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MIMM 211 > Lecture 11: DNA replication > Flashcards

Lecture 11: DNA replication Flashcards

1
Q

In eukaryotes, DNA is organized into […], which are made up of a […] and […] base pairs of DNA.

A

Nucleosomes, histone octamer, 146

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2
Q

In eukaryotes, nucleosomes are linked by […].

A

Linker regions (14 to >100 base pairs), which are themselves bound by histone H1.

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3
Q

Describe the difference in the condensation of DNA between eukaryotes and prokaryotes.

A

In eukaryotes, DNA is condensed approximately 10,000 fold, while in prokaryotes it is only condensed about 1,000-fold.

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4
Q

Explain why the genome is so much smaller and less condensed in the bacterial cell than in the eucaryotic cell.

A

Because bacteria has to be able to replicate itself quickly along with its DNA.

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5
Q

DNA replication in bacteria is […]

A

Semiconservative

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6
Q

Describe the first step of DNA replication in E. Coli along with the associated enzymes.

A

The DNA helix is unwinded by the helicase and use each strand as a template for DNA polymerization, which is done by DNA polymerase III. This creates a replication fork and a replisome is constructed out of 30 different proteins.

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7
Q

Describe DNA replication in E. Coli after the setup is complete.

A

The DNA polymerase III synthesizes DNA from 5’ to 3’ using dNTPs. As this occurs, the DNA polymerase also proofreads what it’s done via a 3’ to 5’ exonuclease activity, which can correct a wrong nucleotide. Basically, every time a nucleotide is added, it looks back to verify that the pairing is correct.

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8
Q

When DNA exonuclease activity fails, the result is […]

A

A mutation, as the mistake is not recognized and corrected.

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9
Q

Explain how the replication of circular bacterial DNA takes place

A

Replication begins at the origin. Replication forks then open up on either side of the replication and the circle “unzips”, creating a second circle. Replication ends when they forks reach the terminus, at which point the chromosomes separate.

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10
Q

Explain how rolling circle conjugation is initiated.

A

There is an origin of replication that is recognized. A single-stranded endonuclease (enzyme) that we call nickase that generates a Nick. The Nick cuts only one phosphodiester bond to operate on the outside strand only. This leaves a 3’ OH that is recognized by the DNA polymerase, which starts to replicate in the 5’ to 3’ direction (blue strand).

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11
Q

Explain how rolling circle conjugation takes place once it has begun.

A

As the new stand is synthesized from 5’ to 3’, it peels off the existing strand, creating a displaced strand. Eventually, the displaced strand reaches an its full length. This can be repeated for several rounds, making the displaced strand longer and longer. The ends are then cut to separate the different units into the displaced strand and re-ligated together to form new circular DNA.

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12
Q

What type of DNA is the rolling circle replication method used for? Why?

A

It is only used for certain conjugative plasmids. This is because chromosomes are too long for this to work, and only plasmids are small enough.

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13
Q

Give 2 reasons why DNA replication in eucaryotic DNA works differently than in prokaryotes.

A
  1. The genome is much larger in eukaryotes
  2. The DNA is linear as not circular
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14
Q

How does DNA replication in eukaryotes differ from replication in prokaryotes?

A

Replication is sparked at different parts along the chromosome, and two replication forks go in opposite directions until they merge, at which point the two copies of DNA separate.

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15
Q

The enzyme that recognizes the origin of DNA replication is called the […]

A

Helicase

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16
Q

The origin of replication in E. Coli is called […] and the helicase that binds to it is called […]

A

oriC, DnaA

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17
Q

Explain how oriC functions as an origin of replication.

A

It is very rich in A-T pairings, which require less energy to break than G-C pairings. This helps the DnaA helicase unwind the strands, as it requires less ATP.

18
Q

Once it has fulfilled its purpose, DnaA is replaced by […]. whose role is to […]

A

2 DnaBs, which form the basis of and recruit proteins to form the replisomes, which will then form the replication forks.

19
Q

Topoisomerases are also called […]

A

DNA gyrase

20
Q

What is the role of toporisomerases?

A

Their role is to release the tension as the DNA strands are being unzipped by the helicase. They cut a phosphodiester bond to release the tension and then re-ligate it. They are located in front of the replisome.

21
Q

What are SSBs?

A

Single-streanded DNA binding proteins

22
Q

What is the role of SSBs?

A

As DNA replication is taking place, they ensure that the two strands remain separated instead of reannealing together. It also protects the single stranded DNA, as it is more susceptible to degradation.

23
Q

The two strands of DNA replication are called the […] and the […]

A

Lagging strand and leading strand

24
Q

Explain how the lagging strand is dealth with.

A

Because the DNA polymerase has to synthesize from 5’ to 3’, it must do so in small chunks along the lagging strand. Since synthesis requires a primer, the primase must deposit small primers consistently. This primer + the synthesized DNA until the next primer are called okazaki fragments. At the end of the process DNA polymerase III gets replaced by DNA polymerase I, which has 5’ to 3’ exonuclease activity. It degrades the RNA primer and synthesizes DNA at the same time. Finally, a ligase comes to join the okazaki fragments together.

25
Q

A gene is also called a […]

A

Cistron

26
Q

What is a gene?

A

It is a nucleotide sequence that codes for an mRNA (protein), tRNA, or rRNA

27
Q

What are the 4 parts of bacterial genes?

A

From 5’ to 3’: Promoter, leader, coding region, trailer

28
Q

Eucaryotic genes are interrupted by […]

A

Introns aka noncoding sequences

29
Q

How do bacterial genes compare to eukaryotic genes in terms of introns?

A

Bacterial genes are more continuous and have fewer introns.

30
Q

Each amino acid in a gene is specified by […]

A

A codon, which consists of 3 consecutive nucleotides.

31
Q

Introns are removed via […]

A

Splicing (after which the coding sequences are ligated together).

32
Q

How many codons are there?

A

64

33
Q

How long is a codon? Why?

A

At least 3 nucleotides, because there are 20 amino acids that need to be coded for using only 4 nucleotides. 4^3 = 64, which is enough, while 4^2 gives 16, which is insufficient.

34
Q

The genetic code is degenerate. What does this mean?

A

This means that most amino acids can be encoded by several codons, as there are 64 possible combinations with only 20 amino acids.

35
Q

Two amino acids have only one codon. What are they?

A

Tryptophan (Trp) and methionine (Met)

36
Q

There are […] sense codons and […] nonsense (stop) codons.

A

61, 3

37
Q

The start codon, […], has the following sequence of nucleotides: […]

A

Met, AUG

38
Q

Explain the effect of wobble pairing in t-RNAs on amino acid coding.

A

This is the reason why there aren’t 61 amino acids despite there being 61 sense combinations. The t-RNA anticodon can read different nucleotides in its 5’ position, as it can have inosine, which can pair with A, C, or U.

39
Q

The glycine (GGC, GGU, GGG, GGA) anticodon is […]

A

GGC, GGU, GGA -> ICC
GGG -> CCC

40
Q

Inosine is a derivative of […]

A

Adenine

41
Q

How are okazaki fragments degraded?

A

By DNA polymerase 1

42
Q

How does the length of okazaki fragments compare in eukaryotes vs prokaryotes?

A

They are much longer in prokaryotes (thousands vs 100s of base pairs)

MIMM 211 (38 decks)

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