chapter 3 p4 Flashcards
Peptides are
polymers made up of amino acid molecules (the monomers).
Proteins consist of
one or more polypeptides arranged as complex macromolecules and they have specific biological functions.
All proteins contain the elements carbon, hydrogen, oxygen, and nitrogen.
Amino acids:
All amino acids have the same basic structure (Figure 1).
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.
general structure of Amino acid
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 is formed between the amino acids and water is produced (this is another example of a condensation reaction,
- The resulting compound is a dipeptide.
polypeptides
- 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 of 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.
Separating amino acids using thin layer chromatography: p1
- 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.
Separating amino acids using thin layer chromatography: p2
- 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.
- Remember, when working with chemicals to take care, wear safety glasses and report any spillages/ breakages to the teacher.
A student carried out the following procedure to separate and identify a mixture of amino acids in solution.
Wearing gloves, the student drew a pencil line on the chromatography plate about 2 cm from the bottom edge. The plate was only handled by the edges.
Four equally spaced points were marked at along the pencil line.
The amino acid solution was spotted onto the first pencil mark using a capillary tube. The spot was allowed to dry and then spotted again. The spot was labelled using a pencil.
The three remaining marks were spotted with solutions of three known amino acids.
The plate was then placed into a jar containing the solvent. The solvent was no more than 1cm deep. The jar was then closed.
The plate was left in the solvent until it had reached about 2 cm from the top. The plate was then removed and a pencil line drawn along the solvent front. The plate was then allowed to dry.
The plate was then sprayed, in a fume cupboard, with ninhydrin spray. Amino acids react with ninhydrin and a purple/brown colour is produced. The centre of each spot present was then marked with a pencil.
Here you can see the TLC plate showing the separated amino acids appearing purple after spraying with ninhydrin.
Suggest why gloves were worn by the student and the plate was only handled by the edges.
to prevent contaminating stationary phase (1); idea of biological material (on skin
A mixture of solvents [such as hexane, water, acetic acid, and butanol) is usually used as the mobile phase when separating an unknown mixture of amino acids. Suggest why.
testing unknown compounds (1); not known whether, polar / non-polar (1); idea that the different solvents will dissolve both polar and non-polar compounds (1)
c. Explain why the solvent was no more than 1 cm deep.
so the concentrated spots were not covered
Suggest why the jar was sealed.
(so) air inside jar is saturated with (solvent) (1); prevents evaporation of solvents
Rf =
distance travelled by component /distance travelled by solvent
Levels of protein structure
Primary structure
this is the sequence in which the amino acids are joined.
It is directed by information carried within DNA
The particular amino acids 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.
Secondary structure
the oxygen, hydrogen, and nitrogen atoms of the basic, repeating structure of the amino acids the variable groups are not involved at this stage) interact.
Hydrogen bonds may form within the amino acid chain, pulling it into a coil shape called an alpha helix (Figure 3a).
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 (Figure 3b).
Secondary structure is the result of hydrogen bonds and forms at regions along long protein molecules depending on the amino sequences.
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 structures brings R-groups of different amino acids closer together so they are close enough to interact and further folding of these sections will occur.
The following interactions occur between the 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 disulfide bridges) - these are covalent and the strongest of the bonds but only form between R-groups that contain sulfur atoms.
This produces a variety of complex-shaped proteins, with specialised characteristics and functions (Figure 4).
Quaternary structure
this results from the association of two or more individual proteins called subunits.
The interactions between the subunits are the same as 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 (Figure 5).
Hydrophilic and hydrophobic interactions:
Proteins are assembled in the aqueous environment of the cytoplasm.
So the way in which a protein folds will also depend on whether the R-groups are hydrophilic or hydrophobic.
Hydrophilic groups are on the outside of the protein while hydrophobic groups are on the inside of the molecule shielded from the water in the cytoplasm.
Breakdown of peptides:
peptides are created by amino acids linking together in condensation reactions to form peptide bonds.
Proteases 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.
Identification of proteins:
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 student carried out the following procedure to test a sample for the presence of protein.
3 cm3 of a liquid sample was mixed with an equal volume of 10% sodium hydroxide solution.
1% copper sulfate solution was then added a few drops at a time until the sample solution turned blue.
The solution was mixed and left to stand for five minutes.
This test is known as the biuret test. A mixture of an alkali and copper sulfate solution is called biuret reagent and can be used instead of adding the solutions individually.
State the colour you would expect to see on addition of the copper sulfate solution if protein is present in the sample.
mauve / lilac / purple
State the colour you would expect to see if the sample contained amino acids instead of proteins.
Explain the reason for this colour.
no peptide bonds present (as no protein) (1); test is negative (1); solution (remains) blue (1); as copper sulfate solution is blue
