1. Option C: Cells & Energy

2. C.1 Proteins
C.1.1: Explain the 4 levels of protein structure, indicating each level’s significance
C.1.2: Outline the differences between fibrous & globular proteins, with reference to two examples of each type
C.1.3: Explain the significance of polar and non-polar amino acids
C.1.4: State six functions of proteins, giving a named example of each

3. 4 levels of Protein Structure
Primary
The unique amino acid sequence
Like the order of letters in a very long word
Slight changes in primary structure greatly affect overall conformation and function

4. 4 levels of Protein Structure
Secondary
Coils and folds of the primary structure as a result of hydrogen bonding
Electronegative O & N attract H
E.g. – alpha helix, pleated sheet

5. 4 levels of Protein Structure
Tertiary
Contortions of molecule by bonding between R groups of amino acids
Hydrophobic interactions important
Core versus outer parts
May be further reinforced by disulfide bonds

6. 4 levels of Protein Structure
Quartnerary
2 or more polypeptide chains aggregated into functional unit
Collagen – 3 proteins together, Hemoglobin 4 proteins together
Shape of subunits together specifies function

8. Fibrous vs. Globular Proteins
Functional Quaternary proteins are either …
Fibrous – long ropelike structures
Collagen – 40% of protein in human body, from skin, bone, tendons & ligaments
Keratin – hair, horns, skin
Globular –spherical
Hemoglobin – oxygen binding protein in blood
Lysozyme – immune enzyme in saliva, tears, sweat that targets bacterial surface proteins

9. Polar vs Nonpolar Polarity of amino acids influences protein behavior
Membrane position (polar portions in or out of cells, nonpolar portions in membrane)
Hydrophobic channel creation
Specificity of enzyme active site – complements properties of the substrate

10. Important Proteins Protein Function Keratin Casein Hemoglobin Actin
Insulin
Lysozyme

11. Important Proteins Protein Function Keratin
Support in hair, horns and feathers
Casein
Storage of AA for babies in milk
Hemoglobin
Transport of O2 by blood
Actin
Movement of muscle fibers
Insulin
Hormone regulates sugar in blood
Lysozyme
Defense against foreign substances

12. C.2 Enzymes
C.2.1: State that metabolic pathways consist of chains and cycles of enzyme catalyzed reactions
C.2.2: Describe the induced fit model
C.2.3: Explain that enzymes lower the activation energy of the chemical reactions which they catalyze.
C.2.4: Explain the difference between competitive and non-competitive inhibition with reference to one example of each.
C.2.5: Explain the role of allostery in the control of metabolic pathways by end-product inhibition

13. Chemical Reaction Types
Exergonic reaction  ENERGY OUTWARD: proceeds with the net release of free energy
Endergonic reaction  ENERGY INWARD: proceeds with the net absorbtion of energy from the surroundings

14. Metabolism
Metabolism = The totality of an organisms chemical processes.
Managing the material and energy resources of the cell.
Metabolic Pathways consist of chains and cycles of enzyme catalyzed reactions
Catabolic pathways: break down molecules and release energy
Anabolic pathways: build complex molecules and absorb energy

15. Reaction types: Exergonic & Endergonic

18. Models of enzyme function
LOCK & KEY MODEL
Each enzyme fits exactly one substrate
Complementary shapes like a lock and a key
INDUCED FIT MODEL
Extension of Lock and key model
Some enzymes can bond multiple substrates
Interaction between enzyme and substrate induces change to fit

20. The induced fit model accounts for the broad specificity of some enzymes

21. Competitive vs. non-competitve
Competitive – inhibiting molecule is structurally similar to substrate, binds to active site, prevents substrate bonding
Inhibition of butanedioic acid dehydrogenase by propanedoic acid in the Krebs cycle
Inhibition of folic acid synthesis in bacteria by sulfonamide protosil (an antibiotic)
Non-competitive – inhibiting molecule binds to enzyme (not at A.S.) causing conformational change to active site
Hg+2, Ag+, Cu+, inhibition of cytochrome oxidase by binding to –SH groups and breaking -S-S- linkages

23. Allosteric Regulation
Form of non-competitive inhibition
Inhibition is a natural mechanism of cell metabolic control
Shape of allosteric enzymes can be altered by binding of end products at the allosteric site
Metabolites or end products can serve in negative feedback by binding to allosteric site and decreasing enzyme function
ATP inhibition of phosphofructokinase in glycolysis

25. Allosteric Reactions
are and example of
feedback inhibition

26. C.3 Respiration
C.3.1: State that oxidation involves the loss of electrons from an element whereas reduction involves the gain of electrons, and that oxidation frequently involves gaining oxygen or losing hydrogen, while reduction involves losing oxygen or gaining hydrogen
C.3.2: Outline the process of glycolysis including phosphorylation, lysis, oxidation, and ATP formation
C.3.3: Draw the structure of a mitochondrion as seen in electron micrographs.
C.3.4: Explain aerobic respiration including oxidative decarboxylation of pyruvate, the krebs cycle, NADH+ + H+, the electron transport chain, and the role of oxygen

27. C.3 Respiration
C.3.5: Explain oxidative phosphorylation in terms of chemiosmosis
C.3.6: Explain the relationship between the structure of the mitochondrion and its function.
C.3.7: Describe the central role of acetyl CoA in carbohydrate and fat metabolism
C.3.8: Analyze data relating to respiration

28. Overall Process Organic compounds + Oxygen
Carbon dioxide + Water + Energy
For convenience we usually start with glucose, but can use lipids, proteins and other carbohydrates.
C6H12O6 + 6 O CO2 + H2O + Energy
Glucose is oxidized and oxygen is reduced

29. Oxidation-Reduction Always coupled
Chemical reactions which involve a partial or complete transfer of electrons from one reactant to another.
Oxidation: partial or complete loss of e- from a substance; e- donor is the reducing agent.
Reduction: partial or complete addition of e- to another substance; e- acceptor is an oxidizing agent.

30. Comparison of Oxidation and Reduction
Addition of oxygen atoms
Removal of H atoms
Loss of e- from a substance
Reduction
Removal of oxygen atoms
Addition of H atoms
Addition of e- to a substance

31. Overview of Cell Respiration

32. 3. Cell Respiration: a)Glycolysis
Catalyzed by enzymes in the cytoplasm
Glucose is partially oxidized and a small amount of ATP is produced
Accomplished without the use of oxygen
Is part of both aerobic and anaerobic respiration

33. Glycolysis overview

34. Energy investment phase: 2 phosphate groups from ATP are added to a molecule of glucose (hexose sugar) to form a hexose biphosphate.
Lysis: The hexose biphosphate is split to form two molecules of triose phosphate.
Oxidation: 2 molecules of NAD+ are reduced to 2NADH + 2H+; so the triose phosphate is oxidized. The energy is used to add another phosphate group to each triose.
NADH can enter the electron transport chain in the mitochondria and be used to produce more ATP in the process called oxidative phosphorylation
4. ATP Formation: Two phosphate groups are removed from the two trioses and passed to ADP to form ATP.
So 4 ATPs are generated for a net gain of 2 ATPs.
ATP is produced by a process called substrate-level phosphorylation because an enzyme transfers a phosphate group from a substrate (organic molecule generated by the sequential breakdown of glucose) to ADP

35. The End of Glycolysis
A 6 Carbon compound has been turned into 2 3 Carbon compounds called pyruvate (A.K.A. oxopropanoate).
Glucose has been oxidized
Net gain 2 ATP, 2NADH + 2H+
ATP made through substrate level phosphorlyation
Glycolysis also yields 2 water molecules for each glucose.

36. Aerobic respiration Each pyruvate must be decarboxylated (CO2 removed)
Remaining 2 carbon molecule (acetyl group) reacts with reduced coenzyme A
During in the process NADH + H+ are formed

37. The Link Reaction: oxidative decarboxylation

38. Summary of One Turn of the Krebs Cycle
1. Acetyl CoA (2C) enters the cycle & joins a 4C molecule.
2. In a series of steps, the remaining H and high energy electrons are removed from the Acetyl CoA.
3. Three NAD+ are converted into 3 NADH & 3H+.
4. One FAD is converted into 1 FADH2.
5. One ATP is made (by substrate phosphorylation).
6. Two CO2 are released.
7. At the end of the cycle, nothing remains of the original glucose molecule

41. Krebs cycle results per glucose
2 molecules of pyruvate are oxidized
2 ATPs by substrate level phosphorylation
6 NADH and 2 FADH2
Starting material is regenerated
Electron transport chain couples electron flow down the chain to ATP synthesis.

42. ETC / Oxidative Phosphorlyation
The purpose of the Electron Transport Chain is to receive the high energy electrons carried by the coenzymes NADH &FADH2 and use the energy from these electrons to pump protons out of the matrix. A high concentration of protons results. As the protons diffuse back to the matrix, their energy is used by the ATP synthase to create 32 ATP.
Oxidative phosphorylation (electron transport) - The creation of ATP via chemiosmosis as a result of electron transport.

43. Electron transport a) Occurs at cristae (Inner membranes)
b) NADH & FADH2 deliver H+ and e- to cristae.
c) Electrons "transport" along cristae through electron acceptors, provide energy to pump H+ from matrix to outer compartment.
d) Concentration of H+ is now higher in outer compartment. H+ pass through ATP synthetases in cristae back to matrix. 32 ATP are made. This is known as chemiosmosis.
e) Last step involves H+ & e- added to oxygen. This frees NAD+ to return to glycolysis & Krebs Cycle to pick up more H+ & e-.

47. Chemiosmosis is the process where protons diffuse from the outer compartment (high concentration) through ATP Synthase in the Cristae to the Matrix (low H+ Concentration). The energy in the protons as they pass is used by ATP synthase to create 32 ATP.

48. XIV: Mitochondria and Chloroplasts
Main energy transformers of cells; transduce energy acquired from the surroundings into forms usable for cellular work.
BOTH:
a) enclosed by double membranes which are NOT part of endomembrane system
b) contain ribosomes and some DNA that programs a small portion of their own protein synthesis
c) are semiautonomous organelles that grow and reproduce within the cell (see Ch. 26 for a discussion of the origins of eukaryotic cells from symbiotic consortiums of prokaryotic cells; Dr. Lynn Margulis’ endosymbiotic theory.

49. Mitochondria
Sites of cellular respiration (catabolic oxygen-requiring process that uses energy extracted from organic macromolecules to produce ATP).
Found in nearly all eukaryotic cells; number directly correlates with cell’s metabolic activity.]
1 um in diameter; 1-10 um in length
Can move, change shape and divide

50. Mitochondrion

51. Mitochondria Structure
BE ABLE TO DRAW AND LABEL
Enclosed by two membranes: smooth outer membrane and convoluted inner membrane which contains embedded enzymes involved in cellular respiration.
Infoldings or cristae increase surface area
Membranes divide mitochondrion into 2 internal compartments:
a) intermembrane space: same solute composition of cytosol.
b) mitochondrial matrix: contains enzymes that catalyze many steps of cell respiration (Krebs cycle)

52. The Role of acetyl CoA
Acetyl CoA is an intermediate in carbohydrate metabolism
In lipid metabolism, the oxidation of fatty acid chains results in the formation of carbon fragments with 2C each
2 carbon fragments are acetyl fragments
They pass into Krebs cycle

53. Proteins and fats in cell respiration: Central role of Acetyl CoA

54. C.4 Photosynthesis
C.4.1: Draw the structure of a chloroplast as seen in electron micrographs
C.4.2: State that photosynthesis consists of light-dependent and light-independent reactions.
C.4.3: Explain the light dependent reactions
C.4.4: Explain phosphorylation in terms of chemiosmosis
C.4.5: Explain the light independent reactions

55. C.4 Photosynthesis
C.4.6: Explain the relationship between the structure of the chloroplast and its function
C.4.7: Draw the action spectrum for photosynthesis
C.4.8: Explain the relationship between the action spectrum and the absorption spectrum of photosynthetic pigments in green plants
C.4.9: Explain the concept of limiting factors with reference to light intensity, temperature and concentration of carbondioxide.
C.4.10: Analyze data relating to photosynthesis

56. Chloroplast

57. B. Chloroplasts BE ABLE TO DRAW AND LABEL
One of a group of plant and algal membrane-bound organelles
Chloroplasts divided into 3 functional compartments by a system of membranes.
1. Intermembrane space: space between the double chloroplast membrane.
2. Stroma: viscous fluid outside the grana (stacks of thylakoids); light-independent chemical reactions take place here. Carbon dioxide converted to sugar.
3. Thylakoids: flattened membranous sacs inside chloroplast; chlorophyll is found in membranes; function in the light-dependent chemical reactions.
4. Thylakoid space: space inside the thylakoids.

58. Absorbance Peaks in: Red & Blue Minimum in Green
Figure Evidence that chloroplast pigments participate in photosynthesis: absorption and action spectra for photosynthesis in an alga
Absorbance
Peaks in:
Red & Blue
Minimum in
Green

59. Photosynthesis consists of the light dependent and light independent reactions

60. 2 step process Light Dependent Reactions = photo
Light Independent Reactions (Calvin cycle) = synthesis
Light dependent reactions are in the thylakoid, light independent reactions in the stroma
Transforming light energy into chemical energy of ATP and NADPH
Creation of Sugars from inorganic compounds

61. Photosystems
In thylakoid membrane chlorophyll organized with other molecules in photosystems
“Antenna array” of Chlor. A, B, & carotenoid pigments, clustered around a reaction center
Reaction center is a single Chlorophyl A associated with the “primary electron acceptor” (PEA)
Chlorophyl A passes electrons to the PEA
PEA traps excited electrons before they fall back to ground state

62. Figure 10.11 How a photosystem harvests light

63. Photosystems
2 types of photosystems in thylakoid membrane cooperate in light reactions
Called Photosystem I & II – different PEA
Photosystem I – P700 best absorbance at 700 nm wavelength (red)
Photosystem II – P680 also in red
Identical chlorophyll but different protein association

64. Electron flow Light drives synthesis of ATP and NADPH
Energy transformation based on flow of electrons
Two routes of electron flow
Noncyclic electron Flow = predominates during light reactions – ejected electrons don’t cycle back to ground state
Cyclic electron Flow = uses Photosystem I not PS II – no production of NADPH or O2

65. Figure How noncyclic electron flow during the light reactions generates ATP and NADPH (Layer 5)

66. Light dependent reactions use solar power to produce ATP and NADPH to fuel sugar production in the Calvin cycle

67. Cyclic electron Flow
Cyclic electron Flow = uses Photosystem I not PS II – no production of NADPH or O2
Short circuit back into electron transport chain
Does produce ATP  cyclic phosphorylation
Light independent reaction consumes more ATP than NADPH, Cyclic electron flow makes up the difference in ATP required

69. Review of chemiosmosis
Mechanism of generating ATP
Electron transport chain pumps protons across the membrane while electrons are shuttled through different carriers
Protons pumped to the inside of thylakoids
Protons accumulate, pH and charge increase  move out to stroma through channels
Movement through channels in ATP synthase drives production of ATP

70. Figure 10.15 Comparison of chemiosmosis in mitochondria and chloroplasts

71. Figure 10.16 The light reactions and chemiosmosis: the organization of the thylakoid membrane

72. The Light Independent Reactions: Synthesis of sugars
Takes place in the Stroma
Carbon enters as CO2 and leaves as sugar
ATP is the energy source
NADPH provides reducing power for adding high energy electrons
Direct product of Calvin cycle is glyceraldehyde-3-phosphate (G3P)
3 cycles to make this product
Actually fixing three molecules of CO2

73. Figure 10.17 The Calvin cycle (Layer 3)

74. Calvin cycle summary For the synthesis of 1 molecule of sugar
Require the input of 9 ATP and 6 NADPH
Light reactions regenerate ATP, NADPH
G3P can be used to produce other sugars

75. Figure 10.20 A review of photosynthesis

76. Limiting Factors
Certain factors in the environment can effect how photosynthesis occurs
Main limiting factors are Temperature, Light intensity, and CO2 concentration
Other factors include nutrient availability, such as nitrogen, phosphorous and iron
Different factors limit plant growth in different areas

77. Effects of Light Intensity & Temperature on Photosynthesis

78. As light intensity increases the rate of photosynthesis increases and
Plateau once photosynthetic machinery is operating at peak capacity
Photoinhibition: sunburn for plants, occurs when too much light overloads photosynthetic machinery
For a given light intensity, Higher temperature  Increased rate of photosynthesis

79. A = at low light intensities light is a limiting factor and temperature has no effect
B = at higher light intensities, temperature is a limiting factor, warmer  higher rate of photosynthesis

80. Effects of Carbon Dioxide on Photosynthetic Rate