DNA Flashcards
A polymer of deoxyribonucloside mono-phosphates covalently linked by a 3’⇢5’
- Hydrogen bond
- Phosphodiester bond
- Peptide bond
Phosphodiester bond
The structure of DNA has the following, which is not an answer
- Double helix with antiparallel chains
- Major groove which binds regulatory proteins
- minor grove which binds drugs
- sugar ribose backbone
sugar ribose backbone, because it is a sugar phosphate backbone
Which DNA base pairing will need a lot of heat to separate them
- AT
- GC
GC - because it has 3 hydrogen bonds vs AT with 2 hydrogen bonds
What is the temperature at which ½ of the helical structure is lost
- heating temperature hm
- melting temperature Tm
- Vaporization temperature
Melting temperature Tm
At temperatures above Tm, DNA is present as a single strand.
Graph: vertical ( absorbance of UV), horizontal (temperature). More UV absorbed to break helical structure= high temperature
Which structural form of the double helix of DNA is the most common?
- B-DNA
- Z-DNA
- A-DNA
B-DNA
A-DNA; right handed helix usually present with non physiological conditions
Z-DNA; left handed helix. Present with methylation and modification of DNA
Eukaryotes have the following characteristics, which one is incorrect?
- Single stranded, circular chromosome associated with non-histone proteins
- linear double stranded DNA molecule associated with histone and non histone proteins
- closed circular DNA in mitochondria of eukaryotes
- All the above
ingle stranded, circular chromosome associated with non-histone proteins. This is a prokaryote
Small circular extra chromosomal DNA molecules are called
- Histones
- Plasmids
- Prions
- Myloid linkage
Plasmids
Enzymes used for DNA synthesis are called
- Ribonucleases
- DNA polymerases
- deoxyribonucleases
- All the above
DNA polymerases
What are the order of the steps in prokaryotic DNA synthesis
- RNA primer
- Separation of the two complementary strands
- DNA ligase
- Chain elongation
- Excision of RNA primers and replacement by DNA
- Formation of the replication fork
- Direction of DNA replication
- Separation of the two complementary strands
- Formation of the replication fork
- Direction of DNA replication
- RNA primer
- Chain elongation
- Excision of RNA primers and replacement by DNA
- DNA ligase
What base pairs are at the origin of replacement site
- AC pairs
- AT pairs
- GC pairs
- GA pairs
AT pairs because they are easier to melt
True or False
Eukaryotes have multiple origin site of replication for rapid replication because they have bigger DNA, prokaryotes have one origin site or replication because it has smaller DNA
True
These 2 things happen at this step of prokaryotic DNA synthesis
- As the 2 strands unwind and separate they form a V where active synthesis occurs
- Replication of dsDNA is bidirectional generating a replication bubble
Formation of the replication fork
Binds to origin and causes the AT rich regions to melt
DnaA protein
unwinds the double helix
DNA helicases
ssDNA binding proteins
keeps the strands apart and protect DNA from nucleases that degrade ssDNA
Cut and rejoin one strand of double helix to remove supercoils
Topoisomerase I
cuts and rejoins both strands e.g. DNA gyrase
Topoisomerase II
The strand that is being copied in the direction of the advancing replication fork which is synthesized continuously
Leading strand
Strand being copied in the opposite direction to the direction of the replication fork, it is synthesized discontinuously
lagging strand
this has okazaki strands
True or False
DNA polymerases read the parental strand in the 3’⇢5’ direction therefore synthesis happens in the 5’⇢3” direction
True
T/F
DNA polymerases require and RNA primer (`10nucleotide) with a free OH on the 3’ end
True
- RNA primer is catalyzed by primase
- RNA polymerases do not need a primer
Which polymerase is responsible for chain elongation during the prokaryotic DNA synthesis
- DNA polymerase III
- DNA Polymerase I
- RNA polymerase IV
- DNA Polymerase II
DNA Polymerase III
- highly processive, it remains bound to template by its beta subunit as it moves along
- it has 3’to5’ exonuclease activity to correct mismatching bases. Goes backwards and corrects mis-matches
Which polymerase is responsible for excising RNA primers and filing the gap during the prokaryotic DNA synthesis
- DNA polymerase III
- DNA Polymerase I
- RNA Polymerase IV
- DNA Polymerase II
DNA Polymerase I
This makes the final phosphodiester linkage between the 5’ phosphate on the DNA chain synthesized by DNA pol III and the 3’ OH on the chain made by DNA pol I
DNA Ligase
True or False
In eukaryotic DNA replication, RNA primers are removed by RNase rather than DNA polymerase I
True
Stage in interphase where a cell prepares to initiate DNA synthesis, biosynthesis also occurs here
G1
Stage in interphase where a cell DNA content doubles, DNA synthesis occurs here
S phase
Stage in interphase where a cell where biosynthesis for mitosis occurs, more DNA synthesis happens here
G2
- If you remove growth factors, cells will end up in this phase of interphase
- this is where cells are sent to reactivate
- Nerve cells exit this cell cycle stage permanently
- Cells that have ceased division
G0
Phase of the cell cycle where cell division happends
mitosis
- DNA polymerase that contains primase
- initiates DNA synthesis
Polymerase Alpha
DNA polymerase that elongates the okazaki fragments of the lagging strand
DNA Polymerase delta
DNA polymerase that elongates the leading strand
DNA polymerase epsilon
- complexes of noncoding DNA plus proteins located at the ends of linear chromosomes
- maintain structural integrity of the chromosomes, preventing attach by nucleases
- Allow repair enzymes to distinguish between a true end from a break in dsDNA
- Consist of several thousand tandem repeats of noncoding AGGGTT paired with a complementary region of Cs and As
- Shorten with every successive division
Telomeres
This enzyme maintains telomeric length in stem cells and cancer cells
telomerase - keeps replacing the telomere region
Enzyme that synthesizes DNA from RNA
Reverse Transcriptase
- Basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei. They act as spools around which DNA winds to create structural units called nucleosomes
- Eukaryotic DNA is associated with these tightly bound basic proteins
Histones
Histones + DNA
Nucleosomes
Each chromosome contains a long molecule of DNA, which must fit into the cell nucleus. To do that, the DNA wraps around complexes of histone proteins, giving the chromosome a more compact shape
DNA damage can happen by the following which is not correct?
- Hydrolysis - lose amino group and get H2O
- Oxidation - loss of electrons
- Methylation - different parts of bases can be methylated
- UV light
- Ionizing radiation
- All the above
All the above
This DNA damage leads to the formation of pyrimidine dimers & thymine dimers ( thymines bond together)
UV light
This type of DNA damage leads to strand breaks in the DNA
Ionizing radiation
