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Cell Biology > Lecture 5 - Exam 2 > Flashcards

Lecture 5 - Exam 2 Flashcards

1
Q

Transcription factors can act as either activators or repressors. Why?

A

Because of each TF consists of three independent domains.

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2
Q

What does the DNA binding domain of a transcription factor recognize?

A

It recognizes a specific DNA sequence.

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3
Q

What does the trans-activation domain interact with?

A

Interacts with the mediator or other components of the transcriptional machinery. They can also interact with coactivators or corepressors that facilitate transcription by modifying chromatin structure.

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4
Q

Some repressors do what?
Other repressors do what?

A

Some repressors block the binding of activators of regulatory sequences.
Other repressors have active repression domains that inhibit transcription by interactions with mediator proteins
And/OR the general transcription factors.
And/OR corepressors that act to modify chromatin structure.

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5
Q

Eukaryotic genes are contained in _________?

A

Chromatin = DNA and protein complexes.

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6
Q

What is the basic unit of chromatin?

A

Nucleosome. This is an octomer of histone proteins wrapped around by 147 base pairs of DNA. More than 6 feet of DNA packed into each human nucleus.

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7
Q

Histones act as what for mRNA transcription?

A

ON/OFF switches.

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8
Q

Condensed nucleosomes mean that histone tails are ?
Which means…?

A

Largely methylated.
GENES OFF (METHYLATED and DEACETYLATED)

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9
Q

Uncondensed nucleosomes mean that histone tails are ?
Which means…?

A

Largely unmethylated and acetylated.
GENES ON (UNMETHYLATED and ACETYLATED)

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9
Q

Histones are important because they appear to be responsible for…?

A

Either facilitating or preventing transcription.

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10
Q

Acetylated histones =

A

Loosened chromatin, allowing transcriptional machinery to get to the DNA.

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11
Q

Methylation of histones usually __________ transcription by…..?

A

Repressed ;
Tightening the interaction between histones and DNA

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12
Q

The core histones have ____________, which extend outside of the nucleosome, and histone-fold domains, which interact with ________ and with _____ in the nucleosome.

A

Amino-terminal tails ;
other histones ;
DNA

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13
Q

HAT = ?

A

Histone acetyltransferase

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14
Q

HDAC = ?

A

Histone deacetylase

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15
Q

Transcriptional activators and repressors are associated with coactivators and corepressors, which have _____ and _______ activities, respectively.

A

HAT and HDAC

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16
Q

REMEMBER - histone acetylation is characteristic of ________.

A

Actively transcribed chromatin

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17
Q

Transcription activity of chromatin is affected by __________ and _________ of specific amino acid residues in histone tails, as well as by their _______.

A

Methylation ;
phosphorylation ;
acetylation

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18
Q

Promoters and enhancers are devoid of ________.
This leaves their DNA available to __________.

A

Nucleosomes.
Transcription factors.

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19
Q

The nucleosomes flanking promoters are marked by?

A

Trimethylated H3 lysine 4
(H3K4me3)

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20
Q

Enhancers are marked by?

A

Monomethylated form of this lysine (H3K4me1).

21
Q

Chromatin remodeling factors alter the ?

A

Arrangement or structure of nucleosomes.
Ex: A chromatin remodeling factor recruited in association with a transcriptional activator could facilitate the binding of general transcription factors and RNA polymerase to chromatin by displacing nucleosomes from the promoter.

22
Q

What is the key concept that is a key to life for eukaryotes?

A

The combinational control of gene expression.

23
Q

It is the combination of the different ______ and associated _____ on the different ________ that ultimately determines when and where the gene will be expressed!!

A

Transcription factors ;
co-factors ;
CREs

24
Q

Without an enhancer, the gene is transcribed at a ______ basal level.

A

Low

25
Q

Addition of an enhancer, _______ transcription.

A

Stimulates

26
Q

The enhancer is active not only when placed just ________ of the promoter.
But also, when inserted up to __________ upstream or downstream from the transcription start site.

A

Upstream ;
several kilobases

27
Q

Enhancers are active in either the ____________ or _____________ orientation.

A

Forward ; Backward

28
Q

Discuss DNA looping.

A

Transcription factors bound at a distant enhancer can interact with mediator or general transcription factors at the promoter because the intervening DNA can form loops, stabilized by cohesin.

29
Q

How is chromatin within the nucleus organized?

A

Chromatin within the nucleus is organized into looped domains formed by the interaction of the CTCF transcription factor and cohesin.

30
Q

Enhancers are restricted to interacting with promoters where?

A

Enhancers are restricted to interacting with promoters in the same domain.

31
Q

CTFC = ?

A

CCCTC-Binding factor

32
Q

Are the CREs the same in every cell?

A

YES!

33
Q

The CRES are the same in every cell. So, what’s different?

A

CREs are modular. Once bound to the CREs, TFs are able to enhance and/or repress the ability of RNA polymerase II to initiate transcription.

34
Q

What is the key technique used to identify gene expression?

A

Reporter gene assay

35
Q

With expanded gene expression, why does gene expression expand when the NRSE sequence is taken out?

A

No silencer (AKA a “negative” CRE).
These bind transcription factors that can turn genes off spatially and/or temporally.

36
Q

While there is modularity between different CREs, there are also ______________ within each CRE.

A

co-dependent units.
In other words, not only is it the combination of CREs that will activate/repress a gene’s transcription…. it is also the combination of TFs within a CRE that will influence whether the CRE promotes or silences transcription.

37
Q

What was the first promoter-CRE ever characterized?

A

Sea Urchin Endo 16 Promoter-CRE

38
Q

What is the combinatorial control of gene expression? Examples?

A

Time and Space.
Ex: Cell A takes out the strongly inhibiting protein, so the gene is more active.
Cell B takes out the strongly activating assembly, so the gene is less active.

39
Q

One of the important consequences of combinatorial association of transcription factors is:

A

Coordinated gene expression.
This is the simultaneous expression of many specific genes.
In many cases, the transcription factors needed for transcriptional activation might be assembled at the CREs so that everything is ready to go EXCEPT they need the binding master control transcriptional factor.

40
Q

It is often that these “___________” transcription factors will bind to CREs of many genes so that a ton of genes are turned on all at once.

A

Master control

41
Q

Global translational activity is modulated in response to…?

A

Stress, nutrient availability, and growth factor stimulation

42
Q

Discuss where translation occurs.

A

Mature mRNA molecules must leave the nucleus and travel to the cytoplasm, where the ribosomes are located.

43
Q

The eukaryotic ribosome is composed of two subunits:

A

60S and 40S
Each subunit exists separately in the cytoplasm, but the two join together in the presence of the mRNA molecule.

44
Q

mRNA is “read” according to…?

A

The genetic code. Each group of three bases in mRNA constitutes a codon, and each codon specifies a particular amino acid (hence, it is a triplet code)

45
Q

____________________ align amino acids with corresponding codons on the mRNA template.

A

Transfer ribonucleic acid (tRNAs)

46
Q

________ is an initiation codon ; _____, _____, _____, are termination (stop) codon.

A

AUG ;
UAA, UAG, UGA

47
Q

All tRNAs fold into compact ____ shapes, to fit onto ribosomes during translation.

A

L

48
Q

tRNAs have the sequence ______ at the 3’ end, and amino acids are _____ attached to the ribosome of the terminal _______.

A

CCA ;
covalently ;
adenosine

49
Q

The anticodon loop binds to the….?

A

Appropriate codon by complementary base pairing.

Cell Biology (33 decks)

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