Biochemistry First Aid- Molecular Flashcards
what is a nucleosome
a nucleosome consists of DNA wrapped twice around a histone octamer
histones are rich in what two amino acids
lysine and arginine
what type of histone molecule connects consecutive nucleosomes
H1
what’s the difference between heterochromatin and euchromatin
heterochromatin is “highly condensed” and inaccessible for transcription; euchromatin is “truly transcribed”
what does DNA methylation do for mismatch repair
DNA methylation (at adenine and cytosine) occurs in new DNA and is absent from old DNA; this allows DNA mismatch repair enzymes to differentiate old and new DNA
what does methylation of CpG islands do?
represses transcription
what does histone methylation do?
can activate or repress transcription depending on the context
what does histone acetylation do
relax DNA coiling allowing for transcription
which base has a methyl group
thymine
which base has a ketone
guanine
from which base is uracil made and how
uracil is made via deamination of cytosine
which base pair has 3 H-bonds
C and G
which base pair has 2 H-bonds
A and T
what does 6-MP do
6-mercaptopurine inhibits purine synthesis from PPRP (phospho-ribosyl pyrophosphate)
how are purines synthesized
PRPP (sugar + phosphate) is added to a base to make IMP which then becomes either AMP or GMP
how are pyrimidines synthesized
carbamoyl phosphate becomes orotic acid which joins PRPP to make UMP. UMP becomes UDP which becomes either CTP or dUDP. (deoxyUDP) dUDP becomes dUMP which becomes dTMP
what does nucleotide reductase do and what drug inhibits it
nucleotide reductase converts UDP to dUDP and it is inhibited by hydroxyurea
what does thymidylate synthase do and what is it inhibited by
thymidylate synthase converts dUMP to dTMP (deoxyuracil monophosphate to deoxythymine monophosphate) by converting THF to DHF; it is inhibited by 5-FU
what does dihydrofolate reductase do and what drug is it inhibited by
dihydrofolate reductase converts DHF to THF and it is blocked by methotrexate and trimethoprim
what does ornithine transcarbamoylase (OTC) do and what does its deficiency cause
OTC is a key enzyme in the urea cycle and its deficiency leads to accumulation of carbamoyl phosphate leading to orotic acid build up
what enzyme defect causes orotic aciduria
defect in UMP synthase which catalyzes conversion of orotic acid to UMP
how do you differentiate between orotic aciduria and OTC deficiency
hyperammonemia in OTC; no hyperammonemia in orotic aciduria
OTC doesn’t cause megaloblastic anemia while orotic aciduria does
name some findings for orotic aciduria
failure to thrive, megaloblastic anemia, high urinary orotic acid
how is orotic aciduria treated
oral uridine administration
what pattern of inheritance does orotic aciduria have
autosomal recessive inheritance
what does adenosine deaminase do and what does its insufficiency cause
adenosine deaminase converts adenosine to inosine;
deficiency of this enzyme leads to excess ATP and dATP causing feedback inhibition of ribonucleotide reductase leading to low lymphocyte count and SCID
what is the inheritance pattern of adenosine deaminase deficiency
autosomal recessive
what causes Lesch-Nyhan syndrome
absence of HGPRT (hypoxanthine guanine phosphoribosyltransferase, which converts hypoxanthine to IMP and guanine to GMP) leading to excess uric acid production and de novo purine synthesis
what is the inheritance pattern of Lesch-Nyhan syndrome
X-linked recessive
what are the clinical findings of Lesch-Nyhan syndrome
H=hyperuricemia G=gout P=pissed off (aggression/ self-mutilation) R=mental retardation T=dystonia (choreoathetosis)
name four features of the genetic code
unambiguous, degenerate (redundant), commaless (nonoverlapping), universal
what does it mean that the genetic code is commaless or nonoverlapping and what kind of organism is an exception to this rule
the genetic code is read from a fixed starting point as a continuous sequence of bases; some viruses are an exception to this rule
what does it mean that the genetic code is degenerate or redundant
most amino acids are coded by multiple codons (except for methionine and tryptophan encoded by AUG and UGG, respectively)
name the four kinds of point mutations
- silent (same amino acid)
- missense (diff. amino acid)
- nonsense (stop codon)
- frameshift
what does helicase do
unwind DNA at the replication fork
what do single-stranded binding proteins do
prevent strands from reannealing
what do DNA topoisomerases do
unwind DNA supercoiling by creating nicks in the helix
what drug inhibits DNA gyrase (prokaryotic topoisomerase II)
floroquinolones
what does primase do
primase makes an RNA primer on which DNA polymerase III can initiate replication
which organisms have DNA polymerase III
prokaryotes only
what two activities does DNA polymerase III perform during replication
synthesis (in the 5’ to 3’ direction)
proofreading (in the 3’ to 5’ direction)
which organisms have DNA polymerase I
prokaryotes only
what does DNA polymerase I do
degrades RNA primer and replaces it with DNA (can excise in the 5’ to 3’ direction)
what does DNA ligase do
catalyzes phosphodiester bonds to anneal fragments of DNA (i.e. joins Okazaki fragments)
what does telomerase do
adds extra DNA to 3’ ends of chromosomes to protect the genetic material
how does nucleotide excision repair work
specific endonucleases cleave oligonucleotides containing damaged bases, DNA polymerase and ligase replace and reseal the gap; this process repairs bulky helix-distorting lesions
what disease is associated with defects in nucleotide excision repair
xeroderma pigmentosum (pyrimidine dimers due to UV persist)
how does base excision repair work
Base-specific glycosylase recognizes altered base and creates AP site (apurinic/apyrimidinic). Nucleotide(s) are removed by AP-endonuclease, which cleaves the 5’ end. Lyase cleaves the 3’ end. Gap is filled by DNA polymerase beta and resealed by DNA ligase.
what specific problem is base excision repair important for
repair of spontaneous/ toxic deamination
how does mismatch repair work
a newly synthesized strand is recognized (via methylation), mismatched nucleotides are removed and the gaps are filled and resealed
what disease is associated with defective mismatch repair
mutation in mismatch repair is associated with hereditary nonpolyposis colorectal cancer (HNPCC)
what does nonhomologous end joining entail
bringing together two ends of double stranded DNA to fix double stranded breaks
in what disease is nonhomologous end joining mutated
ataxia telangiectasia
in what direction is protein synthesized
N to C
in what direction along the DNA is the DNA proofread during DNA replication
3’ to 5’
in what direction do the newly synthesized DNA and RNA strands grow during synthesis and trascription respectively
5’ to 3’
which component of the nucleotide does the incoming nucleotide contribute to the phosphodiester bond
the incoming nucleotide binds with its triphosphate (“the nucleotide provides the energy for the bond”)
the 5’ triphosphate is attacked by 3’OH
which type of RNA is most abundant
rRNA
which type of RNA is the smallest
which is the longest
tRNA is smallest
mRNA is longest
what is the start codon
AUG (rarely GUG)
what are the stop codons
UGA, UAA and UAG
where are enhancers located relative to the genes whose expression they alter
close to, far from or even within (in an intron) the gene
what is a gene silencer
a site where repressors bind
what does eukaryotic RNA polymerase I do
synthesize rRNA
what does eukaryotic RNA polymerase II do
synthesize mRNA
what does eukaryotic RNA polymerase III do
synthesize tRNA
what is the mechanism of action for alpha-amanatin, found in Amanita phalloides (death cap mushrooms)
inhibits RNA polymerase II causing severe hepatotoxicity when ingested
in prokaryotes which RNA polymerases make what
1 RNA polymerase makes all 3 kinds of RNA
what is heterogenous nuclear RNA (hnRNA)
newly synthesized RNA in the nucleus that hasn’t yet been processed
name three kinds of post-transcriptional processing that happens to pre-mRNA in the nucleus
- addition of 5’ 7-methylguanosine cap
- addition of poly A tail
- splicing out of introns
what are the three main steps of pre-mRNA splicing
- primary transcript combines with snRNP’s to form splicesosome
- lariat-shaped intermediate is formed
- lariat intron is released and 2 exons are joined
in what disease are antibodies against splicesosomal snRNPs formed?
Lupus
what is the conserved final sequence of tRNAs
CCA
to which end of the tRNA is the amino acid bound
3’ end
how are tRNAs charged
aminoacyl-tRNA synthetase uses ATP to match an amino acid with its proper tRNA; this match is checked before and after charging and hydrolyzed if it is wrong
how do tetracyclines work
they bind 30S subunit of ribosome preventing attachment of aminoacyl-tRNA
what is tRNA wobble
degeneracy of the genetic code allows for the third base of the codon to be changed without altering the amino acid most of the time
what are the two subunits of the eukaryotic ribosome
40S and 60S
what is ATP used for in protein synthesis initiation and what is GTP used for during this process?
ATP is used for tRNA charging (“activation”)
GTP is used for binding tRNA and translocation (“gripping and going”)
what are the three steps of elongation
- amino-acyl tRNA binds to A side
- ribosomal rRNA catalyze peptide bond between newly added amino acid and the growing polypeptide chain
- ribosome translocates 3 nucleotides toward 3’ end of mRNA and polypeptide is moved to P site
what does the A site do?
what does the P site do?
what does the E site do?
A site is where the amino-acyl tRNA binds
P site is where the growing polypeptide sits
E site is where the empty tRNA exit
how do aminoglycosides act?
they bind the 30S and inhibit initiation complex formation
how do tetracyclines work?
tetracyclines bind the 30S subunit and block entry of aminoacyl tRNA
how does chloramphenicol work
chloramphenicol blocks the 50S subunit and inhibits peptidyl transferase
how do macrolides work?
macrolides bind 50S and prevent exit of uncharged tRNAs
what are the three steps of protein synthesis
initiation, elongation, termination
name three post-translational modifications
- trimming: removal of propeptide components of a zymogen to get mature protein
- covalent alterations: glycosylation, methylation, hydroxylation, acetylation, phosphorylation
- proteosomal degredation: ubiquitin tagging of defective protein
