IAS01 Flashcards
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, read from 5’ to 3’, antiparallel, 10.4 base per turn
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
but cannot return from protein to mRNA
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 RNA polymerase II to promoter –>
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 -> 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 (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
alternative splicing
diff. splicing patterns
exons joined diff. comb. OR diff. exons used in diff. proteins
-> diff. proteins from 1 pre-mRNA
SMA genetics
originated from issues in splicing (autosomal recessive)
SMN2 C->T prevents binding of helper protein in intron -> spliceosome cannot assemble -> exon 7 removed along w/ introns -> protein shorter than normal i.e. alternative splicing (7/8 exons remain)
SMN nonfunctional -> not ensure survival of motor neuron -> motor neuron die
SMA symptoms
muscle wasting, weakness of muscle, infant death
genetic code properties
triplet code (1 codon, 3 nt, 1 AA)
degenerate: multiple codons code for same AA
existence of stop codons w/o tRNA
ribosome structure
rRNA held in place by proteins
large & small subunits, 5’ E P A 3’ site
large: catalyze peptide bond formation
small: mRNA positioning to read as codons i.e. mRNA reading
tRNA
adaptor btn mRNA & protein
carries individual AA, 20 types each carrying 1 type of AA
(charging: binding of tRNA w/ AA by aminoacyl tRNA synthetase)
translation initiation
small sunbunit binds to mRNA & moves to 1st codon -> tRNA carrying Met binds to AUG codon -> large subunit binds to small subunit to form complex while tRNA at P site
translation elongation
tRNA binds A -> P -> E (exit) site
A: match anticodon w/ codon, growing chain in P site added to AA in A site by peptide bond catalyzed by ribosome -> moives to P by ribosome moving 3nt across
P: AA removed i.e. deacylated -> moves to E
E: ejected & recycled
translation termination
stop codon reached, no tRNA & instead recruit release factor -> AA chain & mRNA released -> ribosome disassemble
histone posttranslational modification
methylation, acetylation, phosphorylation, etc. change histone struc, affects part of DNA exposed in nucleosome -> affect gene expression
