BIOL SCI 215 Lecture Notes - Lecture 6: Human Genome, Alternative Splicing, Tata-Binding Protein

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ceriserhinoceros589

28 Jun 2018

School

Northwestern University

Department

Biological Sciences

Course

BIOL SCI 215

Professor

aaronpeterson

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5/2

Telomere - appears at the end of the lagging strand at both ends of the chromosome

- makes the full copy of top strand that would add on sequences, helps solve lagging

strand synthesis

Telomerase synthesizes DNA starting from an RNA template - performs a reaction

that forms more DNA at the end by using piece of RNA to make a template so that a

specialized sequence will form - reverse transcriptase activity

RNA monomer has 2’ Hydroxyl counting base from the first C of sugar attached to

base

DNA monomer does not have 2’ Hydroxyl

Regulation of transcription enables control of protein expression levels

oPromoter - 2 short sequences, 6 nucleotides each -35 and -10, within double

strain DNA, and landing sites for protein sigma factor

o+1 first Nucleotide made in the RNA, proceeds to the right as a bottom strand

as the template

oHairpin loop prevents polymerase from continuing

RNA polymerase is a housekeeping gene because its useful for generic use

DNA in eukaryotes is kept in nucleus so there would be more elaborate interactions.

oProcessing such that it becomes RNA before it leaves the nucleus and is

transported

oTATA box with TATA binding protein TBP which recruits many factors such

as RNA polymerase so that transcription starts

o3D space such that TBP will be able to recognize the TATA box

oTranscription involves activating sequences far away from the start site

Enhancers: DNA sequences/landing sites upstream before the

TATA box which allow for regulated expression of transcripts e.g.

muscle transcription

Protein bound to them called the activator (Tf)

Mediator proteins binds to activator proteins and allow for RNA

polymerase II binding to start the transcription

omRNA synthesis in eukaryotes is more complex than in prokaryotes

Make transcript, cut areas in it called splicing

1) 5’ end: Capping - Made first

Capping special enzyme called 7-methylguanosine

2) 3’ end: Polyadenylation (adds a long set of As)

Special sequence toward the end that would direct an

endonuclease cleavage, an enzyme that would cut an RNA at the

downstream of the signal

Poly-A polymerase adds polyA “tail” which signals sequence

determines effective end of a transcript

RNA looks more mature

Longer tail = longer survival

3’ polyA formation effectively terminates synthesis of mRNA

Why do eukaryotic mRNAs have a cap and polyA tail?

oProtect mRNAs from degradation (so that 5’ to 3’ or

vice versa exonuclease does not eat up the mRNAs and this

would then maintain stability)

oFacilitates translation

3) Splicing

Processed by splicing to remove introns and retain exons in

the mRNA

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Related Questions

1.When a protein binds to DNA at a site defined by a particular nucleotide sequence, with which parts of the DNA does the protein primarily interact?

A. the phosphate and deoxyribose groups in the DNA backbone

B. the phosphate and deoxyribose groups in the DNA backbone, and hydrophobic interactions with the nucleotide bases

C. nucleotide bases within the major grooves of the DNA

D. nucleotide bases within the major and minor grooves of the DNA

E. none of the above

2. Which of the following proteins binds to DNA with sequence specificity?

A. POI Ill holoenzyme

B. DnaA

C. DnaB

D. Dam methylase

E. Both B and D

3. Which of the following is NOT a functional parallel among all known cellular systems of DNA replication?

A. Replication is initiated at specific sites

B. Replication is continuous on the leading strand and discontinuous on the lagging strand

C. DNA replication is semiconservative

D. Replication forks move away from the origin in one direction

E. Nucleases, polymerases and ligases replace RNA primers with DNA and seal the remaining nick

4. A DNA polymerase cannot synthesize a DNA strand de novo (from the beginning) from a mixture of dNTPs. Which of the following explains the role of the primer in the reaction promoted by this enzyme?

A. The primer is an initiation protein with attached nucleotides that binds to the template and to which new nucleotides are added to the 3 ' end.

B. The primer is an initiation protein with attached nucleotides that binds to the template and to which new nucleotides are added to the 5' end.

C. The primer is a preexisting strand of RNA or DNA to which new nucleotides are added to the 3' end.

D. The primer is a preexisting strand of RNA or DNA to which new nucleotides are added to the 5' end.

E. The primer is a preexisting strand of DNA synthesized by DNA pol I, prior to replicative DNA synthesis by DNA pol Ill.

5. Universal features of DNA polymerases include:

A. 5'-3' exonuclease function.

B. Formation of an 'closed' conformation of the polymerase when the template-nucleotide base pair is correct.

C. Use of a single magnesium ion to orient reacting molecules and assist in dissipation of the negative charge that develops during nucleotidyl transfer.

D. Alignment of conserved residues in the active site for attack of the DNA primer by the 3 'OH on the incoming nucleotide.

E. Continuous unbinding and rebinding of the polymerase to the DNA template as each nucleotide is added.

byzantiumscorpion425

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

BIOCHEM QUESTIONS:

Question 1) (1.5 points) True or false: The initial native DNA is usually in an overwound state, making the initial strand separation during replication energetically favorable, with continued strand separation at the replication fork resulting in underwound DNA that is then fixed by DNA gyrase.

Question 2) (1.5 points) True or false: UV based DNA damage largely causes dimerization of C and T bases that are fixed by the NER DNA repair pathway.

Question 3) (1.5 points) True or false: There is no enzyme within humans that has a reverse transcriptase activity.

Question 4) (1.5 points) True or false: One reason why uracil is not observed in DNA is that deamination of cytosine would result in Uracil and therefore potentially changing a GC base bp to an AT bp after a couple of rounds of replication.

Question #5: (1 point) Which of these statements is correct about the RNA polymerase? a) It makes tRNA, mRNA and rRNA b) It uses an RNA template c) It uses ATP, CTP, GTP and TTP d) It requires a primer

Question #6: (1 point) RNA polymerase grows the RNA chain in the 3â to 5â direction. a) True b) False

Question #7: (1 point) The mRNA is copied from the template strand. The mRNA has the exact same nucleotide sequence of the non-template strand except for U instead of T. a) True b) False

Question #8: (1 point) Only a limited portion of the DNA strand is copied by RNA polymerase, and there are initiation and termination signals for transcription. a) True b) False

Question #9: (1 point) The hairpin loop is the only way to conduct transcription termination in Prokaryotes. a) True b) False

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BIOL SCI 215 Lecture Notes - Lecture 6: Human Genome, Alternative Splicing, Tata-Binding Protein

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