Week 5 Flashcards
Gene regulation, transcription, and translation
What is the central dogma of molecular biology
- DNA is transcribed into RNA
- RNA is translated into protein
What is transcription?
The synthesis of an RNA molecule from a DNA template
What are the three major components of transcription?
- A DNA template
- The raw materials to build the RNA molecule
- The transcription apparatus
What is the template strand
The DNA nucleotide strand being used for transcription
What is the transcription unit?
The stretch of DNA on the template stand that encodes an RNA molecule and the sequences needed for its transcription
What three things are included in the transcription unit?
- A promoter
- An RNA coding sequence
- A terminator
What is the promoter in a transcription unit?
DNA sequence that the transcription apparatus recognizes and binds to
What three things are determined by the promoter in a transcription unit?
- Which of the two DNA strands is to be read as the template
- The direction of transcription
- The transcription start site
T or F: In many transcription units, the promoter region is located next to the transcription start site, but it itself is not transcribed.
True
What is the RNA coding region in a transcription unit?
The sequence of DNA nucleotides that is copied into an RNA molecule
What is the terminator in a transcription unit?
The sequence of DNA nucleotides that signals where transcription is to end
Is the terminator sequence typically included in the RNA coding sequence?
Yes because transcription stops after the terminator has been copied into RNA
T or F: Upstream refers to movement from the 3’ end to the 5’ end.
False. Upstream or downstream is relative to the point of reference.
Is the promoter sequence upstream or downstream of the transcriptional start site?
Upstream
Is the termination sequence upstream or downstream of the transcriptional start site?
Downstream
Is the RNA-coding sequence upstream or downstream of the promoter?
Downstream
Is the RNA-coding sequence upstream or downstream of the termination site?
Upstream
What is the orientation of the template strand?
3’ to 5’
In which direction is the template strand synthesized/transcribed?
5’ to 3’
RNA synthesis is ____________ and ____________ to the template strand.
Complimentary, Antiparallel
How does the sequence of the transcribed RNA sequence differ from the non-template strand?
They have the same sequence (both complementary to the template strand), but U is substituted for T in the RNA strand
What is the difference between genes being transcribed on the top (+) and genes being transcribed on the bottom (-) strand of the DNA?
Whether the transcription takes place from left to right or right to left (always read 3’ to 5’ and transcribed 5’ to 3’, but because the strands are antiparallel, the 3’ and 5’ ends are different each)
When being numbered, which nucleotide is labelled as +1?
The first nucleotide being transcribed
Are nucleotides downstream from the start site assigned positive or negative numbers?
Positive numbers
Are nucleotides upstream from the start site assigned positive or negative numbers?
Negative numbers
What is the transcription apparatus made of?
RNA polymerase
What is the role of RNA polymerase during transcription?
Synthesizes RNA from the DNA template
Where does RNA polymerase bind during transcription?
The promoter region
What is RNA polymerase II responsible for?
Generating the majority of mRNA for making proteins
T or F: Transcription in eukaryotes is a complex and highly regulated process.
True
What is an operator?
The binding site for a repressor protein
Where is the operator located?
Between the promoter region and the RNA coding sequence
What is an operon?
The region of DNA consisting of a portion of the promoter, the operator, and the coding sequence
What are negative regulatory proteins?
Proteins that bind to the operator and block the RNA polymerase from initiating transcription
What are positive regulatory proteins?
Proteins that bind to the operator and help initiate transcription
What are the two types of operons?
- Inducible operons
- Repressible operons
What are inducible operons?
When transcription of the operon is normally off and something happens to turn it on
What are repressible operons?
When transcription of the operon is normally on and something happens to turn it off
What is the normal state of a negative inducible operon?
Transcription is turned off by a repressor bound to the operator, which must be relieved to allow transcription
What must happen for a negative inducible operon to allow transcription?
An inducer must bind to the repressor on the operator and inactivate it so it can no longer prevent RNA polymerase from binding, thus inducing transcription
What are negative inducible operons usually involved in?
The degradation/metabolism of molecules
What is one of the most studied negative inducible operon?
The lac operon
What is permase (aka. lac Y)?
An enzyme that transports lactose across the cell membrane to be metabolized
Which enzyme catalyzes the metabolism of lactose?
Beta-galactosidase (lac Z)
In the presence of lactose, what inactivates the repressor that is inhibiting transcription?
Allolactose
How is allolactose produced?
Lactose is broken down into allolactose by lac Z (beta-galactosidase)
How does allolactose induce transcription?
By acting as a ligand and binding to and inactivating the repressor that is inhibiting transcription
In terms of the lac operons, what occurs in the absence of lactose?
The repressor protein (lac I) binds to the operator (lac O) and inhibits transcription
What is the repressor protein called in a lac operon?
Lac I
What is the operator called in a lac operon?
Lac O
When allolactose binds to the lac I, which structural genes can now be transcribed?
Lac Z, lac Y, and lac A
What is translation?
The synthesis of a peptide chain corresponding to the coding sequence present in the previously transcribed mRNA
What are the three major components for translation?
- mRNA
- tRNA
- Ribosomes
Is eukaryotic mRNA monocistronic or polycistronic?
Monocistronic
What does it mean for mRNA to be monocistronic?
The mRNA contains only one coding sequence for a single polypeptide chain
At which end does the ribosome bind to initiate translation?
The 5’ end
What is the codon that initiates RNA translation?
AUG
Which three codons terminate RNA translation?
- UAA
- UAG
- UGA
What is needed to translate the RNA transcript?
- An initiation sequence (start codon)
- A genetic code specifying which amino acid will be incorporated
- A termination sequence (stop codon)
What are four properties of the genetic code?
- Codons are adjacent
- It’s non-overlapping
- It’s degenerate
- It’s (nearly) universal
What is meant when describing the genetic code as non-overlapping?
Each nucleotide is part of one codon
What is meant when describing the genetic code as degenerate?
Most amino acids are specified by more than one codon
What is meant when describing the genetic code as being universal?
With minor exceptions, each codon has the same meaning/codes for the same amino acid in all organisms
How many different codons are possible in the genetic code?
64
How many different amino acids can be coded for in the genetic code?
20
What is included within the large ribosomal subunit used for translation?
Three binding sites for tRNAs
What are the three binding sites for tRNA present in the large subunit of ribosomes used in translation?
- Left side: exit site (E site)
- Middle: peptidyl site (P site)
- Right side: aminoacyl site (A site)
What structures of tRNA are used in translation?
- The amino acid attachment site on the 3’ end
- The anticodon
What role does tRNA play in translation?
Carries the appropriate amino acid to the ribosome for attachment in the polypeptide chain
What is an anticodon?
The sequence of three nucleotides in a tRNA molecule that are complimentary to a codon in the mRNA molecule
What is the difference between a charged and uncharged tRNA molecule?
- Charged tRNA: has an amino acid attached to it
- Uncharged tRNA: does not have an amino acid attatched to it
What are the three steps in translation?
- Initiation
- Elongation
- Termination
What occurs during the initiation stage of translation?
AUG is recognized and Met is established as the first amino acid in the new polypeptide chain
What occurs during the elongation stage of translation?
Successive amino acids are added one by one to the growing polypeptide chain
What occurs during termination of translation?
A stop codon is recognized by a releasing factor that mimics tRNA and the polypeptide chain is released from the ribosome
How is translation initiated?
- The AUG codon is recognized, and the tRNA charged with Met binds to the P site
- The tRNA corresponding to the codon in the A site bring the next amino acid into the A site
- Met is transferred to the amino acid on the tRNA in the A site
How does elongation occur during translation?
- The ribosome moves down one codon, putting the tRNA with the growing polypeptide chain into the P site and ejecting the uncharged tRNA via the E site
- A new tRNA complementary with the next codon binds to the A site and the process continues
How did proteins evolve?
As a result of mutations in DNA
