Biol 40 Chapter 8 & 9 Review

Energy + Enzymes & Cellular Respiration + Fermentation

Kinetic Energy

energy of motion

Potential Energy

energy that is stored in position or configuration (different forms: gravitational, electrical, chemical)

1st law of thermodynamics

energy is conserved; not created nor destroyed, only transferred or transformed

enthalpy

total ENERGY of a molecule

exothermic

when a reaction releases heat (change in enthalpy)

endothermic

when a reaction takes up heat (change in enthalpy)

2nd law of thermodynamics

total entropy in a system always increases

entropy

amount of disorder in a system

exergonic

SPONTANEOUS chemical reaction (releases energy)

endergonic

non-spontaneous (requires energy)

temp vs reaction rule

when temperature is high, reactions collide more, increasing reaction rate

concentration vs reaction rate

when concentration is high, reactants collide more, increasing reaction rate

energetic coupling

exergonic + endergonic reactions pair, transfer free energy from one reaction to another through electron/phosphate transfer

reduction-oxidation reactions (redox)

reactions that involve the loss or gain of electrons (2 half reactions that occur as a pair)

oxidation

the loss of electrons (spontaneous and exergonic)

reduction

the gain of electrons (nonspontaneous and endergonic)

electrons can be gained or lost in what two ways?

1. change in the # of electrons in the valence shell

2. transferred as new covalent bonds are formed w/ other atoms

electron donor

molecule giving up an electron

electron acceptor

molecule receiving electron (most electron donors GAIN potential energy)

flavine adenine dinucleotide (FAD)

cellular electron acceptor that is reduced by 2 electrons and gains 2 protons to form FADH2

nicotinamide adenine dinucleotide (NAD+)

reduced to form NADH (2 electrons reduce NAD+ and it gains 1 proton)

adenine triphosphate (ATP)

ribonucleotide for RNA synthesis

phosphorylation

addition of a phosphate group to a molecule (when ATP is a phosphate donor, phosphorylation is exergonic!)

activation energy

minimum amount of kinetic energy required even in spontaneous reactions (required to sufficiently strain chemical bonds and form products)

transition state

intermediate point between breaking old bonds and forming new ones (free energy of this state is high because old bonds must be destabilized, when products form free energy drops sharply)

What must happen before any chemical reactions can take place?

1. reactants must collide in a precise orientation

2. reactants must have enough kinetic energy to overcome the activation energy barrier + acheive the transition state

substrates

reactants that undergo a chemical reaction by binding to an enzyme

enzymes are catalysts:

bring substrates together in a precise orientation that makes reactions more likely to occur

• enzymes lower activation energy but aren’t consumed in a chemical reaction

active site

where enzymes bring substrates together to collide

• enzymes undergo a conformational/shape change when a substrate binds to an active site

• induced fit = enzyme changing shape when a substrate binds

Steps for enzymes catalyzing reactions:

1. Initiation = enzymes orient substrates as they bind to the active site

2. Transition State Facilitation = catalyst’s active site lets transition state reaction occur much more actively

3. Termination = reaction products have less affinity for active site, products are released, enzyme returns to OG conformation

Cofactors

Enzyme helpers; inorganic ions such as metal ions, that reversibly interact with enzyme

Coenzymes

organic molecules that reversibly interact with enzymes, such as electron carrier

Prosthetic Groups

atoms or non-amino acid molecules that are permanently attached to proteins such as pigments

molecule retinal

involved in converting light energy into nerve impulses

Why does ATP have such high potential energy?

the negatively charged phosphate groups creates an instability making the bonds between them high-energy bonds that store significant energy

What happens when glucose is oxidized?

Much of the potential energy stored in the glucose’s chemical bonds is converted into kinetic energy in the form of heat and light

Glycolysis

one six-carbon molecule of glucose is broken down into two molecules of the three-carbon compound pyruvate

• starting molecule: 1 glucose (C6H12O6)

• CO2 produced: 0

• ATP produced: 4 total, 2 NET

• FADH2 produced: 0

• NADH produced: 2

• ending molecule: 2 pyruvate (C3H3O3)

Pyruvate Processing

each pyruvate produced by glycolysis is processed to release one molecule of CO2 and the remaining 2 carbons are used to form the compound CoA — the oxidation of pyruvate results in more NAD+ being reduced to NADH

• starting molecule: 2 pyruvate (C3H3O3)

• CO2 produced: 2

• ATP produced: 0

• FADH2 produced: 0

• NADH produced: 2

• ending molecule: 2 acetylCoA

Citric Acid Cycle (Kreb’s Cycle)

the 2 carbons from each acetylCoA produced by pyruvate processing are oxidized to 2 molecules of CO2 — during this sequence of reactions, more ATP and NADH are produced, and FAD is reduced to FADH2

• starting molecule: 2 acetylCoA

• CO2 produced: 4

• ATP produced: 2

• FADH2 produced: 2

• NADH produced: 6

• ending molecule: oxaloacetate

Electron Transport + Oxidative Phosphorylation

electrons from the NADH and FADH2 produced by pyruvate processing and the citric acid cycle move through a series of electron carriers that together are called the elctron transport chain — the energy obtained from this chain of redox reactions is used to create a proton gradient across a membrane; ensuring the flow of protons back across the membrane is used to make ATP — because this mode of ATP production links oxidation of NADH and FADH2 with phosphorylation of ADP, it is called oxidative phosphorylation

• starting molecule: 10 NADH, 2 FADH2

• CO2 produced: 0

• ATP produced: 30 - 38

• FADH2 produced: 0

• NADH produced: 0

• ending molecule: NAD+, FAD, H2O, and ATP

cellular respiration

defined as any set of reactions that uses electrons harvested from high energy molecules to produce ATP via the electron transport chain

catabolic pathways

sets of reactions that BREAKDOWN molecules

anabolic pathways

sets of reactions that SYNTHESIZE to larger molecules

Glycolysis Process

1. glycolysis starts by using ATP, not producing it

• glucose is phosphorylated to form glucose-6-phosphate

• 2nd reaction rearranges to fructose-6-phosphate

• 3rd reaction adds a 2nd phosphate group forming fructose

2. energy payoff, consists of exergonic reactions that don’t require energy

• 6th reaction forms 1st high energy molecules: where 2 NAD+ molecules are reduced to NADH

• In reactions 7 + 10, enzymes catalyze the transfer of a phosphate group forming a phosphorylated substrate to ADP, forming ATP (substrate level phosphorylation)

3. for each molecule of glucose processed by glycolysis, the NET yield is 2 molecules of NADH, 2 of ATP, and 2 pyruvate

substrate level phosphorylation

direct enzymatic transfer of a phosphate group from a high-energy substrate molecule to ADP, producing ATP without the help of the ETC

phosphofructokinase

key glycotic enzyme that catalyzes the synthesis of fructose-1,6-biphosphate from fructose-6-phosphate

mitochondrial matrix

compartment enclosed in the inner membrane

• cristae = sac-like compartments formed when portions of the inner membrane protrude into the interior of the organelle and expand

Pyruvate Processing Process

1. pyruvate moves from cytosol across mitrochondrial outer membrane, then transported into matrix via a carrier protein in the inner membrane (prokaryotes don’t have mitochondria, a similar process occurs in the cytosol)

2. pyruvate dehydrogenase couples the oxidation of one carbon in pyruvate to the reduction of a CO2 molecule + production of NADH (CO2 is released and CoA is added)

3. acetyl-CoA is produced, 2 NADH and 2 CO2 are produced

Citric Acid Cycle / Krebs Cycle Process

1. cycle starts with citrate (C6H5O7)

2. energy harvested by oxidizing the acetyl-group

3. substrate level phosphorylation

4. generates 6 molecules of NADH, 2 FADH2, 2 ATP, and 4 CO2

5. produces the molecules oxaloacetate

Electron Transport Chain Process

oxidative phosphorylation

1. starts off with 10 NADH and 2 FADH2

2. components of ETC are organized into 4 large complexes of proteins, complexes 1-11 and protein cytochrome (cyt-c) act as shuttles that transfer electrons between complexes

3. oxidative phosphorylation oxidizes CO2, FADH2, and NADH — oxidizing them to NAD+, FAD, H2O

4. oxidative phosphorylation’s main role is to produce ATP, it produces 30-38 ATP

5. final products = NAD+, FAD, H2O, and ATP

ubiquinoe

pool of nonprotein molecules in the inner membrane of the mitochondrion, belonging to a family of compounds called quinoes (also referred to as coenzyme Q!) = lipid soluable and moves efficiently throughout the hydrophobic interior of the inner mitochondrial membrane

redox potential

an electron acceptor’s ability to accept electrons in a redox reaction

• some molecules gain a proton with each electron, forming bonds to uncharged hydrogen atoms — some only gain electrons

• Coenzyme Q and ETC differ in redox potential, so it should be possible to arrange their redox reactions to a logical sequence (electrons will pass from molecules w/ lower redox potential to one with higher redox potential — the potential energy in each successive bond in ETC would lessen)

role of ETC

generates electron carriers NADH + FADH2, which are needed for glycolysis as well as generating a proton gradient across the mitochondrial inner membrane that powers the synthesis of ATP

ATP synthase

the entire protein complex is known as this — the stalks + knobs of vesicles synthesize ATP + hydrolyze it to form ADP and inorganic phosphate (when knobs were not present the vesicles could not make ATP, but could transport proteins across membrane)

Chemiosmosis Hypothesis

proposed ETC only purpose is to pump proteins across inner membrane of mitochondria from matrix to intermembrane space, after proton gradient was established an inner membrane enzyme will synthesize ATP from ADP and Pi

proton-motive force 

powers production of ATP outside of the vesicle using a proton gradient alone, in the absence of ETC created by the proton pumping activity of the ETC

oxidative phosphorylation

as the shaft spins w/ the knob unit, it is thought to change the shape of the knob subunits in a way that catalyzes the phosphorylation of ADP to ATP

where does the energy for oxidative phosphorylation come from?

comes from an established proton gradient, not phosphorylated substrates as used in substarte level phosphorylation

aerobic respiration

processes used by species that depend on oxygen as an electron acceptor for the ETC for cellular respiration (most efficient)

anaerobic respiration

cells that depend on ETC w/ electron acceptors other than oxygen for cellular respiration

fermentation

metabolic pathway that includes glycolysis and an additional set of reactions that oxidize stockpiles of NADH to regenerate NAD+

• in respiring cells, fermentation serves as an emergency backup so that glycolysis can continue to produce ATP even when ETC + oxidative phosphorylation is shut down

lactic acid fermentation

regenerates NAD+ by reducing pyruvate to form lactate — a deprotonated form of lactic acid

• produced when there is little to no oxygen in muscles, this receives ETC and lactic acid fermentation can convert back to pyruvate and be used as a source of energy to continue cellular respiration

alcohol fermentation

occurs in the eukaryote Saccharomyces Cerevisiae, strains of which make bakers + brewers yeast

• 1st convert pyruvate to the 2 carbon compound acetaldehyde, giving off CO2

• acetaldehyde accepts electrons from NADH, forming NAD+ required to keep glycolysis going, this forms ethanol as a waste product

obligate anaerobes

bacteria + archaea that rely exclusively on fermentation

why is fermentation considered inefficient compared to cellular respiration?

fermentation produces just 2 ATP per glucose metabolized, while cellular respiration produces about 29 ATP

facultative anaerobes

organisms that can switch between fermentation and aerobic cellular respiration

• many human cells function as facultative anaerobes to a certain extent, but we can’t survive for long without oxygen

dehydrogenase

removed a pair of hydrogens

kinase

adds a phosphate group

phosphotase

removes a phosphate group

isomerase

moves atoms around, making isomers but keeping the same molecular formula (ex: turning glucose into fructose)