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 organism.

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

Structure of RNA versus DNA


RNA                                                     DNA

Single stranded                               Double stranded

Ribose                                               Deoxyribose

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 RNA

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.

Genetic Code

• 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 code.

Specifying or Coding for a Polypeptide

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

Protein Synthesis


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

Transcription-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 polymerase. 

• 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

1.       Intrinsic 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.

2.       Extrinsic 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 Processing

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

1.       5' cap with a modified guanine nucleotide is added.

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

       These modifications prevent the mRNA from being degraded

       Signal the ribosome where to attach.

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

3.       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.

Removing Introns

• 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.

Exon 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 proteins.

Ready for Translation

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

Differences in Protein Synthesis between Prokaryotes and Eukaryotes

• Prokaryotes do not have introns like eukaryotes.

• RNA in prokaryotes does not have to be processed like eukaryotes.

• Transcription and translation can be simultaneous in prokaryotes.

• 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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