Notes on Unit 4 – Nature’s Principles

CELLSI. The Cell Theory Cells are the basic unit of life – all life functions can be explained on the cellular level All living organisms are composed of cells Cells come from other cells

II. The Size of Cells Most cells are between 1-100 µm in size. Prokaryotic cells are about 1-10 µm in size, while

eukaryotic cells are 10-100 µm in size. Cell size is limited by constrains of their surface area. If the SA:V ratio becomes too small, cells

are not able to take in nutrients and release harmful waste quickly enough. As the cell grows, its volume grows at a faster rate than its surface area, so the SA:V ratio decreases. This results in less efficient transport into and out of the cell.

Cells have various adaptations to increase the SA:V ratio. There are exceptions to this rule.

o Egg cells are generally larger than usual. This is possible because they are metabolically inactive, produce little waste and don’t really take in too many nutrients from their environment.

o Nerve cells can be very long (1 meter or more) but they are extremely thin, so all parts of the cell are always close to the cell membrane.

o Cells can increase their surface area by having lots of membrane folds.Do Activity on SA:V ratio.

Large size has its evolutionary benefits. Larger organisms have a better chance of defending themselves and larger plants can compete more effectively for sunlight. Multicellular body structure makes larger size possible. However, multicellular structures also result in cell specialization – when cell specialize with their structure (shape, organelles, processes) to perform a certain function. This is going to be a central theme in this unit.

III. Cell Types There are certain properties that all cells have. These are:

o Cell membrane – to separate the cell from its environmento DNA – for storing genetic information for building proteinso Ribosomes – to build proteins for the cello Cytoplasm – to conduct all chemical life processes

All these structures support the common origin of life hypothesis. There are two major types of cells that are quite different in many ways from each other:

A. Prokaryotes – Bacteria and Archaea domains belong here. These organisms don’t have membrane-bound organelles and nucleus. Evolved about 3.5 billion years ago They are about 1-10 µm sized

Most of the life processes of these cells are carried out either in the cytoplasm or in folds of the cell membrane, because they are lacking organelles.

They are usually single-celled, however, can form biofilms, thin layers of millions of cells of different species that help each other with various functions.Be able to draw and label the parts of these cells.

The following structures are found in prokaryotes:o Nucleoid region – holds the circular shaped single bacterial chromosome (DNA) without

a nuclear envelopeo Plasmid – small, circular pieces of DNA, substantially smaller than the chromosome,

which can be passed on from one organism to another – horizontal gene transfer. They usually contain only a few genes that are not vital but beneficial for the bacterium, such as genes for antibiotic resistance.

o Pilus – short extensions of the cell membrane that help with conjugation – passing on genes from one bacterium to another.

o Ribosomes – assemble the primary structure of proteinso Cell wall – made up of peptidoglycan in bacteria, but made up of different materials in

Archaea. The cell wall helps with keeping the cell’s shape and protectiono Glycocalyx – an outer capsule that is mostly carbohydrate based for extra protection.o Fimbriae – also called pili, but these make bacteria stick on surfaceso Flagella – long projections that make the bacterial cells able to move in water

B. Eukaryotic Cells First eukaryotes appeared 2.1 billion years ago. They have membrane-bound organelles including a nucleus. The evolution of these is explained

partially by the endosymbiotic theory Their size range is about 10-100 µm. Because of the compartments that the organelles create, the larger size is possible for these

cells. The compartments make the cell processes more efficient. The organisms with eukaryotic cells include Protists, Fungi, Plants and Animals. These organisms

can be single-celled but for the most part they are multicellular and could reach very large sizes.C. The Endosymbiotic Theory

They have membrane-bound organelles. The evolution of these is explained partially by the endosymbiotic theory

The Endosymbiotic Theory – Mitochondria and chloroplasts evolved from free living bacteria, when they were engulfed by simple but larger cells. Evidence:

1. These organelles have circular DNA2. They reproduce by binary fission like bacteria do3. Some of their metabolic enzymes are similar to bacterial enzymes4. They are about the same size as bacteria5. They have double membranes, one of which was the original bacterial

membrane, the other was the host’s cell membraneEUKARYOTIC CELLS

I. Evolution These cells evolved 2.1 billion years ago as a result of nutrient shortage pressures. These

cells are more efficient at using available sources because of the compartmentalization of their life processes. These organelles (the compartments) restrict chemical reactions to certain areas and with that more complex reactions can go on in each organelle, where the required enzymes are concentrated.

The more complex organization also requires more chromosomes – chromosomal structure changed to linear chromosomes and there are multiple of them in each eukaryotic cell.

II. The Role of the Nucleus It is a control center of the cell, which is processing inputs from the cytoplasm, stores genetic

information and carries out instructions to regulate cell functions. The instructions are coded in DNA. The instructions include genes for making proteins, making RNA and to perform reproduction.

Parts of the nucleus:o Nuclear envelope – made up of TWO phospholipid bilayer with nuclear pores. These

pores are large enough to transport RNA or proteins in and out of the nucleus.o Nucleolus – synthesizes rRNA to assemble the large and small subunits of the

ribosomes. These subunits only combine later in the cytoplasm.o DNA – always remains in the confined and protected area of the nucleus

Ribosomes are used to synthesize proteins. If the ribosomes are free floating in the cytoplasm, they synthesize proteins for the cell. If they are suspended on the rough ER, they form proteins that exit the cell.

III. The Endomembrane System A set of organelles, which are functionally interrelated and located in the cytoplasm. Includes

the nuclear envelope, rough and smooth endoplasmic reticulum, Golgi apparatus, cell membrane and other organelles that form from these listed ones (vesicles, vacuoles).

All other organelles are listed in your book and you can take notes on them on your review sheets.

http://www.youtube.com/watch?v=TYxDoP9ABHc – Harvard cell animation

Mitochondrial disease -- https://www.youtube.com/watch?v=UjIBu0tiXk0

CYTOSKELETON

I. Structure of Cytoskeletal Proteins There is a network of fibers within the cell that is only visible with very high power electron

microscopes. This network collectively is called the cytoskeleton. This network organizes cellular components and cellular activities. They support and preserve the shape of the cell. They participate in moving the cell organelles, substances in or on the cell and the entire cell. The network is composed of three different fibers:

o Microtubuleso Microfilamentso Intermediate filaments

This system is very dynamic, easily reorganizes and breaks apart. The fibers of the cytoskeleton are made up of proteins.

II. Microfilaments The thinnest cytoskeletal structures, that help to support the cell membrane from the inside,

compose microvilli in the small intestinal cells, they form muscle fibers They are made up of a protein called actin which forms two chains that twist together. In muscle fibers, actin is joined by another protein called myosin. Myosin slides along the actin

filaments to generate muscle contraction.

Amoeba uses actin filaments to form pseudopods for motion -- http://www.youtube.com/watch?v=PsYpngBG394http://www.youtube.com/watch?v=pvOz4V699gk

Actin filaments also produce cytoplasmic streaming that moves the cytoplasm of the cell around. http://www.youtube.com/watch?v=pFsty-XyLZc

III. Intermediate Filaments Medium width fibers which are made up of several different types of proteins. They generally

form permanent structures, because they are not as dynamic as the other two types. They form the surface structures of skin cells that they retain even after their death. These

keratin layers protect underlying tissue. They can also support and anchor various organelles in position.

IV. Microtubules They are hollow tubes that are made up of a protein called tubulin. These units come as dimers

(alpha and beta tubulins). Microtubules form tracks within the cell for vesicles to move on, they form cilia and flagella with

a 9+2 microtubule arrangement. They also form centrioles with a 9+0 arrangement of microtubules.

Microtubules use ATP to bend protein arms that connect them to each other. The bending of these protein arms results in an undulating motion.

http://programs.northlandcollege.edu/biology/Biology1111/animations/flagellum.html

V. Cilia and Flagella They are strictly speaking not organelles, because they are outside of the cytoplasm. However,

they are made up of microtubules, so they are part of the cytoskeleton. Cilia are short, many structures outside of the cell. They are made up of the 9+2 microtubule

structures Flagella are long, few structures that have the same arrangement. They are both used to move the cell along, move substances on the cell surface Prokaryotic cells have a different type of flagella arrangement.VI. Centrioles 9+0 arrangement of microtubules. Pair of perpendicular tubes that orient in a certain way and help the formation of

EXTRACELLULAR STRUCTURES

I. Extracellular Structures of Plant and Animal cells Beyond the cell membrane there is a wide range of structures that can cover the cell’s surface.

In plants the cell wall is the most significant, while in animal cells there is an extracellular matrix (ECM).

The basic composition of these structures is similar in plant and animal cells. They both have fibrous components imbedded in a gel-like substance:

o In plants cellulose fibers are imbedded in a substance of polysaccharides and proteinso In animals collagen protein fibers are imbedded into a matrix of carbohydrate

molecules. These structures help with cell identification, cell attachment and anchoring (cells cannot divide

unless they are attached to a solid surface), they also connect cells to other cells for transport purposes and for cell communication.

II. Animal Cell Junctions Cell junctions – direct connections of cells to each other. Types of cell junctions in animal cells:

o Tight junctions – connections between cells that are made by adhesive connections of the cytoskeleton. This usually protects materials from moving from cell to cell

o Desmosomes – Formed by intermediate filaments, which permanently attach cells to each other and form functional units like muscle fibers.

o Gap junctions – passageways between cells that allow the transport of certain substances like sugars, amino acids, ions to pass from one cell to the next.

III. Plant Cell Walls Cellulose fibers are formed from β-glucose monomers. These fibers bind to each other by H-

bonding and various proteins and carbohydrates are deposited in between them to form a gel-like matrix.

The young plant cell only produces a primary cell wall – thin, flexible wall that is able to expand and grow with the cell.

As the plant cell matures, it forms a secondary cell wall – forms between the cell membrane and the primary cell wall, more rigid and does not grow any more.

Plant cells use plasmodesmata for communication. These are holes on the cell wall that allow the cytoplasm of one cell to flow into the next cell and are surrounded by a cell membrane. These cytoplasmic bridges unify an entire plant. Essential materials, such as water, nutrients, and minerals can pass through the plasmodesmata.

PROKARYOTES

I. Prokaryotic Diversity

Don’t forget to be able to draw and label the parts of a prokaryotic cell

Prokaryotes are single-celled organisms with a wide range of metabolic properties. The diversity of prokaryotes relates to their ability to perform horizontal gene transfer – a gene

or part of a gene moves from one organism to another. Types of horizontal gene transfer:

o Transformation – uptake of foreign DNA from the surroundings. In this case, live bacteria can take in pieces of DNA from a decomposing, dead bacterium.

o Transduction – prokaryotic genes are carried from a donor bacterium to a recipient bacterium by using a virus (bacteriophage)

o Conjugation – DNA transfer from a donor to a recipient bacterium by using two cells that connect through a sex pilus.

See next page

Once the gene is incorporated by any of the methods, it remains in the genome of the recipient and is then transferred during reproduction.

Because of the horizontal gene transfer, it is very hard to set up evolutionary relationships among bacteria. As a result, today, metagenomics is used to identify groups of bacteria that tend to live together in the same area. They are genetically related even if they have a more distant ancestry.

Prokaryotes divide by binary fission – a type of asexual reproduction in which the cells double in size, then copy their circular chromosome and split into two new daughter cells that are identical to the parent cell.

In harsh environments, many bacteria produce endospores – dormant forms that survive under adverse conditions. Some of these endospores can remain dormant for thousands of years. Endospores can withstand even boiling for several hours.

II. Prokaryotic Structure Prokaryotic cells can have a wide range of shapes. They are categorized into the following 3

basic ones:o Spheres (cocci)o Rods (bacilli)o Spirals (spirillum)

Bacterial cell walls always contain peptidoglycan, while Archaeal cell wall can vary in structure but usually contain polysaccharides and proteins in various combinations

By using Gram staining, bacteria can be categorized into two basic groups:o Gram positive bacteria possess simple cell walls with peptidoglycan and colors blue or

purple in gram stainso Gram negative bacteria possess a more complex cell wall with an outer membrane over

the peptidoglycan cell wall. These bacteria only faintly color to red or pink with gram stains.

Gram staining is important in determining the possible treatment for a bacterial infection. Gram positive bacteria are usually easier to treat with antibiotics.

III. Quorum Sensing in Bacteria Explains how bacteria can communicate with each other and act together in unison when

certain chemicals are detected.

Take notes while listening to http://www.ted.com/talks/bonnie_bassler_on_how_bacteria_communicate.html

NUTRITIONAL AND METABOLIC ADAPTATIONS OF PROKARYOTES

I. Nutritional Adaptations Prokaryotes adapted to use a wide range of carbon and energy sources. Carbon is used to build

their organic molecules and the energy is required to invest to fuel life processes and perform synthesis of these molecules. According to the sources that they use they can be:

o Photoautotrophs – use energy of sunlight as energy source and CO2 as a carbon sourceo Chemoautotrophs – use chemical energy derived from oxidation reactions of a variety

of chemicals (S, H2S, Fe2+, NH3 etc.) and CO2 as a carbon sourceo Photoheterotrophs – use the energy of sunlight as an energy source, but use organic

substances as a carbon sourceo Chemoheterotrophs – use organic molecules as their energy and carbon source

Prokaryotes can also be categorized by their way of responding to the presence of oxygen (remember the ancient atmosphere):

o Obligate anaerobs are organisms that are not able to tolerate oxygen and die in the presence of it

o Facultative anaerobs/aerobs are organisms that are able to tolerate oxygen but are also able to survive without it

o Obligate aerobs are organisms that are not able to survive without oxygen. Some prokaryotes are vital because of their metabolism of nitrogen.

Think back to the nitrogen cycle and review the following:o Nitrogen fixing bacteriao Nitrifying bacteriao Ammonifying bacteriao Denitrifying bacteria

II. Can Prokaryotes Work Together? Bacteria developed a wide range of mechanisms to deal with environmental changes. Some bacteria, like Anabaena contains genes for both photosynthesis and nitrogen fixation.

However, nitrogen fixation cannot take place in the presence of oxygen which is the product of photosynthesis. So the bacteria can only perform one or the other process at a time. Usually the bacterium performs photosynthesis, but if surrounding bacteria (of different species) run become low on fixed nitrogen and signal to Anabaena, it can start to perform nitrogen fixation.

Prokaryotes can also form biofilms – a community of organisms on a living or non-living surface, surrounded by a slime-like structure. The colony can grow its capsule as a protection for the entire colony, it can burst eventually and start new colonies close by.

Check out Interpreting a Graph of Microbial Fitness in Biofilms in Module 83

CELL MEMBRANES

I. The Fluid Mosaic Model of Biological Membranes This model describes the composition and molecular characteristics of biological membranes

You need to be able to draw and label the parts of the cell membrane. Draw it here:

Because of the molecular composition of the membrane it is said to be selectively permeable – meaning that it only allows certain substances to cross but it serves as a barrier for other substances.

The hydrophobic fatty acid tails make the membrane’s inner region nonpolar. It is hard for polar substances to pass this layer. So the membrane forms a barrier for polar molecules.

Large molecules also are stopped by the membrane because they cannot fit through in between the bilayer molecules.

A. Phospholipids in the membrane: The phospholipids are able to move around in the membrane. They can move sideways or flip-

flop upside down (very rarely). The fluidity of the membrane depends on several factors:

o Unsaturated fatty acids make the membrane more fluid, but saturated ones make it less fluid

o High temperature makes the membrane more fluido Cholesterol make the membrane less fluid on high temperatures, but on lower

temperatures it slows down the solidification of the membrane

B. Proteins in the membrane: Large protein molecules can float in the phospholipid bilayer (integral proteins) or on the

surface of the bilayer (peripheral proteins) The proteins use their side chains to have varying polarity to fit into the nonpolar bilayer or the

polar environment around the membrane Proteins perform a wide range of functions in the membrane:

o Transport proteins – facilitate the movement of materials into and out of the cell. These substances are generally not able to move across the bilayer because they are polar,

large or move against the concentration gradient. These proteins are very specific and can move only certain molecules or ones that are similar to their target molecules

o Structural proteins – these anchor the plasma membrane to the cytoskeleton and to the extracellular matrix. Also can coordinate the migration of cells for example during embryonic development.

o Enzymes – catalyze reactions like chemiosmosis in cellular respirationo Facilitate cell-to-cell interactions – proteins can link cells together by tight junctions (ex.

between skin cells)o Cell communication – gap junctions can act as communication channels between cells.

These gap junctions are also formed by membrane proteinso Cell identification – glycoproteins o Receptors – bind to outside signal molecules and generate changes inside of the cell as a

result of the binding.

C. Carbohydrates of the membrane Carbohydrates are polar molecules that are attached to the outside of the cell membrane. They attach themselves to either a phospholipid – glycolipid or attached to a protein –

glycoprotein. Carbohydrates are used to indicate a cell of the organism (“self”) and also indicate infected,

damaged or foreign cells in the body for the immune system.

D. Cholesterols Membranes should have the consistency of oils. To keep this consistency under different

temperatures, sterols are used. At lower temperatures, the membrane would become too solid and brittle. Cholesterol is

wedged into the hydrophobic fatty acid tails and prevents the fatty acids to pack up too tightly to form solids.

On moderate temperatures, cholesterol prevents the membrane from becoming too fluid and moves the phospholipids around too much.

Cholesterol or some other sterols are used in animal cells, fungal cells and plant cells. However, bacteria and archaea use other substances to accomplish membrane fluidity.

II. The Function of the Cell Membrane: Protect the cell’s internal environment by being selectively permeable. Only allows certain

substances in or out of the cell Maintains the cell’s shape Helps the immune system by presenting ID tags for immune cells to recognize self, defective or

infected cells Connect cells to other cells Participates in cell communication.

MEMBRANE TRANSPORT – Passive Transport

I. Passive Transport The cell must balance its input and output of materials and energy. This balance is partially

accomplished by the cell membrane Passive transport – the process that moves substances across the membrane without using

energy from the cell. This process always moves the molecules down the concentration gradient (from high to low concentration).

Passive transport continues until equilibrium is reached. Random movement of molecules may continue but there is no directionality after equilibrium is reached.

A type of passive transport is diffusion – the random movement of particles due to their kinetic energy. This movement however, can be directional down the concentration gradient (from higher to lower concentration). Usually small, nonpolar substances use diffusion to cross the phospholipid bilayer. Factors that influence diffusion include:

o Temperatureo Concentration gradiento Polarity (when moving across a barrier like the phospholipid bilayer)o Size (when moving across a barrier like the phospholipid bilayer)

Osmosis – a specialized form of diffusion that moves only water molecules. Water can cross the phospholipid bilayer with low efficiency because of its polarity. However, specialized channel proteins (aquaporins) help water to move across the membrane with a higher efficiency.

The pressure that is needed to prevent water from moving across a membrane is osmotic pressure. If the osmotic pressure is too high, water is forced out of an otherwise low water concentration area.

Facilitated diffusion – a special kind of passive transport that requires the help of a transport protein to carry dissolved substances across the membrane that are too polar or larger to get through the phospholipid bilayer. Substances such as glucose or chlorine ions frequently use this process – polar, larger and/or ionic substances. The proteins that are used during facilitated diffusion are generally integral proteins that are constantly open and move substances from the higher to the lower concentration area.

II. The Regulation of Water Content and Homeostasis Controlling the concentration and type of substances that enter and leave the cell is vital for

keeping homeostasis in cells. Osmoregulation – the process by which living organisms control their internal concentration of

water and dissolved substances. On the cellular level, the water level in the cell compared to the environment is measured by tonicity – the measure of water concentration of two solutions separated by a semipermeable membrane. Cells can be the following compared to their environment:

o Hypertonic – higher concentration of dissolved substances and less water inside of the cell than in the environment

o Hypotonic – lower concentration of dissolved substances and more water inside of the cell than in the environment

o Isotonic – equal concentrations of dissolved substances and water inside and outside of the cell

The effect of tonicity on cells depends on the type of cells:o In isotonic solutions animal cells will hold their normal shape, while plant cells are

flaccid – organelles dispersed, low pressure on the cell wallo In hypotonic solutions animal cells swell with water and may lyse (burst), while plant

cells swell up but the cell wall will protect them from bursting (turgid).o In a hypertonic solution animal cells shrink because they lose water, while plant cells

plasmolyse – their cell membranes move away from the cell wall.

You will need to be able to determine the direction of water movement and consequences of this movement across a membrane.

III. Water Potential (not in the book)

In plants it is more complicated to predict which direction water is moving to because of the presence of a cell wall. In the case of plants pressure and solute concentration together determines the direction of water movement. The combined measure of solute concentration and physical pressure are incorporated into water potential (abbreviated with the Greek letter psi, Ψ). Water potential determines the direction of movement of water.

Free water that is not bound by solute or by surfaces always moves from the higher water potential region to the lower water potential region if there is no barrier to its flow.

The unit of water potential is megapascals (MPa). Pure water has a water potential of zero if the container is open to the atmosphere, under standard conditions.

The equation for water potential shows both of its components:Ψ = Ψs + Ψp

Where Ψs is the solute potential and ΨP is the pressure potential.

Solute potential of a solution is proportional to the number of dissolved solute molecules. Because solutes bind to water molecules and lower the capacity of water molecules to do work, adding solute molecules to water always lowers water potential. Because pure water has zero water potential, solutions always have a negative solute potential.

Pressure potential is the physical pressure on a solution. Pressure potential can be both positive and negative relative to atmospheric pressure. The pressure potential in living cells is usually under positive pressure. This positive pressure that presses the plasma membrane against the cell wall is called turgor pressure.

B. Analysis of Water Potential in an Artificial System

Part a: The membrane that separates the two sides of the U-tube is permeable to water but not to solutes. If one side is filled with pure water and the other side is filled with a 0.1M solution, the net water movement will be toward the solution from the pure water, because water always moves from higher water potential to the lower water potential area.

Part b: If a pressure of 0.23 MPa is applied to the solution that the water potential is raised to 0 MPa. There will be no net flow between the two sides.

Part c: If the pressure is further increased to 0.3 MPa than the solution has a water potential of +0.07 MPa. This solution will actually lose water to the pure water part of the U-tube.

Part d: If the plunger would be pulled back on the pure water side, it would create a negative pressure and water would move to the pure water side.

In plant cells, if a plant cell is limp (flaccid) it would have a ΨP of 0 and if it is sitting in a more

concentrated environment, the cell would lose water and would plasmolyze. However, if the plant cell is in pure water, it would gain water and become turgid until the cell wall would produce enough pressure to compensate for the concentration difference and Ψ = 0.

Turgor pressure is an important tool of plant support in nonwoody plants. Solute potential can also be calculated by using the following equation:

Ψs = - i C R T(look in your formula sheet for the meaning and units of these terms)

Problems are on a separate worksheet but here is one for the class to try:What is the solute potential of the solution that has -0.5 M of sugar dissolved in 1 L water on 20 °C temperature? What is the water potential of this same solution if it is in an open container?

Water potential on Bozeman Biology: https://www.youtube.com/watch?v=nDZud2g1RVY

ACTIVE TRANSPORT

I. Membrane-Mediated Transport Some passive transport processes such as facilitated diffusion and osmosis to some extend

require proteins. These proteins are called channels, because they are usually open and simply allow molecules to move from high-concentration area to low concentration area.

Some proteins that are involved only in active transport are called gated channels, these are usually closed and require an electrical or a chemical signal to open.

Both channel proteins and gated channels are highly selective and only allow the transport of one or a few similar substances.

Three types of transports can be performed by these proteins:o Uniport – one molecule or ion type is transported either in or out of the cell o Symport – two or more different molecules or ions are transported in the same

directiono Antiport – two different molecules or ions are transported in opposite directions

II. Active Transport Active transport is a process that moves molecules against their concentration gradient cross

the membrane. This process requires energy provided by the hydrolysis of ATP molecules. This type of transport always requires a transport protein

A special type of active transport is the sodium-potassium ion pump – this process maintains a low sodium and high potassium ion concentration in the cell by carrying 3 Na+ ions out of the

cell and 2 K+ ions into the cell. One third of the cell’s energy is used to keep these ions at their optimal concentrations. Steps of this process:

o 3 Na+ ions bind to the protein in the cytoplasmo This stimulates the hydrolysis of an ATP molecule and the addition of a phosphate to the

protein. This changes the shape of the proteino The protein releases the sodium ions outside and takes in two potassium ions.o This triggers the release of the phosphate group from the protein and the change of the

protein’s shape back to its original shape.o The potassium ions are released into the cytoplasm and the protein is ready to perform

the same action again. The transport of various ions across the membrane can set up a charge difference between the

opposite sides of the membrane. This also results in an electrical difference called membrane potential. This charge difference can be used by the cell as a potential energy source. The difference in concentration of charges on the inside and outside of the cell is called electrochemical gradient.

This electrochemical gradient can be used to move another molecule or ion against its own gradient – secondary active transport. An example of this is the sucrose-proton cotransport (sucrose – H+ cotransport). In this case a proton pump is used to set up a electrochemical gradient and then this gradient is used to cotransport sucrose into the cell with H+ ions in a symport to get sucrose into the plant cells.

http://www.youtube.com/watch?v=2UPqLm-uDnI – summary of all

ENDOCYTOSIS AND EXOCYTOSISI. Bulk Transport Cells use vesicles to move large materials or large quantities of materials. Endocytosis is used to move substances into the cell. There are three types of endocytosis:

o Phagocytosis – nonspecific intake of solid materialso Pinocytosis – nonspecific intake of liquid materialso Receptor-mediated endocytosis – brings in specific molecules that need to bind

with the receptors on the outer surface of the membrane to be able to enter, than the receptors must be able to move back to the outer surface to function again.

Exocytosis is used to move substances out of the cell. This process is used to secrete materials into the external environment. Hormones, digestive enzymes, neurotransmitters, cell wall components are all transported this way.

Vesicles are moved with the targeted materials on tracks of microtubules with the help of motor proteins.

Some cells continuously release molecules while others release molecules, like hormones, only if some signal molecules activate receptors to stimulate release of substances.

Endocytosis is important for the functioning of phagocytes – specialized white blood cells that engulf pathogens.

Sometimes, however bacteria, through natural selection evolved to avoid to be recognized by phagocytes. The glycocalyx can serve as a defensive layer that prevents the binding of phagocytes to bacterial cells and also protects the cells from being digested. http://www.nature.com/news/alzheimer-s-drug-sneaks-through-blood-brain-barrier-1.16291#/ref-link-1 -- animation and article on the blood brain barrier and receptor mediated endocytosis

ANIMAL STRUCTURE AND FUNCTION

I. Anatomy and Physiology Anatomy of organisms refers to the structures that form an organism. These structures

provide details about how the organism lives, what it eats and a wide range of other information.

Physiology refers to the functioning of the anatomical features. What they do and how they perform these functions.

Evolution drives the changes in structure and function among various animals.

Review homologous and analogous traits and how comparative anatomy is used to determine evolutionary relationships. Also differentiate between convergent evolution and adaptive radiation.

II. Levels of Organization within Organisms

We also had this before but you will be expected to know this for this section

III. Tissues of Animals The structure and function relationship shows up in every level of organization. Animal tissue structures are good examples of structure and function relationships as well.

Most animals have the following 4 basic tissue types:o Epithelial tissueo Connective tissueo Muscle tissueo Nervous tissue

A. Epithelial Tissue

Epithelial tissue tightly packed cells with very little extracellular matrix. The blood vessels and nerves are usually underneath the cells on a basal membrane. Three types of epithelium occurs according to the cell shape:

o Squamous epithelium is flattened cells. o Cuboidal epithelium is cube-shaped cells. o Columnar epithelium consists of elongated cells.

Any epithelium can be simple or stratified. Simple epithelium has only a single cell layer. Stratified epithelium has more than one layer of cells.

Functions of epithelial cells include: o movement materials in, out, or around the body o protection of the internal environment against the external environment o covering body surfaceso secretion of substances that are produced by the cells of the epithelium

Glands can be single epithelial cells, such as the goblet cells that line the intestine. Multicellular glands include the endocrine glands – these are glands that release hormones

into the bloodstream. To release hormones they use exocytosis and do not have a separate duct formed for the release

Exocrine glands are formed of ducts and secretory portions. They release their secretions directly to the place where it is used by using their duct.

B. Connective Tissue

Connective cells are separated from one another by an extracellular matrix. The matrix may be solid (as in bone), soft (as in loose connective tissue), or liquid (as in blood). Two types of connective tissue are Loose Connective Tissue and Fibrous Connective Tissue, depending on the amount of fiber that is in the extracellular matrix.

Connective tissue serves many purposes in the body:o binding o supporting o protecting o forming blood o storing fats o filling space

Some specialized connective tissues include cartilage, tendons, ligaments, bone and blood

Adipose tissue has enlarged cells storing fats and reduced extracellular matrix. Adipose tissue facilitates energy storage and insulation.

Bone has calcium salts in the matrix, giving it greater rigidity and strength. Bone also serves as a reservoir (or sink) for calcium. Protein fibers provide elasticity while minerals provide elasticity. Two types of bone occur, dense bone and spongy bone. Spongy bone occurs at the ends of bones and has bony bars and plates separated by irregular spaces.

Blood is a connective tissue of cells separated by a liquid (plasma) matrix. Two types of cells occur. Red blood cells (erythrocytes) carry oxygen. White blood cells (leukocytes) function in the immune system. Plasma transports dissolved glucose, wastes, carbon dioxide and hormones, as well as regulating the water balance for the blood cells. Platelets are cell fragments that function in blood clotting.

C. Muscle Tissue

Muscle tissue facilitates movement of the animal by contraction of individual muscle cells (referred to as muscle fibers). Three types of muscle fibers occur in animals:

o skeletal (striated) o smooth o cardiac

Muscle tissue and organization is shown below:

Muscle fibers are multinucleated, with the nuclei located just under the plasma membrane. Most of the cell is occupied by striated, thread-like myofibrils. The thick filaments are made of myosin and occupy the center of each sarcomere. Thin filaments are made of actin

Skeletal (striated) muscle fibers have alternating bands perpendicular to the long axis of the cell. These cells function in conjunction with the skeletal system for voluntary muscle movements.

Smooth muscle fibers lack the banding, although actin and myosin still occur. These cells function in involuntary movements and/or autonomic responses (such as breathing, secretion, ejaculation, birth, and certain reflexes). Smooth muscle fibers are spindle shaped cells that form masses. These fibers are components of structures in the digestive system, reproductive tract, and blood vessels.

Cardiac muscle fibers are a type of striated muscle found only in the heart. The cell has a bifurcated (or forked) shape, usually with the nucleus near the center of the cell. The cells are usually connected to each other by intercalated disks.

D. Nervous Tissue

Nervous tissue , functions in the integration of stimulus and control of response to that stimulus. Nerve cells are called neurons. Each neuron has a cell body, an axon, and many dendrites. Nervous tissue is composed of two main cell types: neurons and glial cells. Neurons transmit nerve messages. Glial cells are in direct contact with neurons and often surround them.

The neuron is the functional unit of the nervous system. Humans have about 100 billion neurons in their brain alone!

HOMEOSTASIS

I. Regulation and Conformation Animals live in a constantly changing environment with large daily and yearly fluctuations in

temperature, light intensity, moisture etc. Mechanisms that developed to adjust cellular and physiological processes in order to maintain internal equilibrium are called homeostatic mechanisms or homeostasis. Examples of homeostatic mechanisms include temperature regulation, glucose regulation, osmoregulation, pH regulation etc.

Animals that manage external environmental changes by adjusting and mostly keeping a constant internal environment are called regulators. They use complex signaling pathways to keep their body conditions constant. Birds and mammals are mostly considered regulators.

All other animals, like insects, amphibians, fish etc. are considered conformers because they lack complex internal control mechanisms for maintaining their homeostasis in changing environments. Conformers tend to live in environments that are changing less drastically. Many may hibernate when conditions are not ideal. It is beneficial to be a conformer, because it requires less energy to maintain body conditions. However, they tend to be majorly harmed by drastic changes in the environment.

II. Feedback mechanisms Feedback mechanisms – cellular and physiological changes and responses in the body to

maintain homeostasis when conditions change from the ideal. Each condition in living organisms fluctuates around a set point, the ideal condition. However,

the fluctuations can be only within a certain range. If fluctuations in the external environment are great enough, internal feedback mechanisms operate to restore balance.

Steps of the feedback mechanisms to restore homeostatic balance are the following:o Stimulus coming from the environmento Receptors to sense the stimuluso Control center to process the signal and generate adjustmentso Effectors that respond to the stimulus

Negative feedback mechanisms – This type of feedback reduces the deviation from the set point and reducing the impact of the stimulus. Temperature regulation, osmoregulation, pH regulation and most of other homeostatic processes use negative feedback. Regulation of appetite with leptin hormone is another example – watch the animation in your book

Positive feedback mechanisms – they magnify the impact of the stimulus by initiating a series of cascading mechanisms that push the set point beyond normal ranges. Ex. Uterine contractions during childbirth, blood clotting mechanism, pepsin production in the stomach.

http://www.pennmedicine.org/encyclopedia/em_DisplayAnimation.aspx?gcid=000070&ptid=17

http://www.youtube.com/watch?v=_0afKWu4yVg

TEMPERATURE REGULATION

I. Introduction Temperature regulation is a homeostatic mechanism. Organisms require certain temperature

for their normal life processes. If the temperature is too low, metabolic processes can slow down, diffusion of gasses in and out

of cells become dangerously slow and cell membranes can become brittle etc. If the temperature is too high, enzymes can become damaged, heart rate can be too high and other strains can occur on the body.

Temperature regulation helps to establish the ideal body temperature in organisms.

II. Ways of Regulating Temperature in Animals For most animals, the external environment serves as a heat source to provide the ideal

temperature to perform all biological processes. Heat can also come from the energy released during the breakdown of food. Without the proper heat source, animals slow down all their life processes and can eventually die.

Animals can be classified according to the type of temperature regulation that they perform:o Endotherms – mostly derive heat from metabolism (like mammals and birds). They

maintain a constant body temperature even if the environment changes. To maintain a constant body temperature, they require larger calorie intake to cover the energy needs of maintaining a constant temperature.

o Ectotherms – mostly derive heat from the external environment (almost all animals except mammals and birds). Because the heat comes from the environment, these organisms develop certain behaviors to gain the necessary heat but not too much. For example, lizards can bathe on the sun to warm up or move into a shady area or water if it is too hot. Because they don’t use metabolic heat, their calorie needs are a lot lower than endotherms. Crocodiles can go without food for several months.

Both endotherms and ectotherms use temperature regulation but in different ways.

Figure 2 in your book

Bioskill in the book

III. Forces Leading to Heat Gain and Loss Heat exchange occurs when there is a difference between the temperature of an animal and its

surroundings or between different parts of the body. Heat transfer occurs from the higher temperature area to the lower temperature area.

This heat transfer can occur by three processes:o Radiation – release of electromagnetic waveso Evaporation – heat transfer through the transformation of a liquid into a gas, mostly to

cool the surface of an animal downo Convection – heat transfer by moving air or liquids o Conduction – transfer of heat between two objects that are in contact

Book activity – figure 9

IV. Mechanisms to Balance Heat Gain and Loss Insulation – prevents the extreme loss of heat from the body by enclosing heat into the body.

Mammals use fur/hair and fatty tissues (such as blubber) for insulation. Birds use feathers that are covered with oily substances. Filling up the space in between the fur and feathers with warm air also increases insulation and keeps the body warm.

Circulatory adaptations – The circulatory system is important in both heating the body and cooling it. In too warm temperatures, the blood vessels undergo vasodilation – widening, which increases blood flow through the skin and releases more heat from the body. Vasoconstriction occurs when the body decreases heat transfer to the environment mostly to keep heat in and not let the body cool down in cold weather. In these cases the skin blood vessels close up or constrict. (This part is explained differently and not really correctly in your book)

Countercurrent exchange – the transport of heat between fluids circulating in opposing directions. Blood vessels that are located close to each other are a good example of this process. Arteries (blood vessels coming from the heart with O2 rich blood) usually carry warmer blood from the torso to the extremities, while veins (carry CO2 rich blood toward the heart) usually carry cooler blood from the extremities toward the torso. To prevent too much heat loss, veins get closer to arteries in cold weather and warm up the blood before it gets back into the heart. This way the torso does not decrease in temperature.

Evaporative heat loss – evaporation of water from the skin (sweating) or from mucus membranes (panting) prevents the body from overheating. Because of the high heat of vaporization of water, it takes the kinetic energy from the organism to evaporate, in the meantime decreases the temperature. Ectothermic animals would bath in water in the environment instead, they don’t sweat or pant.

Hormones – some hormones such as T3 and T4 of the thyroid gland also generates heat by speeding up metabolism in various tissues. This way more metabolic heat is produced that can heat the body.

Shivering – can increase metabolic heat production by moving muscles and using up more ATP, as a result, generating more heat.

Body position – animals can stretch out on warmer weather to increase the surface area for heat loss by evaporation and convection. In colder weather they curl up to decrease the surface area for heat loss.

Play the story about the man who survived a shipwreck for 3 days in an air hole under water: http://www.youtube.com/watch?v=Vzhi5a0M3jM

Bozeman biology: https://www.youtube.com/watch?v=TSUCdLkI474&list=UUEik-U3T6u6JA0XiHLbNbOw&index=4&feature=plpp_video

OSMOREGULATION

I. Overview Osmoregulation – the process by which a cell maintains the cytoplasmic volume and solute

concentration of an animal’s cells. In invertebrates, fluids, mostly water can simply move across the cell membrane. Most complex animals have interstitial fluid that surrounds cells to provide the proper water and salt concentration.

Transport epithelia – specialized cells develop to form a network of passages and channels to provide large surface area for transport and to connect inner body cells to the environment. This transport epithelium can have many forms depending on the organism and the location of this epithelium. In humans, transport epithelia are found in the kidneys, lungs; in fish on the surface of gills or in sea birds and reptiles in salt glands on the head.

Cells are very efficient at taking in or releasing water by using specialized transport proteins called aquaporins.

Remember and review: water movement is determined by tonicity and water potential.

When the water level in cells is too low, the cell shrivels up, becomes too concentrated and cannot perform various chemical processes. If the cell takes in too much water, it lyses and dies.

On the organismal level, low water levels result in dehydration. This can be a life-threatening process, because metabolic processes stop working, blood becomes too thick to flow, the heart has to work harder, waste removal and nutrient transport becomes ineffective, temperature regulation gets disabled.

Too much water can also have life-threatening consequences such as brain swelling that can result in seizures, coma and respiratory distress.

II. Animal Osmoregulation Osmoconformers – marine animals that maintain the same osmolarity (osmotic concentration)

as their surroundings by keeping uncharged molecules in their body fluids. They live in very stable environments, so they can only tolerate a very narrow range of osmolarity. Most invertebrate belong in this group.

Osmoregulators – these animals actively maintain their internal osmolarity because their internal concentrations of salts and water differ from the environment. These organisms use large amounts of ATP to keep up their internal osmotic concentrations but may be able to tolerate a wider range of osmolarity than osmoconformers. Animals in this category include land animals, marine bony fish, freshwater fish and some crustaceans.

Marine osmoregulators – bony fish – they constantly lose water by osmosis into the sea water. They balance their water by drinking lots of sea water and using their gills and kidneys to get rid of the excess salt. The gills for example have special chloride cells that actively transport chlorine out and Na ions passively follow.

Freshwater animals – These animals are more concentrated than their environment (hypertonic animals). As a result, they constantly gain water by osmosis and lose ions by diffusion. As a solution, freshwater fish drinks almost no water at all and excretes lots of very dilute urine. Salts are replenished by eating or taking in salts through their gills. To take in salts, they use chloride cells to actively transport Cl ions and sodium ions follow passively.

Land animals – Water loss (dehydration) is a major issue for land animals. They must come up with a wide range of evolutionary adaptations to preserve water and reduce water loss – water resistant outer coverings, nocturnal lifestyle, lungs are inside of the body unlike gills, specialized excretion methods. Despite these adaptations, land animals need to drink water and eat moist food or producing water metabolically.

Osmoregulation is an energy requiring process, the requirements depend on how much osmoregulation an organism has to perform. The energy is usually used for active transport and forming channel proteins. The more different osmolarity an organism has compared to its environment, the more energy it takes to regulate it.

Osmoregulation on Bozeman Biology: https://www.youtube.com/watch?v=qfWx8msgHqM

EXCRETORY SYSTEMS

I. Nitrogenous Waste The excretory system is responsible for removing waste, regulating water balance, regulating

salt concentrations. Nitrogenous waste forms during the digestion of proteins and nucleic acids because ammonia

(NH3) is produced from the amino group and other nitrogen containing functional groups. Ammonia is very toxic, because it can change the pH of blood, interfere with oxidative

phosphorylation, and disturb the osmotic balance of the body. In general, the form of waste excreted is related to the evolutionary history of the organisms

and the environment that they live in, mostly the water availability and the reproductive strategy are the defining factors. Types of nitrogenous wastes that are excreted by animals:

o Ammonia – because it is water soluble, aquatic animals can release ammonia with lots of water, without being hurt by the increased water loss during the process. This also requires less energy because the waste ammonia does not need to be converted to any other substance in the body. In fish, most of the ammonia is released through the gills.

o Urea – mammals, most adult amphibians, sharks, some marine body fishes, turtles excrete their nitrogenous waste as urea. It is produced in the liver from ammonia +CO2. Because it is not very toxic, urea can be transported through the circulatory system in higher concentrations and excreted with less water. This way, dry land organisms can preserve water. The disadvantage of excreting urea is that it an energy requiring process to produce it.

o Uric acid – land snails, reptiles, birds excrete nitrogenous waste in the form of uric acid. It is not toxic and does not dissolve in water. As a result, the excretion of these organisms is paste-like. However, making uric acid is even more energy requiring than making urea. Uric acid is beneficial for organisms that reproduce with shelled eggs, because the uric acid can be deposited inside the egg and does not harm the developing embryo.

Humans also release some uric acid, especially if their food contains too much animal tissue – gout is a painful inflammation of the joints when uric acid crystals deposit there.

II. Excretory System Diversity Although there is a variety in the excretory system of organisms, they all share some common

characteristics. All organisms with excretory systems have the same basic 3 processes or some of these processes:

o Filtration – water and certain solutes are transferred through a transport epithelium from the body fluids into the excretory organs. Large molecules, such as proteins remain in the body fluid and do not enter the excretory organ.

o Water reabsorption – many useful molecules, such as amino acids, glucose and others are transported back into the body fluid so they are not excreted and wasted because the body can still use them.

o Secretion – additional waste products such as toxins, excess ions and others can be directly deposited into the excretory organ mostly by active transport.

We are only focusing on the excretory organ of mammals, the kidney, but remember, other animals have a diverse range of other organs for excretion. Kidneys are used to perform all three basic processes of excretion and form the final composition of the urine. They also regulate osmotic concentration of water and various salts. Other organs of the mammalian excretory system include the ureters, bladder and urethra. These are mostly storage organs and channels which helps mammals to get rid of the urine. The kidneys also have a rich blood supply, which is fed by the aorta through the renal artery and collected up by the inferior vena cava connects to the kidneys by the renal vein.

III. The Nephron Your kidneys filter about 180 liters of blood every day (that is more than 47.5 gallon of blood),

so your entire blood volume is filtered through about 36 times – do not memorize this information.

Nephrons are the functional units of the kidneys, located on the border of the outer cortex and the inner medulla. Nephrons function as a dual-system of long tubules and the surrounding blood vessels.

You need to draw the nephron and label its parts.

Afferent arteriole – blood enters the nephron through this small artery Glomerulus – a tangled knot of blood vessels surrounded by a capsule called the Bowman’s

capsule. The blood vessels inside of the capsule have porous walls to allow smaller substances out of the blood vessel into the nephron. Larger molecules, such as proteins are not allowed to pass through.

Efferent arteriole – about 80% of the incoming blood leaves the nephron through this small blood vessel

Proximal convoluted tubule – the filtrate (filtered blood) continues here, many substances will be reabsorbed back into the bloodstream here, including water, sodium ions, potassium ions, chlorine ions, glucose and amino acids. However, some substances will be secreted from the blood into this area such as hydrogen ions to maintain blood pH.

Loop of Henle – the descending loop helps to maintain proper water balance by reabsorbing water back into the bloodstream depending on the body’s needs by using aquaporins. The ascending loop reabsorbs only ions and it is impermeable to water.

Distal convoluted tubule – This region is sensitive to two hormones (aldosterone and vasopressin) which will maintain normal salt and water concentration in the blood to reabsorb the proper amount of water and ions.

Collecting duct – also regulates blood volume and completes the formation of urine.

http://www.biologymad.com/resources/kidney.swf -- step through process

http://argosymedical.com/Urinary/samples/animations/Urine%20Formation/ --- the entire process

http://interactivehuman.blogspot.com/2008/06/animation-kidney-parts-of-nephron.html -- more detailed.

KIDNEY FUNCTION AND HORMONAL CIRCUITS

I. Feedback Mechanisms of Osmoregulation When body water levels decrease, and consequently the solute concentration increases,

osmoreceptors in the hypothalamus of the brain are activated. This triggers the hypothalamus to produce a protein hormone called antidiuretic hormone (ADH), released from the back of the pituitary gland. ADH affects the distal convoluted tubule and the collecting duct of nephrons by causing the transport epithelium there to be more permeable to water. This will result in more reabsorption of water and the return to more ideal water concentrations in the blood stream.

Another regulatory system responds to decreasing blood pressure. The region around the afferent arteriole of the nephron contains a specialized tissue called JGA which responds to decrease in blood pressure and volume by releasing an enzyme called renin. This enzyme produces a protein called angiotensin II. Angiotensin II causes arterioles to constrict, which slows down blood flow and reduces the amount of filtrate that forms. As a result, more water remains in the blood, increasing the blood volume and blood pressure. Angiotensin II also triggers the release of a hormone called aldosterone from the adrenal glands of the kindeys – increases the reabsorption of water and Na+ ions from the nephron, increasing the blood volume and blood pressure. – This entire regulatory system is called the renin-angiotensin-aldosterone system (RAAS)

BLOOD GLUCOSE REGULATION

I. Control of Blood Glucose Levels The islets of Langerhans of the pancreas are responsible for its endocrine function. The

alpha cells of the islets are responsible for releasing glucagon, while the beta cells are responsible for releasing insulin. These two peptide hormones are antagonists of each other.

When blood glucose levels rise above normal, beta cells are stimulated to release insulin. Insulin stimulates liver cells to take in more glucose and store it as glycogen. It also stimulates other cells of the body to take in more glucose.

When blood glucose levels are too low, alpha cells are stimulated to release glucagon. Glucagon makes the liver break down glycogen and release more glucose into the blood stream.

Diabetes mellitus – a disease where glucose homeostasis fails with very serious consequences. People with diabetes mellitus excrete glucose because their kidneys are not able to reabsorb all

the glucose from the blood. Because they excrete glucose in the urine, they also release more water than normal. As a result people with diabetes mellitus excrete larger volumes of urine and feel constantly thirsty. In the meantime, cells are starving for glucose and use more fat for cellular respiration. The fat metabolites can lower blood pH to dangerous, life threatening levels. There are two types of diabetes mellitus with different causes, but each is marked by high blood glucose levels:

o Type I diabetes: is an autoimmune disorder, because the immune system destroys the beta cells of the pancreas with this the body loses its ability to produce insulin. This type of diabetes usually occurs in childhood.

o Type II diabetes: may be somewhat inherited but excess body weight and lack of exercise can also result in Type II diabetes. In this case, insulin is either deficient or the target cells have a reduced responsiveness to insulin because of changes in insulin receptors. This type appears later in life.

This is the end of Unit 4