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PHYS3012: Molecular BioPhysics > Chapter 4: Deoxyribonucleic Acid, DNA, Structure And Synthesis > Flashcards

Chapter 4: Deoxyribonucleic Acid, DNA, Structure And Synthesis Flashcards

1
Q

What is deoxyribonucleic acid (DNA)?

A

DNA is a polymer that carries the genetic instructions for growth, development, functioning and reproduction in all known organisms and many viruses. It is composed of two polynucleotide chains that coil around each other, forming a Watson-Crick double helix.

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2
Q

Describe the shape of a DNA molecule

A

Two helical polynucleotide chains coiled in opposite directions (antiparallel) around a common axis.

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3
Q

What are the two groups of nucleotides?

A

Purines and Pyrimidines

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4
Q

What are the two DNA purines?

A

Adenosine
Guanine

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5
Q

What are the two DNA pyrimidines?

A

Cytosine
Thymine

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6
Q

What are the percentages of each type of base in a DNA molecule?

A

A: 30%
T: 30%
C: 20%
G: 20%

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7
Q

What makes up a nucleotide unit?

A

-Nucleotide base
-Phosphate
-Deoxyribose

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8
Q

What is the diameter of the DNA helix?

A

~20 Å

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9
Q

What is the distance between adjacent DNA bases?

A

~3.4 Å

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10
Q

What is the angle of rotation of the helical structure of DNA?

A

36º

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11
Q

How many bases are there before the helical structure repeats?

A

10

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12
Q

What holds the two polynucleotide chains?

A

Hydrogen bonds

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13
Q

How many hydrogen bonds are between adenine and thymine?

A

2

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14
Q

How many hydrogen bonds are between cytosine and guanine?

A

3

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15
Q

The Watson-Crick model, the B-DNA configuration, has a _____ groove and a _____ groove. These grooves expose the edges of base pairs for _______ ________ by binding proteins.

A

Major
Minor
Chemical recognition

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16
Q

What is the depth of the major groove?

A

12 Å

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17
Q

What is the depth of the minor groove?

A

6 Å

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18
Q

Define supercoiling

A

Where the DNA double helix is packed together densely by the enzyme DNA gyrase (consuming energy in the form of ATP on the process)

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19
Q

Define conformation

A

The possible arrangement of a molecule, due to rotation, without breaking any bonds

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20
Q

What are the 3 key interactions that involve molecular forces in double-stranded polynucleotides?

A
  1. Stacking interactions between aromatic rings in the bases.
  2. Electrostatic interactions between negatively charged phosphates in the sugar-phosphate backbone.
  3. Hydrogen bonds between the base pairs, forming the basis for the complimentary Watson-Crick pairs.
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21
Q

What are stacking interactions between aromatic rings and nucleotide bases?

A

Strong interactions originating from dispersion forces that cause the flat bases to stack together like plates; it is the major driving force in the formation of the double helix.

22
Q

What is the role of electrostatic interactions between negatively charged phosphates in DNA?

A

To keep the strand relatively straight and prevent coiling of a single strand.

23
Q

How much energy does each hydrogen bond contribute?

A

3.3 - 6.6 kJ/mol

24
Q

The stacking interactions and the hydrogen bonds in combination result in a ____ ______ complex being formed and the ability for rapid _____ ________.

A

Very stable
Self-assembly

25
Q

What is DNA origami?

A

Where nanostructures are generated by carefully combined strands of DNA in the hopes of them being made into functional vessels for drug delivery.

26
Q

Define semi-conservative replication

A

The process in which DNA is duplicated during cell division so that both daughter cells have an identical copy of the original DNA strand. Both new DNA molecules contain one of the original strands of DNA, hence, are semi-conservative.

27
Q

Outline the process of DNA replication for one molecule of DNA

A

• A segment of DNA unwinds and the double helix is separated by DNA helicase using energy in the form of ATP.
• Single-strand binding proteins stabilise each individual strand, keeping them in place and easily accessible to act as templates for replication.
• Polymerase III holoenzyme used the single strands as a template to produce copies of the DNA molecule. The leading strand is duplicated from the 3’ end (where there is a ribose on the end) so the copy begins at the 5’ end (where there is a phosphate on the end). The lagging strand is duplicated in short fragments in the 3’ to 5’ direction and are completed by polymerase I before being linked by DNA ligase.
• The process repeats for all nucleotides along the two strands incredibly quickly.

28
Q

Why is DNA replicated so many times?

A

There are a large number of base pairs in the human genome.

29
Q

What is the force required to pull apart DNA strands?

A

~20 pN

30
Q

What is the speed of DNA replication?

A

~1000 nucleotides per second

31
Q

What is the error rate of DNA replication?

A

Less than 10^-8 per base pair

32
Q

What enzyme mediates the process of DNA replication? (EXTRA: why is it so efficient?)

A

Polymerase III holoenzyme

EXTRA: It forms a dimer so synthesis of both strands can be performed simultaneously.

33
Q

What is the purpose if DNA gyrase in DNA replication?

A

To introduce negative supercoils to prevent a topological issue from the double helix constantly unwinding.

34
Q

What is the template for protein synthesis?

A

RNA

35
Q

How does genetic information get converted into a protein?

A

DNA - RNA - protein following protein synthesis.

36
Q

What is ribonucleic acid (RNA)?

A

RNA is a linear polymer that is responsible for coding, decoding, regulation and expression of genes (particularly in controlling the synthesis of proteins). It is a single-stranded molecule made up of nucleotide subunits containing a base, a phosphate group and ribose. These subunits are joined together via phosphodiester bonds, as with DNA.

37
Q

What are the four RNA bases?

A

Adenine
Cytosine
Guanine
Uracil

38
Q

What are the two stages of protein synthesis?

A

Transcription
Translation

39
Q

Define transcription

A

The process by which sections of the DNA sequence, corresponding to a ‘gene’, are transcribed into an mRNA, messenger RNA, sequence.

40
Q

Describe the process of transcription

A

• A portion of DNA is unwound by DNA helicase and the nucleotide bases are exposed on each strand.
• One of the strands then acts as a template for the synthesis of an mRNA molecule. This is known as the template strand.
• Complementary RNA nucleotides form a pool in the nucleus pair with the bases on the DNA template one by one. Each incoming ribonucleotide bonds covalently to the mRNA chain via phosphodiester bonds in a reaction that is catalysed by RNA polymerase II. The bases pair G → C, C → G, T → A, and A → U.
• The mRNA molecule does not remain hydrogen-bonded to the DNA molecule, instead it detaches once a new ribonucleotide has been added and the DNA strands re-join, leaving the double helix as it was initially.
• Once a ‘stop’ triplet code has been recognised, the RNA polymerase II detaches and the production of mRNA is complete.

41
Q

What direction does transcription occur in?

A

The 5’ to 3’ direction.

42
Q

What is the rate of transcription?

A

~20 nucleotides per second.

43
Q

What is the error rate of RNA polymerase II in transcription?

A

1 mistake per 10^4 bases

44
Q

What has a greater mistake rate: DNA replication or transcription? (EXTRA: how is this mitigated?)

A

Transcription

RNA polymerase can return to the error site to cut out the mistake.

45
Q

Define messenger RNA (mRNA)

A

the molecule responsible for transcription whose bases are determined by a DNA template. It acts as a template for protein synthesis by associating itself with ribosomes after it has transported RNA out of the nucleus onto the cytoplasm.

46
Q

Define translation

A

The process by which nucleotides are decoded in consecutive sets of 3 (codons) to form a polypeptide chain.

47
Q

Describe the process of translation

A

• Initially, a ribosome attaches itself to a starting codon on the mRNA molecule.
• The polypeptide sequence can then begin to be constructed. A tRNA, transfer RNA, molecule with a complementary anticodon sequence pairs with the starting codon.
• Another complementary tRNA molecule pairs with the next codon. These two amino acids are joined together by a peptide bond; this reaction is catalysed by an enzyme and ATP.
• The ribosome moves onto the third codon, allowing the tRNA molecule to be released. The pairing process repeated with the second and third amino acids and this continues until the polypeptide chain is built up and the ribosome reaches a stop codon. At this point, all of the molecules separate and the chain is complete.

48
Q

Define transfer RNA (tRNA)

A

The clover shaped, single-stranded molecule that an amino acid attaches to. Each type of tRNA attaches to a different amino acid. The opposite end contains three organic bases known as an anticodon for translation.

49
Q

Describe the structure of tRNA

A

tRNA molecules are about 80 nucleotides long with a three-dimensional clover leaf structure where one end carries the anticodon and the other end has an amino acid attached.

50
Q

What feature of translation makes it more efficient?

A

If multiple polypeptide chains are required, multiple ribosomes can follow directly behind one another to assemble them.

51
Q

How many possible combinations of nucleotide triplets are there to code for amino acids? (EXTRA: how many types of amino acids are found in proteins?)

A

64
EXTRA: 20

PHYS3012: Molecular BioPhysics (12 decks)

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