1. NSCI 314 LIFE IN THE COSMOS 4 - The Biochemistry of Life on Earth Dr. Karen Kolehmainen Department of Physics CSUSB http://physics.csusb.edu/~karen/

2. 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.

3. BASIC FACTS ABOUT LIFE ON EARTH ORGANIC MOLECULE: A MOLECULE COMPOSED OF CARBON AND HYDROGEN ATOMS (AND OFTEN 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

4. 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.

5. 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 PROTEINS AND NUCLEIC ACIDS IN MORE DETAIL.

6. 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.

7. 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.

8. 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.

9. NUMBER OF POSSIBLE PROTEINS EXAMPLE: IMAGINE A PROTEIN THAT CONSISTS OF A CHAIN OF 200 AMINO ACIDS. 20 200 = 10 260 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 10 90. 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 20 312 = 10 406 DIFFERENT POSSIBLE PROTEINS.

10. 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.

11. 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.

12. 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.

13. 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).

14. The 20 Amino Acids Found in Living Organisms 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 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

15. The 20 Amino Acids Found in Living Organisms 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 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.

16. 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

17. 1 2 3 4 5 6 7 89 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y

18. 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

20. 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 AN COPY OF ITSELF DURING CELL DIVISION. WHEN A CELL DIVIDES, ONE COPY OF THE DNA GOES INTO EACH CELL.

21. 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.

22. 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”)

23. 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

24. 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

25. DNA MOLECULE 23 CHROMOSOME PAIRS …….. 1000 GENES CAC TCA AGA CCG TCA TCA …... CODON SEQUENCE

26. 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

27. 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.

28. 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) - later

29. 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)

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

31. 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(E.G., 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 OFTEN DEPICTED IN SCIENCE FICTION CARBON SEEMS LIKE A BETTER CHOICE, BUT IS SILICON-BASED LIFE POSSIBLE? WE DON’T KNOW.