Warm-Up 12/5

Apical meristems	Lateral meristems
Occur in the tips of stems and roots	Occur between xylem and phloem in stems
Produces soft tissues	Produces hard xylem tissue: wood
Lengthens roots and stems	Widens stems to support the weight of tall plants
Allows plants to develop special structures like leaves and flowers	Allows trees to grow tall, helping them to compete effectively for light.
Found in all phyla of plants	Absent in mosses and horsetails.

2. Plants use hormones to control the growth of roots and stems. When a plant releases a growth hormone in response to an external stimulus we call the resulting directional growth a tropism.

One type of tropism is phototropism: growth in response to light. Phototropism may be either positive (towards the light) or negative (away from the light).

Phototropism requires the absorption of light by proteins known as phototropins. Phototropins change to a new conformation (a new shape) when they absorb certain wavelengths of light. The new shape causes phototropins to act as ‘on switches’ for a gene that regulates the activity of auxins.

Auxins cause cells to become longer. Therefore, by releasing auxins on one side of a stem but not on the other side, a stem will bend because one side becomes longer than the other.

When a stem detects directional light it moves auxins from its sunny side to its shady side, which causes the shady side to bend toward the light. Bending toward light allows plants to absorb more sunlight and be able to photosynthesize at a faster rate.

Auxins cause cells to become larger in the following way: 1) they cause cells to actively transport hydrogen ions out of the cell, making the outside acidic; 2) the acid outside the cell makes the cell wall softer; 3) softer cell walls make the cells more stretchable; and 4) stretchy cells are bigger because the internal pressure inside the cell causes the cell wall to bulge out.

3. The xylem is a system of long hollow tubes responsible for replacing water lost during transpiration and photosynthesis. The xylem is made of two kinds of cells: tracheids and vessels. Xylem cells die before they are functional: after they die they become long, narrow tubes with pores at each end that allow water to pass through them.

The xylem sap moves from roots, through the stem, to the leaves without any energy being spent by the plant.

Three processes cause water to rise up the xylem tube:

Root pressure: Water moves into roots by osmosis because the roots have high concentrations of solute. This causes a positive pressure that forces sap up the xylem towards the leaves. Root pressure is highest in the morning before the stomata open and allow transpiration to begin.

Capillary action: The xylem is a long tube that is microscopically thin. When water molecules contact the surface of the xylem there is adhesion. Adhesion tends to pull water molecules upward by a process called capillary action.

Transpiration pull: When water molecules evaporate from leaves the water potential drops at the stomata. The low pressure then pulls new water molecules towards the stomata from the xylem vessels. As these water molecules move they pull on water molecules behind them due to cohesion (caused by hydrogen bonding). The pull is transmitted from one water molecule to the next, all the way to the roots.

Warm-Up

Embryo	The dicotyledons embryo has two cotyledons.	Monocotyledons have one cotyledon.
Leaf venation	Leaf veins are reticulated (branched).	Leaf veins are parallel.
Flowers	Petals in multiples of four or five. May bear fruit ( if tree)	multiples of three
Secondary growth	Often present	Absent
Stem and vascular system	Bundles of vascular tissue arranged in a ring. The vascular system is divided into a cortex and stele.	Bundles of vascular tissue scattered throughout the stem with no particular arrangement, and has no cortex.
Pollen	Pollen with three furrows or pores	Pollen with a single furrow or pore
Examples	Legumes (pea, beans, lentils, peanuts) daisies, mint, lettuce, tomato, oak, tree, etc.	Grains, (wheat, corn, rice, millet) lilies, daffodils, sugarcane, banana, palm, ginger, onions, bamboo, sugar, cone, palm tree, banana tree,grass
Root Pattern	Taproot system	Fibrous roots
Presence or absence of wood	both herbaceous and woody	herbaceous
# of seed leaves	2 seed leaves	1 seed leaf

2. Stem tubers are produced by the stems of some plants. They are used by plants to over-winter and re-grow the next year and as a means of asexual reproduction. Example: ceropegia. A root tuber is an enlarged root that functions as a storage organ. Root tubers store nutrients over periods when the plant can not actively grow, thus permitting survival from one year to the next. Example: sweet potatoes. A bulb is an underground shoot that has modified leaves that are used as food storage organs by a dormant plant. A bulb contains food reserves to enable the plant to survive adverse conditions. Roots emerge from the underside of the base, and new stems and leaves from the upper side. Example: Onions. A tendril is a specialized stem or leaf with a threadlike shape that is used by climbing plants for support and attachment, generally by twining around whatever it touches. Example: garden peas.

Warm Up

1.        Denaturation is when a protein or nucleic acid loses some to all of its function. 

2.      

3.       A competitive inhibitor has a molecular shape similar to the enzyme itself, and binds to the substrate on the active site, thus blocking the enzyme from binding. A noncompetitive inhibitor does not anywhere near the active site, instead it bind to the substrate at another location on its surface.

4.       INDUCED FIT MEANS THAT THE ENZYME RECOGNISES THE SUBSTRATES THEN SLIGHTLY CHANGES IT'S SHAPE, BRING THE TWO SUBSTRATES TOGETHER. LOCK AND KEY----THE SUBSTRATE FITS EXACTLY INTO THE ACTIVE SITE OF THE PROTEIN

Warm-Up 11/4

1. Draw and label a diagram showing the structure of a chloroplast as seen in electron micrograph a

2. Photophosphorylation is the production of ATP using the energy of sunlight. Photophosphorylation is made possible as a result of chemiosmosis. Chemiosmosis is the movement of ions across a selectively permeable membrane, down their concentration gradient. During photosynthesis, light is absorbed by chlorophyll molecules. Electrons within these molecules are then raised to a higher energy state. These electrons then travel through Photosystem II, a chain of electron carriers and Photosystem I. As the electrons travel through the chain of electron carriers, they release energy. This energy is used to pump hydrogen ions across the thylakoid membrane and into the space within the thylakoid. A concentration gradient of hydrogen ions forms within this space. These then move back across the thylakoid membrane, down their concentration gradient through ATP synthase. ATP synthase uses the energy released from the movement of hydrogen ions down their concentration gradient to synthesise ATP from ADP and inorganic phosphate.

3. ATP and NADPH

4. NADPH is generated in the light-dependent reactions as a powerful reducing agent. In the Calvin cycle, it is responsible for the reduction of 1,3-bisphosphoglycerate (1,3-BPG) into glyceraldehyde-3-phosphate. ATP energy is used to run the cycle. 

Warm-Up 10/29

1. chloroplasts - make glucose products for the cell (photosynthesis)
Mitochondrion - break down glucose into ATP energy (cellular respiration)

2. Leaf with greater pigment would have a higher rage of photosynthesis because the green color more easily absorbs light photons

3. Temperature - upside "U" (palabara), too hot or cold is bad
Light intensity - peaks at two different intensities
Carbon dioxide - positive correlation and then plateaus

Warm-Up 10/15

1. Describe chemiosmosis as it relates to oxidative phosphorylation.

The last part of aerobic respiration is known as oxidative phosphorylation. In this process, ADP is phosphorylated to generate ATP using the energy that was released from the oxidation (the main substance that was oxidized being NADH + H⁺). The energy from this is released in a series of small steps and then carried out by the electron transport chain. The method used to couple the release of energy by oxidation to ATP production is known as chemiosmosis, where H⁺ moves across the inner mitochondrion membrane down the concentration gradient releasing energy needed for ATP synthase (enzyme) to form ATP.

2. Describe the role of oxygen in the ETC. 

Oxygen is the "final electron acceptor."  As electrons (usually represented as Hydrogen atoms) are passed down the chain, they lose their energy in the making af ATP by phosphorylation.

Warm-Up 10/9

ETC

- group of compounds that pass electrons via reduction oxidation reactions 

- the transfer of protons across a membrane creates a proton gradient.

Warm Up 10/3

I. Cristae - mitochodrion
II. Folds increase surface area so that there is more area to perform chemical reactions. This especially aids in aerobic cellular respiration.

Warm Up 10/7

 Cellular Respiration outline 

Anaerobic (2 ATP, without oxygen) - glycolysis -> lactic acid fermentation OR alcoholic fermentation
Aerobic (38 ATP, with oxygen) - glycolysis -> pyruvate oxidation -> Krebs cycle -> electron transport chain

Glycolysis (2 ATP)
1. Phosphorylation
- addition of a phosphate group
- 2 phosphate groups added to glucose to form hexose biphosphate (provided by 2 ATP molecules)

2. Lysis
- hexose biphosphate splits to form 2 triose phosphate

3. Oxidation
- 2 hydrogen atoms removed from each triose phosphate
- energy released is used to link on another phosphate group, producing a 3-carbon compound carrying 2 phosphates
- NAD+ is the hydrogen carrier

4. ATP Formation
- pyruvate formed by removing 2 phosphates and passing them to ATP

Krebs Cycle
1. acetyl CoA is combined with oxaloacetate to form a molecule of citrate 
2. hydroxyl group and a hydrogen molecule are removed from the citrate structure in the form of water.  The two carbons form a double bond until the water molecule is added back
3. isocitrate molecule is oxidized by a NAD molecule.  The NAD molecule is reduced by the hydrogen atom and the hydroxyl group. NAD binds with a hydrogen atom and carries off the other hydrogen atom leaving a carbonyl group.  This structure is very unstable, so a molecule of CO₂ is released creating alpha-ketoglutarate.
4. coenzyme A returns to oxidize the alpha-ketoglutarate molecule.  A molecule of NAD is reduced again to form NADH and leaves with another hydrogen.  This instability causes a carbonyl group to be released as carbon dioxide and a thioester bond is formed in its place between the former alpha-ketoglutarate and coenzyme A to create a molecule of succinyl-coenzyme A complex
5. free-floating phosphate group displaces coenzyme A and forms a bond with the succinyl complex.  The phosphate is then transferred to a molecule of GDP to produce an energy molecule of GTP.  It leaves behind a molecule of succinate.
6. succinate is oxidized by a molecule of FAD (Flavin adenine dinucleotide).  The FAD removes two hydrogen atoms from the succinate and forces a double bond to form between the two carbon atoms, thus creating fumarate.
7. An enzyme adds water to the fumarate molecule to form malate.   The malate is created by adding one hydrogen atom to a carbon atom and then adding a hydroxyl group to a carbon next to a terminal carbonyl group.
8. Malate molecule is oxidized by a NAD molecule.  The carbon that carried the hydroxyl group is now converted into a carbonyl group.  The end product isoxaloacetate which can then combine with acetyl-coenzyme A and begin the Krebs cycle all over again.

Electronic Transport Chain

- electrons are transported to meet up with oxygen from respiration at the end of the chain
- the overall electron chain transport reaction is:
2 H⁺ + 2 e⁺ + 1/2 O₂ ---> H₂O + energy
- 2 hydrogen ions, 2 electrons, and an oxygen molecule react to form as a product water with energy released in an exothermic reaction.
- energy released is coupled with the formation of three ATP molecules per every use of the electron transport chain.

Warm Up 10/1

1. What is oxidative decarboxylation?
It is reaction in the Kreb's cycle in which oxygen is used to oxidize two carbon atoms to two molecules of carbon dioxide. The two carbon atoms result from the decarboxylation reactions that occur during the Krebs cycle as the six-carbon compound citrate is converted to the four-carbon compound oxaloacetate.

2. What is substrate-level phosphorylation?
It occurs during glycolysis and the Krebs Cycle and is a precursor for the phosphorylation of glucose. SLP is also the source for the majority of the ATP produced in aerobic respiration.

3. What are the products of Kreb's? Glycolysis?
Kreb's - 6 NADH+H, 2 FADH2, 2 ATP, 4 CO2
Glycolysis - 2NADH, water, net gain of 2 ATP