IB Biology HL Y1 Quarter 4

Blue highlight = example / Green highlight = important info i think probably

Standards - B2.1, D2.3, C1.1, C1.2,

B2.1 Membranes and Membrane Transport

Phospholipids - make up cell membranes as a bilayer, barrier to large as well as hydrophilic molecules

Integral proteins - integrate/go into membrane (sometimes all the way through)

Peripheral proteins - attached to one surface or the other

Glycoproteins and glycolipids - used for cell adhesion + cell to cell recognition

Fluid Mosaic Model - model for the phospholipid bilayer

Fatty acids of lipid bilayer - has varying degrees of saturated vs unsaturated hydrocarbon (fatty acid) chains

  • Animals in colder areas - more unsaturated fatty acids - do not freeze as easily and remain more flexible

  • Saturated fatty acids - stronger membrane but can stiffen at low temperatures

Cholesterol - attached to head of one and tail of adjacent phospholipid, only in animals

  • Modulator of fluidity - lowers at high temperatures, prevents stiffening at low temperatures

  • Lowers permeability

Cell Adhesion Molecules - specialized protein membranes that allow attachment of cells to other cells, either directly attached or indirectly anchored to extracellular matrix, important in many cellular processes (like growth), different molecules mean different cell-cell junctions

Simple Diffusion - small, nonpolar molecules (nonspecific) can move between phospholipids through the membrane, passive, high to low concentration in the gradient, O2 and CO2

Facilitated Diffusion - uses protein channels to facilitate movement of small (typically), polar molecules (specific), passive, high to low concentration in the gradient, Na+ and K+

  • Types of protein channels: leakage, voltage, ligand-gated

  • Osmosis - specialized type of facilitated diffusion (passive) for water, moves through protein channels known as aquaporins, low to high solute

Active Transport - uses protein pumps and ATP (energy = not passive!) to move molecules (specific), low to high concentration in the gradient, Na+ & K+ & glucose

Endocytosis and Exocytosis

  • Allows large molecules/amounts of material to move across plasma membrane

  • Endocytosis is for entering the cell by pinching and exocytosis is for exiting the cell by fusing and releasing - possible due to the fluidity of the membrane

  • Vesicles either form in endocytosis or fuse with the membrane in exocytosis

  • They are essentially the inverse of each other

D2.3 Water Potential

Solvation - interaction of solvent with dissolved solute

  • Hydration - solvation by water

    • Hydrogen bonds form between water molecules and the ions

Water Movement and Effects in Labs

  • Water moves through osmosis from less concentrated (hypotonic) to more concentrated (hypertonic) solutions

    • Hypertonic - more solute

    • Hypotonic - less solute

    • Isotonic - same concentration (water moves back and forth for net 0)

  • Tissue of plants will change in mass and length when put in solutions

    • Osmolarity - the concentration of the tissue, zero percent change on a graph

Animal Cells

  • When in a hypertonic solution, it shrivels; when in a hypotonic solution, it bursts

  • To stop, unicellular organisms have contractile vacuoles

  • Organelles that can capture excess water and expel it to maintain osmotic conditions

Cells with Cell Walls

  • When in a hypertonic solution, it goes through plasmolysis - cell shrinks but maintains overall shape

  • When in a hypotonic solution, it goes through turgor pressure - cell expands

Medical Applications

  • Intravenous (IV) fluids - balanced with blood solute concentration

  • Organs - must be bathed in isotonic solution to prepare for transplant

  • Causes no overall change to cells

Potential energy of water - potential for water to move relative to atmospheric pressure and 20 degrees Celcius, units typically kPa (kilopascals)

  • Water moves from high to low potential (opposite of solute concentration of low to high)

  • Formula: ψw = ψs + ψp — water potential = solute potential + pressure potential

    • Solute potential is always negative - adding solute lowers solute potential

    • Pressure potential (turgor pressure) is positive or negative - amount it’s pushing

C1.1 Enzymes and Metabolism

Metabolism - the complex network of interdependent and interacting chemical reactions occurring in living organisms through the use of enzymes — all enzyme catalyzed reactions

  • generates heat energy - energy lost during a reaction, used by endotherms to maintain body temperature

Catalyst - a substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change — speed up chemical reactions to make more products

Enzyme - a substance produced by a living organism which acts as a catalyst to bring about a specific biochemical reaction

  • they are globular proteins with an active site (small handful of amino acids that bind to substrate - molecules being put in) for catalysis (reacting), overall structure affects binding

  • Induced fit model - both substrate and enzyme change shape when binding occurs

  • graph below: enzymes decrease activation energy of reaction

Types of Reactions

  • Anabolic - condensation reactions to form polymers

    • Protein synthesis, glycogen formation, photosynthesis

  • Catabolic - hydrolysis of macromolecules to monomers

    • Digestion, oxidation in cell respiration

Metabolic pathways - can be cycles or linear

  • Glycolysis - linear, Krebs cycle - cycles, Calvin cycle - cycles

Molecular Motion and Enzymes

  • For a reaction to occur, the enzyme and substrate must collide

  • The faster they are moving, the more likely they are to collide (higher temperature)

  • To enhance likelihood of a collision, embed either the substrate or enzyme into a membrane to lock it in place

Measurements in enzyme-catalyzed reactions - rate of reaction = change in concentration of substance over time, reactants goes down, products goes up

Temp, pH and substrate concentration on Enzyme activity

  • Temperature increases linearly as molecules move faster and then sharp decline as enzyme denatures past optimum temp

  • pH has the denature shape on both sides of the optimum

  • Substrate increases rapidly and then plateaus once all enzymes are being used

Relationships between the structure of the active site, enzyme–substrate specificity and denaturation - the structure of the active site is for enzymes to connect with specific substrates, conditions such as temperature or pH will cause denaturation of enzyme, meaning active site will lose shape and function

Intracellular reactions - inside of cells

  • Examples: cell processes, Krebs cycle, Calvin cycle, glycolysis

Extracellular reactions - outside of cells

  • Examples: releasing enzymes, digestion

Non-competitive or allosteric inhibition

  • Allosteric site - site on enzymes that can bind with a specific inhibitor that will change the shape of the enzyme and stop catalysis

  • Is reversible and slows down a specific reaction

  • End product/feedback inhibition - special type where inhibitor is end product of metabolic pathway

    • Example: Isoleucine is the end product inhibitor of the threonine to isoleucine pathway

Competitive inhibition

  • Substrate and inhibitor are similar and the inhibitor blocks the active site

  • It is only temporary - adding more substrate can overcome it

  • Example: Statins - competitive inhibitors that block cholesterol synthesis

Mechanism-based inhibition - irreversible binding of inhibitor similar to substrate causing irreversible complex with a covalent bond

  • Example: Penicillin - used to kill bacteria

C1.2 Cell Respiration

ATP - stands for adenosine triphosphate, is a ribonucleotide

  • Known as the energy currency - energy stored in phosphate bonds, easily released for use by cell, adenine and ribose allow attachment to enzymes for use in those reactions

  • Supplies energy for life processes - biosynthesis (anabolic), active transport, movement

Coenzymes - non-protein organic compounds that facilitate enzyme reactions

  • ATP is a coenzyme that adds chemical energy to reactions

  • Then ATP will lose a phosphate and release energy to reaction

  • ADP is low energy, must be replenished by adding a phosphate

Cell Respiration makes ATP

  • Main substrates: Glucose and fatty acids

    • Lots of organic compounds can be used for energy including amino acids

  • Put in carbon compounds and break them apart to release energy to regenerate ATP from ADP 

  • NOTE: CELL RESPIRATION IS NOT GAS EXCHANGE! (DOES NOT MEAN BREATHING IN IB)

Glycolysis - the first part of cell respiration, occurs in the cytoplasm

  • Glucose (6 carbons) is phosphorylated (add a phosphate) using ATP, and then again after rearranged

  • Then splits into two 3 carbon molecules each with phosphate

    • The two steps above are energy investments (use of ATP)

  • Those two are rearranged and oxidized (losing electron and H), pairing with the reduction (gaining electron and H) of NAD+ to NADH

  • Phosphate is removed from both and ADP is converted to ATP (substrate level phosphorylation) twice to form pyruvate

    • Both indicating one for each of the two molecules

  • Summary: 1 glucose to 2 pyruvate, net gain of 2 ATP, 2 NADH, anaerobic