Molecular Flashcards
“beads on a string” Condensed DNA
Chromatin, H1 is the only histone that is not in the nucleosome core
Condensed, transcriptionally inactive, sterically inaccessible
heterochromatin
Transcriptionally active chromatin
euchromatin
DNA methylation
at CpG islands will repress transcription
allows mismatch repair enzymes to distinguish between old and new
Histone methylation
reverisbly represses DNA transcription
Histone acetylation
relaxes DNA coiling, allows DNA transcription
Uracil
Deaminated cytosine, found in RNA
C-G bond
3 H bonds, increase in these will increase in melting temp
A-T bonds
2 H bonds
Amino acids necessary for purine synthesis
Glycine, Aspartate, Glutamine
remember purines are A and G
pyrimidines are C, T, U
De novo Pyrimidines
make temporary base (orotic acid)
add sugar + PRPP
modify base
Leflunomide
inhibits dihydroorotate dehydrogenase
interferes with nucleotidee synthesis
Mycophenolate & Ribavirin
inhibit IMP dehydrogenase
Hydroxyurea in ribonucleotide synthesis
inhibits ribonucleotide reductase
inhibits dihydrofolate reductase in humans
methotrexate
inhibits dihydrofolate reductase in bacteria
trimethoprim
inhibits dihydrofolate reductase in protozoa
pyrimethamine
Lesch-Nyhan Syndrome
absent HGPRT, X-linked
hyperuricemia, Gout, agression, self-mutilation, retarded, dystonia
excess uric acid production and de novo purine synthesis
HGPRT
necesary for purine salvage
converts hypoxanthine to IMP and guanine to GMP
Adenosine Deaminase Deficiency
excess ATP and dATP
prevents DNA synthesis and thus decrease lymphocyte count
Unambiguous
each codon specifies only 1 amino acid
Degenerate/Redundant
most amino acids are coded by multiple codons
exceptions: methionine(AUG) and tryptophan (UGG)
Commaless, nonoverlapping
read from fixed starting point as a continuous sequence of bases
Universal
genetic code is conserved throughout evolution except in humans (mitochondria)
Helicase
unwinds DNA template at replication fork
single-stranded binding proteins
prevent strands from annealing
DNA topoisomerases
create a single- or double-stranded break in the helix to add or remove supercoils
fluoroquinolones
inhibits DNA gyrase (prokaryoktic topoisomerase II)
Primase
makes an RNA primer on which DNA polymerase III can initiate replication
DNA polymerase III
5’ => 3’ synthesis and proofreads 3’ => 5’ exonuclease
prokaryotes ONLY
elongates both leading and lagging strands
DNA polymerase I
Prokaryotic ONLY
degrades RNA primer and replaces it with DNA
DNA ligase
joins Okazaki fragments
Telomerase
An RNA-dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material with every duplication
Transition mutation in DNA
purine to purine or pyrimidine to pyrimidine
Transversion mutation in DNA
purine to pyrimidine or vice versa
Silent Mutation
nucleotide substitution by codes for same amino acid
Missense Mutation
nucleotide substitution resulting in a changed amino acid like sickle cell disease
Conservative missense mutation
new amino acids is similar to the replaced one in chemical structure
Nonsense mutation
nucleotide substitution resulting in an early stop codon
Frameshift Mutation
deletion of insertion or # of nucleotides not divisible by 3, results in a truncated non-fx protein
Ex. Duchenne muscular dystrophy
Defective in xeroderma pigmentosum
nucleotide excision repair
nucleotide excision repair
endonucleases to remove damaged bases
DNA polymerase and ligase to fill and reseal gap
repairs pyrimidine dimers from UV light
Base Excision Repair
base-specific glycosylase to recognize altered base
1+ nucleotides are moved with AP-endonuclease cleaving 5’ end
lyase cleaves 3’ end
DNA-polymerase-beta fills gap and DNA ligase seals it
Repair of spontaneous/toxic deamination
base excision repair
Defective in hereditary nonpolyposis colorectal cancer
mismatch repair
Mismatch repair
newly syn strand is recognized, mismatched nucleotides are removed, gap is filled and resealed
DNA repair that is mutated in ataxia telangiectasia
Nonhomologous end joining
repairs double-stranded breaks in DNA
Nonhomologous end joining
Direction that mRNA and DNA are syn in
5’ to 3’
mRNA is read in what direction?
5’ to 3’
Start codon for Prokaryote
AUG, formylmethionine (f-met)
Start codon for Eukaryote
AUG, for methionine
may be removed before translation is complete
Stop codons
UGA, UAA, UAG
Promoter
RNA polymerase finds to DNA upstream from gene locus (TATA box)
Enhancer
DNA that alters gene expression by binding transcription factors
Silencer
site where repressors bind
RNA Polymerase I
in eukaryotes, makes rRNA (most numerous)
RNA Polyermase II
in eukaryotes, makes mRNA, largest RNA
opens DNA at promoter site
RNA Polymerase III
in eukaryotes, makes tRNA, smallest RNA
alpha-amanitin
in Amanita phalloides, inhibits RNA polymerase II
Prokaryotic RNA Polymerase
multisubunit complex, makes all 3 kinds of RNA
initial RNA transcript
heterogenous nuclear RNA, hnRNA
Processes in nucleus following transcription
Capping of 5’ end
Polyadenylation of 3’ end
Splicing of introns
thusly makes mRNA
where mRNA is translated
cytosol
AAUAAA
polyadenylation signal
snRNPs
bind pre-mRNA at intron to aid in splicing
Lariat
looped intermediated for splicing out introns from mRNA
when released, the 2 exons are joined
antibodies to spliceosomal snRNPs
anti-Smith antibodies, highly specific for SLE
Anti-U1 RNP antibodies
highly associated with mixed CT disease
coding segment for protein
exons
non-coding segments of DNA
introns
tRNA 3’ end
CCA - for can carry aminos
T-arm of tRNA
contains thymine, pseudouridine, cytosine, necessary for tRNA-ribosome binding
D-arm of tRNA
contains dihydrouracil necessary for tRNA recognition to correct aminoacyl-tRNA synthetase
mischarged tRNA
reads usual codon but inserts wrong amino acid
aminoacyl-tRNA synthetase
scrutinizes AA before and after it binds to tRNA, if incorrect the bond is hydrolyzed
tRNA wobble
codons differing in the 3rd wobble position may code for the same tRNA/amino acid due to degeneracy genetic code
Protein Synthesis - Initiation
GTP hydrolysis, eIF help assemble 40S with initiator tRNA and are released when mRNA and 60S assemble
2nd step of protein synthesis
Elongation
A site
for incoming aminoacyl-tRNA (except for methionine)
P site
rRNA catalyzes peptide bond formation, transfers growing polypeptide to AA in A site
growing peptide
E site
hold empty tRNA as it exits
Trimming
Post translational modification
removal of N or c terminal propeptides from zymogen to make mature protein
Covalent Alterations
Post translational modification
phosphorylation, glycosylation, hydroxylation, methylation, acetylation, and ubiquitination
Chaperone Protein
Intracellular protein involved in facilitating and/or maintaining protein folding
Heat Shock Protein
Ex of Chaperone protein, in yeast
HSP60, expressed at high temperatures to prevent protein denaturing and misfolding
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