Deevska Review Flashcards
General mechanism of regulation of gene expression in prokaryotes
-Major level of regulation is transcription
The general mechanisms of regulation of gene expression in eukaryotes
- Transcription
- Post-transcription
- Translation
- Post translation
Epigenetics
What allows for more sophisticated regulation in eukaryotic cells compared to prokaryotic cells
Eukaryotic cells have nucleus separation, which allows for more sophisticated control
Repressor operon
Suppress the transcription of a gene. Transcription is usually on, but can be inhibited
Inducible operon (activators)
Transcription usually off, but can be stimulated
Structure of operon
- control region
- structural region
Control region of operon
Contains promoter and operator.
-different factors/molecules that activate/inhibit to regulate (always expressed)
Structural genes on operon
Sequence one after another
- genes required to make AA
- all necessary to code for enzymes
- all controlled by ONE regulator
Lac operon in general
- inducible
- E. coli prefers glucose
- it can use other sugars such as lactos, however, this requires more enzymes (hence more energy) so E coli only produces the enzymes to use other sugars if glucose is absent and another sugar is present
Repressor protein for lac operon when glucose only is present
-encoded by the lac1 gene, always present and bound to the operator, blocks RNA polymerase
Lac operon when glucose is absent
Adenyly cyclase makes cAMP, CAP, cAMP complex forms, binds to CAP binding site, RNA polymerase can efficiently initiate transcription
Lac operon when lactose is present
A small amount of allolactose is produced that binds to the repressor and prevents it from binding to the operator
What role does allolactose have in lac operon function
Binds to the repressor, and prevents it from binding to the operator, lac operon is on
When glucose is present
It inhibits adenyly cyclase, no cAMP, cannot form CAP/cAMP complex, cannot initiate transcription
What happens when there is both glucose and lactose present for the lac operon?
Although the repressor is inactive, the transcription can not be initiated because the cap site is empty. Even though a small amount of allolactose binds to the repressor, the CAP site is still empty due to the lack of glucose, so RNA polymerase cannot efficiently initiate transcription
What is the level of gene expression control that is common between prokaryotes and eukaryotes?
Transcription
Cis-acting elements,
Regulation of transcription is controlled by the regulatory sequences of DNA which are usually embedded in the noncoding regions of the genome. They are called this because they influence expression of genes only on the same chromosome
Trans-acting regulators
Capable of interacting with regulatory molecules (transcription factors). Transcription not possible without these
They are proteins
Enhancers
DNA sequences that increases the rate if initiation of transcription
- on same chromosome
- can be close or far from gene
- upstream or downstream or within intron regions
- tissues specific manner
How can enhancers be brought close to the basal promoter
By bending of the DNA molecule
Transcription factors (trans acting)
- DNA binding domain
- activation domain-stabilize formation of the initiation complex, recruit chromatin modifying proteins
PEPCK inhibited by cortisol
- cortisol diffuses into cytosol
- binds to intracellular receptor
- complex enters nucleus
- binds to GRE
- PEPCK transcription is induced
Alternative splicing and gene expression
- tissue specific isoforms of proteins can be made from the same pre mRNA by the use of alternative splice sites
- over 60% of the genes in humans undergo alternative splicing
- tropomyosin
MRNA editing and gene expression
- additional posttranscriptional modification in which a base in the mRNA is altered
- Apo B mRNA, in the intestine only, the C residue in the CAA codon for glutamine is deaminated to U, changing the sense codon to a nonsens or stop codon
RNAi and gene expression
- mechanism of reducing gene expression by repressing translation or increasing the degradation of specific mRNAs
- cell proliferation, differentiation, apoptosis
- therapeutic potential
RNAi and ARMD
AMD is triggered by VEGF, an siRNA designed to target the mRNA of VEGF and promote its degradation went to clinical trials (1st approved for clinical trials )
Translational control
- eIF-2: phosphorylation of this inhibits translation at the initiation step
- does so by inhibiting GDP to DTP exchange
- phosphorylation catalyzed by kinases in response to environmental conditions
Post translational control
- trimming
- Covalent attachment (phosphorylation)
- Protein folding (chaperones)
- Protein degradation (ubiquination)
Epigenetic regulation
- Euchromatin-loosely packed accessibly for transcription
- Heterochromatin-tightly packed, inaccessible
- methylation of DNA and histones cause nucleosomes to pack tightly together. Transcription factors cannot bind the DNA and genes are not expressed
- histone acetylation results in loose packaging of nucleosomes, genes expressed
CpG islands
Regions in DNA rich in CG that are prone to modifications
Transposons
- mobile segments of DNA that move in a random manner from one site to another on the same or a different chromosome
- direc-cuts out and reinserts
- replicative- copied and inserted elsewhere
- rare cases of hemophilia A, Duchenne muscular dystrophy, antibiotic resistance
What is the urea cycle?
A cycle of biochemical reactions occurring in that produces urea from ammonia
Where does the urea cycle take place?
Primarily in the liver, and to a lesser extend in the kidney
What is the immediate precursor for ammonia and aspartate?
Glutamate
Thermogenics of urea cycle
ATP is used
Irreversible
Large -deltaG
Where doe the nitrogens of the urea cycle come form?
-one from free NH3 and one from aspartate
Purpose of urea cycle
Get rid of nitrogen in form of free ammonia in dehydration of AA. Cannot store AA. 1st step is removing alpha-amino group, producing ammonia. Excreted into kidney, urea operates in liver mostly, some kidney
Sources of ammonia
- diet
- glutamine
- bacterial action
- amines
- catabolism of purines and pyrimidines
Free ammonia present in circulation
Will be removed by the liver and used for the synthesis of urea
What contributes to the acid-base balance of the body by excreting protons?
Free ammonia released in the urine
Glucogenic
An AA that can be converted into pyruvate or an intermediate of the TCA cycle
- may be used as substrates for gluconeogensis
- rise to a net increase in glucose formation in the liver
- pyruvate
Ketogenic
AA that can be converted into acetoacetate or a precursor
-acetyl-CoA
Elevated homocysteine
Produced during methionine metabolism
Elevations in plasma homocysteine
Promote oxidative damage, inflammation, and endothelial dysfunction and are an independent risk factor for occlusive vascular disease
Elevated Hcy during pregnancy
Associated with increases incidence of neural tube defects
Eye abnormalities of Hcy
- ectopia lentis
- myopia
- glaucoma
- optic atrophy
- retinal detachemtn
- cataracts
Albinism
Tryptophan to melanin defect
Lack pigment
High risk of skin cancer
What is homocysteinuria a deficiency of?
Cystathionine synthase
What are the two major pathways in which alcohol is processed in the liver?
- ADH (alcohol dehydrogenase)
- MEOS relying on cyt P450 enzymes
What is rate limiting in alcohol metabolism
ADH
Asians and alcohol metabolism
Mutation for dominant negative mutation
- heterozygotes who still produce the normal enzyme in addition to the defective one, have newer zero enzyme activity
Atypical ALDH
DIsulfiram
- Antabuse
- Accumulation of acetaldehyde after ingestion of ethanol
- Deterrent
- inhibits aldehyde dehydrogenase
What is the most toxic intermediate in ethanol metabolism?
Acetaldehyde
What are symptoms of acetaldehyde toxicity
Flushing of the face and nausea
What has a more immediate affect on ethanol metabolism
NADH
The processing of alcohol produces large quantities of_______ in the liver
NADH
Large amounts of NADH
Alter many metabolic processes
-inhibits many enzymes
Significant effects of NADH build up found in…
Mainly in heavy drinkers and occasional drinkers that binge
Build up of NADH in well fed state
NADH will inhibit PDH complex and cause pyruvate to be converted into lactate resulting in lactic acidosis
Secondary affect of lactic acidosis
Underexcretion of uric acid, hyperuricemia
Hypoglycemia and ethanol metabolism
In the fasting state, the liver will try to perform GNG, however precursors will be diverted at pyruvate to the production of lactate. If the liver glycogen stores become depleted, it will result in hypoglycemia
-can happen to anyone
Is alcohol ketogenic of glucogenic?
Ketogenic
Hyperlipidema and fatty liver
High levels of NADH inhibit the oxidation of fatty acids.
- results in accumulation of TAG as lipid droplets leading to fatty liver
- some of it is releases into the bloodstream as VLDVLs causing hyperlipidemia
Folate deficiency in ethanol metabolism
Results in megaloblastic anemia
Thiamine deficiency in ethanol metabolism
Wernicke-korsakoff syndrome
What are alcoholics usually deficient in?
Folate and thiamine
G1 of cell cycle
Active metabolism and accumulation of building blocks and energy
-cellular metabolism happens here
G2 of cell cycle
Active metabolism and protein synthesis; duplication of organelles
- produces macromolecules
- organelles duplicated
G0 of cell cycles
- resting
- period in the cell cycle in which get cell exists in a quiescent state; the cell is neither dividing nor preparing to divide
- some are capable of going back into the cell cycle
G2 checkpoint
Check for
- cell size
- accurate DNA replication
M checkpoint
Check for
-chromosome attachment to the spindle
G1 checkpoint (restriction)
Check for:
- cell size
- nutrients
- growth factors
- DNA damage
What are the checkpoints of the cell cycle
G2 checkpoint
M checkpoint
G1 checkpoint
Positive regulation of the cell cycle
Cyclins and Cdk
- changes of different cyclins through the cell cycle
- direct correlation between cyclin accumulation and the three major cell cycle checkpoints
- sharp decline of cyclin levels following each checkpoint
- cyclins only active when bound to Cdk
Negative regulators of cell cycle
- Rb
- P53
- p21
Rb
Retinoblastoma protein
-retinoblastoma protein; prevents initiation of the cell cycle in G1 phase
P53
- transcriptional repressor
- repress transcription and promote apoptosis
- induces cell cycle arrest
- checks for DNA damage, cell cycle abnormalities, hypoxia
P21
- prevents cell cycle progression by
- inhibiting the activity of cyclin E-associated CDK2
- therefore preventing E2F-mediated gene transcription and cell cycle progression
Oncogenes
Positive regulators of cell cycle mutated
Protooncogenes
Not mutated, + cell cycle regulated
Tumor suppressor genes
Genes that encode for negative regulator proteins that will suppress uncontrolled cell division
Rb, p53, p21
Role of p53 in cancer
If it is mutated, it will not arrest cell cycle when it comes across cell abnormalities, the damaged cell will continue to divide which results in cancer
