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Metabolism, Molecular, and Pharmacogenomics (MMP) > Molecular Biology (Quiz 1, Chp 9, 10, 11) > Flashcards

Molecular Biology (Quiz 1, Chp 9, 10, 11) Flashcards

1
Q

What is the central dogma?

A

This is a theory that explains the flow of genetic information within a biological system. It states the genetic information flow from DNA to DNA and from DNA to RNA to protein.

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2
Q

What are the two types of nucleic acids?

A

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

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3
Q

What is DNA?

A

DNA contains genetic information used in to development and functioning of all known living creatures. It is the carrier of genetic information.

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4
Q

What is RNA?

A

RNA is involved in the transmission of the genetic information to the cell machinery. It is the transmitter of the genetics encoded into DNA.

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5
Q

What are prokaryotes?

A

Prokaryotes are single-celled organisms that lack a nucleus. It includes things like bacteria and archea.

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6
Q

What are the characteristics of DNA within prokaryotes?

A

The DNA is interspersed throughout the cytosol as there is no nucleus. The DNA is circular. Some prokaryotes have plasmids.

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7
Q

What are plasmids?

A

Plasmids are a small amount of DNA that carry genes for survival such as antibiotic resistance genes. Plasmids replicate independently and do not need genomic DNA to do so. Plasmids are also not infectious.

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8
Q

Will a prokaryote survive if it loses a plasmid?

A

Yes, it does not need a plasmid to survive. The plasmid only provides extra functions.

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9
Q

What are eurkaroyotes?

A

Eukaryotes have DNA within the nucleus of a cell.

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10
Q

In eukaryotes, where does transcription occur?

A

Nucleus

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11
Q

In eukaryotes, where does protein synthesis occur?

A

Ribosomes in cytosol.

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12
Q

Does the mitochondria have it own genetic material?

A

Yes. Mitochondria have their own DNA and RNA so it can make proteins for itself. The DNA is circular which makes sense as millions of years ago the cells incorporated the mitochondria in which was a bacteria.

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13
Q

What are the characteristics of DNA in eukaroyotes?

A

DNA is linear and associated with histone protein to form chromatin.

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14
Q

The primary structure of nucleic acids refers to a _________________ of DNA.

A

Single strand

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15
Q

How is the primary structure of a nucleic acid determined?

A

Order of the nucleotides

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16
Q

The order of what in DNA determines the genetic information?

A

Nucleotides

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17
Q

Each nucleotide (NTP and dNTP) consist of what 3 things?

A
  1. 5-carbon sugar
  2. Nitrogen-containing base covalently attached to the sugar
  3. Phosphate group covalently attached to the sugar
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18
Q

What bond attaches the phosphate group to the 5’ carbon of the sugar ring in nucleotides?

A

Covalent phosphoester bonds

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19
Q

What is the functional unit of the nucleotide?

A

Nitrogenous base

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20
Q

What are the four base nucleotides that make up DNA?

A

Adenine, Thymine, Guanine, and Cytosine

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21
Q

What are the four base nucleotides that make up RNA?

A

Adenine, Uracil, Guanine, and Cytosine

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22
Q

What 3 nucleotides come from pyrimidine?

A

Thymine, uracil, and cytosine

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23
Q

What two nucleotides come from purine?

A

Adenine and guanine

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24
Q

What is a nucleoside?

A

A nucleoside is just a nucleotide without a phosphate group attached

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25
Q

What bond joins together nucleotides?

A

Phosphodiester bond which is a strong covalent bond.

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26
Q

How is DNA and RNA always read?

A

5’ end to 3’ end.

Note: When being replicated and translated it is read by the polymerases from 3’ to 5’.

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27
Q

What is the DNA backbone?

A

The DNA is protected by a sugar and phosphate backbone.

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28
Q

The secondary structure of DNA is referring to ____________.

A

DNA Double Helix

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29
Q

In the DNA double helix, the two chains are _____________.

A

Antiparallel

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30
Q

What is chargaff’s rule?

A

This is the idea of base pairing and how 1 pyrimidine is also paired with 1 purine to make the DNA a 50/50 split of both.

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31
Q

In DNA, adenine and thymine are base pairs. How many and what type of bonds hold them together?

A

2 Hydrogen bonds

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32
Q

In DNA, guanine and cytosine are base pairs. How many and what type of bonds hold them together?

A

3 Hydrogen bonds

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33
Q

Complementary base pairing is the _____________ for _____________ of DNA.

A

Foundation
Replication

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34
Q

The original parental strands of DNA are __________ and seperate to allow access for new base pairs.

A

templates

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35
Q

How do you get from the DNA strand to the complementary strand?

A
  1. Match base pairs

5-ATCG-3 =
3-TAGC-5

  1. Reverse it

3-TAGC-5 =
5-CGAT-3 which is the complementary strand

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36
Q

DNA can exist in both left and right handed forms. What is the most common form?

A

Right-handed form

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37
Q

What are the 3 conformations of DNA and which is most common?

A

B, A, and Z

B is the most common conformation and is right-handed.

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38
Q

What are the characteristics of the B right-handed conformation of DNA?

A
  1. The planes of the nucleotide bases in the double helix basically perpendicular to the helix axis
  2. Each base pair has the same width 2 nanometer diameter)
  3. It has 10 base pairs per helical twist (each base pair is 36 degrees)
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39
Q

Is the Z conformation of DNA left or right handed?

A

Left-handed and is very rare

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40
Q

Can the conformation of DNA (B, A, Z right/left) be switched?

A

It can be switched but not randomly.

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41
Q

What are the 3 bonds that stabilize DNA and which is the strongest?

A
  1. Hydrogen bond
  2. Stacking interaction (strongest)
  3. ionic interaction
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42
Q

Stacking interactions that stabilize DNA result from ____________ forces.

A

Hydrophobic

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43
Q

Do GC pairs or AT pairs alter DNA stability?

A

GC pairs increase DNA stability. The more GC pairs means the more stable the DNA is.

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44
Q

What is DNA denaturation?

A

DNA denaturation/melting is the process is which DNA loses the secondary structure that is present in the native state due to heat or alkali chemicals.

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45
Q

On the UV spectrum, what is the difference between Native and Denatured DNA?

A

Denatured DNA has…
1. Decreased viscosity
2. Increased UV absorbance

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46
Q

Can DNA denaturation be reveresed?

A

Yes. Reversing denaturation is called renaturation or hybridization.

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47
Q

Why is DNA supercoiled?

A

To package it tighter

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48
Q

In prokaryotic cells, is the direction of the supercoil the same or different than the DNA conformation?

A

It is the opposite. If the DNA is right-handed conformation, the supercoil will be left handed

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49
Q

What is the function of type I topoisomerases?

A

Type 1 topoisomerase break one DNA strand in prokaryotic DNA.

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50
Q

What is the function of type II topoisomerases?

A

Type II topoisomerase is also called a gyrase. It breaks both strands of DNA.

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51
Q

What is the general functions of topoisomerase enzymes?

A

They cut and relax DNA so it be used as a template in replication.

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52
Q

What two antibiotics inhibit DNA gyrase (topoisomerase II)?

A

Ciprofloxacin and Novobiocin

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53
Q

The DNA molecules are integrated with proteins allowing it to fold and become compact. What are these called?

A

Chromatin/ chromosomes

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54
Q

What are the two main groups of proteins involved in the folding/packaging of eukaryotic chromosomes?

A

Histones (fixed in the chromatin and + charge) and non-histones (not fixed in the chromatin and less + charge)/=.

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55
Q

What are the 5 different histones proteins?

A

H1, H2A, H2B, H3, and H4

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56
Q

Histones have different percentages of arginine and lysine in them. What do these amino acids do?

A

These allow the histones to be positively charged and therefore attracted to the negatively charged DNA and incorporate themselves into DNA-protein complex.

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57
Q

The basic unit of chromatin organization is the __________.

A

Nucleosome. Nucleosome consists of the DNA double helix strands that twist around the histone protein core as well as the linker DNA and H1 protein. The histone proteins are in the basketball thing.

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58
Q

Each nucleosome contains __________ basepairs of DNA.

A

200

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59
Q

Nuclease digestion releases the nucleosome core particle. This nucleosome core particle consists of ________ base pairs and ____________ histones.

A

150
Octamer

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60
Q

What is contained within the nucleosome octamer?

A

Two H2A/H2B dimers and two H3/H4 dimers. This totals 8 histones proteins

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61
Q

After nuclease digestion, how come 50 base pairs are lost?

A

There are linker DNA strands that are 50 basepairs. So when the nucleosome is digested, the linker DNA is lost resulting in a core particle that is 150 base pairs.

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62
Q

What is the H1 protein for on the nucleosome?

A

The H1 protein binds to linker DNA and attaches the nucleosomes together. It binds to the nucleosome core particle and stabilizes the DNA strand that twists around the octamer.

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63
Q

The nucleosome structure is still not coiled enough. It has to be coiled even further into ______________.

A

30nm fiber

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64
Q

How many nucleosomes are in 1 turn of the 30nm fiber for further condensing?

A

6 nucleosomes per turn

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65
Q

What are 3 drugs that can inhibit topoisomerases to be used as anticancer chemotherapeutic agents?

A

Doxorubicin, Etopiside, and Camptothecin

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66
Q

What is the sequence of condensing a DNA strand into a chromosome?

A

DNA stand —–> double helix —-> nucleosome (supercoil) —-> 30nm fiber——-> chromatin——> chromosome

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67
Q

During what phase of cell division are chromosomes formed?

A

M phase

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68
Q

During what phase of cell division is DNA replicated?

A

S phase

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69
Q

What is the size of the human genome?

A

Over 3 billion base pairs

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70
Q

How many genes does the human genome contain?

A

Between 20,000 and 25,000 genes

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71
Q

What is the definition of a gene?

A

A gene is the functional unit of the chromosome and is a sequence of nucleotides in DNA that codes for a molecule, a polypeptide or a RNA molecule, which has a function. There is a regulatory and intergenic region

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72
Q

What is an allele?

A

An allele is a variant form of a gene. Alleles can have dominant and recessive genetic diseases encoded passed from either mom, dad, or both.

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73
Q

RNA is _________ stranded and connected by __________ bonds. RNA is stabilized by ___________ interactions.

A

Single
Phosphodiester
Stacking

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74
Q

What are the main differences between DNA and RNA?

A

Know this chart

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75
Q

In eukaryotes, DNA has to be replicated _______ a cell _______ during the S phase.

A

Before
Dividies

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76
Q

What provides the mechanism for DNA replication?

A

Complementary base pairing and bi-directionality

77
Q

What does it mean that DNA replication is semiconservative?

A

This means that each new DNA molecule made has one parental strand and one new strand.

78
Q

What are the 3 things that DNA replication requires?

A
  1. DNA template
  2. DNA polymerase
  3. deoxyribonucleotides (dNTPs)
79
Q

What is the function of DNA polymerase?

A

DNA polymerase forms the phosphodiester bonds between to adjacent nucleotides when forming the new DNA strand. It does NOT make the hydrogen bonds between nucleotide base pairs.

80
Q

What type of bond is a phosphodiester bond?

A

Covalent bond

81
Q

Why is DNA replicated semidiscontinously?

A

It is replicated semi discontinuous because DNA polymerase can only go in the 5’ to 3’ direction to make a new strand. Therefore, it can go continuously when making the leading strand (its template is 3’ to 5’) but has to stop and start again for the lagging strand.

82
Q

The DNA chain extends from the ____________ direction due to DNA polymerase only being able to add new nucleotides in this direction?

A

5’ to 3’

This means that parent template is 3’ to 5’

83
Q

What is a leading strand?

A

The leading strand is the strand that is replicated continuously from the point of origin the 5’ to 3’ direction.

84
Q

What is the function of helicases in DNA replication?

A

Helicases separate bases pairs in a double strand of DNA to make a single strand.

85
Q

What is the function of single-strand binding proteins in DNA replication?

A

These cover the template single strands so they do not reform into a double strand as it wants to do.

86
Q

What is the function of topoisomerases in DNA replication?

A

Topoisomerases release the supercoils in DNA

87
Q

What is a lagging strand?

A

The lagging strand is synthesized discontinuously against the overall direction of replication. It is made in many short fragments from the replication fork towards to origin.

88
Q

What are okazaki fragments?

A

These are the short fragments that are made when synthesizing the lagging strands.

89
Q

Why does DNA polymerase require a template and a primer?

A

DNA polymerase needs a template in order to bring in the correct matching base pairs.

DNA polymerase needs a primer that tells it to start replication. In eukaryotes, the primer is an RNA-DNA primer. The location of the primer is denoted as the origin of replication.

90
Q

What is the direction of DNA polymerization done by DNA polymerase?

A

5’ to 3’ as DNA polymerase can only add nucleotides to the 3’ end of DNA where the free hydroxyl group is.

91
Q

What is the origin of replication?

A

This is a particular sequence at which DNA replication is initiated. This area has an increased % of A-T base pairs as these are less stable and aid in the separation of the two DNA strands.

92
Q

What is the replication eye and replication fork?

A

The replication eye is where DNA double strand begins to open and forms an eye shape. The replication fork is the location in which the strands are opening. Prokaryotes have a single replication eye and two forks while eukaryotes have many replication eye and many forks due to its linear shape.

93
Q

What are the major functions of DNA polymerase I for prokaryotic DNA replication ?

A

DNA polymerase I is found in the highest concentration compared to the others (II, III). It adds new nucleotides from the 5’ to 3’ direction while also acting as an exonuclease for both the 5’ to 3’ and 3’ to 5’ direction. Specially when acting as a 5’ to 3’ exonuclease, it cleaves nicked DNA.

It majors functions include removing RNA primers and replacing them with DNA (filling the gap) and repairing damaged DNA. It is NOT a major replicase in the synthesis of DNA strands.

94
Q

What are the major function of DNA polymerase III for prokaryotic DNA replication?

A

DNA polymerase III adds new nucleotides from the 5’ to 3’ direction while also acting as an exonuclease from just the 3’ to 5’ direction. DNA polymerase III is the major replicase in prokaryotic DNA replication as it has two catalytic cores that can synthesize both the leading and lagging strand at the same time.

95
Q

Does DNA polymerase III need sliding clamps?

A

In order to be efficient, yes it needs the sliding clamps. With the sliding clamps, it can replicate around 5,000 nucleotides. Without the sliding clamps, it will fall off and dissociate after around 12 nucleotides.

96
Q

How is the DNA chain elongated in prokaryotes?

A

It is elongated through the actions of DNA polymerase III adding nucleotides from the 5’ to 3’ direction.

97
Q

Describe the mechanism that ensures the high fidelity of DNA replication in prokaryotic cells.

A
  1. Cells maintained a balanced level of deoxynucleotides (dNTPs)
  2. The polymerase reactions are completed in 2 stages
  3. DNA polymerase I and III act as exonucleases to proofread 3’ to 5’
  4. DNA polymerase can’t start replication without RNA primers
  5. There are more intracellular mechanisms that detect and repair DNA mismatch
98
Q

DNA replication in prokaryotes is __________ and __________.

A

Bidirectional, semiconservative, and has multiple initiations.

99
Q

What is the function of DnaA, DnaB, and DnaC?

A

DnaA is a protein that activates the initiation of DNA replication in prokaryotes. It binds to the origin of replication first and the concentration of it determines if replication will start. Once initiated, DnaB and DnaC bind and act as a helicase to separate the two strands.

100
Q

Do helicases and topoisomerases in DNA replication of prokaryotes have the same functions as in eukaryotes?

A

Yes. Helicases separate the strands and topoisomerases relieve the supercoiling.

101
Q

What is the function of primase in DNA replication in prokaryoties?

A

Primase synthesizes the RNA primers to the DNA strands in order to initiate DNA synthesis.

102
Q

Proofreading in DNA replication is a ____________ exonuclease activity.

A

3’ to 5’

103
Q

DNA polymerase initially makes about _________ base pair errors. After proofreading by exonucleases, the error rate is about _____________ base pairs.

A

1 in 10,000
1 in 1 billion

104
Q

What is the function of DNA ligase in prokaryotic cells?

A

DNA ligase together with DNA polymerase I joins the okazaki fragments together and make one long replicated strand. Basically, DNA polymerase I fills the gaps after the primers have been removed and DNA ligase joins the fragments together.

105
Q

Know this chart stating the differences in DNA replication between prokaryotes and eukaryotes.

A
106
Q

When does DNA replication occur in the cell cycle in eukaryotes?

A

S phase

107
Q

What is the function of DNA polymerase alpha?

A

DNA polymerase A along with a primase make the RNA-DNA primer needed to initiate DNA synthesis in eukaryotes. This polymerase does not act as an exonuclease. DNA polymerase alpha mainly has 5’ to 3’ polymerase activity and is involved in the initiation of the leading strand and lagging strand.

108
Q

What is the function of DNA polymerase delta δ in eukaryotic cells?

A

DNA polymerase delta has both 5’ to 3’ polymerase activity and 3’ to 5’ exonuclease activity meaning it can proofread. This polymerase associated with a sliding-clamp protein called PCNA and a clamp loaded called RFC. Its main function is the synthesis of the lagging strand.

109
Q

What is the function of DNA polymerase epsilon ε in eukaryotic cells?

A

DNA polymerase epsilon has both 5’ to 3’ polymerase activity and 3’ to 5’ exonuclease activity but it does not need a sliding clamp. It is mainly involved in the synthesis of the leading strand.

110
Q

How is the RNA-DNA primer removed during eukaryotic DNA replication?

A

The primer is removed by flap endonuclease I and RNase H. The gap left by the primer is filled by DNA polymerase delta.

111
Q

What happens to the nucleosomes during and after replication?

A

The nucleosome can’t be used for DNA replication. It must be disassembled in order for the replication fork to move through. Once it is replicated, the nucleosomes are reassembled.

112
Q

What is a telomere and what are the protecting?

A

DNA polymerase can’t add the the extreme 5’ ends of the lagging strand meaning that without a telomere, the 5’ end of new DNA would continue to get shorter and shorter resulting in the loss of genes. Telomeres are at the end of chromosomes and protect from genes being lost. Without telomeres, chromosomes would be shortened by the length of a primer during each round of replication. They also protect one chromosome from fusing to another.

113
Q

What is the difference in telomeres and the telomerase between normal cells and cancer cells?

A

In normal cells, telomerase activity is typically low, meaning telomeres naturally shorten with each cell division, eventually leading to cell senescence and death; whereas in cancer cells, telomerase is often highly active, allowing for the maintenance of telomere length, enabling continuous cell division and immortality.

114
Q

What is the function of telomerase and why is this enzyme unlike other DNA polymerases?

A

Telomerase carries a small segment of RNA that is complementary to the 6-base pair tandem repeat. This allows it to add new repeats and synthesize telomeres. It function to replace the repeats at the ends of chromosomes. This enzyme is unlike other DNA polymerases as it is an RNA-dependent DNA polymerase.

115
Q

What is DNA damage and what are some causes that can lead to DNA damage?

A

DNA damages are physical damages to nucleotides and DNA strands that are frequent. Sources of damage include replication errors by DNA polymerase, endogenous DNA damage due to ROS, exogenous DNA damage due to UV radiation, X-rays, chemo, etc, and finally, error-prone DNA repair.

116
Q

Why does smoking cigarettes lead to DNA mutation and cancer?

A

Benzoapyrene (BaP) in cigarette smoke is not carcinogenic until it is oxidized within cell. Once oxidized, it binds covalently to guanine residues in DNA therefore interrupting the hydrogen bonding in the G-C base pairs in DNA. This causes distortions in the DNA helix which interferes with replication.

117
Q

What is base excision repair?

A

This is a type of DNA repair. In base excision repair, the glycosylase cleages the glycosidic bond between altered/messed up base pairs and ribose.

118
Q

What is nucleotide excision repair?

A

This is a type of DNA repair. In nucleotide excision repair, the entire nucleotide is removed at once. The gap formed by the incision and excision endonucleases is usually several nucleotides wider than shown.

119
Q

What is mismatch repair?

A

This is a type of DNA repair. It occurs after DNA polymerase proofreads and errors still exist. Mismatch repair detects and repairs post-replication mismatches.

120
Q

What is xeroderma pigmentosum and what causes it?

A

This is a deficiency of nucleotide excision repair therefore DNA repair no longer occurs after UV radiation causes pyrimidine dimers.

121
Q

Is xeroderma pigmentosum a recessive or dominant genetic disease?

A

This is autosomal recessive

122
Q

What is the major cause human hereditary nonpolyposis colorectal cancer syndrome?

A

Defects in mismatch repair result in incidence of human cancers like hereditary nonpolyposis colorectal cancer syndrome.

123
Q

Is human hereditary nonpolyposis colorectal cancer syndrome a recessive or dominant genetic disease?

A

This is autosomal dominant (only 1 mutation in 1 copy of the gene from mom or dad needed)

124
Q

What is the difference between DNA and RNA polymerase?

A

DNA polymerase does require a primer to start while RNA polymerase does not.

125
Q

What is messenger RNA (mRNA)?

A

This is the template for protein synthesis. It is also called the coding RNA.

126
Q

What is ribosomal RNA (rRNA)?

A

This is used for the protein synthesis scaffolding and machinery. This is noncoding RNA as it is not used as the template for protein translation.

127
Q

What is transfer RNA (tRNA)?

A

This is the adapter and decoder for protein synthesis and brings in the amino acids to the ribosome to make proteins. Noncoding RNA.

128
Q

What is the template for RNA polymerase?

A

The template for RNA polymerase is the antisense noncoding strand and is read from 3’ to 5’ and the RNA is made from that is from 5’ to 3’

129
Q

What is the direction of RNA polymerase?

A

RNA polymerase reads a DNA strand from 3’ to 5’ and the new RNA strand is synthesized from 5’ to 3’

130
Q

What is the substrate of RNA polymerase?

A

One DNA strand

131
Q

What is the product of RNA polymerase?

A

RNA

132
Q

What is the error rate for RNA polymerase? How does that compare to DNA polymerase?

A

The error rate is high for RNA polymerase is high, about 1 in 10,000 while DNA polymerase is about 1 in 10 million.

133
Q

What bond does RNA polymerase form?

A

RNA polymerase forms the phosphodiester bonds between NTPs in the new RNA strand.

134
Q

What is the difference between prokaryotic RNA polymerase core enzyme and holoenzyme?

A

RNA polymerase holoenzyme includes 6 subunits: sigma (σ), beta prime (β’), beta (β), omega (ω), and two alpha (α) subunits. The sigma portion is needs to bind to the core enzyme to direct the RNA polymerase to specific promoter regions in the DNA template. After around 10 nucleotides make up the new RNA strand, the sigma complex dissociates leaving the RNA polymerase core enzyme with the 5 subunits (all the same except no sigma).

135
Q

What is the structure of the promoter region for prokaryotic polymerases?

A

The promoter region for prokaryotic RNA polymerases to bind to start with the -35 region and the -10 region. The -10 region is what the sigma factor on RNA polymerase holoenzyme recognizes. The -10 region is also called the Pribnow box. Initiation begins at the initiation site at +1 region.

136
Q

What is the structure of the typical prokaryotic transcription unit?

A
137
Q

What is needed in prokaryotic cells to initiate transcription?

A

To initiate transcription, RNA polymerase must bind to the promoter region that has consensus sequences. The consensus sequence is TATAAT and is called the Pribnow box located the the -10 region in the gene.

138
Q

What is the transcription bubble?

A

A transcription bubble is like the replication eye in DNA replication. When the RNA polymerase with the sigma factor binds to the promoter region, it causes the DNA strands to unwind and seperate the form the transcription bubble.

139
Q

What is the difference between the open and closed complex formed by RNA polymerase?

A

The open complex is when the sigma subunit leaves the RNA polymerase holoenzyme creating the RNA polymerase core enzyme.

140
Q

What is needed in prokaryotic cells to elongate the RNA transcript?

A

To elongate RNA, 4 things are needed:
1. dsDNA (single DNA strand template)
2. RNAP core enzyme (RNA polymerase)
3. Nucleoside triphosphates (NTPs)
4. Topoisomerases

141
Q

How is transcription terminated with the Rho factor?

A

The Rho factor causes the release of the RNA transcript from the template when RNA polymerase meets the termination signal. The Rho protein (an NTP-dependent helicase) chases up the new RNA strand to meet with RNA polymerase to cause termination around 80-100 base pairs before the termination signal is reached.

142
Q

How is transcription terminated without the Rho factor?

A

Without the Rho factor, the RNA strand form a hairpin loop. The strip of U’s tells RNA polymerase to stop.

143
Q

How many stages of transcription do prokaryotic cells have and what are they?

A

There are 3 stages of transcription in prokaryotes and they include 1) initiation 2) elongation and 3) termination

144
Q

Do prokaryotic cells have post-transcriptional processing?

A

Not in the sense that eukaryotes do. In prokaryotes, transcription and translation can happen at the same time. This means mRNA goes directly into translation while the mRNA is still being transcribed from the DNA template.

145
Q

What is the MOA of rifampicin?

A

Rifampicin inhibits transcription by RNA polymerase in prokaryotic cells therefore preventing the RNA chain elongation. Overall used to treat infectious disease.

146
Q

What is a bacterial operon?

A

Bacterial genes are organized into operons, or clusters of coregulated genes. A single promoter may control the transcription of an operon containing many cistrons. The translation of a polycistronic mRNA can result in several polypeptide chains.

Only 1 promoter per 1 operon

A bacterial operon is a cluster of genes on a bacterial DNA strand that are regulated together under a single promoter.

147
Q

Why and how do bacteria use operons to regulate gene expression?

A

One mRNA can produce multiple protein polypeptides. Bacterial genes are organized into operons, or clusters of coregulated genes. A single promoter may control the transcription of an operon containing many cistrons. The translation of a polycistronic mRNA can result in several polypeptide chains.

148
Q

Why do single genes quickly give rise to many copies of it gene products like RNA and proteins in prokaryotes?

A

Many prokaryotic genes are organized in operons, meaning that a single mRNA can carry the instructions for multiple proteins. This polycistronic nature allows several genes to be transcribed and translated together, increasing efficiency. Transcription (RNA synthesis) and translation (protein synthesis) are physically coupled increasing the rate of production.

149
Q

What is the location of the 3 major eukaryotic RNA polymerases?

A

A. RNA polymerase I- nucleolus
B. RNA polymerase II- nucleoplasm
C. RNA polymerase III- nucleoplasm

150
Q

What are the products of the 3 major eukaryotic RNA polymerases?

A

A. RNA polymerase I- mature rRNA
B. RNA polymerase II- hnRNA which matures to mRNA
C. RNA polymerase III- 5S rRNA, tRNA, and snRNA

151
Q

What are the differences between the promoters for prokaryotic and eukaryotic polymerases?

A

Eukaryotic RNA polymerases contain many subunits and require transcription factors for initiation while prokaryotic RNA polymerases only contain 6 subunits and require the sigma factor to initiate.

152
Q

What are the requirements for each stage of eukaryotic RNA transcription?

A

4 stages:
1. Initiation
2. Elongation
3. Termination
4. Transcriptional processing

153
Q

What are the requirements for transcription initiation in eukaryotes?

A

5 things:
DNA with promoters
RNA polymerase
Nucleoside Triphosphates (NTPs)
Transcription factors
Topoisomerases

154
Q

What are the requirements for transcription elongation in eukaryotes?

A

Elongation is done by RNA polymerase II and makes RNA from the 5’ to 3’ direction.

155
Q

What are the requirements for transcription termination in eukaryotes?

A

Polyadenylation signal (AAUAAA) seems to be important in transcription termination as well as stability, nuclear export, and translation.

156
Q

What are the requirements for transcription transcriptional processing in eukaryotes?

A

Transcriptional processing functions to protect the new RNA, export RNA from nucleus, and facilitate protein translation. In transcriptional processing, 3 things are done: 1) 5’cap is added 2) Poly A tail is added and 3) introns are spliced out of immature mRNA

157
Q

What is the 5’ cap that is added to mRNA in transcriptional processing?

A

This is a methylguanosine linked to the 5’ terminal residue of the mRNA via an 5’-5’-triphosphate linkage (covalent bond)

158
Q

How many general transcription factors are needed for eukaryotic transcription?

A

There are 2 categories of transcription factors: 1) general transcription factors. These bind to the TATA box promoter region and facilitate the binding of RNA polymerase II to DNA. In total, 6 basal transcription factors are needed to RNA polymerase II to bind to DNA. 2) Repressors and activators that regulate gene expression. Repressors bind to silencers and inhibit RNA transcription while activators bind to enhancers and promote RNA transcription.

159
Q

What are the post-transcriptional modifications of eukaryotic mRNA (capping, poly-A tail, and splicing)?

A
  1. 5’ cap is added which is a 7-methylguanine (donated from SAM) linked to 5’ terminal residue on RNA via a 5’,5’-triphosphate linkage (covalent bond). This occurs when the new RNA reaches 30 nucleotides.
  2. Splicing occurs next which removes introns which is co-transcriptional (happens as RNA is being made) and proceeds from 5’ to 3’ end. Catalyzed by a spliceosome which is an snRNA protein complex.
  3. Poly-A tail added at 3’ end which is 250 nucleotides catalyzed by Poly(A) Polymerase.
160
Q

How is eukaryotic pre-rRNA processsed?

A
  1. The 5S rRNA is transcribed in nucleoplasma by RNA polymerase III and its moves into the nucleolus
  2. The other rRNAs are transcribed from DNA by RNA polymerase I and mature in the nucleolus.
  3. The mature rRNAs form 40s and 60s ribosomal subunits which then migrate to the cytoplasm.
161
Q

How is eukaryotic pre-tRNA processed?

A
  1. Transcription occur forming the tRNA precursor cloverleaf shape and portions of the 5’ and 3’ ends are cleaved off
  2. Introns are removed by endonucleases
  3. Bases are modified and the CAA portion is added to 3’ end by nucelotidytransferase enzyme (The final A is where the amino acids attach)
  4. Mature tRNA travels into the cytoplasm
162
Q

What are the differences in post transcriptional processing between prokaryotic and eukaryotic cells?

A

Prokaryotes use mRNA immediately and rRNA and tRNA are spliced from a larger transcript. On the other hand, in eukaryotes, mRNA undergoes capping, polyadenylation, and splicing. rRNA is spliced from a larger transcript but tRNA is trimmed, modified, and a CCA group is added.

163
Q

How many double-stranded DNA molecules of 8 base pairs are theoretically possible?

A

65,536

164
Q

Which of the following statements about this structure is true?

A. It contains a phosphodiester bond
B. It contains a pyrimidine base
C. It is a dinucleotide
D. It is a nucleoside triphosphate

A

D. It is a nucleoside triphosphate

164
Q

For 5’ ATCGATCGATCGATCG 3’, determine the
sequence and direction of the complementary DNA
strand.

A. 5’ ATCTATCGATCGATCG 3’
B. 3’ ATCGATCGATCGATCG 5’
C. 5’ CGATCGATCGATCGAT 3’
D. 5’ CGAUCGAUCAUCGAU 3’

A

C. Remember to match and flip

164
Q

Why does the Tm of DNA increase as the % of GC content increases?

A. A CG base pair makes 3H bonds, whereas an AT pair makes 2H bonds
B. GC base stacking interactions are greater than AT bases
C. The bases G and C are more hydrophobic than A and T
C. The bases G and C have a greater combined molecular mass than A and T

A

B. The stacking interactions with GC are greater than that of AT

165
Q

Histone H1 binds to ________, which is between two _____________.

A

Linker DNA
Nucleosomes

165
Q

If a piece of genomic DNA contains 30%
A, what will be its % content of G?

A. 30%
B. 40%
C. 20%
D. 70%

A

C. 20%

165
Q

Which of the following best describes the
structure of a nucleosome core particle?

A. Approximately 150 bp of DNA wrapped around a set of 2
H2A/H2B and 2 H3/H4
B. About 150 bp of DNA wrapped around an octamer of H1 with
H2A,B, H3 and H4
C. About 150 bp of DNA wrapped around a tetramer of either
H2A/H2B or H3/H4
D. About 200 bp of DNA wrapped around a tetramer of
H2A,H2B,H3, and H4

A

A.

166
Q

What RNA takes amino acids to ribosomes that are joined together to make proteins?

A

tRNA

167
Q

Which of the following statements about proof-reading in DNA polymerase is true?

A. Proof-reading is, specifically, a 3’ endonuclease activity.
B. E. coli DNA polymerase III cannot proofread.
C. Proof-reading enhances the rate of DNA polymerase.
D. Proof-reading to remove a wrong nucleotide is a hydrolysis reaction.

A

D. Proof-reading to remove a wrong nucleotide is a hydrolysis reaction

168
Q

Which of the following is not required for the replication fork?

A. DNA gyrase
B. DNA polymerase III
C. DNA A
D. SSB protein (single-strand binding)

A

C. DNA A is not required

169
Q

The replication of DNA is best described by which of the following?

A. It progresses in both directions away from Ori.
B. It requires a DNA template that is in 5’ to 3’ direction.
C. It produces one double helix consisting of two new strands.
D. It requires a 3’ phosphate group to initiate replication.

A

A. It progresses in both directions away from the Ori

170
Q

T or F: Enzyme that is involved in opening the DNA helix into its single strands for DNA replication is Primase.

A

False. It is Helicase

171
Q

A variety of drugs can alter DNA replication in eukaryotic cells.
Which one of the following steps could be a target for such a
drug? Choose the one best answer.

A. The enzyme family of topoisomerases, which copy each parental strand in the 3′-to-5′ direction
B. The enzyme family of helicases, which copy each parental strand in the 5′-to-3′ direction.
C. The enzyme family of DNA polymerases, which unwinds parental strands
D. The enzyme DNA ligase, which joins Okazaki fragments

A

D. The enzyme DNA ligase which joins Okazaki fragments together

172
Q

Primase is not required during DNA repair processes because of which one of the following?

A. DNA would be highly mutagenic at a repair site
B. DNA polymerases can use 3′-OH of the existing Okazaki
fragment for elongation.
C. All of the primase is associated with the origin of replication.
D. DNA polymerases do not require a primer.

A

B.

173
Q

Gene “start” sequences for transcription could be predicted to have which of the following features?

A. Unusual helical structure
B. Relatively high melting temperature
C. Relatively high proportion of A and T base pairs
D. High binding affinity for histones

A

C. The start gene sequences has a high proportion of A and T base pairs as they have less strong bonds

174
Q

The following gene (coding is 5 to 3) is transcribed. What is the sequence of the mRNA produced?

  1. GTAGCTAGCTA
  2. CATCGATCGAT
  3. GUAGCUAGCUA
  4. CAUCGAUCGAU
A

C. The mRNA is the exact copy of the coding strand (just replaces T with U) but it copies the noncoding strand based on base-pairing.

175
Q

Which of the following statements is
FALSE?

  1. RNA synthesis proceeds in the 5 to 3 direction.
  2. Transcription is initiated at specific AUG codon.
  3. Nucleic acid structures are stabilized by stacking interactions.
  4. Transcription terminates at sites that share common features in prokaryotes
A
  1. Transcription is not initiated at a specific AUG codon. Protein translation is initated by the AUG codon.
176
Q

Which of the following statements regarding E.
coli RNA polymerase (RNAP) is not correct?

A. The E.coli RNAP holoenzyme is composed of the core enzyme and a sigma subunit
B. The RNAP core enzyme requires the sigma factor to identify the promoter site.
C. The sigma factor is required by the RNAP core enzyme for accurate transcription
D. RNAP core enzyme tightly binds to template DNA

A

C.

177
Q

T or F: The promoter region of eukaryotic genes contain
consensus sequences at -10 and -35.

A

False

178
Q

T or F: Introns are spliced together in forming the final mRNA molecule.

A

False. Exons are spliced together and introns are taken out.`

179
Q

In DNA, the bond between the deoxyribose sugar and the phosphate group is best described as what?

A

A covalent bond

180
Q

What is a unique aspect of eukaryotic mRNA?

A

A cap structure is found at the 5’end of mRNA

181
Q

The short 5’ AUCCGUACG 3’ transcript would be derived from which of the following DNA sequences?

A

5’ CGTACGGAT 3’

182
Q

What is true from both eukaryotic and prokaryotic gene expression?

A

RNA polymerase binds at the promoter region in a gene inititally

183
Q

Eukaryotic cells contain multiple RNA polymerases, which makes it difficult to block all RNA synthesis with one drug targeted to a specific polymerase. What best describes properties of eukaryotic RNA polymerases?

A

Polymerase I produces most of the rRNA.

184
Q

What enzyme is not required eukaryotic DNA replication?

A

DNA polymerase I

Metabolism, Molecular, and Pharmacogenomics (MMP) (5 decks)

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