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Chapter 5

The Nature of Life on EarthWhat is Life?

Darwinian Evolution – Natural Selection

1. Struggle for Survival – competition for resources

2. Individual Variation – reproduction produces unique individuals. Variation may also occur spontaneously (mutation)

3. Survival of the Fittest – those individuals which are best able to compete for resources will survive and pass these characteristics onto their offspring

Adaptation

Artificial Selection

The Molecular Basis of Evolution

All life on Earth is built of the same fundamental building blocks!

Suggests all life shares a common ancestor

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Natural Selection TodayResistance of bacteria to antibiotics

A Basic Definition of LifeLife is something that can reproduce and evolve through natural selection

Life on Earth is chemically based, consisting of microscopic cells –biological material enclosed in membranes

The simplest organisms like bacteria consist of only single cells (unicellular) while the very complex organisms like humans consist of literally billions of cells (multicellular)

Cells

Chemical Composition of

the Human Body

96% of mass consists of only four elements:

C, H, O and N

All biological molecules are based on the element carbon (C)!

Why is this element so special?

Quantum Mechanics

Energy Levelsn ↑ E ↑

n = 1 ground staten > 1 excited states

n = principle quantum number

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Multi-electron Atoms

Have energy levels like hydrogen

Energy levels in multi-electron atoms hold multiple electrons and are often referred to as

“shells”

The maximum number of electrons allowed in a given shell, n is:

2n2

where:

n = principle quantum number

Valence Electrons of Main Group Elements

A Fundamental Principle of Chemistry

Full valence shells are most stable!

Three ways of obtaining a full valence shell

1. Lose electrons to form a positive ion (cation)

2. Gain electrons to form a negative ion (anion)

3. Share electrons to form a molecule

Lose 1 to form the sodium cation, Na+

[Ne]

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Gain 1 to form the chloride anion, Cl-

[Ar]

Metals lose electrons to form cations

Non-metals gain electrons to form anions Carbon has 4 valence electronsWill it lose 4 or gain 4?

Is the glass half-full or half-empty?

The Octet (Full Shell) Rule

Atoms react with other atoms and molecules in order to obtain a full shell of 8 valence

electrons

What will happen when sodium and chlorine are combined?

Wants to lose an electron

Wants to gain an electron

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A violent reaction! An electron is transferred from sodium to chlorine forming two ions!

Ionic Bonds

The ions are held together by the powerful force of electrostatic attraction!

For this reason, nearly all ionic compounds are high melting point solids!

NaCl melting point = 800 ºC = 1470 ºF

In general, ionic bonds tend to form between

metals and non-metals where there is a

transfer of electrons

On the other hand, non-metals complete their octets by sharing electrons with other non-metals to form covalent bonds

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Two dots or a straight line are drawn between the element symbols to indicate a shared pair

of electrons (called a single bond)

Methane, CH4

Methane (CH4) is held together by covalent bonds

Carbon can share an electron with another carbon atom!

Ethane, C2H6

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Forming long, complex chains!

n-pentane, C5H12

Carbon can even share multiple electrons with itself!

ethylene, C2H4

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acetylene, C2H2

Carbon can also form rings as well as chains!

CH2

CH2

CH2

H2C

H2C

cyclopentane

CH2

CH2

H2C

H2C

H2C

CH2

cyclohexane

H2C

H2C

H2C

H2C

CH2

CH2

CH2

cycloheptane

CH2

CH2H2C

H2C

H2C

H2C

H2C

CH2

cyclooctane

Carbon forms bonds with many other non-metals to form an enormous range of

compounds!

Organic Chemistry

The chemistry of carbon is so complex that it has its own

branch of chemistry!

Organic chemistry gets its name from the fact that the biological molecules

of life are carbon compounds!

organic means living!

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Inorganic Chemistry is the study of the chemistry of all

the rest of the elements!

1. Carbon forms strong chemical bonds with itself in a variety of ways (single, double and triple bonds) to form long complex chains and rings (chemically based life requires complex molecules)

2. Carbon also reacts with many other important elements like hydrogen (H), oxygen (O) and nitrogen (N)

3. Carbon based molecules have the perfect stability for life –not too unstable that they easily fall apart and not too stable that they cannot be rearranged into new forms

Advantages of Carbon for Life

Alternatives to Carbon?

Silicon (Si) seems to be the most likely since it has the same number of electrons (four) in its outer (valence) shell

Unlike C-C bonds, Si-Si bonds are weak!

Silicon forms its strongest bonds with oxygen to form silicates!

Silicates can be very complex and exist in a wide variety of forms!

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However, silicates are nearly all high melting point solids – far too stable for life!

The Biological Molecules of Life

Life on earth consists of four main types of biological polymer:

1. Proteins – used in the basic functioning of cells, including the acceleration (catalysis) of chemical reactions (enzymes)

2. Carbohydrates – used for short-term energy storage and cell structure

3. Lipids (fats) – major components of cell membranes and used for long-term energy storage

4. Nucleic Acids – used for information storage and cell replication

The molecules of life consist of simple molecular units called monomers which are combined together to form complex biological polymers: (A-B-A-C-A-D-A-)n

ProteinsMonomers: amino acids

Of all the many possibilities, proteins in biological molecules consist of only 20 different amino acids!

Amino Acids are Asymmetric!

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All amino acids used in biological molecules are left handed!

Carbon-rich Meteorites contain Amino Acids!

Meteoritic amino acids also contain an excess of the L-form. This may be due to the differences in the way the two forms interact with radiation in space

Meteorites are rocky debris left over from the formation of the solar system that fall to earth

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Life is Specific!

Amino Acid Monomers combine using Peptide Bonds

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The shapes of proteins are very important!

If they are exposed to excessive environmental conditions, they lose their shape and cease to

function!

Hemoglobin Transports Oxygen in our Bloodstream!

CarbohydratesMonomers: monosaccharides

glucose

Sucrose (Table Sugar) Glycogen – an energy storing molecule

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Starch – an important constituent of plants

Glycerol

Fatty Acid

Lipids (Fats)

Lipid Saturation

saturated

unsaturated

polyunsaturated

Cis- and trans-fatty acids

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Cell Membranes Nucleic AcidsMonomers: nucleotides = sugar + phosphate + nitrogen base

RNA uses the sugar ribose, DNA uses the sugar deoxyribose

DNA only uses four nucleotide bases! Complimentary Base Pairing

A--T

G--C

Cross linking of Complimentary Strands

Chains of nucleotides = primary structure

Arsenic (As) may be a possible alternative to the phosphorous (P) backbone of DNA!

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Example:

DNA…TTAGTTCTAGGGAGTGCC…

DNA…AATCAAGATCCCTCACGG…

Both strands carry the same complimentary information and hence can be used to repair

errors in each other!

Data redundancy!

The Double Helix

secondary structure

DNA Replication

Gene = a section of DNA carrying a particular piece of information (typically how to manufacture a particular protein)

Genetic Code – sequences of three nucleotides (codons) code for different amino acids

RNA Bases – Uracil instead of Thymine!

U still complimentary to A!

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RNA is single-stranded and much shorter than DNA!

Protein Synthesis

Section of DNA strand corresponding to gene unwinds Transcription – RNA copy made of gene segment

Example:

DNA…TTAGTTCTAGGGAGTGCC…

mRNA…AAUCAAGAUCCCUCACGG…

Translation – protein made from RNA in ribosome of cell

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The Genetic Code in RNA

Example:

mRNA…AAUCAAGAUCCCUCACGG…

tRNA…UUAGUUCUAGGGAGUGCC…

Protein…LEU-VAL-LEU-GLY-SER-ALA…

Summary

Genome – complete sequence for DNA bases for an organism

The Human Genome contains approximately 3 billion DNA base pairs (organized into 46

chromosomes) with between 30,000 and 120,000 genes. It is currently being mapped by the Human

Genome Project

Every cell contains a complete set of genes. Different types of cell differ only in which genes

that are actually used (expressed)

Cloning – a single cell from a living organism is used to grow a new organism with an identical set of genes

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Synthia – artificial life?

Artificial DNA was synthesized based on DNA from known bacteria and then transplanted into a host

The organism containing the artificial DNA was then able to replicate independently

Prokaryotes –simple, single-celled organisms e.g. bacteria

Most common kind of Life! First kind of Life to appear on Earth!

Prokaryotes – very important!

Help recycle of matter between surface and atmosphere!

Eukaryotes – more complex, genetic material enclosed in membrane (nucleus)

Can be unicellular or multi-cellular

An Amoeba – a simple unicellular eukaryote!The Three Domains of Life

Two branches of Prokaryotes –bacteria and

archaea

Archaea genetically similar to eukaryota! (common ancestor)

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Metabolism – the chemical reactions of Life

• Metabolic processes occur inside cells which act to facilitate reactions

• They require a source of raw materials (carbon compounds) and a source of energy (sunlight, chemical etc) to fuel the reactions

• Enzymes manufacture biological molecules within the cell from a limited number starting materials. Instructions for making these molecule is encoded in DNA

• Energy is stored in cells by the molecule Adenosine Triphosphate (ATP) which releases the energy on demand

Adenosine Triphosphate (ATP) – the cellular energy source

All Life on Earth uses ATP – evidence for a common ancestor!

Metabolic Classifications

Organisms can be classified according to how they obtain raw materials (carbon) and energy for metabolism:

1. Heterotrophs get carbon from preexisting organic compounds (food).

2. Autotrophs get carbon directly from their environment (e.g. air or water) in the form of carbon dioxide (CO2) or some other carbon compound.

3. Organisms that get their energy directly from sunlight (or other source of electromagnetic radiation) are prefixed with the word photo-

4. Organisms which get their energy from chemical reactions (between organic or even inorganic compounds) and use it to make their own energy are prefixed with the word chemo-

Classify these!1. An organism in the soil of Mars which gets its energy from

compounds in the soil and its carbon from carbon dioxide the atmosphere

2. An organism floating in the outer atmosphere of Jupiter which gets its energy from the Sun and its carbon from carbon dioxide in the atmosphere

3. An alien from another planet that gets it carbon and energy from ingesting other organisms

4. An alien is recovered from a crashed spaceship in the Mohave desert. During autopsy it is found to be a carbon based life form which gets its carbon from ingesting organic compounds and its energy from the cosmic microwave background that fills the Universe

Extremeophiles

Organisms which can exist under extreme environmental conditions. Most are simple prokaryotic organisms.

A few examples:

1. Thermophiles – able to survive at very high temperatures

2. Lithophiles – able to live inside porous rocks on the surface or deep below the surface of the earth

3. Endospores – organisms able to survive extreme conditions by generating a protective coat around the cell and then becoming dormant. Can regenerate when conditions change

Life can exist under a very wide range of conditions!

Thermophiles

Black Smokers

Hot Springs

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Lithophiles

Antarctic Dry Valleys – life found inside porous rocks

Columbia River Basalts – life found in rocks kilometers below the surface

Endospores