Chapter 8: Molecular Biology of Transcription and RNA Processing

In one to two sentences each, describe 5' Capping.

5' Capping adds a guanine to the 5' end of the pre-mRNA and methylates newly added nucleotides. This protects the mRNA from rapid degradation.

What is a gene?

A gene is a segment of DNA that contains the information for the transcription of RNA.

What is the meaning of alternative promoter?

Alternative promoters can initiate transcription at distinct +1 start points in different cell types. They are found in variable distance of known promoters.

What is the role of enhancer sequences in transcription of eukaryotic genes? Speculate about why enhancers are not part of transcription of bacterial genes.

Enhancer sequences increase the level of transcription of specific genes by binding with specific proteins that interact with promoter bound proteins. Bacteria mostly regulate gene expression at the level of translation, making transcription enhancers unnecessary.

Describe the difference between introns and exons.

Exons become part of mature mRNA and ecocide protein segments while introns are intervening segments that are removed from pre-mRNA during post-transcriptional processing.

In one to two sentences each, describe intron splicing.

Introns are excess RNA sequences: they are removed from the pre-mRNA by the spliceosome. Removing them ensures correct protein sequences.

How does the use of alternative promoters affect transcription?

It results in a different 5' end than that seen when the known promoter is used. The consequences of this is synthesis of an mRNA that has a different 5' end than what is seen with the regular promoter.

The diagram below shows a DNA duplex. The template strand is identified, as is the location of the +1 nucleotide. 5' __________+1____________________3' template strand 3' ________________________________5' coding strand If this region is a eukaryotic gene transcribed by RNA pol III, where are the promoter consensus sequences located?

Most RNA pol III promoters have internal control regions, which are found within the transcribed region (at approximately +55 to +80).

Eukaryotic promoters are more variable than bacterial promoters. Explain why?

Nearby sequences (in addition to the eukaryotic promoter consensus sequences) are though to be important in modulating the level of transcription initiation. In addition, there are multiple eukaryotic RNA polymerases, each of which binds to a different consensus sequence. There are also multiple eukaryotic transcription factors, which are specific to each polymerase and these bind to different promoter sequences.

In one to two sentences each, describe polyadenylation.

Polyadenylation uses a protein complex to add ~20-200 adenines to the 3' end of the pre-mRNA.

What is the common structure of a bacterial promoter with respect to consensus sequences?

Promoters are double-stranded DNA sequences that direct transcription proteins to the start of transcription. Consensus sequences are short regions of DNA that attract RNA polymerase to promoters.

What role do promoters play in transcription?

Promoters control access of RNA polymerase to the gene.

Compare and contrast the properties of DNA polymerase and RNA polymerase, listing at least three similarities and at least three differences between the molecules.

Similarities: 1. Both DNA pol and RNA pol have polymerization activity. 2. Both govern the catalytic reaction in different stages of the cell cycle. 3. Both polymerases are present in all living organisms. Differences: 1. DNA polymerase is used during DNA replication, whereas RNA polymerase is used only during transcription. 2. DNA polymerase has proofreading ability. 3. DNA replication continues until DNA pol reaches the end of the strand. RNA pol stops transcription once it reaches the stop codon.

What consensus sequences are detected in the mammalian beta-globing gene promoter?

TATA box, CAAT box, GC-rich box

The diagram below shows a DNA duplex. The template strand is identified, as is the location of the +1 nucleotide. 5' __________+1____________________3' template strand 3' ________________________________5' coding strand Assume this region contains a gene transcribed to form mRNA in a eukaryote. Identify the location of the most common promoter consensus sequences.

The most common promoter consensus sequences are the TATA box (-25), the CAAT box (-80), and the GC rich box (-90).

The diagram below shows a DNA duplex. The template strand is identified, as is the location of the +1 nucleotide. 5' __________+1____________________3' template strand 3' ________________________________5' coding strand Assume this region contains a gene transcribed in a bacterium. Identify the location of promoter consensus sequences and of the transcription termination sequence.

The promoter consensus sequences will be upstream of the +1 position. The transcription termination sequences will be downstream of +1, after the coding region.

The following is a portion of an mRNA sequence: 3' - AUCGUCAUGCAGA - 5' Identify the direction in which the promoter region for this gene will be located.

The promoter region for the gene will be located upstream of the start of transcription, in the 5' direction.

Describe the two types of transcription termination found in bacterial genes. How does transcription termination differ for eukaryotic genes?

There are two types of bacterial termination: 1. Intrinsic Termination The transcription of repeat DNA sequences induces a secondary structure needed for termination. This secondary structure is referred to as a hairpin: the hairpin causes the RNA pol to slow down and destabilize, inducing it to release the transcript. 2. Rho-Dependent Termination The rho-utilization site (RUT) is transcribed, and the rho protein attaches to it. The rho protein moves downstream until it reaches RNA pol; once it reaches RNA pol, it catalyzes the release of RNA pol from the transcript.

The following is a portion of an mRNA sequence: 3' - AUCGUCAUGCAGA - 5' During transcription, was the adenine at the left-hand side of the sequence the first or the last nucleotide used to build the portion of mRNA shown? Explain how you know.

Write the transcript going from 5' to 3': 5' - AGACGUACUGCUA - 3' Since the mRNA is transcribed in the 5' to 3' direction, we can assume that the adenine closest to the 3' side was the last nucleotide used to build the transcript.

The following is a portion of an mRNA sequence: 3' - AUCGUCAUGCAGA - 5' Write out the sequence and polarity of the DNA duplex that encodes this mRNA segment. Label the template and coding strands.

Write the transcript going from 5' to 3': 5' - AGACGUACUGCUA - 3' mRNA 5' - AGACGTACTGCTA - 3' coding strand 3' - TCTGCATGACGAT - 5' template strand The coding strand is identical to the transcript. The template strand is complementary to the coding strand and the transcript.

Why are genes for rRNA and tRNA considered to be genes even though they do not produce polypeptides?

rRNA and tRNA are also gene products along with polypeptides.