Biochem Random Flashcards
histone amino acids
lysine and arginine
linker histone
H1
heterochromatin
highly condensed
increase methylation
decrease acetylation
methylation
cystine and adenine
methylation at CpG islands
represses transcription
histone modification
methylation mute
acetylation active
linkage phosphate in nucleotide
3-5’ phosphodiester bond
methyl in base
thymine
deamination of cytosine
makes uracil
deamination of adenine
makes guanine
methylation of uracil
makes thymine
amino acids for purine synthesis
glycine
aspartate
glutamine
inhibits dihydroorotate dehydrogenase
leflunomide
inhibits ribonucleotide reductase
hydroxyurea
adenosine deaminase deficiency
required for degradation of adenosine and deoxyadenosine
increase dATP toxicity to lymphocytes
treatment Lesch-Nyhan
allopurinol or febuxostat
Wobble exceptions
methionine and tryptophan
only encoded by 1 codon
exception of universal genetic cod
mitochondria
AT rich sequences
found in promoters and origins of replication
-poside inhibits
topo II
-tecan inhibits
topo I
FQN inhibits
topo II and topo IV
degrades RNA primer
replaces with DNA
DNA polymerase I
transition mutation
purine to purine or pyrimidine to pyrimidine
transversion mutation
purine to pyrimidine or pyrimidine to purine
early stop
nonsense
UAG, UAA, UGA
examples of frameshift mutation
Duchenne and Tay Sachs
examples of mutation in splice site
cancers, dementia, epilepsy, beta thalassemia
low glucose
increase AC leading to activation of CAP and increased transcription
high lactose
unbinds repressor leading to increase transcription
defective nucleotide excision repair
xeroderma pigmentosum
steps base excision repair
glycosylase removes base and creates AP site
endonuclease cleaves 5’
lyase cleaves 3’ end
polymerase followed by ligase
defective mismatch repair
Lynch syndrome
occurs in G2
defective nonhomologous end joining
ataxia telangiectasia, BRCA1 mutation, Fanconi anemia
start codon eukaryotes vs prokaryotes
methionine to n-formylmethionine
promoter region
AT rich upstream with TATA and CAAT boxes
mutation leads to decrease in transcription
signs of intron
start with GT
end with AG
most numerous RNA
rRNA
alpha amanitin
inhibits RNAP II
causes hepatotoxicity
initial transcript
heterogeneous nuclear RNA
polyadenlation signal
AAUAAA
quality control mRNA
cytoplasmic procesing bodies (P bodies)
contain exonucleases, decapping enzymes and microRNAs
antibodies to snRNPs
SLE
anti-U1 RNP
mixed connective tissue
microRNA
small, conserved, noncoding RNA molecules
target 3’ UTR
T arm tRNA
ribothymidine, pseudouridine, cytidine
D arm tRNA
dihydrouridine residues
detects tRNA by aminoacyl-tRNA synthetase
initiation protein synthesis
GTP hydrolysis
tumor suppressors
p53 induces p21
inhibits CDKs
hypophosphorylation of Rb inhibits G1 to S progression
permanent cells
neurons, skeletal and cardiac muscle, RBCs
stable
hepatocytes and lymphocytes
RER
secretory proteins and N-liknked oligosaccharide addition
RER in neurons
Nissle bodies
free ribosomes
cytosolic and organellar proteins
cells rich in RER
mucus goblet cells and plasma cells
smooth ER
steroid synthesis and detox of drugs and poisons
n-oligosaccharides
asparagine
o-oligosaccharides
serine and threonine
defect in n-acetylglucosaminyl-1-phosphotransferase
I cell disease
cells secreted extracellularly rather than delivered to lysosomes
absent signal recognition particle
protein accumulates in cytosol
cop II vs cop I
two forward
one back
peroxisome
very long chain fatty acids, branched fatty acids, amino acids, and ethanol catabolism
hypotonia, seizures, hepatomegaly
Zellweger syndrome
scaly skin, ataxia, cataracts, shortening of 4th toe, epiphyseal dysplasia
Refsum disease
defects proteasome
Parkinson disease
actin, microvilli
microfilaments
vimentin, desmin, cytokeratin, lamins, glial fibrillary acid proteins, neurofilaments
intermediate filaments
cilia, flagella, spindle, centrioles
microtubules
desmin
muscle
GFAP
neuroglia
dynein vs kinesin
dynein retrograde
kinesin anterograde
9 doublet and 2 singlet arrangement
cliaa
of MT
basal body
9 MT triplets with no central MT
female with Kartagener
increase risk of ectopic pregnancy
sodium potassium
3 Na out
2 K in
oubain
inhibits bining to K site
type I collagen
bone, skin, tendon, dentin, fascia, cornea, late wound repair
type II collagen
cartilage, vitreous body, nucleus pulposus
type III
reticulin-skin, blood vessels, uterus, fetal tissue, granulation tissue
seen in Ehlers-Danlos
type IV
basement membrane, basal lamina, lens
hydroxylation collagen
proline and lysine
problems forming triple helix collagen
osteogenesis imperfecta
problems with cleavage of disulfide rich terminal regions procollagen
Ehlers-Danlos
problems with cross-linking collagen
Ehlers-Danlos and Menkes disease
covalent lysine-hydroxylysine cross linking by copper containing lysyl oxidase
genetics osteogenesis imperfecta
COL1A1 and COL1A2
translucent connective tissue over choroidal veins
blue sclera in OI
aneurysms Ehlers Danlos
berry and aortic aneuysms
classical Ehlers-Danlos
mutation in type V collagen
genetics Menkes disease
X linked recessive impaired copper absorption and transport
ATP7A
brittle, kinky hair, growth retardation and hypotonia
composition elastin
rich in nonhydroxylated proline, glycine, and lysine residues
crosslinking elastin
extracellular
wrinkles of aging
decrease collagen and elastin production
genetics Marfan syndrome
FBN1 on ch 15
AD
lens in marfan
upward and temporally displaced
southwestern blot
DNA binding proteins
like transcription factors
using labeled oligonucleotide probes
microarrays
detect single nucleotide polymorphisms and copy number variations
less specific than Western blot
ELISA
phase karyotyping
metaphase
samples for karyotyping
blood, bone marrow, amniotic fluid, or placental tissue
steps cloning
isolate
expose to RT to produce cDNA
insert cDNA into plasmids with ABX resistance
cre-lox system
manipulate genes at specific developmental points
RNAi
dsRNA complementary to mRNA sequence
pleiotropy
multiple phenotypic effects
dominant negative mutation
heterozygote produces nonfunctional altered protein that also prevents normal product
somatic mosaicism
mitotic errors after fertilization
gonadal mosaicism
only in egg or sperm
suspect if parents do not have disease
mosaicism survivable
McCune Albright
different muations at same locus
beta thalassemia
allelic heterogeneity
mutation at different loci produce similar phenotype
albinism
locus heterogeneity
heteroplasmy
mitochondrial-normal and mutated leading to variable expression
heterodisomy
heterozygous indicates meiosis I error
isodisomy
meiosis II error or postzygotic chromosomal duplication
individual with recessive when only one parent is carrier
uniparental disomy
HW assumptions
no mutation
natural selection not occurring
random mating
no net migration
Prader Willi
maternal imprint
paternal mutated
Angelman
paternal imprint
maternal mutated
genetics hypophosphatemic rickets
X linked dominant
same genetics as fragile X and Alport syndrome
genetics CF
AR on ch7
Phe508 deletion
pathophysiology CF
ATP-gated Cl channel retained in RER leading to increase intracellular Cl and increase Na reabsorption
increase immunoreactive trypsinogen
newborn screening CF
infection CF infancy vs adolescence
Staph aureus early
pseudomonas adolescence
infertility CF
absence of vas deferns
slows progression CF
ibuprofen
lyonization
female carriers variably affected depending on pattern of X inactivation
start weakness Duchenne
proximal
role dystrophin
anchor muscle fibers
connects intracellular cytoskeleton to transmembrane proteins alpha and beta dystroglycan
labs dystrophin
increase CK and aldolase
genetics myotonic type 1 dystrophy
CTG repeat in DMPK
AD
myotonia, muscle wasting, cataracts, testicular atrophy, frontal balding, arrhythmia
myotonic type 1 dystrophy
genetics fragile X
CGG on FMR1
X linked
leads to hypermethylation
macroorchidism, long face with large jaw, large everted ears, autism, mitral valve prolapse
fragile x syndrome
CAG repeat
huntington
GAA repeat
Friedreich ataxia
most common unbalanced Robertsonian translocation Downs
14 and 21
labs first trimester downs
increase nuchal transleucency and hypoplastic nasal bone
decrease PAPP-A
increase free beta hCG
second trimester labs
decrease alpha FP, increase beta hCG, decrease estriol, increase inhibin A
prominent occiput, rocker-bottom feet, intellecutal disability, non-disjunction, clenched fists, low set ears, small jaw, congenital heart disease
Edwards 18
labs edwards
decrease everything
severe intellectual disability, rocker bottom feet, microphthalmia, microcephaly, cleft lip/palate, holoprosencephaly, polydactyly, cutis aplasia, congenital heart sidease
patau
decrease everything in labs
ch 3
VHL, RCC
ch 4
ADPKD (2), achondroplasia, Huntington
ch 5
cri-du-chat syndrome, FAP
ch 6
hemochromatosis
ch 7
Williams syndrome, CF
ch 9
Friederich ataxia
ch 11
Wilms tumor, beta globulin defects (SCD, beta thal, men1)
ch 13
Patau, Wilson, Rb, BRCA2
ch15
Prader-Willi, Angelman, Marfan
ch16
ADPKD1, alpha globin defects
ch17
NF1, BRCA1, p53
ch18
Edwards
ch21
Down
ch22
NF2, DiGeorge
Robertsonian translocation
long arms of 2 acrocentric chromosomes fuse at centromere and 2 short arms are lose
unblaanced-miscarriage, stillbirth, and chromosomal imbalance
cardiac cri-du-chat
VSD
elfin facies, hypercalcemia, extreme friendliness
Williams syndrome
night blindness, dry skin, corneal degeneration, Bitot spots on conjunctiva
vitamin A def
acute vitamin A tox
N/V, vertigo, blurred vision
pseudotumor cerebri tox
vitamin A
teratogenic vitamin A
cleft palate, cardiac abnormalities
thiamine (B1)
pyruvate dehydrogenase
alpha ketoglutarate dehydrogenase
transketolase
branched-chain ketoacid dehydrogenase
diagnosis B1 def
increase RBC transketolase after B1 administration
B2 (riboflavin)
succinate dehydrogenase
B2 def
corneal vascularization and cheilosis
derivation niacin
from tryptophan
synthesis requires B2 and B6
severe b3 def
in Harnup disease, malignant carcinoid syndrome and isoniazid
pellagra symptoms
diarrhea, dementia, dermatitis
treatment hartnup
high-protein diet and nicotinic acid
b5 (pantothenic acid) def
dermatitis, enteritis, alopecia, adrenal insufficiency
function B6
transamination, decarboxylation, glycogen phosphorylation
b6 synthesis for
cystathonine, heme, niacine, histamine, NT (serotonin, epi, NE, dopa, GABA)
b6 def
convulsions, peripheral neuropathy, sideroblastic anemia
inhibition b7
avidin (from eggs)
used in carboxylase reactions
absorption folate
jejunum
labs folate def
increase homocysteine and normal methylmalonic acid
causes of folate def drugs
phenytoin, sulfonamides, methotrexate
cofactor methionine synthase and methylmalongyl-CoA mutase
b12
labs b12 def
increase homocysteine and methylmalonic acid
cofactor dopamine to NE
dopamine beta hydroxylase requires vitamin C
excess vitamin C
risk of iron toxicity
calcium oxalate nephrolithiasis
ergocalciferol
from plants D2
excess vitamin D in granulomatous disease
increase activation vitamin D by epithelioid macrophages
high dose vitamin E
alter vitamin K
enhanced effects of warfarin
vitamin E def
hemolytic anemia, acanthocytosis, muscle weakness, posterior column and spinocerebellar tract demyelination
looks like b12 def but without megaloblastic anemia
def predispose alcholic cirrhosis
zinc
kwashiorkor
protein malnutrition due to decrease plasma oncotic pressure, liver malfunction
marasmus
deficient in caloriesbut no nutrients entireley absent
muscle wasting
fomepizale
inhibits alcohol dehydrogenase
antidote for methanol or ethylene glycol
disulfuram
inhibits acetaldehyde dehydrogenase
kinetics alcohol dehydrogenase
zero order kinetics
ethanol metabolism
increase NADH/NAD ratio
leads to lactic acidosis, fasting hypoglycemia, hepatosteatosis
favors acetyl-CoA for ketogenesis
occurs in both mitochondria and cytoplasm
heme synthesis
urea cycle
gluconeogenesis
occurs in cytoplasm
glycolysis, HMP shunt, steroids, proteins, FA, cholesterol, and nucleotides
carboxylase
requires biotin
regulators of PFK1
+ AMP, F26BP
-ATP citrate
regulators F16BP
+ citrate
-AMP, F26BP
regulators isocitrate dehydrogenase
+ ADP
-ATP NADH
regulators glycogen synthase
+G6P, insulin, cortisol
-epi, glucagon
regulators G6PD
+ NADP
- NADPH
regulators CPS II
+ ATP, PRPP
-UTP
regulators CPS I
n-acetylglutamate +
acetyl CoA carboxylase
+ insulin +citrate
-glucagon, palmitoyl CoA
carnitine acyltransferase I
-malonyl CoA
HMG-CoA reductase
+insulin, thyroxine
-glucaagon, cholesterol
glycerol3phosphate
30 net ATP in muscle
arsenic glycolysis
produce zero net ATP
uses NADPH
anabolic processes
respiratory burst
cytochrome p450
glutathione reductase
glucokinase
in liver and beta cells of pancreas
induced by insulin
has higher Km (lower affinity)
not inhibited by G6P
fasting F26BP
increase PKA due to glucagon
increase FBPase 2 more gluconeogenesis
pyruvate dehydrogenase complex
thiamine pyrophosphate B1 lipoic acid CoA B5 FAD b2 NAD b3
arsenic
inhibits lipoic acid
leads to vomiting, rice-water stools, garlic breath, QT prolongation
findings pyruvate dehydrogenase complex def
neuro defects, lactic acidosis, increase alanine
treatment pyruvate dehydrogenase def
intake ketogenic nutrients
lysine and leucine
NADH enter mitohondria for ETC
malate-aspartate or glycerol 3 phosphate shuttle
FADH straight tocomplex II
rotenone
inhibits complex I
antimycin A
inhibits complex 3
CO/CN
inhibits complex 4
oligomycin
inhibits ATP synthase
uncoupling agents
2,4 dinitrophenol, aspirin, thermogenin in brown fat
even vs odd FA
odd makes 1 propionyl CoA
even cannot produce glucose due to only yielding acetyl CoA equivalents
sites HMP shunt
lactatin mammary glands, liver, adrenal cortex, RBCs
Heinz bodies
denatured hemoglobin within RBCs due to oxidative stress
defect fructokinase
essential fructosuria
fructose in blood and urine
deficiency aldolase B
fructose intolerance
decrease phosphate which inhibits glycogenolysis and gluconeogenesis
reducing sugar in urine
decrease fructose and glucose as treatment
galactokinase deficiency
cataracts
failure to track objects and develop social smile
absence glalactose1phosphate uridyltransferase
accumulation galactitol in lens of eye
failure to thrive
exclude galactose and lactose from diet as treatment
sorbitol to fructose
sorbitol dehydrogenase
glucose to sorbitol
aldose reductase
cells with only aldose reductase
retina, kidneys, Schwann cells
lactase
make glucose and galactose
stool lactase deficiency
decrease pH and breath increase hydrogen content
AA in proteins
L amino acids
essential AA
methioneine, histidien, leucine, lysine, isoleucine, phenylalanine, threonine, tryptophan
AA required during periods of growth
Arg and His
results hyperammonemia
depletes alpha ketoglutarate leading to inhibition TCA
benzoate, phenylacetate and phenylbutyrate MOA in hyperammonemia
react with glycine or glutamine
products renally excreted
increase orotic acid
decrease BUN
hyperammonemia
no megaloblastic anemia
ornithine transcarbamylase deficiency
products phenylalanine
tyrosine (thyroxine) dopa (melanin) dopamine NE epi
products tryptophan
niacin
serotonin (melatonin)
products glycine
prophyrin
heme
products arginine
creatine
urea
NO
defect homogentisate oxidase
alkaptonuria
defect phenylalanine hydroxylase
PKU
defect tyrosinase
melanin
PKU
decrease phenylalanine hydroxylase or TH4 cofactors
phenyl ketones
phenylacetate, phenyllactate, phenylpyruvate
treatment PKU
decrease phenylalanine and increase tyrosine
maple syrup disease
blocked degradation of branched AA (isoleucine, leucine, valine) due to decrease branched chain alpha ketoacid dehydrogenase
treatment maple syrup disease
restrictio of isoleucine, leucine, valine in diet
thiamine supplementation
deficieny of homogentisate oxidase
alkaptonuria
homogentisic acid accumulates
cystathionine synthase def
decrease methionine, increase cysteine and B6, B12 and folate in diet
methionine synthatse def
increase methionine in diet
findings homoxystinuria
increase homocysteine in urine osteoporosis marfanoid habitus ocular changes (down and in) cardio (stroke and MI) kyphosis and intellectual disability
cystinuria
defect in COLA reabsorption
leads to stones (urinary alk as treatment)
diagnostic test cystinuria
cyanide-nitroprusside test
limit dextrin
1-4 residues remaining on a branch after glycogen phosphorylase has shortened it
incrased glycogen in liver, increased blood lactate, increase triglycerides, increase uric acid and hepatomegaly
Von Gierke
defect in G6P
treatment von Gierke
frequent oral glucose or cornstarch
avoid fructose and galactose
cardiomegaly, hypotonia, exercise intolerance
Pompe
lysosomal alpha 1-4 glucosidase
limid dextrin like in cytosol
normal lactate levels
debranching enzyme alpha 1,6
Cori disease
increase glycogen in muscle
cramps and myoglobinuria and arrhythmia
myophosphorylase
McArdle disease
second wind phenomenon
due to increase muscular blood flow
found in McArdle disease
cherry red spot without hepatosplenomegaly
Tay Sach
deficient hexosaminidase A
GM2 ganglioside builds up
Fabry disease
episodic peripheral neuropathy, angiokeratomas, hyphohidrosis
later-renal failure, cardiovascualr disease
defect Fabry
alpha galactosidase A
ceramide trihexoside builds up
defect metachromatic leukodystrophy
arylsulfatase A
cerebroside sulfate builds up
peripheral neuropathy, developmetnal delay, optic atrophy, globoid cells
Krabbe due to defect in galactocerebrosidase
buildup of galactocerebroside and psychosine
pancytopenia, osteoporosis, avascular necrosis, bone crisis and lipid laden macrophages
Gauche due to defect in glucocerebrosidase
hepatosplenomegaly, foam cells, cherry red macula
NPC from defect in sphingomyelinase
corneal clouding and hepatosplenomegaly
Hurler du to alpha L iduronidase def
hunter
no corneal clouding and has aggressive behavior
iduronate sulfatase def
increased in Ashkenazi Jews
NPC, Tay Sachs, Gaucher
X linke lysosomal
hunter and Fabry
required for FA synthesis
citrate to transport from mitochondria to cytosol
in liver, lactating mammary glands and adipose
required for FA degradation
carnitine
systemic primary carnitine def
weakness, hypotonia, hypoketotic hypoglycemia
defect in transport of LCFAs
accumulation fatty acyl carnitines in blood
medium chain acyl CoA dehydrogenase def
avoid fasting
depleted oxaloacetate
in starvation and DKA
leads to buildup of acetyl CoA which shunts glucose and FFA toward ketones
urine test ketones
acetoacetate
source of energy for brain after 3 days of starvation
ketones
pancreatic lipase
degrade dietary triglycerides
lipoprotein lipase
degrades TG in chylomicrons and VLDL
found on vascular endothelial surface
hepatic TG lipase
degrades TG remaining in IDL
LCAT
esterification of 2/3 plasma cholesterol
cholesterol ester transfer protein
mediates transfer of cholesterol esters to other lipoprotein particles
activates LCAT
A1
lipoprotein lipase cofactor that catalyzes cleavage
C-II
mediates chylomicron secretion into lymphatics
B-48
binds LDL R
B-100
alcohol increase synthesis
HDL
abetalipoproteinemia
absent chylomicrons, VLDL, LDL def apoB
findings abetalipoproteinemia
retinitis pigmentosa, spinocerebellar degeneration due to bitamin E deficiency, ataxia, acanthocytosis
treatment abeta
restrict long chain FA
large dose vitamin E
hyperchylomicronemia
defect in CII or lipoprotein lipase
findings hyperchylomicronemia
pancratitis, hepatosplenomegaly, xanthomas
creamy layer in supernatant
familial hypercholestrolemia
defective LDL receptors
findings familial hypercholestrolemia
accelerated atehrosclerosis, tendon xanthomas and corneal arcus
dysbetalipoproteinemia
defective ApoE
findings dysbetalipoproteinemia
preamture atherosclerosis
xanthoma striatum palmare
hypertriglyceridemia
overproduction of VLDL
findings hypertriglyceridemia
hyhpertriglyceridemia
can cause pancreatitis