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Biochem Flashcards

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1
Q

Chromatin

A

histones: + charge, lysine, arginine, octamer
DNA: loops 2X around –>nucleosome
H1=stabilize

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2
Q

Heterochromatin

A

highly condensed

inactive

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3
Q

Euchromatin

A

less condensed

active

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4
Q

DNA methylation

A

CpG methylation silences DNA

template strand methylated to distinguish template strand

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5
Q

Histone methylation

A

represses transcription

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6
Q

Histone acetylation

A

relaxes DNA coiling allowing transcription

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7
Q

Nucleoside

A

base and sugar

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8
Q

Nucleotide

A

base and sugar and phophate

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9
Q

Purines

A

Adenine, Guanine
2 rings
Gly, Asp, Glu needed for synthesis

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10
Q

Pyrimidines

A

C, U, T
1 ring
deamination of cytosine makes uracil

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11
Q

Pyrimidine synthesis

A

Glu +CO2–>Carbamoyl phosphate +Asp–>Orotic Acid +PRPP–>UMP–>UDP–>dUDP etc

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12
Q

Leflunomide

A

inhibits dihydroorotate dehydrogenase

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13
Q

Methotrexate, Trimethoprim, Pyrimethamine

A

inhibit dihydrofolate reductase (decrease dTMP)

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14
Q

5-fluorouracil

A

forms 5-F-dUMP that inhibits thymidlate synthase (decrease dTMP)

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15
Q

Purine synthesis

A

de novo or salvage

Ribose5P–>PRPP–>IMP–>AMP or GMP

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16
Q

6-mercaptopurine

A

inhibit de novo purine synthesis

pro-drug=azathioprine

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17
Q

Mycophenolate, ribavirin

A

inhibit IMP dehydrogenase (IMP–>GMP)

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18
Q

Hydroxyurea

A

inhibits ribonucleotide reductase used in both purine and pyrimidine synthesis

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19
Q

Adenosine deaminase deficiency

A

required for degradation of adenosine so dATP increases–>lympho toxicity–>SCID

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20
Q

Lesch-Nyhan syndrome

A 
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
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21
Q

DNA Pol III

A

Prokaryotic only
5–>3 synthesis
3–>5 exonuclease proofing

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22
Q

DNA Pol I

A

Prokaryotic only
5–>3 exonuclease so degrades RNA primer
5–>3 syn
3–>5 exonuclease

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23
Q

Lac operon

A

low glucose, high cAMP, activate CAP

high lactose unbinds repressor via allolactose

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24
Q

Nucleotide excision repair

A

Endonuclease release damaged nts and DNA pol and ligase fill and reseal
in G1
bulky lesions

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25
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 ```
26
Mismatch repair
usually in G2
27
Nonhomologous end joining
some DNA may be lost
28
mRNA stop codons
UGA UAA UAG
29
Euk RNA Pols
RNA Pol I --> rRNA RNA Pol II -->mRNA RNA Pol III -->tRNA
30
a-amanitin
death cap mushrooms inhibits RNA Pol II hepatotoxicity
31
Prok RNA Pol
only one that makes all 3 kinds
32
Rifampin
inhibits prokaryotic RNA Pol
33
Actinomycin D
inhibits prok and euk RNA Pol
34
RNA processing
in eukaryotes only 5' cap 3' polyadenylation Intron splicing
35
RNA splicing
1. primary transcript combines with snRNPs to form spliceosome 2. lariat intermediate 3. lariat and intron released
36
miRNAs
small RNAs that bind to mRNA and degrade it | can be found in introns
37
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
38
Aminoacyl-tRNA synthetase
1 per amino acid | responsible for accuracy of aa selection
39
Initiation
GTP hydrolysis initiation factors assemble 40S with initiator tRNA 60S assembles
40
Elongation
rRNA - ribozyme catalyzes peptide bond formation
41
Termination
stop codon recog by release factor
42
Ribosome
``` Euk: 40S+60S=80S Pro: 30S+50S=70S A site: incoming aminoacyl-tRNA P site: growing peptide E site: empty tRNA ```
43
Trimming
post-translational | removal of N or C terminal propeptides
44
CDKs
constitutive | inactive
45
Cyclins
phase specific | activate CDKs
46
Cyclin-CDK complexes
phosphorylate other proteins
47
Tumor suppressors
p53 induces p21 that inhibits CDKs-->activation of Rb-->inactivates E2F-->inhibit G1-S
48
Golgi Mods
modifies N-oligosaccharides on Asn adds O-oligosaccharides on Ser and Thr adds Mannose-6-PO4 to traffic to lysosomes
49
I-cell disease
defect in N-acetylglucosaminyl-1 phosphotransferase-->no PO4 on mannose0-->extracellular buildup - coarse facies - clouded cornea - joint restriction
50
Signal Recognition Particle
traffic protein from ribosome to RER
51
COPI
retrograde Golgi->golgi cis-Golgi-->ER
52
COPII
anterograde | ER-->cis-Golgi
53
Clathrin
trans-golgi-->lysosomes | PM-->endosomes (RME)
54
Peroxisome
membrane-encloses | catabolism of long chain FA, branched FA, AA, ethanol
55
Microfilaments
muscle contraction, cytokinesis | actin, microvilli
56
Intermediate filaments
cell structure
57
Vimentin
int. filament | IHC for mesenchymal tissue
58
Desmin
int. filament | IHC for muscle
59
Cytokeratin
int. filament | IHC for epithelial cells
60
GFAP
int. filament | IHC for neuroglia
61
Neurofilaments
int. filament | IHC for neurons
62
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
63
Dynein
retrograde mvmt | postive to negative
64
kinesin
anterograde mvmt | negative to positive
65
Microtubule drugs
``` Mebendazole (anti-helminth) Griseofulvin (anti-fungal) Colchicine (anti-gout) Vincas (anti-cancer) Paclitaxel (anti-cancer) ```
66
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
67
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
68
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
69
Ouabain
Inhibits the Na-K pump by binding to K site
70
Digoxin, digitoxin
cardiac glycosides directly inhibit Na-K pump leads to indirect inhibition of Na/Ca exchange-->increase in intracellular Ca--> increased cardiac contractility
71
Type I Collagen
BONE, skin, tendon, dentin, fascia, cornea
72
Type II Collagen
CARTILAGE, vitreous body, nucleus pulposus
73
Type III Collagen
Reticulin - skin, BV, uterus, fetus, granulation tissue
74
Type IV Collagen
Basement membrane, lens defective in Alport syndrome targeted by auto-Ab in Goodpasture syndrome
75
Collagen Synthesis
1. Pro a-chain (Gly-X-Y): usually proline or lysine 2. Hydroxylaton of proline and lysine (need Vit C) 3. Gycosylation of pro-a-chain hydroxylysine to form procollagen 3 helix 4. Exocytosis into ECM 5. Cleavage of terminal regions to make insoluble tropocollagen 6. link between lysine-hydroxylysine to make collagen fibrils by lysyl oxidase (copper)
76
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 ```
77
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)
78
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
79
Elastin
nonhydroxylated proline, glycine, and lysine tropoelastin and fibrillin broken down by elastase (normally inhibited by a1-antitrypsin)
80
Marfan syndrome
defect in fibrillin
81
Emphysema
a1-antitrypsin deficiency
82
Southern blot
DNA
83
Northern blot
RNA
84
Western blot
protein
85
Southwestern blot
DNA-binding proteins
86
Microarrays
nucleic acid sequences on grids with DNA and RNA probes to detect amount of binding detect SNPs, CNVs
87
ELISA
detect antigen or antibody use of an Ab linked to an enzyme added substrate reacts with enzyme to get signal
88
Cre-lox system
manipuate genes at specific developmental points
89
RNAi
dsRNA promotes degradation of target mRNA -->knock-down

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