Step 1 First Aid - Biochemistry
Chromatin structure - answer:-Negatively charged DNA loops twice around histone
octamer (2 each of the positively charged H2A, H2B, H3, and H4) to form nucleosome
bead. H1 ties nucleosomes together in a string. (Think of "beads on a string"; H1 is the
only histone that is not in the nucleosome core.) In mitosis, DNA condenses to form
mitotic chromosomes. <img src="66a - Euchramatin strxr.JPG" />
Heterochromatin - answer:-Condensed, transcriptionally inactive ("H eteroC hromatin =
H ighly C ondensed.")
Euchromatin - answer:-Less condensed, transcriptionally active (Eu = true, "truly
transcribed")
Purines - answer:-A, G 2 Rings ("PUR e A s G old = PUR ines") <img src="67b - Purine
strxr.JPG" />
Pyrimidines - answer:-C, T, U 1 ring ("CUT the PY (pie): PY rimidines") <img src="67c -
Pyrimidine strxr.JPG" />
Functional groups of the nucleosides - answer:-Guanine has a ketone. Thy mine has a
methy l. Deamination of cytosine makes uracil.
Base differences btw RNA and DNA - answer:-Uracil is found in RNA; Thymine in DNA
Base pair bonds - answer:-G-C bond (3 H-bonds) is stronger than A-T bond (2 H-
bonds). Incr G-C content --< higher melting temperature.
AA's necessary for purine synthesis - answer:-G lycine A spartate G lutamine
Nucleoside - answer:-Base + ribose
Nucleotide - answer:-Base + ribose + phosphate; linked by 3'-5' phosphodiester bond.
Purines are made from...? - answer:-IMP precursor (see bottom/right) <img src="68a -
Nucleotide synthesis.JPG" />
Pyrimidines are made from...? - answer:-Orotate precursor, with PRPP added later.
<img src="68a - Nucleotide synthesis.JPG" />
Deoxyribonucleotide synthesis - answer:-Ribonucleotides are synthesized first and are
converted to deoxyribonucleotides by ribonucleotide reductase. <img src="68a -
Nucleotide synthesis.JPG" />
ABX and anti-neoplastic drugs that function by interfering w/ nucleotide synthesis (list) -
answer:-Hydroxyurea 6-mercaptopurine 5-fluorouracil Methotrexate Trimethoprim
,Step 1 First Aid - Biochemistry
Hydroxyurea - answer:-Inhibits ribonucleotide reductase. <img src="68a - Nucleotide
synthesis.JPG" />
6-mercaptopurine (6-MP) - answer:-Blocks de novo purine synthesis. <img src="68a -
Nucleotide synthesis.JPG" />
5-Fluorouracil (5-FU) - answer:-Inhibits thymidilate synthase (decr dTMP). <img
src="68a - Nucleotide synthesis.JPG" />
Methotrexate - answer:-Inhibits dihydrofolate reductase (decr dTMP) <img src="68a -
Nucleotide synthesis.JPG" />
Trimethoprim - answer:-Inhibits bacterial dihydrofolate reductase (decr dTMP) <img
src="68a - Nucleotide synthesis.JPG" />
Transition vs. transversion - answer:-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 - answer:-Each codon specifies only 1 AA.
Genetic code: degenerate/redundant - answer:-< 1 codon may code for the same AA.
(Methionine is encoded by 1 codon: AUG)
Genetic code: Commaless, nonoverlapping - answer:-Read from a fixed starting point
as a continuous sequence of bases. *some viruses are an exception.
Genetic code: universal - answer:-Genetic code is conserved throughout evolution.
*exceptions include mitochondria, archaebacteria, Mycoplasma , and some yeasts
Silent mutation - answer:-Same AA, often base change in 3rd position of codon (tRNA
wobble)
Missense mutation - answer:-Changed AA (conservative -- new AA is similar in
chemical structure)
Nonsense mutation - answer:-Change resulting in early stop codon ("Stop the nonsense
!")
Frame shift mutation - answer:-Change resulting in misreading of all nucleotides
downstream, usually resulting in a truncated, nonfunctional protein.
Severity of damage in DNA mutations - answer:-Nonsense < missense < silent
,Step 1 First Aid - Biochemistry
Eukaryotic vs. prokaryotic DNA replication. - answer:-Eukaryotic DNA replciation is
more complex, but uses many analogous enzymes. In both: DNA replication is
semiconservative and involves both continuous and discontinuous (Okazaki fragment)
synthesis. For eukaryotes, replication begins at a consensus sequence of base pairs.
Origin of replication - answer:-Particular sequence in genome where DNA replication
begins. May be single (prokaryotes) or multiple (eukaryotes).
Replication fork - answer:-Y-shaped region along DNA template where leading and
lagging strands are synthesized. <img src="70a - DNA replication.JPG" />
Helicase - answer:-Unwinds DNA template at replication fork. <img src="70a - DNA
replication.JPG" />
Single-stranded binding protein - answer:-Prevents strands from reannealing. <img
src="70a - DNA replication.JPG" />
DNA topoisomerases - answer:-Create a nick in the helix to relieve supercoils created
during replication. *Fluoroquinolones inhibit DNA gyrase (a specific prokaryotic
topoisomerase)
Primase - answer:-Makes an RNA primer on which DNA polymerase III can initiate
replication. <img src="70a - DNA replication.JPG" />
DNA polymerase III - answer:-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 w/ exonuclease) <img src="70a - DNA
replication.JPG" />
DNA polymerase I - answer:-Prokaryotic only. Degrades RNA primer and fills in the gap
w/ DNA. (excises RNA primer w/ 5'--<3' exonuclease) <img src="70a - DNA
replication.JPG" />
DNA ligase - answer:-Seals. <img src="70a - DNA replication.JPG" />
Single strand nucleotide excision repair - answer:-Specific endonucleases release the
oligonucleotide-containing damaged bases; DNA polymerase and ligase fill and reseal
the gap, respectively. (mutated in xeroderma pigmentosum)
Xeroderma pigmentosum - answer:-Mutated single strand nucleotide excision repair
gene, which prevents repair of thymidine dimers.; Dry skin w/ melanoma and other
cancers ("children of the night").
, Step 1 First Aid - Biochemistry
Single strand base excision repair - answer:-Specific glycosylases recognize and
remove damaged bases, AP endonuclease cuts DNA at apyrimidinic site, empyty sugar
is removed, and the gap is filled and resealed.
Single strand mismatch repair - answer:-Unmethylated, newly synthesized string is
recognized, mismatched nucleotides are removed, and the gap is filled and resealed.
Mutated in hereditary nonpolyposis colorectal cancer (HNPCC).
Double strand nonhomologous end joining - answer:-Brings together 2 ends of DNA
fragments. No requirement for homology.
What direction is DNA/RNA made? - answer:-They are both synthesized in the 5'--<3'
direction. Remember that the 5' of the incoming nucleotide bears the triphosphate
(energy source for bond). The 3' hydroxyl of the nascent chain is the target.
What direction is mRNA read? - answer:-5'--<3'.
What direction is protein synthesized? - answer:-N--<C
3 Types of mRNA - answer:-rRNA is the most abundant mRNA is the longest tRNA is
the smalles ("R ampant, M assive, T iny")
mRNA start codon - answer:-AUG (or rarely GUG) ("AUG inAUG urates protein
synthesis") In eukartyotes, codes for methionine, which may be removed before
translation is completed. In prokaryotes, codes for formyl-methionine (f-Met).
mRNA stop codons - answer:-UGA, UAA, UAG UGA = U G o A way UAA = U A re A
way UAG = U A re G one
Functional organization of the gene - answer:-<img src="72a - Organization of the
gene.JPG" />
Promoter - answer:-Site where RNA polymerase and multiple other transcription factors
bind to DNA upstream from gene locus (AT-rich upstream sequence w/ TATA and
CAAT boxes). Mutation here commonly results in dramatic drop in amount of gene
transcribed.
Site where RNA polymerase and multiple other transcription factors bind to DNA
upstream from gene locus (AT-rich upstream sequence w/ TATA and CAAT boxes).
Mutation here commonly results in dramatic drop in amount of gene transcribed. -
answer:-Promoter
Enhancer - answer:-Stretch of DNA that alters gene expression by binding transcription
factors.
Chromatin structure - answer:-Negatively charged DNA loops twice around histone
octamer (2 each of the positively charged H2A, H2B, H3, and H4) to form nucleosome
bead. H1 ties nucleosomes together in a string. (Think of "beads on a string"; H1 is the
only histone that is not in the nucleosome core.) In mitosis, DNA condenses to form
mitotic chromosomes. <img src="66a - Euchramatin strxr.JPG" />
Heterochromatin - answer:-Condensed, transcriptionally inactive ("H eteroC hromatin =
H ighly C ondensed.")
Euchromatin - answer:-Less condensed, transcriptionally active (Eu = true, "truly
transcribed")
Purines - answer:-A, G 2 Rings ("PUR e A s G old = PUR ines") <img src="67b - Purine
strxr.JPG" />
Pyrimidines - answer:-C, T, U 1 ring ("CUT the PY (pie): PY rimidines") <img src="67c -
Pyrimidine strxr.JPG" />
Functional groups of the nucleosides - answer:-Guanine has a ketone. Thy mine has a
methy l. Deamination of cytosine makes uracil.
Base differences btw RNA and DNA - answer:-Uracil is found in RNA; Thymine in DNA
Base pair bonds - answer:-G-C bond (3 H-bonds) is stronger than A-T bond (2 H-
bonds). Incr G-C content --< higher melting temperature.
AA's necessary for purine synthesis - answer:-G lycine A spartate G lutamine
Nucleoside - answer:-Base + ribose
Nucleotide - answer:-Base + ribose + phosphate; linked by 3'-5' phosphodiester bond.
Purines are made from...? - answer:-IMP precursor (see bottom/right) <img src="68a -
Nucleotide synthesis.JPG" />
Pyrimidines are made from...? - answer:-Orotate precursor, with PRPP added later.
<img src="68a - Nucleotide synthesis.JPG" />
Deoxyribonucleotide synthesis - answer:-Ribonucleotides are synthesized first and are
converted to deoxyribonucleotides by ribonucleotide reductase. <img src="68a -
Nucleotide synthesis.JPG" />
ABX and anti-neoplastic drugs that function by interfering w/ nucleotide synthesis (list) -
answer:-Hydroxyurea 6-mercaptopurine 5-fluorouracil Methotrexate Trimethoprim
,Step 1 First Aid - Biochemistry
Hydroxyurea - answer:-Inhibits ribonucleotide reductase. <img src="68a - Nucleotide
synthesis.JPG" />
6-mercaptopurine (6-MP) - answer:-Blocks de novo purine synthesis. <img src="68a -
Nucleotide synthesis.JPG" />
5-Fluorouracil (5-FU) - answer:-Inhibits thymidilate synthase (decr dTMP). <img
src="68a - Nucleotide synthesis.JPG" />
Methotrexate - answer:-Inhibits dihydrofolate reductase (decr dTMP) <img src="68a -
Nucleotide synthesis.JPG" />
Trimethoprim - answer:-Inhibits bacterial dihydrofolate reductase (decr dTMP) <img
src="68a - Nucleotide synthesis.JPG" />
Transition vs. transversion - answer:-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 - answer:-Each codon specifies only 1 AA.
Genetic code: degenerate/redundant - answer:-< 1 codon may code for the same AA.
(Methionine is encoded by 1 codon: AUG)
Genetic code: Commaless, nonoverlapping - answer:-Read from a fixed starting point
as a continuous sequence of bases. *some viruses are an exception.
Genetic code: universal - answer:-Genetic code is conserved throughout evolution.
*exceptions include mitochondria, archaebacteria, Mycoplasma , and some yeasts
Silent mutation - answer:-Same AA, often base change in 3rd position of codon (tRNA
wobble)
Missense mutation - answer:-Changed AA (conservative -- new AA is similar in
chemical structure)
Nonsense mutation - answer:-Change resulting in early stop codon ("Stop the nonsense
!")
Frame shift mutation - answer:-Change resulting in misreading of all nucleotides
downstream, usually resulting in a truncated, nonfunctional protein.
Severity of damage in DNA mutations - answer:-Nonsense < missense < silent
,Step 1 First Aid - Biochemistry
Eukaryotic vs. prokaryotic DNA replication. - answer:-Eukaryotic DNA replciation is
more complex, but uses many analogous enzymes. In both: DNA replication is
semiconservative and involves both continuous and discontinuous (Okazaki fragment)
synthesis. For eukaryotes, replication begins at a consensus sequence of base pairs.
Origin of replication - answer:-Particular sequence in genome where DNA replication
begins. May be single (prokaryotes) or multiple (eukaryotes).
Replication fork - answer:-Y-shaped region along DNA template where leading and
lagging strands are synthesized. <img src="70a - DNA replication.JPG" />
Helicase - answer:-Unwinds DNA template at replication fork. <img src="70a - DNA
replication.JPG" />
Single-stranded binding protein - answer:-Prevents strands from reannealing. <img
src="70a - DNA replication.JPG" />
DNA topoisomerases - answer:-Create a nick in the helix to relieve supercoils created
during replication. *Fluoroquinolones inhibit DNA gyrase (a specific prokaryotic
topoisomerase)
Primase - answer:-Makes an RNA primer on which DNA polymerase III can initiate
replication. <img src="70a - DNA replication.JPG" />
DNA polymerase III - answer:-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 w/ exonuclease) <img src="70a - DNA
replication.JPG" />
DNA polymerase I - answer:-Prokaryotic only. Degrades RNA primer and fills in the gap
w/ DNA. (excises RNA primer w/ 5'--<3' exonuclease) <img src="70a - DNA
replication.JPG" />
DNA ligase - answer:-Seals. <img src="70a - DNA replication.JPG" />
Single strand nucleotide excision repair - answer:-Specific endonucleases release the
oligonucleotide-containing damaged bases; DNA polymerase and ligase fill and reseal
the gap, respectively. (mutated in xeroderma pigmentosum)
Xeroderma pigmentosum - answer:-Mutated single strand nucleotide excision repair
gene, which prevents repair of thymidine dimers.; Dry skin w/ melanoma and other
cancers ("children of the night").
, Step 1 First Aid - Biochemistry
Single strand base excision repair - answer:-Specific glycosylases recognize and
remove damaged bases, AP endonuclease cuts DNA at apyrimidinic site, empyty sugar
is removed, and the gap is filled and resealed.
Single strand mismatch repair - answer:-Unmethylated, newly synthesized string is
recognized, mismatched nucleotides are removed, and the gap is filled and resealed.
Mutated in hereditary nonpolyposis colorectal cancer (HNPCC).
Double strand nonhomologous end joining - answer:-Brings together 2 ends of DNA
fragments. No requirement for homology.
What direction is DNA/RNA made? - answer:-They are both synthesized in the 5'--<3'
direction. Remember that the 5' of the incoming nucleotide bears the triphosphate
(energy source for bond). The 3' hydroxyl of the nascent chain is the target.
What direction is mRNA read? - answer:-5'--<3'.
What direction is protein synthesized? - answer:-N--<C
3 Types of mRNA - answer:-rRNA is the most abundant mRNA is the longest tRNA is
the smalles ("R ampant, M assive, T iny")
mRNA start codon - answer:-AUG (or rarely GUG) ("AUG inAUG urates protein
synthesis") In eukartyotes, codes for methionine, which may be removed before
translation is completed. In prokaryotes, codes for formyl-methionine (f-Met).
mRNA stop codons - answer:-UGA, UAA, UAG UGA = U G o A way UAA = U A re A
way UAG = U A re G one
Functional organization of the gene - answer:-<img src="72a - Organization of the
gene.JPG" />
Promoter - answer:-Site where RNA polymerase and multiple other transcription factors
bind to DNA upstream from gene locus (AT-rich upstream sequence w/ TATA and
CAAT boxes). Mutation here commonly results in dramatic drop in amount of gene
transcribed.
Site where RNA polymerase and multiple other transcription factors bind to DNA
upstream from gene locus (AT-rich upstream sequence w/ TATA and CAAT boxes).
Mutation here commonly results in dramatic drop in amount of gene transcribed. -
answer:-Promoter
Enhancer - answer:-Stretch of DNA that alters gene expression by binding transcription
factors.
