BIOC2000 Lecture Notes - Lecture 10: Stop Codon, Start Codon, Tx Network

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ceriseelk223

21 May 2018

School

Department

Biochemistry

Course

BIOC2000

Professor

Dr Justin Ridge

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Lecture 10: Transcription

Replication covered. The next part of the central dogma is Transcription.

Transcription is the process of getting the information out of the DNA and

into a form that can be used for more diverse work in cells than “coding”.

DNA is just functional as a code for production of RNA.

RNA is much more diverse in its cellular roles.

It can function as

1) A messenger (mRNA)

2) A linker (tRNA)

3) A translator (rRNA)

4) A regulator (snRNA and siRNA)

5) A genetic code (in organisms

with an RNA genome)

6) An enzyme (ribozymes)

The essentials of a gene

1. Promoter – sequence of DNA that is used by RNA polymerise to

recognise the start of a gene and begin transcription

- can run either way on a DNA sequence

Promoter has +1 site (TXN start site) – where RNA Pol starts making the

mRNA. Pol jumps on promoter, opens it up and starts synthesizing RNA

(mRNA, tRNA, rRNAetc.) and stops until it reaches TXN stop/terminator site

(-1).

Cell needs to stop transcription, otherwise Pol would continue making

transcripts – expensive for cell as every base added = hydrolyzing a dNTP

If mRNA is synthesized (can be other RNA), it has a start codon and stop

codon – one way cell can tell it is an mRNA

mRNA is the ONLY RNA that is translated.

Ribosome binds to start codon and produces a protein x long. Start codon

has an amino acid. Stop codon does not have an amino acid. Therefore the

protein sequence is 1 amino acid shorter than the total codon sequence of

the mRNA.

The start codon is AUG. Methionine is the only amino acid specified by just

one codon, AUG. The stop codons are UAA, UAG, and UGA. They encode

no amino acid.

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2. Primer – small single stranded piece of DNA or RNA that binds to

another single stranded DNA or RNA sequence. The primer +

template complex is used by DNA/RNA polymerase to start making

a complement

Polymerase gets on 3’ end and end fills till end of template (5’)

Primers copy any piece of DNA, promoter is very specialized and is

recognized by RNA polymerase at the beginning of a gene.

3. Enhancer sequences

- important for particular genes being switched ON/OFF in

eukaryotic systems (do not exist in prokaryotic systems)

- they are varied, gene specific

MAP OF GENE

Making protein is expensive for the cell

Aside:

In ribosome, mRNA runs along the bottom, tRNA brings the matching

amino acid and placing it up top of the ribosome – mRNA doesn’t have

anything to do with the enzymatic activity, it only tells which tRNA to come

in; ribosome adds the amino acid – doesn’t know it has the right amino

acid.

There is machinery to make sure right tRNA gets the right amino acid.

RNA structure is very similar to that of DNA

OH on RNA , H on DNA

U on RNA, T on DNA

How does the polymerase know where to start?

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Promoter is particular sequence; polymerase recognizes promoter

sequence by touching it and conforming its shape to it. Promoters look

different in eukaryotic and prokaryotic systems – in both cases, it is the AT

rich region

What is the point of having an AT rich sequence?

AT forms 2 H bonds – much easier to break it

Polymerase opens DNA by twisting, AT rich with very few H bonds, the

double bonding breaks more easily,

Pol grabs strands and shoves protein in between to keep them separated

Then, it places +1 sequence in active site, that’s where it starts adding

bases

Spacers (between -35 and -10 in diagram ‘-35 = 35 bases away from +1)

Spacers can be modified to make promoter be better or worse promoter.

Make these spaces a bit off (smaller/longer) – polymerase doesn’t grab

strands as well, thus cannot add first base quite as well – not as much RNA

of gene

Cell uses this concept all the time to regulate how good a promoter is.

Consensus – not always perfect but a general agreement

Consensus sequence – taking all the sequences that we know that do this

job, line them up ‘What’s at this position X most frequently’; something that

we worked out

The sequence that tells us that most frequently this is what is happening in

these positions; deviations from the consensus means something is either

less or more optimal – usually most optimal for the protein required

DNA sequences lined up – from databases (millions of genes and proteins

sequenced dumped in data bases)

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Document Summary

The next part of the central dogma is transcription. Transcription is the process of getting the information out of the dna and into a form that can be used for more diverse work in cells than coding . Dna is just functional as a code for production of rna. Rna is much more diverse in its cellular roles. It can function as: a messenger (mrna, a linker (trna, a translator (rrna, a regulator (snrna and sirna, a genetic code (in organisms with an rna genome, an enzyme (ribozymes) The essentials of a gene: promoter sequence of dna that is used by rna polymerise to recognise the start of a gene and begin transcription. Can run either way on a dna sequence. Promoter has +1 site (txn start site) where rna pol starts making the mrna. Pol jumps on promoter, opens it up and starts synthesizing rna (mrna, trna, rrnaetc. ) and stops until it reaches txn stop/terminator site (-1).

Related Questions

Which type of RNA is unique to eukaryotes?

		mRNA
		rRNA
		tRNA
		snRNA
		Its a trick, all cells have all four types of RNA.

1 points

QUESTION 2

The region of DNA to which RNA polymerase binds to initiate transcription is the:

		origin
		promoter
		enhancer
		none of the above are correct

1 points

QUESTION 3

Holoenzyme:

		is RNA polymerase core enzyme.
		is sigma factor.
		is core plus sigma factor.
		none of the above are correct.

1 points

QUESTION 4

Which of these is formed FIRST when RNA polymerase binds to a promoter?

		The closed promoter complex
		The open promoter complex
		A rho-independent terminator
		none of the above are correct.

1 points

QUESTION 5

A hairpin loop followed by a run of Us:

		is the sequence formed in the sense strand of a gene using a rho-independent terminator.
		is the sequence recognized by the rho protein.
		is the structure formed in RNA that causes rho-independent termination.
		is formed immediately after the open promoter complex is formed.

1 points

QUESTION 6

RNA polymerase:

		reads the template strand of the DNA in the 3' to 5' direction.
		synthesizes the RNA in the 5' to 3' direction.
		can begin transcription without a primer.
		all of the above are correct.

1 points

QUESTION 7

Which of the following statements is FALSE?

		Bacteria like E. coli have only one type of sigma factor.
		RNA polymerase has no proofreading activity.
		The promoter of a gene is upstream of the RNA-coding region.
		Bacterial transcriptional terminators are copied into RNA to cause termination.

1 points

QUESTION 8

If the template strand of a gene has the sequence 5' ATGCGAT 3', then:

		the RNA produced will have the sequence 5' AUGCGAU 3'.
		the RNA produced will have the sequence 5' UAGCGUA 3'.
		the RNA produced will have the sequence 5' AUCGCAU 3'.
		None of the above are correct.

1 points

QUESTION 9

The sense strand:

		is the lagging strand
		is also the template strand.
		always goes left to right.
		none of the above are correct.

1 points

QUESTION 10

Which of these is transcribed but not translated?

		mRNA
		tRNA
		rRNA
		all of the above
		tRNA and rRNA are transcribed but not translated.

please help i am a bit confused

5. Alpha amanitin is a drug that binds RNA polymerase andprevents it from functioning in the cell (this is the compound thatis found in poison mushrooms). The reason people die when theyconsume alpha amanitin is:

a) Alpha amanitin prevents gene expression from occurring in thecell

b) DNA replication is directly inhibited by alpha amantin

c) Alpha amanitin binds tightly to the messenger RNAs that aremade in the cell, preventing translation

d) Alpha amanitin binds to nuclear pores preventing thetransport of messenger RNA into the cytoplasm

6. In order for transcriptional initiation to begin in E. colithe following elements are needed:

a) an origin and RNA polymerase

b) initiator protein and a promoter

c) the sigma subunit of RNA polymerase and an RNA template

d) RNA polymerase and a promoter

e) helicase and primase

Questions 7 and 8. You are studying two species of closelyrelated snakes, one species lives in sandy desert area and has paletan skin and the species lives in a volcanic rock area and has darkbrown skin. You a sequence the DNA from each type of snake anddiscover a gene encoding a protein that transports pigment into theskin cells. The pigment transporter protein is responsible for skincolor. When you analyze the DNA coding sequence of the pigmenttransporter from each snake you find these two DNA sequences (hashmarks have been added to indicate the reading frame):

pale tan snake: GCG/TTG/GAC/TGC/ACC (DNA template strand)CGC/AAC/CTG/ACG/TGG (complementary strand) dark brown snake:ACG/TTG/GAC/TGC/ACC (DNA template strand) TGC/AAC/CTG/ACG/TGG(complementary strand)

7. From these sequences you conclude:

a) that the amino acid sequence of the pigment transporters forthe two proteins are almost identical

b) that the amino acid sequence of the pigment transporters forthe two proteins are very dissimilar

c) that the amino acid sequence of the pigment transporters forthe two proteins are identical

8. Since the skin color is different in each snake, you concludefrom the sequence data above that:

a) the genetic code in the skin cells in each of these snakes isdifferent

b) the DNA sequence encoding the entire gene for pigmenttransporters in these two snakes is different

c) that one of the codons in the gene for the pigmenttransporter in these two snakes is different

9. You are analyzing eukaryotic cells that have been exposed tothe radioactive uracil. In most cells the radioactive uracil isinitially localized in the nucleus and then moves from the nucleusto the cytoplasm. However, you observe that in some cells theradioactive molecules stay in the nucleus and never arrive in thecytoplasm. This is most likely a defect in:

a) the transcription of the DNA

b) the processing of the mRNA

c) the translation of the RNA

d) the labeling of the RNA

e) the replication of the DNA

10. Which of the following is true of both eukaryotic andbacterial transcription? (select all that are true)
a) Transcription factors must bind the promoter before RNApolymerase initiates transcription

b) Messenger RNAs must be spliced before translation begins inorder to produce the appropriate gene product

c) During transcription only one DNA strand is used as atemplate to make the messenger RNA

d) Termination of transcription occurs when the RNA polymerasetranscribes a hairpin structure in the RNA followed by a string ofU

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BIOC2000 Lecture Notes - Lecture 10: Stop Codon, Start Codon, Tx Network

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