BIOC 2 Flashcards
(23 cards)
bioinformatics
the development and application of computer science to the analysis of large amounts of biological information.
genomics
study of all genes in an organism
system biology
they study of biological systems taking into account the interaction of the key element of DNA, RNA , proteins and cells with respect to one another, the interaction of this information may be by computer.
met genomics
direct genetic analysis of genome contained with an environmental sample
the study of all genes in a system/environment
biologists
tool users
genomic sequence (diagram)
1- sequence (fragment of gene/cDNA to genome)\
2-sequence clean up
3-similarity search (BLAST)
4- difference between sequence and reference
5-cliinical significance
6-clinincal action
class of genes
house keeping genes or constitutive genes (always expressed)
not highly regulated
inducible genes
expression induced or repressed
highly regulated
operon
a set of co-transcribed genes under the control of a single regulated promoter.
immunization - adaptor
- insertion of foregin DNA from viruses/ plasmids
- a complex of CRISPER associated (cas) proteins is expressed from the cas operon.
- the complex recognises foreign DNA
- it cleaves/cuts a piece out\
- it inserts it into the gene encoding the CRISPER cRNA
- this provides an array of tags of foreign DNA (spacers) with common pieces between (repeats).
immunity -inference
- the CRISPER repeat spacer ncRNA transcribed into pre-CRNA that is processed/cleaved into mature crRNAs.
- these crRNA combine with cas protein and are used as a guide by cas complex to inactive/cleave the corresponding invading nucleic acid
- the centre part of the crRNA (yellow) can base pair to the DNA target.
promoter region
where RNA polymerase binds
rifampicin (RIF)
binds to catalytic (beta) subunit of RNAP
stalls transcription
specific interactions with beta subunits amino acids
(s411)
treatment= amino acid change in this region of rpoB= resistance in TB.
REAL time PCR
- quantitative and diagnostic PCR
1) probes A and E detect MTP rpoB gene- present > need treatment
2) probes B,C,D bind/. detect lack of RIF resistant mutations- if binds to RIF is expected to work
termination of transcription (2 mechanisms)
1) RHO INDEPENDENT
- most common
- specific hair pin/ stem loop structure
- also called intrinsic terminator
2) RHO DEPENDENT
- rho binds to RNA = stops transcription
regulation of transcription (overview)
1- promoter strength
- degree of match of the consensus for a sigma factor
- strong or weak promoters
2-presence of alternative sigma factor
-active under different conditions
3- presence of transcription factors
- positive or negative regulation
- binding affinity - may be modified (allosterically or covalently)
the lac operon
encodes proteins that catabolise lactose and is induced when lactose is available
activation of lac operon
requires both inducer and low glucose- two systems
trp operon - enzymes encode make tryptophan (trp)
- biosynthetic operon
- the order of the gene is the same as the pathway
- the enzyme are not made if tryptophan is already available
feedback loop 1
trp binds TrpR and co-represses operon. TrpR is the repressor and tryptophan =corepressor.
feedback loop 2
the trp operon is also regulated by attenuation - regulated transcription termination
attenuation
trpL mRNA leader can form alternative RNA structures.
when tryptophan is abundant it forms - termination early in mRNA= no trp operon syntheses
summary of trp operon regulation (negative feedback )
1- the operon encodes (trp) biosynthesis enzymes
2- sufficient Trp acts as co repressor to prevent transcription
-negative regulation through - promoter/operator
3- trp triggers attenuation and premature termination of transcription in the leader sequence.
-negative regulation through termination mechanism.
