B1.2 Proteins
Proteins connect amino acid structure, peptide-bond formation, dietary requirements, folding levels, R-group chemistry, denaturation, and functional protein shapes in cells.
- Syllabus
- First assessment 2025
- Topic
- B1.2
- Level
- SL
One Amino Acid Pattern, Three Functional Parts
Every amino acid has an alpha carbon bonded to four groups: an amine group, a carboxyl group, a hydrogen atom and a variable R-group.
H2N−CH(R)−COOH
The amine and carboxyl groups provide the shared chemistry for peptide-bond formation. The R-group varies among amino acids and changes charge, polarity, size and reactivity, thereby influencing protein folding and function.
In two amino-acid diagrams, the backbone groups can be identical while one R-group is non-polar and another charged; both form peptide bonds but interact differently after joining a chain.
The hydrogen on the alpha carbon is part of the generalized structure, and R is not an optional label: it represents the side chain that distinguishes amino acids.
Generalized amino acid structure
Assessment in practice
1 marksHow it is assessed
This objective is assessed through experimental design, commonly using Draw / Identify.
Command terms
Draw / Identify
What earns marks
Build the answer around this relationship: All amino acids have a central alpha carbon bonded to amine, carboxyl, hydrogen and R-group attachments.
Watch for
Omitting either the amine group or carboxyl group when drawing a generalized amino acid.
Representative question
Question 1
[Maximum number: 3]
The molecules of all amino acids include an amine group, a carboxyl group and an R-group. Draw a diagram to show the structure of an amino acid molecule.
a.
b.
and bonded to C ;
c.
Allow a specific amino acid R -
group in marking point c, such
as CH3 (in alanine).
3
max
Peptide Bonds Join Amino Acids
A peptide bond forms when the carboxyl group of one amino acid condenses with the amine group of another, releasing water and creating a covalent C–N link.
amino acid+amino acid→dipeptide+water
OH is removed from the carboxyl group and H from the amine group. Repeating condensation extends the polypeptide from its amino (N) terminus toward its carboxyl (C) terminus.
Two amino acids produce one peptide bond and one water molecule; adding a third amino acid produces a tripeptide with two peptide bonds and releases a second water molecule.
A peptide bond is the covalent link in the backbone, not a hydrogen bond. Hydrogen bonds stabilize later folding levels.
Condensation reactions
Assessment in practice
1–3 marksHow it is assessed
This objective is assessed through experimental design, commonly using Draw / Label / Annotate.
Command terms
Draw / Label / Annotate / State / Identify
What earns marks
Build the answer around this relationship: Peptide bonds form by condensation between carboxyl and amine groups.
Watch for
Calling peptide-bond formation hydrolysis instead of condensation.
Representative question
Question 1
[Maximum number: 4]
Draw molecular diagrams to show the condensation reaction between two amino acids to form a dipeptide.
a. each amino acid with a COO-/ COOH group at one end AND a NH2/NH3+at the other
b. CH in middle with H or R group attached
c. peptide bond correctly drawn between N and C=0
d. C O O-/ C O O H group at one end of dipeptide ANDNH2/NH3+at other end
e. loss of water
eg:
Both needed.
m p a requires the double bond to be shown between the C and O.
Both needed.
4 max
Diet Supplies Some Amino Acids
Essential amino acids cannot be synthesized in sufficient amounts and must be obtained from food; non-essential amino acids can be synthesized from other molecules in the body.
Protein synthesis requires every amino acid specified by the sequence. If one essential amino acid is unavailable, translation of that protein is limited even if all other amino acids are abundant.
A well-planned vegan diet can supply all essential amino acids by including sufficient amounts and a suitable variety of plant proteins. The syllabus does not require memorizing lists of essential amino acids.
If a diet supplies too little of one essential amino acid, that amino acid becomes limiting for synthesis of proteins that require it; consuming more of the other amino acids does not remove the limit.
Non-essential means synthesizable, not biologically unimportant. 'Essential' describes dietary supply, not whether the amino acid has a special position in every protein.
Dietary amino acids
Assessment in practice
1–2 marksHow it is assessed
This objective is assessed through structured response, commonly using Outline / Define / Distinguish.
Command terms
Outline / Define / Distinguish / State / Deduce / Evaluate
What earns marks
Build the answer around this relationship: Essential amino acids must be obtained from the diet.
Watch for
Saying non-essential amino acids are not used by the body.
Representative question
Question 1
[Maximum number: 2]
Some of the twenty amino acids that are linked together to make polypeptides in human cells are essential in the diet and others are not. Distinguish between essential and non-essential amino acids.
a. essential amino acids cannot be synthesized (by human cells)
OR
essential amino acids are required to be obtained by diet / OWTTE;
b. non-essential amino acids can be made (from other amino acids);
Sequence Creates Protein Variety
The genetic code specifies 20 common amino acids, and peptide chains can contain from a few to thousands of residues in any order, creating an immense variety of possible sequences.
At each position there can be many amino-acid choices, so the number of possible sequences grows exponentially with chain length. Genes specify particular orders; different cells express different sets of proteins, forming their proteomes.
Protein variety depends on amino-acid type, number and order. Sequence positions place different R-group chemistries together during folding, helping determine the final three-dimensional form and function.
Two chains with the same numbers of alanine and glycine can have different primary structures—and potentially different folds—when those residues occur in different orders.
A possible sequence is not automatically a stable functional protein, and a sequence change matters only through its effect on folding, stability, interactions or a functional site.
Infinite variety of peptide chains
Assessment in practice
2–7 marksHow it is assessed
This objective is assessed through structured response, commonly using Explain / Describe.
Command terms
Explain / Describe
What earns marks
Build the answer around this relationship: Protein primary structure depends on amino-acid number, type and order.
Representative question
Question 1
[Maximum number: 7]
Cells produce a large variety of proteins with different sequences of amino acids. Explain how this is done.
| a | protein is produced when a gene is expressed / switched on; |
| b | genetic code/codons consists of three nucleotides/bases/base triplet; |
| c | genetic code in DNA is transcribed/transcription (to mRNA); |
| d | mRNA exits the nucleus; |
| e | mRNA (code) is translated/translation into a polypeptide/protein; |
| f | amino acid sequence/polypeptide formation occurs at a ribosome; |
| g | one codon translates to one amino acid; |
| h | tRNA carries code for specific amino acids; |
| i | tRNA anticodon matches with specific codon in mRNA; |
| j | amino acids joined (by peptide bonds) to form polypeptide; |
| k | sequence of amino acids determined by order of bases/nucleotides/codons in DNA/mRNA; |
| l | proteins vary based on which amino acids are used and their order OR protein variety increases by mutations to DNA; |
Protein Shape Depends on Conditions
Protein shape is maintained by weak interactions that can be disrupted by extreme pH or temperature, causing denaturation and loss of function.
Heating increases molecular motion and extreme pH changes charges on R-groups. These changes disturb hydrogen bonds, ionic attractions and other interactions holding the folded chain in its working shape.
Predict a condition effect by asking:
- which interaction is disturbed
- whether the chain unfolds or changes active-site shape
- whether the change is reversible under the conditions
An enzyme may work faster as temperature rises to its optimum, then lose activity sharply when heating disrupts the shape of its active site.
Denaturation changes conformation, not necessarily the amino-acid sequence. Do not treat every loss of activity as peptide-bond hydrolysis.
Effect of pH and temperature
Assessment in practice
1–2 marksHow it is assessed
This objective is assessed through structured response, commonly using Outline / Explain / Identify.
Command terms
Outline / Explain / Identify
What earns marks
Build the answer around this relationship: Denaturation changes protein conformation and can remove biological function.
Watch for
Claiming denaturation changes the amino-acid sequence.
Representative question
Question 1
[Maximum number: 4]
Outline the process of protein denaturation.
change to conformation/shape/tertiary structure/3-D shape;
bonds within the protein/intramolecular bonds broken/changed;
pH and temperature (outside tolerated ranges) can cause denaturation;
vibrations/heat at high temperatures breaks bonds;
high pH/low pH/extreme pH alters ionization/charges (of amino acids and breaks ionic bonds);
protein cannot carry out its function
OR
active site of enzymes cannot bind substrates/catalyze reaction/no enzyme-substate complex;
permanent/irreversible change (usually)
OR
soluble proteins become insoluble/precipitate;
Build And Use Proteins
The core protein story is build -> vary -> function. Amino acids share a backbone but differ in R-groups. Peptide bonds form by condensation between carboxyl and amine groups. Some amino acids must come from diet, or protein synthesis is limited. Twenty coded amino acids create many sequences by type, number, and order. Finally, shape determines function, so denaturation changes performance.
- Amino acids share an alpha-carbon backbone and vary in R-groups.
- Peptide bonds form by condensation and release water.
- Essential amino acids must be obtained from dietary protein.
- Protein diversity depends on amino acid type, number, and order.
- Protein shape determines function; denaturation changes shape and function.
Objective notes
5 learning objectivesB1.2.1Generalized amino acid structure• Amino acids have an alpha carbon bonded to an amine, carboxyl, hydrogen, and R-group• The R-group varies between amino acids and determines chemical properties• Proteins contain C, H, O, N, and usually S4% of analysed papers 5 papers · 5 questionsViewB1.2.2Condensation reactions• Condensation joins the carboxyl group of one amino acid to the amine group of another• A peptide bond forms and water is released• Chains have an N-terminus and C-terminus and are assembled at ribosomes7% of analysed papers 10 papers · 11 questionsViewB1.2.3Dietary amino acids• Essential amino acids cannot be synthesized and must be obtained from dietary protein• Non-essential amino acids can be made by transamination, mainly in the liver• Deficiency of essential amino acids limits protein synthesis and can cause malnutrition8% of analysed papers 11 papers · 11 questionsViewB1.2.4Infinite variety of peptide chains• Twenty coded amino acids can form vast numbers of sequences• Protein diversity depends on amino acid type, number, and order• Genes encode polypeptide sequences; the proteome is the full protein set expressed1% of analysed papers 1 paper · 1 questionViewB1.2.5Effect of pH and temperature• Protein shape determines function, especially enzyme active sites• High temperature or unsuitable pH disrupts weak bonds and denatures proteins• Denaturation may be reversible in small proteins but often becomes irreversible2% of analysed papers 3 papers · 4 questionsView