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Topic 3: Voice of the Genome > How development is controlled > Flashcards

How development is controlled Flashcards

1
Q

Do stem cells have the same genome? Are they able to specialise into a diverse range of cell types? What happens during differentiation?

A
  • all stem cells within an organism have an identical genome
  • despite having same genome, they are able to specialise into a diverse range of cell types because during differentiation certain genes are expressed /switched on
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2
Q

How do stem cells become specialised? What does this mean?

A
  • stem cells become specialised through differential gene expression
  • this means that only certain genes in the DNA of the stem cell are activated
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3
Q

What is an operon? Where are they found? What does it include?

A
  • an operon (are only present in prokaryotes and archaea) is a section of DNA that includes:
  • a cluster of structural genes that are transcribed together
  • control elements, including a promoter region and an operator region
  • some operons may include regulatory genes that code for activators or repressors
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4
Q

What is a promoter region? What is an operator region?

A
  • promoter region = a DNA sequence that RNA polymerase initially binds to)
  • operator region = (where transcription factors bind)
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5
Q

What does the lac operon contain?

A
  • the lac operon contains genes that encode proteins involved in uptake and metabolism of a particular sugar lactose
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6
Q

What is a repressor protein?

A
  • (is an RNA binding protein) that inhibits gene expression (by stopping RNA polymerase from binding to the DNA of a gene)
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7
Q

What is an activator protein?

A
  • (is an RNA binding protein) that stimulates gene expression (by helping RNA polymerase from binding to the DNA of a gene)
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8
Q

What is apoptosis? How does this happen?

A
  • controlled cell death (apoptosis)
  • there is a small group of cell ‘suicide’ genes and when they are expressed this causes the cytoplasm and nucleus to fragment
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9
Q

What is the key to development and why?

A
  • controlling gene expression is the key to development because stem cells differentiate due to the different genes being expressed
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10
Q

What does it mean if a cell becomes specialised?

A
  • cell specialization means that cells change into specific cells
  • when a cell becomes specialised it can carry out different (specific) functions
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11
Q

What are the basic steps that differentiation occurs in?

A
  • under certain conditions, some genes in a stem cell are activated, whilst others are inactivated
  • mRNA is transcribed from active genes only
  • this mRNA is then translated to form proteins
  • these proteins are responsible for modifying the cell, the cell becomes increasingly specialised
  • the process of specialisation is irreversible (once differentiation has occurred, the cell remains in its specialised form)
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12
Q

What is a transcription factor? What do eukaryotes use this for? What does it ensure?

A
  • a transcription factor is a protein that controls the transcription of genes by binding to a specific region of DNA
  • eukaryotes use transcription factors to control gene expression
  • it ensures that genes are being expressed in the correct cells, at the correct times and to the right level
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13
Q

What are activators? How do they work?

A
  • activators are transcription factors that increase the rate of transcription
  • activators work by helping RNA polymerase to bind to the DNA at the start of a gene and to begin transcription of that gene
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14
Q

What are repressors? How do they work?

A
  • repressors are transcription factors that decrease the rate of transcription
  • they work by stopping RNA polymerase from binding to the DNA at the start of a gene, inhibiting transcription of that gene
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15
Q

What happens if transcription factors bind to the promoter region of a gene?

A
  • binding here can either allow or prevent the transcription of the gene taking place
  • transcription factors interact with RNA polymerase, either by assisting RNA polymerase binding to the gene (stimulate gene expression) or by preventing it from binding (inhibiting gene expression)
  • therefore, the presence of a transcription factor will either increase or decrease the rate of transcription of a gene
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16
Q

What does control of gene expression require in prokaryotes?

A
  • in prokaryotes, control of gene expression requires the binding of transcription factors to operons
17
Q

What is an operon? What does it include? What are its control elements?

A
  • an operon is a section of DNA that includes:
  • a cluster of structural genes that are transcribed together (these code for proteins e.g. enzymes)
  • control elements, including a promoter region (a DNA sequence that RNA polymerase initially binds to) and an operator region (where transcription factors bind)
  • some operons may include regulatory genes that code for activators or repressors
18
Q

What is the basic definition of an operon?

A
  • a group or cluster of genes that are controlled by the same promoter
19
Q

What does the lac operon control? And what does this do?

A
  • the lac operon controls the production of the enzyme lactase (aka beta galactosidase) and two other structural proteins
  • lactase breaks down the substrate lactose so that it can be used as an energy source in the bacterial cell
20
Q

Why is lactase known as an inducible enzyme?

A
  • it is known as an inducible enzyme which means it is only synthesized when lactose is present
  • this helps the bacteria avoid wasting energy and materials
21
Q

What are the components of the lac operon?

A

in the following order:
- promoter for structural genes
- operator
- structural gene lacZ that codes for lactase
- structural gene lacY that codes for permease (allows lactose into cell)
- structural gene lacA that codes for transacetylase

22
Q

What is epigenetics the control of? What does it involve?

A
  • epigenetics is the control of gene expression by factors other than an individuals DNA sequence
  • epigenetics involves the switching on and switching off of genes, but without changing the actual genetic code
23
Q

In eukaryotic cells, what is DNA wrapped around?

A
  • in eukaryotic cells, DNA is wrapped around proteins called histones to form chromatin
24
Q

How can chromatin be chemically modified and what would that do? What are these modifications called?

A
  • chromatin can be chemically modified to alter gene expression:
  • by methylation of DNA (chemical addition of -CH3 groups)
  • histone modification via acetylation of amino acid tails
  • these modifications are called epigenetic tags
25
Q

What is an epigenome?

A
  • all the epigenetic tags in an organism is called the epigenome
26
Q

What does the chemical modification of histones and DNA control?

A
  • the chemical modification of histones and DNA controls how tightly the DNA is wound around them as the intermolecular bonding between the histones and DNA changes
27
Q

What would happen to a section of DNA where the DNA is wound more tightly?

A
  • If the DNA is wound more tightly in a certain area, the genes on this section of DNA are ‘switched off’ as the gene and promoter regions are more hidden from transcription factors and RNA polymerase
28
Q

In basic terms, how does methylation cause the gene to be switched off?

A
  • methyl group = attach to DNA (cytosine)
    ===> RNA polymerase cannot bind
    ===> mRNA not made
    ===> no transcription
    ===> switched off
29
Q

How does methylation cause the inactivation of genes?

A
  • methyl groups (-CH3) can attach directly to DNA to change the activity of a gene
  • DNA methylation involves the addition of a methyl group to cytosine bases which influences gene expression
  • methylation inhibits the binding of transcription factors and enzymes needed for transcription (e.g. RNA polymerase)
30
Q

Why do cells use methylation?

A
  • cells use this mechanism to lock genes in the ‘off’ position
  • the gene is said to be repressed or inactivated
31
Q

What are on histones that help DNA coil around the histone protein core?

A
  • Lysine are amino acids on histone proteins
  • lysine has a positively charged R group, this forms ionic bonds with the negatively charged phosphate backbone of DNA
  • this helps DNA to coil tightly around the histone core
32
Q

What happens when adding acetyl groups to lysine residues?

A
  • adding acetyl groups (-COCH3) (acetylation) to lysine residues removes the positive ion and therefore removes a bond between the histone and DNA, this causes the DNA to be less tightly wrapped
33
Q

What happens when DNA is less tightly wrapped? What is the gene said to be?

A
  • when the DNA is less tightly wrapped, RNA polymerase and transcription factors can bind more easily and therefore gene expression can occur
  • the gene is said to be activated
34
Q

In summary, what does methylation do? What does acetylation do?

A
  • methylation adds a methyl group to DNA at cytosine which inhibits transcription
  • acetylation adds acetyl groups to lysine residues which removes the bond between lysine and phosphate backbone which causes DNA to be less tightly wound = gene expression can occur
35
Q

What does deacetylation do?

A
  • deacetylation removes acetyl groups and returns lysine to its positively charged state which has a stronger attraction to the DNA molecule and therefore inhibits transcription and once again stops the gene from being expressed
36
Q

What does acetylation cause chromatin to become? What does this allow?

A
  • acetylation causes chromatin to become less condensed, allowing genes to be transcribed
37
Q

Is the epigenome heritable?

A
  • like the genome, the epigenome is heritable and can be passed on in cell division

Topic 3: Voice of the Genome (5 decks)

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