH goes up Make sure you know about unit conversions (nanogram, microgram, milligram, kilogram etc) And note that: Molarity= moles/Liters Types of Bonds and Interactions—bonds and interactions keep things together 1. Covalent bonds—electrons are shared; (there’s single bonds, double, and triple) 2. Non-covalent bonds A. Ionic or electrostatic bonds (full charges)—obvious positive or obvious negative—compound held by ionic bonds will dissociate into IONS (cations and anions) B. Hydrogen bonds (partial charges) you don’t have to have full charges to be polar (ex. Water) C. Van der Waals interactions (not hydrophobic bonds)— distance dependent. They are very weak individually but many together are strong (like a zipper) 3. Hydrophobic aggregations Not bonds, interactions or even forces between molecules. They are hydrophobic exclusions from water. There are NO hydrophobic bonds. BUT they have hydrophobic aggregations Hydrophobic Aggregations Hydrophilic: “Water loving”. Charged or polar and water soluble. Water is hydrophilic Hydrophobic: “Water fearing”. Uncharged, nonpolar and not very water soluble. Fats (not necessarily have to be lipids) are hydrophobic BASIC THERMODYNAMICS 1. First law:  Energy cannot be created or destroyed.  It is always conserved. Energy is always there.  Different types of energy can be interconverted. Ex: thermo energylight energychemical energy 2. Second law:  The Universe always tends towards disorder. (ΔS for entropy)  Entropy (ΔS) is always increasing.  The amount of energy which is unavailable to do useful work is: TΔS T = Temperature Δ S = Change in entropy SYSTEM AND SURROUNDINGS  Energy of the Universe = energy of the system + energy of the surroundings o To conserve the energy of the Universe, if one changes, the other has got to change. So there’s no change overall o A system can be a defined space, a physically bounded space, an amount of matter, etc. ENTROPY ΔS sys> 0 means that this system becomes more disordered ΔS sys< 0 implies that this system becomes less disordered (more ordered) ΔS of the Universe = ΔS of the system + ΔS of the surroundings First and second laws together The energy (H) of the Universe is constant but entropy (S) continues to increase ΔH = ΔG + TΔS Total energy = usable energy + unusable energy H is enthalpy. Total energy change = ΔH ΔG is the change in free energy (energy available to do useful work) TΔS is Temperature multiplying the change in entropy Can a reaction be driven by a change in entropy of the surroundings? YES  Hydrophobic molecules can aggregate spontaneously (with no energy added) in Water even if the system becomes more ordered. In another words, as long as there is an overall increase in entropy of the universe, hydrophobic aggregation can happen without energy supplied. Some energy will always get loss. You’ll never going to get ALL energy out because some will escape or be used up. That’s why there’s no such thing as “perpetual motion” Gibb’s Free energy ΔG = ΔH – TΔS ΔG must be negative for a reaction to proceed spontaneously as written Reactants  Products ΔG = G products- G reactants The reaction will go if it proceeds to a lower state of free energy If Free energy of reactants is higher than free energy of products, then ΔG is negative. This allows the reaction to proceed as it is written. Change in Gibb’s free energy or ΔG 1. Products have lower free energy than reactant [Exergonic]—Think of exothermic (favored) a. Energy released b. This has a -ΔG Why? We want -ΔG to make things happen 2. Products have a higher free energy than products [Endergonic]—Think of endothermic a. Needs energy b. This has a +ΔG Why? This happens in a cell all the time. 3. Coupled reaction: You want a -ΔG to make things happen that usually don’t happen. You couple -ΔG with + ΔG and run on if -ΔG is bigger than + ΔG What does this mean to us? What’s the point of ΔS and ΔG? 1. A reaction can be driven by changes in either the system or surroundings ΔS of the Universe = ΔS of the system + ΔS of the surroundings Want to increase entropy of universe? Then increase either entropy of system or surroundings. 2. ΔG must be negative for a reaction to proceed as written. This can be driven by either ΔH or TΔS or both ΔG = ΔH – TΔS You want ΔG negative? Then make ΔH more negative or make TΔ S more negative Let’s ignore ΔH; increase entropy will give negative ΔG if ΔH is no change 3. A reaction can be driven by an increase in entropy of the surroundings, even if the system becomes more ordered and no work is done. Yes as long as surroundings become more disordered. You can increase ΔS of universe by increasing ΔS of surroundings even if there’s decreased entropy of system. Just as long as the entropy of surroundings is more than the decrease of entropy of system. ΔG = 0 means equilibrium. Means dead cell  We are fighting against equilibrium and disorder.  Universe says “I want to be disordered!” but you can become ordered if you add energy to it because a cell says: “I don’t want to be disordered because I will die. Give me energy!”  Can hydrophobic molecules aggregate spontaneously (with no energy added) in water if the system becomes more ordered? – YES. As long as there is an overall increase in entropy of the universe, hydrophobic aggregation can happen without energy supplied. o It’s an entropy party! Water molecules are hydrophilic that means they love binding to other water molecules by hydrogen bonding. But there’s hydrophobic molecules which water doesn’t like. o If you let this go for an infinite time, you want to let this go to a lowest state of free energy where you don’t have to do much. o Lowest state of free energy for water molecule is maximum entropy, to do that they need to do “Hydrophobic aggregation”—pushes away hydrophobic molecules. . o Hydrophobic aggregation become an ordered system—but it is okay because the surrounding is more disordered due to hydrophilic water molecules.  Water is in its optimal thermodynamic state (maximum entropy) when each water molecule can bind to as many other water molecules as possible.  Pure water has maximum entropy. They don’t like added substances but they can tolerate for a while. To a matter of extend.  It is thermodynamically unfavorable to get in the way of this (but it happens all of the time--hydrophobic) How much of an unfavorable thermodynamic condition can water tolerate? If too many hydrophobic lipids are suspended in water, they aggregate. This hydrophobic aggregation is driven by exclusion of the hydrophobic molecules from water, not by bonds or interactions between the hydrophobic molecules because there’s no such interaction or bonds! What’s the point?  A hydrophobic aggregation in water is driven by an increase in entropy (Δs) of water. Lipids will spontaneously form aggregation in water without any extra energy added. This is - ΔG Once formed, it can be stabilized by Van der Waals interactions, but these are not “hydrophobic bonds” Two Worlds in a Cell I. Polar, aqueous, hydrophilic. Water-soluble compounds found here. Some examples: Cytoplasm and nucleoplasm. Matrix of mitochondria. (Aquatic worlds inside cell), Lumen of ER, Golgi or lysosomes II. Non Polar, lipid-like (think of fat clogs the artery) Water-insoluble compounds seen here. Example: membranes In Between: Amphipathic Amphipathic means “two natures”. One end is polar (hydrophilic) and the other end is nonpolar (hydrophobic) 1. Neutral Detergent—All detergents must have polar and nonpolar parts. 2. Membrane phospholipids 1. If it is more hydrophilic than hydrophobic, it should be a water soluble detergent  Hydrophobic head and hydrophilic tail. More polar than nonpolar. This is soluble in water 2. If it is more hydrophobic than hydrophilic, it should be a membrane lipid  Hydrophobic tail and hydrophilic head. Amphipathic compound that’s more nonpolar than polar. This is insoluble in water You can turn something phospholipid into detergent by making it less nonpolar and more polar. For example, clip off one tail, the lipid will turn into detergent A detergent micelle—when washing clothes—you dissolve greasy dirt  These are Anionic detergents in water  They are amphipathic  Their hydrophilic heads face the water  Their hydrophobic tails face away from the water, forced into facing the greasy dirt (ordered system) but you get more disorder by getting greasy dirt out, so it’s fine to do so  In the middle of this micelle is a piece of greasy dirt (hydrophobic) What causes this to form?—Hydrophobic aggregation or – ΔG of water. The increase entropy of surroundings drives this. NOT hydrophobic bonds or interactions. This is how the first cell formed. What is a micelle?  You don’t want to see micelle in your cell, you want to see it in your laundry  A glob of detergent around a piece of water-insoluble substance such as a greasy dirt The four main types of organic macromolecules: 1. Proteins 2. Carbohydrates 3. Lipids—not polymers 4. Nucleic acids Polymerize [CONDENSATION] water is removed so the covalent bond forms between monomers-- an monomer and an monomer get together will become a dimer 1. Proteins are polymers of amino acids 2. Polysaccharides are polymers of carbohydrates (sugars) 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. Glycosidase 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 which differ in their SIDE CHAINS 2. Free (unbound) amino acids all have an amino group and a carboxyl group. (Amino on one side, carboxyl on the other when unbound) 3. The amino acids are covalently attached by peptide bonds between neighboring amino and carboxyl groups 4. The charge on the protein is dependent upon the pH 5. Protein is a linear polymer of amino acid but it can fold back at itself to form certain structures PROTEIN STRUCTURES I. Primary Structure (Linear polymer) (the amino sequence) asks: what is the order of the amino acid sequence? II. Secondary Structure: supported by hydrogen bonds, fold the protein into its shape III. Tertiary structure: structure stabilized by covalent and noncovalent bonds IV. Quaternary structure: Two or more proteins together Free amino acid R represents the side chain group. 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 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) 4 general amino acid groups, based on their side chains (R groups) A. Polar and fully charged at pH=7.0. Hydrophilic—ionic bonds B. Polar but uncharged at pH=7.0. (Yes, it is possible to be polar without having a full charge). Hydrophilic—hydrogen bonds C. Nonpolar at pH=7.0. These are hydrophobic (but not lipids) not water- soluble D. Miscellaneous 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 of the protein in solution and its solubility  Side chains determine what amino acid it is  Charged amino acid on inside helps to form and stabilize the conformation with ionic bonds What happens to the net charge on a protein if you change the pH? It depends on what ionizable groups are exposed and what the pH is. Why is the pH important?  At low pH, you deprotonate to go to high pH  Deprotonate means take away a proton; high pH means low proton concentration [H+] 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 (partial charge; hydrogen bonding) Will a protein with many polar, uncharged side chains be water soluble? Could be, but not always It is hard to predict. It depends upon such things as: 1. How many hydrophilic and hydrophobic side chains are exposed to the water? Water solubility depends on relative hydrophobicity and hydrophilicity 2. The pH of the solution. It determines which other side chains are ionized and relative hydrophobicity 3. What else is around for the protein to bind to? 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. Disulfide bond is not peptide bond; these are two covalent bonds we learned so far 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 causing it to become reduced  Reduced compounds are electron donators whereas oxidized compounds are electron acceptors Clarification on Redox: 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 appropriate oxidizing agent 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 by oxidation. Lose one electron means lose one 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 at least two 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 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 as a miscellaneous can form covalent bonds (disulfides) with other cysteines when oxidized. The disulfide bond can be broken when it is reduced What can hold proteins together in their proper conformation? 1. Vander Waals can help stabilize 3D conformation when there’s a lot of them because they’re very weak individually since they are distance-depended. 2. Hydrogen bond—if you have side chains in the polar uncharged group, you can have Hydrogen bonding 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. Hydrophobic 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 Know why there are 4 groups and understand what an amino acid side chain in each group does for a protein Peptide bond formation Proteins are held together as linear polymers by peptide bonds Take out water to make this bond, add water to break this bond (hydrolysis). Putting amino acids together to make a protein 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: 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 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) 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: Biological membranes do not contain fatty acids because they are detergents 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 (left: Palmitic) and unsaturated free fatty acids (right: Linoleic) Palmitic is like uncooked spaghetti. Linoleic has vacancy. An example of a Triglyceride (fat) [Tristearate=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. 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 (3M 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 –linseed Oil. 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) lowering saturation=lowering M.P.  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.  Increasing the unsaturation means more double bonds, more fluid, lower Melting Point.  If a fatty acid is at a temperature above its Melting Point it will be more fluid. 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 it into a phospholipid, you’re turning an insoluble hydrophobic fat 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 Phospholipid head groups: do not waste time memorizing this chart Phospholipids can add charge to a membrane. In nature, we assume there’s no positively charged membrane 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!!! CHOLESTEROL Sterol-> Other membrane sterols  There are many types of sterols. All plant sterols have some moderations.  Cholesterols are essential to animal cells. There are no cholesterols in plants, they have phytosterols. There are no sterols in bacteria or Achaea.  To what extend do plant sterols perform the same functions as cholesterols in our cells? To what extend do they compete in the human cell? (Cholesterols (in yellow) sitting in lipid bilayer)  cholesterols are amphipathic—it is not very water-soluble  Hydrophilic part faces the water.  You can turn cholesterols into detergent!! DNA and RNA—there are three main parts to nucleotides—this is a free nucleotide (on the left) 1. base—tells you what nucleotide it is 2. sugar—pentose sugar—distinguishes carbon on the base and carbon on the sugar by prime notation (‘) (we want to focus on 2, 3 ,5 prime) 3. phosphate—carries negative charge of pH 7 Purine base pairs with a pyrimidine Some of these units repeating to make a polymer (DNA or RNA) The pentose sugar is different in DNA and RNA  This pentose sugar is ribose  If the 2’ OH is replaced with an H, it is called Deoxyribose. (Deoxyribose is the sugar in DNA) Took off OH, it is deoxyribose. BIG DIFFERENCE BETWEEN RNA &DNA: If there’s OH at 2’ then it’s RNA. If there’s a H at 2’ then it’s DNA Hydrogen bonding between base pairs—holds them together as double bonds A = T DNA A = URNA C GBOTH (CG bond is stronger than AT) What’s the point? In DNA there’s A-T and G-C pairs but in RNA there’s A-U and G-C pairs. These pairings are due to hydrogen bonds. Polymerization—got to be in specific order (we lose water during polymerization) Theres 2’ OH so this is RNA!! Polynucleotides <-RNA <-DNA  Is this RNA or DNA? How can you tell? You don’t tell from single stranded or double stranded!  There is no U in DNA  DNA has no OH here at 2 prime (2’)  This is RNA The nucleotides are held together by phosphodiester bonds (polyester)  DNA or RNA? DNA!! Is DNA negatively charged at pH=7.0? o There’s a T o There’s H at 2’ o You can have single stranded DNA and double stranded DNA Double helix formation (Double stranded DNA) DNA can be a template to transcript RNA then RNA is used in translation to make protein. You can either replicate DNA to make more DNA or you can transcript it to make RNA The “Central Dogma”THIS IS WRONG!! How can it be wrong? The Central dogma says that DNA cannot be made from an RNA template BUT Reverse transcriptase can make DNA from an RNA template PROVEN Replication, Transcription, Translation and Reverse Transcription Replication is DNADNA (This is DNA synthesis) Transcrption is DNARNA Translation is RNAprotein (Protein synthesis) Reverse transcription is RNADNA (done by enzyme Reverse Transcriptase) 3 Major Types of RNA [All are made in the Nucleus of eukaryotic (not bacteria) cells—cells with organelles (has membrane bilayer inside a cell) 1. Ribosomal RNA (rRNA)—80 to 90% of the total RNA is rRNA 2. Transfer RNA (tRNA)—rRNA is required for translation 3. Messenger RNA (mRNA)—mRNA is also required for translation DNAtranscriptionmRNAtranslation (needs rRNA and tRNA)protein Examples of double stranded RNA: (Left: tRNA, Right rRNA) RNA can also be double stranded in RNA viruses and RNAi (inhibitory RNA) RNA CAN BE DOUBLE STRANDED!!!! Not all enzymes are proteins!! Some enzymes are RNA!! (catalytic RNA) Two ways to cut RNA 1. Add a ribonuclease (RNAse). This is an enzyme. It is a protein 2. Add a ribozyme. This is a different enzyme. It is catalytic RNA. DNA can be made from an RNA template but RNA cannot be made from a protein  Think: how does structure affect function!  A free fatty acid (satuated) has not covalently attached to anything and no double bonds  A unsaturated free fatty acid has doube bonds  Triglyceride—3 free fatty side chains  Phospholipid—has polar head group and 2 side chains Some types of microscopy Confocal Microscopy  Confocal microscopy has the advantage of producing serial optical sections from thick specimens. (taking a cell, cutting through it not with a knife but the ability to see and focus on various things in a cell—3 Dimensional)  These are like “optical slices” through a specimen.  This also increases optical resolution and contrast by using point illumination Optical Sectioning by Confocal Microscopy  X and y dimensions are in one focal plane  The Z dimension is up and down, like focusing your plane of interest Confocal microscopy can produce serial (one after the other), high resolution focal plane images Centrifugation: 1. Differential Centrifugation: Separation based primarily on size and weight (separating nucleus)—so we can focus on what we’re studying primarily A. Bigger things go into the pellet B. Smaller things go into the supernatant C. Centrifugation speed (g force) and time determine what goes into pellet and supernatant D. If two things are similar in density (g/mL) but have different sizes, use this to separate them 2. Density centrifugation: Separation based primarily on buoyant density (you will float if you have lower density than the density of what you’re floating in)  If two things are similar in size but have different densities, use this to separate them Separating particles based on their size. (Fractioning) 1. A homogenizer breaks open the cell to make a homogenate 2. If you spin it at low speed, you get a P1 (first pellet) with mostly nuclei (nuclear fraction) inside. 3. What’s left behind from supernatant is S1 and centrifuge it at higher speed, P2 has mitochondrial fraction because it is smaller than P1 but bigger than S2. 4. Then you spin S2 at even higher speed, P3 contains ER fractions (Microsomes), left behind is S3 which is the soluble material in cytoplasm P1 has biggest sizes then P2, then P3 Buoyant Density  If you put some beads on top that have a density of 1.25 g/ml and let them settle in until they stop, where would they be? –letting things go to their density and wait until they stop.  Things will float on top of something that has a higher buoyant density Density Gradient Centrifugation. Separation by density  Density is g/ml  1M sucrose is 1.12 g/ml  2M sucrose is 1.23 g/ml From high molar sucrose (bottom—higher density) to lower molar sucrose (top— lower density) Mitochondria are more dense (more g/ml) than lysosomes These organelles band at their buoyant density (Purple shows the particles stopping at their buoyant density)—density centrifugation is better than differential because they have similar sizes. SER Separated from RER by Density Centrifugation: Smooth endoplasmic reticulum (SER) Vesicles 1. Homogenize cells 2. Differential centrifugation to obtain microsome fraction 3. Put microsomes on a density gradient 4. Centrifugation of microsomes on a density gradient separates RoughER from SmoothER vesicles because RER are more dense than SER RER vesicles are denser than SER because they have ribosomes on them:   RER are Rough Endoplasmic Reticulum vesicles Gel electrophoresis:--moving a charged compound at electro field: Electrophoresis can be used to separate, purify and identify proteins, RNA or DNA (RNA and DNA has negative charge at pH 7) Anode: Positive pole, attracts anions (negative charges) Cathode: Negative pole, Attracts cations (positive charges) Positive stuff goes towards negative pole; negative things go towards positive pole  Fill swimming pool with jello, bigger things move slower than small things Two main types of gel electrophoresis 1. Native gels. No detergent added. Keep it real! Migration affected by native conformation (shape), size, solubility and charge Used for separation of charged proteins, DNA at right pH or RNA at right pH  Would pH affect the migration on a native gel? YES! Because only charged things can move, and pH effects charges. 2. Detergent (usually SDS) gels. (De-natured gel)—detergent in shampoo to solubilize greasy dirt Detergent added to the sample and the gel Assumption! That migration is only due to size (doesn’t work all time) SDS-PAGE This stands for SDS-polyacrylamide gel electrophoresis Polyacrylamide is the gel, SDS is the detergent (more soluble than hydrophobic) In SDS-PAGE, all polymeric protein complexes will be broken down into their monomeric forms (not amino acid form) How to look at proteins by SDS-PAGE (assume SDS is always negatively charged) 1. SDS is Sodium Dodecyl Sulfate. It is an anionic detergent at most pHs used 2. It separates proteins on the basis of their size. A. Small proteins move through the gel faster B. ASSUME! That all of the proteins are denatured negatively charged and soluble in the presence of SDS so they all have the same shape and charge. So they’re all running to positive pole C. With no detergent present, proteins could have a net charge of positive, negative or zero and be in their native conformation, depending upon the pH. An idealized animal cell: [not all cells are the same]  Mitochondrion—membrane bound organelle. It is an organelle because it has a membrane around it  Cytoskeleton—support and transport of the cell  Nucleolus is not a membrane bound organelle; not an organelle because it has no membrane around it  Free ribosomes—floating around not bound to anything. They can be floating around not doing anything or they can be bounded to a rough endoplasmic reticulum  Centrioles—organization centers during mitosis  Golgi apparatus—one of the major organelles of a cell  Plasma membrane—this is not the only membrane of the cell. Plasma membrane is on the outside of the cell  Smooth endoplasmic reticulum—Focus on RER instead. The main difference between an animal cell and a plant cell is that the plant cell has a cell wall and chloroplast. And not all plant cells have chloroplast. What are the mitochondria in a plant cell? This is a theory: Explanation of the theory: This cell has no organelles, some mitochondria here used to be free living cells (possibly bacteria). Endosymbiont gets things from the cell and gives things to the cell that it lives in. The theory is that they evolved to stay there forever, so now the cell cannot live without mitochondria. The endosymbiont theory proposes that the intracellular organelles inside eukaryotic cells used to be free-living prokaryotic cells. The theory suggests that they got inside the first prokaryotic cells, liked it and stayed there as endosymbiont. Another theory*: Some eukaryotic cells may have evolved from cells that lost their chloroplasts. Ciliates (a type of protists) may have evolved from a cell that has lost its chloroplast. (Just theories!) The Nucleus: 1. Defining boundary: Nuclear envelope. It is a double membrane with nuclear pores. (a membrane is a bilayer. A double membrane has TWO BILAYERS) 2. Support Structures: Nuclear Lamina (IFs) Nuclear matrix (scaffolding)—holding things in its place. 3. DNA and associated proteins Chromatin in the nucleoplasm—DNA associated (wrapped around) proteins 4. Transcription “machinery” Transcription in the nucleus ONLY in a eukaryotic cell (not bacteria) Translation in the cytoplasm 5. Nucleolus—within the nucleus.—defined area full of cell functions and activities Site of rDNA transcription and ribosomal subunit assembly  Nucleus: you put things together (assemble) in here, you do not create things here.  Ribosomal RNAs are made in nucleus whereas proteins are made in cytoplasm  Ribosomal subunits are ASSEMBLED in the nucleus, ribosomes are assembled in the cytoplasm  You make ribosomal RNA in the nucleus (transcription), so where are things made in a cell? Where do we assemble bigger things? Translation (protein synthesis) Translation starts in the cytoplasm and requires: 1. Large and small ribosomal subunits are made of ribosomal proteins and rRNA 2. Ribosomal subunits bind to mRNA in the cytoplasm— (compartmentalization—why have organelles? Different compartments have different functions) 3. tRNA picks up amino acids and brings them to the ribosome 4. Amino acids are joined together by peptide bonds on the ribosome 5. No translation in the nucleus; no protein synthesis in nucleus; no RNA synthesis in the cytoplasm! They synthesizes in other compartments. Large Ribosomal Subunit Gray is rRNA. It is made in the nucleus (nucleolus) Gold is rProtein. It is made in the cytoplasm Ribosomal RNA Ribosomes are complexes of rRNA and rProteins Ribosomal subunits are assembled in the nucleus Ribosomes are assembled in the cytoplasm Is all RNA translated? mRNA is translated into amino acid sequence; rRNA and transfer RNA (tRNA) are not. They’re a part of translation machinery but they themselves are not translated. Ribosomal subunits and ribosomes—there’s no ribosomes in nucleus, yes ribosomal subunits in nucleus Explanation: Start out in nucleus, transcription and RNA processing; let’s make messenger RNA (mRNA), now it’s in cytoplasm. Let’s make transfer RNA (tRNA), now it’s in cytoplasm. Now mRNA and tRNA can make protein synthesis but not yet, you need RIBOSOMES. So let’s tell the nucleus to make some rRNA. But rRNA is made in nucleus and proteins are made in cytoplasm. Ribosomal proteins are brought into nucleus and they hook up with rRNA to form ribosomal subunits, rRNA does not leave nucleus by its form, they get out with ribosomal subunits and makes ribosomes which makes protein synthesis. (Which came first? The egg or the chicken?) Now we have proteins for transcription: it gets shipped into nucleus and now you have proteins for replication to form DNA replication. Transport through nuclear pores: What goes into the nucleus? A. Ribosomal Proteins—made by translation in cytoplasm and shipped in B. Proteins for Transcription C. Proteins for DNA Replication D. Many other things (IFs, matrix proteins, etc.) What comes out of the nucleus? A. Ribosomal Subunits B. mRNA C. tRNA D. Many other things Two places to make proteins in eukaryotes: Where are we making those proteins and Why? 1. In the cytoplasm on free polysomes (a piece of mRNA with a lot of ribosomes on it and it floats around in the cell. (Soluble proteins)) A. Some can stay in the cytoplasm (like tubulins, actin, etc.) B. Some can be targeted to go to organelles with an NLS, MLS, CLS, etc. 2. On the rough endoplasmic reticulum (RER)—it is rough because there’s ribosomes on it. Proteins made will go into RER A. Integral membrane proteins B. Proteins destined to stay inside the endomembrane system as either biosynthetic or degredative enzymes C. Secreted proteins The Endomembrane System Main Purposes: Manufacturing and Distribution Make proteins and lipids and ship them to their appropriate destinations by vesicular (like a truck with stuff inside) trafficking. Also, some recycling done to save energy Main Parts of the Endomembrane System: (systems within a cell)— manufacturing of protein, lipids, membranes and sugars, so we will leave out the nucleus 1. Rough endoplasmic reticulum (RER)—the endomembrane system starts here 2. Golgi 3. Transition vesicles—transporting stuff 4. Lysosomes—used in recycling things and digesting things 5. Plasma Membrane Possible “fates” of proteins made in this system: (Distribution after manufacturing) 1. Secreted continuously (constitutive) 2. Regulated release—this needs some kind of signal, unlike secreted continuously ones 3. Stay inside lumen of RER, golgi or lysosomes. Each of these needs specific proteins which will stay inside of them. 4. Membrane bound, integral protein on any membrane in this system The nucleus is not generally considered to be part of the endomembrane system. The nucleus is the boss of the factory, but the boss doesn’t manufacture or distribute the products, they just signal where to send the products. Rough Endoplasmic Reticulum (RER)--  Primarily for synthesis of many lipids and proteins as well as their initial glycosylation (take a sugar and covalently attach to it) Destinations for Newly Translated Polypeptides in a Eukaryotic Cell  Cytoplasm and RoughER are protein synthesis sites  Amino acid Localization Sequences direct the proteins to go where they should  Cotranslational translocation happens on RER—it’s a way for the protein to move from cytoplasm into ER into ER’s lumen Nuclear Localization Signal (NLS)-  For proteins to go into the nucleus, the NLS is the “ticket” to get inside  The NLS is part of the amino acid sequence of an NLS protein.  The NLS targets the NLS protein to go to the nucleus  MLS: Mitochondria localization signal  CLS: Chloroplast localization signal You can mislead the protein and use NLS sequence on it. For example a choloroplast protein is given NLS, it will go to nucleus as its being misled. Some examples of targeting sequences Transport to the nucleus (NLS): Pro-Pro-Lys-Lys-Lys-Arg-Lys-Val Transport to the mitochondrial matrix (MLS): Met-Leu-Ser-Leu-Arg-Gln-Ser-Ile-Arg-Phe-Phe-Lys-Pro-Ala-Thr-Arg-Thr-Leu-Cys-Ser-Ser- Arg-Tyr-Leu-Leu- What’s the point?  Specific amino acid sequences can target a protein to its appropriate destination. A change in this sequence could change the protein’s localization. Study tips:  Print out this study guide  Read over everything then highlight things you find important  Try to comprehend instead of memorizing the material  Do all the practice exams for Exam 1 and post-lecture quizzes on UBLearns  Let me know if you have any questions about any material on this study guide.  I’m happy to answer questions and form small study groups in South Campus  Good luck on Exam 1 and I hope this study guide helped!  Share with me your success after the grades have posted   Feel free to email me for Lecture 10 notes. Since it is covered on the test but it’s not in this study guide because I have to upload this a few days prior to the exam.


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