EduNinja
IB Biology SL/Notes/B1.2 Proteins

IB Biology SLB1.2 ProteinsNotes

Read The Amino Acid Backbone

Every amino acid has the same backbone: an alpha carbon bonded to an amine group, a carboxyl group, a hydrogen atom, and an R-group. The R-group is the variable part, so it determines properties such as charge, polarity, hydrophobicity, and later folding behaviour. Proteins contain C, H, O, N, and usually S because some amino acids contain sulfur.

Amino acids have an alpha carbon bonded to an amine, carboxyl, hydrogen, and R-group.
The R-group varies and determines chemical properties.
Proteins contain C, H, O, N, and usually S.
Common backbone lets amino acids link; variable R-group creates diversity.

Use the shared backbone to recognize any amino acid, then look to the R-group for its chemistry.

Label the generalized amino acid.

Label
Labels
5

Label the generalized amino acid.

Choose
1. central carbon
2. NH2/NH3+ group
3. COOH/COO- group
4. H atom
5. variable side chain

Build A Peptide Bond

Peptide bonds form by condensation. The carboxyl group of one amino acid reacts with the amine group of another, water is released, and a peptide bond links the residues. The chain has direction: an N-terminus at one end and a C-terminus at the other. Ribosomes assemble polypeptides in this directional order.

Condensation joins the carboxyl group of one amino acid to the amine group of another.
A peptide bond forms and water is released.
Polypeptide chains have an N-terminus and C-terminus.
Ribosomes assemble polypeptides.

Track which atoms leave as water, then identify the new peptide bond and chain direction.

Put peptide-bond formation in order.

Order
1
water is released
2
peptide bond forms
3
H and OH are removed
4
chain has N-terminus and C-terminus
5
carboxyl group and amine group align

Put peptide-bond formation in order.

Choose
carboxyl group and amine group align
H and OH are removed
water is released
peptide bond forms
chain has N-terminus and C-terminus

Decide Which Amino Acids Must Come From Diet

Practice

Essential amino acids are “essential” because the body cannot synthesize enough of them, so they must come from dietary protein. Non-essential amino acids can be made by transamination, mainly in the liver. If an essential amino acid is missing, protein synthesis is limited because the ribosome cannot complete all needed polypeptides, which can contribute to malnutrition.

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 malnutrition.

Sort each statement into essential, non-essential, or deficiency consequence.

Sort
Unsorted
5
essential amino acids
0
non-essential amino acids
0
consequence of deficiency
0

Explain Protein Sequence Diversity

Protein diversity comes from sequence possibilities. Twenty coded amino acids can be combined in different types, numbers, and orders, creating vast numbers of polypeptide sequences. Genes encode those sequences, and the proteome is the full set of proteins expressed by a cell, tissue, or organism at a given time.

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 expressed.

Match each term to its role in protein diversity.

Match

Predict Denaturation From Shape Change

Practice

Protein shape determines function, especially for enzyme active sites. High temperature or unsuitable pH can disrupt weak bonds that maintain the folded shape. When the active site changes shape, the substrate no longer fits properly and function falls. Small proteins may sometimes refold, but denaturation is often irreversible.

Protein shape determines function, especially enzyme active sites.
High temperature or unsuitable pH disrupts weak bonds.
Denaturation changes conformation and can reduce or stop function.
Denaturation may be reversible in small proteins but often becomes irreversible.

An enzyme is moved to a very acidic solution. Predict what happens.

Predict

Core Transfer: Build And Use Proteins

Exam Practice

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.

Match each core prompt to its answer rule.

Match

Use this for core protein questions on amino acid structure, peptide-bond formation, essential amino acids, sequence diversity, or denaturation.

Label the generalized amino acid and explain that the R-group determines chemical properties.
State that peptide bonds form by condensation between carboxyl and amine groups, releasing water.
Distinguish essential amino acids from non-essential amino acids and link deficiency to limited protein synthesis.
Explain protein sequence diversity by amino acid type, number, and order.
Connect protein shape to function and denaturation to disruption of weak bonds and active-site shape.

Use this for core protein questions on amino acid structure, peptide-bond formation, essential amino acids, sequence diversity, or denaturation.

Proteins are built from amino acids with a shared alpha-carbon backbone and variable R-groups that determine chemical properties. Peptide bonds form by condensation between the carboxyl group of one amino acid and the amine group of another, releasing water and creating directional chains. Essential amino acids must be obtained from dietary protein, while non-essential amino acids can be made by transamination. Protein diversity comes from the type, number and order of the 20 coded amino acids. Protein shape determines function, so high temperature or unsuitable pH can disrupt weak bonds, denature the protein and reduce activity.

Listing terms without explaining how structure leads to function.