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Activation of photoreactivation repair is completely dependent on UV light, hence it is known as light repair which leads to light reaction on the other hand mismatch repair works in absence of UV light and hence is known as dark repair which leads to dark reaction.
Photoreactivation repair has a simple mechanism having only single step reaction whereas mismatch repair has a complex mechanism of two steps, firstly it has to quickly recognize the mismatches and secondly it has to make a correct and accurate mismatch.
Types of enzyme /proteins present in photoreactivation repair is only one and that is photolyase whereas in mismatch repair there are various types of enzymes and proteins like MutS, MutH, MutL proteins, Dam methylase, DNA helicase II, SSB, DNA polymerase III, Exonuclease I, Exonuclease VIII , Exonuclease X, RecJ nuclease and DNA ligase.
Working of photoreactivation repair requires product of one gene whereas working of mismatch repair requires interaction of three element which are as follows, MutS mismatch containing DNA results in MutL, this inturn activates MutH which is an enzyme consisting of incision or nick on one strand near the site of mismatch. Thereafter nicking is followed by helicases and one of the three exonucleases.
In photoreactivation repair enzyme photolyase dependent on energy from the sun cleaves cross link DNA which is caused by UV damage whereas in mismatch repair N-glycocylase cleaves cross links in DNA without utilizing energy from sun.
Type of damage in photoreactivation repair is pyrimidine dimmers and in mismatch repair it is the mismatches.
In photoreactivation repair mechanism there is a removal of photodimers induced by UV radiation of sunlight. The process takes place as follows photoreactivating enzyme known as photolyase bind to thymine dimmers and split them in presence of light and folic acid a co-enzyme of photolyase. Here folic acid takes the light energy and splits the enzyme to photodimers whereas in mismatch repair there are certain enzymes present which are able to recignize and accurately correct the damaged DNA strands.
Photoreactivation repair is applicable to single lesion whereas mismatch repair is applicable to multiple lesions.
Photoreactivation repair is a non-catalytic process, here one protein is required for each removal hence the process is energetically costly then mismatch repair which is a catalytic process.
In comparison to photoreactivation repair in mismatch repair it is expensive to keep accuracy.
Q.2. Give a general definition of the term â€˜consensus nucleotide sequenceâ€™, and list five named prokaryotic/eukaryotic examples of such sequences, their location and functions.
A short linear series or sequence of nucleotides present in a genome, performing a specific function in different organisms is called as consensus sequence. It is an ideal sequence for interaction with regulatory proteins.
Basically, it is a way of representing results of multiple sequence motifs. Therefore they are also know as conserved sequence motifs. It is an ideal sequence for interaction with regulatory proteins.
List of consensus nucleotide sequence present in eukaryotes is as follows:
TATAAAA CONSENSUS SEQUENCE
TATAAAA consensus sequence is called as TATA BOX.
It is a DNA sequence found in promoter region of genes in eukaryotes. It is also called as Goldberg-Hogness BOX. It is surrounded by GC rich proteins.
Approximately24% of human gene contains TATA box within the core promoter.
LOCATION: It is located around 25-30 base pairs upstream of startpoint of transcription. This is a binding site of RNA polymerase II and also for transcription factors to form initiation complex.
It plays an important role in positioning RNA polymerase haloenzyme on a promoter. This process is done by marking a point just before point where transcription begins.
Helps in acquiring optimal transcription.
AAUAAA CONSENSUS SEQUENCE
LOCATION: It is located 100-1000 bases away from actual end of mRNA found near polyadenylation site of eukaryotic mRNA.
- Brings about the process of termination.
- Also leads to accurate and efficient cleavage and helps in invivo polyadenylation of pre-mRNA as well as invitro polyadenylation reaction. In simple words, it promotes polyadenylation.
GGCCAATCT CONSENSUS SEQUENCE
GGCCAATCT is also known as CAAT BOX. It is a highly conserved DNA sequence. It is found within the promoter region of protein encoding genes of many eukaryotic organisms. It is bound by CTF/NF1 family. It consists of distinct pattern of nucleotides.
LOCATION: It is located 75-80 base pair upstream from the starting site of transcription.
It enhances binding of RNA polymerase.
It increases promoter strength.
It also determines efficiency of transcription.
It signals binding site for RNA transcription factor.
GGGCGG CONSENSUS SEQUENCE
GGCGG is also known as GC BOX which is a regulatory DNA elements of eukaryotic genes. This sequence is rich in guanidine and cytidine nucleotides. It binds to transcription factor- Sp1.
LOCATION: It is centred at -90. Located upstream to transcription start site in region of 100-150bp further upstream from TATA BOX.
It functions as an enhancer.
It carries out transcription both upstream and downstream.
A/GCCACCAUGG CONSENSUS SEQUENCE
A/GCCACCAUGG is also known as KOZAK consensus sequence.
LOCATION: It occurs in eukaryotic mRNA and lies within 5â€™ untranslated region.
It plays a major role in the process of initiation of translation.
It targets ribosomes to the initiation codon in eukaryotes and directs translation of mRNA .
Also the cap structure plays an important role in protecting 5â€™end of mRNA from attack of exonuclease enzyme.