MOLECULAR BIOLOGY NOTES FOR FINALS

Dna Methylation :

DNA methylation is a chemical modification of DNA that involves

the addition of a methyl group (-CH3) to cytosine residues within
the genome. This modification is catalyzed by enzymes called
DNA methyltransferases, which transfer a methyl group from S-
adenosylmethionine (SAM) to the cytosine base of the DNA
molecule. DNA methylation is an important mechanism for
regulating gene expression and has been implicated in a variety
of biological processes, including development, aging, and cancer.

DNA methylation occurs at cytosine residues that are followed by

a guanine base, forming a CpG dinucleotide. CpG dinucleotides
are relatively rare in the genome, occurring at a frequency of
about 5%. However, certain regions of the genome, known as
CpG islands, have a high density of CpG dinucleotides and are
often associated with the promoter regions of genes. DNA
methylation at CpG islands can regulate gene expression by
preventing the binding of transcription factors and other
regulatory proteins to the promoter region.
There are several types of DNA methylation, including

Symmetrical methylation which occurs when both strands of the

DNA molecule are methylated

Asymmetrical methylation which occurs when only one strand is

methylated.

DNA methylation patterns are dynamic and can be influenced by

environmental factors, such as diet and stress. DNA methylation
is reversible, and the process of removing methyl groups from
cytosine residues is called demethylation. Demethylation can be
mediated by enzymes called DNA demethylases, which remove
the methyl group and leave the cytosine base unmodified. DNA
demethylation is an important process in development, as it
allows cells to switch between different gene expression
programs in response to changing environments.

DNA methylation has also been linked to a variety of diseases,

including cancer. In cancer cells, DNA methylation patterns are
often abnormal, with either too much or too little methylation at
specific genes. This abnormal methylation can lead to abnormal
gene expression and contribute to the development and
progression of cancer. In addition, DNA methylation has been
used as a therapeutic target in cancer, with drugs that inhibit
DNA methylation or demethylation being developed to treat
cancer.

Transposable Elements :

Transposable elements, also known as transposons or jumping

genes, are sequences of DNA that can move or "jump" from one
location in the genome to another. Transposable elements make
up a significant portion of the genome in many organisms,
including humans, and have been found to play important roles in
the evolution and regulation of gene expression.
Inverted repeats are short DNA sequences that can be found at
the ends of some transposable elements. Inverted repeats are
characterized by the presence of two copies of the same DNA
sequence that are oriented in the opposite direction. Inverted
repeats are thought to play a role in the movement of
transposable elements through a process called transposase-
mediated transposition. Transposase is an enzyme that
recognizes the inverted repeats at the ends of the transposable
element and catalyzes the movement of the transposable element
within the genome.

Direct repeats are characterized by the presence of two copies of

the same DNA sequence that are oriented in the same direction.
Direct repeats can be found at the ends of some transposable
elements and are thought to play a role in the movement of the
transposable elements.

There are several types of transposable elements: Insertion

Sequence, Retrotransposons and DNA transposons.

Insertion sequences (IS) are small pieces of DNA that can move
or "jump" within the genome of an organism. Insertion sequences
are typically a few hundred nucleotides in size and contain only a
few genes, such as those encoding transposase enzymes and
regulatory proteins.

Retrotransposons are transposable elements that are able to

replicate themselves using an RNA intermediate.
Retrotransposons can be classified into two main types: long
terminal repeat (LTR) retrotransposons and non-LTR
retrotransposons. LTR retrotransposons contain long terminal
repeat sequences at their ends, which are involved in the
replication and integration of the retrotransposon into the
genome. Non-LTR retrotransposons do not contain long terminal
repeat sequences.

DNA transposons are larger pieces of DNA that can move within
the genome of an organism. Transposons can contain a variety of
genes, including those encoding enzymes and regulatory proteins,
as well as other functional genetic elements. Transposons can be
classified into two main types: class I transposons and class II
transposons. Class I transposons are able to replicate themselves
using a mechanism called "cut and paste," in which the
transposon is cut out of one location in the genome and pasted
into a new location. Class II transposons are able to replicate
themselves using a mechanism called "copy and paste," in which
the transposon is copied and the copy is pasted into a new
location.

Transposable elements can be classified into two categories

based on their mode of transposition: conservative transposons
and replicative transposons.

Conservative transposons do not make a copy of themselves

during transposition, meaning that the original transposon is lost
from its original location.

Replicative transposons, on the other hand, make a copy of

themselves and leave a copy behind at the original location,
resulting in multiple copies of the transposon in the genome.

Transposable elements can move within and between genomes

through a process called transposition.

There are two main methods are identified for Transposition :

Simple transposition is a type of transposition that involves the

movement of a transposable element within or between genomes.
Simple transposition is mediated by an enzyme called transposase,
which recognizes the direct repeats at the ends of the
transposable element and catalyzes the movement of the
transposable element within the genome. Simple transposition
can occur through cut-and-paste mechanism.Cut-and-paste
transposition involves the excision of the transposable element
from one location in the genome and its insertion into a new
location.

Replicative transposition is a type of transposition that involves

the movement of a transposable element within or between
genomes through a replicative mechanism.Replicative
transposition is mediated by an enzyme called transposase, which
recognizes the ends of the transposable element and catalyzes
the synthesis of a DNA copy of the transposable element. The
DNA copy is then inserted into a new location in the genome
through a copy-and-paste mechanism, which involves the
creation of a double-stranded break at the site of insertion. This
process can result in the disruption of the genes located at the
site of insertion.

Transposable elements can have a variety of effects on the

genome and gene expression. For example, transposons can
disrupt the function of genes by inserting themselves into the
coding region of a gene, or they can alter gene expression by
inserting themselves into regulatory regions of the genome.
Transposons can also cause genome instability by disrupting the
structure of the genome and leading to the formation of
chromosomal rearrangements.

Despite the potential negative effects of transposable elements

on the genome, they have also been found to play important
roles in evolution. Transposons can introduce new genetic
variation into a population, which can be beneficial in some cases.
Additionally, transposons can help to regulate gene expression by
providing binding sites for regulatory proteins or by altering the
structure of the genome.
Translation :

Translation is the process by which the genetic code, or sequence

of nucleotides in DNA or RNA, is decoded and used to synthesize
functional proteins. Translation occurs in cells and is an essential
part of the process of gene expression.

Translation begins with the transcription of DNA into RNA, which

is then transported out of the nucleus and into the cytoplasm. In
the cytoplasm, translation takes place on ribosomes, which are
complex macromolecular structures composed of ribosomal RNA
(rRNA) and proteins.

Translation occurs in three main stages: initiation, elongation, and

termination.

Initiation is the first step in translation process, and involves the

binding of the ribosome to the mRNA molecule, as well as the
recruitment of the tRNA (charged with the correct amino acid) to
the ribosome. The initiation of translation is initiated by the small
ribosomal subunit, which recognizes the start codon (usually AUG)
in the mRNA and binds to it.

Once the ribosome is bound to the mRNA, translation enters the

elongation phase. During elongation, the ribosome moves along
the mRNA molecule, adding one amino acid at a time to the
growing protein chain. This process is facilitated by the enzyme
ribosome-associated synthase, which catalyzes the transfer of
each amino acid from its corresponding tRNA molecule to the
growing protein chain.

Finally, translation reaches the termination stage when the

ribosome encounters a stop codon on the mRNA molecule. Stop
codons are special sequences of nucleotides that signal the end of
translation. Upon encountering a stop codon, the ribosome
releases the completed protein and dissociates from the mRNA
molecule. There are three stop codons in the genetic code: UAG,
UGA, and UAA. These codons are recognized by release factors,
which are proteins that bind to the ribosome and facilitate the
release of the newly synthesized protein.

Translation is a highly regulated process, and a variety of factors

can affect the efficiency and accuracy of translation. These
factors include the concentration of mRNA, ribosomes, and amino
acids, as well as the presence of regulatory proteins that can bind
to the mRNA and affect its translation. Translation is also subject
to errors, which can result in the synthesis of non-functional or
misfolded proteins.
Post-Translational Modification :

Post-translational modification (PTM) refers to a variety of

chemical modifications that can occur to proteins after they have
been synthesized by translation. PTMs are a key mechanism for
regulating protein function and can involve the addition or
removal of various chemical groups, such as acetyl groups,
phosphate groups, or methyl groups. PTMs can also involve the
modification of specific amino acids within the protein, such as
the addition of a hydroxyl group to a proline residue or the
addition of a carboxyl group to an aspartate residue.

There are several different types of PTMs that can occur,

including phosphorylation, acetylation, methylation, ubiquitination,
and sumoylation and Glycosylation.

Phosphorylation involves the addition of a phosphate group to a

protein, which can alter the protein's activity or stability.

Acetylation involves the addition of an acetyl group to a protein,

which can affect the protein's interaction with other molecules or
alter its activity.

Methylation involves the addition of a methyl group to a protein,

which can alter the protein's activity or stability.

Ubiquitination involves the attachment of a ubiquitin molecule to

a protein, which can target the protein for degradation by the
proteasome.

Sumoylation involves the attachment of a small protein called

SUMO to a protein, which can alter the protein's activity or
stability.
Glycosylation involves the addition of carbohydrate groups to the
protein, which can affect its stability or function.

PTMs can occur at specific sites within the protein or can be

distributed randomly along the protein's length. PTMs can be
reversible or irreversible, depending on the specific modification
and the enzymes involved in the modification process.

PTMs play important roles in a variety of cellular processes,

including signaling pathways, protein folding and stability, and
gene expression. Abnormal PTMs have been linked to a variety of
diseases, including cancer, neurodegenerative disorders, and
cardiovascular disease. In cancer, for example, abnormal PTMs
have been observed in a variety of proteins, including signaling
proteins, enzymes, and structural proteins. These abnormal PTMs
can contribute to the development and progression of cancer by
altering the activity or stability of the affected proteins.

The study of PTMs is an important area of research in the field of

molecular biology, and the identification and characterization of
PTMs can provide important insights into the mechanisms of
protein function and regulation.
Rna Editing/Processing :

RNA Editing :

RNA editing is a process by which specific nucleotide residues

within an RNA molecule are modified after the RNA has been
synthesized by transcription. RNA editing can involve the addition
or deletion of nucleotides, as well as the substitution of one
nucleotide for another. RNA editing can occur in a variety of RNA
molecules, including mRNA, rRNA, and tRNA, and can have a
variety of effects on the structure and function of the RNA
molecule.

There are several different mechanisms of RNA editing, including

A-to-I editing, C-to-U editing, and G-to-A editing. A-to-I editing
involves the conversion of an adenine nucleotide to an inosine
nucleotide, which can alter the coding potential of the RNA
molecule. C-to-U editing involves the conversion of a cytosine
nucleotide to a uracil nucleotide, which can alter the structure of
the RNA molecule. G-to-A editing involves the conversion of a
guanine nucleotide to an adenine nucleotide, which can alter the
coding potential of the RNA molecule.

RNA Processing :

RNA processing is the series of chemical modifications that occur

to RNA molecules after they have been synthesized by
transcription. RNA processing plays a key role in the regulation of
gene expression and the production of functional RNA molecules.

There are several steps of RNA processing, including capping,

splicing, and polyadenylation.

Capping involves the addition of a modified guanine nucleotide to

the 5' end of the RNA molecule, which helps to protect the RNA
from degradation Capping is mediated by Capping enzymes which
can recognize the 5' end of the RNA molecule and catalyze the
addition of the modified guanine nucleotide. The modified
guanine nucleotide is usually a 7-methylguanosine triphosphate,
which is added to the 5' end of the RNA molecule through a 5'-5'-
triphosphate linkage.

Splicing involves the removal of non-coding introns from the RNA

molecule and the splicing together of the coding exons. Splicing is
mediated by small RNA molecules called spliceosomes, which
recognize specific sequences within the RNA molecule and
catalyze the removal of the introns. Splicing is a highly regulated
process, and a variety of factors can influence the efficiency and
accuracy of splicing. These factors include the presence of
regulatory proteins and enzymes, as well as the sequence and
structure of the RNA molecule itself.

Polyadenylation involves the addition of a string of adenine

nucleotides, known as a poly(A) tail, to the 3' end of the RNA
molecule. Polyadenylation is mediated by enzymes called
polyadenylate polymerases, which can recognize specific
sequences within the RNA molecule and catalyze the addition of
the poly(A) tail. This process helps to protect the RNA from
degradation and can also help to regulate its stability and
transport.

RNA processing can be regulated at various stages of the process,

and a variety of factors can influence the efficiency and accuracy
of RNA processing. These factors include the presence of
regulatory proteins and enzymes, as well as the sequence and
structure of the RNA molecule itself.

RNA processing is an important mechanism for regulating gene

expression and is essential for the production of functional RNA
molecules. Abnormal RNA processing has been linked to a variety
of diseases, including cancer and neurological disorders. The
study of RNA processing is an important area of research in the
field of molecular biology, and the identification and
characterization of RNA processing pathways can provide
important insights into the mechanisms of gene expression and
regulation.
 RNA EDITING

RNA PROCESSING
Mutation :

A mutation is a change in the sequence of nucleotides within a

DNA molecule. Mutations can occur spontaneously or can be
induced by environmental factors, such as radiation or chemical
exposure. Mutations can have a variety of effects on the structure
and function of the DNA molecule, and can result in changes in
the expression of the genes encoded by the DNA.

There are several different types of mutations, including point

mutations, insertion mutations, deletion mutations, and
chromosomal rearrangements.

A point mutation is a single nucleotide substitution within a DNA

molecule. Point mutations can result in the substitution of one
amino acid for another within the protein encoded by the DNA,
which can alter the protein's structure and function. Point
mutations can have a variety of effects on the organism in which
they occur, depending on the specific mutation and the gene in
which it occurs. Some point mutations may have no effect on the
organism, while others may cause a change in the function or
expression of a gene. In some cases, point mutations can lead to
the development of diseases, such as cancer.
There are several different types of point mutations, including
missense mutations, nonsense mutations, and silent mutations.

A missense mutation is a point mutation that results in the

substitution of one amino acid for another within the protein
encoded by the DNA.

A nonsense mutation is a point mutation that results in the

substitution of a stop codon for a coding codon, which can
prematurely terminate the synthesis of the protein and result in
the production of a truncated protein.

A silent mutation is a point mutation that does not result in a

change in the amino acid sequence of the protein, but may still
affect the protein's structure or function.

Point mutations can occur spontaneously or can be induced by

environmental factors, such as radiation or chemical exposure.

An insertion mutation is a type of mutation that involves the

addition of one or more nucleotides to the DNA molecule.
Insertion mutations can result in the insertion of one or more
amino acids into the protein encoded by the DNA, which can alter
the protein's structure and function. Insertion mutations can have
a variety of effects on the organism in which they occur,
depending on the specific mutation and the gene in which it
occurs. Some insertion mutations may have no effect on the
organism, while others may cause a change in the function or
expression of a gene. In some cases, insertion mutations can lead
to the development of diseases, such as cancer.

A deletion mutation is a type of mutation that involves the

removal of one or more nucleotides from the DNA molecule.
Deletion mutations can result in the deletion of one or more
amino acids from the protein encoded by the DNA, which can
alter the protein's structure and function.

A chromosomal rearrangement is a type of mutation that involves

the rearrangement of large segments of DNA within the genome.
Chromosomal rearrangements can involve the exchange of DNA
between chromosomes, the duplication or deletion of genetic
material, or the inversion of a chromosomal segment.
Chromosomal rearrangements can have a variety of effects on
the organism in which they occur, depending on the specific
rearrangement and the genes affected by the rearrangement.
Chromosomal rearrangements can lead to the development of
genetic disorders, such as Down syndrome or Turner syndrome,
or can contribute to the development of cancer.
The study of mutations is an important area of research in the
field of molecular biology, and the identification and
characterization of mutations can provide important insights into
the mechanisms of gene expression and regulation. Mutations can
also be used as a tool in genetic engineering, allowing
researchers to alter the genes of an organism in order to study
their function or to create new genetically modified organisms.
Lac Operon (E.Coli) :

The lac operon is a genetic regulatory system that controls the

expression of genes involved in the metabolism of lactose in
Escherichia coli bacteria. The lac operon consists of three
structural genes (lacZ, lacY, and lacA) and a regulatory region
known as the operator (O).

The lacZ gene encodes an enzyme called beta-galactosidase,

which catalyzes the breakdown of lactose into glucose and
galactose.

The lacY gene codes for the protein lactose permease, which is
an integral membrane protein that is responsible for the transport
of lactose into the cell.

The lacA gene encodes an enzyme called galactoside

acetyltransferase, which is involved in the synthesis of an
intermediate molecule called galactoside acetyl-CoA.

The expression of the lac operon is regulated by the presence of

lactose and the repressor protein encoded by the lacI gene. In
the absence of lactose, the lac repressor protein binds to the
operator region of the lac operon, preventing transcription of the
structural genes. In the presence of lactose, the lactose molecule
can bind to the lac repressor protein, causing it to dissociate from
the operator region and allowing transcription of the structural
genes to proceed.

The lac operon is an important model system for the study of

gene regulation and has provided important insights into the
mechanisms of gene expression. The lac operon is also a valuable
tool in the field of genetic engineering, as the expression of the
lac operon can be easily controlled and used to study the effects
of gene expression on bacterial metabolism.