Lesson 2: Chemical Biology and Biomolecules PDF

Lesson 2 Chemical Biology and Biomolecules: Essential Concepts  Introduction to Chemical Biology Interdisciplinary field combining chemistry and biology Studies chemical processes within living systems Key focus: Understanding biological systems at molecular level Appl...

Lesson 2 Chemical Biology and Biomolecules: Essential Concepts  Introduction to Chemical Biology Interdisciplinary field combining chemistry and biology Studies chemical processes within living systems Key focus: Understanding biological systems at molecular level Applications in drug discovery, biotechnology, and medicine  Introduction to Chemical Biology Biochemistry is the study of structure, composition (what things are made up of), and chemical reactions that occur in living things. Living things (biotic factors) depend on chemistry for life…so biology and chemistry are closely related!  Fundamental Biomolecules Four major classes of biomolecules: Proteins Nucleic acids Carbohydrates Lipids Each class serves distinct biological functions All are essential for life processes  Lesson 2 – Topic 1 The Chemistry of Life  Organic Chemistry - the study of compounds of carbon and hydrogen (hydrocarbons) and their derivatives Let’s Review! Atomic Structure Atoms - composed of subatomic particles: protons + charge mass = 1 neutrons no charge mass = 1 electrons charge almost 0 mass Let’s Review! Atomic Structure Nucleus dense center of atom protons and neutrons Orbiting the Nucleus electron cloud can remove or add electrons to create ions Let’s Review! Atomic Mass = # protons + # neutrons electrons do not contribute mass Ex. oxygen has 8 protons and 8 neutrons Atomic mass = O16 Let’s Review! Atomic Number Determines the Element Atomic Number # protons each element has a unique atomic number will the number of protons in an atom also determine how many electrons there are in an atom? if an atom has 9 protons, how many electrons will it have? Let’s Review! Atomic Number Determines the Element Atomic Number # protons each element has a unique atomic number will the number of protons in an atom also determine how many electrons there are in an atom? if an atom has 9 protons, how many electrons will it have? Let’s Review! Molecules and Compounds Molecule –when two or more atoms chemically combine Compound –when two or more atoms of different elements chemically combine in defined proportions. Molecular formulas – elements present and the number of each atom present in the molecule H2 C6H12O6 H2 O Let’s Review! Isotopes atoms have same number of protons but a different number of neutrons same atomic number, different atomic weight ex. oxygen forms isotopes (O16, O17, O18) same element! How many protons in O16? O17? O18? How many neutrons? unstable isotopes are radioactive and emit energy – used in medicine and research Let’s Review! Radioactive Tracers A PET scan, a medical use for radioactive isotopes. PET, an acronym for positron- emission tomography, detects locations of intense chemical activity in the body. The bright yellow spot marks an area with an elevated level of radioactively labeled glucose, which in turn indicates high metabolic activity, a hallmark of cancerous tissue. Let’s Review! Radioactive Tracers  Lesson 2 – Topic 2 Water: The Solvent for Biochemical Reaction Properties of Water Hydrogen Bond Positive charges on one molecule and negative charges on another molecule attract each other and form hydrogen bonds. Properties of Water Cohesion Water molecules stay close to each other because of hydrogen bonding. Properties of Water Surface tension Properties of Water Adhesion Due to polarity, water sticks to other surfaces as well (unlike substances, opposites attract). Properties of Water Capillary action/Low Viscosity Due to polarity, water is able to move through small spaces, against gravity. Cohesion and adhesion are also seen in this property. This helps move water to the tops of tall trees and through veins in humans. Properties of Water Density Unlike most substances, water becomes less dense when it freezes. H bonds first condense when water is cold but then expands when water freezes leaving air pockets between the water molecules. Ice floating acts as an insulator to water in a body of water so fish don’t die in the winter. Properties of Water Density Properties of Water Density Properties of Water Solubility/Universal Solvent Because of water’s polarity, it is a universal solvent (can dissolve many things) Solute is the material being dissolved in a solution.  Lesson 2 – Topic 3 Membrane and Membrane Transport Transportation System Figure 7.1 Successful learning relies on communication between brain cells. Here, the vesicles fusing with the plasma membrane of the top cell release molecules (yellow) that bind to membrane proteins (light green) on the surface of the bottom cell, triggering the proteins to change shape. The plasma membrane surrounding each cell regulates its exchanges with its environment and surrounding cells. What is a cell membrane? Cellular membranes are fluid mosaics of lipids and proteins - made up of lipids and proteins, as well as carbohydrates - most abundant lipid are phospholipids - phospholipids are amphipathic (it has both a hydrophilic (“water-loving”) region and a hydrophobic (“water- fearing”) region) FLUID MOSAIC MODEL Factors that affect membrane fluidity Factors that affect membrane fluidity Phospholipid Bilayer - can exist as a stable boundary between two aqueous compartments - create a selectively permeable barrier to the movement of ions and molecules important for cellular function Phospholipid Bilayer - hydrophilic head group consists of a phosphate- containing group attached to a glycerol molecule - hydrophobic tails, each containing either a saturated or an unsaturated fatty acid, are long hydrocarbon chains. Proteins make up the second major component of plasma membranes Proteins - integral proteins (integrins)are permanently embedded in the membrane - majorly acts as channeling or transporting molecules across the membrane - other integral proteins Integral Proteins Integral Proteins Lipid-anchored membrane proteins Type of membrane proteins that are covalently bonded to a lipid group that resides within the membrane. The lipid can be phosphatidylinositol, a fatty acid, or a prenyl Peripheral Proteins (extrinsic proteins) a protein that is found temporarily attached to the cell or mitochondrial membrane Most of them are hydrophilic either attached to integral membrane proteins or can be directly bound to the bilayer’s polar head Functions of Proteins Functions of Proteins CARBOHYDRATES third major component always found on the exterior surface of cells and are bound either to proteins or to lipids form specialized sites on the cell surface that allow cells to recognize each other allows the immune system to differentiate between body cells and foreign cells or tissues Glycoproteins Formed in the endoplasmic reticulum and the Golgi apparatus Responsible for cell signaling, cell-cell recognition, and cell adhesion Serves as marker molecules Glycolipids may act as receptors, be important for cell aggregation and dissociation, and may be responsible for specific cellular contact and for signal transduction. Cholesterol may act as receptors, be important for cell aggregation and dissociation, and may be responsible for specific cellular contact and for signal transduction. TRANSPORT MECHANISMS  TRANSPORT MECHANISM Allow the cell to regulate what solutes enter/exit the cell and the quantity being transported. TRANSPORT MECHANISM PASSIVE TRANSPORT DIFFUSION OSMOSIS FACILITATED DIFFUSION This type of transport relies on the concentration gradient of solutes to move them across the plasma membrane. No energy will be spent to move the solutes across. SIMPLE DIFFUSION The movement of ions and molecules from high concentration to low concentration is known as diffusion. DIFFUSION EXAMPLE DIFFUSION EXAMPLE DIFFUSION and TEMPERATURE DIFFUSION and TEMPERATURE  DIFFUSION and TEMPERATURE When temperature increases, the kinetic energy of the particles increases. The increased motion of the particles causes them to diffuse faster. Therefore, at higher temperatures, the rate at which fluid particles will diffuse is faster than at lower temperatures.  The alveoli in the lungs are filled with oxygen during EXAMPLE OF DIFFUSION IN respiration. As there is a higher concentration of oxygen in the THE HUMAN BODY alveoli compared to in the blood, oxygen will pass down the concentration gradient across the alveoli into the blood via diffusion. OSMOSIS Osmosis is a process by which the molecules of a solvent pass from a solution of low concentration to a solution of high concentration through a semi-permeable membrane. OSMOSIS Osmosis is a process by which the molecules of a solvent pass from a solution of low concentration to a solution of high concentration through a semi-permeable membrane. OSMOTIC SOLUTIONS ISOTONIC Iso = same, tonic = strength Equal amount of water enter and exit the cell, so the size stays constant. HYPERTONIC hyper =more, tonic = strength A solution is hypertonic if it has more solutes (less water) than a cell. HYPOTONIC hypo =less, tonic = strength A solution is hypnotic if it has fewer solutes (more water) than a cell.  TYPES OF OSMOSIS Endosmosis Exosmosis OSMOTIC PRESSURE FACILITATED DIFFUSION Facilitated diffusion is a type of diffusion in which the molecules move from the region of higher concentration to the region of lower concentration assisted by a carrier. Temperature- As the temperature increases, the movement of the molecules increases due to an increase in energy. Concentration- The movement of the molecules takes place from the region of higher concentration to lower concentration. Factors Affecting Facilitated Diffusion Temperature- As the temperature increases, the movement of the molecules increases due to an increase in energy. Concentration- The movement of the molecules takes place from the region of higher concentration to lower concentration. Temperature- As the temperature increases, the movement of the molecules increases due to an increase in energy. Concentration- The movement of the molecules takes place from the region of higher concentration to lower concentration. Factors Affecting Facilitated Diffusion Diffusion Distance- The diffusion rate is faster through smaller distance than through the larger distance. For eg., gas diffuses much faster through a thin wall than through a thick wall. Size of the molecules- The smaller molecules are lighter and hence diffuse faster than the larger molecules.  CHANNEL PROTEIN CARRIER PROTEIN Proteins provide a small hydrophilic Require the molecule being passageway for specific molecules and ions. transported to attach itself to the Some channels can remain open most of the carrier protein. The protein will time (leak channels), while others can be then change its shape opened or closed (gate channels) depending (conformational change) to shuttle on the presence of a stimulus. the molecule across the membrane.  Glucose Transporter are special proteins that are embedded in the Examples of Facilitated phospholipid bilayer of the plasma membrane. They bridge the extracellular fluid and the cytoplasm, allowing glucose molecules to enter Diffusion the cell without needing ATP.  Ion Channels protein molecules (passive conduits) Examples of Facilitated that span across the cell membrane allowing the passage of ions from Diffusion one side of the membrane to the other ions rush down gradients of concentration and electric potential Examples of Facilitated Diffusion Ion Channels Examples of Facilitated Diffusion Ion Channels  Active Transport the movement of molecules or ions across a cell membrane from a region of lower concentration to a region of higher concentration— against the concentration gradient- requires energy in the form of ATP Primary active transport - process uses ATP as an energy source - an example is the sodium-potassium pump the Sodium- Potassium Pump Secondary active transport uses the energy stored in the electrochemical gradients to move other substances against their gradients  Active Transport The movement of macromolecules such as proteins or polysaccharides into or out of the cell is called bulk transport. There are two types of bulk transport, exocytosis and endocytosis, and both require the expenditure of energy (ATP).