Biochemistry III (Plant Processes)

Learn more about Plant Biochemistry

This course will deepen your knowledge of biochemistry with an emphasis on plants. This is an advanced course that will give you a deep understanding on how life processes work, where living organism obtain their energy and nutrients and how these are processed to renew and develop new living materials.  

Lessons cover gycolysis, electron transport, oxidative  phosphorylation, carbohydrate metabolism, lipid metabolism, photosynthesis, nucleotide metabolism, enzymes, reproductive processes, hormones and more.

This is a great course for horticulturalists, environmental managers, technicians, agronomists or anyone interested in plant biochemical processes.  

Prerequisite: Biochemistry I and II or equivalent knowledge.

Lesson Structure

There are 11 lessons in this course:

1. Introduction
   • Introduction to Metabolism
   • Energy Transfer within the Cell - sources of energy, components of the cell, catabolic metabolism, anabolic metabolism, energy exchanges, free energy, enthalpy, entropy, energy transfers, ATP, Oxidation, enzyme catalysed reactions, coenzymes, hydrolysis, hydration reaction, phosphorylation.
2. Glycolysis
   • ATP - ATP Synthase
   • Glycolysis - activation, ATP production from Glycolysis, Metabolism of Pyruvate
   • Pentose Phosphate Pathway
3. Movement Through Membranes
   • Lipids and Fats
   • Membranes
   • Kinetics and Mechanisms of Transport - mediated and non-mediated transport, active transport
   • Ionophores
   • Aquaporins
4. Electron Transport and Oxidative Phosphorylation
   • Mitochondria
   • Electron Transport
   • Oxidative Phosphorylation
   • Citric Acid Cycle/Tricarboxylic Cycle
   • Controls of ATP Production
5. Sugar and Polysaccharide Metabolism
   • Monosaccharides, Disaccharides, Oligosaccharides, Polysaccharides, Glycoproteins
   • Sucrose
   • Starches - Glycogen and Starch
   • Starch Biosynthesis - Transitory Starch in Chloroplasts, Sucrose and Starch Regulation
   • Carbohydrate Metabolism
   • Gluconeogenesis - The Glyoxylate Pathway
   • Cell Wall
6. Lipid Metabolism
   • Lipids
   • Fatty Acid Biosynthesis by Plastids - Saturated Fatty Acid Biosynthesis
   • Glycerolipid and Phospholipid Formation
   • Triacylglycerol (TAG) Formation
   • Fatty Acid Oxidation in the Peroxisomes/Glyoxysomes
   • Wound Sealing
7. Photosynthesis
   • Photosynthesis - Chloroplasts, Light Reactions
   • Dark Reactions - Carboxylation, Regeneration, the Calvin Cycle
   • Photorespiration - C4 Respiration
   • CAM
8. Nucleotide Metabolism
   • Nucleotides
   • Nitrogen Fixation
   • Assimilation of Ammonia into Amino Acids - Purines, Pyramidines
   • Formation of Deoxyribonucleotides
   • Nucleotide Degradation
9. Enzyme Activity
   • Enzymes
   • Enzyme Classification
   • Enzyme Kinetics
   • Enzyme Regulation
10. Reproductive Processes in Plants
    • Types of Plant Reproduction - Sexual and Asexual Reproduction
    • Gene Expression
    • What are Genes?
    • Ribonucleic Acid (RNA) and Protein Synthesis - Overview, Transcription, Translation
    • Eukaryotic DNA Replication - DNA Polymerases, Leading and Lagging Strains, Telomeres and Telomerase
11. Other Processes
    • Hormones
    • Growth Regulators - Auxins, Cytokinins, Gibberellins, Ethylene
    • Other Hormones - Antiauxins, Growth Inhibiters, Growth Retardants, Growth Simulators, Defoliants, Unclassified Plant Growth Regulators
    • Use of Plant Hormones in Horticulture - Hormone Products

Each lesson culminates in an assignment which is submitted to the school, marked by the school's tutors and returned to you with any relevant suggestions, comments, and if necessary, extra reading.

Aims

• Explain the interaction between the various biochemical processes within the plant cell.
• Explain the process of glycolysis.
• Describe the transport mechanism of bio-chemicals through plant membranes.
• Explain the processes of electron transfer and oxidative phosphorylation, and their importance to energy regulation in plants.
• Explain the structure and metabolism of carbohydrates.
• Explain the metabolism of lipids.
• Explain the processes of photosynthesis and the role of the light and dark reactions of photosynthesis in the growth of plants.
• Explain biochemical nucleotide metabolism.
• Explain enzyme reactions and catalysis in biochemistry.
• Explain metabolic processes relevant to reproduction in plants.
• Explain other biochemical processes including biochemical communication through hormones.

Why You need to Understand Plant Metabolism

Metabolism encompasses chemical processes that produce specific products within a plant.

Metabolism within a plant is complex, involving many different chemical reactions; each having an effect upon others. Despite the complexity of living metabolism, organisms maintain relative stability.

There are two main types of pathways in metabolism:

• Catabolism Pathways that result in the degradation of biochemical substances.
• Anabolism Pathways that result in the synthesis or building up of more complex compounds from simpler biochemical substances.

There are four key characteristics common to metabolic pathways:

• Metabolic pathways are irreversible.
• Each metabolic pathway has a first committed step.
• All metabolic pathways are regulated.
• Metabolic pathways in eukaryotic cells occur in specific cellular locations.

ENERGY TRANSFER WITHIN THE CELL

Sources of energy

Plants absorb energy from the sun. (A few plants also absorb energy from trapped insects or by parasitising other plants.) Energy is absorbed by chloroplasts. This energy is converted to carbohydrates (sugars) via the light and dark photosynthetic reactions.

Components of the cell

Eukaryote plant cells contain a cell wall, a cytoplasm, a nucleus, one or more mitochondria and, depending upon the function of the cell, a number of other organelles. 

Within the cell nucleus, DNA provides the blueprint for processes within the organism, in particular the synthesis of proteins. The RNA within the nucleus acts as a ‘negative’ for copying and transferring the DNA code.

The DNA blueprint acts to join together carbohydrates to form amino acids that are then joined to form peptide chains. These peptide chains in turn form proteins and enzymes. 

Proteins form the ‘building blocks’ of many parts of the cell. Enzymes are vital for metabolism as they act to catalyse many different biochemical processes - that is they allow them to occur at lower temperatures.

Mitochondria produce much of the energy needed by organisms, particularly in animals. They also contain some of their own DNA for the synthesis of proteins.   Another organelle responsible for energy production are plastids, the most commonly recognised being chloroplasts.  Through these chloroplasts, light energy is transformed into chemical energy by photosynthesis.

The cell wall and the membranes that enclose the various organelles within the cell are formed from lipids and may also contain proteins and carbohydrates.  Cell walls are outside the plasma membrane and are largely responsible for the structural strength in plants.

Vacuoles occur within both plant and animal cells, however they are more prominent in plants.  They are spaces enclosed by membranes, which fill with fluids.  They predominately serve as storage space for wastes, specialized chemicals and nutrients.  There is a high concentration of solutes in vacuoles; this increases the internal pressure resulting in increased rigidity in non-woody plants.

The cell also contains ATP and NADP, compounds that act as vectors to provide energy during metabolism and to transfer energy within the cell. Some metabolic processes act to synthesise these compounds.

Metabolism within the cell

The metabolic processes within are cell are closely linked.  In many biochemical processes, the by-product of one metabolic process is directed towards another process where it can be re-used.  Similarly, converted energy from one process is transferred within the cell for use in other processes.  Hormones often control these processes. 

For this energy to be transferred within the cell, it must be transferred across membranes.  This phenomenon is known as electron transport. 

Catabolic metabolism

Catabolic processes are the breaking down (degradation) of sugars, amino acids and lipids to form simpler compounds and release energy.  For example, during glycolysis glucose is broken down to form two molecules of pyruvate (or pyruvic acid) and exact a net gain of energy in the form of ATP and NADH.  Pyruvate is broken down further by the citric acid cycle, which takes place in the mitochondria. Similar processes occur via the pentose phosphate pathway.  

Anabolic metabolism

Anabolic metabolic (biosynthesis) processes are typically the reverse of catabolic processes, with the difference being the inclusion of a different enzyme or electron transfer system into the process. Examples of anabolic pathways include gluconeogenesis and photosynthesis. 

Don’t worry if you do not yet understand these metabolic processes; each one is covered in later lessons.

Energy exchanges

All metabolic processes in living beings occur only when there is an exchange in energy between the reactants. In catabolic processes the energy accumulated in larger molecules in the form of chemical bonds is released when the molecules break down. This energy is then transferred to intermediary molecules which carry it to other metabolic processes, generally building up processes (anabolism).
 
Thus the energy is not created or destroyed, but only transferred. Energy is then transferred between exergonic processes, that release energy while chemical bonds break down, and endergonic processes, that take up the energy while new bonds are created. 

Applications for Plant Biochemistry

• Understanding biochemistry allows nurseryman to propagate plants better, by using hormones and other chemicals to do things such as stimulate the production of roots from a cutting
• Biochemical knowledge can be used to manipulate the type and rate of growth in crops, to better manage harvest and post harvest treatment of crops, and increase the overall productivity of plants grown on any type of farm.
• Weedicides could not be developed anywhere near as well without application of biochemistry
• Biotechnology can be used to alter plants in ways that will improve their use in forestry, farming, crop production, landscaping, environmental management, and more.