Regulation Of Gene Expression Flashcards
What is constitutive gene expression?
Gene products that stay more or less constant
Also called house keeping genes
What are the two levels of control for gene expression?
Transcription and translation
What are the 3 ways to measure gene expression?
Northern blot
RT-PCR
DNA microarray
How is RT-PCR done?
- Blood sample from infected person (i.e. HIV)
- Remove cells by centrifugation
- extract viral RNA genome
- Use reverse transcriptase/ PCR amplification
- Do Gel electrophoresis with a control (blood from non infected person)
What is the major determinant for expression of house keeping genes?
Differences in promotor sequences can account for 1000-fold difference in mRNA product
What does deviation from consensus sequence usually do to promotor function?
Reduce expression
What do specifity factors do? Examples?
Alter specificity of RNA polymerase for promotors
I.e.
Sigma factors in bacteria
TBP protein in eukaryotes
What are repressor regulatory proteins? What kind of regulation is it?
They impeded access of RNA polymerase to the promotor.
This is negative regulation
What are activator regulatory proteins? What kind of regulation?
These enhance RNA polymerase-promoter interaction.
This is positive regulation
What are the 3 classes of regulatory proteins?
- Specificity factors
- Repressors
- Enhancers
What sigma factor recognizes most promotor genes?
Sigma factor 70
What sigma factor recognizes genes induced by heat shock?
Sigma factor 32
What sigma factor recognizes gene for stationary phase and stress response?
Sigma factor 28
Do the same sigma factor recognizse the -10 and -35 region on bacteria?
No
What sigma factor recognizes genes involved in motility and chemotaxis??
Sigma factor 28
What sigma factor recognizes gens for nitrogen metabolism?
Sigma factor 54
What sigma factor recognizes genes dealing with misfolded proteins in the periplasm?
Sigma factor 24
What are the things that can act on a repressor protein?
Co-repressor : enhances repressor
Inducer: reduces binding of repressor
What does a co-repressor do?
It enhances the binding of the repressor to the operator
What does an inducer do?
It reduces the binding of the repressor to the operator
What are the molecules that can act on activator proteins?
Co-activator: enhances binding of activator
Repressor: reduces binding
What is a co-activator?
When the signal molecule enhances the binding of the activator to the promoter
What is a repressor in respect to an activator?
When the signal molecule reduces the binding of the activator to the promoter
What is an operan? (Only in prokaryotes)
The promoter region which contains binding site for RNA polymerase (sigma subunit) and adjacent binding sites for activators and repressors.
- The repressor binding sequence is the “operator”
- (cluster of genes involved in the same biochemical pathway)
What produces polycistronic mRNA’s?
Operons
What does the tryptophan operan consist of?
The promoter region and 5 genes involved in tryptophan biosynthesis
What does the promoter of tryptophan have? What kind of promoter is it?
A 15-pair region recognized by a protein.
This protein inhibits further expression and is therefore a repressor
The repressor for the tryptophan operan requires what to bind efficiently to the operator sequence?
Two Trp’s
Trp acts as a co-repressor (it enhances the binding of the repressor)
The repressor is always present in ~20 copies per cell via what kind of expression?
Constitutive expression
Note: this is the house keeping kind of expression
What molecules affect the lac operon?
Glucose and lactose
What is the preferential carbon source for E. coli?
Glucose
What will E. coli use in the absence of glucose?
Lactose
In E. coli the use of lactose coincides with the expression of what gene?
Beta-galactosidase expression
What occurs when both glucose and lactose are present in respect to lac operon?
Operon off because CAP not bound
What occurs when there is glucose (+) and no lactose (-) in respect to the Lac operon?
Operon off
Because Lac repressor bound and because CAP not bound
What happens when both glucose (-) and lactose (-) are not present in respect to the Lac operon?
Operon off because Lac operon is bound
What happens when glucose (-) is not present but Lactose (+) is present in respect to the Lac operon?
Operon on
What does lacZ code for?
Beta-galactosidase
What does LacY code for?
The lactose permease
What does LacI code for?
A constitutively expressed repressor
What does allolactose act as?
An inducer
Binding of allolactose to the repressor results in?
An inactive repressor that has no affinity for the operator
What is cAMP in respect to CAP?
A co-activator
The Lactose operon can only work when it has been first properly activated by?
The cAMP Responsive Protein (CRP) aka the catabolic catabolite activator protein (CAP)
(It must bind cAMP to function)
What kind of effect does glucose have in respect to cAMP?
It lowers intracellular cAMP levels by inhibiting adenylyl cyclase, causing CAP to loose its bound cAMP
-This is called the “glucose effect” or “catabolite repression”
Attenuation is a mode of transcriptional regulation of operons for ____________.
Amino acid biosynthesis
What is transcription attenuation?
Inhibition of gene expression by premature termination of transcription
Upstream of the structural genes in the operon lies a short “open reading frame” (ORF) of about 42 base pairs that functions as?
Codons for particular amino acid whose biosynthesis is directed by the operon
In prokaryotes when does translation start? (In respect to transcription)
Before transcription is completed
The Trp repressor can reduce expression by a factor of?
70
Attenuation can decrease expression by a factor of?
10
When cellular tryptophan concentration is sufficient, the transcription of the trp operon is repressed by?
700 fold
70 from Trp repressor * 10 fold from attenuation = 700
The nucleotide sequence of the 5’ -end of trp mRNA includes the short ORF that encodes a 14 amino acid peptide containing two Trp residues and includes an untranslated attenuator region that can engage in what?
A hair pin formation
Note: The 5’ end is called the Leader region of trp mRNA
What kind of hairpin structure is favored in the absence of obstructions?
2:3 pair
Note: the other hairpin is the 3:4 (atternuator)
What doe high tryptophan levels promote?
The 3:4 hairpin
When there is a 3:4 hairpin from high tryptophan levels what occurs?
Enables Rho-factor independent termination of transcription
When tryptophan levels are high, the ribosome _____ translates sequence 1 (open reading frame encoding leader peptide) and blocks sequence 2 before sequence 3 is transcribed.
Quickly
Note: continued transcription leads to attenuation at the terminator-like attenuator structure formed by sequence 3 and 4.
Activator binding sites are usually _______ of the RNA polymerase binding site.
Upstream
The tryptophan operon is under _____ regulation control in which the molecular signal ( Trp) causes binding of the ______ to the operator.
Negative
Repressor
The lactose operon is under _____ control by lactose and under ____ control for glucose.
Negative
Positive
What causes dissociation of the repressor from the Lac operon?
Lactose (through allolactose)
Glucose (through cAMP) affects binding of ____ (aka ____) to the activator binding site.
Note: high glucose: low cAMP (and vice versa)
CRP (aka CAP)
Regulation of gene transcription is mediated by _____ and/or ______ in concert with molecular signals.
Repressors and/or activators
_________ inhibit operon transcription by binding to a site (operator site) close to the binding site of the RNA polymerase.
Repressors
Attenuation works an an _____ inhibiting transcription that has escaped repressor mediated inhibition
Extra brake
The _______ for genes encoding enzymes involved in amino acid biosynthesis consists of the ORF for the leader peptide and three regions which can engage in a proximal or distal hairpin (downstream of the ORF coding for the leader peptide.
Attenuation region
When there ______ of the amino acid the operon codes for, then the leader peptide is readily synthesized and the distal hairpin is favored, resulting in premature termination of the transcript
Is enough
When there is ________ of the amino acid the operon codes for, the ribosome stall at the sequence coding for the leader peptide (the codons waiting for charged-tRNA)- resulting in complete transcription of the operon
Not enough
DNase hypersensitivity sites differ from tissue to tissue for selected genes: this reflects?
Cell type-specific gene expression
What are the two clases of enzymes that play a role in chromatin remodeling?
- Enzymes that covalently modify the core histones of nucleosomes : Histone Acetyl Transferases (HATs) and Histone DeAcetlyases (HDACs)
- Enzymes that use ATP to remodel nucleosomes on the DNA: SWI/SNF that reposition or remove nucleosomes
What do SWI/SNF complexes do?
Reposition or remove nucleosomes
-create nucleosome-free regions in the chromosome and thus allow for binding of transcription factors
Acetylation status of amino-terminal domains of histone H3 and H4 determines the affinity between histone core particles and DNA. What is responsible for these modifications?
Histone Acetyl transferase (HATs)
Histone Deacetylases (HDACs)
What mutation is involved in Rubinstein-Taybi syndrome?
Caused by mutations in the CBP protein or in the closely related p300 protein both of whom have HAT activity
What are the characteristics of rubinstein-Taybi syndrome?
Characterized by postnatal growth deficiency, microcephaly, specific facial characteristic, broad thumbs and big toes and mental retardation
What kind of mutation is Alpha-thalassemia/mental retardation syndrome?
Caused by mutations in the ATRX protein that is a member of the SWI/SNF family
What are the characteristics of alpha-thalassemia/mental retardation syndrome?
Patients are mentally retarded, have characteristic facial appearance and have a mild form of alpha-thalassemia while their globin genes are normal
Enhancers may be thousand of base-pairs away from the transcription initiation site and make contact with the initiator sites though __________.
Transactivation
______ allows for interactions between distant DNA sites (HMG proteins)
DNA looping
What are cis acting regulators?
Regulatory elements like promotors and enhances that act on the same chromosome as the transcribed gene
What are trans acting regulators?
Activator/repressor proteins that diffuse to the action
What do insulators do?
Limit the action range of enhancers: they may bind to nuclear matrix forming looped domains
A _______ prevents spreading of the heterochromatic state of the DNA back into active area
Barrier sequence
When are basal transcription factors needed at pol II promotor?
They are needed at every pol II promotor
What is needed for RNA pol II binding to a promotor?
Basal transcription factors
DNA-binding transactivators
Coactivators (i.e. TFIID and mediator )
What do DNA-binding transactivators do?
Bind to the enhancers and facilitate transcription
_____ which act indirectly: bride between DNA-binding transactivators and complex composed of Pol II and the general (basal) transcription factors.
Coactivators
_______ are regions devoid of nucleosomes (mediated by chromatin remodeling complexes) and may differ between different tissues
DNase hypersensitive sites
_____ can be classified as proximal and distal elements relative to the initiation start site
Promoter elements
______ devoted to binding of genetic transcription factors
Proximal promotor region
____ devoted to binding gene-specific transcription factors
Distal promotor elements
_______ limit the range of action of an enhancer or a repressor sequence
Insulators
_______ are either involved in binding of transactivators to the RNA pol II complex and TADs or in chromatin remodeling
Co-activators
_____ connects TFIIH to the CTD
Mediator
How do nonpeptide hormones enter the cell?
By diffusion through the membrane
When a nonpeptide hormone binds to a receptor in the cytoplasm what happens?
It causes the receptor to translocations to the nucleus
What does the receptor/hormone complex act as when they bind to the promoter elements of genes regulated by that hormone?
Transcription factors
What are specific hormone response elements (HRE’s?)
The promoter element that the nuclear receptor/hormone complex bind to
Usually the nuclear hormone receptor is __ and the HRE is a _____
Dimer
Palindromic repeat
How does chromatin remodeling occur when hormone/receptor complex are bound to the DNA?
They recruit a co-activator or co-repressor to the promoter region
What is the consensus sequence bound by vitamin D and thyroid hormone?
AGGTCAN3AGGTCA
Note: retinoids acid is similar but a 5 instead of 3
What catalyze transfer of Acetyl group from acetyl coenzyme a to various Lys and Arg residues in amino terminal regions of the histone core proteins
HATs
What are the effects of acetylation of histone tails?
Prevent chromatin from folding into compact structures, thus maintains the euchromatic state (loosening DNA-histone interaction)
*Increased access of specific DNA regions to chromatin remodeling complex proteins
What does epinephrine activate?
G-protein coupled receptors
When epinephrine activates g-protein coupled receptors what do they activate?
Adenylyl cyclase increasing cAMP levels in the cell
When cAMP binds to the regulated subunits of protein kinase A (PKA). What occurs? (Epinephrine)
Releases PKA catalytic subunits that move to the nucleus that phosphorylated the cAMP-Response Element Binding Protein (CREB) in the nucleus
What does P-CREB do?
Binds to cAMP response elements in the promotors of target gens and binds the coactivator CREB Binding Protein (CBP): histone acetylation and chromatin remodeling facilitate transcription
What happens when a ligand binds to remove a negative regulator that is bound without the ligand?
When the ligand binds to the negative regulator to remove it, the gene is turned on
What happens when a ligand is removed from a negative regulator that is bound to DNA when in complex (ligand bound to repressor).
When the ligand is removed, then the repressor is inactive and the gene is turned on.
_______ are only active in the presence of regulatory protein in eukaryotic gene transcription
Promotors
At least 5 _____ for any single eukaryotic gene. It may be 1000s of bps away from from the transcription start site or even downstream
Regulatory sites
Access to eukaryotic promotors is restricted by the structure of?
Chromatin
Note:
Euchromatin = expression
Heterochromatin= no expression
Regions lacking formed up nucleosomes are?
Are open spaces for transcription factors to bind
_____ coactivator is required for both basal and regulated transcription at Pol II promotors. Bind to the C-terminus of the large subunit of RNA Pol II and stimulates phosphorylation of that region by TFIIH
Mediator
_________ is a transcription factor after binding the hormone hormone cortisol.
Glucocorticoid receptor
_________ are translocated into the nucleus upon binding of a steroid hormone
Nuclear hormone receptor
_____ bind to DN as dimers to a repeated DNA sequence
Nuclear hormone receptor
___ often have HAT activity and co-repressors have HDAC activity
Co-activators
______ inhibits gene activation by estrogen though inhibition of the interaction between estrogen receptor and the co-activator
Tamoxifen
_____ hormones regulate gee expression by intracellular signaling through protein phosphorylation follow by chromatin remodeling
Non-steroid
A single transcription factor may regulate ______ genes
Multiple
_________ have subunits with Histone Deacetylase (HDAC) activity.
They lead to transcription repression.
Co-repressors
Co-repressors may bind _______, which compact chromatin (H3-K9 methylation: lysine residue #9 on histone H3)
Histone methyl transferase
Methylation in eukaryotic DNA is limited to cytosine bases in?
CpG dinucleotides
_____ in 5’CpG3’ is the substrate for DNA methylases (Dnmt enzymes/genes)
Cytosine
Methylated DN is associated with?
Gene silencing.
_____of DNA =?
Demethylation
What are some examples of gene silencing?
X-chromosome inactivation in females
Imprinting
what binds to methylated CpG dinuclotides?
MeCP proteins
Methylated CpG-binding Proteins
MeCP2 recruits _____ activity removing acetyl groups from histones and inducing chromatin remodeling.
HDAC
After MeCP2 induces chromatin with HDAC, then does?
Aids H3K9 methylation (Lys9 in histone H3)
what binds to methylated H3P9 and to itself, condensing the chromatin?
HP1 (heterochromatin protein 1)
When chromatin is an open, extended corformation, is it transcriptionally active or inactive?
Active
When chromatin is high condensed, is it transcriptionally active or inactive?
Inactive
When DNA is unmethylated (especially at promoter regions), is it transcriptionally active or inactive?
Active
When DNA is methylated, even at promoter regions, is it transcriptionally active or inactive?
Inactive
When histone is acetylated, is it transcriptionally active or inactive?
Active
When histone is deacetylated, is it transcriptionally active or inactive?
Inactive
What does DNA-protein interaction involve? (Bonding/interactions)
Hydrogen bonding and hydrophobic interactions (methyl group on thymidine)
What is involved in hydrophobic interactions in DNA-protein interactions?
Methyl group on thymidine
What amino acids are involved in DNA binding ?
Asparagine, glutamine, glutamate, arginine, lysine
Asparagine, glutamine, glutamate, arginine, lysine are all involved in?
DNA binding
____ of a particular transcription factor for its target sequence in DNA is a million fold higher compared to other DNA sequences.
Affinity
DNA target site usually ____ to which 2 subunits of a regulatory sequence bind cooperatively. Doubling of the contact sites square the association constant
Palindrome repeat
Many bacterial regulatory proteins interact with DNA through?
Helix-turn-helix motifs in the protein
The helical region interacting with the DNA is called? (In bacterial regulatory proteins)
Recognition helix
What is the recognition helix in bacterial regulatory proteins rich in?
N,Q,E,K or R
Synpolydactyly is caused by mutation in what gene?
HOXD13 gene
Transcription factors in human development have a helix-turn helix domain of 60 aa that is termed the?
Homeodomain
Transcription factors in human development have a ________ domain.
Helix-turn helix
The corresponding segment in the gene is the _________, for homeodomains.
Homeobox
Rephrase?
Zinc is held by what aa?
4 Cys or 2 Cys+ 2 His
(2 aa from an alpha-helical region and 2 aa from beta-sheet region)
Note: domain is about 20 aa long
_____ ion does not directly interact with DNA
Zinc
Interaction between. Single Zn finger and DNA is ?
A weak interaction
TFIIIA is bound to the DNA of what gene?
5S rRNA gene
_____ substantially enhance binding by interacting simultaneously with the DNA.
Multiple zinc fingers
The GATA family of zinc ginger transcriptions factors recognize?
the GATA sequence
What sequence is present in the promotor of many genes promoting embryogenesis, erythropoiesis, muscle development and switching from fetal to adult hemoglobin synthesis.
GATA sequence
SRY gene responsible for male sexual differentiation contains a?
HMG box
What does DNA bending allows interactions with?
Other transcription factors on nearby sites: architectural factors
____name is derived from High Mobility Group (relates to their discovery, but not to their function)
HMG
Note: Three alpha-helical regions interact with DNA
What does mutated SRY gene results in??
Sex reversal
Human protein __ bends DNA ___ derived from the Y-chromosome.
SRY, SRY
What is a leucine zipper?
Leucine-rich regions in two proteins interact to form the dimer (coiled coil of alpha hélices)
What is adjacent to the leucine zipper?
A basic aa segment that interacts with DNA (total is called bZIP domain)
________, proteins involved in cell proliferation, contain both bZIP domains
Fos and Jun
Repertoire of leucine zipper transcription factors is enhanced by?
Formation of heterodimers
MyoD, a transcription factor involved in muscle differentiation contains what domain?
A bHLH domain
What is MyoD?
A transcription factor involved in muscle differentiation
Helix-loop-helix region of 50 aa is involved in?
Protein dimer formation
Helix-loop-helix region of 50 aa is involved in protein dimer formation. DNA binding is mediated by an adjacent short stretch of?
Basic aa (bHLH domain )
Heme is a what kind of inhibitor of Kinase?
Reversible
When iron is available then heme is present in the reticulocyte and the kinase is _______.
Inhibited thus eIF2 is stable and active
When iron is not available there will be no heme DNA all the eIF2 _____
Becomes phosphorylated and will be degraded
What is an example of initiation of translation that is dependent on the phosphorylation state of eIF2?
Globin synthesis in reticulocytes
What form of eIF2 is stable/unstable?
eIF2 is stable
eIF2-P is unstable
If the base pairing between siRNA and mRNA region is very good, then?
RISC complex ribonucleases (often argonauts) degrades the mRNA
If base pairing between siRNA and mRNA is approximate, then?
The RISC complex will just impede translation
____ are preferentially methylated at the C reside (which then favors deamination to a T residue)
CpG dinucleotides
____ bind to methylated cysteine in CpG dinucleotides and then assist in deactylation and subsequent methylation of core histone proteins
MeCP proteins
_____ occurs primarily in eukaryotic cells and involves either phosphorylation of initiation factors (e.g. Regulation of globin synthesis in reticulocytes) or interaction of proteins with hairpins in the 5’ UTR or the 3’ UTR of the mRNA
Regulation of translation
__ from miRNA’s are now known to be important for translation regulation
Silencing RNA’s
____ bind to DNA mainly through glutamine, asparagine, arginine, lysine and glutamine by hydrogen bonding and hydrophobic interactions to nucleotides in the MAJOR DNA groove
Transcription factors
___ protein domains and zinc finger protein domains are involved in transcription factor-DNA interactions
Helix-turn-helix
__ are present in transcription factors that bend the DNA duplex
HMG-box protein domains
Domains involved in interactions between different transcription factors are _____ domains and _____ domains.
Leucine zipper
Helix-loop-helix
The IRE (for ferritin) effect is dependent on what?
It is location-dependent
What is the actual iron sensor?
A 4Fe-4S cluster in aconitase
______ mRNA structure can be involved in translational regulation
Secondary mRNA structure
What protein is needed in case of iron deficiency?
Transferrin receptor
What iron-storage protein is required when there is an excess of (dietary) iron?
Ferritin
What receptor is involved in the uptake of transferrin-bound iron by cells?
Transferrin receptor
Ferritin and transferring receptor are reciprocally regulated by what DNA element?
Iron Responsive Element (IRE)
Where is the IRE for the Ferritin mRNA?
In the 5’-untranslated region of the mRNA
Where is the IRE for the transferrin receptor?
In the 3’ UTR of the mRNA
In the IRE-binding protein the site for ____ and for ____ overlap
Iron binding and for RNA binding
Excess iron causes ___ of Binding protein from the IRE
Dissociation
Binding of IRE-Binding protein to the 5’ IRE ________ translation of ferritin mRNA.
Blocks
Binding of the IRE-binding protein to the 3’ IRE’s ___ the transferrin receptor mRNA
Stabilizes
IRE’s are what kind of structure?
Hairpin
_____ are hairpin structures in the 5’ ITR of the iron-storage protein ferritin and in the 3’ UTR of the iron uptake protein, the transferrin receptor
Iron-responsive elements (IRE)
The ____ dissociates from the iron responsive element in the presence of iron so that at high iron levels ferritin mRNA translation is not inhibited. At low iron concentrations the transferrin receptor protein mRNA is stabilized by bind of the iron-responsive element binding protein to the 3’ UTR (which results in more translation)
Iron-responsive element binding protein
