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This 9 page Class Notes was uploaded by Sheilah Kirui on Tuesday September 20, 2016. The Class Notes belongs to BIO 110 at University of Rochester taught by Dr Clark in Fall 2016. Since its upload, it has received 5 views. For similar materials see Principles of Biology in Biology at University of Rochester.
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Date Created: 09/20/16
1 Sheilah Kirui BIO 110 Study guide for Exam #1 Lecture #2 9.2.16(Friday) The Scientific method; What is it? The aspects that have to be fulfilled? Positive and Negative controls The concept of Electronegativity (eN) Hydrogen bonds (Hbonds) are the result of differences in eN o Found between molecules that have partial charges o If molecules have complete positive/negative charge = ionic interactions o Important for waterwater interactions + behavior and stability for other biomolecules o The individual Hbonds are very weak but together are very strong. Eg: DNA double helix is very stable due to the collective bonds. Q: Why is ice less dense than water? Ice has more permanent hydrogen bonds since cooler temp = less energy needed to break the bonds. Water has all four hydrogen bonds when frozen and it takes less space = less dense Lipids/fatty acids mainly contain CH and thus, are insoluble in water (hydrophobic) Carbohydrates = soluble because they have a lot of hydroxyl (OH) Same rule applies to gases; if polar = soluble, nonpolar=insoluble Glucose is very soluble in water not because of CH but rather, due to the OH groups o Know the structure of Glucose? o Q: Why is glucose hydrophilic? ***Be able to look at the structure of molecules and tell whether hydrophobic/philic? (pg 29) Entropy = amount of order in a system/how spread out is is. The universe moves towards less order Hydrophobic effect: Q: Why is HPE effect important in Biology? o Cell membranes are held together by the HPE, which ensures the folding of proteins o Proteins are: hydrophobic – inside hydrophilic=inside proteins Q: Why does oil not mix with water A: Hydrophobic effect the oil molecules aren’t sticking together. Rather they are being secluded together by water; reduces total # of ordered water molecules Water (roles) o determines how proteins fold – how is it related of eN? o make/break of covalent bonds b/w subunits (e.g.: amino acids) Condensation – forming covalent bond Hydrolysis – breaking a covalent bond using \water molecule 2 Breaking a bond releases a phosphate and provides energy. Q: Why is it important to hydrolyise ATP? Lecture #3 09.07.16 (Wed) Cell membrane = amphipathic (both hydrophobic + hydrophilic) Keq(constant) – tells you the direction that the reaction will take We can make things more acidic by adding more protons Water is a weak acid = doesn’t fall apart easily Q: Do I need to know the titration curve for this exam or in the future? I am guessing not. . pka =determines how tightly an acid holds on to a proton. Types of noncovalent forces **BE SURE TO BE ABLE TO DESCRIBE ALL OF THEM Hydrogen bonds – sharing of H atom Ionic attraction – attraction of opposite fully charged rather than partial charges Hydrophobic – interaction of nonpolar molecules in the presence of polar molecules ; repulsion of molecules from water Van der Waals – the weakest of all forces, which is the interactions of electrons of nonpolar substances **All these forces have something in common: electron and charges Q: Why are they more important than the covalent bonds? A: They are not permanent and since they are weak, they form and break often. The more complicated molecule = the more important the noncovalent interactions The noncovalent forces hold 3D structures of macromolecules ENERGY: Catabolism – breaking down from bigger smaller ; releases energy Anabolism – making/building from smaller bigger size; requires input of energy **Catabolism occurs to produce chemical energy (ATP) that is used to build bigger molecules (Anabolism) The actual energy is called NTP (ATP + other nucleids) ATP produced is used to fight Entropy Fuels – molecules that can be repeatedly oxidized ATP = more valuable fuel that is readily to be used. Glucose has to be trasnformed into ATP in order to be used. ATP’s energy is stored in the bonds between the phosphate. To extract energy from glucose, move electrons from C to O The energy in glucose is found in the covalent bonds (shared electrons) Most humans can oxidize carbon to produce energy 3 Glycogen – temporary energy storage whereas fats = permanent Lipids – insoluble cuss chemical bonds are nonpolar Saturation – with hydrogen Trans – straight rather than kinky saturated fats Triaglycerol – three fatty acids connected to a glycerol Phospholipid – wall of the cell membranes Amino acids: NH2+OOH R – groups aka side chains Pathways (Do we have to know this?) Glucose Glycolysis process to produce high energy electron carriers electron transport chain converts to electrochemical (proton gradient) type of energy conversion to mechanical energy ATP Lecture #3 9.9.16(Friday) Phosphate groups are negatively charged To convert ADP to ATP, you need to add another phosphate. Uses for ATP: o One of the four bases of DNA o Used for energy Electron carriers – holds electrons captured in the oxidation of carbon compounds o NAD+ – used largely in catabolism o NADP – used for anabolism o FAD Deta G = Energy created or used by a reaction that tells you which direction the reaction will proceed (just like eq) Functional Groups **Start knowing their name + be able to identify them though no need to drsw them **BE ABLE TO TELL THEM; NO NEED TO DRAW THEM ON EXAM H,O = water H,O,C = Lipids + Carbohydrates H,O,C,N = Creating of 18/20 Amino acids H,O,C,N,S = All 20 amino acids H.O.C,N,S, P = Nucleic Acids (DNA +RNA) Monosaccharides : 1 sugar Ex: glucose and fructose Oligosacccharides (di, tri…) = 220 sugars 4 Polysaccharides : >20 Glucose is the most common and preferred biomolecule in the whole planet. Therefore, we might often have to convert other molecules into glucose first. Fructose is metabolized in the liver (like alcohol) before converted to glucose to be used by the cells Ribose sugar – RNA ; Deoxyribose DNA Sugars end generally in “ose” whereas enzymes (proteins) have the ending ‘ase’ Most of our sugars are temporarily cyclic, which is more stable than the linear form. Sugars can be modified in order to add other groups Joining two sugars together requires the removal of water molecule; the bond between the sugars is called glycosidic bond (covalent bond that is much stronger than noncovalent forces) Cellulose is largely found in plants and is very stable and insoluble (explains why trees and other plants do not dissolve when it rains) Glycogen and starch In our bodies, we store glucose as glycogen (found mostly in our liver and muscles) The excessive sugar (glucose) is converted into fat – explains why survival is feasible for humans Purposes of polysaccharides(carbohydrates): Energy structure Cellulose structure Cell signaling Blood groups are determined by what carbohydrates are present Shells of athropods Adrenaline tells the liver to break down glycogen as a response to environmental stimuli Branching quickens the breaking down process of bonds **BE ABLE TO EXPLAIN why cellulose and glycogen are different in terms of strength and solubility has to do with hydrogen bonds Starch: the polysaccharide chain is curved/branched rather than as linear as in cellulose. Branching limits the # of hydrogen bonds that can form making it less compact than cellulose Glycogen: the high amount of branching makes its solid deposits more compact than starch Cellulose: unbranched and each glucose molecule is flipped 180 degrees, The parallel chains can create a hydrogen bond to form straight fibers of great strength Lipids – basically, anything that is hydrophobic Roles/purposes: Electron carriers Energy storage (long term storage) Light absorbing pigments 5 Hormones Intracellular messengers Cell membranes are made of lipids Most of our energy is stored in the form of lipids because they’re largely insoluble and stable. Also, it takes less space because there are no water molecules included or exposure. Most enzymes work in a hydrophilic environment Triacylglycerol (a s simple lipid) – used for energy storage + insulation Fatty Acids: Saturated fatty acid: single bonds between hydrocarbon atoms and the chain is straight, which allows molecules to be tightly packed amongst other similar molecules Unsaturated fatty acid: double bonds between two carbons = means fewer oxygen and changes shape to kinky chains. Saturated can pack together better than unsaturated fatty acids. More kinks = less packing Lecture 9.12.16(Monday) AMINO ACIDS Cellulose – insoluble, strong and indigestible Glycogen/starch not very stable but east to break down Both held together by Hbonds but the types of glycosidic bonds is different Q: Why is cellulose insoluble? The potential to have hydrogen bonds is taken by glucose molecules so cellulose has no chance of bonding with water Cell membranes are formed by HPE but held together by the Van der Waals forces The more double bonds = more difficult to pack tightly = so membrane becomes more fluid The cooler the membrane = more fluid. If too cold = becomes like a gel Double bonds are usually found in cis fats rather than trans (related to bad health) Q: Why do we store energy more as fatty acids rather than glucose? Because there is more energy per carbon in f.a. compared to glucose. Fats also take up less space than glucose because there’s no water interacting with the lipids. Things that attach to Carbon in Amino acids: Hydrogen, Amino groups, Carboxyl, R groups Q: We have hundreds of amino acids but we build proteins only with 20 of them. Why? A: We build them out of 20 and then modify them after 6 Roles of Amino Acids Building blocks for Neurotransmitters Energy source Precursors for other biomolecules (they’re turned into other stuff) Anything we use Nitrogen (N) – typically is an amino acid Amino Acids are ionizable The simplest AA: glycine because it’s the simplest Q: Some of our R groups are ionizable (can gain/lose electrons). Why is this important? A: If you change the charge = change the structure = changes the function Peptide bonds (a form of covalent bond) are formed by losing a water molecule; breaking a peptide bond = use water molecule Ribosomes = catalyzes the reaction that removes/adds water to form a peptide bond ***IMPORTANT Note: Be able to tell from structures which group AA belong in and HOW they interact with water or not? Proteins function based on the variety of amino acids Whether or not AA interact with water has an impact on the protein structure and function ** MUST KNOW: Categories of Amino acids: Positively + negatively charged Rgroups hydrophilic (due to the OH groups) Aromatic (ring structures) = largely hydrophobic as a category Polar uncharged =hydrophilic Nonpolar R groups = hydrophobic and cluster together Nonpolar aliphatic = non polar that aren’t cyclic (no rings) The chain in peptide bonds are held together by covalent bonds but in their 3D shape, they are held by noncovalent forces together Adding more covalent bonds = increases stability Biotic = life Abiotic = without life Lecture 9.14.16(Wed) Two amino acids are joined together to form peptide Insulin = regulates blood sugar The typical protein size has hundreds of amino acids 7 Primary – the order of amino acids in a polypeptide. Held together by covalent bonds RNA = determines the primary structure of protein and RNA’s sequence is determined by DNA Secondary structure = 3D shape; interactions between residues that form a stable structure Tertiary = just more 3D structures added Quaternary = when you have more than one polypeptide Held by the four noncovalent forces Protein function = determined by protein structure Protein structure (3D shape) = determined by Amino acid sequences Peptide bonds do not rotate but other bonds may rotate depending on adjacent R groups (size and charge) Q: How can we determine a peptide sequence? Secondary structures Two common ones: alpha helix and beta sheet/strand Held together by hydrogen bonds that have specific angles Alpha – intramolecular Hbonds Beta – intermolecular Hbonds Alpha –helix Forms due to interactions b/w AA separated by four residues Rgroups of the AA point outwards from the axis They have a repeated 3.6 Amino acids/turn Stabilized by the Hbonds between C=O of one aa + NH of another one (these Hbonds are part of the polypeptide backbone not the Rgroup) Beta – sheet/strand More extended than alpha helix Rgroups alternate up and down orientation Hbonds between two strands stabilize the strands that can run in same or opposite directions Functions of proteins Catalysts, Hormones, Toxins and venoms, Growth factor, DNA binding, Ribosomal proteins, Visions, immunoglobins, structure, contractile, transportation, storage, Electron, transport. Lecture 9.16.16(Friday) Primary structure – held by covalent bonds Secondary – held by hydrogen bonds o Alpha/hairpin turn (180 degree turn) 8 o It takes four amino acids to make the turn o Proline and glycine are most likely to be found in alpha turns and least likely in alpha helix Tertiary + Quantenary strcutures– held by four noncovalent forces + disulfide bonding Noncovalent forces hold proteins in shape The diversity of R groups makes proteins unique Functions of proteins ** know the example of proteins for each of the functions below Catalysts, structural, contractile, transport, storage, electron transport, hormones, growth factor, DNA binding, ribosomal proteins, toxins and venoms, vision, immunoglobins All proteins bind to something else (other molecules) Membrane proteins their roles? **Reading for Monday’s class: Circulatory system just focus on the hemoglobin Q: How do proteins fold? Q: Why do small proteins have a higher rate of disulfide A: They have fewer opportunities for covalent bonds because less probability of HPE Disulfide bond; found only between SH and SS bonds Regulating a protein’s shape affects its function as well because they’re related Proteins contain chemical groups other than amino acids (called the prosthetic groups) ****Information that detects how proteins will fold is found in the primary sequence but how does it ‘know’ how to fold? How to test this hypothesis? Cooperative folding – the folding of one element doesn’t affect that of another Protein folding, which can take variety of pathways to occur is driven by Entropy – from high energy lower energy state Reverse of folding = called denaturing and some methods that can cause it: o Heat, detergents, mechanical agitation, urea, extremes of pH, and mercaptoethanol (breaks the SS bonds) o Denaturing causes the proteins to stick together Q: What exactly happens during denaturing? Why are denatured proteins less soluble than native ones and can they be renatured? Alzheimer’s disease is a result of misfolded proteins (exposure of a betastrand outside of the proteins) Ribonuclease A– an enzyme that breaks down RNA **Enzymes ends in “ase” 9 REVIEW Know why proteins form in a certain way Monday’s lecture will be tested if its about proteins, not nucleic acids Hbonds= formed between H atom and the four most eN atoms (O,N,Fl,Cl) Study the amino acids and the groups they belong to, how they interact with water? No need to memorize the AA Histimine = positively charged AA Probability of having a ‘Design your experiment” question