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Biochemistry > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

What are the 3 main components of nucleic acids?

A
  • Base pair
  • Phosphodiester / phosphate
  • Deoxyribose
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2
Q

What do phosphates do and in what position?

A

They link up sugars on the outside of the helix. The 5’ position of the sugar to the 3’ position of the next sugar.

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3
Q

What are the two different types of nucleobases and what is the difference?

A
  • Pyrimidine - Benzene ring but 2 of the C’s are replaced with N’s
  • Purine - Pyrimidine fused to something else
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4
Q

What are the nucleobases?

A
  • Thymine
  • Uridine
  • Cytosine
  • Adenine
  • Guanine
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5
Q

What is the basic chemistry of nucleobases?

A
  • Planar
  • Rigid
  • Aromatic units
  • Sp2 hybridisation
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6
Q

What does adenine compliment?

A

Thymine

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7
Q

What does Guanine compliment?

A

Cytosine

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8
Q

What happens as the strand gets longer?

Complimentsry interactions

A

You get more complimentary interactions and the double helix will become more stable and harder to separate. This is due to more hydrogen bonding

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9
Q

Which complementary pair has more hydrogen bonding and therefore makes the double helix more stable?

A

Guanine and cytosine have more hydrogen bonds, specifically 3 whereas Adenine and Thymine only have 2.

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10
Q

Phosphates & stacking

Why does the DNA duplex have a helical structure?

A
  • Phosphates have negative charges which repel each other so they can get as far away as possible in the helix form
  • The hydrogen bonding between the base pairs
  • Stacking nucleobases through hydrophobic / van der waals vertically compacts the structure. It also stabilises the structure due to the hydrophobic effect.
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11
Q

What are the different forms of DNA?

A
  • B-DNA: Right handed
  • A-DNA: Right handed
  • Z-DNA: Left handed
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12
Q

What is the difference between the different forms of DNA?

A
  • B-DNA: Right handed - Normal helical structure
  • A-DNA: Right handed - More twisted than B, minor becomes huge and major becomes small, anti-parallel
  • Z-DNA: Left handed - less common, sugars are in an alternating arrangement, phosphates are on the outside, interacts differently with enzymes and is associated with diseases.
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13
Q

What is triplex DNA?

Nucleobase

A
  • Purine nucleobase, 4 hydrogen bonds with the additional nitrogen.
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14
Q

What is Quadruplex DNA?

Layers

A
  • Guanine quadruplex, the strand has fewer Gs in them, made of two strands, layers of guanine quartets
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15
Q

nucleophile

What is the difference between DNA and RNA?

A
  • RNA has an additional hydroxyl group attached which provides more ways hydrogen bonding can occur and can act as a nucleophile against a phosphate and catalyse the hydrolysis.
  • Uridine replaces thymine
  • Usually single stranded
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16
Q

What is the difference between thymine and uridine?

Methyl group

A
  • It doesn’t have the methyl group that thymine has which means it has more flexibility.
  • It has the same hydrogen bonding.
17
Q

What are nucleosomes and what are they for?

DNA

A
  • DNA is coiled around proteins called histones which are further packed to produce chromosomes.
  • This provides a way for an organism to find the right bit of DNA easier.
18
Q

How many protein units are required for each nucleosome?

A

Eight

19
Q

What does the central dogma of biology deal with?

Residue-by-residue transfer

A

The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid.

20
Q

Whats it called when DNA is changed to RNA?

A

Transcription

21
Q

What’s it called when RNA is converted into DNA?

A

Reverse transcription

22
Q

What’s it called when RNA is turned into protein?

A

Translation

23
Q

What does copper isomerase do?

A

It’s an enzyme which straightens out the DNA.

24
Q

What does helicase do?

A

It splits up the two strands.

25
Q

What happens on the leading strand during DNA replication?

A

The 5’ end of the strand is copied.

26
Q

What does polymerase do?

Enzyme

A

It’s an enzyme builds a new strand by adding new bases in a complementary sequence from the 5’ end to the 3’ end.

27
Q

What happens on the lagging end?

Another

A

There’s another DNA polymerase which synthesis from 5’ to 3’ but the strand gets liberated in the 5’ to 3’ direction so it has to do it in chunks and get another enzyme to attach the chunks together.

28
Q

What is microscopic reversibility?

A

The energy of going in one direction will be the same as the mechanism going in the reverse direction so any catalyst for making something is also the catalyst for breaking something.

29
Q

What is the polymerase chain reaction for?

A

Amplifying DNA

30
Q

How does polymerase chain reaction work?

Double-strand template, primers

A

Take any double-strand template of DNA and denature it by heating it up (splits into two strands) and attaching primers which are the starting point for replication.
On both strands, you can perform the elongation of the strand by polymerase and get double what you started with and do the same thing over and over again.

31
Q

What do transcription factors do?

Protein clusters

A

They are a protein cluster which signals to RNAP (RNA polymerase) where to begin transcription.

32
Q

How does translation work?

mRNA, enormous complex,

A

mRNA is used to pass on information to make proteins through translation.
It goes into some enormous complex of protein and nucleic acids called the ribosome.
mRNA goes into the groove in the ribosome and then tRNA / transfer RNAs come along
They have a part which will bind to 3 of the nucleotides in the mRNA at the same time they bring along an amino acid. One comes in and binds to the appropriate 3 bases and the amino acid that it has gets delivered onto a growing amino acid chain.
The mRNA moves along one segment, the next one comes in and the next amino acid goes on
A mechanism whereby information in the nucleic acid can be translated in a sequence-specific basis to the protein.

33
Q

What is the purpose of translation?

A

To make proteins.

34
Q

What is the only start codon?

A

AUG = Met

35
Q

What are the stop codons?

A
  • UAA
  • UAG
  • UGA
36
Q

What does tRNA have for mRNA?

A

The anti-codon as they are complementary.

37
Q

What do the larger ribosomal units do?

A

Link amino acids

38
Q

What do the smaller ribosomal units do?

A

Reads RNA

Biochemistry (18 decks)

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