T3- M3&4 Flashcards
What did all cells derive from
Fertilized eggs
What determines a cell’s fate
Which genes are turned on/off
Why are signals important
To control gene expression
Define proteome
The complete set of proteins made by an organism
What are transcription factors
Proteins which bind to specific DNA sequences
Why are transcription factors essential
- Determine pathway for cell type
- Work with other proteins that result in gene expression changes
How are transcriptional regulation in prokaryotes and eukaryotes similar
- Both activate and repress transcription
- both use RNA polymerase to bind to promotors
How are the DNA in eukaryotes and why
Highly compact chromatin- easy way to fit DNA in nucleus
What do chromatin do
Allow DNA to move around in cell divison
Are genes in tight chromatin expressed?
No, need to unwind
What is DNA wrapped around
Histone proteins
How many histone proteins does each nucleosome have
8 with 150 base pairs
What is chromatin remodelling
The rearrangement of chromatin from a condensed state to a transcriptionally accessible state
What is needed for chromatin remodelling
Activator protein or transcription factor
How is DNA tightly bound
Due to positive tails of histones and negatively charged phosphate in DNA
What is the activator protein recruited for histone modifications
Coactivator enzyme histone acetyltransferase
What does coactivator enzyme histone acetyltransferase do
Attaches acetyl groups to lysine amino acids along positive tails of nucleosome histone proteins
What happens once positive tails are acetylated
Positive charge is reduced and interactions between histones and DNA reduced
What other modifications assist in transcription initiation
Methylation of lysine and arginine
Phosphorylaton of serine and theanine
4 types of transcription factor proteins
- include basic helix loop helix
- helix turn helix
- zinc finger
- leucine zipper
What bonds are between alpha helical domains
Hydrogen bonds
What is the promotor sequence in eukaryotes
TATA box
What is a core promotor
A binding site for RNA polymerase and other transcription factors
What is recognized by TATA box
TATA binding protein or TBP subunit of transcription factor TF2D
What is the BRE region
Promoter for eukaryotes
What is BRE region bound by
TF2B factor
What are enhancer regions
Bind cell or region specific transcription factors
- facilitates formation of transcriptional complex
Where are enhancer sequences in eukaryotes
Distant from promotor
What happens once transcriptional components bound
Flexible DNA allows factors and RNA poly to loop
What do adaptor or mediator proteins do
Connect enhancer proteins to promotor proteins
What are silencer proteins
Bind transcriptional repressors to halt transcription
- positioned upstream of target gene
What does silencer region activation cause
Interference of general transcription factor assembly and mediator activity
What type of cells specialize to hemoglobin
Blood cell progenitors/ stem cells
What must happen before progenitor cells differentiate into red blood cells
Transcription of globin proteins
What hemoglobin proteins are in both fetus and adults
2 alpha globin proteins
What hemoglobin protein is unique to fetus
2 gamma globin proteins
What hemoglobin proteins are unique to adults
2 beta globin proteins
Why do fetuses need gamma globin proteins
Gamma globin proteins bind more oxygen, allowing the fetus to use it for development in womb
What does chromatin of beta globin gene do in fetus
It is tightly wrapped to prevent transcription
What does chromatin of beta globin gene do in adult
It is loose to allow transcription
What does methylation of nucleotide bases do
Inhibit transcription
What is the most common nucleotide modification in DNA
Addition of methyl group to cytosine base
What are CpG islands
A string of cytosine and guanine bases where methyl group is added
What does p represent in CpG islands
Phosphate group
Where are CpG islands located
Near promotors
What happens when CpG islands not methylated?
DNA binding proteins recognize promotor and transcription occurs
What happens when CpG islands methylated?
Shape of DNA binding site is changed and protein cannot bind- no transcription
Define HDAC
Histone Deacetylases
- Bind to DNA and promote removal of acetyl group from neighboring proteins
What is the purpose of HDAC proteins
Allow nucleosomes to reassemble and mask enhancer and promotor sequences
* repress transcription
What is the default nature of chromatin in prokaryotes
Default “off”
What is the default nature of chromatin in eukaryotes
Default chromatin “on”
What does amount of gene product vary upon
- changing conditions
- different signals
Where can gene expression be regulated
- transcription/ initiation
- RNA processing
- stability of RNA
- Protein synthesis
- Protein modification/ transport
- Protein degregation
Describe In Situ Hybridization
Lab technique used to identify which cells and tissues express gene by undertaking analysis of finding mRNA in organism development
How was mRNA detected
Complimentary probe with tag
What does complimentary probe have
Fluorescently labelled short, single stranded segment of DNA/RNA which binds complimentary to mRNA
Describe DNA microarray
Lab technique where glass slides with known DNA act as probes to detect gene expression in a pattern
What can microarrays show
Thousands of genes at once and help visualize variation in gene expression in different cell types
What must happen to mRNA to be labelled
Isolated from cell
What needs to be made as a template for mRNA
Complementary cDNA molecules using reverse transcriptase enzyme
- florescent nucleotides used and become part of new cDNA molecule
Describe how mRNA from normal and epithelial cells were combined in hybridization
Equal amounts were placed with normal being green and cancer being red
How to know if gene is active
Produces a lot of mRNA and lots of cDNA- BRIGHT SPOT
What did it mean if the spot was green?
Specific gene is expressed more in normal cells
What did yellow spots mean
Gene equally expressed in both
What does no brightness mean?
Gene not expressed
What must happen to mRNA to stop gene expression
Must be degraded
How was poly a tail affect mRNA
Needed for stability
Describe miRNA
short, non coding regulatory double stranded molecules which to become part of the silencing complex
What does miRNA form
Hairpin loops due to complimentary base pairing
What do the miRNA hairpin loops do
Process into single stranded mRNA fragments which activate RNA interference machinery
What do miRNA and RISC complex do
Bind to target mRNA sequence for translation miRNA
What is siRNA
Small interfering RNA which is associated with RISC complex
- exact compliments of mRNA target
Purpose of proteasomes
Degrade unneeded or damaged proteins by marking them
