Biology 1002B Lecture Notes - Lecture 7: Stem-Loop, Start Codon, Release Factor

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13 Jun 2018

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Lecture 14 Outcomes:

Relative location of such DNA sequence signals as promoter, 5’ and 3’ UTR, SD box,

start codon, stop codon, transcription terminator etc.

- Promoters are located before the gene that is transcribed because they are not transcribed —

they function to attract the RNA polymerase (& protein factor)

- the 5’ UTR (untranslated region) is the sequence that is upstream (before) the start codon

(therefore it does not get translated) — it contains the SD box

- 3’ UTR is the sequence after the gene (also not translated)

- SD box is a region of DNA (in the 5’ UTR) that when transcribed, the sequence on the mRNA

base pairs with corresponding sequence on the rRNA (in the small subunit) and helps with

the initiation of translation by allowing the small subunit to dock onto the mRNA (docking

box) — because it is present on the mRNA it must also be present on the DNA (upstream of

the first start codon, but downstream of the promoter)

- Transcription terminators are sequences included in the mRNA that can pair with itself to a

make loop & causes the RNA polymerase to fall off the double stranded DNA helix (the

sequence on the mRNA is complementary when read in opposite directions)

Mechanism by which each signal is interpreted, or understood, by the cell

- the promoter sequence is upstream of the gene, and where the polymerase binds

- SD box is a region in the DNA that when transcribed, the mRNA base pairs with the rRNA

and helps the initiation of translation

- Start codons are understood by rRNA and interpreted as the place to start translation by

pairing with a Met tRNA (AUG sequence)

- Stop codons are understood by rRNA as the place to stop translation by attracting a release

factor protein in the A site that signals the end of translation (release factor is always trying to

bind with the mRNA but is always outcompeted by the tRNA, but since there is no tRNA to

compete at the stop codon, the release factor binds and signals the end)

- Transcription terminator is transcribed and base pairs with itself to form an mRNA hairpin

loop which signals the polymerase to stop transcription

Relationship between DNA sequence of signals and their function (ie. how would low

efficiency promoters be different than high efficiency promoters?

- mutations in the promoters causes them to be more or less attractive to RNA polymerase

- high efficiency promoters will be more successful in allowing RNA polymerase to bind,

therefore allowing more of the signals of transcription to be made into RNA, and more

functioning of these signals to produce more protein

- there might be a selective advantage for having a constitutively low expressed gene, if its

product is unnecessary or even detrimental in high concentrations

Characteristics of promoters that require a particular position and direction

- either strand of the DNA can function as the promoter, promoters are generally located on the

5’ side of the strand therefore RNA polymerase binds & functions in the 5’ to 3’ direction

- Promoters dictate the genes that get transcribed because they are the initiation point for

transcription

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Document Summary

Relative location of such dna sequence (cid:1688)signals(cid:1689) as promoter, 5" and 3" utr, (cid:1688)sd box(cid:1689), start codon, stop codon, transcription terminator etc. Promoters are located before the gene that is transcribed because they are not transcribed they function to attract the rna polymerase (& protein factor) The 5" utr (untranslated region) is the sequence that is upstream (before) the start codon (therefore it does not get translated) it contains the sd box. 3" utr is the sequence after the gene (also not translated) Mechanism by which each signal is interpreted, or understood, by the cell. The promoter sequence is upstream of the gene, and where the polymerase binds. Sd box is a region in the dna that when transcribed, the mrna base pairs with the rrna and helps the initiation of translation. Start codons are understood by rrna and interpreted as the place to start translation by pairing with a met trna (aug sequence)

Related Questions

Match the following:

1	Region which lies upstream of thetranslation start site contains the Shine Dalgarno sequence
2	Sequence added to the 3' end of thepre-mRNA which affects mRNA stability
3	Establishes the reading frame andspecifies the first amino acid of the protein chain
4	DNA sequence that the transcriptionapparatus recognizes and binds to initiate transcription
5	Expressed sequences of DNA that arenot removed during alternative splicing
6	Signals the end of translation andthe protein molecule
7	Group of three nucleotides that codefor an amino acid
8	Site begins the coding region of thegene and is located 25-30 nucleotides downstream of the TATAbox
9	Non-coding sequences of DNA thatintervene within coding regions of a gene
	10 Ribosome binding site ineukaryotes; functions in the initiation of translation and mRNAstability
11	A sequence which lies downstream ofthe coding region of the gene; determines the location of the 3'cleavage site in the pre-mRNA molecule
12	Sequence of nucleotides at the 3' endof the mRNA that is not translated into protein; affects thetranslation and stability of the mRNA molecule

A.	5' untranslated region
B.	AAUAAA consensus sequence
C.	Promoter
D.	Transcription start site
E.	3' untranslated region
F.	Introns
G.	Initiation codon (AUG)
H.	Poly(A) tail
I.	5' cap
J.	Termination codon (UAA, UGA, UAG)
K.	Exons
L.	Sense codon

ivorymacaw91

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

Fill in the blank. Elongation during translation does NOT involve ____________.

Question 16 options:

	the translation of codons according to the genetic code
	the formation of bonds catalyzed by the ribosome
	complementary base pairing between RNA molecules
	amino acids being linked together in a polypeptide
	reading the DNA template 3' to 5'

For a given gene, what establishes the reading frame for translation?

Question 17 options:

	the location of the enhancer relative to the gene
	the first three nucleotides at the 5' end of the mRNA
	the first three nucleotides at the 3' end of the mRNA
	the start codon in the mRNA
	the location of the promoter relative to the gene

Which of the following is the LEAST likely direct consequence of a substitution mutation?

Question 18 options:

	changing the length of a protein coded for by a gene
	changing one amino acid in a protein
	creating a stop codon
	eliminating a start codon
	changing the length of the DNA molecule containing a gene

Suppose that the pre-mRNA transcript from a eukaryotic gene is 30,000 nucleotides long, and the gene codes for a sequence of 300 amino acids. What is the best explanation for the relationship between these numbers?

Question 19 options:

	only the first 900 nucleotides of the pre-mRNA transcript are translated
	it takes 100 nucleotides to specify a single amino acid
	300 of the nucleotides in the transcript are important, and the rest are "junk"
	only the last 900 nucleotides of the pre-mRNA transcript are translated
	large portions of pre-mRNA transcripts are cut out during RNA processing

Suppose an individual is born into a population with a novel mutation. Is the new mutation an evolutionary change, and why?

Question 20 options:

	no, because it is not a big enough change to count
	yes, because new mutations are always adaptive
	yes, because the appearance of a new genetic variant is a genetic change in a population
	no, because not enough individuals have the mutation for it to matter
	no, because most mutations are not adaptive

Biology 1002B Lecture Notes - Lecture 7: Stem-Loop, Start Codon, Release Factor

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