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MCAT Biochemistry > Chapter 6: DNA and Biotechnology > Flashcards

Chapter 6: DNA and Biotechnology Flashcards

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MCAT flashcards
1
Q

____________ are composed of a five-carbon sugar (pentose) bonded to a nitrogenous base.

A

nucleoside

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2
Q

How are nucleosides formed?

A

By covalently linking the base to the C-1’ of the sugar

carbon atoms in the sugar are labeled with a prime symbol

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3
Q

____________ are formed when one or more phosphate groups are attached to C-5’ of a nucleoside.

A

nucleotides

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4
Q

Nucleic acids are classified according to the ________ they contain.

A

pentose

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5
Q

If the pentose is ________, the nucleic acid is RNA; if the pentose is ____________, then it is DNA.

A

ribose; deoxyribose

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6
Q

The backbone of DNA is composed of alternating sugar and phosphate groups. It determines the directionality of the DNA and is always read from ____ to ____.

A

5’ to 3’

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7
Q

A ________ group linkes the 3’ carbon of one sugar to the 5’ ________ group of the next incoming sugar in the chain.

A

phosphate, phosphate

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8
Q

Phosphates carry a ____________ charge, thus DNA and RNA have this charge.

A

negative

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9
Q

What are the two families of nucleotides?

A
  1. purines
  2. pyrimidines
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10
Q

Purines contain ____ rings in their structure.

A

two

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11
Q

____________ contain only one ring in their structure.

A

pyrimidines

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12
Q

What are the two purines?

A

adenine and guanine

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13
Q

What are the three pyrimidines?

A

cytosine, thymine, uracil

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14
Q

What are characteristics of aromatic compounds?

A
  1. Cyclic
  2. Planar
  3. Conjugated
  4. 4n + 2 pi electrons
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15
Q

What is Huckel’s rule?

A

4n + 2

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16
Q

____________ are ring structures that contain at least two different elements in the ring.

A

heterocycles

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17
Q

The double helix of most DNA is a right-handed helix, forming what is called ________.

A

B-DNA

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18
Q

Another form of DNA is called ________ for its zigzag appearance; it is a left-handed helix. A high ____-content or a high ____ concentration may contribute to the formation of this form of DNA.

A

Z; GC; salt

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19
Q

Denatured, ssDNA can be ____________ if the denaturing condition is slowly removed.

A

reannealed

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20
Q

If a solution of heat-denatured DNA is ____________, then the 2 complementary strands can become paired again.

A

slowly cooled

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21
Q

in PCR, a well-characterized ________ DNA (DNA with known sequences) is added to a mixture of target DNA sequences.

A

probe

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22
Q

When probe DNA binds to target DNA sequences, this may provide evidence of the presence of a gene of interest. This is called ________________.

A

hybridization

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23
Q

The DNA that makes up a chromosome is wound around a group of small basic proteins called ____________, forming ____________.

A

histones; chromatin

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24
Q

2 copies each of the histone proteins form a histone core and about 200 base pairs of DNA are wrapped around this protein complex, forming a ____________.

A

nucleosome

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25
Q

What do nucleosomes accomplish?

A

They create a much more organized and complicated DNA.

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26
Q

Histones are one example of ____________ (proteins that associate with DNA). Most others are acid-soluble and stimualte processes like transcription.

A

nucleoproteins

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27
Q

A small percentage of the chromatin remains compacted during interphase and is referred to as ________________.

A

heterochromatin

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28
Q

Heterochromatin appears ________ under light microscopy and is transcriptionally ____________.

A

dark; silent

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29
Q

Heterochromatin often consists of DNA with what?

A

Highly repetitive sequences

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30
Q

Dispersed chromatin is called ____________.

A

euchromatin

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31
Q

Euchromatin appears ________ under light microscopy and contains genetically ________ DNA.

A

light; active

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32
Q

DNA replication cannot extend all the way to the end of a chromosome. What does this result in?

A

losing sequences and information with each round of replication

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33
Q

Since DNA replication cannot extent to the end of the chromosome, cells form a ____________, which is a simple repeating unit at the end of the DNA.

A

telomere

TTAGGG

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34
Q

Some of the telomere sequence is lost in each round of replication and can be replaced by the enzyme ____________.

A

telomerase

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35
Q

Telomerase is more highly expressed in which cells?

A

rapidly dividing cells

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36
Q

____________ are a region of DNA found in the center of chromosomes.

A

centromeres

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37
Q

Centromeres are composed of ____________, which is in turn composed of tandem repeat sequences that alsoc contain high ____-content.

A

heterochromatin; GC

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38
Q

During cell division, the two sister chromatids can therefore remain connected at the centromere until ____________ separate the chromatids during ____________.

A

microtubules; anaphase

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39
Q

The ____________ or ____________ ________ is a set of specialized proteins that assist the DNA polymerases.

A

replisome, replication complex

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40
Q

To begin the process of replication, DNA unwinds at points called ________ of ____________.

A

origins of replication

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41
Q

The generation of new DNA proceeds in both directions, creating ____________ ________ on both sides of the origin.

A

replication forks

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42
Q

The bacterial chromosome is a closed, double-stranded circular DNA molecule with a ________ origin of replication. Thus there are ____ replication forks that move away from each other inopposite directions around the circle, until they meet and produce two identical circular molecules of DNA.

A

single; two

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43
Q

As the replication forks move toward each other and ________ ____________ are created, the chromatids will remain connected at the ____________.

A

sister chromatids; centromere

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44
Q

____________ is the enzyme responsible for unwinding the DNA, generating two single-stranded template strands ahead of the polymerase.

A

Helicase

45
Q

Unpaired DNA strands are very sticky and the free purines/pyrimidines try to seek each other out. Thus, proteins are therefore required to hold the strands apart: ________-____________ ____-________ proteins will bind to the unraveled strand, preventing both the reassociation of the DNA strands and degradation of DNA by ____________.

A

single-stranded DNA-binding; nucleases

46
Q

As the helicase unwinds the DNA, it causes positive ____________ that strains the DNA helix.

A

supercoiling

47
Q

Supercoiling is a wrapping of DNA on ________ as its helical structure is pushed ever further toward the telomeres during replication.

A

itself

like a telephone cord becoming tangled on itself

48
Q

To alleviate this torsional stress and reduce the risk of strand breakage, ____ ________________ introduce negative supercoils.

A

DNA topoisomerases

49
Q

How do DNA topoisomerases work?

A

They work ahead of helicase, nicking one or both strands, allowing relaxation of the torsional pressure, and then resealing the cut strands

50
Q

DNA ____________ are responsible for reading the DNA template, or parental strand, and synthesizing the new daughter strand.

A

polymerase

51
Q

The ________ strand in each replication fork is the strand that is copied in a continuous fashion. It is read ____ to ____ and synthesized in a ____ to ____ manner.

A

leading; 3’ to 5’; 5’ to 3’

52
Q

The ____________ strand is the strand that is copied in a direction opposite the direction of the replication fork.

A

lagging

53
Q

Because DNA polymerase can only synthesize in the 5’ to 3’ direction from a 3’ to 5’ template, small strands called ____________ ____________ are protduced from the lagging strand.

A

Okazaki fragments

54
Q

Each time DNA polymerase completes an Okazaki fragment, what happens?

A

It turns around to find another gap that needs to be filled in

55
Q

DNA cannot be synthesized de novo, it needs another molecule to “hook onto.” Thus, ________ synthesizes a short ____ ________ (roughly 10 nucleotides) in the 5’ to 3’ direction to start replication on each strand.

A

primase; RNA primer

56
Q

Primers are constantly being added to the lagging strand, why?

A

each Okazaki fragment must start with a new primer

57
Q

DNA ____________ ____ (prokaryotes) or DNA ____________ ____, ____, ____ (eukaryotes) then synthesize the daughter strands of DNA in the 5’ to 3’ manner.

A

polymerase III, polymerases alpha, delta, and epsilon

58
Q

What are the incoming nucleotides for DNA synthesis?

A

5’ deoxyribonucleotide triphosphates

59
Q

As each new phosphodiester bond is made, what is released?

A

A free pyrophosphate is released

60
Q

RNA primers must eventually be removed to maintain the genome’s integrity. This is accomplished by DNA ____________ ____ (prokaryotes) or ________ ____ (eukaryotes).

A

polymerase I; RNase H

61
Q

After the RNA primer is removed, DNA ____________ ____ (prokaryotes) or DNA ____________ ____ (eukaryotes) adds DNA nucleotides where the RNA primer had been.

A

polymerase I, polymerase delta

62
Q

DNA ________ seals the ends of the DNA molecules togehter to create one continuous strand of DNA, e.g. closes gaps between Okazaki fragments

A

ligase

63
Q

Mutated genes that cause cancer are termed ________.

A

oncogenes

64
Q

Before oncogenes are mutated, they are often referred to as ________-____________.

A

proto-oncogenes

65
Q

________ ________ genes, like p53 or Rb, encode proteins that inhibit the cell cycle or participate in DNA repair processes.

A

tumor suppressor

66
Q

They normally function to stop tumor progression, and are sometimes called ____________.

A

antioncogenes

67
Q

How does DNA polymerase discriminate between parent and daughter strands?

A

Looks at the level of methylation - template strand has existed in cell for a longer period of time, and is thus more heavily methylated

68
Q

DNA ligase lacks proofreading ability, thus what?

A

Likelihood of mutations is considerably higher than the leading strand

69
Q

UV light induces the formation of ____________ between adjacent ________ residues in DNA.

A

dimers; thymine

70
Q

Thymine dimers are eliminated from DNA by a ____________ ________ ________ (NER) mechanism, which is a cut-and-patch process.

A

nucleotide excision repair

71
Q

An ____________ ____________ then makes nicks in the phosphodiester backbone of the damaged strand on both sides of the thymine dimer and removes the defective oligonucleotide.

A

excision endonuclease

72
Q

The nick made by excision endonuclease is sealed by DNA ____________.

A

ligase

73
Q

Uracil should not be found in DNA molecules; if it is, ________ ____________ repair occurs.

A

base excision

74
Q

Once the incorrect base is recognized, it is removed by a ____________ enzyme.

A

glycosylase

75
Q

Once a base is removed by a glycosylase enzyme, it leaves behind an ________/____________ site, also called an ________ site.

A

apurinic/apyridiminic, abasic

76
Q

The abasic site is recognized by an ____ ____________ that removes the damaged sequence from the DNA.

A

AP endonuclease

77
Q

____________ DNA technology allows a DNA fragments from any source to be multiplied by either gene cloning or PCR.

A

recombinant

78
Q

DNA ____________ is a technique that can produce large amounts of a desired sequence.

A

cloning

79
Q

Cloning requires that the investigator ligate the DNA of interest into a piece of nuclei acid referred to as a ____________, forming a ________________ ____________.

A

vector; recombinant vector

80
Q

Vectors are usually what? What can they be transferred to?

A

Bacterial or viral plasmid; a host bacterium after insertion of the DNA of interest

81
Q

During cloning, bacteria re then grown in colonies, and then what? How?

A

A colony containing the recombinant vector is isolated; conferring antibiotic resitance to the vector so that you can kill off all the other ones without antibiotic resistance

82
Q

After cloning, the bacteria can be used for what?

A
  1. express the gene of interest
  2. lysed to reisolate the replicated recombinant vectors
83
Q

____________ enzymes are enzymes that recognize specific dsDNA sequences.

A

restriction

84
Q

Restriction enzymes are ____________, meaning that the 5’ to 3’ sequence of one strand is identical to the 5’ to 3’ sequence of the other strand.

A

palindromic

85
Q

Restriction enzymes are isolated from ____________, which are their natural source.

A

bacteria

86
Q

In bacteria, what do restriction enzymes do?

A

They selective cleave foreign DNA

87
Q

Some restriction enzymes produce ________ ________, yielding sticky ends on the fragments. The vector of choice can be cut with the same restriction enzyme, allowing what to happen?

A

sticky ends; allowing the fragments to be inserted directly into the vector

88
Q

DNA cloning can be used to produce DNA ____________ are large collections of known DNA sequences; in sum, these sequence could equate to the ____________ of an organism.

A

libraries; genome

89
Q

How are DNA libraries made?

A

DNA fragments are digested randomly and cloned into vectors

90
Q

Genomic libraries contain what?

A

Large fragments of DNA and include both coding and noncoding regions of the genome

91
Q

________ (complementary )libraries are constructed by reverse-transcribing processed mRNA.

A

cDNA

92
Q

cDNA lacks ____________ regions and only includes genes that are expressed in the tissue from which mRNA was isolated.

A

noncoding

93
Q

____________ is the joining of complementary base pair sequences.

A

hybridization

94
Q

PCR requires ________ that are complementary to the DNA that flanks the region of interest.

A

primers

95
Q

In addition to specific primers, what else does PCR need?

A
  1. nucleotides (dATP, dTTP, dCTP, dGTP)
  2. DNA polymerase
96
Q

Primers have high ____ content, as the additional hydrogen bonds in this region would confer stability.

A

GC

97
Q

PCR also needs ____ to melt DNA part.

A

heat

98
Q

The prferred gel for DNA electrophoresis is ____________ gel; the ____________ the DNA strand, the slower it will migrate.

A

agarose; longer

99
Q

Gel electrophoresis is often used while performing a ____________ blot, which is used to detect the presence and quantity of various DNA strands.

A

southern

100
Q

In a Southern blot, DNA is first cut by ____________ enzymes and then separated by gel electrophoresis.

A

restriction

101
Q

southern blot

After cutting by restriction enzymes, DNA fragments are transferred to a ____________ and their separation is retained.

A

membrane

102
Q

southern blot

Once DNA fragments are transferred to a membrane, the membrane is probed with many copies of a ________ sequence

A

ssDNA

103
Q

southern blot

The ________ binds to its complementary sequence and form ________.

A

probe; dsDNA

104
Q

Probes are labeled with ____________ or ____________ proteins, both of which can be used to indicate the presence of a desired sequence.

A

radioisotopes; indicator

105
Q

Gene ________ now offers potential cures for individuals with inherited diseases. BY transferring a ________ copy of the gene into the affected tissues, the pathology can be fixed.

A

therapy; normal

106
Q

________ mice are altered at their ________ line by introducing a cloned gene into fertilized ova or into embryonic stem cells.

A

transgenic; germ

107
Q

The cloned gene that is introduced to a fertilized ova / embryonic stem cell is referred to as a ____________.

A

transgene

108
Q

____________ mice have a gene that has been initially deleted.

A

knockout

109
Q

The resulting offspring is a ____________, meaning that it has patches of cells, including germ cells, derived from each of the 2 lineages.

A

chimera

MCAT Biochemistry (13 decks)

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