IAS01 Flashcards
nucleoside vs nucleotide
nucleoside: base + pentose
nucleotide: base + pentose + phosphate
pentose of nucleotide characteristics
1’: link to base
2’: determine DNA or RNA
3’: link to phosphate of adj nucleotide
5’: link to phosphate
DNA v RNA
DNA: DS, 2’ hydrogen, thymidine, for info storage, resilient (permanent)
RNA: mostly single stranded, 2’ -OH, uridine, various functions, transient
nucleotide bases & base pairing
adenosine – uridine / thymidine
cytidine — guanosine
purine - pyrimidine
note: T +1 -CH3 group from U
chargaff’s rule: %A=%T, %C=%G
DNA structure & grooves
rh double helix, ds, chiral, read from 5’ to 3’, antiparallel, asymmetric
base in center, backbone at outside
major grooves & minor grooves, major more accessible to transcription factor binding as less distortion of DNA shape
RNA structure
mostly single-stranded, more struc variety, more varied functions, rarely base pairing
can form more H bonds by binding to RNA nts apart from base pairing
RNA functions & types
info transfer (mRNA)
AA carrier (tRNA)
catalyst (rRNA)
sgRNA, snRNA, siRNA
DNA coiling
coil around +vely charged histone octamers, namely H2A, H2B, H3, H4, to form nucleosome (basic subunit of chromatin) -> fiber -> loop (75k nt) -> rosette (6 loops) -> coil (30 rosettes) -> chromatid (10 coils)
central dogma of molecular biology & newer developments
DNA -> RNA -> protein i.e. replication, transcription, splicing, translation
HIV virus do reverse transcription
information harder to return from proteins to nucleic acid, but through epigenetics proteins can modify DNA
collinearity
relationship between DNA base sequence & protein AA sequence
Sense/coding strand (5’ → 3’) = mRNA stand (5’ → 3’) = polypeptide (N->C)
transcription initiation
TATA-box binding protein binds to TATA box of promoter
other components of TFII bind i.e. transcription factors assemble at promoter
mediator carries RNAP to promoter to bind
combine to form transcription initiation complex
transcription elongation
helicase unwinds DNA to expose base in transcription bubble
antisense / template strand act as template for RNA synth which is read in 3’ to 5’, sense / coding strand not involved & go outside
free RNA nt triphosphate enters RNAP -> hydrolyze to form RNA nt & bind to template strand one at a time by CBP -> hybrid helix forms -> nascent / pre-mRNA forms 5’ to 3’ & exits in diff. strand
transcription termination, requirement & energy source
terminator sequence or randomly
Mg2+ dependent
energy from ATP & hydrolysis of RNA TPs to move RNAP & form mRNA chain
splicing major processes
5’ capped with 7-methylguanylate (5’-5’ bond) to stabilize DNA
3’ end polyadenylated
introns removed & cleaved by spliceosome (protein complex) & exons remain
edited mRNA travels out of nucleus by pore to cytoplasm
splicing (OPTIONAL)
spliceosome removes 1 intron
Assembly proteins assemble at intron/exon borders, U1 binds to 5’ end, U2AF & BBP binds to 3’ end, splicing factors act as beacons to guide 5 snRNP, U2, U4, U5, U6, to promote spliceosome formation
Spliceosome brings exons on both intron ends close together
Intron end cuts 5’ end at GU & folded back on itself to A -> loop / intron lariat
Spliceosome cuts 3’ end at AG -> detach intron -> exons joined / splice sites connected
mRNA released, spliceosome disassembles