Week 4_DNA structure/replication/repair Flashcards
what are the components of a nucleotide?
phosphate group
nitrogenous base
ribose sugar (in RNA)
deoxyribose sugar (in DNA)
how do nucleotides join together to form DNA?
(what direction?)
phosphodiester bonds are formed between the existing nucleotide and the new nucleotide to be added
DNA is only is synthesized in the 5’ to 3’ direction by the enzyme DNA polymerase III
what is the backbone of DNA held together by?
covalent phosphodiester bonds
how many bp are in 1 complete turn?
10
what is the 5’ and 3’ end of a nucleotide?
5’ == phosphate group
3’ == OH group on the ribose/deoxyribose sugar
what is at the 5’ end of DNA?
has a free phosphate group attached to the 5’-carbon
what is at the 3’ end of the DNA?
has a free hydroxyl (-OH) group at the 3’-carbon
what does it mean if DNA is antiparallel?
DNA strands are in opposite directions
what are the 3 phases of DNA replication?
initiation
elongation
termination
describe initiation stage of DNA replication
starting of the process
bringing together all the necessary enzymes to replicate DNA
describe elongation stage of DNA replication
actual process of replicating the DNA
describe termination stage of DNA replication
make sure the process is appropriately stopped
what does semiconservative replication mean?
(1) old DNA strands are separated (hydrogen bonds are broken)
(2) each old DNA strand is used as a template for a new DNA strand (semiconservative replication)
(3) the new DNA molecules are 1/2 old strand and 1/2 new strand
what is the replication complex (RC)?
a large complex containing the enzymes needed to replicate DNA, interacts with the DNA
where do RCs bind to the DNA to begin replication?
origin of replication (ori) == particular sequences of DNA where replication begins
eukaryotic chromosomes have thousands of ori’s. Why?
eukaryotic chromosomes are very big
multiple ori’s allow for a much faster replication process
describe how chromosomes get copied beginning at several ORI’s simultaneously
(1) the replication complexes bind to the ORI’s
(2) DNA strands are separated (by helicase) –> forms replication forks
(3) DNA replication proceeds bidirectionally
DNA strands are separated at the ___ by helicase
replication forks
what is the function of helicase?
breaks the hydrogen bonds between strands
on the leading strand, new DNA is synthesized ___ in the ___ direction (by ___)
continuously
5’ –> 3’ direction
DNA Pol III
on the lagging strand, new DNA is synthesized in ___ in the ___ direction (occurs more ___)
discontinuous fragments
opposite directions
occurs more slowly
what are the 4 nitrogenous bases?
what do each of them bind to?
what bonds hold them together?
adenine
thymine
cytosine
guanine
adenine –> thymine
cytosine –> guanine
hydrogen bonds hold the nitrogenous bases together –> hold the two strands of DNA together
what direction does DNA Pol III add nucleotides?
5’ –> 3’ direction
what does DNA Pol III need in order to attach a new nucleotide?
needs a 3’-OH to attach a new nucleotide to
is DNA Pol III able to add the first nucleotide in DNA replication?
no
how does DNA replication get started?
through RNA polymerase enzyme
primase (an RNA polymerase) begins the DNA replication process
DNA replication occurs ___ in the leading strand and ___ in the lagging strand
faster in leading
slower in lagging
what enzyme removes the RNA?
DNA polymerase I removes and replaces the RNA nucleotides with DAN nucleotides
what are nicks?
missing phosphodiester bonds in between Okazaki fragments
what does DNA Pol I do?
1) removes RNA nucleotides
2) and replaces them with DNA nucleotides
3) can’t form the last phosphodiester bond –> leaves a ‘nick’ in the DNA backbone
what does DNA ligase do?
1) enzyme that restores the missing phosphodiester bonds ‘nick repair’
DNA polymerases are enzymes with high ___
processivity
describe why DNA has high processivity
they can add thousands fo nucleotides without falling off the DNA (very stable)
why are DNA polymerases so stable?
Sliding clamp protein helps DNA polymerases remain attached to the DNA
if DNA polymerase adds an incorrect nucleotide, it can…
in other words, DNA polymerase has a ___ function
it can replace it with the correct nucleotide
proofreading
what other proteins also scan DNA for errors and damage?
excision repair enzymes
what do excision repair enzymes do?
detect and repair mismatches and DNA damage
our DNA repair enzymes are constantly at work ___
repairing our DNA
what happens when you have a deficiency in DNA repair enzymes?
xeroderma pigmentosum (XP) –> rare genetic disorder –> excision repair enzymes have significantly reduced ability to repair DNA damage
leads to development of cancers frequently and at young age
ER enzymes are critical for survival
