Biochemistry - Important Concepts Flashcards
Amino acids in histones
Lysine and arginine
His lies made me go “argh!”
Nucleosome core
H2A, H2B, H3, H4
H1
Binds to the nucleosome and to linker DNA, stabilizing the chromatin fiber
During what phase of the cell cycle does histone synthesis occur?
S phase
Heterochromatin
Condensed and inactive
Euchromatin
Sterically accessible
Amino acids necessary for purine synthesis
GAG
Glycine
Aspartate
Glutamine
Leflunomide
Inhibits dihydroorotate dehydrogenase (carbamoyl phosphate + aspartate + PRPP –> orotic acid
Mycphenolate
Inhibits IMP dehydrogenase
My Ribald IMP
Ribavarin
Inhibits IMP dehydrogenase
My Ribald IMP
Hydroxyurea
Inhibits ribonucleotide reductase (which turns UDP –> dUMP or converts ribonucleotides to deoxyribonucleotides)
6-mercaptopurine
Inhibits de novo purine synthesis
Azathioprine
Inhibits de novo purine synthesis
Pyrimethamine
Inhibits dihyrofolate reductase and decreases dTMP
Mnemonic for pyrimidine base production
Gluttons crave carbs as oral porn
Glutamine Carbamoyl phosphate synthase II Carbamoyl phosphate Aspartate Orotic acid PRPP
HGPRT catalyzes what rxns?
Guanine to GMP
Hypoxanthine to IMP
Adenosine deaminase does what?
Adenosine to Inosine (irreversibly deaminates adenosine - substitutes an amino group for a hydroxyl group)
Xanthine oxidase does what?
Hypoxanthine to xanthine, xanthine to uric acid.
Adenosine deaminase deficiency
Leads to excess ATP and dATP, which imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase - DNA synthesis is prevented - lymphocyte count decreases
AR SCID
Purine nucleoside phosphorylase deficiency
Catalyzes the reaction from Inosine to Hypoxanthine. Increased purine nucleosides, decreased uric acid, and impaired T cell function.
Lesch-Nyhan syndrome sx?
HGPRT: Hyperuricemia Gout Pissed off (aggressive, self-mutilating) Retardation DysTonia
Also choreathoid movements
Lesch-Nyhan syndrome treatment?
Allopurinol and Febuxostat (inhibit xanthine oxidase)
Mycophenolate mofetil
Anti-metabolite, anti-proliferative drug that acts as an inhibitor of inosine monophosphate dehydrogenase and is used to treat Wegener’s… somehow
DNA polymerase delta
Major eukaryotic replication polymerase
beta - repair
alpha and epsilon - also involved in replication
gamma - mitochondrial DNA
DNA polymerase beta
beta - repair
delta - major eukaryotic replication polymerase
alpha and epsilon - also involved in replication
gamma - mitochondrial DNA
DNA polymerase III
Prokaryotic only. Proofreads with 3’ to 5’ exonuclease.
III only eats what’s behind it
I is aggressive - chomps as it goes forward, like Pacman
DNA polymerase I
Prokaryotic only. Proofreads with 5’ to 3’ exonuclease. THis is used to degrade RNA primer.
III only eats what’s behind it
I is aggressive - chomps as it goes forward, like Pacman
Transition mutation
purine to purine or pyrimidine to pyrimidine
Transversion mutation
purine to pyrimidine or vice versa
Wobble rules
Third base pair contributes to wobble.
U-G is a valid pair
Inosine can pair with U, C, A
AA with strongly nonpolar side chains have codons with ___s in 2nd position.
Pyrimadines
Polar side chains –> purines
Remember - polar bears are pure.
Xeroderma pigmentosum type of DNA repair problem?
Nucleotide excision repair
Think derma –> skin –> UV exposure
HNPCC repair problem?
Mismatch repair
Ataxia telangiectasia repair problem?
Nonhomologous end joining
Nucleotide excision repair
Repair of pyrimidine dimers or bulky helix-distorted lesions usually from UV light exposure.
A short section is excised using endonucleases and then DNA polymerase and ligase fills and reseals the gap.
Xeroderma pigmentosum
Base excision repair
Altered base - repairs spontaneous / toxic deamination (C –> U, A –> hypoxanthine)
GEL PLease!
Glycosylase (base-specific) recognizes altered base and creates an apyrimidinic, apurinic site
Endonuclease removes nucleotide and cleaves 5’ end
Lyase cleaves 3’ end
Pol beta fills gap
Lyase seals it.
Mismatch repair
Defect in newly synthesized strand.
M2ESS PLease MutS detects mismatch MutL identifies parent strand Exonuclease 1 is activated SSBPs stabilize the construct Pol delta synthesizes new DNA Ligase seals the nick
HNPCC
NHEJ
Brings together 2 ends of DNA fragments to repair double strand breaks; no requirement for homology
Ataxia telangiectasia
DNA denaturation
Hyperchromic effect - increase in UV absorption and A260
Decrease viscosity
Where do capping, splicing, and polyadenylation of 3’ end of RNA occur?
All in the nucleus
hnRNA versus mRNA?
hnRNA - heterogeneous nuclear RNA - not spliced or capped or polyadenylated
Cytoplasmic P-bodies?
These are responsible for mRNA quality control - they contain exonucleases, decapping enzymes, and microRNAs.
Polyadenylation signal
AAUAAA
anti-smith antibodies
Antibodies to spliceosomal snRNPs - highly specific for SLE
anti-U1 RNP antibodies
highly associated with mixed connective tissue disease
Exons
Contain the actual genetic material coding for proton
Introns
Intervening noncoding segments of DNA
Which end is the CCA at in tRNA?
What does it do?
3’ end
Accepts the amino acid
T-arm
Think Tribe
Thiamine, pseudouracil, cytosine
t-RNA ribosome binding
D-arm
Think D-syn
Contains dihydrouracil residues
Necessary for tRNA recognition by the correct amino-acyl tRNA synthetase
Which stages require ATP and which require GTP?
ATP - tRNA activation and charging
GTP - tRNA gripping and going places
Sites on the 60S subunit
A - incoming aminoacyl tRNA
P - accomodates growing peptide
E - holds empty tRNA as it exits
Release factor
Recognizes the stop codon, causes completed polypeptide to be released from the ribosome
Zymogen
Inactive enzyme precursor
CDKs
Constitutive and inactive
Cyclins
Regulatory proteins that control cell cycle events - activate CDKs
Breast cancer, brain tumors, acute leukemia, soft tissue sarcomas, bone sarcomas, and adrenal cortical carcinoma
Li-Fraumeni syndrome
p53 mutation, AD. rare
Nissl bodies
RER in neurons that synthesize peptide neurotransmitters for secretion
Smooth endoplasmic reticulum
Site of steroid synthesis and detoxification of drugs and poisons
Liver hepatocytes and steroid-hormone producing cells in the adrenal cortex and gonads are rich in SER.
Golgi modifications
N-oligosaccharide on asparagine
O-oligosaccharide on serine and threonine
Mannose-6-phosphate addition to proteins for lysosomal trafficking.
Endosomes
Sorting centers for material from outside the cell or from the Golgi, sending it to lysosomes for destruction or back to the membrane / Golgi for further use.
Coarse facial features, clouded corneas, restricted joint movement, and high plasma levels of lysosomal enzymes - fatal in childhood
I cell disease
Inherited lysosomal storage disorder
Defect in phosphotransferase - Golgi fails to phosphorylate mannose residues (mannose 6 phosphate) on glycoproteins so proteins are screted extracellularly rather than delivered to lysosomes
Think clouds and corn on the golf course - restricted movement because you can’t see - Eyes - I cell disease
I cell disease
Coarse facial features, clouded corneas, restricted joint movement, and high plasma levels of lysosomal enzymes - fatal in childhood
Inherited lysosomal storage disorder
Defect in phosphotransferase - Golgi fails to phosphorylate mannose residues (mannose 6 phosphate) on glycoproteins so proteins are screted extracellularly rather than delivered to lysosomes
Think clouds and corn on the golf course - restricted movement because you can’t see - Eyes - I cell disease
Phosphotransferase
I cell disease
Signal recognition particle
Abundant cytosolic ribonucleoprotein that trafficks proteins from the ribosome to the RER. Absent or dysfunctional SRP causes proteins to accumulate in the cytosol.
COPI
Golgi –> Golgi (retrograde)
Golgi –> ER
COPII is anterograde
Gotta go backwards to fix your past before you can go forward! said the Cop
COP II
Golgi -> Golgi (anterograde)
ER -> Golgi
Gotta go backwards to fix your past before you can go forward! said the Cop
Clathrin
Golgi -> lysosomes
Plasma membrane -> endosomes (receptor mediated endocytosis)
Peroxisome
Catabolizes very long chain fatty acids, branched chain fatty acids, and amino acids
Proteasome
Degrades damaged or ubiquitin tagged protein
Peroxisome vs proteasome?
Peroxisome is fatty acids and amino acids
Proteasome is protein
Dynein versus kinesin?
Dynein is Minus end directed microtubule transport - goes TOWARD the cell center
Drugs that act on microtubules?
Pack My Bendy Greasy Collar of Vines Paclitaxel Mebendazole Griseofulvin Colchicine Vincristine/Vinblastine
Axonemal dynein
ATPase ta links peripheral 9 doublets in cilia and causes bending of cilium by differential sliding of doublets.
Infertility, Increased risk of ectopic pregnancy, bronchiectasis, recurrent sinusitis, situs inversus
Kartagener syndrome - primary ciliary dyskinesia
Actin and myosin versus microtubules versus intermediate filaments
Actin / myosin - Muscle contraction
Microtubule - Movement
Intermediate filament - Structure
Intermediate filament stain - vimentin
Stains Connective tissue
Vines connect
Intermediate filament stain - Desmin
Stains muscle
Desmond is muscular
Cytokeratin stain
Epithelial cell
GFAP stain
NeuroGlia
Neurofilament stain
Neurons