What Are Proteins? Making and Breaking Proteins
Making and Breaking Proteins
All amino acids are joined together in exactly the same way, irrespective of the constituent R-group. Each amino acid in the polypeptide chain is joined by a peptide bond (a type of covalent bond); the reaction that forms this bond releases water and so is called a condensation reaction.
The reverse of this reaction is called a hydrolysis reaction because it uses a water molecule to break the bond.
The making and breaking of the peptide bond is central to the building and rebuilding of all protein molecules in organisms, as well as in digestion
Making Polypeptides and Proteins
The diagram to the right shows the formation of a dipeptide. This is formed when two amino acids are joined together; as more and more amino acids are joined together by peptide bonds we have a polypeptide. Proteins can be up to several hundred amino acids long, and in some instances proteins can be several polypeptide chains bonded together, or to another molecule.
But how are they made?
Ribosomes are the cellular machines responsible for selecting, moving and bonding amino acids in a specific sequence according to the instructions on messenger RNA (mRNA). mRNA can be compared to the roll in a player piano. In the instrument, as the roll moves through the piano, notes are played for set lengths of time in a specified order. As the mRNA molecule moves through the ribosome, amino acids are joined together one at a time in a condensation reaction. The sequence of amino acids (known as the primary structure of the protein) produced is determined by the mRNA. Just as a new tune on a player piano requires a different role, to make different proteins, different mRNA molecules must pass through the Ribosome.
A Degenerate Code
The last hub outlined that there are 20 different amino acids, each differing from all the others due to its' unique R-group. You may be thinking that 20 different amino acids does not provide much variety. Let's put that into context.
DNA and RNA encode information using a 4 letter alphabet. As this alphabet is used to write 'words' (codons) that are three letters long, there are 64 possible combinations (4x4x4). Now let's imagine a polypeptide just four amino acids long. Using the same calculation, there are 160,000 possible sequences of four amino acids (20x20x20x20.) The next part of this series shows how important this primary sequence is, but for now, ruminate on this: Even a small protein may be 100 amino acids long - the number of possible proteins of this size is huge!
Transcription and Translation
The synthesis of a protein from the instructions encoded in DNA, via an mRNA intermediary is broken down into two distinct stages:
- Transcription involves the synthesis of an mRNA strand. DNA cannot leave the cell for two reasons - it is too big and too important. Think of mRNA as a photocopy of an important document stored in a library. Just as libraries may not allow an original document to leave their care, they may be happy for you to take a copy of it - mRNA is this copy that you are free to edit and tinker with. Translation copies the DNA onto an RNA strand and then edits it by the removal of non-coding introns, methylation and the addition of a Poly-A tail. The resultant mRNA molecule then leaves the nucleus via the nuclear pores and docks with a ribosome.
- Translation creates the primary structure of the protein (the order of amino acids in the chain). A Ribosome 'reads' the information contained on the mRNA strand: this is encoded as a 'codon' a sequence of three ribonucleotide bases. Each sequence of three bases codes for a different amino acid. The ribosome works with another molecule called tranfer RNA (tRNA). This molecule does what is says on the tin - it transfers specific amino acids to the ribosome for assembly into a polypeptide chain. Once an appropriate amino acid is selected, the ribosome catalyses a condensation reaction forming a peptide bond between the amino acids on the growing polypeptide.
This process has numerous steps and is quite complicated. The resources by John Kyrk below are outstanding and show this process in action, step by step.
Breaking Down Proteins
It is an exercise in common sense that any biomolecule that takes such energy, effort and care to create is not broken down easily. The covalent bonds that bond the amino acids together are extremely strong: peptide bonds do not just fall apart.
It is ironic that these proteins are broken down by during digestion (this is also proof why buying and consuming 'digestive enzymes' is a load of money-spinning tosh. These enzymes are broken down by proteases in your stomach, intestine and pancreas. Let me be clear, purchased digestive enzymes are not used in any meaningful way by the body's catabolic pathways. They are a waste of money.) by a group of proteins called enzymes - specifically proteases. Proteases themselves have to be continually synthesised by the stomach wall (as does the proteins making up the stomach wall lining) as they attack themselves.
These enzymes are where we shall continue our exploration of proteins in the next hub of this series. I look forward to seeing you there!
Knowledge is Power
Where Next? Proteins
Diagrams and explanation of biological molecules including carbohydrates, lipids and proteins. An excellent collection of resources.
- DNA makes RNA - Transcription
Animated overview of DNA transcription. Excellent resource well worth a look
- RNA makes protein - Translation
Animated overview of DNA translation. Step-by-step guide and well worth a look for an in depth understanding of what occurs in this process
What are Proteins Series
- What Are Proteins? (Part 1 of 3)
First part of a series looking at proteins. This hub answers the questions 'Why do we Wee?' 'What are Proteins' and examines the central dogma of molecular biology
- What Are Proteins? (Part 3 of 3)
How is form related to function? How does primary structure influence tertiary structure? What is the secondary structure of a protein? What is tertiary for that matter? This hub answers these questions and more.