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biochem fun


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eukaryotic genome has ____ origin(s) of replication

replication begins at consensus sequence of AT base pairs
xeroderma pigmentosum
defective excision repair (especially of thymine dimers)

AR inheritance
RNA polymerases (eukaryotes)
RNA pol I: rRNA

*a-amantin inhibits RNA pol II

RNA pol has no proofreading fxn, but can initiate chains.

RNA pol II opens DNA at promotor regions
start codon

=methionine in eukaryotes
=f-met in prokaryotes
stop codons
splicing of mRNA
introns sliced out of primary mRNA transcripts
lariat shaped intermediate
snRNPs facilitate splicing by binding to mRNA and forming spliceosomes
RNA processing
occurs in ucleus in eukaryotes
1: capping on 5' end
2: polyadenylation on 3'
3: splicing out of introns

(before all this happens, the initial transcript is referred to as hnRNA)
tRNA structure
antiocodon end is opposite from 3' [aminoacyl] end
all have CCA at the 3' end, where the amino acid is bound
two factors responsible for accuracy of amino acid selection
aminoacyl tRNA synthetase
binding of charged tRNA to the proper codon

**a mischarged tRNA reads the usual codon but inserts the wrong amino acid
energy sources for translation
ATP: tRNA charging (via aminoacyl tRNA synthetase)

GTP: tRNA translocation
site of EXCRETED protein synthesis

goblet cells of small intestine and plasma cells are rich in RER (secrete mucus and antibodies, respectively)
nissl bodies
in neurons: RER

synthesize enzymes (like ChAT) and peptide neurotransmitters
stie of steroid synthesis and detoxification of drugs/poisons

hepatocytes and adrenal cortical cells have lots of SER
I cell disease
failure of addition of M-6-P to lysosomal proteins (so can't be targeted to lysosome)
are instead excreted
Sx: coarse facial features and restricted joint movement
drugs that act on microtubules
taxol (anti-breast CA)
chediak higashi syndrome
due to a microtubule polymerization defect

results in decreased phagocytosis
Kartagener's syndrome
due to dynein [ATPase that causes bending of cilia] arm defect
results in immotile cilia

(dyein = retrograde
vs kinesin = anterograde)
Gq receptor
HAV and M 1, and M 3

act thru phospholipase C

IP3 = increased [Ca]i
DAG = protein kinase C activity
Gs receptor
B1, B2, D1, H2, V2

acts thru adenylyl cyclase

increased cAMP = protein kinase A activity
Gi receptor
M2, A2, D2

INHIBITS adenylyl cyclase
collagen types
Be Cool, Read Books

type I: bones (90% of collagen)
II: cartilage
III: reticulin (skin, vessels, uterus, fetal tissue)
IV: basement membrane
X: epiphyseal plate
collagen synthesis
(inside fibroblasts)
1: alpha chains translated on RER
2: in ER: hydroxylation of proline and lysine [need vit C]
3: golgi: glycosylation of pro-alpha-chain, fomraiton of procollagen (triple helix)
4: procollagen molecules exocytosed into extracellular space
collagen synthesis
(outside fibroblasts)
5: procollagen peptidases cleave terminal regions (tropocollagen formed)
6: tropocollagen moelcules are reinforced by cross-linkage to make collagen fibrils
Ehlers Danlos syndrome
faulty collagen synthesis
->hyperextensible skin
->easy bruising
->hypermobile joints

*associated with berry aneurysms
osteogenesis imperfecta
AD inheritance
abnormal collagen synthesis
->multiple fractures (can occur during birth process)
->blue sclerae
->hearing loss (abnormal middle ear bones)
-> dental imperfections

*type II is fatal in utero
*often confused w/child abuse
found primarily in the liver

lower affinity (higher Km) but higher capacity (higher Vmax)

only HEXOkinase is feedback inhibited by G-6-P
irreversible enzymes of glycolysis
hexokinase/glucokinase (glucose to G-6-P)

PFK-1 [rate limiting]

pyruvate kinase (PEP to pyruvvate)

pyruvate dehydrogenase (pyruvate to acetyl CoA)
PDH complex
3 enzymes that require 4 cofactors:
-> B1 (thiamine): pyrophosphate
-> B2 (riboflavin): FAD
-> B3 (niacin): NAD
-> B5 (pantothenate): CoA
-> lipoic acid

*PDH is activated by:
NAD + : NAD ratio
high ADP
high Ca
PDH deficiency
backup of substrates (pyruvate and alanine)

results in lactic acidosis

*seen in alcoholics due to thiamine [B1] deficiency

Tx: high intake of ketogenic nutrients (fat, lysine, leucine)
cori cycle
transfers excess reducing equivalents (lactate, pyruvate) from RBCs/muscle to liver
allows muscle to fxn anaerobically (net 2 ATPs)
TCA cycle
3 NADH, 1 FADH2, 2 CO2, 1 GTP
= 12 ATP per acetyl CoA
= 24 total ATP per glucose
Can I Keep Selling Sex For Money, Officer?
irreversible enzymes of gluconeogenesis
Pathway Produces Fresh Glucose

pyruvate carboxylase
PEP carboxykinase
fructose 1-6 bisphosphatase
glucose-6 phosphatase

**muscle canNOT participate in gluconeogenesis (only liver, kidney, GI epithelium)

**hypoglocemia caused by deficiency in these enzymes
HMP shunt
produces ribose-5-phosphate from G-6-P for nucleotide synthesis
NADPH from NADP+ for fatty acid and steroid biosynthesis

*occurs in cytoplasm of mammary glands, liver, adrenal cortex
*no ATP produced
G6PD deficiency
rate limiting enzyme in HMP shunt
low NADPH in RBCs = unable to keep glutathione reduced (so can't detox)

*XLR inheritance
fructose intolerance
AR deficiency of aldolase B
fructose-1-phosphate accumulates
* low available phosphate left for gluconeo and glycogenolysis
==>hypoglycemia, jaundice, cirrhosis, vomiting
Tx: reduce intake of fructose and sucrose [glucose + fructose]
essential fructosuria
defect in fructokinase
frucose appears in blood and urine
(earlier enzyme in fructose metabolism pathway)
no galactose-1-P uridyltransferase
AR inheritance
accumlation of toxic substances
Sx: cataracts, hepatosplenomegaly, MR
Tx: exclude galactose and lactose (glucose + galactose)
galactokinase deficiency
galactosemia and -uria

can also lead to toxic accumulation [of galactitol] if too much galactose in diet
essential amino acids
ketogenic: leu, lys
gluco and keto: ile, phe, trp
gluco: met, thr, val, arg, his

acidic and basic amino acids
acidic: aspartate, glutamate
[- charge at pH 7.4]

basic: arginine, lysine
[+ charge at pH 7.4]

neutral: histidine (at 7.4)

**arg and lys found in high amounts in histones that bind to (-) DNA
urea cycle
Ordinarily, Careless Crappers Are Also Frivolous About Urination

ornithine, carbomyl phosphate, citrulline, aspartate, arginosuccinate, fuberate, arginine, urea

*in liver. carbamoyl phos step occurs in mt (rest in cytosol)
amino acid derivatives
phe: tyrosine, DA, NE, Epi, thyroxine, melanin
trp: niacin, 5HT, melatonin
his: histamine
glycine: porphyrin-> heme
arg: creatine, urea, NO
glutamte: GABA
deficiency of either
->phenylalanine hydroxylase ,or
-> THB cofactor
tyrosine becomes essential
Sx: MR, growth retardation, fair skin, eczema, musty body odor
Tx: low phe, high tyr in diet

AR inheritance
deficiency of homogentisic acid oxidase (in tyrosine deg path)
aklapton bodies -> black urine when standing
also have dark connective tissue
benign disease!
deficiency of
->tyrosinase (no melanin)
->tyrosine transporters

may be from a lack of migration of neural crest cells (like Hirschprung disease)
cysteine becomes essential
Sx: MR, osteoporosis, tall stature, kyphosis. lens probs, and atherosclerosis
inherited defect of renal tubular aa transporter for COLA
->cystine, ornithine, lysine, arginie

Tx: acetazolamide to alkalinize the urine
blocked degredation of branched aa's (ile, leu, val)

Sx: severe CNS defects, MR, death
adenosine deaminase deficiency
a cause of SCID
excess ATP and dATP imbalances the nucleotide pool
->feedback inhibition of ribonucleotide reductase
low lymph count (B and T)
Lesch-Nyhan syndrome
absence of HBPRTase
->converts hypoxanthine to IMP
and guanine to GMP
XLR inheritance
Sx: MR, self-mutilation, aggression, hyperuricemia
these organs' cells don't need insulin for glucose uptake

Brain, RBCs, Intestine, Cornea, Kidney, Liver
GLUT2 found in ____

GLUT4 found in ____
B cells of pancreas

muscle and fat
von Gierke's disease
type I glycogen storage disease
G-6-P deficiency
severe fasting hypoglycemia, high glycogen in liver, hepatomegaly, high blood lactate
Pompe's disease
type II glycogen storage disease
lysosomal a-1,4 glucosidase
cardiomegaly and systemic findings
leads to early death
Cori's disease
type III glycogen storage
deficiency of debranching eyzme a-1,6 glucosidase
milder form of von Gierke's
normal blood lactate levels
McArdle's disease
type V glycogen storage
skeletal muscle glycogen phosphorylase
high glycogen in muscle, but can't break it down
painful cramps + myoglobinuria with exercise
mneumonic for glycogen storage diseases
Very Poor Carbohydrate Metabolism

von Gierke's, Pompe's, Cori's, McArdle's
Fabry's disease
XLR inheritance
def: a-galactosidease A
accum: ceramide trihexoside
peripheral neuropathy of hands and feet
cardio/renal disease
Gaucher's disease
def: B-glucocerebrosidase
accum: glucocerebroside
hepatospleno, aseptic necrosis of femur
bone crisis, Gaucher's cells [macs]
Niemann-Pick disease
def: sphingomyelinase
accum: sphingomyelin
progressive neurodegeneration
cherry-red spot on macula
Tay-Sach's disease
def: hexosaminidase A
accum: GM2 ganglioside
progressive neurodegeneration
developmental delay
cherry red spot, onion skin lysozymes
Krabbe's disease
def: B-galactosidase
accum: galactocerebroside
peripheral neruopathy
developmental delay
optic atrophy
metachromatic leukodystrophy
def: arylsulfatase A
accum: cerebroside sulfate
central and periphreal demyelination
ataxia, dementia
Hurler's syndrome
def: a-L-iduronidase
accum: heparan/dermatan sulfate
developmental delay
gargoylism, airway obstruction, corneal clouding, hepatospleno
Hunter's syndrome
def: iduronate sulfatase
accum: heparan/dermatan sulfate
mild hurlers + aggressive behavior
NO corneal clouding
fatty acid metabolism sites
synthesis: citrate shuttle carries acetyl CoA to cytosol

oxidation: carnitine shuttle carries acyl-CoA to mt matrix
major apolipoproteins
A-1: activates LCAT
->catalyzes choesterol esterification (forms new HDL)
B-48: secretion of chylomicrons
B-100: binds to LDL receptor
C-II: cofactor for LPL
E: chylomicron remnant uptake by liver
familial dyslipidemias
I: hyper-chylomicronemia
IIa: hypercholesterol (low LDLR)
IIb: high LDL, VLDL
III: dysbeta (IDL, VLDL)
V: mixed (VLDL, chylos)
acute intermittent porphyria
defciency in uroporphyrinogen I synthetase
porphobilinogen, delta-ALA accumulate in urine
prophyria cutanea tarda
def: uroporphyrinogen decarboxylase
uroporphyrin accumulates in urine (tea colored)
photosensitivity also
symptoms of porphyrias
5 Ps
Painful abdomen
Pink urine
Psychological disturbances
Precipitated by drugs
Vitamin A
deficiency: night blindness, dry skin, impaired immune response
excess: arthralgias, fatigue, headaches, skin changes, sore throat, alopecia
vitamin B1
deficiency: Beriberi and Wernicke-Korsakoff syndrome

=cofactor for oxidative decarboxylation of a-keto acids [pyruvate, a-ketoglut)

dry beriberi: polyneuritis + muscle wasting
wet: high output cardiac failure (dilated cardiomyopathy), edema
vitamin B2
deficiency: angular stomatitis, corneal vasc, cheliosis

FAD and FMN are derived from riboflavin!
vitamin B3
deficiency: PELLAGRA.
->diarrhea, dermatitis, dementia, beefy glossitis
NAD derived from niacin
vitamin B5
deficiency: dermatitis, enteritis, alopecia, adrenal insuff
is a constituent of CoA
vitamin B6
def: confusions, hyper- irritability, periph neuropathy
*is converted to pyridoxal phosphate (AST ALT, decarboxylation, heme synthesis)
vitamin B12
cofactor for homocysteine methylation
stored in liver
only synthesized by bacteria
defic: dermatitis, enteritis [ingestion of raw eggs, antibiotic use]

*is a cofactor for carboxylation rxns
vit C
scurvy: swollen gums, bruising, anemia, poor wound healing
necessary in collagen synthesis
facilitates iron absorption
necessary as cofactor for DA->NE
vit E
defic = increased RBC fragility
is an antioxidant that protects RBCs from hemolysis
zinc deficiency
delayed wound healing, hypogonadism, low adult axillary/facial/pubic hair

can predispose to alcoholic cirrhosis
ethanol metabolism
NAD+ is the limiting reagent

alcohol dehydrogenase operates via zero-order kinetics

*disulfiram: inhibits acetaldehyde dehydrogenase (2nd step)
Kwashiokor: protein [edema, anemia, fatty liver]

Marasmus: protein-calorie [tissue wasting]
ethanol hypoglycemia
high NADH/NAD+ ratio (due to ethanol metabolism using NAD+)
causes diversion of pyruvate to lactate/ OAA to malate
inhibits gluconeogenesis-->hypoglycemia

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