Gene Expression Flashcards
What methods regulate gene expression in prokaryotes on a DNA level
Differential gene transcription by operons, bacterial enhancers and riboswitches
What methods regulate gene expression in prokaryotes at the RNA level
Selective mRNA translation by ribozymes, riboswitches and antisense RNA
What methods regulate gene expression in prokaryotes at the protein level
Differential protein modification
What are operons
Set of different coding genes that are transcribed as a set into a single RNA (important for the synthesis of molecules on a need to need basis)
Discuss the 4 steps of operons
- Operon is a group of structural genes plus sequences that control transcription
- A separate regulator gene, with its own promoter, encodes a regulator protein
- This may bind to the operator site to regulate the transcription of mRNA
- The products of mRNA catalyze reactions in a biochemical payhway
What are the 4 types of operons
- Negative inducible
- Positive inducible
- Negative repressible
- Positive repressible
Discuss negative inducible operons
- regulator y protein
- operon ground state
- activated/repressed when
- pathways controlled
- chemical nature of small molecule
- repressor
- off
- activated when inducer binds to repressor and makes it unable to bind to operator
- biodegradative
- inducer
Discuss positive inducible operons
- regulator y protein
- operon ground state
- activated/repressed when
- pathways controlled
- chemical nature of small molecule
- activator
- off
- transcription activated when inducer binds to activator and enables it to bind to the operator and active the operon expression
- biodegradative
- inducer
Discuss negative repressible operons
- regulator y protein
- operon ground state
- activated/repressed when
- pathways controlled
- chemical nature of small molecule
- repressor
- on
- transcription repressed when co-repressor binds to the repressor and enables it to turn off the operon transcription
- bio synthetic
- co-repressor
Discuss negative inducible operons
- regulator y protein
- operon ground state
- activated/repressed when
- pathways controlled
- chemical nature of small molecule
- activator
- on
- transcription repressed when co-factor binds to the activator and it’s confirmation is changed in such a way that it no longer binds to the operator
- bio synthetic
- co-repressor
What is an inducer
Small substrate molecule for the enzyme encoded by the operon
What is a co-repressor
Small molecule product of metabolic pathway catalyzed but the enzymes encoded in the operon
Discuss the steps of lactose metabolism in E. Cool
- Permeate actively transports lactose into the cell
- Where the enzyme B-galactosidase breaks it k to galactose and glucose
- B-galactosidase also converts lactose into the related compound allolactose
- And converts allolactose into galactose and glucose
Discuss the lactose operon steps
- In the absence of lactose, the regulator protein binds to the operator and inhibits transcription
- When lactose is present, some is converted into allolactose
- Which binds to the regulator protein making it inactive
- The regulator proteins can’t bind the the operator
- Structural genes aren’t translated or transcribed
What is the lactose operon an example of
A negative inducible operon
Discuss bio switches when a regulatory protein is present
regulatory protein binds to riboswitch and stabilizes secondary structure that makes the ribosome-binding site inaccessible, so no translation take place
Discuss bio switches when a regulatory protein is absent
The riboswitch assumes and alternative secondary structure that makes the ribosome-binding site available and translation takes place
Give an example of something controlled by a riboswitch
Vitamin B12 is controlled by riboswitches in bacteria. When B12 is present, synthesis is regulated and when it’s absent B12 is synthesized by the availability of the ribosome-binding site allowing translation
What methods regulate gene expression in eukaryotes on the DNA level
Differential gene transcription by histone acetylation/methylation, DNA methylation and transcriptional control (enhancers, TFs)
What methods regulate gene expression in eukaryotes on the RNA level
Selective nRNA processing by alternative splicing
Selective mRNA translation by differential mRNA longevity, inhibition of translation, ribosomal selectivity, microRNAs
What methods regulate gene expression in eukaryotes at the protein level
Differential protein modification by activation by cleavage, activation by transport to a specific locationX assembly with other proteins, covalent modification
3 important differences between eukaryotes and prokaryotes with respect to gene expression
- Eukaryotes have complex genomes with proteins that help package it
- Eukaryotes have extensive mRMA processing after transcription
- In eukaryotes, transcription and translation are physically separated
3 examples of histone tail modifications
- Methyl group attached
- Phosphate attached
- Acetyl attached
How can you modify histones to activate
- acetylation of Lys residues of H2/H3/H4 tails
- methylation of lysines K4, K38 and K79 of H3
How can you modify histones to repress
- deacetylation of lys residues of H2/H3/H4 tails
- methylation of K9 and K27 of H3 and K20 of H4 (block binding site to specific proteins)
How does acetylation work
Acetyl is negatively charged and lysine is positively charged. Adding Acetyl to lysine neutralizes, removing the electrostatic interactions between lysine and DNA and opening up the chromatin into euchromatin
Where does DNA methylation occur and how does it work
- occurs at CpG nucleotides in promoters/ enhancers
- works by blocking the TFs from binding to enhancers and recruiting histone modifiers that repress chromatin
How are methyl group markers inherited through cell division
- Before replication DNA is fully methylated
At CpG nucleotides - During replication new DNA strands are synthesized without methyl groups
- After replication, each new DNA molecule will have a methylation on one strand but not the other
- Methyl groups attract methyltransferase enzyme, which add methyl groups to the unmethylated strand
- Resulting in fully methylated DNA
How can bad parenting influence experience and phenotype
Bad parenting/ experience in early childhood leads to silencing of the glucocorticoid receptor by DNA methylation and acetylation of histones, leading them to exhibit increased risk-adversity and altered response to stress
Discuss combinatorial association of transcription factors
- each enhancer module consists of several TF binding sites
- all activating TFs must bind before transcription can occur
- the enhancers are the same in all cells but the combination of TFs available are different in each cell type
What are silencers
DNA regulatory element that can actively repress the transcription of a particular gene
What are enhancers
DNA regulatory element that can actively activate the transcription of a particular gene
What are NRSE
- neural restrictive silencer element
- found in genes only expressed in the nervous system
- binds to NRSF which suppress transcription
What are insulators
dna regulatory element that limits the range in which an enhanced can activate gene expression
How do insulators work
They bind to CTCF TFs, keeping the enhancer-mediated complex from binding to and inappropriate promoter and limiting the spread of heterochromatin
