Unit 3

euchromatin

-NOT stained during interphase -central position in the nucleus -promotes gene expression -less compacted

You isolate a mature mRNA from a mixed experimental sample. You want to determine if it is a eukaryotic or prokaryotic mRNA. What can you look for in the mRNA to distinguish between mature prokaryotic and eukaryotic mRNAs? (Check all that apply)

-Presence or absence of a 5' cap -Presence or absence of edited nucleotides not directly encoded by the DNA The key to understanding this question is recognizing that it refers to mature mRNA. Although eukaryotic pre-mRNA contains introns, mature eukaryotic mRNA does not, so that would not be a useful way to distinguish between mature prokaryotic and eukaryotic mRNAs. Similarly, both prokaryotic and eukaryotic mRNAs can have a 3' tail, so this would not be helpful in distinguishing. In contast, only eukaryotic mRNAs have a 5' cap and RNA editing, so these would both be useful ways to distinguish between prokaryotic and eukaryotic mRNAs.

One can conclude that this image is depicting the DNA replication of a eukaryote rather than a prokaryote because ________. (CHECK ALL THAT APPLY)

-the chromosomes are linear rather than circular -there are multiple origins of replication as opposed to a single origin

Operon

A group of two or more genes under the transcriptional control of a single promoter

Repressor

A regulatory protein that binds to the DNA and inhibits transcription

Activator

A regulatory protein that increases the rate of transcription.

Operator

A sequence of bases that provides a binding site for a repressor protein.

Promoter

A sequence of bases that signals the beginning of transcription.

Inducer

A small effector molecule that causes transcription to increase.

The enzyme that travels along the leading strand assembling new nucleotides on a growing strand of DNA is ______.

DNA polymerase

During DNA replication, the lagging strand is synthesized continuously, while the leading strand is synthesized discontinuously. T/F

False

When both glucose and lactose are absent, the highest rate of transcription occurs. T/F

False

This pre-mRNA contains 8 exons and 7 introns. The splice sites surrounding exon 3 are not readily recognized by the splicesome. However, splicing enhancers bind to these sites. In addition, a splicing repressor prevents the recognition of the 3' splice site that precedes exon 7. What exons will be present in the mature mRNA?

If all exons were included, the mature mRNA would contain exons 1, 2, 3, 4, 5, 6, 7, 8. The splice sites surronding exon 3 are not well recognized by the splicesome, but since splicing enhancers bind to these sites, exon 3 should be included. The repressor binding to the 3' splice site that precedes exon 7 will cause the spliceosome to skip over exon 7 and bind to the next available 3' splice site. In this way, exon 7 will be spliced out of the pre-mRNA and not included in the mature mRNA. Therefore the final mature mRNA will contain exons 1, 2, 3, 4, 5, 6, 8.

5′-CAUUAUGCCCGGAGGCACCGUCCAAU-3′Beginning with the first "start" codon, what is the amino acid sequence that will be created from this RNA?

Met-Pro-Gly-Gly-Thr-Val-Gln

Before new DNA nucleotides can be assembled to form a lagging strand, which of the following must occur?

RNA primase constructs a short RNA primer.

Regulatory sequences

Site for the binding of regulatory proteins which influence the rate of transcription.

stop codon

Specifies the end of polypeptide synthesis

Nucleosome-free regions

are found flanking many actively transcribed genes in eukaryotes.

The lac repressor __________.

binds to the operator and prevents transcription

When glucose is present ____________.

cyclic AMP is low, CAP does not bind to the activator binding site, and transcription is turned off

The enzyme that unwinds a segment of the DNA molecule is

helicase

Which amino acids are acetylated in histones?

lysine

Translational regulatory proteins recognize specific areas of what molecule?

mRNA

Which of the following is a mechanism to imprint genes?

methylation of cytosine

terminator sequence

site where transcription ends

promoter

specific region of a gene where RNA polymerase can bind and begin transcription

For each type of gene(s), indicate the eukaryotic RNA polymerase that transcribes it.

tRNA genes-RNA polymerase III rRNA genes except the 5S gene-RNA polymerase I 5S rRNA gene-RNA polymerase III Protein encoding genes-RNA polymerase II

Combinatorial control of transcription factors refers to the phenomenon that

the combination of many factors determines the expression of any given gene.

Feedback inhibition frequently involves

the inhibition of the first enzyme in the pathway by the final product of the pathway.

When both glucose and lactose are present ______________.

the transcription rate is very, very low

regulatory transcription factors

-act at cis-acting elements -can act to repress or activate transcription -activity sometimes modulated by small effector molecules -regulate transcription of specific target genes -activity modulated by covalent modifications

Select all the enzymes that play a role in RNA primer removal in prokaryotes or eukaryotes. (CHECK ALL THAT APPLY)

-flap endonuclease -DNA polmerase I

general transcription factors aka basal transcriptional factors

-necessary for a basal level of transcription -bind to promoter sequence

Heterochromatin

-stained throughout the entire cell cycle -attached to nuclear lamina -inhibits gene expression -more compacted

Place the following events of prokaryotic transcription in the correct order.

1. RNA polymerase holoenzyme binds to the promoter and forms a closed complex 2.DNA is unwound to form an open complex. A short strand of DNA is made and sigma factor dissociates from the core enzyme 3. RNA polymerase slides along the DNA template strand in a 3' to 5' direction, synthesizing RNA in a 5' to 3' direction 4. Either p-dependent or p-independent termination takes place

You are studying a chromosome in a new animal species. The presence of what element would make you most confident that a region is facultative heterochromatin and not constitutive heterochromatin?

H3K27me DNA methylation and repeat elements are found in both types of heterochromatin, so they will not help you distinguish between facultative and constitutive heterochromatin. H3K9me is also found in both types of chromatin. H3K27me is particularly found in facultative heterochromatin, and will help you identify the type of heterochromatin.

Start codon

Specifies the first amino acid in a polypeptide sequence, usually a formylmethionine (in bacteria) or a methionine (in eukaryotes).

There are enzymes that can specifically recognize and degrade single-stranded DNA, while leaving double-stranded DNA untouched. After the addition of which general transcription factor would DNA at a eukaryotic promoter become susceptible to such an enzyme?

TFIIH -TFIIH plays a major role in the formation of the open complex, which is characterized by separated strands of DNA. The DNA at a eukaryotic promoter would become susceptible to these enzymes after the binding of TFIIH.

What is the result when the core histones are acetylated via histone acetyltransferase?

The DNA becomes less associated with the core.

Codon

The group of three nucleotides that specify the different amino acids. The order of these determines the sequence of amino acids within a polypeptide.

Complete the sentences with the correct term about transcriptional termination.

Transcription via RNA polymerase II terminates downstream from a poly A signal. In the allosteric model of transcriptional termination, RNA polymerase II dissociates from the DNA, possibly from the release of elongation factors or the binding of termination factors. In the torpedo model of transcriptional termination, an exonuclease binds to the RNA, catches up to RNA polymerase II, and causes termination. Transcription terminates on the 3' end of the molecule.

Arrange the steps into the correct sequence. (regulation of gene expression)

Transcription->RNA processing->Translation->Post-translation modification

Ribosome-binding site

Translation begins near this site in the mRNA.

Before DNA replication can occur, the hydrogen bonds between the two parental DNA strands must be broken. T/F

True

In the absence of glucose, and in the presence of lactose, allolactose binds to the repressor, allowing RNA polymerase to carry on transcription. T/F

True