Mol Bio Exam 3

Front 1

What is the goal of ENCODE?

Back 1

to fully describe the list of functional elements that make up the human genome

Front 2

"wobble"

Back 2

non-Watson/Crick base pairs where a nucleotide can pair to a few different mRNA nucleotides

Front 3

Aminoacyl - tRNA synthetase

Back 3

1) forms a phosphodiester bond between an amino acid and ATP to get aminoacyl-AMP

2) forms a bond between aminoacyl-AMP and tRNA to get tRNA with amino acid on it

Front 4

Inosine

Back 4

Front 5

Dihydrouridine

Back 5

found in the D loop always in the same position

Front 6

Pseudouridine

Back 6

in the TψC loop

Front 7

A site

Back 7

"aminoacyl tRNA" site, where individual tRNAs enter the ribosome

Front 8

P site

Back 8

"peptidyl site" where growing chain of amino acids come out of the ribosome

Front 9

E site

Back 9

the exit site for tRNA

Front 10

IF-3

Back 10

initiation factor in bacteria that binds to the small subunit, blocks the exit site

Front 11

IF-1

Back 11

initiation factor in bacteria that binds near the A site to prevent any tRNA from coming into the A site so only P site is available

Front 12

IF-2

Back 12

Initiation factor in bacteria that interacts with tRNA(fMet) and can't bind to any other tRNA

has GTP activity - when large subunit is bound, GTP is hydrolyzed to GDP, IF-2 loses affinity and it ejected

Front 13

tRNA(fMet)

Back 13

initiator tRNA where f stands for formal, has formylated amino group to prevent formation of a chain in front of it, goes into the P site

Front 14

Shine Delgarno Sequence

Back 14

sequence in bacterial mRNA, upstream of the start codon, helps recruit the ribosome to the mRNA by aligning the ribosome with the start codon - binds to 16s rRNA when AUG is in the P site

Front 15

riboswitches

Back 15

regulatory segment of mRNA that binds a small molecule - flips RNA between 2 structures (can bind Shine Delgarno, surround tRNA and block ribosome, can be removed)

Front 16

eIF-3

Back 16

eukaryotic initiation factor that binds to 40s subunit and recruits complex with EIF2, tRNA(fmet) and GTP carrying Met

also interacts with eIF-4G

Front 17

eIF-4F

Back 17

is recruited along with mRNA when Met is added to the 40s subunit, recognizes capped mRNA

consists of eIF-4E, -4A, and -4G

Front 18

Kozack sequence

Back 18

sequence in eukaryotic mRNA that is recognized by the 18s rRNA, aligns the ribosome with the start codon and helps start translation

Front 19

eIF-4E

Back 19

cap binding protein, directs ribosome to the mRNA cap

Front 20

eIF-4A

Back 20

helicase, uses ATP hydrolysis to melt secondary structure of mRNA so the ribosome can scan for the start codon

Front 21

eIF-4G

Back 21

the "glue," involved in protein-protein interactions, binds the polyA binding protein that coats the polyA tail of the mRNA -> makes the structure of mRNA circular so translation is more efficient

Front 22

eIF-2

Back 22

a G protein that facilitates binding of Met to the small euk subunit

Front 23

eIF-2B

Back 23

guanine exchange protein that puts GTP on eIF-2 and removes GDP, thereby activating it

Front 24

heme controlled repressor

Back 24

kinase that phosphorylates the GTP-alpha subunit of eIF2 when the cell is experiencing heme starvation; after eIF2 ads Met to the small subunit and binds eIF-2B, GTP and GDP are exchanged but eIF2 and eIF-2B can't dissociate, this makes eIF2 unavailable so translation halts

Front 25

IRES

Back 25

internal ribosome entry site found on viral mRNA, does not depend on cap structure so after the virus stops host translation by decapping its mRNA can still be translated

Front 26

EF-Tu

Back 26

bacterial elongation factor that binds aminoacyl tRNA and GTP and has a high affinity for the ribosome; delivers tRNA

Front 27

GAC

Back 27

GTPase activating center in bacteria, part of the ribosome in the large subunit that catalyzes hydrolysis of GTP on EF-Tu (which puts it into low affinity so it dissociates)

Front 28

EF-Ts

Back 28

GTP exchange factor for EF-Tu

Front 29

EF-G

Back 29

binds and promotes movement of tRNA through the bacterial ribosome, also promotes movement of the ribosome down the mRNA

- binds to A site so small subunit ratches back and forth counterclockwise, EF-G stabilizes structure

-also has G protein activity, when it gets hydrolyzed and changes conformation the ribosome ratchets back to move down the mRNA

-mimics EF-Tu when they are bound to tRNA

Front 30

Accomodation

Back 30

process by which 2 adenosines in 1st codon position swing up and interact with the minor groove of mRNA, if codon/anticodon pairing is correct, a G in the 2nd position will cause a stacking interaction (no real interactions in 3rd due to wobble)

this stabilization is needed to proceed further

Front 31

Paromomycin

Back 31

drug that shifts adenosines to "up" position without the right codon/anticodon pairing so misreading occurs

Front 32

Experiment to prove which part of the ribosome is the peptidyl transferase

Back 32

Treat 50s subunit with protease so only 23s rRNA is left; it still supports 87% of activity and peptide bond formation

Front 33

Hyrbidized State

Back 33

forms after peptide bond occurs; acceptor stem in A site is moved over to the P site, and deacylated tRNA has affinity for the exit site

Front 34

Release Factors

Back 34

-recognize stop codons, hydrolyzes the peptide on tRNA to release it - when RF binds it opens up so GGQ can be involved with hydrolysis and other sequence can recognize the codon

-mimics the structure of tRNA when it is open

-RF1 and RF2 have different conserved sequences and recognize different stop codons

Front 35

GGQ motif

Back 35

motif in the release factors that is involved with hydrolysis of the peptide on tRNA, may be involved with G protein activity

mimics the 3' end of the animoacyl group of tRNA (CCA)

Front 36

Nonsense mediated decay

Back 36

process to get rid of RNA with an accidentally added stop codon

-recognized as "bad" if an exon junction complex is downstread of the "stop codon" so the ribosome slows down, RFs bind, proteins build a bridge to the exon junction complex and phosphorylate it and gets sent to processing bodies

Front 37

processing bodies

Back 37

densities withing the cytoplasm where RNA is degraded; mRNA gets decapped, deacylated and hydrolyzed down as part of nonsense mediated decay

Front 38

siRNA

Back 38

short interfering RNA, protects the prokaryotic cell from viral genome

Front 39

Dicer

Back 39

involved in producing siRNAs; binds to 3' end of dsRNA, cuts it (structurally homologous to RNase 3), gives a staggered end and always a specific length

also has PAZ domain: 3' overhang binding pocket

also cuts pre-miRNA before its tranfered to RISC

Front 40

RISC

Back 40

formed from one of the strands cleaved by Dicer and the protein Ago2

Activity is determined by the strand, or "guide sequence"

Ago2 has nuclease activity, allowing RISC to cleave complimentary mRNA (which can generate more small RNA and amplify effects)

can also engage polyA tail - translational repression

Front 41

miRNA

Back 41

small RNA that regulates ~50% of the human genome, targets mRNA at the 3" UTR end for repression or degradation

consists of strand cleaved by Dicer from pre-miRNA and transferred to Ago/RISC

Front 42

pri-miRNA

Back 42

the origin of miRNA; has lots of stem loop structure, ds stem is cut by Drosha

Front 43

Drosha

Back 43

cuts pri-miRNA 11nt up the stem to create pre-miRNA

Front 44

DGCR8

Back 44

recognizes region between ss and ds on pri-miRNA and orients Drosha

Front 45

pre-miRNA

Back 45

precursor miRNA with a 2 nt overhang at the 3' end, gets cleaved by Dicer

Front 46

piRNA

Back 46

piwi-associated RNA; part of the Ago family and looks like Ago structurally; stops transposon activity by preventing RNA-interferance activity in germ cells

Front 47

GW182

Back 47

bound to Ago2, has affinity for poly-A binding protein

can also bring things into processing bodies

can bind NOT1

complexes with multiple nucleases that interact with polyA tail, also recruits decapping proteins

Front 48

NOT1

Back 48

binds to GW182

can bind eIF4A1 (helicase) and prevent scanning, or eIF4AII and block movement of subunit (?)

Front 49

Ago2

Back 49

binds the guide strand to make RISC

can also engage 4E bound to the mRNA cap, interaction prevents 4G and 4A from binding

PAZ domain binds 3' overhang, piwi domain does cleavage and binds GW182

Front 50

seed region

Back 50

nts 2-8 on miRNA guide sequence that must have perfect base pairing with target RNA

Front 51

PAN2/3, CAF1, and CCR4

Back 51

polyA nucleases recruited by GW182

Front 52

DCP2

Back 52

decapping enzyme recruited by GS182

Front 53

XRN1

Back 53

exonuclease

Front 54

RITS

Back 54

"RNA-induced transcriptional silencing"

occurs in the centromere region where genes are repressed until S phase (heterochromatin)

Ago1 with guide RNA from centromere targets mRNA as it it made in the nucleus

Front 55

ORI

Back 55

origin of replication, consisting of three 13-mers and four 9-mers

Front 56

DnaA

Back 56

bind to 9-mers on ORI and opens up the strands, bacterial

Front 57

DnaB

Back 57

binds to ORI after DnaA has opened up the strands and stabilizes open complex

Has helicase activity, prevents unwinding, bacterial

Front 58

DnaG

Back 58

binds to ORI after DnaB, is a primase that makes the RNA primer that polymerase III will use, bacterial

Front 59

primosome

Back 59

DnaA, B, and G complex

Front 60

Ago1

Back 60

during RITS, binds guide RNA from centromere and recruits methylase, H3H9 (repression) and attracts Swi 6 (recompaction)

inactivates genes in the centromere

Front 61

Dam Sequence

Back 61

sequence at Ori (GATC) where the As can get methylated

Front 62

SeqA

Back 62

binds tightly to hemimethylated Dam sequence after replication, prevents binding to Ori and shuts off replication temporarily

binds the rest of DNA as it gets replicated and hemimethylated (which allows Ori to get fully re-methylated)

Front 63

single stranded DNA binding protein

Back 63

on lagging strand, protects it

Front 64

DNA gyrase

Back 64

DNA unwinding

Front 65

B clamp

Back 65

encloses DNA during replication, put on by the clamp loader, interacts with DNA Pol III during replication and dissociates from it when Pol III reaches end of Okazaki fragment, left behind on DNA

recruits Pol I to remove RNA primer from Okazaki fragment and replace it with DNA,

recruits DNA ligase to fix nick between fragments

Front 66

Bgl II

Back 66

restriction site used to cut fragments of DNA for Okazaki frgament experiment - end up with large fragment from primer to Bgl II that can't fit through the gel and a small fragment from Bgl II to primer

Front 67

clamp loader

Back 67

y-complex, an AAA+ ATPase, opens up 1 of 2 dimer interfaces on B-clamp and guides it onto 3' end of primer, then senses duplex and the junction and dissociates

delta subunit is in excess and exists independently of the loader, can trigger release of B clamp from DNA

Front 68

pol-alpha

Back 68

in euks, puts down primer that is combination of RNA/DNA

Front 69

ORC

Back 69

euk origin of replication complex, stays on DNA throughout cell cycle, binds cdc6, cdt1, and mcm2-7 during G1 phase

Front 70

licensing complex

Back 70

euk pre-replicating complex composed of ORC, cdc6, cdt1, and mcm2-7; in S phase kinase activities are activated to inactivate proteins so so pre-replication complex doesn't start replication again

Front 71

cdc45 and GINS

Back 71

cause strand separation in euk replication, recruited by the replicative complex

Front 72

pol I

Back 72

has 5'-3' exonuclease activity, can removed RNA primer and put down DNA

Front 73

DNase I hypersensitive sites

Back 73

genomic regions that are accessible to enzymatic cleavage as a result of the displacement of nucleosomes

Front 74

replisome

Back 74

DNA pol III bound to the primosome (Dna A, B, and G)