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IB HL Biology > 7.2 Transcription and gene expression > Flashcards

7.2 Transcription and gene expression Flashcards

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1
Q

When a gene is transcribed, the DNA is a ___

A

Template for the RNA polymerase to synthesise (make) a copy of mRNA.

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2
Q

How does RNA polymerase move when a gene is being transcribed?

A

The RNA polymerase starts near a region of the gene called the promoter, located at the 5’ end adjacent to the coding region.

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3
Q

Diagram of the promoter region of a gene and initiation of transcription

A
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4
Q

How many stages does transcription have?

A

3

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5
Q

What are the three stages of transcription?

A

-Initiation

-Elongation

-Termination

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6
Q

When does initiation start?

A

When RNA polymerase binds to the DNA at the promoter region and the double helix unwinds.

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7
Q

What is elongation?

A

-When mRNA becomes longer as nucleotides are added to the 3’ OH group.

-Note that, similar to replication, transcription progresses in a 5’ to 3’ direction.

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8
Q

What is termination?

A

When the mRNA synthesis is complete and the complex of DNA, RNA polymerase and mRNA disassembles.

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9
Q

Diagram of the elongation stage of transcription

A
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10
Q

What does RNA polymerase do once it has attached to the promoter?

A

-It separates the DNA strands at one end while it synthesises a complementary RNA copy from the antisense DNA strand.

-As the DNA template strand (antisense strand) is exposed, ribonucleoside triphosphates line up opposite to their exposed counterpart, according to complementary base pairing rules (A with T or U (found in RNA, not DNA), and C with G.

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11
Q

What happens in transcription once the ribonucleoside triphosphates line up opposite to their exposed counterpart?

A

-This is followed by RNA polymerase forming covalent bonds between the growing mRNA molecule and the ribonucleotides.

-The energy to drive this reaction is released when the bond with the two additional phosphate groups is broken.

-This process continues until the RNA polymerase reaches a terminator region of the DNA; transcription stops when the RNA polymerase detaches from the DNA.

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12
Q

What is the DNA strand that is not transcribed called?

A

-The sense strand

-It has the same sequence of bases as the mRNA molecule except for thymine being replaced by uracil.

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13
Q

What is the transcribed DNA strand called?

A

-The antisense strand

-It is complementary to the mRNA molecule.

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14
Q

How is translation different in prokaryotes and eukaryotes?

A

-In prokaryotes, there is no nucleus or nuclear membrane.

-Once the mRNA has been synthesised, translation begins immediately.

-In eukaryotes, the mRNA that is produced needs to be prepared for translation.

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15
Q

What is post-transcriptional modification of mRNA?

A

In eukaryotes, the mRNA that is produced needs to be prepared for translation.

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16
Q

What is the reason for the extra step of post-transcriptional modification of mRNA?

A

-The reason for this extra step is the introns and exons in eukaryotic genes.

-Introns are DNA sequences in eukaryotic genes that contain no coding information.

-Sometimes they contain controlling sequences that regulate the transcription of the gene.

-Exons are the DNA sequences that code for a polypeptide.

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17
Q

What are introns?

A

DNA sequences in eukaryotic genes that contain no coding information.

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18
Q

What are exons?

A

The DNA sequences that code for a polypeptide.

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19
Q

What are the steps involved in modifying RNA so that it will be used in translation?

A

-Transcription (synthesis of pre-mRNA)

-Addition of a 5’ cap and a poly-A tail (which protect the mRNA molecule from degradation)

-Splicing, which involves removing (excising) the introns and joining (ligating) the exons to form mature mRNA.

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20
Q

Diagram of post-transcriptional modification of mRNA (the steps involved in modifying RNA so that it will be used in translation)

A
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21
Q

The splicing of introns involves a ___

A

Spliceosome

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22
Q

What is a spliceosome?

A

A large ribonucleoprotein (RNP) complex made up of five small nuclear ribonucleoproteins (snRNPs) and several proteins. It acts as an enzyme in the splicing process to remove introns and bind exons together.

(You are not expected to know this definition for the exam.)

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23
Q

Diagram of a spliceosome removing introns and joining exons to form mature mRNA

A
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24
Q

What is the purpose of splicing?

A

It allows several proteins to be synthesised from the same gene.

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25
Q

Give an example of a gene that has 11 exons

A

Tropomyosin in humans

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26
Q

Describe splicing in the tropomyosin gene in humans (reword?)

A

-Some genes, such as tropomyosin in humans, have 11 exons.

-Depending on the tissue, there can be at least five forms of the protein made from this gene by alternative splicing.

-The old theorem: ‘one gene – one polypeptide’ has been overthrown by the discovery of alternative splicing.

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27
Q

Diagram of alternative splicing (splicing allows several proteins to be synthesised from the same gene)

A
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28
Q

Does post-transcriptional regulation of mRNA occur in prokaryotes?

A

-No

-Prokaryotes have no nucleus or nuclear membrane, so once the mRNA is synthesised, translation begins immediately.

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29
Q

In eukaryotes, what does transcription generate?

A

A pre-mRNA, which is modified by splicing out the intron sequences, adding a cap and a poly-A tail.

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30
Q

Why might gene expression be altered at the level of post-transcriptional processing in eukaryotes and not in prokaryotes?

A

Eukaryotic exons may be spliced in alternative patterns.

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31
Q

What is removed from pre-RNA to form mature eukaryotic mRNA?

A

Introns

32
Q

In which direction does transcription occur?

A

5’ to 3’

RNA polymerase adds ribonucleotides to the 3’ OH group of the growing mRNA chain. Thus, translation proceeds from the 5’ end of the molecule to the 3’ end of the molecule.

33
Q

Alternative splicing of exons increases the ___

A

Diversity of proteins that can be made.

34
Q

How is transcription finely tuned to the needs of the organism?

A

-Because a lot of energy is required to produce proteins and not all proteins are needed all the time, it makes sense to regulate the transcription of genes.

-This can be achieved by the contribution of the non-coding regions of DNA such as promoters, enhancers and silencers.

-The promoter directly affects transcription by controlling whether or not RNA polymerase can access the gene.

35
Q

How does the promoter directly affect transcription?

A

By controlling whether or not RNA polymerase can access the gene.

36
Q

Describe the role of the promoter in the regulation of transcription

A

-This is shown in the lac operon of prokaryotes.

-In this case, the presence or absence of certain food sources can trigger the transcription of certain genes.

-When lactose is absent, the active repressor protein, a protein that stops transcription, binds to the operator next to the promoter.

37
Q

What is an operator?

A

-A sequence of DNA in prokaryotes that allows a cell to regulate whether a gene is transcribed or not.

-This stops the binding of RNA polymerase with the promoter.

-Thus, the genes of the lac operon are not transcribed.

38
Q

What happens to the active repressor in the presence of lactose?

A

-The active repressor binds to lactose instead of attaching to the operator.

-As a result, RNA polymerase can bind to the promoter and transcribe the genes of the lac operon. The genes are thus switched on.

-The genes that are transcribed and translated enable the bacterium to break down lactose as a food source.

-Thus the bacterium only expends the energy to produce these enzymes when their substrate is present in the environment.

39
Q

What is a promoter?

A

-A short DNA sequence situated just before a gene, which acts as a binding point for the RNA polymerase enzyme.

-The promoter is a good example of non-coding DNA with a function.

40
Q

Diagram of the lac operon: transcription regulation in prokaryotes activating genes by the presence of a food source

A
41
Q

Describe how transcription is regulated in eukaryotes

A

-Transcription is regulated in a similar way in eukaryotes by the use of promoters.

-When an embryo grows in the uterus, certain tissues need to differentiate to allow the development of certain organs.

-Transcriptional regulation ensures that certain genes are transcribed and others remain silent, meaning that they are not transcribed.

42
Q

Explain how proteins can regulate gene transcription by binding to specific non-coding DNA base sequences, such as enhancers and silencers

A

-For instance, activator proteins bind to enhancers while repressor proteins bind to silencers to increase and decrease the rate of transcription, respectively.

-Enhancers and silencers are also examples of non-coding regions of DNA with specific functions.

-Repressor proteins may block the transcription of specific genes, which plays an important role in the differentiation process.

43
Q

In response to the presence of certain food sources, what can prokaryotes do?

A

Alter the level of transcription of certain genes.

44
Q

Give 3 characteristics of transcription regulation

A

-Is highly efficient at completely preventing transcription

-Can be controlled by a repressor protein

-Allows the cell to only produce proteins that are needed at the time

45
Q

Which of these options is NOT a DNA sequence to which proteins can bind in order to regulate gene expression?

Enhancer

Silencer

Repressor

Promoter

A

-Repressor

-It is not a DNA region, but a protein that can bind to DNA regions such as operators or silencers. The other three options are all DNA regions that have regulatory functions for gene expression when proteins bind to them.

46
Q

What are the two additional ways of regulating transcription known?

A

-These involve small chemical changes to both histones and DNA.

-Histones can be acetylated or methylated, and DNA can be methylated.

47
Q

How do histones influence transcription?

A

Histones have a direct influence on transcription because, when they bind to DNA, they block access to RNA polymerase.

48
Q

Explain the effect of histones on transcription

A

-The tails of histone proteins can be acetylated, that is, adding an acetyl group (–CH 3 COO - ), which prevents binding between nucleosomes.

-This partially unwinds the DNA, allowing the enzymes involved in transcription to access it.

-As a result, acetylation of histones generally keeps the genes active while deacetylation, removal of the acetyl group, silences the gene.

49
Q

Diagram of acetylation of histones and the effect on DNA

A

.

50
Q

Explain how histones can be methylated

A

-Instead of adding an acetyl group (–CH 3 COO - ), a methyl (–CH 3 ) group is added.

-Methylation can have a positive or a negative effect on transcription, depending on where the histones are located on the genome.

51
Q

When can DNA be methylated?

A

-When a methyl group (–CH 3) is added to a cytosine found within a DNA molecule.

-S-adenosylmethionine (SAM) plays a role as a methyl donor.

52
Q

Diagram of the methylation of cytosine

A

.

53
Q

What usually happens to DNA that is methylated?

A

-It is usually not expressed.

-In other words, the genes that have methylated cytosine nucleotides are shut down.

54
Q

Does methylation last for a long or short time?

A

It lasts for a long time

55
Q

How does methylation affect the second X chromosome in females?

A

-It causes the inactivation of the second X chromosome in females.

-Women have two X chromosomes in all their cells (except their ova).

-DNA methylation causes one of the X chromosomes to shut down completely during the life of that cell, a necessary process for the correct functioning of cells with two X chromosomes.

56
Q

What is the level of DNA methylation of the genome or of a specific gene associated with?

A

Various factors including age, diet, environmental conditions during important developmental stages and exposure to infectious agents.

57
Q

Analysis of data highlighting changes in a DNA methylation pattern on exam

A

-You should be able to analyse data highlighting changes in a DNA methylation pattern.

-For instance, you may be provided with graphs showing the DNA methylation level of identical twins brought up in different environments over time, and asked to establish any visible trend or briefly explain the changes observed.

58
Q

Graph showing a three-dimensional plot showing the relation between S1MP2 hypermethylation and clinical parameters of patients

(The relationship between age of patients, stage of a breast tumour and status of methylation.)

A
59
Q

What is the clinical parameter included in the graph of age vs. stage of breast tumor vs. status of methylation

A

-The clinical parameter included is the stage of cancer: stage I is the least advanced, stage IV is the most advanced.

-S1MP2 is a locus that has often been found to be hypermethylated in breast tumour patients.

-Hypermethylation of S1MP2 is shown as green diamonds, whereas no methylation is represented as red diamonds in this sample of patients.

-M and U represent methylated and unmethylated alleles respectively.

60
Q

What can be deduced from the graph of age vs. stage of breast tumor vs. status of methylation?

A

That the hypermethylation event was associated with younger patients of more advanced clinical stages.

61
Q

DNA methylation and histone acetylation are all examples of ___

A

Transcriptional regulation

62
Q

Define epigenetics

A

The study of heritable changes in organisms that are brought about by changes in gene expression rather than by modification of the genetic code.

63
Q

What happens in epigenetic changes?

A

The DNA sequence itself is not altered, but some of the bases are altered.

64
Q

Give examples of factors that favor methylation (reword?)

A

-Most often, a cytosine base is methylated (a methyl group is added) by the enzyme DNA methyl transferase.

-Another factor that favours methylation is when cytosine (C) is followed by guanine (G).

-This CpG (the ‘p’ stands for phosphate linking the two bases) combination is often seen in or near the promoter region of a gene, and when methylated, gene expression will be shut down.

65
Q

Describe the growing evidence about the influence of the environment of a cell or organism on gene expression

A

There is growing evidence that the environment of a cell or of an organism can influence gene expression and even have an effect on the expression of certain genes in following generations if the cells that eventually form sperm or eggs are affected through methylation.

66
Q

Digaram of an example of a methylated promoter region

A
67
Q

What is the CpG?

A

-The CpG is called an epigenetic tag and can be passed to daughter cells during mitosis in the body.

-This means that these tags are copied during DNA replication.

68
Q

What evironmental factors can affect methylation?

A

-Pollution, diet, temperature or stress.

-Scientists have investigated children born before, during, and after times of famine for differences in their health outcomes, and found effects from both parents in the offspring.

69
Q

Give an example of the environmnental effects on methylation (mice)

A

-An example of the environmental effect was shown in mice.

-Their coat colour can be dark or yellow, depending on the methylation of the gene for this trait.

70
Q

Explain the environmental effect on methylation in mice

A

-When methylated, the coat color is brown.

-When not methylated, the gene is active and the coat color is yellow.

-Exposing mice to a diet high in folic acid (which contains the methyl group) during pregnancy increased the proportion of dark mice in their litters.

-This is indirect evidence that increased methylation of genes in the fetus can influence the inheritance of a trait.

71
Q

Diagram of epigenesis in mice: influence of a methylated food source on coat colour

A
72
Q

Give an example of the epigenetic effect in humans

A

-The decreasing similarity observed among identical twins as they age is another example of the epigenetic effect.

-As twins grow up and are exposed to different environmental conditions, their DNA methylation patterns change and they become less similar.

73
Q

During DNA replication, methylation of the DNA ___

A

-Does not change.

-Methylation does not affect replication so the methylated DNA is replicated and passed to daughter cells.

74
Q

The phenotypic features of an organism can be affected by ___

A

Both its genetic code and its environment

75
Q

What is produced during transcription?

A

All types of RNA

All forms of RNA (mRNA, tRNA, rRNA, and others not needed for this course) are encoded in DNA and need to be transcribed to RNA. Only mRNA is translated, however.

76
Q

How does methylation affect DNA?

A

It promotes the supercoiling of DNA by nucleosomes and stops transcription.

77
Q

What is a transcription factor?

A

A protein that binds to specific DNA sequences to control the transcription of mRNA.

IB HL Biology (68 decks)

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