Funbio 2

Biological Molecules: Proteins

• Proteins are derived from the Greek word proteios, meaning "holding first place".
• They are the most abundant organic molecules in living systems. Over 100,000 different proteins exist.
• Proteins are present in every part of a cell and make up approximately 50% of the cellular dry weight.
• Proteins are fundamental for structure and function in life. They significantly influence a cell's appearance and functions.

Learning Outcomes

• Describe amino acid structure and the characteristics of the peptide bond.
• Explain polypeptide primary, secondary, and tertiary structure.
• Describe the role of structural and functional domains in protein tertiary structure.
• Explain the role of molecular chaperones in protein synthesis.
• Explain the role of enzymes in the body.

Proteins

• Proteins are polymers of amino acids.
• Amino acids contain two functional groups; an amino group (-NH2), and a carboxyl group (-COOH).
• Out of approximately 300 amino acids found in nature, only 20 are considered standard amino acids, appearing repeatedly in proteins.

Amino Acids - Building Blocks

• Amino acids are organic compounds.
• They are the basic building blocks of proteins, repeatedly occurring in their structure.

Amino Acid Structure

• All amino acids have a similar structure.
• They are known as alpha-amino acids as both carboxyl and amino groups are bonded to the alpha carbon.
• The alpha carbon also bonds to a R-group (side chain), which varies for each of the 20 amino acids.

Classification Based on Polarity

• Nonpolar: Hydrophobic; lack charge on their R-groups.
• Polar: Possess groups like hydroxyl and amide; participate in hydrogen bonding within protein structure. Lack charge on their R-groups.

Classification Based on Polarity (Electrically Charged)

• Positive charge: Polar amino acids with positive R-groups. (e.g., Lysine, Arginine, Histidine)
• Negative charge: Polar amino acids with negative R-groups. (e.g., Aspartic Acid, Glutamic Acid)

Peptide Bond

• A covalent bond that connects amino acids.
• Formed by removing a water molecule from the amino group of one amino acid and the carboxyl group of the adjacent amino acid.
• Creates a dipeptide, and extends to form polypeptides, and ultimately proteins (starting from the N-terminus).

Protein Structure

• Proteins have four levels of organization:
  • Primary: Amino acid sequence.
  • Secondary: Hydrogen bonding between amino acids results in structures like alpha-helices and beta-sheets.
  • Tertiary: Interactions among side chains fold the protein into a 3D structure.
  • Quaternary: Several polypeptide chains associate to form a larger structure.

Primary Structure

• The linear sequence of amino acids in a protein is its primary structure.
• This structure heavily influences the protein's function.
• Example: The first six amino acids in hemoglobin.

Secondary Structure

• Forming hydrogen bonds, the primary structure organizes into a compact structure.
• The alpha-helix and beta-sheet (parallel or antiparallel) are the most common structures.
• Keratin is an example.

Tertiary Structure

• The interactions between side chains bring about the protein's 3D conformation.
• Hydrogen and ionic bonding influence this process.
• RNA is one example.

Quaternary Structure

• Multiple polypeptide chains bond to form a complex structure.
• This interaction involves hydrogen bonds and Van der Waals forces between nonpolar side chains.
• Hemoglobin is an illustration.

Why Do Proteins Have Different Conformations?

• The amino acid sequence dictates the protein's conformation.
• Proteins normally fold into a single stable conformation initially.
• Environmental factors, like pH and temperature, can cause slight changes or even denaturation (unfolding). Denaturation disrupts hydrogen and ionic bonds, which often leads to a change in shape and loss of biological activity.

Molecular Chaperones

• Specialized proteins that aid in protein folding or unfolding.
• Facilitate and regulate protein conformational changes.
• Assist in the correct folding of proteins during or after synthesis.

What Determines a Protein's Biological Role/Activity?

• The entire protein's structure defines its role.
• Different protein regions can have varying functions.
• Variations in amino acid sequence, and the resulting 3D structure, define protein specialization.

Function of Proteins

• Enzymes: Speed up biochemical reactions. Examples include amylase (digestion) and diastase (starch to maltose conversion).
• Transport: Carry molecules. Examples include hemoglobin (oxygen transport), and albumin (lipoproteins transport).
• Storage: Store molecules. Examples include ferritin (iron).
• Others: Defensive, hormonal, structural, to name a few.

Enzymes

• Enzymes are proteins that speed up metabolic reactions.
• Each enzyme catalyzes a specific reaction.
• Enzymes are reusable.
• Enzymes are needed in small quantities, typically converting thousands of molecules per second.
• Enzyme functions are dependent on their shape and the ‘lock and key’ interactions with the substrate.

Test your knowledge on the structure and function of proteins with this quiz. Covering topics such as amino acid structure, protein synthesis, and the role of enzymes, this quiz will help reinforce your understanding of these essential biological molecules.