It is the sum of all an organism's chemical reactions.

It invovles metabolic pathways.

What are the two main types of metabolic pathways?

For each, describe and give an example.

Catabolic Pathways: Release energy by breaking down complex molecules. Example: Cellular Respiration

Anabolic Pathways: Consume energy to build complex molecules. Example: Photosynthesis

Kinetic Energy: Energy of motion. Example: Thermal energy.

Potential Energy: Stored energy. Example: Chemical energy of structure.

Energy cannot be created or destroyed. It can only be converted into one form or another.

(This is the principle of conservation of energy)

Energy conversions will always increase the entropy of the universe.

This is because some energy is always lost as heat.

The quanity of energy never changes.

The quality of energy changes.

(Heat is random energy of the lowest quality.)

How is order obtained within an organism?

(Regarding the laws of thermodynamics)

Organisms are open systems, so energy and materials are exchanged with their surroundings.

Order can be increased within the organism if entropy is increased in the surroundings. (Order is decreased in the surroundings)

Free energy is energy available to do work.

Its symbol is G (for Gibb's free energy)

When is a process spontaneous?

(In terms of G)

It is spontaneous when (delta)G < 0

Note: Spontaneous DOES NOT mean fast.

It means energy out.

It has a -(delta)G

It releases energy.

It means energy "in."

It has a +(delta)G

It absorbs energy.

Their reactions would reach equilibrium. They would be dead.

(delta)G = 0

ATP stands for adenosinetriphosphate.

It is an energy carrier molecule.

ATP can be created in exergonic reactions.

ATP can by hydrolyzed for endergonic reactions.

Adenine

Ribose

Three phosphate groups ("high energy" bonds)

(delta)G = -7.3 kcal/mol

ATP can be used to phosphorylate molecules.

The transfer of a phosphate group makes the phosphorylated intermediate more reactive.

ATP phosphorylates glutamic acid making the amino acid less stable. Ammonia then displaces the phosphate group, forming glutamine.

Transport Work: ATP phosphorylates transport proteins

Mechanical Work: ATP binds noncovalently to motor proteins and then is hydrolyzed

Yes, ATP is continuously used and regenerated.

Millions of ATP are produced every second by each cell.

It is made of phenylalanine and aspartic acid.

This matters because patients lack the enzyme phenylalanine hydroxylase, which converts phenylalanine to tyrosine. The buildup of phenylalanine can be toxic.

It is energy required to start a reaction.

The state at the 'peak' of an energy graph is called the "transition state"

They bring reactants together

Stress bonds to be broken

Provide the proper environment

Participate direcly in the reaction

1. Substrates enter the active site
2. Substrates are held in active site by weak interactions
3. Active site can lower Ea and speed up a reaction
4. Substrates are converted into products
5. Products are released
6. Active site is available for new substrate molecules

Temperature

pH

Cofactors

They assist the enzyme in reactions. They are called coenzymes if they are organic.

Ex. Metal ions, vitamins

Competative inhibition

Noncompetative inhibition

When another molecules binds to the active site and blocks the way for the intended substrate.

Ex. Penicillin, which blocks the active site of and enzyme for cell wall synthesis.

When an molecule binds to a site other than the active site on an enzyme. This is called "allosteric regulation."

It is accomplished because the molecule alters the protein configuration of the enzyme, rendering it inactive.

Cellular respiration is catabolic

Photosynthesis is anabolic

Redox reactions are oxidation-reduction reactions.

Oxidation is the loss of electrons

Reduction is the gain of electrons

Oxidations and reductions happen together

Oxidating agents accept electrons.

Ex. Oxygen

Reducing agents donate electrons

Ex. Glucose

NAD+ is a coenzyme made from the vitamin nacin.

It is an oxidizing agent (it accepts electrons).

It reduces to NADH and stores energy.

NAD+

NADP

FAD

It converts light to chemical energy. (A 3-Carbon sugar that can easily be made into glucose)

It takes place in the choloroplasts, but is not limited to only plants.

Stomata are pores on the surface of the leaf that are used for gas exchage.

Mesophyll is tissue inside of a leaf that contains chloroplasts.

It takes in water, light, NADP+, and ADP

It produces oxygen, ATP, NADPH

The light reaction takes place in the thylakoid membrane.

The Calvin cycle takes in ATP, NADPH, and carbon dioxide.

It produces NADP+, ADP, and sugar (CH2O).

It is also called the dark cycle and takes place in the stroma.

Thylakoid: Flattened disks

Granum:Stack of thylakoid disks

Stroma: Matrix outside the thylakoids

Wavelenght is the distance between crests (measured in nanometers).

Visible light is between 380-750 nm.

Short wavelengths have high energy.

Long wavelengths have low energy.

Chlorophyll a: It directly participates in light reactions. It is blue-green.

Cholorphyll b: It indirectly participates in light reactions. It is olive-green.

Carotenoids: Used for photoprotection (but can minimally help in photosynthesis). They are yellow and orange.

1. A photo of light is absorbed.
2. The electron is moved from its ground state to a more excitied, unstable state.
3. The electron rapidly returns to the ground state.
4. Energy is then transferred to another molecule (or lost as heat or fluorescence).

Photosystems capture excitied electrons.

Their two major parts are light-harvesting complexes and reaction center complexes.

It includes a cluster of protein and pigment molecules.

The light-harvesting complex transfers energy to the reaction center complex.

It includes a pair of chlorophyll a molecules and a primary electron acceptor.

The reaction-center complex can transfer an electron to an electron transport chain.

Photosystem II (PS II): It absorbs 680 nm wavelength best.

Photosystem I (PS I): It absorbs 700 nm wavelength best.

Light energy and electrons from water are both taken by P680.

P680 is oxidzied and its electrons are transfered to the primary electron acceptor, reducing it.

Electrons are transfered to Pq, then to the Cytochrome complex(where ATP is produced), then to Pc.

Light energy from pigment molecules and electrons from Pc are taken by P700.

P700 is the oxidized, giving up its electrons to the primary electron acceptor, reducing it.

Electrons are then transfered to Fd to NADP+ reductase where NADP+ is combined with H+ and two electrons to form NADPH.

When a hydrogen ion gradient is used to do work?

Such as in the synthesis of ATP by ATP synthase.

It is important for cellular respiration.

The phases are: Carbon fixation, reduction of sugar, and regeneration of carbon-dioxide acceptor.

It produces G3P (Glyceraldahyde-3-phosphate).

CO2 is attached to RuBP, which is catalyzed by the enzyme rubisco.

The resulting 6C sugar is unstable and splits into two 3C sugars.

3C sugars are phosphorylated by ATP.

3C sugars are reduced by NADPH.

One of the 3C sugars is the output G3P

Five G3P molecules are rearragnged using ATP.

Three RuBP are formed.

They are transported to the cytosol by antiporting (traveling oppositely) with Pi.

They are then converted to glucose or sucrose.

C3 Plants: Rubisco intitially fixes CO2 into a 3C compound called 3PG.

Ex. rice, wheat, and soybeans.

C4 Plants:Rubisco initially fixes CO2 into a 4C compound called Oxaloacetate.

Ex. sugarcane, corn, grasses.

Photorespiration occurs on hot, dry days. Plants close their stomata, which makes less CO2 available for the Calvin cycle.

Rubisco adds O2 instead of CO2 to RuBP and the product will be converted into CO2.

No sugar is made, but ATP is used.

They do not use photorespiration extensively because they are adapted for high heat and sunlight.

They utilize bundle sheath and mesophyll cells.

Mesophyll cells help increase CO2 in bundle sheath cells.

Bundle sheat cells can utilize CO2 for the Calvin cycle.

CAM (Crassulacean acid metabolism) plants are water storing desert plants.

Ex. Succulents, cacti, pineapples.

They open their stomata at night and fix CO2 to an organic acid.

During the day they close their somata and utilize that organic acid for CO2.

Glycolysis

Citric Acid Cycle

Oxidative Phosphorylation

This is important for baskeball players.

Glucose is oxidized to pyruvate.

NADH and ATP are formed.

It takes place in the cytosol.

Pyruvate derivative is oxidzied to CO2.

NADH, FADH2, and ATP are formed.

It takes place in the Mitochonria.

The electron transport chain creates a gradient.

This gradient is used for form ATP.

It takes place in the mitochondria.

Glycolysis means "Sugar splitting."

Its two major phases are energy investment and energy payoff.

It yields 2 pyruvate, 2 ATP, 2 NADH.

[Phospho]kinase: Catalyzes transfer of phosphate from ATP to a secondary substrat.

Isomerase: Converts molecules into their positional isomers.

Dehydrogenase: Transfers a hydrogen ion to an electron acceptor, such as NAD+.

It is allosterically regulated.

When a phosphate group from an organic molecule is used to make ATP.

It occurs in glycolysis and the citric acid cycle.

Pyruvate enters the mitochondria via active transport.

Pyruvate is converted into acetyl coenzyme A (acetyl coA).

It was discovered by Hans Kreb.

It begins and ends with oxaloacetate.

There are 8 enzyme mediated steps.

It occurs in the mitochondrial matrix.

4 NADH, 1 FADH2, 1 ATP

(Remember that two pyruvate were formed for each glucose)

Only 4 net ATP are produced via substrate level phosphorylation.

(Most of the energy from glucose is in NADH and FADH2)

The Electron Transport Chain

and

Chemiosmosis

The ETC occurs on the inner mitochonrial matrix because of its high surface area.

Electrons are passed through the ETC and energy is slowly released. The movement of electron is coupled with H+ ions and the H+ ions are pumped across the membrane.

Complexes I-IV: They contain proteins and prosthetic groups.

Mobile Electron Carriers: Ubiquinone (Q) and Cytochrome c (Cyt c).

Final Electron Acceptor: Oxygen (because it is very electronegative)

Electrons pass from NADH to FMN. NAD+ is oxidized, FMN is reduced.

Electrons pass from FMN to Fe*S. FMN is oxidized, Fe*S is reduced.

Fe*S electrons transfer to Q, which carries electrons to complex III.

Electrons move through the ETC until they reach oxygen.

Electrons pass from FADH2 to FAD, then from FAD to Fe*S.

Electrons are then tranferred to Q and moved on through the ETC to oxygen.

As electron move through the ETC, protons are pumped across the membrane.

The resulting H+ gradient is used to form ATP.

It is a multiprotein complex in embedded in the inner mitochondrial membrane.

H+ ions move through the enzyme down their concentration gradient. This activates the catylitic portion that form ATP from ADP and Pi.

The maximum amount of ATP that is produced is about 36 or 38 ATP.

Most of that (32 or 34) is produced via the electron transport chain and chemiosmosis.

Anaerobic Respiration: Involves an ETC, but not oxygen.

Ex. Some marine bacteria use SO4^(2-)

Fermentation: Does not involve an ETC or oxygen. ATP is produced by substrate level phosphorylation.

It includes glycolysis to form 2 ATP and reactions to regnerate NAD+.

The two major types are alcohol and lactic acid fermentation.

It converts pyruvate into ethanol and regenerates NAD+.

It is important for baking, brewing beer, and making wine.

It converts pyruvate into lactate and regenerates NAD+.

It is used in muscle cells when oxygen levels are low.

It is important for making cheese and yogurt.

Obligate: Only perform fermentation OR anerobic respiration.

Facultative: Can perform fermentation or anerobic respiration.

Mitosis: Nuclear division

Cytokinesis: Cytoplasmic division

Reproduction

Growth and Development

 Tissue Renewal

Interphase: G1, S, G2, G0

M Phase: Mitosis and Cytokinesis

Mitosis occurs in somatic cells (non-reproductive cells).

The replicated DNA is divided equally in mitosis. One of each chromosome is distributed to each nuclei.

The total number of chromosomes in a cell.

Human somatic cells have 46 (23 pairs).

Diploid organisms have two sets of chromosomes.

During mitosis, a diploid parent cells produce two diploid daugher cells.

The chromosome number is maintained.

They are duplicated in the S phase, resulting in two sister chromatids.

Centromeres: The region that joins the sister chromatids.

Kinetochore: Stuctures to which the mitotic spindle connects.

Prophase

Prometaphase

Metaphase

Anaphase A

Anaphase B

Telophase

It assembles at the centrosomes.

It also includes microtubuls (MT) and associated proteins.

Kinetochore

Overlapping

Asters

It is not part of mitosis.

The nuclear envelope is present.

Chromosomes are not distinct.

Two centrosomes have been formed, but are not at the poles.

The chromosomes condense.

Centrosomes move apart.

Mitotic spindle begins to form.

Nuclear envelope breaks down.

Microtubules attach to chromosomes.

The mitotic spindle is formed.

Centrosomes are at opposite ends.

Chromosomes line up at metaphase plate.

The M phase chekpoint occurs.

Proteins holding together sister chromatids are degraded.

Sister chromatids move to opposite poles because of the kinetochore microtubules.

They move along the kinetocher microtubules via a motor protein.

In other cell types, they may be pulled in.

Spindle poles move further apart.

Force exerted by non-kinetochore microtubules (Asters and overlapping).

Chromosomes arrive a spindle poles.

Nuclear envelope reforms.

Chromatin fibers decondense.

A cleavage furrow forms in the center of a cell.

Actin and myocin contract and the cell is pinched in two.

Vesicles move to center to form a cell plate. 

Cell plate fuses with plasma membrane.

Cell plate helps form new cell wall.

Kinase: Enzymes that phosphorylate proteins.

Cyclins: Control kinase activity.

Maturation promoting factor is a cyclin-Cdk complex.

It helps cell pass from G2 to M phase. It does this by phosphorylating proteins to activate or inhibit them.

Ex. MPF phosphorylates nuclear lamina to facilitate its breakdown.

Cdk levels remain constant.

Cyclin levels rise and fall.

MPF is only active in G2/M phase.

They have escaped cell cycle control.

They undergo excessive division and can invade other tissues.