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?

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

Cloverleaf: the anticodon loop + acceptor stem (5’ -CCA- 3’)

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

RNA responsible for carrying genetic guidelines from the DNA for protein synthesis (contain monocistronic info)

Structure: 5’ cap (7-methylguanosine) + coding seq. + 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 binding specific TFs (STFs)

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

They are special sequences that increase/decrease transcription rate.

Ex: Enhancers or silencers

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?

1. Processed in nucleus, where pre-mRNA is made → mature mRNA.

2. mature mRNA leaves nuclear pore and enter 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.

Removal of introns and joining of exons.

Define splice sites.

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 → forms mature mRNAs.

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.

What is an example of the start codon?

AUG

List three examples of the stop codon.

UGA, UAA, UAG

What are the genetic code properties?

• Unambiguous (specific) - each codon codes for 1 amino acid

• Degenerate (redundant) - some amino acids encode by more than 1 codon

• Non-overlapping and commaless

• Nearly universal

What is the Wobble hypothesis?

When tRNA recognize and bind to a sequence that is not perfectly complementary.

What initiates termination?

When a STOP codon is reached.

How are codons recognized?

Recognized by RF (release factors) which bind → A site and cause polypeptides on P site → release.

Define polysomes (polyribosomes).

Multiple ribosomes that translate proteins simultaneously.

What are some major post-translational modifications?

1. Phosphorylation (Tyr, Ser, Threo): metabolic regulation and signal transduction.

2. Glycosylation (Ser/threo)

3. Hydroxylation (Pro, Lys): found in collagen

4. Others: carboxylation biotinylation, farnesylation, etc.

What is protein degration?

The destruction of ubiquitin group and the degration of specific proteases.

How is gene expression regulated?

By adaptation (our cell response to external factors for homeostasis) and differentiation

Differentiate heterochromatin and euchromatin.

Heterochromatin: highly condensed part that contains fewer genes in chromosome.

Euchromatin: loosely condensed part that contains many genes in chromosome.

What is the purpose of gene amplification?

To increase gene expression by producing 100-1000 copies of genes.

Define transposons. What is the significance of these?

Mobile fragments of DNA that move between different sites on chromosomes.

They are responsible for structural genomic variation.

What’s alternative polyadenylation?

Proteins with alternative polyadenylation sites that generate coding sequences (or 3’ UTR)

What does RNA interference prevent through inducing gene silencing?

RNA interference can prevent translation or induce degration.

What is RNA editing?

When mRNA processed to include termination sequence before last codon