# Proteins

> IB Biology SL · Theme B: Form and Function
> Source: https://www.owlsprep.com/study/ib-biology-sl-u2-proteins/

This sub-topic covers amino acid structure, peptide bond formation, the four hierarchical levels of protein organization, and the critical relationship between protein shape and function. You will also explore classification and diverse biological roles of proteins.

**Prerequisites:** [Introduction to biological macromolecules](https://www.owlsprep.com/study/ib-biology-sl-u2-intro-to-biological-macromolecules/)

## Learning objectives

- Describe the structure of amino acids and peptide bond formation via condensation
- Outline the four hierarchical levels of protein structure and their stabilizing interactions
- Distinguish between fibrous and globular proteins with named examples
- Summarize the diverse range of protein functions in living organisms
- Explain the relationship between protein structure, denaturation, and function

## Amino Acids and Peptide Bond Formation

**Amino Acid** — The monomeric building block of all polypeptides and proteins. All amino acids share a common core structure: a central carbon atom bonded to an amino group (-NH₂), a carboxyl group (-COOH), a hydrogen atom, and a variable R-group that determines the amino acid's chemical properties.

*Example:* Glycine has a hydrogen atom as its R-group, while alanine has a methyl (-CH₃) R-group.

Amino acids are linked into chains via condensation reactions. During this reaction, the carboxyl group of one amino acid reacts with the amino group of the next, releasing one water molecule and forming a stable covalent peptide bond.

**Worked example:** Describe what occurs when a dipeptide is formed from two amino acids

1. 1. Identify the reactive groups on each amino acid: the carboxyl (-COOH) group on the first amino acid and the amino (-NH₂) group on the second.
2. 2. A hydroxyl (-OH) group is removed from the carboxyl, and a hydrogen atom is removed from the amino group.
3. 3. The removed groups combine to form one water molecule, which is released as a product.
4. 4. A covalent peptide bond (C-N) forms between the two amino acids, creating a dipeptide.

## Four Levels of Protein Structure

**Primary Structure** — The unique linear sequence of amino acids in a polypeptide chain, determined directly by the nucleotide sequence of the gene that codes for the protein.

After a polypeptide is synthesized at the ribosome, it folds into four hierarchical levels of structure, each stabilized by different chemical interactions:

| Level | Description | Stabilizing Interactions |
| --- | --- | --- |
| Primary | Linear sequence of amino acids | Covalent peptide bonds |
| Secondary | Local folding into α-helices or β-pleated sheets | Hydrogen bonds between peptide backbone groups |
| Tertiary | Overall 3D shape of a single polypeptide | Interactions between R-groups (H-bonds, ionic bonds, disulfide bridges, hydrophobic interactions) |
| Quaternary | Assembled structure of multiple polypeptide subunits | Same R-group interactions as tertiary structure |

**Worked example:** Explain why changing one amino acid in the primary sequence can change protein function

1. 1. All higher levels of protein folding depend on the identity and position of R-groups in the primary sequence.
2. 2. For example, in sickle cell hemoglobin, hydrophilic glutamic acid is replaced by hydrophobic valine.
3. 3. The hydrophobic valine on the protein surface causes hemoglobin molecules to stick together, changing the overall 3D shape.
4. 4. The altered shape can no longer carry oxygen efficiently, so function is lost. This confirms primary structure determines final shape and function.

## Fibrous vs Globular Proteins

Proteins are classified into two broad groups based on shape, solubility, and function:

**Comparing methods**

- **Fibrous Proteins** — Long, strand-like proteins with repeating amino acid sequences
  - Pros: Very stable, provide strong structural support
  - Cons: Not suited for binding specific molecules or dynamic functional roles

- **Globular Proteins** — Compact, rounded proteins with irregular amino acid sequences
  - Pros: Fold into specific shapes that can bind other molecules for dynamic roles
  - Cons: Less stable, more prone to denaturation

**Worked example:** Justify why collagen is classified as a fibrous protein

1. 1. Collagen's function is to provide tensile strength to connective tissue (bone, skin, tendons) in animals.
2. 2. It has a repeating amino acid sequence that forms a long, stable triple-helix structure, matching fibrous protein characteristics.
3. 3. It is insoluble in water, which is a key property of fibrous proteins.
4. 4. Its structural role aligns with the function of fibrous rather than globular proteins, so it is correctly classified as fibrous.

## Protein Function and Denaturation

**Denaturation** — A permanent change to a protein's 3D shape caused by disruption of the weak interactions that stabilize folding. Common triggers include high temperature and extreme pH.

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