Category: 1st Semester

Chapter 7 – Membrane Structure and Function Lecture Outline

Chapter 7    Membrane Structure and Function    Lecture Outline

Overview

  • The plasma membrane separates the living cell from its nonliving surroundings.
  • This thin barrier, 8 nm thick, controls traffic into and out of the cell.
  •  Like all biological membranes, the plasma membrane is selectively permeable, allowing some substances to cross more easily than others.

A. Membrane Structure

  • The main macromolecules in membranes are lipids and proteins, but carbohydrates are also important.
  • The most abundant lipids are phospholipids.
  •  Phospholipids and most other membrane constituents are amphipathic molecules.
  •  Amphipathic molecules have both hydrophobic regions and hydrophilic regions.
  • The arrangement of phospholipids and proteins in bi   ological membranes is described by the fluid mosaic model.

1. Membrane models have evolved to fit new data.

  •  Models of membranes were developed long before membranes were first seen with electron microscopes in the 1950s.
  •  In 1915, membranes isolated from red blood cells were chemically analyzed and found to be composed of lipids and proteins.
  •  In 1925, E. Gorter and F. Grendel reasoned that cell membranes must be a phospholipid bilayer two molecules thick.
  • The molecules in the bilayer are arranged such that the hydrophobic fatty acid tails are sheltered from water while the hydrophilic phosphate groups interact with water.
  •  Actual membranes adhere more strongly to water than do artificial membranes composed only of phospholipids.
  • One suggestion was that proteins on the surface of the membrane increased adhesion.
  •  In 1935, H. Davson and J. Danielli proposed a sandwich model in which the phospholipid bilayer lies between two layers of globular proteins.
  • Early images from electron microscopes seemed to support the Davson-Danielli model, and until the 1960s, it was widely accepted as the structure of the plasma membrane and internal membranes.
  • Further investigation revealed two problems.
  • First, not all membranes were alike. Membranes differ in thickness, appearance when stained, and percentage of proteins.
  • Membranes with different functions differ in chemical composition and structure.
  • Second, measurements showed that membrane proteins are not very soluble in water.
  • Membrane proteins are amphipathic, with hydrophobic and hydrophilic regions.
  • If membrane proteins were at the membrane surface, their hydrophobic regions would be in contact with water.
  • In 1972, S. J. Singer and G. Nicolson presented a revised model that proposed that the membrane proteins are dispersed and individually inserted into the phospholipid bilayer.
  • In this fluid mosaic model, the hydrophilic regions of proteins and phospholipids are in maximum contact with water, and the hydrophobic regions are in a nonaqueous environment within the membrane.
  • A specialized preparation technique, freeze-fracture, splits a membrane along the middle of the phospholipid bilayer.
  • When a freeze-fracture preparation is viewed with an electron microscope, protein particles are interspersed in a smooth matrix, supporting the fluid mosaic model.

2. Membranes are fluid.

  •  Membrane molecules are held in place by relatively weak hydrophobic interactions.
  • Most of the lipids and some proteins drift laterally in the plane of the membrane, but rarely flip-flop from one phospholipid layer to the other.
  • The lateral movements of phospholipids are rapid, about 2 microns per second. A phospholipid can travel the length of a typical bacterial cell in 1 second.
  • Many larger membrane proteins drift within the phospholipid bilayer, although they move more slowly than the phospholipids.
  • Some proteins move in a very directed manner, perhaps guided or driven by motor proteins attached to the cytoskeleton.
  • Other proteins never move and are anchored to the cytoskeleton.
  • Membrane fluidity is influenced by temperature. As temperatures cool, membranes switch from a fluid state to a solid state as the phospholipids pack more closely.
  • Membrane fluidity is also influenced by its components. Membranes rich in unsaturated fatty acids are more fluid that those dominated by saturated fatty acids because the kinks in the unsaturated fatty acid tails at the locations of the double bonds prevent tight packing.
  • The steroid cholesterol is wedged between phospholipid molecules in the plasma membrane of animal cells.
  • At warm temperatures (such as 37°C), cholesterol restrains the movement of phospholipids and reduces fluidity.
  • At cool temperatures, it maintains fluidity by preventing tight packing.
  • Thus, cholesterol acts as a “temperature buffer” for the membrane, resisting changes in membrane fluidity as temperature changes.
  • To work properly with active enzymes and appropriate permeability, membranes must be about as fluid as salad oil.
  • Cells can alter the lipid composition of membranes to compensate for changes in fluidity caused by changing temperatures.
  • For example, cold-adapted organisms such as winter wheat increase the percentage of unsaturated phospholipids in their membranes in the autumn.
  • This prevents membranes from solidifying during winter.

3. Membranes are mosaics of structure and function.

  • A membrane is a collage of different proteins embedded in the fluid matrix of the lipid bilayer.
  • Proteins determine most of the membrane’s specific functions.
  • The plasma membrane and the membranes of the various organelles each have unique collections of proteins.
  • There are two major populations of membrane proteins.
  • Peripheral proteins are not embedded in the lipid bilayer at all.
  • Instead, they are loosely bound to the surface of the protein, often connected to integral proteins.
  • Integral proteins penetrate the hydrophobic core of the lipid bilayer, often completely spanning the membrane (as transmembrane proteins).
  • The hydrophobic regions embedded in the membrane’s core consist of stretches of nonpolar amino acids, often coiled into alpha helices.
  • Where integral proteins are in contact with the aqueous environment, they have hydrophilic regions of amino acids.
  • On the cytoplasmic side of the membrane, some membrane proteins connect to the cytoskeleton.
  • On the exterior side of the membrane, some membrane proteins attach to the fibers of the extracellular matrix.
  • The proteins of the plasma membrane have six major functions:

1.       Transport of specific solutes into or out of cells.
2.       Enzymatic activity, sometimes catalyzing one of a number of steps of a metabolic pathway.
3.       Signal transduction, relaying hormonal messages to the cell.
4.       Cell-cell recognition, allowing other proteins to attach two adjacent cells together.
5.       Intercellular joining of adjacent cells with gap or tight junctions.
6.       Attachment to the cytoskeleton and extracellular matrix, maintaining cell shape and stabilizing the location of certain membrane proteins.

4. Membrane carbohydrates are important for cell-cell recognition.

  • The plasma membrane plays the key role in cell-cell recognition.
  •  Cell-cell recognition, the ability of a cell to distinguish one type of neighboring cell from another, is crucial to the functioning of an organism.
  • This attribute is important in the sorting and organization of cells into tissues and organs during development.
  • It is also the basis for rejection of foreign cells by the immune system.
  •  Cells recognize other cells by binding to surface molecules, often carbohydrates, on the plasma membrane.
  • Membrane carbohydrates are usually branched oligosaccharides with fewer than 15 sugar units.
  • They may be covalently bonded to lipids, forming glycolipids, or more commonly to proteins, forming glycoproteins.
  • The oligosaccharides on the external side of the plasma membrane vary from species to species, from individual to individual, and even from cell type to cell type within the same individual.
  • This variation distinguishes each cell type.
  • The four human blood groups (A, B, AB, and O) differ in the external carbohydrates on red blood cells.

5. Membranes have distinctive inside and outside faces.

  • Membranes have distinct inside and outside faces. The two layers may differ in lipid composition. Each protein in the membrane has a directional orientation in the membrane.
  • The asymmetrical orientation of proteins, lipids and associated carbohydrates begins during the synthesis of membrane in the ER and Golgi apparatus.
  • Membrane lipids and proteins are synthesized in the endoplasmic reticulum. Carbohydrates are added to proteins in the ER, and the resulting glycoproteins are further modified in the Golgi apparatus. Glycolipids are also produced in the Golgi apparatus.
  • When a vesicle fuses with the plasma membrane, the outside layer of the vesicle becomes continuous with the inside layer of the plasma membrane. In that way, molecules that originate on the inside face of the ER end up on the outside face of the plasma membrane.

B. Traffic across Membranes

1. A membrane’s molecular organization results in selective permeability.

  • A steady traffic of small molecules and ions moves across the plasma membrane in both directions.
  • For example, sugars, amino acids, and other nutrients enter a muscle cell, and metabolic waste products leave.
  • The cell absorbs oxygen and expels carbon dioxide.
  • It also regulates concentrations of inorganic ions, such as Na+, K+, Ca2+, and Cl−, by shuttling them across the membrane.
  • However, substances do not move across the barrier indiscriminately; membranes are selectively permeable.
  • The plasma membrane allows the cell to take up many varieties of small molecules and ions and exclude others. Substances that move through the membrane do so at different rates.
  • Movement of a molecule through a membrane depends on the interaction of the molecule with the hydrophobic core of the membrane.
  • Hydrophobic molecules, such as hydrocarbons, CO2, and O2, can dissolve in the lipid bilayer and cross easily.
  • The hydrophobic core of the membrane impedes the direct passage of ions and polar molecules, which cross the membrane with difficulty.
  • This includes small molecules, such as water, and larger molecules, such as glucose and other sugars.
  • An ion, whether a charged atom or molecule, and its surrounding shell of water also has difficulty penetrating the hydrophobic core.
  • Proteins assist and regulate the transport of ions and polar molecules.
  • Specific ions and polar molecules can cross the lipid bilayer by passing through transport proteins that span the membrane.
  • Some transport proteins, called channel proteins, have a hydrophilic channel that certain molecules or ions can use as a tunnel through the membrane.
  • For example, the passage of water through the membrane can be greatly facilitated by channel proteins known as aquaporins.
  • Other transport proteins, called carrier proteins, bind to molecules and change shape to shuttle them across the membrane.
  • Each transport protein is specific as to the substances that it will translocate.
  • For example, the glucose transport protein in the liver will carry glucose into the cell but will not transport fructose, its structural isomer.

2. Passive transport is diffusion across a membrane with no energy expenditure.

  • Diffusion is the tendency of molecules of any substance to spread out in the available space.
  • Diffusion is driven by the intrinsic kinetic energy (thermal motion or heat) of molecules.
  •  Movements of individual molecules are random.
  • However, movement of a population of molecules may be directional.
  • Imagine a permeable membrane separating a solution with dye molecules from pure water. If the membrane has microscopic pores that are large enough, dye molecules will cross the barrier randomly.
  • The net movement of dye molecules across the membrane will continue until both sides have equal concentrations of the dye.
  • At this dynamic equilibrium, as many molecules cross one way as cross in the other direction.
  • In the absence of other forces, a substance will diffuse from where it is more concentrated to where it is less concentrated, down its concentration gradient.
  • No work must be done to move substances down the concentration gradient.
  • Diffusion is a spontaneous process that decreases free energy and increases entropy by creating a randomized mixture.
  • Each substance diffuses down its own concentration gradient, independent of the concentration gradients of other substances.
  • The diffusion of a substance across a biological membrane is passive transport because it requires no energy from the cell to make it happen.
  • The concentration gradient itself represents potential energy and drives diffusion.
  • Because membranes are selectively permeable, the interactions of the molecules with the membrane play a role in the diffusion rate.
  • Diffusion of molecules of limited permeability through the lipid bilayer may be assisted by transport proteins.

3. Osmosis is the passive transport of water.

  • Differences in the relative concentration of dissolved materials in two solutions can lead to the movement of ions from one to the other.
  • The solution with the higher concentration of solutes is hypertonic relative to the other solution.
  • The solution with the lower concentration of solutes is hypotonic relative to the other solution.
  • These are comparative terms.
  • Tap water is hypertonic compared to distilled water but hypotonic compared to seawater.
  • Solutions with equal solute concentrations are isotonic.
  • Imagine that two sugar solutions differing in concentration are separated by a membrane that will allow water through, but not sugar.
  • The hypertonic solution has a lower water concentration than the hypotonic solution.
  • More of the water molecules in the hypertonic solution are bound up in hydration shells around the sugar molecules, leaving fewer unbound water molecules.
  • Unbound water molecules will move from the hypotonic solution, where they are abundant, to the hypertonic solution, where they are rarer. Net movement of water continues until the solutions are isotonic.
  • The diffusion of water across a selectively permeable membrane is called osmosis.
  • The direction of osmosis is determined only by a difference in total solute concentration.
  • The kinds of solutes in the solutions do not matter.
  • This makes sense because the total solute concentration is an indicator of the abundance of bound water molecules (and, therefore, of free water molecules).
  • When two solutions are isotonic, water molecules move at equal rates from one to the other, with no net osmosis.
  • The movement of water by osmosis is crucial to living organisms.

4. Cell survival depends on balancing water uptake and loss.

  • An animal cell (or other cell without a cell wall) immersed in an isotonic environment experiences no net movement of water across its plasma membrane.
  • Water molecules move across the membrane but at the same rate in both directions.
  • The volume of the cell is stable.
  • The same cell in a hypertonic environment will lose water, shrivel, and probably die.
  • A cell in a hypotonic solution will gain water, swell, and burst.
  • For organisms living in an isotonic environment (for example, many marine invertebrates), osmosis is not a problem.
  • The cells of most land animals are bathed in extracellular fluid that is isotonic to the cells.
  • Organisms without rigid walls have osmotic problems in either a hypertonic or hypotonic environment and must have adaptations for osmoregulation, the control of water balance, to maintain their internal environment.
  • For example, Paramecium, a protist, is hypertonic to the pond water in which it lives.
  • In spite of a cell membrane that is less permeable to water than other cells, water still continually enters the Paramecium cell.
  • To solve this problem, Paramecium cells have a specialized organelle, the contractile vacuole, which functions as a bilge pump to force water out of the cell.
  • The cells of plants, prokaryotes, fungi, and some protists have walls that contribute to the cell’s water balance.
  • A plant cell in a hypotonic solution will swell until the elastic cell wall opposes further uptake.
  • At this point the cell is turgid (very firm), a healthy state for most plant cells.
  • Turgid cells contribute to the mechanical support of the plant.
  • If a plant cell and its surroundings are isotonic, there is no movement of water into the cell. The cell becomes flaccid (limp), and the plant may wilt.
  • The cell wall provides no advantages when a plant cell is immersed in a hypertonic solution. As the plant cell loses water, its volume shrinks. Eventually, the plasma membrane pulls away from the wall. This plasmolysis is usually lethal.

5. Specific proteins facilitate passive transport of water and selected solutes.

  •  Many polar molecules and ions that are normally impeded by the lipid bilayer of the membrane diffuse passively with the help of transport proteins that span the membrane.
  • The passive movement of molecules down their concentration gradient via transport proteins is called facilitated diffusion.
  • Two types of transport proteins facilitate the movement of molecules or ions across membranes: channel proteins and carrier proteins.
  • Some channel proteins simply provide hydrophilic corridors for the passage of specific molecules or ions.
  • For example, water channel proteins, aquaporins, greatly facilitate the diffusion of water.
  • Many ion channels function as gated channels. These channels open or close depending on the presence or absence of a chemical or physical stimulus.
  • If chemical, the stimulus is a substance other than the one to be transported.
  • For example, stimulation of a receiving neuron by specific neurotransmitters opens gated channels to allow sodium ions into the cell.
  • When the neurotransmitters are not present, the channels are closed.
  • Some transport proteins do not provide channels but appear to actually translocate the solute-binding site and solute across the membrane as the transport protein changes shape.
  • These shape changes may be triggered by the binding and release of the transported molecule.
  • In certain inherited diseases, specific transport systems may be defective or absent.
  • Cystinuria is a human disease characterized by the absence of a protein that transports cysteine and other amino acids across the membranes of kidney cells.
  • An individual with cystinuria develops painful kidney stones as amino acids accumulate and crystallize in the kidneys.

6. Active transport uses energy to move solutes against their gradients.

  • Some transport proteins can move solutes across membranes against their concentration gradient, from the side where they are less concentrated to the side where they are more concentrated.
  • This active transport requires the cell to expend metabolic energy.
  •  Active transport enables a cell to maintain its internal concentrations of small molecules that would otherwise diffuse across the membrane.
  • Active transport is performed by specific proteins embedded in the membranes.
  • ATP supplies the energy for most active transport.
  •  ATP can power active transport by transferring a phosphate group from ATP (forming ADP) to the transport protein.
  • This may induce a conformational change in the transport protein, translocating the solute across the membrane.
  • The sodium-potassium pump actively maintains the gradient of sodium ions (Na+) and potassium ions (K+) across the plasma membrane of animal cells.
  • Typically, K+ concentration is low outside an animal cell and high inside the cell, while Na+ concentration is high outside an animal cell and low inside the cell.
  • he sodium-potassium pump maintains these concentration gradients, using the energy of one ATP to pump three Na+ out and two K+ in.

7. Some ion pumps generate voltage across membranes.

  •  All cells maintain a voltage across their plasma membranes.
  • Voltage is electrical potential energy due to the separation of opposite charges.
  • The cytoplasm of a cell is negative in charge compared to the extracellular fluid because of an unequal distribution of cations and anions on opposite sides of the membrane.
  • The voltage across a membrane is called a membrane potential, and ranges from −50 to −200 millivolts (mV). The inside of the cell is negative compared to the outside.
  • The membrane potential acts like a battery.
  • The membrane potential favors the passive transport of cations into the cell and anions out of the cell.
  • Two combined forces, collectively called the electrochemical gradient, drive the diffusion of ions across a membrane.
  • One is a chemical force based on an ion’s concentration gradient.
  • The other is ann electrical force based on the effect of the membrane potential on the ion’s movement.
  • An ion does not simply diffuse down its concentration gradient but diffuses down its electrochemical gradient.
  •  For example, there is a higher concentration of Na+ outside a resting nerve cell than inside.
  • When the neuron is stimulated, a gated channel opens and Na+ diffuse into the cell down their electrochemical gradient. The diffusion of Na+ is driven by their concentration gradient and by the attraction of cations to the negative side of the membrane.
  • Special transport proteins, electrogenic pumps, generate the voltage gradient across a membrane.
  • The sodium-potassium pump in animals restores the electrochemical gradient not only by the active transport of Na+ and K+, setting up a concentration gradient, but because it pumps two K+ inside for every three Na+ that it moves out, setting up a voltage across the membrane.
  • The sodium-potassium pump is the major electrogenic pump of animal cells.
  • In plants, bacteria, and fungi, a proton pump is the major electrogenic pump, actively transporting H+ out of the cell.
  • Proton pumps in the cristae of mitochondria and the thylakoids of chloroplasts concentrate H+ behind membranes.
  • These electrogenic pumps store energy that can be accessed for cellular work.

8. In cotransport, a membrane protein couples the transport of two solutes.

  • A single ATP-powered pump that transports one solute can indirectly drive the active transport of several other solutes in a mechanism called cotransport.
  •  As the solute that has been actively transported diffuses back passively through a transport protein, its movement can be coupled with the active transport of another substance against its concentration gradient.
  • Plants commonly use the gradient of hydrogen ions generated by proton pumps to drive the active transport of amino acids, sugars, and other nutrients into the cell.
  • One specific transport protein couples the diffusion of protons out of the cell and the transport of sucrose into the cell. Plants use the mechanism of sucrose-proton cotransport to load sucrose into specialized cells in the veins of leaves for distribution to nonphotosynthetic organs such as roots.

9. Exocytosis and endocytosis transport large molecules across membranes.

  • Small molecules and water enter or leave the cell through the lipid bilayer or by transport proteins.
  • Large molecules, such as polysaccharides and proteins, cross the membrane via vesicles.
  • During exocytosis, a transport vesicle budded from the Golgi apparatus is moved by the cytoskeleton to the plasma membrane.
  • When the two membranes come in contact, the bilayers fuse and spill the contents to the outside.
  • Many secretory cells use exocytosis to export their products.
  • During endocytosis, a cell brings in macromolecules and particulate matter by forming new vesicles from the plasma membrane.
  • Endocytosis is a reversal of exocytosis, although different proteins are involved in the two processes.
  • A small area of the plasma membrane sinks inward to form a pocket.
  • As the pocket deepens, it pinches in to form a vesicle containing the material that had been outside the cell.
  • There are three types of endocytosis: phagocytosis (“cellular eating”), pinocytosis (“cellular drinking”), and receptor-mediated endocytosis.
  • In phagocytosis, the cell engulfs a particle by extending pseudopodia around it and packaging it in a large vacuole.
  • The contents of the vacuole are digested when the vacuole fuses with a lysosome.
  •  In pinocytosis, a cell creates a vesicle around a droplet of extracellular fluid. All included solutes are taken into the cell in this nonspecific process.
  • Receptor-mediated endocytosis allows greater specificity, transporting only certain substances.
  • This process is triggered when extracellular substances, or ligands, bind to special receptors on the membrane surface. The receptor proteins are clustered in regions of the membrane called coated pits, which are lined on their cytoplasmic side by a layer of coat proteins.
  • Binding of ligands to receptors triggers the formation of a vesicle by the coated pit, bringing the bound substances into the cell.
  • Receptor-mediated endocytosis enables a cell to acquire bulk quantities of specific materials that may be in low concentrations in the environment.
  • Human cells use this process to take in cholesterol for use in the synthesis of membranes and as a precursor for the synthesis of steroids.
  • Cholesterol travels in the blood in low-density lipoproteins (LDL), complexes of protein and lipid.
  • These lipoproteins act as ligands to bind to LDL receptors and enter the cell by endocytosis.
  • In an inherited disease called familial hypercholesterolemia, the LDL receptors are defective, leading to an accumulation of LDL and cholesterol in the blood.
  • This contributes to early atherosclerosis.

 

Chapter 7 – A Tour of the Cell Objectives

 

 

Chapter 7   Membrane Structure & Function
Objectives
Membrane Structure

1.  Explain why phospholipids are amphipathic molecules.

2.  Explain what freeze-fracture techniques reveal about the arrangement of proteins in membranes.

3.  Describe the fluidity of the components of a cell membrane and explain how membrane fluidity is influenced by temperature and membrane composition.

4.  Explain how cholesterol resists changes in membrane fluidity with temperature change.

Traffic Across Membranes

5.  Distinguish between peripheral and integral membrane proteins.

6.  List six major functions of membrane proteins.

7.  Explain the role of membrane carbohydrates in cell-cell recognition.

8.  Explain how hydrophobic molecules cross cell membranes.

9.  Distinguish between channel proteins and carrier proteins.

10. Define diffusion. Explain why diffusion is a spontaneous process.

11. Explain why a concentration gradient of a substance across a membrane represents potential energy.

12. Distinguish among hypertonic, hypotonic, and isotonic solutions.

13. Define osmosis and predict the direction of water movement based on differences in solute concentrations.

14. Describe how living cells with and without cell walls regulate water balance.

15. Explain how transport proteins facilitate diffusion.

16. Distinguish among osmosis, facilitated diffusion, and active transport.

17. Describe the two forces that combine to produce an electrochemical gradient.

18. Explain how an electrogenic pump creates voltage across a membrane.

19. Describe the process of cotransport.

20. Explain how large molecules are transported across a cell membrane.

21.       Distinguish between pinocytosis and receptor-mediated endocytosis.

 
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Chapter 2 Worksheet BI – Chemistry

 

Chemistry Worksheet

 

Section  2-1    Composition of Matter  

1. Define matter.

2. Define mass.

3. Explain the difference between mass & weight.

4. Why do biologists study chemistry?

5. Define element.

6. Name the 4 elements that make up 90% of the mass of living things. Give the symbol for each of these elements.

7. Explain why some elements such as sodium have odd symbols.

8. Sketch a block from the periodic table and label the atomic number, atomic mass, & symbol for the element.

9. Define atom and tell whether they can be seen.

10. What is the center of an atom called & what 2 subatomic particles are found there?

11. How does the charge of a proton differ from the charge of a neutron?

12. Where is most of the mass of an atom concentrated?

13. How is the atomic number of an element determined?

14. What is the charge on an electron?

15. Explain why the overall or net charge on an atom is zero.

16. Where are electrons found in an atom & describe their movement?

17. In which energy levels do the electrons have more energy?

18. How many electrons can these energy levels hold   — a. first?        b. second? 

19. Define compound and write a formula for water, carbon dioxide, & sodium chloride (table salt).

20. Do compounds have the same chemical properties as the elements that compose them?

21. When would an atom be chemically stable (not react)?

22. What occurs in a chemical reaction?

23. What is a covalent bond?

24. Define molecule.

25. Give an example of a gas that exists as a molecule.

26. Define ionic bond.

27. What is an ion?

28. Name a compound formed from — a. covalent bonding?            b. ionic bonding?

29. If electrons are shared, a(n) ______________ compound forms.

30. If electrons are transferred, a(n) _____________ compound forms.

31. Forming ionic or covalent bonds helps make atoms more ________________.

Section 2-2    Energy 

32. All living things require _____________ to do work.

33. Energy can’t be created or _____________ in a chemical reaction, but it can be _____________ from one form into another.

34. Name 4 forms of energy important to living things.

35. What is free energy?

36. Give an example of energy changing form in an organism.

37. Atoms & molecules are in constant _______________.

38. Name the 3 main states of matter.

39. Explain how the shape and volume of a solid, liquid, and gas differ.

40. Organisms undergo thousands of ____________ as part of their life processes.

41. Where are the reactants and products in a chemical equation?

42. What does a two-direction arrow mean in a chemical equation?

43. _______________ are broken down in chemical reactions in your body to release ___________ and produce _______________ and ______________.

44. What is the difference between an endergonic & exergonic reaction?

45. What is activation energy?

46. What effect does a catalyst have on activation energy?

47. What are biological catalysts called?

48. Redox is the abbreviation for what type of reaction?

49. Redox reactions involve the transfer of energy and _________ between atoms.

50. What happens during oxidation?

51. What happens during reduction?

52. Give an example of oxidation.

53. Give an example of reduction.

Section 2-3        Solutions   

54. Many of the chemical reactions in organisms take place in __________.

55. What is a solution?

56. Give an example of a complex solution in your body.

57. Name & describe the 2 parts of a solution.

58. What is meant by concentration of the solution?

59. How do you get a saturated solution?

60. What are aqueous solutions?

61. Explain dissociation of water molecules.

62. Name and give the charge for the 2 ions formed whenever water dissociates.

63. Write the final equation for the dissociation of water.

64. What is the hydronium ion?

65. How are acidity and alkalinity measured?

66. When would a solution be neutral?    Give an example of a neutral solution.

67. When would solutions be considered as acidic?

68. Acids have what taste?

69. Acids form what ion in water?

70. Give an example of an acid in your stomach.

71. When would solutions be considered as a base?

72. What adjective refers to basic solutions?

73. Give an example of a base.

74. What ion forms whenever a base is dissolved in water?

75. How does a base taste and feel?

76. How is soap made?

77. What is the pH scale used for?

78. What is the range for the pH scale?

79. At what pH would you find each of these solutions on a pH scale:    a. acids?    b. Bases?    c. neutral?

80. How many times stronger is a pH of 3 than a pH of 5?

81. A change of one pH unit reflects a __________ change.

82. Why is controlling the pH range important to organisms?

83. How do organisms control their pH levels?

84. What is a buffer?

85. Give an example of a human body fluid that is:    a. acidic?    b. alkaline?


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Chapter 25 AP Objectives

 

Chapter 25    Tracing Phylogeny
Objectives
Phylogenies are Based on Common Ancestries
1. Distinguish between phylogeny and systematics.
2. Describe the process of sedimentation and the formation of fossils. Explain which portions of organisms are most likely to fossilize.
3. Explain why it is crucial to distinguish between homology and analogy before selecting characters to use in the reconstruction of phylogeny.
4. Explain why bird and bat wings are homologous as vertebrate forelimbs but analogous as wings.
5. Define molecular systematics. Explain some of the problems that systematists may face in carrying out molecular comparisons of nucleic acids.
Phylogenetic Systematics: Connecting Classification
with Evolutionary History
6. Explain the following characteristics of the Linnaean system of classification:
a. binomial nomenclature
b. hierarchical classification
7. List the major taxonomic categories from most to least inclusive.
8. Define a clade. Distinguish between a monophyletic clade and paraphyletic and polyphyletic groupings of species.
9. Distinguish between shared primitive characters and shared derived characters.
10. Explain how shared derived characters can be used to construct a phylogenetic diagram.
11. Explain how outgroup comparison can be used to distinguish between shared primitive characters and shared derived characters.
12. Define an ingroup.
13. Distinguish between a phylogram and an ultrameric tree.
14. Discuss how systematists use the principles of maximum parsimony and maximum likelihood in reconstructing phylogenies.
15. Explain why any phylogenetic diagram represents a hypothesis about evolutionary relationships among organisms.
16. Distinguish between orthologous and paralogous genes. Explain how gene duplication has led to families of paralogous genes.
17. Explain how molecular clocks are used to determine the approximate time of key evolutionary events. Explain how molecular clocks are calibrated in actual time.
18. Describe some of the limitations of molecular clocks.
19. Explain the neutral theory of evolutionary change.
20. Explain how scientists determined the approximate time when HIV-1 M first infected humans.
21. Describe the evidence that suggests there is a universal tree of life.
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Chapter 3 – Water and the Fitness of the Environment – Lecture Outline

Chapter 3    Water and the Fitness of the Environment    Lecture Outline

Overview: The Molecule That Supports All of Life

  • Because water is the substance that makes life possible on Earth, astronomers hope to find evidence of water on newly discovered planets orbiting distant stars.
  • Life on Earth began in water and evolved there for 3 billion years before colonizing the land.
  • Even terrestrial organisms are tied to water.
  • Most cells are surrounded by water.
  • Cells are about 70–95% water.
  • Water is a reactant in many of the chemical reactions of life.
  • Water is the only common substance that exists in the natural world in all three physical states of matter: solid ice, liquid water, and water vapor.

Concept 3.1 The polarity of water molecules results in hydrogen bonding

  • In a water molecule, two hydrogen atoms form single polar covalent bonds with an oxygen atom.
  • Because oxygen is more electronegative than hydrogen, the region around the oxygen atom has a partial negative charge.
  • The regions near the two hydrogen atoms have a partial positive charge.
  • A water molecule is a polar molecule in which opposite ends of the molecule have opposite charges.
  • Water has a variety of unusual properties because of the attraction between polar water molecules.
  • The slightly negative regions of one water molecule are attracted to the slightly positive regions of nearby water molecules, forming hydrogen bonds.
  • Each water molecule can form hydrogen bonds with up to four neighbors.

Concept 3.2 Four emergent properties of water contribute to Earth’s fitness for life

  • Organisms depend on the cohesion of water molecules.
  • The hydrogen bonds joining water molecules are weak, about 1/20 as strong as covalent bonds.
  • They form, break, and reform with great frequency. Each hydrogen bond lasts only a few trillionths of a second.
  • At any instant, a substantial percentage of all water molecules are bonded to their neighbors, creating a high level of structure.
  • Collectively, hydrogen bonds hold water together, a phenomenon called cohesion.
  • Cohesion among water molecules plays a key role in the transport of water and dissolved nutrients against gravity in plants.
  • Water molecules move from the roots to the leaves of a plant through water-conducting vessels.
  • As water molecules evaporate from a leaf, other water molecules from vessels in the leaf replace them.
  • Hydrogen bonds cause water molecules leaving the vessels to tug on molecules farther down.
  • This upward pull is transmitted down to the roots.
  • Adhesion, clinging of one substance to another, contributes too, as water adheres to the wall of the vessels.
  • Surface tension, a measure of the force necessary to stretch or break the surface of a liquid, is related to cohesion.
  • Water has a greater surface tension than most other liquids because hydrogen bonds among surface water molecules resist stretching or breaking the surface.
  • Water behaves as if covered by an invisible film.
  • Some animals can stand, walk, or run on water without breaking the surface.
  • Water moderates temperatures on Earth.
  • Water stabilizes air temperatures by absorbing heat from warmer air and releasing heat to cooler air.
  • Water can absorb or release relatively large amounts of heat with only a slight change in its own temperature.
  • Atoms and molecules have kinetic energy, the energy of motion, because they are always moving.
  • The faster a molecule moves, the more kinetic energy it has.
  • Heat is a measure of the total quantity of kinetic energy due to molecular motion in a body of matter.
  • Temperature measures the intensity of heat in a body of matter due to the average kinetic energy of molecules.
  • As the average speed of molecules increases, a thermometer will record an increase in temperature.
  • Heat and temperature are related, but not identical.
  • When two objects of different temperatures come together, heat passes from the warmer object to the cooler object until the two are the same temperature.
  • Molecules in the cooler object speed up at the expense of kinetic energy of the warmer object.
  • Ice cubes cool a glass of pop by absorbing heat from the pop as the ice melts.
  • In most biological settings, temperature is measured on the Celsius scale (°C).
  • At sea level, water freezes at 0°C and boils at 100°C.
  • Human body temperature is typically 37°C.
  • While there are several ways to measure heat energy, one convenient unit is the calorie (cal).
  • One calorie is the amount of heat energy necessary to raise the temperature of one g of water by 1°C.
  • A calorie is released when 1 g of water cools by 1°C.
  • In many biological processes, the kilocalorie (kcal) is more convenient.
  •  A kilocalorie is the amount of heat energy necessary to raise the temperature of 1000 g of water by 1°C.
  • Another common energy unit, the joule (J), is equivalent to 0.239 cal.
  • Water stabilizes temperature because it has a high specific heat.
  • The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1°C.
  • By definition, the specific heat of water is 1 cal per gram per degree Celsius or 1 cal/g/°C.
  • Water has a high specific heat compared to other substances.
  • For example, ethyl alcohol has a specific heat of 0.6 cal/g/°C.
  • The specific heat of iron is 1/10 that of water.
  • Water resists changes in temperature because of its high specific heat.
  • In other words, water absorbs or releases a relatively large quantity of heat for each degree of temperature change.
  • Water’s high specific heat is due to hydrogen bonding.
  • Heat must be absorbed to break hydrogen bonds, and heat is released when hydrogen bonds form.
  • Investment of one calorie of heat causes relatively little change to the temperature of water because much of the energy is used to disrupt hydrogen bonds, not speed up the movement of water molecules.
  • Water’s high specific heat has effects that range from the level of the whole Earth to the level of individual organisms.
  • A large body of water can absorb a large amount of heat from the sun in daytime during the summer and yet warm only a few degrees.
  • At night and during the winter, the warm water will warm cooler air.
  • Therefore, ocean temperatures and coastal land areas have more stable temperatures than inland areas.
  • Living things are made primarily of water. Consequently, they resist changes in temperature better than they would if composed of a liquid with a lower specific heat.
  • The transformation of a molecule from a liquid to a gas is called vaporization or evaporation.
  • This occurs when the molecule moves fast enough to overcome the attraction of other molecules in the liquid.
  • Even in a low-temperature liquid (with low average kinetic energy), some molecules are moving fast enough to evaporate.
  • Heating a liquid increases the average kinetic energy and increases the rate of evaporation.
  • Heat of vaporization is the quantity of heat that a liquid must absorb for 1 g of it to be converted from liquid to gas.
  • Water has a relatively high heat of vaporization, requiring about 580 cal of heat to evaporate 1 g of water at room temperature.
  • This is double the heat required to vaporize the same quantity of alcohol or ammonia.
  • This is because hydrogen bonds must be broken before a water molecule can evaporate from the liquid.
  • Water’s high heat of vaporization moderates climate.
  • Much of the sun’s heat absorbed by tropical oceans is used for evaporation of surface water.
  • As moist tropical air moves to the poles, water vapor condenses to form rain, releasing heat.
  • As a liquid evaporates, the surface of the liquid that remains behind cools, a phenomenon called evaporative cooling.
  • This occurs because the most energetic molecules are the most likely to evaporate, leaving the lower–kinetic energy molecules behind.
  • Evaporative cooling moderates temperature in lakes and ponds.
  • Evaporation of sweat in mammals or evaporation of water from the leaves of plants prevents terrestrial organisms from overheating.
  • Evaporation of water from the leaves of plants or the skin of humans removes excess heat.
  • Oceans and lakes don’t freeze solid because ice floats.
  • Water is unusual because it is less dense as a solid than as a cold liquid.
  • Most materials contract as they solidify, but water expands.
  • At temperatures above 4°C, water behaves like other liquids, expanding as it warms and contracting as it cools.
  • Water begins to freeze when its molecules are no longer moving vigorously enough to break their hydrogen bonds.
  • When water reaches 0°C, water becomes locked into a crystalline lattice, with each water molecule bonded to a maximum of four partners.
  • As ice starts to melt, some of the hydrogen bonds break, and water molecules can slip closer together than they can while in the ice state.
  • Ice is about 10% less dense than water at 4°C.
  • Therefore, ice floats on the cool water below.
  • This oddity has important consequences for life.
  • If ice sank, eventually all ponds, lakes, and even the ocean would freeze solid.
  • During the summer, only the upper few centimeters of the ocean would thaw.
  •  Instead, the surface layer of ice insulates liquid water below, preventing it from freezing and allowing life to exist under the frozen surface.
  • Water is the solvent of life.
  • A liquid that is a completely homogeneous mixture of two or more substances is called a solution.
  • A sugar cube in a glass of water will eventually dissolve to form a uniform solution of sugar and water.
  • The dissolving agent is the solvent, and the substance that is dissolved is the solute.
  •  In our example, water is the solvent and sugar is the solute.
  • In an aqueous solution, water is the solvent.
  • Water is not a universal solvent, but it is very versatile because of the polarity of water molecules.
  • °         Water is an effective solvent because it readily forms hydrogen bonds with charged and polar covalent molecules.
  • °         For example, when a crystal of salt (NaCl) is placed in water, the Na+ cations interact with the partial negative charges of the oxygen regions of water molecules.
  • °         The Cl− anions interact with the partial positive charges of the hydrogen regions of water molecules.
  • ·         Each dissolved ion is surrounded by a sphere of water molecules, a hydration shell.
  • ·         Eventually, water dissolves all the ions, resulting in a solution with two solutes: sodium and chloride ions.
  • ·         Polar molecules are also soluble in water because they form hydrogen bonds with water.
  • ·         Even large molecules, like proteins, can dissolve in water if they have ionic and polar regions.
  • ·         Any substance that has an affinity for water is hydrophilic (water-loving).
  • °         These substances are dominated by ionic or polar bonds.
  • ·         Some hydrophilic substances do not dissolve because their molecules are too large.
  • °         For example, cotton is hydrophilic because cellulose, its major constituent, has numerous polar covalent bonds. However, its giant cellulose molecules are too large to dissolve in water.
  • °         Water molecules form hydrogen bonds with the cellulose fibers of cotton, allowing you to dry yourself with your cotton towel as the water is pulled into the towel.
  • ·         Substances that have no affinity for water are hydrophobic (water-fearing).
  • °         These substances are nonionic and have nonpolar covalent bonds.
  • °         Because there are no consistent regions with partial or full charges, water molecules cannot form hydrogen bonds with hydrophobic molecules.
  • °         Oils such as vegetable oil are hydrophobic because the dominant bonds, carbon-carbon and carbon-hydrogen, share electrons equally.
  • °         Hydrophobic molecules are major ingredients of cell membranes.
  • ·         Biological chemistry is “wet” chemistry with most reactions involving solutes dissolved in water.
  • ·         Chemical reactions depend on collisions of molecules and therefore on the concentrations of solutes in aqueous solution.
  • ·         We measure the number of molecules in units called moles.
  • ·         The actual number of molecules in a mole is called Avogadro’s number, 6.02 × 1023.
  • ·         A mole is equal to the molecular weight of a substance but scaled up from daltons to grams.
  • ·         To illustrate, how could we measure out a mole of table sugar—sucrose (C12H22O11)?
  • °         A carbon atom weighs 12 daltons, hydrogen 1 dalton, and oxygen 16 daltons.
  • °         One molecule of sucrose would weigh 342 daltons, the sum of weights of all the atoms in sucrose, or the molecular weight of sucrose.
  • °         To get one mole of sucrose, we would weigh out 342 g.
  • ·         The advantage of using moles as a measurement is that a mole of one substance has the same number of molecules as a mole of any other substance.
  • °         If substance A has a molecular weight of 10 daltons and substance B has a molecular weight of 100 daltons, then we know that 10 g of substance A has the same number of molecules as 100 g of substance B.
  • °         A mole of sucrose contains 6.02 × 1023 molecules and weighs 342 g, while a mole of ethyl alcohol (C2H6O) also contains 6.02 × 1023 molecules but weighs only 46 g because the molecules are smaller.
  • °         Measuring in moles allows scientists to combine substances in fixed ratios of molecules.
  • ·         In “wet” chemistry, we are typically combining solutions or measuring the quantities of materials in aqueous solutions.
  • °         The concentration of a material in solution is called its molarity.
  • °         A one molar solution has one mole of a substance dissolved in one liter of solvent, typically water.
  • °         To make a 1 molar (1M) solution of sucrose, we would slowly add water to 342 g of sucrose until the total volume was 1 liter and all the sugar was dissolved.

Concept 3.3 Dissociation of water molecules leads to acidic and basic conditions that affect living organisms

  • ·         Occasionally, a hydrogen atom participating in a hydrogen bond between two water molecules shifts from one molecule to the other.
  • °         The hydrogen atom leaves its electron behind and is transferred as a single proton—a hydrogen ion (H+).
  • °         The water molecule that lost the proton is now a hydroxide ion (OH−).
  • °         The water molecule with the extra proton is now a hydronium ion (H3O+).
  • ·         A simplified way to view this process is to say that a water molecule dissociates into a hydrogen ion and a hydroxide ion:
  • °         H2O <=> H+ + OH−
  • ·         This reaction is reversible.
  • ·         At equilibrium, the concentration of water molecules greatly exceeds that of H+ and OH−.
  • ·         In pure water, only one water molecule in every 554 million is dissociated.
  • °         At equilibrium, the concentration of H+ or OH− is 10−7M (at 25°C).
  • ·         Although the dissociation of water is reversible and statistically rare, it is very important in the chemistry of life.
  • ·         Because hydrogen and hydroxide ions are very reactive, changes in their concentrations can drastically affect the chemistry of a cell.
  • ·         Adding certain solutes, called acids and bases, disrupts the equilibrium and modifies the concentrations of hydrogen and hydroxide ions.
  • ·         The pH scale is used to describe how acidic or basic a solution is.
  •  Organisms are sensitive to changes in pH.
  • ·         An acid is a substance that increases the hydrogen ion concentration in a solution.
  • °         When hydrochloric acid is added to water, hydrogen ions dissociate from chloride ions: HCl -> H+ + Cl−
  • °         Addition of an acid makes a solution more acidic.
  • ·         Any substance that reduces the hydrogen ion concentration in a solution is a base.
  • ·         Some bases reduce the H+ concentration directly by accepting hydrogen ions.
  • °         Ammonia (NH3) acts as a base when the nitrogen’s unshared electron pair attracts a hydrogen ion from the solution, creating an ammonium ion (NH4+).
  • °         NH3 + H+ <=> NH4+
  • ·         Other bases reduce H+ indirectly by dissociating to OH−, which then combines with H+ to form water.
  • °         NaOH -> Na+ + OH−                OH− + H+ -> H2O
  • ·         Solutions with more OH− than H+ are basic solutions.
  • ·         Solutions with more H+ than OH− are acidic solutions.
  • ·         Solutions in which concentrations of OH− and H+ are equal are neutral solutions.
  • ·         Some acids and bases (HCl and NaOH) are strong acids or bases.
  • °         These molecules dissociate completely in water.
  • ·         Other acids and bases (NH3) are weak acids or bases.
  • °         For these molecules, the binding and release of hydrogen ions are reversible.
  • °         At equilibrium, there will be a fixed ratio of products to reactants.
  • °         Carbonic acid (H2CO3) is a weak acid:
  • §         H2CO3 <=> HCO3− + H+
  • §         At equilibrium, 1% of the H2CO3 molecules will be dissociated.
  • ·         In any solution, the product of the H+ and OH− concentrations is constant at 10−14.
  • ·         Brackets ([H+] and [OH−]) indicate the molar concentration of the enclosed substance.
  • °         [H+] [OH−] = 10−14
  • °         In a neutral solution, [H+] = 10−7 M and [OH−] = 10−7 M
  • ·         Adding acid to a solution shifts the balance between H+ and OH− toward H+ and leads to a decline in OH−.
  • °         If [H+] = 10−5 M, then [OH−] = 10−9 M
  • °         Hydroxide concentrations decline because some of the additional acid combines with hydroxide to form water.
  • ·         Adding a base does the opposite, increasing OH− concentration and lowering H+ concentration.
  • ·         The H+ and OH− concentrations of solutions can vary by a factor of 100 trillion or more.
  • ·         To express this variation more conveniently, the H+ and OH− concentrations are typically expressed via the pH scale.
  • °         The pH scale, ranging from 1 to 14, compresses the range of concentrations by employing logarithms.
  • °         pH = − log [H+] or [H+] = 10−pH
  • °         In a neutral solution, [H+] = 10−7 M, and the pH = 7.
  • ·         Values for pH decline as [H+] increase.
  • ·         While the pH scale is based on [H+], values for [OH−] can be easily calculated from the product relationship.
  • ·         The pH of a neutral solution is 7.
  • ·         Acidic solutions have pH values less than 7, and basic solutions have pH values greater than 7.
  • ·         Most biological fluids have pH values in the range of 6 to 8.
  • °         However, the human stomach has strongly acidic digestive juice with a pH of about 2.
  • ·         Each pH unit represents a tenfold difference in H+ and OH− concentrations.
  • °         A small change in pH actually indicates a substantial change in H+ and OH− concentrations.
  • ·         The chemical processes in the cell can be disrupted by changes to the H+ and OH− concentrations away from their normal values, usually near pH 7.
  • ·         To maintain cellular pH values at a constant level, biological fluids have buffers.
  • ·         Buffers resist changes to the pH of a solution when H+ or OH− is added to the solution.
  • °         Buffers accept hydrogen ions from the solution when they are in excess and donate hydrogen ions when they have been depleted.
  • °         Buffers typically consist of a weak acid and its corresponding base.
  • °         One important buffer in human blood and other biological solutions is carbonic acid, which dissociates to yield a bicarbonate ion and a hydrogen ion.
  • °         The chemical equilibrium between carbonic acid and bicarbonate acts as a pH regulator. The equilibrium shifts left or right as other metabolic processes add or remove H+ from the solution.
  • Acid precipitation threatens the fitness of the environment.
  • ·         Acid precipitation is a serious assault on water quality in some industrialized areas.
  • °         Uncontaminated rain has a slightly acidic pH of 5.6.
  • °         The acid is a product of the formation of carbonic acid from carbon dioxide and water.
  • ·         Acid precipitation occurs when rain, snow, or fog has a pH that is more acidic than 5.6.
  • ·         Acid precipitation is caused primarily by sulfur oxides and nitrogen oxides in the atmosphere.
  • °         These molecules react with water to form strong acids that fall to the surface with rain or snow.
  • ·         The major source of these oxides is the burning of fossil fuels (coal, oil, and gas) in factories and automobiles.
  • ·         The presence of tall smokestacks allows this pollution to spread from its site of origin to contaminate relatively pristine areas thousands of kilometers away.
  • °         In 2001, rain in the Adirondack Mountains of upstate New York had an average pH of 4.3.
  • ·         The effects of acids in lakes and streams are more pronounced in the spring during snowmelt.
  • °         As the surface snows melt and drain down through the snowfield, the meltwater accumulates acid and brings it into lakes and streams all at once.
  • °         The pH of early meltwater may be as low as 3.
  • ·         Acid precipitation has a great impact on the eggs and the early developmental stages of aquatic organisms that are abundant in the spring.
  • ·         Thus, strong acidity can alter the structure of molecules and impact ecological communities.
  • ·         Direct impacts of acid precipitation on forests and terrestrial life are more controversial.
  • ·         However, acid precipitation can impact soils by affecting the solubility of soil minerals.
  • °         Acid precipitation can wash away key soil buffers and plant nutrients such as calcium and magnesium ions.
  • °         It can also increase the concentrations of compounds such as aluminum to toxic levels.
  • °         This has done major damage to forests in Europe and substantial damage of forests in North America.
  • °         Progress has been made in reducing acid precipitation.