Lecture

Flow of genetic information in the

cell:

DNA RNA PROTEIN

•Since the structure of DNA was discovered in the
early 1950s, progress in cell and molecular biology
has been astounding.

•We now know the complete genome sequences for

thousands of different organisms, revealing
fascinating details of their biochemistry as well as
important clues as to how these organisms evolved.
 DNA DOUBLE HELIX
In the 1950s, a young American biologist, James
Watson, teamed up with British graduate student
Francis Crick at Cambridge University in England to try
to determine the structure of DNA.

 They proposed that DNA is made of two chains

that wrap around each other in the shape of a double
helix, a shape similar to a winding spiral staircase.

Their final model was correct and was remarkable

because it explained how DNA could replicate.

In 1962, Watson, Crick, and Wilkins received the

Nobel Prize in Medicine for their work on DNA.
 DNA NUCLEOTIDES
DNA is a nucleic
acid made of two
long chains (also
called strands) of
repeating subunits
called nucleotides.
 Each nucleotide
consists of three
parts: a five-carbon
sugar, a phosphate
group, and a
nitrogenous base.
The three parts of
a DNA nucleotide
are illustrated in
Figure 10-6.
 The five-carbon
sugar in a DNA
nucleotide is called
deoxyribose.
The phosphate group consists of a phosphorus (P) atom bonded to
four oxygen (O) atoms. The nitrogenous base contains nitrogen (N)
atoms and carbon (C) atoms and is a base (accepts hydrogen ions).
 Nitrogenous Bases
The sugar and phosphate
group are identical in all DNA
nucleotides.
 However, the nitrogenous
base may be any one of four
different kinds—thymine,
cytosine, adenine, or guanine.
The nitrogenous bases and
their chemical structures, called
rings, are shown above in Figure
10-7.
 The nitrogenous bases are
often represented by the first
letter of their name—T
(thymine), C (cytosine), A
(adenine), and G (guanine).
Nitrogenous bases that have a double ring of carbon and nitrogen atoms,
such as adenine and guanine, are called purines.

Nitrogenous bases that have a single ring of carbon and nitrogen atoms, such
as cytosine and thymine, are called pyrimidines.
The fragment of genetic information
corresponding to one protein is one gene

Individual segments of the entire DNA

sequence are transcribed into separate
mRNA molecules, with each segment coding
for a different protein.

Each such DNA segment represents one

gene
The expression of individual genes is regulated.
Regulatory DNAs are interspersed among the
segments that code for proteins, and these non coding
regions bind to special protein molecules that control
the local rate of transcription.
Genome of the cell is the total of its hereditary
information!
 Most of this information (the genetic information of an
eucaryotic cell) is stored in the nucleus, a small amount
remains in the mitochondria
Eucaryotic genomes are big
• The human genome contains 1000 times more nucleotide
pairs as the genome of a typical bacterium, 20 times as
many genes, and 10 000 times as much noncoding DNA
• Noncoding DNA sequences are components of an
organism's DNA that do not encode protein sequences).
• Eucaryotic genomes are rich in Regulatory DNA
• In eucaryotic genomes there is more noncoding DNA than
coding DNA
• Noncoding DNA regulates the expression of adjacent
genes
DNA directs the synthesis of RNA which than
directs the assembly of proteins
 DNA molecule - two associated polynucleotide
strands - double stranded helix

 DNA molecule is a polymer

 Its monomers are nucleotides – polynucleotide

 Nucleotide is composed of three parts: pentose

(sugar), base, phosphate group

 Sugar is called Ribose in RNA and Desoxyribose

in DNA
 Five bases: A, C, G, T, U.
 A, C, G, T in DNA; A, C, G, U in RNA
• The whole chain is synthesized by DNA polymerase or RNA
polymerase
• The two strands of DNA are held together by hydrogen
bonds
• 2 hydrogen bonds between A and T, 3 hydrogen bonds
between C and G
The Three Roles of DNA

1. Every cell in organism has the same genetic material,

precisely duplicated at every cell division

2. The genetic material has informational content

3. The structure of DNA is stable

 Chromosomes and DNA
Deoxyribonucleic acid (DNA) is the genetic code that allows information
to be transferred from one generation to the next.

DNA molecules consist of two linear chains that are wrapped around
one another forming a double helix structure.

These helical structures are further wound into chromosome structures.

Chromosomes are divided into two parts with a constriction point in the
in the middle which is known as the centromere.

The four types of chromosomes in animal cells are classified by the

position of the centromere.
Structure and Function of
the Centromere
Centromeres consist of a complex combination of proteins and
DNA.

They are essential to the division of cells and ensure the accurate
segregation of chromosomes.

Studies have demonstrated that chromosomes without

centromeres segregate randomly and are eventually lost from
cells.

In contrast, chromosomes that have multiple centromeres can be

subject to fragmentation.
 Metacentric Chromosomes
Metacentric chromosomes have the centromere in the center,
such that both sections are of equal length.

Human chromosome 1 and 3 are

metacentric.
 Submetacentric
Chromosomes

Submetacentric chromosomes have

the centromere slightly offset from
the center leading to a slight
asymmetry in the length of the
two sections.

Human chromosomes 4 through 12

are submetacentric.
 Acrocentric Chromosomes

Acrocentric chromosomes
have a centromere which is
severely offset from the center
leading to one very long and one
very short section.

Human chromosomes 13, 15,

21, and 22 are acrocentric.
 Chromosome Morphology

Under the microscope chromosomes appear as thin, thread-like structures.

They all have a short arm and long arm separated by a primary constriction called the
centromere. The short arm is designated as p and the long arm as q.
The centromere is the location of spindle attachment and is an integral part of the
chromosome. It is essential for the normal movement and segregation of chromosomes
during cell division.
Human metaphase chromosomes can be categorized according to the length of the short and
long arms and also the centromere location.
• Metacentric chromosomes have short and long arms of roughly equal length with the
centromere in the middle.
• Submetacentric chromosomes have short and long arms of unequal length with the
centromere more towards one end.
• Acrocentric chromosomes have a centromere very near to one end and have very small
short arms. They frequently have secondary constrictions on the short arms that connect
very small pieces of DNA, called stalks and satellites, to the centromere.

The stalks contain genes which code for ribosomal RNA.

The diagrams showing region on chromosomes, called ideograms.
 RNA
 is a single-stranded molecule
 3 classes of RNA: mRNA, rRNA, tRNA
 Prokaryotic and Eukaryotic Replication

In prokaryotic cells, which have one circular

chromosome, replication begins at one place
along the chromosome.

Two replication forks are formed and proceed in

opposite directions, like two zippers opening in
opposing directions.

Replication continues along each fork until they

meet and the entire molecule is copied.
In eukaryotic cells, each chromosome is long, but not
circular.
At the rate that DNA polymerase adds nucleotides
(about 50 nucleotides per second in eukaryotic cells), it
would take 53 days to replicate the largest human
chromosome.
Instead, replication begins at many points or origins
along the DNA. As with prokaryotes, at each origin, two
replication forks move in opposite directions.
For example, in a fruit fly chromosome, replication
begins simultaneously at about 3,500 sites in a DNA
molecule.
Only simultaneous replication along chromosomes
could allow rapid enough copying of the organism’s
entire DNA.
Gene expression means the production of protein or a
functional RNA from its gene.
Several steps required:
1) Transcription – a DNA strand is used as a template to
synthesize a complementary RNA strand which is called
the primary transcript
2) RNA processing
3) Nuclear transport
4) Protein synthesis
Transcription is a process in which one DNA strand is used
as a template to synthesize a complementary RNA. U of
RNA is paired with A of DNA. Growth of nucleic acid
strand is always in the 5’ to 3’ direction
DNA replication goes in the 5' to
3' direction because DNA polymerase acts on
the 3'-OH of the existing strand for adding free
nucleotides.
DNA is always synthesized in the 5' to
3' direction.
Since the leading and lagging strand templates
are oriented in opposite directions at the
replication fork, a major issue is how to achieve
synthesis of nascent (new) lagging strand DNA,
whose direction of synthesis is opposite to
the direction of thegrowing replication fork.
 TRANSCRIPTION

Transcription is the process by which the

genetic instructions in a specific gene are
transcribed or “rewritten” into an RNA
molecule.

Transcription takes place in the nucleus of

eukaryotic cells and in the DNA-containing
region in the cytoplasm of prokaryotic cells.
Splicing
In molecular biology, splicing is the editing of
the nascent precursor messenger RNA (pre-
mRNA) transcript into a mature messenger RNA
(mRNA).
After splicing, introns are removed and exons
are joined together (ligated).
• RNA splicing is a process that removes introns
and joins exons in a primary transcript.
• Most introns start from the sequence GU and
ends with the sequence AG (in the 5' to 3'
direction).  ( splice donor and splice acceptor site,
respectively)
•A spliceosome is a large and complex molecular
machine found primarily within the splicing
speckles of the cell nucleus of eukaryotic cells.
•The spliceosome removes introns from a
transcribed pre-mRNA, a type of primary
transcript. 
The Genetic Code
The genetic code is read in triplets
Each amino acid in a protein is specified by a group of three
bases in messenger RNA
The genetic code:
Is redundant – meaning the most of the 20 amino acids are
specified by more than one codon
Is unambiguous – a single codon never codes for more than
one amino acid
It is nearly universal – all codons specify the same amino
acids in all organisms
It is conservative – when several codons specify the same
amino acid, the first two bases are almost always identical
GENETIC CODE
During protein synthesis a ribosome moves along an mRNA chain, interacting
with various protein factors and tRNA and undergoes shape changes
•Three nucleotides - anticodon, form base pairs with the
complementary codon in mRNA.
•Codon a sequence of three nucleotides which together form a
unit of genetic code in a DNA or RNA molecule. Anticodon
a sequence of three nucleotides in a region of transfer RNA tha
trecognizes a complementary coding triplet of nucleotides in
messenger RNA during translation by the ribosomes in protei
nbiosynthesis.
• Aminoacyl-tRNA synthetase attaches the appropriate amino
acid to a tRNA
• Each tRNA molecule is recognized by only one of the 20
aminoacyl-tRNA synthetases An aminoacyl
tRNA synthetase (aaRS) is an enzyme that attaches the
appropriate amino acid onto its tRNA.
• Each of these enzymes links one and only one of the 20
amino acids to a particular tRNA, forming an aminoacyl-
tRNA.
 Translation
Translation has three stages — Initiation, Elongation,
Termination
 Messenger RNAs can be translated simultaneously by several ribosomes
in both prokaryotic and eukaryotic cells

 Once one ribosome has moved away from the initiation site, another can
bind to the mRNA and begin synthesis of a new polypeptide chain

 Thus, mRNAs are usually translated by a series of ribosomes, spaced at

intervals of about 100 to 200 nucleotides

 The group of ribosomes bound to an mRNA molecule is called a

polyribosome, or polysome. Each ribosome within the group functions
independently to synthesize a separate polypeptide chain
TRANSLATION
Although the instructions for making a protein are copied
from DNA to mRNA, all three major types of RNA are
involved in translation—the making of a protein.

Protein Structure
Every protein is made of one or more polypeptides.
Polypeptides are chains of amino acids linked by peptide
bonds.
There are 20 different amino acids found in the proteins
of living things.
The shape of the protein is critical to its function.
Each polypeptide chain may consist of hundreds or
thousands of the 20 different amino acids, arranged in a
sequence specific to each protein.
Steps of Translation
The translation or decoding of the genetic
instructions to form a polypeptide involves five
main steps, as shown in Figure 10-16.

In step 1, two ribosomal subunits, tRNA, and an

mRNA join together.
Enzymes first attach a specific amino acid to one
end of each tRNA according to the genetic code.

The other end of each tRNA contains the

anticodon, three nucleotides on the RNA that
are complementary to the sequence of a codon
in mRNA.
A tRNA carrying the amino acid methionine at one end and
the anticodon UAC at the other end pairs with the start
codon AUG on the mRNA.
The first amino acid in nearly all polypeptides is
methionine, but this amino acid may be removed later.

In step 2, the polypeptide chain is put together.

A tRNA carrying the appropriate amino acid pairs its
anticodon with the second codon in the mRNA.
The ribosome then detaches methionine from
the first tRNA, and a peptide bond forms between
methionine and the second amino acid.
The first tRNA then exits the ribosome.
The ribosome then moves a distance of one codon along the
mRNA. (Codon  a triplet of adjacent nucleotides in the
messenger RNA chain that codes for a specific amino acid in
the synthesis of a protein molecule). 
During step 3, the polypeptide chain continues to grow as the
mRNA moves along the ribosome.

A new tRNA moves in, carrying an amino acid for the next
mRNA codon.
The growing polypeptide chain moves from one tRNA to the
amino acid attached to the next tRNA.

The polypeptide grows one amino acid at a time until step 4. At

this step, the ribosome reaches the stop codon. The newly made
polypeptide falls off 4.

During step 5 , the components of translation come apart. The

last tRNA leaves the ribosome, and the ribosome moves away
from the mRNA.
The translation machinery is now free to translate the same or
another mRNA.