biochem/ cell sci memorize Flashcards
DNA/ histone methylation
inactivates DNA transcription
uses cytosine & guanine (adenine?)
DNA/histone acetylation
activates DNA (relaxes coiling) = + transcription
AAs in histones?
lysine & arginine
inc GC content
inc melting temperature
bc G-C forms 3 H bonds (AT&U = 2 bonds)
nucleotides
base + ribose + phosphate
linked by 3’-5’ phosphodiester bond
AAs needed for purine synthesis?
GAG & THF
Glycine
Aspartate
Glutamine
AA needed for pyrimidine production?
Aspartate
drugs inhibiting purine synthesis
hydroxyurea 6-MP 5-FU MTX TMP
Hydroxyurea MOA
inhibits ribonucelotide reductase
(no UDP –> dUDP) in pyrimidine synthesis
6-mercaptopurine
inhibits de novo purine synthesis
no PRPP –> IMP –> AMP + GMP
5-fluorouracil
inhibits thymidylate synthase
(no dUMP –> dTMP)
decreased dTMP = cell undergoes thymine-less death
Methotrexate
inhibits dihydrofolate reductase (no DHF --> THF) dec dTMP (thymidine-less death)
Trimethoprim
inhibits bacterial dihydrofolate reductase (no DHF--> THF cofactor in dUMP --> dTMP) dec dTMP (thymidine-less death)
Orotic Aciduria path
no orotic acid –> UMP in de novo pyrimidine synthesis pathway
defective UMP Synthase
*AR
Orotic aciduria Sx
inc orotic acid (urine)
megaloblastic anemia (NOT improved with b12 or folate)
FTT
*No hyperammonemia (vs. OTC deficiency in urea cycle– other use of carbamoyl phosphate)
Orotic aciduria Tx
oral uridine
Purine salvage deficiency disorders
Lesch-Nyhan (XLR)-- HGPRT deficiency SCID (AR)-- ADA deficiency APRT deficiency (AR) SCID-- PNP deficiency (AR)
Lesch-Nyhan path
defective pure salvage bc no HGPRT
(no hypoxanthine –> IMP, and no guanine –> GMP)
required de novo purine synthesis
build up of uric acid (end product of purine salvage)
XLR: MALES
Lesch-Nyhan Sx
self-mutilation hyperuricemia --> gout & nephrolithiasis retardation aggression choreoathetosis
Adenosine deaminase deficiency (ADA)
no Adenosine –> Inosine
build up ATP & dATP = feedback inhibition of ribonucleotide reductase = prevent DNA synthesis = dec B & T cell count
*Result = SCID
(AR)
Purine nucleoside phosphorylase deficiency (PNP)
causes SCID (rare) similar to ADA but isolated T cell deficiency, normal B cells.
APRT deficiency
no adenine –> AMP
results in adenine stone urolithiasis and inc uric acid
AR
xanthine oxidase deficiency
no hypoxanthine –> xanthone
or xanthine -> uric acid
Sx: dec uric acid, inc xanthine, + xanthine urine stones
only AAs not under degeneracy/ redundancy rule (AAs encoded by multiple codons)
methionine (AUG- start)
tryptophan (UGG)
severity of damage in DNA point mutations
Frameshift > nonsense > missense > silent
Silent pt mutation
same AA, change in 3rd position = tRNA wobble
normal protein formed
Missense pt mutation
changed AA = base substitution
similar to AA (conservative)
may be dysfxnal protein, but same size
nonsense pt mutation
change = early STOP codon
shorter, non functional protein
frameshift mutation
misreading downstream (deletion or insertion) shorter, nonfunctional protein
splice site mutation
retains introns larger proteins, but nonfunctional retain immunoreactivity (detected by Abs)
DNA ligase forms what bond
phosphodiesterase bonds
DNA pol I
prok only
excises RNA primer with 5’->3’ exonuclease,
replaces it with DNA
DNA pol III
prok only
elongates leading by adding dNT to 3’ (5’->3’ synth)
elongates lagging until primer reached, then insert 3’->5’ exonuclease to proofread
which drug inhibits topoisomerase = increased supercoils during replication
fluoroquinolones
inhibits DNA gyrase (prok top II)
UV light causes dimer of what? Repaired by?
thymine (pyrimidine dimers)
repaired by UV-endonuclease = nucleotide excision repair
Mutated nucleotide excision repair?
Xeroderma pigmentosum AR* mutated endonucleases inc risk CA, severe sunburn, solar keratoses, corneal ulcers. avoid sun (child of the night) Tx- 5-FU, cryotx MC- japan
which enzymes do base excision repair
glycosylases (recognize & remove)
endonuclease (cuts DNA w/o base, removes empty sugar, fills gap and reseals)
*repair toxic deamination
Which disease has mutated mismatch repair?
HNPCC (Lynch Syndrome)
AD*
80% chance CRCA by 50 yo, inc risk other CA (esp endometrial)
What disease has mutated nonhomologous end joining?
Ataxia Telangiectasia
AR* mutated ATM gene (cannot repair ds-breaks)
TRIAD– ataxia, telangiectasias, IgA deficiency
chain terminator Rx have what modified?
3’ OH position
inhibits addition of next NT
blocks DNA replication
stop codons (mRNA)
UGA, UAA, UAG
promotor region
TATA & CAAT boxes upstream
A-T rich
transcription factors bind where?
enhancer regions
alters gene expression
(repressors bind at silencer locations to dec gene expression)
post-transcriptional RNA processing
5’ cap (7-methylguanosine)
poly-A tail (200 A’s at 3’) (no template needed)
splicing out DNA introns (via snRNPs & lariats) (Lupus = Auto-ABs to snRNPs)
- after completed, becomes mRNA then transport out of nucleus
- splicing mutations = alternative splicing (seen in beta-thal)
tRNA structure
CCA @ 3’ end
add AAs via covalent bond
charging of tRNA
aminoacyl-tRNA synthetase (1 per AA) = matchmaker w/ ATP to form peptide bond
*accuracy of AA selection
which drug prevents aminoacyl-tRNA attachment
Tetracyclines
bind 30S subunit
anticodon end of tRNA reads/
CAU (5’ to 3’) to match up with AUG mRNA start codon
4 stages of protein synthesis
1) initiation (IF + GTP, assemble 40S)
2) elongation (amino-acyl tRNA binds a A, ribozyme rRNA catalyzes peptide bond formation & transfers peptide)
3) translocation (ribosome advances 3 NTs and moves peptidyl tRNA to P site, exits via E site)
4) termination (stop codon recognize by release factor, complete protein released from ribosome)
Protein synthesis inhibitors
1) aminoglycosides– 30S inhibitors of initiation complex. cause mRNA misreading
2) Tetracycline– 30S blocks aminoacyl- tRNA from entering A site
3) Chloramphenicol– 50S, inhibits peptidyl transferase via ribosomal rRNA
4) Macrolides– 50S, prevent uncharged tRNA release after donated (stuck at E site)
Post-translational modifications
1) cleavage/ trimming (proenzymes –> enzymes)
2) covalent alterations (-ation)
3) Ubiquitin tag for defective (proteosomal degradation)
tumor suppressor genes in G1 to S
p53
un-P Rb (P via cyclin-CDK to allow progression to S phase)
*both inhibit G1–> S
*mutated = always P-Rb, mut p53 = unregulated cell division
Permanent cell types
always in G0
only hypertrophy, no hyperplasia
*neurons, sk muscle, cardiac muscle, RBC
Stable/ Quiescent cell types
in G0 until stimulated to enter G1
may hypertrophy & hyperplasia
*hepatocytes, lymphocytes, smooth muscle
Labile (stem cell) types
never enter G0, short G1 phase = rapid division
*BM, gut epi (base of crypts), skin BM, hair follicles, germ cells
(commonly complication of CA drugs bc inactivate rapidly dividing cells)
cells rich in RER
protein rich cells
ex) plasma cells (secrete AB), mucus-secreting goblet cells (SI)
cells rich in SER
steroid H production & detox–
ex) Liver hepatocytes (detox), adrenal cortex (steroid-production)
I-cell disease
AR* lysosomal storage disorder
failure of addition of mannose-6-P in golgi to lysosomal proteins
enzymes are secreted outside of cell instead of to lysosome
*Labs= inc lysosomal enzymes in plasma, + inclusion cells, empty lysosomes
*Sx= coarse facial features, clouded corneas, restricted joint mvmt. fatal in childhood.
drugs acting on microtubule
Mebendazole/ thiabendazole (anti-helminthic) Griseofulvin (antifungal) Vincristine/ vinblastine (anti-CA) Paclitaxel (anti-breast CA & ovarian CA) Colchicine (anti-gout)
dyenin
retrograde (+ –> -)
kinesin
anterograde (- –> +)
Chediak-Higashi
AR* mutation in lysosomal trafficking regulator gene (LYST)– product req for Mt-dependent sorting of endosomal proteins into late multivesicular endosomes
(cannot fuse phagosome w/ lysosome)
*TRIAD:
recurrent pyogenic infxns, partial albinism, peripheral neuropathy
alpha-amanitin
found in amanita phalloides (death cap mushrooms)
- inhibits RNA Pol II (mRNA- largest; opens DNA at promotor site)
- severe hepatotoxicity
Kartagener’s Syndrome
AR* dz of primary ciliary dyskinesia
immotile cilia d/t dynein arm defect
*SX: male infertility, dec female fertility, bronchiectasis, recurrent sinusitis
*A/w: situs inversus
immunohistochemical stains for intermediate filaments: Connective Tissue
Vimentin
immunohistochemical stains for intermediate filaments: Muscle
Desmin
immunohistochemical stains for intermediate filaments: Epithelial cells
Cytokeratin
immunohistochemical stains for intermediate filaments: neuroglia
GFAP
glial fibrillary acid proteins
immunohistochemical stains for intermediate filaments: neurons
neurofilaments
Ouabain MOA
inhibits Na/K ATPase by binding to K site
Cardiac glycosides MOA
DIRECTLY inhibits Na/K ATPase
which INDIRECTLY inhibits Na/Ca exchange causing inc intracellular Ca and inc cardiac contractility
*digoxin & digitoxin
Type I collagen
MC bone, skin, tendon dentin, fascia, cornea LATE wound repair *defective in: osteogenesis imperfecta
Type II Collagen
Cartilage (+hyaline)
vitreous body & nucleus pulposus
Type II Collagen
Reticulin– skin, bv’s
uterus, fetal tissue
*Granulation tissue– EARLY wound repair
*defective in: Ehlers-Danlos
Type IV Collagen
BM of skin or basal lamina
*defective in: Alport syndrome
Red safrainin O stain
collagen
mast cell granules
mucin red
Osteogenesis Imperfecta
AD* MC– COL1A1 & COL1A2
abnormal type I collagen– problems forming procollagen triple helix (H & disulf bonds– 3 collagen alpha chains)
brittle bone dz
Sx = multiple fx w/ minimal trauma, blue sclearae (choroidal veins), hearing loss (middle ear bone abn, dental abns (no dentin)
Ehlers-Danlos Syndrome
AR or AD*
defective collagen fibril cross-linking (lysine-hydroxylysine cross link)– MC type I & III?
*SX = hyperextensible skin, easy bleed/bruising, hypermobile joints, poor wound healing, joint dislocation, organ rupture
*A/W: berry aneurysms –> subarachnoid hemorrhage
Alport’s Syndrome
*XLR
abnormal type IV collagen = BM of kidneys, eyes and ears affected
*SX= progressive hereditary nephritis, deafness, ocular distubrances
(Cant pee, cant see, cant hear)
elastin rich in which AAs?
proline & glycine
non-hydroxylated
Marfan’s Syndrome
*AD fibrillin defect (elastin)
Alpha1-antitrypsin deficiency
*co-dom
no elastase inhibition = inc elastin breakdwon
*panacinar emphysema & liver dysfxn
Blotting procedures
SNoWDRoP: Southern = DNA Northern = RNA Western = Protein Southwestern = DNA-binding protein
Indirect ELISA
uses test antigen to find patient antibody
SMOKE
Direct ELISA
uses test antibody to find patient antigen
FIRE
Karyotyping uses chromosomes in what phase?
metaphase
Codominance
both alleles contribute to phenotype of heterozygote
ex) Blood Groups A, B, AB
alpha-1 antitrypsin deficiency
Variable expressivity
phenotype varies among individuals with same genotype
ex) NF1 varying disease severity
Incomplete penetrance/ phenotype
not all with mutant genotype show mutant phenotype
ex) BRCA-1 mutation does not always result in breast/ovarian CA
Pleiotrophy
one gene contributes to multiple phenotypic effects (seemingly unrelated)
ex) PKU sx of MR and hair/skin changes
Imprinting
gene expression differences depend on whether mutation is of maternal or paternal origin
Ex) prader-willi and angelman’s syndrome
Anticipation
inc severeity & earlier onset of disease in succeeding generations
ex) trinucleotide repeat d/o = Huntingtons