B1.2  Proteins

Theme:  Form and Function

Protein structure directly determines protein function through a hierarchical organization where each structural level creates the precise shape needed for specific biological roles.

• Amino acid structure provides the basic building blocks with variable R-groups (hydrophobic, hydrophilic, polar, charged) that create the chemical variety needed for different protein functions.
• Infinite structural possibilities arise from 20 amino acids combining in any sequence and length, creating unlimited functional potential through different molecular arrangements.
• Primary structure (amino acid sequence) determines all higher levels of organization and final function. Secondary structure (helices and sheets) provides stable frameworks through hydrogen bonding. Tertiary structure creates precise three-dimensional shapes through multiple bond types. Quaternary structure combines chains for complex functions.
• Globular proteins have compact, rounded shapes perfect for enzymes and hormones like insulin. Fibrous proteins have long, rope-like structures ideal for structural support like collagen. Membrane proteins have hydrophobic regions that match lipid bilayers for transport functions.
• Environmental sensitivity proves the form-function relationship; when pH or temperature disrupts protein shape through denaturation, biological function is immediately lost.

Guiding Questions:  
Guiding questions help students view the content of the syllabus through the conceptual lenses of both the themes and the levels of biological organization.

• What is the relationship between amino acid sequence and the diversity in form and function of proteins?
• How are protein molecules affected by their chemical and physical environments?

​
​Linking Questions:  
Linking questions strengthen students’ understanding by making connections between topics.  The ideal outcome of the linking questions is networked knowledge.

• How do abiotic factors influence the form of molecules?
• What is the relationship between the genome and the proteome of an organism? 

Key Terms to Know: * higher level only

Acidic*
Alpha-Carbon
Alpha Helix*
Amine
Amino Acid
Basic*
Beta-Pleated Sheet*
Carboxyl
Charged*
Collagen*
Condensation Reaction
Conformation*
Conjugated Protein*
Covalent Bond*
Cryogenic Electron Microscopy*

Denaturation
Dipepetide
Disulfide Bond*
Essential Amino Acid
Fibrous Protein*
Genetic Code
Globular Protein*
Haemoglobin*
Hydrogen Bond*
Hydrogen Ion (H+)*
Hydrophilic*
Hydrophobic*
Insulin*
Integral Protein*
Ionic Bond*

Non-Conjugated Protein*
Non-Essential Amino Acid
Non-Polar*
Peptide Chain
pH
Polar*
Polypeptides
Primary Structure*
Quaternary Structure*
R-Group
Secondary Structure*
Soluble*
Temperature
Tertiary Structure*
Vegan Diet

B1.2.1— Generalized structure of an amino acid.

• Draw the generalized structure of an amino acid.
• Label the amine group, carboxyl group, alpha carbon and R group on an amino acid.​

B1.2.2— Condensation reactions forming dipeptides and longer chains of amino acids.

• Define dipeptide, oligopeptide and polypeptide.  
• Draw peptide bond formation in  a condensation reaction between two amino acids.
• State where in the cell polypeptide formation occurs.

B1.2.3-- Dietary requirements for amino acids.

• ​Compare the source of amino acids by plant and animal cells.
• Define “essential”  and “non-essential” as related to dietary amino acids.
• Outline why vegan diets require attention to food combinations to ensure essential amino acids are consumed.

B1.2.4—  Infinite variety of possible peptide chains.

• State the number of amino acids used by living organisms to make polypeptides.
  
• Outline where there is an infinite variety of possible peptide chains.​
  

B1.2.5— Effect of pH and temperature on protein structure.

• Define denaturation.
• Explain the effect of pH on temperature on protein structure and function.​

AHL ​B1.2.6- Chemical diversity in the R-groups of amino acids as a basis for the immense diversity in protein form and function.

• Outline the effect of R-group structure on the properties of an amino acid, with reference to hydrophilic, hydrophobic, polar and charged.

AHL ​B1.2.7— Impact of primary structure on the conformation of proteins.

• Identify the “backbone” of a polypeptide. 
• Define “confirmation” as related to protein structure.
• Describe the primary structure of a protein, including the type of bonding involved.
• Outline how a DNA sequence codes for a polypeptide that will repeatedly fold into the same precise, predictable protein confirmation.
  

AHL ​B1.2.8- Pleating and coiling of secondary structure of proteins.

• Describe the secondary structure of a protein, including the type and location of the bonds  involved.
• Identify the alpha-helix and beta-pleated sheet in images of protein structure.

AHL ​B1.2.9- Dependence of tertiary structure on hydrogen bonds, ionic bonds, disulfide covalent bonds and hydrophobic interactions.

• Describe the tertiary structure of a protein, including the types of R-group interactions involved.
• Explain the effect of polar and non-polar R-groups of amino acids on tertiary structure of proteins. 
• Explain the effect of positively and negatively charged amino acid R-groups on the tertiary structure of proteins. 
• State that a strong disulfide covalent bond can occur between pairs of cysteine amino acids.

AHL ​B1.2.10- Effect of polar and non-polar amino acids on tertiary structure of proteins.

• State that amino acids can be hydrophobic or hydrophilic depending on the properties of the R-group.
• Discuss the arrangement of amino acids in soluble globular proteins.
• Discuss the arrangement of amino acids in integral membrane bound proteins.
• Discuss the arrangement of amino acids in channel proteins in membranes.

AHL ​B1.2.11- Quaternary structure of non-conjugated and conjugated proteins.

• Describe the quaternary structure of a protein. 
• Compare the structure of conjugated and non-conjugated proteins.
• State an example of a conjugated and non-conjugated protein.

AHL B1.2.12- Relationship of form and function in globular and fibrous proteins.

• Describe, with reference to collagen, the structure and function of fibrous proteins.
• Describe, with reference to insulin, the structure and specificity of globular proteins.