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Biology IB HL > 7.2 Transcription > Flashcards

7.2 Transcription Flashcards

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1
Q

What is a gene?

A

A gene is a sequence of DNA which is transcribed into RNA and contains three main parts:

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2
Q

What is a promoter?

A

The non-coding sequence responsible for the initiation of transcription

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3
Q

Where is the core promoted located?

A

he core promoter is typically located immediately upstream of the gene’s coding sequence

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4
Q

What is the function of the promoter?

A

The promoter functions as a binding site for RNA polymerase (the enzyme responsible for transcription)

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5
Q

What mediates the binding of RNA polymerase?

A

The binding of RNA polymerase to the promoter is mediated and controlled by an array of transcription factors in eukaryotes

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6
Q

Where do transcription factors bind?

A

These transcription factors bind to either proximal control elements (near the promoter) or distal control elements (at a distance)

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7
Q

What happens once RNA polymerase has bound to the promoter?

A

After RNA polymerase has bound to the promoter, it causes the DNA strands to unwind and separate

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8
Q

What is the coding sequence?

A

The region of DNA that is transcribed by RNA polymerase is called the coding sequence

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9
Q

When will RNA polymerase finish transcription?

A

RNA polymerase will continue to transcribe the DNA until it reaches a terminator sequence

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10
Q

Is the mechanism for transcriptional termination in eukaryotes and prokaryotes the same?

A

NO

The mechanism for transcriptional termination differs between prokaryotes and eukaryotes

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11
Q

What is the antisense strand?

A

The antisense strand is the strand that is transcribed into RNA

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12
Q

What is the antisense strand’s sequence relation to the transcribed strand?

A

Its sequence is complementary to the RNA sequence and will be the “DNA version” of the tRNA anticodon sequence

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13
Q

What is another name for the antisense strand?

A

The antisense strand is also referred to as the template strand

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14
Q

What is the sense strand?

A

The sense strand is the strand that is not transcribed into RNA

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15
Q

What is the sense strand’s sequence relation to the transcribed strand?

A

Its sequence will be the “DNA version” of the RNA sequence (i.e. identical except for T instead of U)

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16
Q

What is another name for the sense strand?

A

The sense strand is also referred to as the coding strand (because it is a DNA copy of the RNA sequence)

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17
Q

Is a specific strand always anti/sense?

A

NO
Either of the 2 polynucleotide strands may contain a gene, and hence the determination of sense and antisense is gene-specific

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18
Q

What is transcription?

A

Transcription is the process by which a DNA sequence (gene) is copied into a complementary RNA sequence by RNA polymerase

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19
Q
  1. What is the first step of transcription?
A

Free nucleotides exist in the cell as nucleoside triphosphates (NTPs), which line up opposite their complementary base partner

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20
Q
  1. How are the NTP’s joined? transcription
A

RNA polymerase covalently binds the NTPs together in a reaction that involves the release of the two additional phosphates

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21
Q
  1. In what direction does transcription occur?
A

The 5’-phosphate is linked to the 3’-end of the growing mRNA strand, hence transcription occurs in a 5’ → 3’ direction

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22
Q

What are the 3 main steps of transcription?

A

The process of transcription can be divided into three main steps: initiation, elongation and termination

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23
Q

What occurs during initiation?

A

In initiation, RNA polymerase binds to the promoter and causes the unwinding and separating of the DNA strands

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24
Q

What occurs during elongation?

A

Elongation occurs as the RNA polymerase moves along the coding sequence, synthesising RNA in a 5’ → 3’ direction

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25
Q

What occurs during termination?

A

When RNA polymerase reaches the terminator, both the enzyme and nascent RNA strand detach and the DNA rewinds

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26
Q

Can only 1 gene transcript be generated at a time?

A

Many RNA polymerase enzymes can transcribe a DNA sequence sequentially, producing a large number of transcripts

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27
Q

What must be done in eukaryotes after transcription?

A

In eukaryotes, post-transcriptional modification of the RNA sequence is necessary to form mature mRNA

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28
Q

What 3 post-transcriptional events must occur?

A

capping
polyadenylation
splicing

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29
Q

What does capping involve?

A

Capping involves the addition of a methyl group to the 5’-end of the transcribed RNA

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30
Q

What is the role of the methyl cap?

A

The methylated cap provides protection against degradation by exonucleases

It also allows the transcript to be recognised by the cell’s translational machinery (e.g. nuclear export proteins and ribosome)

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31
Q

What does polyadenylation involve?

A

Polyadenylation describes the addition of a long chain of adenine nucleotides (a poly-A tail) to the 3’-end of the transcript

32
Q

What is the purpose of the poly a tail?

A

The poly-A tail improves the stability of the RNA transcript and facilitates its export from the nucleus

33
Q

What is the purpose of splicing?

A

Within eukaryotic genes are non-coding sequences called introns, which must be removed prior to forming mature mRNA

34
Q

What is done once the introns have been removed? splicing

A

The coding regions are called exons and these are fused together when introns are removed to form a continuous sequence

35
Q

What is the difference between introns and exons?

A

Introns are intruding sequences whereas exons are expressing sequences

36
Q

What is alternative splicing?

A

Splicing can also result in the removal of exons – a process known as alternative splicing

37
Q

What is the purpose of alternative splicing?

A

The selective removal of specific exons will result in the formation of different polypeptides from a single gene sequence

38
Q

Give an example of when alternative splicing is used?

A

For example, a particular protein may be membrane-bound or cytosolic depending on the presence of an anchoring motif

39
Q

What regulates transcriptional activity?

A

Transcriptional activity is regulated by two groups of proteins that mediate binding of RNA polymerase to the promoter

40
Q

What are the two groups of proteins that regulate transcriptional activity?

A

transcription factors and regulatory proteins

41
Q

How do transcription factors and RNA polymerase interact?

A

Transcription factors form a complex with RNA polymerase at the promoter

42
Q

How do transcription factors regulate gene expression?

A

RNA polymerase cannot initiate transcription without these factors and hence their levels regulate gene expression

43
Q

What is the role of regulatory proteins?

A

Regulatory proteins bind to DNA sequences outside of the promoter and interact with the transcription factors

44
Q

What are the 2 types of regulatory proteins?

A

activator and repressor proteins

45
Q

What is the role of activator proteins?

A

Activator proteins bind to enhancer sites and increase the rate of transcription (by mediating complex formation)

46
Q

What is the role of repressor proteins?

A

Repressor proteins bind to silencer sequences and decrease the rate of transcription (by preventing complex formation)

47
Q

Is the presence of transcription factors and regulatory proteins the same in every cell?

A

The presence of certain transcription factors or regulatory proteins may be tissue-specific

48
Q

What may also affect transcriptional activity?

A

Additionally, chemical signals (e.g. hormones) can moderate protein levels and hence mediate a change in gene expression

49
Q

What are control elements?

A

The DNA sequences that regulatory proteins bind to are called control elements

50
Q

Where are control elements located?

A

Some control elements are located close to the promoter (proximal elements) while others are more distant (distal elements)

51
Q

Where do regulatory proteins usually bind, in relation to control elements?

A

Regulatory proteins typically bind to distal control elements, whereas transcription factors usually bind to proximal elements

52
Q

How many control elements do genes have?

A

Most genes have multiple control elements and hence gene expression is a tightly controlled and coordinated process

53
Q

What can cause changes in the internal or external environment cause?

A

Changes in the external or internal environment can result in changes to gene expression patterns

54
Q

How may the external/internal environment affect gene expression?

A

Chemical signals within the cell can trigger changes in levels of regulatory proteins or transcription factors in response to stimuli

55
Q

How do chemical signals affect gene expression?

A

This allows gene expression to change in response to alterations in intracellular and extracellular conditions

56
Q

How do hydrangeas change their gene expression in response to environmental changes?

A

Hydrangeas change colour depending on the pH of the soil (acidic soil = blue flower ; alkaline soil = pink flower)

57
Q

How do Himalayan rabbits change their gene expression in response to environmental changes?

A

The Himalayan rabbit produces a different fur pigment depending on the temperature (>35ºC = white fur ; <30ºC = black fur)

58
Q

How do humans change their gene expression in response to environmental changes?

A

Humans produce different amounts of melanin (skin pigment) depending on light exposure

59
Q

How do fish change their gene expression in response to environmental changes?

A

certain species of fish, reptile and amphibian can even change gender in response to social cues (e.g. mate availability)

60
Q

What do the histone tails determine?

A

These histone proteins have protruding tails that determine how tightly the DNA is packaged

61
Q

How do histone tails typically associate with DNA?

A

Typically the histone tails have a positive charge and hence associate tightly with the negatively charged DNA

62
Q

In what two ways can the histone tails be modified?

A

acetylation and methylation

63
Q

How does acetylation affect the DNA?

A

Adding an acetyl group to the tail (acetylation) neutralises the charge, making DNA less tightly coiled and increasing transcription

64
Q

How does methylation affect the DNA?

A

Adding a methyl group to the tail (methylation) maintains the positive charge, making DNA more coiled and reducing transcription

65
Q

What is heterochromatin?

A

When DNA is supercoiled and not accessible for transcription, it exists as condensed heterochromatin

66
Q

What is euchromatin?

A

When the DNA is loosely packed and therefore accessible to the transcription machinery, it exists as euchromatin

67
Q

Will all cels have the same amount of eu and heterochromatin?

A

NO

Different cell types will have varying segments of DNA packaged as heterochromatin and euchromatin

68
Q

Is this packaging permanent?

A

Some segments of DNA may be permanently supercoiled, while other segments may change over the life cycle of the cell

69
Q

How can DIRECT methylation of DNA affect gene expression patterns?

A

Increased methylation of DNA decreases gene expression (by preventing the binding of transcription factors)

70
Q

Which genes exhibit more DNA methylation?

A

Consequently, genes that are not transcribed tend to exhibit more DNA methylation than genes that are actively transcribed

71
Q

What is epigenetics?

A

Epigenetics is the study of changes in phenotype as a result of variations in gene expression levels

72
Q

What does epigenetic analysis show?

A

Epigenetic analysis shows that DNA methylation patterns may change over the course of a lifetime

73
Q

What can influence epigenetic changes?

A

It is influenced by heritability but is not genetically pre-determined (identical twins may have different DNA methylation patterns)

74
Q

Will the same cell types have the same methylation?

A

NO

Different cell types in the same organism may have markedly different DNA methylation patterns

75
Q

What environmental factors may influence DNA methylation?

A

Environmental factors (e.g. diet, pathogen exposure, etc.) may influence the level of DNA methylation within cells

Biology IB HL (56 decks)

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