Day 8 - Biochemistry - Kreb's Cycle ATP Formation

Major metabolic pathways converging on the TCA cycle

Several catabolic pathways converge on the TCA cycle. Reactions that form intermediates of the TCA cycle in order to replenish them (especially during the scarcity of the intermediates) are called anaplerotic reactions.

The citric acid cycle is the third step in carbohydrate catabolism (the breakdown of sugars). Glycolysis breaks glucose (a six-carbon-molecule) down into pyruvate (a three-carbon molecule). In eukaryotes, pyruvate moves into the mitochondria. It is converted into acetyl-CoA by decarboxylation and enters the citric acid cycle.

In protein catabolism, proteins are broken down by protease enzymes into their constituent amino acids. The carbon backbone of these amino acids can become a source of energy by being converted to Acetyl-CoA and entering into the citric acid cycle.

In fat catabolism, triglycerides are hydrolyzed to break them into fatty acids and glycerol. In the liver the glycerol can be converted into glucose via dihydroxyacetone phosphate and glyceraldehyde-3-phosphate by way of gluconeogenesis. In many tissues, especially heart tissue, fatty acids are broken down through a process known as beta oxidation which results in acetyl-CoA which can be used in the citric acid cycle. Sometimes beta oxidation can yield propionyl CoA which can result in further glucose production by gluconeogenesis in the liver.

The citric acid cycle is always followed by oxidative phosphorylation. This process extracts the energy (as electrons) from NADH and QH₂, oxidizing them to NAD⁺ and Q, respectively, so that the cycle can continue. Whereas the citric acid cycle does not use oxygen, oxidative phosphorylation does.

The total energy gained from the complete breakdown of one molecule of glucose by glycolysis, the citric acid cycle and oxidative phosphorylation equals about 30 ATP molecules, in eukaryotes. The citric acid cycle is called an amphibolic pathway because it participates in both catabolism and anabolism.

Day 8–Homework – Cellular Respiration

1. Diagram the Krebs Cycle paying special attention to the creation of ADP, ATP, NAD and NADH. List appropriate enzymes, cofactors and substrates.

Day 7 - Biochemistry - Cellular Respiration( I & II) Electron Transport and Oxidative Phosphorylation

Cellular respiration describes the metabolic reactions and processes that take place in a cell or across the cell membrane to get biochemical energy from fuel molecules and the release of the cells' waste products. Energy can be released by the oxidation of fuel molecules and is stored as "high-energy" carriers. The reactions involved in respiration are catabolic reactions in metabolism.

Fuel molecules commonly used by cells in respiration include glucose, amino acids and fatty acids, and a common oxidizing agent (electron acceptor) is molecular oxygen (O₂). There are organisms, however, that can respire using other organic molecules as electron acceptors instead of oxygen. Organisms that use oxygen as a final electron acceptor in respiration are described as aerobic, while those that do not are referred to as anaerobic.

The energy released in respiration is used to synthesize molecules that act as a chemical storage of this energy. One of the most widely used compounds in a cell is adenosine triphosphate (ATP) and its stored chemical energy can be used for many processes requiring energy, including biosynthesis, locomotion or transportation of molecules across cell membranes. Because of its ubiquitous nature, ATP is also known as the "universal energy currency", since the amount of it in a cell indicates how much energy is available for energy-consuming processes.

Aerobic respiration

Aerobic respiration requires oxygen in order to generate energy (ATP). It is the preferred method of pyruvate breakdown from glycolysis and requires that pyruvate enter the mitochondrion to be fully oxidized by the Krebs cycle. The product of this process is energy in the form of ATP (Adenosine Triphosphate), by substrate-level phosphorylation, NADH and FADH₂.

Simplified Reaction: C₆H₁₂O_{6 (aq)} + 6O_{2 (g)} → 6CO_{2 (g)} + 6H₂O _(l) ΔH_c -2880 kJ

The reducing potential of NADH and FADH₂ is converted to more ATP through an electron transport chain with oxygen as the "terminal electron acceptor". Most of the ATP produced by aerobic cellular respiration is made by oxidative phosphorylation. This works by the energy released in the consumption of pyruvate being used to create a chemiosmotic potential by pumping protons across a membrane. This potential is then used to drive ATP synthase and produce ATP from ADP. Biology textbooks often state that between 36-38 ATP molecules can be made per oxidised glucose molecule during cellular respiration (2 from glycolysis, 2 from the Krebs cycle, and about 32-34 from the electron transport system).^{[citation needed]} Generally, 38 ATP molecules are formed from aerobic respiration.^{[citation needed]} However, this maximum yield is never quite reached due to losses (leaky membranes) as well as the cost of moving pyruvate and ADP into the mitochondrial matrix.^{[citation needed]}

Aerobic metabolism is 19 times more efficient than anaerobic metabolism (which yields 2 mol ATP per 1 mol glucose). They share the initial pathway of glycolysis but aerobic metabolism continues with the Krebs cycle and oxidative phosphorylation. The post glycolytic reactions take place in the mitochondria in eukaryotic cells, and in the cytoplasm in prokaryotic cells.

Glycolysis

Glycolysis is a metabolic pathway that is found in the cytoplasm of cells in all living organisms and does not require oxygen. The process converts one molecule of glucose into two molecules of pyruvate, and makes energy in the form of two net molecules of ATP. Four molecules of ATP per glucose are actually produced; however, two are consumed for the preparatory phase. The initial phosphorylation of glucose is required to destabilize the molecule for cleavage into two triose sugars. During the pay-off phase of glycolysis, four phosphate groups are transferred to ADP by substrate-level phosphorylation to make four ATP, and two NADH are produced when the triose sugars are oxidized. Glycolysis takes place in the cytoplasm of the cell. The overall reaction can be expressed this way:

Glucose + 2 NAD⁺ + 2 P_i + 2 ADP → 2 pyruvate + 2 NADH + 2 ATP + 2 H₂O

Oxidative decarboxylation of pyruvate

The pyruvate produced in glycolysis is transported across the mitochondrial membranes by a membrane transport protein called the pyruvate carrier.^[1] The pyruvate decarboxylase then produces acetyl-CoA from pyruvate inside the mitochondrial matrix. This oxidation reaction also releases carbon dioxide as a product. In the process one molecule of NADH is formed per pyruvate oxidized.

Citric Acid cycle

This is also called the Krebs cycle or also the tricarboxylic acid cycle. When oxygen is present, acetyl-CoA is produced from pyruvate. If oxygen is not present the cell undergoes fermentation of the pyruvate molecule. If acetyl-CoA is produced the molecule then enters the citric acid cycle (Krebs cycle) inside the mitochondrial matrix, and gets oxidized to CO2 while at the same time reducing NAD to NADH. NADH can be used by the electron transport chain to create further ATP as part of oxidative phosphorylation. To fully oxidize the equivalent of one glucose molecule, two acetyl-CoA must be metabolized by the Krebs cycle. Two waste products, H₂O and CO₂, are created during this cycle.

Oxidative phosphorylation

In eukaryotes, oxidative phosphorylation occurs in the mitochondrial cristae. It comprises the electron transport chain that establishes a proton gradient (chemiosmotic potential) across the inner membrane by oxidizing the NADH produced from the Krebs cycle. ATP is synthesised by the ATP synthase enzyme when the chemiosmotic gradient is used to drive the phosphorylation of ADP.

Anaerobic respiration

Without oxygen, pyruvate is not metabolized by cellular respiration but undergoes a process of fermentation. The pyruvate is not transported into the mitochondrion, but remains in the cytoplasm, where it is converted to waste products that may be removed from the cell. This serves the purpose of oxidizing the hydrogen carriers so that they can perform glycolysis again and removing the excess pyruvate. This waste product varies depending on the organism. In skeletal muscles, the waste product is lactic acid. This type of fermentation is called lactic acid fermentation. In yeast, the waste products are ethanol and carbon dioxide. This type of fermentation is known as alcoholic or ethanol fermentation. The ATP generated in this process is made by substrate phosphorylation, which is phosphorylation that does not involve oxygen.

Anaerobic respiration is less efficient at using the energy from glucose since 2 ATP are produced during anaerobic respiration per glucose, compared to the 30 ATP per glucose produced by aerobic respiration. This is because the waste products of anaerobic respiration still contain plenty of energy. Ethanol, for example, can be used in gasoline (petrol) solutions. Glycolytic ATP, however, is created more quickly. For prokaryotes to continue a rapid growth rate when they are shifted from an aerobic environment to an anaerobic environment, they must increase the rate of the glycolytic reactions. Thus, during short bursts of strenuous activity, muscle cells use anaerobic respiration to supplement the ATP production from the slower aerobic respiration, so anaerobic respiration may be used by a cell even before the oxygen levels are depleted, as is the case in sports that do not require athletes to pace themselves, such as sprinting.

Efficiency of aerobic and anaerobic respiration

Aerobic respiration During aerobic respiration 38 molecules of ATP are produced for every molecule of glucose that is oxidised. C₆H₁₂O_{6 (aq)} + 6O_{2 (g)} → 6CO_{2 (g)} + 6H₂O _(l) + 38 ATP The energy released by the complete oxidation of glucose is 2880KJ per mole. The energy contained in 1 mole of ATP is 30.6KJ. Therefore the energy contained in 38 moles of ATP is 30.6×38=1162.8 kj. Therefore efficiency of transfer of energy in aerobic respiration is=1162.8/2880=40.4%.

Anaerobic respiration (1) Yeast (alcoholic fermentation). During alcoholic fermentation, two molecules of ATP are produced. for every molecule of glucose used.

glucose → 2ethanol + 26CO2 (g) +2 ATP

The total energy released by the conversion of glucose to ethanol is 210kj per mole. The energy contained in 2 molecules of ATP is 2×30.6=61.2kj.Therefore efficiency of transfer of energy during alcoholic fermentation is 61.2/210=29.1%.

(2) Muscle (lactate fermentation). During lactate fermentation, 2 molecules of ATP are produced for every molecule of glucose used.

glucose → 2 lactate + 2ATP

The total enery released by conversion of glucose to lactate is 150kj per mole. Therefore efficiency of transfer of energy in lactic acid fermentation is 61.2/150=40.8%. The amount of energy captured as ATP during aerobic respiration is 19 times as much as for anaerobic respiration.From this point of view Aerobic respiration is more efficient than anaerobic respiration.This is because a great deal of energy remains locked within lactate and ethanol.

Day 6 - Biochemistry - Proteins, Carbohydrates, Lipids & Nucleic Acids

The goal of biochemistry is to describe and explain in molecular terms, all chemical processes of living cells.

The expansive field of biochemistry can be broken up into the following major areas of mechanistic research:

Chemistry of:

• carbohydrates
• lipids
• proteins
• nucleoproteins, nucleic acids, nucleotides
• hemoglobin, porphyrins & relatives

Vitamins
Enzymes
Changes in foodstuffs in alimentary tract
Detoxification mechanisms

• oxidation
• reduction
• hydrolysis
• conjucation

Respiration
Water balance
Acid-Base Balance
Energy metabolism
Metabolism of:

• carbohydrates
• lipids
• proteins
• nucleic acids
• porphyrins & family
• inorganics

Metabolic anatagonism
Blood & other body fluids
Hormones
Urine formation & Renal function

Anatomy of an Animal Cell

General charactoristics:

• Nucleus
• Cytoplasm
• Organelles
• Endoplasmic reticulum (smooth and rough)
• Golgi apparatus
• Lysosomes
• Mitochondria
• Cytoskeleton
• Cell membrane & Extracellular matrix
  

A few comments on Organic Molecules:

• Life as we know it is based on carbon
• Functional groups-clusters of atoms wiht characteristic structure & functions
• Monomers and Polymers
• Condensation-making polymers by lining up monomers and eliminating a water molecule
• Hydrolysis-breaking polymers apart by introducing a water molecule
• Bonds are not physical links. They are links of pure energy
• Covalent bond - sharing electrons (polar and nonpolar)
• Ionic bond - electrons are transferred from one atom to another
• Hydrogen bond - weak attractive force between polar molecules

There are about 50,000 different kinds of proteins in the human body. Proteins are large polypeptides with molecular weights of 10,000 to 1,000,000. The have four levels of structure:

1. Primary structure: sequence of the amino acids that make up the protein
2. Secondary: helical twist
3. Tertiary: a defined 3D geometric shape
4. Quaternary: number & types of polypeptide units & their geometry

Nucleic Acids: Polymers of nucleotides that are made up of 3 components

1. Phosphate group
2. Five carbon sugar called ribose (or deoxyribose)
3. Nitrogenous base

DNA (deoxyribonucleic acid) - the protein which stores the genetic information passed on from parent to offspring

RNA (ribonucleic acid) - serves as the translator of genetic information contained in DNA

Day 6–Biochemistry – Proteins, Carbohydrates, Lipids and Nucleic Acids

1. Define Proteins, Carbohydrates, Lipids and Nucleic Acids. Draw a structure of each.

2. Describe the three types of bonds molecules can take on and give examples of each.

3. True or False, “All carbohydrates are sugars.” Why?

4. Describe the value of Glycogen to the mammalian system.

5. Define Hydrophobic, Hydrophilic and the importance of this in the cellular membrane.

6. List the 10 essential Amino Acids. Draw their structures.

7. Give examples of denatured proteins.

8. What is ATP? Draw the structure. Why is it important to cells?

9. List the 6 classes of enzymes & what they catalyze.

10. Enzymes perform catalysis using 4 main mechanisms.

List & Describe.

Day 5 - Homework Questions due Monday

Day 5–Organic Chemistry – Chemical Bonding & Stoichiometry

1. Which of the following compounds would you expect to be ionic: N₂O, Na₂O, CaCl₂, SF₄?

2. Which of the following compounds would you expect to be covalent:
CBr_4, FeS, P₄O₆, PbF₂?

3. Write the empirical formulas for the compounds formed by the following ions:

a) Na⁺ and PO₄^3-

b) Zn²⁺ and SO₄^2-

c) Fe³⁺ and CO₃^2-

4. Calculate the formula weight of:

a) Al(OH)₃

b) CH₃OH

5. Calculate the molar mass of Ca(NO₃)₂.

Day 5- Organic Chemistry- Electronegativities, Bond Polarity and Moles

Bond Polarity and Electronegativity

Courtesy of Dr. Micheal 1998

The electron pairs shared between two atoms are not necessarily shared equally

Extreme examples:

1. In Cl₂ the shared electron pairs is shared equally

2. In NaCl the 3s electron is stripped from the Na atom and is incorporated into the electronic structure of the Cl atom - and the compound is most accurately described as consisting of individual Na⁺ and Cl^- ions

For most covalent substances, their bond character falls between these two extremes

Bond polarity is a useful concept for describing the sharing of electrons between atoms

• A nonpolar covalent bond is one in which the electrons are shared equally between two atoms
• A polar covalent bond is one in which one atom has a greater attraction for the electrons than the other atom. If this relative attraction is great enough, then the bond is an ionic bond

Electronegativity

A quantity termed 'electronegativity' is used to determine whether a given bond will be nonpolar covalent, polar covalent, or ionic.

Electronegativity is defined as the ability of an atom in a particular molecule to attract electrons to itself

(the greater the value, the greater the attractiveness for electrons)

Electronegativity is a function of:

• the atom's ionization energy (how strongly the atom holds on to its own electrons)
• the atom's electron affinity (how strongly the atom attracts other electrons)

(Note that both of these are properties of the isolated atom)

For example, an element which has:

• A large (negative) electron affinity
• A high ionization energy (always endothermic, or positive for neutral atoms)

Will:

• Attract electrons from other atoms
• Resist having its own electrons attracted away

Such an atom will be highly electronegative

Fluorine is the most electronegative element (electronegativity = 4.0), the least electronegative is Cesium (notice that are at diagonal corners of the periodic chart)

General trends:

• Electronegativity increases from left to right along a period
• For the representative elements (s and p block) the electronegativity decreases as you go down a group
• The transition metal group is not as predictable as far as electronegativity
  

Electronegativity and bond polarity

We can use the difference in electronegativity between two atoms to gauge the polarity of the bonding between them

Compound	F2	HF	LiF
Electronegativity Difference	4.0 - 4.0 = 0	4.0 - 2.1 = 1.9	4.0 - 1.0 = 3.0
Type of Bond	Nonpolar covalent	Polar covalent	Ionic (non-covalent)

• In F₂ the electrons are shared equally between the atoms, the bond is nonpolar covalent
• In HF the fluorine atom has greater electronegativity than the hydrogen atom.

The sharing of electrons in HF is unequal: the fluorine atom attracts electron density away from the hydrogen (the bond is thus a polar covalent bond)

• The 'd+' and 'd-' symbols indicate partial positive and negative charges.
• The arrow indicates the "pull" of electrons off the hydrogen and towards the more electronegative atom
• In lithium fluoride the much greater relative electronegativity of the fluorine atom completely strips the electron from the lithium and the result is an ionic bond (no sharing of the electron)

A general rule of thumb for predicting the type of bond based upon electronegativity differences:

• If the electronegativities are equal (i.e. if the electronegativity difference is 0), the bond is non-polar covalent
• If the difference in electronegativities between the two atoms is greater than 0, but less than 2.0, the bond is polar covalent
• If the difference in electronegativities between the two atoms is 2.0, or greater, the bond is ionic
  
  

Questions on Homework

Some students have had questions regarding the homework. The sheet of Questions that I gave you at the end of class is due tomorrow morning at the beginning of class. The Practice Questions throughout the reading packet (Questions 1-28) are due on Monday. If you have any further questions, feel free to email me or give me a call. Have fun with Stoichiometry!

Day 4 - Organic Chemistry - Stoichiometry, Moles, Molars and Carbon Skeletons in the Closet

Physics: the science of matter, its motion, plus space and time.

Chemistry: the composition, structure and properties of matter & the change it undergoes during chemical reactions.

Inorganic chemistry: inorganic matter

Organic chemistry: organic matter-any compound based on a carbon skeleton

Physical chemistry: energy related studies

Analytical chemistry: analysis of samples to get chemical composition & structure

Biochemistry: chemical processes in living organisms

Here is a great graphic on the overview of Chemistry.

And here is the article I used to describe the different classes and geometry of hydrocarbons.

Here is a link to Polymers. (You can also find organic polymers starting on page 135 of your reading packet)

What is a mole? A moldywarp! No, not that sort of animal! We're into Chemistry now and moles have a whole new description.

The mole (symbol: mol) is the base unit that measures an amount of substance. The mole is a counting unit. One mole contains Avogadro's number (approximately 6.02214 x 10²³) entities (atoms, molecules, elemental particles).

A mole is much like "a dozen " in that both are absolute numbers (having no units) and can describe any type of elementary object (object made up of atoms). The mole's use, however, is usually limited to measurement of subatomic, atomic and molecular structures. (see page 97 of your reading packet)

The Molar (symbol: M) In chemistry, concentration is the measure of how much of a given substance there is mixed with another substance. This can apply to any sort of chemical mixture, but most frequently the concept is limited to homogeneous solutions. Molarity is the moles of solute divided by liters of solution. (see page 103 of your reading packet for more clarity)

Chemical Reactions:
1.) Acids & Bases
2.) Precipitation Reactions (ppt rxns) This link is a GREAT introduction and you get to PLAY!
3.)Oxidation & Reduction (redox rxns) A graphic overview of the reaction systems.

Four major factors affect the rate of a chemical reaction:

1.) Concentration of reactant
2.) presence of a catalyst
3.) increased temperature
4.) larger surface area of a reactant (solids and liquids)

You are responsible for the structure of Families of Organic Compounds (Hydrocarbons):
Alkanes
Alkenes
Alkynes
Aromatics

As well as the functional groups attached to them (hydrocarbons)
Alcohols
Ethers
Aldehydes
Ketones
Carboxylic Acids
Esters
Amines
Amides

R, R' and R" represent hydrocarbon groups

Day 4 –Organic Chemistry – Homework

Stoichiometry, Moles, Molars and Carbon Skeletons in the Closet

1. Why is carbon such a special atom? List its many features.

2. Describe the differences between Alkanes, Alkenes and Alkynes. Are there similarities?

3. What is an isomer? List 3 examples with structures.

4. Draw a cyclic compound and a heterocyclic compound noting differences and similarities. Describe the physical manifestations of these differences.

5. What makes “Superglue” so effective?

6. Using atomic masses of 12.01 for Carbon, 1.01 for Hydrogen, 39.10 for Potassium and 16.00 for Oxygen; what is the formula mass of Potassium Acetate? (C₂H₃KO₂) Show all calculations.

7. Balance the following equation:

NaOH + H₃PO₄ à Na₃PO₄ + H₂O

8. How many grams of CaCl₂ are needed to prepare 250 mL of 0.125M CaCl₂ solution?

Day 3 – Bohr’s Atom, Schrodinger’s Cat, Heisenberg’s Uncertainty & Witten’s Branes

·

· In the Bohr Model the neutrons and protons (symbolized by red and blue balls in the adjacent image) occupy a dense central region called the nucleus, and the electrons orbit the nucleus much like planets orbiting the Sun (but the orbits are not confined to a plane as is approximately true in the Solar System).

· The adjacent image is not to scale since in the realistic case the radius of the nucleus is about 100,000 times smaller than the radius of the entire atom,

· electrons are point particles without a physical extent.

· This similarity between a planetary model and the Bohr Model of the atom ultimately arises because the attractive gravitational force in a solar system and the attractive Coulomb (electrical) force between the positively charged nucleus and the negatively charged electrons in an atom are mathematically of the same form.

· (The form is the same, but the intrinsic strength of the Coulomb interaction is much larger than that of the gravitational interaction; in addition, there are positive and negative electrical charges so the Coulomb interaction can be either attractive or repulsive, but gravitation is always attractive in our present Universe.)

But the Orbits Are Quantized

Quantized energy levels in hydrogen

1. The basic feature of quantum mechanics that is incorporated in the Bohr Model and that is completely different from the analogous planetary model is that the energy of the particles in the Bohr atom is restricted to certain discrete values. One says that the energy is quantized. This means that only certain orbits with certain radii are allowed; orbits in between simply don't exist.

2.

3. These levels are labeled by an integer n that is called a quantum number. The lowest energy state is generally termed the ground state. The states with successively more energy than the ground state are called the first excited state, the second excited state, and so on. Beyond an energy called the ionization potential the single electron of the hydrogen atom is no longer bound to the atom. Then the energy levels form a continuum. In the case of hydrogen, this continuum starts at 13.6 eV above the ground state ("eV" stands for "electron-Volt", a common unit of energy in atomic physics).

Although this behavior may seem strange to our minds that are trained from birth by watching phenomena in the macroscopic world, this is the way things behave in the strange world of the quantum that holds sway at the atomic level.

Atomic Excitation and De-excitation

Atoms can make transitions between the orbits allowed by quantum mechanics by absorbing or emitting exactly the energy difference between the orbits. The following figure shows an atomic excitation cause by absorption of a photon and an atomic de-excitation caused by emission of a photon.

In each case the wavelength of the emitted or absorbed light is exactly such that the photon carries the energy difference between the two orbits. This energy may be calculated by dividing the product of the Planck constant and the speed of light hc by the wavelength of the light). Thus, an atom can absorb or emit only certain discrete wavelengths (or equivalently, frequencies or energies).

However there were concepts in the new quantum theory which gave major worries to many leading physicists. Einstein, in particular, worried about the element of 'chance' which had entered physics. In fact Rutherford had introduced spontaneous effect when discussing radio-active decay in 1900. In 1924 Einstein wrote:-

There are therefore now two theories of light, both indispensable, and - as one must admit today despite twenty years of tremendous effort on the part of theoretical physicists - without any logical connection.

The Elegant Universe is a NOVA special that is excellent at describing the current quandary of physics and string theory.

http://www.pbs.org/wgbh/nova/elegant/program.html

It is available free from this link. (Thank you, Joshua for the reference!)

Day 3 –Homework – Bohr’s Atom, Schrodinger’s Cat, Heisenberg’s Uncertainty & Witten’s Branes

1. Using the atomic models described by John Dalton, J.J. Thomson, Ernest Rutherford, Neils Bohr and Louis de Broglie and Erwin Schrodinger, what elements are the same? What elements differ?

2. What does it mean to have Quantized Energy Levels? How does this effect where an electron will be?

3. What force is described in the QED theory?

4. What force is described in the QCD theory?

5. Describe Schrodinger’s Cat Paradox. Why is this model used everywhere in the Quantum world?

6. Look up the Dirac Equation of 1928 and describe why it was so important to Quantum Mechanics.

7. Why is string theory so novel? What are some of the assumptions that the theory makes that will cause testing the theory to be difficult? What are some of the dangers of string theory?

8. What is the difference between fermions and a bosons?

9. What is Heisenberg’s Uncertainty Principle?

The Particle Adventure

Here is a great link to help you in understanding the different particles in Physics as well as answer many questions regarding supersymmetry, CERN and Fermilab

AS404- Day 2 – Gavity, Light & Failure of Classical Physics

Mass and Weight

The mass of an object is a fundamental property of the object; a numerical measure of its inertia; a fundamental measure of the amount of matter in the object. Definitions of mass often seem circular because it is such a fundamental quantity that it is hard to define in terms of something else. All mechanical quantities can be defined in terms of mass, length, and time. The usual symbol for mass is m and its SI unit is the kilogram. While the mass is normally considered to be an unchanging property of an object, at speeds approaching the speed of light one must consider the increase in the relativistic mass.

The weight of an object is the force of gravity on the object and may be defined as the mass times the acceleration of gravity, w = mg. Since the weight is a force, its SI unit is the newton. Density is mass/volume.

Weight

The weight of an object is defined as the force of gravity on the object and may be calculated as the mass times the acceleration of gravity, w = mg. Since the weight is a force, its SI unit is the newton.

For an object in free fall, so that gravity is the only force acting on it, then the expression for weight follows from Newton's second law.

You might well ask, as many do, "Why do you multiply the mass times the freefall acceleration of gravity when the mass is sitting at rest on the table?". The value of g allows you to determine the net gravity force if it were in freefall, and that net gravity force is the weight. Another approach is to consider "g" to be the measure of the intensity of the gravity field in Newtons/kg at your location. You can view the weight as a measure of the mass in kg times the intensity of the gravity field, 9.8 Newtons/kg under standard conditions.

Weightlessness

While the actual weight of a person is determined by his mass and the acceleration of gravity, one's "perceived weight" or "effective weight" comes from the fact that he is supported by floor, chair, etc. If all support is removed suddenly and the person begins to fall freely, he feels suddenly "weightless" - so weightlessness refers to a state of being in free fall in which there is no perceived support. The state of weightlessness can be achieved in several ways, all of which involve significant physical principles.

c as Speed Limit

The speed of light c is said to be the speed limit of the universe because nothing can be accelerated to the speed of light with respect to you. A common way of describing this situation is to say that as an object approaches the speed of light, its mass increases and more force must be exerted to produce a given acceleration. There are difficulties with the "changing mass" perspective, and it is generally preferable to say that the relativistic momentum and relativistic energy approach infinity at the speed of light. Since the net applied force is equal to the rate of change of momentum and the work done is equal to the change in energy, it would take an infinite time and an infinite amount of work to accelerate an object to the speed of light. (Sorry, Captain Kirk. We can't give you warp speed!)

A common resistance to the speed limit is to suggest that you just accelerate two different objects to more than half of the speed of light and point them toward each other, giving a relative speed greater than c. But that doesn't work! Time and space are interwoven in such a way that no one observer ever sees another object moving toward them at greater than c. The Einstein velocity addition deals with the transformation of velocities, always yielding a relative velocity less than c. It doesn't agree with your common sense, but it appears to be the way the universe works.

Wave-Particle Duality

Publicized early in the debate about whether light was composed of particles or waves, a wave-particle dual nature soon was found to be characteristic of electrons as well. The evidence for the description of light as waves was well established at the turn of the century when the photoelectric effect introduced firm evidence of a particle nature as well. On the other hand, the particle properties of electrons was well documented when the DeBroglie hypothesis and the subsequent experiments by Davisson and Germer established the wave nature of the electron.

The Photoelectric Effect

The details of the photoelectric effect were in direct contradiction to the expectations of very well developed classical physics. The explanation marked one of the major steps toward quantum theory.

The remarkable aspects of the photoelectric effect when it was first observed were: 1. The electrons were emitted immediately - no time lag! 2. Increasing the intensity of the light increased the number of photoelectrons, but not their maximum kinetic energy! 3. Red light will not cause the ejection of electrons, no matter what the intensity! 4. A weak violet light will eject only a few electrons, but their maximum kinetic energies are greater than those for intense light of longer wavelengths!

Experiment

Analysis of data from the photoelectric experiment showed that the energy of the ejected electrons was proportional to the frequency of the illuminating light. This showed that whatever was knocking the electrons out had an energy proportional to light frequency. The remarkable fact that the ejection energy was independent of the total energy of illumination showed that the interaction must be like that of a particle which gave all of its energy to the electron! This fit in well with Planck's hypothesis that light in the blackbody radiation experiment could exist only in discrete bundles with energy

E = hν

This equation says that the energy of a particle of light (E), called a photon, is proportional to its frequency (v), by the Plank constant (h). This means that photons with low frequencies, like radio waves, have lower energies than photons with high frequencies, like x-rays.

Wave-Particle Duality: Light

Does light consist of particles or waves? When one focuses upon the different types of phenomena observed with light, a strong case can be built for a wave picture:

Interference

Diffraction

Polarization

By the turn of the 20th century, most physicists were convinced by phenomena lke the above that light could be fully described by a wave, with no necessity for invoking a particle nature. But the story was not over.

Phenomenon	Can be explained in terms of waves.	Can be explained in terms of particles.
Reflection (mirror)
Refraction (glass)
Interference(soap bubbles & oil on pavement)
Diffraction (image is circle with dark band then a light band)
Polarization (planar & circular) sunglasses
Photoelectric effect

Most commonly observed phenomena with light can be explained by waves. But the photoelectric effect suggested a particle nature for light. Then electrons too were found to exhibit dual natures.

3-6: The Hypothesis of Light Quanta and the Photoelectric Effect

Look up this link Richardson

Average Mean Median and Mode: http://mathforum.org/library/drmath/view/57602.html

Day 2 - Gavity, Light & Failure of Classical Physics-Homework

1. Discuss the wave/particle theory of Quantum Mechanics.

2. What is electromagnetism?

3. What were J.J. Thompson’s contributions? Why did he get the Nobel Prize?

4. George Thompson won a Nobel Prize in Physics? Why? What ramifications did his work have?

5. Discuss Earnest Rutherford’s contributions and the physicists he inspired or taught. Why are his students important?

6. How did Plank’s constant (ħ) help with understanding the Photoelectric effect?

7. You weigh 72 kilograms on earth, how many pounds do you weigh on the Jupiter? (Jupiter’s gravity is 2.5 times greater than earth).

8. Tie your ankles together with a rope or yarn that is five feet long. Without removing the rope, drop your pants and put them back on inside out. Describe your reactions and understanding throughout this process.

The Basics - Definitions

AS404 –Day 1

The Goals of this Class:

· Difference between scientific thought and philosophical thought

· Learn the basic definitions used in the scientific community

· Learn the basic theories of Quantum Mechanics

· Learn the basic models of chemical structure and reactions

· Understand the cycles of sugar, fat and carbohydrate metabolism

· How living organisms breakdown, create, store and retrieve energy

Grading & The Final Exam:

· All the reading is required

· 50% of your grade is the final exam

· 50% of your grade is the homework and I take the median.

· Your final exam will be 60 questions answered in 2 hours or less

· Questions will be taken from class lecture, homework and all the readings

· 30% questions on Physics, 30% of the questions on Organic Chemistry and 30% of the questions on Biochemistry.

· You will be expected to memorize chemical structures, models and cycles

Definitions

A Form – An Outline of Powers and Limits - Mathematics

A System – A decision made before the question arises – A method used to answer a question

A Principle – A basic truth or law or assumption – Natural Laws

What is science? Study of the Natural World

What is religion? A strong belief in a supernatural power or powers

Science is about Cosmic Order: Religion is about Cosmic Purpose

What is physics? The study of matter and energy.

What is chemistry? The science of matter; how is matter put together? The branch of the natural sciences dealing with the composition of substances and their properties and reactions.

What is biology? The study of living organisms. A much more complex science. It is dealing with matter that is alive!

What is mathematics? The study of patterns of structure, change, and space

Physics is the foundation of all the other sciences. An understanding of science begins with an understanding of physics.

Scientists answer questions:

Who?

What? 90% populace & media focus on these

When?

Where?

How? Engineers – Take theory and put it into practice - lubrication & adhesion

Why? Scientists – Theoretical and Experimental arenas

Just a note: most of the lecture notes that I use are drawn from other websites, textbooks, and electronic library resources. Please do not take the following lecture notes as original! I have copied, compiled and collated. Basically, I have borrowed from the work of people MUCH smarter than me to bring this information to you. I have made every effort to put links in place to send you to the original web sites where this information came from.

The Four Known Universal Forces

Strong Nuclear Force

Electromagnetism

Weak Nuclear Force

Gravity

The Strong Nuclear Force

· It is the strongest

· It has the shortest distance of influence

· Its main job is to hold together the subatomic particles of the nucleus: called nucleons.

· like charges repel (+ +, or - -), and unlike charges attract (+ -).

· why would the nuclei of these atoms stay together?

· The strong nuclear force is created between nucleons by the exchange of particles called gluons. This exchange can be likened to constantly hitting a ping-pong ball or a tennis ball back and forth between two people. As long as this gluon exchange can happen, the strong force is able to hold the participating nucleons together.

· The nucleons must be extremely close together in order for this exchange to happen. The distance required is about the diameter of a proton or a neutron

· The dotted line surrounding the nucleon being approached represents any electrostatic repulsion that might be present due to the charges of the nucleons/particles that are involved. A particle must be able to cross this barrier in order for the strong force to "glue" the particles together

· In the case of approaching protons/nuclei, the closer they get, the more they feel the repulsion from the other proton/nucleus (the electromagnetic force). As a result, in order to get two protons/nuclei close enough to begin exchanging gluons, they must be moving extremely fast (which means the temperature must be really high), and/or they must be under immense pressure so that they are forced to get close enough to allow the exchange of gluons to create the strong force.

· Now, back to the nucleus. One thing that helps reduce the repulsion between protons within a nucleus is the presence of any neutrons. Since they have no charge they don't add to the repulsion already present, and they help separate the protons from each other so they don't feel as strong a repulsive force from any other nearby protons. Also, the neutrons are a source of more strong force for the nucleus since they participate in the meson exchange. These factors, coupled with the tight packing of protons in the nucleus so that they can exchange mesons creates enough strong force to overcome their mutual repulsion and force the nucleons to stay bound together.

· The preceding explanation shows the reason why it is easier to bombard a nucleus with neutrons than with protons. Since the neutrons have no charge, as they approach a positively charged nucleus they will not feel any repulsion. They therefore can easily "break" the electrostatic repulsion barrier to being exchanging mesons with the nucleus, thus becoming incorporated into it.

Electromagnetism

One of the four fundamental forces, the electromagnetic force manifests itself through the forces between charges (Coulomb's Law) and the magnetic force, both of which are summarized in the Lorentz force law. Fundamentally, both magnetic and electric forces are manifestations of an exchange force involving the exchange of photons . The quantum approach to the electromagnetic force is called quantum electrodynamics or QED. The electromagnetic force is a force of infinite range which obeys the inverse square law, and is of the same form as the gravity force.

The electromagnetic force holds atoms and molecules together. In fact, the forces of electric attraction and repulsion of electric charges are so dominant over the other three fundamental forces that they can be considered to be negligible as determiners of atomic and molecular structure. Even magnetic effects are usually apparent only at high resolutions, and as small corrections.

Weak Nuclear Force

One of the four fundamental forces, the weak interaction involves the exchange of the intermediate vector bosons, the W and the Z. Since the mass of these particles is on the order of 80 GeV, the uncertainty principle dictates a range of about 10^-18 meters which is about 0.1% of the diameter of a proton.

The weak interaction changes one flavor of quark into another. It is crucial to the structure of the universe in that

1. The sun would not burn without it since the weak interaction causes the transmutation p -> n so that deuterium can form and deuterium fusion can take place.

2. It is necessary for the buildup of heavy nuclei.

The role of the weak force in the transmutation of quarks makes it the interaction involved in many decays of nuclear particles which require a change of a quark from one flavor to another. It was in radioactive decay such as beta decay that the existence of the weak interaction was first revealed. The weak interaction is the only process in which a quark can change to another quark, or a lepton to another lepton - the so-called "flavor changes".

The discovery of the W and Z particles in 1983 was hailed as a confirmation of the theories which connect the weak force to the electromagnetic force in electroweak unification.

The weak interaction acts between both quarks and leptons, whereas the strong force does not act between leptons. "Leptons have no color, so they do not participate in the strong interactions; neutrinos have no charge, so they experience no electromagnetic forces; but all of them join in the weak interactions."(Griffiths)

Beta Radioactivity

Beta particles are just electrons from the nucleus, the term "beta particle" being an historical term used in the early description of radioactivity. The high energy electrons have greater range of penetration than alpha particles, but still much less than gamma rays. The radiation hazard from betas is greatest if they are ingested. Beta emission is accompanied by the emission of an electron antineutrino which shares the momentum and energy of the decay.

The emission of the electron's antiparticle, the positron, is also called beta decay. Beta decay can be seen as the decay of one of the neutrons to a proton via the weak interaction. The use of a weak interaction Feynman diagram can clarify the process.

Gravity

Gravity is the weakest of the four fundamental forces, yet it is the dominant force in the universe for shaping the large scale structure of galaxies, stars, etc. The gravitational force between two masses m₁ and m₂ is given by the relationship:

This is often called the "universal law of gravitation" and G the universal gravitation constant. It is an example of an inverse square law force. The force is always attractive and acts along the line joining the centers of mass of the two masses. The forces on the two masses are equal in size but opposite in direction, obeying Newton's third law. Viewed as an exchange force, the massless exchange particle is called the graviton.

The gravity force has the same form as Coulomb's law for the forces between electric charges, i.e., it is an inverse square law force which depends upon the product of the two interacting sources. This led Einstein to start with the electromagnetic force and gravity as the first attempt to demonstrate the unification of the fundamental forces. It turns out that this was the wrong place to start, and that gravity will be the last of the forces to unify with the other three forces. Electroweak unification (unification of the electromagnetic and weak forces) was demonstrated in 1983, a result which could not be anticipated in the time of Einstein's search. It now appears that the common form of the gravity and electromagnetic forces arises from the fact that each of them involves an exchange particle of zero mass, not because of an inherent symmetry which would make them easy to unify.

Examples of Trajectories

Common misconceptions about guns:

A dropped bullet will hit the ground before one which is fired from a gun.

As shown in the illustration of a horizontal launch, gravity acts the same way on both bullets, giving them the same downward acceleration and making them strike the ground at the same time if the bullet is fired horizontally over level ground.

Bullets fired from high-powered rifles drop only a few inches in hundreds of yards.

Fired at twice the speed of sound, a bullet will drop over 3 inches in 100 yards, and at 300 yards downrange will have dropped about 30 inches. Plug in numbers into the bullet drop calculation to see for yourself. Ammunition manufacturers contribute to this misconception by stating the drop of their projectiles as just the extra drop caused by frictional drag compared to an ideal frictionless projectile.

Drop of a Bullet

If air friction is neglected, then the drop of a bullet fired horizontally can be treated as an ordinary horizontal trajectory. The air friction is significant, so this is an idealization.

Inverse Square Law, General

Any point source which spreads its influence equally in all directions without a limit to its range will obey the inverse square law. This comes from strictly geometrical considerations. The intensity of the influence at any given radius r is the source strength divided by the area of the sphere. Being strictly geometric in its origin, the inverse square law applies to diverse phenomena. Point sources of gravitational force, electric field, light, sound or radiation obey the inverse square law. It is a subject of continuing debate with a source such as a skunk on top of a flag pole; will it's smell drop off according to the inverse square law?

Inverse Square Law, Gravity

As one of the fields which obey the general inverse square law, the gravity field can be put in the form shown below, showing that the acceleration of gravity, g, is an expression of the intensity of the gravity field.

Inverse Square Law, Electric

As one of the fields which obey the general inverse square law, the electric field of a point charge can be put in the form shown below where point charge Q is the source of the field. The electric force in Coulomb's law follows the inverse square law.

Inverse Square Law, Radiation

As one of the fields which obey the general inverse square law, a point radiation source can be characterized by the relationship below whether you are talking about Roentgens , rads, or rems . All measures of exposure will drop off by inverse square law.

The source is described by a general "source strength" S because there are many ways to characterize a radiation source - by grams of a radioactive isotope, source strength in Curies, etc. For any such description of the source, if you have determined the amount of radiation per unit area reaching 1 meter, then it will be one fourth as much at 2 meters.

Homework Day 1 -Quantum Mechanics

1. Define the differences and similarities of a Confederation, a Democracy, a Republic and how they interact with the populations of people under them.

2. Define Science and Religion. Explain the different methods used by each to obtain knowledge. Are there any similarities?

3. Define Physics, Chemistry, Biology, Biochemistry and Mathematics. How do these disciplines build upon one another?

4. Define Classical Physics and Quantum Mechanics. Explain the challenges that Einstein had with Newton’s work and what he had to do to overcome preexisting paradigms.

5. What was the Copenhagen Interpretation and who was involved? Why was Einstein so upset by this?

6. What are the four known forces in our Universe? Give examples of what they do and how they interact with matter.

7. What is the difference between Average, Mean, Median and Mode?

8. What is a positive charge? A negative charge? Why was Benjamin Franklin’s assignments “unfortunate”?