Biomolecules (Synthesis of Biomolecules)

- Synthesis of very large molecules (macromolecules) from small sub-units called monomers
- Monomers join together using covalent bonds
- Condensation reaction (sometimes known as dehydration synthesis)
- For every one bond formed, one molecule of water is released
- All 4 types of biomolecules are made through condensation reaction

For every one bond formed, one molecule of water is released

Overview of Condensation Reaction

Monomer (s)	Polymer Formed	By-product	Bond Name
Monosaccharide (simple sugar)	Disaccharide (di-sugar) à Polysaccharide (complex sugar)	Water	Glycosidic bond
Amino acid	Dipeptide à Polypeptide	Water	Peptide bond
Glycerol Fatty acids	Monoglycerides Diglycerides Triglycerides (Glycerol attached to fatty acids)	Water	Ester bond
DNA /RNA nucleotides	DNA RNA	Water	Phosphodiester bond

Monomer (s)

Polymer Formed

By-product

Bond Name

Monosaccharide (simple sugar)

Disaccharide (di-sugar) à Polysaccharide (complex sugar)

Water

Glycosidic bond

Amino acid

Dipeptide à Polypeptide

Water

Peptide bond

Glycerol

Fatty acids

Monoglycerides

Diglycerides

Triglycerides (Glycerol attached to fatty acids)

Water

Ester bond

DNA /RNA nucleotides

DNA

RNA

Water

Phosphodiester bond

Biomolecules (Synthesis of Nucleic Acids)

- Monomers: DNA and RNA nucleotides
- In DNA replication, each new strand that forms is built up from nucleotides, joined by repeated condensation reactions (polynucleotide chains)

Biomolecules (Hydrolysis Reaction)

- The splitting of a polymer by adding water to a covalent bond
- Catalyzed by a hydrolyses enzyme

Biomolecules (Properties of Water)

1. Water as a Solvent

• Many solvents are dissolved in the water of biological fluids (e.g. Blood plasma)
• Hydroophilic substances dissolve in water and this is important for:
• Transport - Blood plasma consists of about 90% water and is used to dissolve a wide range of useful substances and waste products which can then be easily transported
• Secretion – Most secretions comprise substances in aqueous solution. E.g. digestive juices contain enzymes in solution

2. Thermal Properties of Water

• Water has high heat capacity
• A lot of heat is required to increase or decrease its temperature by 1 degrees Celsius
• Water can act as a thermal buffer, i.e. it can resist large changes in temperature
• Allow for thermoregulation
• Water has high heat of vapourization
• A lot of heat can be lost with negligible loss of water from the body
• This is important for regulating the body temperature of organisms
• Water has high heat of fusion
• A lot of heat must be lost before water freezes
• Contents of cells are less likely to freeze. Ice crystals are extremely damaging if they develop within cells

3. Density and Freezing Properties

• Water is most dense at 4°C
• As water at the surface of a pond decreases from 4 degrees Celsius to 0 degrees Celsius, its density decreases and it remains at the surface and then it freezes
• Water molecules are more closely packed in liquid water than in solid ice. This explains why ice is less dense than water at 0 degrees Celsius
• Hence, water in ponds freezes from the top downwards. The layer of ice insulates the water below, preventing complete solidification

4. Cohesion and Surface Tension

• Cohesion is the force of attraction between like molecules. The cohesion of water molecules is due to the hydrogen bonds between them
•  One effect of the cohesive forces in water formation is surface tension. It is surface tension that allows insects to walk on the surface of water
• Tendency of molecules of a liquid to stick together at the surface due to its polarity and hydrogen bonding

5. Adhesion Forces

• Adhesion is the force of attraction between unlike molecules
• Large adhesive forces exist between the cellulose walls of xylem vessels and the water within them
• Adhesive forces play a role in maintaining a column of water in xylem vessels
• Capillary action
• The tendency of a liquid substance to move along the surface of solid substance due to adhesion (as in water climbing a glass tube or inside a tree), even in spite of gravitational or other forces acting in the opposite direction

6. Penetration by Light Rays

• In clear water, red and yellow light can reach a depth of 50m while blue and violet can penetrate 200m deep
• The ability of light to penetrate water enables photosynthetic organisms to occupy the vast volumes of lakes and oceans
• Light can easily penetrate the water-filled epidermis of leaves and reach the underlying mesophyll cells, which contain chloroplasts  

7. Water has Low Viscosity

• Examples of lubricating fluids which are predominantly water:
• Mucus is used externally to aid movement in animals (e.g. snail and earthworm). It is also used internally in the movement of food along the digestive tract or movement of sperm along the oviduct
• The synovial fluid lubricates movement in many vertebrate joints
• The pericardial fluid lubricates movement of the heart  

8. Metabolic Role of Water

• Water is required for the hydrolysis of many substances (e.g. proteins, lipids and carbohydrates)
• All biochemical reactions in cells occur in an aqueous medium
• Water is needed for the diffusion of materials across surfaces such as in leaf cells
• Water acts as a substrate for photosynthesis

Biomolecules

- All life is cellular
- All living things are from 50 to over 90% water, the source of protons, hydrogen and oxygen in photosynthesis and the solvent of biomolecules
- The major elements of covalently bound biomolecules are carbon (C), hydrogen (H), nitrogen (N), oxygen (O), phosphorus (P) & sulfur (S)
- There is a universal set of small molecules (i.e. sugars, amino acids, nucleotides, fatty acids, phospholipids, vitamins and coenzymes)
- The principle macromolecules are proteins, lipids, carbohydrates and nucleic acids
- There is a universal type of membrane structure (the lipid bilayer)

Organic Molecules vs Biomolecules
- Carbon was a major component, found in any type of organism that was analyzed
- Molecules with carbon in them were assumed to be associated with organisms, and so were called organic molecules
- Elements like H, O, N and S can also be found in organic molecules
- Many of the biomolecules contain carbon, and thus, can be referred to organic compounds as well
- 4 different types of organic molecules 

• Lipids
• Carbohydrates
• Proteins
• Nucleic Acids

Effective Ways to Study

1. Reading materials
2. Lesson slides
3. Worksheet & Practicals (Skills and Theoretical Knowledge)

Systematic Homeostasis

- Maintain a constant internal environment within human body for cells and tissues

- Some examples of homeostasis: 

• Water regulation (Osmoregulation)
• Temperature regulation (Thermoregulation)
• Glucose regulation

Feedback Loops

• Self-regulatory systems (automatic) in which
• It will feedback to the input a part of a system's output (Positive / Negative feedback)
• So as to reverse or enhance the direction of change
• 2 types of feedback loops
• Negative feedback loops (common, e.g. in regulation, the 3 types as stated above: Body temperature (thermoregulation), Amount of water in the body (osmoregulation), Glucose concentration in the blood
• The process can reduce / increase the output of a system in order to re-establish steady state / set point
• Positive feedback loops (rare, not meant to maintain homeostasis, but a mechanism we can see in our body)
• The process increases the output of the system, further enhancing deviation from steady state / set point
• Deviation from set points leads to enhancement of amplification of input
• Examples include: Oxytocin (Giving birth), Histamine (Rashes: the more you scratch, the mort histamine released, due to damaged cells, which makes it swell and itchy), Blood clotting
• Mosquito itch (Anti-coagulant), prevents blood from clotting, recognized as foreign substance by body -> itchy skin

What are the main components in a feedback loop?
1. Stimulus (Produces change in variable)
2. Change detected by receptor -> Receptor (Sensor)
3. Input: Information sent along afferent pathway to -> Control Center
4. Output: Information sent along efferent pathway to -> Effector
5. Response of effector feedsback to influence magnitude of stimulus and returns variable to homeostasis

Cell Membrane (4) - Thinking Exercise

Thinking exercise: Compare channel & carrier proteins

Question: How could regulation of substances in and out of cells result in cellular homeostasis? Give an example to illustrate.

Answer: Homeostasis is the regulation of processes to maintain a constant, stable, living internal environment despite other external conditions. Hence, regulation of substances in and out of cells will result in cellular homeostasis. Example: The cell membrane regulates substances in and out of cells. When the cell is put in a substance with a much higher water potential, osmosis will take place. This is when the molecules of the cells with a higher water potential move towards the cells with a lower water potential, to maintain an equilibrium between the substances. An equilibrium would have been reached when the concentrations of both substances are the same.

Question: Think of a cell within our body that can do this and what is the transport mechanism that is happening that is helping.
Answer: Villi Cell (Small Intestine). The villi cells have a rich blood supply, which has a lower concentration of food molecules as compared to the surroundings. Hence, diffusion of the food molecules will take place and homeostasis will be achieved.

Cell Membrane (3)

Transport of Substances in & out of Cells across Membrane
Passive Transport

• Does not require ATP
• Driven by concentration gradient (concentration difference) – moving down its concentration 
• Occurs in both living and non-living systems
• Mechanism
• Simple Diffusion / Diffusion (Oxygen, CO₂, minerals in soil etc)
• Types of substances that undergo diffusion are:
• Small, hydrophobic
• Lipid, soluble
• Small, hydrophilic (slower)
• Diffusion
• Spread of particles through random motion from regions of higher concentration to regions of lower concentration
• Simple Diffusion
• Hydrophilic molecules diffuse into cells very slowly, because of repulsion faced in the hydrophobic interior core of the lipid bilayer
•       Osmosis (water only)
•        Net movement of water molecules across a selectively permeable membrane from an area of less negative (high) water potential, to an area of more negative (low) water potential
•       Facilitated Diffusion (carrier proteins and pores which increase diffusion rate)
•        Type 1: Transmembrane proteins (Changes shape to facilitate entry and exit of some nutrients, e.g. fructose) create a water-filled pore through which ions and small hydrophilic molecules can pass by diffusion. Channel protein can open and close like gates
  Some molecules are too large for ion channel (e.g. amino acid, glucose etc)
•        Type 2: Some molecules are too large for ion channel (e.g. amino acids, glucose). Solution = carriers. Carrier protein has a specific binding site. Once substance binds-> conformation change of protein occurs. Move substance across. Release and protein returns back to original conformation

Active Transport

• Requires the use of energy (ATP) (E.g. Proton pump)
• Substances are transported against concentration gradient by specific proteins
• Occurs only in living systems
• Transport is specific-- carrier can only recognize certain molecules / ions
• Glucose and amino acids taken in by active transport to the villi cells of small intestine where there is lower concentration of these molecules in the lumen of the small intestines than the blood capillaries 

Endocytosis (Bulk Transport)

• Phagocytosis
• Formation of pseudopodia observed
• Pinocytosis
• Invagination of cell membrane

Exocytosis (Bulk Transport)

• Where secretory vesicles fuse with cell surface membrane
• E.g. Secretion of extracellular enzymes, hormones and antibodies, removal of waste products of digestion
• Are Endocytosis and Exocytosis a form of Active Transport?
• Yes. They require ATP and go against the concentration gradient.

-       

Cell Membrane (2)

Functions of Cell Membrane

1. To compartmentalize the cell as seen in different organelles. Different metabolic processes require different enzymes and conditions. Compartmentalization provides optimum conditions for the reaction to occur without interference from other enzymes and factors. It also prevents the autolysis of cells, e.g. Enzymes of pancreatic juice are found in vesicles prior to their secretion (Auto – self, Lysis – breakdown = Breakdown by itself)
2. Increases surface area for exchange of substances. E.g. Microvilli of intestinal cells making up the villi
3.  Cell recognition. Membranes contain certain protein / glycoprotein / glycolipids molecules which act as identity markers. E.g. Antigens on red blood cells
4.  Cell communication. Some proteins / glycolipids / glycoproteins embedded in the membrane act as receptors for hormones and neurotransmitter
5. Site of chemical reactions. E.g. light reactions of photosynthesis take place on thylakoid membranes found in chloroplasts
6.  Controls entry and exit of substances. Separates cytoplasm from external environment maintaining constant environment inside cell. Cellular homeostasis. 

      Extra

      Liver cells perform 500 different functions. A sign that the liver is not working: Yellow skin