NSCI 314 LIFE IN THE COSMOS 4 – Basic Properties of Life and The Biochemistry of Life on Earth Dr....
-
date post
21-Dec-2015 -
Category
Documents
-
view
218 -
download
0
Transcript of NSCI 314 LIFE IN THE COSMOS 4 – Basic Properties of Life and The Biochemistry of Life on Earth Dr....
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
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 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.