Gene Expression Flashcards
Gene expression
- multi step process that ultimately result in the production of a functional gene product
- RNA or protein
Housekeeping genes
- involved in basic cellular functions that are REQUIRED reguardless of the cell type or environmental cues
- constitutively expressed and not regulated
Regulated genes
- required only in certain cell types and/or certain conditions
- subject to control mechanisms
- determine when and what genes are expressed
How many levels of regulation of gene expression do prokaryotes have?
- 1
- transcription only
- DNA is transcribbed into mRNA then, directly into a protein
How many levels of gene expression regulation are present in eukaryotes and what are they?
- 5
- transcriptional
- post transcriptional
- translation
- post translation
- epigenetics
Epigenetics
- nothing changes to DNA, just accessibility
- euchromatin and heterochromatin
Why are Eukaryotes more regulated than prokaryotes?
- we have more differentiated types of cells
- transcription and translation are in different locations in eukaryotes
Where does transcription, translation, and post-translational regulation occur in eukaryotes?
Transcription: nucleus
Translation: cytosol
Post-translation: golgi
transcription regulatory molecules for prokaryotes
-repressors and activators
Repressor
-suppress the transcription of a gene
Activator
-increase the transcription of a gene
repressible operon
- transcription is usually on, but it can be repressed
- structural genes are on unless inhibited
Inducible operon
- transcription is usually OFF, but can be stimulated
- structural genes are usually off
What are the two regions in an operon?
-control region and structural genes
Control region
-controls ALL genes in the structural region
Structural genes
-genes that are necessary for expression
What is the preferred carbon source for E. coli?
Glucose
When does E. coli use other sources?
ONLY if…
- glucose is absent
- another sugar is present(lactose)
Why does E. coli prefer not to use other sources besides glucose?
-to use other sources, it must use more enzymes, which requires more energy
Is the Lac Operon on or off when glucose only is present?
OFF
repressor protein when glucose only is present?
- encoded by the laclgene, always present and bound to the operator, blocks RNA polymerase
- cannot transcribe gene
adneylyl cyclase when glucose only is present
- glucose inhibits adenylyl cyclase
- no cAMP
- cannot form CAP/cAMP complex
- cannot initiate transcription
Is the lac operon on or off when lactose only is present?
ON
adenylyl cyclase when lactose only is present
- able to make cAMP
- CAP/cAMP complex forms and binds to binding site
- RNA polymerase CAN EFFICIENTLY INITIATE TRANSCRIPTION
allolactose
- isomer of lactose
- when lactose is present, this is produced and binds to the repressor to prevent it from binding to the operator
is Lac operon on of off when glucose AND lactose are present?
OFF
- glucose inhibits adenylyl cyclase so no CAP complex to initiate transcription
- lactose produces allolactose, which binds to the repressor, but if there is no CAP complex, it does not matter
- no transcription
is the transcriptional control from prokaryotes and eukaryotes the same?
- nah bro
- the DNA structure is different, so they both do it, but its different
Eukaryote transcriptional control
- controlled by the regulatory sequences of DNA
- usually embedded in the noncoding regions of the genome
Cis-acting
- influence expression of genes only on the same chromosome
- only control genes downstream from it
- does not influence neighboring genes
- regulatory seguence of DNA that control transcription of eukaryotes
trans-acting
- transcription factors
- proteins
- interact with cis-acting regulatory sequences of DNA
- no trans-acting=no transcription
Binding of trans-acting regulators to DNA is achieved by one of the following…
- zinc fingers
- leucine zipper
- helix-turn-helix in the protein
Enhancers
- DNA sequences that increase the rate of initiation of transcription
- only recognize certain transcription factors
Where are enhancers normally located?
- typically on the SAME chromosome
- gene and enhancer are on same chromosome
- can be close to each other of thousands of base pairs away
- can be upstream OR downstream or in intron regions
- can act in tissue specific manner if the DNA binding proteins are only present in certain tissues
how are enhancers brought closer to the basal promoter?
-by bending the DNA molecule
Transcription factors
- trans-acting molecules
- DNA binding domain
Transcription factor activation domain
- bind to other transcription factors
- interact with RNA polymerase II to stabilize formation of the initiation complex and recruit chromatin modifying proteins
PEPCK gene expression is induced by…
-cortisol
PEPCK transcriptional control
- cortisol diffuses into hepatocyte and binds to intracellular receptor
- cortisol-receptor complex binds to glucocorticoid response element(in nucleus) to induce transcription of PEPCK
cortisol
- steroid hormone
- fat soluble
post-transcriptional control types
- alternative splicing
- mRNA editing
- mRNA stability
alternative splicing
- tissue specific isoforms of proteins can be made from the same pre-mRNA
- make different isoforms
how many genes in humans undergo alternative splicing?
60% of the 25000 genes
tropomyosin
- actin filament-binding protein
- contraction of muscles, in cytoskeleton
- undergoes alternative splicing
mRNA editing
-additional posttranscriptional modification in which base in mRNA is altered
Apo B mRNA in intestine
- the C residue in the CAA codon for glutamine is deaminated to U
- changes codon to a stop codon
- results in a shorter protein
which Apo B mRNA is in intestine and which is in liver?
- Apo B 48 in intestine
- Apo B 100 in liver
What does Apo B 48 mean?
48% of the message was coded
RNA interference (RNAi) types
- mechanism of reducing gene expression by…
- repressing translation
- increasing the degradation of specific mRNA
Which type of RNA interference is more common?
-increasing the degradation of specific mRNA
fundamental role of RNA interference
-cell proliferation, differentiation, apoptosis
RNA interference and AMD
- Neovascular AMD is triggered by over production of VEGF, leading to excess blood vessels behind retina
- RNA interference in trials is trying to degrade VEGF and prevent the making of new blood vessels
microRNA
- miRNA
- very short RNA(20 base pairs)
- mediates RNAi
- acts as a guide strand to traget specific mRNA that contain the complementary sequence
RNAi mechanism
- protein complex(RNA-induced silencing complex) works with miRNA
- expression of gene is reduced by cleaving RNA or blocking translation
siRNA
- double stranded short interfering RNA
- induced into a cell from an outside source can trigger RNAi
- if you know the target, you know what to introduce to fix it
translational control: elF-2 inhibition and promotion
- promoted by dephosphorylation
- inhibited by phosphorylation
phosphorylation of elF-2
- inhibits elF-2 function by inhibiting GDP-GTP exchange
- inhibits translation at the initiation step
- catalyzed by KINASES that are activated in response to environmental conditions
what environmental conditions activate kinases for phosphorylation of elF-2?
- amino acid starvation
- double stranded RNA
- misfolded proteins in rough ER
Post-translational control: modification of polypeptide chain
- after the chain is formed
involves. .. - trimming
- covalent attachments
- protein folding
- protein degradation
triming
- post-translational control
- they are initially synthesized as large precursors then cleaved to become functionally active
- digestive proteins
covalent attachments
- post-translational control
- phosphorylation
- glycosylation
- hydroxylation
- many others
protein folding
-directed by chaperones
protein degradation
- post-translational control
- by ubiquitination
- proteins target molecules to degrade them
euchromatin
- loosely packed DNA
- less dense
- accessible for transcription
heterochromatin
- tightly packed DNA
- not easily accessible for transcription
- more dense
epigenetic regulation is modification in…
- histones
- DNA
CpG islands
-regions in NDA rich in CG that are prone to modification for epigenetics
mechanisms of epigenetic reglation
-acetylation and methylation
acetylation of histones
- results in loose packing of DNA
- transcription factors can bind and transcription can go
methylation of DNA and histones
- makes nucleosomes pack tightly together
- less exposed, less accessible for transcription
what can cause epigenetic changes>
- development
- diet
- chemicals
- drugs
- aging
epigenetic changes can result in…
- cancer
- autoimune disease
- mental disorders
- diabetes
transposons(Tns)
-mobile segments of DNA that move in a random manner from one site to another on the same OR different chromosome
movement of Tns is mediated by…
- transponase
- enzyme encoded by Tn
Direct movement of Tns
- transponase cuts out and then inserts the Tn at a new site
- cut and paste
replicative movement of Tns
-Tn is copied and the copy is inserted elsewhere and original remains in place
diseases associated with transpostion
- hemophilia A
- duchenne muscular dystrophy
- can cause antibiotic resistance
