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Module 1B > 12-13 DNA & Protein Synthesis; Regulation of Gene Expression & Mutations > Flashcards

12-13 DNA & Protein Synthesis; Regulation of Gene Expression & Mutations Flashcards

1
Q

What are nucleic acids composed of?

A

Polymers of nucleotides, also known as polynucleotides

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2
Q

Nucleic acids may be associated with which proteins?

A

Histones

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3
Q

What are the two general types of nucleic acids?

A

Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA).

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4
Q

What is the primary function of DNA in organisms?

A

DNA serves as the genetic repository, containing all the information required for the synthesis of proteins and regulating this synthesis.

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5
Q

What are the different types of DNA, and where can they be found?

A

mtDNA (mitochondrial DNA), nuDNA (nuclear DNA), and plasmid DNA.

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6
Q

Where is mitochondrial DNA (mtDNA) located, and what is its characteristic?

A

In the mitochondria; it is naked and extrachromosomal.

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7
Q

Where is nuclear DNA (nuDNA) located, and how is it packaged?

A

In the nucleus, packaged into chromosomes.

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8
Q

It is extrachromosomal DNA that is not part of the organism’s genome

A

Plasmid DNA

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9
Q

What is the primary function of RNA in cells?

A

RNA plays a role in transferring genetic information by carrying the genetic code.

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10
Q

In which cellular compartments is DNA found in prokaryotes?

A

In prokaryotes, DNA is found in the nucleoid, where it is not separated from other cellular contents and is “naked” (not bound to proteins).

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11
Q

How is DNA organized in eukaryotic cells?

A

In eukaryotes, DNA is enclosed within a nuclear envelope and bound to proteins, forming chromatin; it can also be found in the mitochondria.

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12
Q

Where is RNA typically located in eukaryotic cells?

A

RNA is localized in the nucleolus and the cytoplasm.

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13
Q

True or False: In prokaryotes, DNA is separated from the rest of the cell’s contents by a nuclear envelope.

A

False (DNA is not separated from other cellular contents in prokaryotes).

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14
Q

What is the main role of the nucleolus in eukaryotic cells concerning nucleic acids?

A

The nucleolus is involved in the localization and synthesis of RNA.

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15
Q

How does the packaging of DNA differ between prokaryotes and eukaryotes?

A

In prokaryotes, DNA is “naked” and not bound to proteins, whereas in eukaryotes, DNA is bound to proteins and packaged as chromatin.

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16
Q

What distinguishes mtDNA from nuclear DNA in eukaryotes?

A

mtDNA is found in the mitochondria and is naked and extrachromosomal, whereas nuclear DNA is found in the nucleus and packaged into chromosomes.

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17
Q

What role does RNA play in the genetic material of cells?

A

RNA carries the genetic code and is involved in the transfer of genetic information for protein synthesis.

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18
Q

Where can DNA be found in the mitochondria of eukaryotic cells?

A

DNA in the mitochondria is referred to as mtDNA.

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19
Q

What are polynucleotides?

A

Polynucleotides are long chains of nucleotides, which are the building blocks of nucleic acids like DNA and RNA.

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20
Q

Describe the difference between nuDNA and plasmid DNA.

A

nuDNA is nuclear DNA packaged into chromosomes, while plasmid DNA is extrachromosomal and not part of the organism’s genome.

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21
Q

How is RNA’s role different in prokaryotes compared to eukaryotes?

A

In both prokaryotes and eukaryotes, RNA carries genetic information, but in eukaryotes, RNA is more compartmentalized, being found in the nucleolus and cytoplasm.

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22
Q

What is the significance of histones in relation to DNA?

A

Histones are proteins that DNA associates with to form chromatin, aiding in the packaging and organization of DNA in eukaryotic cells.

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23
Q

What type of sugar is found in RNA?

A

D-ribose

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24
Q

What type of sugar is found in DNA?

A

Deoxyribose (also known as 2-deoxy-D-ribose or Deoxyribofuranose)

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25
Q

What structural feature differentiates the sugar in DNA from that in RNA?

A

The sugar in DNA (deoxyribose) lacks a hydroxyl group (-OH) at the 2’ position, which is replaced with a hydrogen (H+).

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26
Q

Why is DNA’s backbone more flexible compared to RNA?

A

The lack of the 2′ hydroxyl group in DNA provides flexibility for the backbone, allowing it to form the double-helix structure.

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27
Q

Which sugar is more susceptible to alkali hydrolysis, and why?

A

RNA, due to the presence of the 2′ hydroxyl group which acts as an internal nucleophile, facilitating strand scission in an alkali medium.

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28
Q

True or False: Both DNA and RNA can be hydrolyzed under acidic conditions.

A

TRUE

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29
Q

What promotes RNA strand scission in an alkaline medium?

A

The 2′ hydroxyl group (2′OH) acts as an internal nucleophile, enabling transesterification of the 3′, 5′ phosphodiester bonds.

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30
Q

List the five principal nitrogen bases found in DNA and RNA.

A

Adenine, Cytosine, Guanine, Thymine, Uracil

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31
Q

Which nitrogen bases are classified as pyrimidines?

A

Cytosine, Uracil, Thymine

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32
Q

Describe the structure of pyrimidines.

A

Pyrimidines are monocyclic N-heterocycles.

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33
Q

How many hydrogen bonds does cytosine form with guanine?

A

Three hydrogen bonds

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34
Q

Which pyrimidine is found only in RNA, and what base does it pair with?

A

Uracil is found only in RNA and pairs with adenine.

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35
Q

Which pyrimidine is found only in DNA, and what base does it pair with?

A

Thymine is found only in DNA and pairs with adenine.

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36
Q

What structural modification differentiates thymine from uracil?

A

Thymine is a methylated form of uracil (5-methyl uracil).

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37
Q

Which nitrogen bases are classified as purines?

A

Adenine and Guanine

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38
Q

Describe the structure of purines.

A

Purines are bicyclic N-heterocycles.

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39
Q

In DNA and RNA, which base does adenine pair with?

A

In DNA, adenine pairs with thymine; in RNA, adenine pairs with uracil.

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40
Q

How many hydrogen bonds does guanine form with cytosine?

A

Three hydrogen bonds

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41
Q

It is a naturally occurring purine derivative found in the anticodon arm in the form of nucleoside inosine.

A

Hypoxanthine

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42
Q

How is the heterocyclic base linked to the sugar in nucleotides?

A

Through a β-N-glycosidic bond; in pyrimidines, it is between the 1′C of the sugar and N1; in purines, it is between the 1′C and N9.

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43
Q

What type of bond links the nitrogen base to the sugar in nucleotides?

A

β-N-glycosidic bond

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44
Q

How is the nitrogen base linked to the sugar in pyrimidines?

A

The nitrogen base is linked to the 1’ carbon of the sugar at the N1 position.

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45
Q

How is the nitrogen base linked to the sugar in purines?

A

The nitrogen base is linked to the 1’ carbon of the sugar at the N9 position.

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46
Q

What are the two possible conformations resulting from the rotation about the glycosidic bond in purines and pyrimidines?

A

Syn and anti conformations

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47
Q

What is the favored conformation of nucleosides in DNA duplexes?

A

Anti conformation

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48
Q

Which nucleotide is an exception, often adopting the syn conformation in Z-DNA?

A

Guanosine monophosphate (GMP)

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49
Q

A ribose or deoxyribose sugar linked to a nitrogen base

A

Nucleoside

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50
Q

A phosphorylated nucleoside

A

Nucleotide

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51
Q

What type of bond is crucial in nucleotide polymerization?

A

Phosphodiester bonds

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52
Q

How are phosphate groups in a nucleotide specified in its name?

A

As monophosphate, diphosphate, or triphosphate, depending on the number of phosphate groups.

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53
Q

What suffix is added to nucleosides derived from purines?

A

“osine”

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54
Q

What suffix is added to nucleosides derived from pyrimidines?

A

“idine”

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55
Q

When is the prefix “deoxy” added to a nucleoside’s name?

A

The prefix “deoxy” is added when the sugar in the nucleoside is in deoxyribose form.

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56
Q

What is the ribonucleoside name for adenine?

A

Adenosine

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57
Q

What is the deoxyribonucleoside name for adenine?

A

Deoxyadenosine

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58
Q

What is the ribonucleoside name for guanine?

A

Guanosine

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59
Q

What is the deoxyribonucleoside name for guanine?

A

Deoxyguanosine

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60
Q

What is the ribonucleoside name for uracil?

A

Uridine

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61
Q

What is the deoxyribonucleoside name for uracil?

A

Deoxyuridine

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62
Q

What is the ribonucleoside name for cytosine?

A

Cytidine

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63
Q

What is the deoxyribonucleoside name for cytosine?

A

Deoxycytidine

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64
Q

What is the ribonucleoside name for thymine?

A

Ribothymidine

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65
Q

What is the deoxyribonucleoside name for thymine?

A

Deoxythymidine

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66
Q

How is a nucleotide formed?

A

A nucleotide is formed by adding one or more phosphate groups to a nucleoside.

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67
Q

What does the term “nucleoside-3’-monophosphate” indicate?

A

It indicates that the phosphate group is attached to the 3’ carbon of the ribose sugar in the nucleotide.

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68
Q

What does the term “nucleoside-5’-triphosphate” indicate?

A

It indicates that three phosphate groups are attached to the 5’ carbon of the ribose sugar in the nucleotide.

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69
Q

Which carbon of the pentose sugar is most commonly esterified with a phosphate group?

A

The 5’ carbon is most commonly esterified with a phosphate group.

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70
Q

What does the abbreviation AMP stand for?

A

Adenosine monophosphate

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71
Q

What does the abbreviation dAMP stand for?

A

Deoxyadenosine monophosphate

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72
Q

What is the ribonucleoside monophosphate form of adenine?

A

Adenosine monophosphate (AMP), also known as adenylic acid or adenylate

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73
Q

What is the deoxyribonucleoside monophosphate form of adenine?

A

Deoxyadenosine monophosphate (dAMP), also known as deoxyadenylic acid or deoxyadenylate

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74
Q

What is the ribonucleoside monophosphate form of guanine?

A

Guanosine monophosphate (GMP), also known as guanylic acid or guanylate

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75
Q

What is the deoxyribonucleoside monophosphate form of guanine?

A

Deoxyguanosine monophosphate (dGMP), also known as deoxyguanylic acid or deoxyguanylate

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76
Q

What is the ribonucleoside monophosphate form of uracil?

A

Uridine monophosphate (UMP), also known as uridylic acid or uridylate

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77
Q

What is the deoxyribonucleoside monophosphate form of uracil?

A

Deoxyuridine monophosphate (dUMP)

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78
Q

What is the ribonucleoside monophosphate form of cytosine?

A

Cytidine monophosphate (CMP), also known as cytidylic acid or cytidylate

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79
Q

What is the deoxyribonucleoside monophosphate form of cytosine?

A

Deoxycytidine monophosphate (dCMP), also known as deoxycytidylic acid or deoxycytidylate

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80
Q

What is the ribonucleoside monophosphate form of thymine?

A

Ribothymidine monophosphate (TMP), also known as thymidylic acid or thymidylate

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81
Q

What is the deoxyribonucleoside monophosphate form of thymine?

A

Deoxythymidine monophosphate, also known as deoxythymidylic acid

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82
Q

In which nucleic acid is thymine predominantly found?

A

Thymine is predominantly found in DNA.

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83
Q

True or False: The prefix “deoxy” can be omitted for thymine nucleotides in DNA.

A

TRUE

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84
Q

Where else, aside from DNA, can thymine be found?

A

Thymine can also be found in tRNA, where it is termed ribothymidine.

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85
Q

What are the primary roles of nucleotides in DNA and RNA synthesis?

A

Nucleotides serve as the building blocks for DNA and RNA synthesis.

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86
Q

Which nucleotides are used as substrates in DNA replication?

A

GTP, CTP, ATP, TTP are used as substrates in DNA replication.

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87
Q

Which nucleotides are utilized in transcription?

A

GTP, CTP, ATP, UTP are used in transcription.

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88
Q

How do GTP and ATP function as part of cellular energy processes?

A

GTP and ATP serve as the energy currency of the cell, providing energy for various cellular functions.

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89
Q

What role do cyclic nucleotides like cAMP and cGMP play in cellular processes?

A

cAMP and cGMP function as secondary messengers, regulating physiological processes and acting as signaling molecules.

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90
Q

Which enzymes cyclize ATP and GTP to form cAMP and cGMP, respectively?

A

Adenylyl cyclase cyclizes ATP to form cAMP, while guanylyl cyclase cyclizes GTP to form cGMP.

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91
Q

What role do nucleotides play in coenzyme function?

A

Nucleotides function as coenzymes, serving as helper molecules in enzymatic reactions.

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92
Q

Identify the class of compounds that are chemically synthesized analogues of purine and pyrimidine nucleotides.

A

Antimetabolites

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93
Q

How are antimetabolites prepared?

A

Antimetabolites are prepared by altering the heterocyclic ring or sugar moiety of nucleotides.

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94
Q

What is the primary medical use of antimetabolites?

A

Antimetabolites are used to control cancer and infections by interfering with nucleotide metabolism.

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95
Q

Which structural analogues of uracil are used as antimetabolites?

A

5-fluoro or 5-iodo derivatives of uracil (thymine/thymidine analogues) are used as antimetabolites.

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96
Q

What is the structural analogue of inosine used as an antimetabolite?

A

6-mercaptopurine is the structural analogue of inosine used as an antimetabolite.

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97
Q

What is the structural analogue of guanine used as an antimetabolite?

A

6-thioguanine is the structural analogue of guanine used as an antimetabolite.

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98
Q

Identify the nucleoside in which arabinose is used instead of ribose.

A

Cytarabine (arabinosyl cytosine, Ara-C)

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99
Q

Identify the purine analogue that functions as an antimetabolite.

A

4-hydroxypyrazolopyrimidine (allopurinol)

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100
Q

Identify the structural analogue of thymine used as an antimetabolite.

A

Azidothymidine

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101
Q

Identify the nucleoside analogue that interferes with nucleotide metabolism and acts as an antimetabolite.

A

5-iododeoxyuridine

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102
Q

What does DNA stand for?

A

2’-deoxyribonucleic acid

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103
Q

What is the biological function of DNA that ensures the precise duplication of genetic material?

A

Replication

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104
Q

Which biological function of DNA involves the reshuffling or exchanging of genes?

A

Recombination

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105
Q

How does DNA contribute to genetic diversity?

A

Variation/Diversity

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106
Q

True or False: DNA is a double-stranded molecule.

A

TRUE

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107
Q

What is the role of the sugar-phosphate backbone in DNA?

A

Structural role

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108
Q

What forms the backbone of DNA?

A

Sugar-phosphate

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109
Q

How are the two strands of DNA oriented relative to each other?

A

Anti-parallel (opposite polarity)

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110
Q

What kind of bonds hold the DNA strands together?

A

Hydrogen bonds (H-bonds)

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111
Q

How many hydrogen bonds are formed between adenine and thymine in DNA?

A

Two

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112
Q

How many hydrogen bonds are formed between guanine and cytosine in DNA?

A

Three

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113
Q

Which bases are complementary to each other in DNA?

A

A pairs with T, G pairs with C

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114
Q

Who proposed the double helical structure of DNA and in what year?

A

Watson and Crick in 1953

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115
Q

What is the diameter of the DNA helix?

A

200 Å

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116
Q

What is the distance between adjacent bases in the DNA structure?

A

3.4 Å

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117
Q

What kind of molecule is DNA classified as?

A

A large polymeric molecule

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118
Q

What are the monomers of DNA called?

A

Nucleotides

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119
Q

List the four heterocyclic bases found in DNA.

A

Adenine (A), Thymine (T), Guanine (G), Cytosine (C)

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120
Q

What is the pentose sugar found in DNA called?

A

2′-deoxy-D-ribofuranose

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121
Q

True or False: The sequence of one DNA strand can be used to predict the sequence of the other strand.

A

True (The strands are complementary)

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122
Q

What does the precise sequence of bases in DNA carry?

A

Genetic information

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123
Q

What is the characteristic polarity of each DNA strand?

A

3’ to 5’ polarity

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124
Q

What type of biological molecule is DNA considered?

A

Molecular store of genetic information

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125
Q

What is the process by which DNA passes genetic material to the next generation?

A

Transmission

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126
Q

Which of the following is NOT a function of DNA: Replication, Storage, Variation, or Protein Synthesis?

A

Protein Synthesis

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127
Q

What is structural polymorphism in DNA?

A

Variation in the conformation of double-stranded DNA despite the strands running in opposite polarity.

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128
Q

How many structural forms of DNA are there?

A

Three

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129
Q

Name the three structural forms of DNA.

A

A Form, B Form, Z Form

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130
Q

In which direction does the helical formation of DNA A form and B form occur?

A

Right

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131
Q

What is the direction of helical formation in DNA Z form?

A

Left

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132
Q

How many residues per turn of the helix are present in DNA A form?

A

11

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133
Q

How many residues per turn of the helix are present in DNA B form?

A

10

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134
Q

How many residues per turn of the helix are present in DNA Z form?

A

12

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135
Q

What is the rotation of the helix per residue (in degrees) for DNA A form?

A

33°

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136
Q

What is the rotation of the helix per residue (in degrees) for DNA B form?

A

36°

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137
Q

What is the rotation of the helix per residue (in degrees) for DNA Z form?

A

-30°

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138
Q

How is the base tilt relative to the helix axis (in degrees) in DNA A form?

A

20°

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139
Q

How is the base tilt relative to the helix axis (in degrees) in DNA B form?

A

6°

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140
Q

How is the base tilt relative to the helix axis (in degrees) in DNA Z form?

A

7°

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141
Q

Describe the major groove in DNA A form.

A

Narrow and deep

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142
Q

Describe the major groove in DNA B form.

A

Wide and deep

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143
Q

Describe the major groove in DNA Z form.

A

Flat

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144
Q

Describe the minor groove in DNA A form.

A

Wide and shallow

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145
Q

Describe the minor groove in DNA B form.

A

Narrow and deep

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146
Q

Describe the minor groove in DNA Z form.

A

Narrow and deep

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147
Q

What is the orientation of the N-glycosidic bond in DNA A form?

A

Anti

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148
Q

What is the orientation of the N-glycosidic bond in DNA B form?

A

Anti

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149
Q

What is the orientation of the N-glycosidic bond in DNA Z form?

A

Anti for Pyrimidines, Syn for Purines

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150
Q

True or False: All forms of DNA are held together by Watson and Crick base pairs.

A

TRUE

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151
Q

Which form of DNA is the native form under physiologic pH?

A

DNA B form

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152
Q

Which form of DNA is a dehydrated form of DNA B?

A

DNA A form

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153
Q

What is the distinctive contour of DNA Z form?

A

Zigzag

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154
Q

Where are short tracts of Z DNA observed?

A

In prokaryotes and eukaryotes

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155
Q

Given a DNA segment containing 1800 base pairs, what is the total number of nucleotides?

A

3600 nucleotides

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156
Q

If 20% of the base pairs in the DNA segment are AT pairs, what percentage are GC pairs?

A

80%

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157
Q

If the DNA segment contains 3600 nucleotides, and 20% are AT pairs, how many nucleotides contain guanine?

A

1440 nucleotides

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158
Q

True or False: In the given DNA segment, the number of guanine bases equals the number of cytosine bases.

A

TRUE

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159
Q

Explain why the value given as %GC needs to be multiplied by two to obtain the number of nucleotides containing G and C.

A

Because the value given in class represents base pairs, and each base pair consists of two nucleotides.

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160
Q

Why is the double helix of DNA highly negatively charged?

A

Due to the negatively charged phosphates in the backbone.

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161
Q

What type of proteins does the cell make to counterbalance the negative charge of DNA?

A

Histones

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162
Q

What is the charge of histone proteins?

A

Positively charged

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163
Q

How do histones interact with DNA?

A

Through interactions between their positive charges and the negative charges of DNA.

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164
Q

What structure is formed when double-stranded DNA loops around 8 histones twice?

A

Nucleosome

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165
Q

What is the building block of chromatin packaging?

A

Nucleosome

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166
Q

What is formed when nucleosomes are further packaged?

A

Chromatin fibers

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167
Q

When are chromatin fibers condensed into chromosomes?

A

During mitosis (cell division)

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168
Q

During which cellular process is DNA most commonly found in its loosely packaged form?

A

During most of the cell cycle, except during certain stages of mitosis.

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169
Q

True or False: Chromosomes are always visible in the cell throughout its life cycle.

A

False (Chromosomes are most visible only during certain stages of mitosis).

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170
Q

What is the primary role of histones in DNA organization?

A

To bind DNA and aid in its packaging.

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171
Q

Describe the structure of a nucleosome.

A

A nucleosome consists of double-stranded DNA wrapped twice around 8 histones.

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172
Q

What happens to DNA during the process of mitosis?

A

DNA is packaged into condensed chromosomes.

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173
Q

What is the significance of the chromatin fibers?

A

They are a higher level of DNA packaging, formed by coils of nucleosomes.

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174
Q

Why is DNA loosely packaged most of the time?

A

To allow access to the genetic information for processes such as transcription and replication.

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175
Q

True or False: DNA packaging into chromosomes only occurs during mitosis.

A

True (It occurs mainly during certain stages of mitosis).

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176
Q

It is a positively charged proteins that facilitate the packing of DNA into condensed chromatin fibers.

A

Histones

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177
Q

Which amino acids are histones rich in, and why are they significant?

A

Arginine and lysine, which confer a positive charge that easily binds to the negatively charged DNA.

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178
Q

How many types of histones form the histone octamer?

A

Four types: H2A, H2B, H3, and H4.

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179
Q

How is a nucleosome formed?

A

DNA is wound around the outside of a histone octamer, which is formed by two copies each of H2A, H2B, H3, and H4.

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180
Q

What is the term used to describe a series of nucleosomes?

A

“Beads on a string.”

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181
Q

A nucleosome core plus the histone H1.

A

Chromatosome

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182
Q

What role does histone H1 play in DNA packaging?

A

Histone H1 locks DNA on the nucleosome in place and is associated with linker DNA to help package nucleosomes into a 30 nm fiber.

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183
Q

What structure is formed by the packaging of nucleosomes with the help of histone H1?

A

A solenoid-like structure, known as the 30 nm fiber.

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184
Q

How are histones categorized?

A

Into two groups: core histones and linker histones.

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185
Q

Which histones are considered core histones?

A

H2A, H2B, H3, and H4.

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186
Q

What is the composition of the histone octamer?

A

Two H3/H4 dimers and two H2A/H2B dimers form the octamer.

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187
Q

Which histone is classified as a linker histone, and what is its function?

A

Histone H1; it locks DNA in place on the nucleosome and helps in packaging nucleosomes into higher-order structures.

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188
Q

What happens to histones during methylation?

A

Methylation makes histones more hydrophobic by adding methyl groups.

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189
Q

Which enzymes are responsible for adding methyl groups to histones?

A

Histone methyltransferases (HMTs).

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190
Q

How does acetylation affect histones, and what is the outcome for DNA interaction?

A

Acetylation makes histones more negatively charged, loosening their grip on DNA due to repulsion of similar charges.

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191
Q

What is the effect of phosphorylation on histones?

A

Phosphorylation adds a negative charge to histones, similarly loosening their grip on DNA.

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192
Q

Which enzymes add acetyl groups to histones?

A

Histone acetyltransferases (HATs).

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193
Q

Which enzymes remove acetyl groups from histones?

A

Histone deacetylases (HDACs).

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194
Q

True or False: Methylation of histones increases their positive charge.

A

False (Methylation makes histones more hydrophobic, not more positively charged).

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195
Q

What is the relationship between acetylation/phosphorylation and histone-DNA interaction?

A

Acetylation and phosphorylation make histones more negatively charged, weakening their interaction with DNA.

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196
Q

What is the significance of making histones more negatively charged through acetylation or phosphorylation?

A

It reduces the histones’ affinity for DNA, allowing for easier access to the genetic material for processes like transcription.

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197
Q

What are the three major types of modifications that affect DNA packaging?

A

Methylation, Acetylation, Phosphorylation

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198
Q

How does methylation affect DNA packaging?

A

Increases packaging

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199
Q

What is the charge associated with methylation of DNA?

A

Neutral

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200
Q

How does acetylation affect DNA packaging?

A

Decreases packaging

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201
Q

What is the charge associated with acetylation of DNA?

A

Negative

202
Q

How does phosphorylation affect DNA packaging?

A

Decreases packaging

203
Q

What is the charge associated with phosphorylation of DNA?

A

Negative

204
Q

What are the two types of chromatin found in interphase cells?

A

Euchromatin and Heterochromatin

205
Q

Describe euchromatin and its activity.

A

Euchromatin is loosely packaged and transcriptionally active.

206
Q

What structural form does euchromatin generally correspond to?

A

Looped 30 nm fibers

207
Q

It is a tightly packaged, highly methylated, highly condensed, and transcriptionally inactive.

A

Heterochromatin

208
Q

It is the rupture of hydrogen bonds between DNA bases due to increasing temperature or alterations in hydrogen ion concentration.

A

DNA denaturation

209
Q

How does increasing pH affect DNA?

A

Deprotonates ring nitrogens of guanine and thymine, causing the bases to tautomerize and denature the DNA.

210
Q

How does decreasing pH affect DNA?

A

Protonates ring nitrogens of adenine, guanine, and cytosine, but increasing acidity can rupture β-N-glycosidic bonds, and at high temperatures, phosphodiester bonds may be broken.

211
Q

What is the method of choice for denaturing DNA, and what does it involve?

A

Alkali (e.g., Urea), which is used to denature DNA.

212
Q

What happens to DNA when the temperature is increased?

A

The strands separate at a definite temperature, known as thermal melting.

213
Q

What is Tm in the context of DNA?

A

Tm is the temperature at which 50% of the double-stranded DNA is unwound.

214
Q

How can the melting of DNA be studied?

A

By measuring the absorption of light (spectrophotometric analysis) at 260 nm.

215
Q

What is the hyperchromic effect in DNA melting?

A

An increase in absorbance due to the unstacking of bases during melting.

216
Q

How does the base composition of DNA influence its Tm?

A

DNA rich in GC pairs has a higher Tm than DNA with a high proportion of AT pairs.

217
Q

What is DNA renaturation?

A

The reformation of the original double helical structure when the temperature is held at about 20°C to 25°C below the Tm.

218
Q

What is another term for DNA renaturation?

A

Reannealing

219
Q

True or False: Methylation makes DNA more positively charged.

A

False (Methylation is neutral in charge).

220
Q

Why does DNA rich in GC pairs have a higher Tm compared to DNA rich in AT pairs?

A

Because GC pairs have three hydrogen bonds compared to two hydrogen bonds in AT pairs, making GC-rich DNA more stable.

221
Q

What happens to DNA when exposed to high temperatures during denaturation?

A

The strands of DNA separate, resulting in thermal melting.

222
Q

At what wavelength is DNA melting commonly analyzed?

A

260 nm

223
Q

What effect does alkali (such as urea) have on DNA?

A

Alkali denatures DNA by disrupting the hydrogen bonds between bases.

224
Q

True or False: DNA denaturation can be reversed by decreasing the temperature.

A

True (This process is called renaturation or reannealing).

225
Q

A nucleic acid with only a single, helical strand of bases.

A

RNA

226
Q

Characterized by small nucleolar RNA and
associated with chemical modifications of other RNAs

A

snoRNA

227
Q

aid in slicing introns and splicing exons

A

snRNA

228
Q

precursor for mRNA. Contains introns and exons

A

hnRNA

229
Q

contains the sequence of nucleotides that directs the synthesis of polypeptide

A

mRNA

230
Q

subcellular ribonucleoprotein complexes on which translation occurs contains the ribozyme (RNA with catalytic action) peptidyl transferase

A

rRNA

231
Q

arries amino acid to the ribosomes and contains the anticodon complementary to the codon present in mRNA

A

tRNA

232
Q

small RNA molecule that regulates gene expression by reducing the expression of mRNA. It can induce degradation of the target mRNA or block translation of the target mRNA

A

miRNA

233
Q

complementary to mRNA transcribed in the cell. It
can inhibit translation by binding to complementary mRNA

A

antisense mRNA

234
Q

process of producing exact replica of the genetic material.

A

DNA Replication

235
Q

What are the steps of DNA Replication?

A

initiation, elongation, termination

236
Q

Enzyme that recognizes the origin replication element on the autonomously replicating sequences (ARS)

A

Origin Recognition Complex (ORC)

237
Q

Facilitates the unwinding of the double stranded DNA by breaking the H bonds that attach dinucleotide pairs

A

Helicase

238
Q

Prevents the strand of the DNA to reanneal

A

Single-stranded binding proteins

239
Q

an enzyme that adds a stretch of RNA molecules that will assist in initiating polymerization

A

Primase

240
Q

adds DNA nucleotide to the growing DNA chain, it is considered as one of the enzymes of the elongation part of the DNA replication.

A

DNA Polymerase

241
Q

The main replicative enzyme in eukaryotes

A

DNA polymerase delta or epsilon

242
Q

Seals the nick between DNA fragments.

A

Ligase

243
Q

Adds RNA nucleotides to the growing RNA molecule using the instructions in the DNA template.

A

DNA dependent RNA polymerase

244
Q

What are the types of RNA polymerase and their function?

A

RNA polymerase I - Transcribes all rRNA genes except the 5S rRNA
RNA polymerase II - Transcribes all structural genes; Forms all mRNA; Some snRNA genes are transcribed by RNA polymerase II
RNA polymerase III - Transcribes all tRNA genes and the 5S rRNA gene.

245
Q

Essential proteins that aid in initiation, elongation and termination of transcription

A

Transcription Factors (TF IID, TF IIB, TF IIF, TF IIE, TF IIH)

246
Q

Carrier of the genetic code and provides a template for protein synthesis

A

mRNA

247
Q

The adaptor molecule with an amino acid attachment side and anticodon site

A

tRNA

248
Q

What are the 3 binding sites in the ribosome?

A

A site
Binds incoming aminoacyl tRNA as directed by the codon currently occupying the site
This codon would specify the next amino acid to be added to the growing polypeptide chain

P site
The peptidyl tRNA occupies this site
The tRNA is carrying the chain of amino acids that has been synthesized

E site
Occupied by the empty tRNA that is about to exit the ribosome
Empty tRNA = no longer carrying an amino acid

249
Q

proteins synthesized by other genes that help in translation

A

Translation Factors

250
Q

What are some examples of Translation factors and their function?

A

Initiation Factors: aid in AUG codon recognition
Elongation Factors: allow movement of the translation machinery
Release Factors: recognize the stop codon (UAG/UAA/UGA) and then detach the polypeptide from the machinery

251
Q

The primary constriction point where the two chromatids are held together

A

Centromere

252
Q

These are found at the ends of the chromosome

A

Telomere

253
Q

Differentiate Euchromatin and Heterochromatin

A

Euchromatin: regions that are less condensed, gene-rich, and actively transcribed
Heterochromatin: Highly condensed parts of the DNA inactive for expression

254
Q

Non-coding regions located between genes

A

Intergenic; “spacer DNA”

255
Q

Non-coding regions located within the gene

A

Intragenic

256
Q

It is the molecular basis of heredity

A

DNA Replication

257
Q

In DNA replication, genetic materials are duplicated ______ and of ______.

A

accurately and high fidelity

258
Q

Where does DNA replication occurs?

A

S phase

259
Q

Purpose of DNA replication

A

To preserve the chromosome number of species

260
Q

A specific base pairing that occurs between Adenine and Thymine, Guanine ans Cytosine

A

Chargaff’s rule

261
Q

One base at a time and specifically follows the Watson and Crick specific base pairing

A

Polymerization

262
Q

True or False. In DNA replication, each strand can be used as a template to synthesize new strands of DNA

A

TRUE

263
Q

End products of replication

A

Two DNA molecules that are exact replica of the parent molecule having the same sequence of bases and the same DNA content

264
Q

True or False. Each DNA products is composed of old strand from the parents

A

False (DNA replication is a semi-conservative process, wherein each DNA products is composed of the old strand and the newly synthesized one)

265
Q

One of the requirement for DNA replication that is a single-stranded DNA formed by the denaturation of the DNA that guides the synthesis of the complementary strand

A

Template

266
Q

True or False. Polymerization takes place in the 5’ to 3’ direction; thus, template runs from 3’ to 5’ direction

A

TRUE

267
Q

A Y-shaped structure formed with the replisome that forms a replication bubble during replication

A

Replication fork

268
Q

Replicated towards the growing fork; therefore, continuous replication

A

Leading strand

269
Q

Replicated on the opposite direction of the growing fork; therefore, discontinuous replication producing short segments of DNA that are exposed first—called the Okazaki fragment

A

Lagging strand

270
Q

Pertains to the oxyribonucleotides (dNTP’s) of guanine (dGTP), adenine (dATP), cytosine (dCTP), and thymine (dTTP) which is a source of energy that is needed during polymerization

A

Substrates

271
Q

Stretch of RNA molecules which are added by the protein primase. This are important as DNA polymerase can only add to the 3’ hydroxyl end of the DNA chain; thus, RNA molecules essentially provide the free hydroxyl group needed by the DNA polymerase — one in the leading strand, and several in the lagging strand

A

Primers

272
Q

Enzymes involved in DNA replication

A

Topoisomerase

273
Q

Relieves the negative supercoil created by the unwinding of DNA

A

Topoisomerase

274
Q

Two types of Topoisomerase

A

Topoisomerase 1 and 2

275
Q

Makes a transient single strand cut in the backbone of the DNA that nables the two separated strands to swivel around each other, removing the buildup of the twist

A

Topoisomerase 1

276
Q

Creates double strand breaks that enable the double stranded DNA to pass through another. This also removes nuts that are formed within and between the DNA molecules

A

Topoisomerase 2

277
Q

Example of a topoisomerase 2

A

DNA Gyrase

278
Q

Replicative enzymes that catalyze the attachment of nucleotides to make new DNA molecules

A

DNA polymerase

279
Q

3 Types of DNA polymerases

A

DNA Polymerase III

280
Q

Major replicative enzyme for prokaryotic organisms and is highly processive

A

DNA Polymerase III

281
Q

The major replicative enzyme for eukaryotic organisms

A

DNA Polymerase δ and DNA Polymerase ε

282
Q

3 activities of DNA Polymerases:

A

5’ - 3’ Polymerase activity

283
Q

When the enzyme adds nucleotides to the growing chain from the 5’ to 3’ direction of the growing strand

A

5’ - 3’ Polymerase activity

284
Q

Gives DNA Polymerases proof-reading capabilities

A

3’ - 5’ Exonuclease activity

285
Q

When the enzyme cleaves the phosphodiester bonds holding the nucleotides at the end of the growing chain and allows DNA Polymerase to remove primers

A

5’ - 3’ Exonuclease activity

286
Q

Why DNA Polymerase α in eukaryotic cells have primase capabilities?

A

Primase capabilities allows it to be able to form primers

287
Q

Priming in prokaryotic organisms is catalyzed by _____

A

DNAG Primase

288
Q

Subunit composition of DNA polymerase III

A

α-subunits

289
Q

Subunit composition of DNA polymerase III that Has polymerase activity

A

α-subunits

290
Q

Subunit composition of DNA polymerase III that has proofreading functions and act as the sliding clamp

A

β-subunits

291
Q

Subunit composition of DNA polymerase III that acts as clamp loaders that aid the β-subunits in binding to DNA

A

γ-subunits

292
Q

Subunit composition of DNA polymerase III that binds to single-stranded binding proteins

A

ψ and χ-subunits

293
Q

The origin of replication in E. coli

A

oriC (origin of Chromosomal replication)

294
Q

Three types of DNA sequences in oriC that are functionally significant

A

AT-rich region, DnaA boxes, and GATC methylation sites

295
Q

Type of DNA sequences in oriC that serve as control sites for replication; methyl groups are added to adenine by DNA adenine methylase (Dam) in GATC region

A

GATC methylation sites

296
Q

Type of DNA sequences in oriC where DnaA protein binds

A

DnaA boxes

297
Q

Type of DNA sequences in oriC that permits local unwinding or denaturation of DNA

A

AT-rich region

298
Q

2 Types of Bacterial DNA

A

Hemimethylated DNA and Fully methylated DNA

299
Q

One of the types of bacterial DNA where DNA is undergoing replication and is therefore, inactive for another round of replication

A

Hemimethylated DNA

300
Q

One of the types of bacterial DNA where DNA is ready for replication

A

Fully methylated DNA

301
Q

Replication machinery that is responsible for the synthesis of a DNA moelcule

A

Replisome

302
Q

Replication machinery is composed of:

A

specialized number of proteins, including primase, helicase, topoisomerase, DNA polymerase, and DNA ligase

303
Q

Bacterial replication step where replisome is initiated by a specialyzed enzyme called helicase

A

Initiation

304
Q

A special enzyme that facilitates the unwinding of the double stranded DNA to form a single-stranded DNA, which will serve as a template for DNA polymerization

A

Helicase

305
Q

Allows the formation or adding of short RNA segment serving as a primer

A

Primase

306
Q

Overall direction of replication

A

5’ to 3’

307
Q

Bacterial replication step where DNA polymerase enzyme adds DNA nucleotides to the RNA primer

A

Elongation

308
Q

Opposite to oriC is a pair of termination sequences called ter sequences, which are designated T1 and T2

A

Termination

309
Q

A protein that recognizes and binds to the sequences and stops the movement of the replication forks

A

protein tus (termination utilization substance

310
Q

Proteins involved in Eukaryotic DNA synthesis

A

PCNA (Proliferating Cell Nuclear Antigen), RPA (Replication Protein A), RFC (Replication Factor C), MCM (Mini Chromosome Maintenance Complex), and ORC (Origin Replication Complex)

311
Q

Confers high processivity to DNA polymerase delta, which is the major replicative enzyme of a eukaryotic cell and eukaryotic counterpart of the sliding camp of E. coli

A

PCNA (Proliferating Cell Nuclear Antigen)

312
Q

Single-stranded binding protein that facilitates unwinding of helix to create replication forks

A

RPA (Replication Protein A)

313
Q

Loads PCNA on DNA and eukaryotic counterpart of clamp loader of E. coli

A

RFC (Replication Factor C)

314
Q

Ring-shaped replicative helicase

A

MCM (Mini Chromosome Maintenance Complex)

315
Q

Binds to sequences within replicator and interacts with two other proteins resulting in loading of MCM on DNA strand

A

ORC (Origin Replication Complex)

316
Q

True or False. Eukaryotic replication begins with binding of DNA polymerase α, which is the initiator polymerase

A

TRUE

317
Q

After a stretch of about ___ nucleotides have been added, replication protein RFC displaces DNA polymerase α and attracts PCNA. PCNA then binds to DNA polymerase δ or ε. This is known as polymerase switching

A

20

318
Q

True or False. In the end replication problem, New DNA is synthesized in the 5’ to 3’ direction

A

TRUE

319
Q

Type of DNA strand that is continuous and run in 5’ to 3’

A

Leading strand synthesis

320
Q

Type of DNA strand that is discontinuous, runs in 5’ to 3’, and forms Okazaki fragments

A

Lagging strand synthesis

321
Q

Order of the End Replication Problem

A

Double stranded DNA -> Straightforward replication of Leading Strand (5’ to 3’) -> Addition of RNA primers to lagging strand -> Addition of RNA primers to Lagging strand -> DNA polymerase replicates between gaps -> RNA primers removed -> DNA polymerase fills in gaps, but End Replication Problem -> Telomere prevents loss of DNA

322
Q

A tandem repeat of short GC-rich oligonucleotides

A

Telomeres

323
Q

Functions of telomeres

A

Protect chromosomes from fusing with each other, Prevents genomic instability, and Protects cells from degradation

324
Q

Second component of the protective mechanism against the end replication problem and an enzyme that adds telomeric repeat sequence to the 3’ end of DNA strand

A

Telomerase

325
Q

True or False. Telomerase consists of 126 kDal RNA dependent DNA polymerase, other proteins, and a 450 nt RNA

A

TRUE

326
Q

True or False. Telomerase is present in somatic cells and absent in germline cells

A

FALSE ; present in germline cells and absent in somatic cells

327
Q

direction of new DNA is synthesized

A

5’ to 3’ direction

328
Q

Replication occurs bidirectionally from the ___

A

ori

329
Q

TRUE or FALSE: Replication occurs unidirectionally from the ori

A

FALSE: Bidirectionally

330
Q

fragments formed in the lagging strand synthesis

A

Okazaki fragments

331
Q

Leading strand synthesis is ___ (Continuous, Discontinuous)

A

Continuous

332
Q

Lagging strand synthesis is ___ (Continuous, Discontinuous)

A

Discontinuous

333
Q

Get shorter and shorter with each round of replication

A

Telomeres

334
Q

Many short ____ laid down by primase to provide the 3’ OH group for DNA polymerase to add new nucleotide to the growing chain

A

RNA primers

335
Q

RNA primers are removed; then, _____ fills in the gap because each Okazaki fragment has a free 3’ OH end to which the new nucleotide is to be added to

A

DNA polymerase

336
Q

In a linear chromosome, at the very end where the RNA primer has been removed, there is _____ to which DNA polymerase can add new nucleotide

A

no 3’ OH

337
Q

3’ overhang at the end of the chromosome

A

telomere

338
Q

The 3’ overhangs will be lost in the subsequent divisions

A

end replication problem

339
Q

Repeat sequence of the DNA at chromosome end

A

Telomeres

340
Q

Tandem repeat of short GC-rich oligonucleotides

A

Telomeres

341
Q

Specific sequence of DNA repeat vary from eukaryotic to eukaryotic organism
In man, what is the repeated sequence?

A

TTAGGG

342
Q

Role/function of telomeres

A

For chromosome integrity and stability:
Protect chromosomes from fusing with each other
Prevents genomic instability
Protects cells from degradation

343
Q

First component of the protective mechanism against the end replication problem

A

Telomeres

344
Q

Second component of the protective mechanism against the end replication problem

A

Telomerase

345
Q

Enzyme adding telomeric repeat sequence to the 3’ end of DNA strand

A

Telomerase

346
Q

it is a Ribonucleoprotein in the protective mechanism against the end replication problem

A

Telomerase

347
Q

Consist of 126 kDal RNA dependent DNA polymerase, other proteins, and a 450 nt RNA

A

Telomerase

348
Q

The telomerase is ____ in germline cells and ____ in somatic cells

A

Present: Absent

349
Q

Number of times a normal human cell will divide until it no longer can (due to the end replication problem in linear chromosomes)

A

Hayflick Limit

350
Q

How many cell divisions can happen before the Hayflick limit is reached?

A

~ 50–70 cell divisions

351
Q

Once hayflick limit/senescence is reached → cells age → ____

A

Organisms age

352
Q

Occurs because in adult somatic cells, there’s no _____

A

Telomerase

353
Q

The gene for telomerase not expressed in adult somatic cells; but is highly expressed in ___,___,___

A

fetus, stem, cancer cells

354
Q

Genetic information encoded in the DNA has to remain

A

uncorrupted

355
Q

the DNA in the living cell is subjected to many ____ that can cause changes in the DNA

A

chemical alterations

356
Q

These changes must be corrected, otherwise it can cause ____

A

mutations

357
Q

What are the agents that damage the DNA?

A

Radiations, Reactive oxygen radicals, and Chemicals in the environment

358
Q

In the agents that damage the DNA, what are the examples of Radiations under Ionizing radiations?

A

gamma rays and X-rays

359
Q

In the agents that damage the DNA, what are the examples of Radiations under UV rays?

A

UVC Rays and UVB Rays

360
Q

These are produced during normal cellular respiration and can also damage DNA (one of the agents that damage DNA)

A

Reactive oxygen radicals

361
Q

In the agents that damage the DNA, what are the examples of Chemicals in the environment?

A

hydrocarbons found in cigarette smoke

362
Q

What is a structural damage to the DNA molecule that can affect the ability of the cell to replicate or transcribe?

A

​​DNA lesion

363
Q

What are the Types of DNA damage?

A

single-base aberration, two-base alteration, chain breaks, cross-linkage

364
Q

The importance of ______ is highlighted by several diseases affecting people with deficient repair systems

A

effective DNA repair

365
Q

deamination of cytosine to uracil is what tyoe if DNA damage?

A

single-base aberration

366
Q

insertion/deletion of nucleotide is what tyoe if DNA damage?

A

single-base aberration

367
Q

In the single-base aberration tyoe of DNA damage, what is depurination?

A

there is a loss of purine bases by spontaneous fission of the base sugar link

368
Q

In the single-base aberration tyoe of DNA damage, what is deamination of adenine to hypoxanthine?

A

Uracil and Hypoxanthine are not recognized by DNA polymerases

369
Q

Give the examples of the single-base aberration type of DNA damage.

A

[1] depurination, [2] deamination of cytosine to uracil, [3] deamination of adenine to hypoxanthine, [4] alkylation of base, [5] insertion/deletion of nucleotide, [6] base-analog incorporation

370
Q

Give the examples of the two-base alteration type of DNA damage.

A

[1] UV-light induced pyrimidine dimers (thymine-thymine)
[2] Bifunctional alkylating agent cross link

371
Q

Radioactive disintegration of backbone element is what tyoe if DNA damage?

A

chain breaks

372
Q

Between bases in same (intra-strand) or opposite (inter-strand) strands is what tyoe if DNA damage?

A

cross-linkage

373
Q

Give the examples of the chain break type of DNA damage.

A

[1] Ionizing radiation
[2] Radioactive disintegration of backbone element
[3] Oxidative free radical formation

374
Q

Give the examples of the cross-linkage type of DNA damage.

A

[1] Between bases in same (intra-strand) or opposite (inter-strand) strands
[2] Between DNA and protein molecules (histones)

375
Q

What are the two types of DNA repair?

A

Direct Damage Reversal and Excision of DNA Damage

376
Q

This is the simplest repair mechanism that involves a single step reaction of a single polypeptide chain that binds to the DNA damage and restores the genome to its normal state.

A

Direct Damage Reversal

377
Q

Give the examples of Direct Damage Reversal type of DNA repair

A

Photolyase, O6 methylguanine DNA methyltransferase I and II (MGMT, DNA alkyltransferase)

378
Q

Give the two types of Excision of DNA Damage

A

Mismatch repair (Methyl Directed Mismatch Repair) and Nucleotide Excision Repair

379
Q

Major DNA repair in man due to replication errors or mismatches during strand exchange
Main Objective: To remove the error caused by the faulty proofreading activity of DNA polymerase
Involves exonuclease that facilitates excision of the segment of DNA to be corrected in mismatch repair

A

Mismatch repair (Methyl Directed Mismatch Repair)

380
Q

In Mismatch repair (Methyl Directed Mismatch Repair), what do the two sets of proteins do?

A

the first one identifies the mismatch and the second set replaces the excise segment

381
Q

In mismatch repair, In bacteria, this set of proteins is known as the Mut proteins. While in man, homologous Mut proteins are identified as Mut ___ alpha, Mut ___ alpha, replicative PCNA, clamp loader RFC, the five prime three prime exonuclease EXO1, and DNA polymerase δ

A

Mut S alpha, Mut L alpha

382
Q

Loss of function involved in mismatch repair in man can cause two predisposition syndromes, what are these two syndromes?

A

Lynch syndrome (Hereditary nonpolyposis colorectal cancer-HNPCC) and the Turcot syndrome

383
Q

Exposure of a cell to UV light can result in the formation of pyrimidine dimers, usually thymine.

A

Nucleotide Excision Repair

384
Q

This will inhibit replication because DNA polymerase cannot replicate strands beyond the pyrimidine dimer. Pyrimidine dimers can be formed in the skin cells of humans exposed to unfiltered sunlight. The dimers are removed by the UV specific endonucleases (UVrABC proteins) in bacteria and by XP proteins (XPC, XPA, XPF, XPG) in man.

A

Nucleotide Excision Repair

385
Q

Rare autosomal recessive disease, Hypersensitivity to ultraviolet (UV) light with premature aging

A

Xeroderma pigmentosum

386
Q

Involved in lesions caused by alterations or loss of a base due to spontaneous alteration or by radiation means

A

Base Excision repair

387
Q

In base excision repair, when___ is deaminated, there is a loss in its amino group forming ____ that cannot be recognized by DNA polymerase or when adenine is deaminated by nitrate to hypoxanthine and these lesions can be removed by base excision repair

A

cytosine, uracil

388
Q

In base excision repair, the base is excised or removed by ____ that forms an AP site that lacks either pyrimidine or purine base

A

DNA glycosylase

389
Q

The BASE EXCISION REPAIR involves __, __, __, and __

A

Specific DNA glycosylases (apyrimidinic or apurinic site)
AP endonuclease
Lyase
DNA Pol ligase

390
Q

Involved in repair damage caused by ionizing radiations, free radicals and chemotherapy

A

Double Strand Break repair

391
Q

Oxidative free radicals and high energy radiation can cause ____ in the DNA

A

double strand breaks

392
Q

Corresponds to direct joining of the two ends of the two DNA fragments
Some parts of the DNA are lost in the process and is prone to error and mutation

A

Non homologous and end-joining repair

393
Q

A defect in this system is associated with a predisposition to cancer and immunodeficiency syndrome
Errors can cause: Burkitt’s Lymphoma, Philadelphia chromosome, Chronic Myelogenous leukemia and B-cell leukemia

A

Non homologous and end-joining repair

394
Q

causes of the errors in Non homologous and end-joining repair

A

Burkitt’s Lymphoma, Philadelphia chromosome, Chronic Myelogenous leukemia and B-cell leukemia

395
Q

Uses enzymes that perform genetic recombination between homologous chromosomes during meiosis

A

Homologous repair system

396
Q

Gene Expression

A

Conversion of codon, read as triplet nucleotides in the mRNA, into a specific sequence of amino acids in a polypeptide.

397
Q

How many times does gene expression occur?

A

Several times depending on the metabolic demands or needs of the organisms for survival

398
Q

What is Transcription?

A

The process of copying the exact sequence of the oxyribonucleotides of a gene on a DNA into a ribonucleotides known as an RNA molecule

399
Q

What are the end products of Transcription?

A

mRNA, rRNA, tRNA, snRNA and miRNA

400
Q

snRNA

A

for processing the primary mRNA

401
Q

miRNA

A

for gene regulation

402
Q

Gene

A

The portion of the DNA that is being transcribed

403
Q

Regulatory Genes

A

Regions that flunk the coding region

404
Q

Similarities between replication and transcription

A
  • involves steps with 5’ to 3’ polarity
  • the template is a single-stranded DNA (non-coding region)
  • involves large multi component complexes
  • adheres to the Watson Crick based pairing rules
405
Q

DNA atrand

A

Composed of coding and non-coding strand

406
Q

Non-coding strand

A

Serves as the templates for DNA dependent RNA polymerase

407
Q

How does the RNA polymerase discriminate the coding strand from the non-coding strand?

A

Through the location of the promoter sites

408
Q

Promoter sites

A

Contains the regulatory genes that are located to the left of the coding sequence

409
Q

Direction of Transcription

A

runs in the 5’ to 3’ direction and so the template must be in the 3’ to 5’ direction

410
Q

The sequence of bases in the mRNA transcript is _____ as the sequence of bases found in the coding region of the gene

A

Exactly the same

411
Q

In case of a double stranded DNA containing many genes, the template strand for a given gene ______ strand of the DNA double helix

A

may not necessarily be the same

412
Q

Can the given strand of a double stranded DNA be a template strand of 1 gene but a coding strand of another gene?

A

YES

413
Q

Cistron

A

An alternative term for gene and is represented by the primary mRNA

414
Q

Citron Composition

A
  • Specific sequences of bases for the binding of ribosome
  • Sequence of bases for the codons, specifying for a specific polypeptide
  • Stop codon
415
Q

Polycistronic

A

Encodes two or more polypeptides

416
Q

Monocistronic

A

Encodes a single protein

417
Q

Bacterial vs Eukaryotic RNA in cistron number

A

Bacterial: polycistronic :: Eukaryotic: monocistronic

418
Q

Lac Operon

A
  • a polycistronic gene - composed of a cluster of genes needed for the transport and metabolism of lactose in enteric bacteria like E. coli
419
Q

lacZ

A

Encodes for b-galactosidase

420
Q

lacY

A

Encodes for permease

421
Q

lacA

A

Encodes for transacetylase

422
Q

TRUE OR FALSE. lacZ, lacY, lacA are controlled by different promoters and have different regulatory elements

A

FALSE

423
Q

TRUE OR FALSE. lacZ, lacY, lacA are transcribed as a single mRNA

A

TRUE

424
Q

Steps in Transcription

A

Initiation, Elongation, Termination

425
Q

Composition of the pre-initiation complex

A

RNA polymerase, general transcription factors, and associated transcription factors to the binding sites

426
Q

Promoter Region

A

Binding sites

427
Q

What are promoters?

A

The DNA sequences that promote gene expression. They direct the exact location for the initiation of transcription

428
Q

What is the starting point of transcription?

A

the ‘5 end of the mRNA nucleotide designated as +1 and is AT in most organisms

429
Q

The nucleotide in the promoter adjacent to the transcription initiation is designated as ___.

A

-1

430
Q

Where are promoters typically located?

A

upstream of the site where transcription of the gene actually begins

431
Q

The bacterial promoter region includes the _____ and the ______.

A

Pribnow box and -35 sequence

432
Q

Pribnow box

A

Stretch of 6 nucleotide (5’TATAAT3’), otherwise known as the TATA box (Goldberg-Hogness box)

433
Q

TATA box

A

Homologue of the Hogness box in eukaryotic organisms and where transcription factor bind to recruit RNA polymerase

434
Q

-35 sequence

A

2nd consensus sequence, 3 bases to the left of the start site

435
Q

Pribnow box and -35 sequence

A

2 consensus that specifies to other molecuels where transcription begins

436
Q

TRUE OR FALSE. RNA polymerases are DNA dependent enzymes

A

TRUE

437
Q

What are the E. coli RNA polymerase subunits?

A

two identical alpha subunits & similar, but not identical, β and β’ prime subunits

438
Q

β and β’ prime subunits

A

Catalytic subunits

439
Q

β subunits

A

forms the phosphodiester bonds

440
Q

β’ prime subunits

A

binds the DNA template

441
Q

These subunits are the core polymerase, which is nonspecific and becomes a functional holoenzyme upon binding of ______ that recognizes promoter and initiates transcription.

A

Sigma factor

442
Q

When does termination of bacterial transcription occur?

A

It occurs when the short RNA-DNA hybrid of the open complex is forced to separate

443
Q

TRUE OR FALSE. Termination is not the end of RNA synthesis. Therefore, the new RNA and RNA polymerase are not released

A

FALSE

444
Q

Rho-independent

A

requires presence of intragene self-complementary gene sequences in the newly formed RNA transcript. A stable hairpin loop slows down the RNA polymerase and causes it to pause temporarily

445
Q

Rho-dependent

A

involves rho factor. Has ATPase activity which can induce the release of RNA polymerase from RNA.

446
Q

Why is transcription in eukaryotes more complex than in bacterial transcription?

A

Because eukaryotes are larger organisms, have cellular complexity, and multicellular

447
Q

Prokaryotic vs eukaryotic organisms transcription

A
  • In prokaryotic organisms, transcription is usually coupled with translation. Possible because these two processes occur within the cytoplasm.
  • In eukaryotic organisms, transcription occurs in the nucleus while translation occurs in the cytoplasm.
448
Q

RNA pol I

A

Transcribes all rRNA genes except for 5s rRNA

449
Q

RNA pol II

A
  • Transcribes all structural genes
  • Synthesizes all mRNAs
  • Transcribes some snRNA genes
450
Q

RNA pol III

A

Transcribes all tRNA genes and 5s rRNA gene

451
Q

Core promoter-basal transcription

A

Binding site for TATA-binding protein (TBP) and associated factors

452
Q

Promoter proximal elements-true level of expression

A

Binding sites for transcription factors

453
Q

Elements found in most promoters of structural genes

A

the transcriptional start site, the TATA box, and the regulatory elements.

454
Q

Basal transcription factors includes?

A

RNA polymerase, general transcription factors, and mediator elements needed to initiate transcription

455
Q

Basal transcription pertains to a ___ level of transcription.

A

Low

456
Q

Promoter proximal element

A

calls for a high level expression of the gene

457
Q

Regulatory Elements

A

Specific sequences of nucleotides that affect the binding of RNA polymerase to the promoter

458
Q

Enhancers

A
  • Specific binding sites for activators
  • Stimulate transcription
459
Q

Silencers

A
  • Specific binding sites for repressors
  • Inhibit transcription
460
Q

Location of regulatory elements

A

Vary but often in the -50 to -100 region

461
Q

3 mRNA processing steps

A

5’ Capping, Addition of poly A tail, mRNA splicing

462
Q

Conversion of the nucleotide sequence of the mRNA into a polypeptide

A

Protein Synthesis

463
Q

A specific codon always codes for the same amino acid

A

Unambiguous

464
Q

3 steps of Translation

A

Initation, Elongation, Translation

465
Q

The process by which a string of amino acids (the chemical building blocks of protein) interacts with itself to form a stable three-dimensional structure during production of the protein within the cell

A

Protein Folding

466
Q

____ protein molecules sometimes referred to as the stress proteins & They maintain a quality control of proper protein folding of
proteins and edit the wrongly folded proteins

A

Chaperones

467
Q

A specific example of post translational modification involving amino acid modification is the activation of the clotting factors like _______ factors 7, 9, and 10 which require the gamma carboxylation of glutamic acid residues of these clotting factors

A

prothrombin

468
Q

In post translational Modification, addition of phosphate to glycogen phosphorylase makes the enzyme ____ and so glycogenolysis follows (active/inactive)

A

Active

469
Q

In post translational Modification, ______ is being used as a coenzyme. This is required for the binding of calcium

A

Vitamin K

470
Q

Used as an instruction menu for synthesis of proteins, may be in the form of a structure or enzyme needed for survival and proliferation

A

DNA

471
Q

Carry out life processes, DNA to its functional molecule

A

RNA (mRNA)

472
Q

RNA is donw by using the non coding region of the DNA as a template in a process known as

A

Transcription

473
Q

mRNA goes to ________ to form a functional polypeptide

A

translation

474
Q

True or False. All prokaryotic organisms that includes bacteria share the same replicative and transcriptional mechanisms with eukaryotic organisms

A

TRUE

475
Q

Class of antibiotic that targets DNA replication. Ex: ciprofloxacin, levofloxacin, norfloxacin, oflocaxin

A

Quinolones

476
Q

Antimicrobial agent that binds the beta subunit of DNA gyrase and prevents the catalytic activity of the enzyme by impairing the activity of the enzyme to relegate after cleavage

A

Quinolones

477
Q

Cut the strands of DNA, move through the break. Relegate the DNA strands

A

DNA gyrase

478
Q

Antimicrobial agent that directly attaches to DNA causing DNA Damage

A

Metronidazole

479
Q

Antimicrobial agent that needs a reductive activation of its nitro group upon diffusing across the cell membrane of anaerobic bacteria

A

Metronidazole

480
Q

Antimicrobial agent that target the enzyme for RNA transcription in bacteria. Binds to beta subunit of RNA polymerase

A

Rifampicin

481
Q

What happens when the catalytic action of the beta subunit is inhibited

A

No formation of phosphodiester bonds that link one rebonucleotide to another ribonucleotide

482
Q

Antiviral and anti caner agents inhibiting elongation of DNA chain. Ex: 2,3-deoxynucine, cytosine arabinodisde, adenine, arabinoside, acyclovir.

A

Nucleotide Analogs

483
Q

Bacterial protein synthesis is clasified into

A
  1. 30s Subunit 2. 50s Subunit
484
Q

Streptomycin and tratrcycline are examples of

A

30s Subunit

485
Q

erthromycin, lincomycin, and clindamycin are examples of

A

50s Subunit

486
Q

True or False. Inihibitng nucleic acids and protein synthesis is another key approach in battling bacterial infections

A

TRUE

487
Q

True or False. Inihibitors either cleave the DNA resulting to DNA damages that cannot be repaired or Inhibits the formation of the carrier of genetic code or inhibits the formation of polypeptide

A

TRUE

488
Q

What would happen if there is NO DNA duplication, transcription, and translation

A

Cell will not survive and not replicate

489
Q

Polypeptide or proteins are translated from mRNA by a translation machinery called

A

Ribosome

490
Q

Difference between 30s subunit and 50s subunit

A

30s fits mRNA. 50s has catalytic functions

491
Q

Diffrence betrween ribosomes and codons

A

Ribosomes translate the mRNA by reading nucleotides as codon while codons are a sequence of three nucleotidesin mRNA that corresponds to a specific amino acid making the polypeptide

492
Q

How do Quinolones treat bacterial infections

A

Quinolones bind to DNA gyrase inhibitng DNA replication necessary of cell division and bacteria eventually die off

493
Q

Expression of the genetic information is quantitatively increased by the presence of a specific regulatory element

A

Positive regulation

494
Q

Specific regulatory element whose presence quantitatively increases expression of genetic information

A

Activator/inducer

495
Q

Expression of the genetic information is diminished by specific regulatory elements

A

Negative regulation

496
Q

Specific regulatory element that diminishes expression of the genetic information

A

Repressor

497
Q

True or False: Regulation of gene expression occurs only at one step of gene expression

A

False. Regulation occurs at different steps

498
Q

Gene expression is controlled mainly at ____ level

A

Transcription

499
Q

Examples of RNA molecules needed for the formation of a polypeptide chain

A

mRNA, tRNA, rRNA

500
Q

Forms a structural protein or an enzyme

A

Polypeptide

Module 1B (7 decks)

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