III. RNA Synthesis: Transcription

Question 1

What exactly is transcription?

Answer 1

Transcription is the process of copying a segment of DNA into RNA.

Question 2

What are the three main forms of RNA involved in transcription? What is the function of each?

Answer 2

The three main forms of RNA are mRNA (messenger RNA), tRNA (transfer RNA), and rRNA (ribosomal RNA). mRNA carries genetic information from DNA to the ribosome, tRNA brings amino acids to the ribosome during protein synthesis, and rRNA is a component of ribosomes.

Question 3

How is RNA different, chemically, from DNA?

Answer 3

RNA contains ribose sugar, while DNA contains deoxyribose sugar. Additionally, RNA has uracil instead of thymine.

Question 4

Why is the secondary structure of RNA important?

Answer 4

The secondary structure of RNA is important for its function, as it determines how RNA interacts with other molecules.

Question 5

What are ribonucleases? How do the three main types of RNA differ in their susceptibility to ribonucleases?

Answer 5

Ribonucleases are enzymes that degrade RNA. mRNA is generally more susceptible to ribonucleases than rRNA and tRNA, which are more stable.

Question 6

Why is rapid mRNA turnover important?

Answer 6

Rapid mRNA turnover allows for quick responses to changes in the environment by regulating gene expression.

Question 7

What is RNA polymerase? What is its function?

Answer 7

RNA polymerase is an enzyme that synthesizes RNA from a DNA template during transcription.

Question 8

How is RNA polymerase similar to DNA polymerase?

Answer 8

Both RNA polymerase and DNA polymerase synthesize nucleic acids and require a template strand.

Question 9

How is RNA polymerase different from DNA polymerase?

Answer 9

RNA polymerase does not require a primer to initiate synthesis, while DNA polymerase does.

Question 10

What are transcription terminators?

Answer 10

Transcription terminators are sequences in DNA that signal the end of transcription.

Question 11

Why is the regulation of gene expression important?

Answer 11

Regulation of gene expression is crucial for cellular function, allowing cells to respond to environmental changes and maintain homeostasis.

Question 12

What are the five subunits of bacterial RNA polymerase? How many of each subunit is present in the RNA polymerase holoenzyme?

Answer 12

The five subunits are 2 alpha (α), 1 beta (β), 1 beta prime (β’), and 1 omega (ω). The holoenzyme contains 2 α, 1 β, 1 β’, and 1 σ (sigma) factor.

Question 13

How is the RNA polymerase holoenzyme different from the RNA polymerase core enzyme?

Answer 13

The holoenzyme includes the sigma factor, which is necessary for initiation, while the core enzyme does not.

Question 14

What is the function of the sigma factor subunit of RNA polymerase?

Answer 14

The sigma factor helps RNA polymerase recognize and bind to specific promoter sequences.

Question 15

What happens to sigma after transcription begins?

Answer 15

The sigma factor is released from the RNA polymerase after transcription initiation.

Question 16

What are promotors?

Answer 16

Promoters are DNA sequences that initiate transcription by providing a binding site for RNA polymerase.

Question 17

Why are there promotors on both strands of the DNA molecule?

Answer 17

Promoters are present on both strands because each strand can serve as a template for transcription.

Question 18

Is the same gene transcribed from both strands of the DNA molecule? Why or why not?

Answer 18

No, typically only one strand is transcribed for a given gene, as the direction of transcription is determined by the promoter orientation.

Question 19

How does a single sigma factor, such as σ70, recognize promotors with different sequences?

Answer 19

A single sigma factor can recognize different promoters due to its ability to interact with various consensus sequences.

Question 20

What is the Pribnow box? Where is it located (relative to the transcription start site)? What is its consensus sequence?

Answer 20

The Pribnow box is a conserved sequence found in bacterial promoters, located approximately 10 bases upstream of the transcription start site. Its consensus sequence is TATAAT.

Question 21

What is the second consensus sequenced recognized by σ70? Where is it located relative to the transcription start site?

Answer 21

The second consensus sequence is the -35 region, located approximately 35 bases upstream of the transcription start site.

Question 22

What is meant by the term ‘strong’ as it refers to a promotor?

Answer 22

‘Strong’ promoters have sequences that closely match the consensus sequences, leading to higher rates of transcription.

Question 23

What is the importance of having alternative sigma factors (that recognize different promotor consensus sequences)?

Answer 23

Alternative sigma factors allow bacteria to regulate gene expression in response to environmental changes by activating different sets of genes.

Question 24

How do bacterial cells use various sigma factors to control gene expression?

Answer 24

Bacterial cells can switch sigma factors to alter the transcription of specific genes in response to different stimuli.

Question 25

What is a transcriptional unit?

Answer 25

A transcriptional unit is a segment of DNA that is transcribed into a single RNA molecule.

Question 26

What are cotranscribed genes?

Answer 26

Cotranscribed genes are genes that are transcribed together from the same transcriptional unit.

Question 27

What are nontranslated RNAs? What are some examples?

Answer 27

Nontranslated RNAs are RNA molecules that are not translated into proteins, such as rRNA and tRNA.

Question 28

How are individual RNA molecules produced from a single transcriptional unit?

Answer 28

Individual RNA molecules are produced through processes such as splicing or cleavage of the primary transcript.

Question 29

What is an operon?

Answer 29

An operon is a cluster of genes under the control of a single promoter, transcribed as a single mRNA.

Question 30

What is a polycistronic mRNA?

Answer 30

Polycistronic mRNA is an mRNA molecule that encodes multiple proteins, typically found in prokaryotes.

Question 31

What is an open reading frame (ORF)?

Answer 31

An open reading frame (ORF) is a sequence of DNA that has the potential to be translated into a protein.

Question 32

If an operon contains three ORFs, how many promotors does it contain?

Answer 32

An operon typically contains one promoter, regardless of the number of ORFs.

Question 33

What is an inverted repeat?

Answer 33

An inverted repeat is a sequence of nucleotides that is followed downstream by its reverse complement.

Question 34

What is a stem-loop structure?

Answer 34

A stem-loop structure is a common secondary structure formed in RNA, consisting of a double-stranded stem and a single-stranded loop.

Question 35

What is the significance of having a run of adenines following the sequence for a stem-loop structure on the template DNA strand?

Answer 35

A run of adenines can signal termination of transcription in prokaryotes.

Question 36

What is Rho? How is it involved in the termination of transcription in Bacteria?

Answer 36

Rho is a protein that facilitates the termination of transcription by binding to the RNA and moving along it to catch up with RNA polymerase.

Question 37

How many RNA polymerases are found in Bacteria? In Archaea? In Eukarya?

Answer 37

Bacteria have one RNA polymerase, Archaea have one RNA polymerase, and Eukarya have three main types of RNA polymerases.

Question 38

Which eukaryotic RNA polymerase most closely resembles the archaeal RNA polymerase?

Answer 38

Eukaryotic RNA polymerase II most closely resembles archaeal RNA polymerase.

Question 39

How many protein subunits comprise the bacteria, archaeal, and eukaryal RNA polymerases?

Answer 39

Bacterial RNA polymerase has 5 subunits, archaeal RNA polymerase has around 12 subunits, and eukaryotic RNA polymerases have 10-12 subunits.

Question 40

What are transcription factors?

Answer 40

Transcription factors are proteins that help regulate the transcription of specific genes by binding to nearby DNA.

Question 41

What is the TATA box? Where is it located relative to the transcriptional start site? What archaeal protein recognizes it?

Answer 41

The TATA box is a conserved DNA sequence found in eukaryotic promoters, located about 25-30 bases upstream of the transcription start site. The archaeal protein TFB recognizes it.

Question 42

What is the BRE? Where is it located relative to the TATA box? What archaeal protein recognizes it?

Answer 42

The BRE (TFIIB Recognition Element) is located upstream of the TATA box. It is recognized by the archaeal protein TFB.

Question 43

What is the INIT? Where is it located relative to the TATA box? What archaeal protein binds to it?

Answer 43

The INIT is located at the transcription start site and is recognized by the archaeal protein TFIIB.

Question 44

What is TFE?

Answer 44

TFE (Transcription Factor E) is a protein that assists in the initiation of transcription in eukaryotes.

Question 45

How is transcription initiation in eukaryotes similar to and different from transcription initiation in Archaea?

Answer 45

Both involve multiple transcription factors, but eukaryotic initiation is more complex and involves additional proteins and modifications.

Question 46

What is known about how transcription terminates in Archaea?

Answer 46

Transcription termination in Archaea can occur through intrinsic mechanisms similar to bacteria or through Rho-like proteins.

Question 47

What is known about how transcription terminates in Eukarya?

Answer 47

Transcription termination in Eukarya often involves polyadenylation and specific termination factors.

Question 48

Do Archaea or Eukarya have Rho-like proteins?

Answer 48

Archaea have Rho-like proteins that can facilitate transcription termination.

Question 49

What are introns and exons? What group of organisms contains these elements in their genome?

Answer 49

Introns are non-coding sequences, and exons are coding sequences. Eukaryotes contain both introns and exons in their genomes.

Question 50

What is RNA processing?

Answer 50

RNA processing is the modification of RNA after transcription, including capping, polyadenylation, and splicing.

Question 51

What is the difference between a primary transcript and a mature mRNA molecule?

Answer 51

A primary transcript is the initial RNA product that undergoes processing to become a mature mRNA molecule.

Question 52

What is RNA splicing? Where, in the cell, does it occur?

Answer 52

RNA splicing is the removal of introns from the primary transcript, occurring in the nucleus.

Question 53

What is a spliceosome?

Answer 53

A spliceosome is a complex of proteins and RNA that facilitates the splicing of introns from pre-mRNA.

Question 54

What type of archaeal genes contain 'introns' and how are these removed?

Answer 54

Some archaeal genes contain introns that are removed by splicing mechanisms similar to those in eukaryotes.

Question 55

What sequences are conserved at the 5' and 3' ends of an intron splice site (in eukaryotes)?

Answer 55

The conserved sequences are typically GU at the 5' end and AG at the 3' end of the intron.

Question 56

What is capping? When and where (in the cell) does this occur during eukaryotic mRNA processing?

Answer 56

Capping is the addition of a modified guanine nucleotide to the 5' end of mRNA, occurring in the nucleus shortly after transcription begins.

Question 57

What is the function of the 5' cap?

Answer 57

The 5' cap protects mRNA from degradation and assists in ribosome binding during translation.

Question 58

What is polyadenylation?

Answer 58

Polyadenylation is the addition of a poly-A tail to the 3' end of mRNA, which enhances stability and facilitates export from the nucleus.

Question 59

What is the function of the poly-A tail?

Answer 59

The poly-A tail increases mRNA stability and aids in the regulation of translation.