IAS01

Question 1

nucleoside vs nucleotide

Answer 1

nucleoside: base + pentose
nucleotide: base + pentose + phosphate

Question 2

pentose of nucleotide characteristics

Answer 2

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

Question 3

DNA v RNA

Answer 3

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

Question 4

nucleotide bases & base pairing

Answer 4

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

Question 5

DNA structure & grooves

Answer 5

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

Question 6

RNA structure

Answer 6

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

Question 7

RNA functions & types

Answer 7

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

Question 8

DNA coiling

Answer 8

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)

Question 9

central dogma of molecular biology & newer developments

Answer 9

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

Question 10

collinearity

Answer 10

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

Question 11

transcription initiation

Answer 11

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

Question 12

transcription elongation

Answer 12

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

Question 13

transcription termination, requirement & energy source

Answer 13

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

Question 14

splicing major processes

Answer 14

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

Question 15

splicing (OPTIONAL)

Answer 15

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

Question 16

alternative splicing

Answer 16

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

Question 17

SMA genetics

Answer 17

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

Question 18

SMA symptoms

Answer 18

muscle wasting, weakness of muscle, infant death

Question 19

genetic code

Answer 19

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

Question 20

ribosome structure

Answer 20

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

Question 21

tRNA

Answer 21

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

Question 22

translation initiation

Answer 22

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

Question 23

translation elongation

Answer 23

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

Question 24

translation termination

Answer 24

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

Question 25

histone posttranslational modification

Answer 25

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

Question 26

transcription factors

Answer 26

bind to DNA promoters to trigger transcription

Question 27

DNA enhancer region

Answer 27

increase chance of transcription:
cis-acting enhancers few knt away bind to activator, forms loop -> attach to TIC to trigger transcription

Question 28

mediator (transcription)

Answer 28

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

Question 29

methylation

Answer 29

silences gene as transcription factors cannot bind to methylated protein

Question 30

DNA insulator region

Answer 30

reduce chance of transcription
inhibitor protein e.g. CTCF bind to insulator to prevent TIC formation

Question 31

DNA insulator silencing

Answer 31

methylation of C prevent CTCF binding, no CTCF to prevent TIC formation

Question 32

gene expression regulation

Answer 32

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

Question 33

cell variety & gene expression

Answer 33

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

Question 34

reverse transcription application

Answer 34

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