Class+notes

=Area study 1=

Sizes of cells:

 * Sizes of cells vary and they require different tools in order to clearly see their structure. Some examples; human egg 0.1mm, amoeba 0.25mm to 0.75mm, bacteria 0.0002mm.
 * Some rules about measurements; 1000 micrometres in 1 millimetre, 10000 micrometres in 1 cm
 * if the field of view is 0.5mm in diameter we can estimate the size of a cell we are viewing by estimating the number of times the cell would fit across the diameter of this field of view. Eg. if we estimated the cell fits across the field of view 5 times then the size of this cell is 0.1mm (Field of view / number of times it fits across the diameter.) ie 0.5/5
 * Types of cells- you will need to be able to list the characteristics of plant cells vs animal cells as well as Prokaryotic cells vs Eucaryotic cells
 * Animal cells can have a variety of shapes and these shapes support the roles the cells play in a body. eg muscle cells -very long, epidermal skin cells -blocky
 * Shapes and function
 * an extra site for detailed info. http://www.abpischools.org.uk/page/modules/homeostasis_kidneys/index.cfm?coSiteNavigation_allTopic=1

Sizes
Surface area to volume ratio, SA:V something very small - will have a high SA:V eg 6:1 ratio this means there is lots of places for diffusion and osmosis to occur. ie ways for substance to enter into and out of the cell. Something with a low SA:V ratio eg 3:2 will have so much material in the volume of the cell that it would take too long for nutirents to reach it

Structures inside cells DNA is found in the nucleus - forming chromatids during cell division, also inside the nucleus is large inclusions of RNA (nucleoli) || https://www.reference.com › Science › Biology › Cells A pinocytotic vesicle is a structure that aids in transportation as a cell's plasma membrane absorbs molecules from outside. Dictionary.com describes this process as taking place when the exterior membrane enfolds the molecule prior to transport into the cell's cytoplasm. ||
 * Rough Endo plasmic reticulum || Ribosomes on the surfaceof the ER make it rough - Ribosomes are the site of protein synthesis, Rough ER stores proteins, packages proteins ||
 * Smooth Endo plasmic reticulum || makes and stores lipids and steroid ||
 * nucleus || Controls the functions of the cell. It is unique to eukaryotes and is enclosed by a double membrane - called the nuclear envelope. This membrane is perforated with nuclear pore complexes. (protein lined channels) that control teh exchange of materials between the nucleus and cytoplasm.
 * golgi appartus or golgi complex || It produces the membranes that surround the lysosomes. The **Golgi body ** packages proteins and carbohydrates into membrane-bound vesicles for "export" from the **cells. Secrete ** ||
 * vacuole || storage ||
 * ribosomes || protein synthesis ||
 * mitochondria || site of respiration ||
 * cytosol || liquid in the cytoplasm ||
 * cytoplasm || liquid and organelles except the nucleus ||
 * lysosome || lysosome - (also called **cell ** vesicles) round organelles surrounded by a membrane and containing digestive enzymes, sometimes called suicide sacs as the enzymes inside can destroy the cell ||
 * Cytoskeleton || A 3D network of fine protein and microtubules within the cell that holds the organelles in place ||
 * Cell wall || in plants, fungi, algae and bacteria and some other prokaryotes. Made of cellulose, provides structure. ( in some plants (woody plants) there is a primary and secondary cell wall - the primary cell wall is as described the secondary is made of lignin that continues to thicken until the cell dies - this is wood. ||
 * || [|What is the function of a pinocytotic vesicle? | Reference.com]
 * || A raphide crystal occurs in plant cells, and its main function is to repel animals away from plants. The crystals are shaped like needles, and are formed from calcium oxalate.

[|What is the function of a raphide crystal? | Reference.com]
https://www.reference.com/.../function-raphide-crystal-ab29c7bb86649dd1 ||
 * || A druse is a group of crystals of calcium oxalate, silicates, or carbonates present in plants, and are thought to be a defense against herbivory due to their toxicity. Calcium oxalate (Ca(COO)2, CaOx) crystals are found in algae, angiosperms and gymnosperms in a total of more than 215 families.

[|Druse (botany) - Wikipedia]
https://en.wikipedia.org/wiki/Druse_(botany) || [|Microtubules | Celebrate Cytochemistry | Gwen V. Childs, Ph.D.] cytochemistry.net/cell-biology/microtub.htm || Diagram with definitions Rough Endo plasmic reticulum -
 * || Microtubules are conveyer belts inside the cells. They move vesicles, granules, organelles like mitochondria, and chromosomes via special attachment proteins. They also serve a cytoskeletalrole. Structurally, they are linear polymers of tubulin which is a globular protein.Oct 11, 2014

Transport of substances into and out of a cell is governed by the cell Membranes All cells have an active boundary called the plasma membrane - the cell membrane. Its role is to keep things in - intracellular and extracellular outside of the cell.

This membrane can be selectively permeable or semipermeable. It selectively controls the the movement of compounds into or out of the cell via diffusion. NB Fungi, bacteria and plants have a stiff structure outside of the cell membrane. This structure provides shape and does not control entrance into and out of the cell. Only the cell membrane does this. Review the prac on osmosis and diffusion.

definitions Diffusion - movement from hi to lo concentration. eg elements, molecules of compounds can move across the diffusion gradient if their is less of one type of molecule (eg glucose) on one side of the membrane than the other, the same can occur with cations, eg Potassium ions Osmosis ( a special case of diffusion; the movement of water form an are of hi conc of water to an area of lo conc of water through a semipermeable membrane. NB semi permeable membrane tonicity- measure of concentration of the solutes in the solution  osmolality- measure of osmotic pressure  turgidity- Description of the "swollen " state of a cell  hypotonic - Low concentration  hypertonic - High concentration  isotonic - same concentration

Structure of the cell membrane
the size of the cell membrane is 8 nanometres ( 1000 nanometres = 1 micrometre, 1000 micrometres = 1 millimetre, therefore 1000000 nanometres in 1 mm) The cell membrane is made of 2 main substances 1. phospholipids - Phosphate ends are hydrophyllic and are arranged to ward the exterior of the cell and another sett towards the interior of the cell. A hydrophyllic substance is water loving and and is attracted to wards water due to its slight polar charge The hydrophobic ends of hte molecules are pointed toward the centre of the membrane. Water and lipids (fats and oils) do not mix.

proteins- there are 2 types -integral proteins - these are embeded in the phospholipid bilayer (referring to the 2 phospholipids and hydrophylic ends) and generally span the entire width of the cell membrane - hence their name trans - membrane ( trans means across) Peripheral proteins are either anchored to the inside or outside of the membrane. They can only be removed by harsh treatment eg harsh detergents - these are also hydrophobic and hydrophyllic substances. An example is glycoproteins ( proteins with a sugar /carbohydrate molecule attached.)

Fluid mosaic model
of the plasma membrane fluids (thick oily substance) with proteins embedded. The membranes major roll is as gatekeeper controlling entry and exit of materials into and out of the cell. The fatty acidcahins within the membrane make the membrane flexible.

the structure of the membrane of the cell and the organelles.
This model proposes that the plasma membrane should be considered as a 2 dimensional structure the fluids (thick oily substance) with proteins embedded. the mosaic in the name refers to the appearance of the membrane when viewed from above because of the embedded protein.

The function of the plasma membrane
1. it is an active and selective boundary - this icludes the cell membrane as well as membranes that surround various organelles This means teh organelles can have different conditons more favourable to their role, than the surrounding cytosol. 2. denotes the cells identity - this is conferred by the glycoproteins and are cell surface markers or antigens. Glycolipids on the plasma membrane play the roll of tissue recognition. 3. receives external signals eg in the form of hormones 4. transports materials - acts as a selectively permeable membrane, Transport proteins in the plasma membrane enable the movement of substances that cannot cross the lipid bilayer of the membrane. Here is an animation of how the cell membrane functions. this shows the structure of the cell membrane

=How do things cross the plasma membrane?= Generally nutrients entering the cell are already dissolved. A number of conditions have to be met in order to be dissolved in water. The main condition is that it should be polar (ie have a slight positive charge on one end of the molecule and a negative charge on the other end.

So the conditions that have to be met are 1 molecular size - smaller molecules cross more easily than large ones. Macromolecules (proteins and DNA) could not cross the plasma membrane 2. NO Presence of a net charge (+ or -) --Gases such as CO2 and O2 and a small uncharged polar molecules like ethanol can cross the membrane but mineral ions like K+, Na+ and CL- can not because they are repelled by the hydrophobic lipid part of the plasma membrane. 3. Solubility of lipid solvents -- Lipophilic molecules can easily cross but hydrophilic molecules like glucose can not cross because they are repelled by the hydrophobic part of the layer of the membrane (remember hydrophillic substance will dissolve in water) Examples of small lipohilic molecules that can dissolve into the lipid bilayer. egs steroid hormones, alcohol, lipohpilic drugs 4. The direction of the concentration gradient -- Movement down the gradient (from hi down to lo conc) does not require energy input so can happen easily. Movement against this gradient cannot occur by diffusion ( when it does happen it is called active transport because energy is actively required )

http://www.diffen.com/difference/Active_Transport_vs_Passive_Transport
=Simple Diffusion= Movement hi concentration to low concentration

=Osmosis= a special case of diffusion the movement of water form an area of high concentration to an area of low concentration of water through a semipermeable membrane.

Examples of osmosis

Plasmolysis
This is the process of the cell membrane pulling away from the cell wall due to a change in osmotic pressure. Eg. Elodea is irrigated with salt solution. This same dehydrating effect occurs in animal cells, or protozoans etc

Using osmosis to preserve food
salted meat - preserves the meat because the environment is now not suitable microbes. The salt also draws the water out of any living microbes. Water flows down the concentration gradient.

The crying albatross
These birds can only drink seawater so how do they survive? Seawater is hypertonic to the extracellular fluid of the albatross. The salt passes from their blood into salt secreting glands - the cells in these glands take up salt from the birds body fluids and hence is even saltier than seawater. This fluid is then passed out of the birds nostril

Dehydration in people
Prolonged diarrhoea leads dehydration as large quantities of water and salts pass into the large intestine and expelled as a water solution. To rehydrate the patient is given replacement fluid made of saline and glucose. (oral or intravenous) How it works - glucose stimulates the absorption of sodium by the gut cells. The uptake of sodium and glucose creates a hypertonic internal enviroment and this inturn promote osmosis ( water uptake).

Facilitated diffusion
Channel proteins and carrier proteins within the plasma membrane help the transfer of materials into the cell.
 * Channel proteins are transmembrane protein molecules that have a water filled pore through which the dissolved substance (Na+, K+ and small polar molecules) pass along the concentration gradient. This means these structure create a hydrophilic passage that bypasses the phosphlipid bilayer.
 * Carrier proteins are specific for one type of molecule. After binding to its specific cargo molecule the carrier protein undergoes a change in shape as it delivers its cargo to the other side of the plasma membrane.







Endocytosis
Here is an animation describing how a substance is taken into a cell and the biochemistry of how this process occurs  Diffusion, Facilitated Diffusion, Osmosis, and Active Transport The student will be able to compare and contrast the following: diffusion, facilitated diffusion, osmosis, and active transport. |||||||||| How molecules move through the membrane.
 * **__ Diffusion __** is the movement of molecules from an area where the molecule is in high concentration to an area where the molecule is in lower concentration. //A diffusion **animation** is introduced here.// In the animation, the molecules chosen represent a generic molecule (green balls) and carbon dioxide gas (small black and brown three ball structure). The generic molecules being in higher concentration outside of cells will freely diffuse into the cell and carbon dioxide being produced inside the cell due to cellular respiration will increase in concentration inside the cell and diffuse to the outside through the membrane. This allows the cell to obtain nutrients and dispose of carbon dioxide without any energy use. A very fortunate situation for the cell.
 * __ Facilitated diffusion __** is the movement of a molecule from an area of high concentration to an area of lower concentration with the help of a protein channel or carrier. The generic molecules in the previous animation used a channel protein to enter the cell. In the facilitated diffusion **__ animation __** both amino acids and glucose are shown entering the cell facilitated by a protein carrier. In a cell membrane there would be proteins specific to each molecule and the carriers would not be shared in this way. The animation shows that movement occurs until the concentration of the molecules reaches equilibrium.
 * __ Osmosis __** is the diffusion of water through a semi-permeable membrane. Water moves from an area of high water molecule concentration (and lower solute concentration) to an area of lower water molecule concentration (and higher solute concentration). The osmosis **__ animation __** shows water moving into a cell through a channel. Water molecules can be transported in this way, but can also diffuse directly through the membrane lipid bilayer.
 * __ Active transport __** is the movement of molecules from areas of low concentration to areas where the molecule is found in higher concentration. This movement is not spontaneous and requires ATP energy and a protein carrier. The ATP is used to drive conformational changes in the protein to pump molecules against their concentration gradient. This process occurs continuously in nerve cell membranes with sodium-potassium pumps. The active transport **__ animation __** shows a simplified version of how such a pump operates. ||
 * Comparison of the ways molecules move into and out of cells. ||
 * **__ Name __** || **__ Type of Transport __** || **__ Direction of Movement __** || **__ Conditions __** || **__ Examples __** ||
 * Diffusion || passive || towards lower concentration || Concentration gradient || Water, gases (02and CO2), and steroid hormones. ||
 * Facilitated Diffusion || passive || towards lower concentration || Concentration gradient, plus channel or carrier proteins || Water, glucose, and amino acids. ||
 * Osmosis || passive || towards lower concentration || Concentration gradient, channel proteins optional || Water 0nly. ||
 * Active Transport || active || towards higher concentration || Carrier protein and ATP energy || Ions, sugars, and amino acids. ||
 * Active Transport || active || towards higher concentration || Carrier protein and ATP energy || Ions, sugars, and amino acids. ||

the structure of the membran of the cell and the organelles The size of the cell membrane is 8 nanometres

Biochemistry Carbohydrates are made of C H and O. When these are put together in the correct combination and shape (pattern) they make glucose, starch, sugar, fructose, maltose, lactose ( ending in ose tells us they are sugars). They are commonly used to provide energy.

Proteins are made of C, H, O and N. Proteins are generally referred to as chains of amino acids. This means amino acids are made of C H O andN and when chained together in a repeating pattern they form a protein,

Lipids are made of C H and O, they are similar in composition to carbohydrates but always have double bonded O and hydroxyl group at one end

Nucleic acids are made of C H O and N they have an acid group ( like lipids) and a N (like proteins) in their make up. = Energy in the cells =

What is ADP and ATP? ADP = adenosine Di Phosphate ATP = Adenosine Tri Phosphate or ADP + P where P = phosphate see figure 3.10 The ATP and ADP cycle

Photosynthesis simple process whereby the plant produces glucose and oxygen by combining Carbon dioxide and water in the presence of chlorophyll and light energy

Complex the equation you must know : The chloroplast has 2 distinct parts Stroma Granae or Lamellae The photosynthesis has 2 part the light dependent part and the light independent part

The light-independent stage relies on the light-dependent stage for a source of energy in the form of ATP. The light-dependent stage is also a source of hydrogen ions and electrons for the light-independent stage.

the light dependent part occurs on the flat surfaces of the lamella or granae -- here the light energy is used to break down water into ions and to boost the electrons Energy level to store the energy for later use in the light independent stage. And this is done using molecules like ADP to ATP and NADP to NADP+. H+ and OH-

In the light-dependent reactions of photosynthesis, the energy from light propels the electrons from a photosystem into a high-energy state. In plants, there are two photosystems, aptly named Photosystem I and Photosystem II, located in the thylakoid membrane of the chloroplast. The thylakoid membrane absorbs photon energy of different wavelengths of light. lots more detail here

http://www.biotopics.co.uk/a2/light-dependent_reactions.html

The light independent stage ( the Calvin cycle) revolves around joining Carbon dioxides together to form the glucose molecule. much more information here

http://www.biotopics.co.uk/a2/light-independent_reactions.html

Here is another version and comparison of the photsythesis

http://www.shmoop.com/photosynthesis/light-independent-reactions.html

So finally whats the major differences between the light and dark reaction of photosynthesis? http://www.majordifferences.com/2013/12/difference-between-light-and-dark.html#.VsVJb5N96Rs

=Respiration= Takes place in the mitachondrion Two type -anaerobic and aerobic

Aerobic - 3 stages

 * stage 1 || Glycolysis || occurs in the cytosol || Glucose ---> pyruvate (and releases 2 ATP) ||
 * Stage 2 || Krebs Cycle || occurs in the matrix of the mitachondria || Pyruvate + oxygen -> carbon dioxide + water + 32 ATP ||
 * stage 3 || Electron Transport || on the inner membrane of the mitachondria ||  ||

Anaerobic respiration
and then the pyruvate becomes -> Lactic acid || Anaerobic respiration is also used by bacteria and yeast to create ethanol and then the pyruvate becomes -> ethanol + Carbon Dioxide || the production of the CO2 gives rise to the bubbles/ air pockets in bread. or the bubbles in beer or wine. =Detailed slide show of respiration= http://slideplayer.com/slide/6089175/
 * stage 1 || occurs in skeletal muscle cells ||  || Glucose ---> pyruvate (and releases 2 ATP)
 * stage 1 || occurs in yeast ||  || Glucose ---> pyruvate (and releases 2 ATP)

=MAintaining homeostasis= http://homeostasisinhumans.weebly.com/theremoregulation.html this site has notes on all types of homeostasis Feedback loops

=Kidneys= http://interactivehuman.blogspot.com.au/2008/06/animation-kidney-parts-of-nephron.html the animation above describes the way the kidney works

http://www.abpischools.org.uk/page/modules/homeostasis_kidneys/index.cfm?coSiteNavigation_allTopic=1

Things I know about the kidney its role is It has to be careful not to excrete useful molecules and does this by

1. filtration 2. osmoregulation 3. creating diffusion gradients 4. using hormones to control reabsorption

Notes on how the kidney functions
The nephron is the basic part of the kidney. The renal corpuscle (bowmans capsule + glomerulus) and proximal tubule in the Cortex an the loop of Henle in the medulla. 1. Filtration in the renal corpuscle 2. reabsorption of water and ions and nutrients in the proximal 3. The loop of Henle - creates a steep osmotic gradient which allows the kidney to reabsorb water and hence concentrate the urine. 4. the distal tubule reabsorbs water but is under control of hormones 5. urine forms in the collecting tubule/duct

How the loop of Henle works
1. It is a counter current exchange the first part of the loop, the down flow, is permeable to water and not solutes. THe second half of the loop the up flow is not permeable to water but is permeable to ions and partially to urea. 2. Hence osmosis works on the descending limb of the loop 3. the result is the solution inside the loop is becoming more concentrated as the you go deeper into the medulla 4. __diffusion__ works on the bend of the tube of the ascending limb of the loop and __active__ __transport__ of ions works on the remainder of the ascending limb

The loop of Henle is an example of a positive feedback loop because the active transport of ions on the ascending limb creates conditions necessay for osmosis to occur on the descending limb. Because osmosis has occurred on the descending limb the remaining filtrate is Na and Cl concentrated and these are actively pumped out on the top of the ascending limb.

Hormones in the kidney
Remember that the kidney is an area of millions of capillaries. When you consider the above functioning you need to remember that the ions pumped out are reabsorbed into the blood. Therefore, low Na+ in the blood causes the release of aldosterone. Low Na+ means lots of water was in the urine. The release of aldosterone causes Na+ to be reabsorbed by surrounding tissue and hence more is pumped out of the ascending tubule and hence water follows dues to osmosis and this inturn concentrates the urine - urine is not as watery.

ADH (anti diuretic Hormone causes the distal tubule and collecting duct to be more permeable to water This means water will be reabsorbed in to the surrounding tissue instead of being excreted. This decreases water loss.

Inspidus Diabetics produce copious amounts of urine because they produce little or no ADH.

The overall role of the kidney is to maintain homeostasis. This means the removal of waste or maintaining the correct levels of water, salts (ions) int the blood.

Diseases in the kidney and how they affect homeostasis. kidney stones

Tissues and organs of vascular plants
Transport in plants is the role of xylem and phloem. The process of moving water up the xylem is controlled by physical processes that revolve around the physical properties of water ( capillarity, adhesion, water tension, absorption, osmosis Transpiration is the loss of water through the stomata of the leaf. To this extent we can say energy from the sun powers this process. (because evaporation of water from teh leaf leads to the replacement of the water by transpiration.

Translocation is the movement of glucose loaded solution down from the leaf (where photosynthesis has occurred) to the roots. This solution travels in the phloem. Excess glucose can be converted to starch and stored in roots of some plants ( potatoes or in the fruits of others eg pumpkin.

Structure of Xylem and Phloem
1. Xylem vessels The most distinctive xylem cells are the long tracheary elements that transport water. **Tracheids **and vessel elements are distinguished by their shape; vessel elements are shorter, and are connected together into long tubes that are called vessels. Xylem also contains two other cell types: parenchyma and fibers.

Transverse sections When observing xylem look for spiral thickening in the vessels. Also look for larger diameter vessels that me appear hexagonal ( when compared to phloem). Xylem have slots in their ends to allow water to easily pass through.

Longitudinal sections The xylem look like long tubes with almost horizontal stripes. These stripes are the lignin thickenings.

Old xylem often called metaxylem are the components of wood. The lignin that forms the rigid spirals in the xylem get stronger and fills in the metaxylem. These are the ones that form growth rings that can be seen in Transverse sections of wood.

<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 16px;">Phloem cells
<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 16px;">. **<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 16px;">Phloem **<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 16px;"> is composed of several **<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 16px;">cell **<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 16px;"> types including sclerenchyma, parenchyma, sieve elements and companion **<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 16px;">cells **<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 16px;">. The sieve element and companion **<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 16px;">cell **<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 16px;">are found closely associated with each other in what is referred to as the sieve element/companion **<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 16px;">cell **<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 16px;"> complex. <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 16px;">The sieve cells are often compared to the shape of a pepper pot. Small and stout with a dotted plate at either end to allow solutions of glucose (mainly converted to glucose) and sugars to pass through. This solution is actively transported down the phloem also diffusion can occur as sugars are pushed down the phloem from an area of high pressure near its site of production to regions of lower pressure where the sugars are used.

An exercise to examine the different plant tissues and their role in transport in the plant https://vcebiology.edublogs.org/tag/xylem/ = [|Transport in Plants] = [|Photo Source] Biology 4 Kids: [|Xylem and phloem] Look through the [|virtual microscope] at xylem and phloem cells. What Wikipedia says about [|vascular tissue] in plants. WikiAnswers: [|What’s the difference between xylem and phloem?] Different [|types of plant tissues] – including good diagrams. [|Plant structure], including more good diagrams, photos and microscope images of plant tissues. [|Plant Structure II], showing a comparison of monocots and dicots – including arrangement of vascular tissue. Moncotyledons are plants with one seed leaf, parallel venation in their leaves and flowers with petals in multiples of 3 (eg. maize, rye grass). Dicotyledons (such as buttercups, celery and beans) have two seed leaves, reticulate venation and flowers with petals in groups of 4 or 5. How woody plants grow – why trees develop concentric rings- [|Vascular tissue animation.] After completing the practical exercise on pages 64 to 66, describe the distribution of vascular bundles in monocot root xs and dicot root xs. How does this distribution compare to the distribution of vascular bundles in stem tissue of moncots and dicots? How does ring-barking affect trees and why does this occur? This entry was posted in [|Functioning Organisms], [|Uncategorized] and tagged [|phloem] , [|plant transport] , [|tissue] , [|vascular] , [|xylem] on [|May 5, 2009].

=Chapter 5 Adaptations for survival= Lots of this chapter is self evident as long as you remember that living organisms require nutrients, oxygen and shelter for survival.

The amount of each depends on the organism and the environment it is in. See the example rule of 3s p 194

Every organism has a tolerance range - within this its called the optimum range at the periphery its still in the tolerance range but outside this tolerance range survival is not expected (or at the very least it is limited) Outside the optimal range the organism is the the zone physiological stress and beyond that the zone of intolerance. Any condition that approaches or exceeds the the limits of intolerance is called a limiting factor.

Organisms often are selected via natural selection if they have a characterisitc that helps them to survive beyond the limiting factors. Read table 5.1 for examples of limiting factors.

Water is essential for life
water in - water loss = 0 ( water in = water out) Chemistry of water p 200 water is a great solvent _ lots of things (except oil) dissolve easily in water Water resists temperature change - water can store a lots of energy eg it takes 4186 J per Kg to heat water 1 degree whereas it takes 1046 J to heat 1 kg of air 1 degree. This means water will stay hotter than for longer than air - think of how the bay stays warmer even after a cool change comes through. Water has a high heat of vapourisation this means that if water is evaporated from the skin of an animal it will cool it down quickly because 2260 kJ / kg of heat is lost

The high heat of vaporisation and specific heat capacity of water are factors in preventing the death of firefighters in a bushfire (p 233-4)

Water loss in humans
see table 5.2 water is taken in by fluid and water and metabolic water (respiration)

Adaptations for survival desert animals
compare the structure of a kidney thickness of medulla divided by kidney size is positively correlated with the capacity of the kidney to concentrate the urine and so reduce water loss. 1. a reduction in glomerular filtration means less fluid leaves the blood 2. an increase in tubular reabsorption (because the loop of Henle is in the medulla)

Behaviour of an animal
1. keep out of hte sun _ nocturnal 2. fat stores located in the tail away from the main section of the body to allow quicker heat loss 3. SA : vol Greater SA : Vol means quicker heat loss -- think of elephants ears 4. being able to extract more water for a food than animals from temperate environments see fig 5.20 an outline oof water balance for survival of the tarrakawarra ( desert hopping mouse) 5. hibernation or laying dormant eg Frogs in the outback. 6. migration - moving away from hositle conditions see fig 5.22 7. Laying eggs and then dying off 8. specific characterisitic

Vegetation types in arid Australia
1. leaf shape 2. density and size of the shrub (eg Spinifex, salt bush) 3. curling leaf 4. sunken stomata - pit stomata 5. leaf colour (silver) 6. leaf structure - feathered, palmate, divided 7. leaf margins - thinner edgesof the leaf loe heat quicker than the fatt central part of the leaf 8. leaf orientation _ hanging vertically away fro the sun 9. Rolled up leaves 10. no visible leaves 11. leaves that aren't leaves- flattened stalks - phyllodes 12. producing drought resistant seeds - ephemeral plants - they have a life cycle of 2 to 3 weeks flower and produce seeds and the species goes on. 13. dormant plants

Survival in the cold
1 ice kills - water expands when it freezes. Frozen water can explode cells ( plants and animal) 2. water freezes at 0 deg C 3. very Salty water freezes at -18 deg C - animals with hi salt content acts as anti freeze - listen to Dr karl podcast. - the frozen wasp - start from 6min https://www.google.com.au/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0ahUKEwjB-pWQ49fLAhXFq5QKHQcNCAsQFggiMAE&url=http%3A%2F%2Fwww.abc.net.au%2Fscience%2Faudio%2F2011%2F10%2F20%2F3344300.htm%3Fsite%3Dscience%2Fdrkarl&usg=AFQjCNED0_T7N99bfDaH3Yf9_Ca9hqPp5Q

4. Insulation layers - fat, blubber 5. hibernation 6. Countercurrent exchange systems to warm the blood - see fig 5.48 p229

Adpatations of plants
1. high salt content or high sugar content - see table 5.6 2. Bark 3. deciduous - no leaves to freeze 4. thick trunk lo SA to Vol

The BioChallenge p 235
Chapter 6 Homeostasis Thermoregulation and Glucose regulation 1. Thermoregulation





2. Blood sugar regulation (glucose regulation)

<span style="color: #292929; font-family: open_sansregular,'Open Sans',Helvetica,Arial,sans-serif; font-size: 1.4em;">Blood glucose levels: too low
<span style="font-family: Helvetica,Arial,sans-serif;">If the blood glucose level falls below normal, this stimulus is **//__detected by the pancreas__//** and the following responses occur:
 * 1) <span style="font-family: Helvetica,Arial,sans-serif;">(low blood glucose) The **alpha cells** of the pancreas (see figure 6.38) **increase** their production of the hormone **glucagon**. Glucagon acts on liver cells, stimulating the conversion of the storage polysaccharide, glycogen, to glucose that is released into the bloodstream. Glucagon also stimulates the synthesis of new glucose from other compounds in cells, such as amino acids.
 * 2) <span style="font-family: Helvetica,Arial,sans-serif;">The beta cells of the pancreas decrease their production of insulin so that the uptake of glucose from the blood into body cells is reduced.



<span style="color: #292929; font-family: open_sansregular,'Open Sans',Helvetica,Arial,sans-serif; font-size: 1.4em;">Blood glucose levels: too high
<span style="font-family: Helvetica,Arial,sans-serif;">If glucose levels in the blood increase **above** the normal range, glucose must be shifted from the blood into the liver and muscle where it is stored as the polysaccharide, glycogen. <span style="font-family: Helvetica,Arial,sans-serif;">When blood glucose levels rise above normal limits, the **//__beta cells of the pancreas detect this increase and initiate a response in which insulin production is inc__//**reased and glucagon production is decreased (see figure 6.39). The increase in the circulating hormone, insulin, acts on body cells, facilitating their uptake of glucose from the blood into body cells, especially muscle and fat cells.

<span style="background-color: #ffffff; font-family: Helvetica,Arial,sans-serif;">Insulin molecules bind to receptors on the plasma membrane of cells. The binding produces a signal that causes glucose transport proteins enclosed in vesicles within the cytosol to move to the plasma membrane. Once there, the transport proteins form trans-membrane carriers that enable glucose to move into cells by facilitated diffusion.







Chapter 6 - Homeostasis focus on 1 glucose balance - effect of insulin, glycagon 2. temperature balnce 3. water balance Kidney function

Chapter 7 - Biodiversity and its organisation What is biodiversity? Biodiversity is the wide range of species existing in an area. An area very high in biodiversity is called a hotspot. Go here to view the hotspots in Australia http://www.environment.gov.au/biodiversity/conservation/hotspots/national-biodiversity-hotspots

Benefits of classification
 * provides tools for exact communication
 * Predictions can be made due to the nomenclature you can identify close relatives or propose features of extinct species within the same genus
 * provides evolutionary pathways
 * Information about items can be easily retrieved

The 2 kingdom system - first proposed by Carl Linaeus - Animals and PLants - later (1965 Whittaker) changed to a 5 kingdom system The separation of fungi from plants was made due to the presence of chlorplasts being absent from all fungi- advancements in technology and investigation processes allowed moer information to be collected and so the system was changed

Taxonomy is not static and some species may be reclassified into different genus or families An exampleof this is some of the Australian grevillea (plants) Principles of classification up to Phyllum level 1. the kingdoms



FUrther studies have shown the need for DOMAINS. these are higher than kingdoms. This claasification structure was propsed by Woese in 1990. Woese and collegaues eschewed the use of structure, morphology, nutrition modes and focussed on classifying using the molecular criteria such as ribosomal RNA genes and other genes and specific proteins found in all organisms

Here is a link to some further background []

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Its important in this area of study you don't over analyse - after all putting objects into groups is a rather human thing to do - (though some bowerbirds do this also). this taxonomy can be arranged in many ways depending on your focus. However the lateest version of our classification system is thought to be the most efficient way to organise them and identify new organisms. the latest emphasis on DNA has lead to some reclassification. The whole idea is to group similar organisms. At the kingdom level if you are an organism with chloroplasts you are in the plant kingdom.

all the organisms in the kingdom Plantae may have chloroplasts but there are significant differences between them - at the next level of classification they can be divided into those organisms with vascular bundles. And you can further divide this group into those that have flowers and those with cones(pine trees)

So you can see the division is fairly arbitrary. The initial divisions are based on very general characteristics. As you get closer to a more specific grouping more and more specific characteristics must be possessed to belong to each successive grouping as you go down the classification levels

EG Kingdom very general Phylum - still general Class - more characteristics in common Order Family Genus very specific- organisms in this group are very similar but - there are still organisms that be grouped based on very specific characteristics- cannot reproduce and produce fertile young Species—very specific, can reproduce and produce fertile young

SO the overview of the kingdoms can be seen as this-- also see the table below to belong to the Kingdom PLantae - you need chloroplasts to belong to the kingdom Animalia - you need cells without cell walls and be a heterotroph t belong to the kingdom Fungi - you need cell walls - no true vascular tissue and no chloroplasts but feed off cells of other organisms to belong to the kingdom Monera - unicellular and prokaryotic - non membrane bound organelles, extremely tiny - bacteria and archaea to belong to the kingdom Protista - you need to be unicellular and eukaryotic

How classification of living things go in to kingdoms

major phyla of the animal kingdom

CHap 8 Ecology Interactions and trophic levels when you analyse the diversity of species in an ecosystem you can identify the ways each species relates to another. One common interaction is eating or being eaten Autotrophs - plants or poducers - make their own food - Level 1 trophic level heterotrophs - consumers - level 2 trophic level and above eat autotrophs and are called herbivores (first order consumers) or eat herbivores and are called carnivores (second order consumers and above)

We can represent the flow of energy through an ecosystem with a food chain - linear or a food web which combines a number of foodchains

<span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: center;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;">The diagram above really should have arrows to show the direction the energy flows -- ie from the tree to the mushroom to the squirrel to the snake (this is one food chain ) or here is another food chain from the tree to the mushroom to the squirrel to the fox and there are lots of other food chains depicted with in the is food web. <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;">Pyramids of numbers and pyramids of biomass <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;">THe diagrams above show a range of pyramids <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;">note the biomass uses dry weight <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;">Energy uses kcal ( a measure of energy like joules) per square metre per year <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;">Some others <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;">Note how the pyramids can be inverted <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;">And the diagram below clearly shows the difference between the types of pyramids and gives some examples <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: left;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: center;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: center;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: center;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: center;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 10pt; text-align: center;">biodiversity and its organisation <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;">Classification <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;">Sampling ecossytems <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;">To get an understanding of an ecosystem you need to be able to identify the species that live there and then identify their interaction <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;">One aspect of the species is their abundance - ie the size of the population. Just the number is not enough the density is also important as this can also be affected by their distirbution. <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;">Different organism types have their abundance measured in different ways. <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;">eg plants may be measured in numbers per metres squared in the case of weeds. <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;">but for trees it might be better to have numbers per km squared. But amoeba might be bettter measured in numbers per mLs <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;">To measure distribution and abundance in the field 2 main techniques are used

1 transect-- <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: small;">a straight line or narrow section through an object or natural feature or across the earth's surface, along which observations are made or measurements taken. <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: small;">

<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: small;"> <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;">2 quadrat <span style="background-color: #ffffff; display: block; font-family: Calibri; font-size: 13.3333px; text-align: center;"> <span style="color: #222222; display: block; font-family: arial,sans-serif; font-size: 16px;"> How do you use a Quadrat? <span style="color: #222222; display: block; font-family: arial,sans-serif; font-size: small;"> <span class="_Tgc _y9e" style="font-size: 16px;">Ideally every place within the sampling area should have an equal chance of being sampled, each time a sample is taken. To achieve this, place a tape measure along two sides of the area being studied. Then find random coordinates as follows: The length of one side of the **quadrat** forms the sampling interval.

<span class="_Tgc _y9e" style="font-size: 16px;">Count the number of each species some times % coverage is better

<span class="_Tgc _y9e" style="font-size: 16px;">

Putting all this together here is an article that shows the abiotic factor - phosphorous availability in the soil governs the growth of trees in the blue mountain @http://www.regional.org.au/au/asssi/supersoil2004/s11/oral/1840_harringtonb.htm

Our transect and quadrat results go here

Population is the number of organisms of a species in an ecosystem. they can be distributed in a uniform, random or clumped manner
 * Populations**

it can be measured in terms of its abundance - ie how many or measured over a linger term by calculating the Growth Rate = (birth rate + immigration rate) - (Death rate + emmigration rate)

You can also compare numbers of females to males in a population

Factors impacting a populations include Number of predators ammount of food, amount of shelter availabilty of a mate competition for food from other species as well as other members of your species Ammount of disease and parasites favourable weather conditions - eg no blizzards to kill alll the babies. Built in behavioural factors that limit an adults ability to breed - eg kangaroo and joey seasonal factors - number of fertile organisms ( eg not all too old or too young) Mortality rate.

Migration emmigration leaving immigration new organisms of a species arriving general migratory pattern - a population moving off after food

Affecting growth rates 1. r-selection - in general they produce lots of eggs and seed to ensure survival of their species eg insects, turtles, fish, 2. k - selection - in general they go for quality over quantity - these individuals put a lot of effeort into raising the young, eg most mammals, fewre offspring but better prepared for survival

Interactions Ammensalism - I'm all right jack - too bad about you plants that practice allelopathy - the production of chemicals that inhibit the growth of other species and individuals.. Allelochemicals are teh chemicals that inhibit the growht. some seeds have a small amount of allelochemicals which prevents the growth of nearby seeds and hence allow their roots to develop quickly and access resour