Lecture 1 - Exam 3

Question 1

Chromatin within the nucleus is organized into…?

Answer 1

Looped domains formed by the interaction of the CTCF transcription factor and Cohesin.

Question 2

Enhancers are restricted to…?

Answer 2

Interacting with promoters in the same domain.

Question 3

CTFC = ?

Answer 3

CCCTC-Binding factor

Question 4

The CREs are the same in every cell, so what’s different?

Answer 4

CREs are modular.

Question 5

What can transcription factors do once they are bound to CREs?

Answer 5

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

Question 6

Combinatorial gene expression… is it important? What is it?

Answer 6

SO IMPORTANT!
Allows multiple genes to be expressed. For example, Gene A being expressed in brain and limb.

Question 7

The transcription factors bring the _________ to the enhancer. Depending on where the gene will be expressed, those specific TFs will be expressed and that is what determines where the gene will be expressed (slide 6).

Answer 7

Mediator.

Question 8

While there is modularity between different CREs that are also __________ units WITHIN each CRE.

Answer 8

co-dependent

Question 9

While there is modularity between different CREs, there are also co-dependent units within each CRE. In other words, not only is it the combination of CREs that will activate/repress a gene’s transcription…. It is also?

Answer 9

It is also the combination of TFs within a CRE that will influence whether the CRE promotes or silences transcription.

Question 10

Development is controlled by?

Answer 10

Differential gene expression.

Question 11

Every somatic cell contains?

Answer 11

The complete genome.

Question 12

Unused genes retain the potential for?

Answer 12

Expression.

Question 13

How much of the genome is expressed in each cell?

Answer 13

Small percentage.

Question 14

What does the Situ Hybridization show us?

Answer 14

This shows us when and where mRNA is transcribed in the cell. But, this technique does not tell us what CREs and TFs turn these genes on.

Question 15

What is the key technique used in gene expression?

Answer 15

Reporter gene assay. This technique was able to tell us whether or not NRSE sequence is a silencer or an activator.

Question 16

Transcriptional activators and repressors are associated with ____________ and ___________, which have ______ and _______ activities, respectively.

Answer 16

Coactivators ; Corepressors ; HAT ; HDAC

Question 17

REMEMBER: Histone acetylation is characteristic of?

Answer 17

Actively transcribed chromatin.

Question 18

What may be attached to coactivators like HATs?

Answer 18

Pioneer factors.

Question 19

Wherever the TF can bind on the genome, will do what?

Answer 19

It will open up the chromatin and if the correct TFs are around in a cell, they can bind any uncovered TT binding sites in any CREs surrounding a gene.

Question 20

From differentiated fibroblast to induced pluripotent stem cell with four transcription factors. What are these transcription factors called?

Answer 20

Yamanaka factors - Oct3/4, c-Myc, Sox2, Klf4.
Note: These are master control pioneer transcription factors.

Question 21

The Yamanaka factors are virally inserted into differentiated fibroblasts, what will these cells dedifferentiated into?

Answer 21

These cells will dedifferentiate into induced pluripotent stem cells (iPSCs).

Question 22

Like embryonic stem cells, iPSCs can give rise to?

Answer 22

All three germ layers (mesoderm, ectoderm, and endoderm).
Note: Mesoderm includes red blood cells, Ectoderm includes neurons, and Endoderm lineages include pancreatic endocrine cells.

Question 23

What is Antennapedia?

Answer 23

A Hox family master control gene that controls the formation of legs during development.

Question 24

Translation is what stage of gene expression?

Answer 24

The final stage.

Question 25

Global translational activity is modulated in response to what?

Answer 25

Stress, nutrient availability, and growth factor stimulation (AKA cell-to-cell signaling).

Question 26

1. Describe where translation occurs.
2. What is the eukaryotic ribosome composed of?

Answer 26

1. Mature mRNA molecules must leave the nucleus and travel to the cytoplasm, where the ribosomes are located.
2. The eukaryotic ribosome (protein-RNA complexes) is composed of two subunits: 60S and 40S. Each subunit exists separately in the cytoplasm, but the two join together in the presence of the mRNA molecule.

Question 27

1. The prokaryotic ribosome is a ____S ribosome, composed of what subunits?
   2.The eukaryotic ribosome is a ______S ribosome, composed of what subunits?

Answer 27

1. 70S, composed of 50S & 30S
2. 80S, composed of 60S & 40S

Question 28

Ribosomes can be formed ______ by self-assembly from purified ribosomal proteins and rRNAs. What does this provide to experimenters?

Answer 28

in vitro (In a test tube). This provides an important experimental tool, allowing analysis of the roles of individual proteins and rRNAs.

Question 29

Describe the attachment of amino acids to tRNAs.

Answer 29

Attachment occurs in two steps:
1. ATP hydrolysis activates the amino acid and then it forms an aminoacyl AMP intermediate.
2. The amino acids is transferred to the 3’ CCA end of the transfer RNA (tRNA) and AMP is released.

Question 30

Amino acids are covalently attached to the?

Answer 30

Amino acids are covalently attached to the ribose of the terminal adenosine.

Question 31

1. How many Aminoacyl tRNA synthetases are there?
2. What do Aminoacyl tRNA synthetases do?

Answer 31

1. 20
2. Each of the 20 Aminoacyl tRNA synthetases catalyze the reaction for a specific AA and tRNA AND they recognize specific anticodons (*They may work with more than 1 tRNA since there are 40 different tRNAs)

Question 32

How is mRNA read during translation?

Answer 32

The mRNA is “read” according to 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).

Question 33

1. What does tRNA stand for?
2. How do tRNAs align amino acids during the attachment process?

Answer 33

1. Transfer ribonucleic acid
2. tRNAs align amino acids using their anticodon that binds with the complementary codon(s) on the mRNA template.

Question 34

1. What is the initiation codon?
2. What are the termination (stop) codons?

Answer 34

1. AUG
2. UAA, UAG, and UGA

Question 35

The genetic code is…?

Answer 35

Redundant!

Question 36

1. Discuss the “wobble” base.
2. There is a modified guanosine. What is it called, and what can it pair with?
3. Give an example of abnormal base pairing.

Answer 36

1. Base pairing at the third codon position in relaxed, allowing G to pair with U.
2. The modified guanosine is called inosine (I) in the anticodon can pair with U, C, or A.
3. Two examples of abnormal base pairing, allowing phenylalanine (F) tRNA to recognize either UUC or UUU codons and alanine (A) tRNA to recognize GCU, GCC, or GCA. (Look at diagram to understand better)