Final Unit: Gene Expression Flashcards
What is gene regulation?
The ability of cells to control their level of gene expression
Prokaryotes and eukaryotes can control level of gene expression at the levels of …
Transcription, Translation, Post-translation
What are three additional levels of control are unique to eukaryotes?
- Chromatin remodeling
- RNA processing
- Regulation of mRNA life span or stability
What helps DNA condense into such a small size?
Nucleosomes
What are nucleosomes and how are they produced?
Smallest structural component of chromatin
DNA wraps around histones
After the nucleosome is formed, what is next?
The nucleosomes get formed into a 30 nm fiber
What happens to the fiber of nucleosomes?
It is looped into place within the nuclear matrix
What is chromatin remodeling?
When DNA near the promoter is released from tight interactions with proteins
Is DNA unaccessible when the chromatin is condensed or decondensed?
Condensed
What is chromatin?
A complex of DNA and proteins
What is euchromatin?
Lightly stained, more open (decondensed) chromatin
What is heterochromatin?
Darkly stained, more closed (condensed) chromatin
Which type of chromatin contains the majority of eukaryotic genes?
Euchromatin
Which type of chromatin is associated with low gene transcription?
Heterochromatin
In preparation for transcription, nucleosomes are altered by what?
Multiprotein complexes
What are the two types of chromatin remodeling?
- Local histone mobilization
- Histone modifications
In local histone mobilization, what do chromatin remodeling complexes use to reshape chromatin?
ATP
What are the four mechanisms for local histone mobilization?
- Unwrapping
- Sliding
- Ejection
- Dimer exchange
What are the three mechanisms that histone modifications use?
- Acetylation
- De-acetylation
- Methylation
What is the histone code hypothesis?
Particular combinations of histone modifications set the state of chromatin condensation for a gene
Which enzyme facilitates acetylation of histones?
Histone acetyl transferases (HATs)
What does HAT add? To where?
Negatively charged acetyl groups to the positively charged lysine residues in histones
What is the effect of histone acetylation?
Neutralizing a histone’s positive charge
What two things does histone acetylation weaken?
- Weakens histone-DNA interactions
- Weakens nucleosome-nucleosome interactions
What is the end result of acetylation?
Decondensed chromatin –> allow gene expression
Which enzyme facilitates de-acetylation of histones?
Histone deacetylases (HDACs)
What does HDAC remove? What is the effect of this?
Removes the acetyl groups from histones which therefore reverses the effects of acetylation
What is the end result of de-acetylation?
Chromatin condenses –> transcription repressed
Which enzyme facilitates histone methylation?
DNA methyltransferase
What does DNA methyltransferase do?
Adds methyl groups to cytosine residues of DNA
What is the end result of histone methylation?
Transcription repression
What is epigenetic inheritance?
Patterns of inheritance not due to differences in gene sequences
What two patterns do daughter cells inherit?
- Patterns of histone modification
- Patterns of gene expression
What happens to chromatin modifications at fertilization?
Reprogramming resets the chromatin modifications
What are the three requirements for the initiation of transcription?
- Unwinding of DNA
- Basal trancription factors at all gene promoters
- All eukaryotic promoters are bound by the TATA-binding protein (TBP)
What are transcription factors?
Proteins that causes genes to be turned on or off
What is another name for basal transcription factors?
General transcription factors
What do basal transcription factors bind to?
DNA
What do regulatory transcription factors bind to?
Enhancers
What are the three components of eukaryotic promoters?
- TATA box
- Transcriptional start site
- Regulator/response elements
What are the two components of low level basal transcription?
TATA box and transcriptional start site
What is the main component of activated transcription?
Regulatory elements
What is the TATA box’s sequence of bases?
5’ TATAAAA 3’
What is the role of the TATA box?
Determine the starting point for transcription
Where does transcription begin?
At the transcriptional start site
The transcriptional start site and TATA box form the ___
Core promoter
What are regulatory/response elements?
DNA sequences that are recognized by regulatory proteins that control initiation of transcription
What are three examples of regulatory elements?
Enhancers, silencers, promoter-proximal elements
Where are promoter-proximal elements located?
Just upstream of the promoter and the transcription start site
What do enhancers bind?
Specific transcription factors called activators
What do silencers bind?
Specific proteins called repressors to inhibit transcription
Do enhancers increase or decrease gene expression?
Increase
Where can enhancers be located?
Upstream or downstream
What are three differences between promoters and enhancers?
- Promoters are immediately upstream
- Promoters function in only one orientation
- Enhancers determine the rate and efficiency of transcription
How do transcription factors recognize DNA?
The edges of an AT base pair and a GC base pair have different surface shapes
Why do transcription factors bind to a specific enhancer?
Because of complementary interactions between base pairs and its amino acids
Alternative splicing is regulated by proteins that … (2 things)
- Bind to the mRNAs in the nucleus
- Interact with the spliceosomes
Frequency of alternative splicing increases with more _______
Biological complexity
What is RNA interference?
Silencing of an endogenous gene caused by a complementary double-stranded RNA
Which type of RNA is critical for RNA interference?
microRNA
What does miRNA bind to?
The RISC protein complex
What does the RISC protein complex with miRNA bind to?
Complementary sequences of mRNA
What happens once the targeted mRNA is attached to the RISC complex with miRNA?
The target mRNA is degraded
In response to viral infection, translation can be slowed or stopped by …
Phosphorylation of a certain ribosomal protein
What are two differences in chromatin remodeling of bacteria vs eukaryotes?
- Bacteria has limited packaging of DNA whereas Eukaryotes have extensive packaging of DNA
- Chromatin must be decondensed for transcription to begin in eukaryotes, whereas remodeling is not a major issue in bacteria
What are three differences in transcription of bacteria vs eukaryotes?
- In eukaryotes, positive and negative control by regulatory proteins acts close to and far from the promoter. On the other hand, that only happens close to the promoter in bacteria.
- Bacteria needs sigma to interact with the promoter, whereas eukaryotes need a large set of basal transcription factors
- Eukaryotes need a mediator
What is one difference in RNA processing of bacteria vs eukaryotes?
There is no RNA processing in bacteria
What is one difference in mRNA stability of bacteria vs eukaryotes?
Rare used in bacteria, commonly used in eukaryotes
