PDF Module 5.3. DNA and Polypeptide Synthesis

DNA AND POLYPEPTIDE
SYNTHESIS
Inquiry question: Why is polypeptide synthesis
important?
Biology 5.3. DNA and Polypeptide Synthesis (G. Guy - Fort Street High School)
DNA IN PROKARYOTES AND EUKARYOTES
All living things have genetic molecules, DNA. In prokaryotes and
eukaryotes, the chemical composition is the same (with different
order of base pairs).
There is, however, differences in how they are structurally organised
within the different types of cells.
Prokaryotic Cells
Most genetic material in a prokaryotic cell is found in the nucleoid, an
irregular shaped region slightly denser than the rest of the cytoplasm.
The DNA of a prokaryote exists in a large circular simple chromosome,
sometimes accompanied by plasmids – smaller rings of DNA that
contain limited genes.
It does not have the membrane bound nucleus or the histone protein
framework found in eukaryotes.
Plasmids are not essential to
the survival of a cell, but often
provides a selective
advantage, such as
resistance to antibiotics or
other external selective
pressure.
It can be integrated into the
main DNA structure if
needed.
Eukaryotic Cells
DNA in eukaryotic cells are coiled in a histone protein framework
chromosome (see Module 5.2. A) DNA) in a membrane bound nucleus.
Eukaryotes often have some DNA in
other organelles, such as mitochondria
or chloroplasts.
In mammals, mitochondrial DNA
(mtDNA) holds 37 genes in small circular
rings resembling plasmids. These code
for:
 Electron transfer during respiration
 Building RNA molecules (details later
in this module)
In the formation of a zygote (newly formed embryo), half the nuclear DNA comes
from the sperm and half from the ovum (details later in this module).
However, as sperm cells are so small with almost no cytoplasm, all cytoplasmic
organelles in an individual are inherited from their mother’s ovum.
This is why we say mtDNA is used to trace maternal inheritance.
Summary, taken from Pearson Biology
12 New South Wales
GENOTYPES AND PHENOTYPES
The genetic code specific to us as individuals is our genotype.
Our physical appearance, physiology and behaviours are our phenotype,
and are determined partly by the environment, but primarily by our genetic
make up (genotype).
So genes are expressed in an organism’s phenotype (gene expression).
Although some factors are more heavily influenced by the environment in
which the organism lives and the interactions between the two.
The environment can influence how a gene is expressed and the gene
determines how the phenotype is expressed under particular
environmental conditions.
A number of studies with plants and animals have concluded that the
expression of some genes are dependant on the environment.
The colour of Siamese cats that have a particular gene have darker coat
colours where there is poorer circulation, such as in their extremities, or when it
is colder.
Other examples include:
-Hydrangeas, a flower that changes -Human growth height can be restricted
colour based on the alkalinity of the by lack of nutrients or presence of toxic
soil. substances, such as cigarette smoke.
These two men are identical twins
PROTEINS
The driving group of
molecules behind all
process in a body
are proteins. They
are determined by
our genotype and
have important
functions in our
bodies:
 They control all
metabolic
reactions as
enzymes (recall
from Module 1.2.
B) Enzymes)
 Some send intracellular signals (within
cells, between different organelles), or
between cells within the body (such as
insulin)
 Some groups, such as antibodies, are
involved in the adaptive immune system
(details in Module 7 - Infectious Disease)
 Transmembrane proteins alter the
permeability of a cell’s membrane (recall
from Module 1.2. A) Cell Function)
 Some proteins are directly involved in the
building, structure and mechanics of a
whole organism, such as collagen, elastin
and keratin.
In short, the proteins that are found and active in our bodies determine our
phenotype, be it structural or physiological adaptations, with influence from
the external environment.
BEADLE AND TATUM: FROM GENES TO PROTEINS
In 1941, American scientists George Beadle and Edward Tatum working
on mutants of the fungus mould Neurospora crassa.
Their hypothesis was that
one single gene (specific
sequence of base pairs)
controls the production one
specific protein. This
hypothesis was initially
supported, although
rephrased in later decades
as our understanding of
enzymes and proteins
increased.
The base unit of protein structure are amino acids. A chain of amino acids forms
a polypeptide, which is yet to be folded into a protein [Recall from Module 1.2
B) Enzymes].
Beadle and Tatum’s theory that
one gene produced one protein
was changed to the “One
Gene-One Polypeptide” theory,
as scientists realised some genes
and polypeptides can form one
of several proteins.
Although, a specific protein can
only be folded from a specific
polypeptide.
Amino acids are organic
compounds containing a
mine (-NH2) and carboxyl
(-COOH) functional
groups, along with a side
chain (R group) specific to
each amino acid.
These bond together in a
process called
condensation
polymerisation, where a
small water molecule is
released in the bonding
process [details in the HSC
Chemistry course].
Amino acids in a polypeptide chain are attracted to one another through
intermolecular forces, similar to those that hold the bases in DNA together.
This means that a polypeptide chain of amino acids is like a necklace made of
broken magnets – let it go and it will spontaneously form a particular shape. It is
the specific R group that determines how the polypeptide folds.
If one magnet (amino acid) is out of

place, the shape will change.
And, very importantly, some will form
the same shape all the time, some will
have several shapes it might form with
the same sequence of magnets
(amino acids).
It is these shapes that give the protein
its specific role in a body.
Fun Fact
In 1952 American scientists Harold Urey
and Stanley Miller performed an
investigation in a closed system with
conditions that simulated the early Earth.
After several weeks they found a change
in colour in their “ocean”, which with
analysis showed to hold over 20 amino
acids.
It is was significant as it showed that
complex molecules for life can
spontaneously form from non-living
conditions.
PROTEIN STRUCTURE
Protein structure is highly complex with four levels: primary, secondary, tertiary
and quaternary structures.
 Primary Structure
The sequence of amino acids
in a polypeptide chain is the
primary structure of a protein.
The order and positioning of
the functional R-groups in the
polypeptide determine the
higher structure.
 Secondary Structure
This refers to local folded
structures that form within a
polypeptide due to interactions
between atoms of the R-group.
The most common types of
secondary structures are the α
helix and the β pleated sheet.
Both structures are held in
shape by hydrogen bonds,
which form between the
carbonyl O of one amino acid
and the amino H of another.
 Tertiary Structure
This is the overall three-dimensional
structure of a polypeptide. The tertiary
structure is primarily due to various
types of interactions between the R
groups of the amino acids that make
up the protein.
 Quaternary Structure
Many proteins are made up of a
single polypeptide chain and have
only three levels of structure (the
ones we’ve just discussed). However,
some proteins are made up of
multiple polypeptide chains, also
known as subunits. When these
subunits come together, they give
the protein its quaternary structure.
An example of a quaternary
structure is haemoglobin (recall from
Module 2.3 Transport).
RNA (RIBONUCLEIC ACID)
Another molecule that is important
in the production of proteins is RNA
(Ribonucleic Acid).
RNA is a molecule related to DNA,
with some slight chemical
differences:
 The base Thymine (T) is replaced
with Uracil (U), which will bind
with Adenine (A)
 RNA contains the sugar ribose,
compared to the deoxyribose in
DNA
These chemical differences result in some significant structural differences.
RNA does not exist in a double helix; the nucleotide bases are exposed to the external
environment.
This means they are more susceptible to mutations than DNA. This means they are not as
effective at replicating itself as DNA are “mistakes” are more commonly made.
However, one thing RNA can
do that DNA can’t do is
bond with itself. The open
structure and the unbonded
bases allows different parts
of the RNA molecule that
have corresponding bases
to fold and bond with itself
forming an intrastrand.
This allows RNA to fold into
shapes, and these shapes
can have similar functions to
proteins. Not as rigid, specific
or effective, but well enough
to catalyse some basic
metabolic processes.
DNA is an excellent replicating molecule, the best one we know in nature.
Proteins, with their specific folded structures, are excellent enzymes and
mechanical molecules. These two molecule groups working together result
in the complexities of life that exists today.
However, both DNA and proteins are specialists – they can only do the one
job. RNA does a little of both. It replicates itself, but not quite as efficiently as
DNA. It also folds into shapes, but not nearly as effectively and usefully as
proteins.
Fun Fact
Some hypothesis about the origin of
life (abiogenesis) utilise this fact of
RNA. Perhaps it could replicate itself
just well enough, and catalyse this
process just effectively enough to
get by as the base molecule for life
until the team of DNA and proteins
evolved.
POLYPEPTIDE SYNTHESIS
For a gene to expressed as a phenotype it
must be translated into a protein.
This process is polypeptide synthesis, and it
has two main stages: transcription and
translation.
A simplified diagram of protein

synthesis in a cell
https://www.youtube.com/watch?v=2zAGAmTkZNY
TRANSCRIPTION
DNA never leaves the nucleus during Polypeptide Synthesis, and so
transcription occurs in the nucleus. The enzyme RNA Polymerase unwinds
and unzips the DNA double helix and connect complimentary RNA
nucleotides to the DNA. These RNA nucleoids polymerise to form a strand,
which takes the coded message outside the nucleus to be translated.
This specialised
RNA molecule is
called messenger
RNA (mRNA).
Transcription occurs in the 5’
to 3’ direction (similar to
DNA Replication) on one
strand. The coding strand
holds the code that will
eventually give the order of
amino acids in the protein.
This means the mRNA needs
to be the same code as the
coding strand.
The mRNA is not synthesised
on the coding strand, but
the corresponding template
strand of the DNA molecule.
The DNA has a start and stop signal
– a sequence of three specific base
pairs (codon) that tells RNA
Polymerase to start (TAC) or stop
(ATT, ATC or ACT) synthesising.
This is important because not the
whole genome is read, only a small
potion of the cell’s genome is
transcripted.
PROCESSING
Before the mRNA leaves the
nucleus it is matured. The mRNA
has particular nucleotides that are
not used in the final translation.
These are introns. The remaining
nucleotides are exons and are
used in translation.
The complex molecular machine,
spliceosome, cuts out the introns,
like a film editor, to make mature
mRNA that then leaves the
nucleus.
The mature mRNA takes the code from the nuclear DNA to the
ribosomes, that are attached to the rough endoplasmic reticulum,
where translation occurs.
TRANSLATION
Translating the message of the mRNA
and the synthesis of a polypeptide
occurs at the ribosome.
Ribosomes are made from 40% ribosomal RNA (rRNA) and 60% protein by
mass, and are made of two pieces or subunits, one larger than the other.
When protein synthesis is not
underway, the two sub-units
of the ribosome remain
apart. When the cell needs
to make a protein, the two
sub-units of the ribosome join
together and combine with
the mRNA. The completed
ribosome locks onto the
mRNA and begins the
process of protein synthesis.
In the cytoplasm of the cell are transfer RNA
(tRNA) molecules. These are brought to the
ribosomes to create a polypeptide.
tRNA has a specific structure. It has a 3 base pair
to correspond with a codon from mRNA called an
anticodon and an amino acid attached to the
other end.
These are drawn into the ribosome when
translating a mRNA molecule by enzymes called
elongation factors.
The tRNA molecules
move in turn along the
mRNA as it is strung
through the ribosome,
initiated by the start
codon.
The amino acids
polymerise through
condensation reactions
and exit the ribosome as
a polypeptide.
After leaving the
ribosome the polypeptide
folds into a protein.
It is in this way a sequence of base pairs on DNA eventually codes for a specific
trait in the form of a polypeptide or protein, as per the “One Gene – One
Polypeptide” theory.
Fun Fact
During polypeptide synthesis in prokaryotes, translation of an mRNA
molecule occurs while it is still undergoing transcription.
The particular amino acids in the
polypeptide chain correspond to
specific codons, with “STOP” ending the
chain and beginning a new one.
What would be the amino acid
sequence of the following mRNA code?
AUG CCA UCC CGG GGG ACA UGU
CCA CAU UUA CGA UAC CCA UGA
KEY TERMS  Primary Structure  Coding Strand
 Secondary Structure  Template Strand
 Nucleoid
 Tertiary Structure  Codon
 Plasmids
 Quaternary Structure  Introns
 mtDNA
 RNA (Ribonucleic Acid)  Exons
 Genotype
 Intrastrand  Spliceosome
 Phenotype
 Polypeptide Synthesis  Ribosomes
 Beadle & Tatum
 Transcription  Endoplasmic Reticulum
 Amino Acids
 Translation  Transfer RNA (tRNA)
 Polypeptide
 RNA Polymerase  Anticodon
 “One Gene-One
Polypeptide” Theory  Messenger RNA (mRNA).  Elongation Factors
The End

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DNA AND POLYPEPTIDE

These two men are identical twins

If one magnet (amino acid) is out of

A simplified diagram of protein

AUG CCA UCC CGG GGG ACA UGU

CCA CAU UUA CGA UAC CCA UGA

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