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CTO2 - Cells to Organism > Differentiation > Flashcards

Differentiation Flashcards

1
Q

What are organs?

A

Communities of specialised cell types

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2
Q

What is cell differentiation? 2 definitions:

A

The process by which unspecialised cells become specific cell types

– in the embryo (development)

– and continuing throughout life (tissue homeostasis)

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3
Q

How do cells differ?

A

Depends on the presence of different sets of proteins
- diff macromolecules
- different metabolites
- different morphologies and behaviours

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4
Q

Housekeeping vs specialised proteins ?

A

housekeeping = proteins found in most cell types for shared essential cell functions
specialised proteins = proteins specific to particular cell types (luxury functions)

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5
Q

Is insulin and antibody chain house keeping or cell-type specific?

A

cell-type specific

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6
Q

Cell differentiation in embryo development: egg divides to give many cells (initially ______) which must _____ into their various cell types.

A
  • unspecialised
  • differentiate
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7
Q

During early embryogenesis germ layers act as intermediates. what are the 3 germ layers and what does that process lead to?

A

Ectoderm, Mesoderm and endoderm
- eventually leads to cell destiny

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8
Q

Differentiation is driven by interplay between a ____ and its _____.

A

cell’s history (cell lineage)
environment (cell interactions)

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9
Q

What are progenitor cells or precursor cells?

A
  • intermediate states of differentiation
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10
Q

Final cell form is _____ and it is ______

A
  • terminal differentiation
  • irreversible
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11
Q

Germ layers are formed during _____

A

Gastrulation

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12
Q

Mesoderm cells are more differentiated by the virtue of…

A
  • more specific proteins
  • characteristic cell behaviour
  • restricted future differentiation potential
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13
Q

Definitions:
- cell fate determination
- cell lineages
- lineage restriction
- potency

A
  1. The process by which a cell becomes committed to a specific function or identity during development
  2. The developmental history or ancestry of a cell, tracing its progression from a single progenitor cell
  3. The process by which cells become progressively limited in their developmental potential
  4. The ability of a cell to differentiate into different cell types
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14
Q

What are the different types of potency and what cell types they can make?

A

Totipotent: Can form all cell types, including embryonic and extraembryonic tissues.

Pluripotent: Can form all cell types of the body but not extraembryonic tissues.

Multipotent: Can differentiate into a limited range of related cell types

Unipotent: Can produce only one cell type but retains the ability to self-renew.

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15
Q

How are cells differentiated (gene constancy and control of gene expression)

A

Cells differ in protein constituent as well as gene expression. nucleus of fertilised egg contains all genes for all possible proteins. cell specialisation is due to selective activation/inactivation of genes

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16
Q

What is an experiment to prove that genes are not lost in specialised cells?

A

nucleus of differentiated cell supports development of new organism. whole animal or plant can be cloned from a specialised cell

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17
Q

What is gene constancy?

A

all cells in a multicellular organism have a full complement of genes

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18
Q

What are gene expression patterns?

A

Cell-type-specific distribution of proteins and their mRNA

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19
Q

Control of gene expression in cells determines:

  • their____, which in turn determines:
  • their ______
  • their____* during development
A
  • their protein content, which in turn determines:
  • their morphology and function
  • their behaviour* during development
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20
Q

What is not an important concept in embryo development?

A

cell opportunity

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21
Q

Most differentiated cells retain a complete genome known as:

A

Gene constancy

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22
Q

Where is start site of transcription determined by?

A

helper proteins called TATA binding protein coded by TATA box that controls where transcription starts

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23
Q

What is a transcription factor and where does is it interpreted?

A

TF are proteins that are either activators or repressors that bind to enhancers to switch on or off transcription

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24
Q

a gene’s transcriptional activity in a cell depends on:

A
  1. what binding sites are in its DNA enhancer sequences

AND
2. whether approprioate TFs are present in cell

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25
Q

How does TF act via chromatin modifications?

A
  • indirectly recruit RNA polymerase by altering chromatin structure
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26
Q

How does histone acetyl transferase (HAT) work?

A

acetylation loosens histone interaction with DNA, making the gene more accessible

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27
Q

How does chromatin-remodelling complex work

A

chromatin modifying enzymes promote RNA polymerase binding and function

28
Q

Describe the stages of muscle cell differentiation

A
  • Muscles come from mesoderm
  • growth factor secreted to maintain cells in proliferating state
  • turns into myoblast
  • signal to stop growing and start differentiating
  • turns into muscle fibre
29
Q

What is the TF for muscle cell differentiation and what does it activate/suppress)

A
  • MyoD is present in muscle cells during differentiation
  • activates expression of gene for muscle myosin II
30
Q

MyoD coordinated the activation of multiple muscle genes required for cell differentiation. example:

A

muscle myosin II, troponin, tropomyosin

31
Q

These muscle genes are known as target genes. How are they simultaneously switched on? What is this an example of?

A

they all have MyoD’s E box recognition sequence
- example of one TF controlling multiple genes

32
Q

What is the effect of mutating the MyoD gene?

A

undifferentiated myoblasts, failure of cell differentiation

33
Q

What does introducing expression of MyoD in non muscle cells induce?

A

skin cell attempts to function like muscle cell

33
Q

What are the experimental techniques fr genetic analysis of TF function & expression pattern?

A
  • Loss-of-function (l-o-f) – is the transcription factor required for cell differentiation?, Mutate the gene encoding the transcription factor
  • Gain-of-function (g-o-f) – can the transcription factor force cell differentiation (is it sufficient)? Express it in cells that don’t normally have the factor
34
Q

What does plant leaf trichomes (differentiated cell type) do?

A
  • deter insects
  • break up wind current
  • reduce sun exposure
35
Q

how TF recognise their DNA binding site?

A
  • hydrogen bonding is precise at determining bases
  • protein has alpha helix inserted into groove which contacts outside of bases
35
Q

Where in the cell would you find TF?

A

nucleus - near promotor or enhancer regions

36
Q

How many TF in humans, how many % of your genes code for TF?

A

2000-3000
10%

37
Q

Groups of TF binding sites - an enhancer pr cis-regulatory element is a combination which:

A

switches the gene on leading to more complexity and variation in gene expression

38
Q

GATA1 is an important TF in RBC, what does a mutation of that lead to?

A

erythroid precursor cells die so their target genes won’t be expressed (e.g. a and b globin genes)

39
Q

Enhancers of B- globin genes include several different TFs. what are they?

A
  • GATA1
  • CP1
  • NF1
40
Q

Why is GATA1 alone not sufficient?

A
  • GATA1 is expressed in several blood cell lineages
  • GATA1 works in combination with diff TF in each lineage
41
Q

TFs are regulated by:

A
  1. Environmental signals (e.g. signals from other cells, hormones, growth factors)
  2. Developmental history: in cell lineages early TF regulate the expression of later TF
41
Q

Complex regulatory interactions are called:

A

Gene regulatory networks (GRNs)

42
Q

TF activity can be regulated by phosphorylation. How?

A
  • The large negative phosphate group alters protein conformation
  • This may activate or inhibit the transcription factor
42
Q

Example: GF can regulate gene expression via phosphorylation of TFs. how does this happen?

A
  • Growth factors (signals that promote cell proliferation)
  • Activate a protein kinase cascade
  • ‘Mitogen activated protein kinase’ (MAP kinase) enters nucleus and phosphorylates transcription factors
  • This activates them for target gene regulation
43
Q

Binding to EGF receptors leads to phosphoric;ation of MYC on several serines. stabilised MYC drives transcription. what happens if mutation causes serine -> alanine?

A

protein might be unstable because alanine can’t be phosphorylated

44
Q

GATA1 is important in RBC differentiation. EPO is secreted and causes phosphorylation of GATA1. what is the effect?

A
  • EPO causes phosphorylation of GATA1, increasing its DNA binding affinity
  • Conditions of low O2 stimulate greater EPO secretion
45
Q

Why is TF important in embryonogenesis

A
  • orderly progression through to differentiation (cell lineages and cell fate determination)
  • control of cell fate choices
46
Q

Leaf stomata guard cell differentiate relies on 3 related bHLH TF regulated in sequential steps in guard cell differentiation:

A
  1. Speechless
  2. Mute
  3. Fama
47
Q

What does mutants of each gene lead to? SPCH, MUTE, FAMA

A

stomata are missing
SPCH - meristemoid mother cells
MUTE - guard mother cells
FAMA - stomata guard cells

48
Q

Muscle differentiation is an example of :

A

gene regulatory network (GRN)

49
Q

How is moD gene activated?

A

co-regulation by somite specific TF Pax3 and signal activated TF Myf5

50
Q

What activates myf5?

A

Shh triggers it to start differentiating

50
Q

explain the myoD auto regulation:
- myoD activates its _____
- production of myoD binds to its ___
- once it is turned on it____
- boosts initiaal myoD level given by ____ regulation
- myoD expression becomes independent of myf5 and pax3 regulation_

A
  1. own expression
  2. own enhancer region
  3. stays on
  4. myf5/pax3
  5. independent
51
Q

Explain how GF regulates MyoD protein stability?

A
  • Growth factors promote cell division (via cell cycle genes)
  • how it promotes cell proliferation and stops differentiation as it is still growing
  • myoblast secreting GF that binds onto receptors for proliferating
  • myoD has to be prevented from allowing differentiating whilst growth factors are around
  • Cyclin-dependent kinase phosphorylates MyoD and Myf5
  • MyoD is being phosphorylated which leads to degration (unstable and is targetted by proteolytic degration)
  • While growth factors are present, muscle differentiation inhibited;
52
Q

Why and how is pax3 mRNA degraded during differentiation

A
  • Pax3 required for early muscle development
  • It must later be down-regulated for later stages to proceed
  • Its mRNA is degraded specifically by RNA interference
  • microRNA produced which binds to pax3 mRNA and prevents it from being transcribed
  • This is achieved by a specific regulatory RNA called microRNA miR-1
53
Q

What does the cell fate determination by Conrad waddington show

A
  • metaphorical approach to cell determination
  • idea: cell fate and choices can be thought of a landscape with hills and dallies
  • cell represented as a ball going down vallies
  • cells are multipotent in the beginning and are able to choose an path
54
Q

What are the binary cell fate choices of the pancreas?

A

function:
- digestion (exocrine)
- maintaining blood sugar (endocrine - islets of langerhans)

54
Q

Describe the cell fat choices of the pancreas

A
  • pancreatic bud are multipotent for all the pancreatic cell types
  • goes through various binary cell types
55
Q

What decides pre-pancreatic fate in the correct part of the foregut?

A
  • interaction between primitive gut and structure called notochord (source of signals)
  • gut primordium expresses 2 TF, overtime it will expand, grow and start to coil
  • as gut cells proliferate, they loop up to become notochord and becomes in range of a signal being produced by notochord = fgf2
  • cells become close in that region only (the maximus of the curve) and the cells respond by exprerssing the pdx1 gene = pre-pancreatic region
56
Q

Deciding pre-pancreatic fate. How does Cdx2 expression lead to differentiation?

A

Cdx2 expression gives gut cells the potential or competence to become pre pancreatic cells (the only part that is looped up is able to receive signal although the whole strucutre displays it). Cdx2 activates Pdx1 expression only if Fgf2 signal received

57
Q

CMP = stem cell that gives rise to many types of cell. Describe the binary decision in making erythroid or myeloid

A
    • progenitor expresses both GATA1 and PU.1 (antagonistic, competeing to drive the cell down one way or another, they inhibit eachother whilst trying to autoregulate themselves)
  • locks in once one beats the other
58
Q

How does PU.1 repress GATA activity?

A
  • GATA1 bound to a target gene (or GATA1 gene)
  • PU.1 binds to GATA1
  • Knocks off a coactivator protein
  • Recruits chromatin methylation protein
  • (‘tightens’ chromatin – less accessible)
59
Q

in drosophila, eyeless is the mutation of the PAX6 gene that encodes for TF required for the start process of forming an eye. what is the effect of PAX6 gene being expressed in ectopic location?

A
  • eye forms in ectopic location
60
Q

What is the Pax6 known as in terms of regulation?

A

Master regulator

61
Q

What could be the mechanism that explains the lost of eye in cavefish

A
  • PAX6 gene is present but regulation has become defective during evolution
  • PAX6 gene is present and functional but the target genes of PAX6 TF are missing/non-functional

CTO2 - Cells to Organism (8 decks)

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