Biomolecules - Introduction

Biomolecules
- Molecules involved in maintenance and metabolic processes of living organisms
- Organic biomolecules contain:
   - Hydrogen
   - Carbon
   - Oxygen
   - Nitrogen
   - Sulphur
- Formed by condensation reaction
   - The forming of covalent bonds by removing a water molecule
 - Split by hydrolysis
   - The splitting of covalent bonds by adding a water molecule
- 4 main types:
   - Carbohydrates
   - Lipids
   - Proteins
   - Water


Overview of Condensation Reaction

Monomer	Polymer Formed	By-product	Bond Name
Monosaccharide (simple sugar)	Disaccharide --> Polysaccharide	Water	Glycosidic Bond (-O-)
Amino acid	Dipeptide --> Polypeptide	Water	Peptide Bond  (C-N)
Glycerol Fatty acids	Monoglycerides Diglycerides Triglycerides (Glyrcerol attached to fatty acids)	Water	Ester bond (-O-) [amino acids]
DNA/RNA	DNA	Water	Phosphodiester bond

Homeostasis + Cell Structure + Feedback Loop

What is homeostasis?

It is the controlled stability of the internal environment of cells and tissues.
Some examples include:
- Water regulation (osmoregulation)
- Temperature regulation (thermoregulation)
- Glucose regulation

Why is there a need for homeostasis?

It is so that a state of dynamic equilibrium can be achieved. A dynamic equilibrium means a state of balance achieved within an environment as a the result of internal control mechanisms that continuously oppose outside forces that tend to change that environment.


Cell Structure

Component	Organelle Name	Function
A	Nuclear Membrane	- Controls entry and exit of substances
B	Nuclear Pore	- Allows transport of water-soluble substances
C	Nucleolus	- Contains chromatin that controls cell activity; DNA, genetic material - Compartmentalized to increase efficiency of processes and protection
D	Lysosome	- Breaks down worn out organelles - Digests materials
E	Rough Endoplasmic Reticulum	- Isolate and transport proteins synthesized by attached ribosomes - Proteins may undergo further folding
F	Smooth Endoplasmic Reticulum	- Synthesis and transport lipids
G	Cytoplasm	- Contains the cell organelles - Site of cellular reactions - Means of transport for substances in cell
H	Golgi Apparatus	- Process and package complex molecules - Transports proteins and fat molecules to cytoplasm for secretion
I	Cell plasma membrane	- Compartmentalize - Controls entry and exit - Increase surface area - Cell recognition - Cell communication - Site of chemical reactions
J	Vesicle/Vacuole	- Sacs for storage (plant cell), digestion and waste removal (animal cell)
K	Mitochondria	- Produce adenosine triphosphate (ATP) from cellular respiration - Energy currency of cell
L	Ribosome	- Sites of protein synthesis

Cell Plasma Membrane

Organelle	Function
Phospholipid	- Major component of the membrane - When they come into contact with water, they tend to line up heads in water and hydrophobic tails away from the water
Proteins	- Extrinsic    - Loosely attach at hydrophilic surface of phospholipid bilayer - Intrinsic (partially or completely)    - Contain both hydrophilic and hydrophobic regions
Glycoproteins	- Interspersed among phospholipids - Consists of carbohydrate chains bound to peripheral proteins and hydrophilic regions of internal proteins that occur on surface of outer membrane    - Cell recognition or cell adhesion for immune response
Glycolipids	- Interspersed among phospholipids - Consists of carbohydrate chains bound to the head of phospholipid - Involved in cell recognition or cell signalling pathways
Cholesterol	- Interspersed among phospholipids - Essential in maintaining membrane fluidity    - Allow protein movement within cell membrane

Cell Transport

	Transport Mechanism	Type of substances	Energy input	Examples of substances	Importance of mechanism
Simple Diffusion	Across the phospholipid bilayer directly, following a concentration gradient.	Small, lipid soluble and hydrophobic in order to be able to interact with the hydrophobic tails of the bilayer	Passive transport, ATP input not required	Oxygen gas, carbon dioxide, minerals in soil (in high concentration)	To allow for the absorption of small, lipid soluble substances into living cells for essential processes like respiration
Facilitated Diffusion - Ion Channel	Across the phospholipid bilayer through a water, filled pore, following a concentration gradient	Water and water-soluble substances and small lipids	Passive Transport, ATP input not required	Urea, glycerol	To allow for the absorption of water, water-soluble substances and small lipids into living cells for essential processes
Facilitated Diffusion - Carrier Protein	Across the phospholipid bilayer through a carrier protein that has a specific binding site, following a concentration gradient	Too large and too hydrophilic substances	Passive transport, ATP input not required	Amino acids, glucose, fructose	To allow for absorption of too large and too hydrophilic substances into living cells for essential processes
Osmosis	Across a partially permeable membrane, following a concentration gradient	Water	Passive Transport, ATP input not required	Water molecules	To allow for absorption of water into living cells for essential processes such as hydrolysis and condensation and a medium for transport within the cell
Active Transport	Across the phospholipid bilayer through a specific protein pump, against the concentration gradient	Particles	Active Transport, ATP input is required as substances go against the concentration gradient	Amino acids and glucose (in low concentration)	To allow for absorption of large particles against the concentration gradient into living cells for essential processes.
Bulk Transport - Endocytosis	Ingestion of fluids/solids from outside the cell into the cell	Fluid, solids	Active Transport, ATP input is required as substances go against the concentration gradient	Bacteria, food	To allow for the ingestion of fluids and/or solids into living cells for essential processes such as processing food and digestion
Bulk Transport - Exocytosis	Expelling contents from inside of the cell to outside the cell	Waste materials, excess materials	Active Transport, ATP input is required as substances go against the concentration gradient	Enzymes, hormones and antibodies	To allow for the expelling of waste and excess materials from the cell into the outside of the cell
Pinocytosis	Encloses fluid and pinches off to form vesicle	Fluid or suspensions	Active Transport, ATP input is required as substances go against the concentration gradient	-	To allow ingestion of fluid or suspension into the cell
Phagocytosis	Encloses particles and buds off to form vacuole	Bio-organisms	Active Transport, ATP input is required as substances go against the concentration gradient	Food molecules	To allow ingestion of solids from outside the cell

Feedback Loop

It is a self-regulated system in which feedback to the input a part of a system's output so as to reverse or enhance the direction of change.

Positive Feedback Loop (Rare)

- Increases the output of a system, further enhancing deviation from internal equilibrium

eg. Giving birth, rashes, blood clotting

Negative Feedback Loop (Common)

- Reduces the output of a system in order to stabilize or re-establish internal equilibrium

eg. Body temperature, osmoregulation, glucose level

Keywords:

Increase in ____ is detected by the receptors and insulin is released into the blood.

Transport in Animals

The Heart
- It is the involuntary muscle.
- It has 4 chambers
  - Right & left atria (single atrium/auricle)
  - Right & left ventricles

Why is the left ventricle wall so thick?
Blood needs to be pumped to the rest of the body therefore, more pressure is needed.

The Ventricles

- The ventricle pumps blood at high pressure out to the arteries (to the lungs or other parts of the body)
- The pressure generated by the left ventricle is greater than that generated by the right ventricle as the systemic circuit is more extensive than the pulmonary circuit.

Why is the muscle around the atria thinner than the muscle around the ventricles?
Blood from the atria is pumped into the ventricles, therefore less pressure is needed.

The Atrium

- The atrium receives blood at low pressure from the veins (coming from the lungs or other parts of the body)
- The pressure generated the atria is less than that generated by the ventricles since the distance from atria to ventricles is less than that from ventricles to circulatory system.

The Valves

- Ensure that the blood flows in the correct/right direction
- Very important; without them, the flow of blood would be chaotic
- Found in the heart and veins

Tricuspid Valve

- Separates the right atrium from the right ventricle.
- It opens to allow the deoxygenated blood collected in the right atrium to flow into the right ventricle.
- It closes as the right ventricle contracts, preventing blood from returning to the right atrium; thereby forcing it to exit through the pulmonary valve into the pulmonary artery.

Bicuspid Valve (Mitral Valve)

- Separates the left atrium from the left ventricle.
- It opens to allow the oxygenated blood collected in the left atrium to flow into the left ventricle.
- It closes as the left ventricle contracts, thereby forcing it to exit through the aortic valve into the aorta.

Pulmonary Valve

- Separates the right ventricle from the pulmonary artery.
- As the ventricles contract, it opens to allow the deoxygenated blood collected in the right ventricle to flow to the lungs.
- It closes as the ventricles relax, preventing blood from returning to the heart.

Aortic Valve

- Separates the left ventricle from the aorta.
- As the ventricle contracts, it opens to allow the oxygenated blood collected in the left ventricle to flow throughout the body.
- It closes as the ventricles relax, preventing blood from returning to the heart.

Superior & Inferior Vena Cava

- Superior vena cava is one of the 2 main veins bringing deoxygenated blood from the body to the heart.

- Veins from the head & upper body feed into the superior vena cava, which empties into the right atrium.
- Inferior vena cava is the other main vein bringing deoxygenated blood from the body to the heart.
- Veins from the legs & lower torso feed into the inferior vena cava, which empties into the right atrium.

Aorta

-Carries oxygenated blood from the left ventricle to the systemic circulation.
- The aorta is an elastic artery and as such is quite distensible (ability to swell from pressure built within).
- When the left ventricle contracts to force blood into the aorta, the aorta expands. This stretching gives the potential energy that will help maintain blood pressure during diastole, as during this time the aorta contracts passively.

Pulmonary Artery

- The pulmonary artery carry blood from the heart to the lungs.
- They are the ONLY artery (other than umbilical artery in the fetus) that carry DEOXYGENATED BLOOD.
- In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle.
- It is short and wide - about 5cm in length and 3cm in diameter.
- It then branches into 2 pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung.

Pulmonary Vein

- The 4 pulmonary veins carry oxygenated blood from the lungs to the left atrium of the heart.
- They are the ONLY veins in the post-fetel human body that carry OXYGENATED BLOOD.

Chordae tendineae

- The chordae tendineae, or heart strings, are cord-like tendons that connect the papillary muscles to the tricuspid valve and the mitral valve in the heart.
- When the right ventricle of the heart contracts, the blood pressure pushed the tricuspid valve whic closes and prevents a backflow of blood into the right atrium.
- The chordae tendineae prevents the flaps from being averted into the right atrium. Similarly, these cord-like tendons hold in position other flaps like the bicuspid or mitral valve.

Papillary muscle

- In anatomy, the papillary muscles of the heart serve to limit the movements of the mitral and tricuspid valves.
- These muscles contract to tighten the chordae tendineae, which in turn prevent inversion.
- This occurs in response to pressure gradients. Instead they brace the valves against the high pressure, preventing regurgitation of ventricular blood back into the atrial cavities.

Coronary Arteries

- The heart is composed primarily of cardiac muscle that continuously contracts & relaxes, it must have a constant supply of oxygen & nutrients.
- Coronary arteries are a network of blood vessels that carry oxygen & nutrient rich blood to the cardiac muscle tissue.
- The larger vessels travel along the surface of the heart.
- The smaller branches, the capillaries, penetrate the heart muscle.
- The capillaries are so small that the red blood cell must travel in a single file.

Diffusion

What is diffusion?
Diffusion is the net movement of particles from a region of higher concentration to a region of lower concentration.

Is diffusion a spontaneous process (no energy required)? Well, the answer is yes.
What are the factors affecting diffusion rate? One of the factors is temperature.

Diffusion is a spontaneous process (no input of energy required). This explains the below observations:
- Substances tend to spread from an area where they are more concentrated to an area where they are less concentrated
- Two or more substances can become evenly distributed (reach equilibrium) even without external interventions.

Concentration Gradient

First of all, what is concentration?
- Concentration = amount of substance (mass g/kg) / volume of fluid (cm3/ml)
- It is a measure of the amount of a substance in a specific volume.

The change in concentration between 2 regions is known as the concentration gradient.

In other words, the the concentration gradient between points A and B is difference in concentration between points A and B.

Relationship between concentration gradient and diffusion
- Particles diffuse down the concentration gradient.
- The larger the concentration gradient, the faster the rate of diffusion.

Applications of diffusion in Biology

This is a picture of an amoeba, a unicellular organism.

To stay alive, this organism needs to obtain nutrients and remove waste efficiently by diffusion.

"Chemical substances must be able to move from one place to another in order to keep the living organisms alive and growing."
For example, food substance that were absorbed need to :
- Move from one cell to another
- Move in & out of the cell
- Move from one part of the cell to another
One way which these movements would occur is by diffusion.
eg. Substance have to diffuse across membranes.

There are 2 types of membranes:
- Permeable membrane which allows ALL substances to pass through
- Partially permeable membrane which allows SOME substances to pass through; small particles can pass through, large particles cannot pass through

Diffusion across a permeable membrane :

Diffusion across a partially permeable membrane :

The visking tubing encloses a solution of starch while the beaker contains iodine solution.

Starch reacts with iodine to form a dark blue complex.



What type of membrane is the visking tubing? Explain. 
Partially permeable membrane. Iodine solution can enter the visking tubing while starch cannot pass through the visking tubing into the beaker of iodine solution.


Other example of diffusion in Biology include :
- Movement of carbon dioxide during photosynthesis
- Movement of oxygen and carbon dioxide in animals

Conclusion
- Diffusion is an important process where substances are moved without use of energy.
- It is the NET MOVEMENT of particles 9or molecules; or ions) from a region of HIGHER concentration to a region of LOWER concentration.
- Thus the movement is down a concentration gradient.
- The movement is random.
- The GREATER the concentration gradient, the FASTER the rate of diffusion.

Here's a quiz for you to try out!

http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_diffusion_works.html

Ecology

Lithospere, hydrosphere & atmosphere are non-living components of the environment and are called ABIOTIC.
BIOSPHERE: Life supporting zone where the 3 zones meet, interact & make life possible

Lithosphere is the surface of the Earth, including aquatic systems, which contains most of the life.
Lower atmosphere - found to contain windblown organisms, seeds, and spores.

BIOTIC or living components include plants, fungi, animals and microbes living on Earth.
Constant interaction between the abiotic & biotic components of the biosphere results in the transfer of food and energy, making it a stable and dynamic SYSTEM.

A habitat is the physical place where a plant or animal (population) lives. It must supply the needs of organisms, such as food, water, temperature, oxygen, and minerals.
A population is a group of living organisms of the same kind living in the same place at the same time.
All of the populations in the same habitat interact and form a community.
A niche is the role and position of an organism (species) in the community. No two species can occupy exactly the same niche.
The community of living things interacts with the non-living world around it to form the ecosystem.
Ecosystems is a complex interaction of living and non-living processes e.g. as small as a puddle or as huge as the Earth.
Habitats that have similar climate and plants are called biomes.

------------------------------------ACTIVITY------------------------------------

PROCEDURE:
- Locate a small patch of land to examine.
- Use a string to form a circle to mark our study area.
- Record observations about your ecosystem. Include all living and non-living things.
- Record temperatures and other abiotic factors in your ecosystem.
- Turn over a small patch of the turf or vegetation. Observe what's beneath the surface. Replace whatever vegetation you have dug to the original state.

DISCUSSION:
- Consider the variety of living and non-living things in your ecosystem. Which was the largest population?
- How are the survival needs being met in your ecosystem? Air? Food? Water? Sunlight?
---------------------------------------------------------------------------------

Living things cannot exist alone, there must be a relationship between them. Living things are adapted to the environment where they live.
ECOLOGY is the study of how living things interact with each other and with their environment.
ECOSYSTEM consists of a community of living organisms interacting with each other and their environment to form a self-sustaining unit. The environment consists of non-living (abiotic) part and living (biotic) part.

Factors of that affect the ecosystem:

Light
- Affects many living organisms, not just plants.

Temperature
- Affects physiological activities of all living organisms

Water
- Essential for life
- Organisms may have specially adapted features for survival in places with a lot of or very little water.

Oxygen
- Most organisms are aerobes.

Salinity
- Important factor for aquatic organisms
- Also a factor for other organisms

pH
- May be influenced by photosynthetic activity of aquatic plants (freshwater)
Acids pH : 1 - 6.9
Alkali pH : 7.1 - 14.0
Water (neutral) : pH 7.0

--------------------BIOTIC FACTORS----------------------

1. Symbiosis
- a long-term relationship between two different species "living together". The relationship varies in population, can be mutualism, commensalism & parasitism.

Mutualism
- Each population benefits. The interaction is necessary for the survival and growth of each species
+ / + relationship

Commensalism
- One population benefit; the other is unaffected
+ / O relationship

Parasitism
- One population benefits (parasite) while the other is harmed (host). The interaction is necessary for the survival of the parasite.
+ / - relationship

2. Competition
- Both population compete with each other for limited resources in the same ecosystem; both species are adversely affected by the relationship.
Interspecific (a form of symbiosis) or
Intraspecific (same species) competition
- / - relationship

3. Predation
- One population feeds on the other. The interaction is necessary for the survival of the predator.
+ / - relationship

FOOD CHAIN
- A series of organisms through which energy is transferred in material form.
- Carbon compounds move through the flood chains.

- All the energy in an ecosystem comes from the SUN.

The study of food chain helps in understanding of food relationships and interactions among various organisms in an ecosystem.

By studying food chain, we can follow the basic mechanism of transfer of food energy and nutrients through various components of nature.

Food chain helps us understand the movement of toxic substances in an ecosystem and the problems of their biological transfer of food along with toxins substances.

Non-cyclical Nature of Energy Flow in Biological Systems
- Energy flows in one-direction (non-cyclical) and it is either utilised or lost into the surroundings but cannot be recycled.

What happens to the light that falls onto a leaf?

Unidirectional flow of energy
- The amount of available energy in food web decreases with each successive leve.

Food consumed = growth + respiration + heat + egesta (faeces) + excreta (urine)

Only about 10% of the energy is stored as new tissues and is available for transfer to next feeding level.
90% of the energy is lost because some food may not be eaten, or passes through the body without being digested and a lot of the energy is used in respiration.

The total mass of living organisms that can be supported at each higher level also decreases.
The shorter the food chain, the greater is the available food energy.

Decomposers are detritivores that recycle organic matter back to inorganic nutrients (carbon, nitrates) in ecosystems. E.g. fungi, bacteria
Detritus feeder acquire nutrients from dead animals/plants or animal waste products. E.g. certain beetles, earthworm, termites, bacteria, fungi.

Cycling of Nutrients in an Ecosystem

Carbon Cycle and Nitrogen Cycle

Ecological Pyramids

- Pyramids of numbers
  - indicate the relative numbers of individuals at each level

- Pyramids of biomass
  - the dry mass of all the organisms at each trophic level may be estimated

- Pyramids of energy
  - the total energy utilized at each trophic level

CARBON CYCLE

- atmospheric CO2 is 0.03% (main source) important component of all living organisms.
- only plants can take in CO2 & convert it to organic compounds
- carbon compounds move through the food chains
- CO2 is returned to the atmosphere through respiration decay activities also release CO2
- Carbon may be trapped in limestone and fossil fuels

Microscopy

Light Microscope
- Found in most schools
- Uses compound lenses to magnify objects
- The lenses bend or refract light to make the object beneath them appear closer
- Oil immersion lenses can improve quantity of focus and magnification
- Common magnification : 40X, 100X and 400X

Stereoscope
- Allows binocular (two eyes) viewing of larger specimens
- Magnifies 10X to 20X
- Used for thicker specimen
- Creates 3D view of specimen

Guidelines on handling the microscope
- Always carry with 2 hands
- Use lens paper for cleaning
- Do not force knobs
- Always store covered
- Keep objects clear of desk and cords

Magnification
- 3 magnifications : Scanning (Red), Low (Yellow), High (Blue)
- Ocular lends (eyepiece) has a magnification
- Total magnification = ocular lens X objective lens
- We can see better details with higher magnification powers.

Cell Structure and Function

Cell Theory
- All living things are made up of cells.
- Cells are the smallest working units of all living things.
- All cels come from pre-existing cells through cell division.

Definition of cells
A cell is the smallest that is capable of performing life functions.

Two types of Cells
- Prokaryotic
- Eukaryotic

Prokaryotic
- Do not have organelles (specialized structures in cells) surrounded by membranes
- Few internal structures
- One-celled organisms eg. bacteria

Eukaryotic
- Contain organelles surrounded by membranes
- Most living organisms eg plant, animal, fungi

Cell Parts

Organelles - specialized structures in the cell

SURROUNDING THE CELL

Cell Wall

- Most commonly found in plant cells & bacteria

- Surrounds the cell membrane

- Rigid structure that maintains the shape, supports & protects cells

Cell membrane
- Selectively/partially permeable membrane of cell that controls movement of substances in and out of the cell.
- Permeable to small molecules and small proteins only

INSIDE THE CELL

Nucleus
- Contain chromatins that control cell activities
- Chromatins contain DNA which is genetic material
- DNA contain instructions for traits & characteristics and to carry out the cell's function
- Separated from cytoplasm by nuclear membrane

Cytoplasm
- Gel-like mixture
- Surrounded by cell membrane
- Contains organelles

Mitochondria
- Referred to as the "powerhouse" of the cell.
- The food we eat is transformed into energy (ATP) for the cell and our bodies.

Endoplasmic Reticulum
- An interconnected network of tubes and vesicles
- Synthesis of proteins, fats, steroid
- Transports materials around in cell
- Smooth type: lacks ribosomes
- Rough type (in picture) : ribosomes embedded in surface

Ribosomes
- Each cell contains thousands
- Make proteins
- Found on endoplasmic reticulum & floating throughout the cell

Golgi Bodies
- Works closely with the ER
- Primary function is to process and package complex molecules such as proteins and fats that are made by the cell
- Bring these products to the surface of the cell where they can be secreted
- Other secretions include hormones, antibodies and enzymes

Lysosome
- Contain digestive enzymes
- Digest excess or worn-out organelles, food particles and engulf bacteria or viruses
- Also help repair worn-out plasma membrane
- They also provide sugars, amino acids and bases which are the foundation of macromolecules
- Cell breaks down if lysosome explodes

Vacuoles
- Membrane-bound sacs for storage, digestion, and waste removal.
- Central large vacuole-help plant cells maintain shape
- Food vacuoles: formed by phagocytosis
- Contractile vacuoles (in freshwater protist): pump excess water out of the cell

Chloroplast
- Usually found in plant cells
- Contains green chlorophyll
- Where photosynthesis takes place
- Converts light energy into chemical energy in glucose

Difference in plant cell and animal cell
- Chloroplast appears in the plant cell while it does not appear in the animal cell
- The plant cell has a large central vacuole while the animal cell has many mini vacuoles.
- The plant cell has a cell wall but an animal cell does not have a cell wall. Therefore, the plant cell has a fixed shape while the animal cell has an irregular shape.