Christopher Hernandez

Mrs. Dawson

AP Biology 3B

3/3/20

Protein Synthesis

Protein synthesis is the process where DNA encodes for the production of amino acids

and proteins. It is a very complex and precise process as DNA replication is interconnected with

the production of proteins. Malfunction of this precise process in DNA replication can lead to

many well known diseases such as sickle cell anemia which affects the person’s blood cells. In

addition mutations that cause the DNA sequence to change cause physical traits to change such

as albanoism which causes pigment in the skin to not appear. In protein synthesis, malfunction

can lead to toxic function in the protein. However change does not have to happen due to a

mutation. Epigenetic change is a regular and natural occurrence. This process to fully change a

part of the human genome can take millions of years to happen however. It is vital that this

process is precise for the health of the human. As proteins make up over half of the dry mass of a

cell, it is a vital process to the maintenance, growth and development of the cell. Proteins are

widely used in the cell for a variety of reasons and have many different roles, for example some

proteins control biochemical reactions while other form a the complex structure of the cell to

give it its shape. 

The formation of proteins takes place within the cytoplasm, the portion of the cell located

just outside the nucleus. Cytoplasm is a jelly-like substance that holds the cells structures in

place. Proteins are formed through condensation reactions which bond amino acids together with

peptide bonds in a particular sequence and the type of protein that is created is defined by the
unique sequence of the amino acids. DNA and RNA are nucleic acids that are formed in the

nucleotides and are both involved in the process of protein synthesis.

Deoxyribonucleic acid, more commonly known as DNA, is located within the nucleus of

the cell and contains the entire genetic code for an organism within its structure. DNA has two

very important functions which are: to convey information from one generation of cells to the

next by the process of DNA replication and to provide the information for the synthesis of

proteins necessary for cellular function. DNA controls protein synthesis by being it's first step.

DNA is kept in tight packages called chromosomes due to the fact unwinded it wont fit in the

nucleus.

The complex and precise process of protein synthesis begins within a gene, which is a

distinct portion of a cell’s DNA. DNA is a nucleic acid which is made up of repeating

monomers, called nucleotides, and in the case of DNA, these individual monomers consist of a

pentose sugar, a phosphoric acid and four bases known as adenine, guanine, cytosine and

thymine. DNA is a double stranded polymer, which has a twisted ladder like structure, known as

a double-helix. The double-helix of DNA is formed when two polynucleotide chains join

together via base-pairing between nucleotide units within the individual chains. The base pairs

are joined together by hydrogen bonds and the pairings join in a very specific way, for example

guanine will always only join with cytosine and adenine will always only join with thymine. The

sequence of these base pairs along the DNA molecule carries all the genetic information of the

cell. Enhancers, known as transcription factors, on certain genes increase the likeliness that the

gene will undergo protein synthesis. 

Although the DNA does not produce the new proteins itself, it is responsible for

controlling the process of protein synthesis. This is simply because DNA is far too big a structure
to pass through the nucleus into the cytoplasm via its nuclear pore which is a small structure in

the nucleus that allows smaller molecules such as smaller proteins, so instead it sends a message

to the ribosomes in the cytoplasm to start the process. It does this by sending this information via

a chemical similar to DNA called ribonucleic acid (RNA). RNA is single stranded polymer of

nucleotides which is formed on the DNA. There are three types of RNA found in cells, all of

which are involved in the process of protein synthesis. They are Messenger RNA (mRNA),

Ribosomal RNA (rRNA) and Transfer RNA (tRNA). In order for DNA to be copied correctly to

produce the right proteins, single stranded binding proteins are needed for the replication,

recombination, and repair of the DNA. WIthout ssBPs, DNA would fail to have the correct

sequences for proteins thus sometimes having drastic effects on people

Messenger RNA (mRNA) is a long, single stranded molecule which is formed into a

helix on a single strand of DNA. It is manufactured in the nucleus and is a mirror copy of the

part of the DNA strand on which it is formed. The messenger RNA passes through the nucleus

and enters the cytoplasm where it connects with the ribosomes and acts as a template for protein

synthesis. 

Ribosomal RNA (rRNA) is a large, complex molecule which is made up of both single

and double helices. rRNA is formed by the genes which are situated on the DNA and is found in

the cytoplasm which, when bonded with proteins, makes up the ribosomes. The difference

between DNA and RNA is that DNA is a double helix consisting of two strands whereas RNA is

simply a singular strand, RNA also uses uracil instead of thymine as well as DNA consists of a

deoxyribose sugar, whereas RNA consists of a ribose sugar.

Transfer RNA (tRNA) is a very small, single stranded molecule that is manufactured by

the DNA in the nucleus and is primarily responsible for the transfer of amino acids. These amino
acids are found in the cytoplasm, at the ribosomes and operates as an intermediary molecule

between the triplet code of mRNA and the amino acid sequence of the polypeptide chain. There

are at least twenty different types of tRNA, each transporting a different amino acid and at a

central point along the chain there is a significant sequence of three bases, called the anticodon.

These are arranged along the appropriate codon on the mRNA during protein synthesis.

All proteins are encoded in DNA, and the unit of DNA which codes for a protein is its

gene. Since amino acids are regularly found within the proteins, it can then be assumed that the

amino acids must have their own code of bases on the DNA. This relationship between the bases

and the amino acids is called the genetic code. There are just twenty amino acids that regularly

occur in proteins and each must be coded for in the bases of the DNA. With the DNA only

having four different bases present, if each were to code for a different amino acid, then only

four different amino acids could be coded for. With there being twenty amino acids that occur

regularly in proteins, only a code composed of three bases could satisfy the requirements for all

twenty amino acids; this is called the triplet code and this triplet code is more commonly known

as a codon. Out of the 64 codons can be formed, three of these designate the termination of a

message and these are called stop codons (UAA, UGA, UAG) and one codon (AUG) acts as the

start signal for protein synthesis. The codon is a universal code, it is the same triplet code for the

same amino acids in all living organisms. As there is more than one triplet code for most amino

acids, it is called a degenerate code and each triplet must be read separately and must not

overlap. For example, CUGAGCUAG is read as CUG-AGC-UAG.

Protein synthesis is the process that is concerned with transfer of the information from the

triplet code on the DNA to ensure the formation of the proteins. There are four stages in the
formation of the proteins, these are: synthesis of amino acids; transcription; amino acid

activation and translation. These steps often are referred to as the central dogma.

The first stage, the synthesis of amino acids, is concerned with the formation of amino

acids. The human body is able to synthesise amino acids, however it is not able to form the

required amount therefore the remaining amino acids are supplied from the food that is ingested.

For example, many of these amino acids are found in meats and beans which are classified as

proteins.

The second stage, transcription, is the process where a specific region of the DNA

molecule that codes for a polypeptide is copied to form a strand of mRNA. Since the DNA is far

too big a structure to pass through the membrane of the nucleus itself, the process of

transcription takes place within the nucleus. Firstly, a section of the DNA separates as a result of

hydrogen bonds between the bases being broken, causing the DNA to unwind into single strands.

Hydrogen bonds bond both strands of DNA forming the double helix in DNA. One strand

functions as a template and the enzyme called RNA polymerase, along with transcription

initiation factors, moves along the strand attaching RNA nucleotides one at a time to the newly

exposed strand on DNA. Aminoacyl tRNA helps produce tRNA by “charging” the tRNA with

the appropriate amino acid in accordance with the template strand. This mRNA sequence is

known as the sense strand and the complementary DNA sequence which serves as the

transcriptional template is known as the antisense strand. Using complementary base pairing of

nucleotides, the mRNA is an exact replica of the unused strand called the copy strand. The

process of transcription starts at the promoter sequence and continues until the polymerase

reaches the terminator sequence and the fully formed mRNA moves out of the nuclear

membrane, through the nuclear pores, to the ribosomes. Once done, these promoters and
terminators are called start and stop codons as they are the first and last to be translated on an

mRNA . However, just because there is mRNA, doesn't mean there is protein being synthesised.

Inhibitors prevent production by blocking the binding sites of either the gene or blocking

ribosomes.siRNA also plays a role in preventing production of proteins. This molecule inhibits

both gene expression and translation by neutralizing mRNA molecules. Additionally, DNA

methylation also acts as a gene repressor to try to stop transcription of the gene. This happens by

adding a methyl group to the molecule cytosine. In the cell, there are numerous enzymes at work

for basic functions of the cell. These enzymes, if in direct contact with the mRNA, can degrade

mRNA. As a solution, before mRNA is transferred outside the nucleus, an addition of

aproximitly 200 nucleotides is added to the 3’ end of the cell. This structure is called a poly (A)

tail. Not only does this help stop degradation by enzymes, but it aids in the transportation of the

mRNA to the cytoplasm. Along with the 3’ tail, A 5’ cap is added to the 5’ end of the mRNA.

This cap is a 7-methylguanosine cap that also prevents degradation by enzymes in the 5’ end. In

addition, this cap also helps the mRNA to find the ribosome to initiate translation. Before this

can happen however, certain parts of the coded mRNA must be removed as they are not needed

to synthesise this protein. This separated part is called introns while the part of the code that is

used is called exons. This removal is done by a spliceosome. These molecules are formed out of

snRNA and are approximately 80 proteins long. The exon are then allowed to form many

different proteins via alternative splicing through a single gene. 

The third stage, amino acid activation, is the process by which the amino acid combines

with tRNA using energy from ATP. There are twenty different types of tRNA which bond with a

specific amino acid and the amino acid is attached to the free end of the tRNA. The newly

formed tRNA-amino acid begins to move toward the ribosomes in the cytoplasm.
 The fourth and final stage of protein synthesis occurs in the cytoplasm at the ribosomes,

and is called translation. Translation is the means by which a specific sequence of amino acids is

formed in accordance with the codons on the mRNA. Each mRNA molecule becomes attached

to one or more ribosomes to form a structure called a polysome. When translation occurs, the

complementary anticodon of a tRNA-amino acid complex is attracted to the first codon on the

mRNA and binds to the mRNA with hydrogen bonds between the complementary base pairings.

A second tRNA binds to the second codon of mRNA in the same way. The ribosome acts as a

framework which holds the mRNA and tRNA amino acid complex together until the two amino

acids are joined together by the formation of a peptide bond. As the ribosome moves along the

mRNA each codon is recognised by a matching complementary tRNA which contributes its

amino acid to the end of a new growing protein chain. Each nucleotide is assigned to 1 of the 3

sites in the ribosome. They are sequentially in the order of the A site, P site and E site. Each

nucleotide is fitted in one of these sites for translation to happen. This process continues until the

ribosome reaches a stop codon, which then indicates that the polypeptide chain is finished and

the polypeptide chain is then cast off. The formed polypeptides are then assembled into proteins

and by this action. However, in order for a protein to fully function, chaperonin, a capsule shaped

molecule, helps fold the protein correctly and in some cases quicker to their prefered

environment. This molecule prevents misfolding which causes mad cow disease, for example.

Finally protein synthesis is complete.

Protein synthesis is one of the most important synthesis in our body as almost all other

cell actions are dependent on proteins. However, this can be traced even further to say that DNA

is the building block of life as all proteins are synthesised from it as well as it codes for our genes
and traits. Through DNA, our body functions as we can truly call DNA the building blocks of

life.