biochemistry

1. HBC1011 Biochemistry I
Trimester I, 2018/2019
Lecture 2 & 3 – Biochemical evolution
Ng Chong Han, PhD
MNAR1010, 06-2523751
chng@mmu.edu.my

2. Overview
• Key organic molecules
• Reproduction, variation and selective pressure
• Energy transformation
• Cells’ response to changes in their environment
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3. Biochemical evolution
1. The initial generation of some of the key molecules of life—nucleic
acids, proteins, carbohydrates, and lipids—by nonbiological
processes.
2. The transition from prebiotic chemistry to replicating systems. With
the passage of time, these systems became increasingly
sophisticated, enabling the formation of living cells.
3. Conversion of energy from chemical sources and sunlight into forms
that can be utilized to drive biochemical reactions. With the
development of energy-conversion processes and biosynthetic
pathways, a wide variety of unicellular organisms evolved.
4. The evolution of mechanisms that allowed cells to adjust their
biochemistry to different environments. Organisms with these
capabilities could form colonies comprising groups of interacting
cells, and some eventually evolved into complex multicellular
organisms.
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4. Key Organics Molecules are used by
Living Systems
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Earth is approximately 4.5 billion years old.
Approximately 1 billion years after Earth’s formation,
life appeared.
• What is the major process needed to be taken
place before life exist?
– The synthesis of the organic molecules from
simpler molecules found in environment
• How did the building blocks of life come to be?

5. Synthesis of biomolecules
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• Prebiotic (nonbiological) world condition
– Earth early atmosphere was highly reduced, rich in
CH4, NH3, H2O & H2 & subjected to large amount of
solar radiation & lighting
• Can complex molecules be synthesized under these
conditions?
• In 1950’s, Stanley Miller & Harold Urey conducted a
chemical experiment in the lab.
Atmosphere= nitrogen + oxygen + argon +
carbon dioxide + trace gases

6. Figure 2.1 The Urey-Miller Experiment. An
electric discharge (simulating lighting)
passed through an atmosphere of CH4, NH3,
H2O, and H2 leads to the generation of key
organic compound such as amino acids.
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7. Life evolution
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Eukaryotic Cells Evolved from
Prokaryotes in Several Stages
Starting about 1.5 billion years ago, the
fossil record begins to show evidence of
larger and more complex organisms,
probably the earliest eukaryotic cells
Details of the evolutionary path from
prokaryotes to eukaryotes cannot be
deduced from the fossil record alone,
but morphological and biochemical
comparisons of modern organisms have
suggested a sequence of events
consistent with the fossil evidence.

8. Evolution of eukaryotes through
endosymbiosis
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9. Evolution requires reproduction,
variation, & selective pressure
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• Organic molecule life
• How did a living system arise and evolve?
– Before life appear, simple molecular system
complex chemical system
• How does evolution happen?

10. Process of evolution
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• Basic principles common to evolving system
– The ability to replicate/reproduce
– Variation
– Competition

11. Replicate/reproduce
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First, the most fundamental property of evolving systems is their
ability to replicate or reproduce.
Without this ability of reproduction, each “species” of molecule that
might appear is doomed to extinction as soon as all its individual
molecules degrade.
For example, individual molecules of biological polymers such as
ribonucleic acid are degraded by hydrolysis reactions and other
processes.
However, molecules that can replicate will continue to be
represented in the population even if the lifetime of each individual
molecule remains short.

12. Variation
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A second principle fundamental to evolution is variation
The replicating systems must undergo changes. After all, if a system
always replicates perfectly, the replicated molecule will always be
the same as the parent molecule. Evolution cannot occur.
Variation will produce differing populations of molecules.

13. Competition
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A third basic principle of evolution is competition
Replicating molecules compete with one another for available resources
such as chemical precursors, and the competition allows the process of
evolution by natural selection to occur.
Some variant offspring may, by chance, be better suited for survival and
replication under the prevailing conditions than are their parent
molecules.
The prevailing conditions exert a selective pressure that gives an
advantage to one of the variants.
Those molecules that are best able to survive and to replicate themselves
will increase in relative concentration. Thus, new molecules arise that are
better able to replicate under the conditions of their environment.
The same principles hold true for modern organisms.

14. Modern organism applied same principles:
Reproduce
show variation
compete for resources
those variants with a selective advantage
will reproduce more successfully
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15. Evolution
– In 1967, Sol Spiegelman: molecular evolution in the test tube.
– RNA molecules (3300 base) derived from a bacterial virus:
Bacteriophage Qβ
– Qβ replicase: catalyses the replication
– Normal condition: no changes of the composition of
population detected
– When selective pressure is applied: the composition of the
population of molecules change dramatically
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Is there any evidence that evolution can take place at
molecular level?

16. Figure 2.4 Evolution in a Test
Tube. Rapidly replicating species
of RNA molecules were generated
from Qβ RNA by exerting selective
pressure. The green and blue
curves correspond to species of
intermediate size that
accumulated and then became
extinct in the course of the
experiment.
Spiegelman mixed the replicase with a starting population of Qβ RNA molecules.
When selective pressure is applied e.g limiting the concentrations of precursors
or adding compounds that inhibit the replication process, however, the
composition of the population of molecules can change dramatically.
For example, decreasing the time available for replication from 20 minutes to 5
minutes yielded, incrementally over 75 generations, a population of molecules
dominated by a single species comprising only 550 bases. This species is
replicated 15 times as rapidly as the parental Qβ RNA (Figure 2.4).
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17. RNA or related precursors may have
been the first genes and catalysts
• RNA probably played a crucial role in prebiotic evolution, both
as catalyst and as information storage.
• In modern organisms, nucleic acids encode the genetic
information that specifies the structure of enzymes, and
enzymes catalyze the replication and repair of nucleic acids.
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The mutual dependence of these two classes of biomolecules brings
up the perplexing question: which came first, DNA or protein?
The answer may be: neither. The discovery that RNA
molecules can act as catalysts in their own formation
suggests that RNA or a similar molecule may have been
the first gene and the first catalyst.

18. RNA world hypothesis
• One of the earliest stages of biological evolution was the chance
formation whereby an RNA molecule catalyzes the formation of
other RNA molecules of the same sequence.
• The concentration of a self-replicating RNA molecule would
increase exponentially, as one molecule formed two, two
formed four, and so on.
• In the competition for nucleotides, the most efficient of the self-
replicating sequences would win, and less efficient replicators
would fade from the population.
• New variants of self-replicating RNA molecules developed, with
the additional ability to catalyze the condensation of amino
acids into peptides.
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19. RNA world hypothesis
• Occasionally, the peptide(s) thus formed would reinforce the
self-replicating ability of the RNA, and this could undergo further
modifications, generating even more efficient self-replicating
systems.
• The recent, remarkable discovery that, in the protein-
synthesizing machinery of modern cells (ribosomes), RNA
molecules, not proteins, catalyze the formation of peptide
bonds is certainly consistent with the RNA world hypothesis.
• DNA is a more stable molecule than RNA and thus a better
repository of inheritable information.
• Proteins proved to be versatile catalysts and, over time, took
over that function.
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20. DNA-genetic information storage
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• What is the selective advantage of DNA over RNA as the
genetic material?
– RNA with negative charges in the sugar phosphate
backbone: protect it from attack by hydroxide ions
– But 2’-hydroxyl group make it susceptible to base-
catalyzed hydrolysis
• The removal of the 2’ hydroxyl group from the ribose
decreases the rate of hydrolysis by approximately 100-fold
under neutral conditions and perhaps even more under
extreme conditions.
• Thus, the conversion of the genetic material from RNA into
DNA would have substantially increased its chemical stability.

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22. RNA world
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Life originated about 3.5 billion years
ago,
most likely with the formation of a
membrane-enclosed compartment
containing a self-replicating RNA
molecule.
The components for the first cell were
produced by the action of lightning and
high temperature on simple atmospheric
molecules such as CO2 and NH3.
The catalytic and genetic roles of the
early RNA genome were separated over
time, with DNA becoming the genomic
material and proteins the major catalytic
species.

23. Roles of mutation in evolution
• Variation is required for evolution
• Variation in living system: changes that alter the meaning of
genetic message: MUTATION
• Type of mutation:
- point mutation (single nucleotide),
- insertion/deletion of several nucleotides
• More rapid evolution: Gene duplication (entire section of the
coding material being duplicated )
• One of the duplication products may accumulate mutations and
eventually evolve into a gene with a different, but related,
function.
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24. 24

25. Energy Transformations are necessary
to sustain living systems
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Another major event in evolution was the ability to transform
environmental energy into forms capable of being used by living
systems.
Most of the reactions that lead to the biosynthesis of nucleic acids
and other biomolecules are not thermodynamically favorable
under most conditions; they require an input of energy to proceed.
Thus, they can proceed only if they are coupled to processes that
release energy.
How can energy-requiring and energy-releasing reactions be
linked?
How is energy from the environment transformed into a form
that living systems can use?

26. ATP: Energy currency
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• ATP: contains an array of 3 linked phosphates.
• When the bonds linking the phosphate are broken large
amount of energy released
• The energy released is used to promote other processes.
• Synthesis of ATP required energy (from the breakdown of
other chemicals).

27. 27

28. Amino acids are still broken down to produce ATP in modern
organisms. However, sugars such as glucose are a more commonly
utilized as energy source because they are more readily metabolized
and can be stored.
The most important process for the direct synthesis of ATP in modern
organisms is glycolysis
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29. Cells Were Formed by the Inclusion of
Nucleic Acids Within Membranes
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• Modern organisms are made up of cells
• Cell= composed of n.a, proteins & other biochemicals
surrounded by a membrane built from lipids
• Membrane completely enclose their contents: so cells have a
defined inside and outside

30. Phosphatidyl choline is a typical membrane-forming lipid.
Important feature: amphipathic contain hydrophobic &
hydrophilic components.
Hydrophobic: hydros, meaning water, and phobos, meaning fear
Hydrophilic: hydros, meaning water, and philia, meaning love,
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31. When such amphiphatic lipids are in contact with water, they
spontaneously aggregate to form specific structures such that
the hydrophobic parts of the molecules are packed together
away from water, whereas the hydrophilic parts are exposed to
the aqueous solution. The structure for membrane formation is
the lipid bilayer
Figure 2.14. Schematic View of a Lipid Bilayer. These structures define the
boundaries of cells.
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32. Compartmentalization required the
development of ion pumps
• Enclosure of n.a & protein within membranes
complications.
• Effect of osmosis
• Membrane: permeable to water & small nonpolar
molecules/ impermeable to macromolecules (n.a)
• When macromolecules are concentrated inside a
compartment osmotic forces drive water through
the membrane into the compartment.
Without counterbalancing effects, the flow of
water will burst the cell
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33. Figure 2.15. The “Osmotic Crisis.” A cell consisting of macromolecules surrounded
by a semipermeable membrane will take up water from outside the cell and burst.
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34. • Mechanisms for resisting these osmosis force:
- toughen cell wall &
- use of energy-dependent ion pumps.
• Ion pumps: lower the concentration of ions inside a cell relatively to the
outside this will induce an:
Ion gradient: unequal distribution of ions across an
inherently impermeable membrane.
Ion gradients can prevent osmotic crises, but they require energy to
be produced.
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35. Machinery for generating ion gradient: ATP driven proton pump
•Hydrolyze ATP to ADP & phosphate & utilize the energy
released to transport protons from the inside to the outside of
the cell.
•Most likely, an ATP-driven proton pump was the first existing
component of the machinery for generating an ion gradient
Figure 2.16. Generating an Ion Gradient. ATP hydrolysis can be used to drive the
pumping of protons (or other ions) across a membrane.
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36. Molecular Oxygen
• Molecular oxygen, a toxic by-product of some photosynthetic
processes, can be utilized for metabolic purposes.
• Photosynthesis generates electronic “holes” in the photo-
synthetic apparatus on the outside of the membrane.
• These holes are powerful oxidizing agents; that is, they have
very high affinities for electrons and can pull electrons from
many types of molecules.
• They can even oxidize water. Thus, for many photosynthetic
organisms, the electron donor that completes the
photosynthetic cycle is water.
• The product of water oxidation is oxygen gas—that is, molecular
oxygen (O2).
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37. Stromatolites from Hamylin Pool WA. The Stromatolites contain
Cyanobacteria and are found only in a few places on Earth. They are considered
to be the first photosynthetic organisms and evolved to generate molecular
oxygen 2.5 Billion years ago. The appearance of O2 dramatically transformed
earth and was the "Big Bang" for biology that ultimately led to complex
multicellular life.http://biology.anu.edu.au/slideshow/stromatolite/
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38. Through the action of oxygen, a glucose molecule can be
completely converted into carbon dioxide and water,
releasing enough energy to synthesize approximately 30
molecules
of ATP.
Glucose + 6O2 6CO2 + 6 H2O + energy
This number represents a 15-fold increase in ATP yield
compared with the yield from the breakdown of glucose in
the absence of oxygen in the process of glycolysis.
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Evolve mechanism: use O2 for favorable processes such as
oxidation of organic compounds (glucose)

39. Cells respond to changes
• Environments change rapidly, to survive, cells evolved
mechanisms for adjusting their biochemistry
• Adjustment changes:
- activity of pre-existing enzymes molecules,
- rates of synthesis of new enzyme molecules,
- membrane transport processes.
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40. Detecting signals at the cell surface.
• Receptor protein bind to chemical change of
protein structure detected at the inside surface
of cell membrane = chemical outside cell influence
events inside cell
• Signal transduction pathway: 2nd
messenger
spreading news
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1st
messenger
2nd
messenger

41. Intracellular & cellular movements
• The development of the ability to move was another
important stage in the evolution of cells capable of adapting
to a changing environment.
• Without this ability, nonphotosynthetic cells might have
starved after consuming the nutrients available in their
immediate vicinity.
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Filamentous
structures: flagella,
microfilaments &
microtubules

42. Some Cells Can Interact to Form Colonies
with Specialized Functions
• Single cells, competing for resources
• Form colonies, many interacting cell
• communicate by variety of signaling mechanisms &
respond to signals
• Modern organisms: Single cells and multicellular
colonies (differentiated cells)
• Differentiated cell: identical genetic but different
properties
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43. Figure 2.22 Unicellular to Multicellular Transition in Dictyostelium. This scanning electron
migrograph shows the transformation undergone by the slime mold Dictyostelium. Hundreds of
thousands of single cells aggregate to form a migrating slug, seen in the lower left. Once the slug
comes to a stop, it gradually elongates to form the fruiting body. [Courtesy of M. J. Grimsom and R. L.
Blanton, Texas Tech University.]
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44. Figure 2.23. Intracellular Signaling. Cyclic AMP, detected by cell-surface
receptors, initiates the formation of aggregates in Dictyostelium.
The transition from unicellular to multicellular growth is
triggered by cell–cell communication and reveals much about
signaling processes between and within cells.
Under starvation conditions, Dictyostelium cells release the signal
molecule cyclic AMP. This molecule signals surrounding cells by binding to
a membrane-bound protein receptor on the cell surface.
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45. Figure 2.24. Cell Differentiation in
Dictyostelium. The colors represent the
distribution of cell types expressing
similar sets of genes in the
Dictyostelium fruiting body.
The cells aggregate by following cAMP
gradients. Once in contact, they exchange
additional signals and then differentiate into
distinct cell types, each of which expresses the
set of genes appropriate for its eventual role
in forming the fruiting body
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46. The Development of Multicellular Organisms
Requires the Orchestrated Differentiation of Cells
• Multicellular organisms: 600 million years ago.
• i.e.: human, distinct cell make up different
organs
• Different cell types but identical DNA
sequence.
• Single cell complex organism: program of
regulated gene expression, cell division & cell
movement
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47. Figure 2.25. The Nematode
Caenorhabditis elegans. This
organism serves as a useful model
for development.
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48. A Possible Time Line for Biochemical Evolution. Key events are indicated.
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49. http://www.bbc.com/news/science-
environment-39117523
http://www.bbc.com/news/science-
environment-38800987

50. Summary
1. Key organic molecules are used by living
systems.
2. Evolution requires reproduction, variation, and
selective pressure.
3. Energy transformations are necessary to
sustain living systems.
4. Cells can respond to changes in their
environments.
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