Unit 2 notes from textbook + slides Flashcards
functions of DNA
storehouse of genetic information that is encoded in the sequence of subunits along its length (organized in the form of genes)
able to copy itself and transmit its genetic information
directionality of DNA strand
3’ to 5’ end
what bond connects one nucleotide to the next?
phosphodiester bond
give it polarity
how many base pairs per turn?
10
why does a purine pair with a prymidine?
perserves the distance between the backbones along the length of the entire molecule
best bond angles
why do base stacking interactions occur?
the nonpolar flat surfaces of the bases tend to group together away from water molecules
purpose of the PCR
amplify or replicate a targeted region of a DNA molecule into as many copies as desired
what is needed in the test tube for the PCR?
template DNA: region of DNA containing the region to be amplified
DNA polymerase: the enzyme used to replicate DNA
all four nucleotides
two primers: complimentary with the ends of the region of DNA to be amplified
steps of the PCR test
denaturation: heating the solution, breaking the H-bond between bases
annealing: the two primers bind to their complementary sequence via H-bonds
extension: solution is heated to optimal temp for DNA polymerase and it extends each primer
the two strands of the parental DNA double helix unwind and seperate into single strands at a site called..
replication fork
each parent strand is a template for the synthesis of the daughter strand
semi-conservative replication
after replication, each new DNA molecule consists of one strand that was originally parental and one new
enzyme helicase role
seperates the strands of the parental double helix by breaking the H-bonds holding the base pairs
single-strand binding protein (SSBP) role
binds to the single-stranded regions to prevent the template stranf from coming back together
topoisomerase role
works upstream from the replication fork to relieve the stress that results from unwinding the double helix at the replication fork
DNA polymerase role
critical component of a large protein complex that carries out DNA replication
synthesizes a new DNA strand from an existing template
properties of DNA polymerase
1) can only attach a nucleotide to another nucleotide. Can only elongate the end of an existing piece of DNA or RNA
2) each new DNA strand must begin with a primer (short strand of RNA), made by an enzyme called RNA primase
3) can only add nucleotides to the 3’ end of another nuclotide, DNA synthesis or polymerization occurs only in the 5’ to 3’ direction
what provides the energy for DNA synthesis?
as the incoming nucleotide triphosphate is added to the growing DNA strand one of the nucleotides high energy phosphate bonds is broken
leading strand
daugther strand synthesized continously
lagging strand
daugther strand synthesized in small pieces (okazaki fragments) that are later joined
RNA primer is laid down at intervals, which is extended by RNA polymerase
why are leading and lagging strands a thing?
because of the antiparallel nature of DNA and because DNA polymerase can synthesize DNA in only one direction
steps of DNA replication
1) RNA primase lays down an RNA primer
2)DNA polymerase extends the RNA primer
3) a different DNA polymerase removes the primer and replaces it with DNA
4) DNA ligase forms a bond joining the two fragments
origin of replication definition
each point at which DNA synthesis is initiated
replication bubble definition
the opening of the double helix at each origin of replication forms a replication bubble with a replication fork on each side, each with a leading and lagging strand and the respected enzymes necessary
difference between origins of replication in bac and euk
bacteria typically only have one origin of replication whereas eukaryotes have many
DNA Polymerase directionality
reads the DNA template 3’ to 5’ and synthesizes new DNA in the 5’ to 3’ direction
what does polymerization require?
an enzyme
a form of energy (ex. ATP)
enzymes involved in DNA replication
1)Helicase: breaks hydrogen bonds, unwinding DNA double helix
2)Primase: synthesizes RNA primers on leading and lagging strands
3)DNA polymerase: replaces RNA primers with DNA nucleotides
4)DNA Ligase: catalyzes phosphodiester bond formation, joining DNA fragments
5)DNA polymerase: synthesizes DNA 5’ to 3’ on leading and lagging strands
6)SSBPs: coats single stranded DNA to keep them from coming together
7)Topoisomerase: relaxes supercoiled DNA
bacterial DNA replication
bacterial cells can replicate in a circle both directions, the ends will meet up, usually has one origin of replication
three problems the cell has to solve to replicate DNA
1) seperate the DNA strands only a little at a time (use helicase)
2)make primers for DNA polymerase (RNA primase makes RNA primase)
3)allow synthesis to happen simultaneously from the two template strands (okazaki fragments that are later stitched together)
