chapter 3 p4

Question 1

Peptides are

Answer 1

polymers made up of amino acid molecules (the monomers).

Question 2

Proteins consist of

Answer 2

one or more polypeptides arranged as complex macromolecules and they have specific biological functions.
All proteins contain the elements carbon, hydrogen, oxygen, and nitrogen.

Question 3

Amino acids:

Answer 3

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.

Question 4

general structure of Amino acid

Answer 4

Question 5

Synthesis of peptides:

Answer 5

• 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.

Question 6

polypeptides

Answer 6

• 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.

Question 7

Separating amino acids using thin layer chromatography: p1

Answer 7

• 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.

Question 8

Separating amino acids using thin layer chromatography: p2

Answer 8

• 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.

Question 9

A student carried out the following procedure to separate and identify a mixture of amino acids in solution.

Answer 9

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.

Question 10

Suggest why gloves were worn by the student and the plate was only handled by the edges.

Answer 10

to prevent contaminating stationary phase (1); idea of biological material (on skin

Question 11

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.

Answer 11

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)

Question 12

c. Explain why the solvent was no more than 1 cm deep.

Answer 12

so the concentrated spots were not covered

Question 13

Suggest why the jar was sealed.

Answer 13

(so) air inside jar is saturated with (solvent) (1); prevents evaporation of solvents

Question 14

Rf =

Answer 14

distance travelled by component /distance travelled by solvent

Question 15

Levels of protein structure
Primary structure

Answer 15

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.

Question 16

Secondary structure

Answer 16

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.

Question 17

Tertiary structure

Answer 17

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.

Question 18

The following interactions occur between the R-groups in the Tertiary structure:

Answer 18

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).

Question 19

Quaternary structure

Answer 19

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).

Question 20

Hydrophilic and hydrophobic interactions:

Answer 20

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.

Question 21

Breakdown of peptides:

Answer 21

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.

Question 22

Identification of proteins:

Answer 22

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.

Question 23

State the colour you would expect to see on addition of the copper sulfate solution if protein is present in the sample.

Answer 23

mauve / lilac / purple

Question 24

State the colour you would expect to see if the sample contained amino acids instead of proteins.
Explain the reason for this colour.

Answer 24

no peptide bonds present (as no protein) (1); test is negative (1); solution (remains) blue (1); as copper sulfate solution is blue

Question 25

Suggest why this test is not used quantitatively.

Answer 25

Biuret test identifies peptide bonds (1); degree of colour change dependent on number of peptide bonds (1); different proteins have different numbers of peptide bonds (1); idea that different degrees of colour change could indicate different proteins not different quantities of protein (1).

Question 26

complex tertiary and quaternary structures of proteins are built up.
These structures determine the role the protein will play in the body.
The two main groups are

Answer 26

globular proteins and fibrous proteins.

Question 27

Globular proteins

Answer 27

Globular proteins are compact, water soluble, and usually roughly spherical in shape.
They form when proteins fold into their tertiary structures in such a way that the hydrophobic R-groups on the amino acids are kept away from the aqueous environment.
The hydrophilic R-groups are on the outside of the protein.
This means the proteins are soluble in water.
This solubility is important for the many different functions of globular proteins.
They are essential for regulating many of the processes necessary to life, these include processes such as chemical reactions, immunity, muscle contraction, and many more.

Question 28

Insulin:

Answer 28

Insulin is a globular protein.
It is a hormone involved in the regulation of blood glucose concentration.
Hormones are transported in the bloodstream so need to be soluble.
Hormones also have to fit into specific receptors on cell-surface membranes to have their effect and therefore need to have precise shapes.

Question 29

Conjugated proteins:

Answer 29

Conjugated proteins are globular proteins that contain a non-protein component called a prosthetic group.
Proteins without prosthetic groups are called simple proteins.
There are different types of prosthetic groups.
Lipids or carbohydrates can combine with proteins forming lipoproteins or glycoproteins.
Metal ions and molecules derived from vitamins also form prosthetic groups.
Haem groups are examples of prosthetic groups. They contain an ironn ion (Fe2+).
Catalase and haemoglobin both contain haem groups.

Question 30

Haemoglobin:

Answer 30

Haemoglobin is the red, oxygen-carrying pigment found in red blood cells.
It is a quaternary protein made from four polypeptides, two alpha and two beta subunits
Each subunit contains a prosthetic haem group.
The iron n ions present in the haem groups are each able to combine reversibly with an oxygen molecule.
This is what enables haemoglobin to transport oxygen around the body.
It can pick oxygen up in the lungs and transport it to the cells that need it, where it is released.

Question 31

Catalase:

Answer 31

Catalase is an enzyme.
Enzymes catalyse reactions, meaning they increase reaction rates, and each enzyme is specific to a particular reaction or type of reaction.
Catalase is a quaternary protein containing four haem prosthetic groups.
The presence of the iron Il ions in the prosthetic groups allow catalase to interact with hydrogen peroxide and speed up its breakdown.
Hydrogen peroxide is a common byproduct of metabolism but is damaging to cells and cell components if allowed to accumulate.
Catalase makes sure this doesn’t happen.

Question 32

Fibrous proteins:

Answer 32

Fibrous proteins are formed from long, insoluble molecules.
This is due to the presence of a high proportion of amino acids with hydrophobic R-groups in their primary structures.
They contain a limited range of amino acids, usually with small R-groups.
The amino acid sequence in the primary structure is usually quite repetitive.
This leads to very organised structures reflected in the roles fibrous proteins often have.
Keratin, elastin, and collagen are examples of fibrous proteins.
Fibrous proteins tend to make strong, long molecules which are not folded into complex three-dimensional shapes like globular proteins.

Question 33

Keratin:

Answer 33

Keratin is a group of fibrous proteins present in hair, skin, and nails.
It has a large proportion of the sulfur-containing amino acid, cysteine.
This results in many strong disulfide bonds (disulfide bridges) forming strong, inflexible, and insoluble materials.
The degree of disulfide bonds determines the flexibility - hair contains fewer bonds making it more flexible than nails, which contain more bonds.
The unpleasant smell produced when hair or skin is burnt is due to the presence of relatively large quantities of sulfur in these proteins.

Question 34

Elastin:

Answer 34

Elastin is a fibrous protein found in elastic fibres (along with small protein fibres).
Elastic fibres are present in the walls of blood vessels and in the alveoli of the lungs - they give these structures the flexibility to expand when needed, but also to return to their normal size.
Elastin is a quaternary protein made from many stretchy molecules called tropoelastin .

Question 35

Collagen:

Answer 35

Collagen is another fibrous protein.
It is a connective tissue found in skin, tendons, ligaments and the nervous system.
There are a number of different forms but all are made up of three polypeptides wound together in a long and strong rope-like structure.
Like rope, collagen has flexibility

Question 36

The structure of fibrous proteins
Elastin:

Answer 36

Elastin is made by linking many soluble tropoelastin protein molecules to make a very large, insoluble, and stable, cross-linked structure
Tropoelastin molecules are able to stretch and recoil without breaking, acting like small springs.
They contain alternate hydrophobic and lysine-rich areas.
Elastin is formed when multiple tropoelastin molecules aggregate via interactions between the hydrophobic areas.
The structure is stabilised by cross-linking covalent bonds involving the amino acid lysine, but the polypeptide structure still has flexibility.
Elastin confers strength and elasticity to the skin and other tissues and organs in the body.

Question 37

The structure of fibrous proteins
Collagen:

Answer 37

Collagen molecules have three polypeptide chains wound around each other in a triple helix structure to form a tough, rope-like protein (Figure 5d and e).
Every third amino acid in the polypeptide chains is glycine, which is a small amino acid.
Its small size allows the three protein molecules to form a closely packed triple helix.
Many hydrogen bonds form between the polypeptide chains forming long quaternary proteins with staggered ends (Figure 5d).
These allow the proteins to join end to end, forming long fibrils called tropocollagen (Figure 5c).
The tropocollagen fibrils cross-link to produce strong fibres.
Collagen also contains high proportions of the amino acids proline and hydroxyproline.
The R-groups in these amino acids repel each other and this adds to the stability of collagen.
In some tissues, multiple fibres of collagen aggregate into larger bundles (Figure 5a).
This is the structure found in ligaments and tendons. In skin, collagen fibres form a mesh that is resistant to tearing.

Question 38

Suggest what property the arrangement of collagen fibres into large bundles gives to tendons.

Answer 38

• strength, non-elastic

Question 39

As we age the collagen in our skin starts to break down. This leads to the loss of skin structure and the formation of wrinkles. Many beauty products are available that contain collagen in the form of creams and capsules. Using your knowledge of the structure of collagen, suggest why these products are unlikely to have any beneficial effect in reducing or preventing wrinkles.

Answer 39

• (collagen is a) large molecule so unlikely to enter skin (collagen), has a complex structure, idea of individual components arranged in hierarchical structure, idea that new molecules would not incorporate into existing collagen