Lecture 16

Question 1

What are two important promoting factors in rRNA transcription?

Answer 1

CORE & UCE

Question 2

What are the steps to processing tRNA with Pol 3?

Answer 2

1) Transcription product, pre-tRNA, contains additional sequences at 5’ and 3’ ends that are removed (RNase P removes nucleotides at 5’ end)
2) Introns in anticodon arm are spliced out
3) tRNA nucleotidyl transferase adds trinucleotide CCA as a marker of mature tRNA
4) About 10% of additional bases are modified for specific functions

Question 3

What do hormones do to activate transcription?

Answer 3

Hormones such as cortisol, retinoic acid, and thyroxine bind to receptors initially located in the nucleus and cytoplasm. The hormone-receptor complex functions as a transcription factor in the nucleus

Question 4

What is a zinc finger?

Answer 4

A small protein structural motif that is characterized by the coordination of one or more zinc ions in order to stabilize the fold

Question 5

What is a zinc finger domain?

Answer 5

Zinc finger (Znf) domains are relatively small protein motifs that contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not, instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds.

Question 6

What is a hormone response element (HRE)?

Answer 6

A hormone response element (HRE) is a short sequence of DNA within the promoter of a gene that is able to bind a specific hormone receptor complex and therefore regulate transcription.

Question 7

What is a DNA binding domain?

Answer 7

Highly conserved domain containing two zinc fingers that binds to specific sequences of DNA called hormone response elements (HRE)

Question 8

What is NF-κB?

Answer 8

NF-κB is important in regulating cellular responses because it belongs to the category of “rapid-acting” primary transcription factors. This allows NF-κB to be a first responder to harmful cellular stimuli. Known inducers of NF-κB activity are highly variable and include reactive oxygen species (ROS), tumor necrosis factor alpha (TNFα), interleukin 1-beta (IL-1β), bacterial lipopolysaccharides (LPS), isoproterenol, cocaine, and ionizing radiation. Activated by an ubiquitin pathway through phosphorylation

Question 9

What is CREB?

Answer 9

CREB (cAMP response element-binding protein) is a cellular transcription factor. It binds to certain DNA sequences called cAMP response elements (CRE), thereby increasing or decreasing the transcription of the downstream genes. Elevated levels of cAMP cause activation of CREB

Question 10

What is Rubinstein-Taybi syndrome and what causes it?

Answer 10

Rubinstein-Taybi syndrome (RTS) is a genetic disease that involves broad thumbs and toes, short stature, distinctive facial features, and varying degrees of intellectual disability. Caused by a mutation in CREB binding protein, which plays an important role in regulating cell growth and division and is essential for normal fetal development.

Question 11

What type of post-translational modification can regulate gene expression?

Answer 11

Modification of histone side chains. I.E. histone acetyltransferase activity or histone deactylase activity

Question 12

What is the difference between promoting factors in Pol 1 rRNA transcription and Pol 3 tRNA transcription?

Answer 12

In Pol 1, the factors are located upstream of the initiation site. In Pol 3, the factors are located downstream of the initiation site

Question 13

What three promoting binding proteins are involved in the use of Pol3?

Answer 13

TFIIIA, TFIIIB, & TFIIIC. B and C are used for tRNA, while A, B, and C are used for rRNA

Question 14

What are the key promoter elements in Polymerase II?

Answer 14

1) TFIIB Recognition element (BRE)
2) TATA Box
3) Initiator (Inr)
4) Downstream core promoter element (DPE)

Question 15

What are functions of the Carboxyl terminal domain group attached to Pol II?

Answer 15

1) Initiation
2) RNA processing machinery
3) Splicing machinery
4) PolyA tail machinery

Question 16

What is the function of TFIIE?

Answer 16

Recruits TFIIH

Question 17

What are the functions of TFIIH?

Answer 17

1) Helicase activity unwinds DNA for RNA Pol II to utilize
2) Kinase activity phosphorylates DNA once initiation complex has formed to initiate elongation
3) Plays a role in DNA repair

Question 18

What is a CpG island and what is its function?

Answer 18

An area in the DNA with high content C-phosphate-G sequences. Used as a promoter sequence (similar to TATA box in function) to allow Pol II to know where initiation of transcription is located

Question 19

What are differences between genes that use a TATA box as a promoter and genes that use a CpG island as a promoter?

Answer 19

1) TATA box contains 1 major start site of transcription, while the CpG island contains multiple start sites of transcription
2) TATA box starts transcription in a single sense direction, while the CpG island can cause transcription to occur in both directions on both strands (sense & antisense). If Pol II however, transcribes mRNA in the incorrect direction, it will soon terminate and begin in the correct direction

Question 20

How transcription enhancers that are up to 50,000 bp away from the site of transcription carry out their function?

Answer 20

DNA looping allows the enhancer to pair up directly with the site of transcription for enhancement

Question 21

Ligand binding domains are _______ and N-termini often contain ________.

Answer 21

C-terminal; activation domains

Question 22

What is a nuclear localization sequence?

Answer 22

A nuclear localization signal or sequence (NLS) is an amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport. Once the protein binds to its receptor within the cell, nuclear translocation occurs in which the complex moves into the nucleus for transcription/translation

Question 23

What is the CREB activation pathway step by step?

Answer 23

1) High levels of cAMP activates Protein Kinase A (PKA)
2) The catalytic subunits of the tetramer PKA are translocated into the nucleus
3) PKA cause phosphorylation of CREB
4) CREB binds to CBP (CREB binding protein) and the CRE regulatory sequence in the DNA

Question 24

Which protein related to CREB transcription has histone acetyl transferase activity?

Answer 24

CBP, which is important as a developmental factor. Mutation would cause several developmental abnormalities

Question 25

What is a consequence of acetylating a lysine amino acid in a histone side chain?

Answer 25

Loss of positive charge causes histones in nucleosomes to lack ionic interactions with DNA (since DNA is negatively charged). Therefore, the DNA loosens and RNA Polymerase can now attach to a DNA sequence and begin transcription. Histone acetyltransferase activity causes gene activation, in general

Question 26

How is factor IX (9) associated with blood?

Answer 26

It is a blood clotting factor

Question 27

What is Hemophilia B Leyden?

Answer 27

Mutation at -20 site of DNA causes reduced HNF4 (Hepatocyte nuclear factor 4) and therefore increases factor IX levels as puberty progresses (due to increased testosterone)

Question 28

What is Hemophilia B Brandenburg?

Answer 28

Mutation at -26 site of DNA causes reduced HNF4 (Hepatocyte nuclear factor 4) & reduced androgen receptor (AR) binding, causing low factor IX levels throughout life

Question 29

What does the Pax6 gene do?

Answer 29

Paired box protein Pax-6 also known as aniridia type II protein (AN2) or oculorhombin is a protein that in humans is encoded by the PAX6 gene. Pax6 is a transcription factor present during embryonic development. The encoded protein contains two different binding sites that are known to bind DNA and function as regulators of gene transcription. It is a key regulatory gene of eye and brain development.

Question 30

What is aniridia and what is it caused by?

Answer 30

Aniridia is a disease characterized by the absence of the iris in the eyes and is caused by a lack of adequate Pax6 function (heterozygous condition with just a single copy of chromosome 11 affected)