Idl 580 Exam 3 Set Two

Front 1

Features of EUK mRNA

Back 1

5' cap (m'GTP), 5'UTR, AUG start codon, ORF, STOP codon (UGA, UAG, UAA), 3'UTR, polyA tail

Front 2

importance of KOZAK sequence in EUK

Back 2

optimal, most efficient start codon sequence: ACCAUGG. need to know sequence in order to design primer to amplify product in lab.

Front 3

translational frameshifting

Back 3

the act of shifting the reading frame. could be due to fusion protein, and sometimes can be due to the secondary structure of mRNA. It has been described mainly in viruses (especially retroviruses), retrotransposons and bacterial insertion elements, and also in some cellular genes.

Front 4

hydrolytic editing of tRNA

Back 4

accuracy measure performed by trna. editing site double checks that the correct aa is charged on tRNA. it must fit editing site or will be removed before being added to a.a. chain by tRNA synthetase

Front 5

nonsense mediated mRNA decay occurs when?

Back 5

When exons and introns do not splice properly, causing introns to remain in mrna, and exon proteins to be missing. This is recognized when the mRNA is released in the cytosol, step loop structure forms and mRNA is degraded

Front 6

Gel Mobility Shift Assay

Back 6

Protein binds to DNA, which slows movement over electrophoretic gel. Can analyze shift to determine protein binding

Front 7

CHiP assay (immunoprecipitation)

Back 7

use formaldehyde to sheer dna from histone. Add antigen to purify protein, then use PCR to amplify isolated DNA sequence.

Front 8

DNA affinity chromatography

Back 8

add total cell proteins to column with cDNA on beads. Then wash with low salt conc. to remove proteins that did not bind. Medium salt wash to isolate proteins that bind. REpeat in new column, with specific cDNA sequence of interest. Proteins that bind to sequence will be captured, and then follow with med salt wash to remove prots that didn't bind. Then protein of interest can be isolated with High Salt wash

Front 9

DNAse I footprinting

Back 9

Label DNA with P (to help determine sequence with Gel Electrophoresis). Add Specific binding protein, and then follow with DNAse. Run on gel electrophoresis, there will be DNA missing from where binding protein was located=Can determine sequence that Protein binds to.

Front 10

Reporter assay can be used to measure _____activity. ________ site will not show transcription if proposed recognition site does show transcription.

Back 10

Transcriptional.
Mutated.

Front 11

Characteristics of RNA polymerases

Back 11

Reads 3'-5' to synthesize 5'-3'. Either strand of DNA dble helix can serve as a template for RNA synthesis. TFs needed to initiate transcription. RNA polymerases do not possess proofreading activity/no nuclease activity.

Front 12

Structure of EUK Ribosome

Back 12

28S rRNA + 5.8S rRNA + 5S rRNA= 60S subunit (top)
18S rRNA + 35 proteins= 40S subunit (bottom).
Complete Ribosome is called an 80S

Front 13

RNA pol I transcribes multiple copies of_________ and identical sets of the rRNA genes.
______ promoters allow multiple RNA pol I to load and transcribe, found in _______ spacers. Separation between functional products are referred to as __________.

Back 13

Tandemly repeated.
Multiple.
Nontranscribed spacers.
Transcribed spacers.

Front 14

rRNA post transcriptional processing.

Back 14

cleavage (not splicing), and methylation. Then mature rRNA associates with proteins and becomes subunits. 5S MADE BY POL III!

Front 15

RNA pol II characteristics

Back 15

CTD tail (imp for modifications), promoter sequence, TFs, initiation complex needed to recruit and stabilize pol II.

Front 16

Enhancer elements

Back 16

can be far away from promoters to stimulate transcription of a gene/genes. Enhancers may be on the 5' side of 3' side of a gene, occasionally in an intron. Enhancer elements function independent of orientation with respect to a gene, but are "cis acting". Enhancer elements are binding motifs for activators (TFs).

Front 17

Promoters

Back 17

are "cis acting". TFs bind to either promoters or enhancers. TATA boxes, CG boxes are common promoters. Help position pol II on +1 of transcriptional unit.

Front 18

Housekeeping genes have _______ promoters, while most genes restricted to differentiated cell have _________.

Back 18

CG boxes.
TATA boxes.

Front 19

C terminal Domain of RNA pol II

Back 19

52 tandem repeats of 7 a.a. Serine 5 is phosphorylated by TF IIH, which loads RNA processing components to pol. Ser 2 is extensively phosphorylated which facilitates splicing factor binding. TFs bind to sequences and other TFs to position pol II to the gene to initiate transcription.

Front 20

Role of CTD in mRNA processing

Back 20

pSer5= 5' capping
pSer2 + pSer5= Splicing
pSer 2= Poly A tail processing

Front 21

Positive versus Negative regulation

Back 21

Positive regulation is when repressor binding turns gene on. Repressor is active or inactive by addition of ligand.
Negative regulation is when bound repressor shuts gene off. Repressor can be active or inactive, by addition of ligand.

Front 22

Positive versus Negative Feedback loop

Back 22

Positive feedback increases transcription of gene in response to stimulus. Negative feedback degreases transcription in response to stimulus.

Front 23

Feed forward loop

Back 23

ex: A activates B, A and B activate C

Front 24

Steps of transcription initiation in RNA pol

Back 24

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Front 25

steps of translation initiation in Ribozome

Back 25

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Front 26

steps of translation termination

Back 26

insert here

Front 27

levels of control exhibited by transcription and translation:

Back 27

transcriptional control, RNA processing control, RNA transport and localization control, mRNA degradation control, translation control, protein activity control