BIOLOGY 221 FALL - Gene Expression

What is transcription

DNA is transcribed into an RNA copy

What is translation

mRNA is translated into a polypeptide @ the ribosome

Where is transcription and translation in prokaryotes

The cytoplasm

Where is transcription in eukaryotes

The nucleus

Where is translation in eukaryotes

Cytosol

What do gene products result in

Traits aka phenotypes

What is a gene

Specific region on a chromosome that contains/carries information to make a specific gene product

What are the parts of the transcript

1. Regulatory Sequence

2. Promoter

3. Transcribed/Coding Region

   1. Terminator

What is the regulatory sequence

Regulatory protein binding site

What do regulatory proteins influence?

The rate of transcription

What end is the promoter at

The 3’ end

What is the promoter

Signals beginning of transcription

What is the terminator

Signals end of transcription

What direction is DNA synthesis

5’-3’ direction

What direction is the template strand

3’-5’

What direction is transcription

5’-3’

What is the region between 5’ and stop codon

5’ Untranslated region (5’ UTR)

What is the region between 3’ and start

3’ Untranslated region (3’ UTR)

What are exons

Sequences used to make gene products

What are introns

Sequences not used, will have to be removed

What is the first step of transcription

Initiation

What happens on the first step of transcription

• Recognition and binding of promoter by RNA polymerase

  • Melting of the DNA @ the promoter to form and open complex

What is the second step of transcription

Elongation

What happens on the second step of transcription

• Synthesis of RNA molecule that is complementary to the template strand of the DNA

  • Direction of synthesis = direction of RNA polymerase movement along template

What does the direction of synthesis equal

The direction of RNA polymerase movement along template

What does the direction of RNA polymerase movement along the template equal

Direction of synthesis

What is the first step to encoding a protein

Transcription

What does the RNA polymerase consist of in prokaryotic transcription

Core and Sigma factor

What does the sigma factor do?

Recognize and bind to the promoter

When is the sigma factor released

During elongation

What finished transcription after the sigma factor is released

The core factor

What is the core factor

The active site

What does the core factor not do

Cannot recognize promoter

What does sigma factor form

Forms holoenzyme complex

What does RNA polymerase I do

Encodes rRNA

What does RNA polymerase II do

Most genes encoding proteins

What does RNA polymerase III do

Encodes small RNA’s: 

What are examples of small RNA’s

tRNA’s and snRNA’s

What does the recognition and binding of promoters by the eukaryotic RNA polymerases require

Transcription factors

What do transcription factors do

Binds to promoter/enhancer elements and recruit RNA polymerase to the promoter to form an initiation complex

What happens after transcription in prokaryotes

For genes that encode proteins, mRNA is immediately ready to be translated

What can begin even before transcription is complete

Translated

What happens after transcription in eukaryotes

Transcription produces a pre-mRNA that that requires processing before it can be translated

What else happens after transcription in eukaryotes

• Pre-mRNA adds cap to 5’ end

• Pre-mRNA  removes introns

• Addition of poly-A tail to 3’ end

  • Processing occurs in nucleus

When does capping happen

Very soon after transcription begins

What are the functions of the 5’ cap

• Transport

• preventing degradation

• Initiation of translation

What is polyadenylation

Pre-mRNA cleaved within 3’ UTR, poly A polymerase adds poly A tail to the new 3’ end

What are the functions of the poly A tail

• Transport

• Prevents degradation

• Increases efficiency of translation

What does preventing degradation mean

Preserving mRNA

What does preserving mRNA mean

Prevents degradation

What are RNases

Breaks phosphodiester bonds in RNA molecules

What is splicing performed by

snRNP’s

What do snRNP’s form

Spliceosomes

How do introns get remove

Removed by spliceosomes

When are introns removed

Before transcription is complete

What is alternative splicing

Splicing together exons in 2 or more ways

What are self-splicing introns

Spliceosomes not required, removal catalyzed by the RNA

Where does the splicing happen

In the nucleus

What happens on the first step of splicing

2 snRNP subunits bind to the 5’ splice site and branch site

What happens on the second step of splicing

Additional snRNP subunits bind to the 3’ splice site —> Creation of spliceosomes —> Intron forms loop

What happens on the third step of splicing

5’ splice site is cut —> 5. end covalently attached to branch site —> two snRNP’s released

What happens on the fourth step of splicing

3’ splice site is cut. Exon 1 covalently attached to exon 1 intron (now in loop) is released with the rest of the snRNP subunits and degraded

Where is the ribosome binding site in prokaryotic translation

5’ UTR

Why does the ribosome assemble?

So it is correctly positioned at the start codon

What direction is mRNA translated in

5’-3’ direction

Where is the protein synthesized

From the amino terminus to carboxy terminus

What is the bond called in nucleotides

Peptide bond

Where does translation occurs in prokaryotes

The cytoplasm

What other name is the ribosomal binding site called

Shine-Delgarno Sequence

How many different aminoacyl-tRNA synthetases

20

What happens on the first step of charging of tRNA

Species amino acid and ATP bind to aminoacyl-tRNA synthetase

What happens on the second step of charging of tRNA

The amino acid is activated by the covalent bonding of AMP and pyrophosphate is released

What happens on the third step of charging of tRNA

The correct tRNA binds to the synthetase. Amino acid covalently attaches to the tRNA. AMP is released

What happens on the fourth step of charging of tRNA

Charged tRNA is released

Where is the amino acid attachment site

The 3’ ss region

How do anticodons pair

Complementary base pairing

What is the E site on the ribosome

Exit

What is the P site on a riboome

Peptidyl

What is the A site on a ribosome

Aminoacyl

What does the P site do

Base pairs with codon

What does 16S rRNA undergo

Complementary base pairing with Shine-Delgarno sequence in 5’ UTR of mRNA

What is the first step of translation initiation in prokaryotes

mRNA binds to small ribosomal subunits

What is the second step of translation initiation in prokaryotes

Initiator tRNA binds to start codon in mRNA

What is the third step of translation initiation in prokaryotes

Large ribosomal subunit binds

What is the first step of translation initiation in eukaryotes

5’ cap is bound by a cap binding protein (40S subunit binds) (Initiator tRNA charged with methionine binds)

What is the second step of translation initiation in eukaryotes

Complex scans (moves) down the mRNA until start codon in correct context is reached

What is the third step of translation initiation in eukaryotes

60S subunit binds

What is the fourth step of translation initiation in eukaryotes

80S initiation complex is complete

What is the first step in elongation

tRNA entry

What happens in the first step of elongation

Charged tRNA binds to the A site

What is the second step of elongation

Peptidyl transfer reaction

What happens in the second step of elongation

Bond forms between polypeptide chain and amino acid in the A site. Polypeptide then transferred to A site

What is the third step of elongation

Translocation of ribosome and release of tRNAW

What happens on the third step of elongation

Ribosome translocates 1 codon to the right. Uncharged tRNA is released from E site. Process is repeated until stop codon is reached

What are polysomes

Multiplated ribosome translating the same mRNA