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Biology 1A03 > Theme 3: Responding to the Environment - Module 4: Turning Off the Signal > Flashcards

Theme 3: Responding to the Environment - Module 4: Turning Off the Signal Flashcards

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1
Q

How can the relative amount of gene products produced by an organism vary?

A

varies depending on changing conditions and different signals

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2
Q

How do organisms ensure that the right amount of each gene is present at the right time?

A

the expression of genes is regulated

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3
Q

when can gene expression be regulated?

A

at many different points during the synthesis of a functional protein

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4
Q

what are some different points during synthesis in which the expression of a gene can be regulated?

A
  • transcription initiation
  • RNA processing
  • overall stability of the RNA molecule
  • protein synthesis
  • protein modifications and transport
  • protein degradation
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5
Q

what does multi-level regulation enable the cell to do?

A

enables a cell to rapidly alter the levels of active proteins in response to internal and external signals

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6
Q

To understand how cells work, what is it important to know?

A

when and where specific genes/groups of genes are expressed within an organism

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7
Q

what is a straight forward war to examine the patterns of gene expression of specific genes?

A

identify the mRNA products that are produced

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8
Q

How can the mRNA be detected?

A

with a complementary probe that has a fluorescent tag attached to it

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9
Q

what can in situ hybridization be used for?

A

utilized to study the expression of one or a few genes of interest

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10
Q

How can we use in situ hybridization to understand any temporal differences that may exist within the genes of organisms?

A

can do the in situ hybridization at different stages of development and compare them

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11
Q

How many genes were we able to assess using in situ hybridization?

A

a few

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12
Q

what technique was developed that allowed us to examine the expression of thousands of genes at once?

A

DNA microarray technique

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13
Q

what is the DNA microarray technique largely based on?

A

base-pair interactions and binding of complementary strands of nucleic acids

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14
Q

what time of adaptation is this to the in situ hybridization?

A

in vitro adaptation

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15
Q

Since the entire genome of different organisms is not known it is possible to set up glass slides that contain what?

A

tiny spots with known DNA sequences or genes

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16
Q

What do DNA microarray chips contain?

A

DNA molecules that act as probes

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17
Q

What do probes in the DNA microarray do?

A

detect gene expression (also referred to as the transcriptome or the set of mRNA transcripts that are expressed by various genes)

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18
Q

what can genomic DNA sequences as probes be used to investigate?

A

whether specific genes of interest are transcribed and looking at groups of genes to determine whether they’re expressed in any specific coordinated manner

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19
Q

what does the DNA microarray technique make possible?

A

possible to gain insights into possible interacting gene networks within a genome

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20
Q

it is possible to manufacture DNA microarrays containing up to how many oligonucleotides?

A

100, 000 (each representing a different gene)

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21
Q

what are oligonucleotides?

A

short fragments of nucleic acids

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22
Q

are all of our genes active at once since we contain identical genetic material throughout our body?

A

no

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23
Q

what are DNA microarrays useful for?

A

visualizing variation in gene expression during different developmental stages, across different cell types and in response to different signals

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24
Q

investigations about which genes are active or not in different cells can provide information about what?

A

how the cells function normally and what changes when gene expression is altered

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25
Q

DNA microarrays can also be utilized to identify differences in gene expression levels between what kinds of cells?

A

normal and cancerous

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26
Q

what did different types of cancer cells use to be identified by?

A

the organs in which the tumours developed

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27
Q

what does DNA microarray analysis make possible to differentiate with regards to normal vs. cancerous cells?

A

patterns of gene activity

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28
Q

to answer questions about what genes are involved in transforming normal cells to tumour cells what needs to be done?

A
  • growing both cell types in culture
  • isolating gene products or mRNA that is transcribed by the two cell types
  • performing DNA microarray analysis
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29
Q

when the mRNA has been isolate from the cells what can these molecules serve as?

A

templates for making complementary cDNA molecules to mRNA

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30
Q

what enzyme is used to make complementary cDNA molecules to the mRNA

A

reverse transcriptase enzyme

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31
Q

what is used during the reverse transcription process?

A
  • fluorescent nucleotides - they become part of the newly synthesized cDNA molecule
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32
Q

what is it important to label the cDNA from both cell types with? why?

A
  • different coloured fluorescent dyes

- so they can be easily identified during microarray analysis

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33
Q

what does a DNA microarray chip consist of in large numbers?

A

single stranded DNA fragments

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34
Q

what do the single stranded fragments represent?

A

different genes

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35
Q

how are these DNA fragments organized in the glass slide for the microarray analysis?

A

tightly spaced array

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36
Q

what does the DNA fixed to the chip represent?

A

all genes known in the cell (can be differences in gene expression at any time)

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37
Q

what can be done with the normal and cancerous dyed cells?

A

they can be combined in equal amounts and tested for hybridization with the single-stranded DNA molecules that are present in the microarray chip

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38
Q

what is measured after this combination takes place?

A

use scanner at each spot on the microarray slide to measure relative differences in colour and intensity

39
Q

if a particular gene is active what will it produce?

A

many molecules of mRNA

40
Q

what happens as a result of producing many mRNA molecules?

A

more labelled cDNA molecules available after reverse transcription which will be able to hybridize to the DNA on the microarray chip

41
Q

when many molecules of mRNA are produced, more cDNA molecules are available and able to hybridize to the DNA microarray chip, what observation does this lead to?

A

many bright spots

42
Q

what happens when an equal mixture of labelled cDNA of both normal epithelial cells and breast carcinoma cells are applied to a microarray chip?

A

they will compete for the synthetic complementary of DNA fragments that re distributed across all spots of the microarray chip

43
Q

what does a green fluorescent spot mean?

A

gene is more expressed in normal epithelial cells (decreased expression/downregulated in breast carcinoma cells)

44
Q

what does a red fluorescent spot mean?

A

specific gene is unregulated - more expressed in breast carcinoma cells compared to the normal epithelial cells

45
Q

what does a yellow fluorescent spot mean?

A

gene is equally expressed in both cell types

46
Q

how can relative gene activity be measured?

A

measuring intensity of fluorescence

47
Q

how are brighter fluorescent spots produced?

A

by genes that are more active (produce more mRNA)

48
Q

what does it mean if there is no fluorescences at all in a particular spot?

A

gene may be inactive

49
Q

is it vital that gene expression be regulated at many different points during the synthesis of a functional protein?

A

yes

50
Q

is it sufficient to remove proteins from the cell if mRNAs are continually transcribed into new proteins?

A

no

51
Q

how can gene expression be stopped?

A

mRNAs should be degraded

52
Q

what is one way to regulate mRNA stability?

A

through the length of the polyA tail

53
Q

are there more ways to regulate mRNA stability?

A

yes

54
Q

is there evidence that some genes can be transcribed into mRNA but the mRNA never ends up being translated?

A

yes

55
Q

how can genes be transcribed into mRNA but the mRNA is never translated?

A

occurs due to the activation of RNA interfering machinery

56
Q

what is RNA interfering machinery activated by?

A

short, noncoding regulatory double stander RNA molecules

57
Q

what is an example of a small regularity RNA?

A

microRNA molecules

58
Q

what are microRNA molecules transcribed from?

A

from protein-encoding genes using the same RNA polymerase that transcribes other RNA molecules

59
Q

what do the transcribed microRNA often form?

A

form hairpin loops

60
Q

why do the microRNA form hairpin loops?

A

due to complementary base-pairing within these microRNA precursor transcripts

61
Q

what are the hairpin loops processed into? what can they do?

A
  • processed into smaller, single stranded mRNA fragments

- can activate the RNA interference machinery

62
Q

what do the processed microRNA become a part of?

A

incorporated as part of a RNA-induced silencing complex (RISC complex)

63
Q

the single stranded microRNA molecules contain sequences that are complementary to what?

A

specific target mRNA sequences that require regulation

64
Q

the microRNA in the RISC complex with bind in what manner to the target mRNA sequence?

A

non-exact

65
Q

what happens once the microRNA bind to the target mRNA sequence?

A

the proteins within the RISC complex can inhibit translation

66
Q

what type of RNAs are transcribed and process in a similar manner as the microRNAS

A

small interfering RNAs/siRNAs

67
Q

do siRNAs become associated with the RISK complex?

A

yes

68
Q

what is the difference in which the small regulatory microRNAs and siRNAs are able to regulate gene expression?

A

due to manner in which they interact with the target mRNA sequence and how the target mRNA is regulated

69
Q

are siRNAs exact complements of their mRNA target?

A

yes

70
Q

onto of binding to the complementary sequence by an association with the RISC complex, what else do they do?

A

also induce cleavage or cutting of the target mRNA

71
Q

what does the cleavage due to the target mRNA?

A

destabilizes the target mRNA and further contributes to pot-transcriptional regulation of gene expression

72
Q

what are RNA interference mechanisms?

A

endogenous processes that regulate gene expression

73
Q

why have researchers widely adopted this tool?

A
  • used as a technique to turn off desire genes and examine and obtain information about the role of the gene in cells
  • can figure out how misrelated/altered gene expression can lead to various diseases
74
Q

when is one of the final opportunities to control gene expression?

A

after translation

75
Q

what are some of the post-translational modifications that can allow for the production of mature, functional proteins?

A
  • cleavage
  • disulphide bond formation
  • acetylation
  • phosphorylation
  • methylation
76
Q

what does post-translational modifications allow?

A

cell to activate or inactivate specific proteins

77
Q

what does selective degradation do?

A

limits the length of time in which a protein functions in a cell

78
Q

what are proteasomes? where are they found? what are they able to do? what happens as a result?

A
  • very large protein complexes
  • found in cells
  • able to break peptide bonds
  • as a result they degrade unneeded or damaged proteins
79
Q

by degraded unneeded or damaged proteins, what does this enable a cell to do?

A

to regulare the concentrations of specific proteins

80
Q

how are the cells able to regulate the concentrations of specific proteins?

A

by breaking long polypeptides into small fragments of a few amino acids in length

81
Q

what happens after the polypeptides are broken into small fragments of a few amino acids?

A

the small fragments of a few amino acids in length can be further degraded into amino acids and used in subsequent rounds of translation

82
Q

what does the cell need to do with regards to protein degradation?

A

accurately identify and regulate which proteins will be degraded

83
Q

identification of proteins for degradation is largely accomplished through what?

A

a tagging mechanism

84
Q

what happens during protein degradation?

A

target proteins are tagged though an enzymatic cascade

85
Q

what are proteins tagged with?

A

small ubiquitin proteins

86
Q

what is the tagging process largely dependent on?

A

ATP

87
Q

what is the tagging processes facilitated by?

A

ubiquitin activation, conjugation to the target substrate protein, and ligation

88
Q

what does ubiquitin activation, conjugation to the target substrate protein, and ligation result in?

A

polyubiquitin chain

89
Q

what is the polyubiquitin chain attached to? what does it allow?

A
  • substrate target protein

- allows for the proteasome to degrade the tagged protein

90
Q

what else is largely ATP dependent?

A

the passage of the target protein through the proteasome

91
Q

what does the the passage of the target protein through the proteasome allow?

A

allows for the unfolding of the protein and subsequent cleavage into smaller fragments

92
Q

what is another mechanism that can turn off gene expression signals? what does it result in?

A

the ubiquitin-proteaseome pathway

- results in degradation of thousands of proteins in the cell

93
Q

what can those degraded proteins include?

A
  • transcription factors
  • cell-cycle realtors
  • mis-folded or aggregated proteins

Biology 1A03 (5 decks)

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