Light Independent Reaction

The Light Independent Reaction

1.Carbon Fixation

            The cycle incorporates each CO2 molecules by attaching it to a five-carbon sugar RuBP (Ribulose Bisphosphate). The enzyme that catalyzes this step is called rubisco (RuBP carboxylase). The product of phase 1 is a 6 carbon sugar so unstable that it splits in half forming two molecules of 3-phosphoglycerate.

2. Reduction

            Each moleculeof3-phosphoglycerate

receives an additional phosphate group from ATP, becoming 1,3·bisphosphoglycerate. Next, a pair of electrons donated from NADPH reduces 1,3-bisphosphoglycerate, which also loses a phosphate group, becoming G3P. Specifically, the electrons from NADPH reduce a carboxyl group on 1,3-bisphosphoglycerate to the aldehyde group of G3P, which stores more potential energy. G3P is a sugar-the same three-carbon sugar formed in glycolysis by the splitting of glucose Notice that for every three molecules of CO2 that enter the cycle, there are six molecules ofG3P formed. But only one molecule of this three-carbon sugar can be counted as a net gain of carbohydrate. The cycle began with 15 carbons' worth of carbohydrate in the form of three molecules of the five-carbon sugar RuBP. Now there are 18 carbons' worth of carbohydrate in the form of six molecules of G3P. One molecule exits the cycle to be used by the plant cell, but the other five molecules must be recycled to regenerate the three molecules of RuBP.

3. Regeneration

            In a complex series of reactions. the carbon skeletons of five molecules of G3P are rearranged by the last steps of the Calvin cycle into three molecules of RuBP. To accomplish this, the cycle spends three more molecules of ATP. The RuBP is now prepared to receive CO2 again, and the cycle

continues. For the net synthesis of one G3P molecule, the Calvin cycle consumes a total of nine molecules of ATP and six molecules of NADPH. The light reactions regenerate the ATP and NADPH. The G3P spun off from the Calvin cycle becomes the starting material for metabolic pathways that synthesize other organic compounds, including glucose and other carbohydrates. Neither the light reactions nor the Calvin cycle alone can make sugar from CO2, Photosynthesis is an emergent property of the intact chloroplast, which integrates the two stages of photosynthesis.

Light Dependent Reactions

A. Linear Electron Flow

1. Light or photon strikes the leaf and the thylakoid capture it. As it enter the thylakoid it will first undergo a process in the Photosystem II. It will carry the the 2 atoms of hydrogen splitted from water(H2O)

2. The electron “bounce and bounce” in the pigment, as it hit the Chlorophyll A(P680), this will put the electron to the primary electron acceptor.

3. The photoexcited electron will be transferred by the Primacy Electron Acceptor to the photosystem 1 through the Electron Transport Chain (ETC). The electron will cross the ETC through its three parts; first the plastoquinone, after here to the cytochrome complex, the biggest membrane in ETC, in the CC is the ATP mill. The ATP mill pushes a phosphate to ADP present there becoming ATP as the electron roll over. After here it will pass the plastocyanine and at last to the Photosystem 1.

4. In the photosystem 1; the electron is in its ground-state level to ‘excite’ it, another electron enter through and the Chlorophyll A (P700) will again carry the electron to the primary electron acceptor. In both sides of the PEC here, Ferredoxin is situated. Fd is a protein that carries electron to the NADP+ reductase. In here hydrogen is added to NADP+  resulting in the formation of NADPH+H+.

B. Cyclic Electron Flow

1. Light or photon strikes the leaf and the thylakoid capture it. As it enter the thylakoid it will first undergo a process in the Photosystem II. It will carry the the 2 atoms of hydrogen splitted from water(H2O)

2. The electron “bounce and bounce” in the pigment, as it hit the Chlorophyll A(P680), this will put the electron to the primary electron acceptor.

3. The photoexcited electron will be transferred by the Primacy Electron Acceptor to the photosystem 1 through the Electron Transport Chain (ETC). The electron will cross the ETC through its three parts; first the plastoquinone, after here to the cytochrome complex, the biggest membrane in ETC, in the CC is the ATP mill. The ATP mill pushes a phosphate to ADP present there becoming ATP as the electron roll over. After here it will pass the plastocyanine and at last to the Photosystem 1.

4. The electron will be in the ground-state level in the P700 (Chlorophyll A), and a photon will enter PS1 ‘exciting’ the electron again. After that Chlorophyll A will transfer the electron to the Primary Protein Acceptor, in here Ferredoxin will carry the electron back to the Cytochrome Complex. In there it will again roll over the ATP mill. As it did so, ATP is generated by the addition of phosphate to ADP. And the cycle continues. 

Photosynthesis

What  is PHOTOSYNTHESIS?
Photosynthesis is the very nature of plants to produce their own food by converting light energy from the sun to chemical energy in the form of glucose. It occurs in the chloroplast; a part of the leaf that can be found in the mesophyll layer.

Light Dependent Reaction
Light Dependent Reaction is a process in which photosynthesis needs light to work out. In the thylakoid, a part in the chlorophyll, there are two photosystems that are involved in the process. The photosystem II and  photosystem I. They were named in order of discovery but photosystem II functions first in the light reactions.

1. Photosystem II- P680 can absorb light efficiently within 680 nm.
2. Photosystem I- P700 can absorb light efficiently within 700 nm.

Processes in Light Dependent Reaction

1. Linear electron flow
2. Cyclic electron flow

Light Independent Reaction

Light Independent Reaction is a process of undergoing photosynthesis without the presence of light. It is also known as the Calvin-Benson Cycle because it was discovered by Melvin Calvin and Andrew Benson. It is an anabolic process, building carbohydrates from smaller molecules and consuming energy. It produces a carbohydrate called glyceraldehyde-3-phosphate. 

*In the next post, you will learn more about light dependent & independent reactions.

Anatomy of a Leaf

The Anatomy of a Leaf

Outer Structure

1. midrib - the central rib of a leaf - it is usually continuous with the petiole.
2. petiole - a leaf stalk; it attaches the leaf to the plant.
3. stipule - the small, paired appendages (sometimes leaf-life) that are found at the base of the petiole of leaves of many flowering plants.
4. vein (vascular bundle) or small netted vein - Veins provide support for the leaf and transport both water and minerals (via xylem) and food energy (via phloem) through the leaf and on to the rest of the plant.
5. blade - the outline of the leaf

Inner Structure

1. cuticle - the waxy, water-repelling layer on the outer surface of a leaf that helps keep it from dying out (and protect it from invading bacteria, insects, and fungi). The cuticle is secreted by the epidermis (including the guard cells) and is often thinner on the underside of leaves. The cuticle is generally thicker on plants that live in dry environments.
2. epidermis - the protective, outler layer of cells on the surface of a leaf. The guard cells (and stoma) are part of the epidermis. The surface of many leaves is coated with a waxy cuticle which is secreted by the epidermis.
3. guard cell - one of a pair of sausage-shaped cells that surround a stoma (a pore in a leaf). Guard cells change shape (as light and humidity change), causing the stoma to open and close.
4. mesophyll - the chlorophyll-containing leaf tissue located between the upper and lower epidermis. These cells convert sunlight into usable chemical energy for the plant.
5. palisade mesophyll - a layer of elongated cells located under the upper epidermis. These cells contain most of the leaf's chlorophyll, converting sunlight into usable chemical energy for the plant.
6. spongy mesophyll - the layer below the palisade mesophyll; it has irregularly-shaped cells with many air spaces between the cells. These cells contain some chlorophyll. The spongy mesophyll cells communicate with the guard cells (stomata), causing them to open or close, depending on the concentration of gases.
7. stoma - (plural stomata) a pore (or opening) in a plant's leaves where water vapor and other gases leave and enter the plant. Stomata are formed by two guard cells that regulate the opening and closing of the pore. Generally, many more stomata are on the bottom of a leaf than on the top.

Leaf

What is a LEAF?

A leaf is responsible for:

• photsynthesis
• food production
• transforming light energy to chemical energy
• cellular respiration

Classifications of Leaf

A. Phyllotaxy - the fundamental study of leaf arrangement.

1. Opposite - 2 leaves per node
2. Alternate - one leaf per node
3. Whorled - multiple leaves surrounding the node
4. Spiral - leaves swirl around the plant.

*Node - attachment site of the leaf

B. Number of Cotyledon

1. Monocot - has one cotyledon. It has a parallel vein leaf and scattered vascular vessel
2. Dicot - has two cotyledons. It has a netted vein leaf and ring form vascular vessel

Monocot: left, parallel vein leaf; right, scattered vascular vessel

Dicot: left, netted vein leaf; right, ring form vascular vessel

• Vascular Tissues are the transport vessels of plants
• Xylem -upward; water and minerals
• Phloem -downward; nutrients

Membrane Transport

Membrane Transport include the following:

1. Passive Transport
2. Active Transport
3. Exocytosis
4. Endocytosis
5. Phagosytosis
6. Pinocytosis

What is a PASSIVE TRANSPORT?

Passive transport is a diffusion of a substance across a membrane with no energy investment. It is the tendency of molecules of any substance to spread out evenly in space. It is driven by intrinsic kinetic energy of molecules. A molecule or ion that causes a membrane by moving down a concentration of electrochemical gradient and without expenditure of metabolic energy is said to be transported passively.

• Simple diffusion - higher concentration to lower concentration
• Facilitated Diffusion - molecules can go inside the cell membrane by transport protein
• Osmosis - transport of water or gradient through a semi-permeable membrane.

What is an ACTIVE TRANSPORT?

Active transport enables a cell to maintain its internal concentrations of small molecules that would otherwise diffuse across the membrane. It is performed by specific proteins embedded in the membranes. ATP supplies the energy for most active transport. It requires the cell to expend metabolic energy. 

What is EXOCYTOSIS?

Exocytosis takes place when a transport vesicle budded from the golgi apparatus moved by the cytoskeleton to the plasma membrane.

What is ENDOCYTOSIS?

Endocytosis takes place when a small area of the plasma membrane sinks inward to form a pocket.

What is PHAGOCYTOSIS?

Phagosytosis is also known as the "cellular eating" process. The cell engulfs a particle by extending pseudopodia around it in a large vesicle.

What is PINOCYTOSIS?

Pinocytosis is also known as the "cellular drinking" process and is the counterpart of phagocytosis. A cell creates a vesicle around a droplet of extracellular fluid. All included solutes are taken in into the cell in this non-specific process.

Macromolecules

What are MACROMOLECULES?
Macromolecules are molecules needed to survive basic reactions.

Terms that you need to know:

1. Polymers are long molecule consisting of many similar or identical building blocks linked by covalent bonds
2. Dehydration Reaction is the loss of a water molecule to make a bond.
3. Hydrolysis is the addition of a water molecule to break a bond

The Different Macromolecules

• Carbohydrates are composed of hydrogen, carbon, and oxygen. This is the energy used by our body. The building block of carbohydrates is glucose. There are three types of carbohydrates:

1. Monosaccharides are the simplest form of sugar. Examples are glucose, fructose, and galactose.
2. Disaccharides are 2 monosaccharides joined by glycosidic linkage

• Glucose + Glucose = Maltose
• Glucose + Fructose = Sucrose
• Galactose + Glucose = Lactose
• Galactose + Fructose = Lactulose 

3. Polysaccharides are the complex of carbohydrates. An example is the chitin which is the carbohydrate used by arthropods to build their exoskeleton.

• Fats make up the cellular membrane. Fats are the stored energy of our body. They are cushion that protect the internal organs from external force. The building block of fats are fatty acids.

1. Fatty Acid is a long carbon skeleton, usually 16 or 18 carbon atoms in length.
2. Phospholipids are lipids whose head is glycerol (hydrophilic) and tail is fatty acid (hydrophobic) which can be found on the triacylglycerol.
3. Ester linkage is the link of the glycerol to the fatty acid.
4. Saturated fats are animal fats which are solid in form.
5. Unsaturated fats are plant fats which are in liquid form and healthy fats. It has a kink which makes it more stable.
6. Steroids are mistakenly known as proteins that help build muscles. Steroids are fats that strengthen the muscles.

• Nucleic Acid is the basic composition of DNA and RNA.

	Location	# of strands	Nitrogenous bases
DNA	Nucleus	2	C, G, A,T
RNA	In & out of the nucleus	1	C, G, A, U

1. Nucleotide is more stable and the building block of nucleic acid. 
2. Nucleoside is like a nucleotide except that it has no phosphate. It is the building block of nucleotide.

• Protein is made up of amino acids and serves as the building blocks of cells.
• Enzymes are specific proteins that mostly end up in -ase

				20 AMINO ACIDS
Name	Abb	Name	Abb	Name	Abb	Name	Abb	Name	Abb
Glycine	Gly	Isoleucine	Ile	Proline	Pro	Tyrosine	Tyr	Glutamic Acid	Glu
Alanine	Ala	Methionine	Met	Serine	Ser	Asparagine	Asn	Lysine	Lys
Valine	Val	Phenylalanine	Phe	Threonine	Thr	Glutamine	Gln	Arginine	Arg
Leucine	Leu	Tryptophan	Trp	Cysteine	Cys	Aspartic Acid	Asp	Histidine	His

1. Primary Structure is where amino acids and polypeptide chains are formed.
2. Secondary Structure is where coiled protein (alpha helix) and folded protein (beta-pleated sheet) are formed.
3. Tertiary Structure is where interaction of molecules within the protein structure occur.
4. Quaternary Structure is the final stage in which the protein knows its function.

The Protein Synthesis

	Replication	Transcription	Translation
Location	Nucleus	Nucleus	Cytoplasm
Key player	DNA is copied	DNA is transcribed to RNA (codon)	RNA (anti-codon=amino acid)