AP Bio 8-10 Test Review

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

Energy

The capacity to do work. Organisms transform this.

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

The study of energy transformations that occur in matter

1st law of thermodynamics

Conservation of energy. The energy of the 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 the universe. Living systems DO NOT VIOLATE it (open systems with constant input of matter and energy)

Energy equation

ΔG = ΔH - TΔ S

ΔG = change in free energy

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

Exergonic reaction

Releases energy and occurs spontaneously. Energy of products is lower than energy of reactants (negative G/free energy)

Endergonic reaction

Required energy; absorbs free energy from system; not spontaneous. Energy of products is higher than energy of reactants (positive G/free energy)

Spontaneous reaction

Can occur without outside help. Can be harnessed to do work (objects moving down their power gradient)

Energy coupling

Cells manage their energy resources and do work by this process (use energy from exergonic reactions to drive endergonic ones). This is the key role of ATP.

Growth, reproduction, and maintenance of organization in living organisms require constant input of free energy and matter. Loss of order/free energy = death.

Energy input must exceed free energy lost to entropy to maintain order and power cellular processes.

Adenosine triphosphate (ATP)

Primary source of energy in all living things.

Created using ADP and a phosphate. Adding a phosphate group stores energy, removing it releases energy = -ΔG reaction

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 are proteins.

RNA ___= RIBOZYMES

Work by lowering activation energy; don’t change the free energy of reaction.

Unchanged and reusable.

Substrate

Reactant enzyme acts on. Held in active site by weak interactions (ie. hydrogen and ionic bonds).

Active site

Region on enzyme that binds to substrate

Lock-and-key model

Enzyme fits substrate like “lock and key” - only one specific substrate will fit.

Induced fit model

Once substrate bonds to active site, enzyme changes shape slightly to bind the substrate more firmly, placing a strain on the existing bonds in substrate, lowering activation energy.

Optimal energy

Higher temperatures = more collisions among the molecules, so increased rate of a reaction, BUT above a certain temperature activity starts to decline because the enzyme begins to denature.

Rate of chemical reaction increases with temperature up to this, but decreases when it goes above.

Optimal pH

Different enzymes have different pH curves. Extremes in pH and temp can DENATURE enzymes, causing them to unwind/lose their 3D tertiary structure. Breaks hydrogen and ionic bonds; not covalent peptide bonds.

Cofactor

Non-protein helpers for enzymes.

Ex: Metal ions (zinc, iron, and copper)

Coenzyme

Organic helpers for enzymes.

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

C₆H₁₂O6 + 6O₂ → 6 CO₂ + 6 H₂O + energy

Type of oxidation-reduction (redox) reaction

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

Splits apart sugar.

GLUCOSE → 2 PYRUVATE

Occurs in cytosol

Requires 2 ATP to get started

Produces 4 ATP (net gain 2 ATP), Produces 2 NADH

Most widespread metabolic pathway. Present in 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 it 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)

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)

Fermentation

Is done without oxygen (anaerobic). Regenerates NAD+ carriers to allow glycolysis to continue using pyruvate.

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.

Acetyl-CoA Charging

B-vitamin coenzyme

Coenzyme A receives carbons from pyruvate and feeds them into Krebs cycle

Enzyme removes CO2 from pyruvate producing Acetyl CoA

Each glucose produces 2 CO₂ + 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 transport

Stage that produces the most ATP. Attached to cristae inner membrane. Uses energy from NADH and 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 1st 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 (occurs in all living things)

Oxidative phoshorylation

ETC + chemiosmosis = this.

Using proton gradient created by electron transport chain in cristae membrane to make ATP

Substrate-level phosphorylation

Found in glycolysis and Krebs cycle. Addition of a phosphate group directly WITHOUT a 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

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 are a major site. About half a million chloroplasts/mm² of leaf surface. Color of leaf is due to the green pigment chlorophyll.

Chloroplasts mainly in mesophyll cells in the interior of the leaf. 30-40 chloroplasts in the typical mesophyll cell.

O₂ and water vapor exists and CO₂ enters leaf through microscopic pores on the underside of leaf = stoma (plural: stomata)

Guard cells control openings - open if turgid, closed if flaccid

Veins bring water from the roots and carry of sugar from mesophyll cells to nonphotosynthetic areas of plant.

Xylem carries water, phloem carries sugar/nutrients

It 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).

Autotrophs (producers)

• produce organic molecules from CO₂ and other inorganic raw materials obtained from the environment

• ultimate source of organic compounds for heterotrophs

• Photo_____ use light as a source of energy to synthesize organic compounds.

• Photosynthesis occurs in plants, algae, some other protists, and some prokaryotes.

• Chemo_____ 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 oxygen (by-product of photosynthesis)

Pigments

Light absorbing molecules.

Only chlorophyll a participates directly in the light reactions; others have different absorption spectra; funnel energy to chlorophyll a

Chlorophyll a

The dominant pigment. Absorbs best in the red and 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).

Includes 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. A is universal. Other forms found in algae and cyanobacteria.

Spectrophotometer

Measures the ability of pigment to absorb various wavelengths of light

•beams narrow wavelengths of light through a solution containing the pigment

•measures the fraction of light transmitted at each wavelength

•Absorption spectrum plots a pigment’s light absorption versus wavelength

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

Electrons in this state 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)

Light reactions

Convert solar energy to the chemical energy of ATP and NADPH. Use solar power to store chemical energy in ATP and reducing power in electron carrier NADPH. Requires sunlight.

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

Calvin cycle

Light independent reactions, Uses energy from the light reactions to incorporate CO₂ from the atmosphere into sugar.

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

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

Carbon fixation

Phase 1 of Calvin Cycle.

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

Reduction

Phase 2 of the Calvin Cycle.

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

Regeneration

Phase 3 of the Calvin Cycle. 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

CO₂

Where the oxygen in sugar comes from. Experiments with radio-labeled oxygen isotopes showed this.

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, it 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, it synthesizes 160 billion metric tons of carbohydrates

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 these

- 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 = 380-750 nm