The Blueprint of Life,
From DNA to Protein
Chapter 7
The Blueprint of Life
 Characteristics of each cell dictated by
information contained on DNA

DNA holds master blueprint

All cell structures and processes directed by DNA
Overview
 Complete set of genetic information referred
to as genome

Genome of all cells is composed of DNA



Functional unit of genome is the gene
Gene codes for gene product



Some viruses have RNA genome
Gene product is most commonly protein
Study of transfer of genes is genetics
Study of sequence of DNA is genomic
Overview
 Living cells must accomplish two general tasks to multiply
 DNA replication
 DNA expression (gene expression)
 Expression involves two process
 Transcription
 Copies information in DNA to RNA
 Translation
 Interpret RNA to synthesize protein

Flow of information from DNA to RNA to protein
 Central dogma of molecular biology
Overview
 Characteristics of DNA
 Made up of deoxyribonucleotides
 Nucleotides include:
 Phosphate group
 5 carbon sugar
 Deoxyribose

Nucleotides bond covalently
between the 5’PO4 of one
nucleotide and the 3’OH of
another
 Joining of nucleotides creates
an alternating sugarphosphate backbone
Overview
 Characteristics of DNA

Each sugar (deoxyribose) molecule is
connected to a nitrogenous base

Nitrogenous bases




Adenine (A) - purine
Thymine (T) - pyrimidine
Guanine (G) - purine
Cytosine (C) – pyrimidine
Overview
 Characteristics of DNA
 Chemical structure and joining of
nucleotide subunits causes
strands to differ at the ends
 One strand has a phosphate
attached at the number 5
carbon of the sugar.
 Termed the five prime (5’) end

The other strand has a hydroxyl
group attached to the number 3
carbon of the sugar.
 Termed the three prime (3’) end
Overview
 Characteristics of DNA
 DNA occurs as double-stranded
molecule
 Strands are complementary to
each other
 Due to the specific base pairing
of bases
 A:T
 C:G

Strands are held together with
hydrogen bonds
 Specific hydrogen bonding
between bases
 A is bound to T by two
hydrogen bonds
 G is bound to C by three
hydrogen bond
Overview
 Characteristics of DNA
 DNA molecule is antiparallel
 Strands are oriented in
opposite directions
 Strands differ at the ends
 One strand oriented in
the 5’ to 3’ direction.
 The other strand is
oriented in the 3’ to 5’
direction.
Overview
 Characteristics of RNA
 RNA is made up of nucleotides
 Ribonucleotides
 RNA contains nitrogenous bases
 Adenine
 Guanine
 Cytosine
 Uracil
 Uracil replaces thymine in RNA

RNA usually exists as single stranded molecule
Overview
 Characteristics of RNA
 Portion of DNA acts of template for RNA
synthesis

RNA molecule called transcript
 Numerous transcripts can be produced from one
chromosome


Either strand of DNA can act as template
Three different functional groups of RNA



Messenger RNA (mRNA)
Ribosomal RNA (rRNA)
Transfer RNA (tRNA)
Overview
 Regulating the expression of genes


Nucleotide sequence codes for regulation
mechanism for gene expression
Mechanisms determine duration of synthesis
of gene products


Products are only made when required
Key mechanism is regulation of mRNA
synthesis from DNA

Regulation of transcription
DNA Replication
 DNA is replicated to
create second copy of
molecule

Molecule is identical to
original
 Replication is
bidirectional

Replication begins at
specific starting point
 Proceeds in opposite
directions
 Allows replication to
proceed more
quickly
Bi-directional
replication
DNA Replication
 DNA replication


The two strands are unwound and separated
Free, unbound nucleotides match up to the
newly separated nitrogenous bases of the
parent strand

The parent strand is also called the template
strand
DNA Replication
 DNA replication
 Base pairing is specific in DNA replication




Where adenine is present only thymine binds in
the new strand and vice versa
Where guanine is present only cytosine binds in
the new strand and vice versa
Bases that are improperly inserted are
removed and replaced with the correct base
Newly added bases are added by the enzyme
DNA polymerase
DNA Replication
 Specifics of DNA
replication


As the strands of DNA
unwind, it creates an
area of replication
called the replication
fork
As nucleotides are
added, the replication
fork moves down the
parental strand
DNA Replication
 Specifics of DNA replication
 DNA polymerase adds new nucleotides as
they become available.

DNA polymerase can only add nucleotides to the
free hydroxyl at the 3’ end
 DNA polymerase replicates in 5’ to 3’ direction
 Enzymes READS DNA template in 3’ to 5’ direction

Because of the antiparallel nature of the strands
of DNA, the two new strands will grow in opposite
directions
 One strand is the leading strand
 One strand is the lagging strand
DNA Replication
 Specifics of DNA replication

Leading strand


Is synthesized CONTINUOUSLY as the DNA
polymerase moves towards the replication fork
Lagging strand

Is synthesized DISCONTINUOUSLY in pieces as
DNA polymerase moves away from the
replication fork
DNA Replication
 Specifics of DNA replication

DNA polymerase must bind to an RNA primer
to begin synthesis

A second DNA polymerase removes any RNA
primers
 An RNA primer is required at each newly synthesized
section of the lagging strand

DNA ligase joins the fragments of the lagging
strand
DNA Replication
 Specifics of DNA replication


Replication is completed when the replication
fork reaches the end of the parent strands
The original parent strand and the newly
synthesized daughter strand rewind

Each new strand of DNA consists of one parent
strand and one daughter strand
 DNA replication is referred to as semiconservative
DNA Replication
Gene Expression
 Involves two separate but interrelated
process

Transcription


Process of synthesizing RNA from DNA template
Translation

RNA is deciphered to synthesize protein
Gene Expression
 Transcription

Transcription is the synthesis of a strand of
mRNA from a DNA template


mRNA carries the coded information from DNA to
the ribosome, which is the site of protein
synthesis
mRNA also plays an important role in translation
Gene Expression
 Transcription
 During transcription the
enzyme, RNA polymerase,
synthesizes a
complementary strand of
mRNA from a portion of
unwound DNA
Gene Expression
 Specifics of Transcription

RNA polymerase binds to a region of the DNA
called the promoter

Only one strand of DNA acts as a template
 This is called the sense strand
 The strand not transcribed is the nonsense strand
Genet Expression
 Specifics of transcription

Nucleotides in RNA are the same as those in
DNA with one exception

Thymine is replaced with uracil
 Binding in RNA is
 A:U or U:A
 C:G or G:C
Gene Expression
 Specifics of transcription

RNA polymerase continues down strand of
DNA until it reaches a site on DNA called the
terminator

At the terminator RNA polymerase and the new
strand of mRNA are released from strand of DNA
Transcription
Gene Expression
 Translation


Translation is the decoding of information held
in the mRNA to synthesize proteins
Two more RNA molecules become involved in
translation


Ribosomal RNA (rRNA)
Transfer RNA (tRNA)
Gene Expression
 rRNA forms part of the ribosomal machinery
used in protein synthesis

rRNA builds the ribosomes
 tRNA recognizes specific sequences of
mRNA and transports the required amino
acids to form a polypeptide chain
Gene Expression
 Translation

The language of mRNA is in the form of
codons



Codons are groups of three nucleotides situated
next to each other on DNA
Codons are written in terms of their base
sequence in mRNA
The sequence of codons determines the
sequence of amino acids in the protein
Gene Expression
 Translation

There are 64 codons that make up the
“alphabet” of proteins

Of the 64 codons, 61 are sense codons
 Each coding a specific amino acid

The remaining 3 are nonsense codons
 These code for termination of the message

Codons contained in mRNA are read into
proteins through translation

The site of translation is the ribosome
Gene Expression
 In response to each
codon, tRNA brings the
appropriate amino acid to
the site of translation
 Each codon has an
anticodon

The anticodon is
complementary
sequence to the codon
Gene Expression
 Translation

Ribosomes


The 30s and the 50s ribosomal subunits join
together around the mRNA
The ribosomes direct the binding of tRNA to the
correct codon on the mRNA
 tRNA binds to the P site and the A site of the 50s
ribosomal subunit

The ribosomes bind to the mRNA to be translated
Gene Expression
P site A site
 Specifics of Translation

The first tRNA binds to a start
codon in the P site of the
ribosome

AUG is the start codon for
EVERY protein
 AUG codes for the amino
acid methionine

When the second tRNA binds
to the A site, the amino acid
of the first tRNA forms a
peptide bond with the amino
acid of the second tRNA
Gene Expression
 Specifics of translation


After the peptide bond is formed between the
two amino acids, the tRNA P site leaves the
ribosome
The ribosome moves distance of one codon


Amino acid in the A site moves to the P site
A new tRNA fills the now empty A site
Gene Expression
 Specifics of translation
 The ribosome continues down the strand of
mRNA


Translation is terminated when the ribosomes
come to a stop or nonsense codon



Amino acids form peptide bonds along the way
At this point the ribosomes separate
The new polypeptide chain is released
The ribosome and the mRNA are free to begin
translation again
Gene Expression
 Specifics of translation

As the ribosome moves down the strand of
mRNA, the start codon is exposed

Once exposed, a new ribosome will attach and
begin another polypeptide chain
Translation
Regulation of Gene Expression
 Microorganisms posses mechanism to
synthesize maximum amount of cell material
from limited energy

Controls directed at metabolic pathways

Two general mechanism
 Allosteric inhibition of enzymes
 Controlling synthesis of enzymes
 Directed at making only what is required
Regulation of Gene Expression
 Principles of regulation
 Not all genes subjected to regulation
 Enzymes can be classified according to characteristics of
regulation
 Constitutive enzymes
 Constantly synthesized
 Enzymes of glycolysis

Inducible enzymes
 Not regularly produced
 turned on in certain conditions
 Β-galactosidase

Repressible enzymes
 Routinely synthesized
 Generally involved in biosynthesis
Regulation of Gene Expression
 Mechanisms controlling transcription

Often controlled by regulatory region near
promoter

Protein binds to region and acts as “on/off” switch
 Binding protein can act as repressor or activator
 Repressor blocks transcription
 Activator facilitates transcription

Set of genes controlled by protein is called an
operon
Regulation of Gene Expression
 Repressors
 Control mechanism that inhibits gene expression and
decreases the synthesis of enzymes
 Repression is usually in response to the overabundance
of an end product
 Repression decreases the rate synthesis of enzymes
leading to the formation of the particular end product
 Regulatory proteins called repressors mediate repression
 Repressors block the ability of RNA polymerase to bind and
initiate protein synthesis
Regulation of Gene Expression
 Activators


Control mechanism that turns on the
transcription of a gene or set of genes
Inducers are substances that act to induce
transcription

Enzymes synthesized in the presence of inducers
are called inducible enzymes
Regulation of Gene Expression
 Operon model of gene expression
 An operon is a set of genes that includes an
operator, promoter and structural genes
 An operon is divided into two regions, the control
region and the structural region

The control region include the operator and the
promoter
 This region controls transcription
 The operator acts as the “on-off” switch

The structural region includes the structural genes
 This region contains the genes being transcribed
Operon structure
Operator
Gene 1
Gene 2
Gene 3
Promoter
Promoter –
Binding site
for RNA
polymerase
Operator –
binding site for
the repressor
protein for the
regulation of
gene expression
Structural Genes –
DNA sequence for
specific proteins
Regulation of Gene Expression
 Lac operon

Example of induction of gene expression

Near the operon on the DNA is a regulatory gene
called the “I” gene
 This codes for the repressor protein

When lactose is absent, the repressor protein
binds to the operator gene
 Binding of the repressor gene prevents RNA
polymerase from transcribing the structural genes
 No mRNA is made and no enzymes are
synthesized
Regulation of Gene Expression
 Lac operon

When lactose is present the repressor binds to
lactose instead of the operator


With the repressor bound to lactose, RNA
polymerase is able to bind to the promoter and
transcribes the structural genes
Lactose acts as an inducer by keeping the
repressor from binding to the operator
 It induces the transcription of the structural genes
Lac Operon
Operator
Gene 1
Gene 2
Gene 3
1.
Promoter
RNA polymerase
2.
Repressor
3.
Lactose
Lac Operon
Gene Expression and Environmental
Fluctuations
 Many organisms adapt to changing
environments by altering level of gene
expression
 Mechanisms include


Signal transduction
Natural selection
Gene Expression and Environmental
Fluctuations
 Signal transduction
 Process that transmits information from external
environment to inside cell


Allows cell to respond to changes
Two-component regulatory systems

Relies on sensor and response regulator proteins
 Sensors recognize change in environment
 Response regulators activate or repress gene expression

Quorum sensing

Organisms sense density of population
 Enables activation of genes beneficial to the mass
Gene Expression and Environmental
Fluctuations
 Natural selection

Mechanisms to enhance survivability

Antigenic variation
 Alteration in characteristics of certain surface
proteins
 Example: Neisseria gonorrhoeae hides from host
immunity by changing numerous surface proteins

Phase variation
 Routine switching on and off of certain genes
 Altering expression allows portions of population
to survive and multiply