UMN BIOC 3021 EXAM 4 | 343 QUESTIONS AND 100% ANSWERS

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 allowing only the
"right" pairs to form stable interactions

Double Bonded BPs - ANSWER A and T
- the 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
- the 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)

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
- 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

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
- 3' OH of the new NTP can attack the incoming NTP

Transcription Terminology - ANSWER Coding Strand: This strand of DNA is
not used for transcription, runs parallel to RNA

Template Strand: Used for transcription, runs antiparallel direction to RNA

Transcription Initiation - ANSWER Initiated on the DNA template
downstream from promoter sites containing consensus sequences
- Promoter sequence may vary by a couple bases to the consensus sequence

Prokaryotic Promoter Site - ANSWER TTGACA is upstream -35 from
transcription start site
TATAAT (Pribnow box) is upstream -10 from transcription start site