Flashcards in biochem: molecular Deck (68):
condensed, darker on EM, inactive, inaccessible. e.g. Barr bodies
less condensed, lighter on EM. active, accessible.
template strand cytosine and adenine are methylated in DNA replication, allowing repair enzymes to distinguish old and new strands. methylation at CpG islands represses transcription
usually reversibly represses transcription, but sometimes activates it (depending on location).
relaxes DNA coiling, allowing for transcription
2 rings. A, G. PURe As Gold
1 ring. C, T, U. CUT the PY
THYmine has a meTHYl
deamination of cystosine makes
= 3 H bonds = stronger than A-T bond (2 H bonds). so more G-Cs -> higher melting temp
AAs necessary for purine synthesis
GAG = gylcine, aspartate, glutamine
adenosine deaminase deficiency
autosomal recessive cause of SCID. excess ATP and dATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase -? prevents DNA synthesis, so decreases lymphocyte count
defective purine salvage due to avsent HGPRT, which concerts hypoxanthine to IMP and guanine to GMP. results in excess uric acid production and de novo purine synthesis. x-linked recessive. HGPRT: hyperuricemia, gout, pissed off (aggression, self-mutilation), retardation, dysTonia. Tx w/allopurinol or febuxostat
origin of replication
particular consensus sequence of base pairs in genome where DNA replication begins. may be single (prokaryotes) or multiple (eukaryotes)
y-shaped region along DNA template where leading and lagging strands are synthesized
unwinds DNA template at replication fork
single-stranded binding proteins
prevent strands from reannealing
create a single- or double-stranded break in the helix to add or remove supercoils. fluoroquinolones inhibit prokaryotic topoisomerase II (DNA gyrase) and topoisomerase IV
makes an RNA primer on which DNA polymerase II can initiate replication
DNA polymerase III
prokaryotic only. elongates leading strand by adding deoxynucleotides to the 3' end. elongates lagging strand until it reaches primer of preceding fragment. 3'->5' exonuclease activity "proofreads" each added nucleotide. 5'->3' synthesis, 3'->5' proofreading.
DNA polymerase I
prokaryotic only. degrades RNA primer, replaces it w/DNA. similar to DNA polymerase II but also excises RNA primer w/5'->3' exonuclease
seals = catalyzes the formation of a phosphodiester bond w/in a strand of double-stranded DNA (i.e. joins Okazaki fragments).
RNA-dependent DNA polymerase that adds DNA to 3' ends to avoid loss of genetic material w/every duplication. eukaryotes only.
DNA damage mutations severity
duchenne muscular dystrophy mutation
activated in low glucose conditions when lactose is present, allowing lactose metabolism instead
nucleotide excision repair
single strand. specific endonucleases release the oligonucleotides containing damages bases. DNA polymerase fills the gap, DNA ligase reseals it. repairs bulky, helix-distorting lesions. occurs in G1 phase of cell cycle
xeroderma pigmentosum error
= error of nucleotide excision repair, pyrimidine dimers are damaged by UV exposure
base excision repair
single strand. base-specific glycosylase removes altered base and creates AP site. one or more nucleotides are removed by AP-endonuclease, which cleaves the 5' end. lyase cleaves the 3' end. DNA polymerase-beta fills the gap, DNA ligase seals it. occurs throughout cell cycle
repair of spontaneous/toxic deamination
base excision repair
single strand. newly synthesized strand is recognizes, mismatched nucleotides are removed, and the gap is filled and resealed. orrus mostly in G2 phase
hereditary nonpolyposis colorectal cancer (HNPCC) error
nonhomologous end joining
double strand. brings together 2 ends of DNA fragments to repair double-stranded breaks. no reuirement for homology. some DNA may be lost
ataxia telangiectasia and fanconi anemia error
nonhomologous end joining
DNA/RNA/protein synthesis direction
both are synthesized 5'->3'. 5' end of incoming nucleotide bears triphosphate, which is the energy source for the bond. protein synthesis occurs from N-terminus to C-terminus
caused by drugs that blocking DNA replication. modified 3'OH targets triphosphate bond, preventing addition of the next nucleotide
mRNA start codons
AUG (or GUG, rarely). AUG inAURGurates protein synthesis
mRNA start codon in eukaryotes
codes for methionine, which may be removed before translation is completed
mRNA start codon in prokaryotes
codes for N-formylmethionine (fMet), which stimulates neutrophil chemotaxis.
mRNA stop codons
UGA, UAA, UAG. UGA = U Go Away. UAA = U Are Away. UAG = U Are Gone
site where RNA polymerase II and multiple other transcription factors bind to DNA upstream from gene locus (AT-rich upstream sequence w/TATA and CAAT boxes).
commonly results in dramatic decrease in level of gene transcription
stretch of DNA that alters gene expression by binding transcription factors. can be located close to, far from, or even w/in (in an intron) the gene whose expression it regulates.
site where negative regulators (repressors) bind. can be located close to, far from, or even w/in (in an intron) the gene whose expression it regulates.
RNA polymerase in eukaryotes
numbered as their products are used in protein synthesis. No proofreading fxn but can initiate chains.
RNA polymerase I
makes rRNA. most numerous RNA, rampant.
RNA polymerase II
makes mFRNA. largest RNA, massive
RNA polymerase III
makes tRNA. smallest RNA, tiny
found in amanita phalloides (death cap mushrooms). inhibits RNA polymerase II. causes severe hepatotoxicity.
inhibits RNA polymerase in prokaryotes
Actinomycin D MoA
inhibits RNA polymerase in both prokaryotes and eukaryotes
RNA polymerases in prokaryotes
1 RNA polymerase (multisubunit complex) makes all 3 kinds of RNA
= capped, tailed, and spliced transcript of heterogeneous nuclear RNA (hnRNA). transported out of nucleus into cytoplasm, where it is translated.
contain exonucleases, decapping enzymes, and microRNAs, providing quality control for mRNA. mRNA can be stored inside for future translation.
does not require a template.
= AAUAAA. polyadenylation occurs at 3' end (~200 As), forming tail.
splicing of pre-mRNA
1: primary transcript combines w/small nuclear ribonucleoproteins (sRNPs) and other proteins to form spliceosome. 2: lariat-shaped (looped) intermediate is generated. 3: lariat is released to precisely remove intron and join 2 exons
serves as the physical link between the nucleotide sequence of nucleic acids and the amino acid sequence of proteins
protein synthesis: initiation
GTP hydrolysis. initiation factors help assemble the 40s ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal 60S subunit assemble with the complex
protein synthesis: elongation
1: aminoacyl-tRNA binds to A site (except for initiator methionine). 2: rRNA ("ribozyme") catalyzes peptide bond formation, transfers growing polypeptide to AA in A site. 3: ribosome advances 3 nucleotides toward 3' end of mRNA, moving peptidyl tRNA to P side (translocation)
protein synthesis: termination
stop codon is recognized by release factor, and completed polypeptide is released from ribosome
40S + 60S -> 80S = Even
30S + 50 -> 70S = Odd
E, P, and A sites
going APE: A site = incoming Aminoacyl-tRNA. P site = accommodates growing Peptide. E site = holds Empty tRNA as it Exits
removal of N- or C-terminal propeptides from zymogen to generate mature protein (e.g. trypsingen to trypsin)
phosphorylation, glycosylation, hydroxylation, methylation, acetylation, and ubiquitination