Biochemistry Flashcards
Purines
A, G, xanthine, hypoxanthine, uric acid
Transition
Mutations that substitute a pyrimidine for a pyrimidine
Transversion
Mutations that substitute a purine for a pyrimidine or vice versa
Lesch-Nyhan syndrome
X-linked recessive. Failed purine salvage due to absence HGPRT (which converts hypoxanthine to IMP/guanine then to GMP). Thus, excess purine synthesis and uric acid production.
“Lesch Nyhan Syndrome
Lacks Nucleotide Salvage”
Dx-orange crystals in diaper, retardation, cerebral palsy, hyperuricemia
Purine nucleotide synthesis
de novo or salvage pathway. De novo for rapidly dividing cells, salvage pathway recycles from degraded nucleic acids and is the major route of synthesis in adults.
Gout
Hyperuricemia due to either overproduction or undersecretion of uric acid. Since uric acid is less soluble than hypoxanthine and xanthine, sodium urate crystals deposit in joints and soft tissue leading to arthritis
Differential dx for increased uric acid and gout
- Lesch-Nyhan
- Alcoholism
- G6P deficiency, hereditary fructose intolerance, galactose 1P uridyl transferase deficiency
Denatures DNA helix
Heat, alkaline pH, formamide, urea
Hereditary orotic aciduria
Deficiency in orotate phosphoribosyl transferase and/or OMP decarboxylase (pyrimidine metabolism). Presents with retarded growth and severe anemia. White precipitate in urine.
Nucleotide degradation
Purines: uric acid
Pyrimidine: B-amino acids, CO2, NH4+
Increased DNA methylation
decreased gene transcription
Increased histone acetylation
Increased gene transcription
Start codon
AUG
Stop codons
UGA, UAA, UAG
Holoenzyme
Core enzyme with sigma subunit that allows enzyme to recognize promoter sequences
Post-transcriptional modification
5’ capping, poly(A) tail, RNA splicing. Prevents mRNA degradation, allows translation to begin.
5’ capping
7-methyl-guanosine added to 5’ end of RNA. Stabilizes mRNA, facilitates exit from nucleus. Note-not all mRNAs have polyA tail
Poly(A) tail
40-200 adenine nt’s added to 3’ end of RNA by polyadenylate polymerase
RNA splicing
by spliceosome, which is composed of snRNPs. Binds at splice junctions flanked by GU-AG. Function-removes introns, splices together exons. Excised intron released as lariat structure
SLE
Associated with production of antibodies to host protein, including snRNPs.
Defective RNA splicing
Responsible for 15% of genetic diseases
XP
AR. Defective NER. More common in Japanese people. Cannot tolerate sunlight. First signs usu apparent at 6mo -increased pigmentation, diffuse erythema and scaling esp in light exposed areas. Second stage of disease-telangiectasias, skin atrophy, mottled irregular pigmentaiton, other characteristics of poikiloderma. Final stage-malignancies.
Protein synthesis
From N to C terminus. In three steps: initiation, elongation, termination
Post-translational modification
Trimming (e.g. in a zymogen), phosphorylation and glycosylation.
Sickle cell anemia
Change in 6th codon of B-globin gene results in modified Hb structure….Hb S, which polymerizes under low O2 conditions, distorting RBCs.
CF mutations
One of mutations: T substituted for C at nt 1609 of CFTR gene on chromo 7. Converts CAG to stop codon
dF508=most common, 66% worldwide not a nonsense mutation
B thalassemia
Some cases caused by splice site mutation in B globin gene
Splice site mutation
Insertion of nt bases in certain regions of a gene can alter splicing of introns from precursor mRNA, thus contains introns.
Deletion mutations
Generally irreversible
bcr-abl gene
Assoc w CML t( 9;22) -Philedelphia chromosome
Amplification
Multiple copies of whole DNA segments.
Linked to drug resistance in certain cancers –confers resistance to chemo by preventing their uptake into the cell
Reciprocal (non-Robertsonian) translocation
True exchange of DNA fragments between two chromosomes. Can lead to fusion genes or changes level of expression
Robertsonian translocation
Large fragment of chromo attaches to another chromo but no DNA is attached in return. Common ones are confined to acrocentric chromos since short arms of these contain essentially no essential genetic material.
Down syndrome
3% caused by Robertsonian translocation of 1/3 chromo 21 onto chromo 14.
Interstitial deletions
Deletions of large fragments of DNA-results in pairing of two genes not normally in sequence. May lead to formation of fusion oncogenes
Chromosomal inversions
Large segment of single chromo becoming reversed w/in same chromo. Usuallly from rearrangement following chromo breakage. Can create fusion genes.
Two categories of mutagens
Chemical agents and ionizing radiation
Alkylating agents-mechanism
Cross-link guanine nts in DNA causing damage in replicating and non-replicating cells
DNA intercalating agents
Ethidium bromide Aflatoxin Doxorubicin Daunorubicin Thalidomide
Doxorubicin, daunorubicin
cancer chemotherapeutics
Thalidomide
DA intercalating agent.
Last-resort anti-inflamm in erythema nodosum and sarcoidosis
salvage chemo in patients with multiple myeloma
Cell fates when DNA damage surpasses a certain thershold or DNA repair no longer effective
- Senescence (irreversible)
- Apoptosis
- Cancer
BER
Fixes Uracil abasic sites, single strand breaks
NER
Fixes photoproducts, bulky adducts, pyrimidine dimers
Recombinational repair (HR/NHEJ)
Repairs crosslinks, double strand breaks
Mismatch repair (MMR)
Repairs A-G mismatch, T-C mismatch, indel
G1 checkpoint
Largely dependent on p53
Li-Fraumeni syndrome
Mutation in p53 gene
Rb
chromo 13q. Assoc w retinoblastoma and osteosarcoma
G2 checkpoint
Final checkpoint before mitosis. MPF and CDK regulate this step.
Fanconi anemia
AR. Bone marrow failure and DNA repair defects. Often develop pancytopenia as consequnce of aplastic anemia, leukemias, and solid tumors. Cafe-au-lait spots and pigmentation, genitourinary problems and poor growth often present.
Cockayne syndrome
AR. Mutations in NER. Birdlike facies, progressive retinopathy, dwarfism, photosensitivity. Accelerated aging of cells.
Trichothiodystrophy
Rarest NER disorder. Group of AR disorders characterized by sulphur-rich brittle hair and nails, photosensitive, thickened, scaly skin (“fish-skin”); physical and mental retardation. Only over a dozen cases reported.
Ataxia-telangiectasia
Progressive neuro dysfunction, cerebellar ataxia, sinopulmonary infections, telangiectasias, increased risk of malignancy, hypersensitivity to xrays. Can progress to spinal muscular atrophy and peripheral neuropathy. Protein affected required for maintenance of genome stability. Higher freq of chromosome and chromatid breaks and rearrangements esp affecting chromos 7 and 14 (responsible for T cell receptor and Ig regulation). If AR then mutation in ATM gene
Microsatellite instability
Change in number of repeating units of microsatellites in germline alleles. Microsatellites are stretches of DNA made of short repeating motifs (usu b/w 1-5 bases in length).
HNPCC
AD. Mutations in number of genes e.g. MSH2, MLH1, PMS2, ras. 80% risk of CRC, in addition to other malignancies (endometrium, ovary, stomach, brain). Aka Lynch syndrome. Several genes involved in mismatch DNA repair involved leading to significant microsatellite instability resulting in accumulation of malignancies that give rise to malignancies.
Hereditary breast cancer
60-80% lifetime risk (compared to normal average of 11%). Esp serious adenocarcinomas. BRCA2 mutations-ovarian, prostate, pancreatic cancers. Genes typically involve DNA repair. Higher freq of p53 mutations seen.
Hereditary breast cancer-AD. Typ BRCA1, BRCA2. 5% of all breast cancers thought to be hereditary forms.
Bloom syndrome
Rare AR disorder. Growth delay, increased risk of malignancy (300x), recurrent resp and GI infections (compromised immunity). Telangiectatic erythema often seen in butterfly facial distribution. Mutation in gene coding for protein with helicase activity-thought to be involved in maintenance of genomic instabiliy. mutation in BLM gene.
Werner syndrome
AR. Accelerated aging, usu in late teen years. Aka progeria of the adult. Development often normal in first decade of life. Gene involved (WS gene) codes for DNA helicase involved in DNA repair mechanisms and general transcription and replication. Particularly affects CTs. Thought that phenotype results from deficiencies in genome maintenance. 1:1,000,000
B-aminoisobutyrate levels
(Urine) used as indicator of DNA turnover. (Thymine degradation is only source in urine.)
Heterochromatin
Found in mitosis as well as interphase. Condensed, transcriptionally inactive.
RNA primer
Made by primase; necessary for DNA polym III to initiate transcription
DNA polym III
Polymerase and proof-reading functions
Adds dNTPs to 3’-OH end of RNA primer and continues until reaches primer of preceeding fragment.
3’-5’ exonuclease activity
tRNA structure
75-90 nt’s in cloverleaf form. Anticodon is opposite 3’ aminoacyl end
Holoenzyme
(Prokaryotes). Core enzyme with a sigma subunit that allows enzyme to recognize promoter sequences
=Apoenzyme+cofactor
Initiation of transcription (prokaryotes)
Sigma subunit of RNA polym recognizes promoter region of sense strand of DNA, binds to DNA, and unwinds DNA helix. Upstream consensus seqences help RNA polym find promoter.
Termination of transcription (prokaryotes)
RNA poly and/or specific termination factors recognize special DNA sequences that cause their dissociation from DNA template.
Transcription in eukaryotes
Involves both RNA polym and additional transcription factors that bind to DNA. Different RNA polyms are required to synth diff types of eukaryotic DNA
Silencer
Stretch of DNA that decreases the rate of transcription when bound
Enhancer
Stretch of DNA that increases the rate of transcription when bound by transcription factors
Promoter
Eukaryotes-includes TATA sequence and/or CAAT sequence upstream of ATG start codon. Critical for initiation of transcription.. Mutations may decrease the quantity of gene transcribed.
Cofactors
Either metals or small organic molecules. many derived from vitamins.
Thiamine (B1) deficiency
Thiamine pyrophosphate (TPP) deficiency ->pyruvate DH, alpha-ketoglutarate DH and transketolase remain in inactive forms -> drastically reduced ability for cells to produce energy -> beriberi (neuro dysfn, cardiac dysfn, weight loss)
Enterokinase
Only in SI. Cleaves zymogen trypsinogen to active trypsin
Gq protein signalling
Phospholipase C causes lipids to cleave into PIP2 which forms IP3 and DAG. IP3 releases Ca from ER (activates cAM-kinase). DAG
Two main classes of transport proteins
Carrier proteins, channel proteins
MDR protein
Harnesses energy from ATP hydrolysis to pump hydrophobic drugs out of the cell. Overexpressed in many human cancer cells
CF protein
Pumps Cl out of cell. Chromo 7
Gs
Increases adenylyl cyclase and thus increases cAMP and this increases PKA activity
Gi
Decreases adenylyl cyclase and thus cAMP and thus PKA
Cholera toxin
catalyzes ADP ribosylation of alpha-s subunit. GTPase activity blocked so continuously active. Resulting activation of adenylyl cyclase causes large effluxes of Na and water into gut lumen.
Pertussis toxin
Adenylyl cyclase permanently activated
Loose CT
Loosely arranged fibers, abundant cells, ground substance (e.g. lamina propria)
Dense irregular CT
Irregularly arranged collagen fibers and few cells (e.g. reticular layer of epidermis)
Dense regular CT
Densely packed parallel fibers with few cells packed in between (e.g. tendons, ligaments, aponeuroses)
Functions of CT
Structure, support, nutrition, defense
Ground substance
Viscous clear substance that occupies the space between cells and fibers in CT. Three types of macromolecules: proteoglycans, glycoproteins, fibrous proteins
Proteoglycans
Macromolecules consisting of core protein covalently attached to approx 100 GAGs and a linker protein which binds hyaluronic acid. Negatively charged, attract water into ground substance. Resists compressive forces
Basal lamina (Basement membrane)
Specialized ECM. underlies all epithelial cells and surrounds individual muscle, fat, and Schwann cells. Separates from underlying CT, serves as filter in renal glomerulus, functions as scaffolding during tissue regeneration/wound healing.
Contains fibronectin, laminin, heparan sulphate, type IV collagen
Collagen amino acid sequence
Gly-X-Y (X and Y commonly proline or hydroxyproline, respectively)
Fibronectin
Dimer of two large subunits bound together by disulphide bridges that each contain domains specialized for binding a specific molecule (e.g. integrins, collagen, heparan) or cells. Helps cells attach to ECM via different binding domains.
Laminin
Three long polypeptide chains arranged in shape of asymmetrical cross. Individual laminin molecules self-assemble and form extensive networks that bind to type IV collagen and form major structural framework of BMs. Also contains many fn’al domains that bind other ECM components and cell surface receptors, thus linking cells with ECM
Bullous pemphigoid
AI disorder where IgG Ab produced against epidermal BM, resulting in BM’s destruction and subepidermal bullaw. “Bul-low epidemis”
CT fibers
All produced by fibroblasts, composed of long peptide chains.
Types:
Collagen fibers
Reticular fibers
Elastic fibers
Collagen fibers
Flexible, provide high tensile strength to tissues
Three polypeptide chains (alpha chains) wound around each other to form long, stiff helical structure. Glycine and proline rich
Collagen in wound healing
Type III laid down first. As healing progresses, fibroblasts secrete type I which eventually replaces Type III.
Type I collagen
Most abundant (90%). Bone, skin, tendon, dentin, fascia, cornea, late wound repair
Type II collagen
Cartilage, vitreous body, nucleus pulposus
Type III collagen
Skin, BVs, uterus, fetal tissue, granulation tissue
Type IV collagen
Basal lamina (BM), kidney, glomeruli, lens capsule
Type X collagen
Epiphyseal plate
Scurvy
Vit C deficiency -inability to hydroxylate proline and lysine residues of collagen. Thus, weakening of capillaries and many nasty complications (ulceration of gums, gingivial bleeding, loose teeth, tissue hemorrhage, anemia, poor wound healing, impaired bone formation in infants).
Osteogenesis imperfecta (OI)
AD. Variety of gene defects leading to less collagen or less functional collagen than normal
Becker’s muscular dystrophy
Mutated dystrophin
Duchenne’s muscular dystrophy
Frameshift deletion of dystrophin
Cri du chat syndrome
Microdeletion short arm Chromo 5
Hurlers syndrome
No alpha-L-id urokinase
Pataus syndrome
Trisomy 13
Edwards syndrome
Trisomy 18
Down’s syndrome
Trisomy 21 (95%), Robertsonian translocation (4%), mosaicism (1%)
Fragile x syndrome
FMR1 gene-Trinucleotide repeat (CGG)
Cystic fibrosis
CFTR gene
Marfans syndrome
Fibrillin mutation
Huntingtons disease
(CAG) expansion
Hereditary spherocytosis
Defect in spectrin/ankyrin
Familial hypercholesterolemia
Defective/absent LDL receptor
FAP
APC gene mutation
Angelman’s syndrome
Maternal allele deleted. Normally inactivate parternal allele.
Prader Willi
Paternal allele deleted. Maternal allele normally inactivated
Alport syndrome
Type IV collagen defect
Ehlers Danlos
Type III collagen defect (most commonly)
Alkaptonuria
Deficiency homogentisic acid oxidase
Cystinuria
Defect of renal tubular amino acid transporter for cysteine, ornithine, lysine, arginine
Maple syrup urine disease
Decreased alpha ketoacid dehydrogenase
Hartnup disease
Defective neutral amino acid transporter on renal, intestinal epithelial cells
Osteogenesis Imperfecta
Defect in type I collagen
Krabbe’s disease
No beta galactocerebrosidase
Classic galactosemia
Deficient galactose-1-phosphate uridyltransferase
Hyperammonemia
Urea cycle enzyme deficiency, e.g. OTC
Albinism
Deficiency of tyrosinase or tyrosine transporters
McArdle’s disease
No skeletal muscle phosphorylase
Multiple endocrine neoplasia
Ret gene
ADPKD
PKD1 mutation
Achondroplasia
FGF3 cell signaling defect
Lesch Nyhan
HGPRT deficiency
Metachromatic leukodystrophy
No aryl sulfatase A
Tay Sachs disease
No hexosaminidase A
Orotic Aciduria
Orotic acid phosphoribosyl transferase
Von Gierkes disease
No glucose-6-phosphatase
Pompe’s disease
No lysosomal alpha-1,4-glucosidase (acid maltase)
Cori’s disease
No debranching enzyme
VHL
Constitutive expression HIF. Deletion VHL (TSG). Chromo 3.
Homocystinuria
Defic of cystathionine synthase or decreased affinity for pyridoxal phosphate; deficiency of homocysteine methytransferase
Niemann Pick disease
No sphingomyelinase
PKU
Decreased phenylalanine hydroxylated or tetrahydrobiopterin cofactor
Essential fructosuria
Defect in fructokinase
Fructose intolerance
Deficiency of aldolase B
Hunters syndrome
No iduronidase
Fabry’s disease
No alpha galactosidase A
Williams syndrome
Microdeletion short arm Chromo 7
