BIOL 183: Form and Function

Part 1: Plant Biology
 Every Carbon and Nitrogen atom in you…

… went through 
a plant first.

Carbon from CO2 is fixed directly into 

carbohydrates.  Nitrogen from N2 is fixed
by bacteria into amines (or created 
industrially and then added to the soil).
Genomic data from
over 1,000
uncultivated and
little known
organisms, together
with published
sequences are
used to infer an
expanded version
of the tree of life,
with Bacteria,
Archaea and
Eukarya.

Hug et al. 2016. A new view of the tree of 
life.  DOI: 10.1038/NMICROBIOL.2016.48
Excavata – unicellular, flagella
Archaeplastida – red algae, green algae, land plants
Chromalveolata – some protists, brown algae (SAR in text)
Amoeboza – amoeboid protists (Unikonta + Rhizaria in text)
Opisthokonta – animal and fungus  (Unikonta in text)

Note how this grouping is NOT the same 
as in your textbook – why? 
 Figure 28.2

Excavata 5 µm Archaeplastida

20 µm
25 µm

Diplomonads

Excavata
Parabasalids
Euglenozoans
Stramenopiles

Diatoms
Golden algae
Brown algae SAR 50 µm Unikonta
Dinoflagellates
Alveolates
Eukaryotes

SAR
Apicomplexans
Ciliates
Radiolarians
Rhizarians

Forams
Cercozoans

100 µm
Red algae
Archaeplastida

Chlorophytes
Green
algae

Charophytes
Plants
100 µm
Amoebozoans Opisthokonts

Slime molds
Tubulinids
Entamoebas
Unikonta

Nucleariids
Fungi
Choanoflagellates
Animals

© 2017 Pearson Education, Inc.

Boxed groups have photosynthesis in common
Diplomonads

Excavata
Parabasalids

Euglenozoans

Stramenopiles
Diatoms
Golden algae

Brown algae

Dinoflagellates
Alveolates

SAR
Apicomplexans

Ciliates
Radiolarians
Rhizarians

Forams

Cercozoans

© 2017 Pearson Education, Inc.

Figure 28.2ab

Red algae

Archaeplastida
Chlorophytes

Green
algae
Charophytes

Plants
Amoebozoans

Slime molds

Tubulinids

Entamoebas

Unikonta
Nucleariids
Opisthokonts

Fungi

Choanoflagellates

Animals
© 2017 Pearson Education, Inc.
 No animals… except…

Sea Slug able to use

chloroplasts from algae to make
carbohydrates.
Elysia chlorotica, common
name the eastern emerald
elysia, is a small-to-medium-
sized species of green sea slug
(marine gastropod mollusc).
Some members of this group
use chloroplasts from
the algae they eat; a
phenomenon known
as kleptoplasty.
 No animals… except…
Aphids may have a rudimentary
sunlight-harvesting
system.
Aphids are unique among insects in their
ability to synthesize pigments called
carotenoids. Many creatures rely on these
pigments in their diet for a variety of
functions, such as maintaining a healthy
immune system and making certain
vitamins. In aphids, these pigments can
absorb energy from the Sun and transfer it
to the cellular machinery involved in energy
production.

Jean Christophe Valmalette, Aviv Dombrovsky, Pierre Brat, Christian Mertz, Maria Capovilla & Alain Robichon: Light‐ induced 

electron transfer and ATP synthesis in a carotene synthesizing insect. Scientific Reports 2, Article number: 579. 
doi:10.1038/srep00579
Chapter 25, page 531:
Geological time scale

Angiosperms

Gymnosperms

Seed plants

Vascular plants
Non-vascular
Land plants

Eukaryotes
Cyanobacteria
Present
Collision of

Cenozoic
45 mya
India with

Eurasia
Eurasia
Africa
66 mya South India Present-day
America Madagascar
Antarctica
continents

Laurasia

Mesozoic
Laurasia and
135 mya
Gondwana
landmasses

Paleozoic
252 mya The supercontinent
Pangaea

Extensive forests of 
vascular plants, 
insects, reptiles & 
amphibians, fish.
Cyanobacteria (Chapter 25, page 583) are prokaryotes with 
internal membranes called “thylakoids” that support the 
chlorophyll molecules and proteins associated with 
photosynthesis.
About 2.4 billion years ago, photosynthesis by cyanobacteria finally
produced oxygen at a rate exceeding that at which organic matter
and dissolved iron could capture it.
Rising oxygen levels then wiped out nearly all of the Earth's
anaerobic inhabitants, even much of the cyanobacteria itself, leading
to the first known mass extinction.
Free oxygen also combined with the high levels of
methane in the atmosphere to create CO2. Methane is a
far more efficient greenhouse gas than CO2. As
atmospheric methane levels dropped, the earth cooled,
and sheets of ice began to spread across the surface,
triggering the Huronian glaciation. The Huronian Ice Age
lasted about 200 million years.
Anabaena, a cyanobacteria 
species that fixes nitrogen 
and can live freely or in 
symbiosis with other plants. 

http://www.giantmicrobes.com
 Anabaena is used as a model 
organism to study simple vision. 
The process in which light 
changes the shape of the 
pigment rhodopsin and leads to 
vision is studied in Anabaena.

Rhodopsin, also known as visual purple due to its pinkish 
color, is a light‐sensitive receptor protein that acts as a 
proton pump. It is also a biological pigment in 
photoreceptor cells of the retina of vertebrate eyes. 
Rhodopsin is the primary 
pigment found in rod 
photoreceptors in vertebrates.
Chapter 28: Protists  Jumping forward a couple 
(Eukaryotes) hundred million years…
Organelle with • Chloroplasts
four membranes
– Larger proto‐eukaryotes 
Red algal nucleus lost
engulfed smaller 
Nucleus
Brown alga photosynthetic bacteria.
– Chloroplasts come from 
single line of 
cyanobacteria.
Secondary
Nucleus
Endosymbiosis – Hosts are not 
Chloroplast monophyletic (so this 
with two
membranes Eukaryotic cell occurred more than once).
Cyanobacteria Red alga – Brown algae engulfed red 
Nucleus algae that already had 
Primary
Endosymbiosis
chloroplasts.
Eukaryotic cell • Secondary endosymbiosis
Cyanobacteria (Chapter 25, page 583) are prokaryotes with 
internal membranes called “thylakoids” that support the 
chlorophyll molecules and proteins associated with 
photosynthesis… Just like modern plant chloroplasts.  
• Lynn Margulis was an American evolutionary theorist and 
biologist.  She was the primary modern proponent for the 
significance of symbiosis in evolution. 
• Historian Jan Sapp has said that 
"Lynn Margulis's name is as 
synonymous with symbiosis as 
Charles Darwin's is with evolution."
• Throughout her career, Margulis' 
work could arouse intense objection 
(one grant application elicited the 
response, "Your research is crap, do 
not bother to apply again") and her formative paper, "On the 
Origin of Mitosing Cells," appeared in 1967 after being rejected 
by about fifteen journals. 
• Her research was largely ignored for another decade, becoming 
widely accepted only after it was powerfully substantiated 
through genetic evidence.
 Complex Life Emerged on Earth Very Early

• Swedish researchers say 
they’ve discovered 
traces of ancient red 
algae preserved in 
sedimentary rock dating 
back 1.6 billion years.
• These would be the 
oldest plant‐like 
eukaryotic fossils ever 
found. 
Bengtson et al. 2017.  Three‐
dimensional preservation of 
cellular and subcellular structures 
suggests 1.6 billion‐year‐old 
crown‐group red algae. PLoS Biol 
15(3): e2000735. doi:10.1371/
journal.pbio.2000735
 Endosymbiosis and the Origin of The 
Mitochondrion and Chloroplast
● Endosymbiosis has been observed today
● Protozoa like Cyanophora paradoxa and 

photosynthetic bacteria
● Gutless Tube Worms (Riftia pachyptila) and 

chemolithotrophic bacteria
Cyanophora paradoxa
Riftia develop from a free-swimming, non-symbiotic larva, which enters juvenile
development, becoming sessile and subsequently acquiring symbiotic
bacteria. The symbiotic bacteria are acquired from the environment via the
digestive tract. After symbionts are established in the midgut, it undergoes
substantial remodelling while the remainder of the digestive tract has not been
detected in adult specimens
 Photosynthetic Protists
• All the other photosynthetic organisms besides land 
plants and cyanobacteria are protists.
• Most diverse of the four eukaryotic “kingdoms”
• United on the basis that they are not fungi, plants, 
or animals – they are paraphyletic.
• Vary considerably in every aspect
– Unicellular, colonial, and multicellular groups
– Most are microscopic but some are huge
– All symmetries
– All types of nutrition (protists are not just photosynthetic)
26
 Diplomonads

Excavata
Parabasalids

Euglenozoans
Euglenozoa in group Excavata
• Among the earliest eukaryotes to possess mitochondria
• 1/3 also have chloroplasts and are autotrophic
• May become heterotrophic in the dark
• Evolutionarily, from endocytosis of whole green algae
= a secondary endosymbiosis (euglena chloroplasts
have 3 membranes).
• Others lack chloroplasts and are heterotrophic
• All have a flexible pellicle
• No known sexual reproduction

© 2017 Pearson Education, Inc.

 Second flagellum
Stigma Reservoir

Contractile vacuole
Basal bodies
Paramylon granule
Mitochondrion

Pellicle
Nucleus

Flagellum
Chloroplast
 SAR is a supergroup consisting of two photosynthetic 
branches: the Alveolates and the Stramenopila
• They may have arisen by one or more
secondary endosymbiotic events
Stramenopiles
Diatoms
Golden algae

Brown algae

Dinoflagellates
Alveolates

SAR
Apicomplexans

Ciliates
Radiolarians
Rhizarians

Forams

Cercozoans

© 2017 Pearson Education, Inc.

 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Raphe

10 µm 5 µm

Diatoms
– Phylum Chrysophyta
– Photosynthetic, unicellular organisms
– Unique double shells made of silica (glass)
– Some move using raphes
• Two long grooves lined with vibrating fibrils 30
Diatom adhesion is
accomplished through
an adhesion/motility
complex that includes
an intracellular bundle
of actin fibers. The
mucilage strands attach
the cell to the surface,
providing the traction for
gliding movement of the
cell through an as yet
unidentified connection
of the mucilage strands
to the actin bundle.
 Brown algae
• Conspicuous seaweeds of 
northern regions
• Life cycle involves 
alternation of generations
like land plants (more later)
• Not “plants”. Chloroplasts 
have 4 membranes, 
suggesting an origin from an 
endosymbiotic relationship 
between a basal eukaryote 
and another eukaryotic 
organism. 32
Nereocystis

33
 Ptychodiscus

Dinoflagellates  Noctiluca

Gonyaulax

Ceratium

• Photosynthetic, unicellular with flagella
• Live in aquatic environments
• Some are luminescent
• Do not appear to be directly related to any other 
phylum
• “Red tide” are “blooms” – fish, birds, and marine 
mammals may die from toxins
• DNA not complexed with histones
34
 Examples of Important Dinoflagellates
● Gymnodinium breve causes fish kills due to the 
production of neurotoxins
● Alexandrium produces a variety of neurotoxin 
called saxitoxin which causes paralytic shellfish 
poisoning and red tides condition
● Gambierdiscus toxicus causes ciguatera when 
the toxins it produces are accumulated in large 
fish and results in profuse diarrhea, damage to 
the central nervous system, and possibly 
respiratory failure
Figure 27.13 A red tide.
 Red algae

Archaeplastida
Chlorophytes

Green
algae
Charophytes

Plants
Archaeplastida
• This group consists of Red algae, Chlorophyta, 
Charophytes, and land plants.  All 
photosynthetic.

Unikonta
• These photosynthetic organisms acquired their 
chloroplast through a single, primary 
endosymbiosis
© 2017 Pearson Education, Inc.
Red algae (Rhodophyta)
• Red algae range from microscopic to very large 
• Have accessory photosynthetic pigments within 
phycobilisomes (light harvesting protein complexes 
anchored to thylakoid membranes in cyanobacteria, 
red algae).
• Evolutionary origin has been a source of controversy
– Tentatively, treated as a sister clade of 
Chlorophyta (green algae)

40
Herbivory

Red algae

41
Porphyra is a Red Alga (that can look green) that grows in cold, 
shallow seawater (and here in Washington off the coast), made 
into nori.
 Chlorophytes & Charophytes
(Green Algae)
• Land plants arose from an ancestral green 
alga only once during their evolution
• Green alga consist of 2 monophyletic 
groups
– Chlorophyta
– Charophytes
5 µm

43
Multicellular Chlorophytes
– Ulva
• Identical‐looking gametophyte and sporophyte 
generations (more on this later)
• Consist of flattened sheets two cells thick –
why?

44
Charophytes are 
distinguished from 
chlorophytes by their 
phylogenetic relationship 
to land plants.
• Charophytes today form green mats around the 
edges of freshwater ponds and marshes
• One species must have successfully inched its way 
onto land through adaptations to drying.

46
 Sexual Life Cycles
Take out a piece of paper and draw a life
cycle of an animal. Include:

Organism stages
• Multicellular (ploidy ?) “adult”
• Single-celled (ploidy ?) gamete
• Single-celled (ploidy ?) zygote

Processes
• Mitosis
• Meiosis
• Fertilization
 Sexual Life Cycles

• Haplontic = Multicellular stage

is haploid (many fungi)

Fungi

• Diplontic = Multicellular stage

is diploid (animals)

Animals
 Sexual Life Cycles
• Haplodiplontic = "Alternation of generations":
multicellular at both the 1n and 2n stages.

Plants!
 Archaeplastida
• Charophytes have haplontic life cycles (multicellular 
form is haploid)
– Evolution of haplodiplontic life cycle (with diploid 
dominant, like most land plants) occurred after 
the move to land
• Chlorophytes like Ulva have a haplodiplontic life 
cycle (multicellular forms in both haploid and diploid 
stages).
– Difficult to tell the difference between halploid
Ulva and diploid Ulva.

51
 Haplodiplontic Life Cycle
• Multicellular diploid stage – “sporophyte”
– Produces haploid spores by meiosis
– Diploid spore mother cells undergo meiosis in 
sporangia
• Produce 4 haploid spores
• First cells of gametophyte generation
• Multicellular haploid stage – “gametophyte”
– Spores divide by mitosis
– Produces gametes by mitosis
– Gametes fuse to form diploid zygote
• First cell of next sporophyte generation 52
 The Plant Life Cycle words for reference
• Gametophyte (1n): Structures called gametangia
produce haploid gametes by mitosis.
– Antheridia are gametangia that produce sperm
– Archegonia are gametangia that produce an egg
• The zygote is a single cell, the result of fusion of sperm 
and egg.
• Sporophyte (2n): Sporangia produce spores by
meiosis.
– Homospory produces gametophytes that have both 
antheridia and archegonia.
– Heterospory produce gametophytes that are either 
male (microspores) or female (megaspores).
 Evolution of the Plant Life Cycle
• Bryophytes: Dominate gametophytic generation
• With evolutionary time, the sporophyte generation
became dominate and the gametophyte became
reduced

What is 
driving this 
shift to less 
and less time 
spend in the 
haploid, 
multicellular 
state?
 First land Plants May Have Caused (more) Ice Ages
New research reveals how 
the arrival of the first plants 
470 million years ago may 
have triggered a series of ice 
ages.
Timothy M. Lenton, Michael Crouch, Martin 
Johnson, Nuno Pires & Liam Dolan. First plants 
cooled the Ordovician. Nature Geoscience, 2012

At the end of the Ordovician Period, the world entered another
intense ice age, caused by a dramatic reduction in atmospheric 
carbon.  26% of all marine families and about 80% of all 
species went extinct. The expansion of non‐vascular land 
plants accelerated chemical weathering and may have drawn 
down enough atmospheric carbon dioxide to trigger the 
growth of ice sheets, lasting about 1 million years.