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Applied Biochemistry > DNA & RNA Replication (Exam III) > Flashcards

DNA & RNA Replication (Exam III) Flashcards

1
Q

DNA is ___ stranded molecule, while RNA is a _____ stranded molecule

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 this position)

A

Deoxyribose

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4
Q

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

A

Phosphate

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5
Q

What are the purines

A

Pure as Gold

Adenine and Guanine

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6
Q

What are the pyramidines

A

Cut the Pie

Cytosine Uracil and Thymine

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7
Q

Structure of the purines

A

You would rather have more gold than pie

Double ring structure

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8
Q

Describe the structure of the pyrimidines

A

You would rather have more gold than pie

Single ring structure

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9
Q

Difference between uracil and thymine

A

Uracil - RNA
Thymine - DNA

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10
Q

The steps of the staircase when referring to the double helix structure of a DNA molecule are the

A

Bases

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11
Q

What is Chargaff’s rule

A

A=T and G=C

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12
Q

How many bonds form between adenine and thymine?

How many bonds form between guanine and cytosine?

A

AT = 2
GC = 3

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13
Q

What base pairing is more stable and why

A

G-C because they have an extra hydrogen bond

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14
Q

What controls the expression of prokaryotic transcription

A

Promoters and 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

Co-linear

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18
Q

When we refer to the RNA copy as being “co-linear” what we mean is

A

It’s an identical copy of the DNA transcript

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19
Q

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

A

Coding regions or exons

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20
Q

The regions that separate exons that do not get coded

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 a linear fashion and then the introns are removed by a process called

A

Splicing

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23
Q

In prokaryotic organism the RNA copy made from the DNA copy is a ______ copy that is ready for _____

In eukaryotic organisms, everything in the DNA gets copied to the RNA but ____ and ____ must take place to give rise to the mature RNA, which is transported out of the nucleus for use as the template for protein synthesis

A

Exact; protein synthesis
Splicing; subsequent modifications

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24
Q

Translation

A

Protein synthesis

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25
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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26
Q

Alternative splicing gives rise to a possibility of

A

Numerous different proteins from the same transcript

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27
Q

A region of DNA that encodes a protein and includes all of the regulatory elements included in it to control its expression

A

Gene

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28
Q

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

A

Condensed

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29
Q

Prokaryotic organisms condense their DNA by a set of ____ and _____ into back and forth loops

A

Polyamines
Proteins

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30
Q

In eukaryotes, DNA is first condensed into ____

A

Nucleosomes

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31
Q

Each nucleosomes involves around ____ bp of DNA and a set of ____

A

200
Core histone proteins

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32
Q

As DNA is packaged, it exists in what two forms

A

Euchromatin
Heterochromatin

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33
Q

The slightly more relaxed form of chromatin and transcriptionally active

A

Euchromatin

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34
Q

Highly condensed and generally not transcriptionally active form of chromatin

A

Heterochromatin

35
Q

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

A

Solenoids
Supersolenoids
Chromosomes

36
Q

DNA is broken up into fragments called

A

Chromosomes

37
Q

In humans we have 22 chromosomes that are referred to as ____ and each exists as a ____

A

Autosomes
Pair

38
Q

The gametes contain ____ copy of a chromosome

A

One

39
Q

How many protein coding genes in the human genome

A

20,000-25,000

40
Q

The average gene is about _____ bp long, contains about _____ exons and a coding sequence of about ____ bp

A

27,000
9
1340

41
Q

Estimated that on average each gene gives rise to about ___ isoforms, splice variants, etc.

A

8

42
Q

The human genome contains around ____ bp

A

3.2 billion

43
Q

It only takes a single bp change to cause

A

Disease

44
Q

Allie and Abbie have a difference of about how many base pairs

A

1-2 million

45
Q

Abbie and Chelsea have a difference of about how many base pairs

A

Six million

46
Q

Because of the antiparallel orientation of the strains and the fact that the strands are complementary, each strand can

A

Act as template for synthesis of new DNA strand

47
Q

When is DNA replicated

A

During S phase of cell cycle

48
Q

Central dogma of genetic information flow

A

DNA ————————> RNA ——————> Protein
Transcription Translation

49
Q

The first and foremost important principle of DNA replication is that its all driven by

A

base-pairing

50
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

51
Q

Molecule that catalyzes the stepwise addition of deoxyribonucleotide-triphosphate to the 3’ OH end fo a polynucleotide chain

A

DNA polymerase

52
Q

The reason the stepwise addition of a deoxyribonucleotide-triphosphate to the 3’ hydroxyl end of the polynucleotide chain is important is because the addition of the next base is driven by the favorable free energy that is released from the:

A

hydrolysis of the triphosphate molecule to a mono-phosphate phosphodiester bond

53
Q

DNA synthesis on the strand that is being made ALWAYS proceeds

A

5’ ——> 3’

54
Q

For DNA synthesis to occur you need (3)

A
  1. Deoxynucleotide triphosphate
  2. A region of double strand of DNA
  3. A free 3’ hydroxyl group
55
Q

DNA polymerase synthesizes the new strand in what direction

A

5’ ——> 3’

56
Q

DNA polymerase requires a _____ and a strand to build off of with a _____

A

Template strand
Free 3’ OH

57
Q

DNA polymerase contains a _______ polymerase activity and a _______ exonuclease activity

A

5’ to 3’
3’ to 5’

58
Q

The free 3’ hydroxyl group on the deoxyribose will form a ____ bond with the next nucleoside-triphosphate that is going to put there

A

Phoshphodietser

59
Q

The high fidelity of DNA Replication requires

A

Proofreading mechanisms

60
Q

DNA polymerases are a ________ enzyme that remove their own polymerization errors

A

Self-correcting

61
Q

DNA polymerase have a 3’ to 5’ _______ activity during DNA synthesis

A

Exonuclease proofreading

62
Q

If an incorrect base gets put in it creates a ____ that gets removed by the 3’ to 5’ exonuclease, 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 as replication

A

A-T rich regions

64
Q

It is important that the origins of replication are A-T rich because

A

They have weaker bonds making them easier to separate

65
Q

Origins of replication from a

A

Replication fork

66
Q

Daughter strand that is synthesized continuously towards the replication fork

A

Leading strand

67
Q

Daughter strand that is synthesized discontinuously away from replication fork

A

Lagging strand

68
Q

DNA synthesis begins following DNA unwinding and _____ synthesis at replication origins

A

RNA primer

69
Q

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

A

A double-stranded template with free 3’ hydroxyl group

70
Q

What strand do Okazaki fragments get made on

A

Lagging strand

71
Q

Begins with synthesis of short RNA primer by a special nucleotide-polymerizing enzyme

A

Lagging strand DNA synthesis

72
Q

Enzyme that makes the short RNA primers made 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

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

Responsible for joining Okazaki fragments together

A

DNA ligase (doesn’t actually operate in the replication fork)

77
Q

Lagging strand synthesis is:

A

Energetically costly (using a lot of ATP and ATP hydrolysis)

78
Q

Only changes accumulated in the ____ can be inherited

A

Gametes

79
Q

Protein that uses the hydrolysis of ATP to change the shape of the protein, and moves rapidly along the DAN strand, if encountering a region of double stranded helix itch will pry the helix apart

A

DNA helicase

80
Q

Energetically when you have two single stranded regions of DNA they will want to rapidly rejoin. A protein that doesn’t unwind the double helix itself, but aids helicase by stabilizing this unwound helix is

A

Single-strand DNA binding proteins (helix-destabilizing proteins)

81
Q

Anchoring protein that are responsible for holding the DNA polymerase to the replication fork and allow it to move along as the DNA unwinds

A

Sliding clamp /sliding ring

82
Q

Premature aging disease with respect to DNA replication process

A

Werner syndrome

83
Q

Individuals with Werners syndrome either have:

A

Cells that divide ore slowly or stop dividing

84
Q

Werner’s syndrome is caused by a mutation in the

A

DNA helicase

Applied Biochemistry (18 decks)

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