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Microbiology > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

DNA vs. histone methylation

A

DNA - template strand = methylated to label it as “old”; transcription suppressor

Histone - reversible repression of DNA transcription, may activate transcription in some cases

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2
Q

Cytosine, Uracil, Thymine

A

Pyrimidines

Deamination of C makes U

U is in RNA, T is in DNA

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3
Q

De novo pyrimidine vs. purine synthesis

A

Purine: sugar + phosphate, then add base

Pyrimidine: Make temporary base, add sugar and phosphate, then modify base

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4
Q

Purine salvage deficiencies

A

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

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5
Q

Nucleotide vs. base excision repair

A

Nucleotide: swap whole nucleotide due to bulky lesion

Base: leave phosphate-sugar backbone and swap base

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6
Q

Xeroderma pigmentosa

A

Defective nucleotide excision repair prevents repair of thymidine dimers from UV

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7
Q

HNPCC

A

Hereditary non-polyposis colorectal cancer - defective mismatch repair

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8
Q

Ataxia telangectasia

A

Neurodegenerative disease –> poor coordination, weakened immune system, increased cancer risk

Due to mutated nonhomologous end joining

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9
Q

RNA polymerases

A

Eukaryotes:

Pol I makes rRNA

Pol II makes mRNA (inhibited by alpha-amanitin)

Pol III makes tRNA

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10
Q

tRNA structure and charging

A

Amino acid binds to CCA at 3’ end

T-arm binds ribosome

R-arm for recognition by aminoacyl-tRNA synthetase (charging)

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11
Q

Post-translational protein modifications

A

Trimming - remove N- or C-terminal propeptides

Covalent alterations: phosphorylation, glycosylation, hydroxylation, methylation, acetylation, ubiquitination

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12
Q

Hetero vs. euchromatin

A

Hetero = condensed and transcriptionally inactive

Eu = less condensed, transcriptionally active

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13
Q

Lead poisoning

A

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

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14
Q

NF2

A

Bilateral Schwannomas/acoustic neuromas, Schwannomas, Meningiomas

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15
Q

NF1

A

Iris hamartomas (Lisch nodules), cafe au lait spots, neural tumors, skeletal disorders (eg scoliosis)

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16
Q

Niemann-Pick disease

A

autosomal recessive

deficiency in sphingomyelinase –> accumulation of sphingomyelin –> hepatomeg, failure to thrive, neurodegen

Common in Ashkenazi

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17
Q

Gaucher disease

A

autosomal recessive

Glycogen storage disease

deficiency in glucocerebrosidase –> accumulation of glucocerebroside in brain, liver, spleen, and marrow

bone crises, hypersplenism, hepatosplenomeg

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18
Q

Hunter syndrome

A

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)

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19
Q

Morquio syndrome

A

Deficiency in galactosamine-6-sulfatase or beta-galactosidase

Diag around 1yo, short stature, joint laxity, musculoskel problems

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20
Q

Sanfilippo syndrome

A

Enzyme def include sulfamidase

CNS sx (aggressiveness, hyperactivity)

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21
Q

Muscular dystrophies

A

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

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22
Q

Adenosine deaminase deficiency

A

SCID

Part of purine salvage pathway, so without it, B and T lymphocytes especially can’t make DNA

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23
Q

G6PD deficiency

A

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

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24
Q

Von Gierke’s disease

A

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

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25
Q

Nitroblue tetrazolium dye reduction test

A

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)

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26
Q

Chronic granulomatous disease

A

Deficiency in NADP oxidase

Increased susc to catalase positive organisms

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27
Q

McArdle’s disease

A

Deficiency in glycogen phosphorylase in skeletal muscle –> can’t break glycogen down and get muscle cramps and myoglobinuria with exercise

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28
Q

Trinucleotide repeat diseases

A

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

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29
Q

“Blots”

A 
Southern = DNA
Northern = RNA
Western = protein
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30
Q

Homocystinuria

A

ID, marfanoid habitus, lens subluxation, thromboembolus

Cystathione synthase (uses B6) or methionine synthase problem

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31
Q

PKU

A

Phenylalanine hydroxylase deficiency

ID, musty body odor, growth retardation, fair skin, eczema

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32
Q

alpha1-antitrypsin deficiency

A

protein usually inhibits neutrophil elastase in the lung, so without it there’s excess elastase –> destroys elastin and collagen in lungs, liver –> emphysema

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33
Q

Adenosine deaminase deficiency

A

Can’t break down ATP pand dATP, which feedback inhibit ribonucleotide reductase, preventing pyrimidine production –> decreased lymphocytes (SCID)

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34
Q

Lesch-Nyhan defect

A

HGPRT

can’t convert hypoxanthine to PRPP, so keep running purine de novo pathway –> excess uric acid and purines

treat with allopurinol or febuxostat

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35
Q

allopurinol/febuxostat

A

inhibit xanthine oxidase, decreasing conversion of hypoxanthine and xanthine to uric acid (used in gout and lesch-nyhan)

36
Q

leflunomide

A

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

37
Q

mycophenolate, ribavirin

A

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

38
Q

hydroxyurea

A

inhibits ribonucleotide reductase, so don’t convert UDP to dUDP and pyrimidines

used to treat SCD (increases HbF) and myeloproliferative disorders

39
Q

6-mp and azathioprine

A

inhibit de novo purine synth

treat IBD and chemo for leukemia

40
Q

5-FU

A

inhibits de novo pyrimidine synth by inhibiting thymidylate synthase (no dUMP to dTMP) - chemo

41
Q

Chain termination

A

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

42
Q

Protein synthesis direction?I

A

N terminus to C terminus

43
Q

Anti-u1 RNP antibodies

A

Mixed DT disease

Antibodies to spliceosome proteins

Vs anti-smith in SLE (anti-snrps)

44
Q

Vesicular trafficking proteins

A

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)

45
Q

I-cell disease

A

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

46
Q

Drugs that act on MTs

A

Microtubules Get Constructed Very Poorly

Mebendazole (anti-helminth)
Griseofulvin (antifungal)
Colchicine (antigout)
Vincristine/vinblastine (anticancer)
Paclitaxel (anticancer)
47
Q

Osteogenesis imperfecta

A

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

48
Q

Collagen synthesis

A

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)

49
Q

Problems with collagen crosslinking –>

A

Ehlers-Danlos and Menkes (X linked recessive, copper problem)

50
Q

Variable expressivity vs incomplete penetrance

A

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)

51
Q

pleiotropy example

A

phenylketonuria (one gene –> multiple phenotypic effects; here, light skin, musky BO, ID)

52
Q

example of mosaicism

A

mccune-albright (affects g protein signaling) - unilateral cafe au lait spots, fibrous dysplasia, precocious puberty, multiple endo abnormalities

53
Q

Example of locus heterogeneity

A

albinism (mutations at different loci –> same disease)

54
Q

Example of allelic heterogen

A

beta-thal (different mutations at same locus –> same dz)

55
Q

heteroplasmy

A

presence of both normal and mutated mtDNA

56
Q

Prader-Willi vs Angelman

A

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

57
Q

Autosomal dominant diseases

A

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
58
Q

X-linked recessive disorders

A

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
59
Q

Trisomies

A

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

60
Q

Williams syndrome

A

microdel on chromosome 7

“elfin” facies, ID, hypercalcemia, well-dev verbal skills and friendliness, CV problems

61
Q

B vitamins

A 
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])

62
Q

Pellagra

A

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

63
Q

Symptoms of B6 deficiency

A

B6 = pyridoxine

get neuro (convulsions, hyperirritability, peripheral neuropathy) and sideroblastic anemia (impaired hgb synth and iron excess)

64
Q

Drugs that cause folate deficiency

A

phenytoin, sulfonamides, methotrexate (don’t take with pregnancy!)

65
Q

Sx of folate deficiency vs b12 deficiency

A

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

66
Q

Fomepizole

A

inhibits alcohol dehydrogenase (converts ethanol to acetaldehyde); used as antidote for methanol or ethylene glycol poisoning

67
Q

Disulfiram

A

inhibits acetaldehyde dehydrogenase

so acetaldehyde accumulates in breakdown of ethanol –> hangover

68
Q

Role of NADH in alcohol effects on liver

A

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

69
Q

purely ketogenic AAs

A

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)

70
Q

Cahill cycle

A

pyruvate alanine, way to carry amino groups to liver from muscle

71
Q

fates of pyruvate

A

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

72
Q

2 disorders of fructose metabolism

A

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

73
Q

2 disorders of galactose metabolism

A

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

74
Q

why do we care about sorbitol?

A

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)

75
Q

Treatments for hyperammonemia

A

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)

76
Q

OTC deficiency

A

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)

77
Q

Maple Syrup Urine Disease

A

blocked degradation of branched AAs (Isoleucine, leucine, valine) –> buildup of alpha ketoacids –> CNS defects, death

restrict branched AAs in diet, give B1

78
Q

Three forms of familial dyslipidemias

A

I - hyperchylomicronemia (AR)

II - familial hypercholesterolemia (AR)

IV - hypertriglyceridemia (AD)

I and IV can –> acute pancreatitis

79
Q

Fanconi’s anemia

A

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

80
Q

Diamond-blackfan anemia

A

congenital pure rbc aplasia (primary failure of erythroid progenitor cells in marrow)

81
Q

essential fatty acids

A

linoleic and linolenic acids

82
Q

Testing protocol for HIV infection

A

ELISA, then Western to confirm (higher specificity)

83
Q

HbS O2 dissociation curve

A

shifted to the right (decreased affinity, so more unloading of O2 to tissues)

84
Q

Alkaptonuria

A

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

85
Q

Stickler’s syndrome

A

genetic disease affecting type II and XI collagen –> flattened facies, myopia, glaucoma, retinal detachment, hearing loss, hypermobile joints

Microbiology (2 decks)

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