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Chemistry of Life. What are the important molecules in cells? What do they do? Why are these particular molecules used? Could other molecules do the job just as well? How / where were these molecules formed? (prebiotic synthesis). Biological Macromolecules Thousands of atoms Proteins

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slide1

Chemistry of Life

What are the important molecules in cells?

What do they do?

Why are these particular molecules used?

Could other molecules do the job just as well?

How / where were these molecules formed? (prebiotic synthesis)

slide2

Biological Macromolecules

Thousands of atoms

Proteins

Polysaccharides

Nucleic Acids

Building Block Organic Molecules

Tens of atoms

Amino acids

Sugars

Nucleotides

Lipids

Small Molecules

A few atoms

CO2

H2O

NH3, N2

Prebiotic chemistry

Polymerization

slide3

Building Blocks 1 - Amino acids

20 different types of amino acids (different R groups)

peptide bond

polymers called polypeptides or proteins

slide4

Glycine

Gly G

The simplest amino acid

Building up the simpler amino acids

Alanine

Ala A

Valine

Val V

Aspartic acid

Asp D

Serine

Ser S

Leucine

Leu L

Proline

pro P

Threonine

Thr T

Isoleucine

Ile I

Glutamic acid

Glu E

Hydrophilic Acidic

Hydrophobic

slide5

More complex amino acids

Lysine

Lys K

Phenylalanine

Phe F

Asparagine

Asn N

Cysteine

Cys C

Arginine

Arg R

Tyrosine

Tyr Y

Glutamine

Glu Q

Methionine

Met M

Tryptophan

Trp W

Histidine

His H

Amines

Sulphur containing

Aromatic

Hydrophobic

Hydrophilic Basic

protein function enzymes
Protein function - enzymes

Enzymes are catalysts of specific chemical reactions.

Enzymes control metabolism

Why use proteins as catalysts?

Versatile set of chemical groups

Active sites. Substrate binding. Transition states

Specific structures

Folding dependent on sequence

Aldolase with substrate bound

slide8

Protein dynamics – e.g. actin/myosin in muscles

chemical energy => work

ATP synthase in mitochondria and bacteria

A proton gradient across the membrane (created by electron transport chain) causes drives the motor to turn and drives synthesis of ATP.

Storage of chemical energy.

Gee whizz!

slide9

What can’t proteins do?

Replication. Information Storage. Heredity

Central dogma: DNA to RNA to proteins.

Amino acids may be easy to form by prebiotic synthesis but proteins as we know them can only exist after the evolution of translation and the genetic code.

RNA world theory (to be discussed later) – RNAs for both catalysis and information storage.

Cellular organisms always use DNA for information storage. Viruses can use RNA or DNA

Exception? Prion proteins:

Does this count as replication?

Normal form Scrapie form

building blocks 2 sugars
Building blocks 2 – Sugars

Ribose and Deoxyribose are 5-carbon sugars.

Glucose is a 6-carbon sugar.

Sugars can assemble to form polymers (starch, cellulose….)

Function: Metabolism. Energy storage. Structural roles.

Neither catalysis nor information storage.

nucleic acids are polymers composed of nucleotides
Nucleic acids are polymers composed of nucleotides.

Nucleic acids can store information

Double stranded DNA. Both strands contain information to make the other.

Single stranded RNA. Two-stage replication: plus to minus to plus (viruses).

slide13

RNA can also fold to complex 3d structures

Catalytic RNAs (ribozymes) are known – both natural and synthetic

Part of Group II intron structure

building blocks 4 lipids
Building blocks 4 – Lipids

Simple fatty acids

Amphiphiles = polar head + hydrophobic tail

Typical phospholipid in a modern cell membrane

lipids
Lipids

Self-assembly

Micelles

Bilayers

Cell membrane

Fluid and Flexible

Compartmentalization

Selectively permeable

prebiotic synthesis of organic molecules miller urey experiment 1953
Prebiotic synthesis of organic molecules Miller-Urey experiment (1953)

Began with a mixture of CH4 , NH3, H2O and H2.

Energy source = electric spark or UV light.

Obtained 10 amino acids.

Soup recipe!

prebiotic synthesis
Prebiotic synthesis

Begin with simple molecules thought to be common on early Earth

Use reaction conditions thought to exist on early Earth

Show that biomolecules are synthesized

Syntheses have been found for most of the building block molecules.

Purines can be built up from HCN

Sugars can be built up from CH2O (formaldehyde)

Issues:

What were conditions on early Earth? Atmosphere?

Where was the chemistry happening?

Could everything form at the same time?

Concentration?

Stability?

atmospheres and chemistry
Atmospheres and Chemistry

reducing: CH4 , NH3, H2O, H2.

or CO2, N2, H2 or CO, N2, H2

There is hydrogen gas and/or hydrogen is present combined with other elements (methane, ammonia, water)

neutral: CO or CO2 , N2 , H2O

no hydrogen or oxygen gas

oxidizing: O2, CO2, N2

oxygen gas present

Prebiotic chemists favour reducing atmospheres.

Yields in Miller-Urey exp are higher and more diverse in reducing than in neutral atmospheres. Doesn’t work in oxidizing atmosphere.

planetary atmospheres
Planetary Atmospheres

Major element in universe is H (big bang) so doesn’t it make sense that atmosphere was reducing?

Jupiter retains original mixture: H2, He + small amounts CH4, NH3, H2O

  • Smaller planets lose H2
  • New atmosphere created by outgassing from interior
  • Geologists & Astronomers favour an intermediate atmosphere.
  • Venus - 64 Earth atmospheres pressure! Mostly CO2 and N2
  • Carbonates in sedimentary rocks on Earth suggest previously lots of CO2

So maybe Miller and Urey were wrong? :-(

Current Earth: Mostly N2, O2 + small amounts of CO2 H2O – changed by life.

Mars: very low pressure – mostly CO2 and N2

slide20

Alternative suggestion – Hydrothermal vents

Sea water passes through vents.

Heated to 350o C. Cools to 2o C in surrounding ocean.

Supply of H2 H2S etc.

Fierce debate as to whether these conditions favour formation or breakup of organic molecules (Miller & Lazcano, 1995)

slide21

Organic compounds in meteorites

Most widely studied meteorite is the Murchison meteorite. Fell in Australia in 1969. Carbonaceous chondrite.

Contained both biological and non-biological amino acids

Both optical isomers (later shown to be not quite equal)

Compounds are not contamination

Just about all the building block molecules have now been found in carbonaceous meteorites (Sephton, 2002).

Astrochemistry: molecular clouds; icy grains; parent bodies of meteorites....

Delivery by: dust particles; meteorites; comets....

slide22

What to make of all this....?

If we believe in a heterotrophic origin of life, organic molecule supply is crucial.

Observation of organic molecules in meteorites and in space suggests that the chemistry does work!

What were the relative amounts synthesized on Earth and delivered from space?

Maybe delivery from space is very minor but the meteorites are telling us about the chemistry that was happening on Earth at the same time.

Maybe delivery from space is a large part. But the same molecules are supplied as are required by the heterotrophic theory.

Hydrothermal synthesis seems less well documented, and is also rather ‘local’....

Heterotrophic/autotrophic issue still not resolved...(more later)

slide23

Comparison of amino acid frequencies produced non-biologically

concentrations normalized relative to Gly

10 amino acids are found in the Miller-Urey experiments. Very similar ones are also found in meteorites (Murchison and Yamato), an Ice grain analogue experiment, and other places. Maybe these are ‘early’ amino acids that were available for use by the first organisms.

The other 10 are not seen. Maybe these are ‘late’ amino acids that were only used when organisms evolved a means of synthesizing them biochemically.

Higgs & Pudritz : http://www.physics.mcmaster.ca/~odonnedv/OIbook/

slide24

Glycine

Gly G

The early group are simpler and are thermodynamically less costly

Alanine

Ala A

Valine

Val V

Aspartic acid

Asp D

Serine

Ser S

Leucine

Leu L

Proline

pro P

Threonine

Thr T

Isoleucine

Ile I

Glutamic acid

Glu E

Hydrophilic Acidic

Hydrophobic

slide25

The late group are more complex and are more thermodynamically costly

Lysine

Lys K

Phenylalanine

Phe F

Asparagine

Asn N

Cysteine

Cys C

Arginine

Arg R

Tyrosine

Tyr Y

Glutamine

Glu Q

Methionine

Met M

Tryptophan

Trp W

Histidine

His H

Amines

Sulphur containing

Aromatic

Hydrophobic

Hydrophilic Basic

slide26

Why are there only 20 amino acids?

Weber and Miller (1981)

Only  amino acids not  and 

Always one  hydrogen

Some non-biological amino acids are found in meteorites and Miller-Urey exp with concentrations as high as the biological ones

examples:

Norvaline? - don’t know

Homoserine? - lactonization