BOTANY ITHE DEFINITION TABLE

TERM DEFINITIONTHE FLOW OF ENERGY

Free EnergyThe amount of energy in a molecule available for

doing work.

Endergonic Reactions that require net input of energy.Exergonic Reactions that end with net release of energy. Dynamic

EquilibriumThe rate of change is exactly the same in both

directions. No work is done.Activation

EnergyThe minimum amount of energy required to get a

reaction started.Closed system No energy is exchanged with the surroundings.Open system Energy is exchanged with the surroundings.

1st Law of Thermodynami

cs

Energy cannot be crated nor destroyed but can be transferred and changed in form.

The total energy in the universe is constant.In all energy exchanges and conversions, the total energy of the system and its surroundings after the

conversion is equal to the total energy before conversion.

2nd Law of Thermodynami

cs

Disorder in the universe, a closed system, is continuously increasing.

The total energy available for doing in work in a closed system decreases over time.

In all energy exchanges and conversions, if no energy leaves or enters the system under study,

the potential energy of the final state will always be less than the potential energy of the initial state.

Entropy The measurement of randomness or disorder in a system.

Oxidation A substance gives one or more electrons.Reduction A substance receives one or more electrons.Metabolic Pathway

Any system of enzyme – mediated reaction by which a cell builds, rearranges, or breaks down an

organic substance.Anabolic Pathway Builds molecules.Catabolic Pathway Breaks down molecules.

Cyclic Pathway Regenerates a molecule from the first step.Anabolism Series of chemical reactions involved in the

synthesis of organic compounds.Catabolism Series of chemical reactions that break down

organic molecules.ENZYMES

EnzymeIt is a protein molecule specialized as a catalyst

which makes a reaction occur much faster than it would on its own. It hastens the reaction from 106

to 1020 times faster.Substrate It is a specific substance acted upon by an enzyme.Energy of Activation

Energy that must be processed by molecules to react.

CatalystIt is a substance which lowers the activation energy

of a reaction by making a temporary association with the reacting molecules.

Active Sites These are areas on the enzyme where substrate binds and reactions proceed.

Induced Fit Hypothesis

The functionality of an enzyme is determined by the shape of the protein.

The enzyme recognizes, confines, and orients the substrate in a particular direction.

The arrangement of the molecules on the enzyme produces an area known as active

site within which the specific substrate will fit. Suggests than the binding of the substrate to

the enzyme alters the structure of the enzyme placing some strain on the substrate

and further facilitating reaction.Cofactors Non – protein substances essential for

enzyme activity. (e.g. K+ and Ca2+)Coenzymes Non – protein organic molecules bound to

enzymes near the active site. (e.g. NAD)FACTORS AFFECTING ENZYME ACTIVITY

Temperature High temperature boosts reaction rates by

increasing a substrate’s energy. But very high temperatures denature an enzyme.

pH

Each enzyme has an optimum pH range. Change in pH causes side chains in the tertiary

structure of a protein to ionize. The tertiary structure of the protein determines the precise shape of an enzyme. It is held together by weak

bonds (inc. H – bonds) between K – groups.Salinity Salt levels affect the hydrogen bond that holds

enzymes in their three – dimensional shape.Concentration of Substrate

Increasing substrate concentration increases collision rate and reaction rate.

Moreover, high concentration of substrate causes an enzyme to avoid binding to the inhibitor and so

maximum turnover is achieved. INHIBITION

Reversible Inhibitiono Competitive – inhibitor competes with

substrate for active site.o Non – competitive – inhibitor binds at a

different site Irreversible Inhibition – inhibitor combines

with an enzyme and permanently deactivates it, resulting to zero formation of products.

INHIBITORS- Molecules that prevent enzymes in reaching

their maximum turnover numbers. Active Site – directed Inhibitor – Inhibitor

resembles the substrate enough to bind to the active site and so prevent the binding of the substrate.

Inactive Site – directed Inhibitor – Inhibitor does not resemble the substrate and binds to the enzyme disrupting the active site.

ADENOSINE TRIPHOSPHATE

Adenosine Triphosphate

Energy currency of the cell. Donates energy of the third phosphate group. Formed by the phosphorylation of adenosine

diphosphate. (endergonic) ATP ADP + Pi

Amount in any cell is surprisingly small. Average bacteria cell has <5 million ATPs,

only enough to sustain activity for a second or two.

Supply must be continuously replenished. Plays a central role in cell energy metabolism

by linking exergonic and endergonic reactions.

RESPIRATIONCellular

RespirationIt is the process by which cells extract energy from food.

It uses bond energy (electrons) to regenerate ATP.Respiration(in general)

Free energy is released and is incorporated into ATP. It can readily be used for the maintenance and

development of the plant.EQUATION:

C6H12O6 + 6 O2 + 40 ADP + 40 Pi 6 CO2 + 6H2O + 40 ATP

Low temperature oxidation of carbohydrates carried out by living systems and enzymes.

It means to transform carbohydrates into chemical energy (ATP) for many other plant reactions.

It occurs during the night, in developing and ripening fruit and in dormant seeds. It occurs in the mitochondria.It mainly functions for the conversion of potential energy

of food molecules into ATP.

Aerobic Respiration

Requires oxygen; involves the complete breakdown of glucose back into CO2 and H2o.

THREE MAIN STEPS IN AEROBIC RESPIRATION

Glycolysis

The breakdown of glucose into a 3 – carbon compound called PYRUVATE. It occurs in the cytosol.

Some storage energy molecules (ATP and NADH) are also formed.

The synthesis of NADH from NAD involves three phases:

1. Energy Investment Phase2. Cleavage of 6 – Carbon sugar into 2 – 3 Carbon

Sugar3. Energy Regeneration Phase

Overall reaction:Glucose + 2 NAD+ + 2 ADP + 2 Pi 2 pyruvate + 2 NADH + 2 H + 2 ATP + 2 H20

Krebs Cycle/Tricarbo

xylic Acid Cycle/Citric Acid Cycle

It occurs in the matrix of the mitochondria. A cyclic series of reaction that completely

breaks down pyruvate into CO2 and various carbon skeletons.

o Skeletons are used in other metabolic pathways to produce various compounds.

o Includes proteins, lipids, cell wall carbohydrates, DNA, plant hormones, and plant pigments.

Carbon dioxide is given off by the plant. 10 NADH are generated. Overall reaction:

Oxaloacetate + Acetyl CoA + 3 H2O + ADP + Pi + 3 NAD + FAD Oxaloacetate + 2 CO2 + CoA + ATP +3 NADH + 3 H+ + FADH2

Electron Transport

Chain/Oxidative

Phosphorylation

Series of proteins in mitochondria helps transfer electrons from NADH to oxygen.

It releases a lot of energy. It occurs in the inner membrane of the

mitochondria. The released energy is used to drive the

reaction ATP ADP + Pi Oxygen is required and water is produced.

Anaerobic Respiration

Fermentation Occurs in low O2 environments 2 ATP is produced from glucose instead

of 4o from aerobic Same reaction used to produce alcohol

from corn or to make wine. Plant can soon run out of energy and

can suffer from toxic levels of ethanol and related compounds.

Overall reaction:C6H12O6 + O2 2 CH2O3 + 2 H2O + 2 ATPFACTORS AFFECTING PHOTOSYNTHESIS

Kind of Cell or Tissue

Older and Structural Cells = Low Respiration RatesYoung and Developing Flower, Developing and Ripening Fruit = High Respiration Rates

Temperature

Respiration generally has higher optimum and maximum temperatures than photosynthesis reactions.Can have net dry matter loss at high temperatures where respiration exceeds photosynthesis.It refers to the internal temperature of the plant or animal, not air temperature.

OxygenLow levels = reduced aerobic= increased anaerobic= reduced photorespiration

Light Can enhance rate of photorespirationDoes not directly affect other forms

Glucose Concentration

Adequate glucose needed to carry out respirationReductions can occur = reduced photosynthesis, reduced flow of carbohydrates in plants

CO2 Concentration

High levels = reduced respiration rates- Feedback inhibition

Seldom occurs except when oxygen levels are limited- Flooded, compacted soils

ATP Concentration

High levels = reduced respiration rates= occur when other processes slowed down or stopped

Plant Injury Increased respiration rate

Increased growth rate in plants in an attempt to recover from

Mechanical Damage Hail Mowing, Grazing, Cultivation, Wind

Plants synthesize compounds to fight pests.

ENERGY YIELD FROM GLUCOSE OXIDATIONCytos

olMatrix ETC and OP TOTA

L

Glycolysis2 ATP 2 ATP

2 NADH

4 ATP (net yield)

4 ATP

Pyruvate to Acetyl CoA

2 x (1 NADH)

2 x (3 ATP) 6 ATP

Citric Acid Cycle

2 x (1 ATP)

2 ATP

3 x (3 NADH)

3 x (9 ATP) 18 ATP

2 x (1 FADH2)

2 x (2 ATP) 4 ATP

OVARALL TOTAL 36 ATP

PHOTOSYNTHESISGeneral Equation 6 CO2 + 6 H2O C6H12O6 + 6 O2

Triose Phosphate

Considered as the net product of the Calvin Cycle of photosynthesis which is then utilized for the synthesis of glucose and starch.

Leaf and Leaf Structure

The raw materials for photosynthesis enter the cells of the leaf. Products of photosynthesis are transported and are exited through leaf structures:

Palisade layer Spongy layer Vascular tissues

Light

Visible light is part of the EMS of energy radiating from the sun.It is organized into photons and travels in waves.Wavelength – distance between successive crests and troughsPhotons with shorter wavelengths have more energy than longer ones.Radiation within the visible light spectrum excites certain biological molecules, moving electrons into higher energy levels.Visible light wavelengths: 400 – 700 nmWhen light hits an object:

Reflected by the object Absorbed by the object Transmitted through object

Colors we see are actually light reflected from an object.Plants reflect green but absorbs other wavelengths. RED and BLUE wavelengths are the most important for photosynthesis.Action Spectrum – contains effective light needed for photosynthesis.

THE PHOTOSYNTHETIC PROCESS

Photosynthesis

CO2 leaves via stomata.H2O and CO2 diffuse through chloroplasts.6 CO2 + 6 H2O + light C6H12O6 + 6 O230 distinct proteins needed to synthesize sugar molecules.It is a substance which comes from wavelengths of reflected light and absorbs light.

NOTES The amount of energy available for doing work in the universe is

always decreasing. On Earth, energy flows from the sun, through producers, then through

consumers. Cells convert potential energy into kinetic energy to carry out

intercellular processes. The process of photosynthesis converts radiant energy into

chemical energy. Humans can synthesize 8 out of 20 amino acids. 1 NADH = 3 ATP 1 FADH2 = 2 ATP