FIRST AID USMLE STEP 1: BIOCHEMISTRY UPDATED STUDY
GUIDE QUESTIONS AND CORRECT ANSWERS
Chromatin structure Negatively charged DNA loops twice around positively charged histone
octamer to form nucleosome bead, H1 ties nucleosomes together in a string.
Heterochromatin Condensed, transcriptionally inactive, sterically inaccessible.
Euchromatin Less condensed, transcriptionally active, sterically accessible.
Purines A, G 2 Rings
Pyrimidines C, T, U; 1 ring
G-C bond 3 H-bonds-stronger
AA's necessary for purine synthesis Glycine, Aspartate, Glutamine
Nucleoside Base + ribose
Nucleotide Base + ribose + phosphate; linked by 3'-5' phosphodiester bond.
Purines are made from...? IMP precursor
Pyrimidines are made from...? Orotate precursor, with PRPP added after
Transition vs. transversion Transition: Substituting purine for purine or pyrimidine for pyrimidine ("TransI
tion = I dentical type") Transversion: Substituting purine for pyrimidine or vice
versa ("TransV ersion = conV ersion btw types")
Genetic code: unambiguous Each codon specifies only 1 AA.
Genetic code: degenerate/redundant Most amino acids are coded by multiple codons.
Genetic code: Commaless, nonoverlapping Read from a fixed starting point as a continuous sequence of bases. *some
viruses are an exception.
Genetic code: universal Genetic code is conserved throughout evolution
Silent mutation-def, how? nucleotide substitution but codes for same AA; base change in 3rd position of
codon (tRNA wobble)
Missense mutation Nucleotide substitution that results in a changed AA
Nonsense mutation Change resulting in early stop codon
Frame shift mutation Deletion or insertion of a number of nucleotides
not divisible by 3 --> resulting in misreading of all
nucleotides downstream--> truncated, nonfunctional protein.
, Severity of damage in DNA mutations frameshift > nonsense > missense >> silent
Origin of replication Particular consensus sequence of base pairs
in genome where DNA replication begins. May be single (prokaryotes) or
multiple (eukaryotes).
Replication fork Y-shaped region along DNA template where leading and lagging strands are
synthesized.
Helicase Unwinds DNA template at replication fork.
Single-stranded binding protein Prevents strands from reannealing
DNA topoisomerases-definition, clinical -Create a nick in the helix to relieve supercoils created during replication.
Primase Makes an RNA primer on which DNA polymerase III can initiate replication.
DNA polymerase III a. Prokaryotes
a. which type of organism b.
b. requires 1. Leading strand-elongates by adding deoxynucleotides to the 3' end.
c. function 2. Lagging strand-elongates until it reaches primer of preceding fragment.
3. Proofread- Exonuclease activity: 3'-->5'
DNA polymerase I-function excises RNA primer w/ 5'--<3' exonuclease; replaces DNA in the 5'-->3'
direction
DNA ligase Seals.
Single strand nucleotide excision repair Specific endonucleases release the oligonucleotide-containing damaged
bases; DNA polymerase and ligase fill and reseal the gap, respectively.
Xeroderma pigmentosum Mutated single strand nucleotide excision repair gene, which prevents repair of
pyrimidine dimers
Single strand base excision repair -Base specific glycosylases recognizes altered base and creates AP site
(apurinic/apyrimidinic). AP endonuclease- removes one or more by cleaving
the 5- end. Lyase cleaves the 3' end. DNA polymerase-B fills the gap and DNA
ligase seals it.
Mismatch repair-definition, cinical -newly synthesized string is recognized, mismatched nucleotides are removed,
and the gap is filled and resealed. -Mutated in hereditary nonpolyposis
colorectal cancer (HNPCC).
nonhomologous end joining-definition, clinical -Brings together 2 ends of DNA fragments to repair double-stranded breaks.
No requirement for homology -Ataxia telangiectasia
DNA/RNA-synthesis direction, discuss process a. 5'-->3' direction
b.
- 5' of the incoming nucleotide bears the triphosphate (energy source for
bond)
-3′ hydroxyl attacks the 5' end
GUIDE QUESTIONS AND CORRECT ANSWERS
Chromatin structure Negatively charged DNA loops twice around positively charged histone
octamer to form nucleosome bead, H1 ties nucleosomes together in a string.
Heterochromatin Condensed, transcriptionally inactive, sterically inaccessible.
Euchromatin Less condensed, transcriptionally active, sterically accessible.
Purines A, G 2 Rings
Pyrimidines C, T, U; 1 ring
G-C bond 3 H-bonds-stronger
AA's necessary for purine synthesis Glycine, Aspartate, Glutamine
Nucleoside Base + ribose
Nucleotide Base + ribose + phosphate; linked by 3'-5' phosphodiester bond.
Purines are made from...? IMP precursor
Pyrimidines are made from...? Orotate precursor, with PRPP added after
Transition vs. transversion Transition: Substituting purine for purine or pyrimidine for pyrimidine ("TransI
tion = I dentical type") Transversion: Substituting purine for pyrimidine or vice
versa ("TransV ersion = conV ersion btw types")
Genetic code: unambiguous Each codon specifies only 1 AA.
Genetic code: degenerate/redundant Most amino acids are coded by multiple codons.
Genetic code: Commaless, nonoverlapping Read from a fixed starting point as a continuous sequence of bases. *some
viruses are an exception.
Genetic code: universal Genetic code is conserved throughout evolution
Silent mutation-def, how? nucleotide substitution but codes for same AA; base change in 3rd position of
codon (tRNA wobble)
Missense mutation Nucleotide substitution that results in a changed AA
Nonsense mutation Change resulting in early stop codon
Frame shift mutation Deletion or insertion of a number of nucleotides
not divisible by 3 --> resulting in misreading of all
nucleotides downstream--> truncated, nonfunctional protein.
, Severity of damage in DNA mutations frameshift > nonsense > missense >> silent
Origin of replication Particular consensus sequence of base pairs
in genome where DNA replication begins. May be single (prokaryotes) or
multiple (eukaryotes).
Replication fork Y-shaped region along DNA template where leading and lagging strands are
synthesized.
Helicase Unwinds DNA template at replication fork.
Single-stranded binding protein Prevents strands from reannealing
DNA topoisomerases-definition, clinical -Create a nick in the helix to relieve supercoils created during replication.
Primase Makes an RNA primer on which DNA polymerase III can initiate replication.
DNA polymerase III a. Prokaryotes
a. which type of organism b.
b. requires 1. Leading strand-elongates by adding deoxynucleotides to the 3' end.
c. function 2. Lagging strand-elongates until it reaches primer of preceding fragment.
3. Proofread- Exonuclease activity: 3'-->5'
DNA polymerase I-function excises RNA primer w/ 5'--<3' exonuclease; replaces DNA in the 5'-->3'
direction
DNA ligase Seals.
Single strand nucleotide excision repair Specific endonucleases release the oligonucleotide-containing damaged
bases; DNA polymerase and ligase fill and reseal the gap, respectively.
Xeroderma pigmentosum Mutated single strand nucleotide excision repair gene, which prevents repair of
pyrimidine dimers
Single strand base excision repair -Base specific glycosylases recognizes altered base and creates AP site
(apurinic/apyrimidinic). AP endonuclease- removes one or more by cleaving
the 5- end. Lyase cleaves the 3' end. DNA polymerase-B fills the gap and DNA
ligase seals it.
Mismatch repair-definition, cinical -newly synthesized string is recognized, mismatched nucleotides are removed,
and the gap is filled and resealed. -Mutated in hereditary nonpolyposis
colorectal cancer (HNPCC).
nonhomologous end joining-definition, clinical -Brings together 2 ends of DNA fragments to repair double-stranded breaks.
No requirement for homology -Ataxia telangiectasia
DNA/RNA-synthesis direction, discuss process a. 5'-->3' direction
b.
- 5' of the incoming nucleotide bears the triphosphate (energy source for
bond)
-3′ hydroxyl attacks the 5' end
