What causes DNA to be negative? Histones to be positive?
Phosphate- negative DNA
Lysine and Argenine- positive histones
Which histones make-up the nucleosome? Which histone connects the beads?
H1- connects the beads
H2A, H2B, H3, H4- nucleosome
DNA wraps around twice
What type of chromosome is condensed?
Heterochromatin is Highly condensed- transcriptionally inactive
Which nucelotides have 2 rings? Which has a ketone? Which has a methyl?
How do you make uracil?
Purines (A, G)- 2 rings
Guanine has a ketone
Thymine has a methyl
Uracil- deamination of cytosine
Which nucleotides form a triple bond when attached?
G-C is a triple bond, increases the melting point when GC ratio is high
What are the necessary amino acids for purine synthesis?
Which contributes carbon?
Purine- Glycine, Aspartate, Glutamine
Also, THF (folate) needed.
Carbon: CO2, THF, Glycine
What are the necessary amino acids for Pyramidine synthesis? What contributes Carbon?
Pyramidine- Aspartate and Carbamoyl phosphate (from Glutamine and CO2)
Which nucleotides are made from an IMP precursor? What is the starting point? Rate-limiting enzyme?
Purines- IMP (AMP and GMP) from a Ribose 5-P sugar.
Rate-limiting step: Glutamine PRPP amino transferase
Which nucleotides are made from carbamoyl phosphate? What are other important intermediates? Rate-limiting enzyme?
Orotic acid intermediate with PRPP added
Rate-limiting: Conversion of Glutamine and CO2 to carbomyl phosphate by CPS2
What drug interferes with ribonuceotide reductase?
Hydroxyurea (converts ribonucleotides to deoxyribonucleotides)
What drug inhibits PRPP synthetase, what does this block?
5-MP, inhibits de novo purine synthesis
What drug inhibits Dihydrofolate reductase?
Methotrexate and trimethoprim (bacteria)
What drug inhibits Thymidylate synthase? What pathway?
5-FU- inhibits pyramidine synthesis (dTMP)
What are the clinical manifestations of orotic aciduria? Causes?
Inability to convert orotic acid to UMP (de novo pyrimidine synthesis)- Autosomal recessive.
Increased orotic acid in urine, megaloblastic anemia (does NOT improve with folate/B12), failure to thrive, no increased ammonia.
Tx: Oral uridine
What disease is caused by an absence in HGPRT and a defect in purine salvage? What are the clinical manifestations? Treatment?
Lesch-Nyhan syndrome- results in excess uric acid production
Retardation, self-mutilation (lip-biting), agression, hyperuricemia, gout, and chorea.
What disease is caused by an adenosine deaminase deficiency? Clinical symptoms?
SCID- X-linked kind
Excess ATP and dATP cause inhibition of ribonucleotide reductase which prevents DNA synthesis and decrease in lymphocytes.
Chronic diarrhea, repeat infections (yeast, viruses), failure to thrive.
What is a missense mutation? Nonsense?
Missense- changes the Amino Acid
Nonsense- changes the Amino Acid to a STOP codon and
In DNA replication- what unwinds DNA? Makes a nick to relieve supercoils? Makes RNA primer? Seals?
Topoisomerase- creates a nick
(Single-stranded binding proteins hold it open)
Primase- Makes RNA primer
DNA Ligase- seals
Which Eukaryotic polymerase replicates the lagging strand? Leading strand? Mitochondrial DNA? RNA Primer synthesis? Repair?
Alpha- lagging strand and RNA primer
Gamma- Mitochondrial DNA
Delta- Leading strand
Which type of DNA repair has specific endonucleases that cleave an entire segment of damaged DNA, with a DNA polymerase and ligase to close the gap?
Disorders associated with this?
Nucleotide excision repair (good for thyamine dimers)
Xeroderma pigmentosum- 1000x increased risk of cancers, especially melanoma
What type of repair removes only one base?
Base excision repair, AP endonuclease cuts DNA at apyrimidinic site, sugar is removed
What type of DNA repair takes place on unmethylated DNA? Disorders associated?
Mismatch repair- mismatched nucelotides are removed.
HNPCC- colorectal cancer
During DNA/RNA synthesis, what is the energy for the bond formation? Where is the next nucleotide added?
Phosphate at 5' of incoming nucleotide- energy for bond.
OH at 3' end is where the next nucleotide is added
What is the most abundant RNA? The longest? The smallest?
"Rampant, Massive, Tiny"- transcribed in that order as well.
rRNA- most abundant
Start codon? What does it code for in pro/eukaryotes?
Start- AUG coding methionine (eukaryotes) or formyl-methionine (f-Met in prokaryotes)
Stop- UGA, UAA, UAG "U Go Away, U Are Away, U Are Gone"
Where are the promoter regions located? What binds there? What happens if they are mutated?
TATA at -25, CAAT at -75
Binding of Transcription Factors and RNA Polymerase.
Mutations cause major decrease in amount of gene transcribed
What happens when things bind to the enhancer region?
Enhancers/repressors bind here and affect the rate at which genes are transcribed.
What does RNA Polymerase I, II, and III make? Where does it take place?
RNA Polymerase I- rRNA in nucleolus
RNA Polymerase II- mRNA in nuceloplasm
RNA Polymerase III- tRNA in nucleoplasm
What does alpha-amanitin (from death cap mushrooms) affect? Symptoms?
Inhibits RNA Polymerase II- can cause liver failure
What kind of RNA polymerase do prokaryotes have? What antibiotic interferes here?
only one RNA Polymerase that makes rRNA, mRNA, and tRNA
What has to happen to RNA before it leaves the nucleus (after transcription)?
1) 5' cap (7 methylguanosine)
2) Polyadenylation at 3' (200 A's added)
3) Splicing of introns
AAUAAAA is polyadenylation signal, and requires no template
How are introns spliced out? What disease has antibodies to this?
Only in Eukaryotes- snRNPs combine with other ptoeins to form a splicosome.
Lariat-shaped loop is generated, released exactly to join exons.
Lupus has anti-spliceosomal snRNPs antibodies
What is an important characteristic of proteins and TF that bind to DNA?
They have some kind of loop
2) Helix- Turn-Helix
3) Zinc Finger
4) Leucine Zipper
What is the structure of tRNA? Where is the amino-acid covalently bound?
What enzyme is responsible for charging the amino acid?
Cloverleaf- with amino acid at 3' OH (anticodon on opposite end)
All have CCA at 4'end
Aminoacyl-tRNA synthetase uses ATP to attach Amino Acid
Which antibiotic works by preventing attachment of aminoacyl-tRNA at the 30S subunit of prokaryotic ribosomes?
What are the eukaryotic ribosomes? Prokaryotic?
Eukaryotic (even)- 40S + 60S--> 80S
Assembled in nucleus, then transported out
Prokaryotic (odd)- 30S + 50S--> 70S
What is needed to assemble the 40S ribosomal unit with initiator tRNA?
GTP hydrolysis and initiation factors (eIFs)
What happens during the elongation phase of protein synthesis? What catalyzes peptide bond formation?
1) Aminoacyl-tRNA binds to A site (except methionine)
2) Ribosomal rRNA- peptidyltransferase/ribozyme- catalyzes peptide bond formation, transfers growin polypeptide to amino acid
3) Ribosome advances 3 nucleotides toward 3' end moving RNA to P-site (translocation)
What is needed for translocation of RNA from A to P site?
EF-g in prokaryotes
EF-2 in eukaryotes (Diptheria and Pseudomonas Exotoxin A)
Which antibiotics inhibit the formation of the initiation complexes (30S)?
Which antibiotics inhibits peptidyltransferases and 50S?
Which antibiotics bind to 50S preventing translocation?
Macrolides and clindamycine (as well as linazolide)
Which antibiotics bind to 30S and prevent attachment of tRNA?
What phase are chromosomes stained in for Karyotyping? What kind of tissue can be used?
Blood, bone marrow, amniotic fluid, or placenta
What is it called when people have multiple unrelated phenotypes related to one gene?
Pleiotropy- several effects on phenotype. Ex: PKU causes many symptoms from mental retardation to hair/skin changes
What is it called when phenotype depends on whether the mutation is inherited from the mother or father? Example?
Imprinting- Prader Willi (Father- obese, mentally retarded, short) or Angelman's syndrome (Mother- "happy puppet"- laughing and jerky movements)
What is it called when several different genes can cause a single phenotype? Example?
Locus heterogeneity- example: Marfan's
What is heteroplasmy?
When normal and mutated mitochnodrial DNA result in variable expression of a mitochondrial inherited disease
What kind of inheritance is often from defects in structural genes- and both male and female are affected?
What kind of inheritance is usually due to enzyme deficiencies are only seen in one generation?
Autosomal recessive- present in early childhood
What kind of inheritance has no male-to-male transmission and sons have a 50% chance of getting it?
What kind of inheritance affects male and female of the mother, but all offspring of affected father?
X-linked dominant- example: Hypophosphatemic rickets
What kind of inheritance is only transmitted through the mother and all offspring show disease? Example?
Mitochondrial inheritance- variable expression (heteroplasmy).
Ex: Leber's hereditary opti neuropathy- acute loss of central vision from degeneration of retinal ganglion cells
What disease affects FGF 3 receptor? Type of inheritence? Risk factors?
Achondraplasia- dwarfism- advanced paternal age
What disease is associated with mutation in APKD1 and presents with berry aneurysms, mitral valve prolapse, hypertension and hematuria?
ADPKD- autosomal dominant
What disease presents with colon polyps around puberty- will progress to colon cancer? Gene? Inheritance?
FAP- Autosomal Dominant
What disease presents with MI before the age of 20, tendon xanthomas in homozygous?
Familial Hypercholesterolemia Type IIA- absent or defective LDL receptor.
Autosomal Dominant- but heterozygous not as bad
What disease is caused by a spectrin or ankyrin defect? Lab signs? Inheritance?
Hereditary spherocytosis- hemolytic anemia, increased MCHC
What is a disease of trinucleotide repeats (CAG) that shows caudate atorophy and dementia?
Huntington's disease- decreased ACh and GABA-
Chromosome 4- CAG repeats- Autosomal Dominant
What disease is associated with cystic medial necrosis of the aorta, dissecting aortic aneurysms, mitral valve prolapse, and subluxation of lenses?
Marfan's syndrome- Fibrillin gene defect
What disease has cafe-au-lait spots, neural tumors, Lisch nodules (pigmented iris hamartoms)- gene? Inheritance?
NF1- NF1 gene on 17- AKA von Recklinghausen
What disease presents with bilateral acoustinc schwannomas? Gene? Inheritance?
NF2- on chromosome 22
What disease presents with astrocytomas, cardiac rahbdomyomas, seizures, and ash leaf spots? Inheritance?
Tuberous Sclerosis- variable presentation, incomplete penetrance.
What disease presents with hemantioblastomas of retina/cerebellum/medulla and bilateral renal cel carcinomas?
Von Hippel-Laundau- Autosomal Dominant
VHL gene- a tumor suppressor that results in HIF transcription factor and angiogenic growth factors
What disease presents with meconium ileus in newborns and is the number one lethal gene in Caucasians? Gene? Associated infections? Inheritance?
Cystic Fibrosis- Autosomal Recessive
CFTR gene- chloride channels
Pseudomonas infection, steatorrhea from pancreatic insufficiency
How do you diagnose Cystic Fibrosis? Treatment?
CF- diagnose with chloride sweat test (CL> 60mEq/L)
Tx: N-acetylcysteine to cleave disulfide bonds and thin mucous.
Treat with Flouroquionolones for pseudomonas
What are the major X-linked disorders?
Be Wise, Fool's GOLD Heeds Silly Hope
Bruton's agammaglobulinemia, Wiskott-Aldrich,
Fabry's disease (renal failure), G6PD-deficiency, Ocular Albinism, Lesch-Nyhan Syndrome
Duchenne's MD, Hunter's disease, Hemophilia
What disease is caused by a frame-shift mutation that begins as weakness in the pelvic girdle. Also increases of CPK?
Duchenne's MD- deleted dystrophen gene- X linked
Becker's- mutated dystrophin- later onset, less severe
What disease is the 2nd most common cause of mental retardation and also is associated with gigantic testicals, long face, large jaw, and mitral prolapse?
Fragile X- X-linked recessive
FMR1 gene- trinucleotide repeats (CGG)- it is FMRP in the brain and testes that does mRNA translation of axons and dendrites
What disease has CAG repeats? CTG? CGG? GAA?
CAG- Huntington's - AD
CTG- MyoTonic dysrophy
CGG- FraGile X - XR
GAA- Friedreich's ataxia
What are some causes of Down's syndrome? Important symptoms?
95% nondisjunction (advanced maternal age)
5% Robertsonian translocation
1% Down mosaicism
Dudoenal atresia, septum PRIMUM-ASD, endocardial cushions, AML, ALL, Alzheimer's disease (>35yo)
Increased B-HCG, Increased inhibin A
Decreased aFP, decreased estriol
How can you distingues between Down's and Edwards?
In Edward's- there is a decrease in bHCG, in Down's there is an increased
What trisomy presents with clenched hands, migrognathia, and clenched hands?
What trisomy presents with microcephaly, cleft-lip/palate, holoprosencephaly, polydactly, and heart defects?
Patau's syndrome (13)
What genes are involved in Robersonian translocation? What happens?
13, 14, 15, 21, and 22
Long arms fuse at centromere- 2 short arms are lost- Balanced OK, unbalanced- bad.
What disorder is caused by a microdeletion of short arm of chromosome 5 and results in microcephaly, mental retardation and high-pitched crying?
Cri-du-chat- also has cardiac abnormalities and epicanthal folds
What genetic disorder presents with elfin faces, mental retardation, extreme friendliness? What gene is involved?
William's syndrome- deletetion of Chrom 7- including the elastin gene.
Also has extreme sensitivity to Vitamin D
What disorders are associated with a 22q11 deletion? Symptoms?
Cleft palate, Abnormal fascies, Thymic aplasia--> Tcell deficiency, Cardiac defects, Hypocalcemia (lack of parathyroid)
1) DiGiorge- thymic, parathyroid, and cardiac defects
2) Velocardiofacial syndrome- palate, facial, cardiac
Failure of 3rd/4th branchial pouches
Which LSD has renal failure?
Fabry's disease (XR)- deficient in alpha-galactosidase A
Which LSD are X-linked?
Fabry's (renal failure)
Hunter's (MPS)- aggressive, no corneal clouding
Which LSD are associated with death before age 3?
Tay-Sach's (hexosaminidase, cherry red spot)
Neimann-Pick (sphingomyelinase, cherry red spot)
Krabbe (Galactocerebrosidase, optic atrophy, globoid cells)
What is the most common LSD? Hallmark?
Gaucher (B-glucocerebrosidase)- crinkled tissue paper macrophages, bone problems, aseptic necrosis.
What LSD is a demyelinating disease?
Metachromatic leukodystrophy (Arylsulfatase A)-
ataxia and dementia
Which MPS has only corneal clouding? MR? Both?
Corneal Clouding only- Scheie's
Mental Retardation only- Hunter's (XR)
Both- Hurler's or or I-cell (sometimes)
Which LSD has a deficiency in a-L-iduronidase?
Hurler's- MR and Corneal Clouding
Scheie's- no mental retardation
How do you differentiate between Niemann-Pick and Tay-Sachs?
Both cause neural degeneration, cherry-red spot
Neimann-Pick has hepatosplenomegally
Which LSD has a deficiency in iduronate sulfatase?
What LSD has a deficiency in Arylsulfatase A?
Metochromatic leukodystrophy- demylination and ataxia
What LSD has a deficiency in alpha-galactosidase A?
Fabry's disease- renal failure- Xlinked
What LSD has a deficiency in Galactocerebrosidase and an accumulation of this?
Krabbe's disease- globoid cells- death by age 3
What LSD has a deficiency of Beta=glucocerebrosidase leading to accumulation of glucocerebroside?
Gaucher's- most common- bone problems, crumpled tissue macrophages
What LSD has a deficiency in Hexosamidase? Accumulation in GM2 ganglioside?
Tay Sachs- death by 3, cherry red spot, NO hepatosplenomegaly, Jews
What LSD has a deficiency in Sphingomyelinase and accumulation of sphingomyelin?
Neimann-Pick- death by 3, cherry red spot, HEPATOSPLENOMEGALLY
"don't pick your nose with your sphinger"
Which LSD are associated with Ashkenazi Jews?
Tay-Sachs, Neimann-Pick, and Gauchers
What LSD have an accumulation of dermatin sulfate?
MPS- Hunter's Hurler's and Schie's
Hurler's- coreneal clouding
Hunter's- no corneal clouding (have to see to hunt, X-marks the spot)- XR