Cells to Organisms 1

•	When we try to understand life’s humble beginnings, we are looking at the problem from the top down
•	Life is a fact, the structure of life is well known
•	Theories can only suggest possible pathways for a journey already complete

•	Most compelling argument for Miller-Urey models is that laboratory-created biomolecules so closely resemble those found in living systems today
•	Not strong scientific argument, but hard to dispute

•	A road map for the origin of life:
>	Separation from the environment by membranes
>	Metabolic pathways to generate energy for breaking chemical bonds
>	Information and control - RNA, DNA, Enzymes
>	Reproduction

•	Many chicken/egg questions…
>	Which came first, genes or proteins?
>	Which came first, metabolism or genes?

•	Building blocks of life are simple:
>	Amino acids
>	Sugars
>	Purines, pyrimidines
>	Lipids

•	Life’s monomers (single compounds) are usually combined into polymers (chains of monomers)
>	Proteins
>	Carbohydrates
>	Nucleic acids (ACGT)

•	Proteins provide 
>	Structure (hair, fingernails, muscle fibers)
>	Function (ex. flow of materials across membranes) 
>	Control of reactions, systems (enzymes, hormones)

•	Carbohydrates provide 
>	Structure (cellulose in plants)
>	Energy storage (starch in plants, glycogen in animals)
>	Form backbone of RNA (d-ribose) and DNA (deoxy-d-ribose)

•	Lipids (=glycerol + fatty acids) provide
>	Compartments - separate contents from outer world, keep them concentrated
>	Structure - cell membranes (phospholipids)
>	Function - organize flow of reactions (factory floor)
>	Energy storage - fats and oils

•	Cell membranes are critically important to normal cell function
•	Membranes are formed from phospholipids
•	One end is hydrophilic (head likes water), other end is hydrophobic (tail hates water)

•	Molecules line up in water in sheets or spheres
•	Spheres (called vesicles) could serve as tiny empty primordial “cell”

•	An alternate path for lipid bilayer membranes is aerosol formation
•	Single sheets of lipids could have formed on the surface of the water
•	Wind and water creates numerous tiny droplets - aerosols

•	Picked up as aerosols, they form single layer vesicles
•	When these eventually settle back into the water, second layer of lipids could form around the first (Dobson et al. 2000)

•	Murchison meteorite also provided support for Oparin’s ideas on coacervates
•	David Deamer found coacervate-like globules

•	Examination under the electron microscope showed that these coacervates were surrounded by a thin bilayered structure
•	Very suggestive of an early protocell membrane!

•	Primitive cellular membranes can be created in the lab, mix lipid molecules in water
•	Bit harder to do under prebiotic conditions

•	Cell membranes form the infrastructure of all living cells and their organelles - mitochondria, chloroplasts etc...
•	Life also requires metabolism (manufacture) and instructions (genes)

•	Did metabolism come first, or did genetic control mechanisms come first?
•	Now relatively separate functions in cells, unlikely to have been the case early on

•	Metabolism is the total of all the chemical processes that maintain life
•	Making complex biomolecules from free energy sources (like light) and available spare parts (small molecules), or taking them apart to use the energy stored in their chemical bonds

•	Several hypothetical models of early metabolic evolution
•	Must have been some simple set of cyclic reactions, adding or subtracting carbon compounds at each stage
•	Many ideas, but little evidence so far…

•	All living things are assembled from the same basic classes of compounds
•	How are these compounds created in living cells?

•	Instructions for creating, assembling compounds are stored in RNA or DNA
>	Genotype, actual genetic instructions
>	Phenotype, external expression of coded instructions

•	Chromosomes are made up of coiled coils of very long strands of DNA
•	Genes are sections of chromosomes, long stretches of DNA or RNA that code for making a particular protein

•	Chromosomes become visible in the cell just before the cell divides
•	By the time they become visible, the chromosomes have already duplicated themselves

•	Each gene codes for a single protein
•	Each protein is made up of a linear series of amino acids
•	Genes code for the sequence of amino acids used to build each protein

•	DNA (deoxyribonucleic acid) - two strands in a coiled helix, each made up of a series of organic compounds called nucleotides

•	RNA (ribonucleic acid) is a single strand of nucleotides
•	Nucleotides are attached to a backbone of sugar and phosphate molecules

•	Nucleotides form complementary base pairs
>	Adenine (A) pairs with Thymine (T)
>	Guanine (G) pairs with Cytosine (C)
>	Uracil (U) substitutes for Thymine (T) in RNA, so A/U and G/C for RNA

•	Each of the 20 amino acids is coded for by a sequence of three nucleotides (codon)
•	There are 4*4*4 = 64 possible codons that could be represented in DNA or RNA
•	Many codons code for the same amino acid, so the system is redundant

•	Why only 20 amino acids?
•	Many more, but their properties aren’t good
>	Don’t join together in smooth chains
>	Functional (side) groups not diverse, active

•	Properties of compounds depend on
>	Three dimensional structure (lock and key)
>	Pattern of electrical charges on outer surface (attract or repel other molecules)
•	Protein synthesis from amino acids can generate infinite molecular diversity from a small number of building blocks (20)

•	Protein synthesis starts with the creation of a mirror image of each strand of DNA
•	This mirror image is a single strand of messenger RNA (mRNA)

•	Messenger RNA moves from the nucleus out to the cytoplasm

•	Ribosomes attach to mRNA
•	Ribosomes mainly consist of special RNA called ribosomal RNA (rRNA)
•	Ribosomes move along the strand of mRNA, read each sequence of three (codon)

•	Transfer RNA (tRNA) has two binding sites, one is an anticodon, the other attaches to the appropriate amino acid
•	Transfer RNA carries the amino acids to the ribosomes to be attached to the growing chain

•	Once the amino acids are assembled in a row, their positive and negative areas attract or repel each other
•	Amino acid chain spontaneously folds up into a particular shape (electrically stable)
•	The final 3-dimensional shape gives each protein its special properties

•	Higher level structure is built into the sequence of amino acids
•	Doesn’t require extra energy to curl into shape - nifty!
•	Process took 3.5 billion years of trial and error!!

•	Each gene codes for one protein
>	Structural proteins - cell membranes, myosin (muscles) etc…
>	Hormones - proteins that act as chemical messengers
>	Enzymes - most proteins are enzymes

•	Evolution of proteins with catalytic properties (enzymes) was a huge leap forward
•	Genes use enzymes to orchestrate the  complex interlocked networks of chemical reactions that make up a living cell

•	Enzymes are catalysts - they affect chemical reactions, but are not changed by reactions
•	Catalysts have charged areas that attract two molecules, hold them in place so they react
•	Catalysts then separate - each enzyme molecule can catalyze several reactions

•	Enzymes control the direction of reactions -many chemical reactions are reversible
•	Enzymes cause reactions to occur within a narrow range of temperature and pressure
•	Enzymes greatly increase reaction rates
•	Enzyme amount controls amount of product

•	Genes can control growth, development, reproduction etc.
>	By controlling how much of each enzyme is made (amount of catalyst)
>	When an enzyme is made (what enzymes are active at any given time)
>	Can direct traffic, make things happen in a certain way, at a certain time…

•	It is unlikely that early life was based on DNA
•	DNA is a complex molecule, requiring several enzymes to zip it/unzip it, copy it
•	First life must have been based on something simpler

•	Ideal chemical basis for early life would 
>	Carry information
>	Act as a catalyst
>	Reproduce itself

•	Thomas Cech & Stanley Altman discovered that RNA can act as an enzyme
•	Received the Nobel Prize in 1989 for their discovery
•	Opened a new path of speculation on the origin of life - the RNA World

•	RNA is simpler than DNA, easier to form in the lab
•	Many viruses are composed only of RNA (but can’t live without a working cell)
•	RNA can act as a catalyst to form other types of RNA molecules

•	Ribozyme = RNA molecules that catalyze the formation of other RNA molecules
•	Traditional view, only proteins could act as catalysts

•	“RNA world” hypothesis fills in many missing pieces of this puzzle
>	Many types of RNA found in cells, all with different functions (mRNA, rRNA, tRNA)
>	RNA can reproduce itself, small chains (~14 bases long) can be formed in the lab
>	Could explain origin of protein synthesis

•	RNA attached to a solid surface “hunches up” to form a series of hills and valleys
•	Mellersh showed that only certain amino acids fit into these “valleys”
•	RNA on solid surface kinks to expose groups of three RNA bases - origin of triplet codon??

•	May also explain another long-standing problem
•	Lab chemicals are a mixture of left-handed, right-handed forms
•	Life is composed only of the left-handed forms of organic compounds

•	RNA world may explain the ‘handedness” of life
•	Only left-handed forms of amino acids (l-chiral) can fit into these RNA valleys

•	Problems with RNA world hypothesis
>	Not easy to make nucleotides (base + sugar + phosphate) under primordial conditions
>	RNA already a pretty complex molecule itself
•	Must have been an even simpler pre-RNA world…

•	One possible scenario recently proposed by Nick Platts – PAH World
•	PAH – polycyclic aromatic compound,
•	Carbon atoms that form a cyclic ring, other atoms and groups of atoms can attach to the sides of such rings

•	Very common compounds in nature
•	Like lipids they have hydrophilic and hydrophobic ends (attract or repel water molecules = ampiphilic)
•	Like lipids, therefore, they can “self organize”
•	Form stacks of sheet-like compounds

•	Stacks tend to rotate over one another, sheer off small groups of chemicals that might bond to them
•	So favors attachment of “flat” molecules, like purines and pyrimidines (nucleotide bases)

•	PAH molecules in effect could have provided the first scaffolding from which a strand of RNA could constructed
•	Just need to add a “backbone” analogous to the sugar/phosphate backbone of modern RNA/DNA

•	(Hud 2013) takes a different approach, using molecules that are simpler than modern nucleotides
•	Nucleotides don’t pair together unless attached to a polymer backbone (sugar/phosphate)

•	How could modern nucleotides that need polymers to pair together have been selected for? (chicken/egg)
•	Implies an earlier and simpler set of nucleotides
•	Hud created simple ”proto-RNA bases” that spontaneously assembled into linear stacks, like a primitive gene

•	Life is more than a collection of chemical reactions 
•	Life is about organization
•	Organization requires structure
•	Cells provide structure

•	Cellular structure includes:
>	Machines to do work (amino acids, proteins)
>	Separation from environment - closed factory to assemble parts, keep them in proper relative order (cell membranes, organelles)
>	Blueprints / Instructions - RNA, DNA

•	Modern cells are extremely complex
•	Complexity reflected in number of genes added since the LCA, last common ancestor
>	Increased 10 fold over the first 2.5by (~500 to ~6,000 genes
>	Increased 6 fold again in last 1 by (evolution of sex, multicellularity etc)

•	We still don’t know the minimum number of genes an organism needs to function
•	E. coli has ~4,100 genes, strip them away one by one, only 302 are essential
•	Mycoplasma genitalium has only 475 genes, Tremblaya princeps gets by with 120

•	The biggest evolutionary leaps in the history of life were not the evolution of dinosaurs, or flowering plants, or even the evolution of man…
•	Most important transitions occurred at or below the level of the single cell