lecture 1.3: chemistry of life · from the limits of organic life in planetary systems [2]: life on...

Life Chemistry Water

Unit 1: Theoretical Pillars of Biology

Lecture 1.3: Chemistry of Life

John D. Nagy

BIO 181: General Biology for Majors, Scottsdale Community College

2019 Revision

John Nagy Lec 1.3: Chemistry of Life 1/27


Outline

1 Properties of Life

2 ChemistryElementsAtomsCovalent BondsMolecules

3 Water



NASA’s working description of life on Earth

“Life is a self-sustaining chemical sys-

tem capable of Darwinian evolution.”

From The limits of Organic Life in Planetary Systems [2]:

Life on Earth is fundamentally cellular.

Life is chemical: Living things use covalent bonding propertiesof C, H, N, O, P, and S and the ability of O and N to modulatehydrocarbon reactivity.

Biomolecules have evolved to function when dissoved in water.

Metabolism is controlled by enzymes that are inheritedthrough reproduction.

Living systems adapt to changing environments via evolutionby natural selection (Darwinian evolution).

Life exploits thermodynamic disequilibrium (homeostasis).


Life Chemistry Water Elements Atoms Covalent Bonds Molecules

Reivew of basic chemistry

Shown above are coal and a diamond, both pure carbon. Whatis carbon, as shown above?

A compound

A molecule

An atom

An element

None of the aboveJohn Nagy Lec 1.3: Chemistry of Life 4/27


Elementary substances

Definition

An element, or better an elementary substance, is asubstance (solid, liquid, gas) that is composed of the same typesof atoms.



What is an atom?

What are the blue, purple and yellow(ish) objects in thesediagrams?



What is an atom?

Definition: Atom

An atom is the smallest electrically neutral unit of an element.It cannot be decomposed into simpler elements by normalchemical means.



Elements of life

Living things mostly C,H,N,O,P,S and ions Na+, K+, Mg2+,Ca2+ and Cl−.

What is the most abundant element in living things?



Elements of life

Living things mostly C,H,N,O,P,S and ions Na+, K+, Mg2+,Ca2+ and Cl−.

What is the most abundant element in living things?O (60%), C (18%) by mass



A more realistic view of electron shells

The concept of orbitals

Electron densities are 3-dimensional structures surrounding thenucleus. They can have different energies (1, 2, 3, for example).Shown here are s orbitals; there are other shapes (p, d, f , forexample), but different shapes can have similar energies.



C, H, N, O, P, S on the periodic table

Nonmetals



Bonding rules

Nonmetals

A simple bonding rule

Covalent bonds form between nonmetals;

Ionic bonds form between a nonmetal and a metal.









Yay! We biologists only have to worry about covalent bonds.



Metabolism = changing chemical bonds

Principle 1

Atoms with a full outer shell (called the valence shell) tend tobe inert.

Principle 2

Atoms with spaces available for electrons in the valence shellwill react with other atoms until the valence shell is filled.



A more realistic picture of covalent bonds

It is better to think of covalent bonds as atomic orbitalscombining into a smear that encompasses both nuclei (lowerright of the figure).



Examples of covalent bonds



Molecules

Definition: Molecule

A molecule is the smallest electrically neutral structural unitof an element or compound; consists of atoms bonded togetherwith strong (covalent or ionic) bonds.



Not all covalent bonds are the same



Hydrogen bonds between water molecules

Definition: hydrogen bonds

A hydrogen bond is a weak electrostatic interaction betweentwo molecules or parts of the same molecule caused by theattraction between an atom with a slight positive charge andone with a slight negative charge.










Metabolism is controlled by enzymes that are inheritedthrough reproduction.

Living systems adapt to changing environments via evolutionby natural selection (Darwinian evolution).

Life exploits thermodynamic disequilibrium (homeostasis).



Why is life based on water?

Andrew Pohorille (NASA Ames Research Center)

“. . . [the] solvent must promote self-organzation of organicmatter into functional structures . . . [which are] mostly based onnon-covalent interactions [like hydrogen bonds]. . . Hydrophobicinteractions are responsible . . . for many self-organizationphenomena in biological systems, such as the formation of[membranes] and protein folding.”



“Follow the water.” Evidence from MEP landers

One property of life


Mineral evidence of water on the surface (Spirit, Opportunity,Curiosity).

Water-worked boulders (Pathfinder), hydrothermal deposits(Spirit), and ancient mud (Opportunity).

Water ice 10-20 cm under the surface above the arctic circle(Phoenix).

Source: Arvidson (2016) [1].John Nagy Lec 1.3: Chemistry of Life 24/27


“Follow the water.” Evidence from orbit

One property of life


Shallow radar on Mars Reconnaissance Orbiter found evidence oflarge water deposits beneath Mars’ North Pole [3].

Advanced radar on Mars Express found evidence of liquid waterunder Mars’ South Polar cap [4].

Conclusion: Mars once had flowing surface water, maybe even oceans.



Open questions

Was there, at some time in the past, life on Mars?

Is there currently life on Mars?

These questions remain unanswered.



References I

Raymond E. Arvidson.

Aqueous history of Mars as inferred from landed mission measurements of rocks, soils,and water ice.J. Geophys. Res. Planets, 121:1602–1626, 2016.

Commitee on the Limits of Organic Life in Planetary Systems, Space Studies Board, and

Board on Life Sciences.The Limits of Organic Life in Planetary Systems.National Academies Press, Washington, D.C., 2007.

Stefano Nerozzi and J. W. Holt.

Buried ice and sand caps at the north pole of Mars: Revealing a record of climate changein the cavi unit with SHARAD.Geophys. Res. Lett., In Press, 2019.

R. Orosei, S. E. Lauro, E. Pettinelli, and et al.

Radar evidence of subglacial liquid water on Mars.Science, 361:490–493, 2018.


lecture 1.3: chemistry of life · from the limits of organic life in planetary systems [2]: life on...

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