CM05: Gene Expression and Regulation

What is ribonucleic acid (RNA)?

• It is single-stranded (and has stem loops)

• Has uracil instead of thymine

• Sugar is ribose

• Easily degraded than DNA

What is ribosomal RNA (rRNA)? How many types are there in eukaryotes?

It is a type of RNA that assembles with proteins to form ribosomes. There are 4 types in eukaryotes.

What is transfer RNA (tRNA)? What does the cloverleaf structure contain?

It is RNA used to match genetic info to the amino acid sequence during translation.

The cloverleaf structure contains the anticodon loop and the acceptor stem (5’ -CCA- 3’)

What is the messenger RNA (mRNA)? What does its structure contain?

• Largest RNA in size

• It carries out the genetic guidelines from the DNA for protein synthesis (contain monocistronic info)

• It’s structure contains a 5’ cap (7-methylguanosine), coding seq for protein synthesis, and poly(A)tail

What are the three types of RNA polymerases?

• RNA polymerase I (rRNA): most abundant

• RNA polymerase II (mRNA): largest

• RNA polymerase III (tRNA): smallest

Compare the template strand and the non-template strand.

Template: Antisense and non-coding

Non-template: Sense and coding

What is the basal promoter? What are some examples?

It is the minimum sequence necessary for transcription.

Ex: TATA-box and the Inr (Initiator)

What are the TATA-box and Inr required for?

They are required for the binding of general transcription factors (GTFs)

What is the proximal promoter? What are two examples?

They are regulatory elements/TF binding sites.

Ex: CAAT and GC boxes

What are CAAT and GC boxes?

They are regulatory sequences that are for the binding of specific TFs (STFs)

What are some examples of distal promoters? What are they used for?

Enhancers or silencers are some examples. They are special sequences that increase/decrease transcription rate.

What forms the pre-intiation complex? How does this begin transcription?

• 6 GTPs + RNA polymerase II assemble near the transcription start site (TSS)

• GTFs binds TATA-box and recruits the RNA polymerase to the TSS to begin trascription at basal rate.

Explain the process of elongation.

It starts with RNA polymerase unwinding DNA before adding complementary ribonucleotide triphosphates (rNTPs) to 3’- end of RNA.

What forms the transcription bubble?

Melted DNA helix + RNA polymerase + growing RNA

What is the significance of amanitin?

It is responsible for inhibiting RNA polymerase progression in poisonous mushrooms

Explain the process of termination.

RNA polymerase reaches the termination/polyadenylation signal, transcription continues than pre-mRNA/hnRNA is released.

How is RNA processed?

RNA is processed in the nucleus, where post-transcriptional modificiations of the pre-mRNA produce the mature mRNA.

This later leaves the nucleus through the nuclear pore and enters the cytoplasm for translation.

What is the role of the 7-methylguanosine cap at the 5’ end of pre-mRNA?

It serves a protective role due to its resistant to most nucleases.

What is the role of the poly(A) tail at the 3’ end?

It forms a stabilizing role and facilitates export from the nucleus.

Where is the poly(A) tail shortened?

In the cytosol.

Define splicing.

Splicing is the removal of introns and joining of exons.

Define splice sites.

They are intron-exon junctions that are marked by AG at the 3’ end of the exon and GU at the 5’ end of the intron (AG/GU).

Explain what is alternative splicing.

The removal of different regions from the pre-mRNA which forms mature mRNAs with various sequences.

What are the locations and functions of rRNA, mRNA, and tRNA?

• rRNA: Located in the cytoplasm and responsible for structural and functional components of the ribosomes.

• mRNA: Found in the nucleus/cytoplasm and carries the genetic code for proteins.

• tRNA: Located in the cytoplasm and responsible for incorporating amino acids into polypeptide chains.