Biochemistry Flashcards
DNA methylation
- identifies template DNA in replication by methylating Adenine and Cytosine
- blocks DNA transcription by methylating CpG islands
Drugs that inhibit pyrimidine base production pathway
- Leflunomide - inhibits dihydroorotate dehydrogenase which produces orotic acid
- Hydroxyurea - inhibits ribonucleotide reductase which converts UDP to dUDP
- 5-FU - inhibits thymidylate synthase which converts dUMP to dTMP
- MTX, TMP, Pyrimethamine - inhibits DHFR which converts DHF to THF which is needed in conversion of dUMP to dTMP
Drugs that inhibit purine base production pathway
- 6-MP - inhibits conversion of PRPP to IMP
- Mycophenolate and Ribavirin - inhibit conversion of IMP to GMP
Lesch-Nyhan syndrome
- missing HGPRT, can’t convert Hypoxanthine to IMP or guanine to GMP
- get buildup of uric acid and excess de novo purine synthesis
- symptoms: “HGPRT”
Hyperuricemia, Gout, Pissed off (self-mutilation, aggression), Retardation, dysTonia - Tx: allopurinol; febuxostat 2nd line
Adenosine deaminase deficiency
- can’t convert Adenosine to Inosine, get buildup of excess ATP/dATP
- gives feedback inhibition to stop ribonucleotide reductase and block DNA synthesis
- major cause of AR SCID (can’t make LCs)
Fluoroquinolones
inhibit Topo II
Transition vs. Transversion DNA mutation
- Transition: same base type purine to purine or pyrimidine to pyrimidine
- Transversion: changes base type purine to pyrimidine or vice versa
Drugs that block DNA replication MOA
attack the triphosphate bond at the 3’ end of the new DNA strand and add on with their modified OH group, which prevents addition of the next nucleotide and causes “chain termination”
DNA and RNA Polymerases in eukaryotes
DNA: 1 DNA polymerase RNA: I --> rRNA II --> mRNA III --> tRNA
DNA and RNA Polymerases in prokaryotes
DNA:
pol I –> same as pol II but also degrades RNA primer, replaces with DNA
pol III –> elongates strand, proofreads
RNA: 1 RNA polymerase
Nonhomologous end joining
- repairs double stranded breaks by bringing together 2 ends of double-stranded DNA fragments
- mutated in ataxia telangiectasia
Modifications to heterogenous nuclear RNA (makes it into mRNA)
- 5’ cap
- 3’ polyadenylation
- splicing out introns
Splicesosome
the complex of hnRNA combined with snRNPs and other proteins; makes Lariat intermediate, then released when the exons are joined
- *Antibodies to splicesosomal snRNPs are called Anti-Smith Abs, highly specific for SLE!!
- *Abs against U1 RNP specifically (a sliceosome protein) are highly associated with MCTD
tRNA structure
3’ end –> CCA: carries amino acid
T arm –> binds ribosome (closest to 3’ end)
Anti-codon loop –> recognizes codon
D arm –> recognized by tRNA synthetase
Protein synthesis
- Initiation: initiated by GTP hydrolysis
- Elongation: APE site: Aminoacyl tRNA comes in, Peptide bond formed, Empty tRNA exits
- Termination: stop codon recognized (UGA, UAA, UAG)
I (Inclusion) cell disease
- lysosomal storage disorder based on defective phosphotransferase which fails to phosphorylate mannose residues (in Golgi) and proteins are secreted EC instead of delivered as glycoproteins to lysosomes
- coarse facies, clouded corneas, restricted joint movement, high levels of lysosomal enzymes in blood
- often fatal in childhood
vesicular trafficking proteins:
Clathrin
COP I
COP II
Clathrin: from Golgi to lysosomes, plasma membrane to endosomes
COP I: retrograde Golgi to Golgi or Golgi to ER
COP II: anterograde ER to Golgi or Golgi to Golgi
Peroxisome
degrades very long chain and branched chain FA as well as AAs
Proteosome
degrades the damaged or ubiquitin-tagged proteins
Drugs that act on MTs
Microtubules Get Constructed Very Poorly:
Mebendazole
Griseofulvin
Colchicine
Vincristine/Vinblastine - vincas destabilize
Paclitaxel - taxanes stabilize
Cilia structure and Kartagener Syndrome
- structure = 9+2 array (9 MT doublets around outside, 2 MTs in center)
- Axonemal dynein = ATPase that links the doublets ad causes bending by differential sliding
- Dynein arm defect = can’t move, get Kartagener or primary ciliary dyskinesia; infertility in M/F, can also cause bronchiectasis, sinusitis, and situs inversus
Inhibitors of the Na/K pump
- Ouabain - binds K+ site, inhibits
- Digoxin/Digitoxin - directly inhibits ATPase and also indirectly inhibits Na/Ca exchanger which increases cardiac contractility
Locations of each type of Cartilage
I - Bone, skin, tendons; decreased in OI type I
II - Cartilage
III - Reticulin (skin, vessels, uterus, fetus, granulation tissue); deficient in vascular Ehlers-Danlos (uncommon)
IV - Basement membranes; defective in Alport syndrome, auto-Abs in Goodpasture
“Be (So Totally) Cool, Read Books”
Collagen synthesis
All in RER of fibroblasts:
1. Synthesis: Gly-X-Y (where X/Y are proline or lysine)
2. Hydroxylation: by prolyl/lysyl hydroxylase, which require Vitamin C (scurvy)
3. Glycosylation, then make triple helix of 3 collagen alpha chains (if problem here: OI)
Exocytosis of procollagen into EC space where proteolytic processing and cross-linking happens:
4. Cleave disulfide-rich terminal regions of procollagen
5. Cross-link staggered fibers by Cu-containing lysyl oxidase (inhibited by Lathrogens, e.g. sweet peas)
Osteogensis Imperfecta
MCC: AD decreased production of otherwise normal type I collagen; manifests as brittle bones, blue sclera, dental probs (lack of dentin), and hearing issues (abnormal ossicles)
*Glycine in Gly-X-Y is replaced by a bulkier AA and the triple helix can’t be formed
Ehlers-Danlos syndrome
- Classical type - mutation in type V collagen
- Vascular type - mutation in type III collagen
- Can be AD (MCC) or AR because the defect can be in fibrous protein or enzyme genes.
- Manifestations include stretchy skin, bleeding tendency, hypermobile joints; may also see joint dislocation, berry/aortic aneurysm, organ rupture
Menkes disease
- CT disease caused by impaired Cu absorption/transport because lysyl oxidase needs Cu as a co-factor to make CT
- results in brittle hair, growth retardation, and hypotonia
Marfan Syndrom
- defect in fibrillin, a glycoprotein that forms a sheath around elastin
- makes elastin too stretchy because the fibrillin isn’t there to stabilize it
Elastase
- breaks down elastin
- normally inhibited by A1-antitrypsin
- when A1AT is defective, can get panacinar emphysema and cirrhosis
Southern, Northern, Western, Southwestern Blot
Southern = DNA Northern = RNA Western = protein SW = DNA BPs
ELISA - direct vs. indirect
Direct - add labeled antibody to detect presence of antigen in the blood sample
Indirect - add antigen to detect presence of antibody in the blood (which would indicate antigen is/was there at some point), then add a labeled antibody
Cloning DNA
- isolate mRNA
- give it reverse transcriptase to make cDNA (no introns)
- put cDNA into plasmid that also has Abx-resistant genes
- transform bacterial cell with plasmid
- grow bacterial cell on abx medium
The only colonies to grow will be the ones with the plasmid and thus they are also producing more copies of the cloned DNA.
Pleiotropy
one gene contributes to multiple phenotypic effects
ex: PKU - one genotype causes light skin, intellectual disabilities, and musty BO
Dominant negative mutation
a heterozygote (mutation in only 1 allele) produces a non-functional altered protein that also prevents the other allele’s normal protein from functioning, and in this way has a dominant effect on phenotype
Locus vs. Allelic heterogeneity
when a phenotype results from:
- locus: mutation at any 1 of many loci (different loci)
- alleilic: any of many mutations (different alleles) at 1 locus
Heteroplasmy
mosaic mitochondrial DNA, resulting in variable expression of mitochondrial dysfunction
Heterodisomy vs. Isodisomy
Hetero = meiosis I error; get 1 mom, 1 dad, and 1 sperm chromosome Isodisomy = meiosis II error; get one whole homologous pair, plus sperm
Uniparental disomy
- offspring receives a chromosome from only one parent, but receives 2 copies of it
- so there are the correct number of chromosomes but it resulted from 2 mistakes: 2 copies from one parent, none from the other
Prader-Willi syndrome
- case of imprinting where the paternal gene (on chromosome 15) is deleted/mutated and maternal gene is usually silent
- causes hyperphagia/obesity, intellectual disability, hypogonadism, hypotonia
Angelman syndrome
- case of imprinting where maternal gene (on chromosome 15) is deleted and paternal is usually silent
- inappropriate laughter, seizures, ataxia, severe intellectual disability
AD diseases - know mutated gene and chromosome:
- AD PKD
- FAP
- Familial HCL
- HHT/OWR
- Hereditary spherocytosis
- Huntington
- Marfan syndrome
- MEN
- NF1
- NF2
- Tuberous Sclerosis
- Von Hippel Lindau
- ADPKD: PKD1 (85%) - CHR 16; PKD 2 (15%) - CHR 4
- FAP: APC - CHR 5 (5 letters in “polyp”)
- FHCL: LDLR - CHR 19p
- HHT: 80%: ENG - CHR 9; ACVRL1 - CHR 12
- HS: spectrin (SPTAN1/2 - CHR 1/9) or ankyrin (ANK1 - CHR 8)
- HD: CAG repeats - CHR 4 (Hunting 4 food)
- Marfan: FBN 1 - CHR 15
- MEN: Men2A/2B associated with RET oncogene mutation
- NF: NF1 gene - CHR 17
- NF: NF2 gene - CHR 22
- TSc: TSC1 - CHR 9; TSC2 - CHR 16 (contiguous with PKD1)
- VHL: HIF1 gene - CHR 3p (3 words in VHL)
AR diseases - know mutated gene and chromosome:
- Albinism
- AR PKD
- Cystic fibrosis
- Glycogen storage diseases
- Hemochromatosis
- Kartagener
- Mucopolysaccharidoses
- PKU
- SCD
- Sphingolipidoses
- Thalassemias
- Wilson disease
- Albinism:
- ARPKD:
- CF:
- GSD:
- HCT:
- Kartagener
- Mucopolysaccharidoses
- PKU
- SCD
- Sphingolipidoses
- Thalas:
- WD:
DMD and BMD
X-linked mutations
- DMD = frameshift mutation makes truncated dystrophin protein, accelerated muscle breakdown; weakness begins in pelvis and ascends with fatty replacement of muscle esp. calf; COD - dilated cardiomyopathy; diagnose with muscle biopsy, will also have inc. CPK and aldolase
- BMD = point mutation in dystrophin, less severe with onset in early adolescence/adulthood
Myotonic type I MD
CTG nucleotide repeat expansion in the DMPK gene, get myotonia, muscle wasting, frontal balding, cataracts, testicular atrophy, arrhythmia
Fragile X syndrome
X-linked CGG repeats in FMR1 gene; get XL testes/jaw/ears, autism, MVR, and retardation
(FMR = Fragile x Mental Retardation)
Trinucleotide repeat expansion diseases
Try Hunting for My Fried Eggs: Huntingtons - CAG Myotonic dystrophy - CTG Friedrich ataxia - GAA Fragile X syndrome - CGG
Autosomal Trisomies
Pautau - CHR 13 (Puberty)
Edward - CHR 18 (Election)
Down - CHR 21 (Drinking)
- all have CHD; E/P have rocker bottom feet
- 1st Trim: free B-HCG inc. in D, dec. in E/P; inc. nuchal translucency in D/P
- 2nd Trim Quad: AFP and estriol dec. in D/E; B-HCG and inhibin A inc. in D, dec. in E (no info for Patau)
Robertsonian translocation
when two acrocentric chromosomes fuse and lose their short ends, you have one extra large chromosome made of 2 chromosomes and it may be balanced or imbalanced; most commonly happens with CHR 13/14/15/21/22
Cri-du-chat
- microdeletion of CHR 5p
- get microcephaly, mod-severe intellectual disability, high-pitched crying/mewing, VSD, epicanthal folds
Williams syndrome
- microdeletion of CHR 7q (including elastin gene)
- get elfin facies, intellectual disability, hyperCa (hypersensitive to VitD), well-developed verbal skills and extremely friendly to strangers, CV probs
22q11 Deletion syndromes
CATCH-22:
- Cleft palate, Abnormal facies, Thymic aplasia/T cell def, Cardiac defects, Hypocalcemia (2/2 PTG aplasia) - due to microdeletion at CHR 22q11
- due to aberrant development of 3rd/4th branchial pouches (neural crest cell migration defects)
- DiGeorge syndrome - thymic, parathyroid, and cardiac defects (PTA, ToF)
- Velocardiofacial syndrome - palate, facial, cardiac defects
Beriberi
- caused by B1 deficiency (Ber1ber1)
- Wet = HOCF from dilated CM, edema
- Dry = polyneuritis, symmetrical muscle wasting
Wernicke-Korsakoff syndrome
- caused by B1 deficiency
- classic triad: confusion, ophthalmoplegia, ataxia
plus: confabulation, personality change, permanent memory loss
Vitamin A deficiency, excess
- deficiency: night blindness, dry/scaly skin, alopecia, keratomalacia (corneal degeneration), immune suppression
- excess: alopecia, scaly skin, arthralgias, cerebral edema, pseudotumor cerebri, hepatic abnormalities
Vitamin B2 deficiency, function
- deficiency = 2 C’s: Cheilosis, Corneal vascularization
- function: components of FAD and FMN (flavins) used as cofactors in redox rxns
Vitamin B3 (niacin)
- function:components of NAD/NADP used in redox rxns, derived from tryptophan and requires B2/B6 for synthesis
- def: Glossitis, Pellagra (3 D’s: diarrhea, dementia, dermatitis),
- excess: facial flushing (PGs), hyperglycemia, hyperuricemia
Vitamin B5
- component of coenzyme A (CoA) and FA synthase
- deficiency: dermatitis, enteritis, alopecia, adrenal insufficiency
Vitamin B6
- converted to pyridoxal phosphate, a cofactor for synthesis of NTs and other molecules
- deficiency: convulsions, hyperirritability, periph NPY, and sideroblastic anemias
Vitamin B7 (biotin)
- cofactor for carboxylation enzymes to add a 1-C
- deficiency: dermatitis, alopecia, enteritis; rare but may be caused by excessive ingestion of raw egg whites
Vitamin B9 (folic acid)
- converted to THF, an important co-factor for the synthesis of nitrogenous bases into DNA; small reserve pool in liver
- deficiency: anemia, hypersegmented PMNs, glossitis; can be caused by drugs - phenytoin, MTX, sulfonamides
Vitamin B12 (cobalamin)
- cofactor for homocysteine methyltransferase; years’ worth stored in the liver
- deficiency: anemia, hypersegmented PMNs, parasthesias, subacute combined degeneration (of dorsal columns, spinocerebellar tracts, and lateral CS tracts)
- deficiency caused by:
1. insufficient intake (vegan)
2. malabsorption (sprue, enteritis)
3. lack of IF (pernicious anemia or gastric bypass)
4. missing terminal ileum (Crohn’s)
Vitamin C
- needed for: iron absorption, collagen synthesis, conversion of DA to NE
- deficiency causes Scurvy: swollen gums, bruising, hemarthrosis, anemia, poor wound healing, perifollicular/subperiosteal hemorrhages, “corkscrew” hair - all 2/2 collagen def.; also weakened immune response
- excess: N/V/D, fatigue, Ca-oxalate nephrolithiasis; can inc. risk of iron overload in at-risk pts
Vitamin D
- functions to inc intestinal absorption of Ca/P
- deficiency:
1. Rickets - kids; bone pain and deformity
2. Osteomalacia - adults; bone pain, muscle weakness
+ hypocalcemic tetany - excess: hypercalcemia, hypercalciuria, loss of appetite, stupor; seen in sarcoidosis
Vitamin E
- protects erythrocytes/membranes from free radical damage
- def: hemolytic anemia, acanthocytosis, muscle weakness, dorsal column/spinocerebellar tract demyelination
- sx of def may appear similar to B12 deficiency, but won’t see megaloblastic anemia, hypersegmented NTs, or inc. serum methylmalonic acid levels
Vitamin K
- needed for coagulation (warfarin is Vit K antagonist)
- def: neonatal hemorrhage with inc. PT/PTT but normal bleeding time, give Vit K injection at birth to prevent
Zinc
- cofactor for many things
- def: delayed wound healing, hypogonadism, dec. adult hair, dysgeusia, anosmia, acrodermatitis enteropathica
What’s the point of the HMP shunt?
to make NADPH for use in cholesterol synthesis and fatty acid synthesis, as well as for use in the GSSG path
What’s an siRNA and miRNA?
siRNA = silencing RNA
miRNA = microRNA
Both are short (~20-30bp) that induce post-transcriptional silencing; so they basically match and degrade mRNA so it is never translated. This is a potentially therapeutic way to treat oncogenes, because the siRNA can go in and silence the oncogene mRNA transcript.
Will cause degradation if a complete match, but will also jam the ribosome if a partial match.
Operon vs. Promoter
Operons are bound by negative regulators, aka repressors.
Promoters are bound by enhancers.
Example = E. coli’s lac operon which is normally bound by an inhibitor, but lactose will remove the inhibitor and allow the gene to be transcribed.
Insulin binding its receptor and the IC cascades
- Receptor is a TK
- activation of 2 pathways:
- MAPK
- PI3K - MAPK goes to activate TFs for anabolic activity; PI3K goes to put more GLUT4 up in the membrane and activate Protein Phosphatase (dephosphorylates Glycogen synthase so glycogenesis can start)
