NSCI 314 LIFE IN THE COSMOS 4 – Basic Properties of Life and The Biochemistry of Life on Earth Dr. Karen Kolehmainen Department of Physics CSUSB

A CLOSED SYSTEM AND ITS ENVIRONMENT CLOSED SYSTEM MATTER ENERGY MATTER ENERGY

AN OPEN SYSTEM AND ITS ENVIRONMENT OPEN SYSTEM MATTER ENERGY WASTE ENERGY WASTE MATTER

ENTROPY AND ORDER ENTROPY: A MEASURE OF THE DISORDER IN A SYSTEM – LOW ENTROPY = HIGHLY ORDERED – HIGH ENTROPY = VERY DISORDERED OR MESSY SECOND LAW OF THERMODYNAMICS: – IN ANY CLOSED SYSTEM (MEANING THAT NOTHING ENTERS OR LEAVES), NO PROCESS CAN OCCUR IN WHICH THE SYSTEM'S ENTROPY DECREASES. IN OTHER WORDS, A CLOSED SYSTEM CAN'T BECOME MORE ORDERED (LESS MESSY) AS TIME GOES ON. – THEREFORE, THE AMOUNT OF DISORDER IN A CLOSED SYSTEM EITHER INCREASES WITH TIME OR IT DOESN’T CHANGE WITH TIME. USUALLY, THE ENTROPY INCREASES WITH TIME, IN OTHER WORDS, A CLOSED SYSTEM GETS MESSIER AS TIME GOES ON.

ENTROPY AND ORDER SECOND LAW OF THERMODYNAMICS: IN ANY CLOSED SYSTEM, NO PROCESS CAN OCCUR IN WHICH THE ENTROPY DECREASES WITH TIME, IN OTHER WORDS, A CLOSED SYSTEM CANNOT BECOME MORE ORDERED WITH TIME. WHAT ABOUT THE ENTROPY OF AN OPEN SYSTEM? AN OPEN SYSTEM INTERACTS WITH ITS ENVIRONMENT. IF WE INCLUDE THE ENVIRONMENT AS PART OF THE SYSTEM (INSTEAD OF SOMETHING OUTSIDE OF THE SYSTEM), WE NOW HAVE A CLOSED SYSTEM, AND ITS TOTAL ENTROPY CAN'T DECREASE WITH TIME. HOWEVER, THE ENTROPY OF THE ORIGINAL OPEN SYSTEM CAN DECREASE, AS LONG AS THE ENTROPY OF ITS ENVIRONMENT INCREASES BY AN EVEN LARGER AMOUNT. LIFE: ENTROPY DECREASES WITHIN AN ORGANISM AS RAW MATERIALS ARE REARRANGED IN HIGHLY ORDERED WAYS. HOWEVER, THE ORGANISM IS AN OPEN SYSTEM, AND THE ENTROPY OF ITS ENVIRONMENT INCREASES.

LIFE AND ITS ENVIRONMENT ORGANISM ENTROPY DECREASES MATTER ENERGY WASTE MATTER WASTE ENERGY ENVIRONMENT ENTROPY INCREASES

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 SURFACES PLANETARY OR LUNAR INTERIORS THICK PLANETARY OR LUNAR ATMOSPHERES CHEMICAL SOLVENT (LIQUID): WATER (OR SOMETHING ELSE?) ‏ APPROPRIATE TEMPERATURE RANGE: NEEDED TO KEEP THE SOLVENT LIQUID (APPROXIMATELY 0 TO 100 o C IF WATER IS THE LIQUID SOLVENT) ‏ IF IT’S TOO HOT, COMPLEX STRUCTURES ARE BROKEN APART IF 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% Oxygen Iron Silicon Magnesium Sulfur Nickel Aluminum Calcium Sodium Chromium Phosphorus 50% Oxygen Silicon Aluminum Iron Calcium Sodium Potassium Magnesium Titanium Hydrogen Phosphorus Manganese Fluorine Strontium Sulfur 47%

Earth’s Atmosphere Bacteria Human Beings Nitrogen Oxygen Argon Carbon** Neon Helium 78% Hydrogen Oxygen Carbon Nitrogen Phosphorus Sulfur 63% Hydrogen Oxygen Carbon Nitrogen Calcium Phosphorus Sulfur 61%

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 ATOMS EXAMPLES: H 2 O CO 2 CH 4 NH 3 H 2 N 2 O 2 C 2 H 5 O 2 N ORGANIC MOLECULE: A MOLECULE COMPOSED OF CARBON AND HYDROGEN ATOMS (AND OFTEN ATOMS OF OTHER ELEMENTS ALSO) ‏ EXAMPLES: CH 4 C 2 H 5 O 2 N 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

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 (BACTERIA, FOR EXAMPLE) ARE SINGLE-CELLED, AND OTHER ORGANISMS (HUMANS, FOR EXAMPLE) ARE MULTICELLULAR. A CELL CAN DIVIDE, RESULTING IN TWO CELLS.

EXAMPLES OF POLYMERS CARBOHYDRATES: 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.

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 = 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 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 = 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 C 3 H 7 O 2 N C 6 H 15 O 2 N 4 C 4 H 8 O 3 N 2 C 4 H 6 O 4 N C 3 H 7 O 2 NS C 5 H 8 O 4 N C 5 H 10 O 3 N 2 C 2 H 5 O 2 N C 6 H 9 O 2 N 3 C 6 H 13 O 2 N

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 C 6 H 13 O 2 N C 6 H 15 O 2 N 2 C 5 H 11 O 2 NS C 9 H 11 O 2 N C 5 H 9 O 2 N C 3 H 7 O 3 N C 4 H 9 O 3 N C 11 H 12 O 2 N 2 C 9 H 11 O 3 N C 5 H 11 O 2 N *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 (FOR EXAMPLE, 46 IN HUMANS)‏ CAN REPLICATE ITSELF – WHEN A CELL DIVIDES INTO TWO, AN IDENTICAL COPY OF THE ORIGINAL DNA (A COPY OF EACH CHROMOSOME) GOES INTO EACH CELL

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 STRING OF THREE BASES (CALLED A CODON) IN THE DNA SPECIFIES WHICH AMINO ACID IS PLACED NEXT INTO THE GROWING 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.

AGCTAGCT 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 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 STRING 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 …… 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, (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 1/25 th 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 (SiO 2 AND SiH 4 AS COMPARED WITH CO 2 AND CH 4 ) BUT ATOMS CAN’T BE REARRANGED AS EASILY SILICON-BASED LIFE IS SOMETIMES 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.