Tuesday, November 27, 2007

The Cell Membrane

The Cell Membrane

The cell membrane is the barrier that separates the inside of the cell from the outside. The cell membrane is made up of phospholipids,proteins, and other macromolecules. The phosopholipids make up a bilayer. It contains hydrophilic and hydrophobic molecules. The proteins in the cell membrane are located within the phospholipid bilayer. These proteins determine certain funtctions of the cell membrane. There are three types of proteins.

Peripheral Integral Transmembrane
-loosely bound -penetrate lipid bilayer -transport proteins

-on the surface of the cell -across entire membrane -channels,permeases

-identity markers

Nonpolar amino acids - hyrophobic

polar amino acids - hydrophilic

Antigens are markers of a cell and can tell cells apart. It rejects foreign cells, and lets certain cells enter.

Diffusion - is the movement from high concentration to low ( an easy way of thining of it would be H comes before L in the alphabet). Fats and other lipids can get through the phospholipid bilayer directly by diffusion, other larger molecules such as starch can not get into the cell directly.

Facilitated Diffusion (facilitated=with help, open channel=fast transport). Diffusion of hydrophilic molecules. From High to Low.

Active Transport- diffsuion against concentration. Low to High. ATP is needed.

Osmosis = diffusion of water. High to Low. The survival rate of a cell counts on a balance of water loss and uptake. Determined by amount of solute, and water.

Hypertonic=more solute, and less water.EX-shellfish, plant cells

Hypotonic=less solute, and more water. EX- paramecium

Isotonic=equal solute, and equal water. EX-blood cells in blood

Wednesday, November 21, 2007


Explanation: Scientific research often leads to technological advances that can have positive and/or negative impacts upon society as a whole.
Clarification: You would post here examples of how technological innovations have helped advance science whil ethose technolical accomplishments may have also had either beneficial or deleterious impacts on human society.


Explanation: Living organisms rarely exist alone in nature.
Clarification: You would post here examples of how organisms must interact together to live successfully.


Explanation: Everything from cells to organisms to ecosystems is in a state of dynamic balance that must be controlled by positive or negative feedback mechanisms.
Clarification: You would post here examples of how a dynamic equilibrium is maintained at different levels of life, from homesostatic control of cellular and body conditions to maintenance of population levels in ecosystems.


Explanation: The structural levels from molecules to organisms ensure successful functioning in all living organisms and living systems.
Clarification: You would post here examples of structure-function relationships in living organisms. How specific molecules, organelles, cells, tissues, organs, and body structures are structured to support the functions that they perform. (Don't forget plants!)


Explanation: All species tend to maintain themselves from generation to generation using the same genetic code. However, there are genetic mechanisms that lead to change over time, or evolution.
Clarification: You would post here examples of how organisms reproduce while maintaining the same genetic information from generation to generation AND also examples of how organisms reproduce while accumulating changes to their genetic information from generation to generation.


Description: Energy is the capacity to do work. All living organisms are active (living) because of their abilities to link energy reactions to the biochemical reactions that take place within their cells.
Clarification: You would post here examples of how organisms are able to capture energy and utilize it to do the work that supports life.


Description: Biological change of organisms that occurs over time. Which is driven by the process of natural selection. Evolution accounts for the diversity of life on Earth.
Clarification: You would post here examples of evolutionary change in populations of organisms that we have been able to observe or have evidence of.


Description: Science is a way of knowing. It can involve a discovery process using inductive reasoning, or it can be a process of hypothesis testing.
Clarification: You would post here examples of how the scientific process has been used to develop our knowledge about how the biological world works.

Monday, November 19, 2007

A Tour of the Cell

Hey Period 8+9, this was what Monday's lecture was about:

The are different types of cells. There are Prokaryote Cells and Eukaryote Cells which are 2 different domains. The Prokaryotic Bacteria Domain, the cells don't have Membrane Bound organelles and are not specialized. They old consist of Ribosomes and a Cell Membrane/Wall. With Eukarote Domain, there are 2 main cells, the Animal Cells (Of the Animal Kingdom) and the Plant cells (Of the Plant Kingdom). Both these cells have their differences.

Only Plants have a large Central Vacuole, Chloroplasts (for photosynthesis), Centrioles and a Cell Wall.

Now what makes Prokaryotes and Eukaryotes different you ask? Well the answer is organelles. Eukaryotic cells (yes, both plant and animal) have specialized structures withspecialized functions for example cillia or flagella for locomotion. Another reason is that they have "Containers." The cell has compartments in which different local environments are created for example separate pH's. They also have distinct and incompatible functions for example the lysosomes which has its own digestive enzymes. If the lysosome didnt have its own compartment the whole cell would be digested. Also membranes are the sites of Chemical Reactions. There are a unique combination of lipids and proteins and embedded enzymes and reaction centers for example the Choroplasts and Mitochondria where reactions occur.

Now how do cells "make their living"? What jobs do they have to do?

Well their first job is to build proteins. This is because PROTEINS CONTROL EVERYTHING! All the cell functions are controlled by proteins. Their second job is to make energy. This is in order to continue on in daily life and for growth to occur. The third and final job is for the creation of more cells. This gives the opportunity of growth, reproduction and most importantly repair.
Now it is important to study the production of proteins because they are important macromolecules. DNA (Deoxyribnucleic Acid) is the code for creating proteins. Proteins have the job of acting as an enzyme (most enzymes are proteins). Life cannot be run without the influence of proteins. Now in building proteins such organelles as the nucleus, ribosomes, the endoplasmic reticulu, the golgi apparatus and vesicles are involved. Now in the nulcues there obviously is DNA. Proteins go down an assembly line starting with the Nucleus (DNA),onward to the Ribosomes, then to the Endoplasmic Reticulum, the to the Golgi Apparatus and finally to the vesicles.

Now in creating proteins DNA cannot leave the cell, therfore it must make copies of itself inorder to leave and create the proteins that will later have specific functions. There is also no diffusion in the membranes because they are made of lipids. So the RNA travels through out the ER where the ribosomes dwell and read the code to create a polypeptide. Then they travel farther in the ER until they get to the end and bud off in a vesicle to the Golgi Apparatus. There the polypeptide finally folds istelf and travels farther until it is a completed and finsished protein on its way to do its job. An example of this would be the creation of Insulin and the Beta Cells of the Pancreas. If this producton stopped within 3 days a human would be dead.

The next important objective is to create energy in a cell. Once again making energy allows for daily life to continue and for growth to keep occuring. Now cells need lots of energy for power. In order to make energy, cells need to take in food and digest it, take in oxygen and therefore create ATP! (Adenosine triphosphate). Lastly the removal of waste is also needed. On to the Lysosomes!

Now the lysosomes are known as the "little stomach" of the cell (which is a misnomer because in humans digestion takes place mostly in the intestines). The lysosomes digest the macromolecules. The lysosomes are also the "clean up crew" of the cell because they break down the old and damaged organelles. Where Old Organelles go to die! Lysosomes are composed of vesicles with specialized digestive enzymes. Lysosomal Enzymes work best at a pH of about 4.8-5.0. The lysosome creates its own pH levels. It is more acidic than the rest of the cell. This is because the proetins in the lysosome membrane pump up H+ ions from the cytosol into the lysosome. The Cytoplasm happens to be all the contents of the cell while the cytosol is the "Gunk" between the organelles. Now, because the enzymes are sensitve to certain pH's they have to custom make their own and why is that? Well, enzymes are proteins aren't they? So what do we know about them? Yep, pH affects the protein structure and they can denature themselves. Now this is an adaption because if the digestive enzymes were to leak into the cytosol the cell would literally digest itself! But sometimes it is necessary for cells to die and be re-absorbed. Lysosomes can be used to kill cells when it is necessary. Sometimes proper development in an organism requires this process. Apoptosis, an "auto-destruct" process the lysosomes break open and kill the cell. For example the tail of a tadpole gets reabosorbed when it turns into a frog in order to grow legs. Or the loss of webbing between a fetuses fingers during its development (although there are some diseases such as Syndactyly in which the fingers are not dissolved and the fingers stay fused)
and the self-destruction of a cancerous cell in an organisms body (Obviously this doesnt always happen).

But as always, things do go wrong. The diseases of Lysosomes are most often fatal. This occurs when the digestive enzymes in the lysosomes fail to function correctly. What happens is that biomolecules are absorbed but not digested as they cant be. Therefore the lysosomes fill up with lots of undigested materials in which the cell grows larger and larger until the cell is disrupted along with the ogran functions. The are more than 40 known types of lysosomal storage diseases. For example Tay-Sachs disease in which the brain cells build up a number of undigested fats.

Well thats it for Monday's lecture. Tuesday's Sherpa will be Mark, Have Fun and Enjoy! :-) Night


Sunday, November 18, 2007

Nucleic Acids

A Nucleic acids function is to store & transmit hereditary information. Examples of Nucleic Acids are RNA (ribonucleic acid) and DNA (deoxyribonucleic acid). Nucleic Acids are made out of monomers. There are long chains of monomers that you can add repeating units to. These Monomers are Nucleotides. A nucleotide consists of three parts. A nitrogen base (C-N ring) a pentose sugar (ribose in RND deoxyribose in DNA). The deoxy in deoxyribose means the sugar is missing a oxygen. The third part is a phosphate group.
RNA is a single nucleotide chain in a single helix. DNA is a double nucleotide chain consisting of Nitrogen bases bond in pairs across the chains. DNA is spiraled in a double helix. This was first proposed in 1953 by James Watson and Francis Crick.
Types of Nucleotides
THere are two types of nucleotides. THis is because of different nitrogen bases. There are purines which have bigger bases and pyrimidines which have smaller bases. Purines have a double ring nitrogen base. They consist of adenin (A) and Guanine (G).
Pyrimidines have a single ring Nitrogen Base. They conisist of cytosine(C), thymine (T) and uracil (U).

Nucleic Polymers
Nucleic polymers are the backbone of DNA. They are made of sugars and PO4. THE polymers conisist of phosphodiester bonds. These bonds are new bases added to teh sugar of a previous base. The polymer grows in one direction. Nitrogen bases hang out the sugar-phosphate backbone.

Pairing of Nucleotides
Nucleotides bond between DNA strands. These bonds are Hydrogen bonds. They are purines H bonded to pyrimidines. A::T (2 hydrogen bonds) and G::C (3 hydrogen bonds). These matchign bases are important for replication. THis way a T is always bonded to a A and vis versa. The same is with G and C. SInce the bonds are to the same purine or pyramidine there is no confusion when replicating. This way exact copies are made.

Information Polymers
They are a series of bases encoding information. An example would be words ina book. The Stored information is passed from the parent to the child. Because of thisDNA needs to be copied accurately. The information copied is your genes. This is important because if you the parent survived then your offspring have a greater chance of survivng with your genes.

DNA Molecule
The Dna Molecule is a double helix. The hydrogen bonds between the 2 bases join the strands. A::T C::G These bonds are important becaus ethey are easy to break and put back together for replication. Copying DNA is caklled replication. The 2 strands of DNA helixs are complementary. With one strand you can build the other and with one strand you can rebuild the whole molecule. A cell copies DNA during cell reproduction (mitosis) and gamete production (meiosis).

Well thats nucleic acids. The next shurpa will be jesse. Enjoy!

Thursday, November 15, 2007


Proteins are multipurpose molecules. They are the most structurally and functionally diverse group of biomolecules. Proteins are also involved in almost everything. Proteins can act as enzymes such as pepsin and polymerase. Pepsin is the enzyme found in our stomachs which is used in digestion. Proteins such as keratin and collagen form structure, such as a bird's beak or hair. Proteins also take part in carrying and transporting information, and give defense with antibodies. Proteins are also used in contraction, signaling, and storage.


Proteins are made of twenty different amino acids. Amino acids are monomers. Polypeptides are polymers which are made from chain of amino acids bonded together. Proteins can be one or more polypeptide chains folded and bonded together.

Rubisco is a very important polypeptide because it allows plants to go through photosynthesis.

Amino acids have a central carbon with an amino group and a carboxyl group (acid) as well as a sidechain known as an group which confers unique chemical properties of the amino acid.

Nonpolar amino acids are hydrophobic. These are nonpolar and hydrophobic because they are made up of a lot of carbons which are nonpolar and hydrophobic, and so they want to push away from water. Polar amino acids are polar or charged and hydrophilic, meaning that they mix well with water.

The function of proteins depends on the structure. Proteins are twisted, folded, and coiled into a unique shape. Hemoglobin is a protein with both alpha and beta proteins which carry oxygen in the blood.

Primary Structure > Order of Amino Acids

Seconday Structure > "Local Folding"- folding long short sections of polypeptides

Has alpha helix and beta pleated sheet. There are hydrogen bonds against adjacent proteins.

Tertiary Structure > "Whole Molecule Folding" - determined by interactions between R groups. Tertiary structure has hydrophobic interactions and is anchored by disulfide bridges.

Quarternary Structure > more than one polypeptide chain joined together

Denaturing a Protein

This is unfolding a protein by disrupting tertiary structure. Disrupting the pH, salt, or temperature of a protein disruptsH bonds, ionic bonds and disulfide bridges, which destroys functionality. Some proteins can return to their functional shape after denaturation, but many can not.

Sunday, November 11, 2007

Heyy, period 8 and 9!
Today we learned all about Carbohydrates. The name "carbohydrate" means a "hydrate of carbon.” Carbohydrates always have a 1:2:1 ratio of carbon, hydrogen, and oxygen.
The general formula of carbohydrate Cx(H2O)y - x and y may or may not be equal and range in value from 3 to 12 or more. For example glucose is: C6(H2O)6 or is more commonly written, C6H12O6.The chemistry of carbohydrates most closely resembles that of alcohol, aldehyde, and ketone functional groups. The chemistry of carbohydrates is complicated by the fact that there is a functional group (alcohol) on almost every carbon. In addition, the carbohydrate may exist in either a straight chain or a ring structure.
A major part of the carbon cycle occurs as carbon dioxide is converted to carbohydrates through photosynthesis. Carbohydrates are utilized by animals and humans in metabolism to produce energy and other compounds.

Carbohydrate Functions:
Carbohydrates are initially synthesized in plants from a complex series of reactions involving photosynthesis.
-Store energy in the form of starch (photosynthesis in plants) or glycogen (in animals and humans).
-Provide energy through metabolism pathways and cycles.
-Supply carbon for synthesis of other compounds.
-Form structural components in cells and tissues.


is a complex series of reactions carried out by algae, phytoplankton, and the leaves in plants, which utilize the energy from the sun. The simplified version of this chemical reaction is to utilize carbon dioxide molecules from the air and water molecules and the energy from the sun to produce a simple sugar such as glucose and oxygen molecules as a by product. The simple sugars are then converted into other molecules such as starch, fats, proteins, enzymes, and DNA/RNA i.e. all of the other molecules in living plants. All of the "matter/stuff" of a plant ultimately is produced as a result of this photosynthesis reaction.

Metabolism occurs in animals and humans after the ingestion of organic plant or animal foods. In the cells a series of complex reactions occurs with oxygen to convert for example glucose sugar into the products of carbon dioxide and water and ENERGY. This reaction is also carried out by bacteria in the decomposition/decay of waste materials on land and in the water.
Combustion occurs when any organic material is reacted in the presence of oxygen to give off the products of carbon dioxide and water and ENERGY. The organic material can be any fossil fuel such as natural gas oil, or coal. Other organic materials that combust are wood, paper, plastics, and cloth.

The whole purpose of both processes is to convert chemical energy into other forms of energy such as heat.

The monomers of carbohydrates are called monosaccharides and are also called simple sugars. They are usually ring-like and are composed of five or six carbons. They are either a polyhydroxy aldehyde or a polyhydroxy ketone, which means they have more than one hydroxide group (-OH) and one carbonyl group (C=O). Some popular monosaccharides are glucose, fructose, and galactose.However, some very important carbohydrates are composed of thousands of monomers and are called polysaccharides. Here are the main important polysaccharides:- starch: Plants store their energy as starch using photosynthesis. We eat plants, breaking down the starch into its monomers and putting it to good use.- cellulose: The cell walls around plants are composed of cellulose. Cellulose is a very important structural component of plants and it's what makes them snap when you rip them apart. Err, I mean - they provide support for the plant.- glycogen: Animals store energy as glycogen. It's stored in the liver.

A carbonyl group is a functional group composed of a carbon atom double bonded to an oxygen atom : C=O.

An aldehyde is an organic compound containing a terminal carbonyl group. This functional group which consists of a carbon atom which is bonded to a hydrogen atom and double bonded to an oxygen atom (chemical formula O=CH-), is called the aldehyde group.

A ketone (pronounced as key tone) is either the functionalgroup characterized by a carbonyl group (O=C) linked to two other crbon atoms or a chemical compound that contains this functional group. A ketone can be generally represented by the formula:

The major component in the rigid cell walls in plants is cellulose. Cellulose is a linear polysaccharide polymer with many glucose monosaccharide units. The acetal linkage is beta which makes it different from starch. This peculiar difference in acetal linkages results in a major difference in digestibility in humans. Humans are unable to digest cellulose because the appropriate enzymes to breakdown the beta acetal linkages are lacking. Indigestible cellulose is the fiber which aids in the smooth working of the intestinal tract.
Animals such as cows, horses, sheep, goats, and termites have symbiotic bacteria in the intestinal tract. These symbiotic bacteria possess the necessary enzymes to digest cellulose in the GI tract. They have the required enzymes for the breakdown or hydrolysis of the cellulose; the animals do not, not even termites, have the correct enzymes. No vertebrate can digest cellulose directly.

Compare Cellulose and Starch Structures:
Cellulose: Beta glucose is the monomer unit in cellulose. As a result of the bond angles in the beta acetal linkage, cellulose is mostly a linear chain.
Starch: Alpha glucose is the monomer unit in starch. As a result of the bond angles in the alpha acetal linkage, starch-amylose actually forms a spiral much like a coiled spring.

Tommorows sherpa is.. Kim

Later Class!

Saturday, November 10, 2007

Building Blocks of Life

Carbohydrates- function for short-term energy storage
Lipids-function for long-term energy storage, insulate, and are used in the construction of cell membranes.
Proteins- function to build body structures and regulate metabolism
Nucleic Acids – compose all of your genetic material, including DNA and RNA.

All life is built on carbon. There are four major groups of carbon compounds that are important carbohydrates, lipids, proteins, and nucleic acids. A carbon atom is made up of four covalent bonds, and is a stable. Hydrocarbons are stable, and non-polar. As well as hydrophobic which is hydro = water, and phobic = fearful. This means the molecules are not attracted, and are not as close making it a gas. The writing on this picture is really annoying, but I couldn’t find one without it.

Isomers- molecules with the same formula but are different in shape. Each of these diagrams has four carbons, but different chemical properties and biological functions. The structure does have an affect by creating different functions. For example medicine in L-version is active, and D-version is not. So structure does have a significant role.

-Organic compounds with OH are alcohols.
-C=O at end of molecule is an aldehyde, and C=O in the middle is a ketone.
-COOH is an acid.
-N attached to 2 H is amines it acts as the base.
-SH is thios, and it stabilizes the structure of proteins.
-P bonded to 4 O is highly reactive and transfers energy between ATP and GTP.

Monomers link together to create polymers. In synthesis water is taken out, and in digestion water is used to break down polymers.


Wednesday, November 7, 2007

The Chemistry of Life

Chemistry is the foundation of biology. About twenty-five chemicals are necessary for life, and only four create about 96 % of living matter. Those four elements are carbon, oxygen, hydrogen, and nitrogen. We cant live without COHN.

Bonding properties of atoms depend on the number of electrons in the valence shell. Oxygen is the most electronegative element on the periodic table, it is the most reactive. Covalent bonds are strong bonds because the electrons are shared between the atoms. They are very stable. There are polar and nonpolar covalent bonds. In polar covalent bonds, electrons are shared unequally, such as in water.

Hydrogen bonds, ionic bonds, hydrophobic and hydrophilic interactions, and van der Waals forces are examples of weak bonds. Hydrogen bonding can happen anywhere an -OH exists in a larger molecule. It occurs when polar water creates molecular interactions.

All life occurs in water, whether under the sea or inside the cell. Without water life could not exist. Water is very unique. It is cohesive, water molecules are attracted to each other, and adhesive, water molecules stick to other things. These are the reasons that water can reach the top of trees. Its a good solvent, most things can dissolve in water. Hydrophilic substances, which are polar, dissolve in water and hydrophobic substances, which are nonpolar, do not. It has lower density as a solid, which is very rare, actually nothing else has that property. The fact that water does this is not only an amazing phenomenon, but it enables life on Earth to continue. If ice sank, all bodies of water would completely freeze over time and there would not be enough time in the summer for it to thaw, therefore life could not exist. It has a very high specific heat, its very resistant to temperature change, and it takes a lot of energy to heat and cool water. Water moderates temperatures on Earth. And finally it has a high heat of vaporization. When water evaporates off of your skin it cools you off, which is why we sweat and why animals pant when they’re hot.

Water ionizes, H+ splits off leaving -OH, if they’re equal then the solution is neutral. If H+ is greater, the solution in acidic and if -OH is greater, the solution is basic. The pH scale shows how acidic or basic a solution is, 0 is most acidic, 7 is neutral, and 14 is the most basic. There are buffers to help regulate pH levels. The pH of a molecule affects its shape which affects its function. These buffers donate or absorb H+ when it falls or rises to maintain a level of about 7.

Tomorrows sherpa will be Kerrie.

Thursday, November 1, 2007

Animal Behavior (cont...)

today we learned more about animal behaviors. Migration is shown not only in birds but in insects as well. We also learned an interesting fact about migration in that birds navigate their migrations by means of the sun, stars, and magnetic waves. Imprinting shows that learning that occurs during a critical period forms social attachments. Konrad Lorenz studied this with geese. His work has a movie based on it called Fly Away Home here is a clip.


The critical period is the period for the greatest potential learning to take place. Learned behaviors are an association of a stimulus in the environment to a behavior. there are two types of conditioning operant and classical to enforce learned behaviors. Operant condition uses trial and error learning, and association of a behavior with either a punishment or reward. Classical conditioning however assosiates a neutral stimulus with a signifigant stimulus. This type of conditioning is shown in Pavlovs Dogs where pavlov tested salivation in dogs to be associated with a bell by ringing a bell prior to presenting them with food. Habituation is the eventual loss of response to a stimulus once the stimulus happens enough times that the result can be anticipated.
Language is used in all different animals in all different ways in humans we speak, whereas in honey bees they dance to communicate in all different patterns. Some animals communicate via song such as birds and insect some are learned, and some innate. Agnostic behaviors appear violent or hostile but really no harm is generally done, but it is more a test of manhood. Altruistic behavior is when an individual reduces their own fitness for the benefit of the group. Pheromes are chemical signals such as smell used to warn of danger or trigger sex hormones.