1 Flashcards
Rifampacin
binds beta subunit on porkaryotic RNA polymerase and inhibits clearing of the promoter
Puromycin
inhibits translocation, early chain termination AA tRNA analog
Tetracyclines
blocks A site in pokaryotes 30S
Chloramphenicol
inhibits prokaryotic peptidyl transferase in prokaryotes
Cycloheximide
inhibits peptidyl transferase in eukaryotes
Streptomycin
inhibits initiation of translation in prokaryotes distorts mRNA causes misreading
diphteria toxin
inhibits eEF2 in eukaryotic translation
Ricin
binds to eukaryotic 60S subunit
alpha amatin
inhibits eukaryotic pol 2 and pol 3 to a certain extent
actinomycin D
inserts between CG in both eukaryotes and prokaryotes inhibiting elongation of transcription
RAS
G protein family, mutated in 30% of all cancers active form is bound to GTP control transcription- in cancer cells is always on
Protoncogene
EGFR,
IRESSA
drug that binds to the same part of EGFR as ATP, prevents growth signal from being sent to the nucleus CANCER treatement for oncogene EGFR lung cancer
Tumor supressor gene
p53-active form inhibits cell cycle. DNA repair and appopstosis
50% of cancers p 53- prevents continuation of cell cycle until DNA is repaired and also induces apoptosis
Care takers or stability genes
Group 1- Minor mistakes MMS,NER ,BER
Group 2-control processes involving large portion of chromosomes BRCA,ATM, BLM
types of breast cancer
Luminal A- Pt+Er+ HER -
Lumnial B- Pt+ Er+ HER+
HER 2- Pt-ER- HER+
basal like-ER-PT- HER-
Lac Operon
LacI repressor
CRP-CAMP binding to activating promoter site
LAC ZYA- weak promoter(-35 -10)
Tryptophan operon
Trp-R repression of initiation
Trp L- leader
Operator- Binding site for Trp- R
Euploidy
a multiple
aneuploidy
trisomy or monosomy not an exact multiple
KLinefelter syndrome
XXY
tall
hypogonadism and sterility
Turners syndrome
X short stature webbed neck underdevelopped ovaries sterility 40% are mosaicisms
intermediate filaments
tissue stability over cell stability
staining used in cancer detection
they branch
desmasmoses/ hemidesmosomes
phsophorylation dependant not ATP or GTP- no polarity
support nuclear lamina (lamins)
keratins-epithelium/vimentins (Desmin-muscle)/neural/lamin-nuc envelope
actin filaments
cell curface organisaton can be linear to 3 D
branching
in microvilli, zona adherens
ATP dependant ant polarized
Elongation mediated by formins
cross packing for myosin 2 interaction/tight packing (fimbrin) to avoid allowinbg myosin 2 to enter and avoid contraction
ZONULA ADHERENS(dev of tubes and ducts)
microtubules
cell highways MTOC ( centrosomes and basal bodies ) hollow tube
GTP dependent and polarized- DYNAMIC INSTABILITY
cell division
cillia
Liable/stable
tubulin heterodimer
MAPS- Capping proteins (CATASTROPHINS opposite of MAPS lead to microtubule instability)
MBPS-dynein and kinesin
phalloidin
actin specific drugs- stabilizes filaments leukocytes can no longer move
Cholchicine
microtubule specific prevents polymerisation-used for gout treatmnet
vinca alkaloid
microtubule drug, prevents polymerization used as anti cancer agents
secondary cytoskeleton changes due to cell injury
lou gehrig(neurofilament accumulation)
alchoholic liver disease (keratin filaments)
alzeimer
HPV (KOILICYTOSIS)
secondary cytoskeleton changes due to cell injury
cardiomyopathy
immotile cillary syndrom
epidermis bullod
progeria
cell junctions
1-occluding (proteins :Claudin and Occluden)
2-adhering ( microfilament-adherens junction (cell-cell protein: cadherins) and focal adherens(cell-matrix protein: fibronectin)
and intermediate filaments- desmesome (Keratin Filaments protein:cadherens(abnormal desmosomes leads to Pemphyvus vulgaris, sever blisering)
and hemidesmosome Protein: Integrin Bullos Pemphigoid- subemidermal blisters)
3- communicating -cap junctions (close with Ca+ high or pH low) Defect leads to infertility
laminin
sticky proteins that form the basal lamina and allows interation with the epithelium
GAGS
4 types
1-hyoluron:most connective tissues(only one not attached to a core protein all others make BRUSH)
2-Chondroitin/Dermatin Sulfate: Cartilage and skin ( related to aging)
3-Heparan sulfate: Basal Lamina
4-Keratin Sulfate: Cornea and cartilage
Collagen
25% ECM-rich in proline and glycine form intra and inter covalent crosslinks within colagen fibril network forming -type IV ( basal lamina) -type VII(anchoring fibrils)
diseases associated with Collagen
Scurvy:inhibited proline hydoxylation
osteaogenis imperfecta- incorrect collagen fibril assembly
dermatitis herpetiformis- antibodies against anchoring fibrils
adhesive glycoproteins
Laminins
and fibronectin
diseases associated with basal lamina
alports syndrome:gene mutations of collagen IV(develop renal disease)
Goodpastors syndromme: antibodies againt collagen type IV(very rapid)
alpha helix
can be streched to add water
beta sheet
cannot be streched, does not absorb water
beta turns= proline and glycine
commitement
biochemical and genetic restriction on cell fate
2 steps
-specification
-determination
Morphogens:
• Produce a diffusible signal/stimulus for development
• Produced at one location: morphogen concentrations are high near the source, decrease with increased distance from source
• Morphogen concentration affects impact on development
EX- Sonich hedgehog
Sonic hedgehog (SHH)
- The SHH receptor is PTCH1
- SHH is produced in the posterior region of the developing hand, concentrations decrease as a gradient away from the source. Thus, high SHH is a signal for posterior identity, low SHH is a determinant of the anterior portion of the hand.
- Unoccupied PTCH receptor (i.e. no SHH) suppresses another cell surface molecule: SMO (“smoothened”). This allows a cytoplasmic precursor for a transcription factor GLI1/2 to be phosphorylated by PKA, an event which is then permissive for proteolytic cleavage of GLI1/2 to a transcriptional repressor. The GLI1/2 repressor translocates to the nucleus for transcription repression.
- Binding of SHH to PTCH prevents the above-mentioned suppression of SMO. SMO is now free to suppress PKA, which in turn prevent the proteolytic cleavage of GLI1/2. In its uncleaved form, GLI1/2 is a transcriptional activator.
Holoprosencephaly
is a syndrome caused by inactivating mutations in SHH.
• SHH is expressed in the notochord, floorplate and is essential for midline neural structures.
• Holoprosencephaly is a dominant trait, but with variable penetrance.
• Severe form: microcephaly, cleft palate, hypotelorism (narrowly-set eyes)
• Mild: single central incisor
(FGFR3) gene
FGFR3 is unique in that it is actually a suppressor of bone growth. An FGFR3 mutation associated with achondroplasia is G380R, which is not inactivating but rather activating: it causes constitutive activation of the tyrosine kinase function of FGFR3. Constitutive activation of this receptor leads to constant inhibitory signaling during bone growth, explaining the shortening of long bones associated with the disorder.
CHARGE syndrome
newly discovered eitiology CHD7 gene
- colomba
- heart defect
- atresia choanea
- retardation of growth/dev
- ear abnormalities
- genital abnormalities
iPCR
combination of ELISA and realtime PCR to detect protein concentration at the 10^-15
bDNA(branched DNA)
christmass tree model-amplification that is not PCR
capture protein
branche DNA amplifier
enzyme labeled probes
Diagnostic Test parameters
sensitivity(positive) V specificity(negative
Accracy V precision
linear dynamic range for quantification
Sensitivity calculation
True positives/(trues positives + false negatives)
Specificity calculation
true negatives/(true negatives+false positives)
Reciever operator characteristic curve ROC curve
the grpahical trade off between false negatives and false positives. 1/specificity on X axis and 1/sensitivity on Y axsis
melting curve analysis and Tm
1-denaturing
2-tm when dsDNA-ssDNA
3-every DNA sequence has a characteristic melting curve and TM cause it has a specific CG amount
4-single nucleotide mutation can result in a change in Tm
also used in homozygous V heterozygous mutation analysis
Bio bare code assay (BCA)
Using gold nanoparticle
Sandwich
Meat in the middle is what you aretrying to detect
Magnetic particle
And on the other side the gold particule and the BAR code dna
Built DNA into the bar code
Put a magnet - everything will go to that direction- enrichement
Then denature and the bare code can go through the scanner
Detection limit zepotmolar 10^-21
PCR competitor would be able to detect several diseases at a time
applications of indivdual molecular testing in individualized medcicine
1-Theragnositcs= to prescribe ornot
2-pharmacogenomics=dosage
3-prognomics=predict out come of treatement
structural chromosomal abnormalities
1-deletion
2-duplication
3-inversion
4-translocations
wolf hischhorn syndrome
4p deletion microcephaly low birth wiehgt heart probs fish probes used for diagnosis
trisomy 18
(47, +18) Edwards Syndrome omphalacele congenital heart disease clenched hands- limb anomalies high lethality with profound abnormalities in survivors
trisomy 13
Patau Syndrome midline facial clefts holoproencephale congenital heart disease kidney cysts larger chromosome than 18 so even fewer survivors
prader willi
paternal 15q hypotonia food learning disabilities underdevelopped sex organs
FISH prob
flurorescence to detect microdeletion that cannot be seen on a karyotype
method of choice for balanced abnormalities
Digeorge
most frequently ordered FISHprobe test deletion on 22q just bellow centromere cardiac hypocalcemia dev delays cleft palate variable expressivity goes from one generation to the next
Comparative Genome hybridisation (CGH)
microarray tech
usepatient DNA and control DNA and unlike FISH you dont need to know what your target is on the chromosome
uses ratios to detect GENETIC UNBALANCE
Pallister killian
12p disorder lethal if not mocaisism scarce scalp hair streaky pigmentation profound mental retardation
genes that can be imprinted
6 7 11 14 15
4 Paths to uniparental disomy
1-gamete complementation
2-trisomic rescue
3-monosomic rescue(nullesomic gamte is created during meiosis= results in isodisomy)
4- mitotic errors
Fragile X syndrome
unstable trinucleotide repeats - accumulation of CpG repreats unstabile maternal allele hyperextendible joints large ears macrocephaly
huntingtons diseases
unstable trinucleotide repeats on paternal allele
anticipation
phenomen in which the severity of a genetic condtion becomes more severe and earlier on set through subsequent generations
ex:Fragile X and Huntingtons
Enzymes- stabilization of the transition state
1 provide hydrogen bonds
2- provide hydrophobic interactions
3- neutralize charge( ionic interations)
4-chemistry( the serine proteases use covalent chemistry for the formation of the acyl-enzyme intermdiate as well as general acid/base catalysis
