MODULE 3

DNA STRUCTURE AND REPLICATION

1952- The most well-known Hershey-Chase experiment, called the Waring Blender experiment,
provided concrete evidence that genes were made of DNA.

1953 - The discovery in 1953 of the double helix, the twisted-ladder structure of
deoxyribonucleic acid (DNA), by James Watson and Francis Crick marked a milestone in the
history of science.
STRUCTURE OF DNA
 RNA Structure and Function
RNA
● RNA (ribonucleic acid) is a molecule that is present in the majority of livings 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.

Structure of RNA
● Like DNA, RNA is a polymer of nucleotides like DNA. In an RNA nucleotide, the sugar
ribose is attached to a phosphate molecule and to a base, either G, U, A, or C. Notice
that in RNA, the base uracil replaces thymine as one of the pyrimidine bases. RNA is
generally singled stranded, whereas DNA is double stranded. In eukaryotic cell DNA
found in nucleus only while RNA found in nucleus and cytoplasm.

Phosphate
● In DNA and RNA phosphates are used to build the phosphate—sugar backbone, which
fixes the nucleotides bases in place also important for maintaining the structure of DNA
and RNA molecules.

RIBOSE
● Is an essential sugar for present life as a building block of RNA.

NITROGENOUS BASES
● A set of five nitrogenous bases is used in the construction of nucleotides, which in turn
build up the nucleic acids like DNA and RNA. These bases are crucially important
because the sequencing of them in DNA and RNA is the way information is stored.

3 Types of RNA

1. mRNA (messenger ribonucleic acid)

● mRNA is a type of single-stranded RNA involved in protein synthesis. mRNA is made
from a DNA template during the process of transcription.
● mRNA molecules carry the genetic information needed to make proteins. They carry the
information from DNA in the nucleus of the cell to the cytoplasm where the proteins are
made.

2. tRNA (transfer ribonucleic acid)

● Transfer RNA (tRNA) is a small RNA molecule that plays a key role in protein synthesis.
Transfer RNA serves as a link or adaptor between the mRNA molecule and the growing
chain of amino acids that make up a protein.

3. rRNA (ribosomal ribonucleic acid)

 ● rRNA, molecule in cells that forms part of the protein�synthesizing organelle known as a
ribosome and that is exported to the cytoplasm to help translate the information in mRNA
into protein.

❖ mRNA transcribe the genetic code from DNA into a form that can be read and used to make
proteins. mRNA carries genetic information from the nucleus to the cytoplasm.

❖ rRNA is located in the cytoplasm of a cell, where ribosomes are found. rRNA directs the
translation of mRNA into proteins.

❖ Like rRNA, tRNA is located in the cellular cytoplasm and is involved in protein synthesis.
Transfer RNA brings or transfer amino acids to the ribosome that corresponds to each
three-nucleotide codon of rRNA then joined together to make proteins

Definition of Gene Expression

● The process of using a gene sequence to synthesize a protein is called gene
expression.
● Gene expression is a tightly regulated process that allows a cell to respond to its
changing environment.
● It acts as both an on/off switch to control when proteins are made and also a volume
control that increases or decreases the amount of proteins made.
● Gene expression requires two processes called transcription and translation.
● In eukaryotes, transcription takes place in the nucleus and translation takes place in the
cytoplasm.
● During transcription, a portion of DNA serves as a template for mRNA formation. During
translation, the sequence of mRNA bases (which are complementary to those in the
template DNA) determines the sequence of amino acids in a polypeptide.

TRANSCRIPTION
● During transcription, a segment of the DNA called a gene serves as a template for the
production of an RNA molecule.
● The goal of transcription is to make a RNA copy of a gene's DNA sequence.
● For a protein-coding gene, the RNA copy, or transcript, carries the information needed to
build a polypeptide (protein or protein subunit).
● The main enzyme involved in transcription is RNA polymerase, which uses a
single-stranded DNA template to synthesize a complementary strand of RNA.

MESSENGER RNA
● Transcription begins when the enzyme RNA polymerase binds tightly to a promoter, a
region of DNA that contains a special sequence of nucleotides.
● During transcription, complementary RNA is made from a DNA template. At the point of
attachment of RNA polymerase, the DNA helix unwinds and unzips, and complementary
 RNA nucleotides are joined together, after RNA polymerase has passed by, the DNA
strands rejoin and the mRNA transcript is released.
● When mRNA forms, it has a sequence of bases complementary to that of the DNA;
wherever A, T, G, or care present in the DNA template, U, A, C, or G, respectively, are
incorporated into the mRNA molecule. Now, mRNA is a faithful copy of the sequence of
bases in DNA.

PROCESSING OF MRNA
● The newly synthesized primary mRNA molecule becomes a mature mRNA molecule
after processing.
● Most genes in humans are interrupted by segments of DNA that are not part of the gene.
Introns are non-coding segments that interrupt the gene, while exons are ultimately
expressed and produce proteins.
● Primary mRNA contains bases that are
complementary to both exons and introns, but during processing,
(1) one end of the mRNA is modified by the addition of a cap, composed of an altered guanine
nucleotide, and the other end is modified by the addition of a poly-A tail, a series of adenosine
nucleotides.
(2) The introns are removed, and the exons are joined to form a mature mRNA molecule
consisting of continuous exons.

TRANSLATION
● Second process by which gene expression leads to protein synthesis.
● It requires several enzymes, mRNA, and two other types of RNA: transfer RNA and
ribosomal RNA.

THE GENETIC CODE

● The sequence of bases in DNA is transcribe into mRNA, which ultimately codes for a
particular sequence of amino acids to form a polypeptide.
● The genetic code is a triplet code (each triplet is also called a codon) and that this code
is redundant.
● Universal in all living things.

TRANSFER RNA
● Transfer RNA (tRNA) molecules bring amino acids to the ribosomes.
● Each tRNA is a single-stranded polynucleotide that doubles back on itself to create a
boot-like shape.
● On one end is an amino acid
● The other end is an anticodon that complementary to a specific codon of mRNA.
● When a tRNA-amino acid complex comes to the ribosome, its anticodon pairs with an
mRNA codon.
● During transcription, the base sequence in DNA is copied into a base sequence in
mRNA.
 ● During translation, tRNAs bring amino acids to ribosomes in an order determined by the
sequence of codons in the mRNA.
● The sequence of amino acids forms a polypeptide chain or complete protein.

RIBOSOMES AND RIBOSOMAL RNA

● Ribosomes are composed of many proteins and several ribosomal RNA (rRNAS)
● They have binding sites for mRNA and three tRNAs, and help pair tRNA anticodons with
mRNA codons.
● As ribosomes move along the mRNA, new tRNAs enter and the amino acids bond
together, forming a protein

TRANSLATION REQUIRES THREE STEPS:

● Protein synthesis involves three steps: initiation, elongation, and termination.
● Enzymes are required for each of the three steps to function properly. The first two
steps, initiation and elongation, require energy.

INITIATION
● The step that brings all the translation components together.
● Proteins called initation factors are required to assemble the small ribosomal subunit,
mRNA, initiator tRNA, and the large ribosomal subunit for the start of protein synthesis.
● A ribosome has three binding sites for tRNAs. One of these is called the P (for peptide)
site, and the other is the A (for amino acid) site. The tRNA exits at the E site.

ELONGATION
● The protein synthesis step in which a polypeptide increases in length one amino acid at
a time. In addition to the participation of tRNAS, elongation requires elongation factors,
which facilitate the binding of tRNA anticodons to mRNA codons at a ribosome.

TERMINATION
● It is the final step in protein synthesis.
● During termination, the polypeptide of the assembled components that carried out
protein synthesis are separated from one another.
● Termination of polypeptide synthesis occurs at a stop codon.
● Termination requires a protein called a release factor which cleaves the polypeptide from
the last tRNA.
● After this occurs, the polypeptide is set free and begins to take its three-dimensional
shape. The ribo some dissociates into its two subunits.
● Properly functioning proteins are of paramount importance to the cell and to the
organism.
● For example, if an organism inherits a faulty gene, the result can be a genetic disorder
(such as Huntington disease) caused by a malfunctioning protein or a propensity toward
cancer.
● Proteins are the link between genotype and phenotype.
● The DNA sequence underlying these proteins distinguishes different types of organisms.
 ● In addition to accounting for the difference between cell types, proteins account for the
difference between organisms.

REVIEW OF GENE EXPRESSION

● A gene is expressed when its protein product has been synthesized.
● Protein synthesis requires the process of transcription and translation.
● During transcription, a segment of a DNA strand serves as a template for the formation
of messenger RNA (mRNA).
● The bases in mRNA are complementary to those in DNA. Every three mnRNA bases is a
codon (a triplet code) for a certain amino acid.
● Messenger RNA is processed before it leaves the nucleus, during which time the introns
are removed and the ends are modified.
● Messenger RNA carries a sequence of codons to the ribosomes.
● During translation, tRNAs bring attached amino acids to the ribosomes.
● Because tRNA anticodons pair with codons, the amino acids become sequenced in the
order originally specified by DNA.

REMEMBER! The genes we receive from our parents determine the proteins in our cells and
these proteins are responsible for our inherited traits.

Control of Gene Expression

➢ are used by cells to increase or decrease the production of specific gene products

Levels of Gene Control

Pre transcriptional Control
➢ Eukaryotes use DNA methylation and chromatin packing as a way to keep genes turned off.
➢ Genes within heterochromatin are inactive.
➢ Active genes in eukaryotic cells are associated with euchromatin.
➢ The presence of nucleosomes limits access to the DNA by the transcription machinery.
➢ A chromatin remodeling complex pushes the nucleosomes aside to open up sections of DNA
for expression.

Transcriptional Control
➢ Eukaryotic transcriptional control is dependent on the interaction of proteins with particular
DNA sequences.
➢ The proteins are called transcription factors and activators. The DNA sequences are called
enhancers and promoters.
➢ In eukaryotes, each gene has its own promoter.
➢ Transcription factors are proteins that help RNA polymerase bind to a promoter.
➢ Several transcription factors per gene from a transcription initiation complex.

• Transcription Activator
➢ These are the proteins that speed transcription.
➢ They are activated in response to a signal received and transmitted by a signal transduction
pathway.
➢ They bind to a DNA region called an enhancer and stimulate transcription.

Post transcriptional Control

➢ Messenger RNA (mRNA) is processed before it leaves the nucleus and passes into the
cytoplasm.
➢ The primary mRNA is converted to the mature mRNA by the addition of a poly-A tail and a
guanine cap, and by the removal of the introns and splicing back together of the exons.
➢ The speed of transport of mRNA from the nucleus into the cytoplasm can ultimately affect the
amount of gene product following transcription.
➢ There is a difference in the length of time it takes various mRNA molecules to pass through a
nuclear pore.

Translational Control
➢ The longer an mRNA remains in the cytoplasm before it is broken down, the more gene
product can be translated.
➢ Differences in the poly-A tail or the guanine cap determines how long a particular transcript
remains active before it is destroyed by a ribonuclease associated with ribosomes.
➢ Hormones can cause the stabilization of certain mRNA transcripts.

Post translational Control

➢ Some proteins are not active immediately after synthesis.
➢ Insulin is folded into a three-dimensional structure that is inactive.
➢ A sequence of about 30 amino acids is enzymatically removed from the middle of the
molecule, leaving two polypeptide chains that are bonded together by disulfide (S—S) bonds
which activates the protein.
➢ Many proteins only function a short time before they are degraded or destroyed by the cell.