Energy of motion; the energy that you have the potential to use that is stored.

Example: gravitational potential energy

is a boulder at the top of a hill.

Used to measure energy.

"thermodynamics" means "heat changes"

oxidation-reduction

(redox)

total amount of energy in the universe remains constant;

ex: lion eating the giraffe is transferring potential energy from the giraffe into it's own body; giraffe got potential energy from plants.

Some energy dissipates as heat during reactions; it measures kinectic energy and specifically measures "random motion of molecules."

Sun replaces the dissipated energy.

This is the transfer of potential energy into heat, or random molecular motion.

"entropy" is always increasing 

This is the tendency of energy to become disorderly at an increasing rate over time;

The disorder is more spontaneous and the order is energetic

• bricks are more likely to tumble over than to stay in place when stacked.
• bedroom: to get messy is low effort, to clean up is high effort

free energy

this is he energy available to break and make bonds (do work) between molecules after the heat lost from energy dispersal is accounted for.

in equations it is denoted as "G." For Gibbs Free Energy. This that same value as the energy in the bonds.

This is the energy stored in bonds; this is referred to as H in the below equation:

G=H-TS

• G=free energy
• H=enthalpy
• T=temperature in Kelvins
• S=entropy or energy lost

"inward energy" refers to all reactions that require input energy. In these the products have more energy than the reactants.

This is some point between the reactants and the products. It is measured numerically.

this is the extra energy required to destabilize chemical bonds and initiate the chemical reaction.

slower reactions require more activation energy.

speed up reaction by: 

• lowering activation energy
• increasing the energy in the reactants

This is the lowering of the activation energy via a modification of chemical bonds;

enzymes are catalysts.

This process does not change the laws of thermodynamics.

Activation energy speeds up the forward and backward reaction.

ex: the ball in a basin in the dirt; lowering the rim is like catalysis. Gravity then just acts, so direction of the reaction does not change. 

adenosine triphosphate

energy for all processes:

• energy for reactions
• energy for active transport
• movement through the environment

ATP energy storage

store energy via negative charge of the phosphate groups that repel each other

the electrostatic repulsion causes the covalent bonds in the phosphates to be unstable

Adenosine Diphosphate; this includes AMP (the core of ATP) plus one phosphate to make ADP.

This is formed when there is an ATP reaction and the outermost phosphate group comes off.

The ADP then hooks up with an inorganic molecule. 

These are unstable and require low activation energy; they are broken and hydrolysis occurs.

change G is less than 0; (it is exergonic) and there is enough energy to do work in reactions.

This is what hooks onto the ADP when the ATP reacts and loses a phosphate. During this reaction energy is also produced: 7.3 kcal/mol.

amino acids bind with the  substrate; this lowers the activation energy of the reaction

this causes the protein (enzyme) to change its shape

ex: vertebrate red blood cells use an enzym in the cytoplasm called carbonic anhydrase (enzymes all end with "ase").

These couplings typically serve a few specific reactions. 

This powers the endergonic reactions, which have more energy in the reactants than the products and need the enzyme to lower the activation energy.

There is typically more energy yielded by hydrolysis than is needed in one cellular reaction, so it can "power" many (i.e. the endergonic + ATP hydrolysis=net energy)

the modification of the shape of the enzyme to accommodate the substrate.

(i.e. antibody and antigen)

These are teams of enzymes that allow multiple reactions to happen in subsequence.

Some of these may be RNA and not just proteins.

ex: pyruvate dehydrogenase: this catalyzes the oxidation of pyruvate; it is made of 60 protein subunits. This involves three reactions in sequence.

catalytic efficiency:

increases the number of times that an enzyme contacts substrate without peacing

no excess reactions, b/c of proximity

reactions controlled and in one unit

RNA catalyzers 

"ribozymes"

RNA is synthesized by RNA rather than enzymes.

intramolecular catalysis: ribozymes that catalyze themselves

intermolecular catalysis: ribozymes that aren't compositionally changed but catalyze the reactions of other molecules.

this is the temperature at which the enzyme's function maxes rate; it will no longer increase beyond this.

strength too weak to hold bonds (high temp)

strength of bonds too much; the activation site isn't malleable enough to take on the enzyme.

between 6-8

the ones that are high functioning in acidic conditions hold shape despite the high energy level.

The inhibition of the start of the pathway by the end products.

nonprotein organic molecule versions of the cofactors

• vitamins: B, B12 and B6

total of all chemical reactions that an organism carries out

reaction--> product--> used to power new reaction

sequence of enzymatic reacns.

Kreb's Cycle

NAD+

(nicotinamide adenosine dinucleotide)

cofactor that facilitates the catalyzation of the enzyme for redox

• works by accepting the electrons and a proton from a substrate forming NADH+
• made of an NMP + AMP linked by their phosphate groups

Happens in a stepwise way where energy decreases incrementally at each interval.

This is why glucose is oxidized to CO2, because there are intermediate electron transfers and an ultimate arrival at O2.

soluble carriers: move electrons from one molecule to another

membrane-bound carriers: these form the redox chain

membrane carriers: move within the membrane

can all be oxidized and then reduced; some carry protons and electrons/others just electrons

happens incrementally; too much at one time is a waste of energy

• C--H bonds from glucose being stripped at stages in glycolysis and Kreb's 

ATP binds at active site; reactant also binds...the excess energy from changing the ATP site and subsequent reaction results in endergonic power.

ex: ATP synthesis

This happens when the ATP is phosphorylated and becomes ADP.

ex: glycolysis, bonds are shifted and ATP can then form with the excess energy.

ATP is synthesized by ATP synthase from the energy within a proton gradient.

ADP + Pi = ATP

prokaryotes and eukaryotes both use this. 

glyceraldehyde 3-phosphate

(G3P): This is the 3-cabon compound that is made in the first phase of glycolysis and is made from a single molecule of glucose.

• it is endergonic and requires ATP. 

This is the first step in glycolysis that prepares the glucose for splitting into two 3-carbon phosphorylated molecules.

This requires 2 ATP

In the last two reactions of glycolysis, 6-carbon product of glucose priming is divided into two three-carbon molecules: G3P + G3P that is converted from another molecule.

G3P is converted to pyruvate:
oxidation: NADH is made from NAD+ when two electrons and a proton are transferred from the G3P.

one Pi is added to make 1,3 bisphosphoglyecerate (BPG)

and phosphate is transferred to ADP via substrate-level phosphorylization 

BPG is converted to a pyruvate in four reactions

This makes two molecules of ATP per G3P.

This was the pathway for respiration (making ATP) for heterotrophic organisms in early Earth.

It evolved "backward." ATP breakdown of G3P came before the synthesis of G3P from glucose (probably due to the lack of G3P in the atmosphere).

Happens by another molecule accepting electrons from G3P and being reduced in one of these methods:

Aerobic respiration: electrons in the G3P are donated to oxygen and this makes waters. This happens in the mitochondria and it makes ATP. (aka aerobic metabolism)

Fermentation: when oxygen is not available, an organic molecule like acetaldehyde can accept electrons.

aerobic respiration: oxidation of pyruvate to make acetyl co-A

fermentation: reduction of all or part of the pyruvate to oxidize the NADH to NAD+

• happens in the mitochondria for eukaryotes and the cytoplasm and plasma membrane for prokaryotes
• first the pyruvate is oxydized and a 2-carbon compound + CO2 is made. NADH is made from NAD+ via electron transfer
• decarboxylation happens; one of the three carbons detaches and leaves as CO2, the other two form a compound with co-enzyme-A. This is acetyl co-A.
• NAD+ gets a proton and two electrons and NADH is made.
• catalyzed by a multi-enzyme complex

The two carbon acetyl group of acetyl co-A combines with the a 4-carbon oxaloacetate; this makes a 6 carbon citrate. Then oxidation reactions happen, ultimately yielding a oxaloacetate for the next round.

citrate rearrangement and decaroxylation: in five steps, the citrate breaks down to a 5-carbon intermediate and a 4 carbon succinate. 

two NADH and one ATP are produced

citrate forms from oxaloacetate and acetyl co-A, two-carbon acetyl group goes to Krebs

if there is enough ATP, then Krebs stops taking acetyl

two co-A are lost

pyruvate is split

at the end of the chain inorganic molecules accept the electron.

ex: prokaryotes often use nitrate, sulfur, inorganic metals

• less ATP and free energy in the products

the electron acceptor in this case is SO4 instead of CO2 and the reduction=H2S from S

ex: thermoproteous sulfate

NAD+ is recycled in this process; the process uses pyruvate or a derivative in bacteria

reduced compound is usually an organic acid: acetic acid, butyric acid, lactic acid, alchol or propionic acid

made by metabolic breakdown of fats, lipids and proteins

used inanabolic metabolism; can be used in fatty acid synthesis or ATP production

when ATP is too high, the acetyl co-A goes into fat stores

this is the third stage of photosynthesis and happens as the product of a cycle of reactions; can happen with or without light depending on the presence of ATP and NADPH

this is light independent

increased temperature results in increased rate of light-dependent reactions up to 35 degrees; higher temperature than this lower the rate of reactions; 

therfore, he concluded that the light-independent reactions were dependent on enzymes

note: light dependent or independent just means that there is light involved not that light has to be present.

also, temperature and CO2 concentration do not change the rate of photosynthesis.

molecules that absorb light energy in visible range; we see the color that is absorbed not reflected.

ex: in plants this is chlorophyll and cartenoids

This is the efficient range of light absorption or a molecule.

the chemicals in the contact molecule as well as the energy in the photon determines whether or not the light is absorbed.

prefers red and violet-blue light, cannot absorb pigments between 500 and 600 nm light

appear green, found in cyanobacterium and is only one able to transform light energy into chemical energy

an accessory pigment or secondary pigment light absorber; adds to the light absorption of Chlorophyll A. 

prefers green wavelengths and is preferred among specific plants.

the ring structure for chlorophyll; made of alternating single and double bonds.

in chlorophyll a the ring has a CH3 group (methyl)

in chlorophyll b the ring has a CHO group (aldehyde)

single carbon rings with alternating single and double bonds; capture light through wavelengths that are not compatible with photosynthesis; 

protect the plant via antioxidant/reductive process

ex: beta-carotene, this is comprised of two carbon rings linked by 18 carbons that have single and double bonds; when beta carotene is split, vitamin A is produced.

accessory pigments found in cyanobacterium and some algae; these are made of proteins from the tetrapyrrole group.

they can be grouped together to make more light-absorbing entities called phycobiliosomes.

this happens because the light-absorbing capacity of the plant has maxed

light is not absorbed by independent molecules of pigment, but by clusters of photosystems.

one of the components of a photosystem; it is made of hundreds of pigments and feed the light energy from photons to the reaction center of the plant

another component of a photosystem; it is made of chlorophyll molecules embedded in proteins and feeds electrons in and out of the system.

ex: purple photosynthetic bacteria,

a final acceptor is reduced as an electron chain is started by way of a excited electrons being transported across a photosynth membrane

Linked photosystems in plants: photosystem I

Has a reaction center pigment called P700, because it absorbs at 700 nm.

There are two different versions for plants and algae

transfers electrons to NADP+ to make NADPH>

This has pigment P680 at its reaction center; can oxidize water with its oxidaton potential.

Works with photosystem I to create an electron transfer chain that is not cyclic and produces NADPH and ATP; replaces the electrons that are lost in photosystem I.

The amount of light absorbed is maximized by the inclusion of two beams of light at different wavelengths rather than the sum of the two beams absorption rates.

proof that photochemical systems work in concert.

In this process the ATP is made from the electron that remains from photosystem I rather than NADPH. 

the electron just goes back to the b-6 f complex, which pumps the protons back into the thylakoid membranes, creating a gradient leading to chemiosmosis.

Photosystem I: mostly in the grana; the edges of non-stacked grana

Photosystem II: happens mostly in the stroma lamella 

This is made in photosynthesis when the bonds of to intermediates in glycolysis are reassembled. 

Made of five carbons; is a sugar and combines fructose 6-phosphate and GP3.

Reacts with CO2 to form a 6-carbon intermediate that splits into two 3 phosphoglycerate (PGA)'s; it combines CO2 into the PGA in its inorganic form (an acid).

16-subunit enzyme found in the chloroplast stroma

(ribulose biphosphate carboxylase/oxyenase)

Oxygen interferes in the process of carbon fixation; oxygen  ends up mixed up with the RuBP.

In this process 20% of the carbon fixed is lost when the temperatures are 25 degress C.

Loss increases as the temperature rises, eventually the stroma close

C4 plants

Part of the process (decarboxylation) happens in one part of the cell and CO2 fixation happens in another part of the cell.

Can minimize the photorespiration by having photosynthesis occur in both the mesophyll cells and the bundle sheath cells; the carbon is originally stored in the form of an acid at the mesophyll cells. This is then converted so that the carbon can be accessed for the process in the bundle sheath cells. 

include pineapples, cacti, other water-savers..

stomata are open during the night and close during the day; can use the C3 and C4 pathways both.

crussulacean acid metabolism 

decarboxylation happens during the day, PEP is used in the evening for the carbon capture; the processes happen in the same part of the cell.

All abiotic elements of an environment with which communities live an interact.

this includes the biological processes and organisms and the geological (abiotic) systems and processes; they happen on scales of seconds (biochemical reactions)

to millenia (weathering of rocks)

these cross boundaries of the ecosystems; 

Watersheds where we find groundwater; these are permeable, underground layers of rock, sand and gravel. The water in these aquifers represents up to 95% of water in the world.

ex: Oqallala and imbalance..more coming out than staying in.

N2 made into nitrogen containing compounds by way of synthesizing NH3 from N2 .

The second part of nitrogen fixation in which microbes oxidize part of the NO3-.

ex: some prokarotes accomplish this by way of the nitrogenase complex; 

The microbes responsible typically live in symbiosis with legume roots, alders, myrtles and other plants.

Organisms that make their own food; they use inorganic material like CO2, water, and NO3- to make food within their bodies by way of energy from an abiotic source.

Autotrophs that use light as their energy source for making food; these include photosynthetic organisms like plants, algae and cyanobacteria.

Inorganic oxidation reactions allow them to gain energy; these are all prokaryotic.

ex: microbes use hydrogen sulfide in deep water vents; 

Take in organic compounds that other living organisms have made; they obtain energy by breaking up the organic compounds that they consume--bond breaking yields energy.

These are feeding levels in the food chain; organisms are categorized based on roles in an ecosystem (i.e. what they consume/who consumes them).

This is an additional trophic level in which the predators eat only dead organisms; "detritus" is dead organic matter.

decomposers

Microbes and other minute organisms that live by breaking down dead organic matter.

This the rate at which new organic matter is synthesized by organisms at a specific trophic level.

Productivity of the primary producers; includes the organic matter via photosynthesis as well as the breaking down of  organic matter to release energy by way of aerobic respiration.

This is the rate at which organic compounds are broken down by organic compounds.

This is the new rate at which the primary producers synthesize new organic matter.

This is the gross primary productivity with the respiration from primary producers taken out; it contains the food that herbivores can consume as food.

This is the productivity of a heterotroph trophic level; this refers to the rate at which new organic matter is made by individual growth and reproduction in all herbivores in an ecosystem.

These are diagrams that can be used to represent:

1. standing crop biomass
2. numbers of individuals
3. productivity

Occurs when one trophic level has greater biomass than the one below it. 

The process by which effects that happen at a certain trophic level effect multiple other lower levels. 

ex: one species goes extinct, other lower species populations grow, because of absence of a predator.

Effect at the top of the trophic chain impacts below the chain.

Effects flow up through the trophic chain; primary producers up to the higher levels.

ex: one species goes extinct, other go extinct. 

These represent the amount of free energy or potential to do work. 

This often represented at psi with the subscript w; it is used to predict the way in which water will move. 

Water always moves from areas of high water potential to areas of lower potential.

These are the units in which water potential is measured; It is abbreviated as MPa.

The natural movement of water into a cell when the solute concentration inside the cell is lower than that without the cell. 

This describes the cell wall as the cell expands and pushes against the cell wall; this happens as a result of influx of water into the cell. 

The opposite happens when conditions outside of the cell have large amounts of solute; the cell loses water--a plant may wilt as turgor pressure decreases.

This is the turgor pressure that results in pressure against the cell wall of the plant.

Increased turgor pressure increases the pressure potential.

If a solution is not contained, it cannot have a measurable pressure potential.

This is the smallest amount of pressure needed to stop osmosis is proportional to this value;  

The solute potential of pure water is zero. 

Aquaporin-like proteins that speed up osmosis without changing the direction of water movement. 

They maintain water balance and move the water from the cell and move it into the xylem.

This is the movement of water and minerals through the cell walls and the space between cells.

This is the continuum of the cytoplasm between cells connected by the plasmodesmata.

One of the three ways in which molecules can move within the plant.

This is the process of membrane transport between cells and the across the membranes of vacuoles within cells. This route permits the greatest amount of control over what enters and stays within the cell. 

This happens at night; it is caused by the accumulation of ions in roots when transpiration from the leaves is quite low; as a result you end up with a high ion concentration in the cell. As a result, more water will enter the root hairs via osmosis when the solute potential goes down. You get water moving up the plant and through the xylem without transpiration as a result.

A process that happens when there is high root pressure: the water is forced up the leaves and can be lost in a liquid form. 

This the inherent strength of water that happens as a result of the cohesion of molecules; this is made possible by hydrogen bonds.

This makes cohesion-tension theory possible.

This is the expansion of a gas bubble in a plant, which causes water transport to cease and can lead to dehydration or death of all or part of a plant.

This is the loose parenchymal tissue (having large air spaces) that plants growing in water develop to cope with the conditions.

These are plants that can survive in salty areas. 

One of their coping mechanisms is to produce high concentrations of organic molecules in their roots to alter the water potential gradient between the soil and the root. 

This is the model of how carbohydrates in a solution move through the phloem: carbs move from a source to a sink (where they are used).

Process by which carbohydrates enter the plant through of the smallest veins of the plant; from there the carbs may take the symplast path from mesophyll cells to the companion and sieve cells. Otherwise, it may arrive via apoplastic transport and moves across membrane via sucrose and H+.

This is the highly weathered outer layer of the Earth's crust. It is composed of a mixture of ingredients, which may include sand, rocks of various sizes, clay, silt and humus, as well as minerals and other organic matter.

Pore spaces containing water and air occur between the particles of the soil,

This is where the roots are found and is composed of mineral particles of different sizes, living organisms and humus. 

This is the use of plants to concentrate or breakdown pollutants; these plants do this by sequestering and releasing toxic compounds into the atmosphere.

There is no specialization in this type of digestive system, because every cell is exposed to all stages of food digestion. 

Innermost layer of the intestinal tract; it is an epithelium that lines the lumen.

The next major tissue layer--made of connective tissue. Comes after the mucosa, which lines the interior. Nerve networks are located here between muscle layers and regulate the gastrointestinal activities.

This is the first 25 cm of the small intestine; receives the acidic chyme from the stomach, digestive enzymes from the pancreas, and bile from the liver and gallbladder. Enzymes in the pancreatic juice digest larger food molecules into smaller parts. 

These cover the inner walls of the villi on the side facing the lumen (or apical surface); they are comprised of plasma membrane foldings that create cytoplasmic extensions. 

trypsin/chemotrypsin

Pancreatic enzyme that digests fat; released by the duodenum.

These are clusters of endocrine cells that are scattered throughout the pancreas; where insulin and glucagon are made.