Please help me out with these biochemistry questions. Thanks.
Question 1-4 are multiple choice. Question 5-7 are drawing, short, and long question.
1) Which of the following statements about membrane proteins are NOT true?
A) Peripheral membrane proteins must be extracted from lipid bilayers with detergent.
B) A 30 Angstrom membrane can be crossed by an alpha-helix 20 amino acids long.
C) The transmembrane domains of a beta barrel protein can be easily predicted from a
hydropathy plot.
D) Proteins with a single transmembrane domain can flip-flop in the membrane.
E) In the cell, membrane proteins are made on cytosolic ribosomes.
2) Select all the statements that are true about nucleic acid structure:
A) DNA double helices can exist in the right handed A-form, right-handed B-form, or left- handed Z-form.
B) RNA-DNA heteroduplex helices are typically found in the equivalent of the B-form DNA helix with the ribose in the C-2′ endo conformation.
C) In Watson and Crick’s model of the DNA double helix, there were 15 basepairs per turn, with a rise of 3.4 Angstroms per basepair.
D) Hydrogen bonding between basepairs is the driving force for helix formation.
E) Single stranded RNA is less stable than single stranded DNA because the 2’OH can
catalyze cleavage of the phosphodiester bond.
3) Select the following statements about chymotrypsin that are true.
A) Chymotrypsin’s active site consists of a catalytic triad: aspartic acid, histidine, andcysteine.
B) Chymotrypsin increases the speed of peptide hydrolysis by providing an alternative chemical pathway.
C) Chymotrypsin is not an enzyme because it is covalently modified during the reaction.
D) Changes in pH affect chymotrypsin’s Km, but not its Vmax.
E) Chymotrypsin hydrolyzes peptide bonds C-terminal to hydrophobic residues, such as
Phe.
4) Addition of an enzyme to a reaction
A) Increases the initial rate of the reactionB) Decreases the free energy change between substrates and products. C) Increases G‡D) Changes the KeqE) Both A and C
5) Given these molecular components – glycerol, fatty acid, phosphate, and carbohydrate– answer the following:
A) Which is present in a ganglioside but not in a glycerophospholipid?
B) Which two are present in both triacylglycerides and phosphatidylcholine?
C) Which two are in sphingomyelin and phosphatidylcholine?
6) 5-Methylcytosineoccursonapproximately5%ofeukaryoticcytosines. Methylated cytosine can spontaneously deaminate to form thymine, therefore eukaryotic cells have highly specialized enzymes that specifically repair G–T mismatches in DNA that occur when a G-C basepair deaminates cytosine to G-T.
A) Draw a G-C Watson-Crick pair include H-bonds. Your drawing must include the bases and should indicate where the riboses would be (you don’t have to drawribose + phosphates).
B) Draw a G-T mismatch pair (include H-bonds) – note that, like Watson and Crick, you should look for the form that optimizes H-bonding.
C) Given your drawings, name one feature that the G-T mismatch repair enzyme might detect.
7) Cas9isanenzymeformedbyacomplexofRNAandproteinusedbybacteriatobind and cut DNA as part of the bacteria’s defense to phage infection. Unlike other DNA endonucleases that generate double strand breaks, Cas9 cuts DNA at sites specified by the sequence of the bound RNA (“a guide RNA”). Cas9 has been engineered for use as a genome editor in human tissue, which has significant potential for gene therapy.
Go to RCSB PDB online and look up the structure 4OO8 of Cas9 with a guide RNA and target DNA strand.
A) What are the chain IDs (these are letters) associated with the protein, DNA, and RNA?
B) What other molecule is modeled in the structure?
C) There are two nucleic acids present – RNA and DNA. How many basepairs are involved in an RNA-DNA heteroduplex?
D) In this complex, the RNA serves both information encoding and structural purposes. What would be the difference in biological consequences if you mutate nucleotides in the RNA stem loops versus the region that base-pairs with the DNA?
E) Two key features of nucleotides are their phosphate backbone and bases. Please describe how specific amino acid side chains can interact with these two features to stabilize protein-RNA interactions. You should discuss the particular sidechain features that enable the interactions.Hint: Look at 1) the 5’ end of the RNA and 2) Cas9’s “bridge helix” amino acids 63-89.
