Biol 329: mRNA to Gene Expression

Flashcards covering key concepts from lecture notes on mRNA processing, protein translation (Chapter 7), and control of gene expression (Chapter 8), including initiation, elongation, termination, regulatory mechanisms, and epigenetic inheritance.

What modifications does premRNA undergo before becoming active mRNA?

It needs to have a 5' cap and a 3' poly-A tail added, and it needs to be spliced.

What is the function of the 5' cap and 3' poly-A tail on mRNA?

They protect mRNA from degradation. Once the protein is made, the caps and tails are removed, and degradation occurs immediately.

What guiding protein helps attract mRNA to combine with a ribosome?

The initiator protein.

In translation, how many nucleotides make up one codon, and what does one codon code for?

Three nucleotides make up one codon, and one codon codes for one amino acid.

Which codon serves as the universal start codon?

Methionine (AUG).

What are the three stop codons?

UAA, UAG, UGA.

What enzyme links a specific amino acid to its corresponding tRNA?

Aminoacyl-tRNA synthetase (aaRS).

Which site on the ribosome is the arrival site for aminoacyl-tRNAs?

The A-site (aminoacyl site).

Which site on the ribosome holds the tRNA linked to the growing polypeptide chain?

The P-site (peptidyl site).

What are the three main steps in translation?

Initiation, elongation, and termination.

In which direction does a new protein grow, from its ends?

From the amine (N) end to the carboxyl (C) end.

What are ribozymes?

RNA molecules that possess catalytic activity.

What is the typical first amino acid at the N-terminus of all proteins?

Methionine (MET), which is often removed later by specific proteases.

How is translation initiation different in eukaryotes compared to prokaryotes?

In eukaryotes, the small ribosomal subunit binds to the 5' cap of mRNA and scans for AUG. In prokaryotes, a binding sequence binds to a ribosome binding site (polycistronic) directly.

What happens when a stop codon is reached during translation?

Release factors bind to the A-site, catalyzing the addition of H2O instead of an amino acid, which frees the polypeptide from the tRNA.

What are proteases, and what is their function?

Proteases are enzymes that break down proteins through proteolysis (hydrolysis), especially short-lifespan or damaged proteins.

What cellular machines break down proteins in the cytosol and nucleus, particularly those marked by ubiquitin?

Proteasomes.

How is cell differentiation primarily achieved?

By changes in gene expression.

List at least three steps at which gene expression can be regulated.

Transcriptional control, RNA processing control, mRNA transport/localization control, mRNA degradation control, translational control, protein degradation control, protein activity control.

What are regulatory DNA sequences (RDS)?

DNA sequences, in addition to the promoter, that are used to switch a gene on or off.

What is an operon, and where is it typically found?

A cluster of genes transcribed by a single promoter, commonly found in prokaryotes but rare in eukaryotes.

How does a transcriptional repressor typically work?

It binds to an operator within an operon, blocking RNA polymerase from accessing the DNA and preventing transcription.

What kind of protein only binds to DNA if it is also bound to another molecule, such as tryptophan?

An allosteric protein.

In eukaryotes, what are enhancers?

DNA sites where gene activators bind, enhancing the rate of transcription regardless of their position relative to the promoter due to DNA looping.

In eukaryotic gene activation, what protein complex attracts General Transcription Factors (GTFs) and RNA polymerase to form the transcription initiation complex?

The Mediator complex.

How do eukaryotic gene activators promote transcription regarding histones?

They attract chromosome remodeling complexes, such as histone acetyltransferases, which promote the attachment of acetyl groups to lysines in histone tails, making DNA more accessible.

What is combinatorial control in gene expression?

It is when groups of transcription regulators work together to determine the expression of a single gene, requiring the correct combination of regulators.

Give an example of a post-transcriptional control mechanism that regulates mRNA translation.

Translational repressor proteins that bind to the ribosome binding site of mRNA, or thermosensing RNA that blocks/unblocks translation based on temperature.

What are miRNAs, and how do they function?

Small, noncoding RNAs that regulate gene expression by base-pairing with target mRNAs, leading to their destruction or blocking their translation.

What is RNA interference (RNAi)?

The general name for the process where small RNAs (like siRNA) produced from double-stranded foreign RNAs are incorporated into an RNA-induced Silencing Complex (RISC), which destroys complementary foreign mRNA.

Name one mechanism of cellular inheritance (epigenetic inheritance) discussed.

Positive feedback loops from master transcription regulators, DNA methylation, or histone modification inheritance.

How does DNA methylation affect gene expression?

It involves adding methyl (CH3) groups to cytosine bases in DNA, which typically silences the gene, and this methylation pattern can be passed to daughter cells.

What happens to cells when they are 'terminally differentiated'?

They stop dividing.