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Biomolecules > DNA and RNA > Flashcards

DNA and RNA Flashcards

1
Q

Pyramidine vs Purines

A

Pyramidine: hexose, 1 ring, CUT
Purine: 2 rings, AG

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2
Q

what is the difference between thymine and uracil

A

Thymine has a methyl group on the 5th carbon and uracil is less stable than thymine.

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3
Q

What is the difference between DNA and RNA

A

DNA: H on 2nd carbon
ACGT
RNA: OH on 2nd carbon
ACGU

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4
Q

What is the difference between nucleoside and nucleotide

A

Nucleoside: has a 5 carbon ribose sugar with a nitrogenous base linked via B glycosidic linkage.
Nucleotide: same as nucleoside but has phosphate groups attached via ester linkages.

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5
Q

What way can nucleotides be added and where does the addition start?

A

Nucleotides can only be added in the 5’ to 3’ direction, starting at the 3’ part of the strand. On the leading strand, the addition starts due to an RNA primer being attached and on the lagging strand, the RNA primer is attached at every new okazaki fragment beginning.

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6
Q

What makes the RNA primers?

A

Primase enzyme produces primers. Primase enzyme is a form of RNA polymerase.

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7
Q

What three things make sure the lagging strand of the DNA binds together.

A

1.Ligase enzyme sticks the Okazaki fragments together
2.RNA Polymerase I replaces the RNA primers by exonuclease activity.
3.Nuclease enzyme replaces the RNA primers.

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8
Q

What stops the DNA from tangling?

A

Topoisomerase enzyme.

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9
Q

What prevents the two parent DNA strands from joining at the bases?

A

SSBP- Single stranded binding proteins.

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10
Q

Which proteins allow the DNA polymerase to bind to the template strand?

A

Sliding clamp protein.
Clamp loader is the protein that uses ATP to load the sliding clamp onto the template.

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11
Q

Where does DNA replication in prokaryotes (E-coli) start?

A

At origin of replication site. oriC locus on plasmid.
The AT rich tandem repeats regulate replication and is essential to the start of DNA replication.

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12
Q

What is the origin recognition protein in prokaryotes and how many copies are there?

A

DnaA protein and there are 5 copies.

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13
Q

How does replication not reduce the length of the lagging strand due to the constant breakages in fragments?

A

Telomeres on the end of chromosomes protect end from getting shorter. They have tandem repeats of 6 nucleotides, in humans it is TTAGGG. Telomeres are produced by telomerases

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14
Q

What is the difference between A-DNA, B-DNA and Z-DNA.

A

A-DNA=less hydrated
B-DNA= highly hydrated (humans)
Z-DNA= left handed with phosphoryl groups (zig zagging)

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15
Q

What is RNA made of?

A

Ribonucleotides, meaning it has ribose sugar on nucleotide.

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16
Q

Charateristics of mRNA

A
  1. on 5’ end it has 7 methylguanosine triphosphate cap which protects from exonuclease activity and allows for recognition during translation.
  2. Has a poly-A tail on 3’ end. Joins by 5’ to 5’
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17
Q

Characteristics of tRNA

A

75bp
has a clover leaf structure

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18
Q

What kind of RNA do prokaryotes and eukaryotes have?

A

Prokaryotes: monocistronic
Eukaryotes: polycistronic

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19
Q

Characteristics of rRNA

A
  1. is important for the way ribosomes are folded and the parts they have according to whether they are prokaryotes or eukaryotes.
  2. Have catalytic activity, they force mRNA and tRNA through. (ribozymes)
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20
Q

Characteristics of snRNA

A
  1. found in eukaryotes.
  2. less than 300 nucleotides
    3.Highly conserved secondary structure
  3. Involved in splicing of introns and exons
  4. form small nuclear ribonucleoprotein particles
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21
Q

when 3 or more bases interact, what are they stabilized by?

A

Metal ions

22
Q

What are the steps for eukaryotic transcription initiation

A
  1. TFIID + TATA box bind
  2. TFIIA + TFIID
  3. TFIIB + BRE (B responsive complex is on either side of TATA box)
  4. TFIIF and RNA pol II bind (complex forms)
  5. TFIIE + TFIIH start transcription.
23
Q

What protein makes the DNA binding sites in eukaryotes more visible?

A

CRC- Chromatin remodelling complexes. Allows for the DNA to move around the histone proteins to expose the DNA binding sites.

24
Q

What does a mediator protein do in eukaryotes?

A

It is regulated by kinases and regulates transcription factor signals on enhancer region.

25
Q

How is RNA polymerase liberated from the promoter region and what happens when RNA polymerase is finished with transcribing

A

TFIIH has a protein kinase subunit that provides energy for the RNA polymerase to move down the DNA and transcribe the DNA.
When RNA polymerase is finished, the phosphates are taken off by phosphatases.
Only the desphosphorylated form of RNA polymerase can start a new transcription process.

26
Q

What occurs during RNA processing to turn it into mRNA

A
  1. capping
  2. Polyadenylation
  3. splicing
27
Q

what is RNA capping?

A

RNA capping involves adding a guanine nucleotide with methyl group on the 5’ end of the newly formed RNA.

28
Q

What is polyadenylation?

A

Where enzyme cuts end of new RNA and adds many adenine bases as the poly-A tail on mRNA

29
Q

What is the point of capping and polyadenylation?

A

To facilitate transport, make the molecule recognisable (mRNA) and more stable.

30
Q

How does Rho independent work in prokaryotes?

A
  1. The GC-rich site in RNA is highly stable and stops RNAP (RNA pol II)
  2. The Poly-U site between the RNA-DNA complex is weakly bound by hydrogen bonds so the GC rich site
  3. RNA dissociates from DNA
  4. Can be bi-directional
31
Q

How does Rho dependent work in prokarytoes?

A
  1. The GC rich site in RNA is highly stable and stops RNAP
  2. The poly-U site is weakly bonded
  3. RNAP stops around 100 nucleotides away
  4. Rho binds and moves towards the RNAP by ATP hydrolysis and dissociates the RNA-DNA heteroduplex complex.
  5. Can be bi-directional
32
Q

Describe transcription termination in eukaryotes

A

Polyadenylation on RNA triggers it, RNA is cleaved 10-30 nucleotides downstream by the poly-A complex.
RNAPII falls off of DNA.

33
Q

Initiation in prokaryotes

A
  1. Sigma factors are transcription factors.
    They turn RNAP into RNA holoenzyme.
34
Q

How is RNA processed in EUKARYOES only

A
  1. mRNA capping (which is cotranslational) methyl guanylyl adds 7-methyl guanosine cap
  2. CPSF and CSTF bind and cleave at poly A tail
  3. Splicosomes have snRNA’s and cut the introns out at the intron-exon boundary.
35
Q

What is the start codon and stop codon?

A

Methionine is the start codon, there is only one codon for it: AUG
Stop: UAA, UAG UGA

36
Q

What is the point of the codon bias?

A

Different amounts of the same codon in different species means if one species was to affect the other, there would be insufficient tRNA’s produced so is a protective mechanism.

37
Q

PROKARYOTIC TRANSLATION INITIATION: What do the different initiation factors do?

A

IF3: Binds to small subunit and large subunit and stops them from binding
IF1: Binds and blocks A site on ribosomal subunit
IF2: binds initiator (1st) tRNA to the P site, requires GTP hydrolysis.

38
Q

How does PROKARYOTIC TRANSLATION ELONGATION work?

A
  1. EF-TU (Elongation factor thermal unstable) which delivers 2nd aminoacyl tRNA to A site.
  2. Peptidyl transferase catalyses the formation of new peptide bond between incoming amino acid and adjacent one at p site.
  3. tRNA deacylase releases growing polypeptide from tRNA at p site.
    4.Peptidyl tRNA moves the tRNA to P site from A site, promoted by EF-TU.
  4. Spent tRNA released from E site.
39
Q

How does prokaryotic termination work?

A
  1. Release factors RF1 and RF2 resemble tRNA’s that are complimentary to the stop codons because there are no complimentary tRNAs for the stop codons. RF1= UAA, UAG
    RF2=UAA, UGA
  2. tRNA leaves via E site.
  3. peptidyl transferase cleaves polypeptide chain from tRNA in p site.
  4. RF3 makes RF1 and RF2 depart A site (GTP hydrolysis)
  5. Ribosome recycling factor RRF uses GTP to break the 2 subunits.
40
Q

What is a free floating ribosome

A

prokaryotes: ribosomes arent on ER because there is no ER. They are on the RNA, transcription and translation ahppens at the same time.
eukaryotes: detached when they translate mRNAs, attached when on ER.

41
Q

What is gene cloning in molecular biology?

A

Producing clones of a specific gene, not organism.

42
Q

What is classed as a suitable vector?

A
  1. Independent from host chromosome
  2. copied by host cell
  3. maintained through population of cells
  4. allow for selection of those cells that contain vector
43
Q

What enzyme is used to cut the DNA

A

restriction endonuclease.

44
Q

What is the difference between sticky ends and blunt ends?

A

Sticky: bases overhang.
Blunt: Straight cut, no overhangs.

45
Q

What is a multiple cloning site?

A

It is where the unique restriction sites are clustered.

46
Q

Is heat shock inefficient?

A

Yes.

47
Q

In secondary selection which colour proves what in?

A

Blue-white screening:
1. Blue= self-ligated plasmid
2. white= Inserted foreign DNA

48
Q

What does the lac Z gene code for?

A

Beta- galactosidase

49
Q

In trp operon, when is the operon on and off?

A

Trp operon is on when there is no trp (tryptophan)
Trp operon is off when there is trp.

50
Q

What do lac Z,Y,A code for?

A

Lac Z= b galactosidase
Y= permease
A=tranacetylase

51
Q

How does lac operon turn on and off?

A

Off: when there is no lactose, its not required so the lac repressor protein binds to the operator region.
On: when lactose is present, allolactose binds to repressor and the repressor changes shape to get off the operator region.

52
Q

What is the way the lac operon transcription starts?

A

cAMP binds to CRP, this allows for RNA pol to bind and transcribe.

Biomolecules (3 decks)

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