CENTRAL DOGMA OF BIOLOGY

 = name of this process – flow of sequence information: DNA  transcription  RNA  Translation  Protein
NUCLEOTIDE
 NUCLEOTIDE = molecule that consists of a sugar an organic base and phosphate
 RIBOSE SUGAR: 5 carbon sugar arranged like heterocyclic ring – 4 carbons & non-carbon structure participate in ring
structure (ex: O) & carbon 5’ outside the ring

Sugar: DNA Sugar: RNA Base: PURINES

• DeoxyriboNucleic • RiboNucleic Acid • Double rings
Acid – only has – only has Ribose
2’Deoxy-Ribose sugar sugar

Base: PYRIMIDINES
• Double rings
Phosphate
• Inorganic phosphate group
• Attached to 5’ carbon
• Can have up to 3 attached
together in the chain
NUCLEIC
 Polymers, chains of nucleotides
ACID
ATP – Adenosine Tri-Phosphate Naming: Nucleotides in RNA & DNA
 Nucleoside = Base + Sugar
 Nucleotide = Base + Sugar + Mono/Di/Tri-Phosphate
RNA Nucleotides
• Adenosine MonoPhosphate (AMP) = Adenine, Ribose, 1 Phosphate
• Uridine MonoPhosphate (UMP) = Uracil, Ribosome, 1 Phosphate
ADP – Adenosine Di-Phosphate • Guanosine Monophosphate (GMP) = Guanine, Ribose, 1 Phosphate
• Cytidine MonoPhosphate (CMP) = Cytosine, Ribose, 1 Phosphate
DNA Nucleotides
• deoxyAdenosine MonoPhosphate (dAMP) = Adenine, Deoxyribose, 1 Phosphate
• deoxyThymidine MonoPhosphate (dTMP) = Thymine, Deoxyribose, 1
Phosphate
• deoxyGuanosine Monophosphate (dGMP) = Guanine, Deoxyribose, 1 Phosphate
AMP – Adenosine Mono-Phosphate • deoxyCytidine MonoPhosphate (dCMP) = Cytosine, Deoxyribose, 1 Phosphate
• Found in
nucleic
acid
DNA STRUCTURE
Critical Structure
For Its Function
• No 2’ OH group
• Chain of nucleotides linked by phosphodiester
bonds: 5’ phosphate of 1 nucleotide linked to
3’ carbon of another nucleotide above it
• DNA 5’ to 3’ ends polarity: 3’ of DNA =
nucleotide at the bottom has free 3’ hydroxyl
group; 5’ of DNA = free 5’ phosphate at the
top of nucleotide
• Sequence of DNA due to a chain of
nucleotides with different bases = Order of
different bases appearing in the chain
• *(ex: 5’-AGCT-3’)
Double Helix
• Watson-Crick base pairs (A-T, C-G pairs)
• Hydrogen bonds between bases
• Antiparallel strands of DNA = Opposite
direction (strand 1: 5’ – 3’ bottom to top,
strand 2: 5’ – 3’ top to bottom)
• Inside – highly hydrophobic, Outside –
highly charged and hydrophilic
Sequence
• 2 strands REVERSE COMPLEMENT to each other = 2 strands
annealed to each other
• Each strand codes for different proteins BUT only 1 strands codes
for gene’s protein product: strand 1 – template for making coding
RNA strand for DNA replication
• 2 DNA strands for replication & transmission of information
DNA REPLICATION
DNA Polymerase Cell Cycle
• = Synthesize DNA using a template DNA strand
• Create double stranded structure
• Short nucleic acid primer sequence (based paired to larger DNA template)
present = DNA polymerase enzyme can extend from existing one ONLY
(can’t start a new DNA)
• 5’ TO 3’ SYNTHESIS = DNA polymerase adds new nucleotide to the 3’ end
of growing strand/chain
TRIAL & ERROR PROCESS
1. DNA polymerase bring to template and position at free 3’end of primer
2. Deoxynucleotide triphosphate randomly matched up with template strand by DNA polymerase (if wrong, ejected)
3. Correct match, fit correctly with enzyme so enzyme attach it to the growing chain  Release 2 unneeded phosphates
4. DNA polymerase slide forward to next position
RNA Polymerase
• = Synthesize RNA using a template DNA strand (Trial & Error Process)
• DON’T REQUIRE a primer = Can join 2 nucleotides to form new RNA strand = Synthesize RNA de novo
• Uses ribonucleotides instead of deoxyribonucleotides
• Uses different associated proteins
DNA REPLICATION PROCESS 1
Initiation
• Replication begins at special sites, ORIGINS OF REPLICATION
• INITIATION FACTOR specialised protein binds at this site = Cause
small parts of double helix to fall apart = Separating 2 strands, MELTING
(= passive opening of small areas)
• HELICASE recruited to melted area = Actively unwind the DNA = Make
REPLICATION BUBBLE which 2 DNA held apart
• Helicase continue to unwind the DNA as it goes along = Enlarge the
volume
• Bubble is kept open by special SINGLE STRAND DNA BINDING
PROTEIN (SSB)
Replication Forks • Edges of the bubble where helicase unwinds the DNA = REPLICATION
FORKS
• RNA primer synthesised by DNA primase as helicase moves along = To allow DNA polymerase to work
• Replication takes place within the replication bubbles
• TOP STRAND: RNA primer can only be synthesised and extended in 1 direction through the primers 3’ end towards a
replication fork = DNA polymerase can start from the primer and keep synthesizing DNA continuously as helicase moves
along = Create 1 long DNA strand – LEADING STRAND
• BOTTOM STRAND: RNA primer can be synthesised away from the replication fork through the primers 5’ end = Cells
make a series of primers as the replication fork expands = Synthesise DNA in the direction that leads away from the
replication strand = Create 1 long DNA strand discontinuously in the form of short fragments, OKAZAKI FRAGMENTS
– LAGGING STRAND
DNA REPLICATION PROCESS 2
Lagging Strand Synthesis
• The other primers are used by a different
polymerase not attached to helicase =
Make new Okazaki fragments after the
replication fork has moved on
• Primase of left fork primes the leading
strand for the polymerase of the right
fork & vice versa when the replication
bubble is first formed
• DNA helicase for each replication fork, attached to DNA
primase & DNA polymerase
• Helicase moves along = Associated DNA polymerase
continuously synthesise the leading strand & At defined
intervals, primase synthesizes new short primers for bottom
strand

• Leading strand no longer requires a primer

• But primase of each fork continuously primes its own lagging
strand
• After replication fork has moved away = Polymerase uses those • Once replication complete
primers to synthesize the Okazaki fragments = Special enzymes replace
RNA primers with DNA
and join everything
together
DNA REPLICATION PROCESS 3 – microscopic level
Replication Of A Whole Chromosome
• Eventually bubbles merge so long DNA
strand is complicated replicated
• 2 strands are wound around each other =
Force it to coil around each other more
tightly = Stop from unwinding whole
DNA = SUPERCOILING
• Super-coils create a lot of torsional
strain = Eventually stop DNA from
being unwound completely
• DNA TOPOISOMERASE = Cut DNA
= Allow super coils to unwind = Once
super-coils are gone = Relieve torsional
strain = DNA topoisomerase rejoins
DNA
• DNA TOPOISOMERASE = Resolve
tangle/junction where replication
bubbles meet
• DNA POLYMERASE = Repair
damaged nucleotides