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Gamsat notes

Section 3: Reasoning in Biological and Physical Sciences


Curriculum Overview
Physical Chemistry
Bonding
Ions and ionic bonding, Lattice enthalpies, hydrogen bonding, covalent bonds, octet rule, shared electrons, double and
triple bonds
Addition equations; resonance structures, substitution equations

Solution chemistry
Ions in solution, molarity, molality, mole fraction, solubility, concentration, saturation, solubility product K.
Effect of temperature on solubility of solids and of pressure on solubility of gases
Raoults law, BP & MP elevation/depression, osmosis & osmotic pressure, colloids

Reactions
Oxidation/reduction, activity series, balancing equations, use of half-reactions

Gases
Boyles, Charles and ideal gas laws, Avogadros law, STP, Daltons law of partial pressures, diffusion and effusion of
gases, Grahams law
Van der Waals forces and the real gas equation, kinetic theory of gases, Maxwells distribution of gaseous molecular
speeds

Phases and phase equilibria


Melting, vaporising, subliming, phase diagrams, triple point, latent heat
Ion and dipole interaction and effects on MP & BP. vapour pressure, distillation, surface tension, capillary action

Reaction rates
First order and second order reactions, half-life of reactions, rate effects of catalysts/enzymes
Activation energy, Arrhenius behaviour and rate dependence on temperature, reaction paths and rate-determining
steps

Chemical equilibrium
Equilibrium constant in terms of concentrations or partial pressures, reaction quotient, Le Chateliers principle
Effects of changes in concentration on equilibria, effects of pressure and temperature on equilibria

Acids and bases


Arrhenius acids and bases, Bronsted-Lowry acids and bases, conjugate bases, conjugate acids, pH, pOH, pl, pK1, pl
Titrations, indicators, pH curves, titrations between strong/weak acids and strong/weak bases
Common ion effect, buffer solutions, Henderson- Hasselbalch equation, buffer capacity

Thermodynamics and thermochemistry


Enthalpy and the first law of thermodynamics, endothermic and exothermic reactions, Hesss law
Entropy, Boltzmanns constant, standard molar entropies, the second law of thermodynamics
Standard free energies of formation and reaction

Electrochemistry
Galvanic cells, standard reduction potentials and the electrochemical series, standard cell potential, Faradays constant,
Nemst equation
Electrolysis, electroplating, electrochemical corrosion

Nuclear chemistry
Quanta, photons, Plancks constant, Balmer... series, Rydberg constant
Radioactivity, decay and half-life, a and particles, y rays, use of radioactive isotopes, isotopic dating
Nuclear fission and nuclear fusion, nuclear reactions, nuclear binding energy
Organic Chemistry & Biochemistry
IUPAC system
Rules for naming organic compounds (leading to interpreting names in order to determine structures)

Alkanes and cycloalkanes, alkenes and alkynes


Physical and chemical properties of each group, Addition polymers

Aromatic compounds
Nitration, sulfonation, halogenation, benzene derivatives, fused rings

Resonance
Resonance forms, resonance hybrids, stability, contribution of resonance forms to the resonance hybrid

Reaction mechanisms
Addition reactions, Markovnikovs rule
Substitution reactions, SN 1 and SN2 reactions, suitable targets and nucleophiles
E1 and E2 elimination reactions, Aldol condensation

Alcohols
Dehydration to give an alkene, dehydration to give an ether
Oxidation of primary alcohol to aldehyde to carboxylic acid, oxidation of secondary alcohol to ketone
Acidic nature of phenols, physical properties of alcohols and phenols

Ethers, thiols (mercaptans), thioethers (sulfides), disulphides, alkyl and aryl halides

Aldehydes & ketones linking lo carbohydrates


Intermolecular hydrogen bonding, polarity, bonding with water, Tollens and Benedicts tests for aldehydes
Substitution reactions to form acetals, ketals, reduction to alcohols, keto-enol tautomerism

Carboxylic acids
Hydrogen bonding, carboxylic acid salts, acetic acid, oxalic acid, lactic acid, citric acid

Carboxylic esters linking to lipids


Hydrogen bonding, esterification from acid and alcohol by dehydration
Hydrolysis of carboxylic esters by acid or base catalysts, esters and anhydrides of phosphoric acid

Amines
Bonding of hydrogen to nitrogen, dissolve to form ions, separation of amine salts via low pH solutions

Amides & amino acids linking lo proteins as polyamino acids


Hydrolysis of amides by acid or base catalysts, hydrolysis of amides by enzymes catalysts
Amino acids: 19 common L-forms and glycine; ionic nature (zwitterions), act as buffers

Isomers
Constitutional isomers:
Different carbon skeletons, different functional groups, different positions of the same functional group
Stereoisomers:
Fischer projections, chirality, both R & S and D & L enantiomers
cis & trans diastereoisomers in alkenes and in cyclic compounds. E & Z configurations

Spectrometry and spectroscopy


Mass spectrometry, infra-red spectroscopy, ultra-violet & visible-light spectroscopy, NMR spectroscopy

Carbohydrates linking to aldehydes and ketones


Monosaccharides:
a & , D-glucose
a & , D-mannose, D-galactose
D-ribose, a-D-fructose
Disaccharides:
maltose two a-D-glucose rings
lactose -D-ga lactose & -D-glucose
sucrose a-D-glucose & fi-D-fructose
Polysaccharides:
starch a-D-glucose
glycogen a-D-glucose
cellulose -D--glucose

Proteins linking to amino acids


Polyaminoacids: peptides, polypeptides, proteins
Proteins: solubility, isoelectric points, zwitterions; primary structure (disulphide linkages), secondary structure (a-helix, -
pleated sheet.
Triple helix of collagen, hydrogen bonding between CO and NH groups), tertiary structure (disulphide bridges, hydrogen
bond bridges, salt bridges, hydrophobic interactions), quaternary structure
Enzymes: rate of enzymatic activityenzyme and substrate concentrations, temperature, pH, action of inhibitors;
mechanisms of enzyme
Activity; cofactors, regulatory sites, feedback inhibition

Lipids linking to carboxylic esters


Fats: esters based on glycerol; triglycerides, saturated/unsaturated fats: hydrogenation; saponification; lipid bilayers
Complex lipids: phosphoglycerides, particularly lecithin, sphingolipids, glycolipids, particularly the cerebrosides
Steroids: HDL and LDL cholesterol; aldosterone; cortisol and cortisone; testosterone. oestradiol and progesterone

Physics
Translational motion
F=ma, velocity equations, circular motion, friction, motion under gravity alone, projectile motion, gravitational force

Equilibrium
Addition of vectors and components of vectors, forces in statics, forces in pulley systems/muscles, mechanical
advantage

Momentum, work, energy, power


Impulse, change in momentum, work, change in energy, kinetic energy, gravitational potential energy
Hookes law and elastic potential energy, power as the rate of doing work

Waves and periodic motion


Transverse and longitudinal waves, y = f.X , refection of waves, Huygenss principle, phase, refraction, diffraction,
interference
Periodic motion and, in particular, simple harmonic motion, relationship between simple harmonic motion and circular
motion

Light
Laws of reflection, plane and curved mirrors, mirror equation
Refraction, refractive index, Snells law, total internal reflection, optical fibres, concave and convex lenses, lens
equation, optical instruments
Overlapping diffraction and interference patterns

Sound
Transmission and relative speed of sound in solids/liquids/gases
Two source interference, Doppler effect, harmonics and resonance in pipes and strings

Solids, liquids and gases


Density and specific gravity, Archimedes principle
Hydrostatic pressure, continuity equation, Bernoullis equation, viscosity, elasticity

Electrostatics
Charges on insulators, electric fields and field strength
Coulombs law, electric potential energy, potential difference

Electric current
Batteries, resistors, current, voltage, resistance, power, Ohms law, Kirchhoffs laws
Parallel plate capacitors, series and parallel connections of cells, resistors and capacitors

Electromagnetism
Magnets and magnetic fields, magnetic effects of electricity, solenoids, force on a conductor in a magnetic field, electric
motors, electric meters
Coils moving in magnetic fields, Faradays law, transformers, electric generators

Electromagnetic radiation, atomic and nuclear physics


Photoelectric effect, X-rays, photon movement and Compton scattering, wave/particle duality, quantum energy levels
Radioactive decay, a and B-particles, y rays, half-life, isotopes

Note: Biology is a diverse area of knowledge and First Year Biology is not necessarily a meaningful set. However, one
semester of cell biology, including some appropriate biochemistry, is usual followed with genetics or with human
anatomy/physiology.
The key areas are cell biology, with its associated biochemistry, cellular reproduction and genetics, and homeostasis.

Cell Biology and Biochemistry


Structure of animal and plant cells
Plasma membrane, nuclear envelope, chromatin, nucleolus, ribosomes, rough and smooth endoplasmic reticulum, golgi
bodies, mitochondria, microfilaments, microtubules, peroxisome (or microbody), as well as cell wall, plasmodesmata,
plastids, chloroplasts, vacuole, tonoplast, centrioles, lysosome, cilia and flagella

Fluid mosaic model of membranes


Selective permeability, osmosis, facilitated diffusion, active transport, the sodium-potassium pump, the proton pump
Exocytosis, endocytosis

Nucleic acids, genetic codes & protein synthesis


RNA and DNA, bases, nucleotides, primary and secondary structure of DNA, DNA replication, mRNA, tRNA and rRNA
Transcription and translation of genetic codes, genes and gene regulation

Cellular respiration (biochemical approach)


Glycolysis, -oxidation of fatty acids, citric acid cycle (Krebs cycle), electron transport chain, oxidative phosphorylation,
chemiosmosis
ATP synthesis: AMP, ADP, ATP. NAD, FAD, NADH, FADH, acetyl-CoA
Pentose phosphate pathway, ascorbic acid pathway, gluconeogenesis
Glycogen metabolism, formation of ketone bodies, oxidation of amino acids, urea cycle

Photosynthesis
Chloroplasts, light reactions, Calvin-Benson cycle, photo-oxidation of chlorophyll, cyclic and noncyclic
photophosphorylation
Chemiosmosis in chloroplasts and mitochondria, C3, C4 and CAM pathways

Cellular Reproduction and Genetics


Cellular reproduction and embryogenesis
Eukaryote chromosomes, the cell cycle, comparison between mitosis and meiosis, fertilisation, cleavage, gastrulation,
organogenesis

Inheritance and genetic codes


Mendels laws, dominance, recessiveness, chromosomes and genetic variation, incomplete dominance in genes
Codominance, multiple alleles, inheritance of traits and disorders, genotypes and phenotypes, pleiotropy, epistasis,
pedigree analysis
Linked genes, crossing-over, sex linked traits, mutations of genes

Human Biology
Musculoskeletal system
Skeletal system, bone tissue and formation, cartilage, calcium regulation, axial and appendicular skeleton, joints and
movement, disorders/diseases
Muscular system and muscle tissue, functions and properties, disorders/diseases

Human digestive system


Nutrition and nutritional disorders, digestion in mouth, stomach, small intestine, large intestine, disorders/diseases
Structure and functions of pancreas, liver and gall bladder, disorders/diseases

Circulatory system
Components of blood including erythrocytes, leukocytes, platelets, plasma, haemoglobin and their functions
Blood groups, antigens and antibodies, blood vessels, blood flow, materials transported including carriage of O2 and
CO2, disorders/diseases
Structure and action of the heart, blood pressure, circulation, disorders/diseases

Respiratory system
Nose, pharynx, larynx, trachea, bronchi, bronchioles, alveoli
Structure and function of lungs, the control of respiratory gases, gas exchange to circulatory system, disorders/diseases

Urinary system
Homeostasis, structure and functions of kidneys, ureter, urinary bladder, disorders/diseases
Glomerular filtration, selective reabsorption of solutes, reabsorption and regulation of water, regulation of salt

Nervous system
Central nervous system, structure and properties of neurones, neuroglia, meninges, cerebrospinal fluid
Brain, spinal cord, visceral nerves, disorders/diseases
Peripheral, autonomic, sympathetic and parasympathetic nervous systems, disorders/diseases

Reproductive system
Female reproductive system, disorders/diseases, male reproductive system, disorders/diseases
Sexually transmitted diseases, methods of birth control

Endocrine system
Hypothalamus, pituitary, thyroid, parathyroid, adrenal, pineal and thymus glands, disorders/diseases
Major hormones, stress reactions, growth regulation

Disease prevention and the immune system


Non-specific and specific defence mechanisms, antibodies, immunity, allergies, lymphatic system, lymph nodes, effector
cells, disorders/diseases

Homeostasis
Positive and negative feedback
Content Review
PHYSICAL CHEMISTRY
Things to consider
Representation of structures and reactions
Fishcer, lewis, vespr, molecular orbital
What causes reactions, how can I predict them
What are the categories of reaction (substitution, addition, double displacement, combustion, decomposition) and do
they apply to ALL reactions? Where does redox fit into this?
Note the difference between REACTION TYPE (above) and REACTION MECHANISM
Types and subtypes of bonding, where do they apply?
Covalent and ionic big categories
Dative, pi and sigma, resonance, salt bridge, coordination chemistry, hydrogen bond, Van der Waals (and other
polymer type bonds) smaller catagories
Naming conventions rules, sequences and orders
Definitions of things, context of the definition of things (ie. the category being considered (eg. organic or inorganic)
might change the definition)
Electronegativity and Acidity

Chemical equations represent chemical reactions, in either their entirety or in a simplified form
Chemical reactions occur due to intrinsic and extrinsic factors
Intrinsic factors include energetics (single atom based or overall], electron count, shape and geometry, orbital fillings,
and the relationship of all of these factors to themselves (eg. how electron count in their orbitals of a base atom affect
its geometry) and how they relate between atoms (ie. how the geometries affect whether reactions will occur), valence
and oxidation state ie. thermodynamics, electrochemistry, and chemical geometry, and the relation between all
three. Scale is from single atom, molecule, intra-molecular, intermolecular, and entire chemical system
Extrinsic factors include temperature, pressure, volume, general energy, catalysts, other participatory molecules (eg.
water), environmental factors which might affect oxidation state/number
Chemical reaction types can be classified, sometimes based of overall equation (substitution, addition, double
displacement, combustion, decomposition), sometimes based off electron movements, sometimes based off products,
sometimes whether it involves organic or inorganic molecules, the overall thermodynamics and energetics (exogenic,
endogenic, spontaneous or not)
The reaction mechanism defines how the intrinsic factors of a group of atoms and molecules stepwise produce a
chemical reaction, starting from reactants, through to transition states, through to products
Sometimes reaction mechanisms seem to be highly dependent also on extrinsic factors, and a combination of extrinsic,
intrinsic, the relationship between both, seem to produce surface potential maps of chemical reactions and atomic
coordinates. Whether or not a reaction can occur, and why they occur, is thus a combination of intrinsic and extrinsic
factors, and is analysed by Enthalpy calculations/profiles, Gibbs energy calculation/profiles,
Bond types are typically described (ie. ionic, covalent further subtypes) after reaction mechanisms have taken place
Chemical kinetics analyses speed of reactions (typically requires knowledge of reaction mechanisms), dynamic
equilibriums
Combination of thermodynamics and kinetics produces relationships between Free energy of a chemical system and
equilibrium constant

Perhaps best to think of reaction types, mechanisms and bonds in this way
Organic or inorganic reaction type y produced by reaction mechanism x, gives molecule z which contains w bond
type/s

https://en.wikipedia.org/wiki/Chemical_reaction
http://www.chem.canterbury.ac.nz/LetsTalkChemistry/ElectronicVersion/ElectronicVersionNew/theindex.shtml

Atomic theory
Conservation of matter
When a chemical or physical change occurs, matter is actually neither created nor destroyed; the mass remains the
same and the number and types of atoms present before and after the reaction remain the same as well.
In a chemical reaction, the atoms and molecules react with each other to form new combinations.
In a physical reaction, they may be spread further apart or crowded closer together. This phenomenon is called the Law
of Conservation of Mass/Matter.
Law of Constant Composition
The Law of Constant Composition holds that any specimen of a chemical compound will contain the same atoms
combined together in a fixed proportion. Water always consists of two hydrogen atoms and one oxygen atom,
regardless of whether the water fell as rain, was scooped from the ocean, or drawn up from an Artesian well.
Law of Multiple Proportions
The Law of Multiple Proportions holds that any two elements can also combine in different proportions to form
different compounds. The ratio within each compound is constant, but differs between compounds. An example would
be carbon dioxide (CO2) and carbon monoxide (CO).

An atom is now defined as the smallest unit of an element which retains the characteristics of that element and can take
part in a chemical reaction. The one consistent characteristic that now defines an element is its atomic number which is
the number of protons in its nucleus. The atomic number is constant, regardless of whether the atom is bonded in a
compound, free as an ion, or decaying into various isotopes.

Atomic Structure
http://www.chemguide.co.uk/basicorg/bonding/orbitals.html#top

-Original electron peas in positive pudding shown incorrect by Rutherford, who demonstrates positive centre nucleus
surrounded by electrons, predicted that a neutron buffered the protons in the nucleus and allowed them to stay
together
- Refined by Bohr into orbital model for electrons, orbiting the nucleus at a defined distance and on a defined path,
similar to the planets of our solar system orbiting the sun. He proposed four principal energy levels and also realized
that the electrons farthest from the nucleus had a higher energy level than those nearer to the nucleus.
- Further refined by Erwin Schrdinger, who proposed sublevels within Bohr's four orbital shells and developed a
mathematical equation to predict the shape of the orbitals and the likely location of the electrons; and Werner
Heisenberg, who postulated that it is impossible to simultaneously determine the position of an electron and its speed
and direction of movement (Uncertainty Principle).
- Collectively, Bohr, Schrdinger, and Heisenberg together formed the foundation for quantum mechanics. Electron
configurations are essentially maps of atomic structure. Schrdinger's four sublevels eventually came to be called s, p, d,
and f; the letters arose from descriptions of the line patterns of various elements when viewed by spectroscopy, and
stood for Sharp, Principal, Diffuse, and Fundamental. Each sublevel has a defined number of orbitals, and each orbital
can contain up to two electrons with opposite spins.
4 Quantum numbers =
Principle energy level (1,2,3,4) Sublevel (s,p,d,f) Orbital (x,y,z [others too]) Spin (+/- 0.5)
MORE HERE FOR QUANTUM NUMBER RULES

When the electrons fill the orbitals, they occupy the lowest energy orbitals
that are available. However, electron configurations become more
complicated at higher energy levels, because the 4s orbital actually has less
energy than the 3d, 5s has less than 4d, and 5p and 6s have less energy than
4f.

Electron configuration rules:


https://en.wikipedia.org/wiki/Aufbau_principle
-Distribution of electrons into the different levels and orbitals of an atom is
called its electron configuration.
-Atom electronic configuration written as the name of the level followed by
the number of electrons in that level as a superscript, eg. Carbon (atomic
number 6) has a configuration of 1s2, 2s2, 2p2
-Each successive atomic number has the same configuration
as the previous one PLUS one more electron; this is called the Aufbau
Principle.
-The pairing of electrons will start only after each orbital of a sub-shell is occupied by one electron, called Hund's Rule.
For example, carbon's 2p shell, which has three orbitals, the two electrons in that level will occupy separate orbitals
instead of the same one.

The Periodic Table


All known elements are arranged in a table in order of increasing atomic numbers. It is known that the physical and
chemical properties of an element are a function of its atomic number.

Atomic mass is a relative quantity without a standard unit.


MORE HERE
The elements are also informally grouped into categories, based on similarities of reactivity and
other properties. The common designations are as follows:

These informal categories roughly correlate with the groups, especially for the metals, halogens, and inert (noble) gases.
The noble gases are so called because their valence (outermost) shell is full, therefore they do not readily react with
other elements.
The valence shell is the most important, as it determines the element's reactivity. For that reason, regions of the
periodic table are also referred to as blocks, named for the subshell in which the highest-energy electron is located.
The s-block comprises the first two (leftmost) columns of the table, plus helium.
The p-block includes the six rightmost columns of the table, excluding helium which is part of the s-block
The d-block comprises the transition metals
The f-block the rare earth metals
In many ("short") versions of the periodic table, the f-block is placed separately below the rest of
the table.

Compounds, reactivity and Ions


A compound is a pure substance made up of two or more elements in a defined proportion. They are chemically bonded
and cannot be broken down by physical means.

The reactivity of elements is related to their atomic structure and is governed by the "Octet Rule," which states that
because the most stable electron configuration has completely filled s- and p orbitals in the outermost shell (the noble
gases), elements tend to gain or lose electrons to reach the configuration of the nearest noble gas. The elements whose
electron count is one more or one less than a noble gas (the alkali metals and the halogens) are the most reactive.
Atoms react with each other to form molecules by losing, gaining or sharing electrons. When an atom loses an electron
in a chemical reaction, the number of protons in its nucleus exceeds the number of electrons and it acquires a net
positive charge.
Positively charged atoms are called cations.
Similarly, when an atom gains an electron to achieve a stable octet, it becomes negatively charged and is known as an
anion.

The energy required to cause an atom to gain or lose one or more electrons is called ionization energy. As one moves
across a period, the size of the atoms increase with increasing atomic number and therefore, elements toward the right
of the periodic table have higher ionization energies than those toward the left (more protons = more attractive pull
[?]). It follows that elements at the left of the periodic table will lose electrons easily and those towards the right will
gain electrons in order to achieve the noble gas configuration.
Consider the example of sodium chloride (table salt): Sodium (atomic number, 11; electron configuration, [Ne]3s 1) has
only one electron in its outer orbital which can be lost easily to achieve stability. Chlorine (atomic number, 17; electron
configuration, [Ne]3s23p5) can accommodate one more electron in its outer orbital to become stable. So, sodium
"donates" its outer-shell (valence) electron to chlorine and they bond together to form the compound NaCl, sodium
chloride. This is referred to as an ionic bond; sodium is a cation and chlorine is an anion.

More notes on Ionisation Energy


The first ionisation energy is the energy required to remove the most loosely held electron from one mole of gaseous
atoms to produce 1 mole of gaseous ions each with a charge of 1+.
This is more easily seen in symbol terms.

It is the energy needed to carry out this change per mole of X.


The state symbols - (g) - are essential. When you are talking about ionisation energies, everything must be present in the
gas state. Ionisation energies are measured in kJ mol-1 (kilojoules per mole). They vary in size from 381 (which you
would consider very low) up to 2370 (which is very high). All elements have a first ionisation energy - even atoms which
don't form positive ions in test tubes. The reason that helium (1st I.E. = 2370 kJ mol-1) doesn't normally form a positive
ion is because of the huge amount of energy that would be needed to remove one of its electrons.

Periodic Table and factors affecting Ionisation Energies

https://en.wikipedia.org/wiki/Ionization_energy
http://www.chemguide.co.uk/atoms/properties/ies.html

Chemical Bonds and Bonding


https://en.wikipedia.org/wiki/Coordination_complex
http://www.chemguide.co.uk/inorganic/complexions/whatis.html#top
http://www.chemguide.co.uk/atoms/bonding/dative.html#top
http://www.chemguide.co.uk/atoms/bonding/covalent.html#top
A chemical bond is the attractive force which holds two or more atoms within a molecule. Within a given compound,
each molecule is exactly the same as all of the others; the bonded atoms are the same distance apart (bond length) and
arranged with the same geometry (bond angle) I dont believe this is true?
The amount of energy required to break a bond is called the bonding energy. All chemical bonds are the result of
electrical attraction between atoms. They involve atoms either "giving", "receiving", or sharing electrons in order to
reach the most stable noble gas electron configuration, which is to have the outermost or valence shell either
completely filled or completely empty. The two primary types of chemical bonds are: ionic and covalent.

Ionic Bonding
With the exception of the noble gases, a neutral atom of almost any element is not particularly stable. It tends to gain or
lose electrons in order to reach a stable configuration, becoming an ion.
If it loses electrons it becomes a positively charged cation; if it gains
electrons it becomes a negatively charged anion.

Ions of equal but opposite charge are attracted to one another and
form ionic bonds. A common example is sodium chloride (NaCl), table
salt. Sodium, with an electron configuration of 1s22s22p63s1, would be
more stable if it lost its 3s electron and became a cation; its charge
would be +1. Chlorine, with a configuration of 1s22p63s23p5, would be
more stable if it gained an electron to fill its 3p shell to its capacity of 6;
it would be an anion with a charge of -1. Sodium's +1 charge and
chlorine's -1 charge are equal and opposite, thus they attract one
another. Sodium's one 3s electron joins chlorine's 3p shell to fill it. Both
atoms have achieved a stable configuration and a strong bond.

Atoms that become anions (i.e. gain electrons) are said to be highly
electronegative; those that become cations (i.e. lose electrons) are said
to have low electronegativity.

The simplest ionic bond is one between two monoatomic ions.


However, most ions are polyatomic, i.e. made up of multiple types of
atoms see pic to right

Most ionic compounds have very high melting points and are good
conductors of electricity when melted or dissolved in water. The ionic attraction is between masses of atoms and there
are not discrete molecules; rather, they tend to form a crystalline structure.

Covalent Bonds
Compounds formed by covalent bonds do form discrete molecules. They are generally nonmetallic elements, and
involve the sharing of electrons rather than transfer as in ionic bonds. They tend to have low melting points and do not
conduct electricity. The simplest covalent bond occurs between two hydrogen atoms to form the H2 molecule. Each
hydrogen atom has a single electron, with room in its orbital for one more. When two hydrogen atoms are close enough
together, their orbitals overlap and form a single molecular orbital. Both electrons now orbit both nuclei, and a stable
covalent molecule has been formed.

Chemical Bond Energy Considerations


http://hyperphysics.phy-astr.gsu.edu/hbase/Chemical/bondd.html
A chemical bond forms when it is energetically favorable, i.e., when the energy of the bonded atoms is less than the
energies of the separated atoms. Some of the types of tabulated data associated with chemical bonds are:
Ionization energy: the energy required to remove an electron from one mole of gaseous atoms to produce 1 mole of
gaseous ions each with a charge of 1+.
Electron affinity: the energy change when a neutral atom attracts an electron to become a negative ion.
Electronegativity: the ability of an atom in a molecule to draw bonding

Lewis structures rely upon the octet rule, which states that atoms tend to be most stable when their valence
(outermost) shell contains eight (or two for s-block elements) electrons. The dot diagrams show the number of
electrons in the atom's valence shell. That number subtracted from eight if it is more than four, or the number itself if it
is less than four gives the element's covalency, the number of electrons available for bonding.
NOTE: MORE on the skill of making Lewis structures

It is possible for atoms to share more than one pair of electrons and to form multiple covalent bonds, eg. oxygen
molecule, O2, is an example of a double bond oxygen's covalency is two, two atoms share two pairs of electrons,
double bond can be represented by two dashes: O=O.

Covalent compounds are named according to their chemical formula. The first word of the name is the central atom of
the molecule, usually the least abundant element in the formula. The second word of the name is the other atom in the
compound, usually with the suffix -ide added. If there are multiples of the same atom, a prefix such as di- (2), tri- (3),
tetra- (4), penta- (5), or hexa- (6) is added. Thus, CO2 is carbon dioxide.

In some covalent compounds the electrons are not shared equally. The bond in this case is called a polar covalent bond
and the compound is a polar compound. Polarity of bonds is a spectrum, not a fixed category. Ionic bonds are the most
highly polar, and the covalent bonds between identical atoms (as in O2) are nonpolar. The degree of polarity is
determined by the electronegativity of the elements that are bonded. Generally, elements to the right of the periodic
table are more electronegative than those to the left. If the difference between the electronegativities of the two
elements is greater than 1.7, the bond is considered ionic rather than covalent. Research into electronegativity and
polarity of bonds earned Linus Pauling the first of his two Nobel Prizes in 1954.

Chemical Equations
The Mole and Calculations (SKILL)
Quantities of atoms and molecules are expressed in terms of moles. One mole is defined as the number of particles of a
substance equal to the number of atoms in twelve grams of C-12. By various experimental methods that number has
been determined to be 602,000,000,000,000,000,000,000, or 6.02 x 1023. This is called Avogadro's number. One mole
of any substance weighs a number of grams equal to its formula weight. Thus, one mole of NaCl weighs 58.44277 grams.
The mole is used in calculating quantities for chemical equations and concentrations of solutions.

Using the mole concept along with chemical formulas and formula weights, one can calculate the quantities needed of
each reactant to yield a desired product. All of these calculations are collectively called stoichiometry. For example, the
compound FeS (iron II sulfide, used in treating anemia) is made by the following reaction: Fe + S FeS. The formula tells
us that one atom of iron is needed to react with each atom of sulfur. But since individual atoms are too small to be
measured, we can say that one mole of iron is needed for each mole of sulfur. From their atomic masses we then know
that we need 55.85 grams of iron and 32.07 grams of sulfur, and the resulting one mole of the compound would weigh
87.92 grams. Of course, if we need more than 88 grams of FeS, we can multiply the mole weights.

If we need 500 grams of FeS, we divide the desired quantity (500g) by the mole weight (87.92) to find the number of
moles of FeS--5.687. From the formula we know that one mole of each element combines to make one mole of
compound, thus to obtain 5.687 moles of FeS we need that many moles of each element. Multiplying the mole weight
of each element by 5.687 tells us that we need 317.62 grams of iron and 182.38 grams of sulfur. We can also calculate
the mass percentage of each element. 317.62 grams of iron make up 63.5% of the mass of the 500 grams of FeS (317.62
divided by 500).

Writing and Balancing Equations


Chemical equations describe chemical processes or reactions. A variety of symbols are used. Often the physical state of
each compound (solid, liquid, or gas) is indicated, by the letter (s), (l), or (g) beside the name of the compound. If heat is
required to bring about the reaction, is placed above the reaction arrow to indicate that. An example is the
decomposition of solid calcium carbonate (CaCO3) into solid calcium oxide (CaO) and gaseous carbon dioxide (CO2) by
heating. The equation is expressed as follows: CaCO3 (s) CaO (s) + CO2 (g).

Solutions and Solubility


A solution is a homogeneous mixture of two or more substances which do not tend to separate from the solution unless
made to do so by physical means. No chemical bonds are broken when solutions are separated. An example would be
separating a solution of salt and water by evaporating or distilling away the water to leave behind pure salt. A
homogeneous mixture is one in which all parts of the mixture have the same composition. In any solution with two
components, one is the solvent and the other is the solute.
The process of mixing a solvent and solute is called dissolving. The solute is dissolved and spread throughout the
volume of the solvent. The ability of a solute to dissolve in a solvent is called solubility, expressed as the number of
grams of solute that can be dissolved in 100 ml of solvent. Some solutes have infinite solubility, such as ethyl or
isopropyl alcohol in water. There is no limit to the quantity of these alcohols which can be dissolved in 100 ml of water.
Sodium chloride has a solubility of 36 grams in 100 ml of water.
Ie. solubility = grams solute per 100ml solvent

Various factors affect solubility. The most important is the degree of polarity of the compound more polar the bond,
the more soluble it is. Temperature also affects solubility

Molarity and Molality


The concentration of a solution tells how much solute is present in a given quantity of solution or solvent. Concentration
is usually expressed as molarity. Molarity is defined as the number of moles of solute dissolved in one liter of solution; it
is written as the capital letter M after the number.
The formula M1V1=M2V2 makes calculations simpler, where M 1, M2 and V1, V2 are the molarities and volumes
respectively.
A closely related unit of concentration is molality. Molality is defined as the number of moles of solute dissolved in one
kilogram of solvent. It is written as a lowercase m after the number.

Types of Reactions
There are four primary types of chemical reactions, based on the types of reactants and products: combination,
decomposition, displacement, and double displacement.
A combination reaction involves the combining of two reactants to form a single new product. It can be generically
written as A + B A-B. An example is C + O2 CO2.
A decomposition reaction occurs when a compound breaks down into two or more elements or new compounds. Its
generic form is A-B A + B. An example is hydrogen peroxide decomposing to water and free oxygen: 2H2O2 2H2O +
O2.
In a displacement reaction, one substance reacts with a compound and replaces one of its elements. Generically it is
written as A + B-C A-B + C. An example is 2NaBr(s) + Cl 2(g) 2NaCl(s) + Br2(l).
In a double displacement reaction, two compounds react with each other, and one or more atoms or groups of atoms
from each exchanges with the other. The generic form of a double displacement reaction is A-B + C-D A-D + B-C.
An example is a medical test for the presence of calcium in urine. The test reagent ammonium oxalate, (NH4)2C2O4, is
added. If calcium ions are present, the solid calcium oxalate will form. The reaction is as follows: CaCl2 + (NH4)2C2O4
CaC2O4 + 2NH4Cl.

Redox Reactions
Another way to classify types of reactions is to look at electron transfer during the reaction. This is determined by
examining the oxidation numbers of the elements involved. These types of reactions are called oxidation-reduction or
redox reactions. They are required in many biochemical processes such as converting food into usable energy for body
functions.

The oxidation number is a charge assigned to an atom by assuming that the bonded electrons are nearest to the more
electronegative atom of the compound. In ionic compounds, the oxidation number is the same as the charge of the ion.
In covalent compounds, the more electronegative atom will have a negative charge because it "pulls" the electron pair
toward itself even while sharing them with the less electronegative atom. The number will be the number of shared
electrons. The less electronegative atom will have a positive charge with a value equal to the number of electrons it is
sharing. The oxidation numbers in covalent compounds can be easily determined from the Lewis dot structure of the
molecule. In water, for example, each hydrogen atom is sharing one electron with oxygen, and oxygen is more
electronegative. Therefore hydrogen's oxidation number is +1. Oxygen is sharing two electrons, so its oxidation number
is -2. The oxidation number of any given element can be different in different compounds. When the oxidation numbers
of the reactants change as a result of the reaction, the reaction is a redox reaction. For example, when carbon and
oxygen combine to form carbon dioxide, each element starts with an oxidation number of zero. In the product, CO2,
carbon has an oxidation number of +4 because it has lost four electrons to the two oxygen atoms. Each oxygen atom
gains two electrons, so its oxidation number is -2. Therefore the reaction C + O2 CO2 is a redox reaction. Redox
reactions are usually reversible, so they are often written with a double arrow .

In a redox reaction, one compound is oxidized and another is reduced. When an atom gains electrons its oxidation
number becomes negative; it is called an oxidizing agent and it is said to be reduced itself. When it loses electrons, its
oxidation number becomes positive; it is a reducing agent and it is said to be oxidized. Redox reactions are often
represented as two half-reactions, showing the reduction and the oxidation separately.

Thermochemistry
The total energy content of a system is called enthalpy. It is a function of its internal energy as well as pressure and
volume. So,
H=U+PV
where H, U, P and V denote the enthalpy, internal energy, pressure and volume respectively. The SI unit for
measurement of enthalpy is the Joule.
Though it is a macroscopic quantity, internal energy can be explained in microscopic terms by two theoretical virtual
components (for practical considerations in thermodynamics and engineering it is rarely necessary or convenient to
consider all energies belonging to the total intrinsic energy of a system, such as the energy given by the equivalence of
mass or electrical dipole moments; only items relevant to the processes under study. Thermodynamics is chiefly
concerned only with changes in the internal energy, not with its absolute value). One is the microscopic kinetic energy
due to the microscopic motion of the system's particles (translations, rotations, vibrations). The other is the potential
energy associated with the microscopic forces, including the chemical bonds, between the particles; this is for ordinary
physics and chemistry.
https://en.wikipedia.org/wiki/Enthalpy
https://www.khanacademy.org/science/chemistry/thermodynamics-chemistry/enthalpy-chemistry-sal/a/bond-
enthalpy-and-enthalpy-of-reaction
http://www.chemguide.co.uk/physical/energetics/definitions.html#top
http://www.chemguide.co.uk/physical/energetics/bondenthalpies.html

In a chemical reaction, the energy transferred to the environment is the change in enthalpy of the system and can be
calculated as:
H = Hf products - Hf reactants,
when one mole of compound is formed at 25C and 1 atm from elements in their stable form. Heats of formation for
ions and many compounds can be looked up in tables found in many standard textbooks or online. The heat of
formation for an element in its most stable form is defined as zero.

Exothermic vs. Endothermic


A reaction that produces heat is called exothermic, and its H value is defined as negative. A reaction that absorbs or
uses heat is called endothermic, and its H value is defined as positive. A spontaneous reaction is one that tends to
occur without any outside stimulus. The H value is an indicator of the likelihood that a reaction will occur
spontaneously. Generally reactions with negative H values (exothermic) reactions are spontaneous. Endothermic
reactions (positive H values) are not usually spontaneous, but require the addition of energy or a catalyst.
Calorimetry
Calorimetry is the process used to directly measure the amount of energy given off by the combustion of any substance.
The substance to be measured is placed in a "bomb"
that is then sealed and filled with pure O2. The
bomb is placed into a well-insulated container and
immersed in a measured quantity of water. A
temperature sensor is placed in the water and the
container is sealed. A spark is sent into the bomb to
begin the combustion, and the temperature change
of the water is measured. That temperature change,
along with the known specific heat and quantity of
water, can be used to calculate the amount of heat
generated by the combustion of the sample
substance. The device used is called a bomb
calorimeter.

Lattice Enthalpies
The lattice formation enthalpy is the enthalpy change when 1 mole of solid
crystal is formed from its scattered gaseous ions. Lattice formation
enthalpies are always negative. See right.
https://en.wikipedia.org/wiki/Lattice_energy
http://www.chemguide.co.uk/physical/energetics/lattice.html

The two main factors affecting lattice enthalpy are the charges on the ions
(more charge, more attraction, more energy) and the ionic radii (which
affects the distance between the ions).

Hess's Law
The enthalpy change accompanying a chemical change is
independent of the route by which the chemical change
occurs.
Hess's Law is saying that if you convert reactants A into products B,
the overall enthalpy change will be exactly the same whether you do
it in one step or two steps or however many steps. See right.
http://www.chemguide.co.uk/physical/energetics/sums.html
http://www.chemguide.co.uk/physical/questions/q-
energeticshess.pdf
http://www.chemguide.co.uk/physical/questions/a-
energeticshess.pdf

Reaction Rates and Equilibrium


https://en.wikipedia.org/wiki/Chemical_kinetics
If thermochemistry determines the likelihood of a reaction occurring spontaneously and measures how much heat
energy it uses or generates, chemical kinetics determines how fast the reaction will be by tracking what that energy
does

In any reaction, the reactants start with a given amount of energy (their heat of formation). They are at point A on the
above energy diagram. If there is enough energy present to begin a spontaneous reaction, the reactants proceed to
point B, a transition state; this is the point of highest energy. The amount of energy required to get from point A to
point B is called Ea, energy of activation. Once the transition state is reached, the reaction proceeds smoothly to the
end products, point C. This will be a lower energy level than point B. It may or may not be lower than point A. The
difference in energy level between point A and point C is H, the change in enthalpy.
https://en.wikipedia.org/wiki/Energy_profile_(chemistry)
http://www.chemguide.co.uk/physical/energetics/basic.html
http://www.chemguide.co.uk/physical/basicrates/energyprofiles.html
https://en.wikipedia.org/wiki/Reaction_coordinate
https://en.wikipedia.org/wiki/Potential_energy_surface

In general, the higher the energy of activation, the slower the reaction will be. A reaction with a very low Ea, is easily
reversible (IS THIS TRUE??), and at completion there are constant amounts of both reactants and products. This state is
called equilibrium.
http://www.chemguide.co.uk/physical/equilibria/introduction.html
Many things can influence the rate of the reaction. They include;
temperature,
concentration of the reactants,
surface area or physical form of the reactants,
and the presence of a catalyst
Reactions proceed faster at higher temperatures, with greater concentrations of reactants, and if solid reactants are
crushed or dissolved. A catalyst is a substance that is added to a reaction, which increases the reaction rate without
itself being consumed. They create an easier path for the reaction, sort of like a snowplow clearing highways so cars can
travel more quickly and easily. A 10-degree Celsius increase of temperature increases the reaction rate by
approximately a factor of two.

The rate of the reaction is expressed as M/s, the number of moles of reactant that are converted to product per second.
This can be determined experimentally by simply timing how long a reaction takes and then doing a few calculations
based on the known starting quantities and concentrations of the reactants. The behaviour of the reaction is described
in a rate law. There are two types of rate laws: differential and integrated.
A differential rate law describes how the concentration of the reactants affects the rate. For a hypothetical reaction
A + B C, the rate law is rate = k[A]x[B]y
k is the rate constant, which is different for every reaction, while x and y are the "orders" of the reactants: the change in
rate compared to change in concentration.
[SKILL] To derive the rate law for a reaction we need to run and time the reaction several times with different
concentrations of the reactants. So, for example, the first run would be with both A and B at a concentration of 0.1M,
the second with A at 0.2M and B at 0.1M, and the third with A at 0.1M and B at 0.2M. If the experimentally determined
rate is 3.0 x 10-5M/s for the first run and 6.0 x 10-5M/s for the second and third, we see that the rate doubles when the
concentration of either reactant is doubled. The change in rate is the same as the change in concentration, so x and y in
the rate law are both 1. Now we can solve the equation to find k, the rate constant, using the time and concentrations
from the first run of the reaction:
3.0 x 10-5 = k[0.1M][0.1m]. For this reaction the rate constant k is 0.3M/s.
An integrated rate law describes how the concentrations of the reactants change as the reaction progresses over time.
The mathematical calculations involve integral calculus, but the basic form of the rate law for reaction
A B is rate = k[A]
To relate concentration to time, the rate law becomes (after complex calculus)
ln[A] = -kt + ln[Ao]
k is the rate constant, t is time, [Ao] is the initial concentration of A, [A] is the concentration of A after t seconds, and ln
is the natural logarithm. This equation allows determination of the half-life of the reaction--the time it takes for the
concentration of A to decrease by half. The half-life can be graphed as follows:
Swedish chemist Svante Arrhenius developed a method to calculate the activation energy of a reaction in 1889. After
performing a reaction at two different temperatures and finding the rate constant k for each, an equation can be used
to find Ea: [FIND MORE ON ARRHENIUS EQUATION]
ln(k2/k1) = (Ea/R)(1/T1 - 1/T2).
R is the ideal gas constant 8.31J/Kmol; k2 &k1 are the rate constants for each reaction, and T1& T2 are the
temperatures (in Kelvins--C + 273) for each reaction. If we find, for example, the reaction A + B C has a rate constant
of 1.20 mol/s at a temperature of 140 C and a constant of 2.50 mol/s at 340 C, we have the information we need to
find its activation energy.
2.50 mol/s
ln( 1.20 mol/s ) = (Eae 8.31J/Kmol)(1/413K - 1/613K)
ln(2.08 x 105) = (Eae 8.31J/Kmol)0.000790K-1
Ea = 1.29 x 105 J/mol
As noted above, reactions with low Ea are easily reversible and reach a state of equilibrium. Equilibrium doesn't mean
that no reaction is occurring. We have seen that as the concentrations of reactants increase, so does the rate of the
reaction. In the case of a reversible reaction, where the products react to re-form the original reactants, as the
"forward" reaction progresses and concentrations of the products increase, the "backward" reaction starts and
increases its rate. Thus, both the "forward" and "backward" reactions are occurring simultaneously, keeping the
reactants and products in relatively constant proportions

The ratios of products to reactants will be different for each reaction. If the forward reaction is fast and the backward
one is slow, the equilibrium is said to favour the products. In the opposite situation with a slow forward reaction and a
fast backward one, the equilibrium favours the reactants. The ratio can be calculated, and the result is an equilibrium
constant; the larger the constant, the more the equilibrium favours the products. The equilibrium constant is only
"constant" at the same temperature. If the reaction is carried out at a different temperature, Keq will be different. For
the reaction aA + bB cC + dD, the equilibrium constant Keq can be found by solving this equation:
Keq = [C]c[D]d/[A]a[B]b
The bracketed letters represent the concentration (in molarity) of each reactant and product (at equilibrium. The
superscript letters are any quantity coefficients.
[SKILL: Finding equilibrium constant using known equilibrium concentrations]
For example using the reaction C2H3O2H H+ + C2H3O2-, the equation would be Keq = [C2H3O2-][H+]/[C2H3O2H]. If
the concentrations at equilibrium are 0.68M for C2H3O2H and 3.5 x 10-3M for C2H3O2- and H+, the equation becomes
Keq = [3.5 x 10-3] 2/0.68 = 0.00352 /0.68 = 0.00001225/0.68 = 1.80 x 10-5.

Acids and Bases


https://en.wikipedia.org/wiki/Acid
http://www.chemguide.co.uk/physical/acidbaseeqia/theories.html
https://en.wikipedia.org/wiki/Lewis_acids_and_bases

Acids react with certain metals to produce hydrogen gas. They usually cause a stinging sensation on the skin, and edible
acids taste sour. Some common examples of acids are: vinegar, orange or lemon juice, aspirin, and carbonated water.
Bases feel slippery on the skin, react with oils and greases, and edible bases taste bitter. Some common examples of
bases are: ammonia, lye (drain cleaner), chlorine bleach, and baking soda. Soluble bases are called alkalis.

When acids and bases react with each other they produce water and a type of salt; this is a neutralization reaction
[ONLY SOMETIMES, SEE CHEMGUIDE FOR MORE DETAILS]. The strength of an acid or base is any solution is measured
on the pH scale, from 0 to 14. pH actually refers to the hydrogen ion concentration in solution. You could use the
mnemonic percent hydronium as a memory aid. Acids cause litmus paper to turn red, and bases cause litmus paper to
turn blue; an easy way to remember that is that the words acid and red both contain the letter D, and the words base
and blue both contain the letter B.
The pH of a compound can be calculated if the concentration of the solution is known. For a strong acid (one which
almost completely dissociates in water) the equation is
pH = -log[H+].
For hydrochloric acid at a 0.00500M concentration, pH = -log(0.00500M) = 2.30. For a weak acid such as acetic acid,
which does not completely dissociate in water, we first need to know the acid dissociation constant Ka in order to find
the concentration of H+ at equilibrium. The equation for finding the equilibrium constant is used to find the
concentration. For example, acetic acid dissociates in water according to the equation:
CH3COOHCH3COO-- + H+
If we start with a 0.5M solution of acetic acid (C2H3O2H) and the information that its Ka is 1.75 x 10 -5, we can set up the
equation Ka = [C2H3O2-][H+]/[C2H3O2H] and solve it to find [H+], which we will represent as y.
1.75 x 10-5 = [C2H3O2-][H+]/[0.5]
.0000175 x .5 = [C2H3O2-][H+]
0.00000875 = y2
.00296 = y = [H+]
pH = -log[H+] a pH of 2.53

Water dissociation constant is Kw = 10-14 and the equation Kw = [OH-][H+], so that the pH of bases can be calculated.

It is possible to determine the unknown concentration of an acid or base using a process called titration. Place a
measured quantity of the unknown solution in a beaker, and then add acid or base (whichever is needed to neutralize
the unknown) of known molarity in small measured amounts. When the titrated solution reaches the neutral pH of 7.0,
the amount of known solution needed to achieve it allows us to calculate the concentration of the unknown. Perhaps
the bottle from which we pour the unknown tells us that it is NaOH, but doesn't give the molarity. So pour 150 ml of the
NaOH into a beaker along with an indicator such as phenolphthalein. Since NaOH is a base, we will use 1M hydrochloric
acid (HCl) to titrate it. Perhaps it takes 250 ml of the HCl to reach a neutral pH. We can use the equation
MacidVacid = MbaseVbase
M is molarity and V is volume. In this case Mbase is unknown, but the other quantities are known. So, plugging in the
known values we get 1.0M(250ml) = Mbase(150ml). Solving the equation tells us that the concentration of the NaOH
solution is 1.66M.

In the human body, pH is an important consideration in our physiology. Our blood is slightly basic. It also contains a
buffer of a weak acid and its conjugate base to keep the pH stable when we eat or drink acidic foods or beverages. A
buffer prevents drastic pH changes when a strong acid or base is added.

Nuclear Chemistry
Isotopes
Nuclear chemistry studies the spontaneous decomposition of unstable nuclei of atoms, giving out radiations in the
process. As we know, each element has a characteristic atomic number which tells us the number of protons in its
nucleus. Usually there is the same number of neutrons, but not always. Atoms of an element which have different
numbers of neutrons are called isotopes. Collectively the protons and neutrons are referred to as nucleons, and
different isotopes of an element are called nuclides. A radioisotope is one whose nucleus gives off various subatomic
particles. Isotopes of an element are written with the atomic mass as a superscript before the symbol, or with the
symbol followed by a dash and the mass. So uranium could be written as either 238U or U-238.

Radioactivity
Radiation refers to waves of energy passing through a medium. Light, heat and sound are types of radiations but what
we are most concerned about is radiation from radioactive materials. All elements with an atomic number higher than
83 are radioactive, and the ratio of the number of neutrons to the number of protons is a determining factor; most
nuclei with a ratio of between 1.0 and 1.55 are stable. All nuclei with ratios outside that range are unstable, therefore
radioactive. There are several different types of radioactive decay, depending on what type(s) of particles are emitted.
Alpha radiation occurs among nuclides with very high mass. An alpha particle = nucleus of a helium atom, comprising
two protons and two neutrons. Alpha decay causes the atomic number of the atom to decrease by two and it mass to
decrease by four.
https://en.wikipedia.org/wiki/Alpha_decay
Beta radiation converts a neutron to a proton by emitting an electron and a neutrino, OR converts a proton to a
neutron by emitting a positron (anti-electron) and neutrino. The electron or positron is fast moving and is called a beta
ray. The atomic number increases or decreases by one and the mass is unchanged. Nuclides with very high neutron-to-
proton ratios are most likely to undergo beta decay. Neither the beta particle nor its associated neutrino exist within
the nucleus prior to beta decay, but are created in the decay process. By this process, unstable atoms obtain a more
stable ratio of protons to neutrons.
https://en.wikipedia.org/wiki/Beta_decay
Gamma rays are electrically neutral high-energy light particles that are emitted during other
forms of radioactive decay.
In electron capture, an electron from an inner orbital is pulled into the nucleus. As in positron
emission, a proton becomes a neutron, and the effect and occurrence are the same.
[NOTE: MORE ON GAMMA RAYS AND ELECTRON CAPTURE REQUIRED?]
ORGANIC AND BIOCHEMISTRY
Organic chemistry is a study of organic compounds, specifically the physical and chemical properties of compounds
containing carbon. Besides carbon, they also contain hydrogen and oxygen and sometimes nitrogen, phosphorus and
sulphur. They occur naturally in all living things. The word "organic" in the context of chemistry is derived from the word
organism.

Curricula/learning outcomes for this section:

1. Structures Unique to Organic Compounds


Conventions in Notation and Nomenclature
Hydrocarbons
Alcohols
Ethers
Aromatics
Amines
Aldehydes
Polymers

2. Hybridisation in carbon compounds.

3. Stability vs. Volatility

4. Isomerism and Stereochemistry


Chirality
Polarity

http://www.chemguide.co.uk/orgmenu.html#top

Conventions in Notation and Nomenclature


If one atom is significantly more electronegative than the other, that atom will "hog" the electrons. This is called a polar
bond. In organic chemistry polar bonds are often illustrated by the symbol (lowercase delta) with a + or - sign as a
superscript. They can also be shown with a cross-hatch over an arrow on the positive end of the bond. For example,
methanol (CH3OH)

Atoms in molecules and ions often have a formal charge, which is


the number of valence electrons minus the number of bonds minus the number of unpaired electrons.
For example, in the ammonium ion, [NH4+], nitrogen has five valence electrons; it is bonded four times, and has no
unpaired electrons. Therefore its formal charge is +1.

The transfer of electrons during reactions and bonding is represented by arrows showing the formation of covalent
bonds. The arrow originates from the more electronegative atom or molecule, and points toward the less
electronegative one. Convention assumes that a pair of electrons is moved. If only one is moved, the arrow is single
sided. An electron pair acceptor is a Lewis acid and an electron pair donor is a base. [NOTE: LOOK INTO ELECTRON
TRANSFERS AND MOVEMENTS WITHIN REACTIONS]
In some molecules, the electrons move around the molecule without forming stable covalent bonds. An example is
benzene, C6H6. It can be represented as a line drawing in either of two equally valid ways; the difference between the
two is the position of the double bonds. These are called resonance structures. What actually happens is that the
electrons are delocalized and move freely within the benzene ring, and the double bonds are constantly moving.
Therefore the true structure of benzene is represented as a hybrid of the two resonance structures, with an average of
1.5 bonds between each pair of carbon atoms. The dotted line represents a partial bond.

Hybridisation and Physical Bonding Types


http://www.chemguide.co.uk/basicorg/bondmenu.html#top
Carbon, like most elements except hydrogen, behaves differently when forming covalent bonds than when by itself in a
neutral state. When forming a bond, it forms hybrid orbitals. To form a bond, the one 2s and three 2p orbitals are
hybridized and become four sp3 orbitals, each shaped a bit like a bowling pin. Since the electrons repel one another, the
orbitals are arranged in a tetrahedral shape to allow
them to be as far apart as possible. The bond angle is
109. In methane, CH4, carbon bonds with four
hydrogen atoms. The single 1s orbital of each hydrogen
atom overlaps with one of the four sp3 orbitals of the
carbon atom. The same thing happens in ethane, C2H6,
except one sp3 orbital from each carbon atom overlaps
with the other. The remaining three sp3 orbitals overlap
with hydrogen atoms. Single bonds are called -bonds
(sigma bonds).

With double and triple bonds, the hybridization is a bit more complicated, but the principles are similar. Double and
triple bonds are called -bonds (pi-bonds), and the electrons in those bonds are called -electrons.
https://en.wikipedia.org/wiki/Pi_bond

Molecules Unique to Organic Chemistry


Hydrocarbons
Hydrocarbons are compounds that consist of only carbon and hydrogen. The simplest hydrocarbons are called alkanes,
and have only single bonds. The general formula for an alkane is always CnH(2n+2). The nomenclature of all other organic
compounds is based on that of the alkanes. The simplest alkanes are "straight chain" with all of the carbon atoms
arranged in roughly linear fashion (not a truly straight line because of the tetrahedral architecture). If there are side
chains branching off, those are called alkyl groups and named for the number of carbon atoms. Straight chain alkanes
are drawn as zigzag lines, with branches where necessary.
Branched
chain alkanes will have a line representing the alkyl group at the proper location on the parent
chain. The carbon atoms are numbered from the end of the parent chain nearest the first branch.
Branches (substituent groups) are named for the number of carbon atoms they contain and the
position from which they branch from the parent chain. So, for example, the molecule
represented below would be 3-ethyl-2-methylhexane. The parent chain has six carbon atoms,
which makes it hexane. A one-carbon (methyl) group branches at the second carbon, and a two-
carbon (ethyl) group branches at the third. The substituent groups are listed in alphabetical order.

Cycloalkanes are alkanes in which the two ends of the carbon chain are joined, so that the molecule forms a ring. At
least four carbon atoms are needed to form a cycloalkane.
The generic formula for a cycloalkane is CnH2n. They are
named in a similar manner to the straight-chain alkanes.
When there are multiple substituent groups, they are again
listed alphabetically, and the position of the first alphabetical
substituent is number 1. So, for example, the compounds
below are cyclobutane and 1-methyl-3-propylcyclopentane.

The primary type of reaction involving alkanes is combustion. You've probably heard of octane; it's the primary
component in automobile gasoline. Many gas barbecue grills are fueled by propane. Old cigarette lighters used butane.
More complex hydrocarbons are called alkenes, which have at least one CC double bond, and alkynes, which have at
least one CC triple bond. They are named in similar fashion to the alkanes; the longest chain which contains the double
or triple bond is the parent chain, and it is numbered so that the double or triple bond has the lowest possible number.
Naming of substituent groups follows the same rules as for alkanes. The whole molecule name ends with the suffix -ene
or -yne instead of -ane, depending on whether there is a double bond or a triple bond.

Alcohols
The generic formula for an alcohol is ROH. Alcohols are named based on the alkane from which they are derived, and
end in the suffix -anol. The 1-methylcyclopentanol molecule is an example.

Ethers
Ethers have the generic formula ROR' (R' means that the two radicals can be different).
They are now primarily used as solvents, however a form of ether was one of the first
surgical anaesthetics in the mid 1800s. It's no longer commonly used as an anaesthetic,
because it is highly flammable and also causes unpleasant after-effects such as severe
nausea. Since many ethers have been known and commonly used for longer than the IUPAC
has been around, few chemists actually follow the IUPAC guidelines for naming them.
Usually they name the radicals in alphabetical order followed by the word ether. So, for
example, the compound CH3CH2CH3OCH3CH3 would be 1-ethoxypropane according to
IUPAC, but most chemists call it ethyl propyl ether.
Aromatics
Aromatic compounds are molecules based on cyclic hydrocarbons with 4n+2 -electrons (6, 10, 14...an odd number of
-bonds). The most common aromatic compound is benzene. Aromatics are named in similar fashion to other cyclic
organic compounds. A propyl group bonded to benzene would be propylbenzene. A fluorine atom bonded to benzene
would be fluorobenzene. If benzene is
bonded to a larger molecule, it can be called
a benzyl group in the name. There are some
widely used aromatics that have common
names that need to be memorized. They
include toluene, phenol, and aniline.

Amines
Amines are based on ammonia, NH3; one or more radicals are substituted for the hydrogen atoms. They are classified as
primary (1), secondary (2), or tertiary (3) according to how many radicals are present. The radicals can be alkyl
groups or aromatics. Heterocyclic amines have a nitrogen atom substituted for one of the carbon atoms in the aromatic
ring. Most amines have an unpleasant smell. IUPAC nomenclature guidelines for amines are similar to those for alcohols,
but most chemists name them according to the alkyl group followed by the word amine, as in ethylamine.
Aldehydes and Ketones
Aldehydes (R--CHO) and ketones (RCOR) have a very similar chemical structure, but little else in common. They are
part of a much larger groups of compounds called carbonyls; they all contain a
carbonyl group CO. An easy way to remember which is that the word
aldehyde and its formula both contain the letter H. Aldehydes are used as
preservatives (if you've taken an anatomy course you're familiar with
formaldehyde), food flavorings (the sharp tang of cinnamon is a naturally
occurring aldehyde), and in many industrial processes. Ketones are used in
cosmetics (acetone is the main ingredient in nail polish remover), plastics, and
paints.

Polymers
A polymer is a very large molecule composed of 10,000 or more atoms, with a molecular weight of multiple thousands.
Prior to the 1920s, most chemists didn't believe that such large molecules were possible; such compounds must be
simply aggregations of small molecules. Hermann Staudinger, working with natural polymers such as rubber and
cellulose, challenged that view and proposed polymeric macromolecules, made up of many repeating units. The word
polymer is based on Greek words meaning "many parts." He described the molecular structure of rubber, and was
awarded the Nobel Prize for chemistry in 1953.

The way a polymer behaves is at least partly determined by its structure. There are three different types of polymer
structure:
1) linear--like a stalk of bamboo with segments arranged end-to-end;
2) branched--like pine needles on a branch;
3) crosslinked--woven like a mat.
Polymers are also classified by their behaviour when exposed to heat, and by their uses. Thermoplastic polymers
become soft when heated, and can be moulded into many different shapes. Thermosetting polymers are hard even
when heated, and are good insulators. They have a crosslinked structure and are used to make handles for hot objects
such as cooking pans.
Plastic polymers can be moulded, and are used to make dishes, toys, computer keyboards, and many other items. Fibre
polymers are linear strands and are used to make fabrics and carpets. Elastomer polymers, often called synthetic
rubber, are thermoplastic and crosslinked. They are able to stretch and bounce, and are used to make things like latex
gloves, car tires, and sports balls such as basketballs.

[NEED MORE ON ORGANIC CHEM MOLECULES AND RELATED REACTIONS]

Stability vs Volatility
Stability is an indicator of how difficult it is for a molecule to be broken apart in a reaction; more stable molecules
require greater energy to initiate a reaction than less stable ones. Stability is usually a function of molecular structure.
Volatility, on the other hand, refers to how easily a substance evaporates. Volatile organic compounds (VOCs) are
hydrocarbons that have low boiling points, usually less than 100 C. Most are liquids at room temperature, but some are
gases. Examples are benzene and many components of gasoline. Many VOCs are flammable, and also pose human
health hazards with prolonged exposure.

Isomerism and Stereochemistry


https://en.wikipedia.org/wiki/Stereoisomerism
https://en.wikipedia.org/wiki/Chirality_(chemistry)
https://en.wikipedia.org/wiki/Asymmetric_carbon
Isomers are molecules which have the same chemical formula but different structures. There are many different types
of isomers, based on how the structures are related. The structure of the molecule determines the stability, behaviour
and reactivity of the molecule. Constitutional (also called structural) isomers are the simplest; they occur in straight-
chain alkanes. For example, 2-methylbutane and 2,2-dimethylpropane both have the formula C5H12, but their structures,
and hence their behaviour and properties are very different.

Cycloalkanes show cis-trans


isomerism. Although they are
depicted as flat rings on paper,
cycloalkanes are NOT flat.
Cyclohexane, shown below, can take
either a "chair" or "boat" shape. The
hydrogen atoms are bonded to both
free sides of the carbon atoms.

The internal angles of a flat regular hexagon are 120, while the preferred angle
between successive bonds in a carbon chain is about 109.5, the tetrahedral angle.
Therefore, the cyclohexane ring tends to assume certain non-planar (warped)
conformations, which have all angles closer to 109.5 and therefore a lower
strain energy than the flat hexagonal shape. The most important shapes are
called chair, half-chair, boat, and twist-boat.[1] The molecule can easily switch
between these conformations, and only two of them chair and twist-boat
can be isolated in pure form.-
https://en.wikipedia.org/wiki/Cyclohexane_conformation
The "chair" shape is more stable, because it allows greater separation
between the hydrogen atoms. Now let's add some alkyl groups to our chair A cyclohexane molecule in chair conformation.
shaped cyclohexane. If both alkyl groups are on the same side of the ring, it's Hydrogen atoms in axial positions are shown in red,
a cis isomer. If they're on opposite sides, it's trans. Alkenes and many other while those in equatorial positions are in blue.
types of compounds also show cis-trans isomerism. The alkene 2-butene can
be represented with a line drawing as below.

Cis-trans isomers are often symmetrical around an axis of rotation. Cis-2-butene is symmetrical around an axis
perpendicular to the CC double bond; trans-2-butene is symmetrical around two axes, one perpendicular and one
parallel to the CC bond.

Chirality
Stereochemistry deals with isomers that are more complex than the
constitutional and cis-trans types we've examined so far. Stereoisomers have
the same formula, but a different spatial arrangement. Consider the two
isomers of bromochlorofluoromethane.
Both molecules have the same formula, CBrClFH, but are mirror images of each other. There is no axis of symmetry, and
they cannot be superimposed on one another. Each molecule is chiral (normally the carbon is referred to as chiral),
which refers to any object that cannot be superimposed on its mirror image. Chirality is sometimes called "handedness";
the two human hands are chiral mirror images. Enantiomers are chiral isomers that are mirror images but which cannot
be superimposed. They have no internal axis or plane of symmetry--there is no way to cut them in half and have the two
halves be identical. Enantiomers are designated R- or S-, from Latin rectus meaning right and sinister meaning left. To
determine the handedness of a molecule, its substituent groups are ranked based on the atom which bonds to the
parent molecule. The carbon atom to which the substituent groups are bonded is called the stereocenter. The
substituent atom with the highest atomic number gets the
highest rank. Once the substituents are ranked, arrows are
drawn from the highest to the second highest on down to
the lowest. If those arrows point in a clockwise direction,
the molecule is R-. If counter clockwise, it's S-.
https://en.wikipedia.org/wiki/CahnIngold
Prelog_priority_rules
https://en.wikipedia.org/wiki/Absolute_configuration
https://en.wikipedia.org/wiki/Conformational_isomerism
https://en.wikipedia.org/wiki/Enantiomer
The chemical and physical properties of enantiomers are typically identical with one exception. They are optically active;
when struck by a polarized beam of light, the beam is rotated. The degree of rotation is the same for both enantiomers,
but the direction is opposite. R-enantiomers rotate the beam clockwise; they're called dextrorotary. S-enantiomers
rotate the beam counter clockwise; they're called levorotary. Some enantiomers have more than one stereo centre, and
more than one enantiomer.

[MORE ABOUT STEREOCENTRES, ENANTIOMER CHEMICAL/PHYSICAL PROPERTIES, AND R/S ASSIGNMENT RULES]

Diastereomers (or diastereoisomers) are


stereoisomers that are not enantiomers, i.e. not
mirror images of each other. They usually have more
than one stereocenter. Using the same molecule
from above, look at what happens if only one of the
two stereocenters is rotated.
The defining characteristics of diastereomers are that
they have at least two stereocenters, are connected
exactly the same way, that the orientation of at least one sterecocenter of the two molecules is identical, and that the
orientation of the other stereocenter is mirror-image. Diastereomers are optically active, but differ in most other
properties such as melting and boiling points and solubility.

Finally, some molecules have stereocenters but are not chiral because they do have a plane of symmetry. They are
called meso compounds. Often simple rotation of one C--C bond makes them identical.
https://en.wikipedia.org/wiki/Meso_compound

Conventions Unique to Organic Chemistry


Notation
Most organic chemistry reactions are variations on acid-base reactions, therefore it is important to be able to identify
which compounds are acidic, which are basic, and the relative strengths of each. That clarifies where the electrons are
moving as they form bonds. Organic reactions chiefly use the Lewis definition for acids and bases, with compounds
donating or accepting electrons.

Organic chemists use somewhat different terminology than inorganic chemists when discussing reactions. Inorganic
chemists call the compounds on the left-hand side of the equation reactants, while organic chemists call them
substrates if they contain carbon, and reagents if they don't. On the right-hand side of the equation, what inorganic
chemists lump together as products are distinguished by organic chemists as the product of interest (the one created
from the substrate) and by-products. Organic chemists also usually don't write a full, balanced equation; they merely
write a transformation. A transformation is a depiction of the reaction which shows only the substrate(s), reagent(s),
and product(s) of interest. By-products and balancing coefficients are omitted. This can be a source of confusion to
students just beginning organic chemistry after a year of having balanced equations and the Law of Conservation of
Mass drilled into their brains. The fact that the coefficients and by-products aren't written doesn't mean they're not
present; it just means that they are unimportant (even irrelevant) to the reaction being studied. A transformation can
show the sequence of the reaction if multiple steps are involved or if the reagents must be added in a certain order. As
with inorganic reactions, any specific reaction conditions such as temperature are written above the reaction arrow. A
generic example which shows conditions and a sequence of steps is given below.

Classification Of Reagents
As noted above, most organic reactions are Lewis acid-base reactions. Therefore the substrates and reagents are either
acid or base. Reagents can be classified as electrophiles or nucleophiles. Electrophiles are positively charged while
nucleophiles are negatively charged. An electrophilic reagent is a Lewis acid that reacts with an electron-rich substrate
(which is a Lewis base) and accepts an electron pair from it. A nucleophilic reagent is the opposite. It is a Lewis base that
reacts with an electron-poor Lewis acid substrate and donates an electron pair. (Recall that acids in inorganic chemistry
yield protons, H+, and bases give hydroxyl ions, OH-, in solution).

Reaction Mechanisms
https://en.wikipedia.org/wiki/Cycloaddition
https://en.wikipedia.org/wiki/Elementary_reaction
https://en.wikipedia.org/wiki/Organic_reaction
Reaction mechanisms are descriptions of the steps of the process. They detail the movement of electrons and the
sequence of movement from the base to the acid. Reaction mechanisms differ from reaction types in that reaction types
only describe the end result of what is often a multistep process. An analogy from cooking might help you understand it
better: A reaction type is like a menu item, perhaps a steak cooked medium rare. The cooking methods and conditions
are like the reaction mechanisms. The steps of a reaction may convert one functional group to another, or rearrange the
carbon skeleton of a molecule. The mechanisms show how the electrons flow. Understanding the mechanisms of a
reaction allows you to visualize the structural changes that occur, and ultimately to be able to predict the outcome of
new reactions. There are five general electron- flow operations (reaction mechanisms):
A heterolytic bond cleavage operation is the breaking of a bond between two
atoms. One atom takes the electron pair and becomes negatively charged, while the
other loses the electrons and becomes positively charged. It is generically
represented as:
In a heterogenic bond forming operation, an atom with a pair of nonbonding
electrons reacts with an atom that has an empty orbital. The atom with the
pair of electrons donates them to the bond and becomes more positively
charged, while the other becomes more negative. It is essentially the opposite
of the bond cleavage above, and is represented as:
The 1,3-electron pair displacement operation involves a flow of
electrons across three atoms. The first atom, a Lewis base nucleophile
which has a pair of nonbonding electrons, initiates the process by
forming a bond with the second atom. That action displaces a pair of
bonding electrons from the second atom to the third, which is a
Lewis-acid electrophile. The generic form of the process is: One bond
is broken as another is formed. This operation also describes the addition of a nucleophile to a double bond.
To initiate a 1,3-electron pair abstraction operation, and electron-deficient Lewis-acid electrophile draws an electron
pair from a Lewis-base, breaking a bond, forming a new one and causing the displaced atom to become electron-
deficient. This also describes the addition of an electrophile to a double bond. The operation takes this general form:
A 1,5-electron pair displacement operation causes electrons to flow across five atoms. It is initiated by an electron-
donor Lewis-base nucleophile; the electrons pass across three central atoms and finally arrive at a Lewis-acid electron-
acceptor electrophile. Multiple bonds are broken and
reformed. Generically it is written as: An electrophile can
be added to a double bond by this mechanism as well.

Addition, subtraction and elimination Reactions


There are three main types of reactions in organic chemistry: addition, substitution, and elimination. If a reaction
rearranges the carbon skeleton of the substrate molecule, some chemists call that a fourth type. All types use one or
more of the five reaction mechanisms discussed above.
Addition
Addition reactions (also called electrophilic addition reactions) primarily occur in alkenes and alkynes--compounds
which contain double or triple () bonds. An atom or alkyl group is added to a carbon that is part of the -bond, and the
-bond is converted to a single () bond. The substrate does not lose any atoms or electrons in the process. These
reactions occur readily because -bonds are more stable than -bonds. The electrophilic addition reaction is a
bimolecular two-step process. The two molecules involved are the substrate and a polar reagent. When the -bond is
broken, the carbon atom becomes a cation (called a carbocation) intermediate and the electrophilic component of the
reagent forms a -bond at that location by means of a 1,3-electron pair abstraction operation. The second step adds the
nucleophilic portion of the reagent to the carbocation bringing the net charge back to neutral.
For example, when the substrate ethene reacts with the reagent hydrogen bromide, the HBr dissociates and the
electrophilic hydrogen bonds to one of the carbons, creating a fourth - bond for that carbon and creating the
carbocation. In the second step the nucleophilic Br- bonds to the carbocation.

In more highly substituted alkenes, the electrophile will bond to the less-substituted carbon, and the nucleophile bonds
to the more highly substituted carbon.
It is possible to have a trimolecular electrophilic addition, requiring two reagentsone electrophilic, the other
nucleophilic--to act upon the substrate. This is a rare occurrence because of the improbability of three reactive
substances colliding. When it does occur, it uses the 1,5-electron pair displacement operation as its first step.

Substitution
https://en.wikipedia.org/wiki/SN1_reaction
In a substitution reaction (or nucleophilic substitution reaction), an alkyl group (referred to as the leaving group) that is
more electronegative than the SP3-hybridized carbon to which it is bonded breaks that bond, leaving an electrophilic
carbocation. A nucleophilic atom or group of atoms from the reagent then bonds to the carbocation. There are two
possible pathways for a substitution reaction. Which one is used depends upon the nature of the substrate.
In an SN1 (unimolecular nucleophilic substitution) reaction, the first step is the heterolytic bond cleavage of the leaving
group from its carbon, making it an electron-deficient carbocation. The second step is a heterolytic bond forming
operation between the
nucleophile reagent and the
carbocation. The progress of the
reaction depends only on the
substrate.

An SN2 (bimolecular
nucleophilic substitution
reaction) is a single-step 1,3-
electron pair displacement
operation in which the leaving group departs at the same time the nucleophile bonds to the carbon.

Elimination
An elimination reaction removes at least two atoms or functional groups from a molecule, then a multiple () bond
forms between the two carbons that lost their substituents. There are two pathways by which this can occur.
The E1 reaction is unimolecular and has two steps. Step 1 is an ionization reaction, then step 2 is a 1,3-electron pair
abstraction operation. In some cases, the substrate molecule may become cyclic rather than forming a -bond.

The E2 reaction is a bimolecular 1,5-electron pair displacement operation. Its progress depends
on the concentrations of both the substrate and the reagent.

Naming
Organic molecules
https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/nomen1.htm
http://www.chem.uiuc.edu/GenChemReferences/nomenclature_rules.html

Skills to learn
Identifying Stereo-centres in large (mostly aromatic) molecules
Learning how to draw lewis structures
Learning how to identify proper electron movements in resonance structures
Learning basic reaction mechanisms

Bioenergetics
Glycolysis

HUMAN BIOLOGY

PHYSICS
Fulcrums, force and weight

CELL BIOLOGY
Cell Division
Cell Division is the process by which the nuclear (especially genomic) and cytoplasmic components of cells are divided
into two. In metazoan cells, cell division takes two common forms:
1. Mitosis, where the genome is duplicated and then divided, so that the daughter cells contain two (nearly) identical
copies of the genome. For diploid organisms, each daughter cell receives a full diploid complement of chromosomes.
(For example, in humans this represents 23x2 chromosomes.)
2. Meiosis, a specialized form of cell division that is associated with sexual reproduction, where the daughter cells
(gametes) contain a haploid complement of chromosomes (i.e. one copy of each chromosome 1x23, for humans). Cell
division is often called M-phase of the cell cycle. Although this is commonly discussed in terms of nuclear division and
chromosomal segregation, it is important to remember that cell division (M phase) consists of two components:
Nuclear division (e.g. mitosis)
Cellular division (i.e. cytokinesis)

Nuclear Division.
Chromosomal segregation and the mitotic spindle
During S phase the genome is duplicated, but the duplicated chromosomes (sister chromatids) remain attached to one
another.
The aim of mitosis is to segregate those sister chromosomes apart from one another to separate ends of the cell. These
will eventually form the nuclei of the daughter cells. This process must be achieved with fidelity so that each daughter
cell receives a complete set of chromosomes (and only a single set of chromosomes).
The mitotic spindle is the principal apparatus that serves to segregate and separate daughter chromosomes.
The spindle is built out of microtubules (MTs). Key features of spindle organization are:
a. Spindle poles: these are the MT organizing centres (MTOCs) of the mitotic spindle. In mammalian cells they are
composed of centrosomes. We shall assume this for our discussion, though in other types of organisms, other
mechanisms are used for MTOCs.
b. Kinetochore MTs: these will interact with the chromosomes at their kinetochores.
c. Polar MTs: These are oriented into the spindle and interact with other polar MTs from the opposite pole of the
spindle.
d. Astral MTs: these are oriented outwards towards the cell cortex. They interact with the cortex via proteins such as the
minus-end directed motor, dynein.

Microtubule basics.
Because the mitotic spindle is built out of MTs, there are some fundamental things that you need to appreciate (and
study in greater depth see the additional reading):
1. MTs are self-assembling polymers of tubulin. The basic building blocks are heterodimers of -tubulin and -tubulin.
2. MTs are dynamic they have an inherent capacity to assemble and disassemble.
3. MTs are polarized.
The intrinsic dynamic behaviour of their two ends (called the plus- and minus-ends) differs.
There are also structural differences, such that MT-binding motors can distinguish which direction (which end) to move
towards.

4. Dynamic instability.
This is a striking pattern of dynamic behaviour that is seen at the MT ends, although it much more prominent at the
plus-ends. It consists of spontaneous phases of MT growth, sudden (and apparently stochastic) disassembly of the ends
(catastrophe) and regrowth (rescue). This process of growth, disassembly and regrowth of the ends is thought to
represent a mechanism for MTs to probe cellular space. It is the basis of the search-and-capture mechanism by which
kinetochore MTs find their chromosomes.

5. MT motors: generally we think of the motors moving along MTs, carrying cargo (molecular complexes, chromosomes,
vesicles). But remember that if the motor is anchored to something that is less moveable than the MT, the result is
that the motor serves to pull on the MT, moving the MT itself. This is exemplified by the minus-end-directed motor,
dynein, which can be found at the cell cortex, pulling on MTs (such as the astral MTs of the spindle).

Mitosis
The phases of mitosis are commonly described as
1. Prophase.
2. Pro-metaphase
3. Metaphase
4. Anaphase
5. Telophase
However, it is important to note that some of these phases are not so distinct (e.g. prophase vs prometaphase) in some
cells and organisms. Conceptually, it is useful to think of mitosis as falling into two halves (like a football game):
a. The first half leads to the end of metaphase and is designed to have sister chromatids bound to microtubules from
opposite poles of the spindle, ready to be separated into what will be the nuclei of the two daughter cells.
(The association of the kinetochores of sister chromatids onto MTs derived from opposite poles is called bi-orientation.)
b. The second half of mitosis begins with the separation of sister chromatids and their movement to opposite poles of
the spindle and reassembly of nuclei

The key events of mitosis in each stage are:


The first half
1. Prophase
- During the preceding S phase of the cell cycle, the complement of chromosomes has been duplicated; additionally,
many cytosolic components have been produced to meet the need when the cytoplasm is divided.
- During prophase the duplicated chromosomes are prepared for separation and division: elements that were
intertwined (concatenated) during duplication become separated (de-concatenated) and the chromosomes condense.
- The mitotic spindle begins to be built:
Duplication of centrosomes.
Centrosomes are MT organizing centres (MTOCs), which use - tubulin ring complexes (-tubRCs) to nucleate MTs at
their minus-ends.
Duplicated centrosomes then separate and are positioned on opposite sides of the nucleus; the astral MTs play a key
role in separating and positioning the daughter centrosomes.

2. Prometaphase.
- The nuclear envelope disassembles. This entails:
Disassembly of nuclear pore complexes;
Pulling forces exerted on the outer nuclear envelope as the attached centrosomes are moved.
Disassembly of the nuclear lamina (a cytoskeletal scaffold made of specialized intermediate filaments nuclear lamins).
Break down of the nuclear envelope, with much of the membrane of the nuclear envelope absorbed into the
endoplasmic reticulum (ER)

- Note that nuclear envelope disassembly results in the MTs of the developing spindle now having access to many
regulatory factors and MT-associated proteins that are associated with the chromosomes. These influence the ongoing
assembly of the spindle, including beginning to stabilize MTs. One of the key regulatory factors is the GTPase, Ran.

3. Metaphase and the mitotic spindle checkpoint.


A key to metaphase is the arrangement of chromosomes upon the mitotic spindle, so that each sister chromatid is
attached to microtubules from opposite spindle poles. This is called Bidirectionality. Importantly, mitosis does not
proceed unless bidirectionality is achieved. Two factors seem to be crucial:
1) Sister kinetochores must be occupied:
Kinetochores are captured by kinetochore MTs and ultimately associate with the plus-ends of those MTs.
Kinetochore capture occurs by search-and-capture, a process that depends on dynamic instability at the MT plus ends.
The outer kinetochore complex (including DAM-1 and NDC-80) mediates attachment to MTs and is currently thought to
form a sleeve for the MT ends.
Note that the plus ends that are attached to kinetochores remain dynamic.
2) Sister kinetochores are under tension.
Kinetochores appear to sense and regulate tension.
This is manifested as a slight separation of the connections between sister chromatids at the kinetochore regions.
Ultimately tension is balanced (i.e. tension in the connections between a kinetochore and its spindle pole is balanced by
that between its sister and its attached pole).
Productive tension requires:
a) Connections between the sister kinetochores (mediated by cohesin).
b) Force generation which is principally mediated by disassembly at the plus ends of kinetochore MTs (i.e. the ends
linked to the kinetochore itself). This is why the plus ends must remain dynamic.

The second half


4. Anaphase. During anaphase, the sister chromatids are moved to the opposite poles of the spindle to the sites where
daughter nuclei will form. This entails several processes:
a) Sister chromatids must be separated: the physical connections between them must be broken. Those physical
connections are mediated by cohesin, which is degraded by the enzyme, separase. Before anaphase, separase is
inhibited by securin. At anaphase onset, securin is ubiquitylated (and therefore targeted for proteosomal degradation)
by APC.
- So, before anaphase, the pathway is:
Securin, which inhibits separase, which (would otherwise) degrade cohesin.
- Whereas, at anaphase onset, the pathway is:
APC induces the degradation of Securin, which thereby disinhibits separase, thereby allowing it to degrade cohesion.

b) Forces must move the now-separated sister chromatids to their respective spindle poles. These are principally driven
by MT disassembly:
Plus-end disassembly (at the kinetochores); and also
Minus-end disassembly (at the spindle poles).

c) The spindle poles also move apart, driven by forces at the midzone of the spindle which tend to push the poles apart,
and forces at the cell cortex pulling the poles towards the cortex. i.e:
i) Motors (kinesin-5) that cross-link the polar MTs from opposite ends of the spindle at their tips (where polar MTs from
different ends of the spindle overlap at the mid-zone of the spindle). These push apart the polar MTs.
ii) Dynein found at the cell cortex and which interacts with the plus ends of astral MTs. Cortical dynein tends to pull
astral MTs, thereby pulling the poles towards the cell cortices. (Remember this is because the cortically-attached motor
is less moveable than the MTs of the spindle.)

5. Telophase
i) Here the separated chromosomes are packaged into (reformed) nuclei. The chromosomes (chromatin) themselves
play a central role in this process; they can be thought of as scaffolds on which the nuclear envelope is rebuilt.
Rebuilding the nucleus requires :
a) Reforming the nuclear envelop op e. In early mitosis, much of the nuclear envelope is resorbed to the endoplasmic
reticulum. In anaphase, membrane vesicles associate with chromatin, then fuse to first form tubular structures and
eventually the whole nuclear envelope.
b) Reassembling nuclear pores. Proteins of the nuclear pore complex (NPC) first associate with chromatin, then
assemble with each other on the chromatin and interact with lipid.
c) Rebuilding the nuclear lamina. This requires the import of nuclear lamins into the developing daughter nuclei, which
then assemble to form the nuclear lamina.
ii) The central spindle. Most of the mitotic spindle is disassembled. However, a population of polar MTs remain as the
central spindle

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