Biochemistry Flashcards
RNA polymerase I
restricted to nucleolus as it synthesizes majority of rRNA
produces 18S, 5.8S, & 28S
forms essential ribosomal components
mRNA
Produced by RNA pol II
translated by ribosomes to form specific proteins
small nuclear RNA
Produced by RNA pol II
involved in mRNA splicing & transcription regulation
micro RNA
Produced by RNA pol II
cause gene silencing via translation arrest or mRNA degradation
RNA pol III
produces tRNA and 5S ribosomal RNA (essential component of 60S ribosomal subunit)
vitamin A deficiency
sx = night blindness, complete blindness, xerophthalmia, Bitot’s spots (abnromal squamous cell proliferation and keratinization of conjunctiva), corneal perforation, keratomalacia, derm abnl, damage to phagocytes and TC lymphocytes, death
common in Asia, Africa, South America
associated with malnourishment and fat malabsorption (eg CF, cholestatic liver disease)
Give to all children with measles from area with vit A def or with measles mortality >1%
Transformation
Direct uptake of naked DNA from the environment by bacT that are naturally able
- strep pneumo
- Haemophilus influenza
- Neisseria gonorrhoeae & meningitidis
*this is how non-virulent non-capsule-forming strains of s. pneumo can obtain genes that code for capsule and gain virulence
Conjugation
one-way transfer of DNA between bacT cells through direct physical contact
donor cells contain an extra segment of DNA = F factors coding for sex pilus and other prot necessary for transfer to F- recipients
Transduction
transfer of DNA via bacteriophage
during lytic infection when random bacT genes accidentally packaged into viral capsid
lyosgenic infection when selected bacT genes near viral insertion site are excised and packaged into virion
Dry beriberri
think ber1 ber1 –> B1 deficiency
polyneuritis, symmetrical muscle wasting
Wet beriberi
high-output cardiac failure (dilated cardiomyopathy), edema
B1 deficiency
impaired glucose breakdown –> ATP depletion worsened by glucose infusion with highly aerobic tissues affected first (brain, heart)
Thiamine
found in thiamine pyrophosphate (TPP) = cofactor for:
- pyruvate dehydrogenase (links glycolysis to TCA)
- alpha-ketoflutarate dehydrogenase = TCA cycle
- Transketolase (HMP shunt responsible for NADPH production)
vitamin B2
riboflavin
cofactor in oxiation and reduction (eg FADH2)
Mneumonics:
-Fad and Fmn derived from riboFlavin (B2 = 2ATP)
B2 deficiency
Cheilosis
Crneal vascularization
“2 C’s of B2”
B3
niacin
constituent of NAD+, NADP+ (using redox reactions).
Derived from tryptophan – need B6
“NAD derived from Niacin (B3 = 3 ATP)
Niacin deficiency
glossitis
severe = pellagra = diarrhea, dementia, dermatitis
c/b Hartnup dz (dec tryptophan absorption), malignant carcinoid syndrome (inc tryptophan metabolism), INH (dec B6)
niacin excess
flushing - seen at doses used to tx HLD
B5 function and deficiency presentation
pantothenate
essential part of CoA and fatty acid synthase
deficiency = dermatitis, enteritis, alopecia, adrenal insufficiency
B6
pyridoxine
converted to pyridoxal phosphate = cofactor used in transamination (ALT, AST), decarboxylation reactions, glycogen phosphorylase
Needed to make:
- cystathionine
- heme
- niacin
- histamine
- NTs = 5HT, E, NE, GABA
B6 deficiency
convulsions, hyperirritability, peripheral neuropathy, sideroblastic anemia due to impaired Hb synthesis and iron excess
B7 (biotic)
cofactor for carboxylation enzymes (add 1-carbon group):
- pyruvate carboyxlase: pyruvate (3C) –> oxaloacetate (4C)
- acetyl-CoA carboxylase: acetyl-CoA (2C) –> malonyl-CoA (3C)
- Propionyl-CoA carboxylase: propionyl-CoA (3C) –> methylmalonyl-CoA (4C)
deficiency is rare but causes dermatitis, alopecia, enteritis. Occurs if consume too many raw eggs (Avidin binds biotin) or abx.
B9
converted to tetrahydrofolate (THF) = coenzyme for 1-C transfer/methylation rxns
needed to make nitrogenous bases in DNA and RNA
found in green leafy vegetables (“folate in foliage”)
small reserve pool in liver
drugs that cause folate deficiency
MTX, phenytoin, sulfonamides
*remember no neuro sx like in B12 deficiency
B12
cofactor for homocysteine methyltransferase (transfers methyl group as methylcobalamin) and methylmalonyl-CoA mutase
large reserve in liver that lasts years
B12 deficiency
malabsorption (sprue, enteritis, diphyllobothrium latum), lack intrinsic factor, absent terminal ileum
dx with Schilling test
findings = macrocytic, megaloblastic anemia, hypersegmented PMNs, neuro sx (paresthesias) due to abnomral myelin, if prolonged get irreversible nervous system damage
Kwashiorkor
protein deficient MEAL-
Malnutrition
Edema
Anemia
Liver (fatty due to dec apolipoprotein synthesis)
Marasmus
Muscle wasting
loss of SQ fat
variable edema
c/b energy malnutrition
what 3 things are metabolized in both the cytosol and mito.?
HUGs take 2
Heme
Urea cycle
Gluconeogenesis
What 5 cofactors are needed for the pyruvate dehydrogenase complex?
- Pyrophosphate (B1, thiamine, TPP)
- FAD (riboflavin, B2)
- NAD (niacin, B3)
- CoA (pantothenate, B5)
- Lipoic acid
Goal = pyruvate + NAD+ + CoA –> acetyl-CoA + CO2 + NADH
preparing for TCA cycle
Regulation by Fructose-2,6-bisphosphate in the fasting state
inc glucagon –> inc cAMP –> inc protein kinase A –> inc fructose bisphosphatase-2, dec PFK-2, less glycolysis
Remember:
- fasting means you’re low on E –> get back the phosphate to produce glucose/energy
- going from F2,6BP to F6P
Regulation by Fructose-2,6-bisphosphate in the fed state
inc insulin –> dec cAMP –> dec protein kinase A –> dec FBPase-2, inc phosphofructokinase-2, more glycolysis
Remember:
- you’re fed, have to energy to spare, add phosphates to things
- “energy to burn, don’t give a fructo” – phosphoFRUCTOkinase-2
what are the 2 purely ketogenic amino acids
Lysine and Leucine
mutation in pyruvate dehydrogenase complex deficiency
x-linked gene for E1-alpha subunit
sx = neuro deficits tx = ketogenic diet
4 possible targets of pyruvate metabolism and effector enzyme:
- ALT (with B6): alanine carries amino groups to liver from muscle
- pyruvate carboxylase (with B7): oxaloacetate replenishes TCA cycle or used in gluconeogenesis
- pyruvate dehydrogenase (B1, B2, B3, B5, lipoid acid): transition from glycolysis to the TCA cycle
- Lactic acid dehydrogenase (B3): end of anaerobic glycolysis (RBCs, leukocytes, kidney medulla, lens, testes, cornea)
alpha-ketoglutarate dehydrogenase complex
same cofactors as pyruvate dehydrogenase complex
Citric acid cycle major players in order mneumonic
“Citrate Is Kreb’s Starting Substrate For Making Oxaloacetate”
Citrate 6C Isocitrate 6C alpha-ketoglutarate 5C Succinyl-CoA 4C Succinate 4C Fumarate 4C Malate 4C Oxaloacetate 4C
Products of TCA cycle
3 NADH
1 FADH2
2 CO2 –> from the C decreases, i.e. 6C -> 5C -> 4C
1 GTP per acetyl-coA
Total: 10 ATP/acetyl-CoA (multiply by 2 for each glucose since it produces 2 acetyl-CoA)
Electron transport inhibitors
inhibit Complexes of transport chain dec proton gradient and blocking ATP synthesis
Rotenone –| Complex I
Antimycin A –| Complex III
Cyanide and CO –| Complex IV
ATP synthase inhibitors
directly inhibit mito ATPsynthase causing inc proton gradient. No ATP produced bc electron transport stop
Oligomycin –| Complex V
Uncoupling agent of e- transport chain
inc permeability of membrane –> dec proton gradient and inc O2 consumption –> ATP synthesis stops but e- transport produces heat
2,4-DNP, aspirin (fever recurs after overdose), thermogenin in brown fat
Which tissue can’t do gluconeogensis and why?
muscle bc it lacks G6P enzyme
Which fatty acid chains can produce glucose?
Odd chains becaues they yield 1 propionyl-CoA which can enter the TCA cycle as succinyl-CoA
Even chains can’t bc only make acetyl-CoA equivalents
“Odd FAtty’s have Energy thanks to their PROPortionality”
What is the end product of the HMP shunt (pentose phosphate pathway)?
ribose for nucleotide synthesis and glycolytic intermediates
No ATP is used or produced
Sites: lactating mammary glands, liver, adrenal cortex (sites of FA and steroid synthesis), RBCs
What is the end product of oxidative (irreversible) HMP shunt?
CO2, 2 NADPH, Ribulose-5-Pi
What is the end product of nonoxidative (reversible) HMP shunt?
Ribose-5-Pi, G3P, F6P
What is the action of NADPH oxidase and where is it located?
rapid release of reactive oxygen intermediates and found in neutrophils and monocytes
NADPH plays a role in the creation of ROIs and their neutralization –> important for immune response
What type of infections are patients with chronic granulomatous disease at risk for and why?
catalase positive species like s. aureus or aspergillus bc catalase neutralizes the bactericidal effect of H2O2
normally CGD pts use the H2O2 generated by invading organisms and convert it to ROIs but they can’t do that with catalase-positive species bc the catalase will just breakdown the H2O2 made by the organism, i.e. it breaks down its own H2O2 metabolism byproduct
deficiencies in glycolytic enzymes leads to…
hemolysis bc RBCs depend solely on glycolysis for their energy needs
Glucose-6-Phosphate Deficiency
- X-linked recessive disorder
- the most common glycolytic deficiency (and human enz def overall)
- more prevalent in blacks
- inc malarial resistance
RBCs can’t phosphorylate glucose –> don’t carry out glycolysis –> RBC protected from oxidative stress by glutathione –> glutathione regeneration dependent on NADPH produced by glycolysis and HMP shunt neither of which happening –> Hb denatured –> Heinz bodies
*exacerbated by fava beans
Glutathione
in reduced form detoxifies free radicals and peroxides, i.e. protects from oxidizing agents
(eg fava beans, sulfonamides, primaquine, antituberculosis drugs)
which two pathways can give starting substrate of glycolysis (glyceraldehyde-3-P)?
Glucose metabolism
Fructose metabolism
Fructose metabolism pathway
fructose –fructokinase–> fructose-1-P –aldolaseB–> dihydroxyacetone-P and glyceraldehyde –triose kinase–> Glyceraldehyde-3-P
deficiency in fructokinase = essential fructosuria, AR, benign, asx, fructose found in blood and urine
deficiency in aldolase B = AR, fructose-1-P accumulates causing a dec in available phosphate –> inhibition of glycogenolysis and gluconeogenesis
- sx = jaundice, hypoglycemia, cirrhosis, vomiting
- tx = no fructose or sucrose (gluc + fruc)
d/o of fructose and galactose metabolism mneumonic
Fructose is to Aldolase B as Galactose is to UridylTransferase
FAB GUT
these are the two more serious defects because they lead to PO4 depletion (in comparison to essential fructose intolerance from defective fructokinase and galactoskinas deficiency)
glycolysis and gluconeogenesis dependent on metabolism of what?
galactose
uridyl transferase
galactose metabolism
converts galactose-1-P to glucose 1-P with help of 4-epimerase
4-epimerase
galactose metabolism UDP-Gal converted to UDP-Glu facilitating uridyl transferase conversion of galactose-1-P to glucose-1-P to be used in glycolysis and gluconeogenesis
Alternative method of trapping glucose in cells?
- convert it to alcohol counterpart, i.e. sorbitol
- done via aldose reductase
- liver, lens, ovaries, and seminal vesicles also have sorbitol dehydrogenase which converts sorbitol to fructose
- schwann cells, retina, kidneys have only aldose reductase –> risk for sorbitol accumulation and osmotic damage (cataracts, retinopathy, peripheral neuropathy)
*happens with excess galactose too
Essential amino acids
Glucogenic: Met, Val, His
Glucogenic/ketogenic: Ile, Phe, Thr, Trp
Ketogen: Leu, Lys
Acidic aa
Asp and Glu (negatively charged at body pH)
Basic aa
Arg, Lys, His
Arg = most basic, "Argyle print is so basic" His = no charge at body pH, "His style is so neutral"
Arg + His = needed during time of growth bc they are inc in histones wrapped around DNA
Urea cycle
“Ordinarily, Careless Crappers Are Also Frivolous About Urination”
Ornithine Carbamoyl phosphate (made in mito., then out to cyto.) Citruline Aspartate - donates NH4+ to make urea Argininosuccinate Arginine + Fumarate Urea
urea = made in liver, excreted by kidneys
Role of alanine and glutamate in ammonium transport
muscle cell:
- amino acids broken down to alpha-ketoacids
- end up with glutamate that together with pyruvate give alanine
Alanine cycle:
-alanine transported to liver where in combination with alpha-ketoglutarate you get glutamate again and then you make urea
*Cori cycle: glucose -> pyruvate -> lactate in muscle cell –> move to liver as lactate -> pyruvate -> glucose –> back to muscle as glucose and repeat
how do you develop hyperammonemia
acquired in liver disease (e.g. cirrhosis)
hereditary via urea cycle enzyme deficiency
problem is excess NH4+ deplete alpha-ketoglutarate (which is part of the alanine and glutamate transport of urea cycle) –> inhibit TCA cycle
sx = tremor (asterixis), slurring of speech, somnolence, vomiting, cerebral edema, blurring vision –> basically symptoms of an alcoholic
tx = limit protein in diet, benzoate or phenylbutyrate (bind aa and lead to excretion), lactulose
Most common urea cycle disorder
Ornithine transcarbamoylase deficiency which is what combines ornithine with carbamoyl phosphate to make citruline
x-linked recessive (all other urea enz def are AR)
end up with excess carbamoyl phosphate in mito. which is then converted to orotic acid (part of pyrimidine synthesis pathway)
sx = inc orotic acid in blood and urine, dec BUN, sx of hyperammonemia (asterixis, somnolence, vomiting, cerebral edema, blurring vision).
Phenylalanine derivatives
–BH4–> Tyrosine (-> Thyroxine) –BH4–> Dopa (-> melanin) –vitB6–> dopamine –vitC–> NE –SAM–> Epi
Tryptophan derivatives
via B6 get Niacin –> NAD+/NADP+
via BH4 get Serotonin –> melatonin
Histidine derivative
via B6 –> histamine
Glycine derivatives
via B6 –> porphyrin –> heme
Arginine derivatives
Creatine
Urea
Nitric oxide
Glutamate derivatives
via B6 GABA
Glutathione
Enzymes to know involved in catecholamine synthesis and tyrosine catabolism
- Phenylalanine hydroxylase - PKU
- Tyrosine hydroxylase
- Dopa decarboxylase
- Dopamine beta-hydroxylase
- Phenylethanolamine N-methyltransferase
Phenylketonuria
defective or absent phenylalanine hydroxylase ==> Tyrosine is now an essential amino acid
inc Phe leads to excess phenylketones in urine
findings: ID, growth retardation, seizures, fair skin, eczema, musty body odor (d/o aromatic aa metabolism –> body odor)
tx: dec Phe in diet and inc tyrosine
Findings in newborn with maternal PKU
c/b lack of proper diet during pregnancy
microcephaly, ID, growth retardation, congenital heart defects
Alkaptonuria (ochronosis)
congenital deficiency of homogentisic acid oxidase in degradative pathway of tyrosine to fumarate
AR, benign disease
findings; dark connective tissue, brown pigmented sclera, urine turns black on prolonged exposure to air, debilitating arthralgia (homogentisic acid is toxic to cartilage)
Albinism
c/b deficiency in either:
- tyronsinase = AR, can’t make melanin from tyrosine
- defective tyrosine transporters = dec tyr and therefore dec melanin
due to lack of migration of neural crest cells
Homocystinuria forms
all AR, the main problem is excess homocysteine and no cysteine so it cystein becomes essential
- Cystathionine synthase deficiency: needed for conversion of homocys to cystathionine and then to cys
- tx dec Met and inc Cys and inc B12 and folate in diet - dec affinity of cystathionine synthase for pyridoxal phosphate, i.e. B6 cofactor
- tx inc vit B6 in diet - homocysteine methyltransferase (requires B12) deficiency: needed to convert homocys to methionine
findings: inc homocysteine in uria, ID, osteoporosis, tall stature, kyphosis, lens subluxation (down and in) and atherosclerosis (stroke and MI)
Cystinuria
AR defect of renal tubular amino acid transporter for cysteine, ornithine, lysine and arginine in kidney PCT
excess cys in urine –> precipitation –> staghorn calculi
Tx: hydration, urine alkalinization
Maple syrup urine disease
AR, urine smells like maple syrup
“I Love Vermont maple syrup from maple tress with branches”
dec alpha-ketoacid dehydrogenase (B1) –> blocked degradation of branched amino acids (Ile, Leu, Val) –> inc alpha-ketoacids in blood, esp Leu
sx = CNS defects, ID, death
Hartnup disease
AR
defective neutral amino acid transporter on renal and intestinal epithelial cells –> tryptophan excretion and dec absorption in the gut
remember tryptophan –> niacin therefore deficiency in tryp leads to niacin deficiency, a.k.a. PELLAGRA
Glycogen storage disorders
12 types
abnormal glycogen metabolism –> accumulation in cells
Type 1 Glycogen Storage Disease = von Gierke’s Disease
AR, glucose-6-phosphatase deficiency
severe fasting hypoglycemia, inc glycogen in liver, inc blood lactate, hepatomegaly
Type 2 Glycogen Storage Disease = Pompe’s disease
AR, Pome’s trashes the Pump (heart, liver, muscle)
lysosomal alpha-1,4-glucosidase (acid maltase) deficiency which is normally supposed to degrade small amount of glycogen
cardiomegaly and systemic findings leading to early death
Type 3 Glycogen Storage Disease = Cori’s disease
AR, gluconeogensis intact, debranching (alpha-1,6-glucosidase) deficiency
milder form of type I with normal lactate levels in blood
Type 4 Glycogen Storage Disease = McArdle’s disease
AR, McArdle’s = Muscle
skeletal muscle glycogen phosphorylase deficiency
inc glycogen in muscle but can’t break it down –> painful muscle cramps and myoglobinuria with strenuous exercise
Gaucher’s disease
most common lysosomal storage disorder
Deficient Enzyme: Glucocerebrosidase
Accumulated Substrate: Glucocerebroside
Inheritance: AR
Findings:
HSM, aseptic necrosis of femur, bone crises, Gaucher’s cells (macrophages that look like crumpled paper)
Niemann-Pick disease
Deficient Enzyme: sphingomyelinase
Accumulated Substrate: sphingomyelin
Inheritance: AR
Findings:
progressive neurodegeneration, HSM, CHERRY-RED spot on macula, foam cells
Tay-Sachs disease
Deficient Enzyme: Hexosaminidase A
Accumulated Substrate: GM2 ganglioside
Inheritance: AR
Findings:
progressive neurodegeneration, developmental delay, cherry-red spot on macula, lysosomes with onion skin, no HSM (as compared to Niemann Pick)
Krabbe’s disease
Deficient Enzyme: Galactocerebrosidase
Accumulated Substrate: Galactocerebroside
Inheritance: AR
Findings:
peripheral neuropathy, development delay, optic atrophy, globoid cells
Metachromatic leukodystrophy
Deficient Enzyme: arylsulfatase A
Accumulated Substrate: cerebroside sulfate
Inheritance: AR
Findings:
central and peripheral demyelination with ataxia, dementia
Hurler’s syndrome
Mucopolysaccharidoses - missing lysosomal enzymes required to break down glycoaminoglycans
Deficient Enzyme: alpha-L-iduronidase
Accumulated Substrate: heparan sulfate, dermatan sulfate
Inheritance: AR
Findings:
developmental delay, gargoylism, airway obstruction, corneal clouding, HSM
Hunter’s syndrome
Mucopolysaccharidoses - missing lysosomal enzymes required to break down glycoaminoglycans
Deficient Enzyme: Iduronate sulfatase
Accumulated Substrate: heparan sulfate, dermatan sulfate
Inheritance: XR
Findings:
Mild Hurler’s + aggressive behavior, no corneal clouding (Remember it as qualities of a hunter who has to see clearly)
Fatty acid synthesis
inner mitochondrial membrane
citrate in mito matrix
“SYtrate = SYnthesis”
Fatty acid degradation
inner mitochondrial membrane
carnitine brings fatty acids and CoA in from cytosol
“CARnitine = CARnage of fatty acids”
carnitine deficiency
inability to transport long chain fatty acids to mitochondria –> toxic accumulation –> weakness, hypotonia, hypoketotic hypoglycemia
acyl-CoA dehydrogenase deficiency
inc dicarboxylic acids, dec glucose and ketones
number of kcal in 1 g of protein or carb
4
number kcal in 1 g of fat
9
pancreatic lipase
degradation of dietary TG in small intestine
Lipoprotein lipase (LPL)
degradation of TG circulating in chylomicrons and VLDLs
Hepatic TG lipase (HL)
degradation of TG remaining in IDL
Hormone-sensitive lipase
degradation of TG stored in adipocytes
Lecithin-cholesterol acyltransferase (LCAT)
catalyzes esterification of cholesterol, i.e. nascent HDL to mature HDL
Cholesterol ester transfer protein (CETP)
mediates tranfer of cholesterol esters to other lipoproteins particles , i.e. to VLDL, IDL, LDL
Apolipoprotein E
carrier protein
recognized by hepatocytes –> allows liver to remove chylomicron remnants from blood
found in chylomicron, chylomicron remnant, VLDL, IDL, HDL
Apoliprotein B-48
necessary for chylomicrons to be released into the blood from intestinal cells
Apolipoprotein A-I
activates lecithin-cholesterol acyltransferase (LCAT)
Apolipoprotein C-II
lipoprotein lipase cofactor
Apolipoprotein B-100
binds LDL receptor
LDL
transports cholesterol from Liver to Tissues
HDL
transports cholesterol from tissues to liver
type 1 hyperchylomicronemia
inc blood chylomicrons, TG, cholesterol
AR, lipoprotein lipase deficiency or altered apolipoprotein C-II
causes pancreatitis, HSM, and eruptive/pruritic xanthomas (no inc risk for atherosclerosis)
type 2a familial hypercholesterolemia
inc LDL, cholesterol in blood
AD
absent or dec LDL receptors
accelerated atherosclerosis, tendon (Achilles) xanthomas, corneal arcus
type 4 hypertriglyceridemia
inc VLDL and TG in blood
AD
hepatic overproduction of VLDL
causes pancreatitis
abetalipoproteinemia
AR mx in microsomal TG transfer protein (MTP) gene –> dec B-48 and B-100 –> dec chylomicron and VLDL synthesis and secretion
sx first few months of life
findings: failure to thrive, steatorrhea, acanthocytosis, ataxia, night blindness
Gq 2nd messenger pathway
GPCR-Gq stimulation –> Phospholipase C –> splits lipids into PIP2 –> PIP2 split into DAG (activates Protein kinase C) and IP3 (inc Ca2+ concentration and causes smooth muscle contraction)
Gs 2nd messenger pathway
GPCR-Gs stimulation –> adenylyl cyclase –> converts ATP to cAMP –> activates protein kinase A –> inc [Ca2+] in heart cells, inhibits myosin light-chain kinase in smooth muscle
Gi 2nd messenger pathway
inhibits the G2 pathway:
inhibits adenylyl cyclase and the downstream effects (–> converts ATP to cAMP –> activates protein kinase A –> inc [Ca2+] in heart cells, inhibits myosin light-chain kinase in smooth muscle)
