direction- many cells use ATP to drive reactions in a certain direciton.

rate- catalyst called enzyme can speed up rate

1. law of conservation of energy- energy cannot be created or destroyed.

2. tranfer or tranformation of energy from one form to another increases entropy or degree of disorder in a system

negative free energy change- energy is released

spontaneous

favors formation of products

positive free energy change-requires free energy from the environment

requires addition of free energy

not spontaneous

favors formation of reactants

Initial input of energy to start reaction

allows molecules to get close enough for bond rearrangement

can now acheive transition state where bonds are stretched

Overcoming activation energy

2 common ways

1. large amount of heat

2. enzymes to lower activation energy then smaller amount of heat

high affinity/high degree of specificity

induced fit- conformational changes

small molecules permanently attached to the enzyme

aid in catalysis

True/False

Enzymes funciton in a wide range of heat and PH

result in breakdown of reactants

exergonic

promote synthesis

endergonic

can be coupled with exergonic

enzyme directly tranfers phosphate from one molecule to another molecule

makes ATP

exergonic

breakdown of reactants

used to obtain energy for endergonic reactions

energy stored in ATP and NADH

biosynthetic endergonic reaction

made large macromolecules or smaller molecules not available from food

must be couple with an exergonic reaction

with or w/o oxygen

steps identical in all living species

3 phases- energy investment, cleavage, energy liberation

net yield of 2 ATP

process by which living cells obtain energy from organic molecules.

main goal of respiration- make ATP and NADH

1. glycolysis

2. breakdown of pyruvate to an acetyl group

3. citric acid cycle

4. oxidative phosphorylation

pyruvate broken down by pyruvate dehydrogenase.

molecule of CO2 removed each pyruvate

remaining acetyl group attached to CoA to make acetyl CoA

1 NADH made for each pyruvate

metabolic cycle

acetyl removed from acetyl coA and attached to oxaloacetate to form citrate or citric acid

releases 2Co2, 1ATP, 3NADH, and 1FADH2

turns twice per glucose

electrons removed from NADH and FADH2 to form ATP

requires oxygen

electron transport chain- oxidative process

physphorylation occurs by ATP synthase

movement from NADH to O2= negative free energy change

spontaneous in forward direction

highly exergonic

enzyme harnasses free energy as H+ flow through membrane

energy conversion: Energy in H+ gradient converted to ATP

racker and stoeckenius

rotary machine makes ATP as it spins

True/False

Other organic molecules enter glycolysis or citric acid cycle at different points utilizing the same pathways to increase efficiency

lack oxygen

2 strategies

1. use substance other than O2 as final electon acceptor in electron transport chain

2. carry out glycolysis only- does not require oxygen

synthesis of secondary metabolites-not necessary for cell structure and growth.

unique per species

roles in defence, attraction, protection, competition

phenolics- antioxidants with intense flavors and smells (vanilan in vanilla)

alkaloids- bitter-tasting for defense (dark choc)

terpenoids- intense smells and colors

polyketides- chemical weapons

Biological Membranes

What are they made up of/contain?

framework is the phospholipid bilayer

-amphipathic

also contain proteins and carbohydrates

True/False the phospholipid bilayer is symmetrical

False- asymmetrical

p-leaflet faces the cytoplasm

e-leaflet

noncovalently bound to regions of integral membrane proteins that project out from the membrane

or

bound to the polar head groups of phospholipids

length of fatty acyl tails- shorter acyl tails less likely to interact, making membrane more fluid

presence of double bonds- creates a kink in acyl tail, making more difficult for acyl tails to interact and membrane more fluid

cholesterol- tends to stabilize membranes. depends on temperature

ie: in hot weather animals bind cholesterol more solidly to decrease movement

plants increase length of fatty acyl tails

true/false

proteins in the extracellular matrix are bound to molecules outside the cell and therefore cannot move

process of covalently attaching a carbohydrate to a protein or lipid

-serves as recognition signals for other cellular proteins

-often plays a role in cell surface recognition

-protective effects (cell coat or glycocalyx  is a carbohydrate rich zone on the cell surface that shields the cell)

carbohydrate attached to a lipid

carbohydrate attached to a protein

usues a biological sample that is thin sectioned and stained with heavy metal dyes

dyes bind to polar head groups of phospholipids, but do not bind well to fatty acyl chains

a form of TEM, can be used to analyze interiors of phospholipid bilayers

bilayer seperates into p and e faces.

breakdown of ATP to ADP and P

reaction has negative value- favors formation of products.

how do u tell the +/- value of a reaction andy?!?!

True/False

activation site- where reactants are converted to products

allosteric site- where a molecule can bind noncovalently and affect the function of the active site. This causes a conformational change in the enzyme that inhibits catalytic function- often found in a metabolic pathway

glyceraldehude 3 phosphate is oxidized to 1,3 biphosphoglycerate through triose phophate dehydrogenase and 2NADH is released (6); A phosphate is removed from 1,3-bisphosphoglycerate through phosphoglycerokinase and transferred to ADP to make ATP (7);

the resulting 3-phosphoglycerate is moved to a new location, creating 2-phosphoglycerate by phosphoglyceromutase (8); Enolase is used to remove a water molecule from 2-phosphoglycerate to form phosphoenolpyruvate (9); lastly a phosphate is removed from phophenolpyruvate to form pyruvate.  the removed phosphate is transferred to ADP to make ATP (10).

electrons are removed from NADH and FADH2 to make more ATP

typically requires oxygen

series of redox reactions in which electrons are transferred to components with increasingly higher electronegativity.

e-->NADH dehydrgenase(complex I)--> ubiquinone --> cyochrome bc(complex III)---> cytochrome c---> cytochrome oxidase (complex IV)---> oxygen.

The two electrons, now combined with oxygen, also combine with 2H+ to form a molecule of water.  FADH2 tranfers electrons to succinate reducase (complexII) then to ubiquinone and the rest of the chain.

H+ electrochemical gradient

AKA

proton-motive force

H+ is pumped across the inner mitochondrial membrance due to the movement of electrons.  concentration of H+ is higher outside of the matrix and excess positive charge exists outside the matrix.

NADH dehygrogenase, cytochrome b-c, and cytochrome oxidase are H+ pumps

glycolysis-2

citric acid cycle- 2

oxidative phosphorylation- 30-34 (for this process however the actual ATP amount is usually less than the max because the cell may use some H+ molecules to drive anabolic pathways

a H+ channel

9-12 c subunits form a ring in the membrane.  An a subunit with 2 b subunits is attached to this ring.

a hydrogen ion passes through a c subunit causing a conformational change that causes the y subunit to spin clockwise.  Each time the y subunit turns 120 degrees, it changes its ocntacts with the three Beta subunits which in turn causes the Beta subunits to change their conformations.

After conformation 3, beta subunit turns back to conformation 1 to continue the cycle.  Becuase there are 3 beta subunits, each is in a different conformation at a given time.

see page 142.

conformation 1: ADP and P bind with good affinity

Conformation 2: ADP and P bind so tightly that ATP is made

conformation 3: ATP (and ADP and Pi) bind very weakly, and ATP is released.

not essential for cell structure and growth- unique to each species to provide a variety of functions-- protection (bad taste or smell), or attraction (bright colors, sweet smell)

ie: phenolics, alkaloids, terpenoids, and polyketides

compound containing a cyclic ring of carbon with three double bonds known as a benzene ring.

antioxidants that have intense flavors and bright colors

simplest of the phenolic compounds

benzene ring is covalently linked to a single hydroxl group

common categories of phenols: flavanoids, tannins, and lignins

produced by many plant species and create a variety of flavors and smells.  can be deterants or attractants.

contain many antioxidants that inhibit formation of free radicals.

large phenolic polymers. called tannins because they combine with protein from animal skins to form leather.

typically act as a deterrant to animals- bitter taste or toxic effects.

synthesized by plants- strengthens plant cells to withstand environmental stress.

lignin is removed from wood to make paper

lignins bond to cellulose in plant cell walls-enforce

all contain nitrogen and have a cyclic, ring-like structure.

basic alkaline molecules

caffeine, nicotine, atropine, morphine, ergot, and quinine

many serve as a defense function in plants- bitter-tasting and unpleasant odor

poinsonous alkaloid derived from the nightshade plant.

interferes with nerve transmission

in humans it causes the heart to speed up to dangerous rates.

class of secondary metabolites

there are more types of terpenoids than any other family

synthesized from five-carbon isoprene units and are also called isoprenoids.

often responsible for odors in plants: good and bad.

also impart an intense flavor to plant tissues: cinnamon, cloves, traagon

found in many herbal remedies

carotenoids are a type of terpenoid that give species color

another role is cell signaling

group of secondary metabolites that are produced by bacteria, fungi, plants, inescts, dinoflagellates, mollusks and sponges.  synthesized by the polymerization of acetyl and propionyl groups.  Often highly toxic.

type of polyketide- streptomycin which stops protein synthesis in bacteria but not in mammals.

polyketides inhibit growth of fungi and parasites and cancer cells

1. light reactions: energy is captured by the chlorophyll pigments within plants and converted to chemical energy

2. the calvin cycle- ATP and NADH produced in light reactions are used to drive the incorporation of CO2 into carbohydrates (glyceraldehyde)

chloroplasts contain three membranes: outer, inner, and thylakoid.

contains pigment molecules, including chlorophyll

forms thylakoids

shorter wavelengths (gamma rays) have more energy

longer wavelengths (radio waves) less energy

type of pigment found in chloroplasts that impart a color that ranges from yellow to orange to red

responsible for foliage change in color in autumn

light harvesting complex- i the thylakoid membrane

and a reaction center

light harvesting complex in photosystem II

AKA the antenna complex

located in the thylakoid membrane

composed of several dozen pigment molecules that are anchored to proteins.  Role is to directly absorb photons of light, which boosts an electron to a higher energy level

acts as antenna that absorbs energy from light and funnels that energy to P680 in the reaction center

resonance energy transfer

(photosystem II)

P680

(photosystem II)

a special pigment, so named because it is best at absorbing light at a wavelength of 680 nm

located in the reaction center of photosystem II.

role is to quickly remove the high-energy electron from p680* and transfer it to another molecule where the electron will be more stable.

Transfers it to the primary electron acceptor

another function is to replace the electrons that are removed from pigment molecules with electrons from water.

oxidation of water forms oxygen gas.  PhotosystemII creates first product.

Protein Subunits of Photosystem II

(D1, D2; CP43, CP47)

there are 19 total

2 of which are D1 and D2 which contain the reaction center that carries out the redox reactions

CP43 and CP47 bind the pigment molecules that form the light harvesting complex

splits/oxidizes water.  located on the side of D1 that faces the thylakoid lumen.

technique used to determine three-dimensional structure of photosystem II

researchers expose proteins to conditions that make them form crystals, then mathematically calculate the structure

key role is to produce NADPH

light stridkes the light harvesting system of photosystem I, and this energy is transferred to a reacion center where an electron is removed fro ma pigment P700 and transferred to a primary electron acceptor.  A protein called ferredoxin can accept two high energy electrons at a time from the primary electron acceptor.  ferredoxin transfers the electrons to the enzyme NADP+ reductase which transfers the two electrons to NADP+ which combine with H+ to form NADPH

the way in which P680 and P700 receive electrons:

P680+ receives an electron from water, P700+ receives the electron from Pc (platocyanin).  Therefore Photosystem I does not need to split water and therefore does not generate oxygen.

1. oxygen- produced in thylakoid membrane by oxidation of water in photosystem II

2. ATP- produced in the stroma by H+ gradient

3. NADPH- produced in the stroma from electrons that start in photosystem II and are boosted a second time in photosystem I.