Eukaryotes Exam 1

What is the first step of DNA replication in yeast?

The binding of the ORC (origin recognition complex) to the 11 bp consensus sequence. 

What is the second step of DNA replication in yeast?

Binding of Cdc6 to the ORC

What is the third/fourth step of DNA replication in yeast?

Binding of helicase and bound Cdt1 to the DNA, fourth step is just a second helicase.

What is the fifth step of DNA replication in yeast?

The helix is unwound and helicase slides. The ORC and Cdt1 and Cdc6 also leave the complex.

What is the last step of initiation in DNA replication in yeast?

DNA polymerase binds to the complex. 

What does telomerase do after binding to the 3’ overhang?

A series of repeated elongations and translocations result in a repeated TTG-GGG- sequences being produces. 

What is the end result of telomerase activity?

The overhang that is present after telomerase activity is bound by the T-loop which prevents detection from cellular machinery that would destroy it. 

Where is telomerase active?

in germ cells and stem cells

What is the role of RNA Polymerase 1 in eukaryotes?

synthesizes rRNA

What is the role of RNA Polymerase 2 in eukaryotes?

synthesizes mRNA and some non-coding RNA

What is the role of RNA Polymerase 3 in eukaryotes?

synthesizes tRNA, 5S rRNA, and some small nuclear RNAs

Why can’t eukaryotes couple transcription and translation?

Transcription takes place in the nucleus. As a result, it is physically separated from the ribosomes present in the cytoplasm. 

What is the promoter region in eukaryotes?

the TATA box

What is the carboxy-terminal domain (CTD)

AKA c-terminal tail. a protein tail of the RPB1 subunit of RNAP. A sequence of amino acids repeated 52 times. 

What is the role of the CTD?

may be phosphorylated to regulate transcription, recruit post-processing factors, and chromatin modification

What binds to the TATA box?

TATA-binding protein (TBP) of TFIID

What is the first step of initiation in transcription?

Binding of TFIID to the TATA box via its TBP (tata binding protein)

What is the second step of initiation in transcription?

TFIIA and TFIIB bind to stabilize TFIID

What is the third step of initiation in transcription?

TFIIF binds to RNAP II and escorts it to the complex

What is the fourth step of initiation in transcription?

TFIIE and TFIIH are recruited, the Pre-initiation complex is completed.

What is the role of TFIIH?

• it has a helicase factor to unwind DNA

• It also phosphorylates the serine residues of the CTD

What is the torpedo model of termination?

A torpedo RNase cleaves the 3’ end of mRNA and digests the residual transcript, releasing the functional mRNA from RNAPII

What is the allosteric termination model?

A recruited CP complex facilitates the cleavage of the mRNA at the polyA site once a termination sequence is encountered. 

What are two common means of post-transcriptional modification?

• addition of a 5’ cap

• addition of a poly-a tail to the 3’ end

What are three functions of the 5’ cap?

• protects RNA from decay by exonucleases

• serves as a binding site for proteins

• assists in translation

What is polyadenylation?

The process of adding 50-250 adenosine residues to the 3’ end of mRNA.

What is splicing?

The removal of introns and subsequent ligation of exons. 

Why is alternative splicing significant?

It can result in a wider range of proteins based on the order that exons are placed in. Certain splicing patterns can be turned on/off to increase functionality. 

What is the role of eIF1A in eukaryotic translation?

binds to the active site, prevent premature interactions from tRNA. 

What is the role of eIF2 in eukaryotic translation?

Interacts with Met-tRNA and GTP to associate with the small subunit. 

What is the function of eIF4F complex in eukaryotic translation?

associates with the 5’ cap of mRNA

What is the function of eIF3 in eukaryotic translation?

binds to the small ribosomal subunit and prevents the association of the large subunit.

When are the IFs released from the 40s (small) eukaryotic subunit?

After the start codon is found. 

What is the role of eIf5B-GTP?

promotes the association of the large and small ribosomal subunits.

What is the role of eEf1-alpha in elongation?

this elongation factor is responsible for escorting charged tRNA to the active site. 

What is the role of eEF2 in elongation?

drives the repositioning of tRNAs from the P and A sites to the E and P sites. 

What enzyme is responsible for the formation of new peptide bonds?

peptidyl transferase

What is the role of RF1?

RF1 occupies the A site o the ribosome, triggers cleavage o the peptidyl-tRNA.

What are the two eukaryotic release factors?

RF1 and RF3

What is the role of RF3?

promotes action of RF1

What is the key regulator of the galactose pathway in yeast?

Gal4

What are the three domains of Gal4 from superior to inferior?

• Activation domain

• Dimerization domain

• DNA-binding domain

What represses Gal4 activity?

Gal4 is repressed by Gal80

What happens to Gal80 in the presence of galactose?

Gal3 induces a conformational change in Gal80, releasing it from Gal4.

What is a transcription factor?

something that regulates transcription by binding enhancer elements and interacting with coregulators. 

What is a general transcription factor?

something that binds to the promoter region to attract and correctly position RNAPII for transcription.