biology

• The folding of a protein is determined by the interactions between amino acid side chains and the surrounding environment.
• Essential amino acids cannot be synthesized by the body and must be obtained through dietary sources.
• Proteins are made up of elements: Carbon, Hydrogen, Oxygen, Nitrogen, and sometimes Sulphur
• Amino acids are organic compounds that contain both amino and carboxylic acid functional groups
• All amino acids consist of an amino group, a carboxyl group, an alpha carbon bonded to a hydrogen atom, carboxylic group, amino group, and a side chain
• Amino acids can exist as zwitterions, containing both positively and negatively charged functional groups
• There are 20 naturally occurring amino acids that can combine in different ways to form different proteins
• Amino acids can be categorized into nonpolar, polar uncharged, acidic, and basic amino acids based on their side chain properties
• Amino acids are joined together by a condensation reaction involving the amino group and the carboxyl group to form a peptide bond
• Protein structure refers to the 3D structure arising from various bonds
• Primary structure of a protein refers to the sequence of amino acids in a single sequence, involving only peptide bonds
• Secondary structure of a protein includes alpha helix and beta-pleated sheet formations due to hydrogen bonding
• Tertiary structure involves further coiling or folding of the secondary structure to form a precise 3-D shape, based on interactions among side chains
• Bonds involved in tertiary structure include peptide bonds, hydrogen bonds, disulfide bonds, hydrophobic interactions, and ionic interactions
• Quaternary structure involves the association of two or more polypeptide chains held together by various bonds, such as in hemoglobin
• Globular proteins:

  • Molecules are folded into a relatively spherical shape
  • Found inside cells or other aqueous environments outside cells
  • Non-polar, hydrophobic R groups are 'buried' in the center, away from water
  • Hydrophilic R groups remain on the outside of the structure, in contact with water
  • Often soluble in water due to water molecules clustering around outward-pointing hydrophilic R groups
  • Have roles in metabolic and/or physiologic reactions
  • Precise shape is crucial for functioning, enzymes lose functionality when shape is distorted
• Fibrous proteins:

  • Do not curl up into a ball, usually only fold up to the secondary structure
  • Usually occur as straight fibers
  • Examples include keratin and collagen
  • Usually insoluble in water, form insoluble cross-linked structures
  • Have structural roles, e.g., keratin forms hair, nails, and outer layers of skin
• Haemoglobin:

  • Nearly spherical in shape
  • Made of 4 tightly packed polypeptide chains: two alpha (α) chains and two beta (β) chains
  • Each chain contains a haem group, a prosthetic group
  • Responsible for oxygen transport in blood
  • Haem group contains an iron (Fe) atom that binds to oxygen molecules
  • Colour of blood changes depending on oxygen binding status
• Collagen:

  • Makes about 25% of all mammalian protein
  • Important structural protein in almost all animals
  • Consists of three polypeptide chains in a helix shape held together by hydrogen bonds
  • Collagen molecule consists of 3 polypeptide chains wound in helices held together by H bonds and some covalent bonds
  • Every 3rd amino acid is almost always a glycine
  • Forms fibrils by interacting with other collagen molecules running parallel and held by cross-links
  • Many fibrils form fibers with covalent bonds between R groups of amino acids lying next to each other
• Cell membranes and Transport

  • Fluid mosaic membranes
  • All membranes act as barriers, allowing certain substances and not others to pass
  • Cell membranes are flexible to allow the cell to change shape
  • Other organelles are bound by membranes like nucleus, mitochondria, etc
  • Chemical secretions from cells are contained in membrane bags called vesicles
  • Vesicles fuse with the cell membrane to release their contents outside the cell
  • Cell membranes are composed mainly of polar phospholipids and proteins
• Phospholipids form ball-like structures called micelles when shaken up with water
• Two-layered structures called bilayers can form from phospholipids, which is the basis of cell membranes
• Fluid mosaic model of the cell membrane

  • First proposed by S. Johnathan Singer and Garth Nicholson in 1972
  • Referred to as fluid because both the phospholipids and proteins move about by diffusion
  • When viewed from above, it looks like a mosaic structure because of the scattered proteins
• Cholesterol in the cell membrane

  • More rigid than phospholipids, making the membrane more stable and stronger
• Proteins in the cell membrane

  • Some have a hydrophobic part buried in the bilayer and a hydrophilic part exposed on either surface
  • Some are found on the inner or outer surface of the membrane
  • Some proteins go all the way through the bilayer, making pores or channels for passage of polar substances
  • Many proteins and lipids have short, branching carbohydrate chains attached to the side of the molecule which faces the outside, called glycoproteins and glycolipids respectively
• Movement into and out of cells

  • Two types: Passive transport and Active transport
  • Passive transport occurs when there is a concentration, pressure, or electrochemical gradient and requires no energy
  • Active transport involves movement of substances into or out of the cell against the gradient
• Processes of cell signaling


  Main stages leading to specific responses: Secretion of specific chemicals from cells, transport of ligands to target cells, binding of ligands to cell surface receptors on target cells
• Movement into and out of cells

  Processes of simple diffusion, osmosis, active transport, endocytosis, and exocytosis
• Investigations related to movement into and out of cells

  Using plant tissues and non-living materials for simple diffusion and osmosis, calculating surface area to volume ratio of 3D shapes, investigating the effect of changing surface area to volume ratio on diffusion using agar blocks, estimating water potential of tissues by immersing plant tissues in solutions of different water potential, explaining the movement of water between cells and solutions in terms of water potential
• Movement of water on plant and animal cells

  1. Passive transport

  2. Active transport
• Types of cell transport

  • Simple diffusion
  • Facilitated diffusion
  • Osmosis
• Cell transport and diffusion

  3/7/2024
• Simple Diffusion


  1. Substances move down the concentration gradient

  2. Molecules/particles move randomly because of the energy they possess
• When equilibrium is achieved, particles DO NOT stop moving – but there is no net change in distribution
• For many small molecules (e.g., oxygen and carbon dioxide) the cell membrane is not a barrier to stop diffusion
• Facilitated diffusion


  1. Larger substances, or charged substances cannot cross the cell membrane by diffusion alone

  2. Facilitated diffusion involves proteins in the membrane that allow passage of specific substances

  3. Some channels are gated channels – open only when specific substances are present, or when a specific charge is achieved

  4. Another type involves carrier molecules

  5. Carrier molecules pick up the substance to be transported, rotate to the other side, and release the molecule
• Osmosis


  The net movement of free water molecules through a partially permeable membrane, down a water potential gradient
• Water potential


  A measure of free water molecules (H2O molecules not associated with solute molecules)
• Modelling osmosis


  • Osmotic concentration
  • Isotonic solution
  • Hypertonic solution
  • Hypotonic solution
• Animal cells are fragile because they lack a rigid cell wall