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(Biology 211) Cellular Biology > Chapter 14 - DNA structute And Function > Flashcards

Chapter 14 - DNA structute And Function Flashcards

1
Q

What is the definition of a gene

A

A sequence of DNA that codes for a functional protein

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2
Q

The human genome contains between how many functional genes?

A

21-25 thousand

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3
Q

What did Erwin chargaff discover about the amount of the nucleotides?

A

Adenine equaled thymine and cytosine equaled guanine, ect

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4
Q

What is the chargaffs rule?

A

Adenine = thymine and guanine = cytosine

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5
Q

What are the monomers that build DNA?

A

Nucleotides

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6
Q

What is central in the nucleotide structure?

A

A 5 carbon sugar (Pentose)

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7
Q

What is at the 1’ position on the nucleotide?

A

One of the five possible nitrogenous basses is attached to

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8
Q

What is at the 2’ position on the nucleotide?

A

A -OH group attached for DNA, and a -H for RNA

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9
Q

What is at the 3’ position for nucleotides?

A

A -OH group that forms a phosphodiester bond with the phosphate group of the adjacent nucleotide

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10
Q

At the 5’ end of the nucleotide what is attached?

A

The phosphate group

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11
Q

What is a nucleotide made up of all together?

A

A Pentose sugar, a nitrogenous base, and a phosphate group

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12
Q

What are the 2 overall groups of the nitrogenous basses and what are their structures? What nitrogenous bases are present in each group?

A

Purines (double ringed structures)
- Adenine
- Guanine

Pyrimidines (single ringed structure)
-Cytosine
-thymine(DNA ONLY)
-Uracil(RNA ONLY)

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13
Q

Do purines pair with pyramidines, or purines with purines and pyramidines with pyramidines

A

Purines with pyramidines

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14
Q

What does the chargaffs rule state are the pairings for DNA and RNA?

A

DNA:
Adenine = Thymine
Guanine = Cytosine

RNA:
Adenine = Uracil
Cytosine = Guanine

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15
Q

How are base pairs formed? Chemically?

A

Nitrogenous basses extend from the 1’ carbon of the Pentose sugar and hydrogen bond with another nucleotide

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16
Q

Nucleotides combine with each other through what bond? And where chemically?

A

Phosphodiester bonds, 1 water linkage with the 5’ carbon of one nucleotide and another ester linkage with the hydroxyl group of the 3’ carbon of the next nucleotide

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17
Q

Who determined the structure of DNA?

A

James Watson and Francis Crick

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18
Q

It was determined that the DNA molecule was composed of what chemically on the inside of the backbone sugar?

A

2 strands of nucleotides held together by hydrogen bonds between the nitrogenous basses of the nucleotides thus taking the form of a double helix

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19
Q

In the ends of the 2 nitrogenous basses are what molecule?

A

The sugar-phosphate backbone

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20
Q

How many hydrogen bonds are in between A and T vs C and G?

A

A and T has 2 hydrogen bonds while C and G has 3

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21
Q

What are larger pyramidines or purines?

A

Purines are larger than the pyramidines

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22
Q

What does each end of the sugar phosphate backbone always end with?

A

A phosphate attached to the 5’ carbon of the sugar, and the opposite end of the same sugar-phosphate backbone therefore must end at the -OH of the 3’ end

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23
Q

What charge does DNA have?

A

Negative

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24
Q

How does the bands appear in gel electrophoresis?

A

As the DNA moves through the gel the smaller fragments move through the gel faster and appear as bands

Larger amounts of DNA have denser bands

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25
Q

Why are stains used to visualize the bands?

A

Because they are sensitive to UV light

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26
Q

Where is prokaryotic DNA found? In what form?

A

A single circular chromosome which is found in the nucleoid region of the cell?

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27
Q

When are chromosomes at their most compact stage in eukaryotes?

A

Metaphase

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28
Q

Interphase eukaryotic chromosomes contain what 2 distinct regions? Describe each one

A

Heterochromatin - is tightly compact and does not contain expressed genes and is found around the centromeres and telomeres (ends of the chromosome)

Euchromatin - contains genes that are transcribed (copied and sent to the ribosome for translation of proteins) with DNA that are not further compacted than regular nucleosomes

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29
Q

When are the 2 strands of the double helix seperated? And how come?

A

In the copying process since the hydrogen bonds are weak, and each strand can act as a template from which a new complementary strand can be copied

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30
Q

After the copying of a new double helix what is each strand made of?

A

One strand is the old strand and the other is the new strand

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31
Q

How long does prokaryotic DNA replication take in E. Coli. How does the process go? What is the rate of nucleotide production?

A

It takes about 42 minutes and starts at a single site on the circular chromosome and proceeds around the circle in both directions until two new circular chromosomes are produced, about 1000 nucleotides are built per second

32
Q

What is the key enzyme in prokaryotic DNA replication? How does it function?

A

It is DNA polymerase which adds nucleotides one by one to the growing “new” strand by matching nucleotides to its complement which was the nucleotide on the “old” strand

33
Q

The energy for these endergonic reactions in DNA replication comes from what energy source?

A

Nucleotide triphosphate (ATP, GTP, TTP, CTP, NTP)

34
Q

How does the energy release from the nucleotide triphosphate make the growing chains of nucleotides?

A

When the phosphate bond holding the third phosphate to the nucleotide is broken the energy released is used to form the phosphodiester bonds between the incoming nucleotides of the growing chain

35
Q

Briefly what is each DNA polymerase known for?

A

DNA pol 1 is an accessory protein important in DNA polymerization, 2 is required for DNA repairs and 3 is an enzyme necessary for adding new nucleotides onto the growing chain

36
Q

What is the site called where DNA replication starts? How long is it and what is it rich in?

A

It’s called the origins of replication and it is about 245 base pairs long and is rich in AT sequences

37
Q

What is helicase? What does it do?

A

It’s an enzyme that unwinds the DNA by breaking the hydrogen bonds between the nitrogenous base pairs, using an ATP

38
Q

What shape does helicase make the strands into?

A

A Y-shaped replication fork

39
Q

What do single stranded binding proteins do?

A

They coat the single strands of DNA near the replication fork to prevent the single strands from winding back into a double helix

40
Q

What is the only place DNA polymerase 3 can add nucleotides and what does it need?

A

It can only add nucleotides to the 3’ end of the new strand that is in a 5’ to 3’ direction, it needs a free 3’ -OH group to add these nucleotides

41
Q

What does RNA primase do? Also called primer

A

It starts the process by providing a 3’ -OH group to the newly synthesized strand

42
Q

What does topoisomerase do?

A

Prevents overwinding of the DNA ahead of the replication fork

43
Q

Since the double helix is antiparallel what does this mean for the strand orientation?

A

The two templates have opposing orientation, one from 5’ to 3’ and the other from 3’ to 5’

44
Q

Which new strand can add nucleotides to the replication fork? And what is it called?

A

Only 1 new strand can do this, this is the one complementary to the 3’ to 5’ parental strand which can add new nucleotides in the 5’ to 3’ direction toward the replication fork, it’s called the leading strand

45
Q

What does this mean for the other strand that is not the leading strand? What does it become known as?

A

The other strand must add new nucleotides away from the replication fork and then DNA polymerase 1 pieces them together far away from the replication fork, this forms fragments called Okazaki fragments

46
Q

What is this strand with the Okazaki fragments called?

A

The lagging strand

47
Q

What holds DNA polymerase 3 in place?

A

A protein called the sliding clamp

48
Q

What happens to the RNA primers when done?

A

They are removed and replaced by DNA, filling the gaps (done by endonuclease activity)

49
Q

Briefly go over the process of primers removal

A

Primers are removed by DNA polymerase 1 and new DNA is sealed to the rest of the DNA by phosphodiester bonds by the enzyme ligase

50
Q

In summary go over the 9 steps of what happens in prokaryotic DNA replication

A

1- DNA unwinds at the origin of replication

2- helicase opens up the DNA forming replication forks, these extend bidirectionally

3- single stranded binding proteins cots the DNA around the replication fork preventing unwinding, and topoisomerase binds at the region ahead of the replication fork preventing supercooling

4- primase synthesizes RNA primers complementary to the DNA strand

5- DNA polymerase 3 starts adding nucleotides to the 3’ -OH end of the primers

6- elongation of both the lagging and leading strands continues

7- RNA primers are removed by endonuclease activity

8- gaps are filled by DNA polymerase-1

9- the gap between the two DNA fragments are sealed by DNA ligase which helps in the formation of phosphodiester bonds

51
Q

How many origins of replication across the human genome is there?

A

100thousand

52
Q

What is the rate of replication in nucleotides in the eukaryotic genome?

A

About 100 nucleotides per second

53
Q

How many DNA polymerases are known in eukaryotic cells? How many play roles in replication? What are they called?

A

14, 5 of which play roles in replication (Alpha, beta, gamma, epsilon, and delta)

54
Q

What accounts for the slower pace of replication of DNA in eukaryotes compared to prokaryotes?

A

The removal of the histones from the nucleosomes

55
Q

Adding nucleotides to the new strands in strand elongation is done by what dna polymerases in eukaryotes?

A

Alpha, delta, and epsilon

56
Q

What holds the DNA polymerase complex in place in eukaryotes?

A

A sliding clamp protein called proliferating cell nuclear antigen (PCNA)

57
Q

When the replication fork reaches the end of the linear chromosome there is no way to replace the primer on the 5’ end of the lagging strand, what does this cause?

A

The DNA at the ends of the chromosomes thus remain unpaired and over time (aging) these ends can get progressively shorter

58
Q

These shortening ends in eukaryotes are called…

A

Telomeres

59
Q

In humans what six base sequence is repeated up to 1000 times, and why?

A

TTAGGG, this protects the genes from getting deleted as cells divide

60
Q

The enzyme telomerase contains an RNA template that allows what?

A

Nucleotides to be added to the 3’ end of the DNA strand

61
Q

Where are telomerase’s active and not in eukaryotes?

A

Active in germ cell lines and stem cells, but not in regular somatic cells

62
Q

Somatic cells in eukaryotes do not make telomerase, therefore as cells undergo cell division what happens?

A

Their telomeres shorten

63
Q

Cancerous cells can proliferate uncontrollably and migrate to different parts of body in a process called

A

Metasasis

64
Q

Cancerous cells has how much in terms of what in telomeres and telomerase?

A

They have shortened telomeres and telomerase is active in these cells

65
Q

What ability does DNA polymerase have for making correct sequences in DNA replication? What happens

A

They have the ability to proofread by checking for correct base pairing during replication and if the incorrect base is about to be added the phosphodiester bond can be cut and the wrong base is released

66
Q

What happens in mismatch repair?

A

Enzymes recognize mismatched bases and corrects them after replication is complete

67
Q

When does nucleotide excision repair occur? What is the process?

A

It is used to removed damaged bases rather than mismatched ones, DNA polymerases cut the phosphodiester bonds and a new nucleotide is added by DNA ligase, this occurs when UV exposure causes damage by forming pyrimidines dimers

68
Q

What are the 2 categories of mutations?

A

Induced - by chemicals, UV, X rays, environmental agents

Spontaneous - natural reactions

69
Q

What are point mutations?

A

When a single base pair is affected, usually substitutions

70
Q

When do transition substitutions occur?

A

When like nucleotides are wrong

71
Q

When do transversion substitutions occur?

A

When a different nucleotide is wrong (purine for pyrimidine)

72
Q

When do silent mutations occur?

A

When the third base of the codon is substituted which still results in the correct amino acid being translated

73
Q

What do missense mutations result in?

A

The wrong amino acid being translayed

74
Q

What do nonsense mutations result in?

A

A stop codon being translated and an incomplete protein

75
Q

What causes a frameshift mutation?

A

Insertions or deletions of nucleotides which shift the reading frame and the production of a nonfunctional protein

(Biology 211) Cellular Biology (12 decks)

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