• Biology is the scientific study of life

• The cell is the basic unit of life & every organism

consists of one or more cells
• Despite tremendous diversity, coding instructions
of all living organisms are written in nucleic acids
• We can define life by listing its basic components, but
still more is necessary
• Scientists have settled on five qualities that, in
combination, constitute life
• Biology is the scientific study of life
• The cell is the basic unit of life & every organism
consists of one or more cells
• Despite tremendous diversity, coding instructions
of all living organisms are written in nucleic acids
• We can define life by listing its basic components, but
still more is necessary
• Scientists have settled on five qualities that, in
combination, constitute life
• Can we create life synthetically?
• Biology is the scientific study of life
• The cell is the basic unit of life & every organism
consists of one or more cells
• Despite tremendous diversity, coding instructions
of all living organisms are written in nucleic acids
• We can define life by listing its basic components, but
still more is necessary
• Scientists have settled on five qualities that, in
combination, constitute life
• Can we create life synthetically?
• Human Genome
Project cost ~$3
billion
• Celera sequences
human genome for
$300 million
• D. radiodurans can
withstand up to
5kGy
• 1 Gray = 1 Joule γ
radiation absorbed
per kilogram
• Biology is the scientific study of life
• The cell is the basic unit of life & every organism
consists of one or more cells
• Despite tremendous diversity, coding instructions
of all living organisms are written in nucleic acids
• We can define life by listing its basic components, but
still more is necessary
• Scientists have settled on five qualities that, in
combination, constitute life
• Can we create life synthetically? Yes.
• Scientists have settled on five qualities that, in
combination, constitute life
• Scientists have settled on five qualities that, in
combination, constitute life
1. Life is organized into a tremendous hierarchical pattern
ATOM
The smallest chemical
unit of a type of pure
substance (element).
Example: Carbon atom
MOLECULE
A group of joined atoms.
Example: DNA
ORGANELLE
A membrane-bounded
structure that has a
specific
function within a cell.
Example: Chloroplast
CELL
The fundamental
unit of life.
Example: Leaf cell
TISSUE
A collection of specialized
cells that function in a
coordinated fashion.
Example: Epidermis of leaf
ORGAN
A structure consisting
of tissues organized to
interact and carry
out specific functions.
Example: Leaf
ORGAN SYSTEM
Organs connected
physically or
chemically
that function
together.
Example:
Aboveground
part of a plant
ORGANISM
A single living individual.
Example: One acacia tree
ORGANISM
A single living individual.
Example: One acacia tree
POPULATION
A group of the same species of organism
living in the same place and time.
Example: Multiple acacia trees
COMMUNITY
All populations that occupy
the same region.
Example: All populations
in a savanna
ECOSYSTEM
The living and
nonliving
components of an
area.
Example: The
savanna
BIOSPHERE
The global ecosystem;
the parts of the planet
and its atmosphere
where life is possible.
• Emergent properties
(new complex
Sheet of
functions) arise at each Endothelial endothelial
level of biological cell cells

organization

• The capillary has

properties that its
components alone lack

• Emergent properties Capillary

Multiple Agent Simulation System in Virtual Environment
result from all forms of
“And going back to that famous case of the first battle that
organization Endothelial
we did where we had agents running away...
Red blood -- StephencellRegelous
cell (From vfxBlog interview)
• Scientists have settled on five qualities that, in
combination, constitute life
1. Life is organized into a tremendous hierarchical pattern
2. Life requires energy
Energy
from
sunlight

Producers extract energy

and nutrients from the
nonliving environment.
 Heat
Consumers obtain
energy and nutrients by
eating other organisms.
Energy
from
sunlight
 Heat

Energy
from
sunlight
Heat
Heat

Decomposers: consumers
that obtain nutrients from
dead organisms and organic
wastes.
 Heat

Energy
from Note:
sunlight Heat is lost
Heat
Heat every time
energy is
transferred.

Heat
• Scientists have settled on five qualities that, in
combination, constitute life
1. Life is organized into a tremendous hierarchical pattern
2. Life requires energy
3. Life maintains internal consistency
• Cells or organisms maintain an equilibrium state
through homeostasis
• Scientists have settled on five qualities that, in
combination, constitute life
1. Life is organized into a tremendous hierarchical pattern
2. Life requires energy
3. Life maintains internal consistency
• Cells or organisms maintain an equilibrium state
through homeostasis
4. Life reproduces, grows and develops
• Some organisms reproduce asexually, others
reproduce sexually and combine characteristics
• Scientists have settled on five qualities that, in
combination, constitute life
1. Life is organized into a tremendous hierarchical pattern
2. Life requires energy
3. Life maintains internal consistency
• Cells or organisms maintain an equilibrium state
through homeostasis
4. Life reproduces, grows and develops
• Some organisms reproduce asexually, others
reproduce sexually and combine characteristics
• Scientists have settled on five qualities that, in
combination, constitute life
1. Life is organized into a tremendous hierarchical pattern
2. Life requires energy
3. Life maintains internal consistency
• Cells or organisms maintain an equilibrium state
through homeostasis
4. Life reproduces, grows and develops
5. Live evolves: In biology, adaptation occurs through
mutation & natural selection; in engineering, you make
a mock up and troubleshoot
• Now we can catalog and classify life using taxonomy
(the naming & classification of organisms)
• Living organisms are classified into one of three
domains and then further classified from there
• Now we can catalog and classify life using taxonomy
(the naming & classification of organisms)
• Living organisms are classified into one of three
domains and then further classified from there
• What have we learned from the scientific study of life?
• Like all matter, organisms are composed of elements,
BUT not all elements are in living matter…
• Only about 25 elements are essential to life
• Bulk elements make up the vast majority of every
living cell; trace elements are sparse
• What have we learned from the scientific study of life?
• Like all matter, organisms are composed of elements,
BUT not all elements are in living matter…
• Like all matter, living matter contains atoms of these
essential elements chemically bonded to one another

• Each molecule or compound formed is not alive, but

they are utilized to maintain the life of an organism
• What have we learned from the scientific study of life?
• Like all matter, organisms are composed of elements,
BUT not all elements are in living matter…
• Like all matter, living matter contains atoms of these
essential elements chemically bonded to one another
• Water is essential to life!
• Water has extraordinary properties because it’s polar
and can H-bond
• Water is cohesive
• Water is essential to life!
• Water has extraordinary properties because it’s polar
and can H-bond
• Water is cohesive
• Water is a solvent
• Water is essential to life!
• Water has extraordinary properties because it’s polar
and can H-bond
• Water is cohesive
• Water is a solvent
• Water regulates temperature
allowing for homeostasis
• Water is essential to life!
• Water has extraordinary properties because it’s polar
and can H-bond
• Water is cohesive
• Water is a solvent
• Water regulates temperature
allowing for homeostasis
• Water expands as it freezes
• Water participates in life’s
chemical reactions
• In addition to water, carbon-based organic molecules are
essential to life
• They are often polymers of monomeric subunits

Nucleic acid
polymer Monomer

Carbohydrate
polymer

Monomer Monomer

Protein
polymer
• In addition to water, carbon-based organic molecules are
essential to life
• They are often polymers of monomeric subunits
• In addition to water, carbon-based organic molecules are
essential to life
• They are often polymers of monomeric subunits
• Living organisms utilize polymers to make more
complex macromolecules with specialized functions
• Carbohydrates: energy storage, structure
• Lipids: membranes, energy storage, signaling
• Proteins: structure, locomotion, transport, storage,
catalysis and many more functions
• Nucleic acids: information storage and transmission
• Carbohydrates are sugars; simple sugars like
monosaccharides are joined to form disaccharides…
• Complexity grows from there giving polysaccharides
• All lipids are hydrophobic and do not dissolve in water
• Lipids are also known as fats
• But some are used in building membranes and chemical
signaling like cholesterol and testosterone
• Proteins are complex and highly versatile
• Membrane proteins,
hemoglobin, keratin,
polymerases,
antibodies,
enzymes, etc. etc.
• A protein is a chain of amino acids linked together by
peptide bonds to form one or more polypeptides
• We can make some of the 20 naturally occurring amino
acids from scratch, but we get half—the essential amino
acids—from the proteins we eat
• Protein shape is critical for function!
• A protein is a chain of amino acids linked together by
peptide bonds to form one or more polypeptides
• We can make some of the 20 naturally occurring amino
acids from scratch, but we get half—the essential amino
acids—from the proteins we eat
• Protein shape is critical for function!
• Proteins are vulnerable to heat, pH, salts, etc. that can
denature them and render them nonfunctional
• Nucleotide monomers make up long nucleic acid
polymers like deoxyribonucleic acid (DNA) or
ribonucleic acid (RNA)
• DNA is the data storage molecule in
cells and encodes the “blueprints of
life”
• RNA serves multiple roles in the
utilization of the genetic information
stored in DNA
• Cell theory: (1) organisms are made up of 1+ cell(s), (2)
the cell is the fundamental unit of life, and (3) cells come
from preexisting cells
• Cells are small
• Cells all have certain features in common:
• DNA & RNA
• Ribosomes
• Proteins
• Cytosol/cytoplasm
• Cell Membrane
• Membranes are central to life
• They make it possible to and maintain the
exchange of nutrients into and out of the cell
• Also control the ratio of surface area to volume
• Used to only be prokaryotic (“before” nucleus) and
eukaryotic (“true” nucleus) cells
• However, prokaryotes were divided into domains
bacteria and archaea

• Bacteria are the most abundant and diverse organisms

on Earth
• Critical as decomposers & producers, yet structurally
simple
• Nucleoid: cell’s circular DNA molecule congregates
• Most have a rigid cell wall for protection, structural
rigidity (e.g., to prevent lysis if too much water is
absorbed), and shape
• Some have means of
motion like those that
have a flagellum
• Archaean cells resemble bacterial cells in many ways
• Nucleoid: cell’s circular DNA molecule congregates
• Most have a rigid cell wall for protection, structural
rigidity (e.g., to prevent lysis if too much water is
absorbed), and shape
• Some have means of motion like those that have a
flagellum
• However, archaea contain biochemicals that are different
than bacteria or eukaryotes
• Ribosomes are more similar to eukaryotes
• Considered to be closest relative to eukaryotes
• Domain eukarya is very diverse (e.g., animals, yeasts,
mushrooms & other fungi, plants, and protists)
• All are larger than bacteria & archaea and all share many
cellular features
• Most important difference is the presence of a
membrane-bound nucleus and organelles
• An animal cell
• A plant cell
• Note:
Cell wall
Chloroplasts
• Domain eukarya is very diverse (e.g., animals, yeasts,
mushrooms & other fungi, plants, and protists)
• All are larger than bacteria & archaea and all share many
cellular features:
• A cell membrane separates each cell from its
surroundings
• Membranes are composed of a phospholipid bilayer and
proteins that provide selective permeability
• Some prescribe to the fluid mosaic model

• Transport proteins,
• Enzymes,
• Recognition proteins,
• Adhesion proteins, and
• Receptor proteins…

…all float freely within the

plane of the membrane
• Organelles have specialized functions and carry out the
work of the cell
• Many form a coordinated endomembrane system (e.g.,
nuclear envelope, ER, Golgi apparatus, lysosomes,
vacuoles, & cell membrane)
• “Connected” by vesicle transport
• System enables cells to produce, package, distribute
and release complex mixtures of biochemicals
 • Nucleus is the site
of gene expression
• mRNA exits nuclear
envelope through
nuclear pores
• Nucleolus also
provides ribosomes
through pores

• System enables cells to produce, package, distribute

and release complex mixtures of biochemicals
 • Secreted proteins are
synthesized at the
rough endoplasmic
reticulum
• (Soluble proteins in
free ribosomes)
• Lipids are made in the
smooth ER

• System enables cells to produce, package, distribute

and release complex mixtures of biochemicals
• System enables cells to produce, package, distribute
and release complex mixtures of biochemicals
 • Proteins from the
ER pass through
the Golgi apparatus
• Complete folding
and mature
• Enzymes in Golgi
also add sugars to
proteins/lipids
• Golgi sorts and
packages materials

• System enables cells to produce, package, distribute

and release complex mixtures of biochemicals
• System enables cells to produce, package, distribute
and release complex mixtures of biochemicals
• Besides producing molecules, eukaryotic cells break
them down in specialized membranous compartments
• Lysosomes, vacuoles, and peroxisomes are cellular
digestion centers
• Lysosomes: contain break-down enzymes made in
the RER and directed by the Golgi
• Besides producing molecules, eukaryotic cells break
them down in specialized membranous compartments
• Lysosomes, vacuoles, and peroxisomes are cellular
digestion centers
• Lysosomes: contain break-down enzymes made in
the RER and directed by the Golgi
• Vacuoles: “lysosome” of the plant cell; also fills with
water to apply turgor pressure to the cell wall and
keep the plant cell rigid
• Besides producing molecules, eukaryotic cells break
them down in specialized membranous compartments
• Lysosomes, vacuoles, and peroxisomes are cellular
digestion centers
• Lysosomes: contain break-down enzymes made in
the RER and directed by the Golgi
• Vacuoles: “lysosome” of the plant cell; also fills with
water to apply turgor pressure to the cell wall and
keep the plant cell rigid
• Peroxisomes: contain several types of enzymes to
dispose of toxic substances; originate in ER (not
Golgi) and contain different enzymes
• Some organelles are the site of energy transduction or
production in a cell
• Photosynthesis occurs in chloroplasts in plant cells
• Some organelles are the site of energy transduction or
production in a cell
• Photosynthesis occurs in chloroplasts in plant cells
• Double membrane system
• Mitochondria extract energy from nutrients
gives tremendous surface
area on which to conduct
chemical reactions
• Like chloroplasts, mito-
chondria have their own
DNA
• Inherited maternally
• Eukaryotic cells contain a cytoskeleton, an intricate
network of protein “tracks” and tubules
• Actin fibers or micro-
filaments provide
strength for cells to
survive stretching or
compression
• Intermediate filaments
function is a similar
way and help some
bind cells together
• Microtubules have
many functions
• Plant cells have plasmodesmata: channels connecting
adjacent cells for intercellular exchange of nutrients, etc.
• Animal cells may use an extracellular matrix to hold cells
close to one another or junctions to connect cells
• Tight junctions fuse cells
together (e.g., blood-brain
barrier)
• Adhering junctions connect
adjacent cells like “spot
welds” by utilizing
intermediate filaments
• Gap junctions act as protein
channels that link the
cytoplasm of adjacent cells;
allows many cells to act in
unison (like heart muscle)