Thermodynamics Is the Study of Heat

a) Thermodynamics researchers discovered the First law of thermodynamics (energy can neither be created nor destroyed)

4. Entropy is the measure of the amount of energy dispersed in a particular system

5. In the Second law of dynamics, there is a tendency of energy to spread out spontaneously

6. Biologists use the entropy concept because energy flow in a living tissue occurs by making and breaking chemical bonds

C. The one-way flow of energy

1. Work is a result of energy transfer

2. A plant cell does its work by transferring energy from light to molecules that utilize the energy for making ATP

3. Other cellular activities occur by chemical energy transfer from one molecule to the other

4. Glucose synthesis involves chemical energy transfer from ATP to the other molecules.

5. Whenever energy is transferred a bit of it is dispersed.

6. Living things use energy for:

a) Growth

b) Movement

c) Acquiring of nutrients

d) Reproduction

7. Potential energy refers to stored energy.

D. Molecular Energy

Cells store energy in chemical bonds and retrieve it by breaking the chemical bonds

Reaction-processes in which there is a chemical change in molecules

Reactants-molecules entering a reaction

Products-molecules remaining at the end of a reaction

Endergonic reactions-reactions where the free energy of reactants is less than that of the products(energy in)

Exergonic reactions-the free energy of reactants is greater than that of the products (energy out)

Cells access the molecules free energy via exergonic reactions

Aerobic respiration-glucose and oxygen are converted into water and carbon dioxide for energy output

E. The earth does not go up in flames, why?

When lifes molecules combine with oxygen, energy is released

Activation energy minimum amount of energy necessary for a chemical reaction to start

F. Energy currency of a cell

ATP (adenosine triphosphate) energy carrier which couples endergonic reactions and exergonic reactions in a cell.

Phosphorylation involves an addition of phosphate group to a molecule from a donor molecule such as ATP

ATP/ADP cycle is the regeneration of ATP. When ATP loses a phosphate group, ADP is formed, and when ADP gains a phosphate group, ATP is formed.

G. Enzymatic activity

Enzymes catalyzes a specific reaction( occurs faster)

Active sites are pockets where substrates bind to proceed with the reaction.

Active shape complements with the substrate regarding shape, charge, polarity and size.

Enzymes lowers the activation energy and brings a transition state in a reaction by;

Helping substrates get together

Orientation of substrates in a position that will favour the reaction

Inducing a fit between the substrate and an enzyme

Shutting out water molecules

Enzymatic reactions increase with an increase in temperature.

There is a variation in pH tolerance of enzymes. Many have optimal pH between 6 and 8

Excess or too little salt disrupts the hydrogen bonds holding up the enzymes.

Cofactors are atoms or molecules that interact with enzymes is required for the function.

Coenzymes are organic molecules which are cofactors, for example, vitamin C and vitamin B.

The antioxidant prevents reaction of molecules with oxygen.

H. Metabolism is enzyme mediated reactions

There is an interaction of other molecules with ATP and enzymes in an organize metabolism pathway.

Metabolism refers to activities where cells acquire and utilize energy as they synthesize or break down organic molecules.

Metabolic pathways can be linear or cyclic.

Cells can conserve energy and resources by;

Running both the forward and reverse reactions

Feedback inhibition an effect where an end product of an enzymatic reaction inhibits activity of an enzyme in the series

Allosteric sites are sites where regulatory molecules bind.

Redox reactions (electron transfers are reactions where one molecule is oxidized while the other is reduced)

Electron transfer chain- organized reaction steps where membrane-bound enzymes and other molecules surrender and accept electrons in turn.

I. Movements of ions and molecules

Molecules and ions move from one region to the other in response to a concentration gradient

The concentration gradient is the variation in concentration of solute between neighboring regions of a solution.

Diffusion refers to the movement of molecules in response to concentration gradient, and it depends on;

Pressure

Temperature

Concentration gradients steepness

Charge

Size

Hypertonic describes a higher solute concentration, hypotonic describes a lower solute concentration while isotonic describes fluids with similar solute concentration

Osmosis is water diffusion across a semipermeable membrane.

Osmotic pressure turgor pressure that prevents osmosis.

Turgor is the pressure exerted by a fluid against a membrane or wall containing it.

J. Membrane crossing mechanisms

Transport proteins aids specific ions or molecules to cross a cell membrane.

In passive transport, protein is bound by a solute which is released on the opposite membranes side. This movement is initiated by a concentration gradient.

In active transport, a solute is pumped across a membrane by a protein pump against the concentration gradient. Energy in the form of ATP is necessary for this reaction.

A). Calcium pump is an example.

4. Cotransporters are active transport proteins which initiate movements of two substances in two different directions but at the same time.

K. Membrane trafficking

Through endocytosis and exocytosis, cells can take in and get rid of particles which are too large for transport proteins.

In exocytosis, the plasma membrane is fused by a cytoplasmic vesicle thus releasing its contents outside the cell.

In endocytosis, a portion of the plasma membrane is sunk inwardly forming a vesicle in the cytoplasm.

Phagocytosis an endocytic pathway through which particles such as microorganisms are engulfed by cells.

Chapter 6, Where It StartsPhotosynthesis

Green energy

Autotrophs

Harness energy from the environment directly

Uses inorganic compounds to obtain carbon.

Plants, autotrophs, synthesize their food by photosynthesis (use of energy direct from the sunlight for carbohydrate assembly from water and carbon dioxide).

Animals, heterotrophs, obtain carbon and energy from the breakdown of organic compounds assemble by other organisms.

Corns and other food crops have plenty of, starches, oils, or sugars that are converted to biofuels easily.

Sunlight as an energy source.

Photosynthetic organisms utilize pigments in capturing of sunlight.

Properties of lights and pigments

Energy from the sun is organized in form of packets called photons and travels in waves through space.

The radiant energys spectrum includes visible light.

Humans can perceive varying visible lights wavelengths as different colours.

A shorter wavelength leads to a corresponding greater energy

A Pigment is an organic molecule that can absorb light of certain wavelengths

Chlorophyll is the plants photosynthetic pigment

The antioxidant properties of accessory pigments offer protection to the plants and other organisms from the adverse effects of UV lights

The appealing colour of the pigment also attracts pollinators to flowers or animals to ripening fruit.

Chlorophyll is broken down faster than the other pigment hence leaves turn orange, red violet or yellow as the content of chlorophyll declines and the accessory pigments are now visible.

Wavelength refers to the distance between two light waves' crests

Exploring the rainbow

The pigments of photosynthesis work together to harvest light of different wavelengths.

Pigments combination enables photosynthetic organisms to capture efficiently particular wavelengths of light that reach its habitat

According to Englemann, violet and red are the most efficient colours for driving photosynthesis in chladophora.

Overview of photosynthesis

Photosynthesis occurs in two phases in the chloroplast

In the first stage, the formation of NADPH and ATP is driven by light energy.

This reaction takes place in the thylakoid membrane in the chloroplasts of eukaryotes.

The second stage (light independent) takes place in the stroma. The synthesis of carbohydrates from carbon dioxide and water is driven by NADPH and ATP.

Chloroplasts are photosynthetic organelles for plants and a few protists.

Stroma is a semifluid matrix located between thylakoid membrane and two chloroplasts outer membrane.

Thylakoid membrane is a system of a highly folded inner membrane.

Light-Dependent Reactions

Reactions in the initial stage convert light energy to chemical bonds energy.

In the light-dependent stage, chlorophyll and pigments located in thylakoid membrane transfer light energy to photosystems.

Absorption of energy makes electrons leave the photosystems and enters the membranes electron transfer chains.

Electron flow via the transfer chain set up a gradient of hydrogen ion which drives the formation of ATP.

In noncyclic pathway, there is the release of oxygen and electrons are finally located in NADPH.

A cyclic pathway which involves photosystem 1 enables cells to continue synthesizing ATP even if the noncyclic pathway is not functioning.

a) NADPH is not formed, and there is no release of oxygen.

7. Electron transfer phosphorylation is a process where electrons flow via an electron transfer chain creates a hydrogen ion gradient which drives the formation of ATP.

8. A photosystem is a cluster of proteins and pigments that converts energy from light to chemical energy during photosynthesis.

F. Flow of energy during photosynthesis

1. The flow of energy in the first stage reactions shows how organisms harness energy from the environment.

2. Energy inputs from light keep electrons flowing via the electron transfer chains.

3. The energy that is lost as electrons flow through the chains initiates a hydrogen ion gradient which drives ATP synthesis only or NADPH and ATP.

G. Sugar factory-light independent reactions

1. The reactions of Clavin-Benson cycle (enzyme mediated) builds sugars in the chloroplasts stroma.

2. The light-independent reactions utilize NADPH and ATP formed during the light-dependent reaction.

3. The cyclic reactions are the synthesis portion of photosynthesis.

4. Plants use glucose synthesized in the light-independent reactions to make other organic molecules or break it down for energy access in its bonds.

5. Carbon fixation- incorporation of carbon from inorganic sources to an organic molecule.

H. Adaptations: carbon-fixing pathways.

1. There is a difference in the environments and details of photosynthesis.

2. Various adaptations enable plants to thrive where there is a...