NSCI Basic Properties of Life and The Biochemistry of Life on Earth

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1 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

2 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

3 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

4 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%

5 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%

6 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.

7 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 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

8 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.

9 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.

10 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.

11 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.

12 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.

13 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.

14 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.

15 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.

16 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.

17 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.

18 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).

19 The 20 Amino Acids Found in Living Organisms on Earth AMINO ACID* CHEMICAL FORMULA NUMBER OF ATOMS C 3 H 7 O 2 N L-ALANINE 13 C L-ARGININE 6 H 15 O 2 N 4 27 L-ASPARAGINE L-ASPARTIC ACID L-CYSTEINE L-GLUTAMIC ACID L-GLUTAMINE GLYCINE L-HISTIDINE L-ISOLEUCINE 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

20 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

21 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

22 X Y

23 NUCLEIC ACIDS 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)

24

25 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.

26 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.

27 Combinations of Bases in Singlet, Doublet, and Triplet Codes Singlet code Doublet code Triplet code ( 4 words ) (16 words ) (64 words ) A AA AG AC AT AAA AAG AAC AAT G GA GG GC GT AGA AGG AGC AGT C CA CG CC CT ACA ACG ACC ACT T TA TG TC TT ATA ATG ATC ATT GAA GAG GAC GAT GGA GGG GGC GGT GCA GCG FCC GCT GTA GTG GTC GTT CAA CAG CAC CAT CGA CGG CGC CGT CCA CCG CCC CCT CTA CTG CTC CTT TAA TAG TAC TAT TGA TGG TGC TGT TCA TCG TCC TCT TTA TTG TTC TTT

28 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

29 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 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.

30 DNA 23 CHROMOSOME PAIRS 1000 GENES.. CAC TCA AGA CCG TCA TCA... CODON SEQUENCE

31 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

32 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.

33 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

34 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)

35 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

36

37 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 (EXAMPLE: HORTA IN STAR TREK) CARBON SEEMS LIKE A BETTER CHOICE, BUT IS SILICON-BASED LIFE POSSIBLE? WE DON T KNOW.

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