Flashcards in Bicohem Deck (194):
Histones are rich in what two amino acids making it positively charged?
lysine and arginine
What phase do DNA and histone synthesis occur in?
Inactive DNA and histone morphology?
Heterochromatin. Deacetylated and methylated histones allows for tight association and transcriptionally inactive)
Active DNA and histone morphology?
Euchromatin. Acetylated and non-methylated histones allow for loose association and transcriptionally active)
What is methylated in promoter region that can lead to silencing and decreased transcription?
What is methylated in prokaryotic DNA replication to allow for mismatch repair enzymes to distinguish between old and new prokaryotic strands?
Cytosine and Adenine
5 parts needed for purine synthesis
Glycine, aspartate, glutamine ("PURe girls still gag"), THF, CO2
2 parts needed for pyrimidine synthesis
Carbomyl phosphate, aspartate
What is carbomoyl phosphate derived from?
Glutamine + CO2
Nucleoside vs Nucleotide?
Nucleoside-base + (deoxy)ribose
Nucleotide-base + (deoxy)ribose + phosphate; linked by 3'-->5' phosphodiester bond
Thymine has a ______
Guanine vs. Adenine?
Guanine has a =O and can be thought of as "OG"
Rings in purines?
Rings in pyrimidines?
Rate limiting step for pyrimidine production
Glutamine+ CO2-->Carbomyl phosphate (via CPS II)
Mycophenolate and ribavirin inhibit..
6 MP and its prodrug azothioprine inhibits...
de novo purine synthesis
5 FU inhibits
Metotrexate, Trimethoprim, and pyrimethamine inhibit...
How are ribonuclotides converted to deoxyribonucleotides?
Draw the purine/pyrimidine synthesis pathway
p. 63 FA
What is the salvage pathway for thymidylate synthase inhibition?
Thymidine kinase requires thymidine supplementation and normally accounts for 5-10% of dTMP synthesis
Draw the purine salvage pathway
p. 64 FA
Inheritance of adenosine deaminase deficiency?
Inheritanc of Lesch nyhan syndrome?
symptoms of HGPRT deficiency
Hyperuricemia, Gout, Pissed off (aggression, self mutilation) Retardation, DysTonia
Treatment for HGPRT?
Can't treat other symptoms but can treat hyperuricemia/gout with allopurinol and febuxostat
Each codon specifies only 1 amino acid
Most amino acids are coded by multiple codons?
What are the exceptions to AA being coded by multiple codons?
What is commaless, nonoverlappying genetic code?
Read from a fixed starting point as a continuous sequence of bases (exception: viruses)
What is a universal genetic code?
genetic code convserved throughout evolution (exception: mitochondria)
2 enzymes that increase activity of de novo purine synthesis?
PRPP synthetase (Ribose 5-Phosphate-->PRPP) and PRPP amidotransferase (PRPP-->5-phosphoribosylamine)
Rate limiting enzyme of purine synthesis
Glutamine PRPP amidotransferase
Carbon sources in purine synthesis?
Glycine, THF, CO2 (Aspartate, glutamine nitrogen sourceS)
Consensus sequence of base pairs in genome where DNA replication begins. Difference in prokaryotes and eukaryotes?
Origin of replication
Multiple (eukaryotes), single (prokaryotes)
Y-shaped region along dna template where leading and lagging strands are synthesized
Unwinds DNA template at replication fork
Prevents strands from reannealing after unwinding
Single-stranded binding proteins
Create a single-or double-stranded break in the helix to add or remove supercoils
How do replication forks travel?
Travel bidirectionally away from origin of replication as DNA polymerase synthesizes complementary daughter DNA strands
Makes an RNA primer on which DNA pol III can initiate replication
What is ori identified and bound by that locally allows it do dissociate from dsDNA into ssDNA?
DNA A protein. SSB proteins then bind to ssDNA and stabilize and prevent premature reannealing. Helicase then binds ssDNA at ori, moves into rep fork and proceeds to seperate and unwind DNA
What protein triggers DNA replication in bacteria?
5'-->3' synthesis on leading and lagging strand (until reaches primer of preceeding fragment) and proofreads with 3'-->5' exonuclease
DNA polymerase III
5'-->3' synthesis of leading and lagging strand with 3'-->5' exonuclease and also excises RNA primer with 5'-->3' exonuclease+repair of damaged parent DNA
DNA polymerase I
Catalyzes formation of phosphodiester bond within a strand of dsDNA (ie. joins Okazaki fragments)-->seals
RNA dependent DNA polymerase (reverse transcriptase) that adds DNA to 3' ends of chromosomes to avoid loss of genetic material with every duplication?
Inhibit prokaryotic enzyme topoisomerase II (DNA gyrase) and topoisomerase IV
Makes up DNA helicase and primase complex
Coes for tRNA and rRNA and resembles bacterial (prokaryotic) chromosome
Mitochondrial DNA (small circular chromosome similar to bacterial chromosome)
What is an exonuclease?
Removes nucleotides at the end of DNA molecule so it has a particular direction
Sequence added to 3' DNA ends of chromosomes
Telomeres are expressed in what 3 types of cells
Stem cells-long telomeres and act ve telomerase, telomeres shorten with each cell division
Cancer cells-upregulate telomerase activity, preventing cell death by maintaining length of telomeres. Cancer cells immportal b/c cells continue to divide w/o aging and shortening of telomeres
Somatic cells-terminally differentiated and
Transversion and transition apply to which type of mutations?
Point mutations (silent, missence, nonsence)
purine to purine or pyrimidine to pyrimidine "same"
purine to pyrimidine or pyrimidine to purine
Sickle cell disease is a type of what mutation and what happens?
Point mutation that is missence (GAG (glutamic acid) substitution with GTG (valine))
Where is the base change in a silent mutation?
Often base change in the 3rd position of codon (tRNA wobble)
What is it called if new AA is similar in structure to old in missence mutation?
Duchenne muscular dystrophy is what type of mutation?
Frameshift mutation (deletion of dystrophin gene)
Slapped strand mispairing can lead to what?
Insertion and frameshift mutation
What causes the formation of a larger nonfunctional protein, but usually the immunoreactivity of normal proteins (i.e.binding to antibodies?
Splice site mutations (type of point mutation) where mutation of splice sites (not removing all introns from hnRNA in formation of mature mRNA). This is a type of point mutation
Eukaryotic lagging strand building
DNA pol. alpha
Eukaryotic leading strand building
DNA pol. delta
Eukaryotic DNA repair (specifically base excision repair)
DNA pol. beta
replicates mitochondrial DNA
DNA pol. gamma
Mechanism defective in xeroderma pigmentosum
nucleotide excision repair
Repair important in spontaneous/toxic deamination
base excision repair
Mechanism defective in HNPCC
Mechanism defective in ataxia telangiectasia; fanconi anemia
Nonhomologous end joining
What is an endonuclease?
Cut DNA specific DNA sequences within the molecules with no particular direction
When does nucleotide excision repair occur and when does base excision repair occur and when does mismatch repair occur?
Throughout cell cycle-BER
G2 phase-Mismatch repair
Steps in nucleotide excision repair
Specific endonucleases release oligonucleotides by creating a nick on either side. DNA polymerase and ligase fill and reseal gap respectively.
Steps in base excision repair
Base-specific glycosylase (specific endo nuclease) removes base creating an AP site. Following that, one or more nucleotides are removed via AP endonuclease on 5' end and lyase and 3' end. After that DNA polymerase beta adds DNA and is sealed via ligase.
Steps in mismatch repair
Newly synthesized strand is recognized. Mismatched nucleotides are removed. Gap is filled and resealed.
Cause and symptoms of xeroderma pigmentousm?
Most commonly due to absence of UV-specific endonuclease. This is responsible for normally excising thymine dimers by nicking the strand at the thymine dimer.
Symptoms include photosensitivity, poilkiloderma, and hyperpigmentation in sun exposed areas--> increase risk of skin cancer
What brings together 2 ends of DNA fragments to repair ds breaks?
Nonhomologous end joining
DNA and RNA is synthesized in what direction?
mRNA is read in what direction?
N terminus-->C terminus
What is the mechanism behind drugs that block DNA replication?
modified 3' OH, preventing addition of next nucleotide (i.e. cant attach 5' end triphosphate)--> "chain termination"
Mutations in what 2 genes account for 90% of lynch syndrome?
MSH2 and MLH1 genes code for MutS and Mut L homologs. Normally, mismatch repair beings with MutS homolog detecting a mis-match on new daughter strand, which is distinguished from parent strand with occasional nicks in phosphodiester bonds. Mut L recruited slides along complex until nick is recgonized. Exonuclease I loaded onto and activated by repair complex. Daughter strand degraded. DNA pol. delta creates new strand and ligase seals
mRNA start codons (eukaryotes vs. prokaryotes)
Eukaryotes-codes for methionine, which may be removed before translation is completed
Prokaryotes-codes for N-formylmethionine (fMet). fMet stimulates neutrophil chemotaxis.
RNA pol binding?
CAP binding in lac operon (prokaryotic)
At CAP site upstream of promoter
lac l transcribes?
Repressor protein (known as regulatory gene)
lac z codes for?
B-galactosidase (responsible for hydrolysis of lactose into glucose and galactose)
lac y codes for?
Permease (allowing lactose to enter bacterium)
lac A encodes?
B galactosidease transacetylase
Repressor protein binds to (prokaryotic)?
Toxin Inhibits RNA pol II and side effect?
a-amanitin (found in amanita phalloides death cap mushrooms)
Severe hepatotoxicity (increase ALT, AST, bilirubin)
Inhibits RNA pol in prokaryotes
Inhibits RNA pol in eukaryotes and prokaryotes
What opens DNA at promoter site?
RNA pol II
What are specific foci involved in mRNA regulation/turnover in the cytoplasm?
Antibodies to spliceosomal snRNPs
Anti-smith antibodies in SLE
Anti-U1 RNP antibodies
Single gene coding for multiple proteins when same gene is organized differently in different tissues
Abnormal splicing variants implicated in what?
Oncogenesis, genetic disorders (B-thalassemia)
3' end of tRNA
D arm (dihydrouracil residues)
Recognizes specific aminoacyl tRNA synthetase for each AA
T arm (thymine, psuedouracil, cytosine)
Recognizes sequence necessary for tRNA-ribosome binding
Hsp60 in yeast is example of a?
Chaperone protein (facilitating and/or maintaining protein folding)
What helps incoming tRNA bind to A site?
What catalyzes peptide bond formation, transferring growing peptide to AA in A site?
rRNA ("ribozyme") mediates peptidyl transferase activity
How does prokaryotic protein synthesis begin and what is first step for initiation?
mRNA (Shane-Dalgarno sequence) binds to complementary to 16S rRNA (part of 30S ribosomal subunit) and this is necessary for initiation of protein translation.
AA linked by covalent peptide bonds
alpha helix, B-sheet
Compact folding of secondary structure with ionic hdyrophobic hydrogen disulfide stabilizing
Arrangement of multiple folded protein into a multi-subunit complex
Constitutive and inactive regulation of cell cycle
Regulatory proteins that control cell cycle events; phase specific
Phosphorylate other proteins to coordinate cell cycle progression; must be activated and inactivated at appropriate times for cell cycle to progress
2 cells rich in RER
Mucus-secreting goblet cells of small intestine and antibody-secreting plasma cells
3 cells rich in SER
Liver hepatocytes, steroid hormone producting cells of adrenal cortex, gonads
Functions in lipid synthesis and carbohydrate metabolism
Functions in synthesis of proteins (exported)
Two subunits of ribosomes?
Small unit-binds mRNA (template for protein synthesis) and tRNA (carry amino acids)
Large unit-contains peptidyl transferase (catalyzes peptide bond formation in AA)
Membrane enclosed organelle involved in catabolism of very-long chain fatty acids, branched-chain fatty acids, and amino acids
Degrades damaged or uibiquitin-tagged proteins.
Defects of ubiquitin proteoasome system in what disease?
N-oligosaccharides on what in post translational modification?
Asparagine amino group
O-oligosaccharides on what in post translational modification?
serine and threonine hydroxyl group
Mechanism for coarse facial features, clouded corneas, restricted joint movement, and high plasma levels of lysosomal enzymes
Failure of golgi to phosphorylate mannose residues on glyocoprotins so proteins are not delivered to lysososomes.
Golgi-->Golgi (Retrograde); cis golgi-->ER
trans golgi-->lysosomes; plamsa membrane-->endosomes
Which AA can be modified by the golgi apparatus?
Asparagine, serine, threonine
Cyclin D binds to what?
CDK4-->phosphorylation of Rb protein-->Rb protein is released from transcription factor E2F-->w/ E2F unbound, cell is free to transcribe/synthesize components needed for progressing THROUGH S phase (DHF, cyclin E, thymidilate synthase, DNA polymerase)
Cyclin E binds to what?
CDK2-->allows progression INTO S phase.
Cyclin A binds to what?
CDK2 to allow progression from G2-->M (mitotic prophase)
Cyclin B binds to what?
CDK1 complex activated by Cdc 25-->breakdown of nuclear lamnins (skeletal framework) and initiation of mitosis
Nuclear localization signals rich in what AA?
Proline, Arginine, Lysine (PAL). Makes sense b/c histones are in nucleus and rich and lysine and arginine
What are the sorting centers of the cell?
Endosomes. For material from outside of cell or from Goligi, sending it to lysosomes for destruction or back to membrane/golgi for further use.
Cell type: ?
Connective tissue (stain used to identify sarcoma)
Muscle (stain used to identify rhabdomyosarcoma for example)
Epithelial cell (cell used to identify carcinoma)
Neurons (specifically axons. used to identify neuroblastoma)
Predominant function of microfilaments?
Muscle contraction, cytokinesis
Predominant function of intermediate filaments?
Predominant function of microtubules?
Cell division, movement
Drugs that act on microtubules?
Mebendazole, Griseofulvin, Colchicine, Vincristine/Vinblastine, Paclitaxel (Microtubules Get Constructed Very Poorly)
ATPase that links peripheral 9 doublets and causes bending of cilium by differential sliding of doublets
MOA of Ouabain?
Inhibits Na+ K+ ATPase by binding to K+ site.
Most abundant protein in human body
Inhibited by scurvy?
hydroxylation of specific proline and lysine residues
OI has problems forming what?
problems forming triple helix (procollagen)
Ehlers danlos, menkes disease has problems with what?
Cross-linking tropocollagen molecules to make collagen fibrils (secondary to lysyl oxidase covalently linking lysine-hydroxylysine cross-linkage)
Mature collagen is synthetized in what cells?
Fibroblasts, osteoblasts, and chondroblasts
Most abundant AA in collagen?
What catalyzes cleavage of disulfide rich terminal regions of procollagen?
Extracellular precollagen peptidases
2 components of bone matrix
Inorganic hydroxyapatite crystals and organic type I collagen
Common mutations leading to ehlers danlos phenotypes include deficiencies in what two enzymes?
Lysyl hydroxylase (characteristic of kyphoscoliosis and ocular fragility) and pro-collagen peptidase (joint laxity, loos skin, and easy bruising)
3 major differences between collagen and elastin?
1) Very few proline, lysine residues hydroxylated in elastin (thought of as rich in nonhydroxylated proline, glycine, and lysine
2) Triple helix in collagen. No triple helix in elastin
3) Triple helix formation in collagen is initiated by hydroxylation, glycosylation, and inter-chain disulfide bridges @ C-terminus of procollagen. These modifications not happen in elastin molecules
Enzyme catalyzing elastin b linking vs collagen cross linking
Lysyl hydroxylase vs lysyl oxidase
What is unique about elastin crosslinking?
Unique form of desmosine crosslinking between 4 lysine residues between 4 different elastin chains.
DNA sample cleaved into smaller pieces (restriction endonuclease). Electrophoresed on gel. Transferred to filter and filter soaked in denaturant, which is than labeled by DNA probe that recognizes and anneals to complementary strand
Similar to Southern blot except RNA sample is electrophoresed and recognized by DNA probe
Sample protein via gel electrophoresis and labeled antibody used to bind relevant protein
DNA binding proteins (TF, histones, nucleases) used labeled oligonucleotide probes
Describe HIV confirmatory test
Western blot. Antibodies to gp41, gp120/160, p24. Two positive necessary for confirmed positive diagnosis
Direct ELISA used for?
Test for antigen in patient blood
Indirect ELISA used for?
Test for antibody in patient blood
Random insertion of gene into mouse genome
Targeted insertion or deletion of gene thorugh recombination with mouse gene
Inducibly manipulate genes at specific developmental points
dsRNA is synthesized that is complementary to the mRNA sequence of interest. When transfected into human cells., dsRNA seperates and promotes degradation of traget mRNA, "knocking down" gene expression
What explains variable expression in mitochondrially inherited disease
Heteroplasmy due to presence of both normal and mutated mtDNA.
Mccune albright syndrome is an example of
somatic mosaicims that arises from mitotic errors after fertilization and propagates through multiple tissues or organs
4 assumptions of hardy weinberg
No net migration, no mutation at locus, completely random mating, natural selection is not occuring
X-linked recessive diseases:
"Oblivious female will give her boys x-linked disorders"
Ocular albinism, fabry disease, wiskott-aldrich, g6pd deficiency, hunter syndrome, bruton agammaglobulinemia, hemophilia A+B, lesch nyhan, duchenne muscular dystrophy
Hypophosphatemic rickets inheritance
Lifraumeni syndrome commonly causes:
SBLA cancer: sarcoma, brain/breast, leukemia, adrenal gland cancers
Deletion of what 3 nucleotides in cystic fibrosis coding for what?
Phe at position 508
Quad screen Downs, Edwards, Patau?
Down: Increase B-hCG, Decrease afp, decrease estriol, increase inhibin A
Edwards: Decrease b-hCG, decrease afp, decrease estriol, decrease or normal inhibin A
Patau: decrease bCG decrease PAPPA and increase nuchal translucency in 1st trimester screening (not quad screen)
Chromosome 3 disorders
VHL, renal cell carcinoma
Chromosome 4 disorders
ADPKD with PKD2 defect, Huntington disease
Chromosome 5 disorder
Cri-du-chat syndrome, FAP
Chromosome 7 disorders
williams syndrome, cystic fibrosis
Chromosome 9 disorder
Chromosme 11 disorder
Chromosome 13 disorder
Patau syndrome, wilson disease
Chromosome 15 disorder
Chromosome 16 disorder
ADPKD with PKD1 defect
Chromosome 17 disorder
Chromsome 18 disorder
Chromsome 21 disorder
Fragil x, klinefelter, x-linked agammaglobulinemia
what 5 chromosome pairs do robertsonian translocation occur in?