Cell Biology, Chapter 7

Front 1

What is the difference between mRNA and rRNA/tRNA?

Back 1

mRNA codes for a specific polypeptide. rRNA and tRNA are nonspecific, and can be used to make any peptide.

Front 2

What is meant by signal amplification? What molecule is associated with signal amplification?

Back 2

mRNA is associated with signal amplification, because 1x mRNA can be translated many times into hundreds of polypeptides.

Front 3

What is the biological purpose of mRNA?

Back 3

mRNA enables the cell to separate "information storage" from "information utilization".

Front 4

At what stage is polypeptide synthesis usually regulated? What enables this?

Back 4

Polypeptide production is usually regulated at the transcription step. This is made possible because genes can be expressed atvarying levels of efficiencies; a gene is not simply "ON" or "OFF".

Front 5

Why do tRNA, rRNA, snRNA, etc have different functions?

Back 5

The RNAs have different functions because they have different nucleotide sequences, and thus have different shapes. Shape determines function.

Front 6

Describe the terminology for talking about DNA strands and RNA products in transcription. Describe the 5'/3' arrangement.

Back 6

Template/antisense strand is what the RNA polymerase uses to grow an RNA strand.

Non-template/coding/sense strand is not used by RNA polymerase, but (except for T instead of U) has the same order as the RNA produced, and the same.

The template strand will only have a complementary sequence if its 5' and 3' ends are reversed. Otherwise the sequence would be wrong.

Front 7

What are promoters?

Back 7

Promoters are special sequences of DNA that signal RNA-Polymerase to begin transcribing RNA.

Front 8

What direction does RNAP move along the template strand?

Back 8

RNAP always moves from the 3'-->5' end of the template strand.

This means that the RNA "grows" from the 5' end (of its own strand, the RNA itself).

Front 9

What do you need to know about both strands and their genes?

Back 9

Both strands encode genes, but not in the same region of DNA. This is because an RNA product only makes sense when read in one direction (genes aren't palindromes).

Front 10

What do downstream/upstream mean with respect to the template strand? Which way does RNAP move?

Back 10

Downstream is toward the 5' end of the template strand. Upstream is toward the 3' end of the template strand.
RNAP moves from 3'-->5' on the template strand.

Front 11

How does the upstream/downstrem terminology change when referring to genes?

Back 11

For genes, the upstream/downstream terminology is the reverse of RNA-Polymerase because the genes are always discussed wrt the coding strand. On coding strand, the 3' end of the gene is upstream because it is complementary to the 5' end of the template strand (which is ACTUALLY upstream).

Front 12

What determines which strand of DNA will serve as the template?

Back 12

The orientation of the promoter.

Front 13

What are transcription factors?

Back 13

Transcription factors are proteins that help RNAP recognize promoter regions.

Front 14

What are the 3 types of RNA in eukaryotic cells? What is noteworthy about these 3?

Back 14

1. Ribosomal RNA (rRNA)
2. Transfer RNA (tRNA)
3. Messenger RNA (mRNA)

These three must come together in ribosomes to produce protein.

Front 15

What are the 3 types of RNAP? What do each of them transcribe?

Back 15

1. RNAP-I -large (28s, 18s, 5.8s) ribosomal subunits.
2. RNAP-II -mRNA and small nuclear RNA
3. RNAP-III -tRNA and small (5s) ribosomal subunit.

Front 16

What is true about the processing of mRNA, tRNA, and rRNA? What is a transcription unit?

Back 16

All these are made as larger segments called pre-RNAs (a.k.a. transcription unit) that are cut down smaller.

Front 17

Where are promoters on the gene?

Back 17

Promoters are on the 5' end of the gene. Since the terminology of genes is lways with reference to the non-template strand, this makes sense because the 5' end of the complementary strand of the template strand of the gene corresponds to the 3' end of the template, which really is upstream.

Front 18

What are small nuclear RNAs? What RNAP transcribes them?

Back 18

They aid in the cleaving of other RNAs. They are transcribed by RNAP-II.

Front 19

What is rRNA? What are the 3 functions of rRNA? What RNAP transcribes it?

Back 19

Ribosomal RNA:
1. Recognizes other molecules.
2. Provides structural support
3. Catalyzes the formation of peptide bonds between amino acids in ribosomes.

Trick question because 2 RNAPs transcribe rRNA. RNAP-I transcribes the 3 large subunits, and RNAP-III transcribes the 1 small subunit.

Front 20

What are the components of a ribosome?

Back 20

Ribosomes form from the joining of a small and a large subunit. These two subunits are composed of proteins+rRNA.

Front 21

What is the nucleolus?

Back 21

The nucleolus is where rRNA congregates to create the ribosomal subunits.

Front 22

What is snoRNA? What is it very similar to?

Back 22

snoRNA (small nucleolar RNA) aids in the splicing of rRNAs.

It is very similar to snRNA.

Front 23

What does the "Christmas Tree" formation along a DNA strand signify?

Back 23

The "Christmas tree" formation is caused by many RNAs being transcribed simultaneously from the same DNA segment.

Front 24

What is tRNA? What RNAP transcribes tRNA?

Back 24

tRNA is transfer-RNA that delivers amino acids to the ribosome. tRNA is transcribed by RNAP-III.

Front 25

How do the half-lives of rRNA, tRNA, and mRNA differ?

Back 25

rRNA and tRNA have long half-lives. mRNA has a very short half-life.

Front 26

What, specifically, does mRNA refer to? What are the different regions of an mRNA strand from 5'-->3'?

Back 26

mRNA specifically refers to a sequence of nucleotides that can be turned into a polypeptide, so this means that mRNA only exists POST-SPLICING. However, mRNA has non-coding regions for regulatory purposes.

From 5'-->3', mRNA has: 5' cap, untranslated region, coding region, untranslated region, Poly-A tail.

Front 27

What is the different between prokaryotic and eukaryotic mRNA?

Back 27

Prokaryotic mRNA codes for multiple polypeptides. Eukaryotic mRNA codes for a single polypeptide.

Front 28

What 3 things are necessary for mRNA transcription?

Back 28

1. RNAP-II
2. General transcription factors (GTF; not specific for any gene)
3. a promoter region (a.k.a consensus sequence) 25-nt upstream (gene-wise, so more 5' on template strand) to coding region; this is where RNAP-II binds; for mRNA, always a TATA box.

Front 29

What is a TATA box?

Back 29

TATA box is a region 25-nit upstream (gene-wise, so more 5' on template strand) that RNAP-II and GTFs recognize as the pre-initiation site for mRNA transcription.

Front 30

What is the role of TBP?

Back 30

TBP is TATA-binding protetin. It is a GTF for mRNA that recognizes TATA on the minor groove, and induces an acute flexure in the DNA, which allows for other transcription-related proteins to bind.

Front 31

Are there TATA boxes for rRNA and tRNA? Why not?

Back 31

There are no TATA boxes for rRNA or tRNA. They have other consensus sequences that serve as their promoters. TATA boxes are only for mRNA and RNAP-II.

Front 32

What is the preinitian complex? What are the components? Name 2 important GTFs, and 1 other important component.

Back 32

The preinitiation complex consists of various GTFs + RNAP.
1. TFIID (transcription factor 2, component D)- contains TBP; causes kink.
2. TFIIH (transcription factor 2, component H)- contains helicase (uncoils DNA) and kinase (phosphorylates CTD tail, initiating transcription)
3. C-Terminal Domain (CTD) tail- part of RNAP; when phosphorylated, RNAP is released & transcription starts.

Front 33

What happens at the preinitiation site when transcription begins?

Back 33

The CTD tail of the RNAP is phosphorylated by TFIIH. This "unleashes" the RNAP from the preinitiation site, and it starts transcribing. The TFIID remains bound to TATA to allow for more transcription.

Front 34

What is attached to the CTD tail? Why is this biologically significant?

Back 34

1. Capping factors- adds methylated guanosine 5' cap to mRNA.
2. Splicing factors- removes introns.
3. poly-adenylation factors- adds 3' poly-A tail.

Even at this early stage, mRNA is getting processed.

Front 35

What explains why genes can be expressed with different efficiencies? Why can't GTFs alone explain this?

Back 35

If there were only GTFs, then you would expect all genes would be expressed at the same efficiencies since GTFs are gene-independent.
Differential gene expression can be explained by the existence of SPECIFIC TRANSCRIPTION FACTORS (i.e. activator/repressor molecules).

Front 36

What 2 parameters do specific transcription factors control?

Back 36

1. Which promoters assemble preinitiation complexes- this is a cell-specific process.
2. The rate at which new RNAPs can begin transcribing.

Front 37

How does prokaryotic gene expression differ from eukaryotic gene expression? How do eukaryotes compensate?

Back 37

Prokaryotes produce mRNA that translates into all the proteins necessary for a given metabolic pathway. Eukaryotes have all these proteins in different genes. To compensate, eukaryotes have all these scattered genes ACTIVATED by the same specific transcription factor (called an ACTIVATOR), so they'll all be transcribed at once.

Front 38

Describe the general process of how specific transcription factors affect the transcription of a gene.

Back 38

The specific transcription factor (activator or repressor) binds to the enhancer region. The DNA fold so that the bound activator/repressor interacts with a mediator protein on the preinitation complex. This interaction affects transcription.

Front 39

What is the difference between the enhancer region and the promoter region?

Back 39

The promoter is the region where the RNAP+GTFs bind to form the preinitiation complex; it is always ~25nt upstream of the gene itself.
The enhancer is the region that specific transcription factors bind to in order to modulate gene expression; the enhancer can be anywhere upstream, downstream, or within (i.e. on an intron) of the gene its affecting.

Front 40

What is the "committee effect"?

Back 40

The transcription of a single gene is regulated by multiple transcription factors. The net effect of all the activational/repressive influences determines whether the gene will get transcribed. (Like the sum of all excitatory/inhibitory input to a neuron will determine whether there will be an action potential.

Front 41

What is the end result of the action of growth factor on a cell? What 2 important points does this case illustrate?

Back 41

The end result of the action of growth factor is the production of a transcription factor; this makes sense, because the ultimate downstream product has to be something that can affect gene expression.
1. All the genes affected by this newly-produced transcription factor will be involved in the same pathway.
2. These affected genes can be on multiple different chromosomes.

Front 42

What 2 processes is termination of mRNA transcription coupled to?

Back 42

Termination is coupled to:
1. Cleavage (i.e. splicing)
2. Poly-adenylation (appending the poly-A tail to the 3' end)

Front 43

What is the pre-mRNA called? What are the 3 steps in its processing, in the order they occur? What is noteworthy about this process?

Back 43

The unprocessed mRNA is called hnRNA (heterogeneous nuclear RNA).

1. Addition of 5' methylated G cap.
2. Poly-adenylation of 3' end.
3. splicing out the introns.

Some of these steps happen during the transcription.

Front 44

What are the 3 purposes of the 5' methylguanosine cap?

Back 44

1. protects 5' end from exonucleases.
2. facilitates its transport from the nucleus.
3. helps initiate translation.

Front 45

How is the poly-A tails made? What are the two purposes of the poly-A tail?

Back 45

The poly-A tail is a chain of 200-250 adenosines that are added by endonuclease.

1. Protects against degredation (*same a G-cap)
2. helps initiate translation (*same as G-cap)

Front 46

How are eukaryotic and prokaryotic genes organized differently?

Back 46

Prokaryotes have a uniform coding region in their genes. Eukaryotes have coding regions (exons) interspersed with non-coding regions (introns).

Front 47

What 3 things are required for the successful splicing out of introns? What is the end result?

Back 47

Three conserved sequences within all introns ("/" is exon/intron boundary):
1. 5' end: (on exon) AG/G (on intron)
2. center: conserved Adenine NT (interacts with spliceosome)
3. 3' end: (on intron) AG/G (on next exon)
The end result is the linking of both exons by an AGG.

Front 48

What are snRNPs? What is a spliceosome? What are each of these composed of? What does a spliceosome do? How is snRNPs involved?

Back 48

snRNPs (small nuclear riboproteins) are composed for snRNA, which cleave pre-RNA. Spliceosomes are composed of snRNPs. The spliceosome removes introns by forming a lariat structure. The snRNA in the snRNP in the spliceosome recognizes the 3 consensus sequences on the intron (i.e. splice sites.

Front 49

What is alternative splicing? Why is this possible?

Back 49

Alternative splicing is the result of having multiple exons separated by introns. Depending on what exons are spliced together, the final protein product will be different. The introns are NEVER used in the final mRNA!
This is possible because each exon corresponds to a different, independently functioning domain.

Front 50

What are the differences between eukaryotic and prokaryotic transcription?

Back 50

Prokaryotes don;t have exons and introns. Prokaryotes don't do any post-transcriptional processing before translation. Prokaryote genes encode multiple polypeptides.