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Applied Biochem > DNA And RNA Replication- Exam III > Flashcards

DNA And RNA Replication- Exam III Flashcards

1
Q

DNA is ____ stranded and RNA is ____ stranded.

A

Double; single

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2
Q

If a 2’ hydroxyl group is present on the pentose sugar, the molecule is:

A

Ribose

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3
Q

If the 2’ hydroxyl group is absent on the pentose sugar (only a hydrogen in that position)

A

Deoxyribose

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4
Q

High energy ____ molecules are attached to the 5’ carbon of the pentose in both DNA and RNA

A

Phosphate

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5
Q

What are the purines?

A

A and G (pure as gold)

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6
Q

What are the pyramidines?

A

CUT (Cut the py)

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7
Q

Describe the structure of the purines

A

Double ring structure

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8
Q

Describe the structure of the pyrimidines

A

Single ring structure

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9
Q

What is the difference between uracil and thymine?

A

Uracil in RNA
Thymine in DNA

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10
Q

The steps of the staircase when referring to the double helix DNA molecules are:

A

The bases

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11
Q

What is chargaff’s rule?

A

A base pairs with T

G base pairs with T

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12
Q

How many bonds form between adenine and thymine? How many bonds form between cytosine and Guanine?

A

2 on A and T
3 on G and C

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13
Q

What base pairs are more stable and why?

A

G and C because they have an extra hydrogen bond

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14
Q

What control the expression of prokaryotic transcription?

A

Promotors & operons

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15
Q

In prokaryotic organisms the DNA is organized into a ___ or ____ fashion.

A

Linear or contiguous

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16
Q

In prokaryotic gene transcription, the RNA copy made is:

A

Ready for use in translation

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17
Q

As DNA transcription proceeds in a prokaryotic organism, the RNA transcript is described as:

A

Colinear

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18
Q

When we refer to the RNA copy as being colinear, what we mean is:

A

Identical copy of the DNA transcript

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19
Q

In eukaryotic organisms the DNA is broke up into ____ that will give rise to the protein sequence.

A

Coding regions or exons

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20
Q

Regions that do not get coded and separate exons

A

Introns

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21
Q

Regions at the 5’ and 3’ ends that do not encode proteins:

A

Untranslated regions (UTRs)

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22
Q

In eukaryotic organisms, one strand of the DNA is first copied in linear fashion and then then the introns are removed by a process called:

A

Splicing

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23
Q

In prokaryotic organisms, the RNA copy that gets made from the DNA is ready for ________. However, in eukaryotic organism, everything from the DNA gets copied into the RNA but ______ and ______ must take place to give rise to the mature mRNA which is transported out of the nucleus for use as the template for protein synthesis.

A

Protein synthesis; splicing and subsequent modification

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24
Q

In eukaryotic organisms, primary transcripts are often spliced in multiple combinations of exons. This process is called:

A

Alternative splicing

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25
Q

Alternative splicing gives rise to the possibility of ______ from the same transcript.

A

Numerous different proteins

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26
Q

The region of DNA that will encode a protein that includes all the regulatory elements to control its expression

A

Gene

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27
Q

In order to fit inside the cell or nucleus, linear DNA must be:

A

Condensed

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28
Q

in prokaryotic organisms, the DNA is condensed by a set of _____ and _____ in back and forth loops

A

Polyamines and proteins

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29
Q

In eukaryotes, DNA is first condensed into _____.

A

Nucleosome

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30
Q

Each nucleosome involves around _____ BP of DNA and a set of _____

A

200BP and a set of core histone proteins

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31
Q

Chromatin exists in two forms:

A

Euchromatin, and heterochormatin

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32
Q

Slightly more relaxed, transcriptionally active form of DNA

A

Euchromatin

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33
Q

Highly condensed and generally not transcriptionally active form of chromatin

A

Heterochromatin

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34
Q

Chromatin can be further condensed into ___ and _____ ultimately into _________ by function specific sets of proteins.

A

Solenoids; supersolenoids; chromosomes

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35
Q

DNA is broken up into fragments called:

A

Chromsomes

36
Q

In humans we have 22 chromosomes called _____ and each exist as a _____.

A

Autosomes ; pair

37
Q

The gametes contain _____ copy of a chromosomes

A

1

38
Q

What is the number of protein coding genes in the human genome?

A

20,000-25,000

39
Q

The average gene is about ______ BP long, and contains about ____ exons and a coding sequence of about ______ BP.

A

27,000
9
1340

40
Q

On average each gene gives rise to about ____ isoforms or splice variants.

A

8

41
Q

Human genome contains about _____ BP

A

~3.2 billion

42
Q

It only takes a single BP change to cause:

A

Disease

43
Q

Allie and Annie have difference of about ______ BP

A

1-2 million

44
Q

Annie and Jordan have a difference of about _____ BP

A

6 million

45
Q

Becuase the antiparallel orientation of the strands, and the fact that the strands are complementary, each strand can:

A

act as as template for synthesis of new DNA Strand

46
Q

When is DNA replicated?

A

S phase of cell cycle

47
Q

Central dogma of genetic information flow

A

DNA to RNA (transcription)
RNA to protein (translation)

48
Q

The first and foremost principle of DNA replication is that it is all driven by:

A

Base pairing

49
Q

You have a strand of DNA that serves as a template, and the nucleotide bases that make up that strand will dictate:

A

What base gets incorporated at that position in the strand being made

50
Q

The molecule that catalyzes the stepwise addition of deoxyribonucelotide-triphosphate addition to the 3’ OH end of a polynucleotide chain

A

DNA polymerase

51
Q

The reason the stepwise addition of a deoxyribonucelotide-triphosphate to the 3’ hydroxyl end of a polynucleotide chain is important is because that addition of the next base is driven by:

A

the favorable free energy that is released from the hydrolysis of the triphosphate molecule to a mono phosphate phosphodiester bond.

52
Q

DNA synthesis on the strand that is being made, always proceeds:

A

5’—> 3’

53
Q

For DNA synthesis to occur, you need a region of double stranded DNA and a:

A

Free 3’ hydroxyl group

54
Q

DNA polymerase synthesizes the new strand in what direction?

A

5’ - 3’

55
Q

DNA polymerase requires a _______ and a strand to build off of with a ______.

A

Template strand; free 3’ OH group

56
Q

DNA polymerase contains _____ polymerase activity and a ______ exonuclease activity

A

5’-3’ polymerase activity

3’-5’ exonuclease activity

57
Q

The free 3’ hydroxyl group of the deoxyribose will form a _____ bond with the next deoxyribose nucleoside triphosphate

A

Phosphodiester bond

58
Q

The high fidelity of DNA replication requires:

A

Proofreading mechanism

59
Q

The High fidelity refers to:

A

A pairing to T and C to G correctly without error

60
Q

DNA polymerase are a _____ enzyme that remove their own polymerization errors

A

Self-correcting enzyme

61
Q

DNA polymerase have a 3’-5’ ______ activity during DNA synthesis

A

Exonuclease activity

62
Q

If the incorrect base gets put in, it will create a ____ that gets removed by the 3’-5’ exonuclease activity which will leave a _____ to basepair with the correct base.

A

Bulge, free 3’ hydroxyl group

63
Q

DNA synthesis starts at ____ regions known as origins of replication.

A

AT rich

64
Q

It’s important that the origins of replication are AT rich because:

A

They have weaker bonds making them easier to separate

65
Q

Origins of replication form:

A

Replication forks

66
Q

Daughter strand that is synthesized continuously, toward the replication fork

A

Leading strand

67
Q

Daughter strand that is synthesized discontinuously, away from the replication fork

A

Lagging strand

68
Q

DNA synthesis begins following DNA ____ and RNA _____ at replication origins.

A

Unwinding and RNA primer Synthesis

69
Q

The RNA primers that come into the newly opened up area of double stranded DNA provide:

A

A double stranded template w free 3’ hydroxyl group

70
Q

What strand do Okazaki fragments get made on:

A

Lagging strand

71
Q

begins with synthesis ion a short RNA primer by a special nucleotide-polymerizing enzyme

A

The lagging strand of DNA synthesis

72
Q

The enzyme that creates the short RNA primers made up on the lagging strand using DNA as a template

A

DNA primase

73
Q

Unlike DNA polymerase, the DNA primase __________ by joining two nucleoside triphosphates together

A

Can start a new polynucleotide chain

74
Q

The primase synthesizes a short polynucleotide in the 5’ to 3’ direction and then stops, making the 3’ end of the primer available for the ________ to produce the Okazaki fragment.

A

DNA polymerase

75
Q

What is responsible for moving the RNA primers (about 10 nucleotides in length)

A

5’ to 3’ exonuclease activity of DNA polymerase

76
Q

What joins the Okazaki fragments together?

A

DNA ligase

77
Q

Explain the energy of the lagging strand

A

Energetically costly

78
Q

THe DNA ligase uses _____ for energy

A

ATP hydrolysis

79
Q

Only changes accumulated in the _____ can be inherited.

A

Gametes

80
Q

A protein that uses the hydrolysis of ATP to change the shape of the protein and move rapidly along the DNA strand and if encountering a region of double stranded helix, it will pry the helix apart

A

DNA helicase

81
Q

Single Strand DNA binding protein bind to the exposed strand of DNA and aid the helicase by:

A

Stabilizing the unwound helix (to avoid them from repairing together)

82
Q

Single strand DNA binding proteins can also be referred to as:

A

Helix-destabilizing proteins

83
Q

There are some anchoring proteins that are responsible for holding the DNA polymerase to the replication fork and allow it to move along as the DNA unwinds.

A

DNA sliding clamp/ sliding ring

84
Q

DNA ligase works

A

Distally from all the other molecules

85
Q

Premature aging disease with respect to DNA replication

A

Werner syndrome

86
Q

Individuals with Werner’s syndrome cells either:

A

Divide more slowly or stop dividing at all

87
Q

Werner syndrome is caused by a mutation in the:

A

DNA Helicase

Applied Biochem (18 decks)

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