General, Organic, and Biochemistry II Exam 3 Study Guide
General, Organic, and Biochemistry II Exam 3 Study Guide CHEM1031
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This 7 page Study Guide was uploaded by Rachael Chandler on Sunday April 3, 2016. The Study Guide belongs to CHEM1031 at The University of Cincinnati taught by Dr. Ridgway in Winter 2016. Since its upload, it has received 91 views. For similar materials see General, Organic, and Biochemistry II in Chemistry at The University of Cincinnati.
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Date Created: 04/03/16
General, Organic, and Biochemistry II Exam 3 Study Guide ** = There were several clicker/Connect homework questions on this topic -Chapter 19: Enzymes Classification and Naming: Two ways to classify: Traditional/historical and by enzyme commission number Historical/Traditional (The method used in this class) Generally, enzyme names end in –ase Names are generally derived from substrate or reaction catalyzed, though there are classic names that don’t follow either of these rules 6 Basic Types: ** 1. Oxidoreductase ** – Oxidation-Reduction Oxidase: Catalyzes a redox oxidation-reduction reaction involving oxygen (O 2 as an electron acceptor Reductase: Catalyzes a reduction reaction Some can go both ways, acting as an oxidase and reductase; coenzymes can be involved 2. Transferase – Transfer a group Transaminase: Transfers an amino group Kinase: A phosphotransferase (Transfers a phosphate group); usually involved in reactions with ATP/ADP 3. Hydrolase – Hydrolyze Cleave bonds by adding water Example: Phosphatase (Not the same as phosphotransferase) removes a PO 42group 4. Lyase – Lyses (Breaks bonds) Break bonds by method other than oxidation or hydrolysis; often involving double bonds Example: Decarboxylases cleave bonds between the carboxyl group and amino group in amino acids; can also decarboxylate other organic acids 5. Isomerase ** – Changes Stereochemistry Epimerase and Racemase: Change the position of groups on a compound around an asymmetric carbon Epimerase works on compounds with multiple asymmetric carbons, racemase works on compounds with one. 6. Ligase – Links parts Transfers a group to a compound How Enzymes Work: Enzymes lower the activation energy (E )aof a reaction ** Enzyme-Substrate The enzyme combines with the substrate at is active site ** (Usually a pocket/cleft that is complimentary to the shape of the substrate) Substrate held in place by weak interactive forces Lock and key v. Induced Fit Enzyme models Reaction: E + S ES ES* EP E + P ** *Transition State Transition State: Enzymes may put stress on a bond, pull two reactants together, change the pH of a solution, etc. to speed up reactions Classes of Specialty – Enzymes react with specific things Absolute: Enzyme will react with only one type of molecule Group: Enzyme will react with one group, but that type of group can be on several different molecules Linkage: Enzyme reacts with a specific type of bond Stereochemical: Enzyme will recognize one type of enantiomer Nomenclature: Apoenzyme: The part of a multicomponent enzyme that is made of protein and requires a cofactor Cofactor: A component required for some enzymes to function; not made of protein but can be organic compounds, metal ions, etc. Prosthetic Group: A cofactor that is tightly bound (possibly even covalently bonded) to an apoenzyme Holoenzyme: An apoenzyme with its cofactor attached to it. Coenzymes: A secondary, substrate-like compound that is usually an organic or phospho-organic molecule bound to the enzyme by weak interactions or hydrogen bonding. Most carry electrons and have modified vitamins as part of their structure. Things the Affect Enzymes: Optimal pH and pH Range (Temperature, saturation, etc.) Enzymes have unique, optimum pHs at which they work fastest. If they get outside a certain range, they begin to denature The same goes for temperature Similar with saturation, the enzymes can only handle so many substrates before they are saturated. After that point, adding more substrate won’t have an effect on reaction rate. Regulation Some enzymes are produced only when needed; some have on-off switches (Allosteric enzymes); others operate under feedback inhibition; zymogens; etc. There are different types of inhibitors that can bind to enzymes to prevent their catalyzing reactions (Irreversible v. Reversible; Competitive v. Noncompetitive) Proteolytic Enzymes: Cleave peptide bonds in proteins, destroying primary structure -Chapter 20: Genetics Nucleotides ** Basic structure includes a phosphate, a sugar, and a nitrogenous base o Ribose v. Deoxyribose o Purine Bases: Adenine, guanine o Pyrimidine Bases: Cytosine, thymine (DNA only), uracil (RNA only) A nucleoside is just the sugar and nitrogenous base Structure of DNA and RNA ** Nucleotides come together to make a chain of phosphodiester bonds, organized in a 3’ to 5’ structure; the backbone is made up of the sugars and phosphates (Sugar- phosphate backbone) DNA has a double helix structure, held together by hydrogen bonding between the nitrogenous bases of the two parallel strands o The strands are antiparallel (5’ of one lines up with 3’ of the other) and complementary ** o C-G forms 3 H-bonds ** o A-T and A-U form 2 H-bonds (T is only found in DNA, U is only found in RNA) ** RNA has a single helix structure, also held together by the hydrogen bonding mentioned above Cell Types Prokaryotes o No nucleus o DNA is organized in 1 circular DNA molecule that is replicated bidirectionally o Contains nucleoids (A complex in which the DNA is attached to several proteins at around 40 points to form loops) Eukaryotes o Contains a nucleus enclosed by a nuclear membrane o Contains nucleosomes (Strands of DNA wrapped around histone proteins) o Replication begins at several origins and moves bidirectionally DNA Replication (Mostly in Eukaryotes) DNA is replicated before a cell divides so each new cell has a copy of the DNA The replication is semiconservative (1 double helix is used to make two new double helices) Replication Fork: Where the DNA is “unzipped” Leading Strand: Replicates from the 5’ end to the 3’ end continuously Lagging Strand: Replicates from the 3’ end to the 5’ end in segments because DNA must be replicated from 3’ to 5’ Lots of enzymes involved like helicase (‘unzips’ the DNA), DNA polymerase III (catalyzes the addition of nucleotides in the 5’-3’ direction), etc. ** DNA can synthesize more DNA, or it can synthesize RNA that is later translated to proteins RNA 3 Main Types o mRNA (Messenger RNA): Dictates the amino acid sequence of proteins being made; complimentary copy of a gene on the DNA; uses codons (triplet pairs) o rRNA (Ribosomal RNA): Structural and functional component of ribosomes o tRna (Transfer RNA): Transfers amino acids to the site of protein synthesis; each tRNA codes for a specific amino acid; 64 different types of codons/anticodons; more than one base can code for the same amino acid; there are specific start (AUG) and stop codons (UAA, UAG, UGA) ** Protein Synthesis Step 1 – Transcription: DNA serves as a strand template for a new RNA strand o Initiation: RNA polymerase binds to the promoter region at the beginning of the gene ** o Chain Elongation: A 3’-5’ phosphodiester bond is formed, creating a complimentary copy of the DNA o Termination: RNA polymerase releases the newly formed RNA o RNA Splicing: Removing portions of the primary transcript that don’t code for proteins; Introns are portions of the code that don’t correspond to amino acids; Exons are the parts of the sequence that do code for amino acids Step 2 – Translation/Protein Synthesis o Carried out on ribosomes (rRNA); large subunit binds to mRNA, large subunit binds to tRNA ** o Initiation: Initiation factors, mRNA, initiator tRNA, and small and large ribosomes come together o Chain Elongation: tRNAs come into place on the mRNA and join amino acids with peptide bonds, creating primary structure of the protein The A site is where the next tRNA binds The P site is where the tRNA shifts to allow a new tRNA to bind to the A site GTP is used for energy (Instead of ATP) o Termination: When a stop codon is reached a release factor binds to the empty A site, the polypeptide chain is released, and all subunits dissociate; occasionally post-transcriptional modification occurs Mutations: mistakes introduced into the DNA o Silent Mutation: A mistake that causes no change or doesn’t manifest o Point Mutation: Changes one nucleotide in a codon ** Transitions: Replaces a purine with a purine or a pyrimidine with a pyrimidine (A G, C T/U) Transversions: Replaces a purine with a pyrimidine or vice versa (A, G C, T; C, T A, G) o Frame Shift Mutation: A change that disrupts the rest of the chain of codons, completely changing the primary structure of a protein (Almost always lethal) Deletion Mutation: Take one or more nucleotides out of the sequence Insertion Mutation: Adds one or more extra nucleotides to the sequence o UV Damage: Causes covalent linkages of adjacent pyrimidine bases; can result in skin cancer Restriction Enzymes: Bacterial enzymes that cut the sugar phosphate backbone of DNA at specific nucleotide sequences Agarose Gel Electrophoresis: Main method used to study DNA; looks at size of DNA molecules using electric currents Hybridization: Used to identify the presence of a gene in a specific DNA fragment Polymerase Chain Reaction: A technique that allows scientists to clone unlimited identical genes -Chapter 21: Carbohydrate Metabolism Passive and Active Transport The movement of chemicals through cellular membranes Active: Requires energy and moves materials against their concentration gradients Passive: Materials move from a region of high concentration to an area of low concentration; requires no input of energy Facilitated Diffusion: Membrane proteins help the process of passive transport by allowing large and hydrophilic molecules through the membrane ATP: Adenosine Triphosphate Made from oxidation of carbohydrates Cells use an energy conversion that oxidizes glucose and other monosaccharides; small amounts of energy are released at lots of points in this process which are stored in ATP bonds Exergonic – Energy Releasing – Catabolic Endergonic – Energy Requiring – Anabolic Energy is taken from ATP by hydrolyzing phosphoanhydride bonds. ATP ADP + 7 kcal ** Catabolic Processes Catabolism: Breaking larger molecules into smaller molecules or subunits (Opposite of anabolism); Degrading carbs, fats, and proteins to release energy Carbohydrates are the most readily used source All broken parts go into the citric acid cycle Stage 1: Hydrolysis of Dietary Macromolecules Purpose: To degrade foods into subunits Proteins and polysaccharides begin in the mouth being broken down by saliva. Further degraded in the stomach and small intestine Stage 2: Conversion of Monomers to Oxidizable Forms Glycolysis: Glucose or fructose converted to Acetyl CoA and enter the citric acid cycle; Glucose catabolism Proteins and lipids follow similar paths ending in acetyl CoA Stage 3: Complete Oxidation and Production of ATP Glycolysis Begins with D-Glucose and requires no oxygen (Anaerobic); occurs in the cytoplasm ** Products: 4 ATP, NADH (carries anions and electrons elsewhere), pyruvate (used for different purposes based on cell needs) Slightly ineffective because little ATP is produced Ten Steps Catalyzed by Enzymes ** Reaction 1: Glucose phosphorylated by hexokinase; energy used to produce glucose-6-phosphate ** Reaction 2: Glucose-6-phosphate becomes fructose-6-phosphate by phosphoglucose isomerase ** Reaction 3: Fructose-6-phosphate phosphorylated by phosphofructokinase; yields fructose-1,6-bisphosphate and uses energy Reaction 4: Fructose-1,6-bisphosphate split into two separate 3-carbon intermediates by aldolase forming glyceraldehyde-3-phosphate (G-3-P) and dihydroxyacetone phosphate (Later also converted into G-3-P) Reaction 5: Dihydroxyacetone phosphate is rearranged into G-3-P by triose phosphate isomerase + Reaction 6: G-3-P is oxidized to carboxylic acid and reduces NAD to NADH; this is the first step to produce energy Reaction 7: ATP harvested by phosphoylating ADP Reaction 8: 3-phosphoglycerate is isomerized to 2-phosphoglyverate by a mutase Reaction 9: Enolase catalyzes dehydration of 2-phosphoglycerate Reaction 10: Another ATP produced by taking phosphate from phosphoenolpyruvate to ADP; Water is also produced Fermentation: Process that oxidizes NADH and pyruvate for reuse under anaerobic conditions Lactate Fermentation: Occurs in exercising muscles ** Alcohol Fermentation: Yeast breaks down sugars anaerobically (Does not occur in humans); 2 ethanol and 2 CO p2oduced ** The Pentose Phosphate Pathway: The alternative to glycolysis for initial oxidation of glucose in the cytosol Produces parts for biosynthesis, NADPH (Most reduced product), precursors for nucleotides, and precursors for aromatic amino acids ** Steps 1-2.5: Glucose-6-phosphate+2NADP +H ORib2lose-5-phosphate+2NADPH+2H + CO + 2 ~ 1/3 of products converted to ribose-5-phosphate by isomerase (For RNA/ATP) ~ 2/3 products converted to xylulose-5-phosphate by epimerase Final Steps Variety of C5-C7 sugars formed, many of which are also made/used in glycolysis Gluconeogenesis and Glycolysis Gluconeogenesis: Metabolic pathway that makes glucose from non-carbohydrate substances; occurs mostly in liver; converts lactate, glycerol, amino acids, etc. ** Regulation: Step 3 of glycolysis – Phosphofructokinase stimulated by high AMP, ADP, P,iinhibited by high ATP; Reverse in gluconeogenesis is catalyzed by fructose-1,6-bisphosphate, stimulated by high ATP, used during times of high (excess) energy Cori Cycle: Regenerates glucose after anaerobic oxidation; lactate from skeletal muscle transported to liver where it is converted to pyruvate then close and returned to muscles Glycogen is the sole source of energy for mammalian red blood cells and the major source for the brain Glycolysis: Metabolic pathway that makes glucose into pyruvate Gluconeogenesis v. Glycolysis Opposites, but not simple reverses of one another because of several non- reversible steps that are bypassed by new routes Glycogenolysis: Degradation controlled by glucagon and epinephrine in response to low blood sugar and stress Step 1: Glycogen phosphorylase catalyzes removal of an end glucose as glucose-1- phosphate Step 2: Debranching enzyme catalyzes removal of the last glucose at an alpha(16) branch Step 3: Phosphoglucomutase converts glucose-1-phosphate to glucose-6-phosphate Glycogenesis v. Glycogenolysis High blood sugar – Hyperglycemia o Insulin stimulates glucose uptake Elevates glucokinase, activates glycogen synthesis Low blood sugar – Hypoglycemia o Glucagon inhibits glucose uptake **This study guide is just a general overview of all the things we’ve gone over between the last exam and now. To get a better idea of what will be on the test, use the review we’ll be going over later in class. If you want any more detail on any of the topics above you can consult my earlier notes or the PowerPoints on blackboard. For more review, go back over the PRS questions from lectures and old connect and learnsmart assignments. Good luck on exam 3!
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