Biochem Fun

Front 1

eukaryotic genome has ____ origin(s) of replication

Back 1

multiple

replication begins at consensus sequence of AT base pairs

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xeroderma pigmentosum

Back 2

defective excision repair (especially of thymine dimers)

AR inheritance

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RNA polymerases (eukaryotes)

Back 3

RNA pol I: rRNA
II: mRNA
III: tRNA

*a-amantin inhibits RNA pol II

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

RNA pol II opens DNA at promotor regions

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start codon

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AUG

=methionine in eukaryotes
=f-met in prokaryotes

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stop codons

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UGA
UAA
UAG

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splicing of mRNA

Back 6

introns sliced out of primary mRNA transcripts
lariat shaped intermediate
snRNPs facilitate splicing by binding to mRNA and forming spliceosomes

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RNA processing

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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)

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tRNA structure

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antiocodon end is opposite from 3' [aminoacyl] end
all have CCA at the 3' end, where the amino acid is bound

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two factors responsible for accuracy of amino acid selection

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aminoacyl tRNA synthetase
binding of charged tRNA to the proper codon

**a mischarged tRNA reads the usual codon but inserts the wrong amino acid

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energy sources for translation

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ATP: tRNA charging (via aminoacyl tRNA synthetase)

GTP: tRNA translocation

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RER

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site of EXCRETED protein synthesis

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

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nissl bodies

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in neurons: RER

synthesize enzymes (like ChAT) and peptide neurotransmitters

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SER

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stie of steroid synthesis and detoxification of drugs/poisons

hepatocytes and adrenal cortical cells have lots of SER

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I cell disease

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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

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drugs that act on microtubules

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mebendazole
taxol (anti-breast CA)
griseofulvin
vincristine/vinblastine
colchicine

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chediak higashi syndrome

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due to a microtubule polymerization defect

results in decreased phagocytosis

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Kartagener's syndrome

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due to dynein [ATPase that causes bending of cilia] arm defect
results in immotile cilia

(dyein = retrograde
vs kinesin = anterograde)

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Gq receptor

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HAV and M 1, and M 3

act thru phospholipase C

IP3 = increased [Ca]i
DAG = protein kinase C activity

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Gs receptor

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B1, B2, D1, H2, V2

acts thru adenylyl cyclase

increased cAMP = protein kinase A activity

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Gi receptor

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M2, A2, D2

INHIBITS adenylyl cyclase

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collagen types

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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

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collagen synthesis
(inside fibroblasts)

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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

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collagen synthesis
(outside fibroblasts)

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5: procollagen peptidases cleave terminal regions (tropocollagen formed)
6: tropocollagen moelcules are reinforced by cross-linkage to make collagen fibrils

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Ehlers Danlos syndrome

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faulty collagen synthesis
->hyperextensible skin
->easy bruising
->hypermobile joints

*associated with berry aneurysms

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osteogenesis imperfecta

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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

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glucokinase

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found primarily in the liver

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

only HEXOkinase is feedback inhibited by G-6-P

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irreversible enzymes of glycolysis

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hexokinase/glucokinase (glucose to G-6-P)

PFK-1 [rate limiting]

pyruvate kinase (PEP to pyruvvate)

pyruvate dehydrogenase (pyruvate to acetyl CoA)

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PDH complex

Back 28

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

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PDH deficiency

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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)

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cori cycle

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transfers excess reducing equivalents (lactate, pyruvate) from RBCs/muscle to liver
allows muscle to fxn anaerobically (net 2 ATPs)

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TCA cycle

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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?

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irreversible enzymes of gluconeogenesis

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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

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HMP shunt

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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

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G6PD deficiency

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rate limiting enzyme in HMP shunt
low NADPH in RBCs = unable to keep glutathione reduced (so can't detox)
leads to HEMOLYTIC ANEMIA

*XLR inheritance

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fructose intolerance

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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]

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essential fructosuria

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defect in fructokinase
BENIGN, ASYMPTOMATIC
frucose appears in blood and urine
(earlier enzyme in fructose metabolism pathway)

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galactosemia

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no galactose-1-P uridyltransferase
AR inheritance
accumlation of toxic substances
Sx: cataracts, hepatosplenomegaly, MR
Tx: exclude galactose and lactose (glucose + galactose)

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galactokinase deficiency

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galactosemia and -uria

can also lead to toxic accumulation [of galactitol] if too much galactose in diet

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essential amino acids

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ketogenic: leu, lys
gluco and keto: ile, phe, trp
gluco: met, thr, val, arg, his

PriVaTe TIM HALL

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acidic and basic amino acids

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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

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urea cycle

Back 41

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)

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amino acid derivatives

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phe: tyrosine, DA, NE, Epi, thyroxine, melanin
trp: niacin, 5HT, melatonin
his: histamine
glycine: porphyrin-> heme
arg: creatine, urea, NO
glutamte: GABA

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phenyketonuria

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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

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alkaptonuria

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deficiency of homogentisic acid oxidase (in tyrosine deg path)
aklapton bodies -> black urine when standing
also have dark connective tissue
benign disease!

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albinism

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deficiency of
->tyrosinase (no melanin)
->tyrosine transporters

may be from a lack of migration of neural crest cells (like Hirschprung disease)

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homocystinuria

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cysteine becomes essential
Sx: MR, osteoporosis, tall stature, kyphosis. lens probs, and atherosclerosis

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cystinuria

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inherited defect of renal tubular aa transporter for COLA
->cystine, ornithine, lysine, arginie

Tx: acetazolamide to alkalinize the urine

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MSUD

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blocked degredation of branched aa's (ile, leu, val)

Sx: severe CNS defects, MR, death

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adenosine deaminase deficiency

Back 49

a cause of SCID
excess ATP and dATP imbalances the nucleotide pool
->feedback inhibition of ribonucleotide reductase
low lymph count (B and T)

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Lesch-Nyhan syndrome

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absence of HBPRTase
->converts hypoxanthine to IMP
and guanine to GMP
XLR inheritance
Sx: MR, self-mutilation, aggression, hyperuricemia

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these organs' cells don't need insulin for glucose uptake

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BRICK L

Brain, RBCs, Intestine, Cornea, Kidney, Liver

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GLUT2 found in ____

GLUT4 found in ____

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B cells of pancreas

muscle and fat

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von Gierke's disease

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type I glycogen storage disease
G-6-P deficiency
severe fasting hypoglycemia, high glycogen in liver, hepatomegaly, high blood lactate

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Pompe's disease

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type II glycogen storage disease
lysosomal a-1,4 glucosidase
cardiomegaly and systemic findings
leads to early death

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Cori's disease

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type III glycogen storage
deficiency of debranching eyzme a-1,6 glucosidase
milder form of von Gierke's
normal blood lactate levels

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McArdle's disease

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type V glycogen storage
skeletal muscle glycogen phosphorylase
high glycogen in muscle, but can't break it down
painful cramps + myoglobinuria with exercise

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mneumonic for glycogen storage diseases

Back 57

Very Poor Carbohydrate Metabolism

von Gierke's, Pompe's, Cori's, McArdle's

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Fabry's disease

Back 58

XLR inheritance
def: a-galactosidease A
accum: ceramide trihexoside
peripheral neuropathy of hands and feet
angiokeratomas
cardio/renal disease

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Gaucher's disease

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def: B-glucocerebrosidase
accum: glucocerebroside
hepatospleno, aseptic necrosis of femur
bone crisis, Gaucher's cells [macs]

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Niemann-Pick disease

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def: sphingomyelinase
accum: sphingomyelin
progressive neurodegeneration
hepatospleno
cherry-red spot on macula

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Tay-Sach's disease

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def: hexosaminidase A
accum: GM2 ganglioside
progressive neurodegeneration
developmental delay
cherry red spot, onion skin lysozymes

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Krabbe's disease

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def: B-galactosidase
accum: galactocerebroside
peripheral neruopathy
developmental delay
optic atrophy

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metachromatic leukodystrophy

Back 63

def: arylsulfatase A
accum: cerebroside sulfate
central and periphreal demyelination
ataxia, dementia

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Hurler's syndrome

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def: a-L-iduronidase
accum: heparan/dermatan sulfate
developmental delay
gargoylism, airway obstruction, corneal clouding, hepatospleno

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Hunter's syndrome

Back 65

*XLR*
def: iduronate sulfatase
accum: heparan/dermatan sulfate
mild hurlers + aggressive behavior
NO corneal clouding

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fatty acid metabolism sites

Back 66

synthesis: citrate shuttle carries acetyl CoA to cytosol

oxidation: carnitine shuttle carries acyl-CoA to mt matrix

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major apolipoproteins

Back 67

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

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familial dyslipidemias

Back 68

I: hyper-chylomicronemia
IIa: hypercholesterol (low LDLR)
IIb: high LDL, VLDL
III: dysbeta (IDL, VLDL)
IV: VLDL, TG
V: mixed (VLDL, chylos)

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acute intermittent porphyria

Back 69

defciency in uroporphyrinogen I synthetase
porphobilinogen, delta-ALA accumulate in urine

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prophyria cutanea tarda

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def: uroporphyrinogen decarboxylase
uroporphyrin accumulates in urine (tea colored)
photosensitivity also

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symptoms of porphyrias

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5 Ps
Painful abdomen
Pink urine
Polyneuropathy
Psychological disturbances
Precipitated by drugs

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Vitamin A

Back 72

[retinol]
deficiency: night blindness, dry skin, impaired immune response
excess: arthralgias, fatigue, headaches, skin changes, sore throat, alopecia

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vitamin B1

Back 73

[thiamine]
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

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vitamin B2

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[riboflavin]
deficiency: angular stomatitis, corneal vasc, cheliosis

FAD and FMN are derived from riboflavin!

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vitamin B3

Back 75

[niacin]
deficiency: PELLAGRA.
->diarrhea, dermatitis, dementia, beefy glossitis
NAD derived from niacin

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vitamin B5

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[pantothenate]
deficiency: dermatitis, enteritis, alopecia, adrenal insuff
is a constituent of CoA

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vitamin B6

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[pyridoxine]
def: confusions, hyper- irritability, periph neuropathy
*is converted to pyridoxal phosphate (AST ALT, decarboxylation, heme synthesis)

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vitamin B12

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[cobalamin]
cofactor for homocysteine methylation
stored in liver
only synthesized by bacteria

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biotin

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defic: dermatitis, enteritis [ingestion of raw eggs, antibiotic use]

*is a cofactor for carboxylation rxns

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vit C

Back 80

scurvy: swollen gums, bruising, anemia, poor wound healing
necessary in collagen synthesis
facilitates iron absorption
necessary as cofactor for DA->NE

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vit E

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defic = increased RBC fragility
is an antioxidant that protects RBCs from hemolysis

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zinc deficiency

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delayed wound healing, hypogonadism, low adult axillary/facial/pubic hair

can predispose to alcoholic cirrhosis

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ethanol metabolism

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NAD+ is the limiting reagent

alcohol dehydrogenase operates via zero-order kinetics

*disulfiram: inhibits acetaldehyde dehydrogenase (2nd step)

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malnutritions

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Kwashiokor: protein [edema, anemia, fatty liver]

Marasmus: protein-calorie [tissue wasting]

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ethanol hypoglycemia

Back 85

high NADH/NAD+ ratio (due to ethanol metabolism using NAD+)
causes diversion of pyruvate to lactate/ OAA to malate
inhibits gluconeogenesis-->hypoglycemia