Term
| only histone not in nucleosome core! |
|
Definition
|
|
Term
| heterochromatin vs. eutchromatin |
|
Definition
HeteroChromatin -- Highly Condensed, inactive
euchromatin -- active |
|
|
Term
| methylation vs. acetylation |
|
Definition
methylation = mute
acetylation = active |
|
|
Term
purines vs. pyrimidines
C-G vs. A-T
how to tell bases apart |
|
Definition
purines -- 2 rings
pyrimidines -- 3 rings
C-G -- 3 H-bonds
A-T -- 2 H-bonds
THYmine has meTHYl group
guanine has ketone
cytosine has amine group |
|
|
Term
helicase
topoisomerase I vs. II
primerase
DNA polymerase III
DNA polymerase I
telomerase |
|
Definition
helicase -- unwinds DNA
topoisomerase I cuts 1 strand; II cuts 2
primase -- makes RNA primer!!
DNA polymerase III -- adds to 3' end, has 3'-->5' exonuclease activity
DNA polymerase I -- degrades RNA primer and fills the gap with 5'-->3' activity; proofreads with 3'-->5' exonuclease activity
telomerase -- add TTAGGG to 3' end; has RNA template (TERC) and reverse transcriptase (TERT) |
|
|
Term
| nucleotide excision vs. base excision |
|
Definition
nucleotide -- endonuclease --> DNA polymerase --> ligase
base -- glycosylase (remove base ONLY) --> endonuclease --> lysase (remove sugar!!) --> DNA polymerase --> ligase |
|
|
Term
which repair mechanism...
thymine dimers |
|
Definition
nucleotide excision repair
xeroderma pigmentosum (missing UV-specific endonuclease!) -- dry, atrophic, lots of keratin skin; cloudy, ulcerated cornea; skin cancer |
|
|
Term
which repair mechanism...
spontaneous/toxic deamination |
|
Definition
|
|
Term
|
Definition
<100 nucleotides
now that's small! |
|
|
Term
|
Definition
|
|
Term
|
Definition
UGA
UAA
UAG
recognized by RELEASING FACTORS (not tRNA!!) |
|
|
Term
RNA polymerase I vs. II vs. III
alpha-amanitin |
|
Definition
I -- rRNA
II -- mRNA; inhibited by alpha-amanitin (death cap mushroom!!)
III -- tRNA |
|
|
Term
|
Definition
TATA box, CAAT box
where RNA polymerase II opens DNA |
|
|
Term
|
Definition
1. 5' cap -- add guanosine triphosphate, methylate 5' terminal guanine --> 7-metyhlguanine
2. 3' polyadenylation -- find AAUAAA, cleave, then add A's (NO template required)
3. splice introns out! |
|
|
Term
| how many RNA polymerases do prokaryotes have? |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| CCA (Can Carry Amino acid) at 3' end covalently binds amino acid |
|
|
Term
| intiation of protein synthesis |
|
Definition
1. small subunit binds Kozak sequence (gccRccAUGG)
2. Met-tRNA loads in P site
3. large subunit binds to form initiation cmplex |
|
|
Term
|
Definition
eukaryotes -- 40S (18) + 60S (28, 5.8, 5) --> 80S
prokaryotes -- 30S (16) + 50S (23, 5) --> 70S |
|
|
Term
|
Definition
A -- new amino acid
P -- peptide thus far
E -- empty, exit |
|
|
Term
|
Definition
| mRNA regulation, turnover, and storage within cytoplasm |
|
|
Term
|
Definition
| p53 and Rb (hypophophorylated Rb = "stay G1"; hyperphosphorylated Rb lets go of E2F transcription factor = "go to S!!") |
|
|
Term
permanent, stable/quiescent, or labile?
skeletal muscle |
|
Definition
|
|
Term
permanent, stable/quiescent, or labile?
RBCs |
|
Definition
|
|
Term
permanent, stable/quiescent, or labile?
hepatocytes |
|
Definition
|
|
Term
permanent, stable/quiescent, or labile?
lymphocytes |
|
Definition
|
|
Term
|
Definition
RER -- secretory proteins; adds N-oligosaccharide
SER -- cholesterol/phospholipid synthesis; detoxication |
|
|
Term
|
Definition
modifies N-oligosaccharides
adds O-oligosaccharides
adds mannose-6-phosphate -- "to lysosomes, please!" |
|
|
Term
|
Definition
COPI -- retro, Golgi --> ER
COPII -- antero, RER --> cis-Golgi
Clarithin -- trans-Golgi --> lysosomes; plasma membrane --> endosomes (receptor-mediated endocytosis) |
|
|
Term
|
Definition
can't add mannose-6-phosphate
enzymes secreted out of cell!! --> high plasma levels of lysosomal enzymes
dense inclusion bodies b/c can't degrade things in lysosyme!!
course faces, clouded corneas, restricted joint movement, often fatal in childhood |
|
|
Term
| energy for protein synthesis |
|
Definition
load tRNA --> ATP
ribosome stuff --> GTP |
|
|
Term
dynein vs. kinesin
Kartagener's syndrome |
|
Definition
kinesin --> anterograde (- --> +)
dynein --> retrograde (+ --> -) -- Kartagener's syndrome |
|
|
Term
|
Definition
| microvilli, sterocilia, adherens junction, cytokinese, muscle contraction |
|
|
Term
|
Definition
| cilia, flagella, axonal trafficking, centrioles and mitotic spindle |
|
|
Term
|
Definition
| decrease fluidity, increase melting temp |
|
|
Term
| vimentin, desmin, cytokeratin, GFAP, neurofilaments |
|
Definition
| connective tissue, muscle, epithelial cells, neuro glial cells, neurons |
|
|
Term
|
Definition
| inhibits Na/K ATPase by binding to K+ site |
|
|
Term
| collagen -- type I vs. II vs. III, vs. IV |
|
Definition
I -- bone, skin, tendon --> OI
II -- cartilage
III -- reticulin --> Ehlers-Danlos
IV -- basement membrane (kidney, ears, eyes) --> Alports |
|
|
Term
|
Definition
1. synthesis (RER) -- alpha chains, preprocollagen, every 3rd is glycine
2. hydroxylation of proline and lysine (ER) -- vitamin C!!
3. glycosylation of hydroxylysine and forming procollagen triple helix with hydrogen and disulfide bonds (ER) -- forming procollagen impaired in OI
4. exocytosis
OUTSIDE
5. cleave terminal region with lots of disulfide bonds --> insoluble tropocollagen
6. cross-link tropocollagens with covalent lysine-hydroxylsine bonds --> collagen fibrils -- impaired in Ehlers-Danlos |
|
|
Term
|
Definition
| type II -- fatal in utero or neonatally |
|
|
Term
|
Definition
Ehler-Danlos
easy bruising |
|
|
Term
|
Definition
| decr. collagen and elastin PRODUCTION |
|
|
Term
|
Definition
lots of proline, glycine
lysines bind to form desmosine crosslinks --> elasticity and recoil! |
|
|
Term
|
Definition
SNoW DRoP
South = DNA
North = RNA
West = Protein (labeled antibody)
SouthWest = DNA-binding Proteins like transcription factors c-Jun, n-myc (labeled dsDNA) |
|
|
Term
|
Definition
1. random insertion (constitutive)
2. targeted insertion/deletion through homologous recombination (conditional) |
|
|
Term
|
Definition
| inducibly manipulate genes at specific dvelopmental points using antibiotic-controlled promoter (i.e. study gene whole deletion causes embryonic death) |
|
|
Term
|
Definition
| transfect dsRNA, which separates and binds mRNA --> degradation of mRNA --> decrease gene expression |
|
|
Term
| incomplete dominance vs. codominance |
|
Definition
incomplete -- hetero and homo have different phenotypes
co -- neither is dominant (i.e. blood groups) |
|
|
Term
| variable expression vs. incomplete penetrate |
|
Definition
variable expression -- nature and severity of phenotype vary (severity of disease varies)
incomplete expression -- not all with mutant genotype have mutant phenotype (not everyone has the disease!) |
|
|
Term
|
Definition
| pleiotropy -- one gene has multiple effects |
|
|
Term
| dominant negative mutation |
|
Definition
| nonfunctional altered protein prevents normal gene from working |
|
|
Term
|
Definition
| tendency for two alleles to occur more often together than expected |
|
|
Term
| locus heterogeneity vs. allelic heterogeneity |
|
Definition
locus -- mutations at different loci produce same phenotype
allelic -- different alleles at same locus produce same phenotype |
|
|
Term
|
Definition
MITOCHONDRIAL inheritance!
variable expression due to uneven distribution of mitochondria |
|
|
Term
|
Definition
| survival benefit of heretozygotes leads to high incidence of disease allele |
|
|
Term
|
Definition
| two copies of chromosome from 1 parent!! |
|
|
Term
| Hardy-Weinburg assumptions |
|
Definition
1. no mutations
2. no selection
3. no migration
4. random mating |
|
|
Term
| Prader-Willi vs. Angelman |
|
Definition
Prader-Willi -- Paternal gene is mutated (maternal is imprinted, paternal is non-functional)
Angelman -- maternal gene is mutated (paternal is imprinted, maternal is non-functional) |
|
|
Term
|
Definition
dystrophin!!
anchors muscle fibers |
|
|
Term
|
Definition
cystic medial necrosis of aorta --> ascending aortic aneurysm with aortic incompetence, aortic dissection
floppy mitral valve
subluxation of lens UP (vs. down and in in homocysteinuria) |
|
|
Term
|
Definition
CFTR gene -- chromosome 7
Phe 508 deletion --> abnormal post-translational processing --> degradation of channel
CFTR is ATP-binding transporter that pumps out Cl- against gradient with Na+ and H2O following
absence of vas deferens!!
nasal transepithelial potential difference more negative than normal (more sensitive than sweat test!) |
|
|
Term
|
Definition
| >200 repeats --> hyperMETHYLation --> INACTIVATION of FMR1 |
|
|
Term
|
Definition
| also has cataracts, frontal balding, gonadal atrophy, atrophy of type I fibers |
|
|
Term
| random Down syndrome stuff |
|
Definition
excessive skin in posterior neck
gap between first 2 toes
TE fistula
Hirschsprung
#1 septum primum-type ASD |
|
|
Term
| Robertsonian translocation |
|
Definition
| two long arms of chromosomes fuse (13, 14, 15, 21, 22) |
|
|
Term
| DiGeorge syndrome vs. velocardiofacial syndrome |
|
Definition
DiGeorge syndrome -- thymus, parathyroids, cardiac
velocardiofacial syndrome -- palate, cardiac, facial |
|
|
Term
|
Definition
vit A def
(resp, renal pelvis, eyes) |
|
|
Term
|
Definition
B1, thiamine pyrophosphate (TPP)
pyruvate dehydrogenase
alpha-ketoglutarate dehydrogenase
transketolase -- use to diag B1 def!
branched-chain AA dehydrogenase (alpha-ketoacid dehydrogenase) |
|
|
Term
| group of co-factors used in reactions |
|
Definition
B1, B2, B3, B5, lipoic acid
pyruvate dehydrogenase
alpha-ketoglutarate dehydrogenase
branched-chain AA dehydrogenase |
|
|
Term
|
Definition
nerves and heart!
Wernicke-Korakoff
dry beriberi -- polyneuritis, symmetrical muscle wasting
wet beriberi -- dilated cardiomyopathy with cardiac failure
infantile beriberi -- tachycardia, cardiomegaly, convulsions, cyanosis, dyspnea, V, death |
|
|
Term
|
Definition
riboflavin, FAD and FMN
cheilosis, corneal vascularization (two C's of B2!!) |
|
|
Term
| storage of water soluble vitamins?! |
|
Definition
only B12 and folate
stored in liver!! |
|
|
Term
|
Definition
niacin, NAD, NADP
pellagra!! -- diarrhea, dermatitis, dementia, death!!
due to Hartnup, carcinoid syndrome (shunt tryptophan to serotonin!!), low B6 |
|
|
Term
|
Definition
tryptophan --> niacin (with B6)
glutamate --> GABA
dopa decarboxylase: dopa --> dopamine
histadine --> histamine
ALA synthase: glycine --> porphyrin (and heme)
cystathionine synthase: homocysteine --> cystathionine (cysteine)
transamination
glycogen phosphorylase
decarboxylation rxns |
|
|
Term
|
Definition
low GABA --> convulsions
low heme --> sideroblastic anemia
low niacin --> pellagra
hyperirritability, peripheral neuropathy |
|
|
Term
|
Definition
homocysteine methyltransferase: homocysteine (with folate) --> methionine
methylmalonyl-coA mutase: methylmalonyl-coA --> succinyl-coA |
|
|
Term
|
Definition
SAM = ATP + methionine
needs B12 and folate for generation
NE --> E |
|
|
Term
|
Definition
1. pyruvate carboxylase: pyruvate --> OAA
2. acetyl coA carboxylase: acetyl coA --> malonyl coA
3. propionyl coA carboxylase: propionyl coA --> methylmalonyl coA |
|
|
Term
|
Definition
caused by
-- antibiotic use
-- raw eggs -- AVIDin in egg whites AVIDly binds biotin |
|
|
Term
|
Definition
1. helps Fe absorption (keeps Fe in Fe2+ reduced state)
2. dopamine beta-hydroxylase: dopamine --> NE
3. hydroxylation of lysine and proline on collagen synthesis |
|
|
Term
|
Definition
def -- swollen gums!, anemia (iron def!)
excess -- iron toxicity! (too much iron!) |
|
|
Term
|
Definition
antioxidant (protects RBCs and membranes)
hemolytic anemia (can't protect RBCs!)
dorsal column + spinocerebellar tract demyelination (like B12 def and Friedrich's ataxia!!) |
|
|
Term
|
Definition
| inhibits alcohol dehydrogenase (alcohol --> acetaldehyde) |
|
|
Term
|
Definition
| inhibits acetaldehyde dehydrogenase (acetaldehyde --> acetate) |
|
|
Term
|
Definition
uses NAD+ (limiting reagent)
alcohol dehydrogenase is zero-order |
|
|
Term
| metabolic effects of ethanol |
|
Definition
all due to high NADH
1. pyruvate --> lactic acid (NADH down-reg PDH) --> acidosis
2. OAA --> malate --> decrease gluconeogenesis --> hypoglycemia
3. OAA --> malate --> shut down TCA cycle --> coA become ketones
4. shut down beta-ox --> increased FAs --> fatty liver disease |
|
|
Term
|
Definition
Kwashiorkor -- protein deficient; ascites
Marasmus -- energy deficient; waste away |
|
|
Term
where does this take place?
beta-ox |
|
Definition
|
|
Term
where does this take place?
acety CoA prod |
|
Definition
|
|
Term
where does this take place?
TCA cycle |
|
Definition
|
|
Term
where does this take place?
glycolysis |
|
Definition
|
|
Term
where does this take place?
FA synthesis |
|
Definition
|
|
Term
where does this take place?
HMP shunt |
|
Definition
|
|
Term
where does this take place?
heme synthesis |
|
Definition
| mitochondria AND cytoplasm |
|
|
Term
where does this take place?
urea cycle |
|
Definition
| mitochondria AND cytoplasm |
|
|
Term
where does this take place?
gluconeogenesis |
|
Definition
| mitochondria AND cytoplasm |
|
|
Term
| kinase vs. phosphorylase vs. phosphatase |
|
Definition
kinase -- adds phosphate using ATP
phosphorylase -- adds phosphate
phosphatase -- remove phosphate |
|
|
Term
|
Definition
NAD -- catabolism
NADP -- anabolism |
|
|
Term
|
Definition
1. anabolic reactions
2. respiratory = oxidative burst
3. P450!!
4. glutathione reductase
also makes BH4!!
HMP Shunt locations: lactating mammary glands, liver, adrenal cortex, RBCs to make FA, cholesterol, steroids!! |
|
|
Term
|
Definition
glycolysis -- 2 ATP
aerobic with malate-aspartate shuttle (heart, liver) -- 32 ATP
aerobic with glycerol-3-phosphate shuttle -- 30 ATP |
|
|
Term
| hexokinase vs. glucokinase |
|
Definition
glucokinase in liver, beta-cells, high Vmax, low affinity
GlUcokinase is a GLUtton!! |
|
|
Term
|
Definition
pump H+ into intermembranous space (complex I, III, and IV -- NOT II!!)
H+ falls into matrix via ATP synthase |
|
|
Term
| mostly anaerobic glycolysis |
|
Definition
| RBCs, WBCs, kidney medulla, lens, cornea, testes |
|
|
Term
|
Definition
| inhibits complex I (ox phos) |
|
|
Term
|
Definition
| inhibits complex IV (ox phos) |
|
|
Term
|
Definition
| inhibits complex III (ox phos) |
|
|
Term
|
Definition
| inhibits complex IV (ox phos) |
|
|
Term
|
Definition
|
|
Term
|
Definition
uncoupling agent
binds H+ and makes it lipid soluble --> crosses membrane!! |
|
|
Term
|
Definition
|
|
Term
|
Definition
| increase membrane permeability --> decreased proton gradient and increased O2 consumption --> ATP synthesis stops but ETC continues; produces heat |
|
|
Term
|
Definition
uncoupling agent
brown fat
hibernating animals; around kidneys, adrenals in infants (keep them warm!) |
|
|
Term
|
Definition
O2 --> O2 radical --> H2O2 --> HOCl radical --> kills bacteria!!
NADPH oxidase catalyzes first step!!
catalase -- H2O2 --> H2O + O2 (without it, neutrophil/monocyte can use bacterial H2O2 to make reactive oxygen intermediates) |
|
|
Term
|
Definition
glucose --> sorbitol via aldose reductase
some tissues can convert sorbitol --> fructose via sorbitol dehydrogenase
BUT NOT Schwann cells (peripheral neuropathy), lens (cataracts), retina (retinopathy), or kidneys (nephropathy)!! leading to complications of chronic hyperglycemia!! |
|
|
Term
|
Definition
| transports lactate from muscle to liver to be transformed to glucose! |
|
|
Term
| tetrahydrobiopterin reactions |
|
Definition
BH4
tryptophan --> serotonin
phenylalanine --> tyrosine
tyrosine --> dopa |
|
|
Term
| amino acid derivatives (without co-factors) |
|
Definition
serotonin --> melatonin
arginine --> creatine
arginine --> urea
arginine --> nitric oxide
glutamate --> glutathione |
|
|
Term
lysosomal storage disease:
peripheral neuropathy, angiokeratomas, cardiovascular/renal disease |
|
Definition
Fabry's disease
deficiency: alpha-galactosidase
accumulated: ceramide trihexoside |
|
|
Term
lysosomal storage disease:
HSM, aseptic necrosis of femur, bone crises |
|
Definition
Gaucher's disease
deficiency: glucocerebrosidase
accumulated: glucocerebroside
Gaucher cells -- look like crumpled tissue paper! |
|
|
Term
lysosomal storage disease:
progressive neurodegeneration, cherry-red spot on macula, HSM |
|
Definition
Niemann-Pick disease
deficiency: sphingomyelinase
accumulated: sphingomyelin
foamy macrophages!! |
|
|
Term
lysosomal storage disease:
progressive neurodegeneration, cherry-red spot on macula, no HSM |
|
Definition
Tay-Sachs
deficiency: hexosaminidase A
accumulated: GM2 ganglioside |
|
|
Term
lysosomal storage disease:
peripheral neuropathy, optic atrophy |
|
Definition
Krabbe's disease
deficiency: galactocerebrosidase
accumulated: galactocerebroside |
|
|
Term
lysosomal storage disease:
ataxia, dementia |
|
Definition
Metachromatic leukodystrophy
impaired production of myelin
deficiency: arylsulfatase A
accumulated: cerebroside sulfate |
|
|
Term
lysosomal storage disease:
gargoylism, corneal clouding, HSM, airway obstruction |
|
Definition
Hurler's syndrome
deficiency: alpha-L-iduronidase
accumulated: heparan sulfate, dermatan sulfate |
|
|
Term
lysosomal storage disease:
mild gargoylism, HSM, airway obstruction + aggressive behavior, deafness |
|
Definition
Hunter's syndrome
deficiency: iduronidate sulfatase
accumulated: heparan sulfate, dermatan sulfate |
|
|
Term
| glycogenolysis vs. gluconeogenesis |
|
Definition
|
|
Term
| apo proteins on chylomicron "generation" vs. VLDL "generation" |
|
Definition
chylomicrons -- apoB-48
VLDL -- apoB-100 |
|
|
Term
| other apo protein functions |
|
Definition
apoC-II activates LPL --> break down of TGs into FAs that are taken up by peripheral tissue
apoE (after use apoC-II, pick up apoE) binds LDLR
apoB-100 also binds LDLR |
|
|
Term
|
Definition
|
|
Term
|
Definition
has apoA's (apoA-I activates LCAT)
ABCA1 -- gets free cholesterol from peripheral cells
LCAT -- makes cholesterol ESTERS (to form mature HDL)
CETP -- transfers cholesterol to VLDL/LDL |
|
|
Term
|
Definition
HDL -- takes cholesterol from periphery and brings it to liver
LDL -- takes cholesterol from liver and brings to peripheral tissue |
|
|
Term
|
Definition
LPL def or altered apoC-II
increased chylomicrons --> increased TGs and cholesterol
TGs --> pancreatitis
cholesterol --> eruptive/pruritic xanthomas, but NO increased risk for atherosclerosis |
|
|
Term
|
Definition
no LDLRs
elevated LDLs --> super high cholesterol --> xanthomas (Achilles tendon!!), xanthelasmas, corneal arcus, ATHEROSCLEROSIS!! |
|
|
Term
|
Definition
| overprod of VLDL --> high TGs --> pancreatitis |
|
|
Term
|
Definition
can't make apoB-100 or apoB-48
clear/"foamy" cells esp in jejunum
acanthocytosis, ataxia (Vit E def), night blindness (Vit A def), FTT, steatorrhea |
|
|
Term
|
Definition
defective neutral AA transporter
includes tryptophan --> pellagra |
|
|
Term
|
Definition
| defective positive/basic + cysteine AA transporter --> cystine (2 cysteines connected by disulfide bond!!) kidney stones |
|
|
Term
| maple syrup urine disease |
|
Definition
can't degrade branched amino acids (Ile, Leu, Val) -- alpha-ketoacid dehydrogenase
MR, CNS defects, death |
|
|
