2024 Biophysics Mid-Term and Final Exam (PDF)

Exam Raw exam points Hello Credit Points Minimal (Biophysics) (pt.) (CP) Condition Mid-term exam 100 40 min. 25 pt. (10 CP) Final exam 100...

Exam Raw exam points Hello Credit Points Minimal (Biophysics) (pt.) (CP) Condition Mid-term exam 100 40 min. 25 pt. (10 CP) Final exam 100 40 min. 62 pt. (25 CP) 20 (10 attendance and Attendance Activity Points 20 10 exam percentage) min. > 60 % Make-up exam 100 80 min. ~44 pt. (35 CP) 20 (10 attendance and Activity Points 20 20 10 exam percentage) Penalty session exam 100 100 min. 51 pt. (100 CP) (September 2025) NO Activity points - - -  Biological Membranes and Molecular Transport Introduction to Membrane Structure and Function Understanding Molecular Transport Mechanisms  Membranes define the external boundaries of cells and regulate the molecular traffic across that boundary Membranes are flexible, self-sealing, and selectively permeable to polar solutes. Their flexibility permits the shape changes that accompany cell growth and movement (such as amoeboid movement). Within the cell, membranes organize cellular processes such as the synthesis of lipids and certain proteins, and the energy transductions in mitochondria and chloroplasts. Each Type of Membrane Has Characteristic Lipids and Protein. E. g. table below… 4 5 Biological membranes are thin, flexible structures that separate cells and organelles from their environment, and sections the internal environment of cells. Barrier Protects the cell by regulating what enters and exits. Transport Allows selective movement of substances. Communication Hosts receptors for signal transduction. Energy Transduction Involved in energy conversion processes, e.g., in mitochondria and chloroplasts. 6 7 The combined evidence from electron microscopy and studies of chemical composition, as well as physical studies of permeability and the motion of individual protein and lipid molecules within membranes, led to the development of the fluid mosaic model for the structure of biological membranes 8 9 STRUCTURE OF BIOLOGICAL MEMBRANES PHOSPHOLIPID BILAYER Hydrophilic (water-loving) "heads" face outward, toward the aqueous environment. Hydrophobic (water-fearing) "tails" face inward, away from water. PROTEINS Integral proteins Embedded within the lipid bilayer, involved in transport and signaling. Peripheral proteins Loosely associated with the surface of the membrane. CHOLESTEROL Modulates membrane fluidity and stability. Glycocalyx A carbohydrate-rich layer on the extracellular surface of the membrane, involved in cell recognition. 10 Peripheral Membrane Proteins Are Easily Solubilized Membrane proteins may be divided operationally into two groups. Integral proteins are very firmly associated with the membrane, removable only by agents that interfere with hydrophobic interactions, such as detergents, organic solvents, or denaturants. Peripheral proteins associate with the membrane through electrostatic interactions and hydrogen bonding with the hydrophilic domains of integral proteins and with the polar head groups of membrane lipids. 11 12 TYPES OF MEMBRANE TRANSPORT Passive Transport No energy required. Simple diffusion: Movement of small, nonpolar molecules (e.g., O₂, CO₂). Facilitated diffusion: Requires membrane proteins for transport (e.g., glucose via GLUT transporters). Osmosis: Diffusion of water across a semi-permeable membrane. Active Transport: Requires energy (usually ATP). Primary active transport: Direct use of energy to transport molecules (e.g., Na⁺/K⁺ pump). Secondary active transport: Uses electrochemical gradients generated by primary ac ve transport (e.g., Na⁺-glucose cotransporter). Bulk Transport: Involves larger molecules or particles. Endocytosis: Cells engulf materials into vesicles. Exocytosis: Vesicles fuse with the membrane to expel materials. 13  Passive transport is a naturally-occurring phenomenon and does not require the cell to exert any of its energy to accomplish the movement. In passive transport, substances move from an area of higher concentration to an area of lower concentration. Facilitated diffusion is a type of passive transport that uses specialized proteins, such as channel proteins and carrier proteins, to help molecules move across a cell membrane. In this process, molecules can move down their concentration gradient without requiring any energy input from the cell. To move substances against a concentration or electrochemical gradient, a cell must use energy. Active transport mechanisms do just this, expending energy (often in the form of ATP) to maintain the right concentrations of ions and molecules in living cells. Primary active transport that uses adenosine triphosphate (ATP), and Secondary active transport that uses an electrochemical gradient. 14 15 Primary active transport One of the most important pumps in animal cells is the sodium-potassium pump, which moves Na+ out of cells, and K+ into them. Because the transport process uses ATP as an energy source, it is considered an example of primary active transport. 16 Secondary active transport Secondary active transport uses the energy stored in these gradients to move other substances against their own gradients. In secondary active transport, the movement of the sodium ions down their gradient is coupled to the uphill transport of other substances by a shared carrier protein (a cotransporter). For instance, in the figure below, a carrier protein lets sodium ions move down their gradient, but simultaneously brings a glucose molecule up its gradient and into the cell. The carrier protein uses the energy of the sodium gradient to drive the transport of glucose molecules. 17 Secondary active transport 18 Secondary active transport When they move in the same direction, the protein that transports them is called a symporter, while if they move in opposite directions, the protein is called an antiporter. 19 OSMOSIS Osmosis is the spontaneous net movement or diffusion of solvent molecules through a selectively- permeable membrane from a region of high water potential (region of lower solute concentration) to a region of low water potential (region of higher solute concentration), in the direction that tends to equalize the solute concentrations on the two sides. 20 Semi-permeable membranes are very thin layers of material which allow some things to pass through them, but prevent other things from passing through. Cell membranes are an example of semi-permeable membranes. Cell membranes allow small molecules such as oxygen, water, carbon dioxide and glucose to pass through, but DO NOT allow larger molecules like sucrose, proteins and starch to enter the cell directly. 21 OSMOTIC PRESSURE Adding sugars to water will result in a decrease in the water concentration because the sugar molecules displace the water molecules. 22 OSMOTIC PRESSURE If the two containers are connected, but separated by a semi-permeable membrane, water molecules would flow from the area of high water concentration (the solution that does not contain any sugar) to the area of lower water concentration (the solution that contains sugar). 23 OSMOTIC PRESSURE This movement of water would continue until the water concentration on both sides of the membrane is equal, and will result in a change in volume of the two sides. The side that contains sugar will end up with a larger volume. 24 - Water solutions are very important in biology. When water is mixed with other molecules this mixture is called a solution. - Water is the solvent and the dissolved substance is the solute. A solution is characterized by the solute. - For example, water and sugar would be characterized as a sugar solution. 25 The classic example used to demonstrate osmosis and osmotic pressure is to immerse red blood cells into sugar solutions of various concentrations. 1. The concentration of solute in the solution can be equal to the concentration of solute in cells. In this situation the cell is in an isotonic solution (iso = equal or the same as normal). A red blood cell will retain its normal shape in this environment as the amount of water entering the cell is the same as the amount leaving the cell. 26 2. The concentration of solute in the solution can be greater than the concentration of solute in the cells. This cell is described as being in a hypertonic solution (hyper = greater than normal). In this situation, a red blood will appear to shrink as the water flows out of the cell and into the surrounding environment. 27 3. The concentration of solute in the solution can be less than the concentration of solute in the cells. This cell is in a hypotonic solution (hypo = less than normal). A red blood cell in this environment will become visibly swollen and potentially rupture as water rushes into the cell. 28 29 Membrane Dynamics One remarkable feature of all biological membranes is their flexibility—their ability to change shape without losing their integrity and becoming leaky. The basis for this property is the noncovalent interactions among lipids in the bilayer and the motions allowed to individual lipids because they are not covalently anchored to one another. We turn now to the dynamics of membranes: the motions that occur and the transient structures allowed by these motions. Although the lipid bilayer structure is quite stable, its individual phospholipid and sterol molecules have some freedom of motion… 30