BIOL10002 Lecture1 1 Slide

BIOL10002 – Biomolecules and Cells
Assoc Prof Joshua Heazlewood

School of Biosciences
Office: BioSciences 2, Room 305
Email: jheazlewood@unimelb.edu.au
Web: http://heazleome.org/
My research interests include:
• Plant cell walls

• Glycobiology
• Mass Spectrometry
BIOL10002 - Biomolecules and Cells Module 1: What is Life? 1

This subject will look at these big ideas
Evolution
The diversity of life can be explained by the process of evolution
Cells
Cells are the fundamental structural and functional unit of life
Information
Living systems have multiple mechanisms to store, retrieve,
and transmit information
Regulation
Biological processes are chemical in nature; biological organisms
maintain homeostasis
Interconnectedness
Living systems are interconnected and interacting

Background – Joshua Heazlewood
Plant Cell Walls
Fibre / nutrition Paper products
Timber
Biofuels
Clothes

Building a Wall
Golgi apparatus

Transporter activity assay (LC-MS based)
2
_________________________________
_________________________________
Mass Spectrometry 1, CMP1, CMP 11,
11, UDP- UDP-D-GlcNAc
D-GlcNAc
2, UMP2, UMP 12,

12, UDP- UDP-L-Araf
L-Araf
3, UDP-3, UDP-D-GalA 13, PAPS

D-GalA 13, PAPS
4, UDP-4, UDP-D-GlcA 14, GMP
D-GlcA 14, GMP
5, CMP-Neu5Ac15, AMP
5, CMP-Neu5Ac 15, AMP
6, UDP-6, UDP-L-Arap 16, GDP-
L-Arap 16, GDP-D-Man
D-Man
f
7, UDP-7, UDP-L-Rha 17, GDP-
L-Rha 17, GDP-L-Gal
L-Gal
8, UDP-8, UDP-D-Gal 18, GDP-

D-Gal 18, GDP-D-Glc
D-Glc
9, UDP-9, UDP-D-Glc 19, GDP-

D-Glc 19, GDP-L-Fuc
L-Fuc
10,
10, UDP- UDP-D-Xyl 20, ADP-
D-Xyl 20, ADP-D-Glc
D-Glc
_________
P-D-GlcNAc
12, UDP-L-Araf
S
P
P BIOL10002 - Biomolecules and Cells Module 1: What is Life? 5
This module will introduce evolution
Evolution
The diversity of life can be explained by the process of evolution
• The origin of life occurred by natural processes; life continues to evolve

within a changing environment.
• All organisms are connected by lines of descent from common
ancestry; barriers to reproduction foster divergence of lineages.
• Natural selection acts on phenotypic variation, generating adaptations.
• Evolution can occur as a result of processes unrelated to fitness.
• Human interventions can alter the course of evolution.

This module will focus extensively on cells
Cells
Cells are the fundamental structural and functional unit of life.
• All cells come from preexisting cells.

• The molecular and structural properties of cells define their function.
• Cells are bounded by a membrane and maintain internal environments
that differ from their external environments.
• Cells communicate with other cells.
• Cells are able to form organized units capable of more complex function

Module 1 – What is Life?
Lecture 1:
• Defining Life
Lectures 2 & 3:
• The building blocks of life
Lecture 4:
• Prokaryotes
Lecture 5 & 6:
• Eukaryotes

Lecture 1, Part 1: What is Life?
What you should know
• How do we define life – Part 1
• How did life begin on Earth – Part 2
• When did life arise on Earth – Part 3
• The connection between water and life – Part 3
• Evidence of early life on Earth – Part 3

What is Life?
• Composed of a common set of elements
• Grow and change
• Respond to the environment
• Are comprised of cells
• Use molecules and make new molecules Vs
• Extract energy and use it
• Contain genetic information
• Exist in populations and can evolve
• ……..other points (see Google / Biology text books)

Defining Life
• Composed of a common set of elements

• Grow and change
• Respond to the environment
• Are comprised of cells
https://science.sciencemag.org/content/339/6122/936

“Living Crystals”
“Here, we demonstrate a form of self-organization …. in a suspension of synthetic
photoactivated colloidal particles. They lead to two-dimensional "living crystals," which
form, break, explode, and re-form elsewhere.”
Light
TPM polymer colloidal
sphere with protruding
iron oxide cube Hydrogen peroxide Hydrogen peroxide
H2O2 H2O + O2
TPM = 3-methacryloxypropyl trimethoxysilane https://science.sciencemag.org/content/339/6122/936

Defining life is not always simple
Flocking birds are an example of self-organization in active living matter, a similar
process was also observed with the “living crystals”
https://giphy.com/gifs/satisfying-birds-cwn67Rp9Jq6hG

Life is a bit more complex
Vs

What about prions? (also Viroids)
Prions are misfolded proteins that can transmit their misfolded shape onto normal
variants of the same protein
Consensus – Not living
Protein (no DNA), but can replicate
• Prion diseases, also known as transmissible

spongiform encephalopathies (TSEs) i.e.
damage or disease that affects the brain
• Neurological diseases with a progressive

course - usually fatal
• See - mad cow disease

What about viruses?
Pros (alive) See Workshop 1
• Contain nucleic acids (as small as 2–3 kbp) Zombie Viruses
• Viruses can replicate (estimated 1031 virus particles in the oceans)
• Evolve and adapt to the environment
Cons (not alive)

• Viruses are not capable of independent replication
• Do not contain required metabolic processes to be considered “alive”

https://microbiologysociety.org/publication/past-issues/what-is-life/article/are-viruses-alive-what-is-life.html

End of Lecture 1, Part 1
See Activity - Prions


The Origins of Life on Earth
Can biological molecules be formed from
chemicals present in Earths early atmosphere?
Experiments conducted by Miller and Urey in

the 1950s sought to mimic conditions thought
to existed on Earth ~ 4 billion years ago
Early Earth atmosphere = “primordial soup”

Miller-Urey Experiments
A series of experiments (including some conducted at -80°C over 30 years)
have revealed that these early conditions on Earth could result in the
production of organic products:
• The bases present in DNA and RNA (A, C, G, T, U)
• All 20 amino acids found in proteins
• A range of 3- and 6- carbon sugars
• Fatty acids
• Vitamin B6, NAD and organic acids

Formation of protocells from fatty acids
Lipids can form “protocells” https://molbio.mgh.harvard.edu/szostakweb/movies.html

Lipid Building the protocell
bilayer
Nucleic acids
https://molbio.mgh.harvard.edu/szostakweb/movies.html
(RNA)
We have a protocell – but no photocopier

Alien Life – the Murchison meteorite
Life or its building blocks may have originated elsewhere
(presumably under similar conditions as that identified in the
Miller-Urey experiments) and arrived on Earth via meteorites
• Samples from a meteorite that landed in Australia

in 1969 near the Victorian town of Murchison (~2
hours North of Melbourne) were analysed
• Scientists took fragments immediately and analysed

the samples, identifying amino acids, DNA bases
and sugars

Hot off the press – extra extra!
Submitted on 22 Feb 2020
After analyzing samples from the

meteorite Acfer 086……..scientists
identified a protein and found that its
building blocks (side chains) differed
chemically from those found on proteins
from Earth
https://futurism.com/the-byte/scientists-discover-protein-meteorite

What forces created life on earth?
1. Life formed spontaneously on early Earth (a reducing

environment facilitated organic molecule formation,
such as DNA bases)
2. Extra-terrestrial origin – life from another planet or

comet (panspermia)

The cell theory is an important unifying theory
of biology
it states:
• Cells are the fundamental unit of life
• All living organisms are comprised of cells
• All cells come from pre-existing cells
• Modern cells evolved from a common ancestor

What do the similarities among living organisms
indicate?
• All life on Earth has a common ancestry
• Evidence points to a common origin of life on our planet

about 4 billion years ago
• All organisms have arisen from earlier, more primitive

forms over the past 4 billion years through the processes
of evolution
• Because all organisms are related, they share the same

genetic code, chemical composition, and cellular structure
(“biochemical unity of life”)

Evolution occurs by natural selection (Charles Darwin)
• Individuals in a species show a wide range of variation
• ‘Fitter’ individuals with characteristics best suited to the

environment are more like to survive and reproduce
(adaptations leading to differential reproduction)
• Given enough time, a species may evolve into a new form

See Activity – Protocells and Synthetic Biology


Life and water
While water is fairly common

in the universe, most of the
water is in the form of ice
Earth has an abundance of water and it

seems to have existed in a liquid form
from around 3.8 billion years ago

Water is the “Matrix of Life” - Szent-Győrgi
Water molecules
Structure of the Human
lysozyme protein
Water is the “universal solvent”
Solid water (ice) cannot act as a lubricant for the molecular processes of life, so the search
is on for liquid water - a commodity that is far more rare in the universe.

Life arose on Earth ~3.5 billion years ago
Pillow basalt
Evidence for liquid water on Earth (3.8 billion years ago)

Water and the moons of Jupiter (Europa)
A south polar water vapor plume on Europa is

shown in blue in this Hubble Space Telescope
data image, which is superimposed on a visible
light image of the Jupiter moon's leading
hemisphere.
"When we find water here on Earth — whether it be ice-covered lakes, whether it be

deep-sea hydrothermal vents, whether it be arid deserts — if there's any water, we've
found microbes" Brian Glazer (University of Hawaii)

Billions spent looking for extra-terrestrial life
• NASA – Curiosity/Mars Science Lab

• European Space Agency – Mars Express
• NASA - Looking at the Universe – Hubble
• European Space Agency – The Rosetta Mission – investigating comets
• NASA/ESA/ASI – Cassini-Huygens mission to Saturn and its moons
• NASA – The Kepler Mission & Spitzer Space Telescope – the search for
another earth or earth-like planet

When did life arise on Earth?
Life arose soon after the appearance of liquid water

The Cambrian Explosion
• A rapid diversification of life took
place approximately 541 million
years ago, which is commonly
referred to as the Cambrian
Explosion
• Most of the major animal groups

living today appeared during the
Cambrian
• For a long time, scientists had well

preserved fossils from this time
period but nothing earlier
• What did earlier life look like?

Stromatolites – often referred to as “living fossils”
Stromatolites thrive in the hyper-saline water of Hamelin Pools in Shark Bay,

Western Australia
Fossilized stromatolites – Grand Canyon

Fossilized cyanobacteria – 3.5 billion years old

3.7 billion year old fossilized stromatolites
Fossilized cyanobacteria
https://www.theguardian.com/science/2016/aug/31/oldest-fossils-on-earth-discovered-in-37bn-year-old-greenland-rocks-stromatolites

See Activity – The search for stromatolites

on Mars

Summary – Lecture 1
• How we define life is complicated and requires multiple
lines of evidence – but not simple (see viruses)
• Life arose through the formation of large molecules from

smaller molecules on early Earth (and /or beyond)
• Water is a key component associated with life we observe

on Earth
• Life arose on Earth after formation of liquid water
• Stromatolites are evidence of early types of life

Upcoming Lectures
The building blocks of Life
Lecture 2
• Nucleic Acids (DNA and RNA)
• Protein (the workhorse)
Lecture 3
• Carbohydrates (sugar)
• Lipids (bilayers)
• Membrane transport (moving through bilayers)

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BIOL10002 – Biomolecules and Cells

Assoc Prof Joshua Heazlewood

My research interests include:

• Plant cell walls

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 1

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 2

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 3

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 4

2, UMP2, UMP 12,

3, UDP-3, UDP-D-GalA 13, PAPS

8, UDP-8, UDP-D-Gal 18, GDP-

9, UDP-9, UDP-D-Glc 19, GDP-

• The origin of life occurred by natural processes; life continues to evolve

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 6

• All cells come from preexisting cells.

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 7

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 8

• How did life begin on Earth – Part 2

• When did life arise on Earth – Part 3

• The connection between water and life – Part 3

• Evidence of early life on Earth – Part 3

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 10

• Composed of a common set of elements

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 11

TPM = 3-methacryloxypropyl trimethoxysilane https://science.sciencemag.org/content/339/6122/936

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 12

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 13

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 14

• Prion diseases, also known as transmissible

• Neurological diseases with a progressive

• See - mad cow disease

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 15

• Evolve and adapt to the environment

Cons (not alive)

• Do not contain required metabolic processes to be considered “alive”

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 16

See Activity - Prions

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 17

• How did life begin on Earth – Part 2

• When did life arise on Earth – Part 3

• The connection between water and life – Part 3

• Evidence of early life on Earth – Part 3

Experiments conducted by Miller and Urey in

Early Earth atmosphere = “primordial soup”

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 19

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 20

Lipids can form “protocells” https://molbio.mgh.harvard.edu/szostakweb/movies.html

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 21

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 23

• Samples from a meteorite that landed in Australia

• Scientists took fragments immediately and analysed

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 24

After analyzing samples from the

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 25

1. Life formed spontaneously on early Earth (a reducing

2. Extra-terrestrial origin – life from another planet or

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 26

• All living organisms are comprised of cells

• All cells come from pre-existing cells

• Modern cells evolved from a common ancestor

BIOL10002 - Biomolecules and Cells Module 1: What is Life? 27

• Evidence points to a common origin of life on our planet