Lecture 1.4: Foundations of Life

Chem Evol Polypeptides Nucleic Acids

Unit 1: Theoretical Pillars of Biology

Lecture 1.4: Foundations of Life

John D. Nagy

BIO 181: General Biology for Majors, Scottsdale Community College

2019 Revision

John Nagy Lec 1.4: Foundations of Life 1/26

Chem Evol Polypeptides Nucleic Acids

Outline

1 Chemical EvolutionEarly EarthMiller-Urey Experiment

2 PolypeptidesBuilding blocksPolymersProteins

3 Nucleic AcidsBuilding blocksRNAConnections between nucleic acids and proteins


Chem Evol Polypeptides Nucleic Acids Early Earth Miller-Urey

Earth ca. 4.4 billion years ago

See Lunine 2006 [3] for evidence.



Can this environment generate the stuff of life?

Miller-Urey Experiment

Attempt to simulate conditions of early Earth, including earlyatmosphere, heat and lightning. See [4].



Results of the Miller-Urey experiment


Chem Evol Polypeptides Nucleic Acids Building blocks Polymers Proteins

Critical Miller-Urey products—amino acids



The 20 common amino acids in living things



Condensation reactions leading to polymerization



Amino acid polymerization

Polypeptide chains long enough to fold into blobs are calledproteins.



Protein example

Space-filling molecular model:

Protein is called PTEN.

Involved in guarding againstcancer (tumor suppressorprotein).

Shown bound to its ligand,a molecule which binds toanother, usually larger, one.

A chain of 324 amino acidsfolded into into its tertiarystructure.

Proteins are typically > 80 aminoacids long; average about 250.



Composition of cell dry mass

Cell dry mass is about 55% protein.Source: Cell Biology by the Numbersbook.bionumbers.org/what-is-the-macromolecular-composition-of-the-cell.



Proteins: Arguably the most important molecule of life

An estimate of the proportions of proteins in a cell devoted tovarious metabolic functions.

Source: www.cs.cmu.edu/%7Eesefer/metric/index.html



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 [1]:

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).



Enzymes–the central molecule of life

Hexokinase, a key enzyme in glycolysis. Source: Kuser et al. 2000 [2].

Definition: Enzyme

An enzyme is a protein catalyst.

Definition: Catalyst

Substance that increases rate of a chemical reaction withoutundergoing any permanent change.


Chem Evol Polypeptides Nucleic Acids Building blocks RNA Connections

Another product of early Earth experiments



All nucleotides have a 5-carbon sugar...

Sugar = carbohydrate. A carbohydrate is any organiccompound with a formula nearly equal to:

[CH2O]n,

where n is a positive integer (whole number).John Nagy Lec 1.4: Foundations of Life 16/26


...and a nitrogenous base



Nucleotides can bond together by phosphate bridges



Result: Ribonucleic Acid (RNA)

If the sugar is ribose (notdeoxyribose), then

we have ribonucleic acid =RNA;

the bases are A, C, G or U(no T);

bond angles make it a helix(spiral);

but, usually forms a singlehelix.



Sometimes the sugar is deoxyribose

What’s the obvious difference that you see?

Comparison and contrast of RNA and DNA

Both form helicies (spirals).

But, bond angles in deoxyribose allow these polymers towrap around each other.



DNA therefore forms a double helix



DNA base pairing characteristics

If the sugar is deoxyribose then

we have deoxyribonucleicacid = DNA;

the bases are A, C, G or T;

if it forms a double helix, itdoes so typically with acomplementary DNAstrand.



RNA can also form a double helix with itself



Nucleic acids control proteins in a cell

Central dogma of biology

The inappropriately-named central dogma of biology saysthat information flows from DNA to RNA to protein.



Proteins control nucleic acids in a cell

The second-most abundant protein class controls nucleotidemetabolism.

Summary

Proteins and nucleic acids are intimately connected, andtogether they control the metabolic activities of a cell.



References I

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.

Paula R. Kuser, Sandra Krauchenco, Octavio A. C. Antunes, and Igor Polikarpov.

The high resolution crystal structure of yeast hexokinase PII with the correct primarysequence provides new insights into its mechanism of action.J. Biol. Chem., 275(27):20814–20821, 2000.

Jonathan I. Lunine.

Physical conditions on the early Earth.Phil. Trans. R. Soc. B, 361:1721–1731, 2006.

Xueshu Xie, Daniel Backman, Albert T. Lebedev, Viatcheslav B. Artaev, Liying Jiang,

Leopold L. Ilag, and Roman A. Zubarev.Primordial soup was edible: Abiotically produced Miller-Urey mixture supports bacterialgrowth.Sci. Rep., 5:14338, 2015.


Lecture 1.4: Foundations of Life

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