AP Biology

1. AP Biology Exam Critical Concepts Chapters 6, 7, 8 The cell and its processes

2. Chapter 6 The Cell • Prokaryotic cells: • no nucleus • DNA: unbound region called the nucleoid • No membrane bound organelles • Cytoplasm: bound by the plasma membrane • Bacteria cells • Eukaryotic cells: • DNA in a nuclear envelope • Membrane bound organelles • generally much larger than prokaryotic cells • Animal, plant, protist, and fungi cells

3. Chapter 6 The Cell cont.

4. Chapter 6 The Cell cont. • Plasma membrane: • selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell • double layer of phospholipids • logistics of carrying out cellular metabolism sets limits on the size of cells • surface area to volume ratio of a cell is critical • As surface area increases by a factor of n2, the volume increases by a factor of n3 • Small cells have a greater surface area relative to volume

5. Membranes are Great Examples of Form and Function

6. Chapter 6 The Cell cont. • Eukaryotic cell has internal membranes that partition the cell into organelles • Plant and animal cells have most of the same organelles • Nucleus: • contains most of the cell’s genes/DNA • Nuclear envelope: encloses the nucleus, separating it from cytoplasm • a double membrane; each membrane consists of a lipid bilayer • Pores regulate the entry and exit of molecules from the nucleus

7. Chapter 6 The Cell cont. • Ribosomes: • particles made of ribosomal RNA and protein • carry out protein synthesis in two locations: • Free ribosomes: In the cytosol • Bound ribosomes: On the outside of the endoplasmic reticulum or the nuclear envelope • Endomembrane system: • Movement of material in cell • Vesicles: packets of material

8. Chapter 6 The Cell cont. • Endomembrane system components: • Nuclear envelope • Endoplasmic reticulum • Golgi apparatus • Lysosomes • Vacuoles • Plasma membrane • Endoplasmic Reticulum: • Material movement • Accounts for more than half of the total membrane in many eukaryotic cells

9. Chapter 6 The Cell cont. • Endoplasmic reticulum: membrane is continuous with the nuclear envelope • Two distinct regions of ER: • Smooth ER: lacks ribosomes • Synthesizes lipids • Metabolizes carbohydrates • Detoxifies poison and stores calcium • Rough ER: ribosomes studding its surface • Has bound ribosomes: secrete glycoproteins • Distributes transport vesicles • Is a membrane factory for the cell

10. Chapter 6 The Cell cont. • Golgi apparatus: • flattened membranous sacs called cisternae • Functions: • Modifies products of the ER • Manufactures certain macromolecules • Sorts and packages materials into transport vesicles

11. Chapter 6 The Cell cont. • Lysosome: • Hydrolytic enzymes that can digest proteins, fats, polysaccharides, and nucleic acids • Phagocytosis: Some types of cell can engulf another cell by this forms a food vacuole • Fuses with the food vacuole and digests the molecules • Use enzymes to recycle the cell’s own organelles and macromolecules, called autophagy

12. Chapter 6 The Cell cont. • Vacuoles: • plant cell or fungal cell may have one or several vacuoles • Food vacuoles: formed by phagocytosis • Contractile vacuoles: found in many freshwater protists, pump excess water out of cells • Central vacuoles: found in many mature plant cells, hold organic compounds and water

13. Chapter 6 The Cell cont. • Mitochondria and Chloroplasts: • Are not part of the endomembrane system • Have a double membrane • Contain their own DNA • Change energy from one form to another • Mitochondria: sites of cellular respiration • metabolic process that generates ATP • in nearly all eukaryotic cells • have a smooth outer membrane and an inner membrane folded into cristae • The inner membrane creates two compartments: intermembrane space and mitochondrial matrix

14. Chapter 6 The Cell cont. • Chloroplasts: in plants and algae • sites of photosynthesis • a member of a family of organelles called plastids • contain the green pigment chlorophyll, as well as enzymes and other molecules that function in photosynthesis • found in leaves and other green organs of plants and in algae

15. Chapter 6 The Cell cont. • Peroxisomes: • specialized metabolic compartments bounded by a single membrane • produce hydrogen peroxide and convert it to water • Oxygen is used to break down different types of molecules

16. Chapter 6 The Cell cont. • Cell Wall: • Extracellular structure that distinguishes plant cells from animal cells • Found in Prokaryotes, fungi, and some protists • Protects the plant cell • Maintains its shape • Prevents excessive uptake of water • made of cellulose fibers embedded in other polysaccharides and protein

17. Chapter 6 The Cell cont.

18. Chapter 7 The Cell Membrane • Allows movement of material in and out • Boundary that separates the living cell from its surroundings • Selective permeability: allowing some substances to cross it more easily than others • Made of Phospholipids and Protein

19. Chapter 7 The Cell Membrane cont. Phospholipid bilayer Hydrophobic regions of protein Hydrophilic regions of protein

20. Chapter 7 The Cell Membrane cont. • Phospholipids in the plasma membrane can move within the bilayer • Most of the lipids, and some proteins, drift laterally Lateral movement (107 times per second) Flip-flop ( once per month)

21. Chapter 7 The Cell Membrane cont. Viscous Fluid Unsaturated hydrocarbon tails with kinks Saturated hydro-carbon tails

22. Chapter 7 The Cell Membrane cont. • The steroid cholesterol has different effects on membrane fluidity at different temperatures • warm temperatures (such as 37°C), cholesterol restrains movement of phospholipids • At cool temperatures, it maintains fluidity by preventing tight packing • Membrane is a collage of different proteins embedded in the fluid matrix of the lipid bilayer

23. Chapter 7 The Cell Membrane cont. • Proteins determine most of the membrane’s specific functions: • Peripheral proteins are bound to the surface of the membrane • Integral proteins penetrate the hydrophobic core • Transmembrane proteins: Integral proteins that span the membrane • Hydrophobic (nonpolar) molecules, such as hydrocarbons, can dissolve in the lipid bilayer and pass through the membrane rapidly • Polar molecules, such as sugars, do not cross the membrane easily

24. Chapter 7 The Cell Membrane cont. • Cell to cell recognition: • Cells recognize each other by binding to surface molecules, often carbohydrates, on the plasma membrane • Membrane carbohydrates may be covalently bonded to lipids (forming glycolipids) or more commonly to proteins (forming glycoproteins) • Carbohydrates on the external side of the plasma membrane vary among species, individuals, and even cell types in an individual

25. Chapter 7 The Cell Membrane cont. • Transport proteins: • Allow passage of hydrophilic substances across the membrane • Channel proteins, channel certain molecules/ions through membrane • Aquaporinsfacilitate the passage of water • Carrier proteins, bind to molecules and change shape to shuttle them across the membrane • is specific for the substance it moves

26. Chapter 7 The Cell Membrane cont. Signaling molecule Enzymes Receptor ATP Signal transduction (2) Enzymatic activity (3) Signal transduction (1) Transport

27. Chapter 7 The Cell Membrane cont. Glyco- protein (5) Intercellular joining (6) Attachment to the cytoskeleton and extracellular matrix (ECM) (4) Cell-cell recognition

28. Chapter 7 The Cell Membrane cont. • Passive transport: diffusion of a substance across a membrane with no energy investment • Diffusion: tendency for molecules to spread out evenly into the available space • Dynamic equilibrium: as many molecules cross one way as cross in the other direction • Concentration gradient: the difference in concentration of a substance from one area to another without energy

29. Chapter 7 The Cell Membrane cont. • Osmosis: Passive diffusion of water across a selectively permeable membrane • Water diffuses across a membrane from the region of lower solute concentration to the region of higher solute concentration • Tonicity: ability of a solution to cause a cell to gain or lose water

30. Chapter 7 The Cell Membrane cont. • Osmoregulation: the control of water balance • Isotonic solution: Solute concentration is equal in vs. out; no net water movement across the membrane • Hypertonic solution: Solute concentration is greater than that inside the cell • cell loses water to environment • the animal cell becomes flaccid (limp) • the plant may wilt (plasmolysis) • Hypotonic solution: Solute concentration is less than that inside the cell; cell gains water • A plant cell will swells until the wall opposes uptake; the cell is now turgid (firm) • An animal cell may burst (lyse)

31. Chapter 7 The Cell Membrane cont. Isotonic solution Hypotonic solution Hypertonic solution H2O H2O H2O H2O Animal cell Shriveled Normal Lysed H2O H2O H2O H2O Plant cell Turgid (normal) Plasmolyzed Flaccid

32. Chapter 7 The Cell Membrane cont. • Facultative transport: transport proteins speed the passive movement of molecules across the membrane • Channel proteins: provide corridors that allow a specific molecule or ion to cross the membrane • Include: • Aquaporins: for facilitated diffusion of water • Ion channels: open or close in response to a stimulus (gated channels) • Carrier proteins: undergo a subtle change in shape that translocates the solute-binding site across the membrane

33. Chapter 7 The Cell Membrane cont. • Active transport: moves substances against their concentration gradient • Requires energy, usually in the form of ATP • Transport proteins: specific proteins embedded in the membranes to help move substance • Ion pumps: include Na and K pumps • Proton pumps: create electrochemical gradient • Mitochondria and chloroplasts • Cotransport: active transport of a solute indirectly drives transport of another solute

34. Transport Occurs Through Membranes Chapter 7 The Cell Membrane cont. Active Transport = energy (ATP) Passive transport = no energy

35. Chapter 7 The Cell Membrane cont. • Bulk Transport: substances enter or leave the cell through the lipid bilayer or by transport proteins • Large macromolecules, cross the membrane in bulk via vesicles, requiring energy • Occurs by: • Exocytosis: transport vesicles migrate to the membrane, fuse with it, and release their contents • secretory cells exporting their products • Endocytosis: the cell takes in macromolecules by forming vesicles from the plasma membrane • There are three types

36. Chapter 7 The Cell Membrane cont. • Endocytosis types: • Phagocytosis (“cellular eating”) • In a cell engulfs a particle in a vacuole • The vacuole fuses with a lysosome to digest the particle • Pinocytosis (“cellular drinking”) • molecules are taken up when extracellular fluid is “gulped” into tiny vesicles • Receptor-mediated endocytosis • Binding of ligands to receptors triggers vesicle formation

37. Chapter 7 The Cell Membrane cont.

38. Chapter 8 Cell Metabolism • Metabolism: is the totality of an organism’s chemical reactions • emergent property of life that arises from interactions between molecules within the cell • Metabolic pathway: begins with a specific molecule and ends with a product • Each step is catalyzed by a specific enzyme • Catabolic pathway: release energy by breaking down complex molecules into simpler compounds • Cellular respiration: breakdown of glucose in the presence of oxygen, is an example of a pathway of catabolism

39. Chapter 8 Cell Metabolism cont. • Anabolic pathway: consume energy to build complex molecules from simpler ones • The synthesis of protein from amino acids is an example of anabolism • Energy: the capacity to cause change • Kinetic energy: energy associated with motion • Heat (thermal energy): kinetic energy associated with random movement of atoms • Potential energy: energy that matter possesses because of its location or structure

40. Chapter 8 Cell Metabolism cont. • Chemical energy: potential energy available for release in a chemical reaction • Energy can be converted from one form to another • Thermodynamics: study of energy transformations • A closed system is isolated from its surroundings • An open system: energy and matter can be transferred between the system and its surroundings • Organisms are open systems • Catalysts: Substance that change the rate of reaction

41. Chapter 8 Cell Metabolism cont. • First law of thermodynamics: Energy can be transferred and transformed, but it cannot be created or destroyed • also called the principle of conservation of energy • Second law of thermodynamics: Every energy transfer or transformation increases the entropy (disorder) of the universe • During every energy transfer or transformation, some energy is unusable, and is often lost as heat • Exergonic reaction proceeds with a net release of free energy and is spontaneous

42. Chapter 8 Cell Metabolism cont. • Endergonic reaction: absorbs free energy from its surroundings and is nonspontaneous • A defining feature of life is that metabolism is never at equilibrium • A cell does three main kinds of work: powered by ATP • Chemical • Transport • Mechanical • To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one

43. Chapter 8 Cell Metabolism cont. • ATP: energy currency of the cell • The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis • Energy is released from ATP when the terminal phosphate bond is broken • This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves

44. Nucleic Acid Structure is Similar to ATP Chapter 8 Cell Metabolism cont. ATP DNA Nucleotide

45. Chapter 8 Cell Metabolism cont. • Phosphorylation: transferring a phosphate group to some other molecule • ATP drives endergonic reactions • The recipient molecule is now phosphorylated • ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP) • The energy to phosphorylate ADP comes from catabolic reactions in the cell • The chemical potential energy temporarily stored in ATP drives most cellular work

46. Chapter 8 Cell Metabolism cont. • Every chemical reaction between molecules involves bond breaking and bond forming • Activation energy (EA): initial energy needed to start a chemical reaction • often supplied in the form of heat from the surroundings • Enzymes catalyze reactions by lowering the EA barrier • Enzymes do not affect the change in free energy (∆G); instead, they hasten reactions that would occur eventually

47. Chapter 8 Cell Metabolism cont. • Substrate: the reactant that an enzyme acts on is • Enzyme-substrate complex: enzyme binds to its substrate • Active site: region on the enzyme where the substrate binds • Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction • In an enzymatic reaction, the substrate binds to the active site of the enzyme

48. Chapter 8 Cell Metabolism cont. • Enzyme’s activity can be affected by • General environmental factors, such as temperature and pH • Chemicals that specifically influence the enzyme • Each enzyme has an optimal temperature in which it can function • Each enzyme has an optimal pH in which it can function • Cofactors: nonprotein enzyme helpers • may be inorganic (such as a metal in ionic form) or organic

49. Chapter 8 Cell Metabolism cont. • Coenzymes: organic cofactor • include vitamins • Competitive inhibitors: bind to the active site of an enzyme • competing with the substrate • Noncompetitive inhibitors: bind to another part of an enzyme • cause enzyme to change shape, making the active site less effective • include toxins, poisons, pesticides, and antibiotics • Allosteric site: a specific binding site that is not the active site

50. Chapter 8 Cell Metabolism cont. Substrate Active site Competitive inhibitor Enzyme Noncompetitive inhibitor (c) Noncompetitive inhibition (b) Competitive inhibition (a) Normal binding