Welcome to Biol 215!

Brief review of Syllabus

• Please read the entire syllabus on your own.

Students are responsible for this information
• Feel free to contact me if you have questions
regarding the syllabus.
MasteringBiology® by Pearson:
• Online tutorials, assignments and assessments
– weighted as 20% of final course grade
– i.e. same weight as an exam

• Registration instructions posted on Canvas  ‘Modules  ‘Course

Documents’

• Please note: you must complete the registration in one sitting. The
website will log you out after ~5 minutes and your registration will not be
complete.
– So please make sure you have the time and the necessary materials ready
before you begin the process.

• If you started the process and stopped before registration was complete,
you will need to create a new login name.
– e.g. if I used vxh20@case.edu the first time and I didn’t finish my registration, I
can use valerie.haywood@case.edu the second time I attempt to register.
MasteringBiology® by Pearson:
• Important:
– Please register as soon as possible but no later
than noon on Tuesday, 1/14/20
• just in case you encounter any registration issues.

– I may not be able to help anyone who runs into

registration issues after this deadline

*Registration issues are NOT a valid excuse for missing the assignment
deadline 
MasteringBiology® by Pearson:
• Assignments #1 & #2 are due at 5pm this
Friday, 1/17/20
• Syllabus has important information regarding
assignment availability, grading scheme and
due dates.
Announcements:

• Text has end of Chapter Problem Sets

• Solutions Manual available for purchase

– ISBN13: 9780321939111
Announcements:
• Suggested End of Chapter Problem Sets for first few lectures
*Note: this is not an exhaustive list for the exam! These are suggestions in addition to
the learning objectives and other methods of your choice.
Introduction/Chemistry Review:
– Ch. 1:
1-2, 1-3, 1-4, 1-8 (review of scientific method)
– Ch. 2
• 2-1, 2-8, 2-10
• Note: you should be able to answer the following questions from your chemistry
prerequisites: 2-2 – 2-4, 2-7
– Ch. 3
• 3-1 – 3-12 ; 3-13 a, b
Cells:
– Ch. 4
• ALL problems, omit 4-9
– Ch. 12
• 12-1 – 12-3, 12-8 – 12-11
– Ch. 18
• 18-9 – 18-11
– Ch. 22
• 22-1, 22-2, 22-4, 22-5, 22-8 – 22-10
 In-Class ELECTRONICS POLICY
• Personal electronic devices of any kind (e.g. laptops, cell
phones) are not permitted in class.
BUT WHY?! I learn so much more when I take notes on my
computer!

• Taking notes by hand increases retention rates compared

to taking notes on a computer
(Mueller and Oppenheimer, 2014)
http://journals.sagepub.com/doi/full/10.1177/0956797614524581

• In-class electronics:
– lower student engagement
– encourage “multi-tasking” (aka splitting attention away from the
material at hand)
– provide a distraction for neighboring students
(Fried 2008; Sana, Weston, and Cepeda, 2013; Wurts, Smarkola and Gaffney, 2008)
 Announcements: Taking notes in class
• My recommendations:
– Don’t try to scribble down everything that is on the
slides
• The slides are available to you after class…you will already
have that information written down

– Instead, spend class time listening to lecture

• Difficult to hear what’s being said if you are busy writing
down everything (humans cannot ‘multi-task’)
• Rather, summarize important points or highlights
• Ask for any clarification
• Fill in the gaps when studying…slides/LOs/book
 Announcements: Taking notes in class

• “FYI” sections in lecture slides

– “For Your Information” ONLY
– i.e. you are not responsible for this information and
will NOT see it on an exam.
 Announcements: Class Learning Objectives
• Learning Objectives for each class are posted on Canvas
– Tentative list is posted to guide your reading.
– Confirmed list will be updated after each class.

• I use the Learning Objectives to write the exams!

– i.e. Learning Objectives should be your MAIN
study guide for this class!
• The most successful students in the past have shared
with me that they complete the learning objectives after
class that same day
– They do NOT wait until the weekend to cram…NO!!!
Announcements:
FYI: You will be required to memorize structure of
the 20 amino acids (See Fig 3-2)

…You may want to start now so you don’t have to

cram for Exam 1…

Learning Objective: Describe the general structure

of an amino acid. Given an amino acid structure,
name and classify the 20 amino acids as acidic,
basic, polar uncharged, or non-polar. Given the
name of an amino acid, identify the structure and
chemistry. Identify whether a given amino acid
structure is shown in solution (aq) or not.
SI Program run by ESS…
• SI Leader is a fellow undergraduate student
• Course instructors typically are not aware of
SI session content
• While I encourage you to attend if possible,
please understand that I do not (and
cannot) monitor the material presented in
the SI sessions.

*Course instructor is neither responsible nor

accountable for material presented in SI session
What Is Life?

15
 Characteristics of Living Things
- Summary
• Organization
• Evolution of populations
• DNA
• Reproduction
• Growth/development
• Response to environment
• Metabolism
• Homeostasis
• Contain one or more CELLS…
 Living things contain one or more Cells

Cell
= Basic unit of life

• Smallest unit with the

capacity to live and
reproduce,
independently or as
part of a multi-cellular
organism
How do we know this?
To STUDY and UNDERSTAND cells,
we had to OBSERVE them…
 When were ‘cells’ first observed?

a. Early 1400s
b. Late 1500s
c. Mid 1600s
d. Early 1800s
e. Mid 1900s

19
Who is credited with this observation?

a. Watson & Crick

b. Jonas Salk
c. Louis Pasteur
d. Robert Hooke
e. Elon Musk

20
A Very Brief History
of Cytology
(aka. Cell Biology)
 A Very Brief History of Cytology (Cell Biology)
Late 1500s (1595)
• Zacharias Jansen invents the first
microscope
400+ years ago!

…microscopes improve slowly over time…

1665
• “Micrographia”by Robert Hooke
– Credited with coining the term
‘cell’
– Used to describe the Origin of the term 'cell‘. Robert Hooke is credited as the

compartments he viewed in cork originator of the term ‘cell’, which he used in his
description of the structure of cork. This illustration is taken
from his book on microscopy, referred to as 'Micrographia'.
slices
• FYI: Hooke did not really understand what his
observations meant 22
FYI: Hooke’s Microscope

On display at National
Museum of Health &
Medicine, Washington D.C.
 A Very Brief History of Cytology (Cell Biology)
• After 1665…Not many discoveries in Cell Biology

• Scientists were limited by:

1) Optical instruments
• Limited resolving power of microscopes
• Lack of detail
Rembrandt. The Anatomy Lesson of Dr. Nicolaes Tulp. 1632

2) Their way of thinking

• 17th Century was an “Age of Observation”
• Descriptive science
… “Look at this!!!”
• Not really interested in “WHY?”

• More than 150 years later…

 A Very Brief History of Cytology (Cell Biology)
• 1830’s: Advances in Optics
– Lens quality improved
– Development of the Compound Microscope
• Improved both Magnification & Resolution

• 1831: Robert Brown describes the

‘Nucleus’
– Scottish botanist, observed plant cells and
plant fertilization
– Noticed that every plant cell had a ‘rounded
structure’
– Called it a ‘nucleus’…Latin for “kernel”
• FYI: Pollen grains suspended in water also led Brown to the
discovery of ‘Brownian motion’
 A Very Brief History of Cytology (Cell Biology)

1838
• ‘Cell Theory’ put forth by Schleiden & Schwann
– German scientists and colleagues

FYI:
- Schleiden was was a botanist
• Observed cell division in plants
- Schwann was a physiologist
• Observed cell division in animal tissues
FYI: Legend has it:
• Shared their observations over dinner one evening
• Schwann published these findings, omitting Schleiden as author
• Thus, Schwann ‘scooped’ Schleiden!
 A Very Brief History of Cytology (Cell Biology)

Cell Theory - Schwann (1839)

1) The cell is the unit of structure, physiology, and organization
in living things.

2) The cell retains a dual existence as a distinct entity and a

building block in the construction of organisms.

3) Cells form by free-cell formation, similar to the formation of

crystals

WHAT’S WRONG WITH THIS THEORY?

 A Very Brief History of Cytology (Cell Biology)

Cell Theory - Schwann (1839)

1) The cell is the unit of structure, physiology, and organization
in living things.

2) The cell retains a dual existence as a distinct entity and a

building block in the construction of organisms.

3) Cells form by free-cell formation, similar to the formation of

crystals
 “Omnis cellula e cellula”

1855 - Virchow
- German scientist
- Revised Schwann’s postulate
- Based on: Rudolph
Virchow
- Brown’s discovery of the nucleus
- Louis Pasteur’s discoveries of ‘germs’, refuting spontaneous
generation

 All cells arise from only preexisting cells

29
 Cell Theory - Revised

Cell Theory - Schwann (1839)

1) The cell is the unit of structure, physiology, and organization
in living things.

2) The cell retains a dual existence as a distinct entity and a

building block in the construction of organisms.

3) All cells arise from only pre-existing cells

-Virchow (1855)

30
 Founders of Cell Biology

Robert Brown Rudolph Virchow Louis Pasteur

• All provided important contribution that

helped create a foundation for Cell Biology
Welcome to the World of the Cell!!!
 Cells are incredibly diverse…
Plant Cells: Protist Cells: Bacterial Cells:

Human Cells:
FYI: ‘Average’ adult human has ~30+ trillion cells!
Source: Bianconi et al. (2013) Annals of Human Biology. 40, 463-471

33
Images from Figure 1-1
 Plant Cells:

Bacterial Cells:

How can we make meaning out of

ALL of this Diversity?!

Protist Cells:
Phylogenetic Organization of Living Things
There are ____different ‘Domains’ of living
organisms recognized in the contemporary
phylogenetic tree of life.

a) two
b) three
c) four
d) five
e) ten
 Tree of Life
• Tree of Life is continually being redrawn
– Earlier classification systems based largely on morphological
characteristics
• Scala naturae (350 BC)
– Classification scheme outlined in Aristotle’s History of Animals
» All matter organized as decreed by God (see next slide)
» Definition of terms still used today: Vertebrates/Invertebrates
• 2 kingdoms (1700s)
– Classification pioneered by Carl Linneaus & his bionomial taxonomy
– Everything was either a Plant or an Animal
» Bacteria were considered plants
• 5 kingdoms (1960’s)
– Monera (prokaryotes), Protista, Plantae, Fungi, Animalia
» FYI: Original paper published in Science:
Whittaker R.H. (1969). Science 163:150–160.
http://www.sciencemag.org/content/163/3863/150.full.pdf?ijkey=e364e760bafd3ddb27f995f0c1e9b08fdf28eb0f&keytype2=tf_ipsecsha
Scala Naturae = “ladder of complexity”
Five Kingdoms
 Tree of Life
• Current Phylogeny = 3 Domain system
Bacteria = Prokaryotes
Archaea = Prokaryotes, many extremophiles
Eukarya = Eukaryotes
• Group includes Protists, Plants, Fungi, Animals
 Tree of Life
• Current Phylogeny = 3 Domain system
Bacteria = Prokaryotes
Archaea = Prokaryotes, many extremophiles
Eukarya = Eukaryotes
• Group includes Protists, Plants, Fungi, Animals
• Pioneered by Carle Woese & George Fox in the late 1970’s
• Formally recognized in the 1990’s
• Redrawing of phylogenetic relationships based on analysis
of rRNA sequences

Why do you suppose rRNA was used for this purpose?

 Redrawing of phylogenetic relationships based on
analysis of rRNA sequences : Why rRNA?
• All cells require rRNA
Why?
 Component of ribosomes
• rRNA sequences change very slowly with time
– Important sequences that do not evolve rapidly
• Any slight changes in sequence reflect an evolutionary
‘step’

– Can be used to establish evolutionary relationships

between all species

– Conserved regions enable easy in vitro replication

• i.e. we know these sequences, therefore we can design
PCR primers against them to amplify the sequences for
study

• Using such data, phylogenetic relationships were

redrawn…
 3 Domains of Life
‘Hypothetical’ Phylogenetic Tree of Life

Last
Universal
Common
Ancestor
~3.5 BYA

Fig 26.21 43
*Note: Origins of LUCA and Eukarya lineage are hypothetical
Reviews - Nature 440: 623-630; BioEssays 29: 74-84
from Campbell et al., 9 ed.
th
 3 Domains of Life
rRNA analysis revealed
1) two separate groups of
prokaryotes:
- Bacteria & Archaean domains
2) Also suggests that eukaryotes
and archaea are more closely
related to each other than to
bacteria
3) Allowed better understanding of how protists
should be organized phylogenetically
- Revealed how incorrect it was to classify them all together in
one kingdom
- Some protists are not even closely related at all! 44
What is the best way to describe
a PROTIST?

a) Diverse grouping of eukaryotic

organisms
b) A type of prokaryote
c) A group of single-celled organisms
d) A type of delicious pastry
e) None of the above.
 Protists
• Many diverse lineages
of various eukaryotic
organisms

• Can be unicellular
– e.g. dinoflagellates

Red tide dinoflagellate

• Can be multicellular
– e.g. some algae species
kelp