Education

1. CHM043 GENERAL BIOCHEMISTRY
Structure of
DNA and RNA

2. The 3-dimensional double
helix structure of DNA,
correctly elucidated by James
Watson and Francis Crick.
Complementary bases are
held together as a pair by
hydrogen bonds.
Structure of DNA

3. STRUCTURE OF RNA
Ribonucleic acid (RNA) is a molecule
that is present in the majority of living
organisms and viruses.
It is made up of nucleotides, which are
ribose sugars attached to nitrogenous
bases and phosphate groups. The
nitrogenous bases include adenine,
guanine, uracil, and cytosine. RNA
mostly exists in the single-stranded
form, but there are special RNA viruses
that are double-stranded

4. STRUCTURES OF DNA AND RNA
In both DNA and RNA, the primary structure refers to the
linear sequence of nucleotides.
a. Primary Structure

5. STRUCTURES OF DNA AND RNA
b. Secondary Structure
DNA Secondary Structure:
DNA's secondary structure primarily involves the double helix.
The two DNA strands are complementary and anti-parallel, meaning they run in
opposite directions.
Adenine (A) forms hydrogen bonds with thymine (T), and guanine (G) pairs with
cytosine (C), resulting in stable base pairs along the helix.
RNA Secondary Structure:
RNA's secondary structure can vary, but it often forms hairpin loops and stem-loop
structures due to intra-strand base pairing.
Like DNA, RNA strands can also form base pairs (A-U and G-C) within the same
strand, leading to secondary structures such as hairpins and loops.

6. STRUCTURES OF DNA AND RNA
DNA Higher-Order Structure:
DNA is packaged into chromatin, which further condenses into chromosomes during
cell division.
The higher-order structure of DNA involves interactions with histone proteins and
other regulatory proteins, influencing gene expression and accessibility of genetic
information.
RNA Higher-Order Structure:
RNA molecules can fold into complex three-dimensional structures due to
interactions between complementary bases and other molecular forces.
The higher-order structure of RNA is crucial for its various functions, including roles in
protein synthesis (e.g., ribosomal RNA, transfer RNA) and regulatory functions (e.g.,
microRNAs, long non-coding RNAs).
c. Higher-Order Structure

7. Different Classes of RNA
This type of RNA functions by
transferring the genetic material
into the ribosomes and pass the
instructions about the type of
proteins, required by the body cells.
Based on the functions, these types
of RNA is called the messenger
RNA. Therefore, the mRNA plays a
vital role in the process of
transcription or during the protein
synthesis process.
Messenger RNA, mRNA Ribosomal RNA, rRNA
The rRNA is the component of
the ribosome and are located
within the in the cytoplasm of a
cell, where ribosomes are found.
In all living cells, the ribosomal
RNA plays a fundamental role in
the synthesis and translation of
mRNA into proteins. The rRNA is
mainly composed of cellular RNA
and are the most predominant
RNA within the cells of all living
beings.

8. tRNA is the smallest of the 3 types of RNA,
possessing around 75-95 nucleotides. tRNAs
are an essential component of translation,
where their main function is the transfer of
amino acids during protein synthesis.
tRNAs have a cloverleaf structure which is
stabilized by strong hydrogen bonds
between the nucleotides. They normally
contain some unusual bases in addition to
the usual 4, which are formed by methylation
of the usual bases. Methyl guanine and
methylcytosine are two examples of
methylated bases.
Transfer RNA, tRNA

9. DNA REPLICATION

10. DNA DNA
REPLICATION
is the biological process of
producing two identical
replicas of DNA from one
original DNA molecule.
requires the presence of a starting site
called a template, a primer, the four
deoxyribonucleotides (dATP, dGTP,
dCTP, dTTP)
the mechanics of DNA replication were originally
characterized in the bacterium E. coli, contains three
distinct enzymes capable of catalyzing the replication
of DNA. Identified as DNA polymerase I, II, III.
it occurs in all living
organisms acting as the
most essential part of
biological inheritance.

11. DNA Polymerases are a group of enzymes that catalyzes
the synthesis of DNA during replication.
DNA POLYMERASE
The main function od DNA polymerase is to duplicate the
DNA content of a cell during cell division. They do so by
adding nucleotides at 3' -OH group of the growing DNA
stand.

12. DNA Polymerase I is coded by polA gene. It is a single polypeptide and
has a role in recombination and repair. It has both 5’→3’ and 3’→5’
exonuclease activity. DNA polymerase Ⅰremoves the RNA primer from
lagging strand by 5’→3’ exonuclease activity and also fills the gap.
DNA Polymerase II is coded by polB gene. It is made up of 7 subunits. Its
main role is in repair and also a backup of DNA polymerase III. It has
3’→5’ exonuclease activity.
DNA Polymerase III is the main enzyme for replication in E.coli. It is
coded by polC gene. The polymerization and processivity rate is
maximum in DNA polymerase III. It also has proofreading 3’→5’
exonuclease activity.

13. Steps in DNA Replication

14. Initiation: DNA replication starts at specific sites called origins of
replication. Enzymes called helicases unwind and separate the
DNA strands, creating a replication bubble.
How is DNA Replicated?
Unwinding: Single-strand binding proteins (SSBPs) bind to the
separated DNA strands to keep them from rejoining and
stabilizing the single-stranded DNA.
Priming: Primase synthesizes RNA primers complementary to the
DNA template. These primers provide a starting point for DNA
polymerase to begin synthesis.

15. Elongation: DNA polymerase III adds nucleotides to the growing
DNA strand in a 5' to 3' direction. The leading strand is synthesized
continuously in the direction of the replication fork, while the
lagging strand is synthesized discontinuously in short segments
called Okazaki fragments.
How is DNA Replicated?
Okazaki Fragment Processing: DNA polymerase I removes the RNA
primers and replaces them with DNA nucleotides. DNA ligase then
joins the Okazaki fragments together, creating a continuous
lagging strand.
Termination: DNA replication continues bidirectionally until the
entire DNA molecule is replicated. The process terminates when
replication forks from adjacent origins meet.

17. How can DNA polymerase copy both strands of DNA in the 5' to 3' direction
simultaneously?
DNA polymerase is an enzyme responsible for synthesizing new DNA strands
during DNA replication. It can copy both strands of DNA simultaneously
because of the antiparallel nature of DNA strands and the different
mechanisms used for leading and lagging strand synthesis.
Leading Strand Synthesis:
The leading strand is synthesized continuously in the 5' to 3'
direction, which is the same direction as the movement of the
replication fork.
DNA polymerase III synthesizes the leading strand by continuously
adding nucleotides in the 5' to 3' direction as the replication fork
opens up.

18. How can DNA polymerase copy both strands of DNA in the 5' to 3' direction
simultaneously?
Lagging Strand Synthesis:
The lagging strand is synthesized discontinuously in short
fragments called Okazaki fragments.
Primase synthesizes RNA primers along the lagging strand
template at intervals.
DNA polymerase III then synthesizes short segments of DNA
(Okazaki fragments) in the 5' to 3' direction, away from the
replication fork.
As the replication fork progresses, DNA polymerase III synthesizes
new Okazaki fragments, following the movement of the fork.

19. How can DNA polymerase copy both strands of DNA in the 5' to 3' direction
simultaneously?
The key to simultaneous synthesis is that while one strand is
synthesized continuously (leading strand), the other strand is
synthesized in short segments (lagging strand). DNA polymerase III,
along with other proteins and enzymes, coordinates these activities to
ensure efficient and accurate DNA replication.

20. Repair of DNA

21. DNA repair ensures the survival of a species by enabling
parental DNA to be inherited as faithfully as possible by
offspring. It also preserves the health of an individual.
Mutations in the genetic code can lead to cancer and other
genetic diseases.
Repair of DNA

22. Repair of DNA
There are several mechanisms cells use to repair damaged DNA:
Direct Reversal: This mechanism involves the direct reversal of DNA damage
without cutting out any nucleotides. For example, photolyase can repair UV-
induced thymine dimers by using light energy to break the dimer bond.
Base Excision Repair (BER): BER is used to repair small, non-helix-
distorting lesions such as damaged or incorrect bases, or single-strand
breaks. It involves the following steps:
A DNA glycosylase recognizes and removes the damaged base,
creating an apurinic/apyrimidinic (AP) site.
AP endonuclease cleaves the DNA backbone at the AP site.
DNA polymerase fills in the gap with the correct nucleotides.
DNA ligase seals the nick in the DNA backbone.

23. Repair of DNA
There are several mechanisms cells use to repair damaged DNA:
Nucleotide Excision Repair (NER): NER deals with a wide range of
DNA lesions, including bulky lesions caused by UV radiation or
chemical agents. The steps involved in NER are:
Recognition of the damaged DNA region by a complex of
proteins (XPC-HR23B in global genome NER or RNA
polymerase II in transcription-coupled NER).
Excision of a stretch of nucleotides containing the damaged
site by endonucleases (XPF-ERCC1 and XPG).
DNA polymerase fills in the gap, and DNA ligase seals the nick.

24. Repair of DNA
There are several mechanisms cells use to repair damaged DNA:
Mismatch Repair (MMR): MMR corrects errors that occur
during DNA replication and escape the proofreading activity
of DNA polymerases. The steps include:
Recognition of mismatched base pairs by MMR proteins.
Excision of the incorrect nucleotide-containing strand.
Resynthesis of the excised segment by DNA polymerase.
DNA ligase seals the nick.

25. Repair of DNA
There are several mechanisms cells use to repair damaged DNA:
Double-Strand Break Repair (DSBR): DSBR mechanisms
repair breaks that affect both strands of the DNA helix. Two
main DSBR mechanisms are:
Non-homologous End Joining (NHEJ): Joins broken DNA
ends together, often leading to the loss or addition of
nucleotides at the repair site.
Homologous Recombination (HR): Uses an undamaged
homologous DNA sequence as a template to repair the
broken strand accurately.