Flashcards in Molecular EC Deck (110):
Which is transcriptionally active: heterochromatin or euchromatin?
Euchromatin is active
HeteroChromatin is Highly Condenced
What do DNA methylation and acetylation do?
Methylation makes DNA Mute (inactive)
Acetylation makes DNA Active
What amino acids are required for purine synthesis?
Glycine, Aspartate, Glutamine
What does ribonucleotide reductase do?
reduces nucleotides to deoxy forms
What cofactors are required for ribonucleotide reductase action?
thioredoxin and NADPH
*oxidized thioredoxin reduced/recycled by tioredoxin reductase
What is the rate limiting step of purine synthesis?
*converts Ribose-5-P to PRPP
What ensures balance is maintained in purine synthesis? (2 things)
Cross regulation (GMP requires ATP and vice versa)
Each pathway has end-product inhibition
What is the rate-limiting step of pyrimidine synthesis?
CPS-II (formation of carbamoyl phosphate from CO2, glutamine and ATP)
What nucleotides is IMP a precursor to?
AMP and GMP
What nucleotides are UMP a precursor to?
CTP and TMP
What converts dUMP to dTMP?
What causes Orotic aciduria?
How does it present?
What is the treatment?
Defect in UMP synthase (converts orotic acid to UMP)
Presents as megaloblastic anemia UNRESPONSIVE to B12 or folate
Treat with lifetime uridine supplementation
What is the sequence from AMP to Uric acid?
AMP-->Adenosine-->Inosine-->Hypoxanthine-->Xanthine--> Uric acid
What is the sequence from GMP to Uric acid?
What is SCID?
What is its mechanism?
Severe Combined Immunodeficiency Disease
Adenosine deaminase deficiency (inability to convert adenosine to inosine)
*ATP/GTP imbalance inhibits ribonucleotide reductase
*prevents DNA synthesis
*decreased lymphocytes count
What is Lesch-Nyhan syndrome?
What is its mechanism?
What are the findings?
Absence of HGPRT (& thus purine salvage)
"He's Got Purine Recovery Troubles"
Results in excess uric acid production
What is a silent point DNA mutation?
a mutation that codes for the same amino acid
often a change in the 3rd a.a. (tRNA wobble)
What is a missense mutation?
Wrong amino acid but similar chemical structure
What is a Nonsense mutation?
Change resulting in easly STOP codon
"STOP the NONSENSE"
What is a frameshift mutation?
Misreading all nucleotides downstream
Where are the p53 and RB genes located?
p53 is on chromosome 17
RB is on chromosome 13
Describe Mismatch Repair
Mismatch repair enzymes recognize mismatched nucleotides
GATC endonuclease makes incision in daughter strand
Removed and gap filled
Mutations in mismatch repair enzymes gives rise to what disease?
HNPCC (hereditary nonpolyposal colorectal cancer)
Describe base excision repair
Cytosine is spontaneously deaminated to uracil
Uracil DNA glycosylase removes Uracil
AP endonucleases cut DNA and nucleotide is replaced
Describe nucleotide excision repair
thymidine dimmers caused by UV light are removed by excision endonucleases
What is Xeroderma pigmentosum
Caused by a mutation in excision endonucleases responsible for repairing thymidine dimers
Describe direct DNA repair
Alkylation agents (temozolide) cause methylation of Guanine.
MGMT repairs (permanently inactivated and can be depleted)
What is nonhomologous end joining?
Repair of double stranded DNA breaks
Caused by iodinizing radiation or free radical oxidation
Mutated in ataxia telangiectasia
What phase of the cell cycle to 5-FU and Methotrexate act?
What is the mechanism?
Inhibit dTMP synthesis to block DNA replication
(5-FU inhibits thymidylate synthase)
(Methotrexate inhibits DHF reductase)
In what part of the cell cycle do Bleomycin and Etoposide act?
By what mechanism?
S and G2 phases
Inhibit topoisomerase II (preventing strand sepparation)
What is the mechanism of Cyclophosphamide and Nitosoureas?
Alkylating agents that lead to copying errors and expression of abnormal proteins
What is the mechanism of Doxorubicin and Actinomycin D?
Intercalated into DNA rand block DNA/RNA polymerases
What phase of the cell cycle do vinca alkaloids (vincristine and paclitaxel) work?
What are their mechanisms?
Vincristine inhibits mitotic spindle formation
Paclitaxel inhibits mitotic spindle breakdown
BCL2 proto oncogene function and associated tumors
Mutated in follicular B cell lymphoma
ERBB2 proto oncogene function and associated tumors
Binds epidermal growth factor
MYC proto oncogene function and associated tumors
RAS proto oncogene function and associated tumors
G protein that transducers growth factor signals
APC tumor suppressor gene function and associated tumors
Inhibits MYC expression
FAP (familial Adenomatous Polyposis)
BRCA1 and BRCA2 tumor suppressor gene function and associated tumors
Male and female breast
NF1 and NF2 tumor suppressor gene function and associated tumors
Control intra cellular signaling
Neurofibromatosis: optic nerve gliomas, meningioma, acoustic neuroma, pheochromocytoma
TP53 tumor suppressor gene function and associated tumors
Mediates G1 arrest and apoptosis
RB1 tumor suppressor gene function and associated tumors
Mediates G1 arrest
WT1 tumor suppressor gene function and associated tumors
Represses transcription in developing kidney
Defective DNA repair (double stranded breaks)
Cerebellar ataxia; dilation of blood vessels in skin and eyes
Immunodeficiency (B and T cells)
Defective DNA repair
Carcinomas, Leukemias, Lymphoma
DNA repair defect
HNPCC (hereditary nonpolyposis colorectal cancer)
Defective DNA repair (mismatch repair)
Tumors before 40
Defective DNA repair (nucleotide excision repair of thymidine dimers)
BCC, SCC, malignant melanoma
Severe skin lesions
What is a pseudogene?
Produced by a retrovirus DNA from mRNA
Cannot be expressed (lack promoter and introns)
What is a Transposon (jumping gene)?
DNA sequences that insert themselves into different areas of the genome
What is a Retrotransposon?
What are examples of genetic diseases caused by Retrotransposons?
Jumping genes that use reverse transcriptase
Can prevent the expression of normal proteins
ei. Hemophilia and Duchenne Muscular Dystrophy
What are some drugs that inhibit the G2 phase of the cell cycle?
Etoposide and Bleomycin
inhibit the synthesis of tubulin
What are some drugs that inhibit the S phase of the cell cycle?
5-FU and Methotrexate
Inhibit DNA synthesis
What are some drugs that inhibit the M phase of the cell cycle?
What are CDKs and Cyclins?
CDKs phosphorylate proteins and activate them to promote cell cycle progression
Cyclins bind CDKs and activate them
What are p53 and RB?
p53 inhibits G1 to S progression
UN-phosphorylated RB also inhibits G1 to S progression
What is DNA Gyrase (topoisomerase II)?
Relaxes NEGATIVE supercoils in DNA replication
What is DNA Helicase?
Separates DNA strands
What are Single Stranded Binding Proteins?
Prevent strand from re-annealing
What is DNA primase?
Makes RNA primer
(DNA polymerase III can initiate from)
What is DNA polymerase III?
Elongates leading strand
Exonuclease activity "proofreads"
What is DNA ligase?
Seals Okazaki fragments
What is telomerase?
Adds DNA to 3' end to maintain chromosome length
*somatic cells do not have telomerase-aging*
Types of RNA and polymerases used to synthesize
rRNA (rampant) >> RNA polymerase I
mRNA (massive) >> RNA polymerase II
*inhibited by alpha-amanitin
tRNA (tiny) >> RNA polymerase III
What antibiotic inhibits prokaryotic RNA polymerase?
What are 3 common sequences in the eukaryotic promoter?
TATA (binds TBP)
CAAT (binds NF1)
CG (binds SP1)
primary mRNA transcript containing coding and noncoding sequences
(before introns are removed via splicing)
What is the purpose of the cap and tail of the mRNA?
7-methylguanosine CAP orients mRNA on the ribosome
Poly(A) tail increases the half life
aggregate at introns forming spliceosomes
SLE - autoantibodies against snRNPs
lac operon: Low lactose, low glucose
Repressors inhibit expression
lac operon: High lactose, low glucose
No glucose --> cAMP elevated --> CAP-cAMP complex stimulates transcription
lac operon: High lactose, High glucose
Glucose-->cAMP low--> no transcription stimulation
*allows glucose to be used up first*
Describe drugs resistance in cancer cells due to amplication
The gene for dihydro folate reductase can be increased to levels 3000 times the lethal dose of methotrexate in normal cells.
Name two examples of alternative splicing
Fibronectin : extracellular matrix, cell surface, and soluble all from same mRNA
*Removal of carboxy-terminal converts from membrane to soluble protein
IgG heavy chain in B cells
mRNA editing of apolipoprotein B
In the GUT: ApoB-48 do not bind LDLR, encoded not to include binding domain
In the LIVER: Apo-100 has LDLR binding domain
What are some examples of autosomal dominant diseases?
Adult poly cystic kidney disease
What are some examples of autosomal recessive diseases?
Inborn errors of metabolism
What are some examples of X lined diseases?
Duchenne's muscular dystrophy
Hemophilia A and B
What antibiotics work on the 30S subunit?
Tetracyclins: Bind 30S and block incoming aminoacyl tRNA
Aminoglycosides: Inhibit 30S subunit
Streptomycin: Inhibit 30S subunit
What antibiotics work on the 50S subunit?
Chloramphenicol:Inhibits peptidyltransferase activity of 50S
Erythromycin: Inhibits 50S translocation along mRNA
Clindamycin: Inhibits 50S translocation along mRNA
What are some antibiotics that work on eukaryotic 60S subunit?
Shiga-like toxin (EHEC)
~All cleave 28S of 60S subunit which prevents binding of aminoacyl tRNA
How does diptheria toxin inhibit protein synthesis?
Inhibits EF-2 (elongation factor 2), inhibiting ribosome translocation
What antibiotic targets eukaryotic peptidyl transferase?
Cyclohexamide: fungicidal and rat repellant
Describe polypeptide translocation to the RER
Ribosome attaches to ER membrane via SRP
Translocon: directs into ER lumen
Amino end enters first, signal sequence cleaved
Msy be glycosylated in lumen
Cannot form mannose-6-phosphate on enzymes targeted for lysosomes
~deficient in phosphotransferase needed to add M6P
Enzymes produced normally, but secreted into blood instead of lysosome
*presents with coarse facial features, clouded corneas, restricted joint movement.
Tags proteins to be degraded in proteosome
Vesicular trafficking proteins
COP1: golgi>golgi (retrograde)
COPII: golgi>golgi (anterograde)
Molecular motor proteins
Dyenein: Retrograde microtubule (+>-)
Kinesin: Anterograde microtubule (->+)
Mutation in lysosome trafficking regulatory gene (LYST)
Drugs that act on microtubules
Paclitaxel (anti breast cancer)
Dyenein arm deficiency
Associated with siatus inversus
Drugs that inhibit Na/K pump
Ouabain: inhibits binding to K site
Cardiac glycosides (digoxin/digitoxin)
directly inhibit ATPase
Leads to decreased Na/Ca exchange
Increased intracellular Ca and contractility
Type I: Bone, Skin, Tendon
Type III: Reticulin
Type IV: Basement membrane
"Be (So Totally) Cool, Read Books"
Type I collagen
Late wound repair
Defective in osteogenesis imperfecta
Type II collagen
Type III collagen
Reticulin (skin, blood vessels, uterus, fetus, granulation tissue)
Defective in Ehlers-Danlos
Type IV collagen
Defective in Alport syndrome
1) Synthesis (RER): Gly-X-Y
2) Hydroxylation (ER): of proline and lysine (required vit. C)
3) Glocosylation (ER): of hydroxylysine, hydrogen and disulfide bond formation
4) Exocytosis into extracellular space
5) Cleavage: of terminal regions into insoluble tropocollagen
6) Cross-link: Forming fibrils
Multiple fractures, blue sclerae, hearing loss, dental imperfections
Congenital nephritis, deafness, and ocular disturbances
Alport syndrome (type IV collagen)
Paternal allele not expressed
Maternal allele not expressed
Trinucleotide repeat expansion diseases
Fragile X: (CGG)
Friedreich's ataxia: (GAA)
Myotonic dystrophy: (CTG)
"X-Girlfriends First-Aid Helped-Ace My-Test"
18-Edwards (rocker-bottom feet, small jaw)
13-Patau's (rocket-bottom feet, cleft palate, microophthalmia/cephaly, polydactyly)
"Drink at 21, Election at 18, Puberty at 13"
Nonreciprocal chromosomal translocations
Long arms fuse @ centromere and short arms are lost
Microdeletion of short arm of chr 5
microcephaly, retardation, high-pitched crying/mewing, epicanthal folds, cardiac VSD
Microdeletion of long arm of chr. 7
Hypercalcemia (increased vit. D def)
Well-developed verbal skills/extreme friendliness
22q11 deletion syndromes
Aberrant devo of 3rd and 4th branchial pouches