BIO 1027 Exam 2 Highlights

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Universal features of all cells

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Universal features of all cells

Plasma membrane Cytosol Chromosomes Ribosomes

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What kingdoms are prokaryotic

Bacteria and Archaea

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Prokaryotic lack

Nucleus, cytoskeleton, and membrane bound organelles

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Prokaryotic have

Nucleoid Cytoplasm bounded by plasma membrane Fimbriae Cell wall

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What do Eukaryotes have

DNA in nucleus Membrane bound organelles Cytoplasm between plasma membrane and nucleus Cytoskeleton

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What do animal cells lack

Chloroplast Cell wall Central Vacuole

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Nuclear membrane

2x lipid bi layer; inner and outer

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Nuclear Pore

allows transport in and out

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Nuclear Lamina

Reinforces envelope

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Nucleolus

integral ribosomal molecules produced here

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Where are ribsomes found

Cytosol and ER/nuclear envelope

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What makes up the Endomembrane system

Nuclear Envelope ER Golgi Lysosome Vacuole Plasma membrane

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Smooth ER

No Ribosomes Synthesizes lipids Metabolizes carbs Detoxifies drugs/poisons Stores Ca ions

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Rough ER

Ribosomes Secretes glycoproteins Distributes transports vesicles Membrane factory

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Microfilaments (Actin)

Maintain/changes cell shape Muscle contraction Cell motility Cell division

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Intermediate filaments

Maintain cell shape (tension bearing) Anchor Nucleus and other organelles Formation of nuclear lamina

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Microtubules

Maintain cell shape (Compression ressisting) Cell motility (cilia and flagella) Chromosome movement (cell division) Organelle movement Is hollow; has space

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How to Prok and Euk flagella differ

Prok whips around like a weed wacker with t solid protein rod while Euk is more like an animal tail with a sheath

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Extracellular matrix

Replaces cell wall in animal cells Composed of glycoproteins (collagen, proteoglycans, and fibronectin) Binds to receptor proteins in plasma membrane (integrins)

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Plasmodesmata

Plant only Perforate plant cell walls Water and small solutes pass from cell to cell

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Tight Junction

Prevent leaking of extracellular fluid

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Desmosomes

Fastens cells together in sheets

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Gap junction

Provide channels between adjacent cells (communication)

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how phospholipids self-assemble into membranes with both hydrophilic and hydrophobic portions

Due to the watery environment the heads and tails orientate themselves spontaneously

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fluid mosaic model and how proteins are embedded into phospholipid bilayers

The bi-layer creates a semipermeable membrane in which proteins are embedded, much like a blueberry muffin

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six major functions of membrane proteins

Transport Enzymatic Signal transduction Cell-cell recognition Intercellular joining Attachment to cytoskeleton and ECM

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27

Explain how membrane proteins are produced and added and how membranes have distinct faces

Membrane proteins are manufactured in the ER taken to the Golgi body where they are packaged into and vesicle and released into the cell membrane through exocytosis

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28

How does water get through the bi-layer

Water, although polar, can easily pass through due to its size and abundance

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how polar molecules and ions may move across a membrane without input of energy

Transport proteins Channel proteins Aquaporins Carrier protein

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Transport proteins

allow passage of hydrophilic substances

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Channel proteins

hydrophilic channel that certain molecules/ions can use as a tunnel

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Aquaporins

Channel proteins specifically for the facilitation of water

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Carrier protein

bind to molecules and change shape to shuttle them, specific for the substance it moves

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Isotonic

Solute concentration is the same inside and out

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Hypertonic

Solute concentration is greater relative to the other solution

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Hypotonic

Solute concentration is lesser relative to the other solution

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37

Why do organisms osmoregulate

Organisms must osmoregulate in order to maintain homeostasis and continue living

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38

Explain the sodium-potassium pump and how it uses energy to create electrochemical gradient/membrane potential

It loads in Na ions from the cell into the active site of the protein (Na concentration is low inside the cell and high outside) Atp is attached and causes the protein to change shape releasing the Na ions outside the cell and accepting Potassium ions It changes shape again releasing potassium ions inside the cell and repeats This creates membrane potential (voltage difference across a membrane) The voltage is created by a difference in the distribution of + and - ions

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Metabolism

totality of an organism's chemical reactions

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Catabolic pathways

release energy by breaking down molecules into simpler forms Ex. Hydrolysis and cellular respiration

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Anabolic pathway

consume energy to build complex molecules; EX. synthesis of proteins

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Bioenergetics

study of how organisms manage energy resources

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Thermodynamics

The study of how energy is transformed

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first two laws of thermodynamics

Energy cannot be created or destroyed Every energy transfer increases the entropy (disorder) of the universe; every energy transfer is less than 100% efficient

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How do the laws of thermodynamics relate to organisms

The energy of a living organism is consumed by another (transfer of energy) that organisms then runs using that energy to power its movement, but some of the energy is given off as heat and is therefore “lost”

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Spontaneous reaction

occur without energy input; increases entropy; - delta G; free energy decreases and stability increases

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Nonspontaneous reaction

occurs with input of energy; decreases entropy; + delta G; increase free energy and decrease stability

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48

Explain how organisms create order legally while increasing entropy

During the creation of more ordered materials from less ordered materials, some of the less ordered materials used become even more disordered Entropy decreases in an organism but increases overall in the universe

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Free energy

measure of instability and its tendency to change to a more stable state

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50

Explain how spontaneous reactions release energy, increase stability, and increase entropy and non-spontaneous reactions absorb energy, decrease stability, and entropy

Spontaneous reactions release free energy because they do not need an energy input to trigger instead they release it They increase stability by increasing entropy and moving towards equilibrium Non-spontaneous require energy to trigger and therefore consume it They decrease entropy therefore increasing instability

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51

Explain how cells use ATP hydrolysis to drive endergonic processes

ATP couples Exer and Endergonic reactions (uses exer to drive ender) The hydrolysis of ATP breaks off a phosphate group producing a burst of energy used to drive reactions

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52

Explain how cells use ATP hydrolysis to make endergonic reactions exergonic by producing phosphorylated intermediates

ATP attaches ammonia to Glutamic acid in an endo reaction and as a result gets glutamine, ATP, and a gamma phosphate Overall glutamine is much more energy efficient than the starting molecules so although energy was used the net benefit of energy in the end is worth it

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Catalyst

chemical agent that speeds up a reaction without being consumed

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Enzyme

catalytic protein; lower activation energy

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Activation energy

initial energy needed to trigger a chemical reaction (often thermal)

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Substrate

the reactant that an enzyme acts on

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Enzyme-substrate complex

when the enzyme binds to the substrate it forms this

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Active site

the region on the enzyme where the substrate binds

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Induced fit

brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction

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Cofactor

non protein enzyme helper

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Coenzyme

organic cofactor (vitamins)

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Competitive

bind to active site of an enzyme and compete with substrate

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Noncompetitive

bind to another part of an enzyme causing it to change shape and make it less effective

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Allosteric

can either inhibit or stimulate enzyme activity; occurs when a regulatory molecule binds to a protein at one site and affects the proteins function at another site

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Cooperativity

substrate attaches to one part of the proteins and makes the rest of it more efficient; type of allosteric

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66

Explain how energy enters and leaves ecosystems

Energy enters ecosystem through light energy from the sun and leaves through heat

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formula for respiration

C6H12O6+6O2 →6CO2+6H2O+ATP+heat

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redox reactions

Transfer of electrons during a chemical reaction, releases stored energy that is used to synthesize ATP

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69

Recount the order of steps in glycolysis

breaking down glucose to two pyruvate, producing net 2 ATP, 2 NADH+H, and 2H20 (in cytosol)

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70

Recount the order of steps in pyruvate oxidation

Pyruvate oxidation → turning pyruvate into Acetyl CoA → releasing CO2 and converting NAD+ to NADH + H and introducing Coenzyme A to create Acetyl CoA (PER PYRUVATE/DOUBLE FOR PER GLUCOSE)

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71

Recount the order of steps in citric acid cycle

PER PYRUVATE (double for glucose), CIKSSFMO, succinate is late → produces 1 ATP (G3P swap with ADP), 3 NADH, 1 FADH2, and 2CO2

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72

Recount the order of steps in Oxidative phosphorylation

electron goes through ETC to produce 26-28 ATP and 2H20 along with oxidizing NADH and FADH2 to NAD+ and FAD

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73

Explain the role of electron shuttles such as NAD+ and FAD in cellular respiration

NAD+ picks up electrons in glycolysis in the energy payoff phase, as well as oxidizing pyruvate once the CO2 is drawn out, as well as taking electrons from citrate, isocitrate and malate becoming NADH in the Citric Acid Cycle. FAD is only present in the CAC where it picks up electrons off succinate to become FADH2

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substrate-level phosphorylation

when a substrate with a phosphate is bound to an enzyme where an ADP molecule attaches, catalyzing the reaction, binding the phosphate to ADP to create ATP and release the substrate. This occurs in glycolysis and the citric acid cycle

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oxidative phosphorylation

Oxidative phosphorylation is the process of producing ATP through a proton pump concentration gradient

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starting and finishing materials, 2 phases, and the organism that preform glycolysis

Glycolysis starts with a glucose where it then goes into the energy investment phase, where 2 ATP is invested and broken down into 2 ADP and 2 phosphate groups, where then in the energy payoff phase, 4 ADP + 4 Pi is used, and 2 NAD+ is used to produce 2 pyruvate, but also creates a NET of 2 ATP (4 ATP produced overall), 2 H20, and 2 NADH + H+ is produced (this is PER GLUCOSE) THIS PROCESS IS OXYGEN INDEPENDENT and was believed to be an ancient process used to produce energy when O2 was not abundant

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77

For pyruvate oxidation recognize the starting and finishing materials, and where it occurs in the cell

We start with a pyruvate then crossing into the mitochondria we release CO2 and have an electron taken by NAD+ (converting it to NADH +H) before incorporating CoA to make Acetyl CoA

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78

For the citric acid cycle recognize the products and where it occurs in the cell; distinguish between per turn of calculations and per glucose molecule calculations

The CAC occurs in the cristae of the mitochondria (between the folds of the membranes) where it takes in an acetyl CoA, combining it with oxaloacetate to make a 6C citrate, then CO2 is taken out and NAD+ takes an electron to make NADH, then it moves onto Isocitrate which also loses CO2 and an electron to NAD+, then it continues on, CoA reoccurs attaching to succinyl to make succinyl CoA where GDP/G2P comes and grabs a phosphate to become G3P, from there ADP swaps (substrate level phosphorylation) to form ATP and G2P. From S to F, FAD takes an electron and becomes FADH2. Lastly, between M and O, NAD+ takes more electrons becomes NADH, where oxaloacetate is reformed and ready for another crank PRODUCTS FOR ONE CRANK (ONE PYRUVATE/DOUBLE FOR ONE GLUCOSE): 3 NADH, 1 FADH2, 2 CO2, and 1 ATP (from G3P)

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79

For Oxidative phosphorylation (OP) explain the transfer of energy from electrons to the proton motive force to ATP, describe where OP takes place; understand that OP is not the only process that consumes oxygen and that oxygen is converted to water (not CO2); describe ATP synthase; describe how OP produces the great majority of ATP in cellular respiration

OP occurs between the outer and inner membranes of the mitochondria. It begins with NADH dropping off 2 electrons at protein complex I where the electrons power the transport protein and move to complex II. This activity/release of energy stimulates complex I to start pumping H+ protons from the matrix (inner area of mito.) to the intermembrane space (between outer and inner membrane) against the concentration gradient. Then, FADH2 drops 2 more electrons to join the other two at complex II, which causes them to release energy and move across complexes III and IV. These complexes begin to pump ions across the membrane into the intermembrane against the gradient. O2, being the best terminal electron acceptor, picks up the electrons (2 electrons per O2) to form 2 H2O (PRODUCT). The ATP synthase is basically made of a rotor (spinning clockwise), with a stator embedded in the membrane to hold it and a rod spinning with the rotor. The rod spins the knob which contains the catalytic sits where ADP + P to form ATP. As the H+ ions run through the rotor, they spin it, activating the knob to catalyze the synthesization of ATP. In comparison to the 2 ATP in glycolysis and 1 in the CAC, OP creates 26-28 ATP, much more than any of the other processes

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80

Lactic acid fermentation

Glucose goes through glycolysis creating 2 ATP and 2 NADH, as well as 2 Pyruvate (also water but not important to this). The pyruvate has NADH drop off its electrons to it and produce lactate, to recycle the NADH to NAD+ so it can be reused in glycolysis

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81

Alcohol fermentation

Glucose goes through glycolysis creating 2 ATP and 2 NADH and 2 Pyruvate (and 2 H2O but not important). The pyruvate release CO2 to become acetaldehyde and NADH drops off electrons (Recycling to NAD+) to form ethanol (OCCURS IN YEAST)

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82

Anaerobic respiration

all the same steps as aerobic except the terminal electron acceptor is NOT oxygen, rather something like sulfate or iron, and due to them not being as electronegative, it doesn’t push as many H+ and thus less ATP is produced compared to aerobic respiration

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83

What's the difference between lactic and ethanol fermentation

Ethanol fermentation first pulls CO2 out of pyruvate before reducing the acetaldehyde to ethanol to recycle NAD+ and only occurs in yeast; Lactic simply reduces the pyruvate to lactate to recycle NAD+

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terminal electron acceptors other than oxygen used in anaerobic fermentation

Sulfate and iron as well as nitrate

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85

Why do differing electron acceptors produce less ATP than oxygen

These produce less since O2 has a stronger electronegativity and is able to pull more electrons, which leads to creating more ATP than one of the other TEAs

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86

molecules other than glucose can be used to produce energy in cellular respiration

Proteins can be broken into amino acids which can used in pyruvate (and NH3), acetyl CoA, or used in the citric acid cycle Fats can be used with the glycerol forming the glyceraldehyde in glycolysis (the end of energy investment phase molecule) or the fatty acids forming parts of acetyl CoA

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87

Explain the value of photosynthesis to life on earth

Photosynthesis feeds the biosphere and recycles CO2 into oxygen, which most organisms need to survive

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88

Name organisms that are capable of photosynthesis

photoautotrophs/autotrophs, algae (macro- like kelp and seaweed and micro, which are eukaryotic photosynthetic protists), purple sulfur bacteria and haloarchaea (but no PS II, can only do cyclic photorespiration)

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89

Contrast autotrophic organisms and heterotrophic organisms

Autotrophs create their own food without eating anything, the producers of the biosphere, producing organic molecules from CO2 and other inorganic molecules

Heterotrophs obtain organic molecules from other organisms and are the consumers of the biosphere, depending on autotrophs for food and O2

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90

Recognize the structures with a plant leaf that contribute to photosynthesis

Stoma: leaf pores that let CO2 in and O2 out Mesophyll: tissue in between leaf where 30-40 chloroplasts are (in each mesophyll cell) Chloroplast: houses chlorophyll and thylakoid, where photosynthesis occurs Stroma: Where dark reaction occurs, liquid substance in cytoplasm Grana: stacks of thylakoid Thylakoid: membranous sacs where the light reaction occurs in the membrane, contain chlorophyll pigments on surface Chlorophyll: pigment that reflects green light that powers the light reaction

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91

Recognize the anatomy of a chloroplast and the role of each part in photosynthesis

The chloroplasts contain the stroma (where Calvin cycle occurs, where glucose is made) which is its liquid inside

Contains thylakoid where the light reaction happens in the membrane

Chlorophyll: pigment that reflects green light and powers the photosystems in the light reaction

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92

Recognize the formula for photosynthesis and its relationship to the formula for cellular respiration

Light + 12 H2O + 6 CO2 → C6H12O6 (glucose) + 6 O2 (+ 6H2O)

Changing energy to glucose rather than in CR where we turn glucose into energy, reverses electron flow compared to CR

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93

Describe electromagnetic radiation and how it is used in photosynthesis, the relationship between wavelength, energy, and frequency

Smallest to largest: Gamma, xray, UV (all of these previous are ionizing, meaning they do damage and are smaller and more powerful than visible light), visible light (ROYGBIV), Infrared, Microwaves, and Radiowaves

Different chlorophyll pigments pick up different wavelengths with A and B picking up mostly blue and purple and red (reflecting green) and carotenoid picking up only blue and purple (reflecting orange)

The smaller the wavelength (crest to crest), the more energy it has

For visible light, purple light has the smallest wavelength, highest frequency and most energy, red being its opposite (of all that)

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94

Relate photopigments to the absorption of visible light

Different chlorophyll pigments pick up different wavelengths with A and B picking up mostly blue and purple and red (reflecting green) and carotenoid picking up only blue and purple (reflecting orange)

Pigments will reflect light (what we perceive the color to be), absorb it as photons, or transmits it (goes through it, also why we perceive certain colors of things)

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95

Understand the two essential components of photosynthesis: the light reactions and the Calvin Cycle

Light reaction: in thylakoid membrane, has PS II (680P), Plastoquinone, Cytochrome Complex which pumps H ions into the lumen from the stroma, Plastocyanin, then PSI where it goes to Ferredoxin then NADP+ reductase where they are picked up by NADP+ and it turns into NADPH

Calvin Cycle: in stroma, made of carbon fixation, reduction, and regeneration, produces 9 ADP, 6 NADP+, and 1 G3P per crank

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96

LIGHT REACTIONS: describe linear electron flow (aka Z-Scheme) and cyclic electron flow; contrast the products of the two light harvesting reactions and the two photosystems; explain how ATP is produced by ATP synthase in the thylakoids; understand how oxygen is produced by photosynthesis

Z-scheme: Water is split by PSII and electrons are 2 electrons are taken up → PSII chlorophyll harvests light energy that excites the electrons, they are accepted at the top of PS II then move down PQ, CC which releasing energy causes the H+ ions to move through into the lumen (creating gradient) which leads to the production of ATP, then electrons go through PC to PSI where the P700 chlorophyll excited the electrons again where they head up to ferredoxin into NADP+ reductase and are picked up by NADP+ which forms NADPH

Cyclic electron flow: NO PS II, electrons are excited, sent through ferredoxin then transported to cytochrome complex where they power the hydrogen pump and thus allowing ATP synthase to run and create ATP, then it flows to plastocyanin and back into PSI where it gets recycled and the cycle continues, believed to protect plants from harsh sunlight and be more ancient, it also generates ATP surplus

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97

Relate the structure of chloroplasts to the structure of mitochondria

Both have an electron transport chain that occurs in the membranes, with it being in the thylakoid in photosynthesis and in the cristae of the mitochondria

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98

CALVIN CYCLE: describe the three parts of the cycle; understand the products; explain the role of rubisco

3CO2 and 3RuBP combine together and then are broken down by rubisco (an enzyme) into 6 molecules of 3-PGA (carbon fixation - fixing the carbon from CO2 to RuBP), which after charged with 6 ATP and 6 NADPH (gaining electrons, reduced - reduction) it becomes 6 G3P, 5 of which continues on to RuBP regeneration, 1 that goes onto to become glucose (2 G3P needed to make glucose!), the 5 G3P then is charged with 3 ATP to make 3 RuBP again (regeneration).

The product of the CC is 9 ADP, 6 NADP+ and one G3P, and after 2 cranks: 18 ADP, 12 NADP+, and one GLUCOSE molecules

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99

PHOTORESPIRATION: explain why it happens and how plants avoid photorespiration spatially (C4 Plants) or temporally (CAM Plants)

Photorespiration is when Rubisco might pick up O2 instead of CO2 for the CC which causes to the loss of already fixed carbon, wasting energy and decreasing sugar synthesis, it occurs in hot, dry conditions where there is a lot of O2 and little CO2, which could be do the stomata being close din hot conditions to keep water in, allowing little O2 out Rubisco has a high affinity for O2 when it is hot, but when it is mild or cool, it is easier for rubisco to bind to CO2

Most plants, C3 variety, have no special features to prevent this

C4 plants minimize photorespiration by using KRANZ ANATOMY separating the CO2 fixation site from the rest of the calvin cycle. In C4 plants, the light reaction occurs in mesophyll cells while the calvin cycle, instead of occurring in the stroma of those same cells, occurs in bundle-sheath cells (protecting cells around leaf veins). When the CO2 is received in the mesophyll, PEP Carboxylase (NOT RUBISCO) affixes it to oxaloacetate which is converted to malate then sent to the bundle sheath cell where it is broken down into CO2, which is used by rubisco to make sugars, but the remaining pyruvate is phosphorylated by ATP into PEP, which is affixed to CO2 by PEP carboxylase and is started all over. This ATP use can be a toll, but compared to reducing photorespiration, this is ok. This includes crabgrass, sugarcane, and corn, which are common in hot areas but not so much in cooler areas (SPATIAL SEPARATION)

CAM (crassulacean acid metabolism) pathways separate the light dependent and independent (CC) by time of day. At night, the CAM plants open stomata, bringing in CO2 which is fixed onto PEP by PEP carboxylase just like in C4, but then this oxaloacetate is converted into malate or another organic acid that is stored in the vacuoles until day. When day arrives, CAM plants keep stomata closed, but they photosynthesize by releasing these organic acids out of the vacuole which can be broken down to release CO2, which goes through CC. All of this is temporal spacing to maintain a high CO2 concentration around Rubisco. It also uses ATP like C4 plants. It is seen in plants like succulents or pineapples, or plants that are water efficient since they only open stomata on cooler, more humid nights compared to hot, dry days, which helps maintain water.

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