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Nucleic Acids > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

Nucleic acids are found in

A

nucleus and are acidic in nature

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2
Q

True or false: a nucleic acid is a monomer

A

False

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3
Q

The monomer units of a nucleic acid are

A

nucleotides

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4
Q

What are the two types of nucleic acids?

A

DNA: Deoxyribonucleic Acid and RNA: Ribonucleic Acid

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5
Q

DNA :
Found
Function
Transportation

A

Found within cell nucleus
– Storage and transfer of genetic information
– Passed from one cell to other during cell division

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6
Q

RNA:
Occurs where
Primary function

A

Occurs in all parts of cell

– Primary function is to synthesize the proteins

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7
Q

*The components of a nucleotide

A

– Pentose Sugar - Monosaccharide – Phosphate Group (PO43-)

– Heterocyclic Base

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8
Q

Pentose Sugars – Ribose (RNA) vs. 2-Deoxyribose (DNA)

A

Ribose is present in RNA and 2-deoxyribose is present in DNA
• Structural difference:
– a —OH group present on carbon 2’ in ribose – a —H atom in 2-deoxyribose
• RNA and DNA differ in the identity of the sugar unit in their nucleotides.

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9
Q

Nitrogen-Containing Heterocyclic Bases
Bases
Pyrimidine derivatives
Purine derivatives

A

There are a total five bases (four of them in most of DNA and RNAs)
• Three pyrimidine derivatives - thymine (T), cytosine (C), and uracil (U)
• Two purine derivatives - adenine (A) and guanine (G)
• Adenine (A), guanine (G), and cytosine (C) are found in both DNA and RNA.
• Uracil (U): found only in RNA
• Thymine (T) found only in DNA.

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10
Q

Phosphate

A

Phosphate - third component of a nucleotide is derived from phosphoric acid (H3PO4)
• Under cellular pH conditions, the phosphoric acid is fully dissociated to give a hydrogen phosphate ion (HPO42-)

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11
Q

*Nucleotide Formation

A

The formation of a nucleotide from sugar, base, and phosphate can be visualized as a 2-step process

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12
Q

*The pentose sugar and nitrogenous base react to form a

A

Nucleoside

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13
Q

*The Nucleoside reacts with a phosphate group to form a

A

Nucleotide

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14
Q

*Nucleoside

A

A compound formed from a five-carbon monosaccharide and a purimone or pyrimidine base derivative. – The N9 of a purine or N1 of a pyrimidine base is attached to C- 1’ position of sugar (Beta-confirmation) – N-glycosidic linkage
– It is a condensation reaction (H2O released)

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15
Q

*There are 8 nucleosides associated with nucleic acid chemistry.

A

– Four ribonucleosides– RNA

– Four deoxyribonucleosides – DNA

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16
Q

*Nomenclature of nucleoside formation

A

– For pyrimidine bases – suffix -idine is used (cytidine, thymidine, uridine)
– For Purine bases – suffix -osine is used (adenosine, guanosine)
– Prefix “-deoxy” is used to indicate deoxyribose present (example: deoxythymidine)

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17
Q

*Nucleotide Formation

A

Addition of a phosphate group to a nucleoside
– Attached to C5” position through a phosphate-ester bond
– Condensationreaction(H2Oreleased)
– Named by appending 5’-monophosphate to nucleoside name

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18
Q 
*Adenine DNA :
Abbreviation
Nucleoside
Nucleotide 
Abbreviation
A

Abbreviation: A
Nucleoside: Deoxyadenosine
Nucleotide: Deoxyadenosine 5’ monophosphate
Abbreviation: dAMP

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19
Q 
*Guanine DNA:
Abbreviation
Nucleoside
Nucleotide 
Abbreviation
A

Abbreviation: G
Nucleoside: Deoxyguanosine
Nucleotide : Deoxyguanosine 5’ monophosphate
Abbreviation: dGMP

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20
Q 
*Cytosine DNA:
Abbreviation
Nucleoside
Nucleotide 
Abbreviation
A

Abbreviation: C
Nucleoside: Deoxycytidine
Nucleotide: Deoxycytidine 5’ Monophosphate
Abbreviation: dCMP

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21
Q 
*Thymine DNA:
Abbreviation
Nucleoside
Nucleotide 
Abbreviation
A

Abbreviation: T
Nucleoside: deoxythymidine
Nucleotide: Deoxythymidine 5’ Monophosphate
Abbreviation: dTMP

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22
Q 
*Adenine RNA:
Abbreviation
Nucleoside
Nucleotide 
Abbreviation
A

Abbreviation: A
Nucleoside: Adenosine
Nucleotide: Adenosine 5’ Monophosphate
Abbreviation: AMP

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23
Q 
*Guanine RNA:
Abbreviation
Nucleoside
Nucleotide 
Abbreviation
A

Abbreviation: G
Nucleoside: Guanosine
Nucleotide: Guanosine 5’ Monophosphate
Abbreviation: GMP

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24
Q 
*Cytosine RNA:
Abbreviation
Nucleoside
Nucleotide 
Abbreviation
A

Abbreviation: C
Nucleoside: Cytidine
Nucleotide : Cytidine 5’ Monophosphate
Abbreviation : CMP

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25
Q 
*Uracil RNA:
Abbreviation
Nucleoside
Nucleotide 
Abbreviation
A

Abbreviation: U
Nucleoside: Uridine
Nucleotide: Uridine 5’ Monophosphate
Abbreviation: UMP

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26
Q

Sugar-phosphate groups are referred to as

A

nucleic acid backbone - Found in all nucleic acids

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27
Q

True or false: Sugars are different in DNA and RNA

A

True

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28
Q

ribonucleic acid (RNA)

A

a nucleotide polymer in which each of the monomers contains ribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or uracil

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29
Q

deoxyribonucleic acid (DNA)

A

a nucleotide polymer in which each of the monomers contains deoxyribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or thymine.

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30
Q

Primary Structure

A

Structure: Sequence of nucleotides in DNA or RNA
• Primary structure is due to changes in the bases
• Phosphodiester bond between 3’ and 5’ position
• 5’ end has free phosphate and 3’ end has a free OH group
• Sequence of bases read from 5’ to 3’

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31
Q

Comparison of the General Primary Structures of Nucleic Acids and Proteins

A

Backbone: -Phosphate-Sugar- Nucleic acids

• Backbone: -Peptide bonds - Proteins

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32
Q

the DNA Double Helix

A

Nucleic acids have secondary and tertiary structure
• The secondary structure involves two polynucleotide chains coiled around each other in a helical fashion
• The two polynucleotides run anti-parallel (opposite directions) to each other, i.e., 5’ - 3’ and 3’ - 5’
• The bases are located at the center and hydrogen bonded (A=T and GΞC) – # of H-bonds
• Base composition: %A = %T and %C = %G)
– Example: Human DNA contains 30% adenine, 30% thymine, 20% guanine and 20% cytosine

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33
Q

DNA Sequence:

A

the sequence of bases on one polynucleotide is complementary to the other polynucleotide

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34
Q

*true or false: Complementary bases are pairs of bases in a nucleic acid structure that can cavalently-bond to each other.

A

false - HYDROGEN BOND

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35
Q

*True or false: Complementary DNA strands are strands of DNA in a double helix with base pairing such that each base is located opposite to its complementary base

A

true

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36
Q

*Create a complimentary strand for:

5’-A-A-G-C-T-A-G-C-T-T-A-C-T-3’

A

Complementary strand of this sequence will be: 3’-T-T-C-G-A-T-C-G-A-A-T-G-A-5’

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37
Q

*A pyrimidine is always paired with a

A

purine

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38
Q

*true or false: A-T and G-C are called complementary bases

A

true

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39
Q

*Predict the sequence of bases in the DNA strand complementary to the single DNA strand shown below:
5’ A–A–T–G–C–A–G–C–T 3’

A

3’ T–T–A–C–G–T–C–G–A 5’

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40
Q

Replication:

A

Process by which DNA molecules produce exact duplicates of themselves, Old strands act as templates for the synthesis of new strands

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41
Q

DNA polymerase

A

checks the correct base pairing and catalyzes the formation of phosphodiester linkages

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42
Q

Replication:

true or false: The newly synthesized DNA has one new DNA strand and one old DNA strand

A

True

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43
Q

true or false:

DNA polymerase enzyme can only function in the 5’-to-3’ direction

A

true

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44
Q

true or false: The lagging strand grows in segments (Okazaki fragments) in the opposite direction

A

true

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45
Q

DNA ligase

A

connects the segments in replication

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46
Q

true or false: DNA replication one occurs in one site within a molecule (origin of replication)

A

false - occurs in many

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47
Q

true or false:

Multiple-site replication enables rapid DNA synthesis

A

true

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48
Q

Key Enzymes in Replication

A

DNA Helicase, Ligase and Polymerase

49
Q

Upon DNA replication the large DNA molecules interacts with histone proteins to fold long DNA molecules.

A

true

50
Q

The histone–DNA complexes are called chromosomes:

A

– A chromosome is about 15% by mass DNA and 85% by mass protein.
– Cells of different kinds of organisms have different numbers of chromosomes.
– Example: Number of chromosomes in a human cell 46, a mosquito 6, a frog 26, a dog 78, and a turkey 82

51
Q

True or false: Chromosomes occur in unmatched (homologous) pairs.

A

false- they are matched

52
Q

*Human chromosomes are present in…

A

the nucleus

53
Q

Differences Between RNA and DNA Molecules:

A

The sugar unit in the backbone of RNA is ribose; it is deoxyribose in DNA.
• The base thymine found in DNA is replaced by uracil in RNA
• RNA is a single-stranded molecule; DNA is double- stranded (double helix)
• RNA molecules are much smaller than DNA molecules, ranging from 75 nucleotides to a few thousand nucleotides

54
Q

Protein Synthesis

A

Protein synthesis involves RNA but is directly under the direction of DNA
• Proteins are responsible for the formation of skin, hair, enzymes, receptors, hormones, etc

55
Q

Protein synthesis can be divided into…

A

transcription and translation

56
Q

Transcription

A

A process by which DNA directs the synthesis of mRNA molecules

57
Q

Translation

A

a process in which mRNA is deciphered to synthesize a protein molecule

58
Q

Overview (drawing) of protein synthesis

A

DNA–> Transcription–> RNA–> Translation–> Protein

59
Q

Heterogeneous nuclear RNA (hnRNA)

A

Formed directly by DNA transcription.

60
Q

Post-transcription processing converts the hnRNA to

A

messenger RNA (mRNA)

61
Q

Messenger RNA

A

Carries instructions for protein synthesis (genetic information) from DNA
– The molecular mass of mRNA varies with the length of the protein

62
Q

Small nuclear RNA (snRNA):

A

Facilitates the conversion of hnRNA to mRNA.

– Contains from 100 to 200 nucleotides

63
Q

Ribosomal RNA (rRNA):

A

Combines with specific proteins to form ribosomes - the physical site for protein synthesis
Ribosomes have molecular masses on the order of 3 million

64
Q

Transfer RNA (tRNA):

A

Delivers amino acids to the sites for protein synthesis

– tRNAs are the smallest RNAs (75–90 nucleotide units)

65
Q

Transcription:

A

A process by which DNA directs the synthesis of mRNA molecules

66
Q

Two steps of transcription

A

Two-step process - (1) synthesis of hnRNA and (2) editing to yield mRNA molecule

67
Q

*Gene:

A

A segment of a DNA base sequence responsible for the production of a specific hnRNA/mRNA molecule
– Most human genes are ~1000–3500 nucleotide units long

68
Q

*Genome

A

All of the genetic material (the total DNA) contained in the chromosomes of an organism
– Human genome contains approximately 20,000 genes (as of 2014) : http://arxiv.org/abs/1312.7111

69
Q

Steps in the Transcription Process(long)

A

Unwinding of DNA double helix to expose some bases (a gene):
– The unwinding process is governed by RNA polymerase
• Alignment of free ribonucleotides along the exposed DNA strand (template) forming new base pairs
• RNA polymerase catalyzes the linkage of ribonucleotides one by one to form mRNA molecule
• Transcription ends when the RNA polymerase enzyme encounters a stop signal on the DNA template:
– The newly formed RNA molecule and the RNA polymerase enzyme are released

70
Q

Post-Transcription Processing: Formation of mRNA

A

nvolves conversion of hnRNA to mRNA

71
Q

*Splicing

A

Excision of introns and joining of exons

72
Q

*Exon

A

a gene segment that codes for genetic information

73
Q

*Intron

A

a DNA segments that interrupt a genetic message

74
Q

*The splicing process is driven by

A

snRNA

75
Q

*Alternative splicing

A

A process that ultimately leads to the formation of several different protein variants from a single gene
– The process involves excision of one or more exons from hnRNA during splicing process.
– The process occurs in a splicesome (a complex protein-nucleic acid molecular structure responsible for splicing hnRNA)

76
Q

Transcriptome

A

All of the mRNA molecules that can be generated from the genetic material in a genome.
– Transcriptome is different from a genome
– Responsible for the biochemical complexity created by splice variants obtained by hnRNA.

77
Q

Proteome

A

All of the protein molecules generated from mRNAs

78
Q

true or false: The base sequence in a mRNA determines the amino acid sequence for the protein synthesized

A

true

79
Q

The base sequence of an mRNA molecule involves only 4 different bases -

A

A, G, C, U

80
Q

*Codon

A

A three-nucleotide sequence in an mRNA molecule that codes for a specific amino acid
– Based on all possible combination of bases A, G, C, U there are 64 possible codes

81
Q

Genetic code:

A

The assignment of the 64 mRNA codons to specific amino acids (or stop signals)
– 3 of the 64 codons are termination codons (“stop” signals)

82
Q

Characteristics of Genetic Code

A

The genetic code is highly degenerate:
– Many amino acids are designated by more than one codon.
– Arg, Leu, and Ser - represented by six codons.
– Most other amino acids - represented by two codons
– Met and Trp - have only a single codon.
– Codons that specify the same amino acid are called synonyms

83
Q

There is a pattern to the arrangement of synonyms in the genetic code table.

A

– All synonyms for an amino acid fall within a single box in unless there are more than four synonyms
– The significance of the “single box” pattern - the first two bases are the same
– For example, the four synonyms for Proline - CCU, CCC, CCA, and CCG.

84
Q

The genetic code is almost universal:

A

– With minor exceptions the code is the same in all organisms
– The same codon specifies the same amino acid whether the cell is a bacterial cell, a corn plant cell, or a human cell.

85
Q

An initiation codon exists:

A

– The existence of “stop” codons (UAG, UAA, and UGA)

suggests the existence of “start” codons.

86
Q

*The codon

A

coding for the amino acid methionine (AUG) functions as initiation or “start” codon.

87
Q

During protein synthesis amino acids directly interact with the codons of an mRNA molecule.

A

False

88
Q

two important features of the tRNA structure

A

– The 3’ end of tRNA is where an amino acid is covalently bonded to the tRNA.
– The loop opposite to the open end of tRNA is the site for a sequence of three bases called an anticodon.

89
Q

*Anticodon -

A

a three-nucleotide sequence on a tRNA molecule that is complementary to a codon on an mRNA molecule.

90
Q

true or false: tRNA and its anticodon bind to the enzyme aminoacyl-tRNA synthetase to give proper placement of an amino acid on a protein

A

true

91
Q

Translation

A

a process in which mRNA codons are deciphered to synthesize a protein molecule

92
Q

Ribosome

A

an rRNA–protein complex - serves as the site of protein synthesis:
– Contains 4 rRNA molecules and ~80 proteins - packed into two rRNA-protein subunits (one small and one large)
– ~65% rRNA and 35% protein by mass
– A ribosome’s active site – Large subunit
– The mRNA binds to the small subunit of the ribosome.

93
Q

Activation of tRNA:

A

addition of specific amino acids to the 3’-OH group of tRNA.

94
Q

Initiation of protein synthesis:

A

Begins with binding of mRNA to small ribosomal subunit such that its first codon (initiating codon AUG) occupies a site called the P site (peptidyl site)

95
Q

Elongation

A

Adjacent to the P site in an mRNA–ribosome complex is A site (aminoacyl site) and the next tRNA with the appropriate anticodon binds to it. Peptidyl transferase links the A site and P site amino acids via a peptide bond.

96
Q

Termination:

A

The polypeptide continues to grow via translocation until all necessary amino acids are in place and bonded to each other. The process stops when a stop codon is encountered.

97
Q

Post-translational processing:

A

Gives the protein the final form it needs to be fully functional

98
Q

Polysome (polyribosome):

A

The complex of a mRNA and several ribosomes

99
Q

Mutation

A

An error in base sequence reproduced during DNA replication
• Errors in genetic information is passed on during transcription.
• The altered information can cause changes in amino acid sequence during protein synthesis and thereby alter protein function

100
Q

External Mutagens

A

Mutations are caused by mutagens
• A mutagen is a substance or agent that causes a change in the structure of a gene:
– Radiation and chemical agents are two important types of mutagens
– Ultraviolet, X-ray, radioactivity and cosmic radiation are mutagenic –cause cancers
– Chemical agents can also have mutagenic effects

101
Q

*Viruses

A

Tiny disease causing agents with outer protein envelope and inner nucleic acid core
• They can not reproduce outside their host cells (living organisms)
• Invade their host cells to reproduce and in the process disrupt the
normal cell’s operation
• Virus invade bacteria, plants animals, and humans

102
Q

*Zika Virus

A

Known to cause microcephaly in children born to mothers infected with Zika

103
Q

Transduction

A

Use of viral vectors to deliver genes to cells – Used in the lab: Genetically modified animals used in
research

104
Q

Gene therapy

A

Hope to cure genetic diseases in patients

Ex: Gene therapy techniques being developed to treat Hemophila A. Insert gene for factor VIII synthesis

105
Q

*Vaccines

A

riginally discovered by Jenner in 1798: Inactive virus or bacterial envelope (injection or oral dose)
• Antibodies produced against inactive viral or bacterial envelopes will kill the active bacteria and viruses
• Types: Influenza; Measles, Mumps, Rubella (MMR), Polio, Smallpox, Tetanus, Hepatitis B, Human Papilloma Virus (HPV), etc.
• Vaccines – When used by everyone; wiped out several serious diseases such as polio

106
Q

*Vaccines now

A

Resurgence in some diseases – decreased use of vaccines due to fear of side effects.
– Vaccines work most effectively when most of the population receive them
– Ex: Autism: No credible science to connect Autism with vaccines or the preservatives in vaccines.

107
Q

Recombinant DNA:

A

DNA molecules that have been synthesized by splicing a sequence of segment DNA (usually a gene) from one organism to the DNA of another organism.

108
Q

*Genetic Engineering (Biotechnology):

A

A process in which an organism is intentionally changed at the molecular (DNA) level so that it exhibits different traits

109
Q

*Recombinant DNA and Genetic Engineering

Applications

A

First genetically engineered organisms are bacteria (1973) and mice (1974)
• Insulin producing bacteria - commercialized in 1982.
– Bacteria act as protein factories
– Genetically modified (transgenic) animals used in drug development: Ex: knockout mice.

110
Q

*Many plants have now been genetically engineered

A

– Disease resistance – increased crop yield
– Drought resistance – consumption of less water
– Predator resistance – less insecticide use
– Frost resistance – resist changes in temps below freezing.
– Deterioration resistance – long shelf-life.

111
Q

Transgenic Animals: Knock-out mice

A

Used to study importance of a gene in vivo.

112
Q

recombinant DNA Production using a Bacterial Plasmid

A

Dissolution of cells:
– E. coli cells of a specific strain containing the plasmid of interest are treated with chemicals to dissolve their membranes and release the cellular contents
• Isolation of plasmid fraction:
– The cellular contents are fractionated to obtain plasmids
• Cleavage of plasmid DNA:
– Restriction enzymes are used to cleave the double-stranded DNA
• Gene removal from another organism:
– Using the same restriction enzyme the gene of interest is removed from a chromosome of another organism
• Gene–plasmid splicing:
– The gene (from Step 4) and the opened plasmid (from Step 3) are mixed in the presence of the enzyme DNA ligase to splice them together.
• Uptake of recombinant DNA:
– The recombinant DNA prepared in step 5 are transferred to a live E. coli culture where they can be replicated, transcribed and translated.

113
Q

Transformed cell can reproduce a large number of identical cells:

A

clones

114
Q

true or false: Clones are the cells that have descended from a single cell and have identical DNA

A

true

115
Q

true or false: Bacteria grows very slow

A

FALSE

116
Q

Can accelerate process using PCR – Polymerase Chain Reaction

A

true

117
Q

*The polymerase chain reaction (PCR):

A

A method for rapidly producing multiple copies of a DNA nucleotide sequence (gene).
• This method allows to produce billions of copies of a specific gene in a few hours.

118
Q

*PCR is very easy to carryout and the requirements are:

A

– Source of gene to be copied
– Thermostable DNA polymerase
– Deoxynucleotide triphosphates (dATP, dGTP, dCTP and dTTP)
– A set of two oligonucleotides with complementary sequence to the gene (primers)
– Thermostable plastic container and source of heat
– Used in biomedical research, manufacturing, forensics, etc.

Nucleic Acids (1 decks)

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