©FYNDLAY EXAM SOLUTIONS 2024/2025
ALL RIGHTS RESERVED.
BIOC 3021 Exam 4 Study Guide.
Base Pairing - answer✔2 nucleotides on opposite complementary DNA or RNA strands that are
connected via hydrogen bonds
Hydrogen bonding of base pairs - answer✔requires geometrical correspondence of hydrogen
bond donors and acceptors allow only the "right" pairs to form stable interactions
Double Bonded BPs - answer✔A and T
- bond between the amino H and carbonyl O
- bond between the ring NH and the ring N
Triple Bonded BPs - answer✔G and C
- bond between carbonyl O to amino group H
- bond between carbonyl O to amino group H
- bond between amino H and ring N
Larger energy of hydrolysis than double bonded BPs
- higher affinity?
Model of DNA - answer✔-bonds are planar
-bases are slightly tilted
-H bonds and aromatic stacking of the bases stabilize the helix
Flow of Genetic Information - answer✔DNA --> RNA --> Proteins
- DNA is a template for new DNA and RNA
- RNA is the template for protein synthesis
Semi-Conservative model - answer✔2 parental strands--> 2 daughter strands each with one
parental and one new strand --> 2 strands have one new strand and one parental and the other
2 have two new strands (this pattern continues)
1|Page
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Strand Separation and Hybridization - answer✔- light absorbance is less for double strands of
DNA than single strands
- allows monitoring of replication progress
-increased temperature induces separation
- Tm is the temperature where strands of DNA are 50% separated (melting temperature)
-cooling allows strands to rebond
- hybridization will occur id strands have a significant amount of bases in common
-single strand DNA can be hybridized to complementary RNA or DNA
Stem Loop Structure - answer✔formed when single strand DNA or RNA hybridizes to itself
- occasional mismatched regions create bubbles
- branch off from main chain
DNA Replication - answer✔Process by which parental DNA is copied
- General pattern of replication involves the formation of 2 copies of progeny DNA from one
copy of parental DNA (semi conservative)
- Strands have great affinity for each other
- DNA helix is unwound to separate strands
- Replication is highly accurate
- Very rapid
- One strand is synthesized in a continuous fashion and another is synthesized in fragments
discontinuously
- Telomeres are added to the other end to maintain information at the other end of the
chromosome
DNA Polymerase - answer✔Catalyzes the step-by-step addition of deoxyribonucleotide units to
a DNA chain
- New chain is assembled directly onto template by addition onto 5' end of the primer strand
- (DNA)n + dNTP --> (DNA)n+1 + PPi
- Cleavage of dNTP to dNMP allows an addition
- Template can be double or single
2|Page
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ALL RIGHTS RESERVED.
- Double stranded must be broken at 1+ sites
- Single must be bound to a primer strand with a free 3' hydroxyl
- Requires dATP, dTTP, dCTP and dGTP and Mg
Mechanism of DNA polymerase/synthesis - answer✔- Synthesizes 5' --> 3'
- 3' hydroxyl of the terminal deoxyribose attacks the innermost alpha-phosphate residue of the
new dNTP
- Formation of the phosphodiester bridge between the primer and the new unit
- 3' end of the new unit is now ready to do the same to the next dNTP
mRNA - answer✔Template for protein synthesis or translation
- Distinct mRNA is produced for each gene in eukaryotes (less specific in prokaryotes)
- Heterogeneous class of molecules
- Average length is 1.2 kb
- Determines the tRNA to be used
tRNA - answer✔Carries amino acids in an activated form to the ribosome for peptide-bond
formation
- Sequence that AA are polymerized from tRNA is controlled by mRNA
- At least one type of tRNA for each of the 20 AA
- 30 to 50 types
- Relatively small (about 75 nucleotides)
- Contains rare bases (pseudouracil, dihydrouracil)
rRNA - answer✔Constitutes the major component of ribosomes
- Catalytic and structural role in protein synthesis
Types of RNA in E.Coli - answer✔rRNA comprises 80% of RNA
- 23S= 3700 molecules
- 16S= 1700 molecules
- 5S= 120 molecules
3|Page
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ALL RIGHTS RESERVED.
tRNA= 15% of RNA
- 4s= 75 molecules
- Average 75 bases (smallest RNA molecule)
mRNA= 15%
- Average size about 1200 bases
Kilobase (kb) - answer✔a unit of length equal to 1000 base pairs of a double stranded nucleic
acid molecule
RNA Polymerase requirements - answer✔1. A DNA template (Preferably double stranded)
- RNA is not effective template
2. Activated Precursors: ATP, TTP, GTP, CTP
3. DNA-Dependent RNA Polymerase
4. Other Proteins
5. Divalent metal ion (Mg or Mn)
Synthesis of RNA - answer✔Similar to DNA synthesis
- Direction: 5'-->3'
- Strands run antiparallel
- Mechanism: 3' hydroxyl attacks the innermost phosphate of the incoming NTP (nucleoside
triphosphate)
- Reaction is driven by hydrolysis of pyrophosphate (PPI)
Different from DNA synthesis
- RNA polymerase does not require a primer
- Cannot remove mismatched nucleptides
Mechanism of Transcription (RNA Synthesis) - answer✔- RNA synthesis proceeds 5' --> 3'
- Involved terminal ribose residue of the primer
- 3' hydroxyl of terminal ribose attacks the inner most phosphate of the incoming NTP
- Creates a phosphodiester bridge, link primer to new nucleotide unit
4|Page
ALL RIGHTS RESERVED.
BIOC 3021 Exam 4 Study Guide.
Base Pairing - answer✔2 nucleotides on opposite complementary DNA or RNA strands that are
connected via hydrogen bonds
Hydrogen bonding of base pairs - answer✔requires geometrical correspondence of hydrogen
bond donors and acceptors allow only the "right" pairs to form stable interactions
Double Bonded BPs - answer✔A and T
- bond between the amino H and carbonyl O
- bond between the ring NH and the ring N
Triple Bonded BPs - answer✔G and C
- bond between carbonyl O to amino group H
- bond between carbonyl O to amino group H
- bond between amino H and ring N
Larger energy of hydrolysis than double bonded BPs
- higher affinity?
Model of DNA - answer✔-bonds are planar
-bases are slightly tilted
-H bonds and aromatic stacking of the bases stabilize the helix
Flow of Genetic Information - answer✔DNA --> RNA --> Proteins
- DNA is a template for new DNA and RNA
- RNA is the template for protein synthesis
Semi-Conservative model - answer✔2 parental strands--> 2 daughter strands each with one
parental and one new strand --> 2 strands have one new strand and one parental and the other
2 have two new strands (this pattern continues)
1|Page
, ©FYNDLAY EXAM SOLUTIONS 2024/2025
ALL RIGHTS RESERVED.
Strand Separation and Hybridization - answer✔- light absorbance is less for double strands of
DNA than single strands
- allows monitoring of replication progress
-increased temperature induces separation
- Tm is the temperature where strands of DNA are 50% separated (melting temperature)
-cooling allows strands to rebond
- hybridization will occur id strands have a significant amount of bases in common
-single strand DNA can be hybridized to complementary RNA or DNA
Stem Loop Structure - answer✔formed when single strand DNA or RNA hybridizes to itself
- occasional mismatched regions create bubbles
- branch off from main chain
DNA Replication - answer✔Process by which parental DNA is copied
- General pattern of replication involves the formation of 2 copies of progeny DNA from one
copy of parental DNA (semi conservative)
- Strands have great affinity for each other
- DNA helix is unwound to separate strands
- Replication is highly accurate
- Very rapid
- One strand is synthesized in a continuous fashion and another is synthesized in fragments
discontinuously
- Telomeres are added to the other end to maintain information at the other end of the
chromosome
DNA Polymerase - answer✔Catalyzes the step-by-step addition of deoxyribonucleotide units to
a DNA chain
- New chain is assembled directly onto template by addition onto 5' end of the primer strand
- (DNA)n + dNTP --> (DNA)n+1 + PPi
- Cleavage of dNTP to dNMP allows an addition
- Template can be double or single
2|Page
, ©FYNDLAY EXAM SOLUTIONS 2024/2025
ALL RIGHTS RESERVED.
- Double stranded must be broken at 1+ sites
- Single must be bound to a primer strand with a free 3' hydroxyl
- Requires dATP, dTTP, dCTP and dGTP and Mg
Mechanism of DNA polymerase/synthesis - answer✔- Synthesizes 5' --> 3'
- 3' hydroxyl of the terminal deoxyribose attacks the innermost alpha-phosphate residue of the
new dNTP
- Formation of the phosphodiester bridge between the primer and the new unit
- 3' end of the new unit is now ready to do the same to the next dNTP
mRNA - answer✔Template for protein synthesis or translation
- Distinct mRNA is produced for each gene in eukaryotes (less specific in prokaryotes)
- Heterogeneous class of molecules
- Average length is 1.2 kb
- Determines the tRNA to be used
tRNA - answer✔Carries amino acids in an activated form to the ribosome for peptide-bond
formation
- Sequence that AA are polymerized from tRNA is controlled by mRNA
- At least one type of tRNA for each of the 20 AA
- 30 to 50 types
- Relatively small (about 75 nucleotides)
- Contains rare bases (pseudouracil, dihydrouracil)
rRNA - answer✔Constitutes the major component of ribosomes
- Catalytic and structural role in protein synthesis
Types of RNA in E.Coli - answer✔rRNA comprises 80% of RNA
- 23S= 3700 molecules
- 16S= 1700 molecules
- 5S= 120 molecules
3|Page
, ©FYNDLAY EXAM SOLUTIONS 2024/2025
ALL RIGHTS RESERVED.
tRNA= 15% of RNA
- 4s= 75 molecules
- Average 75 bases (smallest RNA molecule)
mRNA= 15%
- Average size about 1200 bases
Kilobase (kb) - answer✔a unit of length equal to 1000 base pairs of a double stranded nucleic
acid molecule
RNA Polymerase requirements - answer✔1. A DNA template (Preferably double stranded)
- RNA is not effective template
2. Activated Precursors: ATP, TTP, GTP, CTP
3. DNA-Dependent RNA Polymerase
4. Other Proteins
5. Divalent metal ion (Mg or Mn)
Synthesis of RNA - answer✔Similar to DNA synthesis
- Direction: 5'-->3'
- Strands run antiparallel
- Mechanism: 3' hydroxyl attacks the innermost phosphate of the incoming NTP (nucleoside
triphosphate)
- Reaction is driven by hydrolysis of pyrophosphate (PPI)
Different from DNA synthesis
- RNA polymerase does not require a primer
- Cannot remove mismatched nucleptides
Mechanism of Transcription (RNA Synthesis) - answer✔- RNA synthesis proceeds 5' --> 3'
- Involved terminal ribose residue of the primer
- 3' hydroxyl of terminal ribose attacks the inner most phosphate of the incoming NTP
- Creates a phosphodiester bridge, link primer to new nucleotide unit
4|Page
