BIOCHEM C785 Final Exam Latest update With Complete Solution

1) What is the basic structure of an amino acid? List the 4 groups and describe what they look like. + alpha carbon ©, Amino group ( NH2 or NH3, Carbonyl group( cooh) and variance or side chain(R group) 2) How do you identify the 3 different types of side chains: non-polar/hydrophobic, polar, and charged? Non Polar:::: ( Hydrophobic)- water hating -Ch3 or C and H ( side) special case: Tryptophan is a hydrophobic nonpolar even tho is has a single N Polar:::: ( Hydrophilic): OH, NH, ( center). Just O! SH is a special polar called Cysteine ending in SH. Charged:::: + or – ( Ionic bond) can be polar. 3) What kind of bonds do each of the 3 different types of side chains make? answered above: The reason we care about what class an amino acid belongs: So, we know what kind of interactions it can form to stabilized a protein tertiary structure. Hydrophobic interact with hydrophobic- C H. Polar interact via Hydrogen bonds. + or – charge interact va Ionic bond -s-s Cysteine side chain can interact via Disulfide bond. 4) Protein Folding: What are the 4 levels of protein structure? List distinguishing features of each. - Primary- Linked by peptide bond. -Secondary-The alpha helix(coil) or pleated sheets. -Tertiary -Protein folding (3 dimensional shape that is necessary for protein to function. -quaternary: 2 or more folded amino acid chains come together to make final working protein. ALL PROTEIN HAVE PRIMARY, SECONDARY AND TERTRIARY BUT SOME ONLY HAVE QUATERNARY STRUCTURE. Ex. Myoglobin only has the first 3. Hemoglobin has 4 subunits . Myoglobin only 1 subunits. - 5) What bonds make up each level of protein structure and how are they formed? Primary: Peptide bond. Formed by dehydration syntheses. Broken by Hydrolysis ( H20ADD) Secondary: Hydrogen BOND. Alpha Helix between above and below. Beta sheets Faraway. Tertiary: hydrophobic interactions: -Weakest but greatest in #! Hydrogen bond: Stronger than hydrophobic. This study source was downloaded by from CourseH on :07:30 GMT -05:00 Ionic bond: Stronger than hydrogen. Disulfide bond: strongest but fewest in number. Quaternary: SAME as ABOVE. 6) What environmental change breaks each type of bond? Disulfide Bond: Strong reducing agent. Ionic and hydrogen bond: Ph change and high salt concentration. Hydrophobic: HEAT Primary – Peptide bonds (backbone) Secondary – Hydrogen bonds (backbone) Tertiary – Hydrophobic interactions, hydrogen bonds, ionic bonds, disulfide bonds (side chain) Quaternary – More than one subunit held by hydrophobic interactions, hydrogen bonds, ionic bonds, disulfide bonds (side chain) 7) What type of amino acid side chain leads to protein aggregation? -Protein that can denature can aggregate. Its BECUZ of HYDROPHOBIC interaction. 8) How do environmental changes affect protein folding? Above: - hydrophobic-Heat. H and I: PH and Salt. Dis: reducing agent. 9) How do mutations affect protein structure? - 10) How do enzymes catalyze reactions? By Lowering activation energy and increasing RATE. This study source was downloaded by from CourseH on :07:30 GMT -05:00 - Special case: ALL ENZYMES ARE PROTEIN THAT CATALYSTS BUT NOT ALL PROTEIN ARE ENZYMES NOR ALL CATAKYSTS ARE ENZYMES, 11) How do enzymes affect reaction rate and activation energy? Increases reaction rate and Lowers activation energy. BY SIMPLIY REDUCING AMOUNT OF ENERGY NEEDED TO GET REACTION. 12) What are the 4 steps of the enzymatic cycle? - A) Starts with enzyme and its substrate floating around in the cytoplasm. Ex. E+S - B) Substrate and Enzyme meet and substrate BINDs TO ACTIVE site. EX. ES ( ENZYME -substrate Complex) - C) Catalysis Occurs, Converting the substrate to product. Forming EP ( ENZYME PRODUCT COMPLEx) - D) The product leaves the active site and we get enzyme and product floating around in solution. Indicate as E+P - 13) How do environmental changes affect enzymes? Increasing temp results in increased reaction. Its crucial that the enzyme retain its proper three-dimensional shape. If we increase temp too much it will denature the enzyme to no longer function. The only way TO INCREASE THE RATE OF THE REACTION WOULD BE TO INCREASE THE AMOUNT OF SUBSTRATE IN THE REACTION UNTIL THE ENZYMES BECOMES SATURATE WITH substrate. What is induced fit? The induced fit refers to the conformational change that the enzyme undergoes when it binds to the substrate to form the enzyme-substrate complex. Therefore, the enzymatic cycle step that occurs after the induced fit is the formation of the enzyme-product complex. 14) What are the differences between competitive and noncompetitive inhibitors? Competitive binds to the active site and Noncompetitive binds to allosteric site. 15) When given an enzyme pathway, be able to analyze that pathway under normal conditions and under inhibition. What molecules increase/build-up or decrease given a specific inhibitor? - When we inhibit an enzyme, its product declines. If we inhibit an enzyme its substrate accumulates. - Kinases: adds a phosphate group into something else ex. Sugar molecule. Kinase always get the phosphate they give from ATP. - Phosphatases: an enzyme that removes a phosphate group from something else. Its mineral ( P) 4 O2, Pi-inorganic phosphate ( mineral);