Chapter 3- 3.6- The structure of proteins Flashcards
What are polymers?
Peptides are polymers made up of amino acid molecules (the monomers).
Proteins consist of one or more polypeptides arranged as what?
Complex macromolecules and they have specific biological functions. All proteins contain the element carbon, hydrogen, oxygen, and nitrogen.
What are amino acids?
All amino acids have the basic structure. Different R-groups (variable groups) result in different amino acids. Twenty different amino acids are commonly found in cells.
Five of these are said to be non-essential as our bodies are able to make them from other amino acids.
Nine are essential and can only be obtained from what we eat. A further six are said to be conditionally essential as they are only needed by infants and growing children.
Explain the synthesis of peptides?
Amino acids join when the amine and carboxylic acid groups connected to the central carbon atoms react.
The R-groups are not involved at this point. The hydroxyl in the carboxylic acid group of one amino acid reacts with a hydrogen in the amine group of another amino acid.
A peptide bond if formed between the amino acids and water is produced (this is an example of a condensation reaction).
The resulting compound is a dipeptide.
When many amino acids are joined together by peptide bonds a polypeptide is formed. This reaction is catalysed by the enzyme peptidyl transferase present in ribosomes, the sites of protein synthesis.
The different R-groups of the amino acids making up a protein are able to interact with each other (R-group interactions) forming different types of bond. These bonds lead to the long chains amino acids (polypeptides) folding into complex structures (proteins).
The presence of different sequences of amino acids leads to different structures with different shapes being produced.
The very specific shapes of proteins are vital for the many functions proteins have within living organisms.
If you look at the way protein structures are built up in stages, it is easier to understood what is happening.
Explain separating amino acids using thin layer chromatography?
Thin layer chromatography (TLC) is a technique used to separate the individual components of a mixture.
The technique can be used to separate and identify a mixture of amino acids in solution.
There are two phases, the stationary phase and the mobile phase which involves an organic solvent.
The mobile phase picks up the amino acids and moves through the stationary phase and the amino acids are separated.
In the stationary phase a thin layer of silica gel (or another adhesive substance) is applied to a rigid surface, for example a sheet of glass or metal.
Amino acids are then added to one end of the gel. This end is then submerged in organic solvent. The organic solvent then moves through the silica gel, this is known as the mobile phase.
The rate at which the different amino acids in the organic solvent move through the silica gel depends on the interactions (hydrogen bonds) they have with the silica in the stationary phase, and their solubility in the mobile phase. This results in different amino acids moving different distances in the same time period resulting in them separating out from each other.
Explain the levels of protein structure in reference to primary structure
The primary structure is the sequence in which the amino acids are joined. It is directed by information carried within DNA.
The particular amino acid in the sequence will influence how the polypeptide folds to give the protein’s final shape.
This in turn determines its function. The only bonds involved in the primary structure of a protein are peptide bonds.
Explain the levels of protein structure in reference to the secondary structure
The oxygen, hydrogen, and nitrogen atoms of the basic, repeating structure of the amino acids (the variable groups are not there at this stage) interact.
Hydrogen bonds may form within the amino acid chain, pulling it into a coil shape called an alpha helix.
Polypeptide chains can also lie parallel to one another joined by hydrogen bonds, forming sheet-like structures. The pattern formed by the individual amino acids causes the structure to appear pleated, hence the name beta pleated sheet.
Secondary structure is the result of hydrogen bonds and forms at regions along long protein molecules depending on the amino sequences.
Explain the levels of protein structure in reference to tertiary structure
This is the folding of a protein into its final shape. It often includes sections of secondary structure.
The coiling or folding of sections of proteins into their secondary structure brings R-groups of different amino acids closer together so they are close enough to interact and further folding of these sections will occur.
What are the interactions that occur between R-groups in the tertiary structure?
Hydrophobic and hydrophilic interactions- weak interactions between polar and non-polar R-groups.
Hydrogen bonds- these are weakest of the bonds formed.
Ionic bonds- these are stronger than hydrogen bonds and form between oppositely charged R-groups.
Disulfide bonds (also known as disulphide bridges)- these are covalent and the strongest of the bonds but only form between R-groups that contain sulphur atoms.
This produces a variety of complex-shaped proteins. With specialised characteristics and functions.
Explain the levels of protein structure in reference to quaternary structure
This results from the association of two or more individual proteins called subunits.
The interactions between the subunits are the same in the tertiary structure except that they are between different protein molecules rather than within one molecule.
The protein subunits can be identical or different. Enzymes often consist of two identical subunits whereas insulin (a hormone) has two different subunits.
Haemoglobin, a protein required for oxygen transport in the blood, has four subunits, made up of two sets of two identical subunits.
What are hydrophobic and hydrophilic interactions?
Proteins are assembled in the aqueous environments of the cytoplasm. So the way in which a protein folds will also depend on whether the R-groups are hydrophobic or hydrophilic.
Hydrophilic groups are on the outside of the protein while hydrophobic groups are on the inside of the molecules shielded from the water in the cytoplasm.
Explain the breakdown of peptides
As you have learned, peptides are created by amino acids linking together in condensation reactions to form peptide bonds.
Protease are enzymes that catalyse the reverse reaction- turning peptides back into their constituent amino acids.
A water molecule is used to break the peptide bond in a hydrolysis reaction, reforming the amine and carboxylic acid groups.
What is a test for identifying proteins?
The biuret test, peptide bonds form violet coloured complexes with copper ions in alkaline solutions. This can be used as the basis of a test for proteins.
A mixture of an alkali and copper sulphate solution is called a biuret reagent and can be used instead of adding the solutions individually.
