Amino Acids and Proteins Lecture Notes PDF

**Lecture Notes: Amino Acids and Proteins** **II. Structure of Amino Acids** Amino acids have a common structure composed of three key components: 1. **Amino Group (-NH₂)** -- A basic group. 2. **Carboxyl Group (-COOH)** -- An acidic group. 3. **Side Chain (R group)** -- Varies for each amin...

**Lecture Notes: Amino Acids and Proteins** **II. Structure of Amino Acids** Amino acids have a common structure composed of three key components: 1. **Amino Group (-NH₂)** -- A basic group. 2. **Carboxyl Group (-COOH)** -- An acidic group. 3. **Side Chain (R group)** -- Varies for each amino acid, determining its properties (e.g., hydrophobicity, charge, and size). - **General Structure of an Amino Acid:** H2N−CH(R)−COOHH\_2N - CH(R) - COOHH2​N−CH(R)−COOH The specific nature of the R group determines the characteristics of each amino acid, making some polar, nonpolar, acidic, or basic. **III. Classification of Amino Acids** Amino acids can be categorized based on the nature of their R group (side chain): 1. **Nonpolar (Hydrophobic) Amino Acids:** These amino acids have side chains that do not interact well with water. They tend to be found in the interior of proteins, away from aqueous environments. - Examples: **Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Methionine, Phenylalanine, Tryptophan.** - *Example:* **Leucine** has a branched hydrocarbon chain, making it hydrophobic and contributing to protein folding. 2. **Polar (Hydrophilic) Amino Acids:** These have side chains that can form hydrogen bonds with water, making them soluble in water. They often participate in enzyme active sites or in signaling functions. - Examples: **Serine, Threonine, Asparagine, Glutamine, Cysteine.** - *Example:* **Serine** contains a hydroxyl group that allows it to form hydrogen bonds with other polar molecules. 3. **Charged Amino Acids:** These are either positively charged (basic) or negatively charged (acidic), making them highly soluble in water and involved in ionic interactions. - **Basic Amino Acids:** **Lysine, Arginine, Histidine** (positively charged at physiological pH). - **Acidic Amino Acids:** **Aspartate, Glutamate** (negatively charged). - *Example:* **Histidine** is crucial for enzyme activity due to its ability to gain or lose protons, depending on the environment. **IV. Essential vs. Non-Essential Amino Acids** - **Essential Amino Acids:** These cannot be synthesized by the human body and must be obtained from the diet. There are nine essential amino acids: - **Leucine, Isoleucine, Valine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Histidine.** - *Example:* **Tryptophan** is a precursor to the neurotransmitter serotonin, which regulates mood, sleep, and appetite. - **Non-Essential Amino Acids:** These amino acids can be synthesized by the human body from other nutrients. Examples include: - **Alanine, Arginine, Asparagine, Aspartic Acid, Glutamic Acid, Cysteine, Glutamine, Glycine, Proline, Tyrosine.** - *Example:* **Glutamine** is important for immune function and is used as fuel by immune cells during periods of stress. Additionally, **conditionally essential amino acids** are those that become essential under certain conditions, such as during illness or stress (e.g., **Arginine** in infants or during wound healing). **V. Peptide Bonds and Protein Synthesis** Amino acids are linked together through **peptide bonds** to form proteins. This bond forms when the amino group of one amino acid reacts with the carboxyl group of another, releasing a molecule of water (a dehydration reaction). H2N−CH(R)−COOH+H2N−CH(R′)−COOH→H2N−CH(R)−CO−NH−CH(R′)−COOH+H2OH\_2N-CH(R)-COOH + H\_2N-CH(R\')-COOH \\rightarrow H\_2N-CH(R)-CO-NH-CH(R\')-COOH + H\_2OH2​N−CH(R)−COOH+H2​N−CH(R′)−COOH→H2​N−CH(R)−CO−NH−CH(R′)−COOH+H2​O - **Peptides:** Short chains of amino acids (usually fewer than 50). - **Polypeptides:** Longer chains that can fold into functional proteins. The sequence of amino acids in a protein is crucial, as even a single change in the sequence can alter the protein\'s function (e.g., **sickle cell anemia** occurs when valine replaces glutamic acid in hemoglobin). **VI. Levels of Protein Structure** Proteins are complex molecules that adopt specific shapes necessary for their function. These shapes are described at four structural levels: 1. **Primary Structure:** The linear sequence of amino acids in a polypeptide chain, determined by the gene encoding the protein. - *Example:* The exact sequence of amino acids in **insulin** allows it to regulate blood glucose levels. 2. **Secondary Structure:** Local folding patterns stabilized by hydrogen bonding between the backbone atoms. The most common secondary structures are: - **Alpha Helix:** A coiled structure stabilized by hydrogen bonds. - **Beta Sheet:** A sheet-like arrangement of chains. - *Example:* **Keratin**, found in hair and nails, is composed of alpha helices that provide strength and flexibility. 3. **Tertiary Structure:** The overall three-dimensional shape of a single polypeptide chain, resulting from interactions between R groups (e.g., hydrophobic interactions, ionic bonds, hydrogen bonds, disulfide bridges). - *Example:* **Myoglobin**, which stores oxygen in muscle cells, has a globular tertiary structure that allows it to bind and release oxygen efficiently. 4. **Quaternary Structure:** The arrangement of multiple polypeptide chains into a functional protein complex. Not all proteins have quaternary structures. - *Example:* **Hemoglobin** consists of four subunits, each capable of binding to oxygen, allowing it to transport oxygen efficiently in the bloodstream. **VII. Protein Folding and Chaperone Proteins** Protein folding is critical for function. During synthesis, proteins fold into their functional three-dimensional shapes. **Chaperone proteins** assist in this process by preventing misfolding or aggregation of newly synthesized proteins. - **Misfolded Proteins:** If proteins do not fold properly, they may become nonfunctional or form aggregates, which can lead to diseases such as **Alzheimer\'s**, **Parkinson\'s**, or **prion diseases**. - **Chaperones (Heat Shock Proteins):** These proteins help other proteins fold correctly, especially under stress (e.g., heat or oxidative stress). *Example:* **Heat Shock Proteins (HSPs)** prevent proteins from misfolding during heat stress, ensuring proper cellular function. **VIII. Protein Denaturation** Denaturation is the process by which a protein loses its native structure, resulting in a loss of function. This can occur due to changes in temperature, pH, or exposure to chemicals. Although the primary sequence of amino acids remains intact, the secondary, tertiary, and quaternary structures are disrupted. - **Heat:** Proteins in food, such as **egg whites**, denature when heated. The clear albumin turns white as its structure unravels. - **pH:** Proteins can also denature in acidic or alkaline environments. For example, when milk turns sour (acidic), the protein **casein** denatures and curdles. Denatured proteins often become insoluble and lose their biological activity, which is critical in many biochemical reactions. **IX. Protein Functions** Proteins are the most diverse biomolecules in terms of function, and they participate in nearly every biological process. Some of the key functions include: 1. **Structural Proteins:** Provide support and shape to cells and tissues. - *Example:* **Collagen** forms the extracellular matrix that supports skin, bones, and connective tissues. 2. **Enzymes:** Act as biological catalysts, speeding up chemical reactions without being consumed in the process. - *Example:* **Amylase** helps digest starch by breaking it down into sugars. 3. **Transport Proteins:** Carry substances within an organism or across cell membranes. - *Example:* **Hemoglobin** transports oxygen in the blood from the lungs to tissues. 4. **Hormonal Proteins:** Regulate physiological processes and signaling in the body. - *Example:* **Insulin** is a hormone that helps regulate blood glucose levels. 5. **Defense Proteins:** Protect the body from pathogens, including bacteria, viruses, and other foreign invaders. - *Example:* **Antibodies** bind to and neutralize foreign substances in the immune response. 6. **Contractile Proteins:** Enable movement and muscle contraction. - *Example:* **Actin** and **myosin** are responsible for muscle contractions, allowing movement in organisms. 7. **Storage Proteins:** Store nutrients and essential elements for later use. - *Example:* **Ferritin** stores iron in the liver and releases it when the body needs it. 8. **Receptor Proteins:** Receive and transmit signals across cell membranes. - *Example:* **G-protein coupled receptors (GPCRs)** detect molecules outside the cell and activate internal signal transduction pathways. **X. Protein Metabolism and Digestion** Proteins in food are digested into amino acids, which are absorbed and used for protein synthesis, energy production, or as precursors for other molecules (e.g., neurotransmitters, hormones). 1. **Digestion:** - In the stomach, **pepsin** breaks down proteins into smaller peptides. - In the small intestine, **trypsin** and **chymotrypsin** further break down peptides into amino acids, which are then absorbed by the intestinal lining. 2. **Amino Acid Metabolism:** - Amino acids are used for building new proteins or, if in excess, they are deaminated (removal of the amino group) and the remaining carbon skeletons are converted into energy or stored as fat. *Example:* After eating a steak, the proteins are broken down into amino acids, which your body then uses to repair muscles and tissues or as fuel. **XI. Protein Deficiency and Malnutrition** Protein deficiency can lead to severe health issues. Two major conditions related to protein deficiency are: 1. **Kwashiorkor:** Caused by severe protein deficiency, characterized by edema, muscle wasting, and a swollen belly. It often occurs in children who have a diet high in carbohydrates but low in protein. 2. **Marasmus:** A condition caused by general energy deficiency, including protein. It leads to extreme muscle wasting, stunted growth, and a weakened immune system. Both conditions are commonly seen in areas where food supply is limited, particularly in developing countries. **XII. Protein Supplements and Their Uses** Protein supplements are widely used, especially by athletes or individuals seeking to build muscle or recover from injury. Common supplements include: - **Whey Protein:** Derived from milk and rapidly digested, often taken post-workout. - **Casein Protein:** Also from milk, but slow digesting, making it ideal for sustained release of amino acids. - **Plant-based Proteins:** For those following a vegetarian or vegan diet, plant-based options like soy, pea, or rice protein are available. *Example:* After a workout, athletes often consume whey protein shakes to help repair and grow muscles quickly. **XIII. Special Functions of Amino Acids** Beyond their role in protein synthesis, some amino acids have specialized functions: 1. **Tryptophan:** Precursor to serotonin, a neurotransmitter that regulates mood, sleep, and appetite. 2. **Tyrosine:** Precursor to dopamine, epinephrine, and norepinephrine, neurotransmitters involved in the body\'s fight-or-flight response. 3. **Arginine:** Plays a role in the urea cycle and helps remove toxic ammonia from the body. It is also important for nitric oxide production, which regulates blood flow. *Example:* Foods rich in tryptophan, such as turkey, are believed to increase serotonin levels, potentially affecting mood and sleep. **XIV. Protein Misfolding and Diseases** Protein misfolding can result in non-functional proteins or toxic aggregates that lead to diseases. Some of these include: 1. **Alzheimer's Disease:** Characterized by the accumulation of misfolded beta-amyloid plaques in the brain, leading to neurodegeneration. 2. **Prion Diseases (e.g., Creutzfeldt-Jakob Disease):** Infectious proteins (prions) cause normal proteins in the brain to misfold, leading to brain damage and death. 3. **Cystic Fibrosis:** A genetic disease where a misfolded protein affects chloride channels in cells, leading to thick mucus buildup in organs. Chaperones, mentioned earlier, are vital in preventing such diseases by ensuring correct protein folding.