Biochemistry Day 1
Terms
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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.
- ketone
- Thymine has a ___ group.
- methyl
- 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
- DNA Pol III =
- elongates DNA chain by adding nucleotides to 3' end; has 3'-5' exonuclease proofreading activity
- DNA Pol I =
- degrades RNA primer
- DNA ligase =
- seals
- 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. -
largest
most abundant
smallest -
RNA Pol I makes ___.
RNa Pol II makes ___.
RNA Pol III makes ___. -
rRNA
mRNA
tRNA - 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 =
-
UGA
UAA
UAG - 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.
- CCA
- 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
- lower
- Km =
- [S] at 1/2 Vmax
-
Competitive inhibitors:
effect on Vmax =
effect on Km = -
unchanged
increase -
Noncompetitive inhibitors:
effect on Vmax =
effect on Km = -
lower
unchanged - Most cells are in which phase?
- G0
- Rapidly dividing cells have a short ___ phase.
- G1
- 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:
vimentin
desmin
cytokeratin
GFAP
neurofilaments -
connective tissue
muscle
epithelial cells
neuroglia
neurons - 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.
- 2
-
Activated carriers: ready?
phosphoryl
electrons
acyl
CO2
1-carbon units
methyl groups
aldehydes
glucose
choline -
ATP
NADH/NADPH/FADH2
coenzyme A, lipoamide
biotin
tetrahydrofolates
SAM
TPP
UDP glucose
CDP choline - ATP + methinonine =
- S-adenosyl methionine (methyl donor)
- Regeneration of methionine and SAM requires Vit__.
- B12
-
Signal molecule precursors:
ATP -->
GTP -->
glutamate -->
choline -->
arachidonate -->
fructose 6P -->
1,3 BPG --> -
cAMP
cGMP
GABA
Ach
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?
- alanine
- 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 -
3 NADH
1 FADH2
2 CO2
1 GTP
= 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?
- oligomycin
- What is the uncoupling agent that inc. mito membrane permeability causing dec. proton gradient, continued O2 consumption, and no ATP production?
- 2,4-dinitrophenol
- 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.
- negatively
-
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
serotonin
melatonin -
AA derivatives:
His --> - histamine (easy peasy)
-
AA derivatives:
Gly --> - porphyrin --> heme
-
AA derivatives:
Arg --> -
creatine
urea
nitric oxide -
AA derivatives:
Glu --> - GABA
- 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 ___.
- OFF, ON
- Insulin turns glycogen synthase ___, glycogen phosphorylase ___.
- ON, OFF
- 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:
inheritance
enzyme
accumulated substrate
findings -
AR
hexosaminidase A
GM2 ganglioside
progressive neurodegeneration, developmental delay, cherry red spot, onion skin lysosomes -
Fabry's disease:
inheritance
enzyme
accumulated substrate
findings -
XR
a-galactosidase A
ceremide trihexoside
peripheral neuropathy of hands/feet, angiokeratomas, CV/renal disease -
Gaucher's disease:
inheritance
enzyme
accumulated substrate
findings -
AR
beta-glucocerebrosidase
glucocerebroside
hepatosplenomegaly, aseptic necrosis of femur, bone crises, Gauchers cells (macs) -
Niemann-Pick disease:
inheritance
enzyme
accumulated substrate
findings -
AR
sphingomyelinase
sphingomyelin
progressive neurodegeneration, hepatosplenomegaly, cherry red spot -
Krabbe's disease:
inheritance
enzyme
accumulated substrate
findings -
AR
beta-galactosidase
galactocerebroside
peripheral neuropathy, developmental delay, optic atropy -
Metachromatic Leukodystrophy:
inheritance
enzyme
accumulated substrate
findings -
AR
arylsulfatase A
cerebroside sulfate
central and peripheral demyelination w/ataxia, dementia -
Hurler's syndrome:
inheritance
enzyme
accumulated substrate
findings -
AR
a-L-iduronidase
heparan sulfate, dermatan sulfate
developmental delay, gargoylism, airway obstruction, corneal clouding, hepatosplenomegaly -
Hunter's syndrome:
inheritance
enzyme
accumulated substrate
findings -
XR
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