BIO CHP 3 - Enzymes and Energy

III. Enzymes and Energy

A. Introduction
-- thermodynamics - the study of energy transformations
-- enzymes - biological catalysts that facilitate reactions by lowering the necessary activation energy - energy needed to be absorbed by the reactants to break the bonds already in place

B. Structure and Function of Enzymes
-- Most enzymes are protein, though some RNA molecules have been found to have enzymatic activity.
-- The almost always large protein is folded so that the active site, where the substrate, or reactant, binds, is accessible.
-- "lock-and-key" theory/model - demonstrates how an enzyme interacts with its substrate: shape of active site matches the shape of the sunstrate exactly.
-- enzymes have specifity, meaning that one enzyme can catalyze only one reaction or a set of related reactions - it benefits the cell because it allows the cell to control different reactions independently by regulating the activity or quantity of the enzyme.
-- Enzymes can be used again, so they typically do not need to be made in large quantities.

BIO CHP 2 - Biological Molecules

II. Biological Molecules

A. Introduction [ugh... intros...]
-- The study of biochemistry - explores structure and function of molecules in living organisms
-- Organic molecules - molecules with the Carbon atom in it. [The only exception is carbon dioxide, CO2... go SAT II Bio book!]
-- Macromolecules - relatively large molecules [organic larger than inorganic... usually] and are usually polymers - molecules formed by adding smaller subunits - monomers. [so many definitions... except you should know all this already.]

B. Carbohydrates [yay carbs... I learned how to spell monosaccharides, disaccharides, and polysaccharides from this outline :)]
-- Carbohydrates - named carbohydrates because it's mainly composed of Carbon and Water, usually in the formula of: [C(H2O)]n [<-- that bracket is not my comment but this is.]
- 1. Monosaccharides - simplest carbohydrate subunits found in nature. They're usually suit and known as "sugars" or "simple carbohydrates". Monosacharides are usually 6-Carbon compounds.
--- glucose - C6H12O6
--- fructose - C6H12O6
--- galactose - C6H12O6
[The general formulas are the same, but the bonds are different]
--- Important 5-Carbon sugars: ribose/deoxyribose [this should sound familiar, if not, you fail at bio :)] - C5H10O5/C5H10O4 [yes that's why it's deoxy-ribose]
- 2. Disacharides - Compose of two monosaccharides [di!] joined by a glycosidic bond. These are also fairly simple sugars.
--- sucrose - table sugar = fructose + glucoses
--- lactose - "milk sugar" = glucose + galactose
--- maltose - "malt sugar" = glucose + glucose
[must be broken down into monosaccharides before bonding]
3. Polysaccharides - composed of many, often hundreds, or monosaccharide units.
-- in nature, all the important polysaccharides are flucose polymers [yay go glucose], differing in their physical arrangement
--- Starch - energy storage in plants and one of the most consumed polysaccharides
--- Cellulose - makes up the cell wall of plants
--- Glycogen - "animal starch" - how animals store excess glucose in their livers and muscles as an energy reserve.

C. Lipids - macromolecules grouped together; lipids do not dissolve in water. They contain nonpolar covalent bonds, largely composed of hydrocarbon chains/rings
- 1. Triglycerides - composed of one molecule of trialcohol glycerol covalently attached to 3 fatty acids.
-- Chains containing double bonds are called unsaturated, the more unsaturated a fatty acid chain is, the more liquidy the triglyceride is. Oils are usually known as polyunsaturated triglycerides.


- 2. Phospholipids - They resemble triglycerides, but a hydrophilic molecule containing a phospate group is in place of one of the fatty acids, giving the molecule a hydrophobic tail and a hydrophilic head [aka amphipathic molecule - one philic, one phobic]. Phospholipids form structures of plasma membranes and can also act as emulsifying agents - agents that allow other lipids to dissolve more easily in the body.

- 3. Steroids - lipids that don't resemble triglycerides but are composed of a series of nonpolar rings. Cholestrol is the most wellknown and prevalent steroid compound in the body. Other important ones include sex hormones and vitamin D.


D. Proteins - polymeric macromolecules made up of subunits called animo acids, which differ by an "R" group.

FOUR LEVELS OF PROTEIN STRUCTURE:
- 1. Primary Structure: linear order of amino acids
- 2. Secondary Structure: hydrogen bonds between atoms of adjacent amino and acid groups. Common secondary structures: alpha-helix and beta-pleated sheets.
- 3. Tertiary Structure: ultimate 3D shape. It folds due to long range interactions between R-groups of amino acids: hydrogen bonding, electrostatic interactions, and hydrophobic interactions. Tertiary structure is responsible for the protein's function.
- 4. Quaternary Structure - not all proteins have a quaternary structure, only those that ave multiple polypeptide chains. Its folding refers to the interactions between multiple chains of amino acids to make a protein that can only function in this state.
-- Proteins also function as enzymes, antibodies, structural components, hormones... etc
-- Hemoglobin: help carries oxygen in blood
-- Collagen and Keratin - major components of hair, skin, and connective tissues
-- Insulin - hormone that regulates blood glucose levels [yay hormones! my fav subject]
-- Pepsin - enzyme that digests other proteins in the stomach, functions best in acidic places with pH between 1.5 - 2 [aka your stomache is acidic... in case you did not know that]

E. Nucleic Acids - macromolecular polymers made up of nucleotide subunits.
-- a nucleotide contains a 5-carbon sugar [yes this is when ribose and deoxyribose comes in handy :)], a nitrogenous base, and a phosphate group.
-- Adenine [purine] - Thymine [pyrimidine]-->(Uracil [pyrimidine] in RNA}
-- Guanine [purine] - Cytosine [pyrimidine]
-- Nucleotides are joined to one another by phosphodiester bonds [a group of strong covalent bonds between the phosphorus atom in a phosphate group and two other molecules over two ester bonds --> go wikipedia].

BIO CHP 1 - INTRODUCTION

I'm gonna start reviewing bio and putting up random notes for my references :) while listening to my HSJ/7 music, which I finally figured out how to upload on my iPod. Hopefully I can get through at least a chapter a day and be done in a month, but knowing me, I'm probably going to do the first like 5-10 chapters today and not do it for a while >.<;.
[my comments will be in brackets...]

I. Introduction [this is like 7th grade review >.<]

A. Biology - the study of life, which includes examining the processes that govern how life is maintained and reproduced, and observing how living things interact with each other and their environments.
- 1. Two perspectives from which one can study biology: in vivo, or in vitro
--- in vivo - "done on the body itself"
--- in vitro - "in glass" experiments one in test tubes aka outside the body
[...experimenting on the person him/herself rather than stuffing the person into a testtube, then experimenting! I see the difference xD.]

B. Scientific Method!!
- 1. Asking questions!
- 2. Form hypothesis and make predictions!
- 3. Testing the hypothesis through experiments [yay this is when u get to blow up stuff]
- 4. Repeating investigations and devising new ways to further test the hypothesis (may include modifying the hypothesis)
- 5. Reporting results and drawing conclusions. [drawing is fun...]
Definition: theory - similar to hypothesis, but theory usually explains a broad range of related phenomena, not just one
Note: "There is no beginning and end in science." All hypothesis are based on previous experiments, and all results/conclusions and be further expanded! Sometimes, experiments might even raise more questions than they answer!

C. Characteristics of Life [What makes us living? aka how to prove to Mr. Waldeck that a candle is NOT alive.]

- 1. Order and Organization - All living things have nucleic acids as the storage mechanism for genetic information, and are made up of cells. [Yes candles are made up of cells... but ...I don't think they have DNA... poll on this?]
- 2. Growth and Development - all living things grow and develop during their life, aka grow into a more complex organism or increase size. [...I don't think candels grow but if you think about it, you can add wax onto it and it'll "grow"...]
- 3. Reproduction - This is sorta self-explanatory, but they must reproduce so their species can survive [candle reproduction = Mr. Waldeck cuts off a piece of the candle. Candles can reproduce! Which is why we still have them in our houses... in case the new technology called electricity fails, but then again we also have firewood...]
- 4. Energy metabolism - all living organisms need energy to survive. Those that make their own food are called autotrophs. All others are called heterotrophs. Nutrients are converted into energy [respiration!] and waste products have to be ELIMINATED. [Of course candles use energy... the fire~]
-- 5. Stimuli response and homeostasis - the ability to respond to the environment(internal or external environment). Organisms must adapt to their environments [naturally or what humans do: create their own environment: A/C!!] [Yes candles adapt to their environment very well. When it gets windy, it just blows out!]
-- 6. Evolution - The ability to change/mutate in order to create diversity!! [Azns, White ppl, etc.] [Yes as you can see, we have many different types of candles in our world.]

D. Structure and function
-- The correlation between the structure and its function is very important in biology! [that's basically what this part says......]

E. Using this book
-- "Remeber: the MCAT stresses your problem solving skills and your knowledge of basic biological concepts. Therefore, you will be better prepared for the test by understanding these concepts rather by just memorizing various facts and terms [lol. tis what Kyumin continuously yells at me for]..."