molecular Flashcards
How is DNA found in the nucleus?
DNA is in condensed, chromatin form
How does chromatin condense to get into the nucleus?
(-) charge DNA loops 2x around (+) charged histone to form nucleosome bead
What are the common amino acids of histone and what holds the beads on a string together?
lysine and arginine where H1 ties nucleosome beads together in a string
Beads (nucleosome core and H1) on a string (DNA)
How is DNA in mitosis?
DNA condenses to form chromosomes
What are the histones of the nucleosome core? are there any other histones present outside of the core?
(2x)nucleosome core histones=> H2A, H2B, H3, H4
H1 only histone not in nucleosome core
describe heterochromatin
condensed, transcriptionally inactive, sterically inaccessible
describe euchromatin
less condensed, transcriptionally active, sterically accessible
What is the importance of DNA methylation?
template strand cytosine & adenine are methylated in DNA replication allowing mismatch repair enzymes to distinguish bw old & new strands in prokaryotes
Result of histone methylation?
inactivates transcription of DNA
result of histone acetylation
relaxes DNA coiling, allowing for transcription
What are the purines and associated nucleotides?
Adenine and guanine => 2 rings
what are pyrimidine and associated nucleotides?
cytosine, thymine and uracil => 1 ring
How is uracil made? where is it found?
deamination of cytosine gives uracil that is found in RNA
What nucleotide has a ketone? a methyl?
ketone=> guanine
methyl=> thymine
What is the binding of the nucleotides? which bond is stronger? what is the significance of more G-C bonding?
G-C bond (3H bonds) is stronger than A-T bond (2H bonds)
G-C bonding will increase melting temperature
What are the amino acids necessary for purine synthesis?
Glycine
Aspartate
Glutamine
What is needed to make a nucleoside?
base + ribose (sugar)
What is needed to make a nucleotide?
base + ribose + phosphate;
linked by 3’-5’ phosphodiester bond
What is the difference in purine vs pyrimidine synthesis?
purines=> 1) start w/ sugar + phosphate (PRPP)
2) add base
pyrimidines=> 1) make Orotic acid (temp. base)
2) add sugar + phosphate (PRPP)
3) modify base
How are deoxyribonucleotides made?
1) ribonucleotides synthesized
2) ribonucleotide reductase converts to deoxyribonucleotides
What are the 2 metabolic pathways that carbamoyl phosphate is involved in?
de nono pyrimidine synthesis;
urea cycle
How does ornithine transcarbamoylase deficiency affect pyrimidine synthesis?
used in urea cycle that deficiency will accumulate carbamoyl phosphate which is then converted to orotic acid
What amino acid does pyrimidine base production require?
aspartate
Where does hydroxyurea mechanism of action work?
inhibits ribonucleotide reductase
where does 6-mercaptopurine (6-MP) MOA work?
blocks de novo purine synthesis
where does 5-fluorouracil (5-FU) MOA work?
inhibits thymidylate synthase (decreases deoxythymidine monophosphate or dTMP)
where does MTX MOA work?
inhibits dihydrofolate reductase (decreases dTMP)
where does trimethoprim (TMP) work?
inhibits bacterial dihydrofolate reductase (decreases dTMP)
What causes orotic aciduria?
inability to convert orotic acid to UMP bc defect in UMP synthase => UMP (de novo pyrimidine synthesis path)
What type of defect is UMP synthase?
bifunctional enzyme of autosomal recessive nature
what are the findings of orotic aciduria?
orotic acid in urine;
megaloblastic anemia (no improve w/ B12 or folate)
failure to thrive;
NO HYPERAMMONEMIA
Tx for orotic aciduria
oral uridine admin
differentiate orotic aciduria from OTC deficiency
orotic aciduria=> no hyperammonemia;
OTC deficiency=> increase orotic acid and hyperammonemia
Name enzyme and what is converted as a result of its presence within the purine salvage pathway
1) HGPRT + PRPP=> converts guanine to GMP; and hypoxanthine to IMP
2) APRT + PRPP => converts adenine to AMP
3) adenosine deaminase => converts adenosine to inosine
4) Xanthine oxidase=> converts hypoxanthine to xanthine and xanthine to uric acid
Adenosine deaminase deficiency results in what disease?
Severe combined immunodeficiency disease;
SCID
How does adenosine deaminase deficiency lead to SCID?
excess ATP and dATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase => prevents DNA synthesis & decreases lymphocytes
An absence of HGPRT results in what disease?
Lesch-Nyhan syndrome
Define how Lesch-Nyhan syndrome’s absence of HGPRT leads to disease
XLR=> defective purine salvage results in excess uric acid production and de novo purine synthesis
Findings of Lesch-Nyhan syndrome
retardation, self-mutilation, aggression, hyperuricemia, gout, choreoathetosis
define unambiguous in genetic code
each codon specifies only 1 amino acid
define degenerate or redundant in genetic code
most amino acids are coded by multiple codons
What are the exceptions of degenerate / redundant principles in the genetic code?
methionine (AUG) and tryptophan (UGG) encoded by only 1 codon
define the principle of commaless, nonoverlapping genetic code features
read from a fixed starting point as a continous sequence of bases
what are the exceptions to commaless, nonoverlapping features of genetic code?
some viruses
define principle of universal features to genetic code and what is the exception?
genetic code is conserved throughout evolution;
human mitochondria
give in order the severity of damage in point mutations in DNA (least to worst)
silent < missense < nonsense < framshift
define silent DNA point mutation
same position amino acid, often base change in 3rd position of codon => tRNA wobble
define missense DNA point mutation
changed amino acid (conservative-new amino acid is similar in chemical structure)
define nonsense DNA point mutation
change resulting in early STOP codon
define frameshift DNA point mutation
change resulting in misreading of all nucleotides downstream => truncated, nonfunctional protein
Describe DNA replication in eukaryotes and important in the synthesis
replication is semiconservative and involves both continuous and discontinuous (Okazaki fragment) synthesis
What is significant about the difference of origin of replication in prokaryotes and eukaryotes?
single => prokaryotes
multiple=> eukaryotes
sequence of base pairs in genome where DNA replication begins
define replication fork
Y shaped region along DNA template where leading and lagging strands are synthesized
define helicase
unwinds DNA template at replication fork
define single-stranded binding proteins
prevent strands from reannealing
define DNA topoisomerases
create a nick in helix to relieve supercoils created during replication
What Rx attacks the DNA topoisomerases of prokaryote?
Fluoroquinolones => inhibit DNA gyrase;
prokaryotic topoisomerase II
define primase
makes RNA primer on which DNA polymerase III can initiate replication (prokaryote)
Define DNA polymerase III (prokaryotic only)
elongates leading strand by adding deoxynucleotides to 3’ end;
elongates lagging strand until reaches primer of preceding fragment
define synthesis and proofreading activity of DNA polymerase III
5’-3’ synthesis;
proofreads w/ 3’-5’ exonuclease
what is role of DNA polymerase I (prokaryotic only)?
degrades & replaces RNA primer w/ DNA;
excises RNA primer w/ 5’-3’ exonuclease
role of DNA ligase
catalyzes formation of phosphodiesterase bond w/in strand of double stranded DNA => seals Okazaki fragments
role of telomerase
enzyme adds DNA to 3’ ends of chromosomes to avoid loss of genetic material w/ every duplication
What are the single strand DNA repair vehicles?
nucleotide excision repair;
base excision repair;
mismatch repair
Which is single strand DNA repair vehicle is mutated in xeroderma pigmentosum? how does it present?
nucleotide excision repair;
prevents repair of pyrimidine dimers bc of UV light exposure
What is the important DNA repair vehicle in repair of spontaneous/toxic deamination?
base excision repair
What is DNA repair vehicle is mutated in HNPCC?
mismatch repair
What is the double strand DNA repair vehicle? what is it mutated in?
nonhomologous end joining =>
mutated in ataxia telangiectasia
What direction are DNA and RNA synthesized?
5’ ->3’
what direction are proteins synthesized?
N terminus => C terminus
When synthesizing DNA or RNA, what provides energy for the process?
1st nucleotide at the 5’ end provides triphosphate
Where do many drugs blocking DNA replication try to modify?
triphosphate bond is target of 3’ hydroxyl attack to prevent addition of next nucleotide => chain termination
What are the most abundant type of RNA? longest type? smallest type?
rRNA=> abundant type;
mRNA=> longest type;
tRNA=> smallest type
mRNA start codon
AUG (eukaryotes=> methionine removed before complete translation)
(prokaryotes=> codes for formylmethionine (f-met)
mRNA stop codons
UGA, UAA, UAG
What is the direction of the sense strand in the gene?
5’=>3’
what is direction of template strand in gene?
3’ => 5’
role of promoter in gene expression
site where RNA polymerase & multiple other transcription factors bind to DNA upstream from gene locus
what makes up the promoter site?
AT-rich upstream sequence w/ TATA and CAAT boxes
what will a promoter mutation result in?
dramatic decrease in amount of gene transcribed
what is enhancer in regulation of gene expression?
stretch of DNA that alters gene expression by binding transcription factors
what is the silencer in gene expression?
site where negative regulators (repressors) bind
What is unique about the enhancers and silencers of gene expression?
may be located close to, far from, or w/in an intron the gene whose expression it regulates
in eukaryotes, what is the role of RNA polymerase I?
makes rRNA (most numerous RNA)
in eukaryotes, what is the role of RNA polymerase II?
makes mRNA (largest RNA); opens DNA at promoter site
in eukaryotes, what is the role of RNA polymerase III?
makes tRNA (smallest RNA)
What is the proofreading vehicle in RNA polymerase?
there is no proofreading function of RNA but can initiate chains
What is the role of RNA polymerase in prokaryotes?
1 RNA polymerase makes all 3 kinds of RNA
A patient is known to have eaten mushrooms. what is the cause of the severe hepatotoxicity?
alpha-amantin from the Amanita phalloides (death cap mushrooms) => inhibits RNA polymerase II
In RNA processing, what is the initial transcript?
heterogeneous nuclear RNA that becomes pre-mRNA
Describe how RNA processing occurs
in nucleus after transcription
1) capping 5’ end
2) polyadenylation on 3’ end (poly-A tail-AAUAAA)
3) splicing out of introns
what is required to get to mRNA?
capped, tailed, and spliced transcript => RNA processed before transported out of nucleus
What do patients w/ lupus make antibodies to in RNA?
Abs to spliceosomal snRNPs
give the splicing process of pre-mRNA
1) 1’ transcript combines w/ snRNPs and other proteins to form spliceosome
2) Lariat-shaped (looped) intermediate is generated
3) Lariat released to remove intron precisely and join 2 exons
differentiate exons vs introns
exons contain actual genetic information coding for protein=> exons exit and expressed
introns intervening noncoding DNA segments => introns intervene and stay in nucleus
what is the structure of tRNA?
secondary structure, cloverleaf form, anticodon end is opposite 3’ aminoacyl end;
CCA at 3’ along w/ high % of modified bases
Why is aminoacyl-tRNA synthetase called the matchmaker?
scrutinizes AA before and after binding to tRNA and has the energy for formation of peptide bond
What occurs if tRNA is mischarged?
reads usual codon but inserts wrong amino acid
what is responsible for accuracy of amino acid selection?
aminoacyl-tRNA synthetase and binding of charged tRNA to codon
Where does tetracyclines bind thus preventing what?
bind 30S subunit and prevent attachment of aminoacyl-tRNA
describe the tRNA wobble
accurate base pairing required in 1st 2 nucleotide positions of mRNA codon so codons in 3rd wobble position code for tRNA/AA
What activates the initiation of protein synthesis?
GTP hydrolysis and initiation factors help assemble 40S ribosomal subunit w/ initiator tRNA
differentiate eukaryote ribosomal subunits w/ prokaryotic subunits
Eukaryotes: 40S and 60S -> 80S
Prokaryotes: 30S and 50S => 70S
differentiate role of ATP from GTP in initiation process
ATP=> tRNA activation (charging);
GTP=> tRNA Gripping & Go places (translocation)
describe the elongation process of protein synthesis
1) aminoacyl-tRNA binds to A site (except for initiator methionine)
2) ribosomal rRNA (ribozyme) catalyzes peptide bond formations, transfers growing polypeptide to AA in A site
3) ribosome advances 3 nucleotides toward 3’ end of mRNA moving peptidyl tRNA to P site (translocation)
describe the termination of protein synthesis
stop codon recognized by release factor and completed protein released from ribosome
where do aminoglycosides bind to block protein synthesis?
bind 30S and inhibit formation of initiation complex and cause misreading of mRNA
where do tetracyclines bind to block protein synthesis?
bind 30S and block aminoacyl tRNA from entering acceptor site
where do chloramphenicol bind to block protein synthesis?
binds 50S and inhibits peptidyl transferase
where do macrolides bind to block protein synthesis?
bind 50S and prevent release of uncharged tRNA after it has donated its amino acid
describe the trimming involved in post-translational modifications
removal of N- or C-terminal propeptides from zymogens to generate mature proteins
describe the covalent alterations involved in post-translational modifications
phosphorylation, glycosylation, hydroxylation, methylation, and acetylation
describe the proteasomal degradation involved in post-translational modifications
attachment of ubiquitin to defective proteins to tag them for breakdown
