Lecture 15

Front 1

Cell-cell contact stimulates transcription of different genes in B. subtilis:

The ________ gene is activated by _______ in the forespore.

The encoded ______ protein becomes associated with the septum separating the mother cell and forespore.

It triggers the proteolytic processing of an inactive form of _________ in the mother cell. This activates it and leads to the recruitment of RNA polymerase and the activation of specific genes in the mother cell.

Back 1

spoIIR, sigma F

spoIIR

SIGMA E OR PRO-SIGMA E

Front 2

cell-cell contact regulation of gene expression:

The neurogenic ectoderm can form 2 types of cells:

However, once a cell becomes a
neuron, that cell ___________ all adjacent
cells from becoming neurons

Back 2

Neurons and epidermis (skin)

inhibits

Front 3

Besides cell-cell contact, the ______________
regulatory switch prevent adjacent
ectodermal cells from becoming neurons

Back 3

Notch-Su(H)

Front 4

Neurons express the _______ ligand
that binds the ______ receptor on
adjacent ectodermal cells.

Back 4

delta, notch

Front 5

An intracellular portion of Notch is _______ and binds to a _______protein that is bound to DNA.

Binding of Notch causes the displacement of 3 co-repressors______, _______, _________, and turns ____ into a transcriptional activator that drives differentiation of cell into skin cells.

Back 5

cleaved, Su(H)


Hairless, CtBP, and Groucho, Su(h)

Front 6

The concetration of the secreted protein called ______ stimulates the formation of different neurons in the neural tube.

What are these neurons starting with the highest conc?

Back 6

sonic hedgehog (Shh)

v3 neurons , motor, v2 intereurons, v1 interneurons

Front 7

What regulatory RNA in bacteria activate and repress translation?

Back 7

sRNA (small RNA)

Front 8

sRNA genes encode RNA ________ nucleotides long.
Nearly ______ sRNA genes in E. Coli.
sRNA functions in trans to:
1. Direct ___________ of mRNA
2. Stimulate _________ (a)
3. ________ translation (b)

Back 8

80-110

100

DESTRUCTION, TRANSLATION, INHIBIT

Front 9

___________ are located on the 5' end of mRNA and bind small molecule ___________. This controls transcription or translation.

The small molecule bnds the _______ region to induce a _______ _________ that affected the _________ __________ region located __________ of the coding sequence.

Back 9

Riboswitches, metabolites


aptemer, conformational change, expression platform, upstream

These conformational changes alter expression of the associated gene by either terminating transcription or inhibiting the initiation of trans- lation.

Front 10

S-ADENOSYLMETHIONINE, AKA _______, binding changes folding to form a __________ structure.

IT can do 2 things when bound to the aptemer...

Back 10

SAM, HAIRPIN
1.TERMINATES TRANSCRIPTION
2. BLOCKS THE RIBOSOME BINDING SITE

Front 11

Riboswitches respond to a range of ____________. such as vitamins, nucleotides and amino acids

Back 11

metabolites

Front 12

What controls transcription of the trp operon?

Back 12

Attenuation

Front 13

At low levels of ____, all the trp genes are transcribed and there is no transcription termination.

What prevents hairpin formation?

Back 13

trp,

stalling at trp codons in leader peptide

Front 14

At high levels of tryptophan, what structure forms to terminate transcription?

Back 14

hairpin

Front 15

2 types of RNA interference (RNAi) in eukaryotes

Back 15

siRNA (SMALL INTERFERING RNA)
miRNA (microRNA

Front 16

Which RNAi is physicall introduced into cells and not encoded/expressed from the genome?

Back 16

siRNA

Front 17

What generate small double stranded RNA from a larger precursor?

Back 17

Dicer Rnase

Front 18

RISC (RNA-inducing silencng complex) can achieve four things:

1. __________ translation
2. _________ mRNA
3. Amplify _________ _________ RNA
4. Remodel __________

Back 18

inhibit
degrade
inhibitory guide
chromatin

Front 19

Pre-miRNA are processed into _____.
They are processed in a sequence _________ manner using the distance from the ____ ________ section as a guide,


Some pre-miRNA encode ____ RNA on each strand.

Back 19

miRNA, indepent, single stranded


guide

Front 20

miRNA are encoded in both _________ and _________.


pre-miRNA can be found in _____ regions and non-coding regions.

They can also be in an __________ of a protein-coding pre-mRNA or in an intron of noncoding RNA.

Back 20

introns, exons

CODING

INTRON

Front 21

Primary miRNA is first cleaved by __________ and then by _______.

Back 21

Drosha, Dicer

Front 22

Drosha associates with a specificity subunit called __________. This form the _____________ complex which cuts the RNA in the _______.

Back 22

Pasha (or DGCR8)
microprocessor
nucleus

Front 23

The RNA is then transported to the _______ where it is cut by _________.

__________ contains 2 ______ domains and a RNA-binding ____ domain.

Back 23

cytoplasm, Dicer,

Dicer, Rnase, PAZ

Front 24

Mehanism of primary miRNA complex by the microprocessor complex:

Drosha cleaves the RNA ____ bp from a single stranded region, leaving a ___bp stem with a ______ of random legnth.

This generates the ____________ (F2) with an overhanging end which is recognized and then cleaved by _______.

Back 24

11, 22, loop

pre-miRNA, Dicer

Front 25

Dicer has a structure of a ______ with a blade and handle.

The PAZ domain anchors the RNA to be cut ___ nucleotides away.

The result is a dsRNA molecule about _____ nucleotides in legnth

Back 25

hatchet

22, 3',

21-25

Front 26

The dsRNA enters the ______ complex. One strand is then removed to form the _____ RNA.

Back 26

RISC, GUIDE

Front 27

The RISC complex contains a protein called __________ that can cleave mRNA that have sequences complementary to the ______ RNA.

the mRNA is cleaved 10-11 bp from the __' end of the _______ RNA.

Back 27

argonaut, guide

5', guide

Front 28

RNAi was first recognized in 1989 when a scientist was trying to engineer ________ flowers to be _________ purple. He instead turned them partly ________.

Back 28

petunia, darker, white

Front 29

In 1998, the mechanism fof RNAi was discovered using _____________ worms. got a nobel prize fo dat.

Back 29

C. elegans nematode

Front 30

iN c. ELEGAN WORMS, it was discovered that the _____ miRNA bound to ___ sites in the __________ 3' untranslated region. This supressed protein expression and worm developement.

Back 30

Lin4
7
Lin14

Front 31

In fission yeast, centromere silencin is induced by a RISC-like compleX ________.

Back 31

RITS
(RNA-induced transcriptional silencing)

Front 32

The centromere encodes RNA from each strand that form dsRNA. The dsRNA is processed by _____ and enters the _____ complex to form ______ RNA.

tHE COMPLEX THEN RETURNES TO THE transcribed centromere mRNA where the RITS complex recruits ___ and _____ nucleosome ________ to silence to centromeric DNA.

Back 32

DICER, RITS, GUIDE

Clr4, Swi6, methylases

Front 33

Chp1 (part of the RITS complex) has a ________ domain that binds to __________ histone tails to prevent RITS FROM LEAVING SO THE silencing can be spread.

Back 33

chromo
methylated

Front 34

Scientists use _______ or _______ (short
hairpin RNA) to specifically _______ ________
expression of a gene. This is easily done
in C. elegans worms that are fed ______
bacteria that contain a _______
expressing shRNA complementary to
the mRNA to be knocked down.

Back 34

siRNA or shRNA
knockdown
E.coli
plasmid

Front 35

normal miRNA expression ________ cancer.

decrease expression of miRNAs thhat suppress cancer causing oncogenes lead to ____________.

Back 35

prevents,
tumorigenesis

Front 36

tumor suppressor mRNAs and oncogene mRNA

Back 36

miR-15a, miR-16, Let-7a

BCL-2 and RAS

Front 37

_______ expression of miRNA that repress tumor suppressor genes lead to tumorigenesis

Back 37

increased

Front 38

miRNAs that repress tumor supressor genes
what are the tumor repressor mRNA

Back 38

miR-17-92, miR- 155, miR-21

PTEN, RB2

Front 39

What are the components of the RITS complex?

Back 39

RITS, argonaute and Chp1

Front 40

The _____ RNA involved in __ chromosome inactivation is expressed from one X chromosome and then coats that X chromosome (a).

Xist RNA then recruits __________ ___________ that __________ gene expression from that X chromosome (b) leading to its ______________.

Back 40

Xist, X

histone deacetylases, silence, inactivation