Biochemistry Flashcards
1
Q
what does methylation do to DNA
A
makes it mute- no transcription
2
Q
acetylation of DNA
A
makes it active
3
Q
which two bases get methylated on template strand?
A
cytoskine and adenine
4
Q
3 amino acids needed for purine synthesis
A
glycine, aspartate, glutamine
5
Q
leflunomide
A
this inhibits dihydroorotate dehydrogenase so you can’t convert carbamoyl phosphate to orotic acid
6
Q
problem in orotic aciduria
A
can’t convert orotic acid to UMP
7
Q
hydroxyurea
A
inhibits ribonucleotide reductase. can’t convert UDP to dUDP
8
Q
5FU
A
inhibits thymidiylate synthase. can’t convert dUMP to dTMP
9
Q
MTX/ TMP and pyrimethamine
A
inhibits dihydrofoalte reductase in humans, bacteria and protozoa respectively.
10
Q
6MP
A
inhibits purine synthesis
11
Q
Mycofenolate and ribavarin
A
inhibits IMP dehydrogenase so can’t make purines
12
Q
amino acid required for pyrimidine base production
A
aspartate
13
Q
adenosine deaminase deficiency
A
excess ATP and dATP because can’t convert adenosine to inosine. makes you go through the pathway one way. major cause of autosomal recessive SCID. via negative feedback you get a reduction in activity of ribonucleotide reductase- decreased lymphocyte count
14
Q
Lesch Nyhan syndrome
A
defective purine salvage due to absent HGPRT. this means you can’t recover them and you end up dumping many more into xanthine then into uric acid. also get increased de novo purine synthesis.
15
Q
genetics of Lesch Nyhan
A
x linked recessive
16
Q
findings in lesch nyhan
A
intelectual disability, self mutilfation, aggresion, hyperuricemia, gout, dystonia
17
Q
difference between DNA pol I and III
A
DNA pol I has an ability to excise the RNA primer in the 5-3 direction- its an exonuclease
18
Q
Which is the polymerse (DNA) that is seen in eukaryotes
A
DNA pol III
19
Q
what is the order of the danger of mutations
A
some men never finish
silent< frameshift
20
Q
disease that is a problem with nucleotide excision repair
A
defective in xeroderma pigmentosum which prevents repair of pyrimidine dimers because of UV light exposre
21
Q
disease that results from a problem with mismatch repair
A
HNPCC-
22
Q
how does base excision repair work
A
AP endonuclease leaves the 5’ end
lyase cleaves the 3’ end
DNA polymerase beta fills the gap
DNA ligase seals it
23
Q
disease from a problem with non homologous end joining
A
ataxia telangiectasia
24
Q
what direction is DNA or RNA read
A
5 to 3
25
mRNA start codons
AUG
26
what is the start codon also indicate (which amino acid)
methionine in eukaryotes and formeylmethionine in prokaryotes
27
mRNA stop codons
U go away
U are away
U are gone.
UGA
UAA
UAG
28
what does rna polymerase I make
rRNA
29
what does rna polymerase II make
mRNA. the most massive.
30
what does rna polymerase III make
tRNA
31
how does alpha amanitin in amanita phalloides (mushroom) make people sick
inhibits RNA pol II. severe hepatotoxicity if ingested
32
how is RNA pol different in prokaryotes from eukaryotes
only one in prokaryotes. 3 in eukaryotes.
33
where do the post transcriptional modifications like caping of the 5' end, polyadenylation and splicing of introns occur?
in the nucleus following transcription
34
what is the mRNA called before it is processed
hnRNA or heterogenous nuclear RNA
35
what are P bodies
mRNA quality control- contain decapping enzymes, endonucleases etc.
36
what diseases are anti splicesome antibodies associated with
anti Smith - lupus
| anti U1 RNP - mixed connective tissue disease
37
disease from abnormal splicing (genetic)
beta thal
38
which end of the tRNA is the amino acid bound?
CCA on the 3' end. "can carry aminoacid"
39
T arm of tRNA
binds to the ribosome
40
D arm of the tRNA
allows for recognition of the right aminoacul tRNA synthetase.
41
what is responsible for the accuracy of amino acid selection
amionacyl tRNA synthetase and binding of charged tRNA to the codon
42
what is the function of aminoacyl tRNA synthetase
to add the amino acid to the tRNA molecule
43
energy source for tRNA activation
ATP
44
energy source for tRNA translocation
GTP
45
function of P53 and rb in cell cycle
they are normally present to inhibit G1 to S migration.
46
Li-Fraumeni syndrome
this is a mutation in the Rb or P53 genes such that there is unrestrained cell division
47
cell type- neurons, skeletal muscle, cardiac muscle and RBCs
permanent
48
stable but quiescent cells
Heptocytes and lymphocytes. normally in Go but can enter G1 if stimulated to do so
49
I cell disease
inherited lyososomal storage disorder. defect in phosphotransferase which means failure of the golgi to phosphorylate mannose residues (doesn't put the mannose 6 phosphate on that would signal it to the lysosome) so the proteins are excreted instead of being sent to the lysosomes. coarse facial features, clouded corneas, restricted joint movement, high plasma levels of lysosomal enzymes. fatal.
50
proteins accumulating in the cytoplasm?
signal recognition particle (SRP) absent or dysfunctional. this normally traffics to the rough ER
51
COPI I
golgi to golgi or golgi to ER
52
COPI II
golgi to golgi or ER to golgi
53
Clathrin
trans golgi to lysosomes or endosomes or plasma membrane.
54
kartagener syndrome
this is primary ciliary dyskinesia. immotile cilia due to a dynein arm defect. results in infertility, immotile sperm, fallopian tube issues, bronchiectasis, recurrent sinusitis, situs inversus
55
vimentin
connective tissue
56
Desmin
muscle
57
cytokeratin or keratin
epithelium
58
GFAP
neuroglia
59
Neurofilaments
neurons
60
type I collagen
most abundant. bone, skin (dermis), tendon, dentin, fascia, cornea, scar
61
deficiency in type I collagen
osteogenesis imperfecta
62
Type II collagen
cartilage, vitreous body, nucleus pulposus
63
Type III collagen
reticulin, epidermis, blood vessels, uterus, fetal tissue, kidney, GRANULATION TISSUE
64
deficiency in type 3 collagen?
EDS vascular type
65
Type IV collagen
basement membrane, basal lamina, lens
66
problem wit type IV collagen
defective in alport syndrome. targeted by antibodies in good pasture syndrome
67
what is the most common aa in collagen
glycine
68
what are the other two aa in collagen
proline and lysine
69
what disease has an issue with collagen hydroxylation
scurvy. hydroxylation of specific proline and lysine residues. requires vitamin C.
70
what disease has a problem with glycosylation of collagen
pro alpha chain is turned into pro-collagen via hydrogen and disulfide bonds. this turns it into a triple helix called procollagen. problems with this are seen in osteogenesis imperfecta
71
proteolytic cleavage of collagen
cleavage of disulfide rich terminal regions of procollagen turning it into insoluble tropocollagen.
72
cross linking of collagen
re-inforcement of many staggered tropocollagen molecules by lysyl oxidase. requires Cu as a co factor to make the collagen fibrils. this is defective in EDS and menkes disease.
73
what is the most common problem in osteogenesis imperfecta
decreased production of otherwise normal collagen type 1
74
pneumonic for Southern, Western, Northern blot
SNoW DRoP
75
indirect ELISA tests for
antigen
76
direct ELISA test for
antibody
77
pleiotropy
one gene effects multiple phenotypes like PKU causing light skin, intellectual issues and musty body odor
78
locus heterogeneity
mutations at different loci can produce a similar phenotype like with albinism
79
allelic heterogeneity
different mutations in the same locus produce the same phenotype such as with beta thal
80
prader willi
chromosome 15. paternal is deleted or mutated while maternal is imprinted. can be caused by maternal uniparental disomy
81
angelman syndrome
chromosome 15. maternal is deleted or mutated and paternal is imprinted.
82
symptoms of angelman syndrome
seizures, atazxia and severe intellectual disability with inappropriate laughter- always happy puppet
83
AD mutations are usually
defects in structural genes
84
AR mutations are usually...
cause enzyme deficiency
85
myopathy with ragged red fibers
this is mitochondrial myopathy- myopathy with lactic acidosis, failure in oxidative phosphorylation.
86
huntington disease chromosome
4
87
PKD1 mutations in ADPKD chromosome
number 16
88
PKD2 mutations in ADPKD chromosome
number 4
89
FAP chromosome
5
90
hereditary hemorrhagic telangiectasia
also known as osler weber rendu syndrome- inherited blood vessel disorder- telangiectasia, recurrent epistaxis, skin discoloration, avms, GI bleed, hematuria,
91
neurofibromatosis type 1 mutation
NF1 gene on chromosome 17
92
neurofibromatosis type 2 mutation
NF2 on chromosome 22
93
what is unique about tuberous sclerosis
incomplete penetrance with variable expression- numerous benign hamartomas.
94
Von hippel lindae disease
chromosome 3 mutation
95
what is the mutation in CF
delta 508 mutation - phenylalanine deletion.
96
treatment for CF
N acetylcystine to break up the mucous plugs and dornase alfa (DNAse) to clear leukocytic debris
97
pneumonic for X linked recessive
He Said He Only Fought With GOLD B
98
mutation in duchene muscular dystrophy
frameshift mutation. truncated dystrophin protein. get pelvic girdle muscle weakness first and then it spread. fibro fatty replacement of muscles.
99
gower maneuver
patients with duchene muscular dystrophy use their hands to help them stand up
100
common cause of death in duchene muscular dystrophy
dilated cardiomyopathy
101
function of dystrophin
anchors muscle fibers, primarily in skeletal and cardiac msucle. connects intracellular cytoskeleton (actin) to the transmembrane proteins alpha and beta.
102
lab values elevated in duchene muscular dystrophy
increased CPK and aldolase
103
Becker muscular dystrophy
this is an X linked point mutation in dystrophin gene (not a frameshift like in duchene. both can be caused by a deletion.
104
myotonia, msucle wasting, frontal balding, cataracts, testicular atrophy and arrythmia
myotonic type 1 dystrophy. this is a CTG repeat.
105
large testicles, long face, large jaw, large everted ears, autism, MVP
fragile X syndrome
106
4 trinucleotide repeat diseases
Huntington, fragile X, mytotonic dystrophy, friedrich ataxia
107
mutations causing downs syndrome
non disjunction in meiosis 1 > RObertsonian translocation > mosaicism (no maternal association, post fertilizaton mitotic error)
108
first trimester findings in downs
increased nuchal translucency, decreased PAPP A and increased bHCG
109
findings in edwards syndrome
this is trisomy 18. rocker bottom feet, small jaw, cross-over of fingers, low set eras, prominent occiput, congenital heart disease. low PAPP A and low BHCG
110
findings in patau syndrome
rocker bottom feet, micropthalmia, microcephaly, cleft lip, cleft palate, holoprosencephaly, poydactylyl, congenital heart disease. increased nuchal tranlucency but decreased bHCG and decreased PAPP A
111
what types of chromosomes do you see robertsonian trans locations on
acrocentric chromosomes - centromeres near the end. if balanced, then no problem. the issue is with unbalanced.
112
cri du chat
chromosome 5. microcephayl, moderate to severe intellectual issues, high pitched crying/mewing, epicanthal folds, cardiac abnormalities like VSD.
113
what chromosome is responsible for Williams syndrome
7
114
what mutation is responsible for DiGeorge syndrome and Velocardiofacial syndrome
22q11. due to abberant development of the 3rd and 4th branchial pouches.
115
which vitamin prevents squamous metaplasia
vitamin A
116
what two diseases can be treated with vitamin A
measles and AML subtype M3 (APL)
117
what is keratomalacia
thickening of the cornea from vitamin A deficiency
118
three things thiamine is used for
ATP so alpha ketoglutarate dehydrogenase, Transketolase and pyruvate dehydrogenase
119
how to test for Wernike Korsakoff syndrome
increased RBC transketolase with B1 administration
120
classic triad of Wernike Korsakoff
confusion, opthalmoplegia, ataxia
121
vitamin used in succinate dehydrogenase reaction
riboflavin B2
122
two things deficiency of B2
chelosis and corneal vascularization
123
what vitamin can you treat lipid issues with
niacin. reduced VLDL and increases HDL
124
what is needed to make thiamin?
derived from tryptophan, need B2 and B6
125
diseases that can cause pellagra
this is a vitamin B3 deficiency.
hartnup disease (tryptophan decreased absorption)
malignant carcinoid syndrome
isoniazid
126
niacin toxicity
facial flushing from prostaglandins
127
vitamin for coA
pantothenate
128
vitamin that is for transamination reactions
B6
129
vitamin assocaited with carboxylation
B7 or biotin
130
deficiency of biotin
rare- antibiotic use or ingestion of raw egg whites
131
how to differentiate B12 def from folate
folate normal MMA and B12 has increased MMA
132
3 drugs that can cause folate deficiency
MTX, sulfonamides, phenytoin
133
bug that likes to eat B12
diphyllobothrium latum
134
what two things require vitamin C
hydroxylation of lysine and proline for collagen synthesis and conversion of dopamine to nor epi. this is the dopamine Beta hydroxylase enzyme
135
what can you use vitamin C to treat
methemoglobinemia- converts Fe3+ to Fe2+
136
what two things are not in breast milk
vitamin D and vitamin K
137
neurologic symptoms of B12 deficiency but NO megaloblastic anemia (hemolytic anemia instead)
think about vitamin E deficiency
138
two reactions that alcohol pushes
it increases NADH so it pushes pyruvate to lactate and oxaloacetate to malate. both of these reactions require NADH and push you away from gluconeogenesis. also make more glycerol 3 phosphate.
139
fomepizole
inhibits alcohol dehydrogenase
140
disulfram
inhibits acetaldehyde dehydrogenase- makes you sick bc the acetaldehyde is not pleasant.
141
glucokinase
found in liver and beta cells of the pancreas. high Km (means low affinity) and high V max means high capacity. not inhibited by G6P and it is induced by insulin. it is what is responsible for MODY diabetes
142
5 enzymes required for pyruvate dehydrogenase
Thiamine TPP, FAD, NAD, CoA and Lipoic acid
143
how does arsenic work
this inhibits the lipoic acid so you make no ATP. produces garlic breath, vomiting and rice water stools.
144
pyruvate dehydrogenase deficiency
buildup of pyruvate that leads to alanine increase and increase in lactic acid production. treat with lysine and leucine- only purely ketegenic amino acids
145
what is pyruvate carboxylase
this is the enzyme that converts pyruvate to oxaloacetate for gluconeogenesis. requires biotin.
146
what inhibits complex 1 in ETC
rotenone
147
what inhibits complex III in ETC
antimycin A
148
what inhibits complex IV in ETC
cyanide, CO
149
what inhibits complex V in ETC
oligomycin
150
what is complex 2
succinate dehydrogenase (part of the krebs cycle)
151
what is oligomycin
ATP synthase inhibitor
152
2,4 dinitrophenol
this is used as an uncouplig agent- illegally for weight loss. aspirin toxicity can also cause this as can thermogenin in brown fat
153
where is glucose 6 phosphatase located
in the ER. turns glucose 6 phosphate into glucose
154
do even or odd chain fatty acids get used for gluconeogenesis
only odd chain fatty acids can be used. even ones are broken down to only yield acteyl CoA
155
first enzyme in respiratory burst that is defective in CGD
NADPH oxidase.
156
second enzyme in oxidative burst
superoxide dismutase
157
third enzyme in oxidative burst
myeloperoxidase.
158
in orer to break down H2O2 you need glutathione redutctase. what element does this require
selenium
159
essential fructoseria
defect in fructokinase. this is basically asymptomatic
160
fructose intolerance
this is a deficiency in aldolase B so you have a buildup of fructose 1 P and this makes peope sick. hypoglycemia, vomiting, cirrhosis.
161
how to treat fructose intolerance
no fructose or sucrose (fructose plus glucose)
162
galaktokinase deficiency
this basically leads to a buildup of galactose which can be converted to galactitol. may cause infantile cataracts which present with failure to follow a finger
163
classic galactosemia
absence of galactose i phosphate uridyltransferase. accumulation of galactitol and galactose 1 phosphate. can lead to sepsis with Ecoli in neonates
164
treatment of classic galactosemia
eclude galactose and lactose from the diet. lactose = glucose plus galactose.
165
aldose reductase
converts glucose to sorbitol
166
sorbitol dehydrogenase
converts the sorbitol into fructose
167
cells that do not have sorbitol dehydrogenase and therefore get a buildup of sorbital
schwann cells, retina, and kidneys. lens has very little
168
essential amino acids that are glucogenic only
methionine, histmaine, valine
169
essential amino acids that are ketogenic only
lysine and leucine
170
essential amion acids that are both glucogenic and ketogenic
isoleucine, phenylalanine, tryptophan and threonine
171
which amino acid is the most basic
arginine
172
which amino acid has no charge in the body but is basic
histmaine
173
function of ornithine transcarmylase
takes carbamoyl phosphate plus ornithine and makes citruline as part of the first step in the urea cycle
174
what is an important cofactor for the carbamoyl phosphate synthetase I reaction?
N acetylglutamate
175
what enzyme is defective in phenylketonuria
phenylalnine hydroxylase and or tetrahydrobiopterin cofactor (malignant pKU). tyrosine becomes essential in this disease.
176
symptoms of pKU
intellectual issues, growth retardation, seizures, fair skin, eczema, musty or mousy body odor
177
what is alkaptonuria
this is a congenital defect in homogentisate oxidase which is part of the pathway to breakdown tyrosine to fumarate
178
findings in alkaptonuria
dark conenctive tissue, brown pigmented sclerae, urine that turns black on prolonged exposure to air. may get arthalgias
179
homocystinuria
this is either a problem with cystathione synthase or homocystine methyltransferase
180
findings in homocystinuria
homocystine in the urine, intellectual issues, osteoporosis, tall stature, kyphosis, lens subluxation (down and inward), thrombosis and atherosclerosis.
181
cystinuria defect
defect in the proximal convoluted tubule and can't recover COLA
cysteine, ornithine, lysine, and arginine
excess cystine in the urine can lead to hexagonal cystine stones
182
what does urinary cyanide nitroprusside test diagnose
cystinuria
183
what is cystine
this is made by two cysteines connected with a disulfide bond
184
maple syrup urine disease
can't break down chain amino acids because of a problem with alpha ketolutarate dehydrogenase. this requires b1 normally. increase in alpha ketoacids in the blood. branched ones are isoleucine, leucine and valine
185
increased ornithine with otherwise normal urea cycle enzymes and hyperammonemia
this is most likely N acetylglutamate deficiency
186
increased orotic acid in blood and urine
check for megaloblastic anemia- this is orotic aciduria and if not, then check for decreased BUN and increased ammonia levels- ornithine transcarbamylase deficiency
187
why does ornithine transcarbamylase deficiency cause increased orotic acid
because there is excess carbamoyl phosphate which can be converted to orotic acid in part of the pyrimide synthesis pathway.
188
what does phenylalnine make
tyrosine, then dopa, then dopamine, then NE and epi
189
what does tryptophan make
seratonin and niacin
190
what does histadine make
histamine
191
what does glycine make
porphyrin (heme)
192
what oes glutamate make
glutathione and GABA
193
what does arginine make
creatine, urea and NO
194
what is the enzyme deficiency in albinism
tyrosinase which is converting dopa to melanin
195
enzyme deficiency in Von Gierke
glucose 6 phosphatase. severe fasting hypoglycemia, increased glycogen in the liver, increased blood lactate
196
enzyme deficiency in Pompe disease
alpha 1,4 glucosidase (this is the enzyme in the lysosomes that breaks down some glycogen) acid maltase. leads to cardiomyopathy and systemic findings
197
cori disease enzyme deficiency
alpha 1,6 glucosidase- this is the debranching enzyme that removes the last glycogen. milder disease with normal blood lactate levels. gluconeogenesis is intact
198
enzyme deficiency in mcardle disease
glycogen phosphorylase in skeletal muscle. this is a muscle disease. it is also known as myophosphorylase. leads to increased glycogen in the muscle that cannot be broken down.
199
fabry enzyme deficiency
alpha galactosidase A
200
what builds up in fabry
ceramide trihexodase
201
gauchers disease- enzyme deficiency
glucocerebrosidase (beta glucosidease)
202
gauche what builds up
glucocerebroside
203
symptoms of gauche-
lipid laden macrophages, hepatomegaly, pancytopenia, aseptic necrosis of the femur, bone crises
204
enzyme deficiency in Neimen pick
sphingomyelinase
205
what builds up in Neimen pick
sphingomyelin
206
symptoms of neimen pick
progressive neurodegeneration, cherry red macula, foam cells- lipid laden macrophages
207
enzyme deficiency in tay sachs
Hexosaminidase A
208
what builds up in tay sachs
Gm2 ganglioside
209
symptoms of tay sachs
cherry red spot on the macula and lysosomes with onion skin, NO HEPATOSPLENOMEGALY (contrast to Neimen pick)
210
krabbe disease enzyme deficiency
galactocerebrosidase
211
krabbe dsiease- what builds up
galactocerebroside and pyshocine
212
metachromatic leukodystrophy what enzyme is deficient
arylsulfatase A
213
metachromatic leukodystrophy what builds up
cerebroside sulfate
214
enzyme deficiency in hurler syndrome
alpha L iduronidase
215
enzyme deficiency in hunter syndrome
iduronate sulfatase
216
what builds up in hunter and hurler syndrome
heparan sulfate and dermatan sulfate
217
how to differentiate hunter and hurler
hunters see clearly (no corneal clouding) and it is X linked recessive
218
liproprotein lipase deficiency or CII alteration
this causes type 1- hyper--chylomicronemia. causes pancreatitis, hepatosplenomegaly and xanthomas
219
defective LDL receptors
this causes type 2a familial hypercholesterolemia. they get very high LDL and cholesterol- heart attacks at an early age etc. can have tendon xanthomas and corneal arcus
220
hepatic overproduction of VLDL
this is type 4 hypertriglyceridemia. you get an increase in VLDL and TG. it can cause pancreatitis.
221
what is B48 for?
this is a marker for chylomicron secretion- on chylomicrons and chylomicron remnants
222
B100 marker
this is somethign that binds to the LDL receptor. it is on the VLDL, LDL and IDL
223
what is CII marker for?
this is a cofactor for lipoprotein lipase. it is on chylomicrons and VLDL. it is also in HDL.
224
what is A1 for?
this activates LCAT which esterifies the cholesterol and turns iit into mature choelsterol. found just on the chylomicron and HDL. mostly an HDL thing.
