Far Eastern University — Institute of Health Sciences and Nursing (2023)

CENTRAL DOGMA
BIOCHEMISTRY LECTURE (Professor: Mr. Lawrence Adrian Tacliad)

CENTRAL DOGMA OF MOLECULAR BIOLOGY - DNA Gyrase/Topoisomerase – prevents DNA from

- Refers to the process of making copies of genetic
information, converting information in DNA into RNA, and
then RNA into proteins.
- Replication- making copies of genetic information.
- Transcription – conversion of DNA to RNA.
- Reverse Transcription – conversion of RNA to DNA;
viruses only .
- Translation – conversion of mRNA into a protein; protein
synthesis
GENES
- Nucleotide sequences that carry specific instructions for the cell,
usually for protein synthesis
- Smallest hereditary unit; smallest form of genetic information
passed from parent to offspring
- A single strand of DNA can carry multiple genes.
GENES: PROKARYOTES and EUKARYOTES
- In prokaryotes, the entire gene codes for a protein/molecule.
- In eukaryotes, the gene consists of coding (exons) and non-
coding (introns) regions.
supercoiling by introducing breaks to the DNA to relieve
stress
- Helicase – ‘unzips’ the double stranded DNA; breaks the
hydrogen bonds between base pairs
- Primase – synthesizes primers
 Primers are short RNA sequences that bind to
the parent DNA strand; serves as the jumping off
paint for DNA polymerase
- Clamp Protein – keeps DNA polymerase in place
- DNA Polymerase – synthesizes the new DNA strand; DNA
polymerase can only add nucleotides to an existing
nucleotide chain and cannot initiate replication, hence the
need for primers
- DNA Ligase - joins the Okazaki fragments in the lagging
strand
- Single-stranded Binding Proteins (SSB) –
stabilizes/protects the single stranded region of the DNA
during replication
LAGGING and LEADING STRAND
- DNA polymerase synthesizes the new strand by adding
nucleotides at the free 3’-hydroxyl group, and therefore the
new strand grows from 5’ to 3’.
- In the leading strand, which runs from 3’ to 5’, replication is
continuous.
- In the lagging strand, which runs from 5’ to 3’, replication is
discontinuous.

- Instead of one long strand of new DNA, the polymerase

makes use of several primers to make fragments of the
new DNA, called Okazaki fragments. These Okazaki
INTRONS and EXONS fragments are then joined together at the end of replication.
- Only 3% of human DNA actually codes for proteins, but
non-coding regions still play a role.
REPLICATION IN SUMMARY
1. OPENING OF DNA Acetylation of histone lysine
- Satellites are highly repetitive, non-coding DNA SUPERSTRUCTURE. residues weakens binding to
sequences; longer satellites provide structural stability to DNA, making DNA available
chromosomes. for interaction with enzymes.
- Mini-satellites and microsatellites are shorter repeats, DNA tends to super coil as
replication proceeds (think of
and are used to monitor mutations implicated in diseases, 2. DNA RELAXATION splitting yarn, where the more it
such as cancer. is split, the tighter the unsplit
portion becomes); DNA gyrase
prevents this.
DNA REPLICATION 3. DNA UNWINDING. Via helicase.
- Process by which DNA makes copies of itself.
4. PRIMER SYNTHESIS. Via primase.
- Occurs in a semi-conservative manner – DNA strands of
the parent DNA becomes the template for the daughter
strands. 5. DNA ELONGATION. Via DNA polymerase.
- Replication occurs on both strands of the DNA.
6. DNA LIGATION Primers are removed, Okazaki
- The strand running from 3’ to 5’ towards the fork is called fragments and any breaks in the
the leading strand. DNA are joined together via
- The strand running from 5’ to 3’ towards the fork is called DNA ligase.
the lagging strand.
- Begins at the origin of replication; a chromosome can
have multiple origins. DNA REPAIR: BASE EXCISION REPAIR
- Base Excision Repair (BER) involves the replacement of
an incorrect of damaged base with the correct nucleotide.
- The replication fork is where replication actively occurs.
 This requires the hydrolysis of the faulty base
from the sugar-phosphate backbone to form an
AP site (apurininc/apyrimidinic), followed by the
- The assembly of proteins that facilitate DNA replication is removal of the sugar-phosphate unit of the
called the replisome. incorrect nucleotide. DNA polymerase then
introduces the correct, and DNA ligase mends
the break to complete the repair.
THE REPLISOME
Panisigan
Far Eastern University — Institute of Health Sciences and Nursing (2023)
CENTRAL DOGMA
BIOCHEMISTRY LECTURE (Professor: Mr. Lawrence Adrian Tacliad)

- Only one base is removed, but depending on the DNA

polymerase used, it may result to a ‘short patch’ (only one
nucleotide is replaced) or a ‘long patch’ (more than one
nucleotide is replaced).

DNA REPAIR: NUCLEOTIDE EXCISION

- Nucleotide Excision Repair (NER) involves the
replacement of a stretch of bases with the correct
nucleotides.
- Similar in principle to BER, but NER removes a section of
the DNA strand instead of a single base and makes use of
a different DNA polymerase from BER.

GENE EXPRESSION: TRANSCRIPTION THE TERMINATOR REGION

- First step in gene expression, occurs in the nucleus - The terminator region is a string of nucleotides at the end
(eukaryotes). of a gene that signals RNA pol to transcription.

- Before transcription, DNA must first be unwound by

binding proteins.
- Helicase attaches to the unwound DNA to break the H-
bonds between base pairs.
- The transcription bubble is the opening in the double
helix where transcription takes place.
ELONGATION
- Template strand – DNA strand that is transcribed; also
- Elongation is the process of adding the appropriate
called (-) strand or antisense strand • Coding strand - DNA
strand that is NOT transcribed; also called (+) strand or complementary nucleotide as RNA pol moves downstream
sense strand . along the gene.

- RNA polymerase (RNA pol) – enzyme responsible for
RNA synthesis; there are three (3) types depending on the
RNA to be produced.
- RNA Pol II for mRNA
- RNA pol reads the DNA template from 3’ to 5’, and
therefore synthesizes RNA from 5’ to 3’.
TRANSCRIPTION
- Transcript is the general term used to refer to the product
of transcription.
- For mRNA, the initial transcript still contains all the introns
and unstranscribed regions, and is referred to as the pre-
mRNA.
- Pre-mRNA undergoes additional reactions before it can be
considered a fully functional mRNA, called the mature
mRNA.

- Recall that genes are DNA sequences that code for a POST-TRANSCRIPTION MODIFICATIONS
specific protein, or carry specific instructions for the body. - Pre-mRNA undergoes three processes before it becomes a
- Genes have coding (exons) and non-coding (introns) mature mRNA:
regions, and these make up the structural gene. - 5’ capping – addition of a methylated guanine group to the
- Genes also have the promoter and terminator regions, 5’ end of the transcript.
which make up the regulatory regions of the gene - 3’ polyadenylation – addition of several adenosine
residues to the 3’ end of the transcript, forming a poly(A)
tail.
THE PROMOTER REGION - RNA splicing – removal of the introns from the transcript
- The promoter region is where the RNA polymerase and joining of the exons.
initially binds, and is found several nucleotides upstream.
- ‘upstream’ means before the beginning of the transcription
- 5’ capping – protects the mRNA from exonucleases; aids in
site • ‘downstream’ means after the beginning of the
mRNA transport to the cytosol; allows for the initiation of
transcription site
translation
- RNA pols cannot recognize the promoter region on their
own, and require the help of transcription factors.
- The promoter also identifies which strand is the template.
- 3’ polyadenylation – protects the mRNA from exonucleases
The coding strand has no promoter region.
- Within the promoter region is the consensus sequence and - RNA splicing – leaves behind the exons that contains the code
the initiation signal. for the amino acids in a protein
- The consensus sequence identifies the precise nucleotide
at which transcription should begin, e.g. the TATA box. TRANSCRIPTION IN SUMMARY
- The initiation signal give RNA pol the signal when to start. 1. DNA UNWINDING Binding proteins and helicase
unwind and opens up DNA.

Panisigan
Far Eastern University — Institute of Health Sciences and Nursing (2023)
CENTRAL DOGMA
BIOCHEMISTRY LECTURE (Professor: Mr. Lawrence Adrian Tacliad)

RNA pol and transcription

factors recognize the promoter
2. INITIATION sequence and bind to DNA.
3. ELONGATION RNA pol reads the template
and synthesizes the pre-
mRNA.
4. TERMINATION. RNA pol recognizes the
terminator region, stops
transcription, and releases
itself from the template.
5. 5’CAPPING.
6. 3’POLYADENYLATION
- The start codon (AUG) also codes for Methionine

7. RNA SPLICING
- Stop codons are UAG, UGA, and UAA
- The genetic code is highly degenerate. This means there
are multiple codons for most amino acids.
- The degeneracy of the genetic code makes it less prone to
mutations.
- Degeneracy – multiple codons per amino acid
- The genetic code is universal
 Codons for humans are the same for other
GENE EXPRESSION: TRANSLATION organisms as well (with some exceptions)
- Synthesis of proteins from mature (spliced) mRNA  Codons are matched with anticodons in
- RNA-protein complexes called ribosomes are used corresponding transfer RNAs (tRNAs)

RIBOSOMES
- Has four rRNA (ribosomal RNA) molecules distributed in two
subunits
- Each subunit: 65% rRNA and 35% protein TRANSFER RNAS (tRNAS)
Anticodons

- The active site is in the ribosomal subunit - Complementary pairs of codons

- Each codon has a corresponding anticodon, therefore a
corresponding tRNA as well.
- rRNA is the active site
TRANSLATION IN SUMMARY
1. tRNA ACTIVATION tRNAs are “loaded” with their
- The predominance of rRNA at the active site gives it the corresponding amino acids.
impression of a ribozyme Ribosome detects start codon,
Met tRNA attaches to P site.
2. INITIATION
- The mRNA binds to the small subunit of the ribosome
3. ELONGATION - Bond between 1st and 2nd
Three sites in the ribosome: amino acid forms
- A site – “attachment site” for tRNAs
- First tRNA goes to E site and
exits ribosome
- P site – polypeptide formation site - At the same time, a new
charged tRNA goes to the A
- E site – “exit site” for tRNAs site
- Cycle repeats until stop codon
GENETIC CODE is encountered
4. TERMINATION - Ribosome detects stop
- The base sequence in mRNA determines the amino acid codon. The Release Factor
sequence in protein synthesis binds to the A site, opening the
ribosome and releasing the
- The base sequence of an mRNA molecule involves 4 newly synthesized polypeptide
different bases - A, C, G, and U

Codon:
- A three-nucleotide sequence in an mRNA molecule that
codes for a specific amino acid
- 64 codons in total
 Genetic code: The assignment of the 64 mRNA
codons to specific amino acids
 3 of the 64 codons are termination codons
(STOP codons)

Panisigan
Far Eastern University — Institute of Health Sciences and Nursing (2023)
CENTRAL DOGMA
BIOCHEMISTRY LECTURE (Professor: Mr. Lawrence Adrian Tacliad)

Panisigan