*Unit+2+Biochemistry

=**__Chapter 2: The Chemical content of life__**= Note: All definitions in this outline are copied word for word. Full credit goes to the book //Biology: AP Edition: 8e// by Niel Campbell and Jane Reece.Outline is copyright of Rick Presman, 2009. Diagrams! [|BioChapter2Diagrams03.doc] [|BioChapter2Diagrams.docx] [|BioChapter2Diagrams03.pdf] [|Chapter 2_0.doc] (Jeff Yoshimura) [|Chapter_2_0.pdf] (Jeff Yoshimura)

**Overview**

 * Duroia hirusta ("devil's garden") mainted for 100s of years b/c of chemical reactions from ants that preserve them

**Concept 2.1: Matter consists of chemical elements in pure form and in combinations called compounds**

 * matter: anything that takes up space and has mass
 * Elements and Compounds**
 * element: substance that can't be broken down to other substances by chemical reactions
 * compound: substance consisting of 2 or more different elements combined in a fixed ratio
 * Essential Elements of Life**
 * 25 out of 92 natural elements are essential; C, O, H, and N make up 96%
 * P, S, Ca, K, and a few more make up the other 4%
 * trace elements : those required by an organism in only minute amounts

**Concept 2.2: An element's properties depend on the structure of its atoms**

 * atom: the smallest unit of matter that still retains the properties of an element
 * Subatomic Particles: parts of the atom**
 * neutrons (neutral): make up atomic nucleus; weighs about 1.7*10^-24 g or 1 dalton
 * protons (positive): make up atomic nucleus; weighs about 1.7*10^-24 g or 1 dalton
 * electrons (negative): circle the nucleus in an electron cloud
 * 1 dalton = 1 amu = 1.7*10^-24 g
 * Atomic Number and Atomic Mass**
 * atomic number: number of protons in a given element
 * mass number: number of protons and neutrons in an atom (NOTE: this is only an __approximation__ of the mass of an atom)
 * atomic mass: total mass of an atom
 * Isotopes: different atomic forms of the same atom due to differing numbers of neutrons**
 * isotopes act identically in chemical reactions
 * radioactive isotope: one in which the nucleus decays spontaneously, giving off particles and energy
 * NOTE: if a radioactive isotope gives off protons, then the element changes (ex: Carbon-14 --> Nitrogen-7)
 * radioactive isotopes ahve many natural and man-made applications, but also have detrimental after-effects
 * The Energy Levels of Electrons**
 * b/c atoms are mostly space, electrons are the only particles coming into contact during chemical reactions
 * energy: the capacity to cause change
 * potential energy: the energy that matter possesses b/c of its location/structure
 * electrons have a potential energy which depends on which electron shell they are in
 * Electron Distribution and Chemical Properties**
 * periodic table of elements organizes the elements by increasing atomic number
 * chemical properties are based on number of valence electrons in valence shell
 * the noble gases are inert (chemically unreactive)
 * Electron Orbitals**
 * although a 2-D diagram of an electron path is convenient, it only shows average distances from the nucleus
 * orbital: the 3-D space an electron is found most of the time
 * ex: 1s, 2s, 2p, etc.

**Concept 2.3: The formation and function of molecules depend on chemical bonding with atoms**

 * chemical bonds: attractions that hold atoms together after interactions
 * Covalent Bonds: sharing of a pair of valence electrons by 2 atoms**

=**__Chapter 3: Water and the Fitness of the Environment__**= [|[BioCh3Notes03.doc]] [|[BioCh3Notes.docx]] [|[BioCh3Notes03.pdf]] (Diagrams are at the end of the notes) THANK YOU TONY


 * Tony Wang** **©**

Yeshhh it works :D

=__**Chapter 4: Carbon and the Molecular Diversity of Life**__= [|Chapter 4 Diagrams.doc]

[|[BioChapter4Notes03.doc]] [|[BioChapter4Notes03.pdf]]

^^^^^^^^^^^^^^^ Notes in word format

Sara Bahmanyar

**CHAPTER 4: CARBON AND THE MOLECULAR DIVERSITY OF LIFE**
~Carbon accounts for large diversity of biological molecules I. Organic chemistry is the study of carbon compounds ~ Study of organic chemistry originated to purify and improve yield of valued substances ~ Vitalism: belief in a life force outside the jurisdiction of physical/chemical laws ~ People didn't believe that organic compounds could be created from inorganic substances until Wohler made urea and Kolbe made acetic acid ~ Abiotic synthesis of organic compounds = early stage in origin of life (Stanley Miller) ~ Mechanism: view that physical/chemical laws govern all natural phenomena (replaced vitalism)

Jonathan Mintz ~//Tetravalence// means that an atom like carbon can branch off in 4 directions due to its valence electrons. ~When carbon atoms link they can chain on to themselves infinitely. ~Hydrocarbons are solely Carbon and Hydrogen molecules, and are also most fuels for combustion. ~Hydrocarbons are hydrophobic and don’t dissolve in water. ~Three types of isomers: Structural, Geometric, and Enantiomers. ~Structural: Only the covalent bonds differ in their placements and configurations. ~Geometric: Differ in spatial arrangements (3-D space), because single bonds can rotate but double bonds are rigid and fixed. ~Enantiomers: Are mirror images of each other, can’t be superimposed atop one another. Have to be asymmetrical.
 * Chapter 4 Section 2 Notes**

Tianyu Yao I.) A small number of chemical groups are key to the functioning of biological molecules ~Organic molecules differ not only upon the carbon arrangements but also due to intermolecular forces. ~Ex. used by book includes the differences of Hydrocarbons, differring amounts as well as shapes lead to drastically different organic molecules. ~Example of two molecules that are similar in chemical components but different organically would be testosterone and estrodiol (demonstrated in diagrams) II.) The Chemical Groups most Important in the Process of Life ~Goes back to testosterone and estrodiol, both of them are steroids, with a structure of 4 rings, however, it is these two similar yet radically different molecules that contribute to the differences between the male and female bodies. ~//Functional Groups// are "A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions." ~There are seven crucial chemical groups required to sustain life: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl groups. ~First six are hydrophillic and help in solubility of organic compounds in water ~Methyl is nonreactive and acts as a recognizable tag to label the biological molecules
 * Chapter 4, Section 3 Notes
 * note: the section titles are copied word-for-word, everything else is genuine**

=__Chapter 5: The Structure and Function of Large Biological Molecules__= Diagrams! [|BioChapter5Diagrams.docx] [|BioChapter5Diagrams03.doc] [|5.4 notes.doc] [|5.4 notes.pdf]

Notes are copyright of Anna Sherman! Excuse the weird styling....

[|chapter5proteins_0.pdf] (Jeff Yoshimura) [|chapter5proteins_0.doc] (Jeff Yoshimura)

[|Macromolecule_Characteristics_0.pdf] (Jeff Yoshimura) [|Macromolecule Characteristics_0.doc] (Jeff Yoshimura)

Biochemistry Unit: Html notes: A. Sherman I. 5.4 – Proteins have many structures and functions A. Roles of Proteins 1. Storage 2. Transport 3. Structural support 4. Defense against disease 5. Catalysts for chemical reactions 6. Cellular communication B. Enzymes 1. Mostly proteins 2. __ Catalysts __ to reactions that regulate metabolism a. chemical agents that speed up reactions without being consumed. 3. Can perform their function over and over again C. __ Polypeptides __ 1. Polymers of amino acids 2. A Protein is 1 or more polypeptides, folded and coiled into a specific structure 3. Amino Acid Monomers a. Amino acids – organic molecules with both carboxyl and amino groups. b. At center is alpha carbon with 4 partners i. Amino group ii. Carboxyl group iii. H iv. Variable R (“side chain”) that changes based on the amino acid c. There are 20 amino acids d. Physical and chemical properties of the side chain R determine the traits of each amino acid 4. Amino Acid Polymers a. __ Peptide Bond __ - 2 Amino Acids will bind via a dehydration reaction (in which a water molecule is lost) if one amino acid’s carboxyl group is facing the other’s amino group. b. Peptide bonds yield __polypeptides__ - polymers of many amino acids linked by peptide bonds. c. Polypeptide chains have one end with a free amino group (N-terminus) d. And one end with a free carboxyl group (C-terminus) e. __ Backbone __ - Repeated sequences of basic amino-carboxyl bonds. D. Protein Structure and Function 1. Protein’s activities result from their unique 3d structure and sequence of amino acids. 2. Frederick Sanger a. Studied insulin breakdown and reconstructed its amino acid sequence 3. Proteins are precisely formed polypeptide chains 4. Folding a. Happens instantly b. Reinforced by bonds from other parts of the chain 5. Structure a. Influences recognition and binding 6. 4 Levels of Protein Structure (LOOK AT THE DIAGRAM IN THE BOOK FOR THIS) a. Primary structure – refers to a protein’s unique sequence of amino acids b. Secondary structure – refers to the coils and folds in polypeptide chains that are a result of hydrogen bonds c. Tertiary structure – refers to the overall protein shape resulting from side chain interactions, coils, and turns d. Quaternary structure – refers to the overall protein structure from multiple polypeptide subunits. 7. Sickle Cell Disease: A Change in Primary Structure a. Sickle cell disease is caused by substitution of the amino acid valine for the normal one, glutamic acid b. The replacement happens in a structure of hemoglobin, a protein that carries oxygen in red blood cells. c. The abnormal hemoglobin causes cells to crystallize into a sickle shape instead of the normal round shape d. These angular cells clog vessels and cause immense problems e. Main idea: a tiny structure change can cause huge problems 8. What determines protein structure? a. Polypeptide chains and their arrangements b. Physical and chemical conditions of the protein’s environment c. __ Denaturation __ – the unraveling/loss of native shape of a protein. i. Due to environmental changes ii. Changes in pH, salt concentration, temperature iii. Misshapen proteins are biologically inactive d. __ Renaturation __ i. A return to functional form ii. May happen if denaturing agent is removed 9. Protein Folding in the Cell a. __ Chaperonins __ – chaperone proteins i. assist in proper folding of other proteins ii. keep protein away from bad influences b. Misfolding is a problem i. Alzheimers and Parkinsons are both causes by large amount of protein misfolding ii. Some cellular systems check with chaperones and fix or destroy badly folded proteins. c. X-ray crystallography i. Way of determining a protein’s 3d structure.

Brion Wood's 5.1-5.3 Notes Overview: The Molecules of Life -The critically important large molecules of all living things fall into 4 main categories. Carbohydrates, lipids, proteins, and nucleic acid. -Carbohydrates, proteins, and nucleic acid are huge and call **macromolecules**.

5.1: Macromolecules are polymers, built from monomers -A **Polymer** is a long molecule consisting of many similar or identical building blocks (**Monomers)** linked by covalent bonds. -Monomers bonded covalently because of the loss of a water molecule, this is called **condensation reaction**, specifically **dehydration synthesis**. -Enzymes facilitate dehydration synthesis. -Disassembling polymers to monomers by **hydrolysis,** essentially the opposite of dehydration. -Hydrolysis used in our bodies during digestion.

5.2: Carbohydrates serve as fuel and building material -**Carbohydrates** include both sugars and polymers of sugars. -Simplest carbs are simple sugars, **monosaccharides**. **Disaccharides** are double sugars joined by a covalent bond. -Monosaccharides have molecular formulas that are some multiple of the unit CH2O. Glucose is the most common. -Source of diversity of simple sugars come from the spatial arrangement of their parts around asymmetric carbons. -Simple sugars, especially glucose, are major nutrients for cells. In cellular respiration, cells extract energy in a series of reactions starting with glucose. -Disaccharide is two monosaccharides joind by a **glycosidic linkage**, a covalent bond between two monosaccharides by a dehydration reaction. -**Polysaccharides** are macromolecules, polymers with a few hundred to a few thousand monosaccharides bonded together. -Some polysaccharides serve as storage material, others serve as building material. -Plants store **starch**, a polymer of glucose monomers. The sugar can later be withdrawn by hydrolysis. -Animals store glycogen, a polymer of glucose. Sugar can be withdrawn. -**Cellulose**, polysaccharide that is a major component of the tough walls that enclose plant cells. It's a polymer of glucose, but the glycosidic linkages differ from those of starch because the shapes of the glucose differ. Cellulose has a distinct 3D shape, while starch is helical. -**Chitin**, a polysaccharide that is used by arthropods to build their exoskeleton.

5.3: Lipids are a diverse group of hydrophobic molecules -**Lipids** mix poorly, if at all, with water. Structure mostly consist of hydrocarbon regions. -**Fat** is constructed from glycerol and fatty acids, two smaller molecules. -Making a fat, add three fatty acid molecules to each glycerol by an ester linkage. This makes a **triacylglycerol**. -Saturated fats are fats with as many hydrogen atoms as possible bonded to the carbon skeleton with no double bonds. Solid at room temp. -Unsaturated is the opposite. Liquid at room temp. -"Hydrogenated Vegetable Oils" Unsaturated fats changed to saturated by adding hydrogen. Also produces trans fats (more double bonds). Bad for health. -Main function of **Fats is energy storage**. They are also cushions. -**Phospholipids** make up the cell membranes. -In phospholipids, two fatty acids attach to glycerol instead of three. Instead, it is a phosphate group (neg charge and has affinity for water). -**Steroids** are lipids characterized by a carbon skeleton consisting of four fused rings. Many hormones are steroids. -**Cholesterol** is a common component of animal cell membranes and the precursor from which other steroids are synthesized (in liver).

=__Chapter 8: An Introduction to metabolism__ (Sections 8.4 and 8.5)= Diagrams! [|BioChapter8Diagrams.docx] [|BioChapter8Diagrams03.doc]

Diagrams for Chapter 8 Cellular Respiration Unit [|chapter 8 bio diagrams.doc]~ Polly

[|chapter 8 notes - 8.4 and 8.5.doc] By Anna Sherman

[|Chapter 8 notespg 144-152.doc] (Jeff Yoshimura) [|Chapter_8_notespg_144_152.pdf] (Jeff Yoshimura)

[|Chapter_8_pg_138_144.pdf] (Jeff Yoshimura) [|Chapter 8 pg 138-144.doc] (Jeff Yoshimura)

Html version:

A. Sherman I. 8.4 – Enzymes speed up metabolic reactions by lowering energy barriers A. __ Enzyme __ – macromolecule that acts as a __catalyst__ 1. __ Catalyst __ – chemical agent that speeds up reactions B. The activation energy barrier 1. All chemical reactions involve bond breaking and bond forming 2. For bonds to break, the starting molecules must be taken to a very unstable state 3. __ Activation Energy ( __ free energy of activation) / E sub a / Ea a. is the energy required by the reactants to bring them to the unstable state in which their bonds can break b. Often absorbed from the surroundings as heat 4. When new bonds of product form, the energy is released back as heat 5. The so-called “unstable condition” is called the __transition state__ 6. To get there: a. Ea is absorbed, usually as heat b. Molecular speed of reactants increases c. Bonds are more likely to break under heat 7. In exergonic reactions, Ea is repaid with interest since the formation of the news bonds releases more energy than what was needed to break the old bonds 8. Ea is usually very very high, and for a reaction to occur, reactants must be heated a lot (A lot of energy needs to be absorbed). C. How Enzymes Lower the Ea Barrier 1. Most complex molecules have lots of energy with potential to break down spontaneously 2. At cell temperatures, their activation energy is too high for random decomposition of molecules 3. Just heating reactants to cause reactions to occur is BAD because a. All reactions would speed up, not just the necessary ones b. Heat kills and denatures proteins 4. __ Catalysis __ – enzymes lower the Ea barrier 5. Enzymes cannot a. modify the overall change in energy of a reaction b. Make an endergonic reaction an exergonic one. 6. Enzymes DO a. Hasten reactions b. Make it possible for cells to have dynamic metabolisms c. Determine which process are going on in the cell D. Substrate Specificity of Enzymes 1. __ Substrate __ – reactant an enzyme acts on 2. __ Enzyme-substrate complex __ – formed when an enzyme binds to its substrate(s). 3. Enzymes can recognize their specific substrate even among isomers. a. Molecular recognition is possible because enzymes are proteins, each with a unique structure and sequence of amino acids that allows them to recognize their unique substrate(s). 4. __ Active site __ – region of enzyme that binds to substrate a. Formed by only a few of the enzyme’s amino acids 5. __ Induced Fit __ – when a substrate enters the active site, the enzyme changes shape for a snugger fit E. Catalysis in the Enzyme’s Active Site 1. Substrate is held in active zone with weak bonds 2. R groups of enzyme’s active zone catalyze reaction 3. Products leave, enzyme can take more substrates 4. Enzymes catalyze extremely fast and are never consumed 5. Enzymes can catalyze forward or reverse reactions, depending on which one has the negative energy change 6. How is the reaction sped up? a. For 2 or more reactants, the active site provides a template for substrates to come together in the proper orientation b. Enzyme stretches the substrate toward transition state form i. Stretches and bends chemical bonds that must be broken in reaction ii. Ea is directly related to the difficulty of breaking the substrate’s bonds iii. Distorting the bonds helps the substrate approach transition and lowers the free energy requirements c. Provides a more conducive microenvironment i. I.E: An enzyme’s R group may have acidic amino acids, and thus the active zone will be a pocket of low pH in an otherwise neutral cell ii. Active group can also be an H+ donor to aid catalysis d. Direct participation of the active site in the reaction i. Brief covalent bonds between substrate and enzyme may be formed ii. Enzyme is always returned to original form 7. Rate of Enzyme Conversion of Substrates a. More substrate molecules means more frequent access to enzyme active sites b. __ Saturation __ – occurs when all enzyme molecules have active sites engagted due to high substrate concentration i. Rate of reaction is directly proportional to the speed at which the active site converts substrates to products ii. The only way to increase the rate is to create more enzymes F. Effects of Local Conditions on Enzyme Activity 1. Optimal conditions favor the most active shape for enzyme molecule 2. Effects of temperature and pH a. Higher temp = higher rate ofr reaction i. Enzymes & substrates move faster and collide more ii. Above a certain temperature, the rate of reaction drops sharply i. Weak bonds that stabilize the active site become disrupted ii. Proteins denature iii. Ideal temp is around 35 – 40 C. b. Optimal pH i. Average: 6 – 8 ii. The optimal pH of Pepsin, an enzyme in the acidic human stomach, is 2 iii. Trypsin, in the intestine, catalyzes fastest at a pH of 8 3. __ Cofactors __ a. Non-protein “helpers” b. May be bound loosely c. May be permanent residents of enzyme d. Inorganic – Zinc, iron, copper ions e. Organic cofactors are called __coenzymes__ i. Vitamins act as coenzymes or help form coenzymes 4. Enzyme Inhibitors a. If an inhibitors attaches itself with covalent bonds, inhibition is usually irreversible b. Most inhibitors bind via weak bonds and ARE reversible c. __ Competitive Inhibitors __ i. Resemble normal substrates and compete for the active site ii. Reduce enzyme productivity by blocking out real substrates iii. An be overcome by increasing substrate concentration i. More substrates get into enzymes than inhibitors d. __ Noncompetitive Inhibitors __ i. Impede enzymes by binding to non-active site ii. Active site becomes less effective if enzyme’s shape is changed (see 8.5) e. Toxins, Poisons, Antibiotics i. Sarin, DDT, and parathion are inhibitors of enzymes in the nervous system ii. Penicillin/other antibiotics block active sites of enzymes that bacteria use to make their cell walls. f. Enzyme Inhibition is not always bad or abnormal. It’s often used in regulation. II. 8.5 – Regulation of Enzyme Activity Helps Control Metabolism. A. Allosteric Regulation of Enzymes 1. __ Allosteric Regulation __ - A protein’s function at one site is affected by a regulatory binding at another. The regulatory molecules act like noncompetitive inhibitors. 2. Allosteric Activation and Inhibition a. Enzymes that are allosterically regulated i. Have 2 or more subunits ii. Each subunit has its own active site iii. The complex oscillates between inactive and catalytically active b. __ Activator __ – binds to enzyme, usually where subjoints join, and lock it into active form. c. __ Inhibitor __ – Binds to enzyme, locks it into inactive form d. Shape changes in 1 subunit cause the same shape change to all others i. A single activator or inhibitor changes the shape of the whole enzyme e. Fluctuating regulator concentrations control each other: i. ATP -> ADP and something else ii. ATP binds allosterically to enzymes that create ATP and inhibits their activity iii. ADP is in activator for the same enzymes iv. If ATP is plentiful, ATP inhibits its own making because that’s a waste of cell resources v. If ADP is plentiful, ATP will not be as plentiful, and ADP will activate enzymes that catalyze reactions that give off ATP. f. __ Cooperativity __ – One substrate primes all of an enzyme’s subunits for more substrates i. Hemoglobin is not an enzyme, but has 4 subunits i. The binding of one oxygen to hemoglobin increases hemoglobin’s affinity for oxygen ii. If oxygen is scarce, hemoglobin does not have this affinity because less oxygen molecules bind to hemoglobin ii. Aspartyl transcarbamoylase is a good example of cooperativity 3. Identification of Allosteric Regulators a. Regulatory sites between enzymes are more distinct than active sites b. Hard to identify allosteric regulators because they bind their enzyme at low affinity for its substrate and make the enzymes and regulators hard to isolate 4. Feedback Inhibition a. A metabolic pathway can be switched off like so: i. As an end product of a metabolic pathway accumulates, it will start inhibiting the first enzyme in its metabolic pathway because it is plentiful, and no more cell resources are needed to create more ii. Metabolic pathway is then switched off 5. Specific Localization of Enzymes within Cells a. Cells have compartments b. Cellular structures bring order to metabolic pathways c. Teams of enzymes can assemble and link i. One enzyme’s end product is another enzyme’s substrate d. Some enzymes have fixed locations e. Others are in solutions, enclosed with their own internal chemical environments.