Week 10 Flashcards
What are the two theories of how eggs can generate whole organisms?
Preformationism and Epigenesis
What is preformationism?
Adult is preformed in egg or sperm, all organisms were generated at the same time
What is epigenesis?
Organisms are progressively built anew in each generation
Aristotle supported this
Which cells contain the complete genome? and what does this mean?
The nucleus of the zygote and every cell that is produced during ontogenesis contains the complete genome.
Every cell, somatic and germ line cells can be used to make a new animal - as in Dolly sheep where a somatic cell was used.
what is differentiation?
Making cells different by regulation of gene expression
In broad terms how are the different cell types established during development?
the genotype contains a developmental programme that unfolds and results in the expression of different sets of genes in different cell types
what are 5 factors that control gene expression?
chromatin structure initiation of transcription RNA processing initiation of translation post-translational modifications
Genes within highly packed ____ are usually not expressed. Why?
heterochromatin
Because dont have access to the genes, it is not naked.
What can affect whether a gene is transcribed?
the location of the gene promoter relative to nucleosome
sites where DNA is attached to the chromosome scaffold or nuclear lamina
Chemical modifications to histones and DNA influence both chromatin structure and gene expression = 3 types?
acetylation
methylation
phosphorylation
What is methylation?
The addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species. The methylation pattern is past on to daughter cell
what 2 things are used in genomic imprinting?
DNA methylation and histone modifications
What is genomic imprinting?
process by which epigenetic modifications regulate expression of either the maternal or paternal alleles of certain genes at the start of development
What is epigenetic inheritance?
Epigenetic modifications can be passed on to emerging cells during development, however, epigenetic tags are removed in germ line cells.
Some epigenetic tags avoid reprogramming and are inherited by the next generation - this is epigenetic inheritance
Example of epigenetic inheritance in plants?
When wild radish plants are attacked by caterpillars they produce distasteful chemicals ad grow protective spines. The offspring of the caterpillar damaged plants also develop these defences, even in the absence of caterpillars.
(no nucleotide changes)
INDIRECT EVIDENCE
Example of epigenetic inheritance in invertebrates?
waterfleas respond to predators by growing helmets. This defensive trait is inherited by the offspring and maintained in the absence of predators over several generations. Not known the substance which induces the helmet growth but something the preadtor does.
INDIRECT EVIDENCE
Example of epigenetic inheritance in mammals?
Rats.
Feeding vinclozolin to pregnant rats causes life long changes in the pups. As adults, the offspring have low sperm counts, among others. this trait is maintained over 3 generations.
DIRECT EVIDENCE - the sperm DNA had an abnormally high level of methyl tags.
Regulation of transcription by transcription factors. How?
Chromatin modifying enzymes provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery.
Transcription factors then control levels of transcription
What is a gene?
a section of DNA that contains the information required for the production of a biologically active RNA molecule
What is the organisation of a typical eukaryotic gene?
most eukaryotic genes have control elements, segments of noncoding DNA that help regulate transcription by binding certain transcription factors.
What is critical to the precise regulation of gene expression in different cell types?
control elements and the transcription factors they bind
Which control elements are located close to the promoter?
proximal control elements
What are enhancers?
groups of distal control elements
where are distal control elements located?
far away from a gene or even located in an intron
what regulates gene expression?
the binding of transcription factors to enhancer control elements regulates gene expression
What is required to initiate transcription?
eukaryotic RNA polymerase requires the assistance of proteins called transcription factors
What are essential for the transcription of all protein coding genes?
General transcription factors
In eukaryotes, high levels of transcription of particular genes depends on what?
control elements interacting with specific transcription factors
A given gene may have many different control elements (enhancers). Expression depends on what?
The complement of activator or inhibitor transcription factors present in the cell that can bind to these control elements
What does TATA BOX do?
it binds TATA binding protein that is necessary for efficient RNA synthesis
promoter elements bind transcription factors that help what?
stabilise the RNA polymerase complex
Enhancer elements are brought into contact with the _______ , BASAL transcription factors are required for ________ to bind to promotor regions and initiate transcription.
basal promotor
RNA polymerase II
Cell specific transcription factors ___ or ____ complex stability and thus increase or decrease _____
increase
decrease
gene expression
What is different with prokaryotic operon genes and eukaryotes?
Unlike the genes of a prokaryotic operon, each of the coordinately controlled eukaryotic genes has a promotor and control elements. These genes can be scattered over different chromosomes, but each has the same combination of control elements.
Copies of the activators recognise specific control elements and promote simultaneous transcription of the genes
What do mechanisms of post transcriptional regulation allow?
a cell to fine tune gene expression rapidly in response to environmental changes
What are post transcriptional regulation mechanisms (3)?
RNA processing
mRNA degradation
initiation of translation
What is RNA processing?
In alternative RNA splicing different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are included.
You can put the exons together in different combinations and each time you end up with a different protein, so from one RNA molecule you can make different proteins.
Explain mRNA degradation
The life span of mRNA molecules in the cytoplasm is a key to regulate protein synthesis.
Eukaryotic mRNA is more long lived than prokaryotic mRNA.
The mRNA life span is determined in part by sequences in the leader and trailer regions
explain initiation of translation
the initiation of translation of selected mRNAs can be blocked by regulatory proteins that bind to sequences or structures of the mRNA. Alternatively, translation of all mRNAs in a cell may be regulated simultaneously.
For example, translation initiation factors are simultaneously activated in an egg following fertilisation.
What are noncoding RNAs?
only a small fraction of DNA codes for proteins in complex organisms. the amount of non-coding DNA increases with the complexity of organisms. a significant amount of the genome may be transcribed into noncoding RNAs.
Noncoding RNAs regulate gene expression at 2 levels?
mRNA translation
chromatin configuration
What are microRNAs?
small single stranded RNA molecules of +- 22nt length. They bind to complementary sequences in the 3’UTR of multiple target mRNAs. This blocks the translation of the mRNA. - gene silencing
What is the phenomenon of inhibition of gene expression by RNA molecules called?
RNA interference (RNAi)
What does RNAi involve?
microRNAs and small interfering RNAs (siRNAs)
siRNAs and miRNAs are similar but form from different ___
RNA precursors
____ can derive from external sources
siRNA
What can siRNAs do to the chromosome?
they play a role in heterochromatin formation and can block large regions of the chromosome
What is a post translational regulation mechanism?
Protein processing and degradation
After translation various types of protein processing, including ___ and ____ are subject to control
cleavage
addition of chemical groups
What are proteasomes?
giant protein complexes that bind protein molecules and degrade them
how can fertilised eggs generate a complex organism?
a programme of differential gene expression leads to different cell types in a multicellular organism
the development from zygote to adult results from 3 major processes??
cell division - need many cells that can be made different
cell differentiation - want different cell types
morphogenesis - specific shapes
what provide the cellular material for the formation of organs and tissues?
mitotic divisions
what is cell differentiation?
the process by which cells become specialised in structure and function
what is morphogenesis?
stands for the physical processes that result in the typical shape of tissues, organs and the whole organism.
what is morphogenesis a consequence of?
the generation of different cell fates
which 4 mechanisms are involved in the generation of different cell fates?
cytoplasmic determinants
induction - short range
induction - long range by morphogens
lateral inhibition
What is an eggs cytoplasm like?
it contains RNA, proteins, and other substances that are distributed unevenly in the unfertilised egg.
What are cytoplasmic determinants in the early development?
they are maternal substances in the egg that for example regulate the formation of the axes.
as the zygote divides by mitosis cells contain different cytoplasmic determinants which lead to _____
different gene expression
what is an example of uneven distribution of cell fate determinants during later stages?
neural stem cells
what is asymmetric cell division?
uneven distribution of cell fate determinants, not uneven cell size but eneven determinants
neural cell fate determinants are localised where?
to the neural precursor
what is induction?
the process whereby one group of cells signals to another group of cells in the embryo and so affects how they will develop.
This signal changes the gene expression in the neighbouring cells.
what occurs in induction?
signal molecules from one group of embryonic cells cause transcriptional changes in nearby target cells and thus interactions between cells induce differentiation of specialised cell types
which transcription factor and which protein direct the differentiation of the endoderm and mesoderm?
VegT - transcription factor
Vg1 - protein
What is VegT?
a transcription factor that directs expression of endoderm specific genes
what is Vg1?
a secreted protein that acts on nearby cells and tells them to become mesoderm : mesoderm induction
What are the 3 types of short range inductive signals?
paracrine signalling
ECM signalling
Juxtacrine signalling
what is paracrine signalling?
short distance; factors secreted from one cell act on nearby cells
what is ECM signalling?
matrix components from one cell may signal to a neighbouring cell
what is juxtacrine signalling?
cell - cell contact
embyonic induction increases ___ during development
complexity
cells can only respond to the inducing signal if they are competent to do so, example?
normal induction of lens by the optic vesicle. Optic vesicle can not induce lens in ectoderm that is not competent - shown in a recombination experiment.
optic vesicle removed no lens induced - shown in a defect experiment
implanted neural cells are not able to induce lens tissue - shown in a transplantation experiment
what is one method of analysing cell fate? example
in vivo labeling of neural stem cells and their progeny in the crustacean. Done by Ungerer & Scholtz 2008
model systems give insight into basic mechanisms, what are some common model systems?
c.elegans, Drosophila, Xenopus, Zebra fish
what are the 3 methods of analysing cell fate?
anatomical
experimental
genetic
what are the 3 ways you can analyse cell fate anatomically?
morphological observation, cell labelling studies and comparative evolution. Using fate maps, the life cycle and evolution
Morphological observation has lead to? (2)
generation of hypotheses
discovery of adhesion factors
What are fate maps?
they provide the basis for experimental biology. They give information about what happens thus generating ideas about how tissues are formed, leading to experiments to test the hypotheses.
comparative embryology contributed to (2)?
concept of the life cycle
evolutionary theory
all animals undergo a similar life cycle that consists of?
fertilisation cleavage gastrulation generation of tissue generation of organs immature (infertile stage) adult
what is the phylotypic stage?
stage of development at which all species within a particular phylum look the same
What are Von Baers principles?
the general features of a large group of animals appear earlier in development than do the specialised features of a smaller group.
Less general characters are developed from the more general, until finally the most specialised appear
Von baers observations coupled with cell labelling led to which concept?
evolution homologous structures
what are homologous structures?
organs whose underlying similarity arises from their being derived from a common ancestral structure
experimental embryology gives information about how development occurs, where the signals come from. What are the 4 kinds of experiments?
isolation experiment
defect experiment
recombination experiment
transplantation experiment
Isolation experiment led to the idea of autonomous development. What is this?
Separation of the 8 cell tunicate embryo into pairs of cells: each pair devlopes along correct path. Interpreted as each cell knowing what it was to become. Develops along path in absence of external signals
What do transplantation experiments provide information about?
when the fate of a cell is set
the ability of a cell to adopt a specific fate changes over time, what are the 2 different stages of development?
specification
determination
What is specification?
a cell can differentiate along the normal path when placed in isolation
but at this stage of development the fate can be changed if the cell is transplanted to a different region of the body
what is determination?
cell differentiates along specified path when placed in different regions of the body. Fate cannot be changed, the cell is committed to that fate.
what are the 3 modes of specification?
autonomous
conditional
syncytial
what is autonomous specification?
some invertebrates
by differential acquisition of cytoplasmic determinants
what is conditional specification?
all vertebrates and many invertebrates
specification occurs by interactions between cells (cell signalling). No invariant fates. Regulative development
what is syncytial specification?
most insect classes
cell fate determinants determine cell fates along anterior-posterior and dorso-ventral axis before cellularization.
no rigid cell fates for particular nuclei.
after cellularisation conditional specification is most often seen
Genetic approaches to development give information about the molecules involved. What are the 2 methods>
forward genetics
reverse genetics
what is forward genetics?
from phenotype to genotype. Identify phenotype and then isolate gene
what is reverse genetics?
from genotype to phenotype.
isolate gene then identify phenotype
Forward genetic approaches rely on the analysis of ____
mutants
in the form of mutagenesis screens to induce mutation or using naturally occurring mutants
If every single cell has the same genetic make up how do we get different cell types?
gene expression is what makes the difference between the blood and the muscles for example. It happens in development when genes are switched on or off.
What is acytelation?
the histone tails are accessible and acytelated then the DNA loosens up and the DNA becomes accessible to transcription etc
Control elements are required for what?
the expression of a gene
If you have genes all over different chromosomes how do you switch them on?
using the same transcription factor - same control element, same enhancer element that bind the same transcription factor
the transcription factors will bind everywhere that has the same enhancer elements allowing you to switch on multiple genes at once
