Chemistry: Atomic Structure 1) An atom is the smallest particle of an element that has the same chemical properties of that

element 2) An atom is made up of subatomic particles:

Protons Charge: +1, Relative mass: 1 Electrons Charge: -1, Relative mass: 1/1836 or 0* Neutrons Charge: 0, relative mass: 1 (Note: The neutron has no charge/ The neutron is neutral. Cannot write neutral charge)

3) The nucleus of an atom is the center of it, made up of densely packed

neutrons and protons (collectively known as nucleons) 4) Overall, the nucleus has a positive charge 5) The electrons spin around the nucleus at nearly the speed of light, and it rotates on an axle (something like how the Earth spins while rotating around the Sun) 6) Most of the atom is empty space. An analogy is using a football stadium as the whole atom. The nucleus is a pea in the center of the stadium and the electrons form a cloud surrounding the nucleus. It takes up the rest of the space in the stadium 7) Overall, an atom has no charge. 8) The atomic structure can be written as a symbol called the Nuclide Notation: A = Mass number (nucleon number): Number of protons + Number of neutrons Z = Atomic number (proton number): Number of protons/ electrons (in an atom with no charge)

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X = Symbol of the element A Z = Number of neutrons Atomic number = Number of electrons

9) Isotopes:

Isotopes are atoms of the same element with the same number of protons but different number of neutrons They have the same proton number but different mass number For example, most hydrogen atoms have 1 neutron and 1 proton, but it has 2 isotopes, containing 2 neutrons and 3 neutrons respectively Isotopes have different masses (refer to mass number of the isotope) as they have a different number of neutrons They have the same chemical properties but different physical properties (e.g. masses and boiling points) Naturally occurring or produced by nuclear reactions

10) Niel Bohr discovered the electron shell model in 1913, which enables us to answer more questions about atoms 11) Based on his model, electrons are arranged into orbits around the nucleus. These orbits are called shells:

Shells are numbered 1, 2, 3, 4 and so on and so forth The first shell can contain at most 2, the second 8, the third 8 For elements 1 to 20, the fourth shell contains a maximum of 2 The 1st shell must be filled before the second can be filled, and so on and so forth This is called electronic configuration

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12) For elements beyond calcium (20), the third shell can hold up to 18 (e.g. krypton/Kr has an electronic configuration of 2.8.18.8) 13) The electronic configuration of magnesium can be represented as 2,8,2 or 2.8.2
14)

The valence electrons of an atom are the electrons in the outermost shell. This is called the valence shell The chemical properties of an element depend on the number of valence electrons. Elements with the same number of valence electrons tend to have similar chemical properties because the valence electrons are responsible for forming the chemical bonds with other atoms in a chemical reaction When filling the electron shells: fill the top first, then the bottom, then the left then the right, and then repeat it Opposites must be filled first The four sides must be filled before there can be a pair of 2 electrons Electrons must be paired when there are more than 4 This applies for only the second and third shell Use only cross or dot for drawing the electronic structure (crosses are faster)
ll 0 lll lV V

15)

16)

Group Vl

l Vll

The Periodic Table

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1) The elements in the periodic table are arranged in atomic (proton) number 2) The vertical columns are called groups and the horizontal rows are called periods 3) Properties of different groups: Group l: Alkali metals Group Vll: Halogens Group 0 (or group Vlll) : Noble gases Transition Metals are those in between group ll and group lll

4) When naming groups, use ROMAN NUMERALS (l, ll, lll, etc.) and not ARABIC NUMERALS (1, 2, 3, etc) 5) The metallic properties of elements decrease as the group number increases
6) Elements in the same period have the same number of electron shells

(1st period 1 shell, 2nd period 2 shells and so on and so forth) 7) Elements in the same group have the same number of valence electrons

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8) Note: Group VII

Melting and 9) Alkali Metals: Boiling Points Reactive Metals (seen from reactions with water) increase

19 F 9 35 Cl 17 80 Br 35 127 I 53 At 85

Have low melting and boiling points Silvery and soft metals. Low density Easily cut with knife Melting and boiling points decrease down the Colour group (Lithium highest, Caesium lowest)
becomes darker Densities increase down the group Reactivity decreases

React easily in air (tarnish) and therefore kept in oil They react with water to give alkaline solutions Reactivity increases down the group (Caesium has the most vigorous reaction while Lithium has the least vigorous reaction). This is because the valence electrons are found further away from the nucleus when the number of electron shells increases and thus held less strongly by the nucleus electrostatic forces of attraction, thus it is lost more easily.

10)

Halogens: Reactive non-metals

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Low melting and boiling points Diatomic molecules Melting and boiling points increase down the group (Fluorine lowest, Astatine highest) Reactivity decreases down the group (Flourine is the most reactive while Astatine is the least reactive). This is because the force from the nucleus that attracts electrons is weaker as the number of electron shells increases, thus, it is harder to gain an electron when the number of electron shell increases A more reactive halogen will displace (take the place of) a less reactive halogen from an aqueous solution of the less reactive halogens ions For example, Chlorine + Potassium Iodide Chloride + Iodine Colour darkens down the group: o F (Fluorine): Pale Yellow o Cl (Chloride): Yellowish Green o Br (Bromine): Reddish Brown o I (Iodine): Purple o At (Astatine): Black Potassium

11)

Noble Gases: Unreactive non-metals due to its noble gas configuration (duplet/ octet configuration) Have low melting and boiling points (gases at r.t.p) Colourless, monoatomic

12) The size of atoms increases down the group as the number of electron shells increases

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13) The size of atoms decreases down the period. Across the period, the number of electron shells remains the same. However, the distance between the valence electrons and the nucleus is shorter down the period as the proton number of the atom increases down the period. This means that there are more protons in the nucleus and the electrostatic forces of attraction acting on the valence electrons are greater and therefore, the valence electrons are pulled more closely towards the nucleus. Chemical Bonding and Structure
1) An atom undergoes chemical bonding to achieve the noble gas

configuration to make them more chemically stable Octet configuration 8 electrons in the valence shell Duplet configuration 2 electrons in the valence shell

2) Ionic bonds:

Electrostatic Force of attraction between positively and negatively charged ions Formed between a metal and a non-metal (metal anion, non-metal cation) The ions are packed into a giant lattice structure (have straight sides) When an atom loses an electron, it has a positive charge, and it is called a cation When an atom gains an electron, it has a negative charge, and it is called an anion These forms when an atom gains or loses an electron/electrons so as to achieve noble gas configuration The electron that is lost by a cation is not necessarily transferred to the anion that it bonds with Are usually formed between ions from group l, ll, lll and group V, VI, VII Group IV atoms usually do not form ions

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3) Properties of ionic compounds:

Hard and crystalline solids at r.t.p. (Most of the time Ammonium nitrate (NH4NO3) boiling point at 170C) High melting and boiling points Explanation: Ionic compounds are held together in fixed positions in a giant lattice structure by strong ionic bonds, thus a lot of energy is required to overcome these strong electrostatic forces of attraction Do not conduct electricity in the solid state, but can conduct electricity in molten or aqueous state Explanation: In the solid state, ionic compounds are held in fixed positions by strong ionic bonds, therefore, the ions are unable to move freely to conduct electricity as they cannot carry the electrical charges. However, in molten or aqueous state, the ions can move freely and therefore can conduct electricity by carrying the electrical charges. Ionic compounds are soluble in water but insoluble in organic compounds (Most of the time Lead (ll) sulfate ((PbSO4) is insoluble in water) Explanation: The ions attract the water molecules, which disrupts the crystal structure, causing the ions to separate and dissolve into the solution. They do not attract the molecules of organic compounds. Basic particle ion Examples Sodium Chloride, Magnesium Oxide, Calcium Chloride, etc. Note: The explanations are model answers for related questions

4) Covalent bonds

Formed by the sharing of electrons between 2 atoms of nonmetal elements

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Can exist as simple covalent molecules or giant covalent structures Simple covalent molecules have a simple molecular structure Giant covalent structure have a large network of atoms held together by strong covalent bonds

5) Properties of covalent bonds

Liquids or gases at r.t.p (Mostly iodine and sulfur are solids) Low boiling and melting points Explanation: Molecules are held together by weak intermolecular forces of attraction, so very little energy is needs to overcome the weak intermolecular forces of attraction Note: The covalent bonds are not broken in state change, it is the force between the covalent molecules that are broken Do not conduct electricity in any states Explanation: There are no free-moving charged particles (ions or electrons) in covalent substances to conduct electricity (or rather no charged particles at all) Insoluble in water (Mostly sugar, hydrogen chloride and alcohol are soluble in water), but soluble in organic solvents Basic particle molecule (A molecule is made up of 2 or more atoms held together by covalent bonds) Examples Carbon Dioxide, Oxygen, Methane, Sulfur, etc. Note: The explanations are model answers for related questions

6) Drawing of the formation of ionic compounds When atoms lose electrons o They have 1, 2 or 3 valence electrons only

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o When drawing electronic structure Write the symbol on the middle (if the element is unknown and named X, use X as the symbol) Bracket the whole electronic structure and write the charge at the top right corner The charge would be: + when 1 electron is lost 2+ when 2 electrons are lost 3+ when 3 electrons are lost When drawing only valence electrons, positive ions must be drawn with only the symbol in the bracket or with an empty shell (not needed for full structure)

When atoms gain electrons o They have 5, 6 or 7 valence electrons only o When drawing electronic structure Write the symbol on the middle (if the element is unknown and named X, use X as the symbol) Bracket the whole electronic structure and write the charge at the top right corner The charge would be: - when 1 electron is gained 2 - when 2 electrons are gained 3 - when 3 electrons are gained Use a different symbol (dot or cross) for the electrons gained to show that it is from another atom When drawing valence electrons, no change

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When the ratio of ions is not 1:1, write a large numeral to in front of the ion to represent the ratio.( E.g. calcium chloride [Ca]2[Cl]) Use cross for ions which have larger proton numbers

Full Electronic Structure of Sodium

Sodium Chloride Showing Only Valence

Full Electronic Structure of Sodium

7) Drawing of the formation of covalent compounds Only the valence electrons are involved so usually only the valence electrons are drawn

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The two atoms are joined like a Venn diagram, with the electrons only inside the shared area (more than one pair can be inside Write the symbol on the middle of atom (if the element is unknown and named X, use X as the symbol) 2 separate atoms have their electrons represented by different symbols If there are more than 2 atoms, alternate the symbols (no 2 atoms joined together can have the same symbols) Valence electrons can be drawn with the electron shell or without Structural formula (as compared to the dot-and-cross diagram) is shown by drawing a line between the symbols of different atoms to represent 1 pair of shared electrons. More than one pair is represented by more than 1 line

8) Note: Polyatomic structures with charges are also bracketed (the whole molecule). They can form ionic compounds

Dot and Cross Diagram of an Oxygen Molecule

Dot and Cross Diagram of a Chlorine Molecule

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Acids and Bases, Chemical Formulae and Equations

1) An acid is a substance that produces hydrogen ions (H+) when

dissolved in water
2) An acid only shows its properties when dissolved in water

because they dissociate in water for form hydrogen ions which are responsible for its acidic properties. They do not dissociate to form hydrogen ions when dissolved in organic solvents (alcohol, oil, etc.) 3) Strong acids:

Hydrochloric Acid HCl Sulfuric Acid H2SO4 Nitrate Acid HNO3 Phosphoric Acid H3PO4

4) Weak acids: Ethanoic Acid (Vinegar) Citric Acid (Citrus Fruits) Lactic Acids (Yoghurt) Tartaric Acid (Grapes)

5) Properties of acids:

Taste sour Hazardous cause skin problems Change blue litmus paper red (Remember Acids are red on the Universal Indictor) Reacts with reactive metals (i.e. not copper, gold or silver) produces a salt and hydrogen Reacts with carbonates produces a salt, carbon dioxide, and water

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Reacts with metal oxides and hydroxides (bases) produces a salt and water (this chemical reaction is also known as neutralization) Do not react with plastic, glass or brick (Labs store them in plastic)

6) A base is a substance that reacts with an acid to form salt and water

only (definition). An alkali is a substance that disassociates when dissolved in water to produce hydroxide ions (OH). It is any metal oxide or hydroxide 7) Difference between alkalis and bases: All alkalis are bases, but not all bases are alkalis. Alkalis are soluble bases.
8) Calcium hydroxide is often used to reduce the acidity of the soil

to better facilitate plant growth. 9) Strong alkalis:

Sodium hydroxide NaOH Potassium hydroxide KOH Calcium hydroxide Ca(OH2) Weak alkalis:

10)

Aqueous ammonia - NH3 Properties of alkalis:

11)

Alkalis feel slippery and soapy Alkalis are hazardous Burn skin when concentrated, irritate skins when dilute Alkalis change red litmus paper blue (Remember alkalis are blue on the Universal Indicator) Alkalis react with ammonium compounds to form a salt, ammonia gas and water Strong alkalis or acids vs Weak alkalis or acids

12)

A strong acid is one that completely ionizes in water

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For example, all the molecules in hydrogen chloride (HCl) dissociates in water to form H+ and Cl. There are no HCl molecules left A weak acid is one that partially ionizes in water For example, only 4 out of 1000 of the molecules in ethanioc acid (CH3COOH) dissociates in water to form H+ and CH3COO. The rest remain as CH3COOH. Therefore, in ammonia solution, there is a pungent smell as most of the ammonia molecules do not dissociate

13) Concentrated and dilute NOT the same as strong and weak

Concentrated refers to having more molecules in the same solution Unit used to measure concentration is known as molarity/ mol/dm3 pH scale:

14)

pH stands for power of hydrogen >7 is alkaline (at r.t.p.) 7 is neutral (pure water) (at r.t.p.) <7 is acidic (at r.t.p.) Indicators:

15)

Chemical substances that change colour in solutions of different pH values but over a definite pH range Table of Indicators:

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Indicator solution Methyl orange Bromothymol blue Phenolphthale in

Colour in acidic solution Red Yellow Colourless

pH level when it changes colour 4 7 9

Colour in alkaline solution Yellow (from pH 5 onwards) Blue (from pH 7 onwards Pink (from pH 9 onwards)

Good indicators are: o Observable and distinct colour change o Required only in small amounts o Does not affect pH level

Universal indicator is a mixture of indicators which change colour at every pH value Advantages of Universal Indicator paper: o pH paper is disposable, so it reduces the risk of contamination o pH paper can be used on small sample size (1 drop is enough) while the sample solution has to cover the whole bulb of the pH meter o pH paper measures the pH faster than the pH meter, as it has to adjust for a while

pH meter measures accurate pH values (1 or more d.p.)

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A probe is dipped into a solution until the whole bulb is covered to show the pH digitally pH probe can be connected to a compute or data logger to collect pH readings.

16) When cleaning up acid spills, calcium oxide (or any other solid base) is used because it can be cleaned up easily. Using an alkali may cause the spill to turn alkaline when used in excess. This is used in factories around the world. 17) 18) Tests for gases: Hydrogen Gas extinguishes a lighted splint with a pop sound Carbon Dioxide White precipitate forms in the solution when bubbled through limewater (calcium hydroxide) Ammonia gas: Turns red litmus paper blue and has a pungent smell Oxides: Acidic oxides: o Oxides of non-metals o React with water to produce acids o Have acidic properties o Examples are: Sulfur trioxide, Carbon dioxide and Phosphorus(V) oxide, Sulfur dioxide Basic oxides: o Oxides of metals o Are bases o Examples are Copper(ll) oxide, Magnesium oxide, Calcium oxide Amphoteric oxides o Behave as an acidic oxide or basic oxide
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o For example: Aluminum oxide + Hydrochloric acid Aluminum chloride + water Aluminum oxide + Sodium hydroxide Sodium aluminate + water o Examples are: Zinc oxide, Lead(ll) oxide, Aluminum oxide Neutral oxides o Do not react with either acids or bases o Examples are: Water, Carbon monoxide, Nitrogen monoxide 19)

Salts The hydrogen ion in acids is replaced by a metal When naming salts, the name of the metal is placed in front, followed by the other part of the acid Hydrochloric Acid - _________ Chloride Sulfuric Acid - _________ Sulfate Nitric Acid - _________ Nitrate Sulfurous Acid - _________ Sulfite Salts are usually in aqueous state Reactions: Acid + Metal Acid + Base Acid + Carbonate Salt + Hydrogen Salt + Water Salt + Carbon dioxide + Water Salt + Ammonia gas

20)

Alkali + Ammonium compounds + Water Neutralization

21)

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Acid + Alkali Produces salt + water The hydroxide ions combine with the hydrogen ions to form water H+ + OH Uses
o

H2O

Controls pH of soil Calcium hydroxide is used, Compost if too alkaline (Compost is made of rotting plat material which gives off carbon dioxide which is acidic when dissolved in water) Treats indigestion due to the excess of hydrochloric acid in stomach due to too much consumption Magnesium oxide is used

o Treats insect stings Add a base as it is acidic o Toothpaste to neutralize the acids produced by bacteria which may corrode the teeth Magnesium hydroxide is used o Treatment of wastewater 22) Table of positive ions MUST REMEMBER

Charge +1

+2

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+3

Name Hydrogen Lithium Sodium Potassium Silver Ammonium (Not Ammonia) Magnesium Calcium Barium Zinc Lead (ll) Copper (ll) Iron (ll) Aluminum Iron (lll)

Chemical Formula H+ Li+ Na+ K+ Ag+ NH4+ Mg2+ Ca2+ Ba2+ Zn2+ Pb2+ Cu2+ Fe2+ Al3+ Fe3+

In cases such as Lead (II) or Copper (II), the charge of the ion can be inferred from the number of I.

23)

Table of negative ions - Important Charge -1 Name Fluoride Chloride Bromide Iodide Hydroxide Nitrate Oxide Sulfide Sulfate Carbonate Phosphate Chemical Formula FlClBrIOHNO3O2S2So42CO32PO43-

-2

-3 24)
25)

Total charge of compound must ALWAYS be equal

When there is more than 1 of the same polyatomic ion in a compound, it must be bracketed (E.g. Mg(NO3)2 or (NH4)2 So4 )

26) The positive ion must be put in front of the negative ion when naming 27) 28) State symbols Solid s (For all metal or metalloid ions, oxides, hydroxides and carbonates) Liquid l (For water) Aqueous aq (For all acids, alkalis, and salts), aq is used when a substance is dissolved in water Gas g (For hydrogen and carbon dioxide) When writing chemical equations Write down the unbalanced equation with state symbols

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Leave spacing between the compounds to accommodate the coefficients Balance it by adding suitable coefficients Find the LCM (Least Common Multiple) For example: CaO (s) + HCl (aq) CaO (s) CaO (s) (l) + HCl (aq) CaCl2 (aq) + H2O (l) CaCl2 (aq) CaCl2 (aq) + + H2O (l) H2O

+ 2HCl (aq)

29)

Note: Atoms cannot be created or destroyed, so the number of each atom on the left must be equal to the number of the same atom on the right. Note: If on the right of the equation you have 3 H and on the left you have H2, you cannot simply change H2 to H3 . Instead you must make it as 6 H on the right of the equation and 3H2 on the left so as to balance the reaction accurately.

30)

Note for All Chemistry Topics 1) Not all ionic solids dissolve readily in water, only some 2) All gas molecules are bonded by covalent bonds (unless ionic compounds are superheated) 3) Carbon conducts electricity sometimes, like graphite. However, diamond does not 4) Noble gases are called inert gases 5) Take note of these equations

Na + H2O

H2 + NaOH H2 + 2NaOH

Balanced Equation: 2Na + 2H2O H2O + K H2 + KOH

Balanced Equation: 2H2O +2 K

H2 + 2KOH

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Physics: Reflection 1) Transparent and opaque materials: Are actually electromagnetic waves that emanates from vibrating electrons in atoms When light is transmitted through a material, the atoms in the material absorb the vibrations given off by the waves of light and then re-emit the vibrations to neighboring atoms which then absorb and re-emit it. This chain of absorption and re-emission passes the light through the material and out the other side. These materials are transparent Materials which are opaque absorb light without re-emitting it, as the vibrations given off by light to its particles are turned into kinetic energy

2) Pin-hole camera: Light rays reflected off an object travels through the pin hole and forms an image on the screen

The image is inverted due to the property of light: Light travels in a straight line

When the pin-hole is enlarged, the Image will become brighter but blurred. The image becomes blurred as the large pin-hole actually acts as many smaller pin-holes. Each pin hole forms its

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own image at a slightly different position. Thus, when the entire screen is observed, a blurred patch of light is seen. However, the image is brighter as there are more light rays entering the pinhole camera When the pin-hole is made larger: o The image size does not change o The image becomes less sharp When the distance between the objet and the pin-hole is increased: o The image becomes smaller o The image sharpness dies not change

3) Laws of reflection:

The incident ray, the reflected ray and the normal at the point of incidence all lie on the same plane The angle of incidence, i, is equal to the angle of reflection, r

4) Properties of a the image of a reflected object

Virtual (Cannot be captured on a screen) Upright Laterally inverted Same size as the object As far behind the mirror as the object is in front of the mirror

5) Drawing reflected light rays: Reflect the image behind the mirror Connect the image to the eye

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Connect the object to the point of intersection on the plane mirror Note: All lines behind the mirror must be dotted.

Refraction
1) If the light ray travels from a substance with a lower refractive index to

a substance with a higher refractive index, the light ray bends away from the normal, and vice versa.
2) Formula: n1 sin theta1 = n2 sin theta2, where n1 and n2 is refractive

index and theta1 and theta2 is angle of incidence and angle of refraction.
3) Total Internal Reflection: occurs when angle of incidence is greater

than critical angle of a particular substance. Only occurs from substances with a higher refractive index to substances with a lower refractive index.
4) To calculate critical angle: sin-1 (Refractive index of substance with

lower refractive index / Refractive index of substance with higher refractive index). Most of the time, for light that is passing from a substance with a higher refractive index that air, the formula is simple: sin-1 (1/Refractive index of substance).
5) If the angle of incidence is 0 (i.e. ray of light strikes surface at 90),

refraction will not occur.

6) Note: Even if it is just normal refraction (No TIR), there will still be a

weak reflected ray of light (MYCT Trick Question!).

7) Note: Refractive index directly corresponds to how fast light travels in

that substance. Just take 3.0 108 Refractive index to get the speed of light in that substance.

Nuclear Physics

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1) Half life: Amount of time taken for half the amount of a substance to decay. Can range from seconds to hundreds of millions of years (e.g. radioactive nuclear waste).

2) Nuclear decay types of radiation released: Alpha Particle radiation a helium atom is released. Can be stopped by a piece of thin paper/ human skin. Beta Particle radiation an electron is released. Can be stopped by aluminum. Gamma rays type of ray on the lowest end of the electromagnetic spectrum, after X-rays. Can be stopped by thick lead.

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Biology: Sexual Reproduction in Humans Haploid cells number of chromosomes = n. Half set of chromosomes (23 in humans), found only in sex gametes. Diploid cells number of chromosomes = 2n, are somatic (body) cells with a full set of chromosomes. Asexual Reproduction

New individual produced by ONE single parent Off-springs are genetically identical to parents Fusion of 2 nuclei not involved (Eg. Binary Fission, Yeast Budding) Mitosis

Sexual Reproduction

New individual produced by two parents Off-springs are genetically not identical to parents Fusion of 2 nuclei to form a zygote Meiosis

Sexual Reproduction in Humans

Only sexually mature male and female organisms can produce reproductive cells Males produce gametes called sperm and females produce gametes called ova.

Puberty Period of rapid growth during which a person becomes sexually mature and capable of reproducing

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Increased secretions of hormones in the body bring about puberty During puberty, reproductive organs develop to produce sperms or mature eggs Dramatic physical, emotional and social changes

Functions of the Male Reproductive System Testes: Produce male gametes (sperms) Secrete male sex hormone (testosterone) which are responsible for the development of male characteristics during puberty

Epididymis: Narrow coiled tube that temporarily stores inactive sperm

Sperm Duct (Vas Deferens): 1 leaving each testis Muscular tubes that rise up the body to the join the urethra Transports sperm from testis to urethra

Seminal Vesicles:

Secretes seminal fluids (contain nutrients that nourish and activate the sperms) which mix with sperms to form semen and stores sperm temporarily

Prostate Gland: Secretes seminal fluid that nourishes sperm

Scrotum: Sac where testes are located Suspended outside main body so as to keep temperature lower than the body for healthy sperm survival

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Urethra: Tube which leads to outside of body through penis Pass sperms into the female body Holds both urine and semen and joins base of bladder

Penis: Erectile organ holding erectile tissue with numerous blood spaces Deposits semen into female during copulation

Sperm:

Has head containing a nucleus with chromosomes where male parent genes are found. Has long tail to help sperm swim to egg Has large nucleus with little cytoplasm and an acrosome. Mitochondria found in middle of sperm and provides energy for sperm activity

Functions of Female Reproductive System Ovaries: Produces one ovum each month Secretes female sex hormones, oestrogen and progesterone

Fallopian Tubes (Oviducts): Narrow and muscular traits Lining of oviducts bear short hairs to move ovum down to uterus Site where fertilization of ovum occurs

Uterus: Thick muscular walls

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Inner surface covered by soft and smooth layer called uterine lining. Lining breaks down and sheds with blood every month from puberty onwards Site of foetus development

Cervix: Ring of muscle at lower narrow end of uterus Keeps foetus in uterus during pregnancy Enlarges to allow foetus to pass through during birth

Vagina: Muscular tube that receives semen from penis during sex Joins cervix to outside of body Serves as birth canal during childbirth

Ovum: Spherical, haploid female reproductive cell Contains nucleus where female parent genes are found One released monthly Cannot move by itself

Menstrual Cycle Menstruation is the start of an event cycle which involves the monthly discharge of tissue and blood out the body through the vagina Occurs in female reproductive organs 5-7 days

Menstrual Cycle: 2 main processes: menstruation and ovulation 28 days on average

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Main function to prepare uterus to received a fertilized egg Events controlled by a variety of hormones

Days 1-6: Uterine Lining shed (menstruation) Bleeding Phase Days 7-10: Uterine Lining grows again Follicular Phase Days 11-18: Ovulation (mature egg released from follicle in ovary) Ovulation Phase Days 19-28: Uterine Lining continues to thicken Luteal Phase Roles of Hormones in the Menstrual Cycle Bleeding Phase:

2-5 days and uterine lining degenerates Occurs only when ovum is not fertilized If fertilization and implantation of embryo occur, no menstruation till birth. Role of Hormones: Oestrogen secreted by Graafian follicle stimulates repair and growth of uterine lining for reception of fertilized egg

Ovulation Phase:

Graafian Follicle ruptures and releases and ovum into oviduct (day 14) Concentration of oestrogen and luteinizing hormone in blood is high Role of Hormones: Progesterone keeps uterine lining thick and well-supplied with blood for implantation of embryo Fertile period: Days 11 17, because sperm can survive for up to 3 days in the oviducts. (Ovum: 1 - 2 days)

If sperm does not fertilize egg, ovary stops producing progesterone Uterine lining would thus break down and bring an onset of menstruation

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Usually occurs on the 28th day

Fertilization & Development Definition: Fusion of nucleus of sperm with nucleus of ovum to form a zygote Process: 1) Semen deposited in vagina during copulation 2) Sperm swims up uterus to enter oviduct 3) If an ovum is in one of the oviducts, one sperm will fertilize the ovum 4) The fertilized egg (zygote) divides repeatedly to form an embryo which moves to uterus and becomes embedded in uterine lining Implantation: When embryo reaches uterus (aft. 4-5 days) and embeds itself into thickened lining of uterus Development of Foetus: Embryo develops in uterine lining to become foetus Embryonic membrane (amnion) develops to enclose embryo (foetus) Foetus connected to placenta by umbilical cord

Functions of amniotic fluid: Supports and cushions foetus before birth Shock absorber Protects foetus against mechanical injury Lubricates and reduces friction during delivery Buoys up foetus and allows it to move freely during growth

Placenta:

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Organ that connects developing foetus to uterine wall to allow nutrient uptake, waste elimination and gas exchange via the mothers blood supply Villi grow from embryo into uterine wall Contains blood capillaries of embryo Partly embryonic tissue, partly mothers tissue Mothers and embryos blood system not continuous due to different blood pressure, blood group; separated by a thin layer of tissue where diffusion of materials occur

Umbilical Cord:

Connects foetus to uterine wall and allows free movement Contains 2 umbilical arteries (which transports waste and carbon dioxide from fetus to mother) and 1 vein (which supplies fetus with oxygen, nutrients etc.)

Birth Control What is it?

Prevents occurrence of ovulation, implantation or fertilization of fertilized egg Methods may be natural, chemical, mechanical, intrauterine devices, hormonal or surgical (sterilization) in nature

Temporary Methods: Allows couple to still have children once they stop using the method May be natural or artificial in nature

Natural Means: Not having sex at all Withdrawal of penis just before ejaculation

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Not having sex during fertile phase of menstrual cycle (rhythm method) Unreliable

Artificial Means: Chemicals devices) such as spermicides, contraceptive (hormonal

Mechanical devices like condoms, diaphragms, IUD Serves to block sperm entry

Condom: Thin rubber tube used to cover erect penis before sex with small tip at end to collect semen Not permeable and does not allow sperm to enter vagina and meet egg

Diaphragm: Dome-shaped rubber cap with elastic rim, inserted into vagina and covers cervix, preventing sperm from entering uterus

IUD: Coil of plastic or metal, many shapes Inserted into uterus by doctor and provides protection for long periods, thus is effective and convenient birth control Prevents fertilization and implantation

Contraceptive Pills: Have chemicals that function like oestrogen and progesterone Inhibit follicle stimulating hormone and luteinizing hormone, preventing ovulation and follicle development

Spermicide:

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Chemicals that inactivate, kill or block sperms from entering uterus (prevents fertilization) May be gel, foam, foaming tablets that are inserted into vagina Unreliable when used on their own

Permanent Methods Requires surgery and usually irreversible Couple should not choose such methods unless they are sure Surgical Methods: Vasectomy and Ligation

Vasectomy: Minor surgery involving the tying and cutting of part of the sperm ducts Sperms will not be ejaculated and male will be sterile

Ligation: Involves surgical tying and cutting of both oviducts Prevents egg from meeting sperm (no fertilization)

Sexually Transmitted Infections Infections that may be transmitted from one to another through sexual intercourse Can contract if having intercourse with infected partner Gonorrhea and syphilis caused by bacteria, curable; AIDS caused by virus, fatal Infected look and feel healthy in early stages Once symptoms are observable, disease may have already caused a lot of bodily harm or become incurable Sign can be observed or measured but symptom can only be felt

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Gonorrhea Caused by spherical bacterium (neisseria gonorrhea) Can be passed from infected mother to baby during birth Signs and symptoms Yellow pus discharged from end of urethra In male, urethra becomes narrow making urinating hard. In severe cases, testes may become fibrous and person may be sterile Burning sensation during urination
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Some women may not show symptoms but dangerous as infection of others continues Can be cured if treated with appropriate antibiotics

Syphilis Caused by spiral bacterium (Treponema palledum) Can be passed from mother to child during pregnancy Stages and Symptoms (3 stages): 1) A few days after infection, a painless sore appears on male penis, female vagina or cervix. Signs may disappear without treatment which does not indicate recovery but progression 2) A few months later, non-itchy rashes appear and sores appear on reproductive organs; disappear without treatment.
3) Highly dangerous as internal organs usually affected. Patient

may become blind, paralyzed. Heart failure, insanity or death may occur. Can be cured if promptly treated by antibiotics Prevention/Control (Syphilis and Gonorrhea) Can be treated with antibiotics Withdrawal Tracing of sex contacts

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Condoms Fidelity to one partner

Acquired Immune Deficiency Syndrome (AIDS) Caused by virus called Human Immunodeficiency Virus Incurable and Fatal White blood cells usually produce antibodies when a virus enters the body to destroy virus HIV attack white blood cells (T helper cells), making them unable to protect the body against infection.

Defense mechanism affected Person loses immunity against disease-causing germs that enter body

Signs and Symptoms: 1) Appear only after a few months/years. HIV-infected may fall sick more easily, lose weight, have diarrhea and fever 2) (Final) Developed AIDS completely destroys immune system. Severe weight loss, chronic diarrhea, fever, lung infection, Kaposis sarcoma (blood vessel cancer), brain infection

Spread of HIV: Sex Blood Transfusion Sharing infected needles From infected mother to foetus during birth and pregnancy

Prevention and Control (AIDS) Prevent casual sex Avoid sharing instruments likely to break skin Used sterilized needles, condoms and safe blood

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Assisted Reproductive Technologies Forms of ART IVF (ICSI, ZIFT, GIFT) Artificial Insemination (IVI, ICI, IUI, ITI) Surrogate Mothers and Gestational Carriers Sperm/Egg Donor

What is ART ? Methods used to achieve pregnancy by artificial or partially artificial means Used primarily in infertility treatments Involves use of third party (eg. Sperm Donor) Techniques often used for women who have irreversible damage to their fallopian tubes or cervical mucus problems Benefits couples with unexplained infertility

In-vitro Fertilisation (IVF) Technique in which fertilization occurs outside the womb Used when fallopian tubes are blocked, damaged or missing Used due to male factors (sperm defects, low count/motility) and unexplained infertility Steps: 1) Ovarian Stimulation: - Fertility drugs used, stimulate ovaries to release multiple ova 2) Ova Retrieval: - Ova aspirated from follicles through needle connected to suction device (Each follicle contains a single egg) 3) Insemination: - Sperm obtained from ejaculation separated from semen

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4) Fertilization: - Motile sperm placed with ova in process of artificial insemination 5) Embryo Culture: - Culture placed in incubator and fertilization takes place hours later 6) Embryo Transfer: - May be transferred to uterus on day 3-5 of development. Tip of transfer catheter (containing culture) passes cervix, fluid with embryo placed in uterus cavity and implantation will take place 1-5 days after transfer. Intracytoplasmic Sperm Injection (ICSI) Used when IVF fails Single Sperm injected directly into ovum Zygote placed in oviduct or uterus Recommended if male partner has few sperms or when other methods are unsuitable

Artificial Insemination Sperm placed directly in uterus, vagina, cervix, fallopian tubes Ensures more sperm are available to access ovum IUI (Intra-uterine Insemination) most commonly used Used when: 1) Womans cervical mucus is hostile to sperm 2) Man has healthy sperm but low sperm count 3) Male infertility due to antibodies to his own sperm 4) Ejaculation problems psychological issues 5) Retrograde Ejaculation 6) Couples who cannot naturally have intercourse Intra-uterine Insemination (IUI) due to vaginal muscle contractions,

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Couples may be offered IUI if sperm quality is reduced, cervical mucus is hostile to sperm, couple has unexplained infertility Selected sperm cells placed directly in womb Insemination takes place at most fertile period (11-17) Can be used concurrently with super-ovulation (More than 1 ovum produced)

Sperm Donor Donors undergo medical and genetic screening, including for AIDS Healthy, viable sperms frozen and quarantined Sperm released if all tests are negative

Surrogacy and Gestational Carrier Surrogate: Using another mothers ovum fertilized with own male partners sperm, conceived by other woman Gestational Carrier: Using own ovum and own male partners sperm, but foetus develops in other womans womb of Sexual

-----------------------------------------------End Reproduction------------------------------------------Heredity Inheritance Why are individuals different?

Fusion of male and female gametes produce individual with genetically unique traits Fertilization allows genetic variation to occur Hereditary characteristics passed down from parents

Mitosis
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Nuclear division by which two diploid daughter cells produced from one diploid parent cell (Internal multiply, then divide)

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Copying division of a single nucleus into two genetically identical daughter nuclei occurs in all cells except sex organs

Meiosis
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Nuclear division by which four haploid daughter cells are produced from one diploid cell (Internal multiply, then divide twice) Reductive division which occurs in sex organs

Variety
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Arises from sexual reproduction

Meiosis shuffles genes to make gametes different - crossing over. Each pair of gametes produce unique offspring

Arises from mutation and environmental factors

Continuous Variation
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No distinct categories with many intermediates Controlled by several pairs of alleles and influenced by environment (eg. Intelligence, eye and skin colour, height)

Discontinuous Variation
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Distinct phenotypes with no intermediates Controlled by one pair of alleles or small number of genes, not influenced by the environment (eg. Blood group, hitchhiker thumb) Continuous Variation Deals with extreme range phenotypes Controlled by many genes Genes show additive effects Affected by environment of

Discontinuous Variation Deals with few clear-cut phenotypes Controlled by a few genes Genes do not show additive effects Not affected by environment

Genetic Terminology (Monohybrid Inheritance)

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Monohybrid Inheritance: Inheritance involving one pair of contrasting traits Chromosomes: Structures containing DNA Genes: Unit of inheritance which occupies a small segment of DNA within chromosome, performs specific function Gene locus: Region on a chromosome occupied by a particular gene Alleles: Different forms of the same gene occupy corresponding loci on homologous chromosomes; express different characteristics, given letters to represent Multiple Alleles: 3 or more alleles giving rise to ABO blood group system, IA, IB, IO, environment influences way genes act Homologous chromosomes exist in pairs, similar size and shape and have same sequence of gene loci but could have different alleles in gene loci Phenotype: Trait which can be seen or observed Genotype: Genetic make-up of organism Homozygous: 2 alleles at locus are identical Heterozygous: 2 alleles at locus are different Dominant allele: Allele shows effect in phenotype in both homozygous and heterozygous Recessive allele: Allele has no effect on phenotype unless it is homozygous Co-dominance: Both traits expressed and equally dominant (eg. Blood group) Incomplete Dominance: Both traits do not express equally. Heterozygous phenotype is intermediate between 2 homozygous phenotypes (eg. Pink), blending of traits Sex Determination in Humans
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Sperm determines childs sex (X/Y) as female only produce gamete with X chromosomes

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Sex chromosomes carry few genes that code for certain traits not concerned with sex May show traits only in 1 sex

Diseases caused by sex-linked traits Haemophilia Lowers level of chemicals that cause blood clots post-injury Genetic defects on X chromosomes (X-linked condition) Women can be carriers but rarely sufferers as they have 2 X chromosomes, so if there is mutation, there is a backup Men are XY, so if they inherit a defective X chromosome, they are guaranteed to develop the condition

Colour-blindness (carried on X chromosome)

Mutation
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Inheritable change in a gene or a chromosome Caused by radioactive emission, certain chemicals (mutagens), UV rays, uneven distribution of chromosomes during cell division Gene mutation:

Alteration of minute part of DNA Produces altered proteins in the cell Sickle cell anaemia, haemophilia

Sickle cell anaemia Mutation in haemoglobin gene

Chromosomal Mutation Through accidents at chromosomal separation in meiosis Extra chromosome in gametes (eg. Downs Syndrome)

Pedigree

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Chart of genetic history of family over generations Include many symbols

Interpretation of Pedigree
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If most males in pedigree are affected, the disorder is likely sex-linked If it is a 50/50 gender ratio, the disorder is likely autosomal If disorder is dominant, one of the parents must have the disorder If disorder is recessive, neither parent has to have the disorder as they can be heterozygous (carrier) End of Heredity

--------------------------------------------------------------------------------------------------DNA Structure DNA

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Each DNA molecule consists of two parallel strands twisted around each other to form a double helix Each DNA molecule is wrapped around proteins to form a chromatin thread During cell division, chromatin threads coil to form chromosomes in cell nucleus

Basic Units of DNA

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Basic unit of DNA is a nucleotide Each nucleotide made of a sugar (deoxyribose), a phosphate group and a nitrogen-containing base joined together 4 nitrogen-containing bases are adenine (A), thymine (T), cytosine (C) and guanine (G) SugarPhosphate Backbone

Nitrogencontaining bases

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Building blocks of DNA

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Nucleotides joined together to form long chains, poly-nucleotides Each gene made of sequence of nucleotides As there are 4 different bases, for a gene made of n nucleotides, there are 4n different nucleotide combinations

Double Helix -

DNA molecule has spiral structure (double helix) Both strands of DNA run in opposite directions are twisted

Rule of Base Pairing

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Two poly-nucleotide strands run anti-parallel Bases of one strand form hydrogen bonds of other strand according to base-pairing rule A bonds with T, C bonds with G Bases that bond with each other are called complementary base pairs In a DNA molecule, the ratios of A:T and C:G are 1:1

RNA Structure RNA

Single strand Made of nucleotides joined to form poly-nucleotides Contains ribose sugar in poly-nucleotide, not deoxyribose sugar 4 bases are adenine, guanine, cytosine and urecil (U, bonds with adenine)

Differences between RNA and DNA DNA RNA Sugar is deoxyribose Sugar is ribose Nitrogen-containing bases are Nitrogen-containing bases are adenine, guanine, cytosine and adenine, guanine, cytosine and thymine urecil

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Ratio of A:T/C:G is 1:1 Large insoluble molecule Permanent molecule in nucleus

Ratios not fixed Small soluble molecule Temporary molecule all over cell, produced when necessary

DNA Replication -

Basis of biological inheritance Biological process that occurs in all living organisms and copies their DNA Starts when one double-stranded DNA molecule produces two identical copies Begins at specific locations in genome called origins Unwinding of DNA at origin by DNA helicase and synthesis of new strands, forming a replication fork DNA polymerase, the enzyme that synthesizes the new DNA by adding free nucleotides matched to the template strands Each strand of original DNA molecule serves as template for production of complementary strand, which is semi-conservative replication (1 original strand, 1 new)

Central Dogma of Molecular Biology

DNA RNA Protein

DNA forms more DNA through replication. DNA forms RNA through transcription. RNA forms protein through translation. Making of Proteins -

Made in cell via 2 processes, transcription and translation One strand of DNA used as template for transcription The other is a coding strand with has the mRNA sequence

Transcription

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Process by which one DNA strand is used as template to copy its information to a messenger RNA molecule (mRNA) Occurs in nucleus Transcription based on complementary base pairing between DNA and RNA

Translation
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mRNA carries message to cytoplasm In cytoplasm, ribosome molecules, together with transfer RNA (tRNA) translate message in mRNA into protein molecule Message on mRNA translated into specified sequence of amino acids Each 3 consecutive bases of mRNA form a codon that specifies a particular amino acid tRNA carries amino acid to mRNA tRNA has anticodon complementary to mRNA codon

Proteins built from amino acids linked up in a chain and folded into a 3D structure

Genetic Code
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Set of rules by which information encoded in genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences) by living cells Defines how sequence of 3 nucleotides called codons, specify which amino acid will be added next to protein synthesis Universal Almost all organisms in nature use same genetic code Same mRNA codons will specify the same amino acids in organisms

Non-overlapping and Continuous Successive triplets read in order

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Each nucleotide is part of only one triplet codon

Degenerate Each amino acid can be specified by more than one codon

Recombinant DNA Recombinant DNA -

DNA taken from two different sources and fused into a single DNA molecule Special DNA cutting enzymes, restriction enzymes, cut DNA at specific sites DNA cut with a restriction enzyme will have single-stranded ends, sticky ends 2 DNA molecules cut with the same restriction will have the same exposed nucleotides and will undergo complementary base pairing Each restriction enzyme recognizes a different nucleotide sequence

Ligase Joins DNA fragments together by repairing the sugar-phosphate backbone

Plasmid Found in bacteria (which has a plasmid and genomic DNA) Used to carry inserted genes into the bacteria

Genetic Engineering Insertion of human insulin into genomic DNA Procedure: 1. Isolate plasmids from bacteria 2. Extract human insulin genes with restriction enzymes 3. Cut plasmids with the same restriction enzyme 4. Splice insulin into plasmids use DNA ligase
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5. Recombinant plasmids inserted into bacteria (transformation) 6. Plasmids serve as vector to carry human gene into bacteria 7. Select transformed bacteria and grow out in culture (cloning)

Human insulin Mass culture of transformed bacteria in fermenter Bacteria produce insulin Extract and purify insulin, used to treat diabetes

Advantages of genetic engineering Wide application: Agriculture, Chemical, Pharmaceuticals, Medicine

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