ch14: DNA structure and function Flashcards
structure of DNA
nucleic acid (polymer of nucleotides)
nucleotide (5-carbon sugar; either deoxyribose or ribose)
phosphate group
nitrogenous base (A,G,C,T/U)
which nitrogenous bases are pyrimidines (one ring)
cytosine, thymine and uracil
which nitrogenous bases are purines (two rings)
adenine and guanine
what is a primer
a short nucleic acid sequence that provides a starting point for DNA synthesis
DNA strand structure is a
polymer of nucelotides
what is a phosphodiester backbone
a repeating sugar-phosphate unit that is joined by a phosphodiester bond
where is the base connected on the 5-carbon sugar
1’ sugar
chain of nucleotides has an orientation of
5’-to-3’ (fifth carbon connected to the third carbon by phosphodiester bond)
double helix
- 2 anti-parallel strands (run in opposite directions)
- bases protrude into center held together by base pairing (hydrogen bonds)
- major and minor grooves (DNA-interacting proteins can fit in these grooves to “read” specific DNA sequences)
- bases stuck on top of each other
G forms — bonds withs C
3 hydrogen
A forms —- bonds with T
2 hydrogen
equal bond distances gives
consistent diameter of helix
Why do you think it’s
important that the
phosphodiester bonds in
the DNA backbone are
covalent (strong) bonds,
and the bonds between the
bases are hydrogen (weak)
bonds?
if you break a phosphodiester bond, it damages the DNA, which causes mutations and all other kinds of problems. but you need those weak hydrogen bonds so that DNA mechanisms can break those bonds in order to copy the DNA into RNA for replication
what does “complementarity of bases” mean
each strand is a template for the opposite base
requirements of DNA replication
- something to copy (parental DNA strand)
- something to do the copying (enzymes; DNA polymerase and other enzymes)
- building blocks to make the copy (nucleotide triphosphates)
process of DNA replication
1) initiation: beginning of replication
2) elongation: new strands of DNA are synthesized by DNA polymerase
3) termination: replication is terminated
DNA is copied by
DNA polymerase
how is DNA copied by DNA polymerase (4)
-it matches existing DNA bases with complementary nucleotides and links them
-adds new bases to the 3’ end of the existing strand
-synthesizes in 5’-to-3’ direction
-requires a primer (usually RNA)
prokaryotic replication (4)
-single circular molecule of DNA
-replication begins at one origin of replication
-helicase unwinds DNA
-DNA replication proceeds in both directions around the chromosome
helicase
clamp onto and unwind DNA
DNA shape in prokaryotes and eukaryotes
prokaryotes: in circular form
eukaryotes: wrapped around histones
supercoiling
unwinding DNA in one area will increase tension in the rest of the strand (one complete helical turn=one supercoil)
unwinding DNA causes
torsional strain
topoisomerase
unwinds DNA to prevent supercoiling (one called DNA gyrase is used in replication)
replication is
semidiscontinous (unwinds a little then lets go to prevent too much tension)
partial opening of helix forms
replication forks
DNA primase
RNA polymerase that makes RNA primer (RNA will later be removed and replaced with DNA)
DNA polymerase III
main replication enzyme
DNA polymerase I
has 5’-to3’ exonuclase activity (acts on lagging strand to remove primers and replace them with DNA)
DNA polymerase II
involved in DNA repair processes
leading strand
-synthesized continuously from a single initial primer
-strand extended by DNA polymerase III
processivity
subunit of DNA polymerase III forms “sliding clamp” to keep it attached to the DNA template
clamp loader
loads clamp onto DNA
DNA primase
produces an RNA primer for each okazaki fragment
DNA polymerase III
synthesizes DNA from each RNA primer
DNA polymerase I
removes all RNA primers and replaces them with DNA
DNA ligase
seals the DNA backbone
okazaki fragments
short sections of DNA formed at the time of discontinuous synthesis of the lagging strand during replication of DNA; allows for the synthesis of both the daughter strands required for cell division
primose
all the proteins involved in DNA synthesis (primase, helicase, clamp loader)
where does termination of replication happen
occurs at a specific site roughtly opposite of the origin of replication
what does termination of replication do
cuts two daughter molecules that are intertwined like a ring; the chromosomes are unlinked by DNA gyrase
