Life in a BottleLife in a Bottle

Lecture Eleven, Feb. 10, 2003Lecture Eleven, Feb. 10, 2003

Course ProjectCourse Project

• Topic of your choosing related to Topic of your choosing related to class.class.

• Proposal (1-2 pages) Feb. 14, 2003. Proposal (1-2 pages) Feb. 14, 2003.

• Project background (3-5 pages) Mar. Project background (3-5 pages) Mar. 28, 2003. 28, 2003.

• Project (10 pages) April 25.Project (10 pages) April 25.

Pathfinder the Race to MarsPathfinder the Race to Mars

• 60 min video on web 60 min video on web site.site.

• 1996 Mars Global 1996 Mars Global Surveyor lunched to Surveyor lunched to orbit and map Mars. orbit and map Mars.

• Also Mars Pathfinder Also Mars Pathfinder with its small rover.with its small rover.

• These followed failed These followed failed Mars Observer in 1993.Mars Observer in 1993.

• See See Manyrovers_full.jpgManyrovers_full.jpg (note, this is a 7.4 MB (note, this is a 7.4 MB image)image)

The Doomsday AsteroidThe Doomsday Asteroid

• 60 min Video 60 min Video about impact of about impact of comet comet Shoemaker Levy Shoemaker Levy 9 with Jupiter 9 with Jupiter and present day and present day threat from threat from impacts.impacts.

• Keck Telescope iKeck Telescope infrared images nfrared images of collision. of collision.

Hubble Image of Impact Hubble Image of Impact PlumPlum

Impact site itself just out of site beyond Impact site itself just out of site beyond rimrim

Gamma Ray BurstsGamma Ray Bursts

• The Nova program The Nova program Death Stars Death Stars discusses Gamma discusses Gamma Ray bursts. These Ray bursts. These are the most are the most energetic explosions energetic explosions since the Big Bang. since the Big Bang. They have now They have now been detected been detected billions of light years billions of light years from Earth.from Earth.

Simulation of Simulation of collapse of giant collapse of giant rotating star to rotating star to produce two gamma produce two gamma ray jets.ray jets.

New Horizons Mission to New Horizons Mission to PlutoPluto

The Kuiper belt: Frontier of The Kuiper belt: Frontier of Solar SystemSolar System

Spacecraft will flyby Pluto Spacecraft will flyby Pluto and then on to a Kuiper belit and then on to a Kuiper belit object. See object. See http://pluto.jhuapl.eduhttp://pluto.jhuapl.edu

Origin of Life According to Origin of Life According to Michelangelo Michelangelo

Origin of life according to Mel Brooks. Real Media Origin of life according to Mel Brooks. Real Media clip of creation of life from clip of creation of life from Young Frankenstein

The Chemistry of LifeThe Chemistry of Life

• Start with very simple chemicals Start with very simple chemicals such as COsuch as CO22, H, H22O, NO, N22, NH, NH33..

• Temperature and pressure allow Temperature and pressure allow liquid Hliquid H22O.O.

• Energy source: could be ultraviolet Energy source: could be ultraviolet radiation from Sun, Lightening, radiation from Sun, Lightening, Chemical reactions.Chemical reactions.

• Somehow produce the building Somehow produce the building blocks of life. blocks of life.

Amino Acids: Building Blocks of Amino Acids: Building Blocks of LifeLife• Amino acids are chemical compounds with amine Amino acids are chemical compounds with amine

groups (containing nitrogen, N) and weak acid groups (containing nitrogen, N) and weak acid groups (HOgroups (HO22C) that can be linked together to form C) that can be linked together to form long chains called proteins.long chains called proteins.

• Example: Amino acid Alanine Example: Amino acid Alanine

HHOO CC

OO

CC

CC

NN

H H

HH

HH

HH

HH HH

Acid groupAcid group

Amine groupAmine group Chemistry Chemistry 101: Note, 4 101: Note, 4 bonds for C, 3 bonds for C, 3 bonds for N, 2 bonds for N, 2 for O and 1 for O and 1 for Hfor H

HHOO CC

OO

CC

CC

NN

H H

HH

HH

HH

HH HH

HHOO CC

OO

CC

CC

NN

H H

HH

HH

HH

HH HH

Two amino Two amino acidsacids

• The amine group of one amino acid can The amine group of one amino acid can react with the acid group of another to react with the acid group of another to produce a molecule of Hproduce a molecule of H22O and the joining O and the joining of the two. of the two.

Acid Acid grougroupp

Amine Amine groupgroup

HHOO CC

OO

CC

CC

NN

H H

HH

HH

HH

HH HH

HHOO CC

OO

CC

CC

NN

H H

HH

HH

HH

HH HH

OO CCCC

CC

NN

H H

HH

HH

HH

HH HH

HHOO CC

OO

CC

CC

NN

H H

HH

HH

HH

HH

Two amino acidsTwo amino acids

One longer chain that still has an amine and an acid One longer chain that still has an amine and an acid groupgroup

HH22O +O +

ThesThese e react react to to form form HH22OO

Proteins are Made of Amino Proteins are Made of Amino AcidsAcids• Amino acids have an amine group (N) and Amino acids have an amine group (N) and

an acid group (COan acid group (CO22H)H)• Can bind amino acids together to produce Can bind amino acids together to produce

long molecules called proteins.long molecules called proteins.• Proteins form the basis for life on Earth.Proteins form the basis for life on Earth.• Earth life uses proteins made from 20 Earth life uses proteins made from 20

different amino acids strung together in different amino acids strung together in definite orders.definite orders.

• Where did the amino acids come from?Where did the amino acids come from?• How were they put together in the correct How were they put together in the correct

order?order?

Life made from 20 amino Life made from 20 amino acidsacids

GlycineGlycine AlanineAlanine

ValineValine LysineLysine

Note, carbons at ends of lines and hydrogens are not Note, carbons at ends of lines and hydrogens are not shownshown

Red is oxygen (acid) and blue is nitrogen (amine) Red is oxygen (acid) and blue is nitrogen (amine) groupgroup

A ProteinA Protein

• To specify a unique protein you must specify To specify a unique protein you must specify which one of the 20 amino acids occurs first, which one of the 20 amino acids occurs first, which amino acid occurs 2which amino acid occurs 2ndnd and so on. and so on.

• A protein may be thousands of amino acids long.A protein may be thousands of amino acids long.• To specify the exact molecule one needs a long To specify the exact molecule one needs a long

string of thousands of numbers each of which string of thousands of numbers each of which goes from 1 to 20. For example, goes from 1 to 20. For example, 5-19-20-1-5-7-8-8-15-20-20-1-1-1-…5-19-20-1-5-7-8-8-15-20-20-1-1-1-…

• Example let 1 be Glycine, 2 be Alanie … So this Example let 1 be Glycine, 2 be Alanie … So this protein has amino acid #5 then #19, #20 and so protein has amino acid #5 then #19, #20 and so on for thousands of links in the long chain.on for thousands of links in the long chain.

The Left Hand of GodThe Left Hand of God

• A given amino acid A given amino acid can come in two can come in two mirror image forms.mirror image forms.

• Life on Earth only Life on Earth only uses the left handed uses the left handed form.form.

• We don’t We don’t understand the understand the origin of this origin of this chirality (Greek word chirality (Greek word for hand).for hand).

Origin of LifeOrigin of Life

• Where did the amino acids come from?Where did the amino acids come from?

• How is the information stored to specify How is the information stored to specify the sequence for each complex protein?the sequence for each complex protein?

• How is the information acted on to How is the information acted on to synthesis the proteins?synthesis the proteins?

• How do the complex proteins function to How do the complex proteins function to form a living organism?form a living organism?

Life is Old Life is Old

• Life arose about 3.8 Life arose about 3.8 billion years ago.billion years ago.

• Clear fossils in 3.5 Clear fossils in 3.5 billion year old rocks. billion year old rocks. Problem, few older Problem, few older rocks have survived.rocks have survived.

• Great bombardment Great bombardment and very hostile and very hostile conditions 4 billion conditions 4 billion years ago and years ago and earlier.earlier.

Isotopes and Age of LifeIsotopes and Age of Life

• A carbon atom has 6 electrons.A carbon atom has 6 electrons.

• Carbon nuclei therefore have six protons. Carbon nuclei therefore have six protons. They can also have either 6, 7 or 8 They can also have either 6, 7 or 8 neutrons to make neutrons to make isotopesisotopes of carbon of carbon 1212C, C, 1313C or C or 1414C. The superscript indicates the C. The superscript indicates the mass number A which is the sum of the mass number A which is the sum of the number of neutrons plus protons.number of neutrons plus protons.

• Isotopes have the same number of protons Isotopes have the same number of protons but different numbers of neutrons.but different numbers of neutrons.

Natural Carbon is: Natural Carbon is:

• 99% 99% 1212C and 1% C and 1% 1313CC• 1414C is radioactive with a half life of about C is radioactive with a half life of about

5000 years. Thus all primordial 5000 years. Thus all primordial 1414C has C has long since decayed.long since decayed.

• Most chemical reactions are the same for Most chemical reactions are the same for different isotopes and will not change the different isotopes and will not change the ratio of ratio of 1212C to C to 1313C.C.

• Reactions important for life work very Reactions important for life work very slightly faster for slightly faster for 1212C than for C than for 1313C because C because it is lighter and so moves faster.it is lighter and so moves faster.

1313C is change in isotope C is change in isotope ratioratio1313C is very small change in ratio of C is very small change in ratio of 1313C to C to 1212C C

compared to the normal value of this ratio.compared to the normal value of this ratio.• Carbon in living material today is slightly Carbon in living material today is slightly

depleted in depleted in 1313C.C.• Interesting evidence that carbon in 3.8 billion Interesting evidence that carbon in 3.8 billion

year old samples also show this slight depletion. year old samples also show this slight depletion. • Suggests that life is at least 3.8 billion years old.Suggests that life is at least 3.8 billion years old.• Note, we have no undisturbed rocks on earth Note, we have no undisturbed rocks on earth

older than about 3.5 billion years old.older than about 3.5 billion years old.

Origin of Amino Acids?Origin of Amino Acids?

• Amino acids can be Amino acids can be made from simple made from simple inorganic chemicals inorganic chemicals such as CHsuch as CH44, NH, NH33, H, H22O…O…

• But how was this done?But how was this done?

• Were the original amino Were the original amino acids extraterrestrial? acids extraterrestrial? Amino acids are found in Amino acids are found in some meteorites.some meteorites.

Allende MeteoriteAllende Meteorite

Miller ExperimentMiller Experiment

• Stanley Miller, a graduate Stanley Miller, a graduate student of Harold Urey, in student of Harold Urey, in 1953 placed H1953 placed H22O, HO, H22, NH, NH33, CH, CH44 in a flask. in a flask.

• He constantly boiled and re-He constantly boiled and re-condensed the Hcondensed the H22O and O and added an electrical discharge added an electrical discharge for energy.for energy.

• Spectacular results: produced Spectacular results: produced lots of amino acids and other lots of amino acids and other organic compounds.organic compounds.

Miller ExperimentMiller Experiment

• Miller thought he was simulating a Miller thought he was simulating a thunderstorm on the primitive thunderstorm on the primitive Earth.Earth.

• He put HHe put H22, NH, NH33, CH, CH44… in the exp. … in the exp. because these had just been seen because these had just been seen (via spectroscopy) in the (via spectroscopy) in the atmosphere of Jupiter. atmosphere of Jupiter.

• We now think early atmosphere We now think early atmosphere was COwas CO22 and had no free and had no free hydrogen. Without free hydrogen hydrogen. Without free hydrogen the experiment does not work and the experiment does not work and few amino acids are made. few amino acids are made.

JupiterJupiter

Miller ExperimentMiller Experiment

• Suggests that amino acids Suggests that amino acids are easy to make under are easy to make under the right conditions and the right conditions and may be common through may be common through out the Universe.out the Universe.

• Thus the building blocks of Thus the building blocks of life may be common!life may be common!

• However, we don’t know However, we don’t know where the correct where the correct conditions occurred. The conditions occurred. The lack of Hlack of H22 on the early on the early Earth appears to be a real Earth appears to be a real problem.problem.

• Perhaps amino acids were Perhaps amino acids were made off the Earth in a site made off the Earth in a site with free hydrogen.with free hydrogen.

DNA the Memory of LifeDNA the Memory of Life

• How does life store the considerable How does life store the considerable information needed to specify a information needed to specify a complex protein?complex protein?

• This information is encoded in This information is encoded in molecules of DNA.molecules of DNA.

• DNA is made from four base pairs: DNA is made from four base pairs: adenine, thymine, guanine, and adenine, thymine, guanine, and cytosine on a double helix backbone.cytosine on a double helix backbone.

The Four Base Pairs in DNAThe Four Base Pairs in DNA

• The molecule The molecule adenine (a) always adenine (a) always pairs with thymine pairs with thymine (t) and guanine (g) (t) and guanine (g) pairs with cytosine pairs with cytosine (c).(c).

• The information in The information in DNA is stored in DNA is stored in which of the four which of the four (a,c,g,t) occur at (a,c,g,t) occur at each position along each position along the double helix. the double helix.

DNADNA

• Double helix structureDouble helix structure

• Genetic code in order of Genetic code in order of the four bases (a,c,g,t) the four bases (a,c,g,t) arranged along one of arranged along one of the helix strands.the helix strands.

• For example, start at For example, start at the bottom with the the bottom with the strand starting to the strand starting to the left: a c t g a t g g g t a left: a c t g a t g g g t a c t t c t t

• Information in 2Information in 2ndnd strand is the same.strand is the same.

DNA can Replicate!DNA can Replicate!

• Double helix “unzips” and Double helix “unzips” and then new base pairs are then new base pairs are added to each single added to each single stand to make two stand to make two identical copies of the identical copies of the original DNA molecule.original DNA molecule.

• This allows cells to divide This allows cells to divide with full copies of the with full copies of the genetic code in each cell.genetic code in each cell.

• The structure of DNA helps The structure of DNA helps explain reproduction. explain reproduction.

DNA Codes for ProteinsDNA Codes for Proteins

• DNA is not a protein and it is not made of DNA is not a protein and it is not made of amino acids.amino acids.

• DNA codes for the synthesis of proteins. DNA codes for the synthesis of proteins. Thus DNA stores the information needed Thus DNA stores the information needed to make a complex protein.to make a complex protein.

• Modern cells have complex machinery to Modern cells have complex machinery to read the DNA information and assemble read the DNA information and assemble amino acids to make proteins.amino acids to make proteins.

• How did early life do this before the How did early life do this before the complex machinery was evolved?complex machinery was evolved?

For next timeFor next time

• Read chap. 4 of Jakosky about the Read chap. 4 of Jakosky about the earliest life and read “Vital Dust", earliest life and read “Vital Dust", pages 1-23 in course packet about pages 1-23 in course packet about origin of life.origin of life.

• Think about your course project. Think about your course project. Proposal (1-2 pages) due Feb. 14, Proposal (1-2 pages) due Feb. 14, 2003.2003.