DNA’s Structure and Function -

Ch 10

Structure of DNA
The structure of DNA, or deoxyribonucleic acid, was discovered by James Watson
and Francis Crick in 1953. They proposed a double helix structure for DNA, which
consists of two strands that are twisted around each other like a twisted ladder.
The strands are made up of nucleotides, which are composed of a sugar molecule
(deoxyribose), a phosphate group, and a nitrogenous base.
The nitrogenous bases in DNA are adenine (A), thymine (T), cytosine (C), and
guanine (G). These bases form complementary base pairs, with A always pairing
with T and C always pairing with G. This pairing is held together by hydrogen
bonds.
The discovery of the structure of DNA was a groundbreaking achievement in the
field of biology. It provided a fundamental understanding of how genetic
information is stored and passed on from one generation to another. The structure
of DNA also laid the foundation for further advancements in genetics and
molecular biology, revolutionizing fields such as biotechnology and medicine.

Denaturation and Reannealing of DNA

Denaturing is the process of separating the double-stranded DNA molecule into
two individual strands. This can occur through various methods such as heating
or exposure to certain chemicals. Denaturation disrupts the hydrogen bonds
between the complementary base pairs, resulting in the separation of the strands.
Reannealing, on the other hand, is the process of bringing the separated DNA
strands back together to reform the double-stranded structure. This can happen
when the denatured DNA is slowly cooled or when the denaturing conditions are
reversed. The complementary base pairs(A-T) and (C-G) will then reform
hydrogen bonds, allowing the strands to reanneal.

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 Denaturing and reannealing processes are essential in various DNA-related
experiments and techniques, such as polymerase chain reaction (PCR) and DNA
hybridization. These processes enable the manipulation and analysis of DNA
strands, facilitating genetic research and various applications in biotechnology
and medicine.

DNA Replication
Replication of the DNA molecule is semi-conservative.

Which means that each parent strand serves as a template for a new strand
and that the two new DNA molecules each have one old and one new strand.

DNA Replication requires:

A strand of DNA serves as a template

Substrates - Deoxyribonucleoside Triphosphates

It begins with an enzyme Helicase - binds to the DNA and separate the 2
strands of DNA, forming a replication bubble.

Another enzyme, DNA polymerase incorporates DNA nucleotides into the

new DNA strand. Nucleotides enter each position acc to base pairing
rules: A - T and C - G.

In prokaryotes, this process begins in only one site called origin of

replication. However in eukaryotes, the replication starts at several places
at the same time.

Genotype can be defined as an organism’s genetic makeup, the sequence of

nucleotide bases in DNA.

Phenotype is defined as the organism’s physical traits.

Replication is highly accurate and error can occur one for every 2 x 10^9
nucleotides which is negligible.

DNA polymerase corrects all these errors.

Transcription and Translation

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 1. Transcription: The transfer of genetic information from DNA into an RNA
molecule.

2. Translation: The transfer of information of RNA into a protein.

Genetic Code
The genetic code is the set of rules by which information encoded in DNA or RNA
is translated into proteins. It is a triplet code, meaning that three nucleotides,
known as codons, specify each amino acid in a protein sequence.
The nitrogenous bases adenine (A), guanine (G), cytosine (C), and thymine (T)
play a crucial role in the genetic code. These bases form codons, with each codon
consisting of three consecutive bases. For example, the codon AAA represents
the amino acid lysine, while the codon GGC represents the amino acid glycine.
Adenine pairs with thymine (A-T), and guanine pairs with cytosine (G-C) in DNA. In
RNA, thymine is replaced by uracil (U), so adenine pairs with uracil (A-U). These
base pairings ensure that the genetic information is accurately transcribed and
translated.
The codons formed by the nitrogenous bases in DNA and RNA determine the
sequence of amino acids in a protein. There are 64 possible codons, including
start and stop codons. Start codons (such as AUG) signal the initiation of protein
synthesis, while stop codons (such as UAA, UAG, and UGA) signal the termination
of protein synthesis.
Here are the images showing the codons corresponding to each amino acid:

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 Three Stages of RNA Transcription
The process of RNA transcription involves three main stages: initiation, elongation,
and termination.

1. Initiation: In the initiation stage, RNA polymerase, an enzyme responsible for

synthesizing RNA, binds to a specific region of DNA called the promoter. The
promoter acts as a signal to indicate the start of a gene. Once RNA
polymerase is bound to the promoter, it begins to unwind the DNA double
helix, exposing the template strand.

2. Elongation: During the elongation stage, RNA polymerase moves along the
template strand of DNA, synthesizing a complementary RNA molecule. As it
moves, RNA polymerase adds nucleotides to the growing RNA chain, following
the base-pairing rules (A-U, C-G). As the RNA polymerase moves forward, the
DNA double helix re-forms behind it.

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 3. Termination: The termination stage marks the end of RNA transcription. In this
stage, a termination signal is reached on the DNA template strand. This signal
causes RNA polymerase to detach from the DNA template, and the newly
synthesized RNA molecule is released. The DNA double helix reforms
completely, and the RNA molecule undergoes further processing before it can
be used for protein synthesis.

The three stages of RNA transcription are crucial for the synthesis of RNA
molecules from DNA templates. This process plays a vital role in gene expression
and the production of proteins in cells.

Exons and introns are regions of DNA that play a role in gene expression and RNA
processing.

Exons are the coding regions of a gene that contain the instructions for producing
a protein. They are transcribed from DNA into RNA and remain in the final RNA
molecule after processing. Exons are crucial for protein synthesis as they provide
the necessary information for the production of functional proteins.

Introns, on the other hand, are non-coding regions of the gene that are
transcribed from DNA into RNA but are removed during RNA processing. Introns
do not contain instructions for protein synthesis and were once considered "junk
DNA." However, recent research has shown that introns may have regulatory
functions and play a role in gene regulation and alternative splicing.

During RNA processing, introns are spliced out from the RNA molecule, and exons
are joined together to form the mature RNA transcript. This process, known as
splicing, allows for the production of different protein isoforms from a single gene
by combining exons in different ways.

The presence of exons and introns in genes contributes to the complexity and
diversity of gene expression in organisms. It allows for the generation of multiple
protein variants and adds an additional layer of regulation to gene expression.

Processing of Eukaryotic RNA

Transcription: The process of copying DNA sequence into a complementary
RNA sequence by RNA polymerase.

RNA Splicing: Removal of non-coding introns and joining of coding exons in

pre-mRNA to produce mature mRNA.

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 5' Capping: Addition of a modified guanine nucleotide to the 5' end of the
mRNA, which helps in mRNA stability and translation.

3' Polyadenylation or Tailing: Addition of a poly-A tail (a sequence of adenine

nucleotides) to the 3' end of the mRNA, which is important for stability and
export of mRNA from the nucleus.

RNA Editing: Post-transcriptional alteration of the nucleotide sequence of RNA

molecules, such as the deamination of adenosine to inosine, which can lead to
codon changes.

Translation:
Initiation:
An mRNA molecule binds to a small ribosomal subunit. A special initiator tRNA
then binds
to the start codon, where translation is to begin on the mRNA. The initiator tRNA
carries the amino acid methionine (Met); its anticodon, UAC, binds to the start
codon, AUG . A large ribosomal subunit binds to the small one, creating a
functional ribosome. The initiator tRNA fits into the P site on the ribosome.

Elongation:
The anticodon of an incoming tRNA molecule, carrying its amino acid, pairs with
the mRNA codon in the A site of the ribosome. The polypeptide leaves the tRNA in
the P site and attaches to the amino acid on the tRNA in the A site. The ribosome
creates a new peptide bond. Now the chain has one more amino acid. The P site
tRNA now leaves the ribosome, and the ribosome moves the remaining tRNA,
carrying the growing polypeptide, to the P site. The mRNA and tRNA move as a
unit. This movement brings into the A site the next mRNA codon to be translated,
and the process can start again with step 1.

Termination:
Elongation continues until a stop codon reaches the ribosome’s A site. Stop
codons—UAA, UAG, and UGA do not code for amino acids but instead tell
translation to stop. The completed polypeptide, typically several hundred amino
acids long, is freed, and the ribosome splits back into its subunits

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 Mutations:
Any change in the nucleotide sequence of DNA.

Mutations can change the amino acid in a protein.

Mutations can involve:

large regions of chromosomes.

a single nucleotide pair.

Types of mutations:

Nucleotide Substitutions:

A substitution is the replacement of one nucleotide and its base-

pairing partner
with another nucleotide pair.

Some substitution mutations have no effect at all. For example, if a

mutation causes an mRNA codon to change from GAA to GAG, no
change in the protein product would result because GAA and GAG both
code for the same amino acid (Glu). Such a change is called a silent
mutation.

Nonsense mutations, change an amino acid codon into a stop codon.

For example, if an AGA (Arg) codon is mutated to a UGA (stop) codon,
the result will be a prematurely terminated protein.

Nucleotide Insertions or Deletions:

Mutations may result from:

Errors in DNA replication or recombination.

Physical or Chemical agents called mutagens.

Mutations:

are often harmful but also useful in nature as a source of genetic diversity,
which makes evolution by natural selection possible and useful in the
laboratory.

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 RNA proccessing:
1. Introduction to RNA Processing

RNA processing refers to the modification and maturation of primary RNA

transcripts into mature RNA molecules.

It occurs in the nucleus of eukaryotic cells before the mature RNA is

transported to the cytoplasm for translation.

2. Types of RNA Processing

a.
Capping: Addition of a 5' cap consisting of a modified guanine nucleotide to
protect the RNA from degradation and assist in ribosome binding.
b.
Splicing: Removal of introns and joining of exons to produce a mature mRNA
molecule.
c.
Polyadenylation: Addition of a poly-A tail to the 3' end of the RNA, which aids in
stability and transport.
3. RNA Splicing

Pre-mRNA undergoes splicing to remove non-coding introns and join together

the coding exons.

This process is carried out by the spliceosome, a complex of RNA and protein
that recognizes splice sites and catalyzes the splicing reactions.

4. Importance of RNA Processing

Proper RNA processing is crucial for gene expression regulation and protein
production.

Errors in RNA processing can lead to genetic disorders and diseases.

5. Regulation of RNA Processing

Alternative splicing allows a single gene to code for multiple protein isoforms,
increasing genetic diversity and specialization of cell functions.

RNA processing is subject to regulation by various cellular factors and

signaling pathways.

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 6. Conclusion

Understanding RNA processing is essential for comprehending gene

expression and molecular biology.

Continued research in this field holds promise for potential therapeutic

interventions.

. Introduction to RNA Stability

RNA stability refers to the lifespan of RNA molecules within a cell before they
are degraded.

It is a crucial factor in determining the abundance and functionality of specific

RNA transcripts.

The lifespan of an mRNA decides how much of a protein is made.

2. Factors Affecting RNA Stability

a.
RNA Structure: The secondary and tertiary structure of RNA can influence its
stability. Stem-loop structures, for example, can protect RNA from degradation.
b.
RNA Modifications: Chemical modifications, such as methylation and
pseudouridylation, can impact RNA stability and degradation rates.
c.
RNA Binding Proteins: Interactions with RNA-binding proteins can either stabilize
or destabilize RNA molecules.
d.
RNA Decay Pathways: Cells employ various mechanisms, such as the exosome
and RNA interference pathways, to degrade unwanted RNA.
3. Mechanisms of RNA Degradation
a.
3' to 5' Exonuclease Degradation: Many RNA molecules are degraded by
exonucleases starting from the 3' end.
b.
Decay Pathways: Different types of RNA, such as mRNA, rRNA, tRNA, and
noncoding RNA, are subject to distinct decay pathways.
4. Regulation of RNA Stability

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 Cells regulate RNA stability as a means of controlling gene expression and
response to environmental changes.

Regulatory elements within the RNA molecule and specific RNA-binding

proteins can influence its stability.

5. Importance of RNA Stability

Proper regulation of RNA stability is crucial for maintaining cellular

homeostasis and responding to developmental and environmental cues.

Dysregulation of RNA stability has been implicated in various diseases,

including cancer and neurodegenerative disorders.

6. Conclusion

Understanding RNA stability is essential for comprehending gene expression

regulation and the dynamic nature of the cellular transcriptome.

Research in RNA stability opens avenues for potential therapeutic

interventions and drug development.

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