Regulation of Gene Expression Flashcards
Are all genes expressed at a given time?
No, only a fraction of the genome is active
What are the 7 levels that regulate gene expression?
1) Transcription initiation
2) Posttranscriptional processing
3) RNA stability
4) Translational regulation
5) Protein modification
6) Protein transport
7) Protein degradation
Where does RNA stability take place?
- In the cytoplasm
- Once RNA is near the ribosomes, the translation takes place
Where does protein synthesis take place?
In the cytoplasm
What are the two classes of genes?
- Housekeeping genes
- Regulated genes
What are housekeeping genes?
- Genes that are expressed by most cells in the body
- Constitutively expressed
- HAVE to be regulated
What are regulated genes?
Genes that are regulated based on the cell’s environment/the cell’s life
Where does RNA polymerase bind to DNA?
At the promoter region
How is DNA represented?
From 5’ to 3’
What happens at the transcription start site?
Where mRNA synthesis beings (RNA start site)
What is left of the RNA start site?
- Upstream
- Regulatory sequence, promoter sequence, binding elements
What is the function of the upstream sequences?
Sequences that regulate/promote gene expression
What do regulatory proteins bind to in order to regulate RNA polymerase operators?
- Transcription factors, coregulators
- Bind to promoter to regulate RNA polymerase operators
- Operators: activators, repressors
What are negative transcription regulators?
- Gene is not being expressed
- The promoter sequence is bound by a repressor
How can a negative transcription regulator be regulated?
- Signal comes in an binds to the repressor and takes it away from the promoter region
- Negative regulator is taken away
- Gene expression is turned on (induced)
What are positive transcription regulators?
- Gene is transcribed
- Promoter is activated
How can a positive transcription regulator be regulated?
- Signal comes in; brings in a repressor that binds to the promoter; gene is turned off
- ALSO, an activator can be brought in to an inactive gene, which will turn it on
Why can bacteria synthesize multiple mRNAs based on one promoter region?
There are common regulatory sequences (promoters in bacteria) for related genes
What is located downstream and upstream of a promoter in a typical procaryote?
Downstream of promoter: repressor
Upstream of promoter: activator
How does a protein bind in gene regulation?
- Specific interaction promoted by HYDROGEN bonds between AA and specific nucleotides
What does thymine and adenine bind to?
Glutamine (H-bonds)
What does cytosine and guanine bind to?
Arginine (H-bonds)
What does arginine bind to?
Cytosine and guanine
What does glutamine bind to?
Thymine and adenine
Depending on the sequence of AA, a transcription factor can identify a specific sequence of ___________
base pairs
What are the most common AA involved and present in DNA binding sequences of transcription factors?
Asparagine, Glutamine, Glutamate, Lysine, Arginine
What are the features of the helix-turn-helix domain?
20 AA long with 2 a-segments (2 flaps)
How does the helix-turn-helix act as a recognition helix?
- One a-segment acts
- Reads the sequence and interacts
What are the features of the zinc finger domain?
- 30 AA long
- Loops are coordinated by Zn2+
How do proteins solve weak DNA binding?
By having several zinc finger domains between them
Which DNA binding motif can read RNA sequences and act as RNA-binding motif?
Zinc finger domain
Which DNA binding motif is found only in Eukaryotes?
Homeodomain
How long is the homeodomain?
60 AA
What does the homeodomain ressemble in terms of function?
Helix-turn-helix
In the leucine zipper, how often does leucine occur?
At every 7th position
How does part of the domain of the leucine zipper interact with DNA?
Through lysines and arginines
Helix-loop-helix contains 1 ____ residue
leucine
How does helix-loop-helix partially interact with DNA? What does the rest interact with?
- Through lysines and arginines
- The rest interacts with other regulatory proteins that still regulate gene expression
Do all transcriptional regulators need to bind to DNA? What could they bind to in order to still regulate gene expression?
- No
- They can bind to helix-loop-helix (which is bound to DNA) and regulate gene expression
How many transcription factors that have DNA binding domain do humans have? How many genes do they regulate?
- 1557 transcription factors
- 20 000 genes
How do transcription factors work together?
- Multiple transcription factors that in different combinations can regulate different genes
- Function by combination (mix-match)
What do transcription factors also interact with?
- TFs and coregulators
What features of gene regulation are different in Eukaryotes?
- Access to promoters is restricted by chromatin structure
- Positive regulation is the most common
- Regulatory proteins are multimeric
- Transcription and translation are separated by the nucleus
In Eukaryotes, what is the access to promoters restricted by?
By the chromatin structures
What is chromatin?
DNA + Histones (proteins)
What is the main function of histones?
- Involved in tight packaging of a long length of DNA to form chromosomes
- Involved in gene expression
In Eukaryotes, what is the access to promoters regulated by?
- By the structure of chromatin
- Tight: less access
- Loose: more access
Which type of regulation is most common in Eukaryotes?
Positive regulation
In Eukaryotes, regulatory proteins are ___________.
multimeric (not individual proteins; present in groups)
In Eukaryotes, where do transcription and translation take place?
- Separated by the nucleus
- Transcription: nucleus
- Translation: cytoplasm
How many histones are there? What are they called?
- 5 different histones
- H1, H2A, H2B, H3, H4
What is the function of the histones?
- H1 histones do NOT play a huge role in transcriptional regulation
- The other 4 make a block around which DNA is wound
What are the two types of chromatin?
Heterochromatin: when chromatin is tightly bound (no access to transcription factors)
Euchromatin: when chromatin is loosely bound (easy access)
When a region of chromatin is transcriptionally active, it is deficient in ___.
H1
When a region of chromatin is transcriptionally active, what variants may form?
- Histone variants
- H3.3 instead of H3
- H2AZ instead of H2
- Occurs when there is gene transcription occurring
Which enzymes are important for histone modifications? What is their function?
- SWI/SNF enzymes
- Modification of histones (replacement, removal, bringing in variants)
When histones are modified, _____ is modified.
Chromatin
Histones are covalently/non-covalently modified.
Covalently
What are the possible modifications of histones that can cause positive or negative effects on gene expression through different combinations?
○ Methylation of lysine and arginine
○ Phosphorylation (serine and threonine)
○ Acetylation (lysine)
○ Ubiquitination and sumoylation (lysine)
Which enzymes regulate histone acetylation?
HATs and HDACs
How can DNA be modified by methylation? In which sequences?
Methylation of cytosine (nucleotide) in CpG sequences (whenever C is followed by a G)
What happens when DNA is methylated?
It is associated with transcriptional inhibition (genes are turned off in that region)
_______________ help in the assembly of the pre-initiation complex.
Regulatory proteins
Which far away region can regulate gene expression?
UAS: upstream activator sequence
What are HMG proteins? What is their function?
- High mobility group
- Bend the DNA to form a loop so that far away sequences come closer to the promoter sequences
Which proteins promote the binding of the polymerase complex?
UAS and HMG
Which complex has to form before a gene is transcribed?
Pol II initiation complex
What will allow the Pol II initiation complex to form?
Binding of various regulator and mediator proteins will allow this to happen
What can inhibit the assembly of the pre-initiation complex?
- Repressors
- Upstream inhibition sequence can repress the Pol II initiation complex and turn off gene expression
Activators and regulators get associated with _________
mediators
What do activation domains activate?
Mediators
What are the three protein interaction domains that display characteristic features?
- “ppp” proline-rich domains
- “QQQ” glutamine-rich domains
- ”—” acidic AA (Aspartate and Glutamate)
Why can sequences be taken to see which genes are affected by nuclear receptors in bioinformatics?
Because specific nuclear receptors recognize specific DNA sequences
What does the transcription activation domain interact with?
- Transcription factors
- Proteins of initiation factors
What does the hormone binding domain interact with?
Binds to hormones
What kind of domains can be located in a transcription factor?
- DNA binding protein
- Transcription activation domain
- Hormone binding domain
Can procaryotes go through alternative splicing?
- No
- Unique to Eukaryotes because genes are not a continuous sequence of DNA that is transcribed
What are exons and introns?
- Exons: genes that are present in blocks
- Introns: anything in between exons
It is the sequence of ______ that results in the sequence of AA from protein synthesis.
exons
What is splicing?
- Introns are removed and exons are joined together
- If certain exons are spliced out and others are retined, they can leave completely different proteins
What is alternative splicing?
- One gene can be spliced to form different proteins that are synthesized
- Achieved by a combination of different exons
What is the reason behind the fact that humans can produce 200 000 proteins from 20 000 genes?
Alternative splicing
How do micro-RNAs regulate mRNAs?
- Prevent translation of mRNA by binding to it
- Cleaves it or blocks it
What happens when micro-RNAs bind to mRNAs?
- mRNA can be degraded
- mRNA’s translation can be inhibited
What are the two classes of micro-RNAs?
1) SiRNA
2) stRNA
How does SiRNA act?
Turns a double-stranded RNA into a single-stranded RNA
How do nuclear receptors function?
Receptor is in the cytoplasm; gets dimerized; gets taken into the nucleus;
transcription
Where can nuclear receptors be located? (2)
- In the cytoplasm
- Directly bound to chromatin
