5/19/2019

Lectures

BIO002 Lecture 1
Lectures 2-3
Introduction: Biology today
Essential Chemistry for Biology
Introductory Biology Lecture 4 Molecules of Life
Lecture 5 Biological Compounds
Lecture 6 Cell Structure
Lecture 7-8 The Working Cell
Lectures 2 and 3 Lecture 9 Photosynthesis
Lecture 10-11 Biotechnology - Recombinant DNA Technology,
DNA Profiling, Genomics and Proteomics.
Lecture 12-13 Ecology and the Biosphere – Overview, the Living
Environment, Global Climate and population.

Lecture 02 The scale of life

Essential Chemistry for Biology
From molecules to the biosphere - more than 40 orders of magnitude
Relevant chapter(s) in textbooks
Electron Ribosome Bacterium Amoeba Human Milky Way

H atom Mitochondrion Cell Bee 1 kg Whale Earth Sun Black Hole

10-30 10-20 10-10 100 1010 1020 1030 1040

Chapter 2 Chapters 1, 4 and 6

SOME BASIC CHEMISTRY

Some Basic Chemistry

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• There’s nothing mystical about biological processes – contrary to what Dr

Frankenstein asserted, there is no magical ‘life force”
• Take any biological system apart, and you eventually end up at the chemical level.
• Chemical reactions occur in the human body constantly.
• Ultimate challenge: is it possible to make a living cell from chemicals?

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Matter: Elements and Compounds Matter: Elements and Compounds

• Matter: anything that occupies space and has • Matter is composed of chemical elements.
mass.
– Element - substance that cannot be broken down
• Found on Earth in three physical states: into other substances by chemical reactions.

– solid – 92 naturally occurring elements on Earth.

– liquid
– gas

Mercury (Hg) Copper (Cu) Lead (Pb)

Chemical Composition of the human body by weight

Atomic number
(number of protons) 6
• 25 elements are essential
Element symbol C for humans Carbon (C): 18.5%

Mass number 12 • 4 major elements:

(number of Oxygen (O):
- Oxygen (O) 65.0%
protons plus neutrons) - Hydrogen (H)
H He Calcium (Ca): 1.5%
- Carbon (C) Phosphorus (P): 1.0%
Li Be B C N O F Ne - Nitrogen (N) Potassium (K): 0.4%
Na Mg Al Si P S Cl Ar - make up of ~96% of the weight of Sulfur (S): 0.3%
most cells Sodium (Na): 0.2%
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Chlorine (Cl): 0.2%
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Magnesium (Mg): 0.1%
Hydrogen (H):
Cs Ba La Hf Ta W Re Os Ir Pt Au Hg TI Pb Bi Po At Rn 9.5%
Trace elements: less than 0.01%
Fr Ra Ac Rf Db Sg Bh Hs Mt Ds Rg Cn Boron (B) Manganese (Mn)
Chromium (Cr) Molybdenum (Mo)
Nitrogen (N):
Cobalt (Co) Selenium (Se)
3.3%
Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Copper (Cu) Silicon (Si)
Fluorine (F) Tin (Sn)
Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr Iodine (I) Vanadium (V)
Iron (Fe) Zinc (Zn)

Matter: Elements and Compounds

• Trace elements are:

– required in very small amounts
– essential for life

• An iodine deficiency causes goitre

• Fluorine:
– is added to dental products and drinking water
– helps to maintain healthy teeth

Goitre - the enlargement of the thyroid gland

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Matter: Elements and Compounds Atoms

• Elements combine to form compounds. • Each element consists of one kind of atom.
– Compounds - two or more elements in a fixed – smallest unit of matter that still retains the properties of
ratio. an element. 2 Protons
subatomic particles

– Common compounds: Nucleus

2 Neutrons
– NaCl
2 Electrons
– H2O (water)
Nucleus
2e–

Electron cloud

The Structure of Atoms Isotopes

• Elements differ in the number of subatomic • Isotopes:

particles in their atoms.
– alternate mass forms of an element.
– Atomic number: determines which element it is.
– same number of protons and electrons, but differ in
– Mass: measure of the amount of material in an number of neutrons.
object.
– Isotope Decay: The nucleus of a radioactive isotope
decays spontaneously, giving off particles and energy.

Atomic number
(number of protons) 6

Mass number
C12
(protons+neutrons)

Isotopes Isotopes

• Radioactive isotopes have many uses in research • There are two types of isotope:
and medicine: ➢ Stable isotopes – nucleus is stable
➢ Radioactive isotopes – nucleus decays giving off particles and energy
– They can be used to monitor the fate of atoms in
living organisms.
e.g. PET scans to diagnose heart disorders
and some cancers.

• Both types have many uses in research and medicine

• They can be used to monitor the fate of atoms in living
organisms.
➢ e.g. PET scans to diagnose heart disorders and some cancers

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A Positron Emission Tomography (PET) Scan

Isotopes

• Uncontrolled exposure to radioactive isotopes can

harm living organisms by damaging DNA.

The 1986 Chernobyl

nuclear accident
released large
amounts of radioactive
isotopes.

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Isotopes Electron Arrangement and the Chemical Properties

of Atoms
• Uncontrolled exposure to radioactive isotopes can
• Only electrons are directly involved in the chemical
harm living organisms by damaging DNA.
activity of an atom.
In 2006, Alexander
Litvenenko was • Electrons orbit the nucleus of an atom in specific
deliberately poisoned
by Polonium-210 – an electron shells.
isotope that can only
be made in nuclear
reactors.
• The farther an electron is from the nucleus, the
greater its energy.
• The number of electrons in the outermost shell
determines the chemical properties of an atom.

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Chemical Bonding and Molecules

• Chemical reactions enable atoms to give up or acquire

First electron shell Outer electron shell electrons, completing their outer shells.
(can hold 2 electrons) (can hold 8 electrons)
Electron

• Usually result in atoms:

– staying close together and
– being held together by attractions called chemical bonds.

Hydrogen (H) Carbon (C) Nitrogen (N) Oxygen (O)

Atomic number = 1 Atomic number = 6 Atomic number = 7 Atomic number = 8

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Ionic Bonds Ionic Bonds

• Atom loses or gains electrons => becomes electrically • Positively charged ions are called CATIONS
charged (Ion)
• Negatively charged ions are called ANIONS
– Ionic bonds: formed between oppositely charged ions
Complete
outer shells Chemist’s joke:

“I think I’m a cation”

Na Cl Na+ Cl–
“Are you sure?”

“Yes – I’m positive!”

Na Cl
Na+ Cl– Na+ Cl–
Sodium atom Chlorine atom
Sodium ion Chloride ion Sodium ion Chloride ion

Sodium chloride (NaCl)

A cation An anion

Covalent Bonds
Electron configuration Structural formula Space-filling model Ball-and-stick model

H H
• Covalent bond: forms when 2 atoms share one or more pairs
Hydrogen gas (H2)
of outer-shell electrons.
• Strongest of the various bonds. O O

• Hold atoms together in a molecule. Oxygen gas (O2)

• The number of covalent bonds an atom can form is equal to H

the number of additional electrons needed to fill its outer

H C H
shell.
H

Methane (CH4)

Hydrogen Bonds Hydrogen Bonds

• Water => compound in which the electrons in its • The polarity of water results in
covalent bonds are not shared equally. weak electrical attractions
between neighboring water
– a polar molecule molecules.
= hydrogen bond Hydrogen bond

Slightly
positive
Slightly
charge
negative
charge

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Chemical Reactions

• Chemical reactions occur when atoms change their

2 H2 + O2 2 H2 O
electron-sharing partners
• Cells constantly rearrange molecules by breaking existing
chemical bonds and forming new ones.
– e.g. the reaction between oxygen gas and hydrogen gas - Hydrogen Oxygen Water
forms water. gas gas

• Chemical reactions:
Reactants Products
– can rearrange matter
– but cannot create or destroy matter

Biology and Society:

More Precious than Gold

• A drought is:
– a period of abnormally dry weather that changes
the environment
Water and Life – a devastating disaster

Biology and Society: Biology and Society:

More Precious than Gold More Precious than Gold

• Droughts can cause: • Throughout human history, droughts have helped

wipe out societies and whole civilizations.
– severe crop damage
• Droughts are catastrophic
– shortages of drinking water
– dust storms • Life cannot exist without water.

– famine
– habitat loss
– mass migration

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Biology and Society: WATER AND LIFE

More Precious than Gold
Hopeful news… • Life on Earth began in water and evolved there for
3 billion years.
– Modern life remains tied to water.
– Cells are composed of 70–95% water.

• The abundance of water is a major reason Earth is

habitable.

https://www.thetimes.co.uk/edition/world/plants-grow-with-a-quarter-less-water-kbzsk7jss

Water’s Life-Supporting Properties (1) Water molecules stick together

Water is weird…

• The polarity of water molecules and the hydrogen bonding • Water molecules stick together as a result of
that results explain most of water’s life- supporting hydrogen bonding.
properties.
– This tendency of molecules of the same kind to stick
(1) Water molecules stick together together = cohesion.
(2) Water has a strong resistance to change in temperature – Vital for the transport of water from the roots to the
leaves of plants.
(3) Frozen water floats

(4) Water is a common solvent for life

(1) Water molecules stick together

The Cohesion of Water

Evaporation from the leaves • Surface tension: measure of how difficult it is to stretch
or break the surface of a liquid.
– Hydrogen bonds give water an unusually high
surface tension.

Microscopic water-conducting tubes

Cohesion due to
hydrogen bonds
between water
molecules
Colorized
SEM

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(2) Water has a strong resistance to change in temperature (2) Water has a strong resistance to change in temperature
How Water Can Moderate Temperature How Water Can Moderate Temperature

• Because of hydrogen bonding, water has a strong • Water can moderate temperatures.
resistance to temperature change.
– Earth’s giant water supply causes temperatures to stay
• Heat and temperature are different. within limits that permit life.

– Heat = amount of energy associated with the molecular movement in a body – Takes energy with it when it evaporates
of matter
– Usually leads to Evaporative Cooling
– Temperature = measures the intensity of heat

• Water absorbs large amounts of heat

without a large increase in temperature

(2) Water has a strong resistance to change in temperature (2) Water has a strong resistance to change in temperature
Wet bulb events – the lethal combination of heat & humidity Wet bulb events – the lethal combination of heat & humidity

• Evaporation of water, e.g. via perspiration, leads to cooling

Spatial distribution of current and
predicted extreme wet-bulb
• However, when dry bulb temperature = wet bulb temperature events on the North
temperature, cooling is impossible China Plain. Historical data is shown in
Panels a) and d).
RCP4.5 and RCP8.5 are two projected
• Death in six hours scenarios for future greenhouse gas
levels.
• Major future problem for North China Plain Panels a) – c) are the data without
irrigation activity and panels d) - f) are
with irrigation activity.
• When the bulb of a thermometer
is wrapped in a wet cloth Taken from: Kang, S. and Eltahir, E.A.B. (2018)
North China Plain threatened by deadly heatwaves
normally it cools. Thus, its due to climate change and irrigation. Nature 9,
temperature will be lower than Article number: 2894 (2018)
dry thermometer
• If there is very high humidity, no
https://www.nature.com/articles/s41467-018-05252-y
cooling is possible.

(3) Frozen water floats (3) Frozen water floats

• When water molecules get cold enough, they move apart, • If ice did not float, ponds, lakes, and even the
forming ice. oceans would freeze solid.

• Ice has fewer molecules than an equal volume of liquid • Life in water could not survive if bodies of water
water. froze solid.

• Ice floats because it is less dense than liquid water.

Source: http://www.dailymail.co.uk/news/article-4208236/Kingfishers-perfectly-preserved-ice.html

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(4) Water is a common solvent for life

Sodium ion
• Solution: a liquid consisting of a homogeneous mixture of in solution
Chloride ion
two or more substances. in solution
Cl– Na+
– Solute: substance that dissolves in solvent
– Solvent: substance that dissolves solute
• Aqueous solution: when water is the solvent
Na+
Cl–

Salt crystal

Acids, Bases, and pH 14

Oven cleaner
OH− 13
OH− OH− Household

Lower H+ concentration
OH− H+ − bleach
OH
OH− H+ 12
Household ammonia
11
• Acid: chemical compound that releases H+ to a solution. Basic
solution Milk of magnesia
10

• Base: compound that accepts H+ and removes them from 9

Seawater
solution. OH− H
+
8
Human blood
OH− H+
OH−
[H ] = [OH ]
+ − 7 Pure water
H+

• pH scale - describes the acidity of a solution

+
OH− H

6 Urine
Neutral
Greater H+ concentration

solution
5
Black coffee
4 Tomato juice

3 Grapefruit juice,
soft drink
H+ H+
+
OH− H H+ 2 Lemon juice,
−
H +OH stomach acid
H+
Battery acid
1
Acidic
solution 0
pH scale

Acids, Bases, and pH Acids, Bases, and pH

• Buffers: substances that resist pH change. Why ocean acidification is bad news (1)
– accept H+ ions when they are in excess • Coral reefs account for 1%
of the ocean’s surface but
– donate H+ ions when they are depleted more than 25% of ocean life
depends on them
• Increases in global CO2 concentrations may lead to: • Hard reefs are composed of
calcite (CaCO3) that harbor
– the acidification of the oceans algae
• Acid dissolves the calcite –
– ecological disasters reefs die.

http://www.picture-newsletter.com/corals/coral-22.jpg

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Acids, Bases, and pH Evolution Connection:

The Search for Extraterrestrial Life
Why ocean acidification is bad news (2) • If life similar to ours has evolved elsewhere in the
universe, then it too would depend upon water.
• Researchers at NASA missions have found evidence
that water was once abundant on Mars.
• Microbial life may exist below the Martian surface.

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http://www.ioccg.org/gallery/seawifs/europe/UK.jpg

Emiliania huxleyi – an example of an algal cell with a Such organisms form algal blooms
brilliant white calcite (CaCO3) shell. Calcite is made from • When they die, they deposit vast amounts calcite
CO2 derived from the air. at the bottom of the oceans
• They also reflect heat from the sun back into space

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