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Molecular Biology Flashcards > Gene Regulation 4 - Regulation of eukaryotic gene expression Packing and unpacking of DNA > Flashcards

Gene Regulation 4 - Regulation of eukaryotic gene expression Packing and unpacking of DNA Flashcards

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1
Q

Learning Outcomes

A

Students will be able to
➢ explain experimental evidence that shows that almost all cell have the same
genome and that this genome is sufficient to give rise to a fully functional
eukaryotic organism.
➢ relate development and differentiation of a multicellular eukaryote to the
regulation of gene expression.
➢ discuss why eukaryotic control of gene expression is more complex than
prokaryotic gene expression.
➢ list levels at which gene expression is regulated in eukaryotes
➢ describe eukaryotic DNA packaging into chromosome structures
➢ relate packaging of DNA to gene expression.

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2
Q

If two cells share the same genome, how come they look
different and have different functionalities?

A
  • Different cells differ in structure and
    function.
    ➢ A neuron cells from the retina
    receives electrical signals from
    many other neurons and carries
    them to many neighbouring
    neurons via neurotransmitters.
    ➢ A liver cell is involved in many
    metabolic processes. One of those
    is the detoxification of alcohol via
    the enzyme alcohol
    dehydrogenase
  • The two cells have the same genes,
    same genome.
  • They express different subsets of
    genes leading to different subsets of
    proteins which determine their
    different shapes and functions.
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2
Q

Differentiation as a consequence of changes in gene expression

A
  • In multicellular organisms, life begins as a single cell.
  • In development, cells commit to specific fates & differentially express subsets of genes.
  • Daughter cells may differ with respect to regulatory instructions & developmental fate, so new cells become different to
    their parent cell.
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2
Q

Frog Embryo Development

A

Frog embryogenesis is characterised by cell division and cellular differentiation of pluripotent cells (in plants
meristem cells).
Pluripotent cell: immature stem cell that has the potential to differentiate into any of the three germ layers:
endoderm (gut, lungs and liver), mesoderm (muscle, skeleton, blood vascular, urogenital, dermis), or ectoderm
(nervous, sensory, epidermis), but not into extra-embryonic tissues like the placenta or yolk sac

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2
Q

Are losses or gains of genes driving changes during development?

A
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3
Q

Undifferentiated and Differentiated cells produce different specific mRNAs and proteins

A

Consider:
▪ A single fertilised egg cell develops into a multicellular organism with trillions of cells, ~ 200 different cell types.
▪ These cells are organised into tissues & organs performing different, specialised functions and morphologies.
▪ This requires that different cell types make different sets of proteins.
* The early embryo is characterised by rapid cell division followed by differentiation ➔ genes expressed will enable
the embryo to fulfil functions associated with division and differentiation appropriate to its developmental state.
* Differentiated cells will express genes that enables them to fulfil a specific function within an organism.

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4
Q

Let’s look at levels of Gene Expression

A
  • Control of gene expression in eukaryotes occurs at
    several levels:
    1) Packing or unpacking DNA
    2) Transcription
    3) mRNA processing
    4) mRNA export
    5) Translation, mRNA stability and degradation
    6) Post-translation protein modification
    7) Protein stability and degradation
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4
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5
Q

How is gene expression regulated in
Eukaryotes?

A
  • Regulation of gene expression in eukaryotes is more complex than in
    prokaryotes.
  • Control of gene expression in eukaryotes occurs at many levels:
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6
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7
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How long is my DNA ?

A

DNA in each of our cells is about 2 to 3 meters long based on 3.2 x 109 nucleotides and
a length of 0.6 nanometers (10-9 m) per nucleotide.
This DNA has to fit into the cellular nucleus which is about 6 µm in size (10-6 metres)
Image result for eukaryotic cell microscope
If we would magnify the nucleus 1000 x to 6 mm, the total length of all the DNA in the
cell’s nucleus would be 2 - 3 km long

DNA in our whole body is about 2.04 x 1010 km ➔ 66.5 trips from
the earth to the sun and back

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8
Q

How to fit 2 meters of DNA into a nucleus of 6 µm diameter:
Package DNA around add histone H1

A
  • The ‘string’ part of the beads on a string is formed by
    unbound linker DNA DNA ~ 20 bp between nucleosomes.
  • The linker DNA is bound by the linker histone protein H1.
  • The nucleosome plus the linker DNA and the linker histone
    form the chromatosome.
  • The chromatosome contains about 166 bp of DNA.
  • This condenses DNA from 2 nm to 11 nm.
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8
Q

How to fit 2 meters of DNA into a nucleus of 6 µm diameter:
Package DNA around core histones

A
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9
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Chromosome structure is regulated

A
  • Gene expression, DNA replication, DNA repair requires access of proteins to the DNA.
  • Along an interphase chromosome we can find regions that are:
    – densely packed: heterochromatin ➔ DNA less accessible ➔ silent genes
    – less densely packed: euchromatin ➔ DNA is more accessible ➔ expressed genes.
  • Eukaryotic cells have several ways to adjust the local structure of chromatin rapidly.
    – Chromatin remodelling complex
    – Reversible chemical modifications of histones
10
Q

How to fit 2 meters of DNA into a nucleus of 6 µm diameter:
Using scaffold proteins

A
  • Multiple nucleosomes wrap into a 30 nm fibre forming
    heterochromatin or chromatin.
  • During mitosis and meiosis DNA can be packaged even more
    into the metaphase chromosome (~1400 nm diameter). This
    requires other sets proteins:
    – Scaffold proteins determine and maintain the authentic
    chromosome shape
    – ensure that DNA winds up and unwinds without tangling.
    – Packaged DNA molecule in a mitotic chromosome is
    10,000 fold shorter than its fully extended length.
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11
Q

Visualising transcribed areas of chromosomes

A

▪ Chromosomes transform into the
lampbrush form in the growing
oocytes of most animals, except
mammals, during the diplotene stage
of meiotic prophase I.
▪ Opened loops of varying length are
areas of active transcription of many
genes.
▪ The light line in the centre of the
chromosome is scaffold made up of
non-histone scaffold protein

11
Q

Chromatin Remodeling Complexes

A
  • Chromatin Remodelling Complex: Regulatory proteins that use ATP (energy) to alter chromatin structure without
    changing histone chemistry.
  • Bind directly to DNA and reposition nucleosomes ➔ DNA is accessible to proteins, e.g. to transcription factors.
  • Example of ways in which remodeling occurs:
    – Nucleosome slides along DNA, DNA that would normally be wrapped around the histones becomes exposed.
    – Conformational change of nucleosomes, DNA or both, so the DNA is more exposed.
  • May work in unison with histone acetylation (see next slides)
12
Q

Histone tail modifications determine active and repressive chromatin

A
  • Histone tail modifications are Post-translational modifications (PTMs).
  • PTMs are covalent modifications of a protein after protein biosynthesis (after translation).
  • These modifications are done by enzymes (proteins).
  • PTMs can regulate protein activities, localization, structure etc.
  • PTMs of histone tails can lead to
  • active, less densely packed DNA in euchromatin
  • or to densely packed DNA in repressive heterochromatin
13
Q

How do histones interact with DNA?

A
  • Chromatin: DNA packaged with protein
  • Most abundant proteins are histones
  • Histone proteins contain basic amino
    acids which are positively charged
    – Lysine
    – Arginine
  • The positive charges of these amino
    acids can interact strongly with the
    negative charges of the phosphate
    groups in DNA = ionic interactions
13
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13
Q

Visualising histone modifications and chromatin structure

A

Chromatin during meiosis prophase:
* Pink shows histone modifications, here methylation of histone
proteins at lysins (K) of histone protein 3
* LEFT (H3K4me3): active chromatin, radially, loop-like structures.
* Bottom (H3K27me3): inactive, repressive chromatin

14
Q

Acetylation of basic amino acids

A

Amino Acid Acetylation:
– Addition of an acetyl (CH3C=O-
) group to Lysine
▪ Acetylation of lysines is done by enzymes called
histone acetyltransferases = HATs
▪ Acetyl groups can be removed by other enzymes
called histone deacetylases = HDACs or HDs

➢Histone modification influences gene expression without changing the nucleotide sequence of the
DNA = type of epigenetic regulation
➢Epi means above or over

14
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15
Q
A

Decondensed chromatin
– Acetylated, active
– Acetylation neutralising positive charge of lysine
– Loose association of less positive histone with negative DNA ➔ prevents
ionic interaction of lysins with DNA
– DNA is accessible for proteins involved in gene transcription (RNA
polymerases, transcription factors…)

15
Q

Histone modifications are a form of Epigenetic Regulation of
eukaryotic gene expression

A

Epigenetic
Modifications:
Heritable alterations that
are not due to changes
in DNA sequence.
▪ DNA methylation
▪ Histone modifications

15
Q
A
16
Q

Acetylation of histone protein tails
remodels chromatin

A

Condensed chromatin
– hypo-acetylated, inactive
– Tight ionic interaction of positively charged histone protein tails with
negative DNA
– Inaccessible DNA, not transcribed

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17
Q

Can you …

A

➢ … relate regulation of gene expression to the creation of a fully functional eukaryotic organism with many
different cell types?
➢ … compare levels of the regulation of gene expression in pro – and eukaryotes?
➢ … list levels at which gene expression is regulated in eukaryotes?
➢ … explain the necessity of DNA packaging into chromosomes?
➢ … describe levels of DNA packaging?
➢ … relate packaging of DNA to gene expression?
➢ … describe different ways in which DNA packaging occurs for example by chromatin remodeling or histone
protein modifications?
➢ … explain the definition for “Epigenetic Regulation” and relate this to histone modifications?

Molecular Biology Flashcards (20 decks)

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