BIOCHEMISTRY USMLE STEP 1 STUDY GUIDE
2024/2025 || WITH QUESTIONS AND CORRECT
ANSWERS GRADE A
histones are rich in which 2 AA's -answer/ lysine & argenine
Barr bodies (what, type of chromatin) -answer/ inactive X chromosomes
heterochromatin (highly condensed, sterically inaccessible)
less condensed, transcriptionally active, sterically accessible chromatin -
answer/ euchromatin
DNA methylation at CpG islands -answer/ represses transcription
"CpG Methylation makes DNA Mute"
DNA methylation (what is methylated and why?) -answer/ template
strand cytosine and adenine are methyated during replication -->
mismatch repair enzymes can distinguish between old and new strands
Histone methylation -answer/ usually reversibly represses DNA
transcription (can activate depending on location)
"histone Methylation Mostly makes DNA Mute"
,Histone acetylation -answer/ relaxes DNA coiling --> permits
transcription
"histone Acetylation makes DNA Active"
function of methylation and acetylation -answer/ change DNA
transcription activity
methylation mutes
acetylation activates
purines (which, ring number) -answer/ A, G
2 rings
PUR As Gold
pyrimidines (which, ring number) -answer/ C, T, U
1 ring
CUT the PY (pie is a single circle)
thymine vs uracil -answer/ thymine has a methyl, found in DNA
deamination of cytosine --> uracil, found in RNA
,base pair with 3 H-H bonds (and consequences) -answer/ G-C
G-C is stronger than A-T (2 H-H)
inc G-C content --> inc melting temperature of DNA
amino acids necessary for purine synthesis -answer/ GAG + THF
glycine
aspartate
glutamine
nucleoside vs. nucleotide vs. nucleotide di/triphosphate -answer/
nucleoside = base + sugar
nucleotide = base + sugar + phosphate
nucleotide diphosphate = base + sugar + 2P's
nucleotide triphosphate = base + sugar + 3P's
de novo purine synthesis -answer/ R5P --> PRPP by PRPP synthetase
(adds 2P's)
add base (hypoxanthine) --> IMP by HGPRT
IMP converted to AMP and GMP
, ribonucleotides --> deoxyribonucleotides -answer/ ribonucleotide
reductase
carbamoyl phosphate involved in which 2 metabolic pathways? -answer/
de novo pyrimidine synthesis (CP synthetase II)
urea cycle
de novo pyrimidine synthesis -answer/ *Make temporary base:*
1. glutamine + CO2 + ATP --> carbamoyl phosphate by CP synthetase II
2. carbamoyl phosphate + aspartate --> orotic acid via dihydroorotate
dehydrogenase
*Add sugar + P (PRPP):*
3. orotic acid + PRPP --> UMP --> UDP
*Modify base*
4a. UDP --> CTP
4b. UDP --> dUDP by ribonucleotide reductase
5. dUDP --> dUMP
6. dUMP + THF --> dTMP by thymidylate synthase = methylates uracil
into thymadine
*THF (which becomes DHF) regenerated by dihydrofolate reductase
differences in de novo purine and pyrimidine synthesis -answer/ purines:
start with sugar + phos (PRPP), add base
2024/2025 || WITH QUESTIONS AND CORRECT
ANSWERS GRADE A
histones are rich in which 2 AA's -answer/ lysine & argenine
Barr bodies (what, type of chromatin) -answer/ inactive X chromosomes
heterochromatin (highly condensed, sterically inaccessible)
less condensed, transcriptionally active, sterically accessible chromatin -
answer/ euchromatin
DNA methylation at CpG islands -answer/ represses transcription
"CpG Methylation makes DNA Mute"
DNA methylation (what is methylated and why?) -answer/ template
strand cytosine and adenine are methyated during replication -->
mismatch repair enzymes can distinguish between old and new strands
Histone methylation -answer/ usually reversibly represses DNA
transcription (can activate depending on location)
"histone Methylation Mostly makes DNA Mute"
,Histone acetylation -answer/ relaxes DNA coiling --> permits
transcription
"histone Acetylation makes DNA Active"
function of methylation and acetylation -answer/ change DNA
transcription activity
methylation mutes
acetylation activates
purines (which, ring number) -answer/ A, G
2 rings
PUR As Gold
pyrimidines (which, ring number) -answer/ C, T, U
1 ring
CUT the PY (pie is a single circle)
thymine vs uracil -answer/ thymine has a methyl, found in DNA
deamination of cytosine --> uracil, found in RNA
,base pair with 3 H-H bonds (and consequences) -answer/ G-C
G-C is stronger than A-T (2 H-H)
inc G-C content --> inc melting temperature of DNA
amino acids necessary for purine synthesis -answer/ GAG + THF
glycine
aspartate
glutamine
nucleoside vs. nucleotide vs. nucleotide di/triphosphate -answer/
nucleoside = base + sugar
nucleotide = base + sugar + phosphate
nucleotide diphosphate = base + sugar + 2P's
nucleotide triphosphate = base + sugar + 3P's
de novo purine synthesis -answer/ R5P --> PRPP by PRPP synthetase
(adds 2P's)
add base (hypoxanthine) --> IMP by HGPRT
IMP converted to AMP and GMP
, ribonucleotides --> deoxyribonucleotides -answer/ ribonucleotide
reductase
carbamoyl phosphate involved in which 2 metabolic pathways? -answer/
de novo pyrimidine synthesis (CP synthetase II)
urea cycle
de novo pyrimidine synthesis -answer/ *Make temporary base:*
1. glutamine + CO2 + ATP --> carbamoyl phosphate by CP synthetase II
2. carbamoyl phosphate + aspartate --> orotic acid via dihydroorotate
dehydrogenase
*Add sugar + P (PRPP):*
3. orotic acid + PRPP --> UMP --> UDP
*Modify base*
4a. UDP --> CTP
4b. UDP --> dUDP by ribonucleotide reductase
5. dUDP --> dUMP
6. dUMP + THF --> dTMP by thymidylate synthase = methylates uracil
into thymadine
*THF (which becomes DHF) regenerated by dihydrofolate reductase
differences in de novo purine and pyrimidine synthesis -answer/ purines:
start with sugar + phos (PRPP), add base
