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Biochemistry Exam 3

Protein Synthesis

What does a sigmodal shaped curve show? The sigmodal shaped curve shows that the binding within the helix has cooperativity.
What important interactions contribute to the sigmodal shape of the melting curve. One of them is hydrophobic forces which causes the hydrophobic bases to move to the center of the helix. the polar sugar phosphates-backbones face the water. the other interactions are base-stacking and H-bonds.
What force holds base-stacking? van der waals forces
Which protein loads the helicase onto the DNA during the initiation phase of prokaryotic DNA replication? DnaC
Consider the following DNA sequence 5'ATGGTCCATTCAG3'. What nucleotide would be trasncribed? 3' UACCAGGUAAGUC5'
From 3' UACCAGGUAAGUC5', what are the first 3 amino acids that are translated? Met- Asp- His
From the previous sequence sequence question, is this enzyme able to synthesize mRNA de novo? The sequence codes for mRNA which can be catalyzed by an RNA ploymerase. It can synthesize mRNA because it does not require a primer to begin transcription and it does not need to check a prior base. DNA on the other hand requires a primer to begin.
Explain the synthesis of the lagging strand of DNA during DNA replication. The lagging strand is synthesized away from the replication fork. The cell overcomes this by synthesizing the parent DNA of the lagging strand in Okazaki fragments. The DNA is pulled to form a loop that resembles a trombone slide.
Continue the explanation of lagging strand after loop. The loop is synthesized by DNA poly III once the primer is laid down. DNA poly I replaces the primer and adds nucleotides. The DNA ligase seals the nick. Once the Okazaki fragment is synthesized, replication machinery detaches and forms another loop.
Why does DNA contain a T and not U? If DNA had U instead of T, after deamination there would be incorrect Us that are identical and not removed. after DNA replication, the DNA would be mutated. DNA has a T instead because the repair enzyme removes the U, places the correct base pair.
Explain a similarity between DNA Poly I and aminoacyl tRNA synthetase. Both have proofreading capacities and can remove an incorrectly added base in DNA Poly I and amino acid fro aminoacyl tRNA.
How does DNA Poly I and aminoacyl tRNA synthetase differ? They differ in the type of substrates they need. DNA Poly I uses a growing strand of DNA with a free 3'OH of deoxyribose and dNTPs as substrates to replicate DNA. aminoacyl tRNA uses an already formed tRNA and adds amino acids to a free 2'OH or 3'OH.
What is a strong promoter? a strong promoter is close to the consensus sequence. it binds RNA poly more often.
What is a weak promoter? a weak promoter differs from consensus sequence and binds RNA poly less often.
What is the name of the enzyme that catalyzes the splicing of hnRNA? snRNPs.
What is the purpose of the 5' cap? The purpose of the 5' cap is to protect the mRNA from nucleases and phosphotases with its 5'-5' GpppA structure and to assist the small ribosome subunit in binding to the mRNA.
What nucleotide almost always forms the 5'cap? The 5'cap is almost always a Guanine.
What amino acid would be added to a tRNA with the anticodon IAG? CUA, CUG, CUU, therefore Leu
What is the degenerate genetic code? A degenrate genetic code has 64 codons with 61 coding for 20 amino acids. this means that most of the amino acids have more than one codon.
What is the wobble hypothesis? The third mRNA nucleotide in the codon and first tRNA nucleotide of the anticodon do not form full base pairs like the other 2 nucleotides.
How does the degenerate genetic code and wobble hypothesis interface one another? they both help prevent negative consequences of mutations. The degenerate genetic code ensures that a mutation in one nucleotide still has a chance of coding fro the same amino acid. The wobble hypothesis lowers the chance of a.a change by not fully inter
How is the reading frame in the translation of mRNA a set in a prokaryotic system? the mRNA binds to the ribosomes through its shine delgamo sequence. tranlsation begins at 1st AUG codon on 3' side of shine delgamo. one of the roles of the 5' cap is to help bind the ribosome so that it starts at the correct postion.
Describe the termination phase of translation. Upon reaching one of the three possible stop codons, no regular tRNA is recognized. the release factors bring water and bind to the stop codon. this stimulates the peptidyl transferase to hydrolyze bond between tRNA and protein, release proteins.
what is a positive supercoiled DNA? an overwound DNA with left handed coil
what is a negative supercoiled DNA? an underwound DNA with right handed coil
Why can supercoils be important? it compacts the size of the DNA, has a smaller volume, and it can fit in a nucleus cell.
Would you expect the promoter regions within DNA to be negatively or positively supercoiled? DNA is typically not found with positively supercoiled cells. If the promoter was supercoiled this would make it harder for transcription to occur, since it would be harder to unwind DNA. also it would affect the rate or the possibility of expression.
Created by: cgalici1