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Eukaryotic Gene Regulation. Flashcards

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1
Q

Define chromatin?

A

The material that is used to make the chromosomes that are found in eukaryotes.

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2
Q

Define a CPG island?

A

Areas of a DNA strand that have a high proportion of cytosines and guanines.

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3
Q

Define a dimer?

A

A molecule that is composed of 2 identical components that are linked together.

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4
Q

Define epigenetics?

A

A change in gene expression that results in a change in phenotype without permanently changing the gene itself.

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5
Q

Can the effects of epigenetic be transmitted to future generations?

A

Yes.

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6
Q

Define euchromatin?

A

Loose chromatin that is active and capable of undergoing transcription.

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7
Q

Define heterochromatin?

A

Densely packed chromatin that makes the DNA less accessible. It is also DNA that is transcriptionally repressed.

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8
Q

Define genetic imprinting?

A

When a parent of the origin transmits the effects of epigenetics to future generations.

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9
Q

In a polypeptide, what does the letter K represent?

A

It is the single letter that is used to represent the amino acid lysine.

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10
Q

Define the promoter region?

A

The region of DNA that RNA polymerase will bind to when initiating transcription.

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11
Q

Define ubiquitination?

A

A method that cells can use to get destroy certain proteins.

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12
Q

What are the 3 main reasons why eukaryotic DNA needs to be regulated?

A

To control the types and quantities of proteins that are produced.

To respond to environmental cues by turning specific genes or specific groups of genes on or off.

To make sure that the correct sequence of genes are turned on during development.

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13
Q

What are the 6 most common mechanisms that are involved in the regulation of eukaryotic genes?

A

Transcriptional control.

mRNA processing.

mRNA transport.

mRNA stability.

Ribosomal selection.

Protein stability.

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14
Q

What is differential gene expression?

A

When gene expression can be turned on or off, or slowed down or sped up at any stage in transcription.

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15
Q

What are the 3 most common components that are involved in the regulation of gene transcription?

A

Cis-regulatory sequences of DNA.

Transcription factors.

Changes of chromatin conformation.

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16
Q

What aspects of transcription are represented by cis-regulatory sequences?

A

This concept involves promoter and enhancer sequences.

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17
Q

What aspects of transcription are represented by transcription factors?

A

Proteins that bind to the the promoter or enhancer regions of genes to stimulate or inhibit transcription.

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18
Q

Can DNA methylation be transmitted to future generations?

A

Yes.

It can lead to parent of origin effects that can be transmitted to future generations.

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19
Q

How does the conformation of DNA regulate transcription?

A

When DNA is supercoiled or tightly packed then the DNA cannot be read by a polymerase.

When the supercoiling is relaxed or the DNA is loosely packaged and it can be read by a polymerase.

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20
Q

How does the methylation of DNA regulate transcription?

A

An enzyme can methylate cytosine residues within DNA and this silences the gene and prevents transcription.

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21
Q

What enzyme is responsible for methylating genes?

A

DNA methyl transferase.

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22
Q

What areas of DNA are most likely to be methylated?

A

CpG islands.

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23
Q

How can transcription factors regulate transcription?

A

Transcription requires certain proteins known as transcription factors.

If these factors are absent then transcription cannot occur.

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24
Q

How can the nuclear matrix regulate transcription?

A

Some proteins may not be able to cross the nuclear membrane.

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25
Q

What proteins will DNA wrap around once it is in the nucleus?

A

Around positively charged histone proteins.

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26
Q

How is a nucleosome formed?

A

When 8 histones and their DNA bind together to create an octamer.

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27
Q

How are the “beads on a string” formed when DNA is packaging occurs?

A

The nucleosomes form the beads and linker DNA forms the string.

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28
Q

What specific histones make up a nucleosome?

A

A nucleosome is composed 2 lots of;

Histone H2A.

Histone H2B.

Histone H3.

Histone H4.

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29
Q

How many histone proteins are found in a nucleosome?

A

8 histone proteins in total.

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30
Q

Which histone and what type of DNA links different nucleosomes together?

A

The H1 histone and linker DNA link different nucleosomes together.

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31
Q

What happens when the beads on a string that makeup DNA condense?

A

When the beads on a string condense they will form chromatin.

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32
Q

What is chromatin?

A

DNA and nucleosomes that have been condensed very tightly.

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33
Q

What are the 2 types of chromatin?

A

Euchromatin.

Heterochromatin.

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34
Q

What type of chromatin is loose and transcriptionally active?

A

Euchromatin.

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35
Q

What type of chromatin is tightly packed and not transcriptionally active?

A

Heterochromatin.

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36
Q

What charge do histones have?

A

They are positively charged.

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37
Q

What amino acid helps to give histones their postive charge?

A

Lysine. (Lysine is a positively charged amino acid)

Histones contain tails that have many lysine residues.

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38
Q

How do histones use lysine residues to bind to DNA?

A

The lysine residues allow the histone to form di-sulphide bridges with the negatively charged DNA molecule.

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39
Q

What happens to lysine-DNA binding when the lysine residues are acetylated?

A

The histones lose their positive charge and will not be able to bind to DNA.

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40
Q

What enzyme is responsible for the acetylation of histones?

A

Histone acetyl transferase (HAT).

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41
Q

When will HAT acetylate histones?

A

Before transcription is due to take place.

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42
Q

What type of chromatin will the acetylation of histones create?

A

Acetylation weakens the bonds between DNA and the histones, creating euchromatin.

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43
Q

What enzyme will de-acetylate histone proteins?

A

Histone de-acetylase (HDAC).

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44
Q

What occurs when the histones are removed from DNA?

A

The bonds can re-form, condensing the molecule and forming heterochromatin.

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45
Q

Is the acetylation of histones heritable?

A

No.

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46
Q

Is the de-acetylation of histones is linked to the methylation of DNA?

A

Yes.

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47
Q

What is DNA methylation also known as?

A

Gene silencing.

48
Q

Why is DNA methylation known as gene silencing?

A

As it is a permanent method of repressing the transcription of genes.

49
Q

What enzyme is responsible for methylating cytosine residfues in CPG islands?

A

DNA methyl transferase which will alter cytosine to form 5-methyl cytosine.

50
Q

How is cytosine altered after methylation by DNA methyl-transferase?

A

It will form 5-methyl cytosine?

51
Q

How does the methylation of cytosine prevent transcription from occurring?

A

It physically prevents the transcription proteins from binding to the gene.

52
Q

What is step 1 of DNA methylation?

A

DNMT-3 will methylate cytosine residues on both strands of the DNA molecule.

53
Q

What is DNNT-3?

A

The 3rd iso-form of DNA methyl transferase.

54
Q

What is step 2 of DNA methylation, after the cytosine residues have been methylated?

A

The methyl groups attract a protein called MeCP-2 which binds to the methylated DNA.

The MeCPG-2 then attracts a number of enzymes.

55
Q

What is MeCP-2 that is involved in the methylation of DNA?

A

A methyl CPG binding protein.

56
Q

What happens after MeCP-2 attracts the enzymes to the methylated DNA in step 2 of DNA methylation?

A

One of these enzymes is HDAC-1 or HDAC-2 and it will bind MeCP-2 along with a protein called MSIN-3A.

57
Q

What are the HDAC-1 or HDAC-2 enzymes?

A

Histone de-acetylase 1 or histone de-acetylase-2.

58
Q

What happens after HDAC-1 or HDAC-2 and MSIN-3A have bound to the MeCP-2 protein in step 2 of DNA methylation?

A

HDAC-1/HDAC-2 de-acetylate the lysine residues allowing heterochromatin to form as the chromatin condenses.

59
Q

What is step 3 of DNA methylation after heterochromatin has been formed?

A

The DNA molecule undergoes replication and each methylated DNA strand is copied.

60
Q

What is formed when a methylated DNA strand undergoes replication?

A

A hemi-methylate DNA strand.

61
Q

What is a hemi-methylated DNA strand?

A

A DNA strand where one strand is methylated and the other isn’t.

62
Q

Which strand of DNA is methylated in a hemimethylated DNA strand?

A

The parent strand.

63
Q

Which strand of DNA is not methylated in a hemimethylated DNA strand?

A

The daughter strand.

64
Q

Are the unmenthylated genes on the daughter strand of a hemi-mathylated strand silenced?

A

No.

They can now undergo transcription.

65
Q

What protien will bind to the methyl groups on hemi-methylated DNA in step 3 of DNA methylation?

A

A MeCP-2 protein will bind to the hemi-methylated strand.

66
Q

What happens when an MECP-2 protein binds to the methylated strand of hemi-methylated DNA in step 4 of DNA methylation?

A

The hemi-methylated strand alters the conformation of the MeCP-2 protein.

67
Q

What happens in step 4 of DNA methylation after the conformation of the MECP-2 protein has been altered?

A

The altered MECP-2 attracts DNMT-1 which will bind to the MeCP-2.

68
Q

What is DNMT-1 also known as?

A

As the maintenance methyl transferase as it maintains the original methylation pattern on the daughter strand.

69
Q

What will the DNMT-1 do once it has bound to the altered MECP-2 in step 4 of DNA methylation?

A

The enzyme adds methyl groups to the same cytosines that were methylated on the original strand.

70
Q

What is the final step of DNA methylation after DNMT-1 has added the methyl groups to the daughter strand?

A

Double stranded methylated DNA is formed which causes the MeCP-2 to go back to its usual conformation.

Transcriptional repression is restored.

71
Q

What is the basal transcription machinery in eukaryotes?

A

The basic transcription factors that are capable of carrying out transcription at very low levels.

72
Q

What are the 7 transcription factors that make up the eukaryotic basal transcription machinery?

A

RNA polymerase II.

TFIIA.

TFIIB.

TFIID and TATA box binding protein subunit.

TFIIE.

TFIIH.

TFIIH.

73
Q

Where do the transcription factors bind to on a gene?

A

To the promoter region.

74
Q

What region of DNA is up stream of the promoter region?

A

A region of DNA called the enhancer region.

75
Q

What is the enhancer region used for?

A

As a binding site for a group of proteins that will interact with the basal transcription machinery.

76
Q

What are cis elements of transcrpition?

A

The enhancer and promoter regions of the DNA strand.

77
Q

What are the trans elements of transcription?

A

The proteins that bind to the promoter and enhancer region are said to be trans elements.

78
Q

What are the cis elements of DNA transcription defined as?

A

Elements that are inherent to the DNA strand.

79
Q

What are the trans elements of DNA transcription defined as?

A

Elements that originate from somewhere that isn’t on the DNA strand. E.g. Proteins.

80
Q

How can cis elements can influence transcription?

A

Cis elements can only influence changes on the same chromosome.

E.g. Factors such as the TATA box and the promoter are cis elements as they are only found on a single chromosome.

81
Q

How can trans elements can influence transcription?

A

Trans elements influence changes on any chromosome.

E.g. Transcription proteins are synthesised by different chromosomes and can travel to and work on multiple chromosomes.

82
Q

What are cis elements of transcription always composed of?

A

DNA.

They are often made up of short consensus sequences that are found within 200 BPs upstream of the transcription site.

83
Q

How do trans elements of DNA transcription regulate transcription?

A

A protein can usually obtain a regulatory response.

E.g. A repressor protein can regulate transcription and basal transcription machinery can enhance transcription.

84
Q

What are trans-acting factors of transcription usually composed of?

A

Proteins that bind to the cis acting sequences of DNA in specific ways.

85
Q

How can the basal transcription machinery of eukaryotes increase the rate of transcription above basal levels?

A

By interacting with additional proteins.

86
Q

Transcription factors are always what kind of molecules?

A

Dimers that consist of 3 domains.

87
Q

What are the 3 domains of a transcription dimer?

A

An activation or repression domain that is used to enhance or repress a certain genetic function.

A dimerisation domain that holds the 2 proteins together.

A DNA binding domain that is responsible for binding to the DNA strand.

88
Q

What are the 3 common structural types of dimer that are produced by transcription factors?

A

Zinc finger.

Helix turn helix.

Leucine zipper.

89
Q

What characteristic of DNA allows for proteins on different regions of DNA to interact with one another?

A

The flexibility of DNA.

90
Q

How does the flexibility of DNA allow proteins in the enhancer region to physically interact with proteins in the promoter region?

A

The DNA molecule can fold, allowing these 2 groups of proteins to form bonds.

91
Q

What about proteins will influence the regulation of transcription?

A

The interactions of different proteins.

E.g. a repressor protein binding to the transcription factors.

92
Q

How many pairs of chromosomes are found in humans?

A

23 pairs.

93
Q

What problem do eukaryotes face when trying to transcribe genes for a protein?

A

Sometimes the expression of different genes on different chromosomes is required at the same time.

94
Q

Are different genes on different chromosomes transcribed during hypoxia?

A

Yes.

95
Q

What is the first step of gene expression under hypoxic conditions?

A

A trans factor known as the hypoxia inducible factor (HIF-1). The HIF-1 will bind to a cis element of DNA that reads TACGTG.

96
Q

Is the cis element that is used by HIF-1 under hypoxic conditions presnt on one chromosome or on multiple chromosomes?

A

It is located on multiple chromosomes.

This allows many HIF-1’s to bind to different chromosomes so multiple mRNAs can be produced at the same time.

97
Q

The binding of HIF-1 protiens to different genes provides what co-ordination of gene regulation?

A

It provides spatial and temporal co-ordination of gene regulation.

98
Q

How does spatial and temporal co-ordination of gene expression affect embryogenesis?

A

It allows for different genes to be expressed during the different developmental stages of embryogenesis.

99
Q

What are the 2 proteins that make up the HIF-1 hetero dimer?

A

2 individual proteins called HIF-1-A and HIF-1-B.

100
Q

What is found on each protein chain of the HIF-1 hetero dimer?

A

Each chain has a trans-activation domain which is responsible for inducing changes in the cell.

A dimeriasation domain in the middle which holds the 2 dimers together.

A binding domain at the bottom that is used for binding to DNA.

101
Q

What are the characteristics of the HIF-1A portion of the HIF-1 protein?

A

The HIF-1-A arm is oxygen sensitive and IT contains 2 sequences of amino acids called the PEST sequence which contain the amino acid proline.

102
Q

What happens when HIF-1-A is expressed in the cytoplasm when high levels of oxygen are present?

A

An enzyme hydroxylates the 2 proline residues on the PEST sequences of the trans-activation domain.

103
Q

What enzyme will hydroxylate the 2 proline residues on the PEST sequences of the HIF-1-A protein when high levels of oxygen are present?

A

Prolyl-hydroxlase

104
Q

Is the HIF-1-A protein bound to the HIF-1-B protein when it is in the cytoplasm?

A

No.

105
Q

What happens when prolyl-hydroxylase hydroxylates the proline residues on the HIF-1-A protiens when high levels of oxygen are present?

A

An enzyme called ubiquitin ligase will add ubiquitin residues to the hydroxylated prolines.

The ubiquitin residues signal for a proteasome to come and ubiquitinate (destroy) the HIF-1-A.

106
Q

What happens when HIF-1-A is expressed in the cytoplasm when low levels of oxygen are present?

A

Prolyl-hydroxylase can’t function and the proline residues on HIF-1-A do not get hydroxylated.

This allows HIF-1-A to move into the nucleus where it will meet and bind to HIF-1-B and form the dimer.

107
Q

What happens to the HIF-1 once the dimer has been formed in the nucleus during hypoxia?

A

The dimer can bind to its cis domain.

108
Q

What is the cis domain for the HIF-1 dimer?

A

A genetic code that reads TACGTG and this is also known as the hypoxic response element (HRE).

109
Q

What happens when the HIF dimer binds to the cis domain during hypoxia?

A

The transcription factors bind to the promoter region and they will make the proteins responsible for factors that combat hypoxia.

110
Q

What protein will interact with both the HIF dimer and the transcription factors to up-regulate or down regulate gene expression during hypoxia?

A

CBP-b300.

111
Q

How many different genes are regulated by HIF-1 during hypoxia?

A

This process will regulate 63 different genes in total.

112
Q

What happens to the glucocorticoid receptor when cortisol is absent from the cytosol?

A

The receptor remains part of a multi protein complex that resides in the cytoplasm.

113
Q

What happens to the glucocorticoid receptor when cortisol is present in the cytosol?

A

Cortisol enters the cell and binds to the receptor.

This causes the GCR to dissociate from it from the multi protein complex.

114
Q

What happens when the glucocorticoid receptor dissociates from the multi protein complex?

A

2 glucocorticoid receptors bind together to form a dimer.

The dimer travels into the nucleus and binds to the hormone response element on the DNA strand.

It induces the expression of target genes.

115
Q

What is the sequence on the hormone response element which the glucocorticoid dimer will bind to on DNA?

A

It is a palindromic sequence of DNA that reads AGAACA-TGTTCT.

116
Q

What happens to the glucocorticoid dimer after it has bound to the hormone response element?

A

A set of co-activators bind to the dimer and the basal transcription machinery.

The co-activators are responsible for the up-regulation, down regulation or repression of gene expression.

Molecular Biology. (22 decks)

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