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343 > FIN > Flashcards

FIN Flashcards

1
Q

What is the difference between a nucleoside and a nucleotide?

A

Nucleosides do not have phophates

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2
Q

What are the components of a nucleotide?

A

Pentose sugar, nitrogenous base, and phosphate

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3
Q

What are purines?

A

These are fused ringed nitrogenous bases: adenine and guanine

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4
Q

What are pyrimidines?

A

These are single ringed nitrogenous bases: thymine and cytosine

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5
Q

What is the arrangement of the DNA strands?

A

They run antiparallel to one another

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6
Q

What is a major groove?

A

This is when there is an abundant space between the bases

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7
Q

What is a minor groove?

A

This is when atoms of bases are exposed to the major groove

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8
Q

How does the DNA in bacteria or archaea coil?

A
  1. Relaxed coil where one part of the circle is laid over another
  2. Helix makes contact in 2 places
  3. Unbroken is passed through the break and the break is resealed by DNA gyrase
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9
Q

What is the role of topoisomerase?

A

To remove or add coils to the DNA against the axis and make a right handed helix

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10
Q

What does DNA gyrase do?

A

It makes dsDNA breaks that lead to negative coiling

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11
Q

What does high temperature do for coiling?

A

Causes positive coiling

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12
Q

What is a chromosome?

A

A collection of genes on a strand all linked together and condensed

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13
Q

What is a plasmid?

A

This is a dsDNA molecule that can be linear or circular and it contains nonessential genes however it does contains genes that can provide antibiotic resistance

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14
Q

What are virulent factors?

A

These are molecules that are encoded and cause infection and they are produced via plasmids

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15
Q

How many replication forks are there?

A

2

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16
Q

How is bacterial DNA replicated?

A
  1. Replisome binds and initiation begins
  2. Replication forks continue to synthesize in opposite directions
  3. The 2 chromosome copies are released when the replication forks reach the terminus of replication
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17
Q

What is a replisome?

A

A replication complex that contains aggregated proteins

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18
Q

What happens to the template as replication occurs?

A

The DNA is pulled through

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19
Q

How does termination happen?

A

When a protein called Tas recognizes a Ter site

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20
Q

What is the haloenzyme?

A

An enzyme that synthesizes RNA and contains 5 factors

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21
Q

What is a core enzyme?

A

When the sigma factor dissociates from the core enzyme

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22
Q

How does a transcription bubble form?

A

When helicase unwinds the DNA strands

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23
Q

What are consensus sequences?

A

These are effective in binding RNA polymerase and are strong promoters

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24
Q

What are cotranscribed genes?

A

RNA from 2 or more genes

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25
Q

What is an operon?

A

This is a DNA region where multiple genes that encode for components of a biochemical pathway are under the control of a single operator and produce a single mRNA

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26
Q

How does termination of transcription happen?

A
  1. There is an inverted repeat region that is followed by a string of U’s the U-A’s bind and form a stem loop which removes the RNA polymerase
  2. A Rho factor identifies a Rho dependent sequence binds and RNA polymerase can’t bind
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27
Q

How does translation happen?

A
  1. EF-Tu loads a charged tRNA to the A (acceptor) site
  2. GTP powers translocation and the tRNA moves to the P (peptide) site
  3. GTP power translocation and the amino acid free tRNA moves to the E (exit) site
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28
Q

What is a transcription factor?

A

This is a protein that binds to activate or repress transcription

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29
Q

What is an effector?

A

This is a substrate or end product that binds to the activator or repressor

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30
Q

What is an inducer?

A

These are effectors that bind to activators and turn ON transcription

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31
Q

What is an activator protein?

A

This is a protein that binds to the promoter and recutirs RNA polymerase

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32
Q

What is a corepressor?

A

These are effectors that bind to repressors and turn OFF transcription

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33
Q

What is an allosteric protein?

A

This is a protein who’s conformation changes when an effector binds

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34
Q

What is enzyme repression?

A

When a product is present the enzyme synthesis via transcription is blocked for example Arg

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35
Q

What is enzyme depression?

A

When a product is present the enzyme synthesis via transcription is activated for example lactose

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36
Q

What does Arg do?

A

It acts as a corepressor to ArgR

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37
Q

What does allolactose do?

A

It acts as an inducer to LacI

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38
Q

Explain the expression patterns of the Arg operon?

A
  1. When Arg is present it binds to ArgR which binds to the operator and inhibits transcription
  2. When Arg is absent ArgR does not bind to Arg and transcription does not occur
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39
Q

Explain the expression patterns of the Lac operon?

A
  1. When allolactose is absent LacI binds to the operator and inhibits transcription
  2. When allolactose is present LacI binds to it and allows transcription
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40
Q

What is a regulon?

A

When an effector is involved in multiple operon activities

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41
Q

Explain the expression patterns of the Mal operon?

A

It is a regulon and has different roles

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42
Q

What is positive control?

A

Turning on transcription

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43
Q

What is negative control?

A

Turning off transcription

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44
Q

What is sRNA?

A

These are small RNA molecules that bind to target mRNA and either lead to translation or inhibit it because ribosomes can’t bind to dsDNA

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45
Q

What are the 4 ways that sRNA is used?

A

1.& 2. Increase or decrease translation by removing the block or blocking the ribosome binding site
3. & 4. Increasing or decreasing degradation of mRNA by decreasing or increasing mRNA stability using ribonuclease

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46
Q

What are 2 situations where sRNA are used?

A
  1. Oxidative-iron limitation
    - RhyB RNA is degraded when Fe is limiting growth
  2. Glucose-phosphate stress
    - Glucose-6-phosphate buildup leads to cell death and the sgRNA is degraded so there are fewer glucose transporters and less G6P in the cell
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47
Q

What is trans-sRNA?

A

The sRNA that are encoded and bind to intergenic regions by Hfq proteins

48
Q

What are Hfq proteins?

A

These are RNA chaperones and forms hexameric rings with RNA binding sites

49
Q

What are riboswitches?

A

RNA molecules that resemble activators and repressors which can bind to small metabolites and regulate gene expression

50
Q

What are ribozymes?

A

These are catalytically active RNA

51
Q

What is the difference between a riboswitch and negative transcription control?

A

Riboswitches lack a specific regulatory protein ie., specific protein repressor

52
Q

Where does the riboswitch bind?

A

To the 5’ UTR region apatamer

53
Q

What are the 2 riboswitch conformations?

A
  1. One small molecule is bound
  2. One small molecule is not bound
54
Q

What control the riboswitch conformation?

A

The expression platform

55
Q

When does the metabolite bind to the riboswitch?

A

When it is in high quantity

56
Q

How do metabolites stop transcription?

A

They bind to the apatamer and form a transcription terminator

57
Q

How do metabolites lead transcription?

A

Remove the stem loop and leads to transcription

58
Q

What is attenuation?

A

This is a method of transcriptional control that occurs before transcription initiation is complete

59
Q

What is the leader sequence?

A

The short transcript that is made before the attenuation happens

60
Q

What are the 2 types of mRNA?

A
  1. Causes premature termination
  2. The other that allows for transcription
61
Q

What does the leader peptide function as?

A

The attenuator

62
Q

How is transcription attenuated?

A

When the newly formed mRNA forms a stem loop and prevents RNA polymerase activity

63
Q

What happens when the Try concentration is low?

A

The ribosome stalls and a stem loop forms allowing RNA polymerase to move past the termination site and encode the Try genes needed to make more Try

64
Q

What is the difference between the alternative and terminator stem loop?

A

The alternative does not stop transcription

65
Q

What influences transcription?

A

Translation

66
Q

What is transformation?

A

When a host uptakes free DNA which causes genetic change

67
Q

What is a competent cell?

A

A cell that can uptake free DNA

68
Q

What are the steps of transformation?

A
  1. Pili pullls DNA through the outer membrane to the periplasm
  2. DNA binds to a competent system on the cytoplasmic membrane
  3. The competence specific proteins include a membrane associated DNA binding protein
  4. Competence proteins degrade the DNA into fragments
  5. Enter the cytoplasm and bind to single stranded donor DNA
69
Q

How can free DNA enter cells with thick cell walls?

A

Electroporation - voltage shock that makes the envelope permeable

70
Q

What is transduction?

A

When a phage inserts DNA from one cell to another

71
Q

What is generalized transduction?

A

When the host genome is accidentally packaged instead of the viral genome as a result the DNA does not replicate

72
Q

What is specialized transduction?

A

Specific region of the host genome is in the virion which is more efficient

73
Q

What is a defective phage?

A

A phage that contains the host genome not the viral genome

74
Q

What is phage conversion?

A

When the phage leads to immunity to a host cell for that phage entering again

75
Q

What is a transducatant?

A

Any gene on the donor chromosome that can be transferred

76
Q

What is conjugation?

A

It is a form of horizontal gene transfer where cell to cell contact can occur between closely or distantly related cells through plasmids from a donor to a recipient cell by a type IV pilus

77
Q

What is a cell with a nonintegrated plasmid?

A

F+

78
Q

What is a cell with an integrated plasmid?

A

Hfr

79
Q

What is a cell with no plasmid?

A

F-

80
Q

What does Hfr stand for?

A

High frequency recombination between the the Hfr and the F- genome

81
Q

What is an F’ plasmid?

A

When the F plasmid is excised from the host genome and it carries genes from the host genome with it

82
Q

What are exoenzymes?

A

Extracellular enzymes

83
Q

Where do secreted proteins need to get from and to?

A

From the site of synthesis (ribosome) through the cytoplasmic membrane

84
Q

What are translocases?

A

These are transport proteins that move into or through membranes

85
Q

What is a Sec translocase?

A

Export unfolded proteins and insert integral membrane proteins into the cytoplasmic membrane

86
Q

What is Tat translocase?

A

Transports the previously forlded protein through the cytoplasmic membrane

87
Q

What is a signal sequence?

A

A sequence that is hydrophobic and positive at the N terminus of the sequence and polar at the other end

88
Q

What is the purpose of the signal sequence structuarally?

A

It prevents protein folding

89
Q

What are signal recognition particles (SRP)?

A

These are particles that export unfolded proteins

90
Q

What do SRP allow?

A

SRP are used to be inserted into the membrane but not released on the oppoiste side and is cotranslation

91
Q

What removes the signal sequence?

A

Protease

92
Q

What are the 2 components of the regulatory system?

A
  1. Sensor kinase on the cytoplasmic membrane
  2. Reponse regulator in the cytoplasm
93
Q

What is quorum sensing?

A

This is a regulatory mechanism that is dependent on the population density

94
Q

What are Koch’s postulates?

A
  1. The pathogen is present in all diseased organisms
  2. Inserting the disease causing pathogen in a healthy organism should cause the disease
  3. The pathogen should be grown on pure culture
  4. The pathogen should be identical to the origingal grown on pure culture
95
Q

What are infections?

A

Growth of a microbe in or on the host

96
Q

What are diseases?

A

Impairment to the host due to a disease

97
Q

What is adherence?

A

The first step of a pathogen entering a host

98
Q

What is pathogenicity?

A

The spread of a pathogen and it causing a disease

99
Q

What is virulence?

A

The measure of the disease causing pathogen LD50

100
Q

What are virulence factors?

A

These are factors that degrade the host tissue in order to allow the pathogen to penetrate for example hyluronidase

101
Q

What are exotoxins?

A

These are pathogens that are secreted as they grow

102
Q

What are enterotoxins?

A

These are pathogens that have a site of infection in the body such as the small intestine

103
Q

What does the B subunit do?

A

The B subunit binds to the host

104
Q

What does the A subunit do?

A

The A subunit crosses the cytoplasmic membrane of the host

105
Q

How does dyptheria cause disease?

A

By preventing the polypeptide growth and ADP-ribosylation preventing tRNA from adding on to the growting chain by EF-2-ADP

106
Q

What does botulism do for the body?

A

It blocks the release of acetylcholine which leads to constant muscle relaxation

107
Q

What does tetanus do for the body?

A

It blocks the release of glycine so the acetylcholine is continuously released leading to continuous muscle contractions

108
Q

What does cholera do to the body?

A
  1. B subunit binds to the intestinal epithelia
  2. A subunit crosses the inner membrane adenylate cyclase converts ATP to cAMP
  3. Cholera blocks Na+ and leads to increased cAMP secreting Cl- and HCO3- to the lumen
  4. This leads to the release of large amounts of water
109
Q

What is the big difference between innate and adaptive immune responses?

A

Time and specificity

110
Q

What are the primary lymphoid organs?

A

Bone marrow and thymus

111
Q

What are the secondary lymphoid organs?

A

Spleen and MALT

112
Q

What are “self” antigens?

A

Harmless antigens

113
Q

What are “not self” antigens?

A

Harmful antigens

114
Q

What is an epitope?

A

The part of the immunogen or antigen that binds to the TCR or the antibody

115
Q

What is the difference between the Th and Tc?

A

The coreceptor:
Th = CD4
Tc = CD8

343 (6 decks)

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