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STRUCTURE OF NUCLEIC ACIDS AND DNA REPLICATION (FUNCTION (capable of…
STRUCTURE OF NUCLEIC ACIDS AND DNA REPLICATION
NUCLEIC ACIDS
are polymers of
nucleotides
STRUCTURE
Pentose sugar (ribose - OH group on C2 for RNA, deoxyribose J group on C2 for DNA)
inorganic phosphate
attached to 5' carbon
causes negative charge on nucleotide (DNA is negatively charged)
nitrogenous base
hydrophobic organic ring
forms H bonds with one another through complementary base pairings
A bonds to T (2 hydrogen bonds) - since it's less H bonds, replication starts at AT rich regions
point 1: % of A in one DNA double helix = % T (Chargaff's Rule)
point 2: purine: pyrimidine is equal (derived from point 1)
but AT%: CG% Is NOT required to be equal
C bonds to G (3 H bonds)
point 1: % C in a DNA molecule (double helix) = % G (Chargaff's rule)
types
purines
adenine and guanine
pyrimidines
thymine and cytosine
PROCESS OF FORMATION of nucleotide from pentose sugar
nitrogenous base undergoes condensation reaction
joins pentose sugar on 1' Carbon
forms a nucleoside
nucleoside and phosphoric acid undergo condensation reaction
forming a phosphoester bond between them, where the phosphate group is added to 5' Carbon
forms nucleoside monophosphate
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Formation of Dinucleotide
requires energy
comes from hydrolysis of nucleotide (nucleoside triphosphate) to form nucleotide (nucleoside monophosphate)
nucleotide (nucleoside monophosphate) join by a condensation reaction
between the phosphate group of the 5' carbon (hydroxyl group removed) and the hydroxyl group (H removed) of the 3' Carbon of the pentose sugar of the other nucleotide
forms a phosphoester bond
Formation of a Polynucleotide
2 Dinucleotides are joined together (ref. formation of dinucleotide)
overall, 2 phosphoester bonds are linked = phosphodiester bond
process is repeated
at the end of the polynucleotide (terminal nucleotide) is a free phosphate group (attached to 5' C of pentose) = 5' end
5' to 3' directionality
at the opposite end (terminal nucleotide) is a free hydroxyl group (attached to 3' Carbon of pentose sugar) = 3' end
STRUCTURE OF DNA
EACH STRAND:
nitrogenous bases project at right angles inwards
each DNA strand is a polymer of nucleic acids (polynucleotide) linked together by phosphodiester bonds -
sugar phosphate backbone
each strand has a
specific base sequence
function: carrier of genetic information
DNA molecule is double stranded
strands are twisted around each other to form a double helical structure
held together by hydrogen bonds between nitrogenous bases
nitrogenous bases form base pairs
through complementary base pairing (ref. structure of nucleotides)
Ensures DNA has a constant width (2nm per base pair)
base pairs are 0.34nm apart
1 turn of the double helix is 3.4nm (10 base pairs)
2 strands are anti-parallel
3' end faces 5' end
importance
: allows for complementary base pairing
allows the 2 strands to be complementary (replicated DNA is genetically identical)
DNA REPLICATION
function: coding and storing of genetic information AND way to replicate accurately
MODELS (TEST)
semi-conservative
both strand separate and act as templates
each daughter DNA molecule composed of one parental and one daughter strand (H bonds formed between them)
conservative
both strands of DNA molecule act as templates
2 parental strands re-associate, while 2 newly synthesised daughter DNA strands form another DNA molecule
dispersive
Parental DNA molecule breaks up into short segments, which act as templates
segments are joined together, so each strand of daughter molecules is a mixture of old and newly synthesised parts
EXPERIMENT
mechanism
15N isotope of DNA (greater density) cultivated in E Coli (all bases in DNA have 15N element
heavier DNA
bacteria transferred into medium with 14N and allowed to divide once (replication occurs)
new DNA synthesised is lighter because it uses 14N DNA
bacteria divides in 14N medium a second time
differences in density measure using caesium chloride density gradient (shown by DNA bands in centrifuge tubes)
results
generation 0 (grown in 15N)
One band of heavy type
100% 15N
generation 1 (grown in 14N once)
one band of intermediate type
100% 15N14N
disproves dispersive as the density wouldn't have been so even
disproves conservative as conservative model assumes 50% 25N 50% 14N
DOESN'T prove semi-conservative fully
generation 2 (grown in 14N twice)
2 bands of equal thickness
50% 14N15N (from the 15N) 50% 14N14N
proves semiconservative
one intermediate and one light
SEMI-CONSERVATIVE PROCESS
unwinding and separation of DNA strands
each strand acts as a template for the synthesis of a new daughter strand
forms 2 daughter DNA molecules
each daughter DNA molecule has 1 parental DNA strand and 1 newly synthesised DNA strand
Semi conservative (half parental half daughter)
END REPLICATION PROBLEM
in eukaryotes (linear DNA)
prokaryotes have circular DNA so there'll always be.a free 3'OH end at the other end
RNA primer at 3' end of parental template strand is not replaced with corresponding DNA nucleotides--
DNA polymerase I (same as 3, needs to add onto 3' OH end) has no 3'OH end available to add onto (for lagging strand)
5' end of growing strand has no 3'OH free to add once primers are exised
newly formed daughter DNA strand is shorter than parental strand
when replication occurs, DNA shortens and critical genes is lost
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FYI when you add nucleotides on one by one to replace every nucleotide of primer it's actually 3' to 5' direction (wrt chain)
PRIMING
Single stranded DNA binding protein attaches to single stranded DNA to stabilise it
primase catalyses the synthesis of an RNA primer (short chain of RNA)
RNA primer is complementary to DNA nucleotides on template
RNA primer is needed because DNA polymerase III can't initiate DNA synthesis (needs a preexisting 3'OH end to add on DNA nucleotides to)
ELONGATION by DNA polymerase III
DNA polymerase III adds on free DNA nucleotides (nucleoside triphosphate) to exposed bases on the parental DNA strand by complementary base pairing
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catalyses formation of phosphodiester bonds between 2 adjacent DNA nucleotides
only works in 5' to 3' direction wrt growing chain
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takes place at the origin of replication (note: eukaryotes have many origins of replication)
helicase moves 3' to 5' with reference to (wrt) template, breaking the hydrogen bonds between complementary bases
helicase unwinds and separates 2 DNA strands
as the 2 strands separate, a replication bubble is formed with
replication fork
at each end
MUTATION IN DNA
strand slippage
newly synthesised strand loops out
insertion of additional nucleotide base
template strand loops out
deletion of nucleotide base
FUNCTION
store genetic information
long polymer : stores large amounts of information as linear sequence of bases
must be stable to prevent mutation
large number of H bonds
strong phosphodiester bonds
hydrophobic interactions between stacked bases
no hydroxyl group at carbon 2 (reduces reactivity)
double helix structure = reduced reactivity of bases
histone proteins reducing acidic properties
capable of accurate replication
complementary base pairing
double helical structure: semi-conservative replication
each strand can act as a template
original DNA molecule gives 2 copies of DNA with identical structure and base sequence
DNA repair (repair changes from environmental factors) - prevents mutations
intact complementary strand is template for repair
genetic variation (for offspring)
mutations to form new stable forms of genes (alleles)