Notes on Cellular Respiration/Photosynthesis

Chapter 6-Intro to Metabolism
METABOLISM= all the chemical reactions in an organism
CATABOLIC PATHWAY (CATABOLISM)• release of energy by the breakdown of complex molecules to simpler compounds

EX: digestive enzymes break down food
ANABOLIC PATHWAY (ANABOLISM)
• consumes energy to build complicated molecules from simpler ones

EX: linking amino acids to form proteins
ORGANISMS TRANSFORM ENERGY
ENERGY- capacity to do work
KINETIC ENERGY- energy of moving objects
POTENTIAL ENERGY- energy stored as a result of position or structure
CHEMICAL ENERGY- form of potential energy stored in chemical bonds in molecules
THERMODYNAMICS- study of energy transformations that occur in matter
1st LAW OF THERMODYNAMICS = Conservation of energy
• energy of universe is constant; energy CAN BE transferred and transformed, but NEVER created or destroyed

2nd LAW OF THERMODYNAMICS
• every energy transfer or transformation increases the entropy (disorder or randomness) in universe

Equation that describes energy of system;

G= H-T S
- change in free energy is represented by  G
S = ENTROPY
G = FREE ENERGY of a system
(energy that is able to perform work when the temperature is uniform)
H = Total energy in system
T = Absolute temperature in °Kelvin

You don’t need to be able to do G problems; just know that there is an equation;

EXERGONIC REACTION- releases energy and occurs spontaneously
Energy of products is lower than energy of reactants (negative G)
ENDERGONIC REACTION- requires energy; absorbs free energy from system; not spontaneous
Energy of products is higher than energy of reactants (positive G)
SPONTANEOUS REACTION
- can occur without outside help
- can be harnessed to do work (objects moving down their power gradient)
Cells manage their energy resources and do work by ENERGY COUPLING
(use energy from exergonic reactions to drive endergonic ones)
Key role of ATP = ENERGY COUPLING
ADENOSINE TRIPHOSPHATE (ATP)
= primary source of energy in all living things
ADP (adenosine diphosphate) + Pi → ATP;
-adding phosphate group stores energy;
-removing it releases energy

ACTIVATION ENERGY = amount of energy required to get chemical reaction started
CATALYST- substance that changes the rate of a chemical reaction without being altered
ENZYMES = biological catalysts; most enzymes are PROTEINS (Ch 17 & 26: RNA enzymes = RIBOZYMES)
ENZYMES work by LOWERING ACTIVATION ENERGY; Don’t change the FREE ENERGY of reaction
SUBSTRATE= Reactant enzyme acts on
ACTIVE SITE = region on enzyme that binds to substrate
Substrate held in active site by WEAK interactions (ie. hydrogen and ionic bonds)
SUBSTRATE(S) + enzyme → Enzyme-substrate complex → enzyme + PRODUCT(S)
ENZYMES are UNCHANGED & REUSABLE
LOCK-AND-KEY MODEL: enzyme fits substrate like “lock and key”
-only specific substrate will fit
INDUCED FIT MODEL: once substrate binds to active site, enzyme changes shape slightly to bind the substrate more firmly placing a strain on the existing bonds in substrate lowering act energy
Enzymes have OPTIMAL TEMPERATURE for activity
Higher temperatures = more collisions among the molecules so increase rate of a reaction BUT. . . above a certain temperature, activity begins to decline because the enzyme begins to DENATURE
So rate of chemical reaction increases with temperature up to optimum, then decreases.

Enzymes have own OPTIMAL pH
Different enzymes have different pH curves
Extremes in pH and temp can DENATURE enzymes
-causing them to unwind/lose their 3-D TERTIARY structure
-breaks hydrogen, ionic bonds; NOT covalent peptide bonds
Many enzymes require helpers:
NON PROTEIN helper
= COFACTOR
Ex: METAL IONS
(zinc, iron, and copper)

Hemoglobin
ORGANIC helpers = COENZYMES
Ex: vitamins
-part of NAD+, NADP, FADH2,
Coenzyme A molecules

COMPETITIVE INHIBITORS
- reversible
- compete with substrate for active site

NONCOMPETITIVE INHIBITORS
- bind another spot on enzyme
- cause shape change making active site nonfunctional
ENZYME REGULATION:
REGULATORS bind to ALLOSTERIC site
- binding site on enzyme (not active site)
- binding changes shape of enzyme
- ACTIVATORS can stimulate
INHIBITORS inhibit enzyme activity

NEGATIVE FEEDBACK (FEEDBACK INHIBITION)
- switches off pathway when product is plentiful
- common in many enzyme reactions;
- saves energy; don’t make it if you don’t need it

POSITIVE FEEDBACK – speeds up pathway
- Less common
EX: Chemicals released by platelets that accumulate at injury site, attract MORE platelets to the site.

CELLULAR RESPIRATION-Chapter 7
C6H12O6 + 6O2 → 6 CO2 + 6 H2O + energy
Type of oxidation-reduction (redox) reaction

OIL RIG
Oxidation Is Losing electrons
Reduction Is Gaining electrons

MITOCHONDRION STRUCTURE
Double membrane- allows compartmentalization
OUTER MEMBRANE
INNER MEMBRANE (CRISTAE) –contains Electron transport proteins
MATRIX- contains enzymes for KREBS CYCLE
INTERMEMBRANE SPACE- between cristae and outer membrane
Place where H+ ions accumulate during ETC
GLYCOLYSIS
“Glykos”= sweet; “lysis”=split apart
GLUCOSE → 2 PYRUVATE
Occurs in cytosol
Requires 2 ATP to get started
Produces 4 ATP (net gain 2 ATP)
Produces 2 NADH
GLYCOLYSIS PATHWAY
Regulated by phosphofructokinase
ALLOSTERIC enzyme near beginning of pathway
AMP turns pathway on
(AMP is high when ATP is needed)
ATP turns pathway off
(don’t waste energy making ATP when not needed)

EVOLUTIONARY LINKS
Glycolysis = Most widespread metabolic pathway
• Earliest fossil bacteria (3.5 billion years ago) but large amounts of oxygen not present until 2.7 BYA
• Works without oxygen
~suggests ancient prokaryotes probably used glycolysis to make ATP before oxygen was present
• happens in cytoplasm without mitochondria
~ suggests it was in early prokaryotic cells before eukaryotes appeared eukaryotes appeared 1 billion years after prokaryotes (Endosymbiotic theory)

WITHOUT OXYGEN (anaerobic)
Pyruvate → FERMENTATION
Regenerates NAD+ carriers to allow glycolysis to continue
ALCOHOLIC FERMENTATION
Pyruvate → CO2 + alcohol + NAD+
Used by microorganisms to make beer/wine
Used by yeast to make bread
LACTIC ACID FERMENTATION
Pyruvate → lactic acid + NAD+
Human muscle cells when oxygen is low during exercise

WITH OXYGEN
GLYCOLYSIS → KREBS CYCLE → ETC
HIGH ENERGY ELECTRON CARRIERS:
(B-vitamin coenzymes)
NAD+ → NADH

FAD → FADH2

FACULTATIVE ANAROBES (Ex: yeast/some bacteria) can switch back and forth between fermentation/respiration depending on O2 availability
Pyruvate transported into mitochondrial matrix
Uses 1 ATP/pyruvate for active transport
ACETYL CO-A CHARGING (B-vitamin coenzyme)
Co enzyme A receives carbons from pyruvate feeds them into Krebs cycle
Enzyme removes CO2 from pyruvate producing Acetyl CoA
Each glucose produces 2 C02 + 2 NADH
KREBS (CITRIC ACID) CYCLE
Releases 6 original carbons in glucose as 6 CO2;
Stores energy in NADH/FADH2
Occurs in Mitochondrial MATRIX
OAA (oxaloacetic acid) receives 2 carbons from Acetyl CoA to make CITRIC ACID
Each glucose requires TWO turns of cycle
1 GLUCOSE produces: 6 CO2, 2 FADH2, 2 ATP, 8 NADH

ELECTRON TRANSPORTstage that produces the MOST ATP
Attached to CRISTAE inner membrane
Uses energy from NADH & FADH2 to create proton gradient and make ATP
Includes:
THREE transmembrane PROTON PUMPS;
Carrier molecules between pumps =
UBIQUINONE (Q); and CYTOCHROMES
Each NADH makes 3 ATP (drops its electrons at top of ETC; hits all 3 proton pumps)
Each FADH2 makes 2 ATP (drops its electrons at Q; skips 1 st proton pump; so makes less ATP)
Electrons passing down ETC provide energy for pumping H+ ions into INTERMEMBRANE SPACE
Final electron acceptor at end of ETC = O2 (O2 + 2e- +2H+ → H2O)
1 glucose yields 36 net ATP
Proton gradient powers ATP SYNTHASE to ADP + Pi → ATP
PROTON MOTIVE FORCE = potential energy of hydrogen ion gradient
CHEMIOSMOSIS = Generation of ATP from a proton gradient
(It occurs in all living things)
OXIDATIVE PHOSPHORYLATION using proton gradient created by electron transport chain in cristae membrane to make ATP
ETC + CHEMIOSMOSIS = OXIDATIVE PHOSPHORYLATION
SUBSTRATE LEVEL PHOSPHORYLATION (found in glycolysis & Krebs cycle)
Addition of phosphate group directly WITHOUT proton gradient and ATP synthase
OTHER FUEL MOLECULES
Fats, proteins, carbohydrates can be broken down to release energy
1 g of fat → twice as much ATP as 1 g of carbohydrate
BETA OXIDATION = breakdown of fatty acids into 2 carbon fragments can enter Krebs cycle as acetyl CoA
Intermediates from glycolysis and Krebs cycle can be diverted into anabolic pathways to provide building blocks for many macromolecules

CHAPTER 8-Photosynthesis

• Life on Earth is solar powered
• Photosynthesis nourishes almost all the living world directly or indirectly
 All organisms use organic compounds for energy and for carbon skeletons.
 Organisms obtain organic compounds by one of two major modes: autotrophic or heterotrophic

AUTOTROPHS (=producers)
• produce organic molecules from CO2 and other inorganic raw materials obtained from the environment
• ultimate source of organic compounds for heterotrophs
Photoautotrophs use light as a source of energy to synthesize organic compounds.
• Photosynthesis occurs in plants, algae, some other protists, and some prokaryotes.
Chemoautotrophs
• harvest energy from oxidizing inorganic substances, such as sulfur and ammonia
• unique to prokaryotes
HETEROTROPHS (=consumers)
• live on organic compounds produced by other organisms
• dependent on photoautotrophs for food and for oxygen (by-product of photosynthesis)
PHOTOSYNTHESIS:
• converts light energy to the chemical energy of food
6CO2 + 6H2O + light energy  C6H12O6 + 6O2
• Happens in all green parts of plants but leaves = major site
~ about half a million chloroplasts/mm2 of leaf surface
• Color of leaf due to green pigment chlorophyll
Chloroplasts mainly in mesophyll cells in the interior of the leaf
30–40 chloroplasts/typical mesophyll cell
O2 and water vapor exits and CO2 enters leaf through microscopic pores on underside of leaf = stoma (pl. stomata)
GUARD CELLS control openings- OPEN if TURGID; CLOSED if FLACCID

VEINS bring water from the roots and carry off sugar from mesophyll cells to nonphotosynthetic areas of plant
XYLEM-carries water/PHLOEM carries sugar/nutrients
CHLOROPLAST:
• Surrounded by DOUBLE membrane
• Central fluid filled space = STROMA
• System of interconnected membranous sacs = THYLAKOIDS
• Stack of thylakoids = GRANUM (pl. GRANA)
• Fluid filled compartment inside thylakoid
=THYLAKOID SPACE (lumen)
• Chlorophyll is located in membranes of thylakoid sacs
Photosynthetic prokaryotes lack chloroplasts
- photosynthetic membranes = infolded regions of the plasma membrane

LIGHT
= form of electromagnetic radiation
Energy = inversely related to its wavelength
(ie, shorter wavelengths pack more energy)
Visible light = 380-750 nm
PIGMENTS = light absorbing molecules
• Only chlorophyll a participates directly in the light reactions;
• Other pigments have different absorption spectra; funnel energy to chlorophyll a
Chlorophyll a (the dominant pigment)
• ABSORBS best in the red & violet-blue wavelengths;
• REFLECTS green wavelengths = reason plants “look” green
Chlorophyll b- slightly different structure
• funnels energy to chlorophyll a
CAROTENOIDS = accessory pigments (red, yellow, orange);
• Include: CAROTENES (orange) and XANTHOPHYLLS (yellow)
• funnel the energy to chlorophyll a
• photoprotection- protect chlorophyll from excessive light
CHLOROPHYLL
Porphorin ring with MAGNESIUM cofactor in center
Plants have a and b forms- slight difference in functional groups
Chlorophyll a is universal
Other forms found in algae and cyanobacteria

EXCITING ELECTRONS:
When a molecule absorbs a photon of light an electron is elevated to an orbital with more potential energy
Electron moves from ground state → excited state
Excited electrons are unstable
They drop to their ground state in a billionth of a second, releasing heat energy

Some pigments, including chlorophyll, can also release a photon of light when excited (= FLUORESCENCE)
Outside of chloroplasts, if chlorophyll is illuminated, it will fluoresce and give off heat
PHOTOSYSTEMS in thylakoid membranes
• reaction center containing chlorophyll a and “primary electron acceptor”
• surrounded by a light-harvesting complex of other pigments and proteins (chlorophyll b, carotenoids)
• act as “antenna” to collect light energy → chlorophyll a → “primary electron acceptor”
Photosystem I (PS I) reaction center absorption peak at 700 nm (P700)
Photosystem II (PS II) reaction center absorption peak at 680 nm (P680)
TWO STAGES OF PHOTOSYNTHESIS:
1) LIGHT REACTIONS (Light dependent reactions) convert solar energy to the chemical energy of ATP and NADPH
2) CALVIN CYCLE (Light independent reactions)

uses energy from the light reactions to incorporate CO 2 from the atmosphere into sugar.
Named for Melvin Calvin (Got Nobel in 1961 for figuring out pathway)

LIGHT REACTIONS:
• Use solar power to store chemical energy in ATP and reducing power in electron carrier NADPH
• REQUIRE sunlight
•Two possible routes
1) NONCYCLIC ELECTRON FLOW (= predominant route) produces both ATP and NADPH
- Photosystem II absorbs a photon of light
- One of the electrons of P680 reaction center is excited to a higher energy state
- Electron is captured by the primary electron acceptor, leaving the reaction center oxidized

- Electrons are replaced by splitting a water molecule in thylakoid space
- Oxygen released from water splitting combines with another oxygen atom; released as O2 to atmosphere
- Hydrogen released from water splitting accumulates in thylakoid space
- Photoexcited electrons pass along electron transport chain ending up at Photosystem I reaction center
- energy from electrons “falling down” ETC is used by CYTOCHROMES to pump H+ ions into thylakoid space • When chloroplasts are illuminated, thylakoid space pH ~5; stroma pH ~ 8 (1000 fold difference)
- Photosystem I absorbs a photon of light
- One of the electrons of P700 reaction center is excited to a higher energy state
- Electron is captured by the primary electron acceptor, leaving the reaction center oxidized
- Electrons are replaced by electrons passed from PS II down ETC
- Photoexcited electrons pass down a second electron transport chain through the protein FERRIDOXIN
(Fd)
- Enzyme transfers 2 electrons to NADP+ (nicotinamide adenine dinucleotide phosphate) to produce
NADPH
- H+ ions in thylakoid space provide energy to produce ATP as they diffuse down their gradient (ELECTROMOTIVE FORCE) back into the stroma through ATP SYNTHASE
2) CYCLIC ELECTRON FLOW
• alternative pathway for photoexcited electrons from photosystem I = CYCLIC PHOTOPHOSPHORYLATION
• Photoexcited electrons return to CYTOCHROMES instead of passing to Ferridoxin
• So produces only ATP; NO NADPH; no OXYGEN
• Used because NON CYCLIC FLOW makes equal amounts of ATP and NADPH
• Calvin cycle requires more ATP than NADPH
• Way to regulate amounts of ATP and NADPH needed for Calvin cycle
CHEMIOSMOSIS IN CHLOROPLASTS AND MITOCHONDRIA
SIMILARITIES
• Used by chloroplasts and mitochondria to generate ATP
• Energy from ELECTRON TRANSPORT CHAIN used to pump protons across a membrane
• Creates a H+ gradient across membrane
•ATP SYNTHASE uses energy from diffusion of H+ ions back across membrane to generate ATP
• Some electron carriers (cytochromes) are similar in both chloroplasts/mitochondria
DIFFERENCES:
OXIDATIVE PHOSPHORYLATION in MITOCHONDRIA
• Mitochondria transfer chemical energy from food molecules to ATP
• Mitochondrial INNER MEMBRANE pumps protons from MATRIX out to the INTERMEMBRANE SPACE
• ATP made as H+ ions diffuse back to stroma
PHOTOPHOSPHORYLATION in CHLOROPLASTS
• Chloroplasts transform light energy into the chemical energy of ATP
• Chloroplast THYLAKOID membrane pumps protons from the stroma into the thylakoid space
CALVIN CYCLE (= LIGHT INDEPENDENT PHASE)
Originally called “Dark reactions” but don’t just happen at night
Happens in stroma
Uses ATP and NADPH (made in Light Reactions) to convert CO2 to sugar regenerates its starting material after molecules enter and leave the cycle
= anabolic -uses energy to build sugar from smaller molecules
Carbon enters the cycle as CO2 and leaves as sugar
Actual sugar product = three-carbon sugar, glyceraldehyde-3-phosphate (G3P)
Each turn of the Calvin cycle fixes carbon from 1 CO2; 3 turns to make 1 G3P; 6 turns to make 1 glucose
Uses 18 ATP’s and 12 NADPH’s to make 1 glucose

CALVIN CYCLE
Phase 1: Carbon fixation
Each CO2 molecule is attached to a five-carbon sugar, RIBULOSE BISPHOSPHATE (RuBP)
 This is catalyzed by RuBP carboxylase (=RUBISCO)
 Rubisco = most abundant protein in chloroplasts; probably the most abundant protein on Earth
 Unstable six-carbon intermediate splits in half to form two three carbon 3-phosphoglycerate for each
CO2
Phase 2: Reduction
ATP provides energy; NADPH provides reducing power to reduce intermediates
Three carbon GLYCERALDEHYDE-3-PHOSPHATE (G3P) is produced
G3P exits the cycle; = starting material for metabolic pathways that synthesize other organic compounds, including glucose and other carbohydrates
Phase 3: Regeneration
Rest of molecules rearrange to regenerate the starting RuBP molecules
For the net synthesis of one G3P molecule, the Calvin cycle consumes nine ATP and six NADPH (X 2 for glucose)
Light reactions regenerate ATP and NADPH
WHERE DOES THE OXYGEN IN SUGAR COME FROM: H2O or CO2?
CO2 + H2O + light energy  [CH2O] + O2
[CH2O] represents the general formula for a sugar
Before 1930’s thought splitting H2O provided oxygen for sugar
Experiments with radio-labeled oxygen isotopes in H2O and CO2 showed oxygen in carbo’s comes from CO2

Evidence that chloroplasts split water molecules enabled researchers to track atoms through photosynthesis. Powered by light, the green parts of plants produce organic compounds and O 2 from CO2 and H2O
Photosynthesis is a REDOX REACTION
 It reverses the direction of electron flow in cellular respiration
 H2O is OXIDIZED (loses electrons)
 CO2 is REDUCED (gains electrons) to make sugar
 Process requires energy (provided by light)
C3 PLANTS = Most plants (EX: rice, wheat, and soybeans)
Rubisco fixes CO2 into three carbon compound (3PGA)
Calvin cycle happens during day when ATP and NADPH are available from light reactions

OIL RIG
Oxidation Is Losing
Reduction Is Gaining

PROBLEM: Closing stomata on hot dry days to conserve water, reduces CO2 needed for photosynthesis
When CO2 is low Rubisco adds O2 to RuBP instead of CO2
= PHOTORESPIRATION
Rubisco adds O2 to RuBP, RuBP splits into a three-carbon piece and a two-carbon piece
Two-carbon fragment is exported from chloroplast and degraded to CO 2 by mitochondria and peroxisomes.
 Unlike normal respiration, consumes ATP instead of making it


Unlike photosynthesis, siphons organic material from the Calvin cycle instead of making sugar



Photorespiration can drain away as much as 50% of the carbon fixed by the Calvin cycle on a hot, dry day. PHOTORESPIRATION may be evolutionary baggage
When rubisco first evolved, the atmosphere had far less O 2 and more CO2 than it does today
Inability of the active site of rubisco to exclude O2 would have made little difference then,
BUT makes a difference today when O2 in atmosphere is higher

Alternative mechanisms of carbon fixation
Certain plant species have evolved alternate modes of carbon fixation to minimize photorespiration
C4 PLANTS- EX: sugarcane and corn

Minimizes photorespiration and allows plant to efficiently fix CO 2 at low concentrations Allows plants to thrive in hot regions with intense sunlight
Unique leaf anatomy; spatial separation of CO2 fixation from air/into sugar
BUNDLE SHEATH cells arranged into tightly packed sheaths around leaf veins
MESOPHYLL cells more loosely arranged cells located between bundle sheath cells and leaf surface
PEP CARBOXYLASE in mesophyll cells has very high affinity for CO2 ;
Can fix CO2 efficiently at low levels when rubisco can’t
CO2 fixed into a FOUR CARBON compound/ pumped into BUNDLE SHEATH cells CO2 is released in Bundle sheath cells, keeping CO2 levels high enough for rubisco to work in Calvin cycle

PEP Carboxylase also found in some bacteria, but not animals or fungi.
CRASSULACEAN ACID METABOLISM (CAM) PLANTS- EX: Succulents, cacti, pineapples
Evolved in hot, dry environments
TEMPORAL separation of CO2 fixation from air/into sugar
Open stomata during night when temps are lower and humidity higher
Close them during the day to save water
AT NIGHT: Fix CO2 in mesophyll cells
Use PEP carboxylase, like C4 plants, to fix CO2 forming four carbon compounds
Stored in vacuoles
DURING DAY:
Light reactions supply ATP & NADPH;
CO2 is released from organic acids to complete Calvin cycle
IMPORTANCE OF PHOTOSYNTHESIS:
Energy from sunlight = stored as chemical energy in organic compounds
Sugar made in the chloroplasts supplies the entire plant with chemical energy
AND with carbon skeletons to synthesize all the major organic molecules of cells
- Carbohydrate (as disaccharide sucrose) travels via the veins to nonphotosynthetic cells
-About 50% = consumed as fuel for cellular respiration in plant mitochondria
Also provides raw materials for anabolic pathways, including synthesis of proteins and lipids and formation of the extracellular polysaccharide cellulose
Cellulose = main ingredient of cell walls; = most abundant organic molecule in the plant, maybe on Earth
Plants also store excess sugar by synthesis of starch in chloroplasts and in storage cells in roots, tubers, seeds, and fruits.
On a global scale, photosynthesis is the most important process on Earth
 Provides food energy for heterotrophs, including humans
 It is responsible for the presence of oxygen in our atmosphere.
 Each year, photosynthesis synthesizes 160 billion metric tons of carbohydrate