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Phgy209 > Fuck Bio Haha > Flashcards

Fuck Bio Haha Flashcards

1
Q

Antennapedia

A

Transcription factor that tells specify genes to turn on during development

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2
Q

What’s a vector?

A

Specialized plasmid that was engineered to carry out specific functions

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3
Q

cDNA

A

DNA synthetised from a single stranded RNA (mRNA or miRNA) by the action of the ez reverse transcriptase

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4
Q

Ribonuclease H or RNase H

A

Enlève le segment de RNA dans un dsRNA:DNA (une solution alkaline peut aussi imiter cette fonction en brisant tous les liens H)

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5
Q

cDNA libraries

A

-Quand on veut se concentrer sur les protéines coding genes
-Isoler le mRNA de tRNA et de rRNA : oligo T nucleotides linked to a solid support. Wash the junk.
Poly A linked avec T: ça sert de primer pour RT
-On enlève le RNA avec solution alkaline ou RNase-H.
-On ajoute un polydG adapter. On prime avec un poly dC. Là on obtient un ds cDNA.
-Ajouter des restrictions sites aux deux bouts pour pouvoir insérer dans un plasmid.
-la library est représentative du nombre de mRNA de chaque sorte dans l’organisme

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6
Q

Polynucleotide Kinase

A

Phosphorylation of nucleotides by adding gamma (y) phosphate of ATP to the free hydroxyl at 5’end of the oligonucleotides. Ça rend radioactif : utiliser pour faire des probes qui sont visibles

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7
Q

Lac promoter

A

Quand on ajoute du galactose, le gène downstream se fait transcrire

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8
Q

How to transfect a vector in animal cell

A

Lipid treatment or electroporation

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9
Q

Solid support

A

Nitrocellulose for RNA

Nylon for DNA

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10
Q

Probe

A

Single stranded nucleic acid complementary with target (acts as a visual aid, donc a quelque chose pour qu’on le voit)

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11
Q

2 ways to make probes

A

Polynucleotide kinase: takes the y phosphate of ATP and put it on free hydroxyl of 5’end of the oligonucleotide (makes radioactive)

By PCR: sauf qu’on utilise certains nucleotides radiolabeled on their alpha phosphate (watch out, you have to make it single-stranded before using it)

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12
Q

Why alkaline solution dénature DNA

A

Bc less H in the solution, plus OH- qui attire les H des liaisons entre bases

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13
Q

Ca2+ binding protein

A

Calmodulin: quand avec Ca, binds to other prots (because other conformation) in a Ca2+ dépendant manner

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14
Q

Plastid

A

Organelle for transcription in plants and algae

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15
Q

Poison that affects Pol

A

Alpha-amanitin

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16
Q

SDS

A

Sodium Dodecylsulfate

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17
Q

ChIP-chromatin immunoprecipitation

A

Antibody + agarose beads.
Antibody recognizes phosphorylated residues on CtD of elongating (or pausing) Pol II.

Centrifugation.

Next-gen sequencing of DNA/RNA bound to the Pol II

To find actively transcribed genes

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18
Q

Reporter genes

A

Gives info about relative efficiency of transcription (luciferase, bc gives light or GFP)

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19
Q

Recognition helix

A

Alpha-helical domain of the transcription factors that binds with non-covalent interactions with the bases in the major groove

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20
Q

EMSA

A

Electrophoretic mobility shift assays

Savoir quel bout de ton promoter est bound par des transcription factors

Make dsDNA radiolabbeled probe de ton cis-element qui est important + electrophoresis. Ceux qui vont pas loin: bound to proteins

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21
Q

Acetylation

A

Rend histone + chargé donc interagit plus avec DNA

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22
Q

P-TEFb or CDK9

A

Phosphorylation of Ser2

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23
Q

Hybridation experiment

A

To find existence of introns!

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24
Q

RNP

A

Ribonucleoprotein

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25
Q

Self splicing introns

A

Group I: nuclear rRNA in protozoan

Group II: tRNA and rRNA in mitochondria and chloroplasts

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26
Q

Ce qu,on fait avec le lariat intron

A

Debranching enzyme: rend ça linéaire et après chewed up

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27
Q

Sequence that contains the polyadenylafion signal (AAUAAA)

A

Recognized by cleavage and polyadenylation stimulating factors

Cleaved at the polyA site
+ PAP

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28
Q

RNA editing

A

Ça change À to I et C to U (attention Ca peut causer un stop codon plus tôt)

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29
Q

NLS

A

Nuclear localisation signal : sur protéine qui doit aller dans le noyau

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30
Q

mRNA exporter

A

2 subunits: NXF1 and NXT1

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31
Q

2 organismes vraiment importants

A

E.Coli + bacteriophage lamba

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32
Q

Autoradiography

A

To see hybridized probes

33
Q

Shine Dalargo in mammaliens

A

Kozak sequence

34
Q

Kozak sequence

A

ACCAUGG

35
Q

De U2snRNP à U1snRNP

A

Cross-exon recognition complex

36
Q

SR proteins bind to

A

Exonic splicing enhancers

37
Q

Enzyme to oxydate SH groups on cysteine to make disulfide bridges

A

PDI: Protein disulfide isomerase (only present in ER)

38
Q

Chaperonins for humans

A

TriC and GroEL for bacteria

39
Q

Oxydation

A

Perte d’un H

40
Q

Enzyme pour créer des disulfide bridges

A

PDI (protein disulfide isomerase). On la trouve juste dans ER

41
Q

Chaperones

A

Hsp70, Hsp90
Dans ER: BiP and Calreiculin/Calnexin (BiP qui lache Ire1 crée une dimerisation de celle-ci + UPR : augmentation transcription factor pour chaperones)

42
Q

Sequence in the 3’end of UTR in mRNA that tend to shorten lives of mRNA

A

Repeats of UAAAU

43
Q

Which amino acid are phosphorylated?

A

Serine, Threonine, Tyrosine

44
Q

Protein modification (post-translational)

A

Phosphorylation
Glysosylation
Lipid moieties
Methylation / acetylation

45
Q

Amino acid pour ubiquitin

A

Lysine

46
Q

What is linked scanning mutation?

A

(To find which part of the promoter/upstream region is really important for transcription initiation / what part binds proteins)

47
Q

EMSA

A

Electrophoretic mobility shift assays

48
Q

Recognition helix

A

Alpha helix dans DNA binding domain des transcription factors

49
Q

Acetylation

A

Rajout d’un acetyl, rend l’histoire moins positif, donc la chromatine est plus ouverte donc plus de transcription : actif.

50
Q

YSPTSPS

A

Repeat dans CTD

51
Q

CPSF

A

Cleavage and polyadenylation stimulating factors

52
Q

CDK9 / P-Tefb

A

Phosphorylation of Serine 2

53
Q

eIF5

A

Arrive avec tRNAi bound to eIF2-GTP

54
Q

ABCE1 complex

A

A les eIF 1, 3 and 1A

55
Q

Polysome

A

mRNA avec pleins de ribosomes dessus

56
Q

IREs

A

Iron response element (in 3’UTR)

57
Q

Isomers of amino acids

A

L (common), D (rare)

58
Q

Topoisomerase

A

Relieves supercoil avant la réplication fork

59
Q

polycistronic mRNA

A

Suite à un opéron, se fait translate de plusieurs manières (donné plusieurs protéines)

60
Q

Transposons

A

Interspersed repeated DNA elements that can move everywhere in the genome (also referred to as jumping genes)

61
Q

Primer for reverse transcription

A

tRNA

62
Q

Forme normale de DNA

A

B form (right-handed)

63
Q

Signal for polyadenylation

A

AAUAAA

64
Q

Chromosome des procaryotes

A

Souvent juste un et seulement ORI est nécessaire!

65
Q

Diameter nucleosome

A

10 nm (linked DNA is between 10 and 90 bp in length)

66
Q

Number of bp around a nucleosome core

A

147 bp (almost 2 full turns)

67
Q

SAR

A

Scaffold associated region (sert à la chromatine (30 nom fiber) pour bind le scaffold de protéines)

68
Q

Telomerase

A

Ribonucleoprotein (RNA et reverse transcriptase)

69
Q

Orthologous

A

Same gene in different species! (Alpha tubulin in fly and alpha-tubulin in human)

70
Q

Paralogous

A

2 gènes that look alike in same specie (duplication) (alpha-tubulin and bet-tubulin in human)

71
Q

Reverse genetics

A

Analyse la fonction d’un gène en trouvant son effet sur le phénotype

72
Q

Forward analysis

A

Trouver la bas génétique d,un phénotype

73
Q

Chaperonine

A

E.Coli: GroEL

Human: TriC

74
Q

SIR2 in yeast

A

Deacetylated tails proche d’elles

75
Q

Histone methyltransferase

A

Reconnaît H3K9me3 pour methylate les histones natifs autour (ça permet de transférer à la progeny les epigenetic traits)

76
Q

CDK9

A

P-TEFb

77
Q

La stabilité de ton mRNA

A

Ca se passe dans ton 3’ UTR

78
Q

Genomic library

A

Juste avec DNA (pas cDNA libraries)

Phgy209 (4 decks)

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