Gene Expression and Regulation 2-2

Class 19

What does mRNA do?

It is the "message" transcribed from the gene.

What does rRNA do?

It makes up part of the ribosome.

What does tRNA do?

It brings amino acids to the ribosome during translation.

Why can prokaryotes do transcription and translation simultaneously?

They lack a nucleus.

Do prokaryotes have introns?

No, they do not have introns.

What are the three stages of transcription?

Initiation, elongation, termination.

What enzyme produces mRNA during transcription?

RNA polymerase.

Where does RNA polymerase bind to start transcription?

The promoter region.

What is the transcription terminator?

A nucleotide sequence that signals RNA polymerase to stop.

What helps RNA polymerase initiate transcription in prokaryotes?

A sigma factor.

What do transcription factors do?

They determine which genes are transcribed in eukaryotes.

In which direction does RNA polymerase synthesize RNA?

5' to 3'.

What is the template strand?

The DNA strand that is copied into RNA.

What is the coding strand?

The DNA strand with the same sequence as the mRNA (except T instead of U).

What happens when RNA polymerase reaches the termination sequence?

A hairpin loop forms and the mRNA + polymerase dissociate.

Given DNA (sense): 5' ATGGCCTATGAATCG 3'

what is the mRNA sequence?,5' AUGGCCUAUGAAUCG 3'.

Do introns code for amino acids?

No, introns do not code for proteins.

What are exons?

The coding regions that remain in the mRNA.

What is the primary RNA transcript?

The initial pre-mRNA copy made from the gene.

Where does RNA processing occur?

In the nucleus.

What removes introns from pre-mRNA?

Enzyme-RNA complexes (spliceosomes).

What joins exons together?

Spliceosomes (snRNPs + pre-mRNA).

What is added to the 5' end of mRNA?

A 5' cap.

What is added to the 3' end of mRNA?

A poly-A tail.

What is the function of the poly-A tail?

It protects mRNA from degradation.

How much of a human gene is typically introns?

About 90%.

What is alternative splicing?

Using different combinations of exons to produce different proteins.

How many mRNA transcripts can humans make from 25

000 genes?,Around 120,000 transcripts.

What is a spliceosome made of?

Pre-mRNA + small ribonucleoproteins (snRNPs).

When does RNA processing occur?

Immediately after transcription.

Translation occurs on what structure?

Ribosomes; the protein-making factories of the cell.

Where are ribosomes found?

Free in cytoplasm or attached to rough ER.

What is each ribosome made of?

Proteins + several segments of ribosomal RNA (rRNA).

What are the two ribosomal subunits?

Small subunit and large subunit.

What does the small ribosomal subunit do?

Exposes a short rRNA sequence complementary to mRNA's leader sequence; binds mRNA.

What does the large ribosomal subunit contain?

Three tRNA binding sites: A, P, and E sites.

Role of tRNA

Transfers amino acids to the ribosome during translation.

What is a codon?

Three-nucleotide mRNA sequence that codes for an amino acid.

How is mRNA read?

In three-nucleotide units called codons.

What does each codon correspond to? A specific amino acid.

Function of the A site

Aminoacyl-tRNA entry site; new tRNA with amino acid enters.

Function of the P site

Peptidyl site; holds growing polypeptide; peptide bonds form here.

Function of the E site

Exit site; empty tRNA leaves the ribosome.

What is the anticodon?

Three-nucleotide sequence on tRNA complementary to an mRNA codon.

What attaches amino acids to tRNA?

Activating enzymes (aminoacyl-tRNA synthetases).

What happens when mRNA binds the small ribosomal subunit?

Large subunit attaches → complete ribosome forms.

How does mRNA move through the ribosome?

Three nucleotides at a time.

What enters the A site during translation?

A new tRNA carrying an amino acid to be added.

Before a new tRNA can enter the A site

what happens?,Previous tRNA moves from A site to P site.

What happens at the P site?

Peptide bond forms between the new amino acid and the growing chain; uses GTP for energy.

Which enzyme catalyzes peptide-bond formation?

Peptidyl transferase.

What happens to the empty tRNA?

Moves to the E site and is released.

Translation occurs on what structure?

Ribosomes—the protein-making factories of the cell.

What are ribosomes made of?

A complex of proteins + ribosomal RNA (rRNA).

What are the two ribosomal subunits?

Small subunit + large subunit.

How does mRNA bind to the ribosome?

mRNA binds to a complementary rRNA sequence on the small subunit.

What are the three ribosomal binding sites?

A site, P site, and E site.

What binds at the A site?

tRNA carrying an amino acid enters at the A site.

What binds at the P site?

tRNA holding the growing polypeptide chain.

What happens at the E site?

Empty tRNA exits the ribosome.

What is a codon?

A 3-nucleotide sequence on mRNA that codes for an amino acid.

How many possible codons exist?

64 possible codons (4×4×4).

How many amino acids exist?

20 amino acids.

Why can multiple codons code for the same amino acid?.Due to redundancy of the genetic code—silent mutations can occur.

What is an anticodon?

A 3-nucleotide sequence on tRNA complementary to an mRNA codon.

What attaches amino acids to the correct tRNA?

Activating enzymes (aminoacyl-tRNA synthetases).

What happens once mRNA binds the small ribosomal subunit?

The large subunit joins forming a complete ribosome.

How does mRNA move through the ribosome?

Three nucleotides at a time (one codon).

What happens when a new tRNA arrives?

It enters the A site carrying an amino acid.

What happens before a new tRNA can enter?

The tRNA in the A site shifts to the P site.

What reaction forms peptide bonds?

Peptidyl transferase catalyzes peptide bond formation.

What happens after the tRNA in the P site is empty?

It shifts to the E site and exits.

When does translation stop?

When a stop codon is reached.

What happens at a stop codon?

The ribosome falls apart and releases the protein.

Can multiple ribosomes translate one mRNA at once?

Yes—polyribosomes increase efficiency.

Why can bacteria translate and transcribe simultaneously?

They lack a nucleus, allowing both processes to occur at the same time.

What happens to proteins after translation in eukaryotes?

They fold into secondary and tertiary structures; some are modified by the Golgi.

What is post-translational modification?

Further processing in the Golgi where proteins are packaged into vesicles.

What are lipoproteins?

Proteins combined with lipids (e.g., LDLs).

What are glycoproteins?

Proteins combined with sugars (e.g., blood type markers A, B, AB).

What must every cell regulate?

Which genes are transcribed.

How can prokaryotes turn genes OFF?

Using a repressor that binds DNA and blocks the promoter.

How can genes be turned ON?

An activator increases promoter access for RNA polymerase.

What is an operon? A cluster of genes transcribed as a single unit under one promoter.

What is the best example of an operon?

The lac operon in E. coli.

What genes does the lac operon contain?

Genes coding for lactose-breaking enzymes.

What regulatory elements does the operon have?

Operator and promoter.

How does lactose affect the lac operon?

Lactose binds the repressor → repressor falls off → operon is transcribed.

Why does this matter?

Allows bacteria to produce enzymes only when lactose is present.

What is CAP?

An activator protein required for RNA polymerase to work efficiently at the lac operon.

When does CAP bind DNA?

When glucose AND lactose are low.

Why is CAP important?

It ensures transcription only happens when lactose is present and glucose is scarce.

Why do eukaryotes need histone proteins?

To condense their complex chromosomes so the DNA fits in the nucleus.

What limits which DNA a cell can transcribe?

Only DNA that is accessible to RNA polymerase can be transcribed.

Are all chromosomal regions equally condensed?

No—different regions have different levels of condensation.

What happens to highly condensed regions of DNA?

They are not transcribed.

What is methylation?

Addition of methyl groups (-CH₃) that prevents transcription—gene silencing.

What does methylation do to gene expression?

It shuts genes off by making DNA inaccessible.

What is alternate splicing?

Only certain exons are included in the final mRNA, producing different protein products.

Why is alternate splicing important?

It allows over 100,000 proteins to be made from only ~25,000 genes.