Biology 30: Organization of Life

To study life we need to consider the most important aspects for living things, primarily obtaining energy and transferring that energy at the whole and at the cellular level. We will also look into the classification of living organisms, as well as compare organisms with the use of dissections.

BI30-OL1 Investigate cell structure and processes, including energy transfer, and transport of materials, in unicellular and multicellular organisms.

a. Analyze the processes (e.g., chemosynthesis, photosynthesis, and cellular respiration) by which organisms from different kingdoms create and transfer energy in the form of ATP. (K)

http://www.pmel.noaa.gov/eoi/nemo/education/images/chemosynthesis.jpg

There is no easy way to show what photosynthesis is, so …

This video helps me:

http://www.bozemanscience.com/science-videos/2012/5/6/photosynthesis.html

A. Photosynthesis Transforms Solar EnergyB. Organic molecules built by photosynthesis provide both the building blocks and energy for cells.C. Plants use the raw materials: carbon dioxide and waterD. Chloroplasts carry out photosynthesisE. Chlorophylls and other pigments involved in absorption of solar energy reside within thylakoid membranes of chloroplasts

A. Solar Radiation - Only 42% of solar radiation that hits the earth’s atmosphere reaches surface; most is visible light.B. Photosynthetic Pigments - Pigments found in chlorophyll absorb various portions of visible light; absorption spectrum. Two major photosynthetic pigments are chlorophyll a and chlorophyll b. Both chlorophylls absorb violet, blue, and red wavelengths best. Very little green light is absorbed; most is reflected back; this is why leaves appear green. Carotenoids are yellow-orange pigments which absorb light in violet, blue, and green regions. When chlorophyll breaks down in fall, the yellow-orange pigments in leaves show through.

Photosynthetic Reaction

1. In 1930 C. B. van Niel showed that O2 given off by photosynthesis comes from water and not from CO2.2. The net equation reads:

.

Two Sets of Reactions in Photosynthesis

Light Dendendent and Light Independent

1. Light reactions cannot take place unless light is present. They are the energy-capturing reactions.b. Chlorophyl within thylakoid membranes absorbs solar energy and energizes electrons.c. Energized electrons move down the electron transport system; energy is captures and used for ATP production.d. Energized electrons are also taken up by NADP+, becoming NADPH.

2. Calvin Cycle Reactions (Light Independent)a. These reactions take place in the stroma; can occur in either the light or the dark.b. These are synthesis reactions that use NADPH and ATP to reduce CO2.c. The end product is glucose which can be used by the plant

Please try to complete the photosystem colouring diagram. Can we make a table that shows the inputs and products of each stage? After completing the diagram, we will try to complete the online assessment:

http://www.biologycorner.com/quiz/qz_photosynthesis.html

Factors the Affect Photosynthesis

1. Light Quality (color)2. Light intensity3. Light Period4. Carbon Dioxide Availability5. Water Availability

Are leaves specialized in any way? Please do quick research to find three ways that leaves are specialized for photosynthesis or any process related to photosynthesis. This could be an exam question!

Other Pathways of Photosynthesis

1. The Calvin Cycle is the MOST Common Pathway for Carbon Fixation. Plant Species that fix Carbon EXCLUSIVELY through the Calvin Cycle are known as C3 PLANTS.

2. Other Plant Species Fix Carbon through alternative Pathways and then Release it to enter the Calvin Cycle.

3. When a plant's Stomata are partly CLOSED, the level of CO2 FALLS (Used in Calvin Cycle), and the Level of O2 RISES (as Light reactions Split Water Molecules).

4. A LOW CO2 and HIGH O2 Level inhibits Carbon Fixing by the Calvin Cycle. Plants with alternative pathways of Carbon fixing have Evolved ways to deal with this problem.

5. C4 PLANTS - Allows certain plants to fix CO2 into FOUR-Carbon Compounds. During the Hottest part of the day, C4 plants have their Stomata Partially Closed. C4 plants include corn, sugar cane and crabgrass. Such plants Lose only about Half as much Water as C3 plants when producing the same amount of Carbohydrate.

6. THE CAM PATHWAY - Cactus, pineapples have different adaptations to Hot, Dry Climates. They Fix Carbon through a pathway called CAM. Plants that use the CAM Pathway Open their Stomata at NIGHT and Close during the DAY, the opposite of what other plants do. At NIGHT, CAM Plants take in CO2 and fix into Organic Compounds. During the DAY, CO2 is released from these Compounds and enters the Calvin Cycle. Because CAM Plants have their Stomata open at night, they grow very Slowly, But they lose LESS Water than C3 or C4 Plants.

The Calvin Cycle Reactions (also called the Light Independent or Dark Reactions)

A. Overview1. The Calvin Cycle is a series of reactions producing carbohydrates.2. The cycle is named for Melvin Calvin who used a radioactive isotope of carbon to trace the reactions.

3. The Calvin Cycle includes: carbon dioxide fixation, carbon dioxide reduction, and regeneration of RuBP.

B

Respiration

http://www.bozemanscience.com/science-videos/2012/5/6/cellular-respiration.html

Cellular respiration is the enzymatic breakdown of glucose (C6H12O6) in the presence of oxygen (O2) to produce cellular energy (ATP):

C6H12O6 + 6O2 -->6 CO2 + 6H2O + 36 ATP (it is 38 ATP in plants)

This formula shows the net reactants and products of this process! It must be known!

1.Glycolysis:a) 6 carbon glucose is split into two 3 carbon pyruvatesb) anaerobic - proceeds whether or not O2 is present ; O2 is not requiredd) net yield of 2 ATP per glucose moleculee) net yield of 2 NADH per glucose ---> sent to the ETC in mitochondria

The pyruvic acid diffuses into the inner compartment of the mitochondrion where a transition reaction occurs that serves to prepare pyruvic acid for entry into the next stage of respiration, this converts them an acetyl CoA which enters the Kreb's cycle.

If oxygen is not present, pyruvate is converted to lactic acid in the cytoplasm -- anaerobic respiration

2. Citric Acid or Krebs Cycle

a)occurs in the inner mitochondrial matrixb) an aerobic process; will proceed only in the presence of O2c) net yield of 2 ATP per glucose molecule d) net yield of 6 NADH and 2 FADH2 (NAD+ is reduced to NADH, FAD+ is reduced to FADH) e) in this stage of cellular respiration, the oxidation of glucose to CO2 is completed. See Graphic on Citric Acid Cycle

3. Electron Transport System:

a) consists of a series of enzymes on the inner mitochondrial membraneb) electrons are released from NADH and from FADH2 and as they are passed along the series of enzymes, they give up energy which is used to fuel a process called chemiosmosis, which drives the process of ATP synthesis using an enzyme called ATPase. c) net yield of 32 ATP per glucose moleculed) 6 H2O are formed when the electrons unite with O2* at the end of electron transport chain. * Note: This is the function of oxygen in living organisms!

Please copy down the diagram summarizing respiration.

Please complete the respiration review.

d. Explore the structural and biochemical adaptations that enable some Archaen’s (e.g., halophiles, thermophiles, and methanogens) to live in extreme environments. (K) Begin by completing the Big Squeeze Lab. Do all living things obtain their cellular energy in the same way? Please follow this link and read the information:http://www.ucmp.berkeley.edu/precambrian/archean_hadean.php

So, if no oxygen present, how are these organisms be different?

g. Research the tools (e.g., light and electron microscopes) and techniques (e.g., cell fractionation and cell cultures) that have enabled scientists to develop deeper understandings of cell structure and processes. (K, STSE)

In this section, we must begin by determining what each type of microscope is, as well as the different types of slides and process that can be used to study cells.

Types of MicroscopesLight Microscope - the models found in most schools, use compound lenses to magnify objects. The lenses bend or refract light to make the object beneath them appear closer. Common magnifications: 40x, 100x, 400x

Stereoscope - this microscope allows for binocular (two eyes) viewing of larger specimens.

Scanning Electron Microscope - allow scientists to view a universe too small to be seen with a light microscope. SEMs do not use light waves; they use electrons (negatively charged electrical particles) to magnify objects up to two million times.

Transmission Electron Microscope - also uses electrons, but instead of scanning the surface (as with SEM's) electrons are passed through very thin specimens.

In simple terms a cell culture is group of cells growing together and fractionation is to break into pieces (think fraction) to study certain parts. These techniques allow scientists to use electron microscopes.

We use light microscopes and you will need to complete Microscope Basics.

c. Examine the diversity of ways in which unicellular organisms are able to exhibit all the characteristics of living things. (K)

f. Examine the structures (e.g., pseudopods, cilia, and flagella) and processes that enable locomotion in unicellular organisms (e.g., amoeba, paramecium, dinoflagellates, and euglena). (K)

Unicellular organisms are often called Protists or Protozoa. One of the best places to look for them is in pond water and a great diversity of living organisms can be found. You will need to be patient and complete the following assignments:

Protozoa Virtual LabBiodiversity of Ponds Microscope

e. Examine how some bacteria meet their needs by interacting with other organisms through symbiotic relationships (e.g., parasitism, commensalism, and mutualism). (K)

Begin by writing a definition for symbiotic relationships, followed by for parasitism, commensalism and mutualism. How do bacteria use each of these of types of relationships? If possible, find examples with humans, but it is also important to recognize these types of relationships can occur with other organisms.

b. Compare the structure and composition (e.g., chitin, cellulose, and peptidoglycan) of cell walls in a variety of organisms representing different kingdoms. (K)

Cell Walls:http://www.biologyreference.com/Ce-Co/Cell-Wall.html

i. Design a model to demonstrate transport of materials at the interface of the cell membrane through processes such as endocytosis, exocytosis, and active and passive transport. (A, STSE, S) j. Analyze how intercellular and intracellular processes, including osmoregulation and biofeedback maintain homeostasis at the cellular level. (K, A)

http://www.biologycorner.com/APbiology/cellular/notes_cell_membrane.html

The Plasma Membrane

--the fluid mosaic model (S.J Singer) -- semi-permeable--fluid portion is a double layer of phospholipids, called the phospholipid bilayer

Jobs of the cell membrane

Isolate the cytoplasm from the external environment Regulate the exchange of substances Communicate with other cells Identification

The Plasma Membrane is also called the Phospholipid bilayer

Phospholipids contain a hydrophilic head and a nonpolar hydrophobic tail

Hydrogen bonds form between the phospholipid "heads" and the watery environment inside and outside of the cell Hydrophobic interactions force the "tails" to face inwardPhospholipids are not bonded to each other, which makes the double layer fluid

Cholesterol embedded in the membrane makes it stronger and less fluid

Proteins embedded in membrane serve different functions

1. Channel Proteins - form small openings for molecules to difuse through2. Carrier Proteins- binding site on protein surface "grabs" certain molecules and pulls them into the cell3. Receptor Proteins - molecular triggers that set off cell responses (such as release of hormones or opening of channel proteins)4. Cell Recognition Proteins - ID tags, to idenitfy cells to the body's immune system5. Enzymatic Proteins - carry out metabolic reactions

Video to watch:

http://www.bozemanscience.com/015-cell-membrane

Passive and Active Transport

Passive does not require energy, active requires energy.http://www.biologycorner.com/bio1/notes_diffusion.html

Diffusion-the process by which molecules spread from areas of high concentration, to areas of low concentration. When the molecules are even throughout a space - it is called EQUILIBRIUM

Concentration gradient - a difference between concentrations in a space.

Molecules will always move down the concentration gradient, toward areas of lesser concentration. Think of food coloring that spreads out in a glass of water, or air freshener sprayed in a room.

Selectively Permeable - membranes that allow some things through, the cell membrane is selectively permeable, water and oxygen move freely across the cell's membrane, by diffusion

Test Yourself: Diffusion Quiz

Review with: Passive Transport Tutorial and How Diffusion Works

Osmosis - the diffusion of water (across a membrane)

Water will move in the direction where there is a high concentration of solute (and hence a lower concentration of water.

A simple rule to remember is: 

Salt is a solute, when it is concentrated inside or outside the cell, it will draw the water in its direction. This is also why you get thirsty after eating something salty.

Type of SolutionsIsotonic Solutions

If the concentration of solute (salt) is equal on both sides, the water will move back in forth but it won't have any result on the overall amount of water on either side.

"ISO" means the same

Hypotonic Solutions

The word "HYPO" means less, in this case there are less solute (salt) molecules outside the cell, since salt sucks, water will move into the cell.

The cell will gain water and grow larger. In plant cells, the central vacuoles will fill and the plant becomes stiff and rigid, the cell wall keeps the plant from bursting

In animal cells, the cell may be in danger of bursting, organelles called CONTRACTILE VACUOLES will pump water out of the cell to prevent this.

 

Hypertonic Solutions

The word "HYPER" means more, in this case there are more solute (salt) molecules outside the cell, which causes the water to be sucked in that direction.

In plant cells, the central vacuole loses water and the cells shrink, causing wilting. In animal cells, the cells also shrink. In both cases, the cell may die.

This is why it is dangerous to drink sea water - its a myth that drinking sea water will cause you to go insane, but people marooned at sea will speed up dehydration (and death) by drinking sea water.

This is also why "salting fields" was a common tactic during war, it would kill the crops in the field, thus causing food shortages.

Diffusion and Osmosis are both types of PASSIVE TRANSPORT - that is, no energy is required for the molecules to move into or out of the cell.

Sometimes, large molecules cannot cross the plasma membrane, and are "helped" across by carrier proteins - this process is called facilitated diffusion

Active Transport- When cells must move materials in an opposite direction - against a concentration gradient. - Active transport requires Energy.- Proteins or Pumps are found in the cell membrane transport molecules across the membrane.

Molecular Transport - Proteins are used to move small molecules such as calcium, potassium, and sodium ions across the membrane

Endocytosis- cell takes in large particles by engulfing them

Phagocytosis - "cell eating" - extensions off cytoplasm surround a particle and package it within a food vacuole and then the cell engulfs it. Ex. Amoebas use this process.

Pinocytosis - the process of taking up liquid from the surrounding environment. Tiny pockets form along the membrane, fill with liquid, and pinch off.

Exocytosis- cell gets rid of particles, opposite of endocytosis- remember the vesicles created by the Golgi Body? These are removed from the cell by exocytosis

 

Sodium - Potassium PumpThe cell removes 3 sodium ions for every 2 potassium ions that enter the cell. This mechanism requires energy.

Think about it.....why does the cell NOT want sodium to build up within its cytoplasm?

http://www.youtube.com/watch?v=yz7EHJFDEJs

http://www.biologycorner.com/quiz/qz_cell_membrane_and_parts.html

h. Analyze how fungi perform extracellular digestions and absorption at the cellular level to acquire energy and nutrients. (K) Most Fungi, mushrooms, digest there food outside of their cells and then absorb. They secrete digestive enzymes that will break down the material into a liquid that can be absorbed. They play a role in decomposing material, but some can eat in different ways:

http://archives.microbeworld.org/microbes/fungi/eat.aspx