molecular biochem Flashcards
Chromatin structure
DNA exist in the condensed, chromatin form
DNA loops 2x around the histone octomer to form a nucleoSOME
H1 binds the nucleosone and to linker DNA and stabilize the chromatin fiber
Phosphate groups give DNA a negative charge
Lysine and argininge give histone a + charge
DNA and histone synthesis occurs in S phase
mito have their own DNA which is circular and doesnt utilize histones
Heterochromatin
condensed, darker, inaccessible and inactive, increased methylation makes DNA mute
decreased acetylation that makes the DNA active
Barr bodies (inactive x chromosome in the periphery of nucleus)
Euchromatin
less condensed, appears lighter on EM
transcriptionally active, stericallu accessible
Euchromatin is expressed
DNA methylation
Changes the expression of a DNA segment without changing the sequence, involved with aging, carcinogenesis, genomic imprinting, transposabl eelement repression and inactivation of the X chromosome
impriming – dna methylation,
Methylation is within a gene promoter (CpG islands)
typically silences gene transcription
CpG islands for methylating the DNA segment
Histone methylation is reversible, can also cause activation in the right spot
histone acetylation removes the histones positive charge–> relaxed DNA coiling,
nucleotides
Nucleoside = base + deoxy ribose (sugar) NucleoTide= base + deoxyribose + phosphaTe, linked by 3'-5' phosphodiester bond
5’ of incoming base what joins the regular 3’ end
Pur As Gold (adenin, Guanin are purines and double ringed) CUT the Py (pyrimidines -cytosine, adenin guanine
CG triple bonds, AT only double bongs (increased C-G content–> melting temp increases )
Amino acids necessary for purine synthesis (cats purrr untile they GAG)
Glycine, Aspartate, Glutamine
Purine synthesis
PRPP synthase is the rate limiting step of both purine and pyrimidine (ribose 5 P to PRPP)
PRPP -> IMP is inhibited by 6MP (Azathioprine) inhibit denovo purine synthesis
PRPP-> IMP -> AMP
PRPP-> IMP -> GMP (mycophenolate and ribavirin - inhibit Inosine monophosphate dehydrogenase)
Pyrimidine production
needs Aspartate
Glutamine+CO2 –> Carbamyl phosphate synthetase 2 CPS2)
Carbamoyl phosphate–> orotic acid (with PRPP)
UMP synthase (orotic aciduria-> UDP Ribonucleotide reductase->dUDP ->dUMP -> dTMP (thymidylate synthase)
DHF to THF (DHFr)
methotrexate, TMP and pyrimethamine inhibit dihydrofolate reductase (deoxy
DNA repplication
single in prokaryotes and multiple in eukaryotes
Helicase unzips DNA, deficient in Bloom syndrome (BLM gene mutation
SS-binding proteins- proteins that prevent from reannealing
DNA topoisomerases- Create single or ds breats (1 and 2)- in eukaryotes irinotecan and topotecan inhibit topoisomerase TOP 1, etoposide/teniposide inhibit TOP2, In prokaryotes: fluoroquinolones inhibit TOP 2 (DNA gyrase and TOP 4)
Primase- Makes an RNA primer on which DNA polymerase 3 can initiate replication
DNA polymerase 3
Prokaryotes only, elongates leading strand by adding deoxy nucleotides to the 3’ end, elongates lagging strand until it reaches primer of precedign fragment
DNA polymerase 3 has 5’–> 3’ synthesis and proofreads with 3’–> 5’ exonuclease
Drugs blocking DNA replicaiton often have a modified 3’ OH, thereby preventing addition of the next nucleotide (chain termination)
DNA Polymerase 1
Prokaryotes only Degrades RNA primer, replaces it with DNA
Same functions as DNA polymerase 3 also excises RNA primer with 5’-> 3’ exonuclease
DNA ligase
Catalyzes the formation of a phosphodiester bond within a strand of ds DNA
Joins Okazaki fragments, Ligase Links DNA
Telomerase
Eukaryotes only, A reverse transcriptase (RNA dependent DNA polymerase) that adds DNA (TTAGGGO to 3’ ends
Lac operon
Glucose is the preferred metabolic substrate in E coli, but when glucose is absent and lactose is present, the lac operon is activated to switch to lactose metabolism
Low glucose–> increased adenylate cyclase activity–> generation of cAMP from ATP–> activation of catabolite activator protein (CAP)–> increased transcription
High lactose–> unbinds repressor protein from repressor/operator site–> increased transcription
Nucleotide exicision repair
Specific endonucleases release the oligonucleotides containing damaged bases, DNA polymerase and Ligase fill and reseal the gap, respectively, Repairs bulky helix distorting lesions, Occurs in G1 phase of cell cycle
Defective in xeroderma pigmentosum (inability to repair DNA pyrimidine dimers caused by UV exposure)
Dry skin extreme light sensitivity, skin cancer
Base excision repair
base specific Glycosylase removes altered base and creates AP site (Apurinic/apyrimidic )
One or more nucleotides are removed by AP-Endonuclease, which cleaves 5’end
AP lyase cleaves 3’ end
Glycosylase-> Endonuclease-> lyase-> Polymerase-> ligase
Mismatch repair
mismatched nucleotides in newly synthesized unmethylated strand are removed and gap filled and resealed, occurs predominantly in S phase
Defective in lynch syndrome (hereditary nonpolyposis colorectal cancer)
Non homologous end joining
brings together 2 ends of DNA fragments to repair double stranded breaks
Defective in ataxia-telangiectasia
No requirement for homology, some DNA may be lost
Homologous recombination
requires 2 homologous DNA duplexes, A strand from damaged dsDNA is repaired using a complementary strand from intact homologous dsDNA as a template
Defective in breast/ovarian cancers with BRCA1 mutation and in Fanconi anemia
does not lose nucleotides
regulation of gene expression
Promoter- where RNA polymerase 2 and multiple other transcription factors bind to DNA upstream from gene locus (AT rich upstream sequence with TATA and CAAT boxes
Promoter mutation commonly results in dramatic decrease in level of gene transcription
Enhancer- DNA locus where regulatory proteins (activators bind increasing expression of a gene on the same chromosome
Silencers where regulatory prototeins repressors bind, decreasing expression of a genen on the sm
RNA processing
initial transcripts is called heterogenous nuclear RNA (hnRNA) then modified and becomes mRNA
Capping of the 5’end (addition of 7 methylguanisine cap)
Polyadenylation of 3’ end (200 As on 3’)
Splicing out of introns
Capped, tailed, and spliced transcript is called mRNA
mRNA quality control occurs at cytoplasmic processign bodies (P-bodies) which contain exonucleases, decapping enzymes, and microRNAs, mRNAs
Poly A polymerase does not require a template AAUAAA - polyadenylation signal
RNA polymerase
RNA polymerase 1 makes rRNA (nucleolus)
RNA polymerase 2 makes mRNA, microRNA, snRNA
RNA polymerase 3 makes 5S rRNA, tRNA (tiny)
No proofreeding,
a-amanitin- found in amantina phalloides (death cap mushrooms) inhibits RNApolymerase 2 –> severe hepatotoxicity
Actinomycin D- also called dactinomycin, inhibits RNA polymerase in both prokaryotes and eukaryotes
Prokaryotes 1 RNA pol (mutisubunit complex) makes all 3 kinds of RNA - Rifampin inhibits DNA dependent RNA polymerase in prokaryotes
tRNA
<100 nucleotides, anticodon end is opposite 3’ aminoacyl end. All tRNAs both eukaryotes and prokaryotic, have CCA at 3’ end along with a high percentage of chemically modified bases, the amino acid is covalently bound to the 3’ end of the tRNA, CCA Can carry Amino acids
t- arm- contains the TC site for tRNA- ribosome binding, T arm, Tethers tRNA molecule to ribosome
D-arm- contains Dihydrouridine residues necessary for tRNA recognition by the correct aminoacyl-tRNA synthetase, D-arm allows Detection of the tRNA by aminoacyl tRNA synthetase
Charging- aminoacyl tRNA synthease uses ATP
Start and stop codons
AUG, inAUGurates protein synthesis
codes for methionine
stop UGA, UAA, UAG
Protein synthesis
initiation- eukaryotic initiation factors (eIFs) identify the 5’ cap , eIFs assemble the 40s ribosomal subunit with the initiator tRNA, eIFs released when the mRNA and the ribosomal 60s subunit assemble with the complex, Requires GTP
elongation- Aminoacyl-tRNA binds to A site, rRNA,
Permanent vs stable vs Labile cells
Permanent- Remain in G0 regenerate from stem cells
Stable- Enter G1 from G0 when stimulated
Labile- never go to G0 divide rapidly with short G1 , most affected by chemo
Cell trafficking
Golgi is distribution center for proteins and lipids from ER to vesicles and plasma membrane, Post translational events in Golgi inculde modifying N-oligosaccharieds on asparagine, adding O-oligosaccharides on serine and threonin, and adding mannose 6 P to proteins
I cell diseasep- inherited lysosomal storage disorder autosomal recessive defect in N-acetylglucosaminyl –< failure of the golgi to phosphorylate mannose residues on glycoproteins, –> proteins are secreted extracellulary rather than delivered to lysosomes, results in coarse facial features, gingival hyperplasia, clouded corneas, restricted joint movements–> claw hand, fatal in kids
SRP (signal recognition particles)
abundant, cytosolic ribonucleoprotein that traffics polypeptide-ribosome complex from the cytosol to the RER . Absent or dysfunctional SRP–> accumulation of protein in cytosol
Vesicular trafficking proteins- COPI- golgi –> cis Golgi–> ER
COP2 ER–> cis golgi
Clarthrin- trans golgi–> lysosomes, plasma membrane–> endosomes (receptor-mediated endocytosis) LDL receptor
Peroxisomes
B-ox of VLCFA, a ox of Bchain FA, catabolism of amino acids and ethanol, synthesis of cholesterol, bile acids, and plasma logen, important membrane phospholipid, especially in white matter of brain
Adrenoleukodystrophy- X linked recessive disorder of B-oxidation due to mutation in ABCD1 gene–> VLCFA buildup in adrenal glands, white (leuko matter of brain testes, progressive disease that can lead to adrenal gland crisis coma, and death
Microtubules
cylindrical outer structure composed of a helical array of polymerized heterodimers of a-B tubulin, each dimer has 2 GTP bound, incorporated into flagella, cilia, mitotic spindle, grows slowly collapses quickly
C tetani- HSV, Polio, rabies use dynein for retrograde transport to the neuronal cell body
Microtubule drugs- Mebendazole, Griseofulvin, Colchicine, Vincristine, paclitaxel
Negative near nucleus
Positive poits to periphery
cilia structure
9 doublet and 2 singlet arrangement of microtubules
Base body- below cell membrane, with 9 microtubyle triplets and no central microtubules
Axonemal dynein- ATPase that links peripheral 9 doublets and causes bending of cilium by sliding
Gap junctions enaple fordinated ciliary movement
Kartagner syndrome- immotile cilia due to dynein arm defect- autosomal recessive, dysfunctional sperm and fallopian tubes, increased risk of ectopic pregnancy
Bronchiectasis, recurrent sinusitis, ear infection, conductive hearing loss, and situs inversus, nasal nitric oxide,
Collagen
most abundant proteins in human body, extensively modified by posttranslational modification, organizes and strengthens extracellular matrix
Type one- Bone, skin, tendon, dentin, fascia, cornea, late wound repair, made by osteoblasts,, decreased production in osteogenesis imperfecta type 1
Type 2- Cartwolige (including hyaline), vitresous body, nucleus pulposus
Type 3- reticulin, skin, blood vessels, uterus, fetal tissue, early wound repain,
Type 4- basement membrane- basal lamina- lens, floos, defective in ALport syndrome, and AB against in good pasture syndrome
Synthesis
Translation of collagen a chains (Preprocollagen) GLy xy, collagen is mosly Glycine
Hydroxylation fof specific proline and lysine residues, requires vitamin C, deficiency –> scurvy
Glycosylation- of pro a chain hydroxylysine, residues and formation of procollagen via hydrogen and disulfide bonds (triple helixes of 3 collagen a chains), problems forming triple helix–> osteogenesis imperfecta
Exocytosis of procollagen into extracellular space
Proteolytic processing- cleavage of disulfide rich terminal regions of procollagen–> insoluble tropocollagen
Cross linking- reinforcing staggered tropocollagen molecules by covalent lysine-hydroxylysine cross linkage by copper lysul oxidase to make collagen fibrils, problems with cross linking–> Menkes disease
Osteogenesis imperfecta
COL1A1/2 autosomal dominant with decreased production of otherwise normal type 1 collagen, manifestation include
Blue sclera- connective translucent cT over choroid
Abnormalities
hearing loss
treat with bisphosphonates to decreased fracture risk, BITe
Bones, I eyes, teeth, ear
Ehlers Danlos syndrome
Faulty collagen sunthesiso
skin, hyper mobile easy bruising
berry aneurysms
Type 5 collagen
vascular type 3 gives vessles issuew
Elastin
Stretchy protein within skin, lungs, large arteries, elastic ligaments, vocal cords, ligamenta flava (connect vertebrae–> relaxed and stretched conformations)
Rich in nonhydroxylated proline glycine, and lysine (vs collagen that needs to have hydroxylation)
Tropoelatin with fibrillin scaffolding
Crosslinking takes place extracellularly and gives elastin its properties
a1 antitrypsin, an elastase inhibitor, (a1 antitrypsin deficiency–> unopposed elastase activity)
Changes with aging- decreased dermal collagen and elastin, decreased synthesis of collagen fibrils, crosslingking remains normal
Marfans–> AD skeleton, heartm eyes Fibrillin 1 gene mutation in chromosome 15 (FiFteen) no sheath around elastin, tall with long extremities, pectus carnitum and excavatum, cystic medial necrosis of aorta, mitral valve prolapse, subluxation of lenses upward and temporally (downward and medially in homocystinuria)
codominance
both alleles contribute to the phenotype of the heterozygote
blood groups , a1 antitrypsin deficiency, HLA groups
variable expression vs incomplete penetrance vs pleiotropy
variable expressivity- same genotype diffrent phenotypes (severity)
incomplete penetrance- not all individuals with the gene get the disease (Brca1 doesnt=cancer)
pleiotropy- one gene contributes to multiple phenotypic effects
loss of heterozygosity
mutation in a tumor supressor gene
the complemenatry gene needs to be mutated
RB, Lynch syndrome, Li fraumeni
dominant negative mutation
exerts a dominant effect
a heterozygote==> nonfunctional altered protein that also prevents the normal gene from frunctioning
p53
linkage disequilibrium
tendency for certain alleles at 2 linked loci occure together more or less oftern than expected by change
in populations not in families (brown hair and brown eyes in asia)
Mosaicism
presence of genetically distinctly cell lines in teh same individual
Somatic mosaicism- mutation arises from mitotic errors after fertilization and propagates through multiple tissues or organs
Gonadal mosaicism- mutation only in egg or sperm, if parents and relatives do not have the disease, suspect gonadal (or germline mosaicism)
McCune-Albright syndrome- due to Gs protein activating mutation, presents with unilateral CAL spots with ragged edges, polyostotic fibrous dysplasia (bone is replaced by collagen, fibroblasts) and at least one endocrinopathy, lethal if mutation occurs before fertilization affecting all cells, but survivable in pts with mosaicism
Locus heterogeneity, Allelic heterogeneity, heteroplasmy, uniparental disomy
Locus heterogeneity- mutations at different loci can produce a similar phenotype (albinism)
Allelic heterogeneity- Different mutations in the same locus produce the smae phenotype (b-thalassemia)
Heteroplasmy- both normal and mutated mtDNA resulting in variable expression in mitochondrially intherited disease
Uniparental disomy- offspring receives 2 copies of a chromosome from 1 parent and no copies from the other parent, heterod1somy (heterozygous) indicates a meiosis 1 erroe, IsoIsomy (homozygous) indicates a meiosis 2 error or postzygotic chromosomal duplication of one of a pair chromosomal
disorders of imprinting
imprinting one gene copy is silenced by methylation, and only the other copy is expressed–> parent of origin effects
Prader Willi syndrome
Maternally derived genes are silenced, Disease occurs when the Paternal allele is deleted or mutated
Hyperphagia, obesity , intellectual disability, hypogonadism, hypotonoa
Chromosome 15 of paternal origin
Prader has no Dad
Angel Man syndroem
Paternally derived UBE3A is silenced, Disease occurs when Mom allele is deleted or mutated
Seizures, Ataxia, severe intellectual disbility , inappropriate Laughter (happy puppet), set SAIL for angel Island
UBE3A on maternal copy of chromosome 15
MD are angels (maternal Deletion)
cystic fibrosis
encodes ATP Cl- that secretes CL in lungs and GIT
Reabsorbs CL in sweat glands
No Cl (with H20) in Lungss and GIT- thinck mucus
with increased CL in sweat
S aureus as kids, P aeruginosa in adults
Rett syndrome
Sporadic disorder seen in girls ( affected males die in utero)
De novo mutation of MECCP2 on X chromosome,
ages 1-4
regression, in motor, verbal and cognitive abilities, ataxia, seizures, growth failure hand wringing
Fragile X syndrome
Trinucleotide repeat in FMR 1 gene- hypermethylation –> decreased expression
down syndrome is most common genetic cause, but mostcases occurs sporadically
post pubertal macroorchidism, long face jaw, everted ears, mitral valve prolapse
trisomy 21
Atrioventricular septal defection,
Alzheimer disease
AML ALL
high hCG, increased inhibin
Edwards syndrome trisomy 18
Prince
Prominant occiput, Rocker bottom feet, Intellectual disability, Non disjunction, Clenched fists with overlapping fingers, low set Ears,
Patau syndrome trisomy 13
severe disability, rocker bottom feet, microphthalmia, microcephaly, cleft liP/ Palate
holoprosencephaly, poly dactyly, cutis aplasia, congenital heart disease (pump)
Polycystic kidney disease, omphalocele
death at 1
Robertsonian translocation
21 22 13 14 15 (chromosomal translocation)
long arms of 2 acrocentric chromosomes centromeres near their ends) fuse at the centromere and the 2 short arms are lost
Balanced translocations do not cause abnormal phenotype, unbalanced translocations can result in miscarriage stillbirth and chromosomal imbalance (down patau)
Criduchat
deletion on short arm of chromosome 5
microcephaly, mod- to severe intellectual disabilty, high pitched crying/ meowing, epicanthal folds, cardiac abnormalities
Williams syndrome
deletion of chromosome 7 (deleted ergion incledes elastin gene)
elfin facies,
Fat soluble vitamins
DEAK
Absorption dependent on ileum and pancreas
Toxicity more common than water soluble vitamins because fat soluble vitamins accumulate in fat
Malabsorption syndromes with steatorrhea (CF and celiac disease) or mineral oil intake can cause fat soluble vit deficiency)
Vitamin A
includes rets
Antioxidant, constituent of visual pigments (reinal)
essential for normal differentiation of epithelial cells into specialized tissue (pancreatic cells, mucus secreting cells) prevents squamous metaplasia, usted to treat measels and acute promyelocytic leukemia (APML)
liver leafy veg,
acne
deficiency– night blind, dry scaly skin, corneal squams, bitot (keratin debris foamy appearance on conjuctiva) corneal degeneration, immunosuppression
Acute toxicity- nausea, vomiting, vertigo and blurred vision, alopecia, dry skin hepatic problems, teratoges
Vitamin B1 (thiamine )
Be APT
Branched chain ketoacid dehydrogenase, a-ketoglutarate dehydrogenase (TCA cycle) Pyruvate dehydrogenase (links glycolysis to TCA cycle) Transketolase (HMP shunt)
Deficiency- impaired glucose breakdown–> ATP depletion worsened by glucose infusion, highly aerobic tissues (brain, heart) are affected first. in alcoholic or malnourished patients, give thiamine before dextrose to decrease risk of precipitating Wernicke encephalopathy
Diagnosis made by increased RBC transketolace activity following B1 infusion
Wernicke encephalopathy vs Korsakoff syndrome
Wernicke encephalopathy- acute, life-threatening neurologic condition classic triad of confsion, opthalmoplegia ataxia
Korsakoff syndrome- amnestic disorder due to chronic alcohol consumtpion, presents with confabulation, personality changes, meomry loss (permanent damage)
Wernicke-korsakoff syndrome- damage to medial dorsal nucleus of thalamus, mammillary bodies, presentation is combination of Wernicke encephalopathy and Korsakoff syndrome
Dry and wet beri beri
Dry beri beri- polyneuropathy, symmetric muscle wasting
Wet beriberi- high out put cardiac failure (dialated cardiomyopathy), edema
Vitamin b2
riboflavin
Component of flavins FAD and FMN used as cofactor in redox reactions Succinate dehydrogenase reaction in the TCA cycle
Cheilosis (inflammation of lips, scaling and fissures at the corners of the mouth
Corneal vascularization
FAD and FMN are derived from riboFlavin
B2=2ATP
the 2 Cs of B2
Vitamin B3
Niacin (B3= 3ATP)
Constituent of NAD, NADP (used in redox reactions) derived from TRYPTOPHAN
Synthesis requires B2 B6
used to treat dyslipidemia
Lowers levels of VLDL and raises levels of HDL
Deficiency= Glossitis, Severe deficiency leads to pellagra which can also be caused Hartnup disease, malignant carcinoid syndrome (increased Tryptophan metabolism) and isoniazid (decrease vit B6)
Pellagra- Diarrhea, menentia, Dermatitis, hyperpigmentation fo sun exposed limbs
Hartnup disease- AR deficiency of neutral Amino acid (TRYPTOPHAN) transporters in proximal renal tubular cells and on enterocytes–> neutral aminoaciduria, and decreased absorption from the gut–> decreased tryptophan for conversion to niacin–> pellagra like symptoms
High protein diets and nicotinic acid, Deficiency of vit B3–> pllegra
Excess- facial flushing (induced by PG) take aspirin with niacin, hyperglycemia, hyperuricemia–> Podegra
Vitamin B5
pantothenic acid
Essential component of coenzyme A (CoA a cofactor for acyl transfers and fatty acid synthase)
deficiency– dermatitis, enteritis, alopesia, adrenal insufficiency)
Vitamin B6
Pyridoxine
Converted to PLP
For TRANSMAINATIONS, Decarboxylation
Glycogen phosphorylase
Synthesis of GSH, cystathionine, heme, niacin, histamin, and neurotrasmitters including serotinin, epinephrine, NE, dopamine, and GABA
Deficiency- Convulsions, hyperirritability, peripheral neuropathy, deficiency inducible by INH and oral contraceptives, siderblastic anemia (due to impaired hemoglobin synthesis and iron excess
B7
biotin
Cofactor for Carboxylation enzymes
add a 1 carbon group
Pyruvate carboxylase: pyruvate (3C)–> oxaloacetate (4C)
AcetylCoA carboxylase: AcetylCoA (2C)–>malonylCoA (3C)
PropionylCoA carboxylase: PropionylCoA (3C) –> methylmalonyl CoA (4C)
deficiency rare- Dermatitis, enteritis, alopesia, caused by long term ABx use or ingestion of Raw egg whites (avidin in egg whites)
B9
FOLATE
Converted to THF, a coenzyme for 1 carbon transfer/methylation reactions,
Important for the synthesis of nitrogenous bases in DNA and RNA
absorbed in jejunum, Folate from foliage
Small reserve pool
Macrocytic megaloblastic anemia, hypersegmented PMNs, glottitis, no neuro symptoms
Labs- increased homocysteine, normal methymalonic acid levels seen in alcohol and pregnancy
Deficiency from lots of drugs- phenytoin, sulfonamides, methotrexate
decreased neural tube defects
Vit B 12
cobalamin
Cofactor for methionine synthase (transfers CH3 groups as methylcobalamin and methyl malonyl CoA mutase, important fo DNA Synthesis
Macrocytic, megalo blastic anemia, with PMNS, paresthesias and subacute combined degeneration of dorsal columns, lateral corticospinal tracts and spinocerebellar tracts due to abnormal myelin, associated with increased serum homocystein and methylmalonic acid levels, along with 2’ folate deficiency
Prolonged deficiency –> irreversible nerve damage
animals, very large reserve pool, in liver, deficiency caused by malabsorption (sprue, enetritis, Diphyllobothrium latum, achlorhydia, bacterial overgrowth, alcohol)
Lack of IF ( pernicious anemia, gastric bypass) or abcesnce of terminal ileum certain drugs metformin, or insufficeint intake
Anti IF Abs diagnostic for pernicious anemia, Folate supplementation can mask the hmeatologic symptoms of B12 deficiency but not the neuro symptoms
vit C
antioxidant, iron absoprtion by reducing it to Fe 2+ state
necessary for hydroxylation of proline and lysine in collagen syntheisi, necessary for dopamine B hydroxylase which converts dopamine to NE
treatment for methemoglobinemia by reducing Fe3+ to Fe2+
Def- scurvy gums easy bruising peticiae, hemarthrosis, weak immune responce
Excess - NVD fatigue, calcium oxolate nephrolithiasis, increased iron toxicity
Vitamin D
D3 (cholecalciferol) from exposure of skin (stratum basale) to sun, ingestion of fish, milk, plants
D2 (ergocalciferol) from ingestion of plants, fungi and yeasts
Both converted to 25 OH D3 (storage form) in liver and to the active form 1,25 OH 2 D3 (calcitriol) in kidney
Function- increased intestinal absorption Ca and PO4 3-, increased bone mineralization at levels, increases bone resorption at higher levels
PTH increase, low CA or low PO43- –> increased 1 25 OH2 D3 production
Deficiency- rickets , osteomalacia in adults (bone pain and muscle weakness, hypocalcemic tetany
Caused by malabsorption, decreased sun exposure, poor diet, CKD advanced liver disease
Give oral vit D to breastfed infants, deficiency is exacerbated by pigment skin, premies
Excess- hypercalcemia, hypercalciuria, loss of appetite, stupor . Seen in granulomatous diseases (increased activation of vitamin D by epithelioid macrophages
Vit E
Tocopherol and tocotreinol
Antioxidant (protects RBCs and membranes from free radical damage)
Deficiency: Hemolytic anemia, acanthocytosis, muscel weakness, demyelination of posterior columns, and spinocerebellar tract (ataxia). Neurologic presentation may appear similar to vitamin B12 deficiency, but without megaloblastic anemia, hypersegmented neutrophils, or increased serum methylmalonic acid levels
Excess- risk of enterocolitis in infants, high dose supplementeation may alter metabolism of vit K–> enhanced anticoagulation of warfarin
Vit K
Activated by epoxide reductase to the reduced form, which is a cofactor for the gamma carboxylation of glutamic acid residues on various proteins required for blood clotting synthesized by intestinal flora
2 7 9 10 C S, vit K dependent (warfarin inhibits it)
Deficiency- neonatal hemorrhage with increased PT and increased aPTT, but normal bleeding time (neonates have sterile intestines and are unable to synthesize vit K) can also occur after prolonged use of broad spectrum antibiotic
Not in breast milk, neonates are given vitamin K injection at birth to prevent hemorrhage disease of the newborn
Zinc
FUNCTION- mineral essential for the activity of 100+ enzymes, important in the formation of zinc fincters
Transcription factor motif
Deficiency- delayed wound healing, suppressed immunity, male hypogonadism, decreased adult hair ( axillary, facial, pubic) dysgeusia anosmia
Acrodermatitis enteropathica defect in intestinal zinc absorption, may predispose to alcoholic cirrhosis
Kwashiorkor, Marasmus
Kawaskikor - protein malnutrition –> skin lesions, edema due to decreased plasma oncotic pressure, liver malfunction (fatty change due to decreased apolipoprotein synthesis) Clinical picture is small child with swollen abdomen
Kwashiorkor- Malnutriton, edema, Anemia, fatty liver, skin lesions
Marasmus- malnutrition not causing edema, diet is defieicnt in calories but no nutrients are entirly absent- Marasmus results in muscle wasting
ethanol metabolism
Ethanol (NAD+) –> acetyladehyde (NADH) ALCOHOL DEHYDROGENASE
Cyp2e1
Acetylaldehyde (NAD+) –> Acetate (NADH) ACETYLALDEHYDE DEHYDROGENASE
FOMEPIZOLE- blocks alcohol dehydrogenase, antidote for overdoses of methanol or ethylene glycol
DISULFRAM- blocks acetylaldehyde dehydrogenase–> increased acetylaldehyde –> increased hangover symptoms–> discouraging drinking
NAD+ is a limiting reagent
Alcohol dehydrogenase operates via zero order kinetics
Ethanol metabolism increases NADH to NAD+ ratio in liver causing:
EtHanol increases nadH
- Lactic acidosis (increased Pyruvate–> Lactate (anion gap metabolic acidosis)
- Fasting hypoglycemia– decreased gluconeogenesis due to increased conversion of OAA to malate (in TCA cycle)
- Ketoacidosis- diversion of Acetyl CoA into ketogenesis rather than TCA cycle ( you need NAD+ in TCA)
- Hepatosteatosis- increased conversion of DHAP to glycerol 3 P (acetyl CoA diverges into Fatty acid synthesis, which combines with glycerol 3 P to synthesize Triglycerides
Increased NADH/NAD ratio inhibits TCA cycel–> increased acetyl CoA used in ketogenesis, lipogenesis
Rate determining enzymes of metabolic processes Glycolysis Gluconeogenesis TCA cycle Glycogenesis Glycogenolysis HMP shunt De novo pyrimidine synthesis De novo purine sythesis Urea cycle Fatty acid synthesis Fatty acid oxidation Ketogenesis Cholesterol Synthesis
Glycolysis- PFK 1, ( activators AMP, F 2* 6 bisphosphate, inhibitors -ATP citrate)
Gluconeogenesis- Fructose 1* 6 bisphosphate (inhibitors- AMP F 2 6 bisphosphate)
TCA cycle- Isocitrate dehydrogenase (activators ADP, inhibitors ATP, NADH)
Glycogenesis- Glycogen synthase (Activators- G6P, insulin, cortisol. Inhib- Epinephrine, glucagon)
Glycogenolysis- glycogen phosphorylase (Activators- epinephrine, glucagon, AMP, inhibitors. Inhibitors- G6P, insuin, ATP)
HMP shunt- G6P dehydrogenase (Activators- NADP+. Inhib NADPH)
De novo pyrimidine synthesis- Carbamoyl phosphate synthetase 2 (Activators- ATP, PRPP. Inhibitors- UTP)
De novo purine sythesis- PRPP (inhibitors AMP, IMP GMP)
Urea cycle- Carbamoyl phosphate synthetase 1 (act- Nacetyl glutamate)
Fatty acid synthesis- Acetyl CoA carboxylase (Act. Insulin, citrate. Inhib- Glucagon, palmitoyl CoA)
Fatty acid oxidation- Carnitine Acyltransferase 1 ( inhibit- Malonyl CoA)
Ketogenesis- HMG coA synthase
Cholesterol Synthesis- HMG coA reductase (activators - Insulin thyroxine, estrogen, Inhib- glucagon, cholesterol)
hexokinase vs glucokinase
Phosphorylation of glucose to yield glucose 6 phosphate is catalyzed by glucokinase in the liver and hexokinase in the rest of the body tissue
Hexokinase sequesters glucose in tissues where it is used even when glucose concentrations are low, at high glucose concentrations, glucokinase helps to store glucose in liver
Hexokinase- in tissues except liver and pancreatic B cells, Km (lower, higher affinity) , Vmax (lower, low capacity) not induced by insulin, feedback inhibition by G6P
gLucokinase- in liver, B cells of pancreas, higher KM (lo affinity), Higher VMax (higher capacity), induced by insulin, inhibited by Fructose 6 phosphate
Glycolysis regulation, key enzymes
Net Glycolysis (cytoplasm)
Glucose +2Pi +2 ADP + 2NAD–> 2 pyruvate, 2ATP, 2 NADH, 2H+ 2H20
Glucose–> G6P (hexokinase/glucokinase) (G6P inhibits hexokinase, F6P inhibits glucokinase)
F6P–> F16 BP ( Phosphofructokinase 1 (RLS) - AMP+, F26 BP +, ATP -, Citrate-
The first steps require ATP
1,3 BPG –> 3 PG ( Phosphoglycerate kinase), PeP (pyruvate kinase)–> Pyruvate (F1 6 bisphosphate+ , ATP -, alanine -
Regulation by fructose 2 6 bisphosphate
Fructose bisphosphatase gluconeogenesis, Phosphofructokinase glycolysis
Fructose bisphosphatase 2 (FBPase 2) and phosphofructokinase 2 (PFK 2) are the same enzyme thats reversed by phosphorylation by protein kinase A
Fasting state– increased glucagon–> increased cAMP–> increased protein kinase A–> FBPase 2, PFK2, less glycolysis, more gluconeogenesis
(FaBian the peasant has to work hard when starving)
Fed state: insulin–> decreased cAMP–> decreased protein kinase A–> decreased FBPase2, increased PFK 2, more glycolysis, less gluconeogenesis
(Prince FrederiK) works only when fed
Pyruvate dehydrogenase complex
mitochondrial enzyme complex linking glycolysis and TCA cycle
redulated in fed vs fasting states
pyruvate+ NAD+ + CoA–> Acetyl-CoA +Co2 + NADH
Contains 3 enzymes requiring 5 cofactors
Thiamine, Lipoic acid, CoA (B5), FAD (B2), NAD (B3)
B 1 2 3 5, and lipoic acid
activated by NAD, ADP, Ca
Arsenic inhibits lipoic acid (Lipoic acid fucking up the sequence)
Vampire (loss of pigment in skin, and skin canger), vomiting and having diarrhea, running away from a cutie (QT prolongation with garlic breath
Pyruvate dehydrogenase complex deficiecny
Causes a buildup of pyruvate that gets shunted to lactate (via LDH) and alanine (via ALT)
X linked
Findings- neurologic defects, lactic acidosis, increases serum alanine starting in infancy
increased intake of ketogenic nutrient (high fat content or lysin and leucine)
Pyruvate metabolism
Aanine amino transferase (ALT) with B6, alanine carries amino groups to the liver from muscle
Pyruvate carboxylase (biotin ) oxaloacetate can replenish TCA cycle or be used in gluconeogenesis
Pyruvate dehydrogenase (B 1 2 3 5, lipoic acid - transitions from glycolysis to the TCA cycle)
Lactic acid dehydrogenase (B3)- end of anaerobic glycolysis (major path in RBCs WBCs kidney medulla, lens, testes, and cornea)
TCA cycle
Pyruvate to acetyl CoA produces 1 NADH and 1 CO2
TCA cycle produces 3 NADH, 1 FADH2, 2 CO2, 1 GTP per acetyl CoA= 10 ATP/ acetyl CoA (2x everything per glucose)
in mitochondria
a KG dehydrogenase same cofactors as PDH (B1 2 3 5 lipoic acid
Citrate Is Krebs Starting Substrate For Making Oxaloacetate
Electron transport chain and oxidative phosphorylation
NADH electrons from glycolysis enter mitochondria via the malate aspartate or glycerol 3 phosphate shuttle
FADH2 electrons are transferred to complex 2 (at a lower energy level than NADH)
The passage of electrons results in the formation of proton gradient that coupled to ox phosphroylation drives the production of ATP
Gluconeogenesis, irreversible enzymes
Pyruvate carboxylase- in mitochondria, pyruvate–> oxaloacetate, (required biotin, ATP, activated by acetyl CoA)
Phosphoenolpyruvate carboxylase- in cytosol, oxaloacetate–> phosphoenolpyruvate ( Requires GTP)
Fructose 1, 6 bisphosphatase- in cytosol, Frutose 1,6 bisphosphate–> fructose 6 phosphate (Citrate+, AMP-, fructose 2,6 bisphosphate -)
glucose 6 phosphatse- in ER, Glucose 6-phosphate–> glucose
Occurs in liver, euglycemia during fasting, kidney, intestinal epithelium, deficiency in of the key gluconeogenic enzymes causes hypoglycemia
muscle cant participate in gluconeogenesis, lacks G6P
Odd chain fatty acids yield 1 propionyl CoA during metabolism, and can enter TCA cycle
Pentose phosphate pathway
HMP shunt
produces a source of NADPH from abundantly available glucose 6 P NADPH is required for reductive reactions, GSH reduction inside RBC, Fatty acid and cholesterol biosyntheisis
Additionally makes ribose for nucleotide synthesis
not ATP is used or produced
Lactating mammary gland, liver, adrenals
G6PD deficiency
NADPH is necessary to keep GSH reduced, to detox free radicals and peroxides
Decreased NADPH in RBCs leads to hemolytic anemia due to poor RBC defense against oxidizing agent- Fava beans, sulfonamides, nitrofuratoin, PMquining, anti TB, can also precipitate hemolysis, infalmmatory response produces free radicals that diffuse into RBC causing oxidative damage
X linked recessive disorder, African americans, increased malarial resistnace, heinz bodies (denatured glocin chains precipitate within RBCs due to oxidative stress, bite cells, result from the phagocytic removal of heins bodies by splenic macrophages
Hereditary fructose intolerance
aldolase B deficiency
Fructose 1 phosphate accumulates causing a decreased in available phosphate, which results in inhibition of glycogenolysis and gluconeogenesit
Symptoms after juice
dipstick will be - for glucose
Reducing sugar can be detected in the urine (nonspecific test for in the urine (nonspecific test for inborn errors of carbohydrate metabolism)
Symptoms: hypoglycemia, jaundice, cirrhosis, vomiting
Treatment: decreased intake of fructose, sucrose and sorbitol
galactokinase deficiency
deficiency of galactokinase
galactitol accumulation if galactose is present in diet
galactose in blood, urine, infantile cataract
classic galactosemia
Galactose 1 phosphate uridyltransferase
accumulation of toxic substances (galactitol, in lens of eye)
infant feeding
FTT, jaundice, hepatomegaly , infantile cataracts, intellectual disability
E coli sepsis
treatment- exclude galactose and lactose from dite
Sorbitol
an alternative method of trapping glucose in the cell is to convert it to its alcohol counterpart, sorbitol via aldose reductase
Some tissues then convert sorbitol to fructose using sorbitol dehydrogenase, tissues with an insufficient amount–> increased intracellular sorbitol accumulation, cuasing osmotic damage (cataracts, retinopathy and peripheral neuropathy seen with chronic hyperglycemia in diabetes)
high blood levels of galactose also result in conversion to the osmotically active galactitol via aldose reductase
Lens has primarily aldose reductase Retina kidney, schwann cells only aldose reductase (LuRKS0
Amino acids
L amino acids are found in protiens
Essention
PVT TIM HLL
Phenylalanine, Valine, Tryptophan Threonine, Isoleucine, Mehtionine, Histidine, Leucine, Lysine
Glucogenic - Met His Valantine (so sweet)
Glucogenic/ ketogenic- Isoleucine, phenylalanine, threonin, tryptophan
Ketogenic- Leucine, Lysicine
Basic - His Lys Arg basic
Urea cycle
Amino acids give metabolic fuels-nitrogenous
Ordinarily careless crappers are also frivoulous about urination
Hyperammonemia
Liver disease or hereditary
Flapping tremor (asterixis) Slurring speech, somnolence, vomiting, cerebral edema, blurring of vision NH3 changes relative amounts of a KG, Glutamate, GABA, and glutamine to favor increased glutamine
CNS tox may involve dcreased GABA, decreased a kG, TCA cycle inhibition, cerebral edema
limit protein, Lactulose to acidify GIT and trap NH4, ABxrifaximin, neomycin to decreased ammoniagenic bacteria, Benzoate phenylacetate or phenylbutyrate react
ornithine transcarbamanylase deficiecny
Most common urea cycle disorder
X linked recessive (vs other urea cycle enzyme deficiencies)
cant eliminate ammonia
carbamoyl phosphate is converted to orotic acid
increased orotic acid in blood and urine, decreased BUN , symptoms of hyperammonemia, no megaloblastic anemia
PKU
decreased phenylalanine hydroxylase or decreased Tetrahydrobiopterin
Tyrosine becomes essential
Intellect, growth retartadation, seizures, fair complexion, eczema, musty body odor
TRT- decreased phenylalanine and increased tyrosine in diet, Tetrahydrobiopterin supplementation
aromatic amino acid metabolism–> musty body odor
stop artificial sweetener
MAple syrup urine disease
branched amino acids deficiency
Isoleucine, leucine Valine
aketo acid dehydrogenase
Treatment- restriction of isoleucine, leucine and valin ein diet, and thiamine supplementation
vomiting poor feeding, urine smells like maple serup CNS
I Love Vermont maple syrup (B1racnhes)
alkaptonuria
congenital deficiency of homogentisate oxidase in the degenerative pathway of tyrosine to fumarate
–> pigment forming homogentisic acid builds up in tissue
Autosomal recessive
benign
Findings- bluish black connective tissue, ear cartilage, and sclerae
black urine–> debilitating arthralgias
homocystinuria
cystathionine synthase deficiency- treat with methionine decrease, increase cysteine, B6, B12, folate in diet)
Decreased affinity of cystathionine synthase for pyridoxal phosphate (treatment - increased B6 and cysteine in diet)
Methionine synthase deficiency (homocysteine methyltransferase) treat with increasing methionine in diet
Methylenetetrahydrofolate reductase (MTHFR)- deficiency– increase folate in diet
All forms result in excess homocysteine
HOMOCYstinuria– increased Homo cystein in urine, osteoporosis, MArfanoid habitus, Ocular changes (downward and in subluzation), Cardiovascular effects (thrombosis and atherosclerosis–> stroke and MI), kYphosis, intellectual disabiility fair complexion, in homocystinuria, lens subluzes
Cystinuria
Hereditary defect of renal PCT and intestinal amino acid transporter that prevents reabsorption of cystine, ornithine, lysine and Arginine
Excess cystine in urine can lead to recurrent precipitation of hexagonal cystine stone
treat with urinary alkalinization (potassium citrate, acetazolamide) and chelating agent (penicillamine)
increases solubility of cystine stones, good hydration
AR, urinary cyanide nitroprusside test is diagnostic, cystine is made of 2 cysteines connected by a disulfide bond
Organic acidemias
most common presents in kids with poor feeding, vomiting, hypotonia, high anion gap metabolic acidosis, hepatomegaly, seizures
Organic acid accumulation
Inhibits gluconeogenesis–> decreased fasting blood glucose levels, increased ketoacidosis–> high anion gap metabolic acidosis
Inhibits urea cycle–> hyperammonemia
Propionic acidemia- deficiency of propionyl CoAcarboxylase–> increased propionyl coA, decreased methylmalonic acid
methylmalonic acidemia- deficiency of methylmalonyl CoA mutase or vitamin B12
Treat with low protein diet limited in substances that metabolize into propionyl CoA
Valine, odd chain fatty acid, MEthionine, Isoleucine, threonien
Glycogen
branches have a(!,6) bonds, links have a1,4 bonds
Skeletal muscle- Glycogen undergoes glycogenolysis–> glucose 1 phosphate–> glucose 6 phosphate, which is rapidly metabolized during exercise
Hepatocytes- glycogen is stored and undergoes glycogenolysis to maintain blood sugar at appropriate levels
Glycogen phosphorylase liberates glucose 1 phosphate residues off branched glycogen until 4 glucose remain on branch, then 4a d glucanotransferase (debranching enzymes) moves 3 of the 4 glucose units from the branch to the linkage, then a 1,6 glucosidase (debranching enzyme) cleaves off the last residues remaining on a branch after glycogen phosphorylase has already shortened it
glycogen storage diseases test
abnormal glycogen metabolism and an accumulation of glycogen within cells
Periodic acid Schiff stain identifies glycogen and is useful in identifying these diseases
Von Gierke disease
Severe fasting hypoglycemia, increased Glycogen in liver and kidney, increased blood lactate, increased triglycerides, increased uric acid (Gout) and hepatomegaly, renomegaly
Liver doesnt regulate blood glucose
Glucose-6- phosphatase deficiency
Treatment- frequent oral glucose/ cornstarch, avoidance of fructose and galactose, impaired gluconeogenesis and glycogenolysis
Pompe disease
Cardiomegaly, hypertrophic cardiomyopathy, hypotonia, , exercise intolerance, and systemic findings lead to early death
lysosomal acid a 1-4 glucosidase deficiency (acid maltase with a 16 glucosidase acitivty
PomPe trashes the PumP and 4th letter, heart liver, and muscle)
cori disease
similar to von Gierke disease, but milder symptoms and normal blood lactate levels. Can lead to cardiomyopathy, limit dextrin-like structures accumulate in cytosol
Deficiecny in debranching enzymes
Gluconeogenesis is intact
McArdle disease
increased glycogen in muscle but muscle cannot break it down–> painful Muscle cramp, Myoglobinuria (red urine)
with strenuous exercise, and arrythmia from electrolyte abnormalities
Second wind phenomenone noted during muscle blood flow
deficiency in skeletal muscle glycogen phosphorylase, myophosphorylase
Characterized by a flat venous lactate curve with normal rise in ammonia levels during exercise
Blood glucose levels typically unaffected
McArdle= Muscle
Lysosomal storage disease
each is caused by a deficiency in one of the many lysosomal enzymes, results in an accumulation of abnormal metabolic products
Tay sachs disease
Progressive neurodegeneration, developmental delay, hyperreflexia, hyperacusis (noises), cherry red spot on macula, lysosomes with onion skin, no hepatosplenomegaly
tAy saX (heXosaminidase A deficiency)–> GM2 ganglioside accumulation
Fabry disease
Early on- triad of episodic peripheral neuropathy, angiokeratomas, hypohidrosis)
Later on- progressive renal failure, cardiovascular disease
X linked resessive
a-galactosidase A deficiency–> ceramide trihexoside
Metachromatic leukodystrophy
central and peripheral demyelination with ataxia, dementia
Deficiecy of Arylsulfatase A
Increased cerebroside sulfate
Krabbe disease
Peripheral neuropathy, destruction of oligodendrocytes, developmental delay, optic atrophy, globoid cells
Galactocerebrosidase deficiecny
Galactocerebroside increases
Gaucher disease
Most common, hepatosplenomegaly, pancytopenia, osteoporosis, avascular necrosis of femur, bone crises, Gaucher cells - lipid laden macrophages resembling crumplided tissue paper
Gaucher gaches tissue paper
Glucocerebrosidase deficiecy –> Glucocerebroside increases
Niemann Pick disease
Progressive neurodegenation, hepatosplenomegaly foam cells (lipid laden macrophages
Cherry red spot aswell
Sphinomyelinase deficiecny
Sphingomyelin increased
fatty acid metabolism
FA synthesis required transport of citrate from mitochondria
in liver lactating mammary glands, and adipose
LCFA degradation requires carnitine-dependent transport into the mitochondrial matrix
Sytrate Synthesis
CARnitine- Carnage of FAs
Systemic 1’ carnitine deficiency- no cell uptake carnitine–> no transport of LCFAs into mitochondria–> toxic accumulation of LCFAs in the cytosol, causes weakness, hypotonia, hypoketotic hypoglycemia, dilated cardiomyopathy
MC acyl CoA dehydrogenase deficiency- cant break down fatty acids into actetyl CoA –> fatty acids in blood with hypoketotic hypoglycemis
Lethargy, seizures, coma, liver dysfunction, hyper ammonia
sudden death, dont fast
What do you need to break down FA and to build them up
Break down- AcetylCoA carboxylase
Build up- Acyl CoA dehydrogenase (B oxidation)
Ketone bodies
acetone, aacetoacetate, B-hydroxybutyrate
starvation and DKA, oxaloacetate is depleted for gluconeogenesis
in alcohol, excess NADH shunts oxaloacetate to malate, all of these processes lead to buildup of acetyl CoA which is shunted into ketone body synthesis
metabolic fuel use
1 g CARB/protein= 4 letters 4 kcal
1 g alcohol= 7 cal
1 gram fo fatty acid- 9 kcal
hyperchylomicronemia
AR, Lipoprotein lipase or apoC2 deficiency
increased chylomicrons, TG and cholesterol
Pancreatitis, hepatosplenomegalu, eruptive, pruritic xanthomas, (no increased risk of atherosclerosis)
Familial cholesterolemia
AD
Absent or defective LDL receptors, or defective ApoB 100
2a- LDL cholesterol
2b- LDL cholesterol, VLDL
Heterozygotes- have really high cholesterol, Accelerated atheroscloris and cornea
Dysbeta lipoproteinemia
Defective ApoE
Chylomicrons and VLDL
Premature atherosclerosis, tubereruptive and palmar xanthomas
hypertryglyceridemia
Hepadic overproduction of VLDL
increased VLDL and TG
HypertG can cause acute pancreatitis, Related to insulin resistance
