IAS01 Flashcards

1
Q

pentose of nucleotide characteristics

A

1’: link to base
2’: determine DNA or RNA
3’: link to phosphate of adj nucleotide
5’: link to phosphate

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2
Q

DNA v RNA

A

DNA: DS, 2’ hydrogen, thymidine, for info storage, resilient (permanent)
RNA: mostly single stranded, 2’ -OH, uridine, various functions, transient

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3
Q

nucleotide bases & base pairing

A

adenosine – uridine / thymidine
cytidine — guanosine
purine - pyrimidine
note: T +1 -CH3 group from U
chargaff’s rule: %A=%T, %C=%G

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4
Q

DNA structure & grooves

A

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

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5
Q

RNA structure

A

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

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6
Q

RNA functions & types

A

info transfer (mRNA)
AA carrier (tRNA)
catalyst (rRNA)
sgRNA, snRNA, siRNA

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7
Q

DNA coiling

A

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)

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8
Q

central dogma of molecular biology & newer developments

A

DNA -> RNA -> protein i.e. replication, transcription, splicing, translation
HIV virus do reverse transcription
but cannot return from protein to mRNA

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9
Q

collinearity

A

relationship between DNA base sequence & protein AA sequence
Sense/coding strand (5’ → 3’) = mRNA stand (5’ → 3’) = polypeptide (N->C)

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10
Q

transcription initiation

A

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

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11
Q

transcription elongation

A

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

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12
Q

transcription termination, requirement & energy source

A

terminator sequence or randomly
Mg2+ dependent
energy from ATP & hydrolysis of RNA TPs to move RNAP & form mRNA chain

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13
Q

splicing major processes

A

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

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14
Q

splicing (OPTIONAL)

A

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

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15
Q

alternative splicing

A

diff. splicing patterns
exons joined diff. comb. OR diff. exons used in diff. proteins
-> diff. proteins from 1 pre-mRNA

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16
Q

SMA genetics

A

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

17
Q

SMA symptoms

A

muscle wasting, weakness of muscle, infant death

18
Q

genetic code properties

A

triplet code (1 codon, 3 nt, 1 AA)
degenerate: multiple codons code for same AA
existence of stop codons w/o tRNA

19
Q

ribosome structure

A

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

20
Q

tRNA

A

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)

21
Q

translation initiation

A

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

22
Q

translation elongation

A

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

23
Q

translation termination

A

stop codon reached, no tRNA & instead recruit release factor -> AA chain & mRNA released -> ribosome disassemble

24
Q

histone posttranslational modification

A

methylation, acetylation, phosphorylation, etc. change histone struc, affects part of DNA exposed in nucleosome -> affect gene expression

25
Q

transcription factors

A

bind to DNA promoters to trigger transcription

26
Q

DNA enhancer regions & insulator regions

A

enhancers increase chance of transcription:
cis-acting enhancers few knt away bind to activator, forms loop -> attach to TIC to trigger transcription
insulators reduce chance of transcription:
inhibitor protein e.g. CTCF bind to insulator to prevent TIC formation

27
Q

DNA methylation & e.g. in gene silencing & activation

A

e.g. silences gene as transcription factors cannot bind to methylated protein
e.g. in DNA insulator silencing, methylation of C prevent CTCF binding, cannot prevent TIC formation

28
Q

mediator (transcription)

A

binds several transcription factors & controls transcription, can enhance or silence gene
demonstrates complexity as multiple TF needed to activate mediator

29
Q

gene expression regulation

A

histone posttranslational modification
enhancers, insulators, transcription factors
posttranscription processing & posttranslational processing control
mature mRNA degrade into nt
modified protein degrade into AA

30
Q

cell variety & gene expression

A

diff. proteins expressed in diff. cells & diff. dev. stages for diff. function due to gene expression
failure to do so lead to cancer

31
Q

reverse transcription application

A

reverse transcription of mRNA into cDNA analyzes mRNA expression in cancer cells (overexpression or underexpression) by fluorescing cDNA & adding into microarray
compare amount of cDNA reversely transcripted from one sample w/ cDNA of another sample (w/ CBP)
used in diagnosis & management of cancer