MIBO 3500 Exam 2 |Questions and Answers 2023/2024
what is the monomer unit of DNA - nucleotide
3 parts of a nucleotide - 1. Deoxyribose Sugar
2. Phosphate Group
3. Nitrogenous Base
- purines: adenine (A) and guanine (G)
- pyrimidines: cytosine (C) thymine (T) and uracil (U)
difference between a ribose sugar and a deoxyribose sugar - RNA ribose has a 2' OH group while DNA
deoxyribose does not
- 2' OH group makes RNA less chemically stable
- the minor chemical difference is recognized by most of the cellular enzymes that interact preferentially
with either DNA or RNA
the phosphate group on DNA - gives DNA its negative charge and makes it acidic
how does DNA assemble - phosphate on the 5' carbon
nitrogenous base on the 1' carbon
5' phosphate attaches to the 3' OH group of the next sugar
nucleoid - bacteria pack their DNA into a series of loops or domains, collectively called the nucleoid
- loops are supercoiled and anchored by histone-like proteins
3-step mechanism for introducing a supercoil into a chromosome - 1.) produce a double-strand break
in the circular chromosome
2.) pass an intact region of the DNA through the break
3. Seal the ends to generate a twist in the chromosome
,enzymes that control DNA supercoiling - topoisomerases
vertical transmission - flow of genetic information from one generation to the next
horizontal transmission - transfer of genes between cells of the same generation
central dogma - DNA -> RNA -> Protein
topoisomerase I - Single protein that makes single-stranded DNA breaks to relieve negative supercoiling
a
topoisomerase II - An multiple subunit protein that cleaves both strands of DNA and uses ATP to
introduce negative supercoils
- ex.) DNA gyrase
direction of DNA replication - 5' to 3'
What kind of replication does DNA undergo? - semi-conservative replication
where does DNA replication begin - OriC
- A 245-bp sequence that includes a series of repeats bound by specific replication factors
DnaA protein - initiator protein complexed with ATP; binds to specific 9-mer sequences within OriC
- Distorts DNA at oriC leading to strand separation at the 13-mer repeats
- assembles a replication machine (replisome) containing DnaC and DnaB
DnaC - helicase loader
- Opens DNA helicase protein rings and then are released
, DnaB - helicase; unwinds helix to expose template strands
- Uses energy from ATP hydrolysis to unwind DNA at each of the replication forks
- Recruits DnaG
DnaG - primase; synthesizes short RNA primers against each template strand
- Has 3' OH group on end; required as starting point for DNA polymerase to add DNA nucleotides
DNA pol III - major replication enzyme
Completes the replisome
- Sliding clamp holds polymerase in place and DNA polymerase III adds nucleotides one by one in the 5'
to 3' direction
- The continuous strand is leading strand
- Lagging strand built in fragments: Behind origin, can only add in short pieces as the DNA molecule
unzips
single-stranded binding proteins - coat exposed regions of ssDNA to protect it
DNA pol I - replaces RNA primers with DNA
DNA gyrase - relaxes supercoiling ahead of the replication fork
- introduces negative supercoiling to relieve the positive supercoiling caused by helicase
How are new dNTPS added - The 3' OH group of the last nucleotide on the strand attacks the 5'
phosphate group of the incoming dNTP
- Two phosphates are cleaved off
- A phosphodiester bond forms between the 2 nucleotides
removal of RNA primers - RNaseH or the exonuclease activity of DNA pol I
what is the monomer unit of DNA - nucleotide
3 parts of a nucleotide - 1. Deoxyribose Sugar
2. Phosphate Group
3. Nitrogenous Base
- purines: adenine (A) and guanine (G)
- pyrimidines: cytosine (C) thymine (T) and uracil (U)
difference between a ribose sugar and a deoxyribose sugar - RNA ribose has a 2' OH group while DNA
deoxyribose does not
- 2' OH group makes RNA less chemically stable
- the minor chemical difference is recognized by most of the cellular enzymes that interact preferentially
with either DNA or RNA
the phosphate group on DNA - gives DNA its negative charge and makes it acidic
how does DNA assemble - phosphate on the 5' carbon
nitrogenous base on the 1' carbon
5' phosphate attaches to the 3' OH group of the next sugar
nucleoid - bacteria pack their DNA into a series of loops or domains, collectively called the nucleoid
- loops are supercoiled and anchored by histone-like proteins
3-step mechanism for introducing a supercoil into a chromosome - 1.) produce a double-strand break
in the circular chromosome
2.) pass an intact region of the DNA through the break
3. Seal the ends to generate a twist in the chromosome
,enzymes that control DNA supercoiling - topoisomerases
vertical transmission - flow of genetic information from one generation to the next
horizontal transmission - transfer of genes between cells of the same generation
central dogma - DNA -> RNA -> Protein
topoisomerase I - Single protein that makes single-stranded DNA breaks to relieve negative supercoiling
a
topoisomerase II - An multiple subunit protein that cleaves both strands of DNA and uses ATP to
introduce negative supercoils
- ex.) DNA gyrase
direction of DNA replication - 5' to 3'
What kind of replication does DNA undergo? - semi-conservative replication
where does DNA replication begin - OriC
- A 245-bp sequence that includes a series of repeats bound by specific replication factors
DnaA protein - initiator protein complexed with ATP; binds to specific 9-mer sequences within OriC
- Distorts DNA at oriC leading to strand separation at the 13-mer repeats
- assembles a replication machine (replisome) containing DnaC and DnaB
DnaC - helicase loader
- Opens DNA helicase protein rings and then are released
, DnaB - helicase; unwinds helix to expose template strands
- Uses energy from ATP hydrolysis to unwind DNA at each of the replication forks
- Recruits DnaG
DnaG - primase; synthesizes short RNA primers against each template strand
- Has 3' OH group on end; required as starting point for DNA polymerase to add DNA nucleotides
DNA pol III - major replication enzyme
Completes the replisome
- Sliding clamp holds polymerase in place and DNA polymerase III adds nucleotides one by one in the 5'
to 3' direction
- The continuous strand is leading strand
- Lagging strand built in fragments: Behind origin, can only add in short pieces as the DNA molecule
unzips
single-stranded binding proteins - coat exposed regions of ssDNA to protect it
DNA pol I - replaces RNA primers with DNA
DNA gyrase - relaxes supercoiling ahead of the replication fork
- introduces negative supercoiling to relieve the positive supercoiling caused by helicase
How are new dNTPS added - The 3' OH group of the last nucleotide on the strand attacks the 5'
phosphate group of the incoming dNTP
- Two phosphates are cleaved off
- A phosphodiester bond forms between the 2 nucleotides
removal of RNA primers - RNaseH or the exonuclease activity of DNA pol I
