Protein Synthesis

Protein Synthesis


At the end of this
lecture, student will be able to

• Describe the steps involved in protein synthesis


• Proteins are the “workhorse” molecule found in organisms.

• The blue print for proteins is coded in the DNA of the

• DNA contains genes that determine the phenotype of an
organism or “what we look like”. 
DNA codes for the synthesis of proteins. 
Proteins are responsible for the phenotype.

• Humans can make over 200,000 proteins actually much more
than that if the immune system is taken into consideration.

• Made of polypeptide chains.  Proteins have primary, secondary, tertiary
and quaternary structure.

• There are 20 different amino acids and the average
polypeptide chain is 400 amino acids long.

• The part of the DNA that codes for a particular
polypeptide chain is known as a gene.

Uses of proteins

• Enzymes (catalase)

• Structure (silk, hair, nails)

• Antibodies

• Movement (muscle, flagella)

• Hormones (insulin)

• Carry gases (hemoglobin)

• Storage of amino acids (albumin)


• In 1909, British physician Archibald Gerrod first
suggested that genes dictate phenotypes through enzymes that catalyze specific
chemical reactions.

• He thought symptoms of an inherited disease reflect an
inability to synthesize a certain enzyme.

• Linking genes to enzymes required understanding that cells
synthesize and degrade molecules in a series of steps, a metabolic pathway.

• Archibald Garrod was the first to connect a human disorder
with Mendel’s laws of inheritance. He also proposed the idea that diseases came
about through a metabolic route leading to the molecular basis of inheritance.

• Garrod was studying the human disorder alkaptonuria. He
collected family history information (as well as urine) from his patients.
Based on discussions with Mendel advocate William Bateson, Garrod deduced that
alkaptonuria is a recessive disorder. In 1902, Garrod published a book called The
Incidence of Alkaptonuria: a Study in Chemical Individuality
. This is the
first published account of a case of recessive inheritance in humans.

• Beadle and Tatum’s key experiments involved exposing the
bread mold ,Neurospora crassa to x-rays, causing mutations. In a series
of experiments, they showed that these mutations caused changes in specific
enzymes involved in metabolic pathways. These experiments led them to propose a
direct link between genes and enzymatic reactions, known as the “one gene,
one enzyme” hypothesis.  They received
the Nobel Prize for Physiology or Medicine in 1958 for their research.


• One gene produces one enzyme.

• Later it was modified

• One gene produces one protein.

• One gene produces one polypeptide chain.

• Today the definition for a gene is a sequence of DNA
molecules that can direct the synthesis of some sort of molecule product.  i.e. genes do not all code for a protein, but
all do code for an RNA molecule. Some of those RNAs are translated into
protein, but many serve other functions, such as gene regulation.

• The molecules can be a polypeptide chain, protein, or
RNA.  There are genes that make pieces of
RNA that do not produce a protein product. 
For example tRNAs are coded for by a DNA gene but yet it does not make a
polypeptide chain.

• The DNA that codes for the proteins is located in the
nucleus but proteins are actually made in the cytoplasm.  There must be an intermediate that can take
the code (instructions) out to the cytoplasm so that the protein can be made.

• RNA is the intermediate that takes the code out to the
ribosome so that the protein can be made.

• Protein synthesis has two major parts.

  1. Transcription-DNA
    nucleotides found in a gene are used as a template to make a molecule of

  2. Translation-
    RNA template or mRNA is used in conjunction with ribosomes, tRNA with
    attached amino acids to produce a polypeptide chain.

of RNA versus DNA


RNA                                                     DNA

Single stranded                               Double stranded


U instead T                                         T
instead of U

Nucleus and cytoplasm                 Restricted
to nucleus & organelles

Multiple uses                                     Used
as template for RNA synthesis and proteins

Types of

There are different types of RNA

mRNA-carries the information from the DNA gene to
the cytoplasm.  Determines the sequence
of amino acids for a protein

tRNA-brings the correct amino acid to the ribosome
and mRNA in translation

rRNA-found on ribosomes and used to
“connect” the  tRNA to the mRNA

snRNA-found on spliceosomes.  Used to remove introns.

SRP RNA-part of the signal recognition particle
used to bring a translating ribosome to the E.R. and threads the emerging
polypeptide chain into the lumen of the E.R.


• Amino acids are coded for by a triplet of DNA nucleotides
called a codon.


1. There 64 codons- 61 code for amino acids. There is
“redundancy” in the code; more than one codon codes for the same
amino acid.

2. Three codons code for stop.

3. One codes for start and also for methionine.

• Since DNA code is transcribed into mRNA, the genetic code
in books is described in terms of mRNA codons.

• The Nirenberg and Matthaei experiment was a scientific
experiment performed on May 15, 1961, by Marshall W. Nirenberg and his post-doctoral
fellow, Heinrich J. Matthaei. The experiment cracked the genetic code by using
nucleic acids, tRNA, and amino acids to translate specific polypeptide chain.

• In the experiment, they prepared an extract from bacterial
cells that could make protein even when no intact living cells were present.
Adding an artificial form of RNA, poly-U, to this extract caused it to make a
protein composed entirely of the amino acid phenylalanine. This experiment
cracked the first codon of the genetic code and showed that RNA controlled the
production of specific types of protein.

• Nirenberg was awarded the 1968 Nobel Prize in Physiology
or Medicine.

• Nirenberg later worked with Phillip Leder and
performed an experiment to determine the triplet nature of the genetic code and
allowed the remaining ambiguous codons in the genetic code to be deciphered.

• Marshall Nirenberg and Heinrich Matthaei determined the
first codon for an amino acid.  It was
found that UUU coded for the amino acid phenylalanine by creating mRNA entirely
of uracil.  The mRNA

• (UUU..UUU….) added it to a test tube with amino acids,
ribosomes, RNA polymerase and other needed materials.  It resulted in a protein made of only phenylalanine.  Further research determined the rest of the

or Coding for a Polypeptide

This gene designates that the following peptide chain be
made with the amino acids in this particular order.



• Transcription is the first step of gene expression, in
which a particular segment of DNA is copied into RNA (mRNA) by the enzyme RNA

synthesis from a DNA template




RNA processing

1. Initiation

Initiation-There is a
region prior to beginning of a gene where the RNA polymerase attaches called
the promoter region. 

• The promoter region determines which side of the gene will
be transcribed. 

• In a prokaryotic cell, the RNA polymerase attaches
directly to the region, but in a eukaryotic cell there are transcription
factors (proteins) which help facilitate the attachment of the RNA

• Within the promoter region, there is a sequence of TATA
nucleotides, called the TATA box, that helps identify where the RNA polymerase
should bind.

• Once the RNA polymerase attaches, there are even more
transcription factors that attach.  Now
the RNA polymerase unwinds the DNA at the start point of the gene.

• In prokaryotes there is only one type of RNA polymerase,
but in eukaryotes there are three types of RNA polymerase.

2. Elongation

• Elongation- RNA polymerase unwinds the DNA and base pairs
RNA nucleotides to the DNA gene.  RNA is
made 5’ → 3’ so the DNA gene is 3’ →5’.

• The base pairing for RNA is adenine with uracil and
guanine with cytosine. 

• The approximate rate of base paring by RNA polymerase is
about 60 RNA nucleotides/minute. 

• The RNA molecule will peel off of the DNA gene and DNA
molecule will reform.  

• The average mRNA is 8000 base pairs long. 

• A gene can be simultaneously transcribed by a number of
transcription factors. 

• This is important when many copies of the same protein are
needed, such as albumin in an egg, or hemoglobin in a red blood cell. 

• Do the math, if the average protein is 400 amino acids
long then the number of nucleotides absolutely necessary to code for an average
protein is 1200 nucleotides. 

• However the average mRNA is 8000 base pairs long.  There seems to be some extra nucleotides.

3. Termination


• RNA synthesis proceeds until the RNA polymerase encounters
a sequence that triggers its dissociation.

• This process is not well understood in eukaryotes.  

• In eukaryotic cells, the RNA polymerase actually passes
the termination point before the RNA molecule is released.

Termination —there
are two different methods for prokaryotic cells

termination —
RNA transcription stops when the newly synthesized RNA
molecule forms a G-C-rich hairpin loop followed by a run of U’s. When the
hairpin forms, the mechanical stress breaks the weak rU-dA bonds.  This pulls the poly-U transcript out of the
active site of the RNA polymerase, in effect, terminating transcription.

termination —
a protein factor called rho destabilizes the interaction
between the template and the mRNA, thus releasing the newly synthesized mRNA
from the elongation complex.

4. RNA

• RNA processing- In eukaryotic cells the RNA is processed.

5′ cap with a modified guanine nucleotide is

At the 3′ end 30-200 adenine nucleotides are
added (poly-A-tail).

modifications prevent the mRNA from being degraded

the ribosome where to attach.

poly-A-tail also determines how many times the mRNA can be translated before it
is destroyed.

The average immature RNA is 8000 nucleotides
long but the mature mRNA is 1200 nucleotides long.   There are noncoding regions (introns) that
are removed in eukaryotic cells.  The
remaining regions (exons) are joined together to form the cistron.


• A spliceosome removes the introns. 

• Spliceosomes are composed of smaller particles called
snRNP (made of proteins and snRNA). 

• The spliceosome will splice the intron at a specific RNA
sequence releasing a “lariat” RNA.

RNA Processing

• Different exons are recombined in different ways for
certain mRNAs.  This increases the number
of different proteins.

Shuffling and Different Proteins

• Proteins often have a modular architecture consisting of
discrete regions called domains

• In many cases, different exons code for the different
domains in a protein

• Exon shuffling may result in the evolution of new

Ready for

• This mRNA has been processed and is called mature mRNA. It
is ready to go to the cytoplasm for translation.

in Protein Synthesis between Prokaryotes and Eukaryotes

• Prokaryotes do not have introns like eukaryotes.

• RNA in prokaryotes does not have to be processed like

• Transcription and translation can be simultaneous in

• The major difference between prokaryotic and eukaryotic
protein synthesis is prokaryotes do not have a nucleus so transcription and
translation can be simultaneous. 

• Also, the mRNA is not processed like eukaryotic RNA. 

• Both types of cells use the same genetic code.

End Product
–The Protein!

• The end products of protein synthesis is a primary
structure of a protein

• A sequence of amino acid bonded together by peptide bonds


• Protein synthesis is of three steps

• The ribosome binds to the mRNA at the start codon (AUG)
that is recognized only by the initiator tRNA

• The ribosome moves from codon to codon along the mRNA

• A release factor binds to the stop codon, terminating
translation and releasing the complete polypeptide from the ribosome

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