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UA / Biology / BIOL 1543 / replacement electrons for the reaction center of photosystem ii

replacement electrons for the reaction center of photosystem ii

replacement electrons for the reaction center of photosystem ii


School: University of Arkansas
Department: Biology
Course: Principles of Biology
Professor: Shadwick
Term: Fall 2016
Tags: Biology and pob
Cost: 25
Name: Principles of Biology Chapters 1-4, 6-8 & 25
Description: Principles of Biology Chapters 1-4, 6-8, & 25. Includes textbook notes and lecture notes
Uploaded: 02/23/2017
59 Pages 156 Views 0 Unlocks

• What causes gravity?

What is the mechanism behind it?

• Science: Why did that happen?

Chapter 8 - Plant Biology 8.1 Overview of Photosynthesis I. Photosynthesis: converts solar energy into chemical energy of a carbohydrate  A. Autotrophs: Organisms that capture energy and make their own food 1. example: plants, algae, and cyanobacteria B. Photosynthetic organisms, that include cyanobacteria, algae like kelp, typically live in  water and can range in size froIf you want to learn more check out Define what Interplanetary Theory is.
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We also discuss several other topics like the time it takes food to travel the length of the gi tract is called the transit time.
We also discuss several other topics like cgspay
We also discuss several other topics like What are ways to shift towards products?
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m microscopic to macroscopic, and plants such as  sequoia, which typically live on land C. It’s possible to trace majority of food chains back to plants and algae  1. Producers, who can synthesize carbohydrates, feed not only themselves but also  consumers with takes in performed organic molecules  D. Heterotrophs: Consumers who cannot synthesize must take in organic food  E. Pigments allow photosynthetic organisms to capture solar energy, which is a “fuel” that  makes photosynthesis possible  F. Chlorophyll: a pigment that gives them a green color G. Carotenoid: gives cells a yellow to red color  II. Flowering Plants as Photosynthesizers A. Parts, like leaves, contain chlorophyll and other pigments that allow the plants to carry  on photosynthesis  B. The raw materials used for photosynthesis are water and carbon dioxide  C. After entering a leaf, carbon dioxide and water diffuse into the cells and enter the  chloroplasts, the organelles that carry on photosynthesis D. Figure 8.2 1. Stroma: A double membrane surrounds a chloroplast and it’s fluid-filled interior a) Filled with enzymes, where carbon dioxide is first attached to an organic  compounds and is reduced to a carbohydrate b) Associate the absorption of solar energy with thylakoid membranes making up  the grana c) Associate the reduction of carbon dioxide to a carbohydrate with the stroma of a  chloroplast  2. Thylakoids: A different membrane system within the stroma forms flattened sacs III. Photosynthetic Reaction A. 6 CO2 + 6 H20 —> (solar energy, pigments) C6H12)6 + 6 O2 IV. Two sets of reaction A. Photo: lights, referring to reaction that capture solar energy B. Synthesis: reactions that produce carbohydrate  C. Light reaction: first set, light dependent reactions D. Calvin Cycle Reactions: light independent reaction E. Light reactions release oxygen and provide the molecules that allow the Calvin cycle  reactions to reduce carbon dioxide to a carbohydrate F. NADP+: coenzyme that carries hydrogen atoms from the light reactions to the Calvin  cycle reactions 1. When NADP+ accepts hydrogen atoms, it becomes NADPH8.2 Plants as Solar energy Converters I. Solar energy, can be described in terms of its wavelength and its energy content II. Figure 8.4 Listing different types of radiant energy, from shortest wavelength, gamma ras, to  the longest radio waves  A. White, or visible light is only a small portion of this spectrum  III. Visible Light A. Contains various wavelengths of light B. When passed through a prism, we see different colors that make up visible light C. The sensory areas of our brains identify these wavelengths as distinct colors D. The colors in visible light range from the violet (shortest wavelength) to indigo, blue,  green, yellow, orange, red (the longest wavelength) E. Energy consent is highest for violet and shorter for red F. Pigments found in photosynthesizing cells, the chlorophyll and the carotenoids are  capable of absorbing different portions of visible light G. Figure 8.5 1. Chlorophyll a and b absorb violet, indigo, blue and red  2. Green light is reflected and minimally absorbed leaves appear green to us 3. The yellow and orange carotenoids are able to absorb light in the violet-blue-green  range IV. Light Reactions A. light reactions occur in the thylakoid membrane consisting of 2 electrons pathways  called the noncyclic electron pathway and the cyclic electron pathway B. Both electron pathways produce ATP, but only the noncyclic pathways also produces  NADPH V. Noncyclic Electron Pathway A. Noncyclic Electron Pathway: electron flow can be trace from water to a molecules of  NADP+ 1. Uses 2 photosystems 2. Photosystems: consist of a pigment complex (molecules of chlorophyll a and b and  the carotenoids) and an electron acceptor within the thylakoid membrane 3. The pigment complex serves as an “antenna” for gathering solar energy  4. Begins with photosystem II: a pigment complex absorbed solar energy, and then is  passed from one pigment molecule to another until it is concentrated in a particular  pair of chlorophyll a molecules called the reaction center  5. Electrons (e-) in the reaction center chlorophyll come so energized that they escape  from the reaction center and move to a nearby electron acceptor 6. Photosystem II disintegrates without replacement electrons 7. Replacement electrons are provided by water, which splits, releasing oxygen to the  atmosphere 8. Organisms, including plants and even ourselves use this oxygen 9. Hydrogen ions (H+) stay in the thylakoid space and contribute to the formation of a  hydrogen ion gradient 10. Water is used up and oxygen is produce 11. The electron accepter that got the energized electrons from the reaction center will  send the electrons down a series of carriers that pass electrons from one to the other  known as the electron transport chain12. As the electrons pass from one carrier to the next, the energy is realized and is used  to move hydrogen ions (H+) from the stroma into the thylakoid space forming a  hydrogen ion gradient  13. These hydrogen ions flow down their electrochemical gradient through ATP Synthase  complexes, ATP product occurs as will described shortly  14. ATP Synthase: complex of proteins in the cirstae of the mitochondria and thylakoid  membrane of chloroplasts that produce ATP from the diffusion of hydrogen ions  across a membrane 15. This ATP will be used in the Calvin cycle reactions in the stroma to reduce carbon  dioxide to a carbohydrate  a) Photosystem I pigment complex absorbs solar energy, energized electrons lead  its reactions center and are captured by a different electron acceptor 16. After going through the electron transport chain, the electrons from photosystem II  are now low-energy electrons  17. These electrons are used to replace those lost by photosystem I 18. The electron accepter in photosystem I passes its electrons to NADP+ molecules 19. Each NADP+ accepts two electrons and an H+ to become a reduced form of the  molecules - NADPH 20. This NADPH will also be used by the Clavin Cycle reactions in the stroma to reduce  carbon dioxide to a carbohydrate  VI. The organization of the Thylakoid Membrane A. Photosystem II: consists of a pigment complex and an electron acceptor molecules,  receives electrons from water, which splits, releasing oxygen B. The electron transport chain carries electrons from photosystem II to photosystem I and  pumps H+ (hydrogen ions) from the stroma into the thylakoid space C. Photosystem I, which also consists of a pigment complex and an electron acceptor  molecules, is adjacent to NADP reductase, which reduces NADP+ to NADPH D. The ATP synthase complex crosses the thylakoid membrane and contains an interior  channel and a protruding ATP synthase, an enzyme that joined ADP+ VII. Cyclic Electron Pathway A. Under high oxygen levels, NADPH levels may accumulate the cell, and photosynthetic  cells may enter the cyclic electron pathway  B. Cyclic Electron Pathway: Alternate form of light dependent reactions in photosynthesis  that does not produce NADPH 1. Found in many prokaryotic cells 2. Different from noncyclic reactions by the electrons are recycled back to photosystem  I C. This pathway begins when the Photosystem I pigment complex absorbs solar energy  that is passed from one pigment to the next until it becomes concentrated in a reaction  enter 1. But with Photosystem II, electron (e-) becomes so energized that they escape from  the reaction center and move into a nearby electron acceptor molecules 2. Figure 8.8  VIII. ATP Production A. Thylakoid space acts a s reservoir for hydrogen ions (H+)  B. Each time oxygen is removed from water, two H+ remain in the thylakoid space C. As the electrons move from carrier to carrier along the electron transport chain, the  electrons give up energy which is used to pump H+ from the stroma into the thylakoid  space which is like pumping water into a reservoirD. The end result is that there are more H+ in the thylakoid space than in the stroma E. Beaucse H+ is charged, this is an electrochemical gradient F. There are also more positive charges within the the thylakoid space that the stroma G. When a channel is opened in the ATP synthase complex, H+ flows from thylakoid space  into the stroma, just like water flowing out of the reservoir H. The flow of H+ from high to low concentration across the thylakoid membrane provides  energy that allows the ATP synthase enzyme to enzymatically produce ATP from ADP+  I. This method of producing ATP is called chemiosmosis because ATP production is tied to  the establishment of an H+ gradient  8.3 Plants as Carbon Dioxide Fixers I. The Calvin cycle reactions take place after the light reactions A. A series of reactions that produce a carbohydrate before returning to the staring point B. The cycle is named for Melvin Calvin, who used radioactive isotope 14C as a tracer to  discover the reactions making up the cycle C. Figure 8.9  D. The Clavin cycle includes (1) carbon dioxide fixation (2) carbon dioxide reduction and (3)  regeneration of RuBP (ribulose-1, 5-bisphosphate) that staring material of the cycle II. Fixation of Carbon Dioxide A. Carbon Dioxide Fixation: the first step of the Clavin cycle 1. The molecules of carbon dioxide from the atmosphere are attached to 3 molecules of  RuBP resulting in three 6carbon molecules 2. The enzyme that speeds this reaction is called RuBP carboxylase a) RuBP carboxylase: a protein that makes up about 20% to 50% of the protein  content in chloroplasts b) It’s abundance may be that is unusually slow(it processes only a few molecules  of substrate per second compared to thousands per second for a typical enzyme)  and so there has to be a lot of it to keep the calvin cycle going  III. Reduction of Carbon Dioxide A. Each of two 3PG molecules undergoes reduction to G3P in two steps B. First step: converts 3PG into BPG using ATP  C. Second step: convert BPG into G3P using NADPH D. Figure below IV. Regeneration of RuBP A. Calvin cycle reactions are multiplied by 3 because it takes 3 turns of the calvin cycle to  allow one G3P to exit B. For every 3 turns, 5 molecules of G3P are used to reform 3 molecules of RuBP and the  cycle continues C. 5 x 3 (carbons in G3P) = 3 x 5 (carbons in RuBP) D. figure below V. Importance of the Calvin Cycle A. G3P is a product of the cabin cycle that can be converted to other molecules a plant  needs B. Plants use G3P for glucose, sucrose, starch, cellulose, fatty acids, and amino acid  synthesis C. Glucose phosphate is one of the organic molecules that results from G3P metabolism 1. Glucose is the molecules that plants and animals use most often to metabolize to  produce the ATP molecules they require for energy needsD. Glucose phosphate is also the starting point of the synthesis of starch and cellulose  1. Starch is the storage form of glucose 2. Some starch in stored in chloroplasts, but most is stored in roots 3. Cellulose is a structural component of plants cell walls and becomes fiber in out diet  because we are unable to digest it 4.Chapter 2 Lecture 4 Notes Molecule of Cells - Lactose: a sugar in milk - Lactase: an enzyme that breaks down lactose • People who are lactose intolerant do not produce lactase into adulthood  - Life’s molecular diversity is based on the properties of carbon • Almost all the molecules a cell makes are composed of carbon bonded to - Other carbons and atoms of other elements • Carbon based molecules are called organic compounds - Carbon atomic number: 6  - 6 protons and 6 neutrons  - Isotopes • Isotope: Are atoms of the same element with different numbers of neutrons • Radioactive isotopes emit various types of energy as they decay - Carbon 14 decays  - Uses of low level radiation • The messing area in thyroid scan indicates the presence of a tumor that does not take up  the radioactive iodine - Uses of high level radiation • Radiation kills bacteria and fungi • Irradiated peaches spoil less quickly and can be kept for a longer length of time • Physicians use radiation therapy to kill cancer cells - Ionic bonding • Ions: form when electrons are transferred from one atom to another - Example: Na, with 1 electron in its 3rd orbital, tends to be an electron donor • Becomes positive after giving up one electron - Example: Cl, with 7 electrons in its 3rd orbital, tends to be an electron acceptor.  • Become negative after gaining 1 electron - Covalent bonding • Covalent bond: is a result from when atoms share electrons in such a way that each atom  has an octet of electrons in the outer orbital (shell) - An atom may share electrons with one or more atoms • After sharing electrons, each atom has completed an outer orbital  - Nonpolar and polar covalent bonds • Nonpolar: if the sharing of electrons between 2 atoms is fairly equal • Polar: As in water, the sharing of electrons between oxygen and each hydrogen is unequal • Electronegativity: the attraction of an atom for electrons in a covalent bond- Polar Covalent Bonds • Pole covalent bonds: The sharing between 2 atoms is unequal, the covalent bond is  described as polar • Oxygen is more electronegative than hydrogen  - Hydrogen Bonding • Polarity within a water molecule causes the hydrogen atoms in 1 molecule to be attracted  to the oxygen atoms in other water molecules • The attraction between partially (-) oxygen and partially (+) hydrogen results in a hydrogen  bond • Bond is weak individually but strong collectively  - Properties of water • High heat capacity - Does not change temperature easily • High heat of vaporization - Makes cooling by evaporation efficient • Can dissolve many molecules - Hydrophilic: molecules attract water - Hydrophobic: molecules do not attract water • Water molecules are cohesive and adhesive - Cohesion: water molecules cling together because of hydrogen bonding - Adhesion: water’s positive and negative poles allow it to adhere to polar surfaces • Water has a high surface tension - Acids and Bases • When water ionizes, it releases an equal number of hydrogen ions (H+) and hydroxide ions  (OH-) • Acidic Solutions: (High H+ concentrations) • Basic Solutions: (Low H+ concentrations) • Acid: HCl -> H+ + Cl- • Base: NaOH -> Na+ + OH- • Acids usually have a sour taste (like lemon juice) - pH Scale • The pH scale: indicates the acidity or alkalinity of a solution • Scale ranges from 0-14 • A pH below 7 is acidic • A pH above 7 is alkaline • A pH of 7 is neutral  - Organic Molecules • Organic molecules always include: - Carbon (C) and Hydrogen (H) - Those with only (H) and (C)are called hydrocarbons • Example of hydrocarbon is gas from a car- Carbon Bonds • 4 electrons on outer shell • Can make up to 4 bonds - Functional Groups • Functional groups: are a specific combination of bonded atoms that always react in the  same way - Different functional groups change the function of a molecule  • Hydroxyl group- OH • Amino Group - NH2 • Methyl Group - CH3 all 3 will be on test - Monomers and Polymers • Macromolecules: contain many molecules joined together - Monomers: Simple organic molecules that exist individually - Polymers: Large organic molecules, formed by combing monomers • Dehydration reaction: an -OH and -H are removed as water \ - Carbohydrates • Carbohydrates: function for quick fuel an shorter energy storage in organisms - Play a structural role in plants - Cell walls, wood • Monosaccharides and Disaccharides - Monosaccharides: are sugars with 3-7 carbon atoms • Frutose • Glucose • C6, H12, O6 - Disaccharides: contain two monosaccharides joined by the dehydration reaction • Maltose • Sucrose • Lactose  - Polysaccharides: long polymers that contain many glucose subunits • Starch is: - A polymer of glucose - Used b y plants for energy storage - Potatoes and grains - Glycogen is: • A polymer of glucose • Used by animals for energy storage • We use - Cellulose is: • A polymer of glucose • Forms plant cell walls - Chitin is: • A polysaccharide • Used by insects and crustaceans to build an exoskeleton• High-fructose corn syrup - Most sodas and fruit drinks contain it (HFCS) - Fructose is sweeter than glucose - Glucose atoms are rearranged fructose - In a factory - Most scientific studies have not shown health consequences associated with replacing  sucrose with HFCS - Lipids • Types of lipids: - Fats and oils used for energy storage - Phospholipids from membranes - Steroids include sex hormones - Lipids have on common characteristic - they do not dissolve in water (hydrophobic) • Fats and oils are mostly energy-storage molecules - Fats: • Usually of animal storage • Solid at room temperature • Store energy, insulate again heat loss, form protective cushion for internal organs  (visceral fat) • Know as triglyceride  - Consists of one glycerol backbone - Three fatty acids - Oils: • Usually of plant origin  • Liquid at room temperature • Store energy in seeds • Saturated vs. Unsaturated fats - Some fatty acids contain one or more double bonds, forming an unsaturated fatty acid • olive oil • corn - These have one fewer hydrogen atom and are bent • Do not pack tightly - Double bonds cause oils to be liquid at room temperature  - Fats with maximum number of hydrogens are called saturated fatty acids • Most animals fat are saturated fats • Hydrogenated veggie oils are unsaturated fats that have been converted to saturated  fats by a dying hydrogen • this hydrogenation creates trans fats, which are associated with health risks - Partially Hydrogenated Oils = Trans Fats • Hydrogenation of oils - Increases shelf life - Allows reheating for drying - reduced need for animal fats • Many foods have hydrogenated oils, trans fats  • Trans fats are indeed a greater health risk the saturated fats - Phospholipids: • Two fatty acids and a phosphate group• Phosphate group forms a polar head (hydrophilic) while the rest of the molecule is a  non polar (hydrophobic) tail • Spontaneously form a bilayer in which the hydrophilic heads face outward toward  watery solutions and the tails form the hydrophobic interior  - Steroids • Have a backbone of four fused carbon rings - Cholesterol - Testosterone - Estrogen - Hormone Analogs: • A chemical that acts like hormones in the body - Many act like estrogen in animals - Proteins: • Are polymers composed of amino acid monomers • Amino acids - Amino group (-NH2) - Acidic group (-COOH, carboxyl) - R group varies  • 20 different amino acids vary by the R Group • `20 different functional groups  • Have a wide range of functions and structures - Proteins perform many functions • Structural: proteins give support (keratin, collagen) - Nails • Enzymes: speed up chemical reactions - More functions to come  • Peptides - A polypeptide is a single chain of amino acids - A peptide bond joins two amino acids • Levels of Protein Organization - Proteins have up to 4 levels of structural organization • Primary: is the linear sequence of the amino acids • Secondary: occurs when the protein make certain types of structures in different  places - Two types include: alpha helix and beta sheet  • Tertiary: the final 3 dimensional shape - Maintained by various types of bonding between R groups • Quaternary: is found in proteins with multiple polypeptide chains - Separate polypeptide chains are arranged to give this highest structure - Has to have the same 4 proteins stuck together to work • The final shape of a protein is very important to its function • A protein is denatured when it loses structure and function - Occurs when proteins are exposed to extreme heat or pH • Nucleic Acids - Two types of nucleic acids are: • DNA: - Stores genetic information in the cell and in the organism- DNA replicates to transmit its information when a cell divides or an organisms  reproduces • RNA • DNA Structure:  - A polymer of nucleotides • Nucleotide is a molecule with: phosphate, sugar, and nitrogen containing base • Contains Adenine, Thymine, Guanine, and Cytosine  - The nucleotides form a linear molecule called a strand - DNA is a double helix of two strands - The two strands held together by hydrogen bonds - Rungs of the ladder are formed by complementary paired basesChapter 7: Cellular Respiration I. Overview of Cellular Respiration A. Cellular Respiration: the release of energy from molecules such as glucose  accompanied by the used of this energy to synthesize ATP molecules 1. Aerobic - O2 2. Gives off CO2 II. NAD+ and FAD A. Cellular respiration involves any individual reactions, requiring its own enzyme 1. Certain enzymes use 2 coenzymes a) NAD+  b) FAD 2. Each carries two electrons and two hydrogen atoms B. NAD+ and FAD are transporters for high energy electrons  III. Phases of Cellular Respiration A. Glycolysis B. Preparatory Reaction C. Citric Acid Cycle D. Electron Transport Chain IV. Outside the Mitochondria: Glycolysis A. Glycolysis: is the breakdown of glucoses to 2 molecules of pyruvate 1. In the cytoplasm 2. Requires no oxygen 3. Transforms one 6 carbon molecules into 3 carbon molecules  B. Energy Investment Steps 1. 2 molecules of ATP is used to activate glucose as glycolysis begins C. Energy Harvesting Steps 1. Oxidation of G3P results in NADH synthesis 2. Additional chemical changes lead to direct substrate-level phosphorylation,  formation of 4 ATP D. Substrate-level ATP Synthesis: phosphate passed directly to ATP from enzyme V. Outside the Mitochondria: Fermentation A. In animal cells, pyruvate from glycolysis accepts 2 hydrogen ions and 2 electrons  and is reduced to lactate B. 2 NADH pass electrons to pyruvate to reduce it to lactate in animals C. Fungi, yeast, produce alcohol as ethanol  VI. Why fermentation? A. Quick burst of energy B. Recycles NADH C. Problems: 1. Ethanol and lactate can be toxic to cells 2. Provides much less ATP than aerobic respiration  VII. Inside the Mitochondria: the Preparatory reaction A. Acetyl group attaches to CoA to become acetyl CoA B. Carbon dioxide is produced C. Hydrogen atoms are removed from pyruvate and picked up to form NADH + H+D. This reaction occurs twice per glucose VIII. Citric Acid Cycle A. Cyclical pathway that occurs in the matrix of mitochondria 1. A 2 carbon acetyl group of acetyl CoA combines with a C4 molecules to  produce C6 citrate 2. The CoA is recycled to the preparatory reaction  B. Each 2 carbon acetyl group os oxidized to 2 CO2 molecules C. Reactions produce NADH + H+ and one FADH2 D. One ATP is produced by substrate-level ATP synthesis E. Cycle turns twice per original glucose molecule F. Inputs: 2 acetyl groups, 6 NAD+, 2 FAD, 2 ADP + 2 phosphates G. Outputs: CO2, NADH + H+, FADH2, 2 ATP IX. Electron Transport Chain A. Located in cristae of mitochondria 1. Electrons are passed to a series of electron carriers 2. Some carriers are cytochromes, iron-containing proteins B. High energy electrons enter the system and low-energy electrons leave the  system C. 2 electrons per NADH + H+ and FADH2 enter the electron transport chain X. Electron Transport Chain A. Electrons pass from one carrier to another, energy is captured, and stored as a  hydrogen ion concentration gradient B. Oxygen combines with hydrogen ions to form water C. NAD+ and FAD are recycled to pick up more electrons from glycolysis, prep reaction,  and citric acid cycle  XI. Generating ATP A. Electron carriers are located in the cristae of the mitochondria B. NADH pass electrons to the first acceptor of the electron transport chain C. Energy released is used to pump H+ into the inter membrane space of mitochondrion D. Protons accumulate in the inter membrane space (proton gradient) E. The cristae also have ATP synthase complexes F. The H+ ions through an ATP synthase complex, back into the matrix G. As the H+ pass through the complex, energy is released and captured to form ATP from  ADP  1. Called chemiosmosis XII.Energy Yield from Cellular Respiration A. Total of 4 ATP by substrate-level ATP synthesis 1. 2 net from glycolysis 2. 2 from citric acid cycle B. 32-34 ATP produced by electron transport chain and chemiosmosisChapter 7 SB Notes 7.1 Overview of Cellular Respiration  I. Cellular Respiration: the release of energy from molecules such as glucose accompanied by  the use of energy to synthesize ATP molecules A. Cellular respiration is an aerobic process that requires oxygen (O2) and gives off carbon  dioxide (CO2) B. It usually involves the complete breakdown of glucose as shows here (draw figure below  the sentence) C. Glucose is a high-energy molecule and its breakdown products, CO2 and H2O are low  energy molecules D. As glucose is broken down, energy is released E. This energy is used to produce ATP molecules F. The breakdown of one glucose module results in the production of between 36 to 38 ATP  molecules G. This represents about 39% of the potential energy within a glucose molecule H. The rest of the energy dissipates I. This conversion is more efficient than many others J. Only between 14% and 30% of the energy within gasoline is converted to the motion of a  car II. NAD+ and FAD A. NAD+ ( Nicotinamide adenine dinucleotide): enzymes that utilize the coenzyme as an  electron carrier 1. Coenzymes help an enzyme do its job and sometimes participate in the reaction 2. In that instance, NAD+ receives 2 electrons (is reduced) as the substrate glucose is  oxidized 3. Each electron by NAD+ as part of a hydrogen atom 4. A hydrogen atom consists of a hydrogen ion (H+) and an electron (e-)  5. NAD+ receives two e- and 2 H+ to give NADH + H+ a) Figure 7.1 and explanation B. FAD (flavin adenine dinucleotide): coenzyme frequently used as an electron carrier 1. FAD accepts two e- and 2 H+, FADH2 results 2. NAD+ and FAD are analogous to electron shuttle buses 3. They pick up electrons at specific enzymatic reactions in either the cytoplasm or the  matrix of the mitochondria and carry these high- energy electrons to an electron  transport chain in the cristae of the mitochondria, where they drop them off 4. They empty NAD+ or FAD is then free to go back and pick up more electrons III. Phases of Cellular Respiration  A. The metabolic pathways of cellular respiration couple the release of energy within a  glucose molecule to the production of ATP B. The coupling of these reactions reduces the amount of energy of lost heat, which would  be significant if glucose breakdown occurred all at once. C. First phase: glycolysis, takes place outside the mitochondria and does not utilize oxygen D. Anaerobic: the chemical reaction that in the absence of oxygen E. Aerobic: Where oxygen is the final acceptor of electrons7.2 Outside the Mitochondria: Glycolysis I. Glycolysis: takes place within the cytoplasm, is the breakdown of glucose to two pyruvate  molecules A. Evolves before the citric acid cycle and the electron transport chain B. Most likely evolved when environmental conditions were anaerobic and before cells had  mitochondria C. This is why glycolysis does not require oxygen and occurs in the cytoplasm II. Energy-Investment Steps A. As glycolysis begins, 2 ATP are used to activate glucose and the molecule that results  splits into 2 C3, molecules ( G3P - glyceraldehyde 3 phosphate) each of which has  attached phosphate group B. Figure 7.4 and explanation III. Energy-Harvesting Steps A. Oxidation of G3P occurs by the removal of hydrogen atoms (H+ + e-) B. The hydrogen atoms are picked up NAD+ and NADH + H+ results C. Later, NADH will pass electrons on to the electron transport chain D. Oxidation of G3P and subsequent substrates results in 4 high-energy phosphate groups,  which are used to synthesize 4 ATP E. Substrate-level ATP synthesis: in which an enzyme passes a high-energy phosphate to  ADP, and ATP results  IV. Inputs and Outputs of Glycolysis A. The inputs and outputs are as follows: figure 7.3  7.3 Outside the Mitochondria: Fermentation I. The complete breakdown of glucose requires an input of oxygen to keep the electron  transport chain working II. If oxygen is limited pyruvate molecules accumulate in the cell, and intermediate, such as  NAD+ and FAD, cannot be recycled III. To correct this, cells may use anaerobic pathways such as fermentation IV. Fermentation: Anaerobic breakdown of glucose that results in the gain of 2 ATP and end  products such as lactic acid and alcohol A. Two types of fermentation: lactic acid and alcohol V. Lactic Acid Fermentation A. Electrons needed to reduce pyruvate to lactic acid are supplied by the NADH molecules  from glycolysis  B. Figure 7.5 and explanation C. Lactate is toxic to cells D. First, blood carries away all the lactate formed in muscles E. Eventually lactate begins to build up, lowering the pH and causing the muscles to “burn” VI. Alcohol Fermentation A. Pyruvate is reduced to produce alcohol B. Electrons needed to reduce the pyruvate are supplied by NADH molecules C. In the process, NAD+ molecules are regenerated for use in glycolysis VII. Energy Yield of Fermentation A. ATP produced during fermentation are products of glycolysis B. That’s because fermentation follows glycolysis  C. Anaerobic pathways produce only 2 ATP by substrate-level atp synthesisChapter 1 Lecture 1.20.17 Introduction to the Study of Life and the Scientific Method - What is a virus?  • Viruses are acellular structures that require a living cell to reproduce (obligate parasites) - Two main components to all viruses • Capsid: outer portion comprised of proteins • Nucleic acid core: DNA or RNA - Life and Emergent Properties • Emergent Property: a property that a complex system has but the individual members of  the system do not - Example: saltiiness • NaCl is salty (table salt) • Is sodium salty? No • Is chlorine salty? No. Very reactive.  - All aspects of life contain emergent properties - Qualities of Life • Living things: - Are organized - Acquire materials and energy  - Reproduce - Respond to stimuli - Are homeostatic - Grow and develop - Have the capacity to adapt - Viral Life Cycle • Moves into cell, viral replication (attachment) • Entry (get into the cell) • Replication  • Biosynthesis  • Assembly • Budding (can bud off from the cell and go off) • Repeat • Video on blackboard - Chapter 1 folder - Virus Structure  • Whether or not the virus is alive or not is a gray area • Are not homeostatic - Assembled from their parts and then released from the host cell • Do not grow and develop - Evolutionary adaptation = population changes - Some mutation are adaptive - Best adapted viruses reproduce more than others - Mutations arise as virus particles are produced - The process of science • Science is a way of knowing that tens from our curiosity about ourselves and the world  around us • Using observation, reason, and logic • Understand the rules that govern the physical universe- Strengths of Science • Science is publicly understandable - If you are willing to make the observations, you can verify scientific claims  • Science is self-correcting - New data may require new or altered theories • Science is predictive  - Tools of science • Ability to observe - Using sense, often enhanced with instruments  • Microscopes • Scientific Method - A tool to keep us from fooling ourselves • Science: Why did that happen? - Law or Principle: a description of a pattern in nature • Law of gravity: objects with mass attracted to each other • Law of Evolution: life on earth has changed - Theory: explanation as to why a pattern (law) exists. What is the mechanism behind it? • What causes gravity? • Theory of Evolution by Natural Selection - Hypotheses are based on theories • The hypothesis describes what we should see in an experiment to help us support or  refute a theory  “Browned toast and potatoes are ‘potential cancer risk’, says food scientists” BBN News - Cooking foods that have sugars and amino acids may form acrylamide - Toast, potatoes - Acrylamide showed to produce cancer in lab rats - Safety levels for humans unknown  - Observational clinical study - Scientists use two types of reasoning • Inductive reasoning: makes generalizations based on collecting and analyzing a large  number of specific observations  - All living organisms checked so far are made of cells. So all organisms are made of  cells. • Deductive reasoning: flows from general premises to predicted and specific results - Since humans are organisms, I will probably find that they are made of cells - Experimental Design • Background Information - Most stomach and intestinal ulcers are caused by the bacterium Heliobacter pylori - Antibiotics are used to treat this condition • A new antibiotic is found and needs to be tested in humans for stomach ulcer  treatment - Hypothesis • No difference expected between control and experimental groups or the experimental  variable will have no effect • Alternative hypothesis - Expect a difference between the groups or the experimental variable will have an  effect  • Experimental design, needs to be a blind study  - Don’t know which group they are in• Results: what happened in the experiment - After 2 weeks a higher percentage of those treated with Antibiotic B were effectively  treated • Conclusion - On the basis of their data, the investigators conclude that their alternative  hypothesis has been supported  - Good experiments only have one experimental variable • Extra variables are called confounding variables - Sometimes very easy - Usually very difficult, especially in biology - Antibiotic experiment controlled to prevent confounding variables? - A way to control for confounding variables • Replicates: - The same experiment should be performed many times and still get similar results - Each time is a replicate - Presenting data in graphs • X axis • Y axis • Data - Standard error/Standard deviation Chapter 2  2.1 Basic Chemistry  I. Matter: anything that takes up space and has mass  A. Forms of matter: solid, liquid, gas, plasma  B. All matter is composted of elements  II. Elements: Substance that cannot be broken down to a simpler substance with  different properties by ordinary chemical means  A. Each elements has it’s own properties: density, solubility, melting point, and  chemical reactivity  III. Atomic Structure  A. English scientist John Dalton championed the atomic theory, which says that  elements consist of tiny particles called atoms  1. Atoms: smallest part of an element that displays properties of the element  B. 3 best known subatomic particles: protons, electrons, neutrons  1. Protons: Positively charged atom  2. Neutrons: “neutral” or uncharged atom  3. Electrons: Negatively charged atom  4. Protons and neutrons are located within the nucleus, while the electrons  move around the nucleus  C. Atomic number: all atoms of the element have the same number of protons  1. Each atom has the same number of protons and electrons  D. Mass number: sum of the protons and the neutrons in the nucleus  E. Isotopes: Atoms of the same element that differ in the number of neutrons  F. Atomic mass: The average mass for all isotopes of the atom  1. Example: Majority of carbon is carbon 12, the atomic mass of carbon is closer  to 12 than to 13 or 14.  2. To find the number of neutrons from the atomic mass, you subtract the  number of protons from the atomic mass and take the closest whole number  IV. The Periodic Table  A. Vertical columns = groups  B. Horizontal rows = periods  V. Radioactive Isotopes  A. Example: carbon 14 changes into nitrogen 14 over time, which is a stable  isotope. When carbon 14 decays, it releases various types of energy in the form  of rays and subatomic particles.  B. Geiger counter detects radiation  VI. Electrons  A. Valence shell: The outermost shell of the electron  1. Determines many of an atom’s chemical properties  B. Octet Rule: If an atom only has one shell, the valence shell is complete when it  has two electrons. In atoms with more than one shell, the valence shell is most  stable when it has eight electrons 2.2 Molecules and Compounds  I. Molecule: formed when two or more atoms bond together  A. Example: Oxygen does not exist in nature as a single atom. Two oxygen atoms  are joined to form a molecule of oxygen, O2.  II. Compound: When two or more different elements bond together  III. Ionic Bonding  A. Ions form when electrons are transferred from one atom to another  B. Example: Sodium Chloride  1. This electron transfer becomes imbalanced because the sodium atoms has  one more proton than it has electrons. (net charge of +1 Na^+)  2. The chlorine atoms has one more electron than it has protons. (net charge of  -1 Cl^-)  C. Ions: Charged particle that carries a positive or negative charge  D. Ionic bond: when ionic compounds are held together by an attraction between  negatively and positively charged ions  IV. Covalent bonding: when two atoms share electrons in such a way that each atom  has an octet of electrons in the outer shell  A. Example: Hydrogen atom - the outer shells complete when it has two electrons,  If hydrogen is in the presence of a strong electron acceptor, it gives up its  electron to become a hydrogen ion (H^+) But if it’s not possible, hydrogen can  share with another atom and thereby have completed an outer shell.  V. Nonpolar and polar covalent bonds  A. Nonpolar covalent bond: sharing of electrons between two atoms is fairly equal  B. Electronegativity: the ability of an atom to attract electrons toward itself in a  chemical bond  1. Example: Water sharing electrons between oxygen and hydrogen is not  completely equal. That’s because one atom is able to attract electrons to a  greater degree than the other atom.  C. Polar covalent bond: unequal sharing of electrons in a covalent bond  1. Called polar because it different in polarity (the electrical charge) across the  molecule  D. Hydrogen bonding: a weak bond arising between a slightly positive hydrogen  atom of one molecule and a slightly negative atom of another molecule, or  between parts of the same molecule.  2.3 Chemistry of Water  I. The fires cells evolved in water, organisms composed of 70-90% water.  II. Calorie: the amount of heat energy needed to raise the temperature of 1 gram of  water by 1 Celsius  A. Other covalent bonded liquids are not require input of only about half this amount  of energy to rise 1 Celsius in temperature  B. The many hydrogen bonds that link water molecules help water absorb heat  without a great change in temperature  III. Water has a high heat of vaporization A. Water has a high heat of vaporization because hydrogen bonds must be broken  before water boils and changes to a vaporized state  B. Water’s high heat of vaporization gives animals in a hot environment an efficient  way to release excess body heat  1. Example: When we sweat, or get water splashed on us, our body heat is  used to vaporize the water, thus cooling us down  C. When body temperature increases, sweat produced by glands in the dermal  layer of the skin  IV. Water is a solvent  A. Because of its polarity, water facilitates chemical reactions, inside, and outside  living organisms  B. Solution: contained dissolved substances called solutes (solid)  C. Solutes: Substance that is dissolved in a solvent, creating a solution  1. Example: Salt in water. Salt is the solute, the saltwater is the solution  D. Hydrophilic: Molecules that can attract water  1. Ions and molecules disperse in water, they move about and collide creating a  reaction  E. Hydrophobic: Nonionized and non polar molecules, such as oil, the cannot  attract water  V. Water molecules are cohesive and adhesive  A. Cohesion: the ability of water molecules to cling to each other due to hydrogen  bonding  1. Because of cohesion, water exists as a liquid under the condition of  temperature and pressure  B. Adhesion: the ability of water molecules to cling to other polar surfaces  1. Liquid portion of our blood, transports dissolved and suspended substances  all over the body, is 90% water  C. Surface tension: the force that holds moist membranes together due to the  attraction of water molecules through hydrogen bonds  1. Acts as a barrier between the surface of the water and the atmosphere  D. Frozen water is less dense than liquid water  VI. Acids and bases  A. When water ionizes, it releases an equal number of hydrogen ions and hydroxide  ion into the solution  VII.Acidic Solutions (High H^+) Concentrations)  A. Lemon juice, vinegar, tomatoes, and coffee are all acidic solutions  B. Acids: substances that release hydrogen ions (H^+) when they dissociate in  water.  VIII.Basic Solutions (Low H^+ Concentrations)  A. Bases: substances that either take up hydrogen ions (H^+) or release hydroxide  ions (OH^-)  1. Examples: baking soda and antacids  B. NaOH ->> Na^+ + OH^-  IX. pH Scale: used to indicate the acidity or basicity (alkalinity) of solutions  A. Ranges from 0 to 14 B. pH of 7 represents a neutral state in which the hydrogen ion and hydroxide ion  concentrations are equal  C. A pH below 7 is an acidic solution  D. a pH above 7 is basic  X. Buffers and pH  A. Buffer: a substance that keeps pH within normal limits  1. Examples: aspirin, shampoos, and deodorants  2. Resist pH changes because they can take up excess hydrogen ion (H+) or  hydroxide ion (OH-)  2.4 Organic Molecules I. Inorganic molecules constitute nonliving matter, but inorganic molecules such as  salts and water play important roles in living organisms  II. The molecules of life are organic molecules  III. Organic Molecules: always contain carbon (C) and hydrogen (H)  IV. Isomers: molecules with the same molecular formula but a different structure, and  therefore a different shape  A. Organic molecules get its unique chemical characteristics are the combinations  of atoms, called functional groups, that are attached to the carbon skeleton.  V. Functional Groups  A. Chemical reactivity of an organic molecule is determined by the type and  locations of functional groups on the organic molecule  B. Functional group: a specific combination of bonded atoms that always have the  same chemical properties and therefore always react in the same way  C. Draw the functional groups chart  VI. From Monomers to Polymers  A. Carbohydrates, lipids, proteins, and nucleic acids are macromolecules, meaning  that they contain smaller subunits joined together  B. Polymers: macromolecule consisting of covalently bonded monomers  1. Lipids are not polymers because they contain two different subunits  C. Monomer: Subunit of a polymer  1. constructed by linking together a large number of the same type of subunit  2. Glucose is a monomer of starch  D. Dehydration reaction: chemical reaction in which a water molecule is released  during the formation of a covalent bond  E. Hydrolysis reaction: splitting of a chemical bond by the addition of water, with the  H+ going to one molecule and the OH- going to the other  1. To degrade polymers, the cell uses a hydrolysis reaction in which  components of water are added  2. draw figure 2.13 a & b with explanation for both under figure 2.13 2.5 Carbohydrates I. Carbohydrates: universally used as an energy source for living organisms, including  humans  A. Also play a role in structural woody plants, bacteria, and animals such as insects.  B. On cell surfaces, they are involved in cell-to-cell recognition  C. Characterized by the presence of the atomic grouping H-C-OH D. Single sugar molecules and chains of sugars  E. Chain length varies from a few sugars to hundreds of sugars  F. The monomer subunits, called monosaccharides, are assembled into long  polymer chains called polysaccharides II. Monosaccharides - Simple Sugars  A. Monosaccharides: consist of only a single sugar molecule and are commonly  called simple sugars  B. Have a carbon backbone of 3 to 7 carbons  C. Pentoses: monosaccharides with 5 carbons  D. Hexoses: monosaccharide with 6 carbons  E. Glucose: a hexose sugar found in our blood  1. Our bodies use glucose as an immediate source of energy  III. Disaccharides A. Contains two monosaccharides that have joined during a dehydration reaction  B. draw figure 2.15 and explanation for it at bottom of image  IV. Polysaccharides - Complex Carbohydrates  A. Polysaccharides: long chains of glucose subunits  1. Long polymers such as starch, glycogen, cellulose  2. Because of their length, they are referred to as complex carbohydrates  V. Energy Storage Polysaccharides  A. Starch: storage found in plants that are composed of glucose molecules joined in  a linear side chain  B. Glycogen: Storage found in animals composed of glucose molecules joined in a  linear chain with several branches  C. Some polymers in starch are long chains of up to several thousand glucose units  D. Starch has fewer side branches, or chains or chains of glucose that branch off  from the main chain, than does glycogen  E. Draw figure 2.16 and 2.17 and explanation  VI. Structural Polysaccharides  A. Cellulose: found in plant cell walls, which helps account for the strong nature of  these walls  1. Glucose units are joined by a slightly different type of linkage than that found  in starch o glycogen 2.6 Lipids  I. Lipids: contain more energy per gram than other biological molecules while fats and  oils function as energy storage molecules in organisms  A. Phospholipids form a membrane that separates the cell from its environment and  forms its inner compartments as well  B. Lipids are diverse in structure and function  C. They all do not dissolve in water, they are hydrophobic  D. Fats and Oils  1. Most familiar lipids  2. Fats: tend to be of animal organ and are solid at room temperature  a) Lard  b) Butter  c) Long-tem energy storage, insulates against heat loss, forms a protective  cushion around major organs  3. Oils: usually plant origin, are liquid at room temperature  a) Corn oil  b) Soybean oil  4. Fats and oils form when one glycerol molecule reacts with 3 fatty acid  molecules  5. Triglyceride: Fat molecule of glycerol with 3 fatty acids  6. Draw figure 2.19 and explanation  II. Saturated, Unsaturated, and trans-fatty acids  A. Fatty acids are either saturated or unsaturated  B. Fatty acid: hydrocarbon chain that ends with the acidic group -COOH  C. Most cells contain 16 and 18 carbon atoms per molecule  D. Smaller ones with fewer carbons are known  E. Saturated fatty acids: no double bonds between carbon atoms  1. Solid at room temperature  F. Unsaturated fatty acids: have double bonds between carbon atoms where the  number of hydrogens is less than two per carbon atom  1. Makes a bend in the fatty acid chain  2. Liquid nature of veggie oil at room temperature  G. Trans-fats: often produced by hydrogenation, or the chemical addition of  hydrogen to vegetable oils  H. Draw figure 2.20 and explanation  III. Phospholipids  A. Phospholipids: contain a phosphate group  1. Constructed like fats, but in place of the 3rd fat, there is a polar phosphate  group or grouping that contains both phosphate and nitrogen  2. The phosphate group forms the polar (hydrophilic) head of the molecule,  while the rest becomes the non polar (hydrophobic) tails  3. Primary components of cellular membranes  4. Draw figure 2.21 and explanation IV. Steroids:  A. Steroids: have a backbone of 4 fused carbon rings  B. Each one is different primarily by the arrangement of the atoms in the rings and  the type of functional groups attached to them  C. Cholesterol is a steroid formed by the body that all enters the body as part of our  diet  1. A component of an animal cell’s plasma membrane  2. Bile salts and sex hormones testosterone and estrogen  2.7 Proteins  I. Proteins: polymers composed of amino acid monomers  II. Amino acid: central carbon atom bonded to a hydrogen atom and 3 functional  groups  A. Group 1 - Amino group (-NH2)  B. Group 2 - Acidic group (-COOH)  C. Group 3 - R group  1. Determine uniqueness of each amino acid  2. Varies from having a single carbon to being a complicated ring structure  D. Draw figure 2.23 and explanation  E. Enzymes: speed chemical reactions  1. Chemical workings of the cell  F. Proteins in the plasma membrane have several functions:  1. Some form channels that allow substances to enter and exit cells  2. Some are carrier that transport molecules into and out of the cell  3. Some are enzymes  III. Peptides  A. Polypeptide: a chain of amino acids that are joined to one another by peptide  bond  B. Peptide bond: type of covalent bond that joins 2 amino acids  C. Draw figure 2.24 and explanation  IV. Levels of Protein Organization  A. Level 1: Primary structure. The linear sequence of the amino acids joined by  peptide bonds  1. Can be made of any combination of 20 different amino acids  2. Draw 2.25 figure and explanation  B. Level 2: Secondary Structure  C. Level 3: Tertiary Structure  D. Level 4: Quaternary Structure  E. Final shape of protein is important to its function  F. Enzymes cannot function unless they have their normal shape  G. When proteins are exposed to extremes in heat and pH, they undergo an  irreversible change in shape (denatured)  H. Denatured: When the normal bonding of the R group has been disturbed  1. Once it loses it shape, it can no longer function normally 2.8 Nucleic Acids I. Two types of nucleic acids  A. DNA: stores genetic information in the cell and in the organism  1. Cell replicates and transmits this information when the cell copies itself as  well as the organism reproduces  B. RNA: produced from covalent bonding of nucleotide monomers that contain  sugar ribose  II. Structure of DNA and RNA  A. Nucleotide: molecular complex of 3 subunits phosphate, a pentose sugar, and a  nitrogen-containing base  1. DNA contain the sugar dosyribose and the nucleotides in RNA contain the  sugar ribose  2. Different types of bases in DNA: a) Adenine (A)  b) Thymine (T)  c) Guanine (G)  d) Cytosine (C)  e) The base can have 2 rings (adenine or guanine) or one ring (thymine or  cytosine)  3. RNA bases: a) Uracil (U) replaces the base thymine  b) These structures are called bases because their presence raises the pH  of a solution  c) draw figure 2.2 and explanation  4. Double helix: DNA is double stranded, with two strands twisted about each  other  a) Figure 2.7 and explanation  5. RNA is a single stranded and is formed by complementary base paring with  one DNA strand  6. There are several types of RNA a) mRNA or messenger RNA  (1) carries information from DNA strand to the ribosome where it is  translated into the sequence of amino acids specified by the DNA  III. ATP (Adenosine Triphosphate)  A. ATP: an energy carrier in cells  1. ATP can be said to be the energy “currency” of the cell  B. ADP (Adenosine Diphosphate): a molecule of inorganic carbohydrates and  proteins]  1. After it breaks down, it is rebuilt by the addition of P to ADP  2. Figure 2.28 and explanation Chapter 8 - Photosynthesis  I. Overview A. Photosynthesis: converts solar energy into chemical energy of carbohydrates B. Pigments allow photosynthetic organisms to capture solar energy C. Most photosynthetic organisms contain the pigment chlorophyll D. Another common pigment group is the carotenoids E. Photosynthesis occurs in the green part of plants 1. Particularly leaves, contain chlorophyll and other pigments F. Leaves contain mesophyll tissue specialized for photosynthesis G. Raw material are water and CO2 H. Water is taken up by roots and transported to leaves by veins I. Carbon dioxide enters through opening in the leaves called stomata J. Light energy is absorbed by chlorophyll K. The chloroplast and stroma are surrounded by a double membrane L. Thylakoids are a different membrane system within the stroma M. Thylakoid space is formed by a continuous connection between individual thylakoids II. Photosynthetic Reaction A. Glucose and oxygen are the products of photosynthesis B. The oxygen given off comes from water C. CO2 gains hydrogen atoms and becomes a carbohydrate D. 6 CO2 + 6 H@0 —> C6H12O6 + 6 O2 1. Arrow is solar energy/pigmentsChapter 3 Lecture Notes - Cell Structure and Function  - Do not need to know peroxisomes and intermediate filaments I. The Microscope A. A revolution for understanding life B. Robert Hooke described cells in 1665, cork cells C. Light Microscope: visible light passes through a specimen, then through glass lenses,  and finally is projected into the viewer’s eye D. Specimens can e magnified by up to 1,000 times II. The cell theory A. All organisms are composed of one or more cells B. Cells are the basic living unit of structure and function in organisms C. All cells come only from other cells  III. Magnification and Resolution A. Magnification: the increase in an object’s image size B. Resolution: measure of the clarity of an image 1. The ability of an instrument to show two nearby objects are separate  IV. Contrast A. Most cells are clear B. Must stain cells to make out certain structures  V. Scanning Electron Microscope A. SEM: Study the detailed external architecture of cell surfaces  B. Images from an electron microscope are black and white VI. Transmission Electron Microscope A. TEM: Study of the details of internal cell structure  VII. All cells have a plasma membrane, cytoplasm, ribosome, and DNA VIII. Plasma membrane A. All cells are surrounded by a plasma membrane 1. Boundary and gatekeeper B. The semifluid medium inside of a cell is the cytoplasm 1. It is composed of water, salts, and dissolved organic molecules  IX. Prokaryotic cells A. Ribosome B. Flagellum C. Capsule D. Cell Wall E. Plasma membrane F. Nucleoid G. FImbriae X. The Nucleus A. Nuclear Envelope: 2 layers 1. Filled with nuclear pores B. Chromatin: DNA + protein C. Nucleolus: RNA, protein, and unfinished ribosomes XI. Vacuoles and Vesicles A. Membrane bound sacks B. Vesicles are usually smaller 1. Lysosome: centaines enzymes to digest food or damaged organelles  2. Turgor pressure is inside the vacuole C. Solar energy + carbon dioxide + water -> carbohydrate + oxygen 1. Photosynthesis a) Plants, algaie, and cyanobacteria have this ability b) Solar energy is the ultimate source of energy for most cells D. Carbohydrate + oxygen -> carbon dioxide + water +energy 1. Cellular respiration a) All organisms convert chemical energy to ATP b) ATP is used for all energy-requiring processes in cells  c) All organisms used ATP  XII. Parts of Mitochondria  A. Double membrane: outer and inner membrane B. Cirstae C. matrix XIII.The cell’s internal skeleton helps organize its structure and activities A. Cells contain a network of protein fibers, called the cytoskeleton: organizes the  structures and activities of the cell 1. Proteins of the cytoskeleton stained with fluorescent dye  XIV. Actin (Micro) Filaments A. Two long, thin, flexible, actin chains twisted in helix B. Microfilaments C. Roles: 1. Provide structure as dense web under plasma membrane 2. Form projections in intestinal cells as microvilli 3. Allow for formation of pseudopods in amoeboid movement 4. Provide the movement for muscle contraction  D. Actin interacts with motor molecules for movement  1. Example: muscle cells E. In the presence of ATP, myosin pulls actin along XV.Microtubules A. Hollow cylinders of tubular protein B. Assembly: controlled by microtubule organizing center (MTOC) 1. Most important MTOC is centrosome C. Roles: 1. Help maintain cell shape 2. Interact with motor molecules kinesin ad dynein to cause movement of organelles 3. Form spindle apparatus during cell division XVI.Evolution of the Eukaryotic cell A. Endosymbiotic theory: mitochondria and chloroplasts derived from prokaryotes that were  taking up by a larger cell 1. Mitochondria were originally hereotrophic bacteria 2. Chloroplasts were originally cyanobacteria 3. After exerting the host cell, the bacteria began living together cooperatively Chapter 4 SB  4.1 Plasma Membrane Structure and Function I. Plasma membrane separates the internal environment of the cell from the external  environment A. Regulates the entrance and exit of molecules in the cell B. Helps the cell and organism maintain a steady internal environment, called homeostasis  C. Made primarily of phospholipids II. Fluid mosaic model of plasma membrane structure A. Membrane is composed of a phospholipid bilayer in which proteins are embedded with  the cytoplasmic side B. Steroids (cholesterol) help regulate the fluid of the membrane C. Cytoskeleton filaments are attached to the inside surface by membrane proteins  D. Peripheral proteins are associated with only one side of the plasma membrane 1. These proteins on the inside of the membrane are often held in place by the  cytoskeletal filaments E. Integral proteins span the membrane 1. Protrude from one or both side  F. They form a mosaic pattern and this combination of protein, steroids, and phospholipids  is called the fluid mosaic model, of membrane structure  G. Both phospholipids and proteins can have attached carbohydrate (sugar) chains 1. These molecules are called glycolipids and glycoproteins 2. Glycolipids: lipid in plasma membrane that contains an attached carbohydrate chain 3. Glycoproteins: protein in plasma membrane that contains an attached carbohydrate  chain  III. Function of the Membrane Proteins  A. Peripheral proteins: a structural role that they help stabilize and shape the plasma  membrane  B. Also function in signaling pathways  C. Integral proteins largely determine a membrane’s specific function D. Types of integral proteins 1. Channel proteins: Involved in the passage of molecules through the membrane a) They have a channel that allows a substance to simply move across the  membrane  b) Example: a channel protein allows hydrogen ions to flow across the inner  mitochondrial membrane c) Without the movement of hydrogen ions, ATP would never be produced d) Channel proteins may contain a gate that must be opened by the binding of a  specific molecule to the channel  2. Carrier proteins: also involved in the passage of molecule through the membrane a) They combine with a substance and help it move across the membrane b) Example: A carrie protein transports sodium and potassium ions across a nerve  cell membrane c) Without this carrier protein, nerve conduction would be impossible  3. Cell Recognition Proteins: glycoproteins a) These proteins help the body recognize when it being invaded by pathogens so  that an immune reaction can occur 4. Receptor proteins: Have a shape that allows the molecule to bind to ita) Binding of the molecule causes the protein to change its shape and thereby bring  about a cellular response  b) Coordination of the body organs is totally depending on such signal molecules c) Example: the liver stores glucose after it is signaled to do so by insulin 5. Enzymatic proteins: carry out a metabolic reaction directly a) The integral membrane proteins of the electron transport chain carry out the final  steps of aerobic respiration b) Without the presence of enzymes, some of which re attached to the various  membranes of the cell, a cell would never be able to perform the metabolic  reactions necessary to its proper function  6. Draw figure 4A and describe what is going on in the process  4.2 The Permeability of the Plasma Membrane  I. Plasma membrane regulates the passage of molecules into and out of the cell II. Selectively permeable: certain substances can move across the membrane while others  cannot III. Small, non charged molecules (like carbon dioxide, oxygen, glycerol, and alcohol) can freely  move across the membrane A. They slip between the hydrophilic heads of the phospholipids and pass through the  hydrophobic tails of the membrane B. The molecules are said to go “down” their concentration gradient as they move from an  area where their concentration is high to an area where the concentration is low C. Some molecules are able to go “up” they concentration gradient, or move from an area  where their concentrations low to an area where the concentration is high, but this  requires energy  IV. Draw Table 4.1  V. Diffusion and Osmosis A. Diffusion: the movement of molecules from a higher to a lower concentration 1. Down their concentration gradient - until equilibrium is achieved and they are  distributed equally B. A solution contains both a solute (usually a solid) and a solvent (usually a liquid) C. Gases can diffuse through the lipid bilayer 1. In which oxygen centers cells and carbon dioxide exits cells 2. Consider the movement of oxygen from the alveoli (air sacs) of the lungs to the blood  in the lung capillaries 3. After inhaling, the concentration of oxygen in the alveoli is higher than that in the  blood 4. Therefore, oxygen diffuses into the blood 5. Several factors influence the rate of diffusion: temperature, pressure, electrical  currents and molecular size a) Example: as temperature increases, the movement of molecules increases which  in turn increases the rate of diffusion D. Osmosis: diffusion of water across a selectively permeable membrane due to  concentration differences  1. Osmotic pressure: the pressure that develops in a system due to osmosis a) The greater the osmotic pressure, the more likely it is that water will diffuse in  that directionb) Because of osmotic pressure, water is absorbed by the kidneys and taken up by  the capillaries in the tissues VI. Isotonic Solution: solution that is equal in solute concentration to the of the cytoplasm of cell  A. Allows them to neither gain nor lose water because of osmosis  B. The solute concentration and the water concentration both inside and outside the cell  are equal, and therefor there is no net gain or loss of water  VII.Hypotonic Solution  A. Hypotonic Solution: solution that cause cells to swell or even burst because of an intake  of water  B. Hypo: less than and refers to a solution with a lower concentration of a solute (higher  concentration of water) than inside the cell  C. If a cell is placed in a hypo tonic solution, water enters the cell D. The new movement of water is from the outside to inside of the cell E. Any concentration of a salt solution lower than 0.9% is hypotonic to red blood cells F. Cytolysis: referred to disrupted cells, but with red blood cells, hemolysis is used G. Turgor pressure: When a swelling of a plant cells in a hypotonic solution 1. When a plant cell is placed in a hypotonic solution, the cytoplasm expands because  the large central vacuole gains water and the plasma membrane pushes against the  rigid cell wall 2. The plants cell does not burst because the cell does not give away 3. Turgor pressure is important to the maintenance of the plant’s position 4. When you forget to water plants, they wilt due to decreased turgor pressure  H. Organisms that live in fresh water have to prevent their internal environment from  becoming hypotonic I. Protozoans, such as paramecia, have contractile vacuoles that rid the body of excess  water J. Freshwater fishes have well-developed kidneys that excrete a large volume of dilute  urine 1. They would be not be able to survive in either distilled water or marine environment  VIII. Hypertonic Solution: solutions that cause cells to shrink or shrivel due to loss of water  A. Hyper: more than referring to a solution with a higher percentage of solute (lower  concentration of water) than the cell B. If a cell is placed in a hypertonic solution, water leaves the cell C. The cell movement of water is from the inside to the outside of the cell D. Any concentration of a salt solution higher than 0.9% is hypertonic to red blood cells E. Animals cells are placed in this solution, they shrink F. Crenation: shriveling of a cell in a hypertonic solution G. Plant cells in this solution, the plasma membrane pulls away from the cell wall as the  large central vacuole loses water H. Plasmolysis: shrinking of the cytoplasm due to osmosis  I. Marine animals coping with hypertonic environment: 1. Sharks increase or decrease the urea in their blood until their blood is isotonic with  the environment 2. Marine fishes and other animals excrete salts across their gills IX. Transport by Carrier Proteins A. Can combine with only a certain type of molecule or ion, which is then transported  through the membraneB. The carrier undergoes a change in shape that moves the molecule across the  membrane C. Carrier proteins are required for both facilitated transport and active transport X. Facilitated Transport: explains the passage of such molecules as glucose and amino acids  across the plasma membrane even though they are not lipid-soluble A. Passage of glucose and amino acids is facilitated by reversible combination with carrier  proteins, in which some manner transport them through the plasma membrane 1. Example: sugar molecules of identical size might be present inside or outside the  cell, but glucose can cross the membrane hundreds of times faster than other sugars 2. Example: aquaporins, allow water to rapidly move across the plasma membrane  XI. Active transport: molecules or ions that move through the plasma membrane, accumulating  either inside or outside the cell A. Example: iodine collects in the cells of the thyroid gland, glucose is completely absorbed  form the gut by the cells lining the digestive tract, sodium can be almost completely  withdrawn from urine by cells lining the kidney tributes 1. Molecules moved to the region of higher concentration, exactly opposite to the  process of diffusion  B. Carrier proteins and expenditure of energy are needed to transport molecules against  their concentration gradient 1. Chemical energy, in the form of ATP, is required for the carrier to combine with the  substance to be transported 2. Cells involved primarily in active transport, like kidney cells, have a larger number of  mitochondria near membranes where active transport is occurring  C. Proteins involved in active transport are called pumps 1. One type is in active transport in all animal cells, associated with nerve and muscle  cells move sodium ions (Na+) to the outside of the cell and potassium ions (K+) to  the inside of the cell a) 2 events are linked, and the carrier protein in called sodium-potassium pump b) Sodium-potassium pump: carrier protein in plasma membrane that moves  sodium ions out of and potassium ions into the cell (1) A change in carrier shape after the attachment of a phosphate group, and  again after its detachment, allows the carrier to combine alternately with  sodium ions and potassium ions (2) Draw figure 4.9 and explain(highlighted, picture right above) (3) The phosphate group is donated by ATP when it is broken down  enzymatically by the carrier (4) Sodium-potassium pump results in a solute concentration gradient and an  electrical gradient for these ions across the plasma membrane  XII.Bulk Transport A. Video on exocytosis and endocytosis  B. Exocytosis is a way substances can exit a cell C. Endocytosis is a way substances can enter a cell XIII.Exocytosis A. Exocytosis: vesicle fuses with the plasma membrane as a secretion occurs B. Hormones, neurotransmitters and digestive enzymes are secreted from the cell in this  manner C. Golgi apparatus often produces the vesicles that carry these cell products to the  membraneD. During exocytosis, the membrane of the vesicle becomes a part of the plasma  membrane, which is hereby enlarged  E. Exocytosis can be a normal part of cell growth  F. 4.10 figure and explanation highlighted below  XIV.Endocytosis: cells take in substances by vesicle formation  A. A portion of the plasma membrane invaginate to envelop the substances, and then the  membrane punches off to form an intracellular vesicle  B. Occurs in 3 ways: 1. Phagocytosis transports large substances such as viruses 2. Pinocytosis transports small substances such as macromolecules into cells 3. Receptor-mediated endocytosis is a special form of pinocytosis 4. 4.11 figure  XV.Phagocytosis A. When a material is taken in by endocytosis is large (food particle or another cell)  B. Common in single-celled organisms (amoebas) and also occurs in humans C. Certain types of human white blood cells are amoeboid, mobile like amoeba, and they  are able to engulf debris such as worn out red blood cells or viruses  D. When an endocytic vesicle fuses with a lysosome, digestion occurs 1. Preliminary step toward the development of immunity or bacterial diseases  XVI. Pinocytosis  A. Occurs when vesicles form around a liquid or around very small particles B. Blood cells, cells that line the kidney tubules or the intestinal wall, and plant root cells all  use pinocytosis to ingest substances XVII. Receptor-Mediated Endocytosis  A. Form a pinocytosis that is quite specific because it uses a receptor protein shaped so  that a specific molecule (vitamin, peptide hormone or lipoprotein) can bind to it B. Receptor for these substances are found at one location in the plasma membrane 1. Called a coated pit because there is a layer of protein on the cytoplasmic side of the  pit 2. Once formed, the vesicle become uncoated and may fuse with a lysosome 3. When empty, used vesicles fuse with the plasma membrane and the receptors return  to their former location  4. It is selective and much more efficient than ordinary pinocytosis a) Involved in uptake and also in transfer and exchanged of substances between  cells b) Example: Take place when substances move form maternal blood into fetal blood  at the placenta  5. Importance demonstrated by a get disorder called familial hypercholesterolemia  a) Cholesterol is transported in the blood by a complex lipid and protein called low density lipoprotein (LDL)  b) Body cells take up LDL when LDL receptors gather in a coated pit c) In some individuals LDL receptors is unable to properly bind to the boated put  and the cells are unable to take up cholesterol d) Cholesterol accumulates in the walls of arterial blood vessels, leading to high  blood pressure, occluded (blocked) arteries, and heart attacks 4.3 Modifications of Cell Surfaces I. Two types of animal cell surface features A. Extracellular matrix: observed outside cells B. Junctions: occur between some types of cells C. Both connect to the cytoskeleton and contribute to communication between cells and  therefore tissue formation II. Extracellular Matrix A. ECM: A meshwork of proteins and polysaccharides in close association with the cell that  produced the 1. Collagen and elastin fibers are well known structural proteins in the ECM Collagen resists stretching and elastin gives the ECM resilience B. Fibronectin: adhesive protein that binds to a protein in the plasma membrane called  integrin C. Proteoglycans: Amino sugars in the ECM that form multiple polysaccharides that attach  to protein III. Junction between cells A. Behave in a coordinated manner B. 3 types: 1. Adhesion junction: serve to mechanically attach adjacent cells a) Desmosomes are on form of adhesion junction  b) Sturdy flexible sheet of cells c) Most common type of intercellular junction between skin cells 2. Tight Junction: bring cells even closer than desmosomes a) Connect plasma membranes between adjacent cells together producing zipper  like fastening 3. Gap junction: allows cells to communicate a) Formed when two identical plasma membrane channels join b) Lined with 6 plasma membrane proteins c) Important to the heart muscle and smooth muscle - they permit the flow of ions  that is required for the cells to contract as a unit IV. Plant Cell Walls A. Surrounded by a porous cell wall that varies in thickness depending on the function of  the cell B. All have a cell wall C. Pectins allow the wall to stretch when the cell is growing and noncellulose  polysaccharides harden the wall when the cell is mature D. Plasmodesmata: in a plant cell, the cytoplasm of living cells is connected by numerous  narrow, membrane-lined channels that pass through the cell wall Chapter 6 SB Notes 6.1 Life and the Flow of Energy I. Energy: the ability to do work or bring about change A. To maintain their organization and carry out metabolic activities, cells (as well as  organisms) need a constant supply of energy B. Carries on the process of life, growth, development, response to stimuli, and  reproduction C. Majority of organisms gets their energy from organic nutrients produced by  photosynthesizers (algae, plants, and some bacteria) D. Life on Earth is dependent on solar energy II. Forms of energy A. Kinetic energy: the energy of motion 1. A ball rolling down a hill  B. Potential energy: stored energy - has the capacity to accomplish work that is not  being used at the moment C. Chemical energy: contains energy in the chemical bonds of organic molecules D. Mechanical energy: type of kinetic energy associated with the position, or motion  of an object 1. A moose walking is converting chemical energy into a type of kinetic energy III. Two Laws of Thermodynamics A. Explains why energy flows in ecosystems and in cells B. First law(The law of conservation of energy) explains the ability of organisms to  convert chemical energy to mechanical energy 1. Energy cannot be created or destroyed but it can be changed form one form  to another C. The second law states that energy cannot be changed from one form to another  without a loss of usable energy 1. No process requiring a conversion of energy is over 100% efficient 2. Much of the energy is lost in the form of hear 3. Glucose tends to break apart carbon dioxide and water IV. Cells and Entropy A. Second law can be stated in another way: every energy transformation makes  the universe less organized and more disordered. B. Entropy: used to indicate the relative amount of disorganization 1. Processes that occur in cells are energy transformations, the second law  means that every process that occurs in cells always does so in a way that  increases the total entropy of the universe 2. Then any of these processes makes less energy available to do useful work  in the future6.2 Energy Transformations and Metabolism C. Cellular metabolism: the sum of all chemical reactions that occur in a cell 1. A significant part of cellular metabolism involves the breaking down and the  building up of molecules D. Catabolism: refers to the breaking down of molecules  E. Anabolism: refers to the building up(synthesis) of molecules F. Reactants: in a chemical reaction, they are substances that participate in a  reaction G. Products: substances that form a a result of a reaction 1. Example: in the reacting A + B -> D, A and B are the reactants and C and D  are the products  H. Free energy: the amount of energy available, that is, energy that is still “free”to  do work after a chemical reaction has occurred.  1. The change in free energy after a reaction occurs is calculatedly subtracting  the free energy content of the reactants from that of the products  2. A negative result means that the products have less free energy than the  reactants and the action will go forward I. Exergonic reactions: spontaneous and release energy J. Endergonic reactions: require an input of energy to occur 1. In the body, many reactions, such as protein synthesis, nerve impulse  conduction, or muscle contraction, are endergonic and they are driven by the  energy released by exergonic reaction 2. ATP is a carrier of energy between exergonic and endergonic reactions V. ATP: Energy for Cells A. ATP: the common energy currency of cells 1. All cells require energy, and they spend ATP B. ADP (Adenosine diphosphate): a molecule of inorganic phosphate C. Figure 6.3 The ATP Cycle 1. In cells, ATP carries energy between exergonic reactions and exergonic  reactions. When a phosphate group is removed by hydrolysis, ATP releases  the appropriate amount of energy for most metabolic reactions VI. Function of ATP A. In living systems: 1. Chemical work: ATP supplies the energy needed to synthesize  macromolecules (anabolism) that make up the cell, and therefore the  organisms 2. Transport work: ATP supplies the energy needed to pump substances across  the plasma membrane 3. Mechanical work: ATP supplies the energy needed to permit muscles to  contract, cilia, and flagella to bind chromosomes to move and so forth VII. Coupled Reactions A. Coupled reactions: the energy released by exergonic reaction is used to drive an  endergonic reaction 1. ATP breakdown is often coupled to cellular reactions that require an input of  energy2. Coupling, requiring that the exergonic reaction and the exergonic reaction be  closely tied, can be symbolized like this: figure 6.4 6.3 Enzymes and Metabolic Pathways I. Reactions do not occur haphazardly in cells II. They are usually a part of a metabolic pathway which is a series of linked reactions A. They begin with a particular reactant and terminate with an end product B. Metabolic energy is captured and utilized more easily if it is released in small  increments rather than all at once C. Diagram below III. Enzymes: typically proteins that function as catalysts to speed a chemical reaction A. Some forms of RNA molecules called ribozymes can act as catalysts IV. Substrates: the reactants in an enzymatic reaction for that enzyme V. Energy of Activation A. Molecules do not react with one another unless they are activated in some way B. Energy of activation: the energy that must be added to cause molecules to react  with one another (figure 6.5) 1. Shows E, when an enzyme is not present compared to when an enzyme is  present, illustrating that enzymes over the amount of energy required for  activation to occur 2. The addition of the enzyme doe not change the end result of the reaction 3. Notice that the energy of the products is less than the energy of the reactants 4. This results in a negative, so the reaction will proceed 5. The reaction will not go at all unless the energy of activation is overcome 6. Without the enzyme, the reaction rate will be very slow 7. By lowering the energy of activation, the enzyme increases the rate of the  reaction VI. How enzymes function A. Active site: one small part of the enzyme complexes with the substrate 1. It is here that the enzyme and substrate fit together seemingly like a key fits a  lock 2. Cell biologists now know that the active site undergoes a slight change in  shape in order to accommodate the substrate 3. Induced fit model: The enzyme is induced to undergo a slight alteration to  achieve optimum fit 4. After the reaction has been completed, the product is released, and the active  site returns to its original state, ready to bind to another substrate molecule 5. Only a small amount of enzyme is actually needed in a cell because enzymes  are not used up by the reaction 6. Every reaction in a cell requires that its specific enzyme be present because  enzymes complex only with their substrates, they are often named for their  substrates with the suffix -ase  VII. Factors Affecting Enzymatic Speed A. To get maximum product per unit, there should be enough substrate to fill the  enzyme’s active sites mot of the timeB. Addition to substrate concentration, the rate of an enzymatic reaction can also be  affected by environmental factors (temperature or pH) or by cellular mechanisms  such as enzyme activation, enzyme inhibition and cofactors VIII. Substrate Concentration A. Enzyme activity increases as substrate concentration increases because they  are more collision between substrate molecules and the enzyme B. As more substrate molecules full active sites, more product results per unitize C. When the enzymes active sites are filled almost continuously with substrate, the  enzyme’s rate of activity cannot increase any more and the maximum rate has  been reached IX. Temperature and pH A. If the temperature rises beyond a certain point, enzyme activity eventually levels  out and then declines rapidly because the enzyme is denatured B. Denatured: loss of proteins or enzyme’s natural shape so that it is no longer  functions 1. Occurs when temperature or pH is less than optimal C. Most enzymes and proteins and the shape of the protein responds to  temperature D. Temperature influences the proteins secondary and tertiary structure preventing  it form binding its substrate efficiently E. Therefore, as the structure of the enzyme changes, its activity decreases F. Each enzyme also has a preferred pH at which the rate of the reaction is the  highest (figure 6.9) shows that the preferred pH for the enzymes pepsin and  trypsin 1. At this pH value, these enzymes have their normal configurations 2. The globular structure of an enzyme is depending on interactions, such as  hydrogen bonding, between R groups 3. A change in pH can alter the ionization of R groups and disrupt normal  interactions and under extreme pH conditions , denaturation eventually  occurs 4. If the enzymes shape is altered, then is it unable to combine efficiently with its  substrate X. Enzyme Activation A. Activation of enzymes occur in many different ways B. Some enzymes are covalently modified by the addition or removal of phosphate  groups C. An enzyme called a kinase adds phosphates to proteins, as shown below, and  an enzyme called a phosphate removes them D. In some proteins, adding phosphates activates them; in others, removing  phosphates activates them E. Enzymes can also be activated by cleaving or removing part of the protein or by  associating with another protein or cofactor XI. Enzyme Inhibition A. Enzyme inhibition: occurs when the substrate is unable to bind to the active site  of an enzyme B. Regulated by feedback inhibitionC. Figure 6.10 XII.Enzyme Cofactors A. Most enzymes require an inorganic ion or an organic, but nonprotein, helper to  function properly B. The inorganic ions are metals such as copper, zinc or iron.  C. Cofactors: what the helpers are called D. Coenzyme: the organic, nonprotein molecule E. These cofactors assist the enzyme and may even accept or contribute atoms to  the reactionsPrinciples of Biology Chapter 1 Section 1.1 Notes A. Life is organized (the hierarchy of levels) I. Atom: Smallest particle of an element -trees, humans, and other organizations, atoms join together to form molecules II. Molecules: 2 or more atoms joining together of the same element III. Cell: Smallest unit of life  - Some organisms are single-celled -Multicellular organisms, the cell is the smallest structural and functional unit IV. Tissue: a group of similar cells that perform a particular function  - Nervous tissue has millions of nerve cells transmitting signals all over the body V. Organ: Two or more tissues join together  - The main organ that receives signals from the nerves is the brain VI. Organ System: Organs working together to form  - Ex: Trees & humans are a collection of organ systems B. Levels of Biological Organizations I. Species: Group of similar organisms capable of producing fertile offspring  - Share a common gene pool II. Population: Group of organisms of the same species in a certain area sharing a  common gene pool - Ex: Tropical grassland having a population of humans, zebras, and acacia trees III. Community: One species interacting with another within the same environment IV: Ecosystem: A community of populations interacting with the physical environment  V. Biosphere: All of Earth’s ecosystems together C. Life requires materials and energy  I. Living organisms need an outside source of materials and energy to maintain their  organizations  - Ex: Trees use carbon dioxide, water, and the sun to make their own food II. The food we eat provides nutrients, while cells use as building blocks or for energy III. Energy: The capacity to do work IV. Metabolism: the sum of all chemical reactions in a cell V. Plants and certain organisms capture solar energy and carry on photosynthesis VI. Photosynthesis: The process within chloroplasts using solar energy to reduce carbon  dioxide (CO2) to carbohydrates D. Chemical cycling and energy flow in an ecosystem I. (Visual in textbook and chapter 1 notes) II. The process - Begins when producers, like grass, take in solar energy to produce food by  photosynthesis  - Chemical cycling (blue arrows in visual) move from one population to another in  the food chain until decomposition returns to the producers once again - Energy (red arrows in visual) flows from the sun to plants and along the food  chain as they feed on one another  - Energy does not cycle E. Living organisms reproduce and develop I. Reproduction: process of producing a new individual of the same kind  II. Single-celled: bacteria, protists, and other single-celled organisms split in two III. Multicellular organisms: reproductive process starts with pairing a sperm from one  partner and an egg from the other partner.  - When the egg and sperm come together, followed by cell division, it results to  the immature stage  - It then goes onto stages of development, or change, to become an adult IV. When living organisms reproduce, their genes are passed on to the next generation  V. Genes: hereditary existing as alleles on chromosomes, one from each parent  -Genetic instruction VI. Random combination of sperm and egg, containing unique genes, makes the  offspring have new and different characteristics  VII. An embryo develops into a whole, a yellow daffodil, or a human because of specific  genes inherits from its parents VIII. In all organisms, genes are made of DNA (deoxyribonucleic acid) molecules IX. DNA: nucleic acid polymer produced from covalent bonding X. DNA has blueprints, or instructions, for organizations and metabolism of the organism XI. Multicellular organisms: contain the same set of genes, but only certain genes are  turned on in each type of specialized cell XII. Species are different, like humans, because of mutation XIII. Mutation: inheritable changes in the genetic information F. Living organisms respond to stimuli I. Organisms respond to external stimuli by moving toward or away from a stimulus, such  as smelling food II. Movement in humans and animals depend on their nervous and musculoskeletal  systems III. Behavior: observable, coordinated responses to environmental stimuli G. Living organisms are homeostatic I. Homeostasis: “staying the same” II. Internal environment of an organism stays relatively constant H. Humans have the capacity to adapt I. Adaptations: as environment changes, individuals of a species possess certain  features that make them more suited for the new environment  II. Natural selection: Individuals of a species are better adapted to their environment tend  to live longer and produce more offspring than others III. Evolution: Genetic change in a species over time  Section 1.2 Notes A. Classification of organisms  I. Taxonomy: Branch of biology identify, describing and naming organisms - also known as categories II. Systematics: Study of evolutionary relationships between organismsIII. Describe how living organisms are classified - (1) Domain: largest category - Three domains are Archea, Bacteria, and Eukarya - (2) Kingdom - (3) Phylum - (4) Class - (5) Order - (6) Family - (7) Genus - Contains species the most closely related through evolution - (8) Species - Organisms able to interbred and produce fertile offspring B. Domains I. Domain Archea: contains prokaryotic cells living in extreme habitats II. Domain Bacteria: Contains prokaryotic cells that differ from archer because they have  their own unique genetic, biochemical, physiological characteristics III. Domain Eukarya: Consisting of eukaryotic cells - Includes protists, fungi, plants, and animals IV. Domain Archea and Domain Bacteria both contain prokaryotes lacking membrane bound nucleus found in the cells of the eukaryotes V. Prokaryotes: Organism lacking a membrane-bound nucleus VI. Eukaryotes: Has a membrane-bound nucleus C. Kingdoms I. Protists: single-celled organism - Some make their own food and some ingest their food II. Fungi: molds and mushrooms that help decompose dead organisms III. Plants: multicellular photosynthesizers IV. Animals: multicellular and ingest their food  1.3 The Process of Science - Scientific method: series of steps used to gain knowledge - Steps: Oberservation, hypothesis, experiment, conclusion, support/or not support the  hypothesis  A. Hypothesis I. Inductive reasoning: a person used creative thinking to combine facts into whole II. One famous case was the antibiotic penicillin in 1928 with Alexander Flemmiing III. A hypothesis is not a guess, but an educated guess B. Predictions and Experiments I. Scientists perform an experiment  II. Experiment: series of procedures to tes a hypothesis III. To determine how to test a hypothesis, scientists use deductive reasoning IV. Deductive reasoning: if/then logic V. Experimental design: methodology in which an experiment seeking support by the  hypothesisVI. A good experiment design makes sure the scientists examine a specific variable  called the experimental variable to the observation VII. Responding variable: the dependent variable in which a change happens when an  experiment variable is used VIII. Control: does not change and does not get tested  IX. A test group get experimented, but the control group does not XI. Model: A hypothesis that describes how a particular process could possibly be  carried out - Ex: Cell biologists could use mice as a model for effects of a new drug C. Presenting and Analyzing Data I. Statistical data - Scientists who publish research articles use statistics to help them evaluate  their experimental data - In Statistics, the standard error, or standard deviation tells us how uncertain a  value is II. Statistical Significance - When they calculate the probability value (p), their results were due to chance  alone III. If probability value is low, the results are statistically significant IV. The value is less than 5% (p<0.05) V. The lower the p value, the less likely it has results due to chance D. Scientific Publications I. Published in scientific journals II. Before published, experts review the research to make sure it is accurate, credible,  unbiased, and well executed E. Scientific Theory I. Theories: concepts joined together well-supported and a related hypotheses II. A scientific theory is supported by observations, experiments, and data III. Basic Theories -Cell Theory: All organisms are composed of cells, and new cells only come from  preexisting cells -Homeostasis Theory: The internal environment of an organism stays the same -  within a range that is protective of life - Evolution Theory: A change in the frequency of traits that affects reproductive  success in a population or species across generation  F. Experimental Design I. 1 control II. 2 Test groups III. Reduce the number of variables among the groupsChapter 25 Part 1 - DNA Structure and Gene expression I. DNA is the genetic material of life A. DNA: Nucleic acid polymer produced form covalent bonding of nucleotide monomers  that contain sugar deoxyribose II. The Nature of the Genetic Material A. Griffith experiment 1. injected S strain has capsule and kills mice 2. Injected live R strain has no capsule and mice does not die  3. Injected heat-killed S strain does not cause mice to die 4. If hear-killed S strain and R strain are both injected into the mice, they die because  the R strain bacteria have been transformed into the virulent S strain B. By the 1940’s scientists recognized that genes are on chromosomes and that  chromosomes contain both proteins and nucleic acids C. Some debate about whether protein or DNA was the genetic material D. Many thought that the protein component of chromosomes must be the genetic material  because proteins contain up to 20 different amino acids that are set in any particular way E. Nucleic acids - DNA and RNA - contain only 4 types of nucleotides as basic building  blocks  1. Some argued that DNA did not have enough variability to be able to sore information  be the genetic material III. Hershey-Chase Experiment Figure 25.2 A. Finding the Structure of DNA 1953 James Watson and Francis Crick B. DNA is a polymer of nucleotides, each one having a phosphate group, the sugar  deoxyribose and a nitrogen-containing base C. Erwin Chargaff, a chemist, in the late 1940’s, decided that the number of purines in DNA  always equal the number of pyrimidines 1. The amount of adenine equals the amount of thymine (A=T) and the amount of  guanine equals the amount of cytosine (G=C) a) Known as Chargaff rules D. Rosalind Franklin, working with Maurice Wilkins prepared X-ray diffraction photograph of  DNA 1. Showed that DNA is a double helix of constant diameter and that the bases are  regularly stacked on top of one another IV. DNA Replication: DNA Structure A. DNA is a chain of nucleotides 1. Each nucleotide is a complex of 3 subunits - phosphoric acid (phosphate), a pentose  sugar (deoxyribose), and a nitrogen-containing base B. There are 4 possible bases 1. 2 of them are purines: a double ring a) Adenine b) Guanine 2. 2 of them are pyrimidines: a single ring  a) Thymine b) Cytosine 3. They attached to the sugar and go to one side 4. The 2 strands of the double helix are held together by hydrogen bonding between  the basesa) Always pairs with T by forming 2 hydrogen bonds b) G always pairs with C by forming 3 hydrogen bonds 5. Purine is always bonded to pyrimidine 6. Complementary base pairing: hydrogen bonding between particular purines and  pyrimidines 7. When the helix unwinds, it creates a ladder a) The side of the ladder are the sugar-phosphate backbones  b) The rungs of the ladder are the complementary paired bases 25.2 DNA Replication I. When the body grows or heals, cells divide A. Each new cell requires an exact copy of DNA contained in the chromosomes B. DNA replication: process of copying one DNA double helix into 2 identical double helices II. S phase of interphase during mitosis when DNA is replicated A. The double stranded structure of DNA allows each original strand to serve as a template  for the formation of a complementary new strand B. As a result, DNA replication is termed semiconservative because a new double helix  has one conserved old strand and one new strand C. Replication results in 2 DNA helices that are identical to each other and to the original  molecules D. At a molecular level, several enzymes and proteins participate in the synthesis of new  DNA strands  1. The enzyme DNA helices unwinds and and unzips the double strand DNA by  breaking weak hydrogen bonds between the paired bases 2. New complementary DNA nucleotides fit into place by the process of complementary  base pairing. These positioned and joined by the enzyme DNA polymerase. The  DNA polymerase uses each original strand as a template for the formation of a  complementary new strand 25.3 Gene Expression I. Gene expression: process of using information within a gene to synthesize a protein A. Relies on several different forms of RNA molecules 1. Messenger RNA (mRNA) 2. Transfer RNA (tRNA) 3. Ribosomal RNA (rRNA) II. Transcription: first stage of gene expression; where DNA serves as a template for the  formation of mRNA A. Takes place in the nucleus  III. Translation: sequence of mRNA bases that determines the sequence of amino acids in a  polypeptide A. Takes place in the cytoplasm  IV. Genetic information lies in the sequence of the bases in DNA, which through mRNA  determines the sequence of amino acids in a protein V. Transfer RNA assists mRNA during protein synthesis by bringing amino acids to the  ribosomes  VI. Proteins differ from one another by the sequence of their amino acids VII.Proteins determine the structure and function of cells and the phenotype of the organismsA. Figure 25.6 VIII.Transcription A. Gene: serves as a template for the production of a RNA molecules  B. All 3 classes of RNA are formed by transcription, we will focus on transcription to form  messenger RNA (mRNA) which is the first step in protein synthesis IX. Messenger RNA (mRNA) A. mRNA: carry genetic information from the DNA to the ribosomes for protein synthesis B. Formed by the process of transcription, where eukaryotes occurs in the nucleus C. Transcription begins with the enzyme RNA polymerase D. RNA polymerase: an enzyme that creates mRNA transcript by joining nucleotides  complementary to a DNA template 1. Binds to a promoter E. Promoter: a region of DNA that contain a special sequence of nucleotides F. When mRNA forms, it has a sequence of bases complementary to that of the DNA 1. A T G or C are present, then U A C or G are incorporated into the mRNA molecule 2. mRNA is a “faithful copy” of the sequence of bases in DNA G. Figure 25.7 X. Processing of mRNA A. Eukaryotic cells, the mRNA molecule, produced by transcription, called pre-mRNA, is  processed before exiting the nucleus and becoming a mature mRNA molecule B. The information that is needed to produce the functional product, like protein, is  contained in DNA sequences called exons 1. Exons: segment of mRNA containing the protein coding portion of a gene that  remains within the mRNA after splicing as occurred 2. Introns: intergeneric sequences a) Region between exons b) Do not contain information that contributes to the final structure of a protein,  these regions have important regulatory functions XI. Translation A. Second process of gene expression that leads to protein synthesis  B. Occurs in ribosome and requires several enzymes  C. Requires several different types of RNA molecules, including mRNA, tRNA, and rRNA XII.The Genetic Code A. Codon: triplet of nucleotides B. 64 possible  1. Also degenerate, most amino acids are coded for by more than one codon 2. Figure 25.9 XIII.Transfer RNA A. tRNA: molecules that bring amino acids to the ribosomes, the site of protein synthesis B. A single stranded polynucleotide that doubles back on itself such that complementary  base pairing creates a rootlike shape C. One send is an amino acid, the other is a anticodon D. Anticodon: triplet of 3 bases complementary to a codon of mRNA XIV.Ribosomes and Ribosomal RNA A. Site of translation B. Both found in the cytoplasms and on the rough endoplasmic reticulum C. Ribosomes are composed of many proteins and several ribosomal RNA’s (rRNA’s) 1. rRNA: Structural form of RNA found in ribosomes a) produced in a nucleolus within the nucleusb) The rRNA joined with proteins manufactured in and imported from the  cytoplasms to form 2 ribosomal sub units ,one small and one large c) The subunits leave the nucleus and join together in the cytoplasm to form a  ribosome when protein synthesis begins 2. A ribosome has a binding site for mRNA and 3 tRNA molecules a) Figure 25.1 1b 3. The biding sites facilitate complementary base pairing between tRNA anitcodons and  mRNA codons 4. As the ribosome moves down the mRNA molecules, new tRNA’s arrive and a  polypeptide is formed and grows longer 5. Translation terminates once the polypeptide is fully formed and an mRNA stop codon  is reached 6. The ribosome then dissociates into its 2 sub units and falls off the mRNA molecule XV.Translation requires 3 steps A. Codons of an mRNA base pair with the anticodons of tRNA molecules carrying specific  amino acids B. The order of codons determines the order of the tRNA molecules at a ribosome and the  sequence of amino acids in a polypeptide C. The process is very orderly so amino acids of a polypeptide can be sequence correctly D. Protein synthesis involves 3 steps: initiation, elongation, and termination 1. Needs all 3 to function properly XVI. Initiation  A. Initiation: the step that brings all the components of translation together B. Required to assemble mRNA, tRNA, and the large ribosomal sub unit for the start of  protein synthesis  C. Figure 25.12 D. Begins with a small ribosomal sub unit attaches to mRNA in the vicinity of the start  codon XVII.Elongation A. Elongation: the protein synthesis step where a polypeptide increases in length one  amino acid at a time  B. Figure 25.13 C. 4 steps 1. A tRNA with an attached peptide is at the p site, and a tRNA carrying the next amino  acids in the chain is just arriving at the A site 2. Once the next tRNA is in place at the A site, the peptide chain is transferred to this  tRNA 3. Energy and part of the ribosomal sub unit are needed. Energy contributes to peptide  bond formation, where it makes the peptide one amino acid longer by adding peptide  from the A site 4. Translation then occurs, the mRNA moves forward on codon length and the peptide bearing tRNA is now at ribosome P site  5. “spent tRNA wits and the new codon is at the A site and is ready to receive the next  complementary tRNA 6. Completed cycle at a rapid rate (15 times per second in bacteria) XVIII. Termination A. Termination: the final step in protein synthesis 1. Figure 25.14B. The polypeptide and the assembled components that carried out protein synthesis are  separated form one another C. Termination of polypeptide synthesis occurs at a stop codon D. Requires protein called a releases factor, which cleaves the polypeptide from the last  tRNA E. After, the polypeptide is set free and begins to take on its 3 dimensional shspe F. Ribosome dissociates into 2 sub units XIX.Review of Gene Expression A. Expressed when product, in our case a protein has been synthesizedChapter 25 DNA Structure and Gene Expression Part 2 Notes 25.4 Control of Gene Expression I. Control of Gene Expression in Prokaryotes A. Operon: a cluster of genes usually coding for proteins related to a certain metabolic  pathway, along with short DNA sequences that coordinately control their transcription B. The control sequence consists of a promoter, a sequence of DNA where RNA  polymerase first attaches to begin transcription  C. Also an operator, a sequence of DNA in the lac operon where a repressor protein binds 1. Figure 25.16 D. In lac operon, the structural genes for 3 enzymes that are needed for lactose  metabolism are under the control of 1 promoter/operator complex E. If lactose is absent, a protein (repressor) binds to the operator F. When the repressor is bound to the operator, RNA polymerase cannot transcribe the 3  structural genes of the operon G. The lac repressor is encoded by a regulatory gene located outside the operon  H. The lac operon is considered an inducible operon 1. It’s only activated when lactose induces its expression II. Control of Gene Expression in Eukaryotes A. In prokaryotes, a single promoter serves genes that make up a transcription unit or  operon  B. In eukaryotes, each gene has its own promoter where RNA polymerase binds 1. Contrast to prokaryotes, eukaryotes employ a variety of mechanisms to regulate  gene expression  a) These mechanisms affect whether the gene is expressed, the speed with which it  is expressed and how long it is expressed  III. Levels of Gene Control A. Pretranscriptional control B. Transcriptional control C. Posttranscriptional control D. Translational control E. Posttranslational control IV. Pretranscriptional Control  A. Genes with darkly staining, highly condensed portions of chromatin, heterochromatin,  are inactive B. Each in activated X chromosome, called a Barr body in honor of its discoverer, can be  seen as small, darkly staining mass of condensed chromatin along the inner edge of the  nuclear envelope C. Figure 25.17 D. Active genes in eukaryotic cells are associated with more loosely packed chromatin,  called euchromatin  V. Transcriptional Control A. Dependent on the interaction of protein with a certain DNA sequence B. Transcription factors: proteins that help RNA polymerase bind to a promoter  C. Transcription activators: proteins that speed transcription dramatically VI. Post-transcriptional Control A. Following transcription messenger RNA (mRNA) is processed before it leaves the  nucleus and passed into the cytoplasmB. The primary mRNA is converted to the mature mRNA by the addition of a poly-A-tail and  a guanine cap, and by removing the introns and splicing back together of the exons C. The same mRNA can be spliced in different ways to make a different product in different  tissues 1. EX: hypothalamus and the thyroid gland produce the hormone calcitonin, but the  calcitonin, mRNA that exits the nucleus contains different combinations of exes in the  2 tissues D. The speed of transport of mRNA from the nucleus into the cytoplasm can affect the  amount of gene product following transcription E. There is a different in length of time it takes different mRNA molecules to pass through a  nuclear pore  VII.Translational Control A. The longer an mRNA remains in the cytoplasm before its broken down, the more gene  product can be translated  B. Differences in the poly-A-tail or the guanine cap can determine how long a certain  transcript remains active before it is destroyed by a ribonuclease associated with  ribosomes C. Hormones can cause the stabilization of certain mRNA transcripts 1. EX: the mRNA for vitelline, an egg membrane protein can persist for 3 weeks if its  exposed to estrogen as opposed to 15 hours without estrogen  VIII.Posttranslational Control A. Some proteins are no active immediately after synthesis B. After translation, insulin is folded into a 3 dimensional structure that is inactive C. Then a sequence of 30 amino acids is enzymatically removed from the middle of the  molcule, leaving 2 polypeptide chains that are bonded together by disulfide (S-S) bonds D. This activates the protein E. Other modifications such a phosphorylation also affect the actively of a protein F. Many proteins only function a short time before they are degraded or destroyed by the  cell  G. Figure 25.18 25.5 Gene Mutations and Cancer I. Gene mutation: a permanent change in the sequence of bases in DNA A. Gene mutation may have a variety of effects on a cell 1. EX: it may change how the gene is expressed in the cell 2. EX: may also change the structure of a protein so that its function is altered, or  completely inactivated B. Mutation is the remainder of the cells of the body C. Somatic cells: passed on to daughter cells by cell division 1. Not passed to future generation but may lead to the development of cancer II. Causes of Mutations A. Some are spontaneous - they happen for no reason - where others are induced by  environmental influences B. Spontaneous mutations: arise as a result of abnormalities in normal biological processes C. Induced mutations: result from exposure to toxic chemicals or radiation that cause  changes in the base sequence of DNA III. Mutagens A. Mutagens: environmental influences that cause mutations in humansB. include radiation, radioactive elements, X-rays, UV radiation and certain organic  chemicals IV. Transposons A. Transposons: specific DNA sequences that have the remarkable ability to move within  and between chromosomes B. Their movement to a new location sometimes alters neighboring genes, particularly by  increasing or decreasing their expression C. Figure 25.19 V. Effects of Mutations on Protein Activity A. Point mutations: involve a change in a single DNA nucleotide 1. Alters transcription and possibly changes the specific amino acid B. Base substitution: one type of point mutation that results in one DNA nucleotide being  replaced with another incorrect nucleotide 1. Figure 25.20 Note that the base different in the second row and how it changes the  resultant amino acid sequence  C. Figure 25.20 1. Frameshift mutations occurs most often because one or more nucleotides are either  inserted or deleted from DNA 2. The result from it can be a completely new sequence of codons and nonfunctional  protein 3. How it occurs: the sequence of codons is read from a specific starting point, as in  this sentence (the cat are the rat). If the C is deleted from this sentence and the  reading frame is shifted we read (the ata tet her at) which is something that doesn’t  make sense VI. Mutations cause cancer A. In the U.S the 3 deadliest forms of cancer are lung cancer, colorectal cancer, and breast  cancer  B. Cancers vary greatly, they usually follow a common multistep progression 1. Most cancers begin with benign 2. Benign: abnormal cell growth that is not cancerous and does not grow larger 3. Figure 25.22 VII.Benign VS Malignant Tumors A. Cancer cells continues is unregulated division, it may form a population of cells called a  tumor  VIII. Characteristics of Cancer Cells A. Cancer cells are genetically unstable 1. Generation of cancer cells are linked to mutagenesis 2. Cell acquires a mutation that allows it to continue to divide 3. One of the progeny cells will acquire another mutation and gain the ability to form a  tumor 4. More mutation occurs and the most aggressive cell becomes the dominant cell of the  tumor 5. Tumor cells undergo mutations and also tend to have chromosomal aberrations and  rearrangements B. Cancer cells do not correctly regulate the cell cycle 1. Normal controls do not operate to stop the cycle and allow the cells to differentiate 2. Because of that, cancer cells tend to be nonspecialized  3. Both rate of cell division and number of cells increase  C. Cancer cells escape the signals for cell death1. A cell that has a genetic damage or problems with the cell cycle will initiate  apoptosiss or programmed cell health 2. But cancer cells do not respond to internal signals to die and they continue to divide  even with genetic damage 3. Cells from the immune system when they detect an abnormal cell, will send signals  to that cell, inducing apoptosis  4. Cancer cells also ignore these signals D. Telomeres: sequences at the ends of chromosomes that keep from fusing with each  other 1. Each cell division, the telomeres shorten and get short enough to signal apoptosis  2. Cancer cells turn on the gene that encode the enzyme telomere, which is capable of  rebuilding and lengthening the telomeres E. Cancer cells can survive and proliferate elsewhere in the body 1. Many of the changes that occur for cancer cells to form tumors elsewhere in the  body are not understood 2. They disrupt normal adhesive mechanism and move to another place in the body 3. Metastasis: travel through the blood and lymphatic and the invade new tissues where  they form tumors 4. Angiogenesis: as a tumor grows, it must increase its blood supply b forming new  blood vessels IX. Prevention of cancer A. Be tested B. Be aware of occupational hazards C. Use sunscreen D. Check your home for radon E. Avoid unnecessary X Rays F. Practice safe sex G. Carefully consider hormone therapy H. Maintain a heathy weight I. Exercise regularly  J. Increase consumption of foods that are rich in vitamin A and C K. Include veggies from the cabbage family in your diet L. Limit consumption of salt-cured, smoked, nitrite-cured foods M. Be moderate in the consumption of alcohol N. Don’t smokeChapter 25 - DNA Structure and Gene Expression Lecture Notes I. Will not cover The Nature of Genetic Material (p 497-498)  II. Will not cover 25.4 Control of Gene Expression I. DNA and RNA are polymers of nucleotides A. DNA and RNA are nucleic acids consisting of long hairs (polymers) of chemical units  (monomers) called nucleotides II. 4 DNA Nucleotides A. Each type of DNA nucleotide has a different nitrogen-containing base 1. Adenine (A) 2. Cytosine (C) 3. Thymine (T) 4. Guanine (G) III. RNA is also a polymer of nucleotides A. DNA  1. Nucleic referring to DNA’s location in the nuclei B. RNA is unlike DNA in that it 1. Uses the sugar ribose (instead of deoxyribose in DNA) 2. Has a nitrogenous base uracil (U) instead of thymine 3. Is single stranded  IV. Discovery of the structure of DNA A. James Watson and Francis Crick worked out a 3 dimensional structure of DNA< based  on work by Rosalind Franklin B. The structure of DNA consists of 2 polynucleotide strands wrapped around each outer in  a double helix  V. Structure of DNA A. 4 possible bases 1. 2 purines a) Adenine b) Guanine 2. 2 pyrimidines a) Thymine b) Cytosine B. DNA is a polynucleotide strand with a backbone of alternating phosphate and sugar  groups  C. 2 strands make up a double helix D. 2 strands are held together by hydrogen bonding 1. Complementary Base Pairing a) Adenine always pairs with Thymine b) Guanine always pairs with Cytosine  VI. DNA Replication A. DNA replication: the process of copying one DNA double helix into 2 identical double  helices B. DNA polymerase: the key enzyme in DNA replication 1. Semiconservative replication uses each original strand as a template to produce a  new complimentary strand C. Semiconservative Replication 1. Each daughter DNA molecule consists of one new chain of nucleotides and one from  the parent DNA molecule  2. Daughter DNA molecules identical to the parent molecule  D. Steps 1. Strands start as hydrogen bonded 2. DNA helicase: unwinds and unzips the double stranded DNA 3. New strands built complementary base pairing of nucleotides by DNA polymerase 4. DNA ligase seals and breaks in the sugar-phosphate backbone 5. The 2 double helix molecules are identical to each other and to the original DNA  molecule  VII.Gene Expression A. Gene expression: the process of using a gene sequence to synthesize a protein 1. Depends on different types of RNA (ribonucleic acid) a) Messenger RNA (mRNA) b) Transfer RNA (tRNA) c) Ribosomal RNA (rRNA) 2. Depends on 2 processes a) Transcription (1) In the nucleus (2) Part of DNA serves as a template for mRNA formation (3) During transcription, a gene (segment of DNA) serves as a template to  produce an RNA molecule  b) Translation (1) Takes place in the cytoplasm (2) Sequence of mRNA bases determines the sequence of amino acids in a  polypeptide (3) tRNA assists by bringing amino acids to the ribosome VIII.Messenger RNA (mRNA) A. Messenger RNA carries genetic information form DNA to the ribosomes B. mRNA is formed by the process of transcription C. First RNA polymerase binds to a promoter (in DNA) D. The RNA polymerase adds complementary RNA nucleotides to DNA  E. Processing of mRNA 1. Primary RNA contains to both introns and exons a) Introns: intragene segments which get removed b) Exons: are the portion of a gene that is expressed  2. A guanine cap is added at one end 3. A poly-A-tail is added to 3’ end 4. The mature mRNA molecule is ready (read and turns into protein) IX. Translation A. Creation of proteins from RNA sequence B. Translation requires several enzymes and different types of RNA molecules 1. mRNA 2. tRNA 3. rRNA C.Lecture Notes Chapter 6 I. Metabolism: sum of all the chemical reactions in a cell A. Breaking down and building up of molecules 1. Catabolism: breaking down molecules 2. Anabolism: Building molecules II. Energy transformations and metabolism A. exergonic reactions: are one where energy is released 1. Products have less free energy than reactants 2. Spontaneous B. Endergonic reactions: require n input of energy 1. Products have more free energy than reactants 2. Require an input of energy to run C. ATP: energy for cells 1. ATP stands for adenosine triphosphate a) Common energy currency for cells b) ATP generated from ADP+ phosphate molecule (P) c) Glucose breaking down provides the energy to build up ATP d) Mitochondria is the main organelle that recycles ADP and inorganic  phosphate into ATP D. Coupled reactions 1. The energy released by an exergonic reaction i used to drive an endergonic  reaction  III. Enzymes and Metabolic Pathways A. enzymes: proteins that function as catalysts to speed up chemical reactions 1. Ribozymes are RNA’s that can act as catalysts 2. Participate in chemical reactions, but are not used up by the reaction B. Metabolic pathway: series of linked reactions 1. Reactions do not occur haphazardly in cells 2. Begin with a specific reactant and product an end product 3. Metabolic energy is captured and utilized because it is released in increments  IV. Energy of Activation A. Energy that must be added to cause reactants to react with one another 1. Need a match to start wood burning B. Enzymes lowers the energy of activation 1. Do not change the end result of the reaction 2. Increase the reaction rate V. How enzymes function A. An enzyme binds with a substrate to form a complex B. The active site is a small part of the enzyme that complexes with the substrate C. The following equation indicates the sequence of steps in an enzyme catalyzed  reaction D. Enzyme + substrate -> enzyme-substrate complex -> product  E. Each reaction requires a specific enzyme F. Enzymes are often animus for their substrate because they only complex with  their substrateG. -ase = enzyme VI. Factors affecting enzymatic speed A. Substrate concentration 1. More collisions between substrate and enzyme 2. As more active sites are filled with substrate, more product will form B. Temperature and pH C. Enzyme activation D. Enzyme inhibition E. Enzyme cofactors F. Substrate concentration VII. Temperature A. Enzyme activity increases as the temperature rises B. Higher temperatures cause a larger number of effective collisions between  enzymes and substrates  VIII.pH A. Each enzyme has an optimal pH at which its activity is the highest B. Enzyme structure is also pH dependent C. Extremes of pH can denature an enzyme by altering its structure  IX. Enzyme Inhibition A. Feedback inhibition: when product is abundant it binds to enzyme’s active site  and blocks further production 1. When product is used up it is removed from the active site a) Enzyme begins to function again 2. Or product binds to a site other than the active site, which changes the shape  of the active site a) Poison are often enzyme inhibitors (1) Cyanide inhibits an essential respiratory enzyme (2) Penicillin blocks the active site on a bacterial enzyme

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