Protein Synthesis

PROTEIN SYNTHESIS

• All metabolic reactions are catalyzed by proteins  in the form of enzymes, including energy releasing and energy capturing reactions.
• Proteins offer structure to cells and organisms, such as the cytoskeleton.
• DNA has the stored information needed to determine the sequence of amino acids in proteins.
• It is essential to understand how proteins are synthesized in order to fully understand how they work.
• The building of proteins is called protein synthesis.
• The assembly of proteins occurs outside the nucleus in the ribosomes.

The ribosome will translate the mRNA molecule until it reaches a termination codon on the mRNA. When this happens, the growing protein called a polypeptide chain is released from the tRNA molecule and the ribosome splits back into large and small subunits.

The newly formed polypeptide chain undergoes several modifications before becoming a fully functioning protein. Proteins have a variety of functions. Some will be used in the cell membrane, while others will remain in the cytoplasm or be transported out of the cell. Many copies of a protein can be made from one mRNA molecule. This is because several ribosomes can translate the same mRNA molecule at the same time. These clusters of ribosomes that translate a single mRNA sequence are called polyribosomes or polysomes.

---

DNA and RNA

• DNA sends instructions for building proteins to the ribosomes in the form of messenger RNA (mRNA).

RNA

• RNA is a nucleic acid.  RNA is made up of a chain of nucleotide (phosphate + sugar + nitrogen base).

• RNA - consists of only a single strand of nucleotide (Remember DNA is two strands).  RNA is half a ladder or zipper.

• The sugar in RNA differs from the DNA sugar.  The sugar in RNA is ribose.
• The bases found in RNA differ as well.  DNA is made up of adenine, guanine, thymine and cytosine.  Adenine, guanine and cytosine also are found in RNA.  But instead of thymine RNA contains the base uracil.

• In RNA, cytosine bonds to guanine, and adenine bonds to uracil.

---

Types of RNA

RNA are the “workers” for protein synthesis.  DNA provides the workers with the instructions for making the proteins and the workers build the proteins amino acid by amino acid (Remember amino acid + amino acid + amino acid = Protein).

3 Types of RNA that makes proteins (Workers in the protein assembly line)

1. mRNA – RNA messenger – brings instructions from the DNA in the nucleus to the cells factory floor, the cytoplasm.  Once the mRNA is on the factory floor (cytoplasm) it moves to the assembly line, a ribosome.
2. The ribosome is made up of ribosomal RNA (rRNA); it binds the mRNA and uses the instructions to assemble the amino acids in the correct order.
3. The transfer RNA (tRNA) is the supplier – tRNA delivers the amino acids to the ribosome to be assembled into a protein. 

---

Transcription

The process by which the DNA message is copied into a strand of mRNA is called transcription.  This mRNA is then used for the construction of a protein molecule.

Transcription takes places in the NUCLEUS because DNA cannot leave.

The steps:

1. The DNA double helix starts to uncoil.
2. Once the two strands of DNA separate from one another only one strand participates in the synthesis of a complementary mRNA strand.
3. The mRNA strand is synthesized “made” with the help of an enzyme called RNA polymerase.
4. After mRNA synthesis is complete, the two strands of DNA recouple and the molecules of DNA recoils to assume its double helix.
5. The proceeded mRNA leaves the nucleus and enters the cytoplasm.                                

mRNA carries the instructions that direct the assembly of a specific protein to a designated area on the ribosome.  The instructions are carried in a sequence of three nitrogen bases called a codon.

---

Codon Chart

Codon is the code – needed to convert mRNA into protein language.   Each codon (3 nitrogen bases) codes for one amino acid.  This is the genetic code.  The genetic code is universal.

64 possible combinations– Note some do not code for an amino acid, but provide instructions for making a protein (UAA is a STOP codon indicating that the protein chain ends at that point).

AUG is a START codon as well as  the codon for methionine.

Note that more than one codon can code for the same amino acid. 

---

Translation

Once the message has reached the ribosome, the protein is ready to be assembled.  The process of building the protein from the mRNA instructions is called translation.  The transfer RNA (tRNA) and the ribosomal RNA (rRNA) are involved in translation.

In the cytoplasm, a ribosome attaches to the strand of mRNA like a clothes pin clamped to a close line.

tRNA is responsible for carrying the amino acid acids (the building blocks of proteins) to the ribosome so they can be linked in a specific order that makes up a single protein.  Each tRNA attaches to only one type of amino acid (correct translation of mRNA depends on the joining of each mRNA codon with the correct tRNA molecule).

How does this happen? One end of the tRNA carries a three-base sequence called an anticodon, which matches up with a particular codon on the mRNA.  They are complementary to each other.  

The Translation Process

1. The tRNA carries the first amino acid to the to the mRNA strand (see Figure 11.9A).  
2. The anticodon forms as base pair with codon mRNA (see figure 11.9B).  This places the amino acid in the correct position for forming a peptide bond with the next amino acid (Remember peptide bonds bond amino acids together in proteins). 
3. The ribosome slides down the mRNA chain top the next codon and a new tRNA  molecule bring another molecule (Figure 11.9C).  
4. The amino acids bond, the first tRNA releases its amino acid and detaches from the mRNA (Figure 11.9D).  The tRNA molecule is now free to pick up and deliver another molecule of its specific amino acid to a ribosome.  Again the ribosome slides down to the next codon; a new tRNA molecule arrives and its amino acid bonds with the previous one.   rRNA helps bond the amino acids together to form the final protein.
5. When the STOP codon is reached on the mRNA strand translation ends and amino acid strand is released from the ribosome (Figure 11E)
6. Amino acid chains become proteins when they are released from the ribosome.

The Central Dogma

Crick and Watson had a model for the flow of information in cells. This model incorporates  DNA, RNA, and proteins.

DNA may replicate itself
DNA may be transcribed to RNA
RNA may be translated into proteins
RNA and DNA are NOT  made from protein
DNA is NOT made from RNA

Called the Central Dogma of Molecular Biology – DNA to RNA to protein

---

The genetic code between DNA and protein is in the sequence of nucleotides in DNA within genes.

DNA is transcribed into mRNA
mRNA is translated into a polypeptide with the help of tRNA
tRNA with a specific sequence that matches mRNA,  carries the specific amino acid to the ribosome to help form a polypeptide
Ribosomes are the site of protein synthesis.

Transcription involves making a strand of RNA complementary to DNA.
RNA is single stranded-only one strand of DNA is transcribed.
RNA produced is messenger RNA (mRNA) because it carries the genetic message from DNA to the site of protein production.
DNA does not leave the nucleus!!!

this information is used to code for a protein made up of amino acids

if there are 4 letters in DNA language, and there are 20 amino acids that make up proteins

Amino acids are coded for by groups of 3 nucleotide, called CODONS.

• There are 4x4x4 = 64 codons.
• With these and only 20 amino acids, there are extra codons.
• Each amino acid is coded by more than 1 codon.
• NO codon codes for more than 1 amino acid

Four codons have special functions in the genetic code

• one start AUG codes for methionine
• 3 stop codons you do not have to memorize these.
• These determine the beginning and end of the polypeptide production.ate