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This 10 page Study Guide was uploaded by Manna Notetaker on Monday February 15, 2016. The Study Guide belongs to BIO 120 at State University of New York at Oswego taught by Dr.Cruickshank in Spring 2016. Since its upload, it has received 21 views. For similar materials see Molecular and Cellular Foundations in Biology at State University of New York at Oswego.
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Date Created: 02/15/16
Manna Job Test 1 Atoms come together and forms molecules. Molecules atoms held together by chemical bonds. Covalent bonds are formed when electrons are shared. Ionic bonds are formed when electrons are transferred. Ion an atom or molecule with a net electric charge due to gain or loss of electron/s.Eg Na+ Cl forms an ionic salt NaCl. Water 1 oxygen covalently bonded to two hydrogens. Water is POLAR! partial () charge on oxygen and partial (+) charge on hydrogens. Electrons are spending most of their time around the oxygen atom rather than hydrogen atom which makes oxygen more negative and H more positive. Hydrogen Bonds Bonds between water molecules. WEAK BONDS! always breaking off and reforming. Ice isless dense than liquid water hence it floats on water. This is because in Ice atoms are farther apart and hydrogen bonds are forming and breaking at a lesser rate when compared to liquid water.Molecules are still moving in ice.Ice melts when hydrogen bonds break. Solution Solute substance being dissolved. Solvent substance that does the dissolving. Solution Solute + Solvent. E.g. When salt is dissolved in water, water molecules attach to the Na+ and Cl, breaks their ionic bond and as a results dissolves in water. Need a crew of H2O molecules to do this. Most proteins are soluble in water because they have regions that are attracted to water molecules. Hydronium Sometimes when two water molecules come together, a H+ proton moves from one molecules to other making that molecule H3O+ (hydronium )and the one left behind OH (hydroxide). pH When [H+]=[OH] the pH = 7. pure water has a pH of 7. The solute in the sol’n is going to influence the pH by shifting the values of H+ and OH . pH indicates the acidity of the solution. If pH is not 7 there is more H+ and OH free to react. pH scale number differs by a factor of 10. If pH of a sol’n is 7 and pH is 6 for another the one with 7 is 10 times more basic than the sol’n with pH 6. add acid → raises [H+] lowers [OH] → lowers pH add base → lowers[H+] raises [OH] → raises pH Buffers minimizes change in pH. usually made of weak acid base combo. Earth has carbon based life carbon is looking for four electrons to share. Hydrocarbons are hydrogen and carbon. used as fuels. nonpolar covalent molecules. E.g. butane, propane, ethane. Hydrophilia vs. hydrophobic Hydrophilia likes water, polar molecules, charged molecules Hydrophobia fears water, nonpolar molecules. LARGE BIOLOGICAL MOLECULES 1. Carbohydrates . monomer monosaccharide polymer polysaccharide 2.Proteins monomer amino acids polymer polypeptide, protein 3.Nucleic acids monomer nucleotide polymer polynucleotide, nucleic acids 4.Lipids monomer fatty acids polymer fats, phospholipids, steroids and waxes. polymer many, oligomer few, dimer two, trimer three, tetramer four Synthesis of polymers Dehydration/ condensation assembles polymers through the process of losing a water molecule. E.g. trimer becoming a tetramer and wa water molecule going out. Hydrolysis process of breaking down polymers by adding a water molecule. E.g. tetramer becoming a trimer. 1. Carbohydrates monosaccharides linear form. When in aq, form a ring form. mono to disaccharide dehydration rxn. 2 glucose coming together to make a maltose Glucose critical sugar. multicellular organisms store glucose for functions like cellular respiration. Polysaccharides (carbohydrate polymers ) 1. Starch function: energy storage. in: plants broken down by: plants 2. Glycogen function: energy storage in : animals broken down by : animal enzymes 3. Cellulose function: structural in : plants broken down by : microbial enzymes 4. Chitin function: structure in : fungi, plants, animals broken down by: plant enzymes, fungal enzymes Humans are not very good at breaking down cellulose. Sheeps, cows etc have bacteria in their gut that can break down cellulose for them. 2. ipids ● Fats : triacylglycerol formation triacylglycerol = glycerol 3 fatty acids (condensation/dehydration) Fatty acids can vary in length depending on the number and location of C=C. Saturated acids NO double bond. lies straight Unsaturated acids Double bond. (cis or trans) bent a little. Hydrogenation of fatty acids polysaturated fatty acids cis fatty acids (natural) and trans fatty acids (artificial ) ● Phospholipids : hydrophobic tail, hydrophilic heads forms a bilayer so hydrophobic tails are away from water and hydrophilic head are in water. makes the layer flexible ● Waxes : extremely hydrophobic. water impermeable barrier can be created with waxes. ● Steroids: e.g. cholesterol. serves as a base for hormones, estrogen and testosterone 3.Nucleic Acid monomer nucleotide. components phosphate group, pentose sugar (5 sugar), nitrogenous base 5 nitrogenous bases : cytosine, thymine, uracil, (pyrimidine) adenine and thymine (purine) DNA (deoxyribonucleic acid ) phosphate + deoxyribose + A,C,G, or T (one of the four) phosphate and deoxyribose forms a sugar phosphate backbone. Phosphodiester linkage between the 3’ carbon and 5’ carbon. DNA is typically double stranded (2 polynucleotides). The two halves are complimentary. 3 →5, A→ T and C→ G Bases form hydrogen bonds.Lots of hydrogen bonds makes the DNA stable. A=T and C triple bond G (one purine and one pyrimidine). Double bond between A&T and triple bond between C&G also adds to the stability. Base Pair sugars, phosphate and nucleotides. One molecule of DNA can be millions of base pairs long. Chromosome a really big molecule of DNA. RNA ( ribonucleic acid) components phosphate, ribose and nitrogen base (A,G,C,U ) Phosphate and ribose forms the sugar backbone. Difference between DNA and RNA DNA deoxyribose, Thymine. Function : information storage RNA ribose, Uracil Function: information transfer, enzymatic activity and regulatory activity 4. Proteins monomer : amino acid Structure : amino group, alpha carbon, hydrogen, side group and a carboxyl group The carboxyl and amino group remains the same. The side group changes. can be polar(serine which is hydrophillic) or nonpolar (lucine which is hydrophobic) There are 20 amino acids. Smallest Glycine. Largest Tryptophan. Amino acid polymer polypeptide. Amino group at end is N terminus and carboxyl group end is C terminus. ● Primary Structure long, linear structure. ● Secondary structure coils and folds. alpha helix and beta sheets. whether or not you get the alpha helix and beta sheets depends on the particular amino acid order. you can get either one or none at all. Alpha helix and sheets are formed by hydrogen bonds ● Tertiary structure held together by hydrogen and ionic bonds. disulfide bridges (comes from sulfur ) these bridges are covalent bonds ● Quaternary structure two or more subunits e.g. chaperonin from Ecoli. formed from multiple subunits. Protein Functions: enzymatic functions structural functions transport functions signaling (hormones, receptors) storage movement defensive venoms and toxins CHAPTER 8 METABOLISM Metabolism biochemical modification and use of organic molecules to support the activities of life Catabolism breakdown of complex molecules ( releases energy) Anabolism making complex molecules from simpler molecules ( requires energy) Energy forms: chemical, thermal, light,magnetic, electrical energy Energy states : kinetic (energy of motion), potential (stored energy) Laws of Thermodynamics : 1. Energy cannot be created or destroyed. it can only be transformed or change form. 2. ENtropy in universe increases with transfer of energy. Free Energy (G) G is the energy in a system available to do work. (uniform temp and pressure) e.g of work : small molecules in a cell becoming larger molecules, moving silia, particle moving through phospholipid. delta G= change in free energy. Delta G = Delta H+ T delta S Delta G : final stage energy initial stage energy Delta H: change in enthalpy (total energy in sys. ) T : Temp in Kelvin Delta S : change in system’s entropy Delta G ● spontaneous rxn, exergonic (energy exits) ● Gproducts < Greactants. Reactants have more free energy. ● +delta S entropy increases ● delta H nthalpy decreases +Delta G ● rxn requires energy to start, endergonic (energy enters) ● Gproducts > Greactants. Reactants have less free energy ● Delta S ● +Delta H Entropy in universe increased. Delta G + Delta S Delta H + Delta G Delta S + Delta H Chemical reactions, energy and Enzymes e.g of a biochemical reaction: H2O+Sucrose → glucose + fructose Delta G hydrolysis rxn (breaking down), catabolic, spontaneous,exergonic Reverse reaction : Glucose + Fructose → H2O + Sucrose +Delta G dehydration rxn( making complex molecules), anabolic, not spontaneous , endergonic Sometimes endergonic and exergonic rxns are coupled together. Most commonly used Exergonic rxn in cells isTP hydrolysis ATP Triphosphate group, ribose sugar and adenine. similar to RNA but RNA only has two phosphate groups. Phosphate groups in ATP are all negatively charged and thus unstable so ATP hydrolysis occurs ATP + H2O → ADP + P + energy hydrolysis, exergonic, Delta G Example of pairing ATP dephosphorylation with an endergonic rxn is converting glutamic acid to glutamine. SInce endergonic, DeltaG is + amines belong amino acids ATP regeneration: ATP + H2O → ADP + P + Energy from catabolism(spontaneous, exergonic) → used for cellular work (anabolic , endergonic) Enzymes Cells cannot rely on random collisions to produce energy to do cell work. Enzymes come in. they effectively enable chemical reactions by lowering activation energy and making bond forming/breaking much more likely to happen. Enzymes : mostly proteins act as catalysts effectively enabling chemical rxns and do not affect delta G substrates (what the enzyme acts on) are chemically changed not the enzyme itself. specific for particular substrates often ends with _____ ase eg. glutamine synthetase Enzyme and substrate Active sitesbind substrates with weak bonds orient substrate stresses substrate ( strain bonds and stabilize transition state ) provides favourable microclimate and may directly participate in chemical rxn through formation of temporary covalent bonds. An enzyme can have multiple active sites. Glutamine synthetase has 12. Catalytic Cycle : Substrates enter active site of an enzyme and forms enzymesubstrate complex. Substrates are held in active site. Active site lowers the activation energy and effectively enables the rxn. Substrates are converted into products and products are released. The enzyme is unchanged and its active site is available for new substrates. What affects enzyme activity level? 1. pH 2. temperature (both affects enzyme's ability to function) E.g. Tyrosinase is an enzyme involved in pigment introduction and it is affected by temperature as seen in the bunny with dark ears and feet and the cat with dark ears and feet. 3. Presence/ concentration of substrate If we inc. the conc. of substrates, overall enzyme activity is higher. If substrate conc. decreases overall enzyme activity is lower. 4. Presence/ concentration of cofactors Cofactors may be required to allow or enhance enzyme activity. inorganic or organic cofactors can exist. 5. Presence/Concentration of inhibitors Inhibitors negatively affects enzyme’s ability to function. Competitive inhibitor : binds to active site and thus substrate is unable to bond. noncompetitive inhibitor :binds to another site and changes the shape of active site and it wil not recognize substrate. Irreversible inhibitor:permanently binds to an enzyme which is dangerous because then substrates cannot bind and the enzyme is ruined. inhibitor level goes up, enzyme activity goes down inhibitor level goes down, enzyme activity goes up 6. Presence/ concentration of activator Activator enhances enzyme activity If activator level goes up, enzyme activity goes up. Feedback inhibition: When products acts as activators. eg. Isoleucine (noncompetitive inhibitor) binds allosterically so threonine cannot bind. Regulated by the product. CHAPTER 6 The more surface is exposed the more interaction the surface will have with the environment. A mouse will have a higher surfacevolume ratio when compared to a bear. a mouse will lose moe heat to the environment than a bear. Cells and Basic Cell anatomy Prokaryotes: Bacteria and archea 110um. Features: plasma membrane, chromosomes, ribosomes,nucleoid,cytoplasm, flagellum Eukaryotes 10100um. Features: plasma membrane, chromosomes, ribosomes, cytoplasm, flagellum (mostly protists) Cytoplasm cytosol + organelles(except nucleus) Cytosol mostly water. also contains amino acids, ions, P inorganic phosphate and other small molecules. Plasma membrane Components : phospholipids → hydrophilic heads and hydrophobic tails. Proteins Cholesterol in animal cells Plant cells are rigid because of cell wall. Animal cells are more flexible due to the lack of cell wall and the cholesterol provides flexibility in animal cells. Parts of the cell 1. Nucleus: surrounded by nuclear envelop(double membrane) with pores and continuous with endoplasmic reticulum. Contains chromosomes(made of chromatin), nucleoli( ribosomes are made here). The pores regulate the enter and exit of materials. hromatin DNA + associated proteins Chromosomes One DNA molecule plus associated proteins 2. Ribosomes: composed of ribosomal RNA and proteins. Lots of ribosomes in one cell. can be free floating in cytosol or attached to ER. Function is protein synthesis. Components of endomembrane system. Endoplasmic reticulum: extensive network of membrane tubules and sacs. separate lumen from cytosol continuous with nuclear membrane. Rough(ribosomes) and Smooth ER Function: (rough) synthesis of proteins from ribosomes,adds carbs to proteins to make glycoprotein, produces new membrane. (smooth) Synthesis of lipids, Ca2+ storage, detoxification of drugs and metabolism of carbs. Golgi Apparatus: s tacks of flattened membranous sacs no ribosomes attached. has polarity. cis and trans phases Function: modification of proteins, carbs, phospholipids, synthesis of polysacchs, sorting and transport of vesicles. Vacuoles : plant cells, paramecium.Large membrane bound vesicle. digestion, storage, waste disposal,water disposal. Function: cell growth and protection. Lysosomes : membranous sac of hydrolytic enzymes (animal and fungi) Function: breakdown of digestive materials, cell macromolecules and damaged organelles for recycling. Not endomembrane system Peroxisomes: specialized metabolic structure bounded by one membrane contains enzymes that transfers hydrogen atoms from substrates to oxygen producing H2O2 and the water from that. Peroxisome, chloroplast and mitochondria a re all membrane bound but not from endomembrane system because the did not originate from the ER pH is different in different areas of a cell: mitochondria 8, ER 7.2 , Lysosomes 4 lowest pH and most acidic hence the membrane around so that the digestive materials stays in the sac and separate from rest of the cells. Components of Cytoskeleton Microtubules hollow tubes. made from protein tubulin. functions: maintenance of cell shape,cell motility(cilia and flagellum) organelle movement, chromosome movements during cell division. Microfilaments two intertwined strands of Actin (protein). each a polymer of actin subunits. function: maintenance of cell shape,changes in cell shape, muscle contraction, cytoplasmic streaming, cell motility(pseudopods in amoeba) , cell division Intermediate filaments: fibrous proteins supercoiled into thicker cables.one of proteins from keratin function: maintenance of cell shape,anchorage of cell nucleus and other organelles, formation of nuclear lamina. Cilia and flagella ( specialized microtubule arrangement) Cilia move the cell itself or moves the stuff around the cell ex: human respiratory flagella moves the cell. ex. sperm, unicellular organisms. Organelles responsible for energy generation Mitochondrion bounded by double membrane. inner membrane has infoldings called cristae. has ribosomes inside mitochondrial matrix and also has its own chromosomes. function: cellular respiration. Chloroplast (plants and algae) Two membranes around the fluid stroma which contains thylakoid stacked into grana. also has its own ribosomes. function: photosynthesis. Flow of energy. Light to ATP to cellular work. Cellular respiration Organic Compound + O2 → → → CO2 + H20 + energy C6H12O6 + 6 O2 → → → 6CO2 + 6 H20 + ATP + heat Delta G = 686 (exergonic, spontaneous, catabolic) Cellular resp. proceeds in many steps with enzymes. Electrons move around, lose energy that ends up in ATP. Redox Rxn CH4 + 2 O2 → CO2 + energy + 2 H20 Methane: reducing agent Oxygen: oxidizing agent Reducing agent is oxidized, loses e , and loses energy Oxidizing agent is reduced, gains e , gains energy and is often oxygen. Sometimes products of redox rxn has charges. sometime products are uncharged but bonds are polar. Reduction of NAD+ to NADH NAD+ has a nucleotide format. Dehydrogenase (enzyme) catalyzes this rxn of NAD+ to NADH. Stages of cellular respiration initial stage of cellular respiration ( glycolysis ) occurs in the cytosol. Glycolysis is a 10 step rxn. Pyruvate Oxidation pyruvate is transported across the mitochondrial membrane by transporter protein. Oxidized to acetyl CoA Producing 1 acetyl CoA 1 CO2 and 1 NADH Citric Acid cycle ( The Krebs Cycle)
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