Biology Notes 2008

BIOLOGY NOTES

I LOVE BIO:D

Biology Notes 2008

Topics to Study for End of Years

Homeostasis

Generalisations of HOMEOSTASIS - Definition of homeostasis - Boundaries - Externals VS Internal environments - Case studies - Why water?

Cell Organelles Cell Transport

- Differences - Definitions

PASSIVE TRANSPORT ACTIVE TRANSPORT Definition Types: Diffusion, facilitated diffusion, osmosis

Definition Types: Ion pumps, Exocytosis, Endocytosis, Pinocytosis, Phagocytosis

Diffusion - Surface Area: Volume ratio ATP (Adenosine Triphosphate) Facilitated Diffusion

- Protein Channels Channel Proteins Carrier Proteins (2)

Ion Pumps - What are they - Functions

Osmosis - Definition - Plasmolysis - Turgidity - Isotonic - Hypertonic - Hypotonic - Surface Area: Volume ratio

Exocytosis and Endocytosis - Processes

Plasma Membrane Functions - What does the membrane do?

STRUCTURE OF MODEL 5 KEY PARTS:

Phospolipid Bilayer - Hydrophilic and hydrophobic parts - Structure of each phospolipid molecule - Saturated and Unsaturated fat - What keeps it together?

Cholesterol - Functions - Where it is located

Glycoprotein (Carbohydrate + Protein)

- Functions - Where it is located

Integral Protein (channel protein is ONE type)

- Functions - Types - Where it is located

Fluid Mosaic Model

Peripheral Protein - Where it is located - Functions

Membrane Fluidity

- Why must it be fluid? - Which part of the membrane allows it to be fluid? - How do we know it is fluid?

Case Study Beetroot Experiment

Biology Notes 2008

Bio Molecules

Condensation and Hydrolysis Reactions - Definitions - Examples (Drawings) - Purposes - Uses

Carbohydrate - Definitions of Carbohydrates - Components - Functions

Types of Carbohydrate Monosaccharide - Examples

- Components - Different types

Disaccharides - Definition - Examples, including the type of monosaccharide’s it consists of - Properties - Detailed composition of the examples

Polysaccharides - Definition Storage polysaccharides - Detailed examples - Different types Structural polysaccharides - Properties that make them suitable to be storage/ structural polysaccharides

Fats/ Lipids - Definition - Uses - Compositions - Hydrolysis and condensation processes - Fats VS Oil - Functions of fat

Type of Fat Saturated fat Unsaturated fat

- Where is it located - Characteristics - Properties - Definition

Types of Lipids Simple Compound Steroid/ Sterols

- Definition - Example - Hydrolysis Reactions

Protein - Definitions - Location - How they are formed (amino acids) - General Characteristics - Functions

Amino Acids - Different groups - Chemical Structure - Hydrolysis/ Condensation Reactions - Properties - Linkages to form a protein Different types of bonds between amino acid residues

Structures of Protein Primary Secondary Tertiary Quaternary

- Definition - Different types? (Secondary) - Characteristics - Examples

Classification of Protein According to SHAPE, and COMPOSITION

Biology Notes 2008

Enzymes

- Definitions - Functions - Characteristics - Examples of reactions involving enzymes - Properties of enzymes - MUST know examples of enzymes and the substrates they work on

How Enzymes Work Structure of Enzymes - Active site Functions of enzymes How the active site helps the enzyme to catalyze reactions

2 ways enzyme work Catabolic Reaction or Anabolic Reaction Theories for enzyme specificity Lock and Key theory Induced Fit theory

- Definition - Understand the systems - Draw them to represent the sequence

Factors Affecting Enzyme Activity Enzymes and pH - Must know specific enzyme

action at specific pH levels (Which enzyme)

Enzymes and temperature - Which enzymes work at which temperature? (based on their locations)

Enzymes and substrate concentration

Enzymes and enzyme concentration

- Must know the graph - Explain the curve shape - Relationship - Reasons for relationship

Inhibitors - What are they? - What do they do?

Types Competitive Non-Competitive Allosteric

- Shape, size - How it inhibits the enzyme (reasons why it works) - How to overcome it - The graphs of enzyme activity when exposed to all 3 types of inhibitors-

EXPLAIN Co-enzymes

- What are they? - How do they help? - Structure

Energy Transfer in Organisms

Autotroph VS Heterotroph - Definitions - Understand their roles in the food chain

Autotroph Nutrition: Photosynthesis Heterotroph Nutrition: Respiration

Biology Notes 2008

Energy Transfer in Autotrophs: Photosynthesis

- Definition of process - General Equation of Photosynthesis - Inputs, outputs, process

Structure of a Leaf Parts of a leaf - Adaptations for

photosynthesis - Turgid Pressure

Features/ characteristics of those parts

Functions of leaf

Use these 3 parts, combine the 3 concepts and understand how the lead is suited and adapted for photosynthesis How do plants obtain: - water - oxygen/ carbon dioxide - Light

Opening and Closing of the Stomata Factors Affecting Photosynthesis

- Carbon dioxide - Water - Light - Chlorophyll - Know all graphs

VERY IMPORTANT: UNDERSTAND THE LIMITING FACTOR CONCEPT. MUST MUST. Reactions Light-dependent Stage Light-Independent Stage

- Equations - Where - What happens - Inputs - What are the products - What are the processes

Energy Transfer in Heterotrophs: Respiration

Aerobic Respiration

- How our body is adapted for gaseous exchange with our surroundings? Take in oxygen, give out carbon dioxide

- How do the respiratory system and circulatory system work together? - The system of inhaling/ exhaling (how the lungs work)

Different gaseous exchange systems in other organisms - Mammals - Amphibians - Aquatic organisms - Insects

Common properties of gaseous exchange surfaces - what is required for efficient gaseous exchange

Gaseous Exchange

Fick’s Law (Diffusion rate) Cellular Respiration

- Definition of process - General equation - Uses of energy

Glycolysis Krebs Cycle

3 metabolic stages of cellular respiration

Electron Transport and oxidative phosphorylation

- Where does it occur? - What are the inputs? - What are the products?

Anaerobic Respiration - Definition of process - Inputs, processes, products - Fermentation

Comparing Aerobic and Anaerobic Respiration - Which is more efficient?

Biology Notes 2008

Ecology

Definition of Terms Levels of Ecological Organisation

- Individual - Population - Community - Ecosystem - Biome - Biosphere

Recycling of Nutrients - Different roles in an ecosystem - Carbon Cycle - Nitrogen Cycle

Energy Flow Food chains and Webs - Examples

- Roles in a food chain/ food web - Trophic levels

Ecological Pyramids - Pyramid of numbers

- Pyramid of Biomass

- Pyramid of energy

- Limitations and strengths of each pyramid - Which is more commonly used? Why? - Compare 3 pyramids

Relationships and Interactions between organisms

- Predator-prey relationship - Types of Mutualism - Strategies for Mutualism

Hierarchy of Organisms (Classification) Distribution of life on earth

- Prerequisites for life - Where most life form is found - Conditions for life - Various biomes

Sampling to understand distribution of life - Types of sampling methods - Objectives

Harsh Environments Factors Affecting the Abundance of Biodiversity Distribution across Kingdoms

Biology Notes 2008

Evolution

Definition of Evolution Theories of Evolution

- Lamarck’s Theory - Darwin’s Theory - Neo-darwinism - Theory of Natural Selection - Differences between Lamarck and Darwins’ theories

Theory of Natural Selection

- Processes - Assumptions made

Why are there variations within a species? Why sex? Are males necessary? Speciation Conditions for Speciation Geographic Isolation / Restriction of Gene Flow

- Allopatric Speciation - Sympatric speciation - Founder’s Effect

Evidence for Evolution - Homologous VS analogous

Man’s Impact on the Environment Tragedy of the Commons

- Concept - Apply it to many many situations

Overfishing Vanishing Cod Global Warming

- All examples of the Tragedy of the Commons concept - Know how to apply it - Read articles

Sustainability Possible Solutions Putting a price on the environment

- Conservationists

Biology Notes 2008

Homeostasis.

Biology Notes 2008

GENERALISATIONS OF HOMEOSTASIS 1. Definition of Homeostasis - The process of maintaining equilibrium in living organisms To maintain the conditions within the body, such as:

- Body temperature - Oxygen supply

For Body Functions to occur, so that chemical processes can occur. The three main processes are: Breaking Down Transportation Repairing

- Water Supply - Nutrient Supply

2. Boundaries & External and Internal Environments

- Living Organisms have boundaries to distinguish between the internal and external environments - External environments can cause changes in the internal environment of living organisms - Different organisms have different strategies for coping with external changes

3. Case Studies Lungfish

- Bladder modified to breeding chamber - Burrows itself as an artificial boundary - By burrowing itself in the ground, there is shelter from external environment - As it is less exposed to the sun, there is LESS HEAT, LESS EVAPORATION and MORE HUMIDITY - Hence, there is LESS FLUCTUATION OF HEAT - Coats itself with a layer of mucus, as an additional barrier

Desert Frog

- Burrows itself as an artificial barrier, protecting it from the external environment - Sheds many layers of skin - Waterproof skin barrier

Thorny Devil

- Eats ants for water in the desert Metabolic water (during respiration)

- Rough Ridges on its skin Appear fierce and intimidating to ward off predators Capillary Action

Requires a narrow channel Only water has the necessary qualities for capillary action to take place (Look under: Why Water?) Channels water up to its mouth

Thorny Lizard - Increases the blood pressure in its eye sinuses - Breaks through the capillary wall at the tear duct - Blood bursts out from its eye - Blood can squirt up to 20 consecutive times

What for

Labyrinth structure - Has many folds to absorb as much air as possible by increasing surface area

Biology Notes 2008

Jesus Christ Lizard

- It walks on water to escape from dangers/ predators - The lizard spreads out its legs to balance out its weight on the water, and to trap cushions of air in its legs - As water has high surface tension, the air bubbles do not burst easily - Before the air bubble bursts, it will step onto the next bubble, hence walking on water - It can walk at the speed of 10km/hr - It walks up to 40m

Flying Snake Lizard/ Paradise tree lizard - Found in Singapore! - It is actually a glider - Flattens its ribs into a ribbon-like shape, allowing it to glide from tree to tree

Flying Dragon

- Lizard with “wings” - Glider, with a small degree of direction control - Can glide up to 30 feet

4. Why Water?

Why is Water the medium to carry electrolytes? Water molecules are attracted to each other, creating hydrogen bonds. These strong bonds determine almost every physical property of water and many of its chemical properties too.

4.1 Thermal properties Water absorbs or releases more heat than many substances for each degree of temperature increase or decrease. Because of this, it is widely used for cooling and for transferring heat in thermal and chemical processes. 4.2 Surface tension Surface tension is a measure of the strength of the water's surface film. The attraction between the water molecules creates a strong film, which among other common liquids is only surpassed by that of mercury. This surface tension permits water to hold up substances heavier and denser than itself. Water has a very high surface tension. In other words, water is sticky and elastic, and tends to clump together in drops rather than spread out in a thin film. The hydrogen atoms are "attached" to one side of the oxygen atom, resulting in a water molecule having a positive charge on the side where the hydrogen atoms are and a negative charge on the other side, where the oxygen atom is. Since opposite electrical charges attract, water molecules tend to attract each other, making water kind of "sticky." 4.3 Molecules in motion Surface tension is responsible for capillary action, which allows water (and its dissolved substances) to move through the roots of plants and through the tiny blood vessels in our bodies. Water molecules as well as binding to each other, bind to many other substances such as glass, cotton, plant tissues, and soils. This is called adhesion. For example, in a thin glass tube, when the molecules at the edge reach for and adhere to the molecules of glass just above them, they at the same time tow other water molecules along with them. The water surface, in turn, pulls the entire body of water to a new level until the downward force of gravity is too great to be overcome. This process is called capillary action. Capillary action is defined as the movement of water within the spaces of a porous material due to the forces of adhesion, cohesion, and surface tension. Plants and trees couldn't thrive without capillary action. Plants put down roots into the soil which are capable of carrying water from the soil up into the plant. Water, which contains dissolved nutrients, gets inside the roots and starts climbing up the plant tissue. As water molecule #1 starts climbing, it pulls along water molecule #2, which, of course, is dragging water molecule #3, and so on. 4.4 Water – the universal solvent An extraordinary property of water is its ability to dissolve other substances. There is hardly a substance known which has not been identified in solution in the earth's waters. Were it not for the solvent property of water, life could not exist because water transfers nutrients vital to life in animals and plants.

Folds of skin that are supported by 4-5 ribs

Biology Notes 2008

4.5 Boiling and Freezing Point Water freezes at 32o Fahrenheit (F) and boils at 212o F (at sea level, but 186.4° at 14,000 feet). In fact, water's freezing and boiling points are the baseline with which temperature is measured: 0o on the Celsius scale is water's freezing point, and 100o is water's boiling point. Water is unusual in that the solid form, ice, is less dense than the liquid form, which is why ice floats. 4.6 Pure water has a neutral pH of 7, which is neither acidic nor basic. 4.7 Specific Heat Index Water has a high specific heat index. This means that water can absorb a lot of heat before it begins to get hot. This is why water is valuable to industries as a coolant. The high specific heat index of water also helps regulate the rate at which air changes temperature, which is why the temperature change between seasons is gradual rather than sudden, especially near the oceans. 4.8 Viscosity: Viscosity deals with the resistance to internal friction between molecules. Some liquids like water have a low viscosity where other liquids like honey or shampoo have a high viscosity. Viscosity will be affected by the temperature. At higher temperatures the viscosity decreases as the molecules take on more kinetic energy allowing them to move past each other faster.

CELL ORGANELLES 1. Plant Cell Structure

Biology Notes 2008

2. Plant Cell Organelle Functions

Cell Organelle Function Cell Wall - Prokaryotic Cells (e.g. plant cells)

- Maintains the firm shape of the plant cell - Protects the organelles - Made of cellulose

Cell Membrane - Contains the cytoplasm and all the organelles - Regulates passage of molecules in and out of cell - Maintains homeostasis - Barrier between the internal and external environment of the cell

Nucleus - Processes Information - Stores the cell's hereditary material, or DNA, - Coordinates the cell's activities (e.g. growth, intermediary metabolism,

protein synthesis, and cell division) - Contains nucleoplasm, surrounded by nuclear envelope

Chloroplasts - Converts light energy to chemical energy for photosynthesize Mitochondria - Break down carbohydrate and sugar molecules to provide energy,

particularly when light isn't available for the chloroplasts to produce energy

- Converts glucose into ATP Golgi Apparatus - Distributes and ships the cell's chemical products

- Modifies and packages proteins and fats built in the endoplasmic reticulum and prepares them for export as outside of the cell.

Endoplasmic Reticulum - Manufactures, processes, and transports chemical compounds for use inside and outside of the cell

- Connected to the double-layered nuclear envelope, providing a pipeline between the nucleus and the cytoplasm

Vacuole - Stores compounds (food, water, waste) - Contains cell sap, which contains dissolved substances such as sugars,

mineral salts and amino acids - Enclosed by tonoplast - Helps in plant growth - Plays an important structural role for the plant, providing the turgidity

and firmness for the plant Ribosome - 60 percent RNA and 40 percent protein

- Protein synthesis Peroxisome - Single membrane bounded and most common microbody

Biology Notes 2008

ACTIVE VS PASSIVE TRANSPORT

Plasma Membranes are selectively permeable membranes. They serve as boundaries for the cell, fencing off the cell’s interior from the external environment. Plasma membranes allow water, certain molecules and ions into the cell, as well as excrete substances. 1. Definitions

ACTIVE TRANSPORT Attributes/ Comparisons PASSIVE TRANSPORT

Needs energy - in the form of ATP

Energy expenditure No need energy - Spontaneous

Against/ up concentration gradient - Region of low concentration to region of high concentration

Direction Across/ down concentration gradient - Region of high concentration to region of low concentration

Protein Doorways Entry Point Protein Doorways 1. Ion Pumps 2. Exocytosis 3. Endocytosis 4. Pinocytosis 5. Phagocytosis

Types 1. Diffusion 2. Facilitated Diffusion 3. Osmosis

2. Passive Transport Diffusion Definition Diffusion is the spontaneous net movement of ions or molecules from a region where

they are in higher concentration to a region where they are in lower concentration (down a concentration gradient) Diffusion will continue until both regions are of equal concentrations, and equilibrium has been reached. Diffusion may involve the movement of molecules ACROSS a membrane, or not.

Rate of Diffusion - The steeper the concentration gradient, the faster the rate of diffusion. - The shorter the distance, the faster the rate of diffusion. - The larger the area, the faster the rate diffusion across the area. - The thinner the barrier (or presence of pores), the faster the rate of diffusion.

Surface Area: Volume Ratio (applies to diffusion across membranes)

- The rate of diffusion across a membrane depends on how much cell membrane is available.

- The greater the area of cell surface membrane, the faster the rate of diffusion. The greater the surface area: volume ratio, the faster the rate of diffusion.

- Evident in our body- Intestines! With folds, SA: Volume ratio is increased. Therefore, rate of absorption is

increasing, increasing the effectiveness of the intestines as this is where nutrients and water from the food is absorbed into the body. (A long tube will have a small SA: volume ratio)

Biology Notes 2008

2.2 Facilitated Diffusion

Definition Facilitated diffusion is a process of diffusion, a form of passive transport

facilitated by transport proteins.

Rationale Polar molecules and charged ions are dissolved in water. However, they are unable to diffuse freely across cell membranes due to the hydrophobic nature of the lipids (fats) that make up the phospholipid bilayers of the membrane, which is 80% fat. Therefore, the water is repelled by the hydrophobic center of the bilayer (phosphate tails). Only small nonpolar molecules, such as oxygen can easily diffuse across the membrane. Therefore, there is a need for specialized integral proteins to serve as transmembrane channels, allowing the molecules and ions to pass through the plasma membrane in and out of the cell. Protein Channels, ionophore, (a type of integral protein) creates a pathway, “blocking out” the fat so that hydrophilic molecules and ions can pass through.

Channel Proteins

- Proteins that are always “open” for simple diffusion across the membrane

Ion channels - Do not bind the solute - Hydrophilic pores through the membrane that open and allow certain types

of molecules, usually inorganic ions, to pass through. - Quite specific for the type of molecule they will transport - Faster than transport by carrier proteins. - Additionally, many channels contain a "gate" which is functions to control

the channel's permiability. When the gate is open, the channel transports, and when the gate is closed, the channel is closed.

- These ion channels are said to be 'gated' if they can be opened or closed. There are three types of gated ion channels: Ligand gated Open or close in response to the binding of a small signalling

molecule or "ligand". Some ion channels are gated by extra cellular ligands; some by intracellular ligands. In both cases, the ligand is not the substance that is transported when the channel opens.

Mechanically gated Mechanical deformation of the cells of stretch receptors opens ion

channels leading to the creation of nerve impulses Voltage gated Found in neurons and muscle cells Open or close in response to changes in the charge (measured in

volts) across the plasma membrane. For example as an impulse passes down a neuron, the reduction in the voltage opens sodium channels in the adjacent portion of the membrane. This allows the influx of Na+ into the neuron and thus the continuation of the nerve impulse.

Protein Channels

Carrier Proteins (also known as permeases or transporters)

- Changes shape naturally when the molecules come near - Binds a specific type of molecule and are thereby induced to undergo a series

of conformational changes which has the effect of carrying the molecule to the other side of the membrane.

- The carrier then discharges the molecule and, through another conformational change, reorients in the membrane to its original state.

- Typically, a given carrier will transport only a small group of related molecules.

Biology Notes 2008

2.3 Osmosis

Definition - A type of diffusion

- Osmosis is the net movement of water molecules from a solution of higher water potential to a solution of lower water potential through a selectively permeable membrane

- Osmosis is the net movement of water molecules from a solution of lower solute concentration to a solution of higher solute concentration through a selectively permeable membrane

- - Water moves down the water potential gradient

Water potential: Measure of the tendency for water to move from one place to another - Osmosis occurs when 2 solutions are separated by a selectively permeable

membrane and have different water potentials (different solute concentrations as well), until both solutions have an even distribution of water molecules and equilibrium has been reached

Isotonic - Provides an environment in which the concentration of solutes outside the cell

equals the concentration of solute inside. ISOTONIC DRINKS: e.g. Gatorade, H20, 100 plus - Replenish the salts that we lose when we sweat

Magnesium Sodium Potassium Chloride

Hypertonic - Provides an environment in which the concentration of solutes outside the cell is more than the concentration of solute inside. (less water potential)

- E.g. Concentrated salt solution

Types of Solutions

Hypotonic - Provides an environment in which the concentration of solutes outside the cell is less than the concentration of solute inside. (more water potential)

- E.g. Most hypotonic substance: Pure water Isotonic There WILL still be movement of water. However, there will be equal amounts of

water moving in and out of the cell, maintaining a ZERO net movement of water molecules.

What happens when plant cell is placed in solutions

Hypertonic - Water moves out of the plant cell - Plant cell loses water, causing vacuole to decrease in size

Contains urea (waste product)

Biology Notes 2008

- Cytoplasm shrinks away from the cell wall (plasmolysis) - Plant cell is PLASMOLYSED.

that are…

Hypotonic - Vacuole increases in size as water enters cell and pushes the cell contents against the cell wall

- Cell wall prevents over expansion of cell by exerting an OPPOSING PRESSURE (turgor) and hence, prevents the entry of more water.

- Plant Cell becomes TURGID. - Plant cell does not burst because the cell wall is STRONG and slightly

ELASTIC. Turgor: - Plays an important role in maintaining the shape of the soft tissues in plants - Helps plant remain firm and erect - When there is a high rate of evaporation of water from cells, cells lose

turgidity and plant wilts

Isotonic There WILL still be movement of water. However, there will be equal amounts of water moving in and out of the cell, maintaining a ZERO net movement of water molecules.

Hypertonic - Animal cell loses water - Membrane of cell forms little spikes and cell shrinks (crenation) - Animal cell will become dehydrated and will eventually die - Animal cell CRENATES.

What happens when animal cell is placed in solutions that are…

Hypotonic - Vacuole increases in size as water enters cell and pushes the cell contents against the cell membrane

- Animal cell will swell - Animal cell may BURST, killing the cell

Drinking too much water can kill! - Cells will swell preventing more entry of water, and be too dilute. The salt

concentration will be too low, which may be harmful as salts are necessary for bodily functions.

Contractile Vacuole Paramecium and other single-celled freshwater organisms are usually hypertonic relative to their outside environment, hence water will tend to enter the cell, swelling the cell and eventually bursting it. The contractile vacuole is the Paramecium's response to this problem. The pumping of water out of the cell by this method requires energy since the water is moving against the concentration gradient. Water is collected into the central ring of the vacuole and actively transported from the cell.

Biology Notes 2008

Animal Cell

Plant Cell

3. Active Transport Process in which energy is consumed to move the particles/ molecules against a concentration gradient The work of active transport is performed by specific carrier proteins in the membrane.

3.1 Carrier Proteins These transport proteins harness the energy of ATP to pump molecules from a low to a high concentration. The carrier protein first binds to the molecule. When ATP transfers a phosphate group to the carrier protein, the protein changes its shape in such a way as to move the bound molecule across the membrane.

Sodium-potassium pump - Na+ is maintained at low concentrations inside the cell and K+ is at higher concentrations. The reverse is the case on the outside of the cell.

- When a nerve message is propagated, the ions pass across the membrane, thus sending the message.

- After the message has passed, the ions must be actively transported back to their "starting positions" across the membrane.

- Unequal balance of Na+ and K+ across the membrane creates a large

concentration gradient that can be used to drive other active transport mechanisms.

Proton pump - Use ATP to remove hydrogen ions (H+), moving them from inside to outside the cell

- Creates a large difference in proton concentration (inside becomes NEGATIVELY CHARGED)

- Can be used to drive transport of other molecules

Biology Notes 2008

Coupled transport - Plant cells use gradient in PROTON PUMPS (hydrogen ions) to drive active transport of nutrients into plant cell

- SPECIFIC transport protein couples return of H+ ion to transport of sucrose into phloem cells

- Sucrose rides with H+ as it diffuses down the concentration gradient - Don’t really need ATP, because the concentration gradient is

maintained by either sodium-potassium pump or proton pump

3.2 ATP - Adenosine Triphosphate - Product of RESPIRATION (Glucose + Oxygen) - 1 glucose molecule = 34 ATP

P A P

P - The phosphate molecules are highly excitable and there is a high tendency to lose ONE phosphate molecule - When 1 molecule is lost, the bond is broken ENERGY RELEASE!

P Adenosine Triphosphate (ATP) becomes Adenosine Diphosphate (ADP) A P

- Also used in muscle contraction - Which is why dead people cannot move, as they have used up all the ATP , thus, muscles are unable to move - Rigor Motif: Corpses can “stand” or “sit up” because their muscles are hard and firm and inflexible. If

pressure is applied on one part of the body, the body acts like a hard rod and another part will move upwards (like a see saw)

3.3 Exocytosis and Endocytosis

CYTOSIS

- Form of active transport involving the in/out folding of the plasma membrane. (Plasma membrane needs to be flexible)

- Results in the bulk transport in/out of the cell - Achieved through the localised activity of microfilaments and microtubules in cytoskeleton -

- Engulfment of material - Typically occurs in protozoans and certain white blood cells of mammalian defense

system - Invagination of plasma membrane, which then forms vesicles or vacuoles that get

detached and enter cytoplasm Phagocytosis: “Cell- eating” - Engulfment of SOLID MATERIAL

- Results in formation of vacuoles

ENDOCYTOSIS

Pinocytosis: “Cell- drinking” - Uptake of liquids or fine suspensions - Results in formation of pinocytic vesicles

EXOCYTOSIS - Vesicle moves within the cytoplasm to the plasma membrane

- Vesicle membrane and plasma membrane fuses - Vesicle contents are released to outside of the cell - Typically in secretory cells

3 Phosphate Molecules are attached

Biology Notes 2008

Biology Notes 2008

PLASMA MEMBRANE

1. Functions of the Plasma Membrane

- Barrier between the external and internal environments of the cell as it is selectively permeable, allowing

only certain molecules and ions to enter/ leave the cell - Essential for homeostasis - Separate reaction and chemical activities of the cell - Divide the Organelles into compartments - Provide reaction surfaces and organizes enzymes and substrates

2. Fluid Mosaic Model 2.1 Structure

Biology Notes 2008

2.2 Five Key Parts Phospholipid Bilayer Hydrophilic Heads and Hydrophobic Tails- Stable Arrangement

- Has a polar (hydrophilic) head and two nonpolar (hydrophobic) tails- one saturated, one unsaturated.

- Phospholipids are aligned horizontally, tail to tail - This is the only stable arrangement as the hydrophobic tails repel the hydrophilic

heads - In addition, water is present on the inside and outside of the cell - As the hydrophobic tails repel water, the only stable arrangement formed is when 2

layers of phospholipids face each other, such that the hydrophobic tails are enclosed by the hydrophilic heads.

- Nonpolar regions of the molecules face the interior of the bilayer, where they are shielded from water.

- Polar regions of the molecules face outward where they interact with the water inside and outside of the cell.

Phospholipid Molecule

- Head is connected by glycerol to two fatty acid tails. - One of the tails is a straight chain fatty acid (saturated). - The other has a kink in the tail because of a double bond (unsaturated). - This kink influences packing and movement in the lateral plane of the membrane. It

allows for fluidity of the membrane, so that the lipids can MOVE. It prevents tight packing and makes the bilayer difficult to freeze.

All carbon valence electrons are used to bond with other atoms

Biology Notes 2008

Movement of Each Phospholipid Molecule - Individual molecules are free to move laterally; flips exist, though very rare. - It is the lack of flip-flopping that maintains the asymmetry of membranes (e.g.,

different components are present in different layers)

Cholesterol - Another lipid in the Fluid Mosaic Model - Plasma memb - ranes have nearly one cholesterol per phospholipid molecule (Amount of cholesterol

may vary with the type of membrane) - The cholesterol molecule inserts itself in the membrane with the same direction as

the phospholipid molecules (Note that the polar head of the cholesterol is aligned with the polar head of the phospholipids

- Functions Immobilize the first few hydrocarbon groups of the phospholipid molecules.

This makes the lipid bilayer less deformable and decreases its permeability to small water-soluble molecules. Without cholesterol (such as in a bacterium) a cell would need a cell wall.

Cholesterol prevents crystallization of hydrocarbons and phase shifts in the membrane.

Lower down, near the center of the bilayer, the flexible tail of the cholesterol molecule allows more movement, making the central part of the bilayer the most fluid.

Plays an important role in membrane fluidity and stability

Glycoprotein 1. Proteins produced by ribosome 2. Proteins pass into the interior of rough endoplasmic reticulum, carbohydrates

are added, forming glycoproteins - Carbohydrates: Different kinds of sugar linked together - A type of integral protein

Functions: - Carbohydrates act as markers that determine the destination of the glycoprotein

within the cell/ for export - Carbohydrates help position/ orientate glycoproteins - Carbohydrates prevent glycoproteins from rotating in membrane - Carbohydrates on cell surfaces are important in intercellular recognition

(recognition of different cells to form tissues and detection of foreign cells by immune system)

- Glycoprotein play important role in cellular recognition and immune response, and act as receptors for hormones and neurotransmitters

- Together with glycolipids, stabilize membrane structure

Integral Protein - Proteins that completely penetrate or partially penetrate lipid bilayer. - Functions:

Play a role in the selective transport of certain substances across the phospholipid bilayer, either acting as channels or active transport molecules.

Others function as receptors, which bind information-providing molecules, such as hormones, and transmit corresponding signals based on the obtained information to the interior of the cell.

Membrane proteins may also exhibit enzymatic activity, catalyzing various reactions related to the plasma membrane

Sometimes known as gateway proteins Proteins also function in cellular recognition

Biology Notes 2008

Peripheral Protein - Proteins that are stuck to surface of membrane - Typically this attachment is via attachment to portions of integral membrane

proteins jutting out of the membrane interior 2.3 Fluidity - Lipids in membrane are not fixed

Lipids can move in the membrane (semi-fluid nature of membrane) - Interior of membrane attached to cytoskeleton to give cell membrane FIRMNESS and SHAPE

Why must the membrane be fluid? - A frozen membrane cannot:

Move Carry out cytosis Heal small punctures

- Allow interactions to take place easily among membrane components - Allow newly synthesized protein to reach destinations quickly - Membrane fusion and subsequent mixing of components allowed - Even distribution of components at cell division What allows it to be fluid? - Phospholipid Bilayer gives the plasma membrane its FLUIDITY - Individual molecules are free to move laterally due to their one unsaturated tail, which allows the lipids to

move, increasing fluidity - Cholesterol helps stabilize animal cell membranes at different temperatures.

At higher temperatures cholesterol serves to impede phospholipid fluidity. Cholesterol keeps lipids attached to each other through van der waals forces so that the plasma membrane will not disintegrate

At lower temperatures cholesterol interferes with solidification of membranes (e.g., cholesterol functions similarly, in the latter case, to the effect of unsaturated fatty acids on lipid-bilayer fluidity). Cholesterol serves as a physical entity, keeping a minimum distances between phospholipids so fluidity is maintained.

- Depending on a number of factors, including the exact composition of the bilayer and temperature, plasma

membranes can undergo phase transitions which render their molecules less dynamic and produce a more gel-like or nearly solid state.

- Cells are able to regulate the fluidity of their plasma membranes to meet their particular needs by synthesizing more of certain types of molecules, such as those with specific kinds of bonds that keep them fluid at lower temperatures

Biology Notes 2008

Biological Molecules;

Biology Notes 2008

Condensation and Hydrolysis Reactions

Carbohydrates Definition: Organic Compounds that are made up of elements carbon, hydrogen and oxygen General Formula: CX(H2O)y where there are always twice as many hydrogen atoms as oxygen atoms.

- Come mainly from plants, and are a good source of energy for the body Functions of Carbohydrates

- Good source of energy - Form supporting structures - Can easily be converted to other organic compounds - Help in the formation of nucleic acids (e.g. DNA) - Synthesize lubricants (e.g. mucus- carbohydrate and protein) - Produce nectar - Fuel cell metabolism

Types of Carbohydrates There are three groups of carbohydrates:

Carbohydrates

Condensation Reaction Condensation is a chemical reaction whereby 2 simple molecules are joined together to form a larger molecule with the removal of 1 molecule of water

Hydrolysis/ Hydrolytic Reaction Reaction where a water molecule is added to split complex sugar into simpler component molecules by

- Heating with dilute acids at 100°C (chemical method) - Treating with suitable enzyme at room temperature/ optimum temperature of the enzyme

(enzymatic method)

Monosaccharide Simple Sugars

- Glucose - Fructose - Galactose

Disaccharide Complex sugars

- Maltose - Lactose - Sucrose

Polysaccharide - Starch - Cellulose - Glycogen

Other Derivatives - Pectins - Chitin

Biology Notes 2008

1. Monosaccharide General Formula: (CH2O)n

n Monosaccharide 3 Triose 4 Tetrose 5 Pentose 6 Hexose

- Monosaccharides differ ONLY in terms of the details of arrangement of atoms within a molecule, which gives them their different chemical and biological properties

- Hence, they show isomerism Aldose and Ketose Monosaccharides contain either an ALDEHYDE (-CHO) group or a KETONE (-CO) group

Formula Aldose Ketose C5H10O5 Ribose Ribulose C6H12O6 Glucose Fructose

Open-chain form and ring form

Isomers have different structural formulae but same molecular formula Types of isomers: aldose and ketose, open-chain and ring forms, alpha and beta

Biology Notes 2008

Enzymes.

Biology Notes 2008

Enzymes Definition: Enzymes are biological catalysts made up of PROTEIN or RNA which can alter or speed up the rate of chemical reactions without themselves being changed at the end of the reaction Without enzymes, biochemical reactions will proceed too slowly to sustain life. The rate of a reaction can be speeded up by raising the temperature. However, this is not the best the solution as it would be detrimental to the cell if temperatures are too high.

- Enzymes can speed up the rate of reactions WITHOUT increasing the temperature Properties of Enzymes

- Effective in small amounts as they remain chemically unaltered throughout the reaction - Highly efficient> enzyme-catalysed reactions proceed 103 to 108 times faster than uncatalysed reactions - High turnover number (no. of substrate molecules converted into products by one enzyme molecule in one

second when enzyme is fully saturated with substrate) - High degree of specificity > due to the configuration of its active site (shape determines function) - Enzyme activity affected by pH, temperature, [substrate] and [enzyme] - Enzyme activity can be altered by inhibitors/ co-enzymes

Examples of Enzymes-Catalysed Reactions

Biological Molecule

Enzyme Location

Carbohydrases

starch (+ water) maltose

Digestive enzymes - digestive tract or nearby organs like the pancreas or liver

maltose (+ water) glucose + glucose

sucrose (+ water) glucose + fructose

Carbohydrate

Cellulase digests cellulose

Proteases Digestive enzymes - digestive tract or nearby organs like the pancreas or liver

proteins (+ water) polypeptides

Stomach

Protein

liquid milk proteins (+ water) coagulated milk solids

Lipases Digestive enzymes - digestive tract or nearby organs like the pancreas or liver

Lipid

fats/oils (+ water) fatty acids + glycerol

Steapsin in pancreatic juice

Other (non-digestive) enzymes -

hydrogen peroxide water + oxygen

Biology Notes 2008

How Enzymes Work Structure of Enzymes

- Globular proteins that are much larger than the substrate molecules - Only a small portion of the enzyme comes into contact with the substrate: Active Site - There are 2 types of amino acid residues at the active site: Contact residue: Responsible for specificity and induces the conformational change in shape of active site

to fit the substrate molecules Catalytic residue: Responsible for catalyzing the reaction; act on the bonds of the substrate

- The other amino acid residues (not at active site) maintain the globular shape of the enzyme => enables optimal function of active site

Function of Enzyme Activation Energy: The energy required for substances to react (energy barrier that has to be overcome before a reaction can occur)

- The greater the activation energy, the slower the reaction at any particular temperature What Do Enzymes Do

- Enzymes decrease the activation energy required for a reaction to occur without increasing the temperature (Heat can supply this energy, but it is detrimental to the cells)

- There are several ways that enzymes lower activation energy: 1. Orientation of Substrate Molecules

The substrates and enzyme must collide at the correct orientation so that the substrate molecules can bind to the enzyme at the active site to form enzyme-substrate complex where the chances of reaction are much higher. Enzyme molecules hold the substrate molecules in an arrangement that forces them in the correct orientation so the complex can be formed easier. Without enzymes, it is unlikely that the substrate molecules will collide into each other in the correct orientation to react.

2. Put stress on substrate molecule Within the enzyme-substrate complex, the enzyme will exert stress on certain bonds in the substrate molecule, increasing likelihood that the bonds will break

3. Changing charge of substrate

When the R groups of amino acid residues at active site are very close to the substrate, they can change the charge of the substrate, alter the distribution of electrons within the bonds of the substrate (or activates the functional groups of substrates) that increases reactivity of substrate

Catabolic VS Anabolic Reactions Catabolic Reactions Anabolic Reactions

- 1 substrate molecule drawn to active site - Substrate subjected to stress, breaking the

chemical bonds - Substrate molecule breaks apart to form 2

separate substrate molecules

- 2 substrate molecules drawn to active site - Molecules subjected to stress, aid in formation of

bonds - Molecules form bonds and become a single molecule

e.g. Digestion, cellular respiration e.g. protein synthesis, photosynthesis

Theories for Enzyme Specificity Enzymes are highly specific in the reactions they catalyse. Most enzymes catalyse reactions of one type of substrate molecule only, while some have lower specificity and catalyse reactions of a group of similar molecules. Lock and Key Induced Fit Enzyme active sit has a particular fixed shape, into which the substrate molecules fit exactly. Once products are formed, they no longer fit into the active site and hence, leave the active site. Shape of the active site is complementary to shape of substrate molecule

Initial shape of active sit may not be complementary to shape of substrate molecule, only after substrate binds. Binding of substrate to active site induced a conformational change in shape of active site, enabling the substrate to fit snugly into the active site. Hence, the enzyme can perform its catalytic function more effectively.

Biology Notes 2008

Factors Affecting Enzyme Activity Enzyme and temperature The higher the temperature, the faster the rate of the reaction until optimum temperature is reached. Reason 1: As temperature increases, the kinetic energy of enzyme and substrate molecules increases. Therefore, there are an increased number of effective collisions between the enzyme and substrate molecules, increasing the number of enzyme-substrate complexes. Reason 2: When temperatures increase, the kinetic energy of the molecules increase. When molecules collide, the kinetic energy of the molecules can be converted into chemical potential energy of the molecules. With increased kinetic energy, the amount of chemical potential energy produced when the molecules collide may become great enough to achieve the activation energy of the reaction. Thus, it is possible that more molecules per unit time will reach the activation energy, increasing the rate of reaction. - For most enzymes, the rate of increase is doubled for every increase of 10°C.

If the temperature is increased beyond the optimum temperature, the rate of reaction will decrease rapidly because the enzyme will DENATURE. Reason: Excessive heat will disrupt the intra-molecular bonds that serve to stabilize the secondary and tertiary structures of the enzyme molecule, causing the enzyme to unfold and lose the precise shape of the active site. [irreversible] If the temperature is decreased to near or below 0°C, the rate of reaction will also decrease rapidly because the enzyme is INACTIVATED. [reversible- enzyme activity will regain pace when higher temperatures are restored]

Enzyme and pH If the pH is lower/ higher than the optimum pH, the rate of reaction will decrease. Reason: The concentration of hydrogen ions (H+) would change, altering the charge on the R groups of the amino acid residues of the enzyme molecule. This would disrupt the ionic and hydrogen bonds that help maintain the conformation of the enzyme molecule, affecting the binding of the substrate to the enzyme. [reversible if pH is altered by a small extent] Enzyme pH Optimum Lipase (pancreas) 8.0

Lipase (stomach) 4.0 - 5.0

Lipase (castor oil) 4.7

Pepsin 1.5 - 1.6

Trypsin 7.8 - 8.7

Urease 7.0

Invertase 4.5

Maltase 6.1 - 6.8

Amylase (pancreas) 6.7 - 7.0

Amylase (malt) 4.6 - 5.2

Catalase 7.0

Optimum Temperature: temperature at which the enzyme functions at its maximum

Optimum pH: pH at which the rate of the enzyme-catalysed reaction is at its maximum; the intra-molecular bonds that maintain the secondary and tertiary structures of the enzyme are intact- thus the conformational of active site is most ideal for binding the substrate and the enzyme

Biology Notes 2008

Enzyme and [substrate] For a fixed enzyme concentration, The rate of reaction increases with increasing substrate concentration, until a point where further increase in substrate concentration no longer produces a significant change in the reaction rate Reason: More substrate molecules result in more successful collisions between the substrate and enzyme molecules, forming more enzyme-substrate complexes and hence, increasing the rate of reaction. When the active sites of all the enzyme molecules are saturated with substrate molecules (that’s why enzyme activity begins to plateau). Any extra substrate molecule has to wait until the enzyme-substrate complex releases the products Limiting Factor: Substrate concentration When maximum velocity is reached, the limiting factor becomes the enzyme concentration. Km value is a measure of affinity of an enzyme for its substrate. Low Km = high affinity High Km = low affinity Enzyme and [enzyme] [Substrate] maintained at a high level, constant pH and temperature Rate of reaction is proportional to the enzyme concentration Reason: As enzyme concentration increases, there is a higher chance of substrates colliding with an enzyme molecule, thus more enzyme-substrate complexes are formed, increasing rate of the reaction. At high [enzyme], increasing [enzyme] would not increase the rate of reaction if the [substrate] is limiting.

Biology Notes 2008

Inhibitors and Co-Factors Allosteric Enzyme Enzyme whose activity can be altered by molecules acting at a site other than the active site (non-competitive), called the allosteric site. The binding of a regulatory molecule at the allosteric site changes the overall shape of the enzyme, can either ENABLE or PREVENT binding of substrates. Inhibitor Substance that prevents an enzyme from catalyzing its reaction => Decreases the rate of the reaction How? It combines with enzyme and forms an enzyme-inhibitor complex, which cannot bind with substrates Types of Inhibitors

Non-competitive Competitive Non-Competitive Allosteric

(Allosteric Inhibitor, a type of regulatory

molecule)

Poisons (Allosteric Inhibitor, a

type of regulatory molecule)

- Close structural resemblance to substrate

- Competes with substrate for the active site

- When the competitive inhibitor is bound to the enzyme active site, the substrate molecules cannot bind to it

- No structural resemblance to substrates

- Combines with enzyme at a site other than the active site

- Changes the conformation of the enzyme, including the active site

- The substrate can still bind to the active site, though the rate of reaction is slower

# Increase the concentration of enzymes to increase rate of reaction

- No structural resemblance to substrates

- Combines with enzyme at the allosteric site

- Changes the conformation of the enzyme, including the active site

- Active site is totally distorted, the substrate cannot bind to the active site AT ALL

- Causes a proportion of enzyme molecules to be out of action (not functional), thus the concentration of effective enzymes is decreased.

# Increase the concentration of enzymes to increase rate of reaction

- Some heavy metals Cadmium Arsenic Lead Mercury

- Most act as non-

competitive inhibitors - Bind strongly to the

sulfhydryl groups of protein and destroy catalytic activity by changing the conformation of the enzyme and active site

- Active site is totally distorted, the substrate cannot bind to the active site AT ALL

- Causes a proportion of enzyme molecules to be out of action, thus decreasing the concentration of effective enzymes

Reversible Reversible Reversible Irreversible - Increasing the

[substrate] can decrease the effect of competitive inhibitor

Reason: Increases the probability of enzyme-substrate collision instead of an enzyme-inhibitor collision - At very high

[substrate], the rate of reaction can almost reach the maximum value (without inhibitor)

Increasing [substrate] will not increase the rate of reaction, the number of effective enzymes is limited, and there is only a fixed number of substrate molecules it can bind with at any given time.

Biology Notes 2008

Allosteric activators - Enhances enzyme activity by enabling substrate to bind to the active site by changing the shape of active site - Without the activator bound to the allosteric site, the active site is unable to bind the substrates to catalyse the

reaction. When the allosteric activator binds to the enzyme at the allosteric site, the shape of the active site changes so it can bind the substrates.

- Reversible process Cofactors Co-factor: Non-protein component of an enzyme Some enzymes consist of just protein, while some require the addition of other components in order to complete their catalytic properties, if not the active site would be unable to bind the substrate to catalyse the reaction. These additional components may be permanently attached parts (prosthetic groups) or temporarily attached pieces (coenzymes) that detach after reaction. Details Inorganic Ions (Enzyme Activator) - Mould enzyme into a shape that allows an enzyme-substrate complex to

be formed easier - E.g. Chloride ions enhances salivary amylase activity

Prosthetic groups - Cofactors that are bound to enzyme permanently - Organic molecules - Iron-containing haem group is the prosthetic group of catalase enzyme

Coenzymes - Organic molecules - Derived from vitamins - Temporarily attached, detaches from enzyme after reaction

Biology Notes 2008

Energy transfer.

Biology Notes 2008

Energy Transfer In Organisms

Autotroph Heterotroph Able to synthesize their own food Unable to synthesize their own food Captures energy from the sun and convert it to chemical energy Able to use simple inorganic materials as starting materials for synthesis of complex organic compounds using either: - light energy (photoautotroph) - Chemical energy (chemoautotroph)

Captures energy from the autotrophs and convert it to chemical energy

Photosynthesis Respiration

Energy Transfer in Autotrophs: Photosynthesis Definition: Photosynthesis is defined as the process by which organisms use carbon dioxide and water to manufacture food, using energy supplied by light that is absorbed by the organisms and converted to chemical energy. General Equation: 6 CO2 + 6 H2O C6H12O6 + 6 O2

How do Plants Obtain the Necessary Inputs for Photosynthesis? Water - Via vessels running from the root, through the stem to the leaves. - Xylem: vessels for conducting water - Phloem: vessels for conducting nutrients The cohesion-tension theory of water flow from roots to leaf in xylem:

1. Water Molecules evaporate from the leaf to the surroundings via the openings (stomata) through transpiration

2. Other water molecules from the xylem replace those that evaporated 3. The water molecule chain (from leaf veins to roots) is pulled up by evaporation Cohesion of water molecules to each other and adhesion to xylem wall through hydrogen bonds create

water chain 4. As water retreats up the xylem, the water pressure in the xylem in the roots decreases. Due to osmosis,

water molecules will travel from a region of higher water potential to lower water potential. Thus water enters the vascular cylinder of the root, replenishing the bottom of the chain

Carbon Dioxide - Via openings on the leaf surface called stomata - Diffusion of CO2: Concentration of carbon dioxide in the leaf must be LOW, thus due to the concentration

gradient, carbon dioxide will enter the leaf from the air space How does the leaf control the opening and closing of the stomata?

Light, chlorophyll

1. The sun rises, and light intensity rises. 2. Photosynthesis begins in the guard cells 3. Glucose is formed, and the water potential drops

in the guard cells 4. Water enters the guard cell via osmosis 5. The volume of the guard cells increase 6. The guard cell becomes turgid 7. Due to uneven thickness of the cell wall, the

guard cell will curve outwards 8. Stoma opens

1. Sun sets, light intensity drops 2. Photosynthesis does not occur 3. Glucose will be converted to starch or used up

in other process (e.g. respiration) 4. Water potential in guard cell increases 5. Water leaves guard cell 6. Guard cell becomes flaccid 7. Guard cell shrinks, and straightens 8. Stoma closes

Biology Notes 2008

Alternate method of Opening and Closing of Stomata

How is the Leaf Adapted for Photosynthesis

Part of the Leaf Characteristic How it helps Cuticle Transparent and thin Prevents water loss and focuses sunlight Upper Epidermis 1 cell thick As it is thin, it allows the light to pass through Palisade - Lie just below the upper

epidermis - High layer of cells closely

packed with chloroplasts

Allows maximum absorption of sunlight

Chloroplasts - Numerous - Located near the periphery of

the cell - Phototactic

Maximum absorption of sunlight Facilitates gaseous exchange with intercellular air spaces Move within cell towards light

Spongy Mesophyll Oval in shape; Loosely packed with air spaces

Allow efficient diffusion of carbon dioxide

Vascular Bundle Connects leaf to rest of plant Transport water for photosynthesis; removes glucose; provides support to keep the leaf up, so that leaf blade is held at right angles to incident light

1. High light intensity, high humidity 2. Proton pump drives protons (H+ ) from guard

cells 3. Electrical potential of cell decreases 4. Potassium ions are pumped into the guard cells

through active diffusion 5. Increases osmotic pressure in the guard cell 6. Water enters cell through osmosis 7. Increases cell volume and turgor pressure 8. Rings of cellulose microfibrils prevent the width

of guard cells from swelling, allows extra turgor pressure to elongate guard cells

9. Guard cells lengthen

1. Roots experience water shortage 2. Abscisic acid is released, which binds to certain

receptors in the guard cells’ plasma membranes. 3. Raises the pH of cytosol of the cell 4. Increase the concentration of free Ca2+ in the

cytosol (due to influx from outside cell, and the release of calcium ins form internal stores)

5. Chloride and inorganic ions exit cells 6. Loss of K+ in cells 7. Reduce osmotic pressure 8. Cell flaccid 9. Stoma closes

Biology Notes 2008

Xylem: Transports water and mineral salts to leaf cells, preventing leaf from wilting and 1% of water is used for light reactions of photosynthesis Phloem: Transports products of photosynthesis away from leaf

Stomata Guard cell opening and closing Allow passage of air into plant, prevents excessive water loss

Large Surface Area Allows maximum absorption of sunlight Thin Carbon dioxide only needs to diffuse cross short distance to reach mesophyll cells More stomata on the lower epidermis then upper epidermis

Allows entry of carbon dioxide into leaf, and still minimise water loss from the plant - Upper epidermis directly exposed to sun and a lot of water will be lost

Guard Cell See above Factors Affecting Photosynthesis - Carbon Dioxide concentration - Water - Light Intensity - Chlorophyll levels Photosynthesis and Light Intensity At low light intensities, Rate of photosynthesis increases linearly with increasing light intensity Very high light intensities Chlorophyll may be damaged, decreasing the rate of photosynthesis - plants living under such conditions are usually

adapted to be protected by thick cuticles Compensation point: light intensity at which the rate of photosynthesis= rate of respiration - All the carbon dioxide produced during respiration is

used for photosynthesis - All the oxygen produced during photosynthesis is used

for respiration. - No gaseous exchange between the plant and

environment - Reached at low light intensities Below compensation point (dark)

Compensation point Above compensation point (bright)

Respiration No photosynthesis

Rate of Respiration = Rate of Photosynthesis

Rate of Respiration < Rate of photosynthesis

Intake: Oxygen Release: Carbon dioxide

Intake: - Release: - No gaseous exchange with surroundings

Intake: Carbon dioxide Release: Oxygen

Photosynthesis and Light Wavelength Peak at 470 and 650 nm (red + blue/violet light) Absorption Spectrum and Action Spectrum - Chlorophylls a and b absorb red and blue/ violet light - Carotene and xanthophyll absorb only blue/violet light - Different photosynthetic pigments effectively increase the range of wavelengths from which plants can obtain

energy - Action spectrum similar to absorption spectrum, indicating that those pigments are responsible for light

absorption for photosynthesis

Biology Notes 2008

Photosynthesis and Carbon Dioxide Concentration - CO2 required for dark reactions - Rate of photosynthesis can be increased by increasing the carbon dioxide concentration - Short term optimum: 0.5% - Long term optimum: 0.1% Photosynthesis and Temperature Why is photosynthesis affected by temperature? Reactions of photosynthesis are catalysed by enzymes, whose activity is greatly affected by temperature Rate of photosynthesis would double for every 10°C increase (same as enzyme activity) until the optimum temperature. At temperatures higher than optimum temperature, the enzymes will denature and rate of respiration decrease. Photosynthesis and Water If the plant has low water content, it will close its stomata in response to wilting. This prevents carbon dioxide from entering the plant for photosynthesis. A deficiency in water will decrease the rate of photosynthesis. Photosynthesis and Oxygen concentration A high concentration of oxygen will inhibit photosynthesis (decrease rate of photosynthesis) as oxygen will compete with carbon dioxide for the active site in RuBP carboxylase Photosynthesis and Chlorophyll Concentration - Not normally a limiting factor - Decrease in chlorophyll levels will decrease rate of photosynthesis, and cause leaves to turn yellow Reasons for decrease in chlorophyll levels

Disease Ageing Nitrogen and magnesium deficiency Lack of light

Limiting Factors - Rate of biochemical process, which consists of a series

of reactions, is limited by the slowest reaction in the series - Rate of biochemical process, which is affected by several

factors, is limited by the factor that is nearest minimum value. At A, light is the only limiting factor. Light saturation occurs at C, B, D, where an increase in light intensity will not increase the rate of photosynthesis. This means that another factor that affects photosynthesis is obstructing the rate of photosynthesis from increasing. Single: At C, an increase in light intensity would not cause the rate of photosynthesis to increase. This is because of light saturation. There is “excess” light, and another factor has “too little” and unable to “keep up” with the increasing light intensity. This other factor is carbon dioxide concentration 0.04%. At C, carbon dioxide concentration is too little and hence, despite increase in light intensity, photosynthesis would not speed up. Compare B and C: A higher concentration of carbon dioxide would increase the rate of photosynthesis. D and B: A higher concentration of carbon dioxide would increase the rate of photosynthesis. HOWEVER, if D is changed to be at B: - Despite differences in carbon dioxide concentration, the rate of photosynthesis would not increase. This means

that even though the carbon dioxide concentration increases, another factor is obstructing photosynthesis. Different conditions (e.g. 0.4% and 0.04%) - Likened to advancing right on the x-axis, increase in one factor=> would the rate increase? If yes, then that factor is the limiting factor. If no, then there is another limiting factor.

Biology Notes 2008

Chemistry of Photosynthesis

Photosynthesis consists of 2 stages: - Light-dependent Stage (light reactions) - Light-independent stage (dark reactions) Light-dependent Stage (Light Reactions) - Occurs in the Thylakoid membrane (chlorophyll) - Sets of integral protein - Where light energy is converted to chemical energy to be used in the dark reactions - Produce ATP and NADPH for dark reactions Formula

12 H2O + 12NADP + 18ADP + 18Pi 6 O2 + 12 NADPH + 18 ATP

Chlorophyll is found in the thylakoid membrane

light and chlorophyll

Biology Notes 2008

Photosystem 2- Light Harvesting Complex - Light-harvesting system acts like a funnel - When an accessory pigment molecule in the light harvesting system absorbs light energy, its energy level

increases and gets ‘excited’. - The ‘excited’ accessory pigment molecule transfers its energy to neighbouring accessory pigment molecules,

until it reaches the reaction centre - At the reaction centre, energy is absorbed by special chlorophyll a molecule - An electron of choloropyl a molecule is boosted to a very high energy level and displaced

Chlorophyll a -> chlorophyll a+ + electron

However, the light harvesting complex cannot afford to keep losing electrons. Water is split by manganese complex to produce electrons to replace those that are released.

2H2O 4e++ O2 + 4 H+

Photosystem 2- Electron Transport Chain - the electron that was displaced is transferred to an electron acceptor Y which passes it on to a chain of electron

carriers (of progressively lower energy levels) - The electron transport chain is used to pump hydrogen as well - Hydrogen (H+) will be attracted to the electron and the momentum of electron passing through will cause the

hydrogen to pass through the chain, an into the thylakoid space - Transport of electrons down the chain provide energy for active transport of hydrogen ions from stroma, across

the thylakoid membrane and into thylakoid space - High concentration of hydrogen ions in the thylakoid space, must be diffused out - ATP synthase (enzyme to create ATP; integral protein in thylakoid membrane)

Active site only ready to catalyse reaction of ADP and Pi when there’s hydrogen Hydrogen concentration gradient drives ATP synthase Everytime 1 hydrogen ion leaves via the ATP synthase, 1 ADP is released

Photosystem 1- Light Harvesting Complex - Electron from the electron transport chain is fitted into the light harvesting system - Electrons get excited from the light energy again, and releases one electron from the reaction centre (see above)

(this time, this electron is replaced by the electron from photosystem 2) Photosystem 1- Electron Transport Chain - The electron passes through the chain of electron carriers again, and hydrogen ions are pumped into the

thylakoid space through active transport again (see above) - The hydrogen ions in the thylakoid space and the electron at the end of the electron transport chain creates the

active site to reduce NADP+ to NADPH

NADP+ + 2H+ + 2e NADPH + H+

1st product of photosynthesis

Biology Notes 2008

Light-Independent Stage - Occurs in the stroma - Fixes CO2 to produce glucose 12NADPH + 18ATP + 6CO2 Glucose + 12NADP+ + 18ADP + 18Pi + O2 Caboxylation

1. Ribulose Biphosphate Caboxylase (enzyme) binds carbon dioxide (Input of photosynthesis) with a five carbon compound (Ribulose Bisphosphate RuBP) to form an unstable 6 carbon compound

2. 6-carbon compound breaks down to form 2 molecules of 3-carbon compound called glycerate-3-phosphate (3pGA)

Reduction

1. 3PGA is reduced to glyceraldehyde-3-phosphate (G3P) NADPH -> NADP + H+ ATP-> ADP + Pi The hydrogen needed for this reduction comes from NADPH and the energy comes from the breaking

down of ATP 2. 2 G3P molecules combine to form a six-carbon sugar

Regeneration

3. The rest of the G3P molecules enter a series of reactions driven by ATP to regenerate RuBP, to ensure continued fixation of carbon dioxide

Biology Notes 2008

Energy Transfer in Heterotrophs: Respiration Definition Respiration is an energy-releasing process. Cells can undergo respiration if the presence of oxygen (aerobic) or absence of oxygen (anaerobic) Gaseous Exchange The process by which oxygen is acquired and carbon dioxide is removed. Cellular respiration creates a constant demand for oxygen and a need to eliminate carbon dioxide gas. - We breathe as a reflex because we need to get rid of carbon dioxide in our body Gaseous Exchange Systems in Animals Animal Gaseous Exchange System Aquatic Insects - some develop tracheal gills to increase surface area across which gases diffuse

- some are dependent on getting oxygen from the surface with a siphon and releasing carbon dioxide straight into the air (e.g. mosquito larva)

Tadpoles Juvenile amphibians usually have gills, which are lost as adult takes on terrestrial existence

Animal like protists (e.g. amoeba)

Simple diffusion across cell surface

Air Breathing Vertebrate Lungs Marine mammals come to the surface to breathe.

Bony fish, sharks, rays Gills to breathe dissolved oxygen in water - 80% extraction rates - Over 3 times the rate of human lungs from air

Insects System of branching tubes (tracheal tubes) - Gases diffuse across the moist lining directly to and from tissues - End of each tube contains a small amount of fluid (spiracle) to regulate the

movement of gases by changing surface area of air in contact with cells Amphibians Surface Gas Exchange

- Surface must be kept moist by secretions from mucous glands

Birds - Air sacs in addition to lungs - Air sacs ventilate the lungs, where gaseous exchange takes place - Anterior and posterior air sacs serve as bellows that keep air flowing through

lungs continuously in one direction Common Properties of Gaseous Exchange Systems Property How it aids gaseous exchange Thin Membrane Facilitates Diffusion Large surface area Facilitate EFICIENT diffusion Moist For gas to dissolve in the transport medium, which is water in the blood Surface Area X Difference in concentration across membrane = Diffusion rate across gas exchange surfaces Larger SA + Bigger difference in concentration + Thinner membrane = Faster diffusion rate

Thickness of Membrane

Biology Notes 2008

Human Gaseous Exchange System

Bronchiole and Alveolus help to increase surface area Alveolus is MOIST. - Near blood vessels, so gases can diffuse into blood stream and be carried to the heart and pumped all over the

body - Direct contact with blood vessels - Gases dissolve into the blood stream - Alveolar surface: gas exchange embranes are

only 0.5 think, allowing for rapid and efficient diffusion

Alveolus and Lung Capillary - Lung capillaries surround the alveoli very

closely, allowing for rapid and efficient diffusion of gases

- Oxygen and carbon dioxide diffuse from the alveoli to the capillary and vice versa respectively

- When oxygen levels in the capillary are high, haemoglobin binds with a lot of oxygen Body Tissue Capillary and Body Cells - Capillaries are very close to body cells, allowing for rapid diffusion back and forth - When carbon dioxide levels of the body tissues are high, haemoglobin releases oxygen

Oxygen will diffuse into the body cells from the capillaries - Carbon dioxide from the body cells diffuse into the capillary

Most of the carbon dioxide in the blood is carried as bicarbonate (formed in red blood cells and diffuse out into the plasma)

Biology Notes 2008

Breathing Mechanism Inhalation Exhalation Forced Breathing External intercostal muscles contract External intercostal muscles relax Internal intercostal muscles and

abdominal muscles contract to increase force of expiration

Ribcage moves UP and OUT Ribcage moves DOWN and IN Lungs Expand Lungs shrink Diaphragm contracts and moves down Diaphragm relaxes, elasticity of diaphragm causes recoil and moves up Thoracic volume increases, a partial vacuum is created, decrease in pressure - Air flows in, in response to pressure

gradient

Thoracic volume decreases, pressure increases - Air flows out in response to pressure gradient

Breathing Control Why can’t we hold our breaths for long? Why do we have a reflex to breathe? If we don’t breathe, there will be raised CO2 levels in our blood, increasing carbonic acid levels and H+ ions, lowering the blood pH. Chemoreceptors will monitor this decrease in pH, and stimulate respiratory centre to increase breathing rate and depth. Cellular Respiration (Aerobic Respiration) - Glucose is broken down/ oxidized to give carbon dioxide, water and energy

Energy released is used to manufacture ATP from ADP and Pi. Oxidation of 1 glucose molecule = energy to synthesize 38 ATP molecules

General Formula

C6H12O6 + 6 O2 6 CO2 + 6 H2O + Energy - Aerobic Respiration occurs mainly in the mitochondrion Uses of Energy - Muscle contraction - Protein synthesis - Cell division - Active transport - Building up of protoplasm for growth - Transmission of nerve impulses - Maintenance of a constant body temperature End Product of Respiration: ATP molecules ATP is a convenient store of energy for a cell because - It stores energy in relatively small amount. - It is quickly hydrolysed in a one-step reaction to release energy. - It can move around inside cells easily, but cannot pass through cell membranes.

Chemoreceptors (in aorta and carotid arteries) monitor the blood’s pH. Low pH (high CO2) will stimulate the respiratory centre to increase breathing rate and depth

Respiratory Centre connects to the cerebral cortex, allowing voluntary control over breathing

Vagus nerve carries impulses from stretch receptors to respiratory centre to inhibit inspiration

Stretch receptors monitor the amount of lung inflation

Intercostal nerves stimulate inspiration

Phrenic nerve sends impulses to diaphragm to stimulate contraction

ATP (High energy compound) => Free phosphate + ADP (Low energy compound with no available energy to fuel metabolic activity) ATP: 30.7 kJ of energy

10% captured by cell for processes 90% lost to heat

Biology Notes 2008

Glycolysis - Occurs in the cytoplasm - Breaks down glucose into pyruvate - Releases ATP - Forms NADH - Occurs during aerobic respiration AND anaerobic respiration

Phosphorylation: addition of phosphate group to a molecule (ATP-> ADP) Hydrolysis: Transfer of phosphate group from molecule to ADP (ADP-> ATP) Oxidation: Removal of hydrogen from a molecule (NAD+ -> NADH) Products: 2 ATP (4 ATP- 2 ATP) 2 NADH (Oxidative phosphorylation) 2 Pyruvate (converted to acetyl CoA)

Conversion of pyruvate to acetyl CoA - ONLY occurs in aerobic respiration

Products: 2 acetyl CoA molecules (Krebs Cycle) 2 NADH (Oxidative phosphorylation) 2 CO2 (Exhaled from lungs)

Biology Notes 2008

Krebs Cycle - Can ONLY occur in aerobic respiration - Occurs in the mitochondrial matrix - Oxidise acetyl CoA through decarboxylation and dehydrogenation - Not oxidized directly, but only after being added to oxaloacetate Products: 2 oxaloacetate molecules (reused for krebs cycle) 6 NADH molecules (Oxidative phosphorylation) 2 FADH2 molecules (Oxidative phosphorylation) 2 ATP molecules 4 CO2 molecules (Exhaled from lungs) Oxidative Phosphorylation - Occurs in the inner membrane of mitochondria - ATP is formed as electrons are transferred from

NADH or FADH2 to oxygen via electron carriers in the electron transport chain

(NADH -> NAD+ , FADH2 -> FAD) - Final electron acceptor is oxygen (BREATHE IN) - As electron is transported along this electron

transport chain, energy from electron transfer used to pump hydrogen ions from mitochondrial matrix, across the inner mitochondrial membrane and into intermembrane space through active transport

- Creates a proton gradient across inner mitochondrial membrane

- Hydrogen ions diffuse from intermembrane

space into mitochondrial matrix through F0 protein

- ATP synthase synthesize ATP from ADP and Pi - Proton gradient is the source of potential energy

from gradient synthesizes ATP

Products: 34 ATP

* 1 NADH -> 3 ATP 1 FADH2 -> 2 ATP

Biology Notes 2008

ATP Produced from Aerobic Respiration Stage No. of NADH or

FADH2 No. of ATP formed in oxidative phosphorylation (from NADH or FADH2)

No. of ATP formed by substrate level phosphorylation

Total No. of ATP formed

Glycolysis 2 NADH 6 2 8 Pyruvate to acetyl CoA

2 NADH 6 6

Krebs Cycle 6 NADH 2 FADH2

18 4

2 24

34 4 38 For animals going through hibernation, they can survive despite having no glucose because fat/ protein/ glucose can all be converted to pyruvate (though glucose -> pyruvate is the fastest, simplest process) Anaerobic Respiration - Absence of Oxygen - All organisms can metabolize glucose anaerobically using glycolysis in the cytoplasm - Energy yield is very low and it produces much more toxic waste products. - In yeast and plants, alcoholic fermentation occurs. - In animals, production of lactic acid. Formula: Plants & Yeast C6H12O6 C2H5OH (Ethanol) + CO2 + small amount of energy ethanol Animals C6H12O6 C3H6O3 (Lactic acid) + small amount of energy - Muscle cells can respire anaerobically for short periods of time when there is a shortage of oxygen - Produces lactic acid - It incurs an oxygen debt, which is the amount of O2 required to oxidise the lactic acid produced - Lactic acid is produced which causes fatigue - Lactic acid is transported to the liver and converted back into glucose when the body is no longer short of O2.

Biology Notes 2008

Comparing Photosynthesis and Respiration Photosynthesis Respiration

Produces sugars for energy Burns sugars for energy

Energy is stored Energy is released

Occurs only in cells with chloroplasts Occurs in most cells

Oxygen is produced Oxygen is used

Water is used Water is produced

Carbon dioxide is used Carbon dioxide is produced

Requires light Occurs in dark and light

ATP production in photosynthesis and respiration Photophosphorylation (photosynthesis)

Oxidative phosphorylation (respiration)

In thylakoids of chloroplasts Mitochondria membrane

Energy source is electrons excited by light Energy source is transfer of electrons during oxidation reactions.

NaDP is the electron acceptor NAD is the electron acceptor

Chlorophyll is necessary No chlorophyll in mitochondria

Most ATP produced is used in the light-independent reaction

ATP is used in a wide variety of reactions

Carriers of Energy-rich electrons Photosynthesis Respiration Source Light Glucose

Types NADP NAD+ FAD

Products of Electron Transport Photosynthesis Respiration ATP + NADPH ATP

Chloroplast Mitochondrion

Inner Membrane Electron and H+ ion transport ATP Synthesis

Electron and H+ ion transport ATP Synthesis

Direction of H+ ions transport

Outside to Inside Inside to outside

Carbon reactions DNA Stroma Matrix

ATP Synthesis Photosynthesis Respiration

Pumps H+ ions Yes Yes

H+ gradient drives ATP formation Yes Yes

ATP synthase Yes Yes

Biology Notes 2008

Ecology;

Biology Notes 2008

Ecology Definition Ecology is the study of all those complex interactions referred to by Darwin as the conditions of the struggle for existence. Ecology is the study of how organisms interact with each other and their environment - Living things cannot exist alone, there must be a relationship between them. - Living things are adapted to the environment where they live. The environment in which organisms live can be divided into the abiotic and biotic environments: Abotic environment Biotic environment Non-living factors

Soil factors Climatic factors Topographical factors Light, Temperature, Humidity, Water,

Oxygen, pH, Salinity

Living organisms Prey Predator Parasites/ competitors

Habitat: Physical location in which an organisms lives

Levels of Ecological Organisation Individual - No 2 species can occupy the same niche (position a species occupies within its habitat, including physical space,

interactions with other organisms and effects on environment) Population Individuals of the same species occupying a certain area= population Community Different populations in an area which interact with each other form a community Ecosystem Consists of different species of a community, and their non-living environment - 4 basic elements: Abiotic component, biotic component, energy, nutrients - Usually “open” Biome Ecosystem is a part of a biome Biosphere All life is restricted to a zone (about 22.4km) called the biosphere- the region of earth’s land, water and air in which organisms are found.

Recycling of Nutrients - Organisms can be categorised into 3 nutritional groups: producers, consumers, decomposers Carbon Cycle - Passage of carbon within ecosystem Nitrogen Cycle - Passage of nitrogen in an ecosystem - More complex than carbon cycle - Though atmosphere contains 79% nitrogen, only a few microorganism can tap this resource

Biology Notes 2008

Food chains and Food Webs - Elements which make up living organisms are recycled - Except for energy, which flows from organism to organism and finally lost to the atmosphere as heat Food Chains - Consists of a series of organisms through which energy is transferred - Each organism in the series feeds on and derives its nutrients/ energy from the preceding one Producer - Autotrophs: Able to synthesis complex organic substances from simple inorganic substances - E.g. plants, algae, some bacteria Primary Consumer - Heterotrophs: Unable to synthesize complex organic substances from simple inorganic substances - Feed on complex organic substances made by producers - Feed on producer: Herbivores/ Omnivore Secondary Consumer - Feed on primary consumer: Carnivore/ Omnivore Tertiary Consumer - Feed on secondary consumer: Carnivore/ Omnivore * Decomposers - Act on dead organisms - Break down organic mater into simple inorganic substances - Make nutrients available to the producers (recycles nutrients) - Example: Bacteria, fungi - Not part of the food chain (They are not “predators”) *Detritivore - Animals that feed on dead decaying matter (detritus) - Dead decaying matter passes through a detritivore, partly digested and absorbed, remains comes out in faeces. Trophic Level: One stage in a food chain, a feeding role - Food chains usually have less than 5 trophic levels:

There is inadequate energy in ecosystems to support more than 5 trophic levels Only 1% of sun’s energy reaching the earth’s surface is trapped by producers Only 10% of the energy in each trophic level is transferred to the next level The more levels there are in a food chain, the more unstable it becomes. (vulnerable to changes in species

and populations) Food Webs - Food chains interconnected in a criss-cross network if nutritional relationships - Single species may form part of many different food chains, occupying different trophic levels - The complexity of a food web makes it stable Transfer of Energy between Trophic Levels - Only about 10% of the energy in a trophic level is converted to biomass in the next tophic level - Transfer of energy from producers to primary consumers is the LEAST efficient (1% to 10%) of producer

biomass: Plants contain high levels of cellulose and lignin, which many animals are unable to digest Leaves of some plants are poisonous and thus, not consumed by animals Certain parts of the plant are inaccessible Some plants die before being eaten

- Transfer of energy from primary consumers to secondary consumers: 10% to 20%

Bulk of Energy lost to respiration Lost to Excretion/ Egestion Lost to Death Certain parts of the primary consumer are inedible Some primary consumers are inaccessible to the secondary consumers

Biology Notes 2008

Possible things that can happen to the energy taken in by the organisms in each trophic level: - It can be passed on to the biomass of the next trophic level in the food chain when the organism is eaten. - It can become stored in detritus. This energy is passed on to decomposers when the detritus decays. - It can be converted to heat energy by inefficient chemical reactions, radiated by warm bodies, or in friction due

to movement. The heat energy is lost to the surroundings, and cannot be regained by living organisms. Energy Losses in an Ecosystem Only 10% of the energy available in food is incorporated into biomass, the remaining 90% is lost as: - Faeces - Used in respiration and lost as heat - Used to increase biomass of herbivore (energy of production = 10%) - Lost in urine Ecological Pyramids - Quantify feeding relationships in a community to enable us to compare the different ecosystems and assess the

potential of an ecosystem for the production of food Pyramid of Numbers - Indicates the no. of organisms for each species at each trophic level in a unit area at a given time - As pyramid ascends, the number of organisms decrease but the size of each organism increases - Limitations:

May be inverted (does not show how an ecosystem works) Difficult to represent an entire community using the same scale as the number of individuals for each

species may vary very widely Does not account for immature forms of species Amount of biomass/ energy available to next trophic level is not known

Pyramid of Biomass - Represents the total biomass of organisms of each species at each trophic level in unit area at a given time - Procedure:

Estimate no. of individuals of each species Determine average dry mass of individuals Total biomass of species = no. of individuals X average dry mass of individuals

- Limitations: Determination of biomass is destructive! Affect actual food chain/ web Usually, only a small sample of individuals in a population is taken to measure for biomass, and thus may

not be representative Pyramid of Energy - Represents flow of energy through each trophic level in unit area in an interval of time (usually 1 yr) - Advantages:

Takes account productivity of species (amount of energy produced by a species) An upright pyramid is always obtained (shows how an ecosystem works) Takes into account that different chemicals and species may not have the same energy content per unit

mass - Limitations:

One needs to combust organisms to construct pyramid -> destructive! Affect actual food chain/ web Usually, only a small sample of individuals in a population is taken to measure for biomass, and thus may

not be representative Time interval is usually quite long (1 year) Difficult to measure energy due to problem of heat loss

Relationships between Organisms

Relationship Explanation Example Predator-prey OBVIOUS. 1 species kills and feeds on

another. - Predator population usually less then prey - Important relationship to regulate and

maintain stability in the ecosystem - Prey needs the predator just as much as

predator needs prey

ME AND FISH.

Biology Notes 2008

Mutualism Intimate association between 2 species that offers advantage to both (both benefit)

Fungus and Alga (cyanobacteria) - Gives rise to lichens

Parasitism Common exploitation relationship in plants and animals. A parasite exploits the resources of its host (e.g. food, shelter, warmth, protection) to its own benefit. The host is harmed, but usually not killed.

Endoparasites (e.g. liver flukes, tapeworms, nematodes) are highly specialised to live inside their hosts, attached by hooks/ suckers to host’s tissues Ectoparasites (e.g. ticks, mites, fleas) live attached to the outside of the host, where they suck body fluids, cause irritation or act as vectors for disease causing micro-organisms.

Symbiotic

Commensalism 2 species form an association where 1 organism (commensal) benefits and the other is neither harmed or helped (1 benefit, 1 is not affected)

- Gouper and remora - Anemone shrimp and sea anemone

Inter/Intra-specific Competition

Competition for resources (e.g. food, water, land territories) - Interactions involving competition for

the same food resources are dominated by largest and most aggressive species

- Interspecific usually less tense than intraspecific (competition between individuals of same species)

-

Storks, Vultures and hyena’s compete for carcasses

Strategies/ Defence Mechanisms: - Predators have numerous adaptations for locating, identifying and subduing prey - Prey has its own defences such as hiding, escaping/ defending Prey Capturing Strategies Predator Avoidance Defences Concealment (camouflage) - Strike only when prey is within reach

Mimicry - Prey gain immunity from attack by mimicking

harmful attacks to scare off the predator

Filter Feeding - Filter water to extract tiny organisms (e.g. marine

animals filer water to find plankton)

Poisonous - Poisonous animals advertise and broadcast that they

are unpalatable by using brightly coloured and gaudy markings

Tool Use - Use natural resources found in habitats to make

tools to capture prey - E.g. Chimpanzees use carefully prepared twigs to

extract termites from mounds

Visual Deceptions - Deceptive markings (e.g. Fake eyes) can deceive

predators, allowing prey time to escape

Stealth - Night hunting ability enhanced by infrared senses

Chemical Defence - Offensive smelling chemicals - E.g. American skunks squirt nauseous fluid at

attackers Lures - Use lures to attract prey within striking range - Example: Angler fish

Offensive Weapons - Vital to actively fend off an attack by predator

Traps - Traps to capture prey so they cant escape - E.g. Spiders use strong silky silk threads

Camouflage - Cryptic shape and colouration allows some animals

to blend into background

Biology Notes 2008

Classification Kingdom- Prokaryote, Plantae, Animalia, Protista, Fungi Phyllum Class Order Family Genus Species

What are the prerequisites for life? - Climate - Oxygen, water, food - Temperature (rainfall) - Sunlight - Substrate Most life forms are found in the tropics, near the water (along equator) Because of limited sources, there is a limit as to how much a population can grow => Competition for resources How if Life distributed on Earth? - Temperature - Latitude - Soil - Fresh water Various Biomes on Earth

• Tropical rainforest • Deserts • Tundra • Savannah • Temperate forests • Corals

Name: Group: characteristics: criteria for

breadth:

Eukarya Domain eucaryotes subjective

Animalia Kingdom animals subjective

Chordata Phylum notochord containing subjective

Vertebrata Subphylum spinal chord containing subjective

Mammalia Class hair and breasts subjective

Primates Order nails, grasping digits, binocular vision subjective

Hominoidea Superfamily apes and humans subjective

Hominidae Family genus Homo, genus Australopithecus subjective

Homo Genus our genus subjective

sapiens Species our species objective

Distribution of Life on Earth

Biology Notes 2008

Terrestrial Biomes and Biodiversity: A Comparison Biome: Temperate

Rainforest Artic Artic Tundra Boreal Forest

(Taiga) Tropical Rainforest

Physical Conditions

- One long wet winter/spring season, dry foggy summer

- Greater variation in daily temperatures (compared to tropical rainforests)

- Moist climate (~ 400 cm of precipitation)

- Mainly conifers and deciduous trees

- Immediately below the polar ice caps

- Temperatures can reach below -55oC)

- Average precipitation - 25 cm

- “Freezing desert” - Soil permanently frozen

(permafrost) - No trees can survive there,

why? - Small herbs and mosses

- Uniformly warm (25-30°C)

- moist climate (250 - 400cm rainfall)

- Only 6% of Earth’s total surface

- Home to 5-8 million species (1/2 to 2/3s of the world’s total)

- Very efficient nutrient cycling system

- Huge trees

Unique Climate and physical features

4 Seasons, Spring, Summer, Autumn, winter (extreme cold, little water)

4 seasons (I think), Cold winters and cool summer

4 seasons, long cold winters, cold, desert like

4 seasons Short, moist,

moderately warm summers Long, cold

winters Precipitation is

normally in the form of snow

1 season generally, spring/summer

Landscape, terrain, substrate, Distribution of Flora and fauna

Very fertile soil with extensive coverage of animal and plant life.

Ice covered ocean, surrounded by treeless, frozen ground

- Permafrost – a layer of permanently frozen subsoil. - Low shrubs, sedges, reindeer moss, grasses. - 400 varieties of flowers - Ponds, bogs - No trees - About 1700 kinds of plants

Forms around 1/3 of earth’s forests Snow is harder than in the artic tundra Soil is thin, nutrient poor, acidic Canopy permits low light penetration, thus understory is limited

Greatest diversity of species Soil is nutrient poor and acidic. Decomposition is rapid and soil are subject to heavy leaching Canopy in tropical forests is multilayered and continuous, allowing little light penetration

Animal Biodiversity including examples

Mammals: bear, squirrel, raccoon, deer; birds, reptiles, amphibians

Mammals: polar bear Fish: erm, fish?

Mammals: Artic wolf, Caribou (3 million of them) Birds

Birds: Woodpeckers, Hawks

Mammals: Moose, Fox, Deer, chipmunk

Numerous birds, bats, small mammals and insects

Unique Animal Features

Adapt to winter by migration, hibernation or keeping active, Depend on trees for shelter, food and water. Animals are camouflaged to look like ground.

Polar bear: after 5 months of not eating, still able to feed milk to young. Hibernates.

- Caribou migrates, in search for warmer places and food. Artic wolves goes along with them (predator) - Adapted to handle long winters: additional insulation from

Not much Varies E.g. Sloth

The sloth survives on little energy and only moves very little. Also, it only needs to go down to the forest floor for a “toilet break” very rarely and thus is able to survive well in the tropical forest where its tall branches are hard to reach.

Biology Notes 2008

Plant biodiversity including examples

Deciduous plant life: Large Trees (oak), saplings, shrubs (rhododendrons), Herbs, ground(mosses)

Zilch. - Low shrubs, sedges, reindeer moss, grasses - 400 varieties of flowers

Evergreen conifers, pine, fir, spruce

Mostly evergreen, tall, with buttressed trunks and shallow roots

Orchids, bromeliads, vines(lianas), ferns, mosses, palms

Unique Plant Features

Trees shed leaves in fall/ winter.

Zilch. All plants are adapted to sweeping winds and disturbances of soil

Plants are short and grouped together to resist the cold temperatures and are protected by the snow during winter

Able to carry out photosynthesis at low temperatures and low light intensities (even though the sun does not set in the artic tundra, because of the angle the sun shines, sunlight hardly gets to the tundra)

Growing seasons are short and most plants reproduce by budding rather than sexually by flowering

No deep root systems

Needle-like leaves – virtually inedible

Depends on the plant

Orchids: have the ability to “climb” up trees

Tropical

Rainforest Temperate Forest

Grasslands Deserts Tundra

Elaboration - Uniformly warm (25-30°C)

- moist climate (250 - 400cm rainfall)

- Only 6% of Earth’s total surface

- Home to 5-8 million species (1/2 to 2/3s of the world’s total)

- Very efficient nutrient cycling system

- Huge trees

- One long wet winter/spring season, dry foggy summer

- Greater variation in daily temperatures (compared to tropical rainforests)

- Moist climate (~ 400 cm of precipitation)

- Mainly conifers and deciduous trees

- Mainly dry with one wet season which the entire year’s precipitation falls (30cm or less)

- Only few specialized trees

- Only grasses survive?

- Lots of large mammals present

- Extreme climates (e.g. Gobi desert, temperature average below freezing for 6 months, then 41-43oC in summer.

- Very dry (less than 30cm rainfall annually)

- Plants and animals adapted for dry conditions and extreme heat

- Immediately below the polar ice caps

- Temperatures can reach below -55°C)

- Average precipitation - 25 cm

- “Freezing desert”

- Soil permanently frozen (permafrost)

- No trees can survive there,

- Small herbs and mosses

Sampling Census It involves counting entire population; only possible with very obvious individuals and ability to cover entire spread of population range (eg. census of dogs in a park). Sampling It involves counting just part of the population and then extrapolating to estimate total population size. One will need to know how reliable samples are and the degree of errors involved when extrapolating depends a lot on variability across the range of the population. - Use variables and factors to identify each organism’s role in environment and its niche - Compare with previous sample to observe any changes in population in relation to changes in environment

Biology Notes 2008

Direct Counts It involves: - Relevé: for vegetation sampling - Quadrats: markers that isolate a sample area to count the population size of different species within the area. - Capture Techniques: for animals Indirect Counts Inferences from: - Evidence of animals’ presence (eg. nests, droppings) - Evidence from human activities (eg. fishing quotas and catch rates) Sampling Designs 3 types: - Regular / Uniform: samples are taken in a regular pattern (eg. a line) - Random: samples are taken from randomly chosen spots (eg. numbers of grid coordinates) - Stratified Random: random samples are allocated deliberately to each of the recognised different environmental patches in the sample area No. Of Samples

- Calculate running mean and plot the graph - The point where the running mean stops fluctuating and stabilizes is the optimum number of samples to

take Methods of Sampling For Sessile Species (Don’t move around) For mobile species Quadrat Sampling Sampling unit of known area (usually square frames)

- Point Quadrats Estimate percentage cover of species in an area

- Quadrats of different sizes > Percentage cover of species within a communiry

- Mark & Recapture Animals must live normally even after being

marked Marking cannot affect behaviour and health Cannot make organism more vulnerable to

predation Cannot allow for trap-shyness or develop

trap-favouritism Random Sampling For results to be valid, there must be an objective approach to quadrat siting Simple random sampling Area under study is divided into grid system of boxes. Random numbers are chosen as coordinates for the grid box to place quadrat Transect Sampling

- Belt Transect Strip about 0.5 m across study area. Quadrat is laid at regular intervals along this belt -> good idea of the numbers and distribution of organism

- Line Transect Quicker, though less quantitative and less representative method. A line is laid across the area and marked off at regular internals.

Factors Affecting Abundance of Biodiversity

- Sunlight - Water - Climate - Substrate - Non-seasonality

Abundance of Biodiversity Animalia: 74.88% Plantae: 18.80% Fungi: 3.55% Monera: 0.36% Virus: 0.08% Protozoa: 2.33% Total: 1,392,485

Biology Notes 2008

Evolution.

Biology Notes 2008

Definition of Evolution Evolution is one of the most important concepts in all of science Has become a unifying principle It is a biological theory and not intended to be useful outside of science Definition Evolution is a process that results in heritable changes in a population spread over many generations.

Biological evolution is change in the properties of populations of organisms that transcend the lifetime of a single individual.

Biological evolution refers to populations and not to individuals Changes must be passed on to the next generation- heritable Therefore it can also be defined as:

any change in the frequency of alleles within a gene pool from one generation to the next

Theories of Evolution Lamarck’s Theory Lamarck used giraffes as an example

- As the trees grew taller in the African savannah, the leaves and fruits became out of reach - The giraffes stretched their necks to reach for the leaves, and this active use of the necks resulted in the

enlargement and lengthening of the necks - The giraffes passed on these acquired genes to the next generation, which continued to “grow” their necks - This ultimately resulted in giraffes with long necks

His Theory - The hypothesis of The Inheritance of Acquired Characteristics - A changing environment creates a need for certain features to be developed in order to survive. - “Acquired Characteristics”: Through use and /or non-use, those features needed for survival are developed

in each individual - Inheritance: Those beneficial characteristics developed (“acquired”) by individuals are somehow passed on to

their offspring, who can continue that development. - New species: Eventually, over many generations, enough differences have developed that we can say we have a

new species. Charles’ Darwin’s Theory His Observations and Deductions - Darwin noticed 13 different species of finches within the different islands of the Galapagos - The finches appeared to be related to the only finch found on the mainland of South America - The finches all had different beaks that appeared to have different functions - An ancestral stock had migrated to the islands where they underwent profound changes under the different

conditions of the individual islands. A single ancestral group could give rise to several different varieties or species.

Observations

Deductions

Populations have the potential to increase exponentially Populations are fairly constant in size Natural resources are limited There is variation within a species, and variation is inherited

- Only some organisms survive. There is a struggle for existence among individuals in a population.

- Individuals with favourable variations are more likely to survive and reproduce.

- Accumulation of variation over many generations is evolution.

His Theory of Natural Selection Stage Explanation

Overproduction of Offspring All individuals of a population are capable of reproducing large numbers of offspring. If all the offspring survived, there would be a geometric increase in the size of the population.

Biology Notes 2008

Constancy of Numbers Although organisms are capable of producing large numbers of offspring, most populations remain relatively constant in numbers. This is because most of the offspring die before the reach reproductive age.

Variations within a population

Individuals of a population differ from each other. These variations are a PRE-REQUISITE for evolution by natural selection. - These variations arise spontaneously before a change in the environment - Not formed as a result of the new environment to make the individuals better

adapted - Environment does not determine what structures an individual should develop

during its lifetime - The environment only selects those individuals who by chance happen to be

better adapted

Change in Environment Changes in climate, topography, food supply, predators, etc

Struggle for survival Because of overproduction of offspring and constancy of numbers, individuals are constantly competing with each other for the limited resources (e.g. food/ shelter) - In the struggle for survival, only a few individuals reach maturity and reproduce

Survival of the Fittest “Fitness”: Ability of individuals to survive to produce viable offspring - Within the population, some individuals are more adapted to the existing

environmental conditions than others - Some are better adapted to survive till maturity and produce viable offspring - These individuals are selected by environment of nature

Like produces like - Individuals who can survive to maturity and likely to produce offspring similar to themselves

- The beneficial characteristic which gave them a edge over others are likely to be passed on to the offspring

Formation of a new species - Individuals possessing an advantage characteristic, have a greater chance to

survive to maturity and reproduce as compared to those without the characteristic

- Over generations, the proportion of individuals with the trait increases. The inheritance of 1 trait may lead to formation of a new strain, but not a new species.

- Formation of a new species: formed only after the development of several characteristics in a particular direction over many generations.

- In other words, natural selection that occurs over a long period of time results in evolution - As long as the environment changes, a population will continue to evolve

• E.g. changes in predators, changes in climate, changes in natural resources for life - Evolution may result in the organisms changing to a new species Summary of the Natural Selection Theory 1. Overproduction: More offspring produced than will ultimately survive and reproduce 2. Variation: Inheritable features vary from individual to individual 3. Change in environment: Changes in climate, topography, food supply, predators, etc 4. “Struggle for existence”: Mainly competition within the species, for food, habitat, survival from being eaten 5. “Survival of the fit” (not necessarily the strongest): Those with more adaptive traits tend to survive longer

and/or produce the most offspring; these are the “naturally selected” 6. Inheritance of “selected” features: Traits involved are already inheritable, but may involve new

combinations 7. New species, better adapted to the new environment: when the collective traits of the population differ

significantly from the earlier population, and can no longer reproduce with the earlier population Assumptions Made In order to have natural selection, some basic assumptions were made: - The traits seen must be found in the genes and hence be able to be passed on to the next generation - Traits arose from random events like meiosis and mutation and not by intent (they are not directed)

Biology Notes 2008

Differences between Lamarck and Darwin’s Theories - Lamarckian theory was incorrect as the traits acquired by overuse of an organ can be transferred to the next

generation. Lamarck also believed that traits can arise due to intent, with organisms seemingly able to “will” their organs to grow or develop

Darwin’s natural selection was based on passive processes like random variation in a population while Lamarck’s theory was based on active response to change

Lamarck Darwin

Environment changes thus creating a “need” to change

Variations of inheritable features which already normally exist

Development of new features, “in order to survive” or “so that one can survive”.

Environment “screens out” features contributing to survival, & tends to eliminate the others

Newly acquired traits somehow get passed down to offspring

Those with traits which kelp survival tend to survive & have offspring, who inherit those traits

New Species, eventually New species, eventually

Lamarck’s theory was based on active response to change

Darwin’s natural selection was based on passive processes like random variation in a population while

Neo-darwinism/ Theory of Evolution by Natural Selection Modification of Charles Darwin’s theory of evolution by natural selection - Emphasis on natural selection as main driving force of revolution Neo-darwinism Charles Darwin’s theory - incorporates the principles of Mendelian genes and

knowledge of molecular biology

- Such knowledge was unknown at the point of time when this theory was published

Neo-darwinism

1. Populations have great reproductive potential but the number of individuals remain relatively constant as: Many fail to survive, Being checked by environmental factors Competition for resources Predation

2. Variations within population arise as a result of spontaneous mutation and not in response to needs of individuals. Genetic variation arises from gene mutations, chromosomal mutations, meiosis, random fusion of gametes.

3. Individuals with genetic variations that are best suited to the new environment are more likely to survive till maturity and REPRODUCE

4. Environment selects pre-existing forms that have selective advantage 5. Proportion of individuals at a selective advantage increases. Natural Selection alone is inadequate in explaining show new species are formed- only if populations of a species are separate so they do not interbreed. Separated populations adapt to their own environments and may diverge, eventually forming new species. Geographical Isolation is one way. 6. Lead to a change in allele frequencies and over a long period of time, lead to evolutionary changes and

possibly, formation of a new species.

Causes of Genetic Variation Gene mutation - Change in structure of DNA which occurs at a single locus on a chromosome - Result in the formation of new alleles - Processes/ Mechanisms:

Deletion: one or more nucleotides are moved from a sequence of nucleotides

Theory of Natural Selection

Biology Notes 2008

Insertion: one or several nucleotides added to sequence of nucleotides Substitution: A nucleotide is replaced by another Inversion: When sequence of nucleotides becomes separated from the allele; rejoins at original position

but it is inverted (reverse sequence) - New alleles increase the gene pool for natural selection - E.g. Sickle cell anaemia (substitution) Chromosomal Mutation - Change in the structure of a chromosome (involving gene loci) or change in number of chromosomes - Mechanisms:

Deletion: 2 points of chromosome breaks, middle part falls out Inversion: 2 points of chromosome breaks, middle part falls out and rejoins after turning 180° Translocation: a section of a chromosome breaks off, attach to another Duplication: section of chromosome replicates Non-disjuction: failure of sister chromatids to separate during anaphase

- result in reshuffling of alleles on chromosome - less important role in evolution (only reshufflement of alleles already existing in the same gene pool) - e.g. Down Syndrome Mutation (on the whole) - bring about changes in phenotype, hence allows natural selection - Particularly important in asexually reproducing organisms because it is the only source of genetic variation - Most are disadvantageous (a useful one is RARE) - Natural selection prevents harmful mutations from accumulating, but ensures useful ones spread Sexual Reproduction (Meiosis) - Crossing over during meiosis - Combinations of gametes between individual Why sex? - Making an egg requires A LOT of energy, and may even be detrimental to the organism - Sexual reproduction is energy consuming and a very risky process - In terms of energy used, splitting of cells is better and less risky (still can get variety through spontaneous

mutation) - Sex loses some good genetic sequences - WHY DO WE INVEST SO MUCH ENRGY IN SEXUAL REPRODUCTION, EVEN WHEN THE SUCCESS IS

NOT ASSURED? IS IT WORTH IT? - Do the advantages of variety outweigh the risk of losing good genetic combination? - The variety from sexual reproduction is much more than asexual reproduction and it is necessary to maintain

and ensure survival - One is that males are necessary to combat disease: without sexual reproduction, a clonal species is vulnerable to

increasing parasitic attack. - The other theory holds that sex helps purge the species of genetic mutations by shuffling the genes in each

generation.

Speciation Lineage splitting event that produces 2-3 more species - Same ancestral group split into different species Geographic Isolation/ Restriction of Gene Flow 1 species goes through mutation - 2 groups of the same species - Geographically isolated (don’t mix) - Natural selection in EACH group - Results in 2 different species Allopatric Speciation Sympatric Speciation 2 groups separated; speciation caused by geographic isolation - Both groups evolve different -> 2 different species

Speciation occurs when there’s NO geographic isolation - Same island, separated - 2 groups still don’t mix

Biology Notes 2008

Evidence for Evolution Evidence can be found in the following areas: - paleontology, biogeography, comparative anatomy, vestigial structures, embryology, and molecular biology 1. Fossils Fossils can reveal the immediate environment of an ancient organism, clues to a scene, or even global change. - Found in layers - Most bottom: oldest IF A HUMAN FOSSIL IS FOUND IN THE SAME AGE AS DINOSAURS, EVOLUTION CAN BE DISPROVED :D 2. Biogeography: The study of the past and present distributions of plant and animal species. - As evidence for his theory of evolution, Darwin noticed that species all over the world are most closely

related to species that live nearby> indicating descent with modification from a common ancestor.

3. Similar Skeletal Organisation (comparative anatomy)

Homologous Structure Analogous Structure Structures in different organisms that have a similar function and the same origin. (same vertebrae ancestor) E.g. Pentadactyl limb

Modified from pre-existing design e.g. feathers are modified scales

Structures that have similar functions, but from different origins. e.g. bat wing (limb) VS butterfly wing (not a limb)

Biology Notes 2008

4. Embryo Resemblances - Similar embryo - Developed into the different parts of the body of each organism 5. Vestigial Organs - Structures with little or no known function that are thought to be remnants of a structure that at one time had a

function in an ancestral species - E.g. TAIL BONE 6. Amino Acids - The less the number of amino acid differences from man, the more similar (shared a more recent common

ancestor)

Misconceptions of Evolution 1. Only groups of organisms can evolve (populations or species); individuals never evolve 2. Adaptations, in the evolutionary sense, can only “develop” as characteristics of a species - Generally over a long period of time, involving many generations - These must not be confused with the “adjustments” an individual might make, consciously or otherwise,

enabling it to survive better (such as “developing resistance to a disease” or “adapting to higher altitude”

Micro and Macro Evolution Micro Macro Refers to the changes in traits within a population in response to the selection pressures, resulting in changes of phenotype of the population - Based on Darwinian theories of changes in allele

frequency due to natural selection within a species

- E.g. Antibiotic resistance in bacteria

Refers generally to the formation of major groups of organisms from other groups that are distinctly different. - E.g, the evolution of whales from terrestrial

mammals. - The mechanism for this process is generally

considered to be the same as for microevolution - But carried on accumulatively over many millions of

years, resulting in the ever increasing diversity of life we see today.

Antibiotic Resistance of Bacteria - Simple organisms like bacteria and viruses show us examples of evolution in a very short space of time as

they reproduce fast. Their numbers double every 20 minutes! - Bacteria have different antibiotic resistance genes in their chromosomes and plasmids - Bacteria are known to be able to exchange genetic material with one another, as well as with bacteria of different

species This mechanism allows antibiotic resistance genes to be passed on to many other bacteria

- In a bacterial population, there is variation and a very small proportion of the bacteria has antibiotic resistance

genes which is caused by mutation. - If the patient did not finish the entire antibiotic course prescribed, not all the bacteria will be wiped out - Those that survive would mainly be those that are resistant or just tolerant of the antibiotic prescribed - Those bacteria will rapidly divide and soon the body may fall under infection by antibiotic resistant bacteria - The change in allele frequency and traits of the population to being antibiotic resistant is an example of micro

evolution

Leads to