Protein's Cont'd

Hey guys, well I know the structure of proteins is kind of difficult to learn, but I will try to do the best I can to help you guys understand this.

The primary structure is basically the order of amino acids in chains. Even a slight change in the amino acid can affect a protein's structure and then FUNCTION. One protein can determine the difference between sickle cell anemia and the normal red blood cells.

The secondary structure is local folding. This folds along short sections of polypeptide. They are hydrogen bonds between each R groups.

The dotted lines between the diagram are hydrogen bonds.

The tertiary structure is also known as whole molecule folding. This is determined by interactions between R groups. Hydrophobic bonds want to stay away from water so they cluster together so that the hydrophobic bonds are next to each other, clustered together. This is important in the structure of the the cell membrane. The hydrophobic tails basically face each other in a cell membrane, away from the water and cluster together, while the heads are hydrophylic and face the water. This forms a phospholipid bilayer.

The quaternary structure is when more than one polypeptide chain is joined together. However, it is important to note that not all proteins have subunits and more than one polypeptide. This polypeptide take different shapes and this then determines their functions. Its basically HYDROPHOBIC INTERACTIONS.

The unfolding of a protein has a fancy name for it called denaturing. When a protein unfolds, the tertiary structure, or 3' structure is disrupted. The pH, otherwise the acidity, is one of the factors. Another is salty environment, as well as temperature. Size doesn't matter, shape matters. Denaturing of proteins disrupts the H bonds, ionic bonds, and disulfide bridges. Ms. Foglia had boiled milk and added vinegar. Vinegar is an acid which disrupting the shape of the proteins. And believe it or not, it is the process of making cheese!!!

Proteins

Proteins

The most important job of a cell is to make proteins. Proteins are made in the ribosomes of a cell. Protiens are used for almost anything. They have many different structures, with each different structure having a different function. They are also known as multipurpose molecules.






Some examples of proteins are keratin and collagen which makes up hair nails and skin.

Proteins are made of two structures monomers and polymers. Monomers are amino acids, and there are 20 different ones. Polymers are polypeptides. Proteins can be one or more polypeptide chains that are folded and bonded together. They are large and complex molecules.

The structure of amino acids have a central carbon, and amino acid groups. The carboxyl group are acids. The R group is a side chain. This is a variable group confers unique chemical properties of the amino acids.

Nonpolar amino acids are nonpolar and hydrophobic. Nonpolar meaning there are carbons in it. Hydrophobic means that it does not like water so it tends to try and push the water away. On the other hand amino acids can be polar and hydrophilic. By polar it means that it has a nitrogen in it. Hydrophilic means that it likes water and wants to be in or as near as possible to water as it can. They are polar and hydrophilic because they fold in order to make a protein.

Sulfur containing amino acids allow a link between sulfers and amino acids to be created called disulfide bridges. It smells like rotten eggs or permed hair.

Peptide bonda are building proteins that link the NH2 of one amino acid to COOH of another. Part of the buildin proteins are polypeptide chains that involve N-terminus= NH2 end and the C- terminus which ends in a COOH.


One of the four levels of structure is primary (1 degree) stucture pattern. The DNA of the gene decides the amino acid sequence and even a slight change in the sequence can make it a change in the protein's stucture and funtion. The perfect example of this is Sickle Cell Anemia, where the structure of the cell of hemoglobin goes from a 'doughnut' shape to one that looks like a 'sickle' or 'cresant moon'.

Carbohydrates !

Ahhh yes Per. 1&2
It is time to unveil my most devious plan everr, preparations A through G were complete failures... but now it is time to initiate.... Preparation H.







On Friday we had the wonderful opportunity of learning all about my good friend, the standard Carbohydrate. Now mah boy "carbohydrate" means a "hydrate of carbon.” Back in college him hydrogen and oxygen were near inseparable with a 1:2:1 ratio..

"I’d say they were pretty tight"

Now 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.

Photosynthesis:
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:
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 functional group characterized by a carbonyl group (O=C) linked to two other carbon atoms or a chemical compound that contains this functional group. A ketone can be generally represented by the formula:
R1(CO)R2.


Cellulose:
The major component in the rigid cell walls in plants is cellulose
(Fat B@$tard also seems to be composed of a similar substance)

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 & 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.

I leave you with the mugshots of two alleged carb jackers

(Known only as Moonshine the Hippie & Lil Red) previously taken into custody for posession of carbs with intent to distribute.

Although uneasy on the eys I urge to look beyond the mundane and horror to identify these criminals for whoever does... would most worthy of tomorrows sherpa report!

Chemistry of Carbon

Today we learned about Carbon, which just reinforces the idea presented in Paiges post about how terrible Chemistry really is.

- All life is built on carbon. Cells are made up of 72% water, 25% carbon, and 3% Salt.



That is us, mostly made of water.
- And thats the carbon we're made of!

• First off theres the BIG 4: Carbohydrates, Lipids, Proteins, and Nucleic Acids
  

Carbon atoms are very versatile building blocks because they equally share electrons with hydrogen. They have 4 stable covalent bonds.

Hydrocarbons are combinations of carbon and hydrogen. They are non-polar, hydrophobic (fear of water), stable, and are gases at room temperatures. They are gases because there is no close attraction between the molecules so therefore they stay far apart.

• Isomers: are molecules with the same molecular formula but different structures or shapes.

*Form affects function!*
Small structural differences can create important functional significance. For example the amino acid alanine has an L-version and a D-version. They are mirror images of each other and are called stereoisomers. In medicine, only the L-version is active and this is important to know because of tragic effects such as in the case of Thalidomide. It was intended to reduce morning sickness but instead caused severe birth defects in limb development.

Diversity of Molecules :
Substitute other atoms or groups around the carbon. Ethane can become Ethanol (alcohol) when an H is replaced by a hydroxyl group (-OH). This change makes ethane non-polar, and ethanol polar, and ethane a gas while ethanol is a liquid. Below is an example of what ethanol can do to you and your belly.

• Functional Groups are parts of organic molecules that are involved in chemical reactions. These groups are hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate. These groups are all the difference in the case of female and males. They have the same carbon skeleton but different functional groups are attached and one becomes estrogen while the other is testosterone.

Macromolecules- smaller organic molecules join together to form larger molecules. The big 4 are the major classes of macromolecules.
-Polymers are long molecules built by linking repeating building blocks in a chain.
-Monomers are small building blocks.

Building Polymers

• Dehydration (Condensation) Synthesis: a water molecule is removed
• - one monomer donates OH- and another donates H+, these two combine to form H2O
  

Breaking down Polymers

• Digestion (Hydrolysis) - use H2O to break down polymers. The water is split into H+ and OH-
• Requires Enzymes
  

Carbon are the building blocks of life, so I guess I dont hate them after all<3 Tom and the lunchbox are the next sherpas.

the Good, the Bad, and the BIOCHEMISTRY!
We all took chemistry over the past two years and it was terrible and its back.

We spent the entire period studying the properties of water which are super important because all life occurs in water, inside and outside of the cell.

COHESION AND ADHESION
COHESION: H bonding between water molecules

-just like Tom and his girl pictured above, water likes to stick together. That’s why we can suck it up through a straw.

- water has an extremely high surface tension, so that’s why not a lot of organisms can walk on it, except for Jesus and insects like the water strider of course. The strider’s impact on the water is less than H2O’s surface tension so they don’t sink.

ADHESION: H bonding with H2O and other substances
Ex: capillary action, meniscus, water on paper towel

SO LETS APPLY THESE TO REAL LIFE: trees.
Trees are built on cohesion and adhesion. The stomates on the tree’s leaves open to allow water molecules to evaporate. As one molecule leaves the leaf, it pulls another water molecule along, and it continues.

-polarity makes H2O a stellar solvent because water molecules surround positive and negative ions.
-hydrophilic and polar: DISSOLVE IN WATER
-hydrophobic and non-polar: SEPERATES FROM WATER (no attraction)

ICE ICE BABYYY.

All substances are denser as a solid right? NOPE, not water. Ice floats!
-At 4 degrees Celsius, water is at its densest.

So why is floating ice so important in real living things?
When lakes freeze over, the surface ice insulates the water below it making it possible for fish and other organisms to live through winter. Floating Ice also attributes to the cycling of nutrients.

FOGLIA ICE TIP OF THE DAY:
Make sure you always mix your drinks at the bar,

this way you never have to drink a weak mix, and you save cash!

SPECIFIC HEAT: how much energy is required to heat a substance
-water has a very high specific heat. It takes more to heat up and cool down water than anything else.
-specific heat’s important because H2O moderates all temperatures on earth.
-areas surrounded by land: extremes (super hot in summer, freezing in winter)
-areas near water: moderate temperatures year round

IONIZATION OF WATER AND pH
1. if H+ = -OH then water is neutral
2. if H+ > -OH then water is acidic
3. if H+ < -OH then water is basic

These three points make up the base of the pH scale

pH Scale- how acidic or basic a solution is measured on a 1 through 14 scale

1 being super acidic, 14 being super basic, 7 is neutral

Buffers- chemicals that allow control of pH measure

Lastly, here are a couple of lameo macaques

On Monday, we learned about the chemistry of life. Although this is an AP Biology class, we study chemistry because it is the foundation of Biology.

As many of us have learned across the hall in the Chemistry rooms, everything is made of matter. Matter is made of atoms that are made up of electrons, protons and neutrons.
In this biology course, we only need to worry about ten elements on the periodic table: hydrogen, magnesium, potasium, sodium, calcium, carbon, nitrogen, oxygen, phosphorus and sulfate. Hydrogen, carbon, nitrogen, and oxygen are the key elements that our human body is made up of. Phosphorus is in DNA and ATP.

We also went on to learn about the bonding properties and the effect of electrons. Electrons determine the chemical behavior of an atom, depending on the the number of electrons in an atom's outermost shell. The valence shell is nonactive.
Atoms with many electrons in its valence shell have high electronegativity and tend to want to "steal" electrons from other atoms while atoms with fewer electrons have low electronegativity in their valence shell and tend to want to "donate" to other atoms. These atoms with fewer electrons donate bececause they cannot hold that many electrons themselves. These tendencies drive chemical reactions and create bonds. A chief principle that we learned Monday was that when we think of weak bonds, hydrogen bonds should be the very first thing we think of while when strong bonds are mentioned, covalent bonds should be thought of immediately. Covalent bonds are strong because two atoms share a pair of electons and both atoms hold onto the electrons, making them very stable. This forms molecules. The more pairs of electrons shared, the stronger the bond. More is better!


PAGEMASTER will be our next sherpaaaaa!

And That's The Way The Cookie Crumbles!

IMPORTANT NOTE: The following post does not reflect the views of it's author. It is simply reflective of what we learned in class, and the information provided is not supported by it's provider.

Welcome folks, to another exciting round of Biology Jeapordy with your host....

The wonderfully talented (and good looking!) Alex Trebek!

So basically, today in class we covered Critical Periods, Various Animal Behaviors (operant and classical conditioning), Social Behaviors, and BioMagnification. So our categories will be.....

1) Critical Periods 2) Various Animal Behaviors 3) Social Behaviors and.....

4) BioMagnification-----surprise!

CRITICAL PERIODS

So, what are these things anyway?

Critical periods are just what they sound like: critical periods of time in which an organism is expected to learn something, which can usually only be learned within the critical period.

For example, language in humans is learned during a critical period. Children who don't learn to speak within this critical period aren't usually able to grasp the complexity of our language.

Critical periods are interesting, aren't they? Why can an organism learn to do something at one period in their life, but not after that? Like they say, you can't teach an old trick a new dog. Or something like that.

Various Animal Behaviors

To easily understand how and why animals act the way they do, it's best to split the topic up into two sections:

1) Innate Behaviors (or instinctive behaviors)
2) Learned Behaviors

While I would love to take the time to explain both to you, I'm not going to! We learned about learned behaviors today, and innate behavior yesterday. So if you need help on innate, consult Sean's post.

--Learned Behaviors--

Learned behaviors are behaviors that organisms learn throughout their lives. For example, most species of birds learn their song from their parents and the birds around them.


When studying learned behaviors, it is imperative that you know the following terms.

Associative Learning-learning to associate one feature of the environment with another.

Operant Conditioning-trial and error learning; associating behavior with reward or punishment.

Classical Conditioning-Associating a "neutral stimulus" with a "significant stimulus"

Operant Conditioning is easy enough to remember. Just think about Skinner's box, and the mouse's repeated action of pressing the lever to get food.

After pushing the lever for the first time (and every time after that), the mouse gets a piece of food. The mouse then learns to associate the act of pushing the lever with a reward.

The ingenious man who came up with this experiment was B.F. Skinner.

Classical Conditioning should be no problem for us AP students either! Just think about Ivan Pavlov and his experiments with the dog and the bell.

Before each time Pavlov fed the dog, he rang a bell. Then, by just ringing a bell, he could get the dog to salivate, expecting food. This experiment demonstrates classical conditioning because the dog is connecting a reflex behavior (salivating at the sight of food) to associated stimulus (the ringing bell).

Let's give it up for Ivan Pavlov!

(Ivan Pavlov)^^^

Next we should talk about Social Behaviors.

Social Behaviors

To understand the social behaviors of animals, we should know:

Habituation-loss of response to stimulus (think of "The Boy Who Cried Wolf", in which animals learn not to repond to repeated occurrences of stimulus).

--Language--
Many animals use some form of language to communicate. Communication between individuals is necessary for mating, protection, and finding food.

Examples of language in animals are the songs birds use to find mates, and the honey bee's waggle dance.

--Agonistic Behaviors--
Agonistic behaviors are behaviors that animals perform to outcompete others. These behaviors are generally not threatening, but are instead ritualistic behaviors performed to impress mates, and to establish a social rank.

--Altruistic Behaviors--
Altruistic behaviors are behaviors which are performed which reduces individual fitness but increases fitness of recipient.

A perfect example of this is found in the Belding ground squirrel. These crazy squirrels make noise when predators are near, endangering themselves but incresing the chance of survival of their families and offspring.

The next important thing to understand is the concept of pheromones.

--Pheromones--
Pheromones are chemical substances that stimulate a response from other individuals. The most common pheromone types are alarm pheromones and sex pheromones.

These are vital to the animals success, protection, and reproduction.



So the next time that sweaty person stting next to you smells of bad B.O., just think....

...is this disgusting, or seductive?

--Cooperation--

Some animals cooperate with eachother to help get food, protection, or resources. This can best be associated with a mutualistic symbiotic relationship, because both individuals benefit.

Examples of cooperation include:

1) African dogs who hunt together in packs to help bring dow prey more quickly.

2) White pelican and dolphins who "herd" fish to make it easier for the whole group to eat.

--Colonial Mammals--

Colonial mammals are those who have a queen, breeding and non-breeding workers, and a whole social heirarchy.

Some examples of these include:

1) Bees

2) Ants

3) Termites

4) Mole Rats

And since mole rats are all your favorite animals to look at.....

And now....... (finally)

BioMagnification

BioMagnification is a pretty easy concept to grasp. Basically, it's just the idea that if a substance is introduced to an organism on the bottom of the food chain, then it will increase in concentration as it travels up the food chain. This is due to the fact that a secondary consumers eat several primary consumers, and get more of a concentration of the substance. In turn, tertiary consumers eat more than one of the secondary consumers, and obtain an even greater concentration of the substance.

So the overall lesson of this post? There is a reason why animals act the way they do, and it's important to know the reason.

HOWS MY POSTING??

CALL 1-800-GUD-POST

All those in favor of having Mrs. Foglia dress up as a witch everyday post "I."

All those in favor of having Mrs. Foglia dress up as a pirate everyday post "Aye."

Let me end this post with a quote: "Mo money, mo money, MO MONEY!"