Planets & LifePlanets & LifePHYS 214PHYS 214

Dr Rob ThackerDr Rob ThackerDept of Physics (308A)Dept of Physics (308A)

thacker@astro.queensu.cathacker@astro.queensu.caPlease start all class related emails Please start all class related emails

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Today’s LectureToday’s Lecture Biochemistry and DNABiochemistry and DNA

Chemical basis of lifeChemical basis of life Alternative chemistriesAlternative chemistries Sugars to DNASugars to DNA

LAWKILAWKI In the rest of the course we will In the rest of the course we will

frequently refer to life similar to that frequently refer to life similar to that on Earthon Earth Carbon based, water solventCarbon based, water solvent

To save time, we’ll refer to this as To save time, we’ll refer to this as “Life as we know it” or LAWKI“Life as we know it” or LAWKI

The elements: in life, on The elements: in life, on Earth, and in the universe Earth, and in the universe

Table 1.1 from Gilmour & Sephton (G&S from Table 1.1 from Gilmour & Sephton (G&S from here on) shows the elemental abundances of here on) shows the elemental abundances of the Universe, Earth (total), crust, ocean, and the Universe, Earth (total), crust, ocean, and human beings human beings

Human beings have a very different proportion Human beings have a very different proportion than their terrestrial environs than their terrestrial environs

The implications are: The implications are: The chemistry of life is innate and not simply a result The chemistry of life is innate and not simply a result

of what chemicals are available of what chemicals are available There is, for example, something special about carbon chain There is, for example, something special about carbon chain

chemistry, water as a solvent... chemistry, water as a solvent... Beware, it was thought at one point that oxygen based Beware, it was thought at one point that oxygen based

chemistry was chemistry was requiredrequired The chemicals in LAWKI are to be found though out The chemicals in LAWKI are to be found though out

the universe, so the the universe, so the potential potential for life elsewhere is for life elsewhere is great great

In the solar system H & He are the predominant elements

In the Earth (as a whole), O is the most abundant, closely followed by Fe.

The Earth’s crust has comparatively low amount of Fe, but much higher amounts of Si and Al

Organic ChemistryOrganic Chemistry Originally organic chemistry referred to the Originally organic chemistry referred to the

molecules to be found only in and via lifemolecules to be found only in and via life Until urea synthesized by Wohler in 1824 (“organic” Until urea synthesized by Wohler in 1824 (“organic”

molecule synthesized from “inorganic” materials) molecule synthesized from “inorganic” materials) Now we think of organic chemistry as the complex Now we think of organic chemistry as the complex

chemistry of the carbon atom chemistry of the carbon atom Biologically, carbon tends to form molecules with H,  O Biologically, carbon tends to form molecules with H,  O

and N -- and to a lesser extent P (nucleic acids) and S and N -- and to a lesser extent P (nucleic acids) and S (aminos)  [collectively called CHONPS]. (aminos)  [collectively called CHONPS].

Carbon chemistry gives rise to a large variety of Carbon chemistry gives rise to a large variety of stable, but not inert, molecules stable, but not inert, molecules Potential for information storage and many reactionsPotential for information storage and many reactions

In many cases smaller molecules In many cases smaller molecules monomersmonomers can can be chained (polymerized) together to form longer be chained (polymerized) together to form longer molecules, molecules, polymerspolymers

What about alternatives to What about alternatives to carbon?carbon?

Carbon's versatility due partly to its 4 valence electrons. Next obvious choice would be Silicon, also 4 valence electrons

Carbon vs SiliconCarbon vs Silicon Chemistry of Si much Chemistry of Si much lessless flexible flexible than Cthan C

C can form C can form double bondsdouble bonds, Si can't: , Si can't: less varietyless variety though Si though Si cancan form form polymerspolymers ( (e.g.e.g. silicones with silicones with

Si,O)Si,O) C-C bonds C-C bonds twice as strongtwice as strong as Si-Si bonds: as Si-Si bonds:

carbon chains carbon chains more stable more stable ((silanessilanes Si SinnHH2n+22n+2 compared to compared to alkanesalkanes C CnnHH2n+22n+2))

Silicon reacts Silicon reacts very strongly very strongly withwith oxygen to oxygen to form a protective layer that is unstable only form a protective layer that is unstable only above temps > 940 K above temps > 940 K e.g.e.g. silane (SiH silane (SiH44) only forms when T > 1000K. SiH) only forms when T > 1000K. SiH44

very unstable: very unstable: decomposes into SiOdecomposes into SiO22 in presence in presence of oxygen or water vapourof oxygen or water vapour

Compare to CHCompare to CH44, which is much more stable, which is much more stable Jupiter: HJupiter: H22O, CHO, CH44, NH, NH33, PH, PH33, but , but no no SiHSiH44

Life based on Si seems Life based on Si seems improbableimprobable

SiOSiO22 (silicon equivalent of CO (silicon equivalent of CO22) is not helpful:) is not helpful:

solid below 2000 C (too high for stable polymers). solid below 2000 C (too high for stable polymers). A Si-based organism would exhale sand!A Si-based organism would exhale sand!

very insolublevery insoluble except in hydrofluoric acid except in hydrofluoric acid cf. COcf. CO22, which easily dissolves in water, and remains a gas , which easily dissolves in water, and remains a gas

down to -75 C. This means that Si will stay down to -75 C. This means that Si will stay locked uplocked up in in SiOSiO22, and not available for “organic” uses., and not available for “organic” uses.

On the Earth, Si is ~600 times more abundant than On the Earth, Si is ~600 times more abundant than C, but life is carbon-based not silicon-based. No C, but life is carbon-based not silicon-based. No silanes/silicones in comets, meteorites, or silanes/silicones in comets, meteorites, or interstellar cloudsinterstellar clouds

“Devil in the Dark”

Life stranger than fiction?Life stranger than fiction?

Shewanella oneidensisDiscovered in 1988Energy source is hydrogen or formaldehydeBreathes rocks! Mn oxides or Iron oxides

SolventsSolvents Solvents are important for:Solvents are important for:

dissolvingdissolving chemical compounds, to allow chemical compounds, to allow transport of nutrients and carrying off of waste.transport of nutrients and carrying off of waste.

as a as a mediummedium in which chemical reactions can take in which chemical reactions can take placeplace

to to regulate temperaturesregulate temperatures in organisms in organisms

solvents need to solvents need to remain liquidremain liquid for a large range for a large range of temperature and pressureof temperature and pressure

Comparison of possible Comparison of possible solventssolvents

Note water can be supercooled down to -42 C at atmospheric pressure. You needvery pure water and the container to be very still though. Once motion begins anda crystal nucleus is formed the rest of the water will crystallize almost immediately.

Ammonia – liquid at temperatures that are too low for promoting rapid reactionsMethyl alcohol, can be very reactive, latent heat of vapourization quite low too

SolventSolvent Liquid Liquid temperaturtemperature range / Ce range / C

Heat Heat Capacity/ J Capacity/ J

KK-1-1 g g-1-1

Heat of Heat of vapourizativapourization/ kJ gon/ kJ g-1-1

WaterWater -50 to 110 -50 to 110 4.2 4.2 2.5 2.5 AmmoniaAmmonia -78 to -33 -78 to -33 5.15.1 1.3 1.3 Methyl Methyl AlcoholAlcohol

-94 to 65 -94 to 65 2.52.5 1.21.2

Water as a solventWater as a solvent It is a good It is a good solventsolvent: dissolves things well: dissolves things well Has a high Has a high heat capacity heat capacity and and latent heat of latent heat of

vaporizationvaporization latter latter twicetwice that of ammonia and methyl alcohol that of ammonia and methyl alcohol water environment water environment more stable more stable against temperature changesagainst temperature changes water is an excellent water is an excellent temperature regulator temperature regulator (can absorb large (can absorb large

amounts of heat); important for maintaining amounts of heat); important for maintaining reaction ratesreaction rates e.g.e.g. sweating twice as efficient sweating twice as efficient

Since HSince H22O is a polar molecule it will tend to dissolve O is a polar molecule it will tend to dissolve polar solvents by forming weak hydrogen bondspolar solvents by forming weak hydrogen bonds Molecules that can be dissolved in water are dubbed Molecules that can be dissolved in water are dubbed

hydrophyllichydrophyllic Molecules that have a low affinity and are relatively insoluble in Molecules that have a low affinity and are relatively insoluble in

water are hydrophobicwater are hydrophobic Non-polar solvents required for dissolving non-polar moleculesNon-polar solvents required for dissolving non-polar molecules

More about waterMore about water Water has unique property: it Water has unique property: it expands expands

when it freezeswhen it freezes ice layer on top with liquid water underneath ice layer on top with liquid water underneath also means that ice can burst cells!also means that ice can burst cells! ammonia-based life forms could have advantage ammonia-based life forms could have advantage

for interstellar travelfor interstellar travel Water has very high surface tension, Water has very high surface tension,

important for creating important for creating membranesmembranes Water also provides Water also provides UV shieldingUV shielding, via , via

dissociation of Hdissociation of H22O and formation of OO and formation of O33 So it looks like water is really our best betSo it looks like water is really our best bet

Sugars and Sugars and Carbohydrates Carbohydrates

The most abundant single class The most abundant single class of organic substances. of organic substances.

Made of carbon, oxygen, Made of carbon, oxygen, hydrogen (H to O ratio of about hydrogen (H to O ratio of about 2 to 1 as in water) 2 to 1 as in water)

Sugars form ring like Sugars form ring like structures in waterstructures in water

Monomers of sugar are linked Monomers of sugar are linked into carbohydrate polymersinto carbohydrate polymers

Water is lost in the processWater is lost in the process In animals the chief carb is In animals the chief carb is

glycogen glycogen This is a polymer of glucose This is a polymer of glucose

(see Fig 1.5 G&S). (see Fig 1.5 G&S). Plants are chiefly cellulose Plants are chiefly cellulose

(making up the cell walls, also (making up the cell walls, also polymer of glucose) polymer of glucose)

Cellulose is the most common Cellulose is the most common bio-organic substance making bio-organic substance making up about 50% of biologic up about 50% of biologic carbon if we ignore the carbon if we ignore the possibility of a major possibility of a major contribution from the 'deep hot contribution from the 'deep hot biosphere' biosphere'

C OHH

HCH

OGlycolaldehyde

C OHH

HCH

OCH

OH

CH

OHCH

OHD-ribose

OH = hydroxyl group

LipidsLipids Made of (usually 3) fatty acids

(CnH2n+1COOH -- e.g. acetic acid with n=1) and a 3-carbon glycerol backbone (C3H5)

Used for energy storage and transport for higher organisms (plants and animals) also role as steroids

(hormones) testosterone, cholesterol

More fundamental role in cell membranes as phospholipids

Phosphate group induces polar behaviour

Membranes are result of their amphiphilic (one end likes water, other end doesn't) nature

COOH

“Carboxyl group”

Amino AcidsAmino Acids Remember: acids Remember: acids donatedonate H H++: bases : bases

acceptaccept H H++

Acids release HAcids release H++ in solution (ionization) in solution (ionization) There are twenty amino acids (Fig. There are twenty amino acids (Fig.

1.6 G&S) found in life (as monomer 1.6 G&S) found in life (as monomer units in proteins, see below) on the units in proteins, see below) on the Earth Earth

They all share a They all share a carboxyl groupcarboxyl group, , and and amine groupamine group attached to an attached to an alpha carbon atom alpha carbon atom

Other than the most simple amino Other than the most simple amino acid (glycine) all show a acid (glycine) all show a handedness (chirality -- see Section handedness (chirality -- see Section 1.6.2, G&S) 1.6.2, G&S)

C H

O

C OH

N H

H

R

Amine group –basic since it canaccept an H+

Carboxyl group –acidic since it can donate an H+

Variable

Aside: ChiralityAside: Chirality The amino acids in LAWKI are left-handed

Non-biological is symmetrical -- equally left and right-handed

This allows us one way of knowing, for example, when studying amino acids found on meteorites to know if they are: potentially terrestrial contamination (ie if left-handed), non-biological (equal), or potentially due to extraterrestrial life (right-handed)

This depends in part on assumptions, i.e. if life on meteorite not possible...

Sugars also display chirality, and life has chosen right-handed (D) as in e.g. ribose and deoxyribose. L type sugars are frequently (but not always) tasteless Smell different too

In 1953, Stanley Miller and Harold In 1953, Stanley Miller and Harold Urey set up an experiment to test Urey set up an experiment to test whether a simulation of the whether a simulation of the primordial Earth ocean+atmosphere primordial Earth ocean+atmosphere could reproduce amino acidscould reproduce amino acids

The “atmosphere” includedThe “atmosphere” included CH CH44, NH, NH3 3 and was subject and was subject

to to sparks sparks designed to simulate designed to simulate lightninglightning

Allowed to run for 1 weekAllowed to run for 1 week Produced nearly 20 amino Produced nearly 20 amino

acids + numerous other acids + numerous other organic compounds organic compounds

Miller-Urey & the Miller-Urey & the Murchison MeteoriteMurchison Meteorite

Murchison meteorite: a carbon rich meteorite (carbonaceous chondrite) preserved from the formation of the solar system

Fell in 1969 in the town of Murchison, just outside Melbourne, Australia

Analysis of the amino acids on the meteorite showed a remarkable to match to the relative productions of amino acids in the Miller-Urey experiment

Main problem with Miller-Urey is that there is expected to have been much less NH3 and CH4 than assumed Makes synthesis of amino acids harder

ProteinsProteins Chains of amino acids bond to form Chains of amino acids bond to form

polypeptides* -- in the context of life these are polypeptides* -- in the context of life these are proteins proteins

Proteins are the stuff from which are bodies Proteins are the stuff from which are bodies are primarily made are primarily made If our bodies were dehydrated, proteins would If our bodies were dehydrated, proteins would

make 75% of the remaining mass make 75% of the remaining mass In our bodies, proteins make up (In our bodies, proteins make up (e.g.e.g.): ):

Enzymes (insulin), Enzymes (insulin), Collagen (skin, cartilage, blood vessels) Collagen (skin, cartilage, blood vessels) Hemoglobin (part of blood which carries oxygen) Hemoglobin (part of blood which carries oxygen)

*peptide bond formed when carboxyl group reacts with an amine group to form an amide linkage

Information carrying Information carrying potential in a proteinpotential in a protein

A protein chain with N amino acid units A protein chain with N amino acid units can be made in 20can be made in 20NN different ways different ways

Thus protein has a vast potential to Thus protein has a vast potential to store (genetic?) information store (genetic?) information Given an average protein length of 100 Given an average protein length of 100

amino acids there are 20amino acids there are 20100100 (about equal to (about equal to 1010130130 -- cf. the visible universe with about -- cf. the visible universe with about 10108080 particles) possible different proteins particles) possible different proteins Yet most organisms make do with less than Yet most organisms make do with less than

10,000 10,000

Bases, Nucleosides, Bases, Nucleosides, Nucleotides and ATP Nucleotides and ATP

DNA and RNA (slide 26) are built from monomer units (nucleotides) which are in turn composed of: A phosphate group (PO4) A sugar

deoxyribose for DNA (deoxyribonucleic acid)

ribose for RNA (ribonucleic acid)

A nitrogen-containing compound called a nitrogeneous base

In DNA four different nucleotides are used, each with the same sugar and phosphate groups but different bases

The four bases…The four bases… Nucleotide names:

adenosine (A) corresponding base: adenine thymidine (T) corresponding base: thymine cytidine (C) corresponding base: cytosine guanosine (G) corresponding base: guanine

The nucleotides with additional phosphate groups bonded to them are called, for example: diphosphate, triphosphate etc. e.g.: adenosine diphosphate (ADP)

adenosine triphosphate (ATP) ATP is the basic energy currency of life

DNA-RNADNA-RNA Structure of DNA and RNA

(Watson and Crick, 1953) The nucleotides form a chain by

linking phosphates to sugars producing a sugar-phosphate backbone (polymer) with side bases Somewhat akin to proteins, which

are a glycine polymer backbone with various amino side groups.

The proteins are actually more capable of carrying info as they can link together 20 independent amino acids.

Base-pairing (Watson-Crick pairs): C always bonds with G A always bonds with T (DNA), U

(RNA) The bonded chains spiral together

in the famed "double helix" in DNA

Base pairings:

A T T A G C C G

ReplicationReplication One of the necessary roles of the genetic factor One of the necessary roles of the genetic factor

is to replicate itself.  How does DNA do this? is to replicate itself.  How does DNA do this? The double helix (parent) splits down the The double helix (parent) splits down the

middle like a zipper coming undonemiddle like a zipper coming undone The base-pairing implies that each strand carries The base-pairing implies that each strand carries

the same information the same information Nucleotides floating around pair up with the Nucleotides floating around pair up with the

appropriate bases to form two new (daughter) appropriate bases to form two new (daughter) strands strands Both of these steps are mediated by enzymes Both of these steps are mediated by enzymes

(proteins) (proteins) See later discussion of mitosis and meiosisSee later discussion of mitosis and meiosis

The genetic codeThe genetic code The bases of the DNA form

a triplet code whereby each unit of three bases (codon) represents an amino acid

In a triple of four possible choices there are 43 = 64 possibilities This is greater than the 20

amino acids (plus a stop) so there is some redundancy

e.g. glycine is represented by GGT, GGC, GGA, or GGG

If we went to a doublet code only 42 = 16 possibilities, so not enough to code for the aminos needed.

Summary of lecture 19Summary of lecture 19 Chemistries based on anything other than Chemistries based on anything other than

carbon seem unlikely at bestcarbon seem unlikely at best Similarly, water seems uniquely positioned as Similarly, water seems uniquely positioned as

an effective solvent that has numerous other an effective solvent that has numerous other benefits (high heat capacity and so forth)benefits (high heat capacity and so forth)

Organic monomers can be easily synthesized in Organic monomers can be easily synthesized in conditions similar to the primordial Earthconditions similar to the primordial Earth However, strong solar UV means there is probably However, strong solar UV means there is probably

very little NHvery little NH33 and CH and CH44 Much harder to produce amino acids in NMuch harder to produce amino acids in N22, CO, CO22 environment environment

Next lectureNext lecture Cell evolution & relation to Earth’s Cell evolution & relation to Earth’s

historyhistory Guest lecture next Friday (8Guest lecture next Friday (8thth March) by March) by

Dr Virginia Walker (Biology) on Dr Virginia Walker (Biology) on extremeophilesextremeophiles