General properties of proteins
AQA
A-Level
Amino acids are the monomers from which proteins are made. Each amino acid has a central carbon atom bonded to four groups: an amine group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a variable side chain called the R group. The amine and carboxyl groups must be drawn on the same central carbon. The twenty amino acids common to all organisms differ only in their R group. For example, glycine has a hydrogen atom as its R group, whereas cysteine has a side chain containing sulfur. The sequence of R groups influences a protein's properties because R groups vary in size, charge and polarity, so they determine the bonds that form when the protein folds.
27
Objectives
24
Exam Tips
40
Pitfalls
43
Key Terms
45
Mark Points
Subtopics in this area
Amino acids are the monomers from which proteins are made. The general structure of an amino acid as: where NH represents an amine group, COOH represents a carboxyl group and R represents a side chain. The twenty amino acids that are common in all organisms differ only in their side group.
A condensation reaction between two amino acids forms a peptide bond.
Dipeptides are formed by the condensation of two amino acids. Polypeptides are formed by the condensation of many amino acids.
A functional protein may contain one or more polypeptides.
The role of hydrogen bonds, ionic bonds and disulfide bridges in the structure of proteins.
Proteins have a variety of functions within all living organisms.
The relationship between primary, secondary, tertiary and quaternary structure, and protein function.
The biuret test for proteins.
Students should be able to relate the structure of proteins to properties of proteins named throughout the specification.
General properties of proteins Revision Guide
Learning Objectives
What you need to know and understand
- Draw and label the general structure of an amino acid, naming the amine group, the carboxyl group and the R group.
- State what is the same and what differs between the twenty amino acids common to all organisms.
- Explain how variation in R groups leads to variation in the bonds that can form within a folded protein.
- Describe how a peptide bond is formed, naming the two functional groups involved and the molecule released.
- Explain why a peptide bond involves the backbone of an amino acid rather than its R group.
- Describe how peptide bonds are hydrolysed, naming the molecule required to break the bond.
- Calculate the number of peptide bonds formed and water molecules released when a stated number of amino acids condenses.
- Describe the formation of a dipeptide and a polypeptide by condensation.
- Explain how hydrolysis reverses condensation and breaks peptide bonds.
- State what quaternary structure means and name a protein that has it and one that does not.
- Describe the interactions that hold two or more polypeptides together in a functional protein.
- Explain why haemoglobin needs four polypeptide chains to show cooperative binding of oxygen.
- Name the bonds and interactions that hold secondary, tertiary and quaternary structure together, and say where each forms.
- Explain why a change in pH breaks ionic bonds within a protein and what this does to its tertiary structure.
- Suggest why a protein containing many disulfide bridges is more resistant to high temperatures than one with none.
- Name four different functions of proteins and give a named protein for each.
- Explain why proteins can perform such a wide range of roles, referring to the three-dimensional shape of each molecule.
- Describe the role of specific proteins in transport, structural support, and regulation.
- Describe each of the four levels of protein structure and name the bonds responsible for each.
- Explain how the primary structure of a polypeptide determines its tertiary structure and therefore its function.
- Explain how quaternary structure, including multiple polypeptides and prosthetic groups, contributes to protein function.
- Describe the biuret test, naming both reagents and stating the positive and negative results.
- Explain why a solution of free amino acids gives a negative biuret result while a protein gives a positive one, referring to peptide bonds.
- Describe how the biuret test can be used to compare the protein concentrations of two solutions.
- Relate a named protein's property, such as the cooperative binding of haemoglobin, to a specific feature of its structure.
- Explain how the tertiary structure of an enzyme, antibody or carrier protein produces its specificity.
- Explain how denaturation changes a protein's tertiary structure and so removes its function.
Marking Points
Key points examiners look for in your answers
- one mark for drawing the general structure of an amino acid with the amine group (-NH2), carboxyl group (-COOH), hydrogen atom and R group all bonded to the same central carbon
- one mark for labelling the amine group, the carboxyl group and the R group correctly on the general structure
- one mark for stating that the twenty amino acids common to all organisms differ only in their R group or side chain
- one mark for stating that amino acids are the monomers from which proteins are made
- one mark for explaining that R groups vary in size, charge and polarity, so they determine the bonds that form when the protein folds
- State that amino acids are joined by peptide bonds.
- State that the bond is formed by a condensation reaction.
- Identify the reacting groups as the carboxyl group of one amino acid and the amine group of the next.
- State that one molecule of water is released per peptide bond formed.
- State that peptide bonds are hydrolysed, using water, when the polypeptide is broken down into amino acids.
- one mark for a dipeptide being two amino acids joined by condensation, forming one peptide bond
- one mark for a polypeptide being many amino acids joined by condensation
- one mark for calculating that n amino acids form n-1 peptide bonds and release n-1 water molecules
- one mark for stating that hydrolysis breaks a peptide bond and uses a molecule of water
- one mark for distinguishing a polypeptide (a chain of amino acids) from a protein (a folded, functional molecule)
- one mark for quaternary structure meaning more than one polypeptide chain in the functional protein
- one mark for the chains being held together by bonds or interactions between polypeptides, not by peptide bonds
- one mark for naming those interactions as hydrogen bonds, ionic bonds, disulfide bridges or hydrophobic interactions
- one mark for a correct named example, such as haemoglobin with four polypeptides or insulin with two
- one mark for identifying a prosthetic group, such as haem, as part of the functional protein
- one mark for hydrogen bonds forming the secondary structure, the alpha helix or beta pleated sheet
- one mark for tertiary structure being formed by interactions between R groups
- one mark for naming hydrogen bonds, ionic bonds, disulfide bridges or hydrophobic interactions as those R group interactions
- one mark for disulfide bridges being covalent bonds between two cysteine R groups and stronger than hydrogen or ionic bonds
- one mark for heat or pH breaking hydrogen and ionic bonds, so the tertiary structure changes and the protein is denatured
- one mark for each named function with a correct example, such as enzymes as catalysts or antibodies binding antigens
- one mark for identifying a structural role with a named protein such as collagen or keratin
- one mark for a transport role, naming haemoglobin or channel and carrier proteins
- one mark for linking each function to the specific three-dimensional shape of the protein
- one mark for identifying a regulatory role, such as hormones binding to receptors or transcription factors regulating gene expression
- one mark for primary structure as the sequence of amino acids in the polypeptide
- one mark for secondary structure as the alpha helix or beta pleated sheet formed by hydrogen bonding
- one mark for tertiary structure as the three-dimensional folding formed by interactions between R groups
- one mark for quaternary structure as two or more polypeptide chains held together
- one mark for explaining that specific tertiary or quaternary structures create functional regions, such as active sites
- one mark for adding sodium hydroxide solution to make the sample alkaline
- one mark for then adding dilute copper(II) sulfate solution, or for using biuret reagent
- one mark for a positive result being a colour change from blue to purple, lilac or violet
- one mark for stating that the solution stays blue if no protein is present
- one mark for using a colorimeter with a calibration curve of known concentrations to make the test quantitative
- naming the level of structure responsible for a stated property, such as quaternary structure in haemoglobin
- linking the tertiary structure of an active site or binding site to specificity and complementary shape
- explaining a loss of function through broken hydrogen and ionic bonds changing the tertiary structure
- relating an antibody's specificity to the tertiary structure of its variable region
- making the link explicit between the structural feature and the property, rather than stating them separately
Examiner Tips
Expert advice for maximising your marks
- 💡Learn the general structure well enough to draw it from memory, labelling the amine group, carboxyl group, hydrogen atom and R group.
- 💡When discussing protein structure, remember that the R groups are the variable part that determines specific bonding interactions, such as ionic bonds, hydrogen bonds and disulfide bridges.
- 💡Always explicitly state both 'condensation reaction' and 'peptide bond' when describing the joining of amino acids, as both terms are essential for a complete biological description.
- 💡Remember that the peptide bond is a backbone bond, and that R group interactions belong to tertiary structure.
- 💡Do the n-1 calculation on paper rather than in your head; the off-by-one error is the single most common slip in this topic.
- 💡Reserve the word protein for a folded, functional molecule and use polypeptide for the chain itself.
- 💡When asked about hydrolysis, state that it is the reverse of condensation and that water is used to break the peptide bond.
- 💡Never write peptide bond when describing what holds polypeptides together in quaternary structure - it is an explicit exclusion.
- 💡Keep two examples ready, one single-chain and one multi-chain, so you can answer either direction of the question.
- 💡Mention prosthetic groups where relevant; haemoglobin without haem is an incomplete description.
- 💡Match the disruption to the bond: pH changes break ionic bonds, heat breaks hydrogen and ionic bonds, and disulfide bridges resist both.
- 💡Say 'interactions between R groups' when describing tertiary structure - it is the phrase the mark scheme uses.
- 💡Do not offer peptide bonds as an answer about tertiary or quaternary structure; they belong to primary structure only.
- 💡Always attach a named example to a named function; a bare list of functions rarely scores.
- 💡Where a question asks about a protein you have not met, work from its shape and its binding site rather than trying to recall it.
- 💡Use the specific term 'tertiary structure' rather than just '3D shape' to ensure clarity in your answers.
- 💡Set out the causal chain in order: primary sequence, R group interactions, tertiary structure, and resulting function.
- 💡Remember that quaternary structure can involve non-protein prosthetic groups, like the haem group in haemoglobin, which are essential for function.
- 💡Remember what the test actually detects - peptide bonds - because that explains both the positive and the negative results.
- 💡Name both reagents, sodium hydroxide and copper(II) sulfate, even if you also mention biuret reagent, and leave heating out of the method - biuret is done at room temperature.
- 💡If asked to compare protein concentrations, describe a colorimeter and a calibration curve built from known standards.
- 💡Build a table of every named protein in the specification with its level of structure and the property that follows from it.
- 💡In extended answers, integrate the topics rather than listing them; the highest bands reward linked, clearly explained points across several areas.
- 💡Use complementary, tertiary structure and binding site as your standard vocabulary for any protein-function explanation.
Common Mistakes
Pitfalls to avoid in your exam answers
- drawing the amine and carboxyl groups on different carbon atoms; correction: both groups, plus the hydrogen atom and R group, must be bonded to the same central carbon
- saying the twenty amino acids differ in their amine or carboxyl groups; correction: they differ only in their R group or side chain
- writing carbonyl instead of carboxyl for the -COOH group; correction: the carboxyl group is -COOH, and the amine group is -NH2
- describing the R group vaguely as 'the rest of the molecule' with no reference to it being variable; correction: state that the R group is the variable side chain that differs between amino acids
- Saying the peptide bond forms between the R groups of two amino acids. Correction: State that the peptide bond forms between the carboxyl and amine groups of the backbone, not the R groups.
- Writing that water is added when the peptide bond forms, rather than eliminated. Correction: Specify that water is eliminated (or released) during a condensation reaction, whereas it is added during hydrolysis.
- Naming the bond as a glycosidic or ester bond in a protein question. Correction: Ensure you use 'peptide bond' for proteins, reserving glycosidic for carbohydrates and ester for lipids.
- Using 'broken down' about a polypeptide without naming the peptide bond or the hydrolysis. Correction: Use precise terminology by stating that peptide bonds are hydrolysed.
- saying a dipeptide contains two peptide bonds - a dipeptide of two amino acids has one peptide bond
- stating that ten amino acids release ten molecules of water rather than nine - the number of water molecules equals the number of peptide bonds, which is n-1
- using polypeptide and protein as if they always mean the same thing - a protein is a folded, functional molecule and may contain more than one polypeptide chain
- forgetting that hydrolysis is the reverse of condensation and requires a molecule of water to break the peptide bond
- miscounting peptide bonds in a tripeptide - a tripeptide has two peptide bonds, not three
- saying the polypeptides of a quaternary structure are joined by peptide bonds, which is not credited
- claiming every protein has a quaternary structure
- giving haemoglobin two polypeptide chains instead of four
- omitting the haem groups when describing haemoglobin as a functional protein
- treating a polypeptide and a functional protein as identical
- saying disulfide bridges can form between any two R groups rather than between two cysteines
- describing ionic bonds as covalent, or disulfide bridges as weak
- claiming peptide bonds hold the tertiary structure together
- stating that a single hydrogen bond is strong, instead of many weak bonds acting together
- saying denaturation breaks peptide bonds and changes the primary structure
- writing that proteins are needed 'for growth and repair', which is not an A-level answer
- assuming all proteins are enzymes, ignoring structural or transport roles
- giving energy storage as a primary function of proteins, which is a role for carbohydrates and lipids
- using the vague term 'shape' instead of specifying 'tertiary structure' when describing 3D folding
- saying secondary structure is held by ionic bonds or disulfide bridges
- claiming every protein has all four levels of structure (many lack quaternary structure)
- describing primary structure as the number of amino acids rather than their sequence
- stating that a mutation changes the tertiary structure directly, without mentioning the change to the primary structure first
- heating the biuret test in a water bath, as for Benedict's
- giving the positive result as brick-red, confusing it with the reducing sugar test
- omitting the sodium hydroxide, so the reaction cannot occur in alkaline conditions
- saying the test detects amino acids, when free amino acids have no peptide bonds and give a negative result
- reporting the blue starting colour as the positive result
- describing a protein's structure and its property in separate sentences without linking them
- attributing enzyme specificity to primary structure directly, missing the tertiary structure step
- saying denaturation breaks peptide bonds rather than hydrogen and ionic bonds
- using shape rather than tertiary structure when explaining how a binding site works