Control of Gene Expression Flashcards
Blood cells
Erythroid cells
Lymphocyte
Monocyte
Platelets
Neutrophil
Basophil
Eosinophil
Different cell types contain the same DNA
Differentiated cells retain the ability to ”de-differentiate”
a group of cells that can be grown indefinitely in a lab
Cell line
Cell line examples
Embryonic stem cell
Liver cell
Muscle cell
Blood vessel cell
Blood cell precursor
Skin cell
Lung cell
Cells become different because they synthesize and accumulate different sets of RNA and protein molecules.
Some RNAs and proteins are abundant in specialized cells in which they function and cannot be detected elsewhere
GENE REGULATION
During development different cells express different sets of genes in a precisely regulated fashion
a group of genes that are transcribed at the same time.
They usually control an important biochemical process.
Rare in eukaryotes
Operon
_________________________
*Genes whose expression is turned off by the presence of some substance (co-repressor)
*__________ represses the trp genes
*__________ is typically the end product of the pathway
Repressible Genes -Operon Model
Tryptophan; Co-repressor
Tryptophan Operon
*When E. coli is swimming in tryptophan (milk & poultry), it will absorb the amino acids from the media
*When tryptophan is not present in the media, then the cell must manufacture its own amino acids.
*E. coli uses several proteins encoded by a cluster of 5 genes to manufacture the amino acid tryptophan
a.) Tryptophan absent = repressor inactive = operon on
_______________
*Genes whose expression is turned on by the presence of some substance
*___________ induces expression of the lac genes
*An antibiotic induces the expression of a resistance gene
*Catabolic pathways
Inducible Genes -Operon Model
Lactose
This enzyme hydrolyses lactose into glucose and galactose
β-galactosidase
*E. coli can use either glucose, which is a (monosaccharide, disaccharide), or lactose, which is a (monosaccharide, disaccharide)
*However, (glucose, lactose) needs to be hydrolyzed (digested) first
*So the bacterium prefers to use (glucose, lactose) when it can
Monosaccharide, disaccharide
lactose; glucose
- When lactose is absent
- A repressor protein is continuously synthesized. It sits on an Operator site
*The repressor protein blocks the Promoter site where the RNA polymerase settles before it starts transcribing
- When lactose is present
_________ binds to the lac repressor and makes it change shape so it can no longer bind DNA
Allolactose
- When both glucose and lactose are present
RNA polymerase can sit on the promoter site but it is unstable and it keeps falling off (low transcription)
- When glucose is absent and lactose is present
High transcription
+ Glucose
+ Lactose
Operon OFF
Because CAP (Catabolite Activator Protein) is not bound
+ Glucose
- Lactose
Operon OFF
Because Lac repressor bound and CAP (Catabolite Activator Protein) is not bound
- Glucose
- Lactose
Operon OFF
Because Lac repressor is bound
- Glucose
+ Lactose
Operon ON
4 situations are possible
- When glucose is present and lactose is absent the E. coli does not produce β-galactosidase.
- When glucose is present and lactose is also present the E. coli does not produce β-galactosidase.
- When glucose is absent and lactose is absent the E. coli does not produce β-galactosidase.
- When glucose is absent and lactose is present the E. coli produce β-galactosidase.
How does a cell determine which of its thousands of genes to transcribe?
Transcription regulators
*Recognize specific sequences of DNA cis-regulatory sequences
Transcription regulators
The region of the chromosome must be opened up in order for enzymes and transcription factors to access the gene
Chromatin remodeling
The elements of transcriptional control: a model
- Regulatory transcription factors recruit chromatin-remodeling complex and HATs. Chromatin decondenses.
- When chromatin decondenses, a region of DNA is exposed, including the promoter.
- Regulatory transcription factor recruits proteins of the basal transcription complex to the promoter. Note looping DNA.
- RNA polymerase and the basal transcription complex join to form the initiation complex; transcription begins.
*Contains 8 histone proteins
*DNA is wrapped around each
_________, like a string wrapped around a bead
nucleosome
- DNA packing as gene control
- Tightly wrapped around histones (no transcription and genes turned off)
- Darker DNA (H)=tightly packed
- Highly condensed transcriptionally inactive region.
Heterochromatin
- Lighter DNA (E)
- Lesser coiled transcriptionally active region which can be easily accessed by RNA polymerase
Euchromatin
- DNA methylation
- Blocks transcription factors (genes are turned off)
- Attachment of methyl groups
(-CH3) to cytosine
*Addition of methyl groups can condense chromatin
Histone methylation
are genomic regions that contain a high frequency of CG dinucleotides.
particularly occur at or near the transcription start site of housekeeping genes.
CpG islands
A gene involved in basic functions is required for the sustenance of the cell.
_________ are constitutively expressed e.g. enzymes in metabolic cycle (e.g. glycolysis)
Housekeeping gene
are those coding for specialized functions synthesized (usually) in large amounts in particular cell types.
e.g. insulin (beta cells) & serum albumin gene (liver cells)
Luxury gene
Histone acetylation unwinds DNA
- Attachment of acetyl groups
(-CoCH3) to histones
Acetylation of histone tails promotes loose chromatin structure that permits transcription
- DNA transcription control elements may be located many kilobases away from the promoter they regulate
These proteins bind to selected sets of genes at sites known as silencers and thus slow transcription
Repressors
These proteins bind to genes at sites known as enhancers and speed the rate of transcription
Activators
These “adapter” molecules integrate signals from activators and perhaps repressors.
Coactivators
________: mask the activation surface
- binds to the activation domain of the activator protein thereby preventing it from carrying out its activation functions
- binds tightly to the activator without having to be bound to DNA directly
- Interacts with an early stage of the assembling complex of general transcription factors, blocking further assembly.
Repressor
In response to injunctions from activators, these factors position RNA polymerase at the start of transcription and initiate the transcription process
How repressor works
- Masking the activation surface (binds tightly to activator)
- Competitive DNA binding
- Direct interaction with the general transcription factors
- Recruitment of chromatin remodeling complexes
- Recruitment of histone deacetylases
- Recruitment of histone methyl transferase
- Repressor that is expressed preferentially in the developing kidney
*Children that produce no functional WT1 protein, invariably develop kidney tumors
Wilms’ tumor (WTI) gene
Cytoplasmic Polyadenylation promotes translation in oocytes
- Provides a point where the expression of a gene can be controlled
- This allows a variety of different polypeptides to be assembled from the same gene
RNA Splicing
- RNA-binding proteins that bind to exonic splicing enhancer sequences in exons
- Critical in defining exons in the large pre-mRNAs of higher organisms.
SR Proteins
- Result from mutations in a region of the genome containing two closely related genes, SMN1 and SMN2
SMN2 encodes a protein identical with SMN1, but it is expressed at much lower level because a silent mutation in one exon interferes with the binding of an SR protein, leading to exon skipping in most of the SMN2 mRNAs.
SMN2 mRNAs that are correctly spliced is sufficient to maintain cell viability during fetal development, but insufficient of spinal cord motor neurons in childhood, resulting in their death and associated disease
Spinal muscle atrophy
- Mechanism of silencing gene after transcription by causing degradation of some specific mRNA molecules
RNA interference (RNAi)
specific mRNA molecules for RNA interference (RNAi)
- Small interfering RNAs (siRNAs)
-dsRNA of 20-25 bps
*Micro RNAs (miRNA)
-Small non-coding RNAs of 21-22 nucleotide long, that hybridize to the 3’ untranslated regions of specific target mRNAs
is an RNAse III nucleases that converts either long dsRNAs or hairpin RNAs into siRNAs
Dicer
RNA-induced silencing complex (RISC) contains ________ which is an endonuclease capable of degrading mRNA whose sequence is complementary to that of the siRNA guide strand
argonaute
RNAi Pathway
- Long double-stranded RNA (dsRNA) is processed in the nucleus by _______ (RNAse enzyme). The resulting shorter dsRNA is exported to the cytoplasm, binds to dicer (RNAse enzyme), and is cleaved into small fragments, called small interfering RNAs (siRNAs) or microRNAs (miRNAs), 21-25 base pair RNA strands.
- The siRNA or miRNA is recruited by the RISC complex, unwinds, and incorporates into a protein-RNA complex
- RISC + siRNA or miRNA bind to a complementary, targeted messenger RNA (mRNA).
- mRNA is cleaved in a specific site and then degraded in the cell, thereby disrupting protein synthesis of the target gene.
Drosha
(add* DGCR8 recognizes this double-stranded miRNA)
(add* transported to the cytoplasm by the protein Exportin 5)
(add* it is recognized in the cytoplasm by dicer which cleaved the stem loop leaving a short ds miRNA molecule)
(add* AGO2 binds to the miRNA and 1 strand is released and the guide strand left forms the RISC complex)
(add* 2 types of RNAi at work 1. Cut off mRNA 2. inhibition of translation)
- Steroid hormones that regulates the metabolism of glucose
- Stimulate breakdown of fat
- Is released during time of starvation and intense physical activity, stimulating liver cells to increase the production of glucose form amino acids and other small molecules
Glucocorticoid hormone
a DNA sequence that activates a transcriptional enhancer when bound by a glucocorticoid receptor (GR). GREs are involved in the regulation of genes that are responsive to glucocorticoids.
required for maximal initiation of transcription
Glucocorticoid response element (GRE)
*enhancer
When the GRE is absent, the GRE receptor dissociations
- Iron storage protein that stores surplus iron and release it when the body needs it.
Ferritin
Where do erythropoiesis take place
In the bone marrow
Protein synthesized in the liver that serves as the main transporter of iron in the body
Transferrin
Control mediated by Iron
*An increase in iron concentration in the cytosol lead to the increase synthesis of ferritin that bind to extra iron
*Also, this decreases the synthesis of transferrin receptor in order to import less iron across plasma membrane
*Mediated by _________ an iron-responsive regulatory protein which can recognize stem loop structure
aconitase
The binding of aconitase of the ferritin mRNA blocks translation initiation.
During iron starvation
- Cytosolic aconitase bound to mRNA
- no ferritin made, transferrin receptor made
During excess iron
- Cytosolic aconitase not bound to mRNA
- ferritin made, no transferrin receptor made
Roles of miRNA
Metabolism
Stem cell division
Development
Apoptosis
Cell proliferation
Cell cycle control
Protein that allows import of lactose from outside the cells inside
Permease
