Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MCBG TEST 2!!! > 8-21 Gene Xprsion Post-tx regulation > Flashcards

8-21 Gene Xprsion Post-tx regulation Flashcards

0
Q

Why does implanted eggs with nuclei from SOMATIC cells have defects? [2]

A

1) Somatic Cells have DNA that may not be fully de-methylated
- –>important genes are INACTIVATED due to extra methyls!

2)Imprinting (methylation of certain genes for differentiation) may not occur or is flawed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
1
Q

What type of effects does methylation have on DNA gene expression?

A

Methylation INHIBITS DNA Gene Xpression!

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Alternative Splicing

A

Regulated process in which family of related proteins can be made from a SINGLE gene

(20,000 genes= 100,000 proteins thru Alternative Splicing)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Tx factors with Bromodomains?

A

Bromodomains = found in the Tx factors that ONLY BINDS to DNA with ACETYL groups attached

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Name 2 Fibronectin mRNA genes produced by ____ ____

A

Fibroblast fibronectin mRNA=archictecture of the tissue[Has EIII-B and EIII-a splicing regions]

Hepatoycyte fibronectin mRNA=involved in clot formation

(Both are related/same family but have differences made by ALTERNATIVE SPLICING)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

DSCAM in Drosophila (Drosophila Down Syndrome Cell Adhesion Molecule)

A

Can produce over 38,016 different splicing patterns (but only 3 are chosen-1 from each exon area)

*Is an Axon Guidance Protein=helps axons grow to the appropriate neuron in DROSOPHILA FLIES
(In humans=alteration of brain wiring=mental retardation
-Found in Chromosome 21

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Integrins

A

CELL SURFACE RECEPTORS expressed on variety of cells and involved in adhesion
-used on the surface of Fibroblast fibronectin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

How is DSCAM related to Down-Syndrome?

A

When DSCAM (found on Chromosome 21) is over expressed in human=alters with brains wiring=mental retardation seen in Down syndrome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Negative Control of Splicing

A

Happens when a REPRESSOR PROTEIN binds to regulatory silencer sequences of splice sites to STOP SPLICING on that mRNA [it does not PHYSICALLY BLOCK THE SPLICE SITE] –>It just “silences” it

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Positive Control of Splicing [++++]

A

Happens when a mRNA with a weak splice site is boosted up with an ACTIVATOR/SR Protein. SR Protein binds to regulatory enhancer

sequence and encourages splisosome to use a weak site.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Alternative Splicing includes both ____control and ____control

A

Alternative splicing includes both POSITIVE AND NEGATIVE control regulations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

what’s unique about the sequences which overhead positive/negative control of splicing

A

Enhancer and Silencer seq. can be in both introns and exons but have to be close to the splice site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Name and describe the Two parts of Translation initiation

A

1) Prepare small ribosomal subunit and bind it to eIF3–> then initiating tRNA is bound with EIFII/GTP.
2) sRBSunit bound with eIF3 then is recruited to mRNA and then it scans with initiating tRNA to find AUG USING ATP.
3) GPT from eIF2 is hydrolyzed->conformational change->releases initiating tRNA and EIFII/nowGDP [recycled by EIFIIB] is released
2) Prepare the mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

1) How do we stop/slow the initiation of translation (in regards to eIF-2)?
2) How do we reverse these effects?

A

1) Cellular Stress causes Phosphorylation of eIF2 when it is in its GDP form –> prevent eIF2B[guanine nucleotide xhcnge factor] from binding and giving eIF2 another (P) to be active again= NO RECYCLING to eIF2/GTP = No initiation of translation
2) Phosphotase can cleave/clip off the bound P from eIF2 =can bind to eIF2B again

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is eIF4G?

A

EIF4G=scaffold protein that binds to eIF4E and eIF4A(helicase) and then BINDS TO SMALL RIBOSOMAL SUBUNIT 40s –> how floating ribosome is recruited to the mRNA gene

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How does different levels of EIF4E relate to translation?

A

1) High levels of EIF4E promote cellular growth [can be in CANCER!]
2) Helps with translation of disadvantage transcripts (not mRNAs are created equally)
3) Low levels

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What does 4E-BP do [eIF4E-BP]

A

eIF4E-BP is inhibitor protein that stops eIF4E cap binding protein from binding to 5’N7MG cap.—-> eIF4G which uses 4E to attach to the cap now won’t bind to mRNA transcript recruit small ribosome to mRNA transcript

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Why are some transcripts mrNA disadvantaged?

A

There’s a secondary structure int he 5’start region which makes it difficult for ribosome to find the AUG

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

T or F: All tl is cap-dependent

A

FALSE Not all tl is cap dependent

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q
  • —–WHat is IRES? ——- [2]

- Is this common?

A

WE’RE BYPASSING THE 5’CAP FOR INITIATION MAN!
Internal Ribosome Entry Sites= *translation initiation mechanism in which the 5’cap (eIF4E–normally needed for rbsome recruitmnt) is bypassed and eIF4G can bind to mRNA on its own thru this site!

  • Requires wayy less translation initiation factors, and these factors can assemble DIRECTLY onto an IRES and still recruit a 40S sRbsme to the mRNA WITHOUT eIF4E! #BOOM!
  • **This occurs in only small subset of eukaryotic mRNA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is the normal way translation initiated?

A

EIF4E binds to 5’cap which then binds to EIF4G–>Small ribosome will then come to bind to EIF4G

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

How does a cell commit suicide via translation?

A

Shut off protein expression and make apoptosis proteins thru IRES and produce variant of EIF4G

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q
  • How is Rate of mRNA degradation related to steady state?

- short half life=_____rate of degradation=_____[short/long]time to reach NEW mRNA steady state

A

Rate of Synthesis and Rate of Degradation both maintain mRNA steady state (amount of mRNA in a cell)

*****Time it takes to get to a NEW mRNA steady state during fluctuation=only depends on RATE OF DEGRADATION/HALF-LIFE of that specific mRNA

(short half life=fast rate of degradation=will reach new steady state real fast)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Rate of mRNA Degradation dictates what….

A

absolute amount of cellular constitutent depends on both rate of synthesis and rate of degradation. but Time required to achieve the new level depends ONLY RATE OF DEGRADATION?

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

How are mRNA half-life and Rate of degradation related?

A

INC Half-life of mRNA to degrade = DEC Rate of degradation=MORE STABLE mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What does the stability of the mRNA depend on?

A

Stability of an mRNA depends on how quickly the polyA tail is shortned

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

miRNA [2]

A
  1. (2,500 types of miRNA) regulates 20-30% of mRNA gene expression by binding to mRNA seed seq. [7 bases]
  2. After Drasha and Dicer cleave the ends of miRNA, miRNA interacts w/both Argonaute and active target mRNA binding to tht mRNAs seed sequence—-> stop translation
27
Q

Describe the 2 mRNA degradation components involving Deadenylase [3]

A

Deadenylase DEGRADES mRNA
1st: SLOWLY shortening the 3’ end poly-A tail to LESS THAN 30 bases –>makes mRNA unable to support binding to polyA binding proteins

2nd: Associates onto & Decaps the 5’ N7methylguanine cap
- -»promotes degradation [faster process thn tail removal]

3rd: After 5’ Decap occurs, Exonuclease can now degrade
5–>3 and then 3—>5 FROM BOTH ENDS!!!!

28
Q

Argonaute

A

“the killer machine” apart of the RISC complex. Works with and uses ss miRNA to target old/bad mRNA (via seed seq.) and degrade it after it’s been cleaved by nucleases Drosher(nucleus) and Dicer(cytosol).

29
Q

How does rapid mRNA degradation occurs?

A

“slicing” of the mRNA by Argonaute proteins occurs with ATP. RISC is released and rapid mRNA dgradation happens

30
Q

How does miRNA associate with cancer?

A

miRNA will work with ARgonuate to degrade mRNA important for tumor suppression = Cancer INC

31
Q

Nonsense-mediated Decay

A

Removes transcripts with STOP codons in the middle of the coding region->(happens when there are splicing problems–>truncade proteins and aggregation).

32
Q

Exon junction complexes

A

Bind to splicing site after splicing has been done and these EJC help to signal to ribosome that there is a premature stop codon present—>that mrNA is rapidly degraded

33
Q

Ubiquitin Tags

A

recyclable tags that bind to Bad protein Substrates–> degradation by Proteosomes

34
Q

What is the mechanisms behind Ubiquitin

A

small ubiquitin
E1(activating enzyme) binds to ubiquitin–>trnfr to E2 and E2 and E3(ligase) form a complex where multiple chains of ubiquin are placed on the mRNA for degradation

35
Q

What recognizes Ubiquitin

A

recognized by 19S cap on the Proteosome [Central 20S cylinder+2 supplemental cap]

36
Q

mitotic castrophe

A

when cyclins are present in the wrong cell cycle and so cyclin have to be rapidly degraded when transitioning between cycles. All cyclins began with ARG and if mutated cyclyins can’t be ubiquianated.

37
Q

Cell Cyclin destruction

A

Involves E3 being expressed toward the end of the cell cycle which then degrades cyclins BEFORE ENTERING NEXT STAGE OF CELL CYCLE

38
Q

Proteosome and Cancer

A

I-kappa B kinase
NF-kappaB(normally an inactive complex bound to inhibitor I-kappaB) translocates to the nucleus when I-kappaB is unwarrantedly phosphorylated and released from it and then destroyed by Proteasomes! NFKB then activates genes associated with cell growth and survive,

Cancer treatment= Block proteasome which destroys I-kappaB after it’s been phosphrolated allowing I-kappaB to possibly adhere back to the NFKB

39
Q

Explain competition between mRNA trnslation & mRNA degradation

A

The same 2 processes use the same 2 landmarks (5’N7MGcap/3’polyA tail) when both degrading or translating===mRNA mssges not actively trnsltd will likely be deadenylated instead

40
Q
  • VHL protein?

- Mutation in VHL would lead to what?

A
  • E3 ubiquitin ligase complex that regulates/tethers ubiquitin onto HIF(HIF is a tx factor that promotes angiogenesis) for ULTIMATE DESTRUCTION BY A PROTEOSOME
  • Mutation in VHL means HIF acts in excess and –>cancer!
41
Q

1) There are __ main types of Alternative Splicing. What are they?
2) What are the minor patterns of alt splicing?

A

4 MAIN TYPES OF ALTERNATIVE SPLICING!
1. Exon Skipping (40% occurrence)

  1. alternative 3’ splice site (20%)
    {***l&raquo_space; #2and#3=occur when 2 or more splice sites exist at one end of an exon}
  2. alternative 5’ splice site (10%)
  3. Intron retention (5%)

minor–=(mutually exclusive exons vs. alternative promoter usage vs. altrnative polyadenylation)

42
Q

WHAT are the 6 post-tx control mechanisms for regulating Eukaryotic Gene Xprssion?

A
  1. ATTENUATION/RIBOSWITCH(rare)->mRNA transcript aborts degradation
  2. RNA PROCESSING [Alt splicing vs. 5’capping vs. cleavage/polyadenyltn]–>diffrnt transcripts producd from 1 gene &nonfunctional transcript degradation
  3. NUCLEAR EXPORT(rare)->transcript degradation
  4. TRANSLATN CONTROL0>Trnsltion is blocked or diff. transcript
  5. mRNA STABILITY->transcript degradation
  6. protein control [turnover vs. modification vs. inhibition]->protein activation/inactivation
43
Q

What is an SR Protein?

A

(Serine Arginine Rich Protein) which acts as an ACTIVATOR/SR Protein for boosting up weak splice sites on mRNA.
-Binds to regulatory enhancer sequences on mRNA that hve weak splice sites on them

44
Q

Why are the LOCATIONS of polyadenylation and cleavage sites important in pre-mRNA?

A

The site of RNA cleavage and poly A addition determines whethr an antibody molecule is secreted in blood or membrne bound.

45
Q

Explain the Immunoglobulin polyadenylation site selection for an unstimulated B-lymphocyte

A

unstimulated B-cells make long RNA transcripts and the intron sequence near its 3’end is REMOVED by splicing—>mRNA for a membrane bound antibody (hydrophobic peptide)

46
Q

Explain polyadenylation site selection for antigen stimulated B-lymphocytes

A

B-cells w/antigen stimulation have RNA transcript cleaved in front of splice site right behind last exon seq.->cuts off 3’ acceptor splice junction and INTRONS AREN’T REMOVED as they should be.=
hydrophillic peptide that is secreted to travel in blood

47
Q

Explain the mechanism of how the Ribosome is drawn and attached to the start codon of mRNA [3]

A
  1. eIF2 forms 3*complex w/GTP &initiator methinyl-tRNA
  2. Complex binds to 40s sRbosmal subunit and are recruited to mRNA by the 5’cap binding complex
  3. Interaction between [initiator met-tRNA__sRbosme-40s] combo with initiation codon triggers GTP hydrolysis from eIF2—>assembly of functional ribosome on the mRNA
48
Q

Translation
1)WHAT IS eIF4E? WHat is eIF4E-BP?
2)What happens when you phosphorylate eIF4E-binding protein
(eIF4E-BP)?
3)When is eIF4E-BP naturally DePhosphorylated?

A

1) eIF4E=cap binding protein which binds to 4G during translation so sRbosmal subunit is recruited to mRNA. IT CAN BE BOUND UP AND STOPPED BY eIF4EBP
2) If we Phosphorylate eIF4EBP then we BOUND IT UP so it will no longer bound up eIF4E–>4E attaches to 4G like it supposed to–>recruitment of small ribosome for translation
3) Phosphates are taken off eIF4E-BP when cell is entering M phase and during viral infection–>bounds up eIF4E :-(–>No recruitment and No translation

49
Q

What effects would phosphorylating and dephosphorylating eIF4E-BP have on mRNAs that have IRES in them?

A

INC Phosphorylation of eIF4E-BP=INC ability for eIF4E (5’cap binding protein) to do its job and bind to 4G for recruit smribsme to mRNA.

**Since IRES bypasses this entire cap-dependent mechanism!–>There is NO EFFECT ON mRNAs THAT HAVE IRES IN THEM WHEN PHOSPHRYLTNG eIF4E-BP

50
Q

Why do mRNAs exclusively active during Apoptosis (cell death) likely contain IRES?

A

IRES allows you to destroy the eIF4E^eIF4G rbsomal recruitment duo without stopping the synthesis of proteins needed to kill the cell. IRES bypasses the 5’cap recruitment cascade

51
Q

Constitutive Splicing

A

Splicing in which all exons are spliced and ligased together IN THE SAME ORDER they were in prior to splicing

[opposite of Alternative=exons are ligased in unique combinations]

52
Q
  • What is the primary purpose of miRNA?

- Where are miRNA usually located?

A

-Purpose: DECREASE or SILENCE GENE XPRESSION of proteins
-Location: Within introns of protein coding genes OR
between genes (intergenic DNA) within NON-protein coding regions

52
Q

Describe the mechanism of action for miRNA processing and RISC (RNA-induced SILENCING complex) [5]

A
  1. in nucleus, nuclease DROSHER cleaves ds miRNA precursor & that’s trnsported to cytosol
  2. In cytosol Dicer cleaves some more->even smaller ds miRNA
  3. This binds to Argonaute(apart of RISC)

4.1 of the ds miRNA is degraded and remaining strand is used by RISC to identify target genes w/1 or more “seed” seq. at least 7 bases and complimentary

  1. *good compliment between miRNA and mRNA target=silencing[R hand]
    * EXTENSIVE COMPLIMENT=ENDONUCLEOLYTIC CLEAVAGE by ARGONAUTE [L hand]
53
Q

What happens to mRNAs after they are affected by the miRNA-RISC complex?

A

The mRNAs are translationally inhibited and will accumulate at
cytoplasm P-body sites to eventually be
DECAPPED, DEADENYLATED–>DEGRADED

54
Q

What are some of the INDIRECT targets of miRNA?

A
  • Regulatory proteins
  • Protein Kinases
  • tx Factors
  • Chromatin remodeling complex
  • *stuff that controls expression of other genes
55
Q

1) Explain how Ubiquitin tags for protein destruction are actually added to the protein
2) What happens to this ____(finished product) once it’s complete?

A
  • USING ATP, 76-AA ubiquitin forms an isopeptide covalent bond between its carboxyl-terminal glycine and a Lysine E-amino group on the bad protein.–>then more ubiquitin molecules are added to the lysine side chain=polyubiquitinated chain!
    2) The POLYUBIQUITINATED PROTEIN(finished product) is then degraded by the multiprotein PROTEASOME!
56
Q

Describe how the Enzymes CATALYZE the protein destruction ubiquitination process? [5]

A

1st: [76 AA Ubiquitin] binds to E1[ubiquitin activating enzyme]
2nd: E1 transfers Ubiquitin to E2(ubiquitin conjugating enzyme)

3rd:E2 (~20 members present) then HAS ITS UBIQUITIN TETHERED to DOOMED PROTEIN by E3 {ubiquitin ligase} (~500 members present) after E2 and E3 mix

4th: After ubiquitin is tethered to DOOMED Protein–>goes to
[26S multiprotein Proteasome] which DEGRADES DOOMED PROTEIN

5th: Ubiquitin chains are Recycled :-) and small peptides remain from degradation

57
Q

1) What are Proteasomes for?

2) Describe both the inner and Outer significances of the multiprotein PROTEASOME

A

1) Proteasomes degrade BAD/misfolded proteins which are tagged with Ubiquitin by E1, E2 and E3
- ————————————————————————-
2) Inner=protease subunits form central rings in a cylinder and have active sites ONLY ACCESSIBLE from inside the cylinder

OUTER=CENTRAL CYLINDER (contains proteases) IS CAPPED BY PROTEIN SUBSTRATE RECOGNITION CAPS
–>RECYCLES UBIQUITIN, UNFOLDS PROTEIN & THREADS PROTEIN INTO INNER ACTIVE SIDE OF CYLINDER

58
Q

Protein Digestion by Proteasomes is ____ and the ___ ___ is responsible for recognizing the ubiquitin-tagged protein substrate. The Proteasome requires ATP to _____ and then transport into the ________. Proteins are digested into_______

A

Proteasome Protein Digestion is PROCESSIVE and the PROTEASOME CAPS recognize ubiquitin tagged protein substrate. Proteasomes require ATP to UNFOLD THE DOOMED PROTEIN and transport it into the ACTIVE INNER CENTRAL CORE. Proteins are digested into short peptides 7-12 AA long.

59
Q

*What is the Ubiquitin-Proteasome system? [3]

A

2 groups of E3 ubiquitin ligases regulate cell cycle

A. APC=recognizes to trigger chromosome separation and terminate mitosis

B. SCF=promotes G1–>S phase transition and progression throughout S phase

C. Mdm2=destroys p53 tx factor(controls cell cycle progression/apoptosis)—>causes cell cycle arrest, over-progression and death

60
Q

Mitotic Cyclin Destruction Box [2]

A

1)AA seq. found in cyclins of the M-phase that allows
[APC-E3 ubiquitin ligase] to bind, induce chromosome separation & mitosis termination.
2)Cyclin A/B1/B2 all start with [Arg] AA

61
Q

1) What is SCF type 3 E3 ubiquitin ligase
2) What is I-kappa B? What happens if it’s Phosphorylated?
3) What about NF-kappaB?

4)What’s the overall significance to these 3?

A

1)SCF type 3 is Part of the ubiquitin-protesome system and regulates levels of I-kappaB by joining with E2-ubiquitin conjugating enzyme to ubiquitinize I-kappaB THATS BEEN PHOSPHORYLTD :-(

2) I-kappaB=inhibits tx factor NF-kappaB.
* *****(P)=NO ACTIVITY FROM IkappaB–>eventual proteasome destruction due to ubiquitination from SCT type3

3)NF-kappaB=activates cellular growth and survival genes. NF-kappaB is usually ELEVATED IN CANCER CELLS

**DEC Proteasomes=INC I-kappaB (able to stay around longer w/out proteasomes destroying it)–>=DEC NF-kappaB=DEC CANCER!

64
Q

How are Proteasome inhibitors able to treat autoimmune and inflammatory disorders in humans?

A
  • DEC Proteasomes or SCF type3 =
  • *INC I-kappa B (they stay around longer becuz not being destroyed by proteasomes when phosphrylted) =

***DEC NF-kappaB = DEC CANCER & INFLAMMATION/ AUTOIMMUNE SYMPTOMS

65
Q

What is Alternative Polyadenylation

A
  • Activator/Repressor proteins DECIDE what site to use for either Polyadenylation OR Splice site
  • if we want shorter segment/free antibody=need enhancer to bind to mRNA since we want shorter segment requires FIRST Splice site which is the weakeer splice site in antibodies
66
Q

Mitochondria DNA can be HETEROPLASMIC! What does this mean?

A

Some cells of a person can HAVE normal types of mitochondrial DNA in 1 cell WITH ABNORMAL MUTANT types of mitochondria DNA in the same cell depending on the random sorting in Mom’s egg

MCBG TEST 2!!! (13 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions