CENTRAL DOGMA

• The progression of information within a cell; from DNA to protein

• DNA —> RNA —> Protein
•TAKE NOTE: The central dogma's main goal is the production of protein but other important processes and
products can be produced from this process as well.

HOW DOES THE CENTRAL DOGMA OCCUR?

•STEP 1 — DNA Replication
- DNA acts as a template to form new DNA
• Replication - duplication of DNA, giving rise to new DNA molecule

•STEP 2 — TRANSCRIPTION
• Transcription – a process of making RNA from DNA
- In some viruses, RNA can serve as a template strand
to produce new RNA in a process called RNA REPLICATION
- Also, in some viruses, RNA can serve as a template strand for
new DNA in a process called REVERSE TRANSCRIPTION
- RNA REPLICATION AND REVERSE TRANSCRIPTION ONLY HAPPEN IN VIRUSES
- RNA that is made up of DNA is specific for mRNA

•STEP 3 — TRANSLATION
• Translation - RNA sequence of mRNA is used to direct the synthesis of proteins
• The genetic sequence in RNA is changed into amino acid sequences to form PROTEINS.
- amino acids are very specific in terms of sequencing
- amino acids grouped together to form PROTEINS

3 CHALLENGES TO OVERCOME
••Two DNA strands are separated from each other
••Synthesizing of DNA from 5' to 3' end
- Newly formed DNA has 2 antiparallel strands:
- Template strand is 5' to 3'
- New strand is 3' to 5'
•• Guarding against the error of replication

SEMICONSERVATIVE REPLICATION
••DNA replication involves the separation of 2 original strands and
the production of 2 new strands with the original strands as templates.

KEY ENZYMES
Helicase — helix-destabilizing protein
- most important enzyme because it separates the 2 strands
- responsible for breaking down hydrogen bonds between nucleosides and nucleotides bases

DNA Gyrase (Class II topoisomerase)

- prevents positive coiling
- has 2 types:
• Negative supercoiling — if the DNA is right turning, the curling will be on the opposite side
• Positive supercoiling — if the DNA is right turning, it will turn right turn more. They will constrict curls with
each other.

Primase — catalyzes the synthesis of RNA primer

- basis of DNA polymerase where it starts to copy the DNA strands
DNA Polymerase — replicates DNA molecules to form the new strand

DNA Ligase — glues that fragment together

IN DETAIL:

STEP 1: UNWINDING OF THE DOUBLE HELIX

••Helicase unwinds the double-helix

- Unwinding of the helix introduces positive supercoiling

- Positive supercoiling will make further replication impossible

••DNA Gyrase places negative supercoils ahead of the replication forks

- DNA Gyrase - guard up separated strands and will place negative supercoils

••Single-stranded DNA is susceptible to degradation by nucleases

- Single-Strand Binding (SSB) Protein binds tightly to the single-stranded portions, protecting them from
degradation
*Hydrogen bonds can be denatured and renatured anytime at a higher frequency so we need proteins to
stabilize DNA strands so they won’t stick again

STEP 2: PRIMING
••Primase catalyzes the synthesis of an RNA primer

- copies a short stretch of the DNA template producing the RNA primer sequence
- DNA strands are anti-parallel
- new strands will be called lagging strands (replicated in 5’-3’ direction)
- responsible for making new strands
••Primer has a free 3'hydroxyl to which the growing chain can attach
STEP 3: FORMATION OF THE NEW STRAND
••DNA Polymerase III starts the synthesis of 2 new strands
- Newly formed DNA Is linked to the 3'hydroxyl of the RNA primer
••DNA Polymerase I - repair function
- removes the RNA primer (exonuclease activity) and
- replaces it with deoxynucleotides (polymerase activity)
••All synthesis of nucleotide chains occurs in the 5' - 3' direction
••Leading strand - formed continuously from its 5' to 3' end
- Template: 3' to 5'
••Lagging strand - semi discontinuously in small fragments - Okazaki fragment.
- Template: 5' to 3'

Addition of nucleotide to a growing chain:

••The 3'-hydroxyl group at the end of the growing DNA chain is a nucleophile.
••It attacks the phosphorus adjacent to the sugar in the nucleotide to be added to the growing chain
- eliminating the pyrophosphate
- a new phosphodiester bond is formed

PROOFREADING AND REPAIR

••Accuracy of the replication process should be high to prevent mutations.
••Proofreading - refers to the removal of incorrect nucleotides immediately
- Improves the fidelity of replication to one error in every 10^9 to 10^10 base pairs
- most unique function in DNA replication
••Replication resumes when the correct nucleotide is added

STEP 4: LINKING OF THE NEW STRAND

••DNA Ligase is responsible for linking the small fragments of DNA

POST-DNA REPLICATION
What if a mutation managed to escape?
• Mismatch-Repair System
 - The repair system identifies which of the two strands is the correct one
- Area with mismatch is removed
- DNA polymerases replicate the area again

• Base-Excision repair
- A base that has been damaged by oxidation or chemical modification is removed by DNA glycosylase

• Nucleotide-Excision repair
- Common for DNA lesions caused by ultraviolet or chemical means - leading to deformed DNA structures

TRANSCRIPTION

• Process of using a DNA template to produce RNA (mRNA)

• Produces all types of RNA