Biochem Flashcards
Chromatin
histones: + charge, lysine, arginine, octamer
DNA: loops 2X around –>nucleosome
H1=stabilize
Heterochromatin
highly condensed
inactive
Euchromatin
less condensed
active
DNA methylation
CpG methylation silences DNA
template strand methylated to distinguish template strand
Histone methylation
represses transcription
Histone acetylation
relaxes DNA coiling allowing transcription
Nucleoside
base and sugar
Nucleotide
base and sugar and phophate
Purines
Adenine, Guanine
2 rings
Gly, Asp, Glu needed for synthesis
Pyrimidines
C, U, T
1 ring
deamination of cytosine makes uracil
Pyrimidine synthesis
Glu +CO2–>Carbamoyl phosphate +Asp–>Orotic Acid +PRPP–>UMP–>UDP–>dUDP etc
Leflunomide
inhibits dihydroorotate dehydrogenase
Methotrexate, Trimethoprim, Pyrimethamine
inhibit dihydrofolate reductase (decrease dTMP)
5-fluorouracil
forms 5-F-dUMP that inhibits thymidlate synthase (decrease dTMP)
Purine synthesis
de novo or salvage
Ribose5P–>PRPP–>IMP–>AMP or GMP
6-mercaptopurine
inhibit de novo purine synthesis
pro-drug=azathioprine
Mycophenolate, ribavirin
inhibit IMP dehydrogenase (IMP–>GMP)
Hydroxyurea
inhibits ribonucleotide reductase used in both purine and pyrimidine synthesis
Adenosine deaminase deficiency
required for degradation of adenosine so dATP increases–>lympho toxicity–>SCID
Lesch-Nyhan syndrome
X-linked recessive absent HGPRT which converts hypoxanthine to IMP and guanine to GMP excess uric acid production and de novo purine synthesis Hyperuricemia Gout Pissed Off Retardation dysTonia Treat: allopurinol or febuxostat
DNA Pol III
Prokaryotic only
5–>3 synthesis
3–>5 exonuclease proofing
DNA Pol I
Prokaryotic only
5–>3 exonuclease so degrades RNA primer
5–>3 syn
3–>5 exonuclease
Lac operon
low glucose, high cAMP, activate CAP
high lactose unbinds repressor via allolactose
Nucleotide excision repair
Endonuclease release damaged nts and DNA pol and ligase fill and reseal
in G1
bulky lesions
Base excision repair
gylocosylase removes base and creates AP side AP-endonuclease cleaves 5 end Lyase cleaves 3 end DNA Pol B fills throughout cycle
Mismatch repair
usually in G2
Nonhomologous end joining
some DNA may be lost
mRNA stop codons
UGA
UAA
UAG
Euk RNA Pols
RNA Pol I –> rRNA
RNA Pol II –>mRNA
RNA Pol III –>tRNA
a-amanitin
death cap mushrooms
inhibits RNA Pol II
hepatotoxicity
Prok RNA Pol
only one that makes all 3 kinds
Rifampin
inhibits prokaryotic RNA Pol
Actinomycin D
inhibits prok and euk RNA Pol
RNA processing
in eukaryotes only
5’ cap
3’ polyadenylation
Intron splicing
RNA splicing
- primary transcript combines with snRNPs to form spliceosome
- lariat intermediate
- lariat and intron released
miRNAs
small RNAs that bind to mRNA and degrade it
can be found in introns
tRNA
T arm: contains TYC for ribosome binding
D arm: contains dihydrouridine for correct aminoacyl-tRNA synthetase
Acceptor stem: 5’-CCA-3’ is amino acid acceptor site
Aminoacyl-tRNA synthetase
1 per amino acid
responsible for accuracy of aa selection
Initiation
GTP hydrolysis
initiation factors assemble 40S with initiator tRNA
60S assembles
Elongation
rRNA - ribozyme catalyzes peptide bond formation
Termination
stop codon recog by release factor
Ribosome
Euk: 40S+60S=80S Pro: 30S+50S=70S A site: incoming aminoacyl-tRNA P site: growing peptide E site: empty tRNA
Trimming
post-translational
removal of N or C terminal propeptides
CDKs
constitutive
inactive
Cyclins
phase specific
activate CDKs
Cyclin-CDK complexes
phosphorylate other proteins
Tumor suppressors
p53 induces p21 that inhibits CDKs–>activation of Rb–>inactivates E2F–>inhibit G1-S
Golgi Mods
modifies N-oligosaccharides on Asn
adds O-oligosaccharides on Ser and Thr
adds Mannose-6-PO4 to traffic to lysosomes
I-cell disease
defect in N-acetylglucosaminyl-1 phosphotransferase–>no PO4 on mannose0–>extracellular buildup
- coarse facies
- clouded cornea
- joint restriction
Signal Recognition Particle
traffic protein from ribosome to RER
COPI
retrograde
Golgi->golgi
cis-Golgi–>ER
COPII
anterograde
ER–>cis-Golgi
Clathrin
trans-golgi–>lysosomes
PM–>endosomes (RME)
Peroxisome
membrane-encloses
catabolism of long chain FA, branched FA, AA, ethanol
Microfilaments
muscle contraction, cytokinesis
actin, microvilli
Intermediate filaments
cell structure
Vimentin
int. filament
IHC for mesenchymal tissue
Desmin
int. filament
IHC for muscle
Cytokeratin
int. filament
IHC for epithelial cells
GFAP
int. filament
IHC for neuroglia
Neurofilaments
int. filament
IHC for neurons
Microtubules
movement, cell division
cilia, flagella, axon, spindle
-composed of helix of heterodimers of a and b-tubulin each with 2 GTP
-dynein and kinesin
Dynein
retrograde mvmt
postive to negative
kinesin
anterograde mvmt
negative to positive
Microtubule drugs
Mebendazole (anti-helminth) Griseofulvin (anti-fungal) Colchicine (anti-gout) Vincas (anti-cancer) Paclitaxel (anti-cancer)
Cilia
9+2 arrangement of mt doublets
base is called the basal body with 9 mt triplets and no central mts
axonemal dynein-ATPase cause bending
Kartagener Syndrome
Primary Ciliary Dyskinesia
immotile cilia due to defective dynein arm
- male and female infertility
- ectopic preg risk
- bronchiectasis, sinusitis
- situs inversus with dextrocardia
Na+-K+-ATPase
For each ATP consumed, 3Na+ go out of the cell when the pump is phosphorylated and 2K+ come into the cell when the pump s dephosporylated
Ouabain
Inhibits the Na-K pump by binding to K site
Digoxin, digitoxin
cardiac glycosides
directly inhibit Na-K pump
leads to indirect inhibition of Na/Ca exchange–>increase in intracellular Ca–> increased cardiac contractility
Type I Collagen
BONE, skin, tendon, dentin, fascia, cornea
Type II Collagen
CARTILAGE, vitreous body, nucleus pulposus
Type III Collagen
Reticulin - skin, BV, uterus, fetus, granulation tissue
Type IV Collagen
Basement membrane, lens
defective in Alport syndrome
targeted by auto-Ab in Goodpasture syndrome
Collagen Synthesis
- Pro a-chain (Gly-X-Y): usually proline or lysine
- Hydroxylaton of proline and lysine (need Vit C)
- Gycosylation of pro-a-chain hydroxylysine to form procollagen 3 helix
- Exocytosis into ECM
- Cleavage of terminal regions to make insoluble tropocollagen
- link between lysine-hydroxylysine to make collagen fibrils by lysyl oxidase (copper)
Osteogenesis Imperfects
COL1A1, COL1A2 defects autosomal dominant decreased production of type I collagen with issues making triple helix -fractures -blue sclerae -hearing loss -tooth issues
Ehlers-Danlos Syndrome
faulty cross-linking in collagen
- hypermobility type: hypermobie joints
- classical type: joint and hyperextensible skin (type V collagen)
- vascular type: easy bruising, aortic aneurysms, organ rupture (type III coll)
Menkes disease
X-linked recessive
impaired copper absorption due to bad ATP7A
decreased activity of lysyl oxidase needed for crosslinks
-kinky hair
-growth retardation
-hypotonia
Elastin
nonhydroxylated proline, glycine, and lysine
tropoelastin and fibrillin
broken down by elastase (normally inhibited by a1-antitrypsin)
Marfan syndrome
defect in fibrillin
Emphysema
a1-antitrypsin deficiency
Southern blot
DNA
Northern blot
RNA
Western blot
protein
Southwestern blot
DNA-binding proteins
Microarrays
nucleic acid sequences on grids with DNA and RNA probes to detect amount of binding
detect SNPs, CNVs
ELISA
detect antigen or antibody
use of an Ab linked to an enzyme
added substrate reacts with enzyme to get signal
Cre-lox system
manipuate genes at specific developmental points
RNAi
dsRNA promotes degradation of target mRNA –>knock-down
