Biology Chapter on Proteins and Enzymes

Chapter 3: Protein Structure and Function

• This chapter examines protein structure and function, including amino acids, primary structures, secondary, tertiary, and quaternary structures, and factors influencing enzyme activity.

3.1 Proteins and Amino Acids

• Proteins originate from the Greek word "proteios," signifying "first," highlighting their crucial roles in living organisms.
• Proteins function as essential biological agents, with amino acids serving as their building blocks.
• The remarkable diversity of proteins in nature arises from the intrinsic properties of only 20 common amino acids.
• These properties include the capacity to polymerize, diverse acid-base properties, varied structures and chemical functionalities in side chains, and chirality (handedness in molecules). A chiral molecule cannot be superimposed on its mirror image.

3.2 Proteins: Primary Structure

• The primary structure of a protein is defined by its linear sequence of amino acids.
• Peptide bonds link adjacent amino acids, forming a polypeptide chain.

3.3 Proteins: Secondary, Tertiary, and Quaternary Structures

• Secondary structure refers to the repeating, regular patterns formed by the polypeptide chain. Common examples of these patterns include alpha-helices and beta-pleated sheets. Hydrogen bonds between the amide hydrogens (N-H) and carbonyl oxygens (C=O) stabilize these structures.
• Tertiary structure describes the three-dimensional arrangement of a polypeptide chain, resulting from interactions like hydrophobic interactions, hydrogen bonding, salt bridges (ionic interactions), and disulfide bridges.
• Quaternary structure exists in proteins composed of more than one polypeptide chain. This structure describes how multiple polypeptide subunits or peptides (subunits) arrange to form a functional protein.

3.4 Enzymes

• Enzymes are proteins that act as biological catalysts.
• Enzymes speed up biochemical reactions that would otherwise take days or weeks to occur, or require extremely high temperatures.
• The digestive enzymes pepsin, trypsin, and chymotrypsin, for example, break down dietary proteins into smaller, absorbable subunits.
• Without enzymes, the body cannot effectively absorb nutrients.
• Antibodies are proteins that play a crucial role in the body's immune response to fight off foreign invaders like bacteria and viruses.

3.5 Factors Affecting Enzyme Activity

• Several factors can influence enzyme activity including temperature, pH value, and the presence of inhibitors or activators.
• Various factors can influence protein structure and function, influencing their activity.

Classification of Some Proteins and Their Functions

• Structural Proteins: Provide structural components, e.g., collagen, keratin,
• Contractile Proteins: Enable muscle movement, e.g., myosin and actin;
• Transport Proteins: Transport essential substances, e.g., hemoglobin, lipoproteins;
• Storage Proteins: Store nutrients, e.g., casein, ferritin;
• Hormonal Proteins: Regulate body metabolism, e.g., insulin, growth hormone;
• Enzymes: Catalyze biochemical reactions, e.g., sucrase, trypsin;
• Protective Proteins: Recognize and destroy foreign substances, e.g., immunoglobulins.

Amino Acids: A Deeper Dive

• Amino acids have particular side chains (R-groups) that distinguish them and influence their properties including their polarity.
  • Nonpolar: Hydrophobic;
  • Polar neutral: Hydrophilic;
  • Polar acidic: Hydrophilic and negatively charged;
  • Polar basic: Hydrophilic and positively charged.
• All amino acids are vital for normal tissue growth and development.
• Essential Amino Acids: must be acquired through diet. They include:- PVT. TIM HALL – Phe, Val, Thr, Trp, Ile, Met, His, Arg, Leu, Lys
• Non-essential amino acids can be produced by the body.
• Chirality refers to a property of amino acids and their molecules where a molecule cannot be superimposed onto its mirror image.

Protein Functions (Detailed)

• Movement Proteins: Essential to maintain movement, e.g., muscles, actin, and myosin.
• Regulatory Proteins: Control diverse functions including cell metabolism and reproduction, like hormones such as insulin and glucagon.
• Transport Proteins: Carry substances throughout the body like oxygen and iron. Hemoglobin, transferrin are examples of these.
• Nutrient Storage Proteins: Supply amino acids for developing embryos and infants, e.g. egg albumin, casein.

Important Peptides and Protein Hormones

• Various peptides and protein hormones are produced from different tissues in the body for various physiological functions.

Myoglobin and Hemoglobin

• Myoglobin is an oxygen-storage protein, especially within muscle tissue.
• Hemoglobin transports oxygen throughout the body in the blood.
• Myoglobin has a higher affinity for oxygen than hemoglobin, allowing it to facilitate efficient oxygen transfer and uptake.
• Each hemoglobin contains a heme group that can hold one oxygen molecule. The iron in the heme group binds oxygen.

Protein Denaturation

• Denaturation disrupts the secondary, tertiary, and quaternary structures of proteins, causing them to lose their biological functions.
• Physical and chemical factors like high temperature, pH extremes, and heavy metal ions cause denaturation.

Protein Hydrolysis

• Hydrolysis is the process of splitting peptide chains into simpler compounds.
• In a laboratory setting, protein hydrolysis uses acidic or basic solutions and heat to catalyze peptide bond breakage.
• In the human body, enzymes like peptidases catalyze protein hydrolysis for digestion purposes

Protein Sequencing

• Determining amino acid sequences involves hydrolysis, identifying the products, and assembling the sequences like a puzzle.
• Methods of hydrolysis include acid hydrolysis, and enzymatic hydrolysis using proteases/ peptidases (exo/endopeptidases), including trypsin, chymotrypsin, and others.
• Additional techniques, like chemical methods (Sanger's method, Edman degradation, hydrazine method) are used for determining the specific amino acid sequence.

Electrophoresis

• Electrophoresis is a method used to separate proteins and other charged molecules based on the difference in their net charge under the influence of an electric field.

Quaternary Structure

• Quaternary structure refers to how multiple polypeptide chains (subunits) arrange to form larger, functional protein molecules.
• This arrangement is stabilized by various forces similar to those holding tertiary structures together.

Conjugated Proteins

• Conjugated proteins are proteins with additional chemical components or prosthetic groups . These groups (e.g. carbohydrates, lipids, metals) attached help modify the proteins' structure and function.