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4BBY1013 > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

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1
Q

What is semi-conservative replication?

A

When one strand of the parent strand is in the daughter strand. The new DNA contains an ‘old’ strand and a ‘new’ strand.

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2
Q

What are replication forks?

A

It is created by helicases. When the DNA strand is broken apart for replication or transcription, the resulting structure has two branching “prongs”, each one made up of a single strand of DNA.

http://img.sparknotes.com/figures/A/a0d1b3a1aaed46e29034f996722dd1a1/repfork2.gif

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3
Q

Where does the energy for DNA synthesis come from?

A

The energy comes from hydrolysis of nucleotide triphosphate.

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4
Q

What is special about polynucleotide synthesis?

A

New nucleotides are always added to the free -OH group of the growing polynucleotide strand.

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5
Q

What are the differences between DNA polymerase I and III?

A

DNA polymerase I makes removes RNA primers on the lagging strand and fills in the nucleotides between the Okazaki fragments.

DNA polymerase III makes DNA in both the leading and lagging strand in the 5’->3’ direction.

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6
Q

What is the difference between Type I and Type II tropoisomerase?

A

Type I tropoisomerase relaxes the supercoil

Type II tropoisomerase (DNA gyrase) cuts and reseals DNA strand to relieve supercoiling

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7
Q

What are the enzymes used in DNA replication?

A

Type I and Type II tropoisomerase, DNA polymerase I and III, DNA ligase and DNA helicase

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8
Q

What do DNA helicase and DNA ligase do?

A

DNA helicase unwinds the DNA double helix and separates the DNA double strand by breaking the hydrogen bonds between the two strands, forming replication forks.

DNA ligase joins the discontinuous DNA fragments by making phosphosiester bonds

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9
Q

What are proof reading functions?

A

Proof reading function is found in RNA and DNA polymerase.

As the polynucleotide is being synthesised, sometimes an incorrect base will be added. The polymerase stops synthesis to goes back and ejects the base before continuing synthesis.

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10
Q

How do alkylating agents damage DNA?

A

Adds alkyl groups (we only learn about methyl) to guanine leading to guanine modification.

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11
Q

How does UV light damage DNA?

A

Causes dimer formation between two adjacent thymines or adjacent cytosines.

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12
Q

How do Nitrous Acids damage DNA?

A

They remove amine groups off of bases.

Needs to be known:
cytosine is converted to uracil

May need to be known:
adenine is converted to hypoxanthine and guanine is converted to xanthine

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13
Q

How do free radicals damage DNA?

A

Cause strands to break and base modification. They have unpaired electrons so try to take the electrons of whatever it makes contact with, meaning it does’t only damage DNA, but anything in the cell

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14
Q

How do carcinogenic chemicals damage DNA?

A

Cause chemical modifcations to bases causing cancers

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15
Q

How does ionising radiation lead to damage DNA?

A

They break the strands.

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16
Q

What is special about the structure of the origin of replication?

A

There is a high density of A-T bonds.

A-T bonds have 2 hydrogen bonds and G-C bonds have 3 hydrogen bond which means it takes less energy to break apart the A-T bonds in comparison to G-C, meaning the DNA strands are easier to separate at origin of replication.

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17
Q

What are the differences between the leading and lagging strand?

A

The leading strand has the daughter strand being built backwards and utilises DNA polymerase III.

The lagging strand uses (various enzymes and other things) to build the DNA strand in the normal direction and utilises DNA polymerase I and III

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18
Q

What is special about the lagging strand?

A

Lagging strand is synthesised ‘backwards’. (3’->5’)
It isn’t possible to directly synthesise DNA backwards, so DNA is synthesised in segments in the 5’->3’ directions (known as Okazaki fragments) which are linked by DNA ligase.

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19
Q

What direction is RNA synthesised?

A

5’->3’

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20
Q

What is the difference between a ribose and deoxyribose sugar?

A

On the 2’ carbon, there is a hydroxyl group on the ribos, but no hydroxyl on the deoxyribose sugar.

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21
Q

What is the UTR?

A

Untranslated region of the mRNA. They don’t code for anything ans there is a 3’ UTR and a 5’ UTR.

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22
Q

What is the initiation step for prokaryotic transcription?

A

Sigma factor binds to the Pribnow box of the DNA. The sigma factor acts as an intiation factor for the transcription. The sigma factor helps the RNA polymerase to bind to exactly where it needs to to be.

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23
Q

What is the elongation step for prokaryotic transcription?

A

The RNA polymerase forms a transcriptional bubble and reads the template DNA in order to synthesise the mRNA. It moves along the DNA and synthesises the mRNA until it reaches the termination stage.

24
Q

What is the termination step for transcription?

A

There is a sequence that leads to a structural element being synthesised which signals that the mRNA has finished being synthesised. The structural element is a hairpin loop (G-C rich stem loop) signalling that the RNA polymerase should stop.

25
Q

What is the hairpin loop structure?

A

http://img.sparknotes.com/figures/5/531c62f0d28ea4ccc5bf20ebe5828d16/rhoindept.gif

26
Q

What is capping?

A

GTP reacts with 5’ end of the mRNA to form 7-methylguanosine at the 5’ end of an mRNA. A 5’-5’ bond is made and the mRNA is ‘capped’ and every mRNA synthesise in eukaryotic cells will be ‘capped’.

27
Q

What is polyadenylation?

A

Adenine chains (Just a whole bunch of A’s, AAAAAAAAAA…..) are added by an enzyme to the mRNA to add stability to the mRNA of eukaryotic cells.

28
Q

What is alternative splicing?

A

Combination of different exons to make different proteins for the same sequence of DNA. Exons and Introns are swapped to make different mRNA for translation.

29
Q

Which bases are purine?

A

Guanine and Adenine

30
Q

Which bases are pyramidine?

A

Thymine, Uracil and Cytosine

31
Q

Griffith pneumococcus experiment (1928)

A

.

32
Q

Avery pneumococcus experiment (1944)

A

.

33
Q

Hershey-Chase experiment (1952)

A

.

34
Q

Early 20th Century

A

.

35
Q

Mendel (1865)

A

.

36
Q

Erwin Chargoff

A

.

37
Q

James Watson and Francis Crick

A

.

38
Q

What are the names of the bonds broken to give energy from triphosphate nucleotides?

A

Phosphoanhydride bonds

39
Q

What does it mean for DNA to be degenerate?

A

Some proteins are coded for by different codons, so if DNA mutates there’s a chance that the same amino acids will be coded for.

40
Q

What is the start codon? What does it code for?

A

ATG codon in the DNA
AUG codon in mRNA

Codes for Methionine protein (Met or M)

41
Q

What are the stop codons? What do they code for?

A

TAA, TGA and TAG in the DNA
UAA, UAG and UGA in mRNA

Doesn’t code for anything. Just ends the polypeptide chain.

42
Q

What mutations are there?

A

Point mutations: Nonsense mutations, Missense mutations and Silent mutations

Frame shift mutations: Insertions and Deletion

43
Q

Describe the structure of tRNA.

A

Forms a cloverleaf structure.
Theres 75-90 nucleotides
Theres the CCA-OH sequence at 3’ end plate where amino acids binds to.
Theres a D-arm, an anticodon arm and a T-arm.
Theres also a lot of modified bases

44
Q

What is the ‘wobble’ mechanism?

A

Some amino acids can be coded for by multiple codons. If the first two codons for the multiple codons are the same, the third base doesn’t need to be read for the amino acid to be accepted by the ribosomes. This saves time when translating mRNA.

45
Q

How are the amino acids added to the tRNA?

A

Specific aminoacyl-tRNA-synthases load tRNA molecules with amino acids. As there are 20 amino acids, there are 20 types of aminoacyl-tRNA-synthases.

46
Q

What is the chemical reaction that occurs for when tRNA is loaded by aminoacyl-tRNA-synthases?

A

Amino acids + tRNA + ATP —> PPi + aminoacyl-tRNA + AMP

47
Q

What are the binding sites on ribosomes?

A

A-site (Attachment), P-site (Polymerisation) and E-site (Exit)

48
Q

What is the intiation step for translation?

A

The 30S subunit bind to IF1 and IF3 (Initiation Factor) which then binds to the mRNA thats going to be translated.
tRNA^[fMet] (the tRNA containing fMet) binds to GTP-IF2 and enters the P-site of the 30S subunit
tRNA^[fMet] anticodon lines up with AUG codon
The 50S subunit binds to the 30S subunit and GDP + Pi (from the GTP of the GTP-IF2) is released (along with energy)

49
Q

What is the elongation step for translation?

A

The 2nd aminoacyl tRNA is bound EF-Tu GTP (Elongation Factor thermo unstable GTP).
It is delivered to ribosome and enters at the A-site where proof reading occurs (energy for which is provided by GTP hydrolysis) and EF-Tu GDP and Pi are expelled from ribosome.
Peptidyl transferase occurs where the 2nd AA is added to the 1st AA (fMet) and the shape of the tRNA changes within the ribosome.
EF-G-GTP binds and is hydrolysed which provides energy for translocation of tRNAs
Discharged tRNA leaves ribosome and the ribosome now has the same structure as it did at the start of elongation, except it now has one additional AA.
Cycle continues until termination.

50
Q

What is the termination step for translation?

A

Stop codon of mRNA causes the binding of the release factor at the A-site of the ribosome. Translocation of the tRNA and release factor causes the 70S to split into the 50S and the 30S. The polypeptide chain is finished being translated.

51
Q

Describe how the DNA strand of the lagging strand is synthesised.

A

On the lagging, Primase adds RNA primers allowing Okazaki fragments to be synthesised in the normal (5’->3’) direction. DNA on the lagging strand must be looped to achieve synthesis of Okazaki fragments. The RNA primers are removed by DNA polymerase III and the Okazaki fragments are joined by DNA ligase.

52
Q

What is the Pribnow box?

A

A series of bases at the -10 region of the transcription start site.
TATAAT is the sequence.

53
Q

What are the differences between eukaryotic and prokaryotic transcription?

A

Eukaryotes

  • 40S + 60S = 80S ribosome
  • hnRNA (pre-mRNA) is modified by capping, polyadenation, and splicing before translation
  • Initiator tRNA is met-tRNA^(met)

Praokaryotes

  • 30S + 50S = 70S ribosome
  • mRNA is unmodified before translation
  • Initiator tRNA is fmet-tRNA^(fmet)
54
Q

In transcription, what is splicing?

A

This only occurs in eukaryotic cells. Introns are removed and Exons are brought together. Splicing occurs at specific regions of the mRNA to allow Introns to be removed.

55
Q

What is the Shine-Dalgarno sequence?

A

The ribosomal binding site for prokaryotic mRNA.

56
Q

Where does the energy for peptidyl transferase come from?

A

No nucleotide triphosphate hydrolysis needed, the energy comes from the charged tRNA itself.
After the transfer has happened, charged tRNA is just tRNA.

57
Q

What are the stop codons?

A

UAA, UGA, UAG

4BBY1013 (6 decks)

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