Secondary 2 Science Notes

JLTPS
Year 2 Science Notes

Chemistry, Pg 1-10
Physics, Pg 11-20 user
Biology, Pg 21-42
2012
No part of this production is to be reproduced or

sharedwithout the consent of the creator.
Year 2 Chemistry Notes
Topics:
1. The basics about atoms.

 Structure of an atom
 Nuclide notation
 Isotopes
 Electronic configuration
2. The Periodic Table
 Reading the periodic table.
 Alkali metals, halogens and noble gases.
3. Chemical bonding
 Ionic bonding
 Covalent bonding
 Comparison
 Drawing
4. Acids and bases
 Properties of acids
 Properties of bases
 Acid reactions
 pH scale
5. Chemical formulae
 Table of charges
 Writing and balancing chemical equations
Atomic Structure
An atom is the smallest particle of an element that has the same chemical
properties of that element. Atoms of the same element are all identical.
An atom is made of three types of subatomic particle. These are the proton,
the neutron and the electron. The proton and neutron are in the centre of the atom
and electrons spin around the nucleus.
Year 2 Science Notes ©JLTPS 2012 Page 1

Each of these subatomic particles has important properties – the charge and
the relative atomic mass.
Subatomic particles Relative mass (in atomic Relative charge

mass unit)
Proton 1 +1
Neutron 1 0
Electron 1/1836 ≈ 0 -1
Nuclide notation
In nuclide notation, there are two important terms: mass number and atomic
number. The mass number is basically the mass of the atom in atomic mass units (i.e.
number of neutrons + number of protons), and the atomic number is the number of
protons.
The nuclide notation is basically the structure of the atom being written in
symbol form:
Isotopes
Isotopes are atoms of the same element with the same number of protons but
a different number of neutrons. Therefore, they have the same atomic number but a
different mass number. Isotopes of the same element have similar chemical
properties (chemical reactions) but different physical properties (melting point,
boiling point, density, etc.).
Isotopes are usually expressed in the form {element – mass number}. Some
examples are carbon-12, carbon-13, carbon-14, uranium-235, uranium-239, etc. They
can also be expressed in nuclide notation. Some isotopes, such as the isotopes for
hydrogen, even have special names (hydrogen-1 is protium, hydrogen-2 is
deuterium and hydrogen-3 is tritium).
(NOTE: This becomes very important in nuclear physics later on.)
Electronic configuration
Electrons are arranged in groups of varying energy levels called electron

shells. The first shell can hold 2 electrons, the second can hold 8, the third can hold 8
and the fourth holds the rest in the first 20 elements of the periodic table. The

electron shells must be filled in increasing order of energy levels – the first shell is filled,
then the second, then the third and so on (for the first 20 elements).
Electronic configuration basically tells us the number of electrons in each shell.

To work out an elements electronic configuration (for the first 20 elements), we first
find the number of electrons. This is usually the same as the atomic number (but in
some troll questions where ions are involved, this may not be the case!!!). After we
find this number, we can find the electronic configuration, which can be
represented by (A,B,C,D) A must be equal to 2 before B can exist, B must be equal
to 8 before C can exist and C must equal to 8 before D can exist. A+B+C+D = the
number of electrons. Some examples are hydrogen (1), carbon (2,4), oxygen (2,6),
magnesium (2,8,2), aluminium (2,8,3), chlorine (2,8,7) and potassium (2,8,8,1).
Electronic configuration bonus
The reason why this only applies for the first 20 elements is because of
subshells. In an atom, there are not only shells; there are also the subshells s, p, d and
f. The first shell only has subshell 1s, the second shells has 2s and 2p, the third shell has
3s, 3p and 3d, while the fourth shell has 4s, 4p, 4d and 4f. After we factor in these
subshells, we then can actually derive a formula for the maximum number of
electrons in each shell – 2(shell number)2. This means that the first shell can hold 2
electrons, the second can hold 8, the third can hold 18, and the fourth can hold 32.
It then follows that s subshells can hold 2 electrons, p subshells can hold 6, d subshells
can hold 10 and f subshells can hold 14. These subshells also require different energy
levels to fill up. 1s is the easiest to fill up, followed by 2s, 2p, 3s, 3p, 4s then 3d.
(Mnemonic: We can assume the amount of energy needed to fill up a subshell as 1
+ the letter, where s is 1.4, p is 2.3, d is 3.2 and f is 4.1. Then 1s would require 2.4, 2s
would require 3.4, 2p would require 4.3 and so on. It then applies that 4s requires 5.4,
while 3d requires 6.2, followed by 4p which requires 6.3.) This then shows that 4s is
easier than 3d to fill up, and will be filled up before 3d. In the first 20 elements, 3d
isn’t filled up (it is only filled up from element 21) since 1s, 2s, 2p, 3s, 3p and 4s must
be filled up with exactly 20 electrons. :D
The subshell configuration is given by 1snumber of electrons here, 2snumber of electrons here
and so on.
Atomic orbitals
The quantum theory says that electrons are not found in fixed orbits, but can
appear randomly in a 3D probability field. These probability fields, called atomic
orbitals, are different for different subshells, and actually look quite cool :P
Periodic Table
The periodic table is probably one of the most useful things in chemistry. It is a
way of arranging and classifying the elements, which are arranged in order of
proton number.

The vertical columns are called groups (written in roman numerals) and the
horizontal rows are called periods. Certain groups are very important, namely Group
I, Group VII and Group 0, the alkali metals, halogens and noble gases respectively.
Some elements have no group number written over the columns they are in. These
are the transition metals.
As the group number increases, the elements become less and less metal-like
(their metallic characteristics/properties decrease). A zigzag staircase can be drawn
through the periodic table, from boron downwards to polonium. This line divides
metals and non-metals. Some of the elements which are touched by this line are
metalloids, which exhibit properties of both metals and non-metals.
This is a picture of a colour-coded periodic table, indicating which elements

are metals, metalloids and non-metals:
Going back to the three important groups, elements of these groups have
notable characteristics that are important.
Group I – Alkali Metals Group VII – Halogens Group 0 – Noble gases

Reactive metals. Reactive non-metals. Unreactive non-metals.
Have low melting and Have low melting and Have low melting and
boiling points. boiling points. boiling points.
Silvery, soft metals with low Exist as diatomic Colorless, monoatomic
densities. molecules. gas.
General trends as the row number increases

Melting and boiling points Melting and boiling points None. All are colorless and
decrease. increase. unreactive.
(Lithium is a solid at room (Fluorine is a gas; iodine is
temperature; caesium a solid.)
melts if you hold it in your
hand.)
Reactivity increases. Reactivity decreases.
(Lithium sizzles in water; (Fluorine is explodes when
caesium explodes in set on fire; iodine only
water.) smolders.)
Colour darkens.
(Fluorine is a pale yellow
gas; iodine is a blackish
solid.)
Uses
Lithium – batteries. Chlorine is used in bleach, Helium – balloons!
disinfectants and
swimming pools.
Sodium vapor – street Iodine + alcohol = Neon in argon in light
lamps. disinfectant for wounds. bulbs – won’t explode.
Imagine using fluorine in a
light bulb which would last
a few minutes/seconds
before exploding. (good
prank though :P)
Sodium compounds, e.g. Neon in advertising strip
salt (NaCl) lights.
KNO3 is used as a fertilizer. Argon in steel
manufacturing.
Chemical bonding and structure

In the earlier part on Group 0 elements, we can see that Group 0 elements
are the most stable. This is because their electron shells are filled. This sort of
configuration, called a noble gas configuration is extremely stable and atoms will try
to reach this state by chemical bonding.
There are basically three types of bonding – ionic bonding, covalent bonding
and metallic bonding. Of the two, only ionic bonding and covalent bonding are
tested.
Ionic bonding
An ionic bond is the electrostatic force of attraction between positively and

negatively charged ions. (Atoms lose or gain some electrons to achieve the noble
has configuration and thus acquire a charge, which is determined by number of

protons – number of electrons in noble gas configuration. With a charge, they are
then called ions.)
In ionic compounds, the ions are packed closely together in a regular pattern.
The positive and negative ions are strongly attached to one another by ionic bonds
and arranged into a giant lattice structure.
Examples: Sodium chloride (table salt), magnesium oxide, calcium chloride.
Covalent bonding
A covalent bond is the bond formed by the sharing of electrons between 2

atoms of non-metal elements.
Many covalent substances exist as molecules with a simple molecular

structure, made up of 2 or more atoms held together by covalent bonds. A
molecule of an element contains atoms of the same element covalently bonded
together while a molecule of a compound contains atoms of different elements
covalently bonded together.
Examples: Carbon dioxide, oxygen gas, methane, sulfur.
Differences between covalent and ionic compounds
Property Ionic compounds Covalent compounds

Physical Hard Ions are held in their Usually Molecules are held
State at crystalline fixed positions in a liquids or together by weak
room temp. solid with a giant lattice gases. intermolecular forces
and giant structure by very (except of attraction (van
pressure. lattice strong ionic bonds, iodine and der Waals’ forces),
structure. which require a lot sulfur.) very little energy is
Melting and High. of energy (in this Low. required to
boiling case heat) to overcome these
points. overcome these weak intermolecular
strong electrostatic forces.
forces of attraction. Only small molecules
held together
strongly by
intermolecular forces
are not separated.
Electrical Does not In the solid state, Do not No free moving
conductivity conduct the ions fixed in conduct charged particles
electricity position by strong electricity (ions and electrons)
in solid ionic bonds and in all states. to conduct
state; only cannot move freely electricity.
does so in to conduct
molten or electricity.
aqueous In the molten or
states. aqueous states, the
ions can move
about freely to

conduct electricity.
Solubility Usually - Usually -
soluble in insoluble in
water. water.
Drawing these compounds – dot and cross diagrams
Ionic
1. The electrons of 1 type of atom are represented by dots, while those of

different neighboring atoms are represented by crosses.
2. Read the question carefully and see if it requires drawing of all electrons or
only valence electrons.
3. If it is all electrons, just draw all of them but make sure that the atoms have a
noble gas configuration.
4. If it is only valence electrons, draw something as shown in the diagram.
5. Draw square brackets around the atoms and indicate the number of such
atoms with a big number at the left. Also indicate the charge of a single atom
at the top right.
Covalent
1. Most of the time, only valence electrons need to be drawn.

2. It is actually not necessary to draw the rings as shown in the above diagram.
3. Cheat: if you don’t know how the molecule is supposed to be drawn, then
you add the number of valence electrons (A) and also the number needed
for a noble gas configuration (B). You can then take (B-A)/2 to get the
number of bonds (e.g. if there are 3 atoms and you calculate 3 bonds, there
is a single bond (one shared electron pair) between each atom). This will
make your life easier.

4. Sometimes, the bonds are represented by lines, with one dot and cross
representing one line between the atoms. Usually, these line diagrams
(structural formulae) will come out in the question, and to answer it, simply
copy the whole thing out, but replace the lines with a dot and a cross and
add electrons to ensure all atoms have the noble gas configuration.
Acids and Bases

Acids
- An acid is a substance that produces H+ ions when dissolved in water.

- As such, it only displays it properties when dissolved in water, and not when
dissolved in other organic solvents.
- There are strong acids (lowest pH) and weak acids (lower pH – below 7).
Strong acids include sulfuric acid (H2SO4), nitric acid (HNO3) and hydrochloric
acid. Weak acids include ethanoic acid and citric acid.
- Properties of an acid
 Sour taste.
 Turn blue litmus paper red.
 pH value is less than 7.
 Good conductor of electricity – has free moving ions to conduct
electricity.
Bases
- A base is a substance that reacts with an acid to form a salt and water only.
- It can be any metal oxide or hydroxide.
- Soluble bases are called alkalis.
- Alkalis dissociate to produce hydroxide ions (OH-) when dissolved in water.
- There are strong bases (highest pH) and weak bases (higher pH – above 7).
Strong bases include potassium hydroxide (KOH) and sodium hydroxide
(NaOH), and weak bases include aqueous ammonia.
- Properties of a base
 Bitter taste.
 Slippery and soapy feel.
 Turn red litmus paper blue.
 pH value is more than 7.
 Good conductor of electricity.
Reactions involving acids – VERY IMPORTANT!!!
1. Acid + reactive metal = salt + hydrogen gas.

2. Acid + base = salt + water.
3. Acid + carbonate = salt + water + carbon dioxide.

pH scale
- The pH (power of hydrogen) scale is basically a measure of the acidity or

alkalinity of a solution.
- Scale from 1-14: Lower pH below 7 = acidic; higher pH above 7 = basic;
neutral pH equal to 7 = neutral.
- Methods of measuring pH
 indicators such as phenolphthalein (strongly acidic = orange; acidic or
near neutral = colorless; slightly basic = pink/fuchsia; strongly basic =
colorless), methyl orange (reasonably strong acid = red; very weak
acid/base = yellow), litmus paper (acid = red; base = blue) and
Universal Indicator (colours of the rainbow – acid = red; base = violet;
neutral = green)
 pH probe attached to a data logger.
Chemical Formulae
Basically, positive ions react with negative ions such that the overall charge
becomes 0. However, you have to memorize the charges of some elements.
Charge (+/-) Positive Negative

Hydrogen (H) Fluoride (F)
Lithium (Li) Chloride (Cl)
1 Sodium (Na)
Potassium (K)
Bromide (Br)
Iodide (I)
Silver (Ag) Hydroxide (OH)
Ammonium (NH4) Nitrate (NO3)
Magnesium (Mg) Oxide (O)
Calcium (Ca) Sulfide (S)
Barium (Ba) VS
2 Zinc (Zn) Sulfate (SO4)
Lead (II) (Pb) Carbonate (CO3)
Copper (II) (Cu)
Iron (II) (Fe)
3 Aluminium (Al)
Iron (III) (Fe)
Phosphate (PO4)
Most of this stuff can actually be derived from the periodic table except the
stuff in green.
Anyway, now that we know the charges, we can mix and match according
to the name of the chemical to make the charge 0.
For example, silver (+1) nitrate (-1) is AgNO3, sulfuric (-2) acid (acid =
hydrogen, which is +1) is H2SO4 (number of hydrogen atoms must be doubled as

hydrogen is only +1 and there need to be two to get +2 to counter -2) and
zinc(+2) phosphate(-3) is Zn3(PO4)2 because the LCM of 3 and 2 is 6.
Now that we know how to convert substances into their chemical formulae,
we can now write chemical equations :D
Step 1: Identify the type of reaction (acid-base, acid-metal, acid-carbonate).

Write the word equation.
Step 2: Convert the chemicals in the word equation to chemical formulae (which
you can get from the periodic table and the table above).
Step 3: Balance the equation (make sure that the left side has exactly the same
number of atoms of each element as the right side) by adding numbers at the
left side of the chemical formula (e.g. 2H2O = 2 water molecules = 4 hydrogen
atoms + 2 oxygen atoms).
Step 4: Write down the state symbols. (solid, liquid, gas, aqueous)

Year 2 Physics notes
Topics:
1. Optics
 Light
 Pinhole cameras
 Reflection
 Drawing reflection diagrams
 Geometrical properties used in this topic
 Refraction and Snell’s Law
 Total internal reflection and critical angle
2. Nuclear physics
 Types of decay
 Nuclear reactions and atomic notation
 Half life
 Applications of radioactivity
 Nuclear fission
 Nuclear power plants
Optics
What is light?
Light is a form of energy. Light travels in a straight line. It is both a wave (EM
waves) and a particle (photons) – wave-particle duality, which has to do with
quantum mechanics. In this whole topic, however, light will be represented as a ray.
The direction of this light ray will be represented by arrows drawn on the ray.
When a light hits a material it will either be reflected, absorbed or transmitted

through the material. If the light is reflected or absorbed, the material is opaque. If
light is transmitted through the material, than the material is transparent.

Pinhole cameras
Pinhole cameras work because light travels in straight lines. It is basically a

light-proof box with one hole at the side. This is a ray diagram of light going into a
pinhole camera:
Important things to note:
1. =
2. As the size of the hole increases, the image become brighter but blurrier.
3. The image is inverted and real.
Reflection
Reflection is basically the object reflecting light that is shone on it. Reflection is
how we see things – light is cast onto the thing and is reflected into our eyes.
There are two laws of reflection – the incident ray, the reflected ray and the
normal (the imaginary line perpendicular to the surface; in a circle, this is a line from
the centre of the circle) lie on the same plane, and the angle of incidence is equal
to the angle of reflection.
There are two types of reflection. These are regular reflection and diffuse
reflection. Regular reflection involves all the light rays striking a smooth, regular

surface and then being reflected away in the same direction. Diffuse reflection,
however, involves the light rays hitting an irregular surface. Each ray obeys the laws
of reflection, but the normal for these rays is different, so the rays will be reflected in
different directions. A regular reflection can result in glare, or a very bright light
shining into your eyes because all the rays would be travelling in the same direction,
i.e. your eyes, whereas diffuse reflection results in only a few light rays being
reflected into our eyes and is not as glaring.
The reflected image has certain properties – it is laterally inverted and is virtual
(cannot be captured on a screen; opposite of real). The distance of the reflected
image from the mirror is always the same as the distance of the real object from the
mirror. There are some special cases however, which involve having two mirrors
placed at a certain angle. In these cases, a greater number of images can be seen,
with the angle between the mirrors, α, determining the number of images formed.
This number is -1. The distance from the object to the place where the mirrors
meet and the distance from the images to this point is equidistant, and the object
and images themselves are also equidistant. In these cases, not all the reflections
are laterally inverted. All of them are still virtual, however.
Drawing reflection ray diagrams (cheat)
1. Reflect the object into the mirror (i.e. draw the image in the mirror). This image
has the same distance from the mirror as the object.
2. Draw lines from the image to the eye. You will have to draw two rays to the
top and bottom of the eye, and these rays should both be straight.
3. The rays in the mirror should be dotted lines, while the lines out of the mirror
should be solid lines. Draw 2 more solid lines to the place where the dotted
lines hit the mirror from the object.
4. Draw the normal for both these light rays.

Geometry having to do with reflection
1. Triangles
Formulae:
Similar triangles:
= if AB and EC are parallel.
Isosceles triangle:
If point F is drawn in line with AB, and angle BAD = angle BFD, then triangle AFD is an
isosceles triangle. In this case, AD = FD and AB = BF.
Refraction
Refraction is the bending of light as it passes from one transparent medium

into the other. The light ray can bend away from or towards the normal depending
on the optical density of the two mediums.
The optical density of a medium can be determined by its refractive index (n).
The refractive index indicates how much light slows down compares to when light is
in a vacuum (i.e. if the refractive index is greater, the light slows down more). When
a light travels from medium A to medium B, the incident ray will bend towards the
normal if medium B has a higher refractive index, and will bend away from the
normal if medium B has a lower refractive index.
There are basically 2 formulae to remember for this section:
1. Snell’s Law
n1 1 = n2 2 (this is like the most important law of refraction and almost all
other equations can be derived from this.)
2. Speed of light (v) in the two mediums

n1v1 = n2v2
Critical angle and total internal reflection
When a light ray travels from an optically denser medium (with a greater
refractive index) to an optically less dense medium (with a smaller refractive index),
the light ray will bend away from the normal. When the angle of the refracted ray
from the normal becomes 90 , the angle from the incident ray to the normal is the
critical angle. When the angle from the incident ray to the normal surpasses the
critical angle, there will be total internal reflection. The reflected ray in total internal
reflection follows the normal laws of reflection. Theoretically, if the two surfaces are
parallel, a ray that has experienced total internal reflection will never get out from
the interior of the optically denser medium (such as in optical fibers).
The formula for the critical angle, which can be derived using Snell’s Law, is:
sin-1( )*
*in this case, n1 is the refractive index of the medium
Obviously, the critical angle is inversely proportional to the refractive index of

the medium from which means that there is a higher chance of TIR in an optically
denser medium.
Refraction extras :D
Reversibility of a light ray
When a light ray enters a certain set of mediums at n , it will escape from that
set of mediums at n away from the normal assuming the mediums are all parallel.
Real depth and apparent depth
If you look straight down at an object in an optically denser medium (such as

water), it appears to be closer than it actually is. Conversely, when you look up from
an optically denser medium, the object appears to be lower than it actually is.

Nuclear physics
Nuclear physics is basically the physics behind why some things are
radioactive, and how these things emit radiation. Although radiation is invisible, it
can be detected through photographic detectors, gold leaf electroscopes, Geiger-
Muller counters and diffusion cloud chambers. So how is radiation caused?
Types of decay
Unlike chemistry, where we learnt about the reactions of different elements to

each other due to their electrons, nuclear physics involves fundamental changes in
the atomic nucleus, which include the decay of the nuclei of radioactive elements,
and also nuclear reactions, which will be elaborated upon later. So, what are the
types of decay?
Particles emitted Charge Speed Ionizing Penetrating

power power
Alpha Alpha particles, +2 0.1c High Low
decay which are helium
nuclei.
Beta Beta particles, which -1 0.9c Medium Medium
decay are electrons.
Gamma Gamma rays, which 0 c Low High
emission are electromagnetic
waves.
In the table, there are probably two unfamiliar terms:
 Ionizing power: The power to ionize gas, or to make molecules in gas lose an
electron to become ions, and thus become ionized.
 Penetrating power: The power to pass through blockage. For example, alpha
particles have low penetrating power as they can be blocked by 1-2 sheets
of paper, beta particles have medium penetrating power as they can only
be blocked by 5mm of aluminum, while gamma rays need a few cm of lead
to be blocked.
Nuclear equations
Remember the nuclide notation in atoms used to describe the number of

protons and neutrons in an atomic nucleus? Well, since nuclear physics involves
changes in the atomic nucleus, this information will be useful for nuclear equations.
A nuclear equation looks something like this:

Basically, the sum of atomic numbers and mass numbers on both sides must
be equal. In the above example, the mass number on both sides is 18, while the
atomic number is 9. Also note that the element changes as the atomic number
changes.
So, what is the equation like in nuclear decay? Let’s first look at the nuclide
notation of the various particles.
The nuclide notation for alpha particles is:
The nuclide notation for beta particles is a bit trickier. In beta decay, although
the electron is emitted, it is actually caused by a neutron turning into a proton and
an electron, and the emission of the electron. Therefore, the notation is:
Since gamma rays are only photons, they have no nuclide notation. Gamma
rays are basically given out when there is extra energy in the nucleus after one of
the other decays.
Anyway, now that we know the nuclide notations, we can determine what
will happen to the mass and atomic number of an atom after a certain type of
decay.
Type of decay Mass number Atomic Change in element?

(difference number
from original) (difference
from
original)
Alpha -4 -2 Yes, move 2 to the left of the
periodic table.
Beta No change +1 Yes, move 1 to the right in the
periodic table.
Gamma No change No change No, but the atom will no longer
be in its excited state (shown by
*)
Examples
Alpha decay:
Beta decay:

Gamma radiation:
Half life
Half life is basically the average time taken for half of the nuclei in a sample of
a radioactive isotope to undergo decay. It is a probability, so the amount left after a
half life may not be half, although it probably will be half.
The main format of questions that could be asked is:
There are x grams of an element with half life y minutes. How much is left after
z minutes? Answer: x/2z/y.
For some questions, however, the numbers they give may not be nice powers
of two. So, what do you do? There are 3 options:
1. Approximate to the nearest power of 2. This is the easiest but least accurate
solution. And what if it can’t be approximated properly?
2. Draw the graph of time against amount left based on the information. Then
find the point that you want. This is darn irritating and nobody will ever waste
time doing this. Might as well lose the 2 or so marks…
3. Formula. Yes, there is actually a formula linking original amount, amount left
and time. You can utilize the equation to suit your purposes. However, the
math involved is challenging (involves “e” and “In”, don’t use formula if you
can’t utilize this!). Nevertheless, just dumping all the values into the equation is
reasonably simple. The equation is (in a few forms):
Nt is the remainder.
N0 is the original.
t is the time that has passed.
λ is the disintegration constant. (only for
that element)
For half life OR disintegration constant, use
equation 1 and take Nt/N0 = ½ (assuming
you know either one).

Applications of radioactivity
Radioactivity has a few applications:
 Tracing – weak radioisotopes are injected into the body as tracers to trace
their motion, usually caused by the body’s motions.
 Sterilizing – radioactivity can be used to kill bacteria in syringes and in food.
 Thickness control – Beta radiation can be used to check how thick an object
is by seeing how much can pass through.
 Radiotherapy – used to kill malignant cancer cells.
Nuclear fission
This is the main process used to produce nuclear energy as the temperatures
required for nuclear fusion are currently unachievable.
A neutron is shot at a U-235/Pu-239 atom. The U-235/Pu-239 atom is then

converted into an unstable U-236/Pu-240 atom, and then decays into 2 other
radioactive atoms and some neutrons. The difference in binding energy causes a
decrease in mass of the products compared to the original, and this mass is
converted to energy (e=mc2). The extra neutrons released will trigger more reactions.
These are some examples of fission reactions:
 U-235 + 1n > U-236* > Kr-92 + Ba-141 + 3n

 U-235 + 1n > U-236* > Kr-90 + Ba-144 + 2n
 U-235 + 1n > U-236* > Br-85 + La-148+3n
 Pu-239 + 1n > Pu-240* > Ce-148 + Kr-89 +3n
Nuclear power plants
Nuclear power plants are powered by the heat produced from the energy
generated in nuclear fission.
In the reactor vessel, water is superheated and flows through a pipe system.
This pipe system is in contact with water in a steam generator. When the
superheated water flows through the pipe system, it will heat up the water in the
steam generator, and will then lose heat and flow back into the reactor vessel. The
water in the steam generator, after being heated, will boil, and the steam would
turn a turbine, which turns a generator, generating electricity. The steam will then
travel through a pipe system into a condenser and will condense and flow back into
the steam generator.
This cycle will then continue to produce huge amounts of electricity, while
leaving behind some nuclear waste.

This is the picture of a nuclear power plant:

Year 2 Biology notes
Topics:
1. Human reproduction
 Puberty
 Parts of the human reproductive system
 The menstrual cycle
 Pregnancy
 Assisted Reproductive Technologies (ARTs)
 Birth control methods
 Abortion
 STIs
2. Heredity
 Key terms
 Mitosis and meiosis
 Variation
 Monohybrid inheritance
3. DNA
 Structure of DNA
 DNA replication
 Central dogma
 Genetic engineering
Human reproduction
Puberty
Puberty is defined as the period of human development during which physical

growth and sexual maturation occurs. It is triggered by hormones – mainly testosterone
in men and mainly oestrogen in women. During puberty, a human will start to develop
sexual characteristics. These sexual characteristics are classified into primary and
secondary sexual characteristics. Primary sexual characteristics are those directly
involving the development of reproductive organs which are necessary for sexual
reproduction, while secondary sexual characteristics are traits that characterize the
male and female in a species, but are not directly necessary for reproduction.

Some examples are:
Male sexual characteristics Female sexual characteristics

Primary Secondary Primary Secondary
Size of penis and Change in behaviour Vagina and uterus Change in
testes increase. (become grow in size. behaviour (become
aggressive/territorial; maternal;
attracted to girls). attracted to boys).
Production of Growth of hair (on Menstruation Growth of hair
sperm begins. face, body, under occurs. (under armpits and
armpits and in the in the pubic
pubic region). region).
Breaking of voice. Breasts develop
and enlarge.
Growth spurt, growth Growth spurt.
of muscles.
Broadening of chest Hips broaden.
and shoulders.
Skin becomes oilier, Increase in fat
acne may occur. deposition at the
abdominal, buttock
and thigh areas.
Parts of the human reproductive system
All humans need reproductive systems to reproduce. These reproductive

systems develop during puberty. The reproductive systems of males and females are
obviously different.
These some important parts of the male and female reproductive systems and
their functions:

Male
1. Testes – Produce sperm.

2. Epididymis – Store sperm.
3. Scrotum – bag that holds the testis outside the body (sperms are sensitive to
heat).
4. Sperm duct (vas deferens) – tube which connects to epididymis to the prostate
gland.
5. Prostate gland – One of the glands that produce fluid and nutrients for the
sperm (the fluid part of semen).
6. Cowper’s (bulbourethral) gland – Another gland that produces a clear, salty,
viscous, alkaline solution known as pre-ejaculate.
7. Seminal vesicles – Produce a sugar-rich fluid (fructose) that provides energy for
the sperm.
8. Urethra – The tube that transports both sperm and urine but at different times.
9. Penis – Contains blood vessels that fill with blood to make the penis rigid and
erect, allowing for penetration.

Female
1. Ovary – Produces and stores eggs.

2. Oviduct – Passageway for egg.
3. Uterus – Where the fetus develops (if fertilization occurs).
4. Uterine wall – The wall of the uterus.
5. Uterine lining – The lining on the uterine wall, which changes in thickness during
the menstrual cycle. It is the site where the embryo is implanted.
6. Cervix – Opening of the uterus.
7. Vagina – Birth canal.
The menstrual cycle
The menstrual cycle begins in females during

puberty. The whole cycle takes approximately one
month:
Day 1-5: Menstruation
 Uterine lining breaks down.

 Broken uterus lining flows out through the
vagina in a bloody discharge.
Day 6-12: Follicular phase
 One follicle in the ovary begins to develop

and produce the hormone oestrogen.
 Oestrogen causes the uterine lining to
thicken.

Day 13-15: Ovulation
 A mature ovum is released from one ovary at peak oestrogen levels.

 A ruptured follicle in the ovary becomes a corpus luteum.
 The ovum is swept into the fallopian tube (oviduct) and moved along by
peristalsis and wave-like movement of cilia.
Day 16-28: Luteal phase
 Corpus luteum in the ovary produces the hormone progesterone, which helps to
maintain the uterine lining.
 If fertilization does not occur (what usually happens), the corpus luteum begins
to degenerate, and the production of progesterone ceases.
 Oestrogen and progesterone levels decline.
 Uterine lining begins to degenerate.
NOTE: Teachers may troll and make Day 1 of the menstrual cycle different from the
first day of the month in the question. Day 1 is ALWAYS when menstruation starts. So
don’t get trolled and throw marks away. :D
Pregnancy
During the menstrual cycle, there is a short period called the fertile period.
This period is Day 11-17 of the menstrual cycle. It can be found by taking into account
the ovulation stage (Day 13-15) in menstrual cycle. Since the ovum is able to survive for
1-2 days in the woman, the sperms are able to fertilize it as late as Day 17. The sperms
are able to survive for about 3 days waiting in the oviduct and thus can start waiting
from Day 11.
During this period, if sexual intercourse without contraception (will be covered

soon) occurs, the male and female gametes will be able to meet and fertilization will
occur.
Gametes
Male gamete (sperm) Female gamete (ovum)

Size Relatively smaller. Relatively larger.
Approximates: head = 0.003 by 0.005 Approximately 0.1mm
mm; tail = 0.04mm large.
Structural Head (nucleus and acrosome). Sphere, in which there is
components Mid-piece (mitochondrion). a disproportionately large
Tail. amount of cytoplasm, a
jelly coat and polar
bodies.

Relative numbers 50-500million sperms released at a 1.
time during ejaculation.
During fertilization, the nuclei of the male and female gametes fuse to form a
zygote. The zygote then divides and develops into an embryo over about 3-5 days in a
process known as embryo development in the oviduct. Finally, after all of this
development, implantation of the embryo (not the zygote) in the uterine lining occurs,
in which the embryo simply attaches itself to into the uterine lining of the uterus.
After this, pregnancy occurs.
Pregnancy
During pregnancy, the embryo basically develops into a fetus, and then finally is
born as a baby. There are some important parts involved in pregnancy:
1. Placenta: It is basically a disc for the transport of nutrients to the fetus and
the removal of waste material from fetus. It is the place where exchange of
materials takes place between the mother’s and fetus’ blood, and is made up of
the villi and the uterine wall. The waste materials consist of carbon dioxide and
urea, while the nutrients consist of dissolved food substances and oxygen.
2. Umbilical cord: The fetus is attached to the placenta by the umbilical cord. The
cord contains the umbilical artery, which transports waste materials, and the

umbilical vein, which transports nutrients (different from other veins and
arteries, which transport waste materials and nutrients respectively).
3. Amniotic sac: Contains amniotic fluid.
4. Amniotic fluid: The fetus lies in the amniotic cavity that contains amniotic fluid,
which cushions the fetus against mechanical shock, maintains a constant
temperature (water has a high heat capacity) and acts as a lubricant during
birth.
Extra – twins
Identical twins are formed when the zygote divides into two identical zygotes,
which then divide separately to form two identical embryos, which develop and
gradually become identical twins.
Fraternal twins are formed when two eggs are fertilized to form two different
zygotes, which then develop into two different fetuses and gradually become fraternal
twins. This can also be caused by IVF, in which two or more eggs may implant into the
uterine lining and lead to fraternal twins.
Extra – pregnancy test kit
These are placed in the woman’s urine to detect certain hormones. Monoclonal
antibodies are used in these kits to detect human chorionic gonadotropin (HCG) which
is produced as soon as an embryo implants into the uterus. If HCG is detected, the
woman is probably pregnant.
Assisted Reproductive Technologies (ARTs)
Some couples simply cannot have children due to a problem with the
reproductive system of either parent – they are infertile. Infertility is defined as the
inability to conceive after a year of regular unprotected intercourse. Therefore, ARTs,
which are methods used to achieve pregnancy by artificial or partial artificial means,
are used to help them to get a child. There are many different types of ART:
ART Details
IVF  In-vitro fertilization.
 Firstly, fertility drugs are used to stimulate the ovaries to
superovulate (release multiple ova).
 Secondly, an operation using ultrasound is used to retrieve the
ova.
 Thirdly, sperm obtained using ejaculation is placed together with
the ova and fertilization occurs.

 Finally, one or more embryos are transferred to the uterus
through the cervix using a catheter.
GIFT  Gamete Intrafallopian transfer.
 Gametes are transferred to the fallopian tubes rather than the
uterus, and fertilization takes place in the fallopian tubes (in
vivo).
ZIFT  Zygote Intrafallopian transfer.
 Fertilization takes place outside the human (in vitro) and the
resultant zygotes are transferred to the fallopian tubes.
ICSI  An extension of IVF or ZIFT.
 A single sperm is injected directly into an ovum to aid the sperm
if the man has very few sperms, or when other fertilization
methods are unsuitable.
AI  Sperm is artificially placed in the uterus with the help of a
catheter after the semen has been removed.
 Occurs in 4 locations (vagina-IVI, cervix-ICI, uterus-IUI and
fallopian tubes-ITI), with IUI being the most common.
 Used when a woman’s cervical mucus is scant or hostile to sperm,
man has low sperm count but healthy sperm, male infertility or
ejaculation issues.
Sperm donor  Healthy, viable sperms from a sperm bank are used to fertilize
an egg.
 Used when the male has extremely unhealthy/mutated sperm.
Surrogacy  Surrogacy – Pregnancy is carried by the surrogate mother (with
/gestational biological relations) using her ova (through ART).
carrier  Gestational carrier – Pregnancy carried by another woman
(without biological relations) , but uses mother’s ova and father’s
sperm.
Birth control methods
Some people want to have children but can’t, but others can have children but
don’t want to. These people would then use birth control methods. Birth control
methods are classified into these categories: natural, chemical/ mechanical, hormonal,
intrauterine devices, and sterilization.
Obviously there are many different types of birth control:
Natural
Name Details (how it works, how it’s used, cost, effectiveness,
duration and limitations)
Rhythm method  Avoid having unprotected sex during ‘fertile period’ of the female.
 Keep sperm out of vagina on fertile days of the female. 3 methods to
track fertile period:

o Body temperature
o Cervical mucus
o Calendar
 Free
 ~75%
 Track daily
 Difficult to adhere to, requires discipline and cooperation from both
partners.
Withdrawal  Man must know when he’s about to ejaculate, pull out penis before
semen comes out and move penis away.
 Withdrawal prevents sperms from entering vagina during sex, thus
preventing sperm from fertilising egg
 Free.
 ~80%
 Use with each act of intercourse.
 Requires strong willpower from the male partner; May reduce sexual
pleasure, causing frustration/anxiety; Male may have pre-ejaculate
that contains sperms.
Chemical/mechanical
Name Details
Condom  Male: Thin cover that fits snugly over erect penis
 Female: Plastic tube with flexible ring at each end to help stay in
place in the vagina
 Condoms acts as a barrier to prevent sperms from entering the
vagina during sexual intercourse; protects against STIs.
 $1 per male condom
 $4 per female condom
 ~80%
 Use and dispose with each act of intercourse
 Irritation due to latex allergy and spermicide allergy, requires
cooperation from both partners to be effective
Diaphragm  Flexible rubber cup inserted into vagina and fit snugly over cervix
 Can only be obtained by prescription from healthcare provider.
 Diaphragm acts as a barrier to prevent sperms from entering the
uterus
 $15 - $75 (lasts up to 2 years)
 ~80%
 Use with each act of intercourse, reusable
 Irritation due to latex allergy
 Increased risk of vaginal infection
Spermicide  Comes in a few forms: Cream, Foam, Gel, Suppository, Film
 Kills or inactivates sperms, preventing them from fertilising the egg
 ~$8 per package
 ~71%
 Use with each act of intercourse
 Nonoxynol-9, a common ingredient, is known to increase risk of HIV
& other STI transmission; Frequent use can induce lesions and

ulcerations to genital mucosa lining – increase probability of
transmitting infectious agents.
Hormonal
Name Details
Emergency  Hormones in pill stop ovulation and cause cervical mucus to thicken,
contraception preventing sperm from entering uterus
 $10-$77 for consultation/prescription
 ~80%
 Use after unprotected intercourse
 Nausea & vomiting
 Abdominal pain, sore breasts, irregular bleeding, headaches
“Pill”  Hormones in pill prevent ovulation and thicken cervical mucus to
block sperm from entering uterus
 $15-$50 every month
 92%
 Taken daily for 21 days (rest 7 days)
 Nausea & vomiting; Abdominal pain, tender breasts, irregular
bleeding, headaches; Easy to forget taking pills daily
Intrauterine devices (IUDs)

Name Details
Copper IUD  IUD is inserted into uterus by health care provider
 Prevents sperm from reaching egg by interfering with movement of
sperm and disrupting implantation by irritating uterine lining.
 $175 - $950 (lasts up to 12 years)
 99%
 Effective for 10-12 years .
 Increased bleeding & cramping initially, but lessens over time.
Sterilization
Name Details
Vasectomy  Simple outpatient procedure where healthcare provider numbs the
area round the scrotum and makes a small incision into the scrotum
to cut and tie the vas deferens.
 The sperm ducts are tied, cut or sealed to prevent sperms from
entering the semen.
 $350-$1000 for consultation/procedure
 99%
 Permanent
 Possible short-term tenderness or bruising after procedure;
Permanent/irreversible
Tubal Ligation  Fallopian tubes are tied, cut or sealed, through incisions into the

abdomen
 Blocks fallopian tubes and prevent eggs from reaching the uterus
 $1500-$6000 for consultation/operation
 Permanent
 99%
 Mildly invasive surgery; Possible complications from anaesthesia and
surgery; Permanent/irreversible
Abortion
As seen above, the success rate is not 100%. If a woman really becomes
pregnant, but does not want to, she has to remove the fetus through a process called
abortion.
Abortion is basically the gruesome process of destroying the unborn fetus and
sucking the dismembered parts out of the mother’s uterus using a vacuum. It is
extremely controversial since it is like murder (gruesome murder) and there are many
ethical issues related to abortion. Also, it may cause harm to the mother’s uterus,
disallowing her from having children even when she wants to. Therefore, it’s obviously
not recommended.
STIs
During intercourse, even with birth control (except for condoms) some
infections can be passed on from one partner to the other. They are called STIs
(Sexually Transmitted Infections), and are transmitted by the exchange of bodily fluid,
for example through blood, saliva, semen, vaginal secretion or breast milk. STIs are
quite severe and not easy to get rid of. The only way to prevent them is by using the
aforementioned condom, or, even better, don’t have multiple sexual partners.
There are three main STIs that will be focused on:
AIDS Gonorrhea Syphilis

Causes HIV (Human Bacterium Bacterium Treporema
Immunodeficiency Virus) Neisserin pallidum, Spirochaete
gonorrhoeae
Symptoms 1. Upon infection, minor 1. Painful Stage 1: Painless sore
flu-like symptoms or no burning known as chancre
symptoms at all. sensation when appears on sex organs
2. No further symptoms urinating. for 10-90 days.
for 10 years BUT immune 2. Pus discharge Stage 2: Non-itchy
cells are slowly being from the sexual rashes appear on other
destroyed. organ. parts of the body,
3. Full-blown AIDS 3. May spread which disappear with

(Kaposi’s sarcoma, Weight to surrounding or without treatment.
loss/loss of appetite, organs, leading Latent stage: No
Prolonged fatigue, Swollen to infertility if symptoms for 10-20
lymph nodes, left untreated. years.
fever/diarrhoea, etc.) Late stage: paralysis,
blindness, insanity,
heart disease and bone
and joint deformity.
Transmission 1. Unprotected sex with 1. Contact with 1. Direct contact with
infected person and the mouth, syphilis sores on sex
contact with the body vagina, penis or organs/anus.
fluids. anus. 2. From a mother to
2. From mother to child, 2. From a her fetus.
during mother to the
pregnancy/childbirth. fetus during
3. Sharing syringes when birth, causing
injecting drugs through eye infections
the blood. and blindness.
Treatment No cure, only antiviral Treated by Treated by antibiotics
treatments which slow antibiotics quickly (stage 1/2)
down the progression. quickly upon upon diagnosis.
diagnosis.
Heredity
Mitosis and meiosis
Before we even start on this topic, we need to understand a few key terms:
1. Chromosome – something in the nucleus of a cell that carries genetic information.

2. Gene – a unit of inheritance borne on a particular locus (position) in a
chromosome. Each gene controls a particular characteristic.
3. Allele /er-leel/ NOT /ah-ley-ley/ - different form of the same gene that
control a certain trait. The different forms are represented by a capital and
small version of the same letter (e.g. T and t), with the dominant allele being
capital and the recessive one being small. (Remember! Will gain great importance
soon!)
4. Haploid – having n chromosomes (in humans, n=23).
5. Diploid – having 2n chromosomes.
6. Sister chromatids – identical chromosomes attached together at the
centromere.

7. Homologous chromosomes – chromosomes in the same pair, which have the same
length and carry the genes for the same traits.
Mitosis is a type of cell division that takes place during cell growth in asexual
reproduction. It results in the production of 2 daughter cells from 1 parent cell. The
number and type of chromosomes in the nuclei of the daughter cells are identical to
that of the parent cell. The daughter cells have a diploid number of chromosomes. In
this process, the chromosomes are duplicated with sister chromatids and then they are
split and form 2 identical cells.
Meiosis, however, is another type of cell division that results in the production
of gametes for sexual reproduction. 4 haploid daughter cells are produced from 1
diploid parent cell. In this process, the chromosomes are duplicated and homologous
chromosomes are paired up through the centromere and crossing over (swap of alleles
at a chiasma [crossing-over point]) takes place. They then separate and split into 2 non-
identical (due to crossing over) daughter cells with the sister chromatids remaining
together. Finally, the sister chromatids are separated into 4 haploid cells.
Variation
Human beings belong to the same species, but look different from each other.
These differences are called variations. Genes determine the inherited characteristics
of an individual and are carried on a specific locus (position) in a given chromosome, and
thus cause these variations.
There are two main types of variation: continuous and discontinuous variation:
Continuous variation Discontinuous variation

 Features vary gradually from one  Features show no in-between
extreme to the other. forms.
 Results from the combined effects  Results from the effect of one or
of many genes. only a few genes.
 Affected by the environment (e.g.  Not influenced by the environment.
diet, living conditions)  Examples: Albinism, mid-finger
 Examples: Height, weight, finger hair, attached earlobes, widows
length, eye colour, IQ. peak, cystic fibrosis (disease),
blood group.
Variations are caused by:
1. Random fertilization during sexual reproduction.

2. Meiosis (crossing over/independent assortment).

3. Mutation (gene mutation [sickle cell anaemia]/chromosomal mutation [more
serious as many genes are affected, an example being trisomy-21, a.k.a. down
syndrome])
Monohybrid inheritance
Monohybrid inheritance is basically the passing down of a single trait from a

parent to an offspring. Using the techniques learnt in this section, we can predict the
probability of certain outcomes. Firstly, however, we need to know some key terms:
1. Mendel’s Law of Segregation: A pair of alleles for a gene segregates into

different gametes during gamete formation. The outcome is that for any given
gene, half of the gametes will carry one allele and the other gametes will carry
the other allele.
2. Mender’s Law of Independent Assortment: Each pair of alleles segregates
independently during gamete formation. This applies when genes for two
characters/traits are located on different pairs of homologous chromosomes.
3. Phenotype: How the organism looks. (e.g. black or white)
4. Genotype: The alleles the organism has (e.g. TT, Tt or tt)
5. Homozygous: Having 2 identical alleles for a certain trait. (e.g. TT, tt)
6. Heterozygous: Having 2 different alleles for a certain traits. (e.g. Tt) In these
cases, the dominant trait is always the phenotype.
Genetic diagram
The phenotypes of the offspring of 2 parents with given genotypes can be

worked out using a genetic diagram. This is worth 4 marks, so draw it right! This is what
you have to include in a genetic diagram in this order:
1. Let big letter be allele for dominant trait, small letter be allele for recessive
trait.
2. Parental phenotype: Father’s phenotype x Mother’s phenotype.
3. Parental genotype: Father’s genotype x Mother’s genotype.
4. Gametes: From the genotype, just split the two letters and circle them.
5. Draw lines from gamete 1, 3 to F1 genotype 1, 1,4 to F1 genotype 2 and so on. (1,3;
1,4; 2,3; 2,4).
6. F1 genotype (should have 4 of these, as derived from the line-drawing.
7. F1 phenotype: Write the phenotype of the offspring based on the genotype.
Remember that heterozygous always follows the dominant allele.
8. Phenotypic ratio: Always 3:1, 1:1 or all of a certain phenotype. Put in simplest
terms.

Punnett square
This is a method for rough working. Firstly, draw a 2x2 square. Then draw the
gametes of one parent above the square and the gametes of the other parent at the
left of the square. Circle the gametes. Then, in the 1x1 squares in the 2x2 square, write
the genotypes of the offspring based on the allele in the gamete to the direct left and
directly above the 1x1 square. You have just derived the genotypes :D
Cheat sheet
Homozygous dominant x anything = All dominant.
Heterozygous dominant x Heterozygous dominant = 3 dominant: 1 recessive.
Heterozygous dominant x (Homozygous) recessive = 1 dominant: 1 recessive.
Sex-linked traits
Sex-linked traits are traits associated with the sex chromosomes. In humans,
the X chromosome usually carries the allele, and these traits are usually diseases like
colour-blindness and haemophilia (causing you to bleed to death). Before you start
cackling with joy about how only females get these diseases, think again. Males have
the genotype XY. The alleles for these traits are recessive. This means that once a
male gets one recessive allele for the disease, he’s screwed, while a female (XX) can
have one recessive allele but would have the dominant allele to mask it, and she would
be defined as a carrier. There are some questions associated with these sex-linked
traits and how they are passed over to the offspring so here’s the cheat sheet:
Normal mother x Normal father = All normal children. (you don’t say)
Normal mother x Diseased father = 100% carrier daughters, 100% normal sons.
Carrier mother x Normal father = 50% normal daughters, 50% carrier daughters, 50%
normal sons, 50% diseased sons.
Carrier mother x Diseased father = 50% carrier daughters, 50% diseased daughters,
50% normal sons, 50% diseased sons.
Diseased mother x Normal father = 100% carrier daughters, 100% diseased sons.
Diseased mother x Diseased father = All diseased children. (you don’t say)
This may be tested for genetic diagrams, and drawing these will still be the
same as in the normal genetic diagrams.
Pedigree chart

A pedigree chart is basically a family tree, which shows whether or not
individuals have a certain trait. There are a few questions asking you to interpret it, so
these are the possible interpretations:
 trait is autosomal (carried on 1st

22 chromosomes), it should affect
an equal number of males and
females.
 trait is sex-linked, it will affect
more males than females.
IF  trait is dominant, parents who
have it may have children who do
not have it, and parents who don’t
have it will not have children who
have it.
 trait is recessive, parents who
have it will definitely have
children who have it, and parents
who don’t have it may have
children who have it.
Test cross
This involves crossing an organism with a dominant trait with another organism
with a recessive trait to determine the genotype of the organism with the dominant
trait (homozygous dominant or heterozygous). If some offspring have the recessive
trait, the genotype of that parent is heterozygous, whereas if no offspring have the
recessive trait, the genotype of that parent is homozygous dominant.
Co-dominance and incomplete dominance
Co-dominance is when both traits are shown in the organism which has both the
dominant alleles of the same thing.
Incomplete dominance, on the other hand, is when a fusion of the traits is shown.
An easier way to remember:
Incomplete dominance: Red + White = Pink (snapdragon flowers)
Co- dominance: Red + White = Red spots on white/white spots on red. Like a cow.

An example of co-dominance is the blood group of humans. As we should all know,
humans have 4 blood groups – AB, A, B and O. These are determined by the alleles IA,
IB and IO. IA and IB are co-dominant, while IO is recessive. This is a list of the blood
groups and the possible genotypes:
Blood group Possible genotypes

AB IAIB
A IAIA or IAIO
B IBIB or IBIO
O IOIO
Implication: if one parent has the blood group AB, he or she cannot have an
offspring with blood group O.
This may be tested for genetic diagrams, and drawing these will still be the
same as in the normal genetic diagrams.
DNA
DNA Structure
DNA (deoxyribonucleic acid) is the essence of life. Without it, life as we know it
probably would not exist. DNA is normally found in the nuclei of cells, in the
chromosomes. In each chromosome, DNA is coiled around histones (some proteins, we
don’t need to know) and compacted into a chromosome.
DNA is a double helix. That means it looks something like the picture at the
extreme left. However, in exams, for simplification, DNA is usually drawn like the
diagram next to the nice-looking double-helix.

In the simplified model, the different shapes depict different parts of DNA:
 Orange pentagon: Usually colorless in exam papers due to stinginess. These

represent pentose (5-sided) sugars in DNA. In DNA, as can be guessed by the
named, this sugar is deoxyribose.
 P with Os connected to it: Usually depicted as white circles in exam papers.
These are basically the phosphates in DNA. They are held together by strong
phosphodiester bonds to form the sugar-phosphate backbone of DNA.
 Blue, pink, green and purple stuff in center: Usually depicted as white rectangles
in exam papers. These are the nitrogenous bases in DNA, which will be
elaborated upon later. They are held to each other by weak hydrogen bonds.
 Pentose sugar + Phosphate + Base = Nucleotide.
Complementary base pairing
In the diagram, you will notice that some colors are always paired with other
bases. This is called complementary based pairing. DNA basically has 4 different
nitrogenous bases – Adenine, Thymine, Cytosine and Guanine. Adenine bonds with
Thymine, and Cytosine pairs with Guanine. Therefore, the percentage of Adenine is
around that of Thymine, and the percentage of Guanine is around the same as that of
Cytosine. Note that this is very important and without this complementary base pairing,
nothing would work the way we are used to.
DNA Replication
Obviously, DNA must replicate itself for stuff like mitosis and meiosis, which
are essential for life. So, how does it do this?
Remember that DNA has 2 strands, and that the strands are complementary to
each other. Also note that the strands are antiparallel, i.e. one of them runs from the 3’
to 5’ direction and the other from the 5’ to 3’ direction.
In DNA replication, the 2 strands must basically be split to form 2 new double
helixes, each with 1 old and 1 new strand.
First, the double helix is unzipped into 2 strands so it can be photocopied. This
process is greatly sped up by an enzyme called helicase, and is done with relative speed
and ease due to the weak hydrogen bonds holding the bases together.
Secondly, the single strands of DNA act as templates for their complementary
bases to attach onto. The free nucleotides will basically find a complementary base to
attach to, and these nucleotides will form the new DNA strand. The main enzyme
speeding up this process is DNA polymerase.

However, DNA can only be replicated from the 3’ to 5’ direction. The strand in
the 3’ to 5’ direction, known as the leading strand, is replicated easily as it is in the
correct direction. But what of the lagging strand in the 5’ to 3’ direction?
NOTE: You don’t need to know the info in the rest of this section.
On the lagging strand, primase joins RNA nucleotides into a primer. From the
primer, DNA polymerase III adds DNA nucleotides to the primer until it reaches the
next primer, forming an Okazaki fragment. Finally, the RNA primer is replaced by DNA
by DNA polymerase I and is added to the 3’ ends of the neighboring Okazaki fragment.
Finally, DNA ligase joins up the gaps between the fragments of DNA, which forms the
strand of DNA complementary to the lagging strand. Note that this actually happens
just as quickly as the synthesis of the complementary strand to the leading strand.
Telomeres
Due to the method in which the lagging strand is replicated, it cannot be fully
replicated due to one of the primers having no 3’ end to bind to. Basically, small bits of
DNA at the tips of the DNA strand will be gone as the DNA replicates itself. To
counter this, DNA has junk ends with a rubbish sequence. These are called telomeres.
As the DNA replicates, instead of having important bits of DNA cut out, the telomeres
are shortened instead, prolonging the life of the cells.
Central dogma
Now that we know how DNA is replicated, we can now see how DNA is used.
First, however, we must understand another important acid – ribonucleic acid (RNA).
RNA is quite similar DNA, except for a few important differences:
DNA RNA
Contains deoxyribose. Contains ribose.
Double-stranded. Single-stranded.
Contains the four bases Adenine, Thymine, Contains the four bases Adenine, Uracil,
Guanine and Cytosine. Guanine and Cytosine.
Uracil basically replaces Thymine as the
base to be complementary to Adenine.
Now that we know what RNA is, we can go into the central dogma, which explains
how genes in DNA are read to produce proteins and then make up life.
Transcription

To a cell, RNA is seemingly less useful than DNA. Therefore, it is used as a
photocopy for the DNA in a process called transcription. As the name implies, DNA is
transcribed onto a strand of RNA. The strand of DNA used for transcription is called
the template strand, and the strand complementary to this is called the coding strand
(will have the same bases as mRNA except that T is replaced with U). The template
strand basically provides the template for RNA to form on it through complementary
base pairing (A-U, C-G). The newly formed strand of RNA is called messenger RNA, or
mRNA for short. This mRNA is basically a messenger which carries a photocopy of the
DNA code on itself and brings it out of the nucleus for the second stage of protein
synthesis.
Translation
DNA is made of 4 letters – A, T, C, G. Obviously, the language on the DNA, is not

the language of proteins. Thus, this language of DNA has to be translated into amino
acids, forming a polypeptide chain and then a protein.
After the mRNA leaves the cell, it is processed by a ribosome. In this process,
another type of RNA called transfer RNA (tRNA). tRNA basically has an amino acid
attached to one end of it and an anticodon on the other end. This anticodon is
complementary to a codon on the mRNA that codes for the certain amino acid.
These codons on mRNA are made up of a set of 3 nitrogenous bases. A set of

three is needed as it is the minimum that provides a sufficient number of combinations
to make the 20 amino acids (2 bases have only 16 combinations). What the set of 3
codes for will be found in the Universal Genetic Code, which will be given. Just note
that Methionine (AUG) is usually the start codon.
Anyway, this set of three codons basically has a tRNA attach to it in the
ribosome from the anticodon through complementary base pairing. The amino acid then
detaches itself from the tRNA and starts a polypeptide chain from the ribosome.
After the first tRNA leaves, the next codon is then bonded to by the tRNA and the
next amino acid detaches and joins the first amino acid, continuing the chain. This
process continues until a stop codon, which basically has no anticodon coding for a
protein that can attach to it. From this process, a polypeptide chain, and later proteins,
will be formed, and the proteins can be used to repair cells, make enzymes and so on,
allowing the organism to survive.
Note that key structures that have been highlighted are required to be labeled
in the exam, and may even have to have their function described.

Genetic engineering
Genetic engineering is basically the process of editing an organism’s genes,

usually by adding genes to that organism, so that the organism will have a specific trait
that it cannot have otherwise.
Genetic engineering is normally done through recombinant DNA technology.

Recombinant DNA is DNA taken from 2 different sources and fused into a single DNA
molecule. This is done through a complicated process. However, to understand this
process, we first have to understand certain key terms (Red words are extras):
 Restriction enzyme: These enzymes act like scissors. They recognize certain
sequences of bases and cut the DNA at these portions.
 Sticky end: The single-stranded ends of DNA that has just been cut by a
restriction enzyme. Note that sticky ends cut by the same restriction enzyme
can join together through complementary base pairing.
 DNA ligase: This enzyme acts like a glue for DNA. It basically glues any bits of
DNA back together by repairing the sugar-phosphate backbone.
 Plasmid: Circular DNA often found in bacteria that are outside of the
chromosomes, but influence the cell’s characteristics and can be replicated
independently.
 Vector: A DNA molecule used as a carrier to transfer genetic material from one
cell to another.
 cDNA: Complementary DNA, which is DNA synthesized from mRNA.
 Reverse transcriptase: An enzyme that allows mRNA to be used for cDNA
synthesis.
Now, let’s talk about this epic process :D
1. mRNA is extracted from the organism from which you want to get the trait (e.g.
bioluminescence, insulin production, etc.)
2. Reverse transcriptase and DNA polymerase converts this mRNA to cDNA.
These two steps may seem a bit extra, but remember that DNA has a lot of
junk DNA in it. Only the useful bits for protein production are converted to
mRNA. Therefore, converting mRNA back to cDNA instead of just taking DNA
would result in a lot less junk that you have to sieve through to get the required
trait.
3. A plasmid is extracted from the bacterium.
4. cDNA and the plasmid are cut by the same restriction enzyme, allowing the
sticky ends to be complementary.

5. DNA ligase sticks everything back together. The plasmid is now a ring of
recombinant DNA.
6. The plasmid is then placed back into the bacteria. The bacteria may now have
the trait that you want. If not, try again until the bacteria gets the trait. Got it?
Good, proceed to step 7 :D
7. The bacteria divide so there is a whole colony of bacteria with the trait that you
want! Yay!
Note that the protein the bacteria produce is exactly the same as the protein
the cell you took the mRNA from produces. This only works because the genetic
code is universal. If not, if you take the human gene coding for insulin production
and insert it into an E. Coli, it may produce some poisonous protein and kill the
person this poison is injected into.
It is also worth noting that it is much easier to use this technology on bacteria
than other organisms, since editing the organism’s chromosomal DNA has a high
chance of causing that cell not to be able to divide due to the mutation.
This is the end of the notes for Science by jltps. If you

are familiar with all of it, you will probably get full
marks without carelessness. Note that some parts
are extra info so don’t panic if you have no idea what
it means. Good luck for the EOYs :D

Secondary 2 Science Notes

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Secondary 2 Science Notes

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JLTPS

Year 2 Science Notes

No part of this production is to be reproduced or

1. The basics about atoms.

Year 2 Science Notes ©JLTPS 2012 Page 1

Subatomic particles Relative mass (in atomic Relative charge

(NOTE: This becomes very important in nuclear physics later on.)

Electrons are arranged in groups of varying energy levels called electron

Year 2 Science Notes ©JLTPS 2012 Page 2

Electronic configuration basically tells us the number of electrons in each shell.

Electronic configuration bonus

Year 2 Science Notes ©JLTPS 2012 Page 3

This is a picture of a colour-coded periodic table, indicating which elements

Group I – Alkali Metals Group VII – Halogens Group 0 – Noble gases

Year 2 Science Notes ©JLTPS 2012 Page 4

Chemical bonding and structure

An ionic bond is the electrostatic force of attraction between positively and

Year 2 Science Notes ©JLTPS 2012 Page 5

Examples: Sodium chloride (table salt), magnesium oxide, calcium chloride.

A covalent bond is the bond formed by the sharing of electrons between 2

Many covalent substances exist as molecules with a simple molecular

Examples: Carbon dioxide, oxygen gas, methane, sulfur.

Differences between covalent and ionic compounds

Property Ionic compounds Covalent compounds

Year 2 Science Notes ©JLTPS 2012 Page 6

Drawing these compounds – dot and cross diagrams

1. The electrons of 1 type of atom are represented by dots, while those of

1. Most of the time, only valence electrons need to be drawn.

Year 2 Science Notes ©JLTPS 2012 Page 7

Acids and Bases

- An acid is a substance that produces H+ ions when dissolved in water.

Reactions involving acids – VERY IMPORTANT!!!

1. Acid + reactive metal = salt + hydrogen gas.

Year 2 Science Notes ©JLTPS 2012 Page 8

- The pH (power of hydrogen) scale is basically a measure of the acidity or

Charge (+/-) Positive Negative

Year 2 Science Notes ©JLTPS 2012 Page 9

Step 1: Identify the type of reaction (acid-base, acid-metal, acid-carbonate).

Year 2 Science Notes ©JLTPS 2012 Page 10

When a light hits a material it will either be reflected, absorbed or transmitted

Year 2 Science Notes ©JLTPS 2012 Page 11

Pinhole cameras work because light travels in straight lines. It is basically a

Important things to note:

Year 2 Science Notes ©JLTPS 2012 Page 12

Drawing reflection ray diagrams (cheat)

Year 2 Science Notes ©JLTPS 2012 Page 13

= if AB and EC are parallel.

Refraction is the bending of light as it passes from one transparent medium

There are basically 2 formulae to remember for this section:

other equations can be derived from this.)

2. Speed of light (v) in the two mediums

Year 2 Science Notes ©JLTPS 2012 Page 14

Critical angle and total internal reflection

*in this case, n1 is the refractive index of the medium

Obviously, the critical angle is inversely proportional to the refractive index of

Reversibility of a light ray

Real depth and apparent depth

If you look straight down at an object in an optically denser medium (such as

Year 2 Science Notes ©JLTPS 2012 Page 15

Unlike chemistry, where we learnt about the reactions of different elements to

Particles emitted Charge Speed Ionizing Penetrating

In the table, there are probably two unfamiliar terms:

Remember the nuclide notation in atoms used to describe the number of