Proteins

• Proteins


  Proteins are composed of long chains of recurring monomers called amino acids

  • Each amino acid contains a central alpha carbon linked to an amine group, carboxyl group, a variable group and a hydrogen atom

  There are 20 different amino acids which are universal to all living organisms

  • Each type of amino acid differs in the composition of their variable side chain (denoted ‘R’)

  
• Dietary requirements for amino acids


  • Essential
  • Non-essential
  • Conditional
• Essential amino acids


  Cannot be produced by the body and must be present in the diet.There are nine essential amino acids.

  Name some dietary sources of these:

  • Meat
  • Fish
  • Eggs
  • Dairy products
  • Quinoa
  • Soy products
  • Legumes
  • Nuts and seeds
  • Whole grains
• Non-essential amino acids


  Can be produced by the body (from other amino acids) and are therefore not required as part of the diet
• Conditional amino acids


  Can be produced by the body, but at rates lower than certain conditional requirements. Conditional amino acids are essential at certain times only (such as during pregnancy, infancy or illness). A shortage of one or more essential amino acids in the diet Will prevent the production of specific proteins
• Protein deficiency malnutrition


  The health effects will vary depending on the amino acid shortage. Certain diets (e.g. vegan) require particular attention to ensure essential amino acids are consumed and malnutrition is avoided
• Condensation reactions forming dipeptides and longer chains of amino acids


  Amino acids can be covalently joined together via condensation reactions to form a dipeptide and water

  The bond that is created is called a peptide bond and forms between the amine and carboxyl groups of adjacent amino acids

  Long chains of covalently bonded amino acids are called polypeptides and these chains can be broken down via hydrolysis reactions (requires water to reverse the process)

  
• Proteins


  • A very diverse class of compounds
  • May serve a number of different roles within a cell
• Functions of Proteins


  Proteins perform an array of functions:

  • Structure (collagen, spider silk)
  • Hormones (insulin, glucagon)
  • Immunity (antibodies)
  • Transport (protein channels)
  • Sensations (rhodopsin)
  • Movement (actin, myosin)
  • Enzymes (Rubisco, amylase)
• Denaturation


  Denaturation is a structural change in a protein that results in the loss (usually permanent) of its biological properties. Because the way a protein folds determines its function, any change or abrogation of the three dimensional structure will alter its activity

  Denaturation of proteins can usually be caused by two key conditions – heat (high temperatures) and pH

  
• Effect of temperature on protein structure

  High levels of thermal energy may disrupt the hydrogen bonds that hold the protein together

  As these bonds are broken, the protein will begin to unfold and lose its capacity to function as intended

  Temperatures at which proteins denature may vary, but most human proteins function optimally at body temperature (~37ºC)
• Effect of pH on protein structure

  • Amino acids are zwitterions, neutral molecules possessing both negatively (COO–) and positively (NH3+) charged regions
  • Changing the pH will alter the charge of the protein, which in turn will alter protein solubility and overall shape
  • All proteins have an optimal pH which is dependent on the environment in which it functions (e.g. stomach proteins require an acidic environment to operate, whereas blood proteins function best at a neutral pH)

  
• Composition and Variety


  Polypeptide:

  Infinite variety of possible structures.

  Composed of 20 different types of amino acids.

  Each amino acid has a specific variable side chain.
• Chemical Properties and Protein Folding

  • Amino acids have distinct chemical properties (e.g., charged, non-polar, etc.).
  • These properties cause the protein to fold differently according to its specific position within the polypeptide chain.
  • Protein folding plays a critical role in determining its function and level of biological activity.
• Natural Polypeptide Chains and Organism Capabilities

  Most natural polypeptide chains contain between 50 – 2000 amino acid residues.

  Organisms can produce a huge range of possible polypeptides.
• Insulin


  Regulates blood sugar levels.

  A hormone produced by the pancreas that helps cells absorb glucose from the blood.
• Hemoglobin


  Transports oxygen in the blood.

  A protein in red blood cells composed of four polypeptide chains, each containing an iron atom that binds to oxygen.
• Collagen


  • Provides structural support.
  • A structural protein found in connective tissues, skin, bones, and cartilage, composed of three polypeptide chains wound together.
• Antibodies (Immunoglobulins)


  • Immune response.
  • Proteins produced by B-cells that recognize and help neutralize pathogens like bacteria and viruses.
• Enzymes (e.g., Amylase)


  • Catalyze biochemical reactions.
  • Amylase is an enzyme that helps break down starches into sugars during digestion
• Actin and Myosin


  • Muscle contraction.
  • Proteins involved in muscle contraction and cell motility. Actin forms microfilaments, while myosin interacts with actin to generate force.
• Growth Hormone


  • Stimulates growth and cell reproduction.
  • A hormone that stimulates growth, cell reproduction, and cell regeneration in humans and other animals.
• Glucagon


  • Regulates blood glucose levels.
  • A hormone produced by the pancreas that raises blood glucose levels by promoting the conversion of glycogen to glucose in the liver.
• List of the Nine Essential Amino Acids

  For completeness, here are the nine essential amino acids:

  1. Histidine
  2. Isoleucine
  3. Leucine
  4. Lysine
  5. Methionine
  6. Phenylalanine
  7. Threonine
  8. Tryptophan
  9. Valine
• Histones 


  • Structural Protein
  • Histones are proteins that help organize and package DNA into structural units called nucleosomes.
  • They play a critical role in gene regulation by controlling access to DNA for transcription (gene expression).
  • Histones are found in the nucleus of eukaryotic cells and are essential for maintaining the structure and function of chromosomes.
• Keratin


  Structural Protein

  • Keratin is a fibrous protein that provides strength and protection to cells and tissues.
  • It is a key component of the outer layer of the skin (epidermis), as well as hair, nails, claws, hooves, and feathers.
  • Keratin helps protect epithelial cells from damage or stress.
• Lipase


  • Enzyme
  • Lipase is a type of enzyme that catalyzes the hydrolysis (breakdown) of lipids (fats) into fatty acids and glycerol.
  • It is essential for the digestion and absorption of dietary fats.
  • Lipase is produced in various tissues, but primarily in the pancreas, stomach, and small intestine.
• How do cells produce a variety of proteins with different sequences of amino acids?

  1. DNA sequences encode instructions for proteins.
  2. DNA is transcribed into mRNA in the nucleus.
  3. mRNA is processed (splicing and adding cap/tail) before leaving the nucleus.
  4. mRNA is translated by ribosomes in the cytoplasm.
  5. tRNA carries amino acids to ribosomes, matching codons with anticodons.
  6. Ribosomes form peptide bonds between amino acids.
  7. Polypeptides fold into specific shapes and undergo modifications to become functional proteins.
• Proteome


  The entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time. In cells of different tissues, the genome is the same while the proteome varies. The proteome of a species contain a larger number of proteins than genes that code for these proteins because there are genes that code for several proteins.

  Represents the functional output of genetic information and is dynamic, changing in response to various biological and environmental factors.
• Rhodopsin


  It's the light-sensitive protein pigment found in the rod cells of the retina. It is responsible for allowing us to see in low-light conditions.
• Spider silk 


  Is known to have the highest tensile strength among natural materials, making it an excellent choice for the question.
• Tensile


  It's strength refers to the maximum stress a material can withstand before breaking when pulled apart. It is a measure of a material's ability to resist breaking under tension.