Biochemistry Flashcards
DNA vs. histone methylation
DNA - template strand = methylated to label it as “old”; transcription suppressor
Histone - reversible repression of DNA transcription, may activate transcription in some cases
Cytosine, Uracil, Thymine
Pyrimidines
Deamination of C makes U
U is in RNA, T is in DNA
De novo pyrimidine vs. purine synthesis
Purine: sugar + phosphate, then add base
Pyrimidine: Make temporary base, add sugar and phosphate, then modify base
Purine salvage deficiencies
Adenosine deaminase deficiency - Excess ATP –> feedback inhibition of ribonucleotide reductase –> decreased DNA synthesis, especially in lymphocytes –> SCID
Lesch-Nyhan syndrome: defective purine salvage b/c HGPRT is absent –> excess uric acid and de novo purines (hyperuricemia, gout, aggression, ID, dystonia); tx = allopurinol or febuxostat
Nucleotide vs. base excision repair
Nucleotide: swap whole nucleotide due to bulky lesion
Base: leave phosphate-sugar backbone and swap base
Xeroderma pigmentosa
Defective nucleotide excision repair prevents repair of thymidine dimers from UV
HNPCC
Hereditary non-polyposis colorectal cancer - defective mismatch repair
Ataxia telangectasia
Neurodegenerative disease –> poor coordination, weakened immune system, increased cancer risk
Due to mutated nonhomologous end joining
RNA polymerases
Eukaryotes:
Pol I makes rRNA
Pol II makes mRNA (inhibited by alpha-amanitin)
Pol III makes tRNA
tRNA structure and charging
Amino acid binds to CCA at 3’ end
T-arm binds ribosome
R-arm for recognition by aminoacyl-tRNA synthetase (charging)
Post-translational protein modifications
Trimming - remove N- or C-terminal propeptides
Covalent alterations: phosphorylation, glycosylation, hydroxylation, methylation, acetylation, ubiquitination
Hetero vs. euchromatin
Hetero = condensed and transcriptionally inactive
Eu = less condensed, transcriptionally active
Lead poisoning
inhibition of several enzymes involved in heme synthesis, including the enzyme aminolevulinic acid dehydratase. This leads to the accumulation of various products in the heme synthesis pathway, causing the patient to develop a lead-induced porphyria.
Loss of developmental milestones and abdominal sx
In adults: basophilic stippling, anemia due to lack of fxal hemoglobin (inhibits synthesis of heme by blocking delta-aminolevulinic acid dehydratase and decrease iron incorporation into heme); inherited defects in same enzyme can –> peripheral neuropathy and photosensitivity
NF2
Bilateral Schwannomas/acoustic neuromas, Schwannomas, Meningiomas
NF1
Iris hamartomas (Lisch nodules), cafe au lait spots, neural tumors, skeletal disorders (eg scoliosis)
Niemann-Pick disease
autosomal recessive
deficiency in sphingomyelinase –> accumulation of sphingomyelin –> hepatomeg, failure to thrive, neurodegen
Common in Ashkenazi
Gaucher disease
autosomal recessive
Glycogen storage disease
deficiency in glucocerebrosidase –> accumulation of glucocerebroside in brain, liver, spleen, and marrow
bone crises, hypersplenism, hepatosplenomeg
Hunter syndrome
Deficiency in iduronate sulfatase
Coarse facial features, aggressive social behavior, pearly skin lesions on scapulae
Similar to Hurler syndrome (alpha-L-iduronidase, but hurler has corneal clouding
Hurler = similar in presentation to Sly syndrome (defect in beta-glucoronidase)
Morquio syndrome
Deficiency in galactosamine-6-sulfatase or beta-galactosidase
Diag around 1yo, short stature, joint laxity, musculoskel problems
Sanfilippo syndrome
Enzyme def include sulfamidase
CNS sx (aggressiveness, hyperactivity)
Muscular dystrophies
Becker’s = X-linked recessive, less severe than Duchenne’s (frameshift mutation –> dysfxal dystrophin protein and inhibited muscle regeneration in skel and heart muscle –> myonecrosis)
Myotonic type 1 = autosomal dominant, CTG trinucleotide repeat in DMPK gene –> myotonia, muscle wasting, cataracts, testicular atrophy, frontal balding, arrhythmia
Adenosine deaminase deficiency
SCID
Part of purine salvage pathway, so without it, B and T lymphocytes especially can’t make DNA
G6PD deficiency
X-linked recessive
NADPH is a cofactor for glutathione reductase, so without it, can’t reduce peroxides
Erythrocytes especially susc to oxidative stress, can be triggered by sulfa drugs or bacterial infxns –> HEINZ BODIES (denatured Hgb) and BITE CELLS
G6PD converts glucose-6-P to 6-phosphogluconolactone (RLS of pentose phosphate) so without it, no pentose phosphate, no NADPH, and thus no reduced form of glutathione to detox ROS
Von Gierke’s disease
Glucose-6-phosphatase deficiency (glycogen storage disease)
Presents in infancy with hypoglycemia, seizures, hepatomeg, lactic acidosis
Usually presents when babies start spending more time “fasting” between meals
Nitroblue tetrazolium dye reduction test
Diag chronic granulomatous disease (neative result indicates lack of ROS and presence of dz)
can also use dihydrorhodamine flow cytometry to look for fluor green pigment (conversion of DHR to rhodamine if NADPH oxidase = present)
Chronic granulomatous disease
Deficiency in NADP oxidase
Increased susc to catalase positive organisms
McArdle’s disease
Deficiency in glycogen phosphorylase in skeletal muscle –> can’t break glycogen down and get muscle cramps and myoglobinuria with exercise
Trinucleotide repeat diseases
Huntington’s (CAG on chrom 4)
Myotonic dystrophy (CTG on chromosome 19) - AD, late childhood - gait abnormalities and atrophy of facial muscles
Fragile X (CGG on X chromosome) - ID
Friedrich’s ataxia (GAA on chrom 9) - AR, cardiomyopathy
“Blots”
Southern = DNA Northern = RNA Western = protein
Homocystinuria
ID, marfanoid habitus, lens subluxation, thromboembolus
Cystathione synthase (uses B6) or methionine synthase problem
PKU
Phenylalanine hydroxylase deficiency
ID, musty body odor, growth retardation, fair skin, eczema
alpha1-antitrypsin deficiency
protein usually inhibits neutrophil elastase in the lung, so without it there’s excess elastase –> destroys elastin and collagen in lungs, liver –> emphysema
Adenosine deaminase deficiency
Can’t break down ATP pand dATP, which feedback inhibit ribonucleotide reductase, preventing pyrimidine production –> decreased lymphocytes (SCID)
Lesch-Nyhan defect
HGPRT
can’t convert hypoxanthine to PRPP, so keep running purine de novo pathway –> excess uric acid and purines
treat with allopurinol or febuxostat
allopurinol/febuxostat
inhibit xanthine oxidase, decreasing conversion of hypoxanthine and xanthine to uric acid (used in gout and lesch-nyhan)
leflunomide
inhibits dihydroorotate dehydrogenase, which converts carbamoyl phosphate to orotic acid (temporary base used in pyrimidine synth)
used to decrease dna synthesis and thus get rid of lymphocytes in RA and psoriatic arthritis
mycophenolate, ribavirin
inhibit IMP dehydrogenase, so don’t convert IMP to GMP,
myco –> decreasing lymphocytes to prevent organ rejection
ribavirin acts as guanosine analog and decreases viral replication in RSV, HCV etc
hydroxyurea
inhibits ribonucleotide reductase, so don’t convert UDP to dUDP and pyrimidines
used to treat SCD (increases HbF) and myeloproliferative disorders
6-mp and azathioprine
inhibit de novo purine synth
treat IBD and chemo for leukemia
5-FU
inhibits de novo pyrimidine synth by inhibiting thymidylate synthase (no dUMP to dTMP) - chemo
Chain termination
drugs etc that have modified OH on the nucleotide base, so that when the nucleotide is incorporated into dna, it can’t attack the incoming nucleotide’s triphosphate, and thus can’t elongate the chain
Protein synthesis direction?I
N terminus to C terminus
Anti-u1 RNP antibodies
Mixed DT disease
Antibodies to spliceosome proteins
Vs anti-smith in SLE (anti-snrps)
Vesicular trafficking proteins
COPI: retrograde (eg Golgi to Golgi, or Golgi to ER)
COPII: anterograde (eg cis-Golgi, or ER to golgi)
Clathrin: (trans-golgi to endosome, or receptor mediated endocytosis)
I-cell disease
defect in N-A-1-phosphotransferase, so can’t get phosphate onto mannose, which means those proteins don’t get into lysosomes
junk builds up inside lysosomes –> inclusion bodies
and lysosomal enzymes float around in plasma
Drugs that act on MTs
Microtubules Get Constructed Very Poorly
Mebendazole (anti-helminth) Griseofulvin (antifungal) Colchicine (antigout) Vincristine/vinblastine (anticancer) Paclitaxel (anticancer)
Osteogenesis imperfecta
aka brittle bone dz
problems forming triple helix of collagen (glycosylation step in fibroblasts –> H and disulfide bonds that allow triple helix to form)
so collagen that is there is normal, just not much of it
autosomal dominant
Collagen synthesis
RER of fibroblasts: translation (1/3 glycine), hydroxylation (requires vit C), and glycosylation (make H and diS bonds for triple helix formation) –> exocytosis
–> proteolytic cleavage of diS terminal regions –> insoluble tropocollagen –> crosslinking (by lysyl oxidase)
Problems with collagen crosslinking –>
Ehlers-Danlos and Menkes (X linked recessive, copper problem)
Variable expressivity vs incomplete penetrance
VE - same genotype can –> different phenotypes (eg NF1 varying severity of syndrome)
IP - same genotype can lead to phenotype in some people, no phenotype in others (not varying severity; eg brca1)
pleiotropy example
phenylketonuria (one gene –> multiple phenotypic effects; here, light skin, musky BO, ID)
example of mosaicism
mccune-albright (affects g protein signaling) - unilateral cafe au lait spots, fibrous dysplasia, precocious puberty, multiple endo abnormalities
Example of locus heterogeneity
albinism (mutations at different loci –> same disease)
Example of allelic heterogen
beta-thal (different mutations at same locus –> same dz)
heteroplasmy
presence of both normal and mutated mtDNA
Prader-Willi vs Angelman
chromosome 15
prader-willi = maternal imprinting (gene from mom is usually silent, so paternal gene = screwed up) –> hyperphagia, obesity, ID, hypogonadism, hypotonia
Angelman = paternal imprinting (gene from dad is usu silent and mom’s gene is deleted/mutated) –> inappropriate laughter, seizures, ataxia, severe ID
Autosomal dominant diseases
Tend to be defects in structural genes (vs recessive = enzyme deficiencies, generally more severe)
ADPKD FAP Familial hypercholesterolemia Hereditary hemorrhagic telangectasia/Osler-Weber-Rendu Hereditary spherocytosis Huntington dz Li-Fraumeni syndrome Marfan MEN NF1 and NF2 Tuberous sclerosis VHL
X-linked recessive disorders
Be Wise Fool’s GOLD Heeds Silly Hope
Bruton agammaglobulinemia Wiskott-Aldrich syndrome Fabry disease G6PD deficiency Ocular albinism Lesch-Nyhan Duchenne/Becker musc dystrophy Hunter syndrome Hemophilias OTC deficiency
Trisomies
21 = Down (beta hcg up, papp-1 down) - in addition to all physical findings (eg duod atresia, single palmar crease, brushfield spots etc), increased risk of AD, ALL, AML
18 = Edwards (beta hcg down) - rocker bottom feet, micrognathia, low-set ears, clenched hands, prominent occiput; early death
13 = Patau (beta hcg down, papp-1 down) - ID, rocker bottom feet, microphthalmia, microcephaly, holoprosencephaly/cleft lip/palate, polydactyly; early death
alpha fetoprotein down in all (vs up in neural tube defects and other holes)
congen heart defects in all three
Williams syndrome
microdel on chromosome 7
“elfin” facies, ID, hypercalcemia, well-dev verbal skills and friendliness, CV problems
B vitamins
1 = thiamine 2 = riboflavin 3 = niacin 5 = pantothenic acid (CoA) 6 = pyridoxine (PLP) 7 = biotin (carboxylation) 9 = folate 12 = cobalamin
ones like 5 and 7 that are ubiquitous: when deficient, get alopecia, dermatitis, enteritis (fastest dividing cells = affected most); 1 and 3 = needed for energy processing, so affect neuro and heart [1 only - beri beri])
Pellagra
B3 (niacin) deficiency
need B2 (riboflavin) and B6 (pyridoxine) + tryptophan to make B3, so seen in hartnup disease (decreased Trp abs), carcinoid (increased Trp metabolism to make serotonin), and isoniazid/b6 deficiency
sx = 3D’s: diarrhea, dementia, dermatitis
Symptoms of B6 deficiency
B6 = pyridoxine
get neuro (convulsions, hyperirritability, peripheral neuropathy) and sideroblastic anemia (impaired hgb synth and iron excess)
Drugs that cause folate deficiency
phenytoin, sulfonamides, methotrexate (don’t take with pregnancy!)
Sx of folate deficiency vs b12 deficiency
Folate: no neuro sx! (unlike b12)
hypersegmented polys, macrocytic, megaloblastic anemia, glossitis
labs: increased homocysteine but normal MMA
B12: megaloblastic anemia, hypersegmented polys + PARESTHESIAS AND SUBACUTE COMBINED DEGEN OF SPINAL CORD, increased homocysteine and mma
Fomepizole
inhibits alcohol dehydrogenase (converts ethanol to acetaldehyde); used as antidote for methanol or ethylene glycol poisoning
Disulfiram
inhibits acetaldehyde dehydrogenase
so acetaldehyde accumulates in breakdown of ethanol –> hangover
Role of NADH in alcohol effects on liver
breakdown of ethanol –> NAD+ –> NADH, so increased NADH:NAD+ ratio –> more glycolysis (fasting hypoglycemia), lactic acidosis, and hepatosteatosis (DHAP –> G3P)
also favors utilization of acetyl-CoA for ketogenesis over TCA so more NADH isn’t made –> ketoacidosis and lipogenesis
purely ketogenic AAs
lysine and leucine
increase their intake in pyruvate dehydrogenase complex deficiency (b/c glucose –> pyruvate, which is shunted to lactate and alanine, since it can’t be made into Acetyl-CoA and enter TCA cycle)
Cahill cycle
pyruvate alanine, way to carry amino groups to liver from muscle
fates of pyruvate
converted to alanine in muscle, which is transported to liver, converted back to pyruvate, releasing NH3 to make glutamate and excrete urea (Cahill cycle)
converted to OAA (to enter TCA cycle or be converted back to PEP to start gluconeo - need biotin/B7)
converted to acetyl coa for TCA
converted to lactate (cori cycle) for anaerobic glycolysis - needs B3
2 disorders of fructose metabolism
essential fructosuria = defect in fructokinase (1st step, fructose –> fructose-1-p), benign and asymp b/c fructose isn’t trapped in cells
fructose intolerance = BAD, aldolase b deficiency, so get fructose-1-p (trapped inside cells), but can’t convert it to DHAP and glyceraldehyde; buildup decreases phosphate, inhibiting glycogenolysis and gluconeo, so when eat fruit, juice, honey (things with fructose or sucrose) –> hypoglycemia, jaundice, cirrhosis, vomiting
both aut rec
2 disorders of galactose metabolism
Galactokinase deficiency (1st step, galactose –> galactose-1-P doesn’t happen, so galactitol accum instead; relatively mild but can cause CATARACTS)
Classic galactosemia (SEVERE - no G-1-P uridyltransferase, so can’t make glucose-1-P; galactose-1-P and galactitol accum in lens etc –> FTT, jaundice, hepatomeg, cataracts, ID)
both aut rec
why do we care about sorbitol?
alternative pathway of glucose metabolism, catalyzed by aldose reductase
in most cells, sorbitol can be converted to fructose by sorbitol dehydrogenase, but this enzyme doesn’t exist in schwann cells, retina, lens, and kidneys, so excess glucose and galactose –> sorbitol acumulates –> osmotic damage (eg cataracts, periph neuropathy in DM)
Treatments for hyperammonemia
lactulose (non-absorbable sugar that acidifies GI tract and traps NH4 for excretion)
rifaximin (decrease colonic ammoniagenic bacteria)
benzoate or phenylbutyrate (bind AA and increase their excretion)
OTC deficiency
X-linked recessive
urea cycle disorder –> buildup of carbamoyl phosphate (–> increased pyrimidine synthesis and buildup of orotic acid) + hyperammonemia
vs. orotic aciduria (can’t convert orotic acid to pyrimidines, so get megaloblastic anemia, no hyperammonemia since not involved in urea cycle)
vs. N-acetylglutamate synthase deficiency (cofactor for carbamoyl phosphate synthetase I, so get hyperammonemia b/c can’t do urea cycle, but no buildup of CP and thus no increased orotic acid)
Maple Syrup Urine Disease
blocked degradation of branched AAs (Isoleucine, leucine, valine) –> buildup of alpha ketoacids –> CNS defects, death
restrict branched AAs in diet, give B1
Three forms of familial dyslipidemias
I - hyperchylomicronemia (AR)
II - familial hypercholesterolemia (AR)
IV - hypertriglyceridemia (AD)
I and IV can –> acute pancreatitis
Fanconi’s anemia
most common cause of inherited aplastic anemia, can cause AML
defective DNA repair –> chrom breakage, rearrangement,s deletions
other sx: kidney malform, hypogonadism, microcephaly, high fetal hgb conc
Diamond-blackfan anemia
congenital pure rbc aplasia (primary failure of erythroid progenitor cells in marrow)
essential fatty acids
linoleic and linolenic acids
Testing protocol for HIV infection
ELISA, then Western to confirm (higher specificity)
HbS O2 dissociation curve
shifted to the right (decreased affinity, so more unloading of O2 to tissues)
Alkaptonuria
deficiency in homogentisate oxidase –> buildup of homogentisic acid (in urine –> black, in cartilage/skin, in sclerae and ears, on heart valves, in kidney–> stones)
can cause severe arthralgias with increasing age
Stickler’s syndrome
genetic disease affecting type II and XI collagen –> flattened facies, myopia, glaucoma, retinal detachment, hearing loss, hypermobile joints
