Advanced Biology

1. Advanced Biology Semester 1 Review Part II Chapters 5 - 9

2. Chapter 5 The Working Cell • Things to know and Be Able To Do • Types of energy • Laws of Thermodynamics • ATP • Enzymes • Membranes • Cellular Transport • Review notes, study guides, and labs

3. Energy is the Capacity to Perform Work • Kinetic Energy: Energy that is actually doing work • Heat and Light • Potential Energy: Stored energy due to location or arrangement of matter • Chemical energy is a form of potential energy due to the arrangement of atoms in a molecule due to the chemical bonds

4. Laws of Thermodynamics • 1st law: Energy can not be created or destroyed. It can be transformed from one form to another. • Cells do not make energy or consume energy, they transform energy from one form to another. • From the chemical energy of glucose to the chemical energy of ATP • 2nd Law: Energy transformations reduce the order of the universe • Energy transformations are not 100% efficient • In all energy transformations some energy is lost in the form of heat.

5. Chemical Reactions Store or Release Energy • Exergonic reactions release energy by breaking bonds. • Endergonic reactions store energy by forming new bonds • Energy Coupling: Cells use energy released by exergonic reactions to power essential endergonic reactions. • Most energy released by exergonic reactions is stored in the bonds of ATP • ATP molecules shuttle this energy to places where it is required for essential endergonic reactions

6. Enzymes • Enzymes are proteins • Enzymes speed up chemical reactions by lowering the activation energy of the reaction but are not consumed in the chemical reaction (biological catalysts) • Enzymes are specific to the reactions they catalyze • Active site: Region of the protein that binds to the substrate • Substrate: a reactant in the chemical reaction that the enzyme acts on, must fit in the active site

7. Factors Affecting Enzyme Activity • pH, Temperature, and salinity can denature an enzyme • Inhibitors can block an enzymes active site • Competitive: Sit in the active site and prevent substrate from entering the active site • Noncompetitive: Bind to the enzyme outside of the active site, but cause the protein to change its overall shape, thus altering the active site. • Reversible: When inhibitors bind to the enzyme by weak H-bonds, can be easily be undone • Irreversible: When inhibitors bind to the enzyme with strong covalent bonds

8. Membranes • Organize cellular activities • Phospholipid Bilayer • Two layers of phospholipid molecules • Polar heads face away from each other, nonpolar tails face towards each other • Allow small, nonpolar molecules to diffuse through the membrane and into the cell • Proteins • Embedded in the phospholipid bilayer • Many functions depending on the type of protein • Enzymes, receptors, connnect cell to its surroundings, transport molecules into and out of the cell • Carbohydrates • Cell ID tags to allow the cell to be recognized by other cells that are part of the same organism

9. Cellular Transport • Diffusion: the movement of molecules from areas where they are highly concentrated to areas where they are less concentrated • Results from random motion of molecules • Requires no work • Molecules diffuse down their concentration gradient, unaffected by the concentration of other molecules • Passive Transport: The diffusion of molecules across the membrane of a cell

10. Osmosis • The diffusion of water across a selectively permeable membrane • Water can diffuse easily across a biological membrane • Solute molecules can not diffuse across biological membrane • Water will diffuse until the concentration of water is equal on both sides • Hypertonic: Solutions with a high solute concentration compared to another solution • Hypotonic: Solutions with a low solute concentration compared to another solution • Water will move by osmosis from hypotonic regions to hypertonic regions

11. Osmoregulation • In Hypotonic Solutions • Animal cells will lyse • Plant cells become turgid but do not lyse, due to rigid cell wall • In Hypertonic Solutions • Animal cells will shrivel • Plant cell membranes will shrivel, cell wall will not change dimensions. • Osmoregulation: Organisms must use energy to control water loss or gain in their cells due to osmosis. They can not stop osmosis. • Example: Freshwater fish pee constantly Saltwater fish constantly drink, and concentrate urine in their tissues

12. Facilitated Diffusion and Active Transport • Facilitated diffusion is the movement of molecules across a membrane by diffusion through transport proteins • Transport proteins form channels that allow large, polar, or charged molecules to cross the cell membrane • Active Transport uses energy and transport proteins to move molecules against their concentration gradient • Active transport like all cellular work is powered by ATP

13. Chapter 6 • Things to Know and Be Able to Do: • Overall chemical equation for aerobic cellular respiration • Inputs and outputs for all stages of cellular respiration • Location of each of the stages • Fermentation • Review Chapter 6 notes, labs, and review packets

14. Aerobic Cellular Respiration • C6H12O6 + 6O2 ---> 6CO2 + 6H2O + 36-38 ATP • Glucose is broken down into Carbon dioxide and water • Requires oxygen • Produces between 36 and 38 ATP molecules • Has three major steps • Glycolysis • Kreb’s Cycle • Electron Transport Chain and Chemiosmosis

15. Glycolysis • First stage of Aerobic cellular respiration AND fermentation • Takes place in the cytoplasm of all cells • 2 molecules of pyruvic acid result from the splitting of glucose • 2 molecules of NADH shuttle electrons and hydrogen ions to the Electron Transport Chain • 2 molecules of ATP are made directly during glycolysis by substrate level phosphorylation

16. Chemical Grooming • Intermediate step between Glycolysis and the Krebs Cycle • 2 molecules of CO2 are produced; 1 from each pyruvic acid • 2 molecules of NADH shuttle electrons and hydrogen ions to the Electron Transport Chain from the break down of pyruvic acid; 1 NADH from each pyruvic acid molecule • 2 molecules of Acetyl CoA are formed from the break down of pyruvic acid • No ATP is made directly in this stage

17. Kreb’s Cycle • Second major step of aerobic cellular respiration • Occurs in the matrix of the mitochondria in eukaryotic cells • 4 molecules of carbon dioxide result from the break down of the Acetyl CoA; 2 molecules from each Acetyl CoA • 6 NADH and 2 FADH2 shuttle electrons from the breakdown of Acetyl CoA to the ETC; 3 NADH and 1 FADH2 from each Acetyl CoA • 2 ATP are made directly by substrate level phosphorylation; 1 ATP from each Acetyl CoA

18. Electron Transport Chain and Chemiosmosis • Final stage of aerobic Cellular respiration • Takes place along a chain of protein molecules embedded in the inner mitochondrial membrane • Produces about 34 molecules of ATP using the NADH and FADH2 produced in previous stages; 3 ATP per NADH and 2 ATP per FADH2

19. Electron Transport Chain and Chemiosmosis (continued) • Electrons from NADH and FADH2 move down the Electron Transport Chain by redox reactions and release energy. • Oxygen is the last electron acceptor in the chain • The released energy is used to actively transport H+ across the inner mitochondrial membrane from the matrix to the intermembrane space • H+ flows back into the matrix through ATP synthase which powers the phosphorylation of ADP to ATP

20. Alcoholic and Lactic Acid Fermentation • Fermentation is an alternative to aerobic respiration when oxygen supplies are limited or not present. • Both use glycolysis to make ATP • Alcoholic Fermentation • Breaks glucose down in to pyruvic acid • Converts pyruvic acid into ethanol and CO2 to recycle NAD+ • Produces 2 ATP per glucose • Common in yeast and bacteria, used to make beer and wine • Lactic Acid Fermentation • Breaks glucose down in to pyruvic acid • Converts pyruvic acid into lactic acid to recycle NAD+ • Produces 2 ATP per glucose • Occurs in muscle cells, causes muscle soreness

21. Chapter 7 • Things to know and be able to do: • The overall equation and purpose of photosynthesis • The inputs and outputs of each stage of Photosynthesis • The location of each of these stages • Review all chapter 7 notes, labs, and review packets

22. Photosynthesis • CO2 + H2O + light ---> C6H12O6 + O2 • Organisms that can photosynthesize are called autotrophs or producers • Photosynthesis occurs in the chloroplasts of eukaryotic cells and in green pigment molecules (chlorophyll) of some photosynthetic bacteria • Photosynthesis uses energy from sunlight to convert water and carbon dioxide into glucose. • Oxygen gas is released as a by-product • The glucose is used to make ATP by cellular respiration in the mitochondria • Excess glucose is stored as starch • Occurs in two major steps: • Light reactions and Calvin Cycle

23. Light Reactions (PS I) • Occur in photosystems (PS I and PS II) that are embedded in the thylakoid membranes of chloroplasts. • Photosystems are groups of chlorophyll molecules that absorb photons of light • Chlorophyll electrons in PS I are energized by sunlight, captured by a primary electron acceptor, and passed down an electron transport chain to NADP+ which becomes NADPH • NADPH shuttles these energy rich electrons to the Calvin cycle which occurs in the stroma of the chloroplast.

24. Light Reactions (PS II) • Electrons lost from PS I are replaced by electrons from PS II. • Electrons from chlorophyll molecules in PS II are energized by photons of sunlight, captured by a primary electron acceptor, and passed down an electron transport chain to reach PS I. • As the electrons move down the electron transport chain the energy lost is used to pump H+ across the thylakoid membrane, from the stroma into the thylakoid compartment. • The H+ then flow through ATP synthase to power the production of ATP

25. Products of the Light Reactions • Electrons lost from PS II are replaced by electrons that come from the splitting of water at PS II using the energy absorbed from sunlight. • Splitting water makes O2 which is released from the stomata of plant leaves • ATP and NADPH made during the light reactions are used in the Calvin Cycle • The Calvin cycle also requires CO2 which the plant brings in through the stomata of its leaves

27. Calvin Cycle • Occurs in the stroma of the chloroplast • 3 molecules of CO2 enter the Calvin Cycle and form a chemical intermediate • This chemical intermediate is phosphorylated by ATP and reduced by NADPH • G3P is formed and leaves the Calvin cycle. • This process is repeated, producing a second molecule of G3P. • The two molecules of G3P combine to form 1 molecule of glucose • ADP and NADP+ are recycled back to the thylakoids

28. Chapter 8: Cellular Basis of Reproduction and Inheritance • Things to know and be able to do: • Binary Fission • Chromosomes vs. chromatin • Cell cycle stages and control mechanisms • Stages of Mitosis and its purpose in organisms • Cell division and relationship to cancer • Meiosis • Purpose in organisms • Stages • How meiosis causes genetic variation • Potential accidents during meiosis • Review all notes, labs, review packets and study guides

29. Cell Division • Binary Fission • Occurs in bacteria • Results in exact clones of bacteria cells • The single bacterial chromosome is copied and the cell divides in half • Mitosis • Occurs in Eukaryotes • Results in 2 daughter cells that are genetically identical to each other and the parent cell • Used for growth, repair and development in multicellular organisms • Meiosis • Occurs only in the ovaries and testes of Eukaryotes. • Makes 4 haploid daughter cells called gametes

30. Chromatin and Chromosomes • Refers to the DNA of all organisms when it is in thin threadlike fibers during interphase • Prokaryotic DNA forms a single circular chromosome • Eukaryotes form numerous chromosomes made of DNA densely coiled around proteins • Always found in the nucleus • At the beginning of cell division chromosomes consist of 2 identical copies of DNA called sister chromatids joined together by a centromere

31. Stages of the Cell Cycle • Interphase • G1: Cell grows, copies organelles, makes proteins, carries out its function in the organism • S: Cell replicates (copies) its DNA • G2: Cell continues growing and makes proteins involved in cell division • Mitotic Phase: • Mitosis: Nucleus and chromosomes are divided • Cytokinesis: The rest of the cell including the cell membrane organelle copies and cytoplasm divides

32. Stages of Mitosis (PMAT) • Prophase • Chromatin coils and condenses into chromosomes • Spindle fibers form and attach to kinetochores on each sister chromatid • Nuclear membrane breaks up • Metaphase • Spindle fibers align chromosomes on the metaphase plate • Anaphase • Spindle fibers pull sister chromatids apart and move them towards the poles of the cell • Telophase • Chromatids uncoil • New nuclear membranes begin to form • Cytokinesis begins during the end of mitosis

33. Cytokinesis • The process that divides cells • Eukaryotic Animal Cells • Microfilaments form a ring around the center of the cell • Microfilaments begin to contract and pinch the center of the cell together forming a cleavage furrow • Eukaryotic Plant cells • Vesicles containing cellulose line up in the center of the cell • Vesicles fuse with each other and the edges of the cell forming a membrane covered cell wall down the middle of the cell

34. Control of the Cell Cycle • Density Dependent Inhibition • As cell density increases, cell division slows down and eventually stops • Anchorage Dependence • Most cells must be attached to other cells in order to continue dividing • Growth factor • Proteins secreted by neighboring cells that stimulate cell division in surrounding cells. • As cell density increases the volume of growth factor declines and cell division slows

35. Control of the Cell Cycle (checkpoints) • Cells do not proceed through the cell cycle unless they get “go-ahead” signals at key check points • End of G1: Growth factors signal go ahead if the cell is large enough, has copied organelles and made enough proteins. Most important. • End of G2: Growth factors signal go ahead if cell has correctly replicated DNA during S phase • Metaphase of Mitosis: Growth factors signal go ahead if chromosomes are correctly aligned at metaphase with spindle fibers attached

36. Cancer is a Disease of the Cell Cycle • Cancerous cell divide out of control. • They do not respond to density dependence and continue to grow to much higher densities than normal cells thus creating a tumor • Some cancer cells, those in malignant tumors, do not respond to anchorage dependence and can metastasize. In other words they can break free from the tumor and begin growing even when not attached to other tissues, thus spreading the cancer through the organism

37. Life Cycles • Somatic (non-reproductive) cells are diploid. • They contain pairs of homologous chromosomes. • Gametes (reproductive cells) are haploid. • Meiosis divides diploid cells in the testes or ovaries to produce haploid gametes • Gametes contain one chromosome from each homologous pair in an organisms diploid cells • Fertilization is the union of gametes from two different individuals as the result of sexual reproduction. • Fertilization produces diploid zygotes. • Zygotes develop into offspring through repeated rounds of mitosis

38. Meiosis • Meiosis is the process that makes haploid gametes from diploid cells in reproductive organs. • Meiosis involves two consecutive rounds of cell division • Meiosis results in four haploid daughter cells with different genetic combinations in each daughter cell. • Meiosis has 8 stages divided between meiosis I and meiosis II

39. Meiosis I (PMAT I) Prophase I: • Pairs of homologous chromosomes, each consisting of identical sister chromatids, attach to each other and form tetrads • Crossing over between non-sister homologous chromosomes Metaphase I: • Tetrads line up along the imaginary metaphase plate Anaphase I • Tetrads separate, homologous chromosomes in each tetrad get pulled to opposite poles of the cell. Each chromosome still consists of 2 connected sister chromatids Telophase I • Chromosomes may or may not unwind and new nuclei may or may not form depending on the species. • Occurs simultaneously with cytokinesis, which divides the parent cell into two haploid daughter cells

40. Meiosis II (PMAT II) • Prophase II • Spindle fibers reform in each daughter cell and begin moving chromosomes towards the center of the cell • Metaphase II • Chromosomes line up at the metaphase plate of each daughter cell • Anaphase II • Sister chromatids separate and are pulled to opposite poles of each cell • Telophase II • New nuclei form around the groups of sister chromatids • Cytokinesis begins dividing each cell into two daughter cells, for a total of four daughter cells at the end of meiosis II.

41. Sources of Genetic Variation • Independent Orientation: Homologous pairs of chromosomes can line up in two different orientations. Each pair orients itself independently of all other pairs. • Crossing Over: Non sister homologous chromosomes can exchange pieces with each other during synapsis of prophase I. This leads to new combinations of traits not seen in either parent • Random fertilization: The two processes above produce varied gametes in all parents. Which male gamete fertilizes a specific female gamete during sexual reproduction between 2 parents is due to random chance

42. Accidents During Meiosis • Nondisjunction • Homologous chromosomes fail to separate during meiosis I • Results in 4 gametes with abnormal chromosome # (2 with extra, 2 with less) • Sister chromosomes fail to separate in Meiosis II • Results in 2 gametes with normal chromosome #, and 2 with abnormal chromosome # (1 with extra, 1 with less) • Usually results in miscarriage if nondisjunction occurs between autosomes, but there are exceptions (down syndrome) • More survivable if nondisjunction occurs between sex chromosomes (Turners, Klienfelter)

43. Accidents During Meiosis • Alterations of chromosomes: Results from chromosomes breaking during meiosis • Deletions: missing a piece altogether, usually the most serious • Duplication: When a piece of one chromosome breaks off and is added to its homolog, Resulting in 2 copies of the genetic information • Inversion: When a piece breaks off of one chromosome and then is reattached upside down to the same chromosome • Translocation: When a piece breaks off and attaches to another non-homologous chromosome