Theme 3- Module 3 Flashcards
Development of a eukaryotic organism from a single fertilized zygote is dependent on the ____________
Molecular communication between cells
What determines the fate of an embryonic cell?
The signals that are exchanged
Which genes are switched on or off at specific times
On what type of cell did differentiation occur (that eventually led to the variation in specialized cell types)?
Stem cells
What does the body use to control which genes get activated along the chromosome during development?
Transcription factors (det pathway)
Proteins (that can result in various changes in gene expression)
All embryonic stem cells are
a) Different
b) The same
B) The same
Muscle cells and liver cells are different because:
a) They have different DNA blueprints
b) They were transcribed differently
c) They removed unnecessary genes from the genome
b) They were transcribed differently
How does winding the DNA into chromatins affect gene expression?
Genes within this tightly wound heterochromatin are usually not expressed. To be able to transcribe a specific gene product, it is necessary to unwind the DNA.
Describe the structure of a nucleosome
Octamer of 8 histone proteins around which approximately 150 DNA base pairs wrap around
Describe the basic steps of chromatin remodeling
1) Activator protein recruits histone acetyltransferase (or methyltransferase, etc)
2) Add acetyl group to lysine (or specific amino acid) along histone tails
3) (+) charge of tails reduced
4) Interaction b/w histones and DNA are weakened
What is the histone code?
Degree of modifications to histone tails controls activation and repression of transcription
Does acetylation and methylation with a single methyl group allow for transcriptional activation or repression?
Activation
Does methylation with three methyl groups allow for transcriptional activation or repression?
Repression
Why are transcription factors able to recognize and bind to nucleic acid sequences in DNA?
Bc of structural and chemical complementarity between the proteins and DNA
Most transcription factors are classified based on what?
The structures of their distinct DNA binding motifs (basically, they’re classified based on their structure and how it helps them bind to DNA)
What are the four different types DNA binding motifs?
Basic helix- loop-helix
Helix-turn-helix
Zinc finger
Leucine zipper
Most of these transcription factors have _________ that tend to fit nicely within the major grooves of DNA
Alpha-helical domains
What is the core promoter?
Binding site that is required for binding of RNA polymerase and associated transcription factors
What elements are part of the core promotor?
TATA box
BRE region
Transcriptional start site
The TATA box region is usually recognized by the __________ subunit of the transcription factor ___________
TATA-binding protein (or TBP)
TFIID
What is another region that is recognized by TFIID?
BRE (B recognition element)
- closely related to the TATA box
How are enhancer regions able to facilitate the formation of the transcriptional complex?
Enhancer regions are able to bind cell or region specific transcription factors. These transcription factors interact with the basal machinery at the promoter to enhance the transcription of a gene
What binds to enhancer regions?
a) Transcriptional activator proteins
b) General transcription factors
a) Transcriptional activator proteins
What binds to promotrr regions?
a) Transcriptional activator proteins
b) General transcription factors
b) General transcription factors
How do transcriptional activator proteins and general transcription factors work together to help regulate transcription?
Loop the DNA and bring regulatory sequences (which are situated far from the actual transcription sites) close to transcription sites
What do adaptor or mediator proteins do?
Connect the proteins that are bound to the enhancer regions with proteins that are bound to the core promoter region
What do silencer regions and repressor proteins do?
Interfere with the general transcription factor assembly and mediator activity
What are blood cell progenitors?
Stem cells
In order for blood cell progenitors to differentiate into functional red blood cells that contain haemoglobin, progenitor cell must activate transcription of what protein?
Globin proteins
How many alpha- globin proteins does a fetus have compared to an adult?
Both have 2 (making up half of their tetrameric hemoglobin protein)
How many gamma- globin proteins does a fetus have compared to an adult?
Fetus has 2
Adult has 0
How many beta- globin proteins does a fetus have compared to an adult?
Fetus has 0
Adult has 2
Why do fetuses have gamma proteins while adults have beta proteins?
Gamma globin binds oxygen more strongly than beta globin
Allows fetus to be able to sequester enough oxygen while growing in the womb
Both a fetus and adult have both the beta-globin and gamma-globin genes. Why the difference between the two then?
In the fetal blood cell progenitors, the chromatin is WOUND UP around the beta-globin gene to inhibit transcription
The chromatin around the gamma-globin gene is OPEN to allow transcription
(opp in adults)
How does the body switch from gamma to beta-globin proteins after birth? (what is it regulated by)
Specific transcription factors silence gamma-globin gene transcription
Others activate the beta-globin gene transcription
Besides histone modifications, what else affects transcription in eukaryotes?
Chemical modification of cytosine bases in the DNA sequence
What is the common chemical modification of cytosine bases?
Addition of a methyl group
True or false: if methylation occurs, it happens on every cytosine
False
It happens within a “CpG” island (a string of cytosine and guanine bases)
What does the “p” rep in CpG island?
The phosphate in the backbone between the two bases
Where are CpG islands frequently located?
In or near promoter sequences (or mammalian genes)
When a CpG island contains many methylated cytosine bases, why can’t transcription occur?
Bc methylations causes the shape of the DNA binding site for the proteins to change
Therefore, the proteins can no longer bind
True or false: methylation state can change in response to environmental and developmental cues
True
it’s an epigenetic mechanism
True or false: methylation state is heritable from mother cell to daughter cell
True
It maintains the same state of transcriptional activation with subsequent cell divisions
What are histone deacetylases (HDAC) and what do they do?
Proteins that can only bind to methylated DNA
They promote the removal of the acetyl groups from the neighbouring histones
Why is deacetylation of the histones important?
Allows nucleosomes to reassemble and can once again lead to the masking of enhancer and promoter sequences (and repressing transcription)
Is the default chromatin transcription conformation of eukaryotes “on” or “off”?
Off
Genes are only transcribed when chromatin is remodelled to expose the promoter sequences
Is the default genome transcription conformation of prokaryotes “on” or “off”?
On
