NSCI 314

LIFE IN THE COSMOS

4 – Basic Properties of Life and

The Biochemistry of Life on Earth

Dr. Karen KolehmainenDepartment of Physics

CSUSB

http://physics.csusb.edu/~karen/

WHAT IS LIFE? HARD TO DEFINE, BUT LET'S LIST SOME OF ITS

PROPERTIES. NECESSARY PROPERTIES:

– USES ENERGY– INTERACTS WITH ITS ENVIRONMENT– MAINTAINS A LOW ENTROPY (HIGH DEGREE OR ORDER

OR COMPLEXITY) INTERNALLY LIKELY (BUT MAYBE NOT NECESSARY) PROPERTIES:

– GROWS AND DEVELOPS– REPRODUCES– MUTATES AND EVOLVES

REQUIREMENTS FOR LIFE MATTER:

PRODUCED IN BIG BANG (H & He) AND STARS (HEAVIER ELEMENTS) ARE CERTAIN ELEMENTS NEEDED? STABLE ENERGY SOURCE:

LOW MASS MAIN SEQUENCE STARS (OR SOMETHING ELSE?) PROTECTED ENVIRONMENT:

PLANETARY OR LUNAR SURFACESPLANETARY OR LUNAR INTERIORSTHICK PLANETARY OR LUNAR ATMOSPHERES

CHEMICAL SOLVENT (LIQUID): WATER (OR SOMETHING ELSE?) APPROPRIATE TEMPERATURE RANGE: NEEDED TO KEEP THE SOLVENT LIQUID (APPROXIMATELY 0 TO 100o C IF WATER

IS THE LIQUID SOLVENT)IF IT’S TOO HOT, COMPLEX STRUCTURES ARE BROKEN APARTIF IT’S TOO COLD, INTERACTIONS ARE TOO SLOW

Sun Earth Earth’s Crust

Hydrogen

Helium

Oxygen

Carbon

Neon

Nitrogen

Magnesium

Silicon

Iron

Sulfur

Argon

Aluminum

Calcium

Sodium

Nickel

Chromium

Phosphorus

90.99%

8.87

0.078

0.033

0.011

0.010

0.004

0.003

0.003

0.002

0.0003

0.0003

0.0002

0.0002

0.0002

0.00003

0.00003

Oxygen

Iron

Silicon

Magnesium

Sulfur

Nickel

Aluminum

Calcium

Sodium

Chromium

Phosphorus

50%

17

14

14

1.6

1.1

1.1

0.74

0.66

0.13

0.08

Oxygen

Silicon

Aluminum

Iron

Calcium

Sodium

Potassium

Magnesium

Titanium

Hydrogen

Phosphorus

Manganese

Fluorine

Strontium

Sulfur

47%

28

8.1

5.0

3.6

2.8

2.6

2.1

0.44

0.14

0.10

0.10

0.063

0.038

0.026

Earth’s Atmosphere Bacteria Human Beings

Nitrogen

Oxygen

Argon

Carbon**

Neon

Helium

78%

21

0.93

0.03

0.0018

0.00052

Hydrogen

Oxygen

Carbon

Nitrogen

Phosphorus

Sulfur

63%

29

6.4

1.4

0.12

0.06

Hydrogen

Oxygen

Carbon

Nitrogen

Calcium

Phosphorus

Sulfur

61%

26

10.5

2.4

0.23

0.13

0.13

BOTTOM LINE:

THE ELEMENTS THAT MAKE UP TERRESTRIAL LIVING ORGANISMS ARE VERY COMMON IN STARS AND IN THE INTERSTELLAR MATERIAL FROM WHICH STARS AND PLANETS ARE FORMED.

IN LIVING THINGS, THE ATOMS OF THESE ELEMENTS ARE ORGANIZED IN ORGANIC MOLECULES, MANY OF WHICH ARE LARGE AND COMPLEX.

ORGANIC MOLECULES

MOLECULE: A COMBINATION OF TWO OR MORE ATOMSEXAMPLES: H2O CO2 CH4 NH3 H2 N2 O2 C2H5O2N

ORGANIC MOLECULE: A MOLECULE COMPOSED OF CARBON AND HYDROGEN ATOMS (AND OFTEN OTHER ELEMENTS ALSO)

EXAMPLES: CH4 C2H5O2N

MONOMER: A SIMPLE ORGANIC MOLECULE SUCH AS AN AMINO ACID, SIMPLE SUGAR, FATTY ACID, OR GENETIC BASE

POLYMER: A LARGE ORGANIC MOLECULE COMPOSED OF A CHAIN OF REPEATING MONOMERS

EXAMPLES OF POLYMERSCARBOHYDRATES: STARCHES, CELLULOSE, SUCROSE.

MONOMERS: SIMPLE SUGARS, GLUCOSE

LIPIDS: FATS, CHOLESTEROL, HORMONES, CELLULAR MEMBRANES.MONOMERS: FATTY ACIDS

NUCLEIC ACIDS: DEOXYRIBONUCLEIC ACID (DNA) & RIBONUCLEIC ACID (RNA).MONOMERS: GENETIC BASES

PROTEINS: STRUCTURAL PROTEINS FOR BONE, ORGANS, TISSUE, AND MEMBRANES; ENZYMES, CHEMICAL SENSORS AND TRANSPORTERS.MONOMERS: AMINO ACIDS

LET’S EXAMINE NUCLEIC ACIDS AND PROTEINS IN MORE DETAIL.

ORGANIC MOLECULES

CARBON ATOMS OCCUPY CENTRAL POSITIONS IN MOST MONOMERS. WHEN THE MONOMERS COMBINE TO FORM POLYMERS, THE CARBON ATOMS FORM THE CENTRAL STRUCTURE OF THE CHAIN, WITH ATOMS OF OTHER ELEMENTS STUCK TO THE SIDES.

H H H | | | C – C – C

| | |

H H H

LIFE ON EARTH IS CARBON-BASED.

BASIC FACTS ABOUT LIFE ON EARTH

LIVING ORGANISMS ON EARTH ARE MADE OF CELLS.

EXCEPTION: VIRUSES

A CELL IS TINY DROP OF WATER AND VARIOUS ORGANIC MOLECULES, SURROUNDED BY A MEMBRANE. SOME CELLS CONTAIN CERTAIN STRUCTURES, TO BE DISCUSSED LATER. SOME ORGANISMS (e.g., BACTERIA) ARE SINGLE-CELLED, AND OTHER ORGANISMS (i.e., HUMANS) ARE MULTICELLULAR. A CELL CAN DIVIDE, RESULTING IN TWO CELLS.

STRUCTURE OF PROTEINS

A PROTEIN IS A LONG POLYMER MADE OF MONOMERS CALLED AMINO ACIDS.

EACH PROTEIN IS COMPOSED OF A CHAIN OF HUNDREDS OF AMINO ACIDS.

PROTEINS USED IN LIFE ON EARTH ARE FORMED FROM ONLY DIFFERENT 20 TYPES OF AMINO ACIDS.

ADDITIONAL TYPES OF AMINO ACIDS EXIST AND COULD BE USED BY LIFE ELSEWHERE.

PROTEIN STRUCTURE

EXAMPLE:

AA1—AA3—AA3—AA1—AA17—AA11—AA11—AA11 —

AA2—AA9—AA9—AA9—AA9—AA9—AA10—AA15 —

AA8—AA5—AA5—AA1—AA16—AA12—AA4—AA20 —

AA19—AA7—AA3—AA5—…. CONTINUING ON FOR

HUNDREDS MORE OF AMINO ACIDS.

PROTEIN STRUCTURE

CHANGING EVEN ONE OF THE AMINO ACIDS OUT OF THE HUNDREDS IN THE CHAIN CHANGES THE PROTEIN.

AA1—AA3—AA3—AA1—AA17—AA11—AA11—AA11 —

AA2—AA9—AA9—AA9—AA9—AA9—AA10—AA15 —

AA8—AA5—AA6—AA1—AA16—AA12—AA4—AA20 —

AA19—AA7—AA3—AA5—…. CONTINUING ON FOR

HUNDREDS MORE OF AMINO ACIDS.

THIS IS NOW A DIFFERENT PROTEIN FROM THE ONE ON THE PREVIOUS SLIDE.

NUMBER OF POSSIBLE PROTEINS EXAMPLE: IMAGINE A PROTEIN THAT CONSISTS OF A CHAIN OF 200 AMINO ACIDS.

20200 = 10260 DIFFERENT PROTEINS ARE POSSIBLE.

(NUMBER OF POSSIBLE ORDERINGS OF A CHAIN OF 200 AMINO ACIDS OF 20 DIFFERENT TYPES)

IN COMPARISON, THE TOTAL NUMBER OF PROTONS, NEUTRONS, AND ELECTRONS IN THE ENTIRE UNIVERSE IS ESTIMATED TO BE LESS THAN 1090.

ANOTHER PROTEIN OF A DIFFERENT LENGTH WOULD HAVE A SIMILARLY LARGE NUMBER OF POSSIBLE COMBINATIONS.

EXAMPLE: A SEQUENCE OF 312 AMINO ACIDS WOULD RESULT IN 20312 = 10406 DIFFERENT POSSIBLE PROTEINS.

CONSEQUENCE: EVEN IF EXTRATERRESTRIAL LIFE

USES THE SAME 20 AMINO ACIDS AS LIFE ON EARTH …

IT IS VERY UNLIKELY THAT ANY OF THE PROTEINS WILL BE THE SAME AS THOSE USED BY LIFE ON EARTH.

THIS MAKES IT UNLIKELY THAT WE COULD EAT EACH OTHER'S FOOD, BE INFECTED BY EACH OTHER'S DISEASES, ETC.

AMINO ACIDS

AMINO ACIDS ARE THE MONOMERS THAT MAKE UP PROTEINS.

AMINO ACIDS ARE FOUND:IN ALL TERRESTRIAL FORMS OF LIFE.IN METEORITES (ROCKS THAT FALL TO

EARTH FROM SPACE).IN INTERSTELLAR CLOUDS OR NEBULAE.

NOTE: AMINO ACIDS CAN BE PRODUCED BY NON-BIOLOGICAL CHEMICAL REACTIONS. THEREFORE, THE PRESENCE OF AMINO ACIDS DOESN’T NECESSARILY INDICATE THE PRESENCE OF LIFE.

HANDEDNESS OF AMINO ACIDS

EACH AMINO ACID CAN HAVE TWO “ISOMERS” OR MOLECULAR VERSIONS: L (LEVO- OR LEFT-HANDED) D (DEXTRO- OR RIGHT-HANDED)

THE TWO ISOMERS ARE MOLECULAR MIRROR IMAGES OF EACH OTHER.

HANDEDNESS OF AMINO ACIDS AMINO ACIDS FROM NON-BIOLOGICAL

SOURCES (INCLUDING THOSE IN METEORITES AND INTERSTELLAR CLOUDS) ARE 50% LEFT- HANDED AND 50% RIGHT-HANDED.

AMINO ACIDS IN TERRESTRIAL LIVING ORGANISMS ARE ALL LEFT-HANDED.

EXTRATERRESTRIAL LIFE COULD USE EITHER LEFT-HANDED AMINO ACIDS OR RIGHT-HANDED AMINO ACIDS (OR POSSIBLY BOTH, ALTHOUGH NOT LIKELY).

The 20 Amino Acids Found in Living Organisms on Earth

AMINO ACID* CHEMICAL FORMULA NUMBER OF ATOMS

L-ALANINE

L-ARGININE

L-ASPARAGINE

L-ASPARTIC ACID

L-CYSTEINE

L-GLUTAMIC ACID

L-GLUTAMINE

GLYCINE

L-HISTIDINE

L-ISOLEUCINE

13

27

17

15

14

18

20

10

20

22

C3H7O2N

C6H15O2N4

C4H8O3N2

C4H6O4N

C3H7O2NS

C5H8O4N

C5H10O3N2

C2H5O2N

C6H9O2N3

C6H13O2N

The 20 Amino Acids Found in Living Organisms on Earth

AMINO ACID* CHEMICAL FORMULA NUMBER OF ATOMS L-LEUCINE

L-LYSINE

L-METHIONINE

L-PHENYLALANINE

L-PROLINE

L-SERINE

L-THREONINE

L-TRYPTOPHAN

L-TYROSINE

L-VALINE

22

25

20

23

17

14

17

27

24

19

C6H13O2N

C6H15O2N2

C5H11O2NS

C9H11O2N

C5H9O2N

C3H7O3N

C4H9O3N

C11H12O2N2

C9H11O3N

C5H11O2N*For those amino acids that have both a left-handed (L) and a right-handed (D) form, we have indicated that only the left-handed member of these stereoisomer pairs appears in living organisms. Only glycine, the simplest of the amino acids, has no L and D forms, and thus requires no L or D designation.

ROLE OF DNA PROVIDES A “BLUEPRINT” OR “RECIPE” FOR

MAKING PROTEINS– CARRIES INFORMATION ABOUT THE SEQUENCE

OF AMINO ACIDS IN A PARTICULAR PROTEIN

FOUND IN EVERY CELL IN A LIVING ORGANISM– IN “HIGHER” ORGANISMS, THE DNA IS

SEPARATED INTO LARGE PIECES CALLED CHROMOSOMES (e.g., 46 IN HUMANS)

CAN REPLICATE ITSELF – WHEN A CELL DIVIDES INTO TWO, AN IDENTICAL

COPY OF THE ORIGINAL DNA (i.e., A COPY OF EACH CHROMOSOME) GOES INTO EACH CELL

1 2 3 4 5 6

7 8 9 10 11 12

13 14 15 16 17 18

19 20 21 22 X Y

A NUCLEIC ACID IS A POLYMER CHAIN CONSISTING OF PAIRS OF GENETIC BASES (PLUS SOME SUGARS AND PHOSPHATES). THE BONDING OF GENETIC BASES IS VERY SPECIFIC – EACH TYPE OF BASE BONDS ONLY WITH ONE OTHER TYPE OF BASE, AS SHOWN BY THE

DASHED LINES.

DNA (DEOXYRIBONUCLEIC ACID)

Adenine (A)---------Thymine (T)

Guanine (G)----------Cytosine (C)

RNA (RIBONUCLEIC ACID)

Adenine (A)-----Uracil (U)

Guanine (G)-------Cytosine (C)

NUCLEIC ACIDS

DNA STRUCTURE AND FUNCTION A DNA MOLECULE CAN “UNZIP” AND

SEPARATE INTO TWO STRANDS. THIS HAS TWO IMPORTANT CONSEQUENCES:

1. EACH STRAND CAN BE USED AS A TEMPLATE FOR CONSTRUCTING A DUPLICATE OF THE OTHER STRAND. IT IS AN EXACT DUPLICATE (EXCEPT FOR OCCASIONAL MISTAKES CALLED MUTATIONS) BECAUSE OF THE SPECIFICITY OF THE BONDING BETWEEN BASES. THE BASES THAT ARE USED TO MAKE THE NEW STRAND ARE PULLED FROM A “SOUP” OF BASES AND OTHER MOLECULES BY SPECIAL PROTEINS. THIS ALLOWS THE DNA TO MAKE A COPY OF ITSELF DURING CELL DIVISION. WHEN A CELL DIVIDES, ONE COPY OF THE DNA GOES INTO EACH CELL.

DNA STRUCTURE AND FUNCTION A DNA MOLECULE CAN “UNZIP” AND

SEPARATE INTO TWO STRANDS. THIS HAS TWO IMPORTANT CONSEQUENCES:

2. ONE OR BOTH STRANDS CAN BE USED AS A TEMPLATE FOR MAKING A PROTEIN. THE SEQUENCE OF BASES IN THE DNA SPECIFIES THE SEQUENCE OF AMINO ACIDS IN THE RESULTING PROTEIN. TO BE MORE PRECISE, A GROUP OF THREE BASES (CALLED A CODON) IN THE DNA SPECIFIES WHICH AMINO ACID IS PLACED NEXT INTO THE PROTEIN.

WHY THREE BASES PER CODON? THERE ARE ONLY 4 DIFFERENT KINDS OF BASES USED, BUT THERE MUST BE INSTRUCTIONS FOR 20 DIFFERENT TYPES OF AMINO ACIDS.

A

G

C

T

Combinations of Bases in Singlet, Doublet, and Triplet Codes

AAT

AGT

ACT

ATT

GAT

GGT

GCT

GTT

CAT

CGT

CCT

CTT

TAT

TGT

TCT

TTT

AAC

AGC

ACC

ATC

GAC

GGC

FCC

GTC

CAC

CGC

CCC

CTC

TAC

TGC

TCC

TTC

AAG

AGG

ACG

ATG

GAG

GGG

GCG

GTG

CAG

CGG

CCG

CTG

TAG

TGG

TCG

TTG

AAA

AGA

ACA

ATA

GAA

GGA

GCA

GTA

CAA

CGA

CCA

CTA

TAA

TGA

TCA

TTA

AT

GT

CT

TT

AC

GC

CC

TC

AG

GG

CG

TG

AA

GA

CA

TA

Singlet code Doublet code Triplet code

( 4 “words”) (16 “words”) (64 “words”)

TTT

TTC

TTA

TTG

CTT

CTC

CTA

CTG

ATT

ATC

ATA

ATG

GTT

GTC

GTA

GTG

DNA Codons for Amino Acids (the genetic code).

}

}

}

}

}

phenylalanine

leucine

leucine

isoleucine

valine

TCT

TCC TCA

TCG

CCT

CCC

CCA

CCG

ACT

ACC

ACA

ACG

GCT

GCC

GCA

GCG

TAT

TAC

TAA

TAG

CAT

CAC

CAA

CAG

AAT

AAC

AAA

AAG

GAT

GAC

GAA

GAG

TGT

TGC

TGA TGG

CGT

CGC

CGA

CGG

AGT

AGC

AGA

AGG

GGT

GGC

GGA

GGG

}}}}

serine

proline

threonine

alanine

valine/”initiator”

methionine/”initiator”

}

}

tyrosine

“terminator”

}

}

}

}

}

}

histidine

gluatamine

asparagine

lysine

aspartic acid

glumatic acid

}

}

}

}

}

cysteine

“terminator”tryptophan

arginine

serine

arginine

glycine

CODON: A GROUP OF 3 GENETIC BASES GIVING THE CODE (OR INSTRUCTION) FOR PLACING A PARTICULAR AMINO ACID INTO A PROTEIN THAT IS UNDER CONSTRUCTION.

GENE: A STRING OF ROUGHLY 1000 CODONS THAT IS THE RECIPE FOR A PARTICULAR PROTEIN.

CHROMOSOME: A LARGE PIECE OF DNA CONTAINING A LARGE NUMBER OF GENES.

GENOME: ENTIRE SEQUENCE OF DNA IN AN ORGANISM.

IN HUMANS, THE GENOME CONTAINS ABOUT 3 BILLION GENETIC BASES, AND 30,000 TO 100,000 GENES, ORGANIZED INTO 23 CHROMOSOME PAIRS.

(THERE IS ENOUGH DNA FOR 1 MILLION GENES, BUT FEWER THAN 100,000 EXIST. THERE IS A LOT OF “JUNK” DNA BETWEEN GENES.)

GENETIC STRUCTURE

DNA

23 CHROMOSOME PAIRS

……..

1000 GENES

CAC TCA AGA CCG TCA TCA …...

CODON SEQUENCE

DNA MOLECULE

…….

23 CHROMOSOME PAIRS

CODON SEQUENCE

CAC TCA AGA CCG TCA TCA ……..

DNA SEQUENCE TRANSCRIBED INTO mRNA

mRNA TRANSLATED INTO PROTEIN

HISTIDINE SERINE ARGININE PROLINE SERINE SERINE…..

PROTEIN

TRANSCRIPTION AND TRANSLATION

TRANSCRIPTION: DNA UNZIPS AND ONE STRAND IS USED AS A TEMPLATE FOR CONSTRUCTING A NEW STRAND. THIS IS SIMILAR TO DNA REPLICATION, EXCEPT THAT THE NEWLY CONSTRUCTED STRAND IS RNA INSTEAD OF DNA. (RNA USES U INSTEAD OF T, AND THE SUGAR IN BACKBONE IS SLIGHTLY DIFFERENT.)

TRANSLATION: RNA MOVES TO A DIFFERENT PART OF THE CELL, WHERE THE GENETIC CODE IS READ AND CONVERTED TO AN AMINO ACID SEQUENCE.

NOTE: RNA ALSO PLAYS OTHER ROLES IN ORGANISMS. IN SOME VIRUSES, RNA REPLACES DNA AS THE GENETIC MATERIAL.

LIFE ELSEWHERE COULD HAVE: Very similar proteins and DNA sequences to us

(if so, a common origin is likely) Same 20 amino acids and 4-5 genetic bases as

us, but combined into different proteins and DNA sequences (if so, common origin?)

Amino acids and genetic bases, but not the same 20 amino acids and 4 or 5 bases as us

Different monomers, (i.e., not amino acids and genetic bases), but still carbon-based polymers of some sort

Different kind of chemistry? (based on some element other than carbon)

No chemistry at all! (exotic matter or interactions other than electromagnetic) - to be discussed later

ADVANTAGES OF CARBON ABUNDANT

A CARBON ATOM CAN COMBINE WITH MANY OTHER ATOMS (AS MANY AS 4 AND ALMOST ANY OTHER ELEMENT), THUS MAKING COMPLEX MOLECULES

MOLECULES ARE REASONABLY STABLE, BUT NOT TOO STABLE (CAN BE BROKEN APART TO FACILITATE INTERACTIONS)

SUBSTITUTES FOR CARBON? ANY ELEMENT IN THE SAME COLUMN IN THE

PERIODIC TABLE WILL COMBINE WITH OTHER ATOMS IN MUCH THE SAME WAY, BUT…

AS THE SIZE OF ATOM GROWS, BONDING BETWEEN ATOMS GETS WEAKER, MAKING FORMATION OF COMPLEX MOLECULES MORE DIFFICULT

AS SIZE OF ATOM GROWS, ABUNDANCE OF ELEMENT DECREASES

THEREFORE, THE BEST CHOICE (BESIDES CARBON) IS SILICON, THE ELEMENT JUST BELOW CARBON IN THE PERIODIC TABLE

SILICON INSTEAD OF CARBON? ONLY 1/25th AS ABUNDANT (BUT STILL

REASONABLY ABUNDANT) MOST BONDS WEAKER (ESPECIALLY Si-Si

BONDS), SO MORE DIFFICULT TO BUILD LONG CHAINS (POLYMERS)

Si-O BOND STRONGEST, SO MOST SILICON STAYS BONDED TO OXYGEN (AS IN ROCKS)

SIMILAR COMPOUNDS EXIST(E.G., SiO2 AND SiH4 AS COMPARED WITH CO2 AND CH4) BUT ATOMS CAN’T BE REARRANGED AS EASILY

SILICON-BASED LIFE IS OFTEN DEPICTED IN SCIENCE FICTION (EXAMPLE: “HORTA” IN STAR TREK)

CARBON SEEMS LIKE A BETTER CHOICE, BUT IS SILICON-BASED LIFE POSSIBLE? WE DON’T KNOW.