CHAPTER 6 - GENE EXPRESSION

Question 1

What do chromosomes contain?

Answer 1

A long piece of DNA (circular in prokaryotes)

Question 2

What are the 3 parts of a gene?

Answer 2

1) the promoter sequence helps to control when and where transcription starts.
2) the coding sequence is what gets transcribed onto RNA
3) the terminator sequence signals the end fo the gene

Question 3

TRANSCRIPTION (in prokaryotes)

STEP 1 is called……?

Answer 3

Initiation.
- This is when several transcription factors bind to the promotor of the gene. The factors help RNA polymerase to bind correctly so it’s ready to start transcription at the site.
-Since the promotor is upstream of the start site, it does not get transcribed.

Question 4

TRANSCRIPTION (in prokaryotes)

STEP 2 is called……?

Answer 4

Elongation.
-RNA polymerase slides along the gene, briefly separating the 2 strands of DNA and using the TEMPLATE STRAND of DNA to form complementary base pairs with each new RNA nucleotide before its added to the growing RNA strand.

Question 5

TRANSCRIPTION (in prokaryotes)

STEP 3 is called……?

Answer 5

Termination.
- The termination sequence has a GC-rich region followed by many nucleotides.
- When it is transcribed: the GC- rich region of the resulting RNA causes it to fold over and base-pair with itself to form a hairpin loop.
-Since A-U base pairs are less stable because it has 2 H-bonds. Instead of 3 H- bonds like GC pairs. The RNA polymerase must backtrack to find a GC pair to stabilize before continuing. However, the hairpin loop blocks it, therefore, terminating the transcription.

Question 6

TRANSLATION (in prokaryotes)

What happens next, for the RNA molecule?

Answer 6

-If this gene for a functional RNA molecule (e.g. a tRNA) no translation is needed
-However, if there is a gene for a protein: this mRNA must now be translated to produce a protien.

Question 7

What is transcription?

Answer 7

The process by which a cell makes an RNA copy of a piece of DNA.

Question 8

What is translation?

Answer 8

Converting from 4 bases to another 20 amino acids. The process by which a cell makes proteins using the genetic information carried in messenger RNA (mRNA).

Question 9

TRANSLATION (in prokaryotes)

STEP 1 is called……?

Answer 9

Initiation.
We must assemble the ribosome and the first tRNA at the correct starting location.
1) the small ribosomal subunit binds to Shine Dalgarno sequence, which is on the mRNA near its 5’ end because you read 5’ —>3’
2) An initiator tRNA carrying a modified amino acid binds to the start codon, a few bases downstream of the Shine-Dalgarno sequence. (Step 1 and 2 happens at the correct AUG start codon)
3) The Large ribosomal subunit joins the small subunit to complete the translation initiation complex.

Question 10

What is the Shine Dalgarno?

Answer 10

It enables the initiation of protein synthesis by aligning the ribosome with the start codon.

Question 11

TRANSLATION (in prokaryotes)

STEP 2 & 3 is called……?

Answer 11

Elongation and Termination.
-The genetic code table lets you take each 3-base mRNA codon (e.g. 5’-UCC-3’), which is like a 3-letter word in the language of DNA/RNA and translate it into a specific amino acid which is a building block for the protein that’s being made.

Question 12

TRANSCRIPTION IN EUKARYOTES (compared to prokaryotes)

STEP 1 is……?

Answer 12

Initiation.
In eukaryotes, when and where transcription begins still depends on the promoter sequence found upstream of the RNA-coding sequence, and transcription factors still help RNA polymerase bind properly at the +1 transcription start site.

Question 13

What is the difference in transcription step one for Eukaryotes compared to Prokaryotes?

Answer 13

The transcription facts and the DNA sequences that they recognize within the promoter sequence (TATA BOX) are different, and the process is more complex, involving other more distant regulatory regions.

Question 14

TRANSCRIPTION IN EUKARYOTES (compared to prokaryotes)

STEP 2 is……?

Answer 14

Elongation.
-elongation is essentially the same in all cells, with RNA polymerase building the growing RNA strand by complementary base pairing with the template strand of DNA.

Question 15

TRANSCRIPTION IN EUKARYOTES (compared to prokaryotes)

STEP 3 is……?

Answer 15

Termination.
-eukaryotes do not use hairpin loops to terminate transcription.
-They use much more complex mechanisms.

Question 16

RNA PROCESSING (in eukaryotes only)

Answer 16

-The RNA transcript (or pre-mRNA) produced during transcription in eukaryotes is not ready to be translated it must of through 3 types of RNA Processing.

Question 17

What is the 3 types of RNA processing?

Answer 17

1) a 5- cap is added to tell the eukaryotic ribosomes where to start binding (similar to prokaryotes using Shine-Dalgarno Sequence)
2) A Poly-A Tail is added to signal to the cell that this is a valid mRNA from the nucleus (not viral RNA), so it should be allowed to cross the nuclear envelope, and enzymes should not destroy it in the cytoplasm.
3) Non-coding regions (introns) of the RNA. The transcript must be removed, & the coding regions (exons) spliced together.

Once RNA processing and transcription is completed, the resulting mRNA is ready to exit the nucleus and be translated by ribosomes in the cytoplasm.

Question 18

Summary Question:
RNA PROCESSING (EUKARYOTES ONLY)
Which of the following statements is true?
A. Prokaryotic mRNA is shorter than the coding sequence of its gene.
B. Eukaryotic mRNA is shorter than the coding sequence of its gene.
C. Eukaryotic pre-mRNA is shorter than the coding sequence of its gene.
D. Eukaryotic pre-mRNA is shorter than the completed mRNA.
E. None of the above statements are true.

Answer 18

B.

Question 19

TRUE OR FALSE.

The same exons can be removed (with the introns) during RNA splicing, which means one gene can actually produce serval different mRNAs and, therefore several different proteins.

Answer 19

FALSE.
DIFFERENT exons can be removed (with the introns) during RNA splicing, which means one gene can produce serval different mRNAs and, therefore, several different proteins.

Question 20

Is the one gene- one enzyme hypothesis false in many ways or true?

Answer 20

FALSE.
-genes can encode functional RNA
-Genes can encode polypeptides that join other parts to form functional proteins.
-One gene can make more than one polypeptide/protein ( by alternative splicing)
-Not all proteins function as enzymes (e.g. hormones, transport proteins etc..

Question 21

TRANSLATION IN EUKARYOTES (compared to prokaryotes)

STEP 1 is……?

Answer 21

Initiation.
The small ribosomal subunit binds with the initiator tRNA first, which carries normal Methionine (MET) instead of the modified one.
- This complex then starts at the 5’ cap and scans the mRNA until it reaches the first AUG, which is the start codon
-After, the large ribosomal subunit binds to complete the transcription initiation complex, much like in prokaryotes.

Question 22

TRANSLATION IN EUKARYOTES (compared to prokaryotes)

STEP 2 is……?

Answer 22

Elongation
that’s precisely what happens. As the ribosome shifts 3-bases to the right:
- The empty tRNA slides into the E-site of the ribosome, where it is ejected.
-the newer tRNA holding the polypeptide slides into the P-site.
- the next codon of mRNA is in the A-site, waiting for the newest aminoacyl-
tRNA to arrive.
And so the cycle repeats until the stop codon reaches
the A-site of the ribosome

Question 23

TRANSLATION IN EUKARYOTES (compared to prokaryotes)

STEP 3 is……?

Answer 23

Termination.
1. There are no aminoacyl-tRNAs that match the stop codons, so a protein release factor
binds instead.
2. This release factor releases the polypeptide from the last tRNA, and that tRNA exits
from the E-site.
3. The large and small subunits of the ribosome separate, releasing the mRNA.

Question 24

What do you think happens to those ejected tRNAs that have given up their amino acids to make this polypeptide?

Answer 24

Specific amino acids are attached to them, and they’re reused for translation. Enzymes (aminoacyl-tRNA synthetases) attach the correct amino acid to match that tRNA’s anticodon!

Question 25

Since prokaryotc genes do not have introns that need to be spliced out of the RNA transcript, does this mean that the entire mRNA molecule is translated? Justify your answer.

Answer 25

No, there are still untranslated regions (UTR) at the 5’ & 3’ ends of the mRNA:
1) For the 5’ UTR: the start codon (where translation starts) is not right at the
+1 site (where transcription began)… there are some essential bases in the 5’ UTR,
such as the Shine-Dalgarno sequence, where the small ribosomal subunit binds.
2) For the 3’ UTR: there are still many bases after the stop codon, e.g. the terminator.