BIOCHEMISTRY II

Lesson Structure

There are 9 lessons in this course:

1. Introduction to Biochemical Molecules
   • What is Biochemistry?
   • Cells – Prokaryote Cells, Eukaryote Cells, Viruses and Prions
   • Biomolecules – Proteins, Carbohydrates, Lipids, Nucleic Acids, Vitamins and Co-enzymes, Hormones and Nuerotransmitters
   • Metabolic Processes – Catabolism and Anabolism
2. Amino Acids
   • Amino Acids – Biochemical Nomenclature
   • Amino Acid Properties – Acidic and Basic, Hydrophilic and Hydrophobic, Polarity of the Side Chain, Amino Acid Polarity and Non-standard Amino Acids
   • Genetic Coding of Amino Acids
   • Terminology
3. Structure of Proteins
   • Proteins Functions
   • Protein Structure – Primary Structure, Secondary Structure, Tertiary Structure, Quaternary Structure
   • Fibrous Proteins – Collagen, Elastin, Keratin, Globular Proteins, Albumin
   • Cofactors and Conformation
   • Post-Translational Modifications
   • Protein Denaturation
   • Protein Degradation
4. Protein Dynamics
   • Protein Folding
   • Molecular Chaperones
   • Heat Shock Proteins – HSP90, HSP70, HSP60, Small Heat Shock Proteins
   • Chaperones
   • The Importance of Understanding Protein Structure
   • Structural Evolution of Proteins
   • Dynamics of Haem Proteins – Haemoglobin Co-operativity
5. Sugars and Polysaccharides
   • Saccharides – Monosaccharides, Oligosaccharides, Polysaccharides, Lectins
   • Polysaccharide Bonds
   • Polysaccharide Function – Classification of Monosaccharides, Ring or Chain Types, Complex Sugars
   • Monosaccharides – Glucose, Fructose, Galactose
   • Disaccharides – Sucrose, Maltose, Lactose
   • Polysaccharides – Starch, Dextrin, Glycogen, Cellulose
6. Lipids (Fats) and Membranes
   • Lipids – Fatty Acids, Triacilgliceroles, Neutral Lipids, Phospholipids, Glycolipids, Terpenoids
   • Cholesterol
   • Cellular Membranes
   • Terminology
7. Enzymes, Vitamins and Hormones
   • Enzymes - Coenzymes
   • Vitamins – Vitamin Classification, Reviewing Vitamin C
   • Hormones – Plant Hormones
8. DNA and RNA
   • Nucleic Acids – Structure of DNA, Types of RNA
   • DNA Replication
   • Inheritance
   • Interesting facts about DNA
9. Laboratory Techniques
   • Laboratory Health and Safety
   • Common Experimental Methods – DNA Methods, Protein Methods, General Methods

Aims

• Explain characteristics of biochemical molecules and to distinguish between different groups of biochemical molecules.
• Describe the structural characteristics and other properties that differentiate standard amino acids one from another.
• Explain the structures of different proteins (both covalent and 3-dimensional).
• Describe common protein dynamics including folding, structural evolution and haemoglobin function.
• Describe the structure and dynamics of different types of saccharides and polysaccharides.
• Explain the composition and structure of both lipids and membranes.
• Describe the structure and dynamics of different types of enzymes, vitamins and hormones.
• Describe the structure and function of different types of nucleic acids including DNA and RNA.
• Discuss some of the basic laboratory techniques used in biochemistry and to appreciate the importance of safety in the laboratory.

Where and How Do We Use Our Knowledge of Biochemistry

Much of what we learn about biochemistry comes from analytical and research work in a laboratory. The application of biochemical knowledge extends well beyond the laboratory.

This course can be valuable training for work in a laboratory; but it can be equally valuable for anyone working with plants or products derived from plants, outside of a laboratory 

Understanding more about plant biochemistry is fundamental to better understanding the characteristics of crops that are grown and plants in natural or man made landscapes. The complex mixture of chemicals found in plants are what affects the food value of crops, the toxic affects of some garden plants, and many other features of a plant.

LABORATORY WORK

Most people who work with plants, may rarely need to work in a laboratory themselves; but they may at times need the knowledge derived from, or the services of a laboratory.

Understanding laboratory work may be valuable; even if you don't actually undertake lab work directly yourself.

Within scientific laboratories you can expect to find chemicals that are carcinogenic, teratogenic, caustic and radioactive.  Chemicals may be able to directly penetrate the skin, may interact with the fats on the skin, irritate the delicate membranes of the nose and throat through inhalation, and damage the eyes.  Some chemicals can react violently, are unstable in certain states and many are extremely flammable.  When working with biomolecules, contamination is an important issue, as well as degradation.  Proteins, in particular need to be stored correctly, and not left at room temperature.  Finally, many of the reagents used in a laboratory are extremely expensive.

Before you enter a laboratory, you should receive some sort of safety training.  Laboratories working with micro-organisms and specimens (plant/animal/human) are generally off limits without more specialised training and there are numerous protocols to be aware of as well as specialist protective clothing, ventilation systems and waste removal procedures.  However, some basic key safety points to remember include:

• You should know the location of all safety equipment in the lab as well as all emergency and evacuation exits.
• Safety equipment should include safety shower, eye wash, first aid kit, fire extinguisher and fire blanket.
• A laboratory coat and gloves should worn for all laboratory work as well as enclosed shoes covering the entire foot and heel and are at least water resistant (leather, for example, not canvas). Clothing should not be overly loose and hair should be securely tied back.  In many cases safety glasses should be worn.  In other cases, face masks, double gloves, face shields or temperature proof safety clothing might be required.  Working with radioactive reagents requires additional safety precautions and a monitor should be warn to track your exposure.
• Clear your bench top of all unnecessary material before starting your work.  It is a good idea to sanitise the area, 70% ethanol is commonly used.  In other cases, chemicals that will destroy biomolecules from previous experiments are also used.
• Check chemical labels twice to make sure you have the correct substance and the correct concentration of a solution. Some chemical formulas and names may differ by only a letter or a number.  When you are making up solutions, particularly if they are clear and/or odourless, be sure to label them well, and clearly, including your name and the date.
• Ensure chemicals are stored properly and be aware of the hazards of each chemical before you use it (MDS sheets should be available and standard information is generally packaged with the chemical by the manufacturer).
• You may be asked to transfer some laboratory chemicals from a common bottle or jar to your own container. Do not return any excess material to its original container unless authorized, as you may contaminate the common bottle.
• Laboratory glassware should be autoclaved before reuse to avoid contamination.
• Avoid unnecessary movement and talk in the laboratory, it can disturb concentration of others and in some situations, such as in tissue culture facilities, can cause contamination problems.
• Do not bring food and drinks into the laboratory. Do not put fingers, pens, or pencils in your mouth while in the laboratory. Do not taste any laboratory items.
• If you are instructed to smell something, do so by fanning some of the vapour toward your nose. Do not place your nose near the opening of the container.  Smelling is a very bad way of trying to determine what an unknown chemical is, as many are toxic if inhaled directly.
• Never look directly down into a test tube view the contents from the side. Never point the open end of a test tube toward yourself or anyone else. Never heat a test tube directly in a Bunsen burner flame unless it was designed for that purpose.  Use the correct test tube for your application, there are numerous different types available.
• Any laboratory accident, however small, should be reported immediately to supervisors
• The procedure for chemical spills will vary, this is why it is crucial to know what you are working with. While many situations will require rinsing with copious amounts of water, some chemicals will react violently with water and should be rendered inert by another product.  A minor spill may be easily cleaned up, but if a spill is large, or involves a caustic, flammable, unstable, radioactive etc chemical, specific procedures must be followed.  If the eyes are affected, rinsing with water must begin immediately and continue for at least 10 to 15 minutes. Professional assistance must be obtained.  For safety reasons, you should never work alone in a laboratory.
• Minor skin burns should be placed under cold, running water.
• When discarding or disposing of used materials, carefully follow the instructions provided. Waste chemicals are not generally permitted in the sewer system.  Some can be flushed with set amounts of water, some are autoclaved and disposed of as contaminated waste, some are incinerated.  There are steep penalties for incorrect disposal of laboratory chemicals and waste.
• Return equipment, chemicals, aprons, and protective goggles to their designated locations.
• Before leaving the laboratory, make sure that gas lines and water faucets are shut off.
• Wash your hands before leaving the laboratory with a suitable anti-bacterial soap.
• Be aware that some reagents cannot be left in, or exposed to light, some must be kept on ice. 
• Take extreme care using centrifuges, they must be properly balanced, using blank tubes in some cases.  They will have inserts for certain specimens, weights and speeds.  Ensure you don’t overload a centrifuge and always use test-tubes that are able to withstand the centrifugal force.  Some centrifuges have temperature controls, do not leave a cold centrifuge open to warm it – you will only end up with a build up of ice.  Centrifuges, even small ones are very expensive, do not use one without being shown how first.
• Never use any piece of equipment without being shown how first.  Many items will require specific introductory training first.
• Transport of laboratory specimens, chemicals and equipment between laboratories, or out of the laboratory is, in most countries, regulated by very specific regulations.  Be familiar with them, and authorised to transport before you take anything out of the laboratory.

What Types of Chemicals are Found in Plants?

All of the chemical compounds in plants come originally from carbohydrates that were synthesised during photosynthesis. There are two main groups: of these compounds:

Primary Metabolites
These are found in all plant cells. They are used in basic plant processes and biochemical reactions concerned with growth and metabolism. They include fats, proteins, and carbohydrates. From a commercial perspective primary metabolites are harvested for use in large quantities as relatively low value raw materials for industry, or foods such as vegetable oils, as well as food additives such as proteins and carbohydrates like starch, cellulose and sucrose. Some primary metabolites can have physiological impacts on the human body; though such impacts are mainly caused by secondary metabolites.   

Secondary Metabolites
Secondary metabolites are derived from primary metabolites. There are different ways to classify them but one method which is widely adopted is to group them into alkaloids, phenolic compounds, and terpenoids. Alkaloids and phenolic compounds are synthesised by the shikimic pathway. Terpenoids are synthesised via the acetyl-CoA mevalonic acid pathway.

There are thousands of these secondary metabolites, and most are not involved in human growth and metabolic processes, More commonly they are used by plants to fight against pathogens or to ward off attacks from herbivores - by being toxic or repellent to them. Others may inhibit the growth of other competitor plants, and some are responsible for pigments and odours which attract pollinating insects to plants.