Biochemistry Flashcards

1
Q

RNA polymerase I

A

restricted to nucleolus as it synthesizes majority of rRNA

produces 18S, 5.8S, & 28S

forms essential ribosomal components

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2
Q

mRNA

A

Produced by RNA pol II

translated by ribosomes to form specific proteins

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3
Q

small nuclear RNA

A

Produced by RNA pol II

involved in mRNA splicing & transcription regulation

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4
Q

micro RNA

A

Produced by RNA pol II

cause gene silencing via translation arrest or mRNA degradation

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5
Q

RNA pol III

A

produces tRNA and 5S ribosomal RNA (essential component of 60S ribosomal subunit)

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6
Q

vitamin A deficiency

A

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%

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7
Q

Transformation

A

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

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8
Q

Conjugation

A

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

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9
Q

Transduction

A

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

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10
Q

Dry beriberri

A

think ber1 ber1 –> B1 deficiency

polyneuritis, symmetrical muscle wasting

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11
Q

Wet beriberi

A

high-output cardiac failure (dilated cardiomyopathy), edema

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12
Q

B1 deficiency

A

impaired glucose breakdown –> ATP depletion worsened by glucose infusion with highly aerobic tissues affected first (brain, heart)

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13
Q

Thiamine

A

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)
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14
Q

vitamin B2

A

riboflavin

cofactor in oxiation and reduction (eg FADH2)

Mneumonics:
-Fad and Fmn derived from riboFlavin (B2 = 2ATP)

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15
Q

B2 deficiency

A

Cheilosis
Crneal vascularization

“2 C’s of B2”

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16
Q

B3

A

niacin

constituent of NAD+, NADP+ (using redox reactions).

Derived from tryptophan – need B6

“NAD derived from Niacin (B3 = 3 ATP)

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17
Q

Niacin deficiency

A

glossitis
severe = pellagra = diarrhea, dementia, dermatitis

c/b Hartnup dz (dec tryptophan absorption), malignant carcinoid syndrome (inc tryptophan metabolism), INH (dec B6)

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18
Q

niacin excess

A

flushing - seen at doses used to tx HLD

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19
Q

B5 function and deficiency presentation

A

pantothenate

essential part of CoA and fatty acid synthase

deficiency = dermatitis, enteritis, alopecia, adrenal insufficiency

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20
Q

B6

A

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
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21
Q

B6 deficiency

A

convulsions, hyperirritability, peripheral neuropathy, sideroblastic anemia due to impaired Hb synthesis and iron excess

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22
Q

B7 (biotic)

A

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.

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23
Q

B9

A

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

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24
Q

drugs that cause folate deficiency

A

MTX, phenytoin, sulfonamides

*remember no neuro sx like in B12 deficiency

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25
B12
cofactor for homocysteine methyltransferase (transfers methyl group as methylcobalamin) and methylmalonyl-CoA mutase large reserve in liver that lasts years
26
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
27
Kwashiorkor
protein deficient MEAL- Malnutrition Edema Anemia Liver (fatty due to dec apolipoprotein synthesis)
28
Marasmus
Muscle wasting loss of SQ fat variable edema c/b energy malnutrition
29
what 3 things are metabolized in both the cytosol and mito.?
HUGs take 2 Heme Urea cycle Gluconeogenesis
30
What 5 cofactors are needed for the pyruvate dehydrogenase complex?
1. Pyrophosphate (B1, thiamine, TPP) 2. FAD (riboflavin, B2) 3. NAD (niacin, B3) 4. CoA (pantothenate, B5) 5. Lipoic acid Goal = pyruvate + NAD+ + CoA --> acetyl-CoA + CO2 + NADH preparing for TCA cycle
31
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
32
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
33
what are the 2 purely ketogenic amino acids
Lysine and Leucine
34
mutation in pyruvate dehydrogenase complex deficiency
x-linked gene for E1-alpha subunit ``` sx = neuro deficits tx = ketogenic diet ```
35
4 possible targets of pyruvate metabolism and effector enzyme:
1. ALT (with B6): alanine carries amino groups to liver from muscle 2. pyruvate carboxylase (with B7): oxaloacetate replenishes TCA cycle or used in gluconeogenesis 3. pyruvate dehydrogenase (B1, B2, B3, B5, lipoid acid): transition from glycolysis to the TCA cycle 4. Lactic acid dehydrogenase (B3): end of anaerobic glycolysis (RBCs, leukocytes, kidney medulla, lens, testes, cornea)
36
alpha-ketoglutarate dehydrogenase complex
same cofactors as pyruvate dehydrogenase complex
37
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 ```
38
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)
39
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
40
ATP synthase inhibitors
directly inhibit mito ATPsynthase causing inc proton gradient. No ATP produced bc electron transport stop Oligomycin --| Complex V
41
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
42
Which tissue can't do gluconeogensis and why?
muscle bc it lacks G6P enzyme
43
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"
44
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
45
What is the end product of oxidative (irreversible) HMP shunt?
CO2, 2 NADPH, Ribulose-5-Pi
46
What is the end product of nonoxidative (reversible) HMP shunt?
Ribose-5-Pi, G3P, F6P
47
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
48
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
49
deficiencies in glycolytic enzymes leads to...
hemolysis bc RBCs depend solely on glycolysis for their energy needs
50
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
51
Glutathione
in reduced form detoxifies free radicals and peroxides, i.e. protects from oxidizing agents (eg fava beans, sulfonamides, primaquine, antituberculosis drugs)
52
which two pathways can give starting substrate of glycolysis (glyceraldehyde-3-P)?
Glucose metabolism | Fructose metabolism
53
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)
54
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)
55
glycolysis and gluconeogenesis dependent on metabolism of what?
galactose
56
uridyl transferase
galactose metabolism converts galactose-1-P to glucose 1-P with help of 4-epimerase
57
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
58
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
59
Essential amino acids
Glucogenic: Met, Val, His Glucogenic/ketogenic: Ile, Phe, Thr, Trp Ketogen: Leu, Lys
60
Acidic aa
Asp and Glu (negatively charged at body pH)
61
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
62
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
63
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
64
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
65
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).
66
Phenylalanine derivatives
--BH4--> Tyrosine (-> Thyroxine) --BH4--> Dopa (-> melanin) --vitB6--> dopamine --vitC--> NE --SAM--> Epi
67
Tryptophan derivatives
via B6 get Niacin --> NAD+/NADP+ via BH4 get Serotonin --> melatonin
68
Histidine derivative
via B6 --> histamine
69
Glycine derivatives
via B6 --> porphyrin --> heme
70
Arginine derivatives
Creatine Urea Nitric oxide
71
Glutamate derivatives
via B6 GABA Glutathione
72
Enzymes to know involved in catecholamine synthesis and tyrosine catabolism
1. Phenylalanine hydroxylase - PKU 2. Tyrosine hydroxylase 3. Dopa decarboxylase 4. Dopamine beta-hydroxylase 5. Phenylethanolamine N-methyltransferase
73
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
74
Findings in newborn with maternal PKU
c/b lack of proper diet during pregnancy microcephaly, ID, growth retardation, congenital heart defects
75
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)
76
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
77
Homocystinuria forms
all AR, the main problem is excess homocysteine and no cysteine so it cystein becomes essential 1. 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 2. dec affinity of cystathionine synthase for pyridoxal phosphate, i.e. B6 cofactor - tx inc vit B6 in diet 3. 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)
78
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
79
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
80
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
81
Glycogen storage disorders
12 types abnormal glycogen metabolism --> accumulation in cells
82
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
83
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
84
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
85
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
86
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)
87
Niemann-Pick disease
Deficient Enzyme: sphingomyelinase Accumulated Substrate: sphingomyelin Inheritance: AR Findings: progressive neurodegeneration, HSM, CHERRY-RED spot on macula, foam cells
88
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)
89
Krabbe's disease
Deficient Enzyme: Galactocerebrosidase Accumulated Substrate: Galactocerebroside Inheritance: AR Findings: peripheral neuropathy, development delay, optic atrophy, globoid cells
90
Metachromatic leukodystrophy
Deficient Enzyme: arylsulfatase A Accumulated Substrate: cerebroside sulfate Inheritance: AR Findings: central and peripheral demyelination with ataxia, dementia
91
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
92
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)
93
Fatty acid synthesis
inner mitochondrial membrane citrate in mito matrix "SYtrate = SYnthesis"
94
Fatty acid degradation
inner mitochondrial membrane carnitine brings fatty acids and CoA in from cytosol "CARnitine = CARnage of fatty acids"
95
carnitine deficiency
inability to transport long chain fatty acids to mitochondria --> toxic accumulation --> weakness, hypotonia, hypoketotic hypoglycemia
96
acyl-CoA dehydrogenase deficiency
inc dicarboxylic acids, dec glucose and ketones
97
number of kcal in 1 g of protein or carb
4
98
number kcal in 1 g of fat
9
99
pancreatic lipase
degradation of dietary TG in small intestine
100
Lipoprotein lipase (LPL)
degradation of TG circulating in chylomicrons and VLDLs
101
Hepatic TG lipase (HL)
degradation of TG remaining in IDL
102
Hormone-sensitive lipase
degradation of TG stored in adipocytes
103
Lecithin-cholesterol acyltransferase (LCAT)
catalyzes esterification of cholesterol, i.e. nascent HDL to mature HDL
104
Cholesterol ester transfer protein (CETP)
mediates tranfer of cholesterol esters to other lipoproteins particles , i.e. to VLDL, IDL, LDL
105
Apolipoprotein E
carrier protein recognized by hepatocytes --> allows liver to remove chylomicron remnants from blood found in chylomicron, chylomicron remnant, VLDL, IDL, HDL
106
Apoliprotein B-48
necessary for chylomicrons to be released into the blood from intestinal cells
107
Apolipoprotein A-I
activates lecithin-cholesterol acyltransferase (LCAT)
108
Apolipoprotein C-II
lipoprotein lipase cofactor
109
Apolipoprotein B-100
binds LDL receptor
110
LDL
transports cholesterol from Liver to Tissues
111
HDL
transports cholesterol from tissues to liver
112
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)
113
type 2a familial hypercholesterolemia
inc LDL, cholesterol in blood AD absent or dec LDL receptors accelerated atherosclerosis, tendon (Achilles) xanthomas, corneal arcus
114
type 4 hypertriglyceridemia
inc VLDL and TG in blood AD hepatic overproduction of VLDL causes pancreatitis
115
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
116
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)
117
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
118
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)