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Biochemistry Day 1


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Which histones form the nucleosome octamers that DNA loops around?
H2A, H2B, H3, H4
H1 ties nucleosomes together in a ___-nm string.
30 nm
Heterochromatin is ___ and transcriptionally ___.
condensed, inactive
Euchromatin is ___ and transcriptionally ___.
loose, active
Purines consist of ___ & ___, and have ___ ring(s)
Adenine & Guanine; 2 rings
Pyridimidines consist of ___, ___, & ___ and have ___ ring(s).
Cytosine, Uracil, Thymine; 1 ring
Guanine has a ___ group.
Thymine has a ___ group.
Nucleotides are linked by ___'-___' ___ bonds.
3'-5' phosphodiesterase bond
Silent mutation =
same AA, often base change in 3rd position of codon
Missense mutation =
changed AA (new AA is similar in chemical structure)
Nonsense mutation =
early STOP codon
Frame shift mutation =
misreading of all downstream nucleotides, result in truncated protein (WORST damage!)
DNA topoisomerases =
create nick in helix to relieve supercoils
Primase =
makes RNA primer for DNA Pol III to start replication
elongates DNA chain by adding nucleotides to 3' end; has 3'-5' exonuclease proofreading activity
DNA Pol I =
degrades RNA primer
DNA ligase =
DNA repair: ___ locates damaged base, ___ makes a break upstream, ___ removes the chunk of nucleotides, ___ fills gap, ___ seals.
excision repair-specific glycosylase, endonuclease, exonuclease, DNA pol, DNA ligase
DNA repair defects:
Xeroderma pigmentosum ~ ___
Ataxia-telangiectasia ~ ___
Bloom's syndrome ~ ___
Fanconi's anemia ~ ___
XP ~ UV light
AT ~ xray
BS ~ radiation
FA ~ crosslinking agents
Xeroderma pigmentosum is where you can't repair ___ ___ which form in DNA when exposed to UV light. Associated with ___ & ___.
thymine dimers
dry skin, melanoma
mRNA is the ___ type of RNA.
rRNA is the ___ type of RNA.
tRNA is the ___ type of RNA.
most abundant
RNA Pol I makes ___.
RNa Pol II makes ___.
RNA Pol III makes ___.
alpha-amanitin (from mushrooms) inhibits RNA Pol ___.
RNA Pol II --> cannot open DNA to start transcription
Prokaryotic RNA Pol makes ___.
all 3 kinds of RNA.
Stop codons =
Promoter =
site where RNA Pol and TFs bind DNA upstream from gene locus
Enhancer =
piece of DNA that alters a gene expression by binding TFs
Operator =
where gene repressors bind
Exons =
encode the actual genetic info
After mRNA transcription, 3 processes:
1) capping 5'end (7-methyl-G)
2) polyAAA tail
3) splice out introns
* then transport out of nucleus
All tRNAs have _ _ _ at the 3' end which binds AA.
What is the enzyme that links an AA to the 3'end of tRNA?
aminoacyl-tRNA synthase - 1 per AA, uses ATP
What is tRNA wobble?
mRNA codons differing in 3rd base position may still code for same tRNA/AA
Methionine sits in the ___ site on the ribosome, the incoming AA lands in the ___ site.
P site, A site
How is GTP used in protein synthesis?
"tRNA gripping & going places" - translocation along the ribosome
___ Km = higher affinity
Km =
[S] at 1/2 Vmax
Competitive inhibitors:
effect on Vmax =
effect on Km =
Noncompetitive inhibitors:
effect on Vmax =
effect on Km =
Most cells are in which phase?
Rapidly dividing cells have a short ___ phase.
How can enzymes be regulated?
1) synthesis/destruction
2) zymogen cleavage
3) phosphorylation
4) feedback inhibition
5) transcriptional regulation
What happens in the RER?
1) make secretory proteins
2) add N-linked oligosaccharide to proteins
What are Nissl bodies?
neuronal RER that make enzymes and NTs (not found in axon hillock or axon)
What happens in the SER?
1) steroid synthesis
2) detox of drugs/poisons
Which cells have a lot of RER?
goblet cells, plasma cells
Which cells have a lot of SER?
hepatocytes, adrenal cortex
I-cell Disease =
Caused by failure to add mannose-6-phosphate to lysosome proteins --> enzymes secreted out of cell instead of going to lysosome. Have coarse facial features and restricted joint movement.
What are the 6 functions of Golgi?
1) distribute proteins/lipids
2) modify N-oligosaccharides
3) add O-oligosaccharides
4) assemble proteoglycans
5) sulfation of sugars
6) add mannose-6-phosphate to lysosomal proteins which targets protein to lysosome
Drugs that act on microtubules:
1) mebendazole/thiabendazole for worms
2) griseofulvin for fungi
3) taxols for breast cancer
4) vinca alkaloids for cancer
5) colchicine for gout
Chediak-Higashi syndrome =
microtubule polymerization defect --> dec. phagocytosis
Cilia structure =
9 + 2 arrangement microtubules, dynein for retrograde axon transport, kinesin for anterograde axon transport
Microtubules are found in what cell structures?
flagella, cilia, mitotic spindles
Kartagener's syndrome =
dynein arm defect --> immotile cilia (infertility, chronic respiratory infection)
What is the function of cholesterol in plasma membrane?
promote stability, makes up ~ 50% of membrane
Phosphatidylcholine =
aka lecithin; component of RBC membrane, myelin, bile, surfactant (dipalmitoyl phosphatidylcholine); helps esterify cholesterol
Na/K pump =
3 Na out: 2 K in (1 ATP used)
Oubain inhibits Na/K pump by:
binding to K site
Digoxin and digitoxin inhibit Na/K pump -->
inc. heart contractility
Gq goes to which receptors to activate phospholipase C?
H1, a1, V1, M1, M3
IP3 -->
DAG -->
inc. intracellular calcium
protein kinase C
Gs subunit goes to which receptors to activiate adenylyl cyclase?
B1, B2, D1, H2, V2
Gi subunit goes to which receptor to inhibit adenylyl cyclase?
M2, a2, D2
Type 1 collagen found in:
BONE, tendon, skin, fascia, teeth, cornea, late wound repair
Type 2 collagen found in:
CARTILAGE, vitreous body, nucleus pulposus
Type 3 collagen found in:
skin, vessels, uterus, fetal tissue, granulation tissue (early wound repair)
Type 4 collagen found in:
basement membrane
Type 10 collagen found in:
epiphyseal plate
Preprocollagen =
collagen alpha chains, Gly-X-Y (proline, lysine)
Scurvy =
VitC deficiency, cannot hydroxylate preprocollagen in ER
Procollagen =
triple helix of 3 alpha chains, made in Golgi
Osteogenesis imperfecta =
AD disorder, abnormal collagen synthesis at triple helix step --> multiple fractures, blue sclera, bad teeth, hearing loss
Once triple helix procollagen get outside fibroblast:
procollagen peptidases cleave terminal ends --> insoluble tropocollagen
Ehlers-Danlos syndrome =
faulty collagen synthesis at terminal cleavage step --> hyperextensible skin, hypermobile joints, easy bruising, associated with BERRY ANEURYSMS!
Tropocollagen is crosslinked by ___ to make collagen fibrils.
lysyl oxidase
IHC stains:
connective tissue
epithelial cells
Metabolism sites: mitochondria
1) fatty acid oxidation
2) acetyl CoA production
3) TCA cycle
Metabolism sites: cytoplasm
1) glycolysis
2) fatty acid synthesis
3) HMP shunt
4) protein synthesis (RER)
5) steroid synthesis (SER)
Metabolism sites: both mito and cyto
1) gluconeogenesis
2) urea cycle
3) heme synthesis
Aerobic metabolism of glucose yields ___ ATP via malate shuttle, ___ ATP via G3P shuttle.
38, 36
Anaerobic glycolysis yields ___ ATP per glucose.
Activated carriers: ready?
1-carbon units
methyl groups
coenzyme A, lipoamide
UDP glucose
CDP choline
ATP + methinonine =
S-adenosyl methionine (methyl donor)
Regeneration of methionine and SAM requires Vit__.
Signal molecule precursors:
ATP -->
GTP -->
glutamate -->
choline -->
arachidonate -->
fructose 6P -->
1,3 BPG -->
PGs, LTs, TX
fructose 1,6 BP (via PFK)
2,3 BPG
NAD+ is generally used in catabolic or anabolic processes?
catabolic, H+ away as NADH
NADPH is used in ___ processes as a supply of reducing equivalents. It is a product of which pathway that takes place in cytoplasm?
anabolic, HMP shunt
NADPH needed for 3 things:
1) anabolic processes
2) respiratory burst
3) P-450
NADPH oxidase deficiency -->
chronic granulomatous disease, cannot do first step in respiratory burst!
Superoxide dismutase =
turns O2- into H2O2
Myeloperoxidase =
turns H2O2 into HOCl (bleach), lyses phagocytosed bacteria!
Catalase =
converts H2O2 into water, and oxidizes GSH to GSSH
Glutathione reductase =
Duh. Reduces glutathione by oxidizing NADPH
Glucose 6 phosphate dehydrogenase =
makes NADPH, first step in HMP shunt (G6P to 6PG)
Hexokinase is found ___.
Glucokinase is found ___.
throughout body
in Liver
Glycolysis, irreversible enzymes (4):
1) hexokinase/glucokinase
2) phosphofructokinase
3) pyruvate kinase
4) pyruvate dehydrogenase
Glycolytic enzyme deficiency -->
hemolytic anemia, because RBC only use glucose anaerobically (no mito)
Pyruvate dehydrogenase complex requires which 5 cofactors?
1) pyrophosphate (B1/thiamine; TPP)
2) FAD (B2, riboflavin)
3) NAD (B3, niacin)
4) CoA (B5, pantothenate)
5) lipoic acid
What other complex uses the same cofactors as pyruvate dehydrogenase?
a-ketoglutarate dehydrogenase
Pyruvate dehydrogenase is activated by exercise which inc. 3 things:
1) inc. NAD/NADH ratio
2) inc. ADP
3) inc. calcium
Reaction catalyzed by pyruvate dehydrogenase:
pyruvate + NAD + CoA --> acetyl CoA + CO2 + NADH
What happens in pyruvate dehydrogenase deficiency (vitamin def, alcoholism)?
backup of pyruvate & ala --> lactic acidosis, neurologic defects!
* TX ~ eat ketogenic nutrients like fat or lys & leu
Which AA serves as a carrier of amino groups from muscle to liver?
2 functions of Oxaloacetate:
1) TCA cycle (mito)
2) gluconeogenesis (mito & cytoplasm)
What catalyzes reaction of pyruvate --> lactate?
Lactate Dehydrogenase (LDH)
Which enzyme converts pyruvate --> Oxaloacetate?
pyruvate carboxylase
Which enzyme converts oxaloacetate --> PEP for gluconeogenesis?
PEP carboxykinase
What is the purpose of the Cori cycle?
allows muscle to function anaerobically (net 2 ATP); muscle glucose --> pyruvate --> lactate which goes to Liver and is made into glucose again
TCA cycle produces:
___ NADH
___ FADH2
___ CO2
___ GTP
= ___ ATP
2 CO2
= 12 ATP per acetyl CoA
What are the elements (in order) of the TCA cycle? Start after pyruvate --> acetyl CoA.
acetyl CoA + oxaloacetate --> citrate --> isocitrate --> a-KG --> succinyl CoA --> succinate --> fumarate --> malate --> oxaloacetate
Which ETC inhibitors directly inhibit electron transport, causing dec. proton gradient and block of ATP synthesis?
rotenone, antimycin A, CN, CO
Which is the ATPase inhibitor that directly inhibits mito ATPase, causing inc. proton gradient but no ATP production?
What is the uncoupling agent that inc. mito membrane permeability causing dec. proton gradient, continued O2 consumption, and no ATP production?
Gluconeogenesis, irreversible enzymes (w/o which leads to hypoglycemia):
1) pyruvate carboxylase
2) PEP carboxykinase
3) fructose 1,6-BPase
4) glucose 6 phosphatase
Which organs can do gluconeogenesis?
liver, kidney, intestine
* muscle cannot!!
What are the 2 functions of the HMP shunt (in cytoplasm)?
1) make ribose-5P from glucose-6P for nucleotide synthesis
2) generate NADPH for FA synthesis, steroid synthesis, reducing glutathione
G6PD deficiency:
- what kind of anemia?
- inheritance?
- epidemiology?
- intracellular body?
- hemolytic anemia due to low NADPH in oxidative situations
- XR
- blacks more
- Heinz body (Hb precipitate)
Which oxidizing agents can precipitate a G6PD deficiency attack?
- fava beans
- anti-TB drugs
- sulfonamides
- primaquine
What is the missing enzyme in fructose intolerance (AR dz)?
aldolase B - accumulate fructose 1P causing dec. in available P and inhibit glycogenolysis & gluconeogenesis
What is the defective enzyme in essential fructosuria?
fructokinase - benign, asymptomatic, just fructose appears in blood/pee
What is the absent enzyme in galactosemia (AR disease)?
galactose-1P uridyltransferase - accumulate toxic substances causing mental retardation, hepatomegaly, cataracts!
* TX ~ don't eat lactose or galactose
Who gets lactase deficiency?
blacks, Asians
Essential AA:
ketogenic (2)=
glucogenic (5)=
both (3)=
Leu, Lys
Met, Thr, Val, Arg, His
Ile, Phe, Trp
What are the si/sx of fructose intolerance?
hypoglycemia, jaundice, cirrhosis, vomiting
* TX ~ don't eat fructose or sucrose!
Which 2 essential AA are required during periods of growth?
Arg, His
Which 2 basic, positively charged AA are found in histones because they bind to negatively charged DNA?
Arg, Lys
At body pH 7.4, acidic AA glutamate and aspartate are ___ charged.
Urea cycle:
CO2 + NH4 --> carbamoyl P... then what?
carbamoyl P + ornithine --> citrulline, + aspartate --> argininosuccinate, - fumarate (join TCA cycle) --> arginine, + H2O --> UREA!
AA derivatives:
Phe -->
tyrosine --> thyroxine, Dopa --> melanin, dopamine --> NE --> Epi
AA derivatives:
Trp -->
niacin --> NAD/NADP
AA derivatives:
His -->
histamine (easy peasy)
AA derivatives:
Gly -->
porphyrin --> heme
AA derivatives:
Arg -->
nitric oxide
AA derivatives:
Glu -->
What is missing in Phenylketonuria?
either low phenylalanine hydroxylase, or low tetrahydrobiopterin cofactor - can't make Tyrosine
How does PKU present?
mental retardation, growth retardation, musty odor, fair skin, eczema
* AR disease, 1:10 000
* TX ~ lower Phe and raise Tyr in diet
What disease makes urine turn black on standing and makes connective tissue dark? May have arthralgias but otherwise benign condition.
Alkaptonuria, deficiency of homogentisic acid oxidase in degradative pathway of Tyrosine
What are the causes of albinism?
1) no tyrosinase - can't make melanin from Tyr
2) defective Tyr transporters
What are 3 forms of homocystinuria?
1) cystathionine sythase def.
2) dec. affinity of cystathionine synthase for B6
3) methionine synthase def.
What are the si/sx of homocystinuria?
mental retardation, tall stature, osteoporosis, kyphosis, lens subluxation, atherosclerosis
Which AA transporters are missing from kidney tubules in the disease Cystinuria?
COLA - cysteine, ornithine, lysine, arginine
What is a result of cystinuria?
Cystine kidney stones, TX acetazolamide to alkalinize urine
What is the disease where you can't degrade branched AA (Ile, Leu, Val)?
Maple Syrup Urine disease - deficient a-ketoacid dehydrogenase lead to inc. Leu in blood
How can Maple Syrup Urine disease present?
severe CNS defects, mental retardation, death
What happens if there is deficient Adenosine deaminase?
Build up ATP and dATP --> inhibit ribonucleotide reductase --> prevent DNA synthesis and lymphocyte production --> SCID!!
What is the enzyme missing in Lesch-Nyan syndrome?
HGPRTase, which converts hypoxanthine to IMP and guanine to GMP
What are some manifestations of Lesch-Nyan syndrome?
- hyperuricemia, gout
- retardation
- self-mutilation, aggression
In fasted state, Liver glycogen will eventually become ___ and ___.
glucose (via G6P --> glu), ketones (via G6P --> pyruvate --> acetyl CoA)
Insulin is needed for glucose uptake in ___ and ___.
skeletal muscle, adipose
GLUT 2 receptors are found:
beta cells
GLUT 4 receptors are found:
muscle and fat
5 anabolic effects of insulin:
1) glucose uptake
2) glycogen synthesis
3) TG synthesis
4) Na retention in kidney
5) protein synthesis in muscle
Glucagon turns glycogen synthase ___, glycogen phosphorylase ___.
Insulin turns glycogen synthase ___, glycogen phosphorylase ___.
Von Gierke's disease =
glucose 6-phosphatase deficiency; hypoglycemia, hepatomegaly, inc. blood lactate
Pompe's disease =
lysosomal a-1,4 glucosidase deficiency; cardiomegaly, hepatomegaly, lack muscle tone or weakness (ie exercise intolerance, difficulty breathing)
Cori's disease =
lysosomal a-1,6 glucosidase; mild hypoglycemia, normal lactate
McArdle's disease =
skeletal muscle glycogen phosphorylase deficiency; can't break down glycogen; get cramps and myoglobinuria upon exercising
Tay-Sach's disease:
accumulated substrate
hexosaminidase A
GM2 ganglioside
progressive neurodegeneration, developmental delay, cherry red spot, onion skin lysosomes
Fabry's disease:
accumulated substrate
a-galactosidase A
ceremide trihexoside
peripheral neuropathy of hands/feet, angiokeratomas, CV/renal disease
Gaucher's disease:
accumulated substrate
hepatosplenomegaly, aseptic necrosis of femur, bone crises, Gauchers cells (macs)
Niemann-Pick disease:
accumulated substrate
progressive neurodegeneration, hepatosplenomegaly, cherry red spot
Krabbe's disease:
accumulated substrate
peripheral neuropathy, developmental delay, optic atropy
Metachromatic Leukodystrophy:
accumulated substrate
arylsulfatase A
cerebroside sulfate
central and peripheral demyelination w/ataxia, dementia
Hurler's syndrome:
accumulated substrate
heparan sulfate, dermatan sulfate
developmental delay, gargoylism, airway obstruction, corneal clouding, hepatosplenomegaly
Hunter's syndrome:
accumulated substrate
iduronate sulfatase
heparan sulfate, dermatan sulfate
mild Hurler's + aggressive behavior, no corneal clouding
What are si/sx of Fanconi's anemia?
AR disease of DNA repair defect, pancytopenia, cafe au lait spots, short stature, radial arm deformities (no thumbs), small testicles, small head, mental retardation, small kidneys

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