Biology 1010

Cellular Basis of Life

Igor KOVALCHUK

Textbook
CAMPBELL BIOLOGY, THIRD CANADIAN EDITION

9/6/2024
9/6/2024
 Dr. Igor Kovalchuk HEAL R &D

B. Med. (1993) – general practitioner

M.D. (1996) - ObGyn
PhD (Medical Genetics, 1998) – molecular biology of breast cancer

Expert in plant biotechnology, medicinal plants (cannabis), magic

mushrooms, epigenetics and epigenomics of health and disease,
genome stability, transgenerational responses

Office: SA9238 – by appointment – mainly zoom, but Tue/Thur in person

is possible
Welcome to Biology 1010
Laboratories!
Information and FAQs
When do Labs start the week
labs start? of September 9th
Do I need to come to lab?

Missing labs will result

in a grade of 0/35
Yes – attendance will
being assigned.
be taken for each lab
Review your lab
manual for details
Is there a • Yes! Lab manuals are available
as .pdf on the Biology 1010 All
Labs Moodle page
lab manual • Lab manuals are NOT available
through the Bookstore
and where • Lab manuals are free to
download BUT you MUST have

can I find a bound copy (eg binder,

duotang) for your lab – you
can print off at any of the

one? photocopiers on campus, or

send the manual to a third
party service such as Staples.
Make sure you ask for black
and white to save on costs.
 Contact the folks in the Teaching
Centre as soon as possible to ensure
that you have access to all of the lab
I can’t access materials!

Moodle –
what do I do? (403)380-
1856 | [email protected]
 Yes – electronic copies on
Do I need to your phone or tablet or
laptop are NOT permitted
bring a paper
version of the
lab manual to There are grade penalties
every lab? associated with not
bringing the entire lab
manual to every lab
 How can I print my lab manual?

For guidelines,
please see:
Web based interface
allows you to upload
from your computer
and print to the Ricoh
photocopiers
https://www.ulethbridge.ca/printing
/follow-you-printing
 Lab coat – Bookstore, KOST, Amazon

Safety glasses (see above)

What else do
Close toed shoes, long pants or long skirt with
I need for boots (no bare toes or legs!)
labs? Lock for a locker (Bookstore, dollar store) to store
your stuff (no food, drink, coats, backpacks in lab)

Notebook, ruler, calculator, pen, pencil

What do I Complete
If you haven’t already done so for other courses, complete
WHMIS training and the Lab Safety course. These are posted
on YOUR personal Moodle page (not the 1010 page). Save

need to do to your certificates!

prepare for
my first lab Upload
Upload your certificates to the Crowdmark link on the All
Labs Moodle page. They are due Monday, September 9th at

during the 9:00 AM (MST) (value: 1% for completion)

week of
September Read the lab policies on attendance and grading. Read Cell
Read Structure and Function Week 1 and watch the associated
9th? videos. Review the associated appendices.
 If your questions deal with:

Moodle access: The Teaching Centre - (403)380-

I have more 1856 | [email protected]

questions –
who can I talk WHMIS and Lab Safety course access, obtaining
certificates: The Teaching Centre – see information
above
to?
1010 labs themselves: Your lab instructors and/or
Laurie Pacarynuk ([email protected]). In the
subject line, please include who you are, and what
lab section you are in when you email!
Biology 1010

Midterm Exam 1 Oct 7-8, 2024 15%

Midterm Exam 2 Nov 4-5, 2024 20%
Final Exam Dec 12-14, 2024 30%
Lab 35%

! Bonus marks opportunity – short essays – 5% bonus maximum !

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Biology 1010

Letter Percent Grade Point Letter Percent Grade Point

A+ 90-100 4.0 C+ 67-69.9 2.3

A Excellent 85-89.9 4.0 C Average 64-66.9 2.0

A- 80-84.9 3.7 C- 60-63.9 1.7

B+ 77-79.9 3.3 D+ 56-59.9 1.3

B Superior 74-76.9 3.0 D Poor 50-55.9 1.0

B- 70-73.9 2.7
F Failing 49 or less 0

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Why study biology?
9/6/2024
PUBLIC: Coordinated by the National Institutes of Health and the U.S. Department of Energy.
Additional contributors - universities across the USA and international partners in the United
Kingdom, France, Germany, Japan, and China.

PRIVATE: Celera Genomics

HGP fueled the discovery of more than 1800 disease genes
 All cells in our bodies have the exact same
DNA, yet they differ in shape, size and function

https://genographic.nationalgeographic.com/genetics-overview/
 Genetics vs Epigenetics

NATURE NURTURE
Nature: due to inherited
characteristics and innate drives

Nurture: due to environmental

influences and learning
 Centenarians

Nature: due to inherited characteristics and innate

drives
Nurture: due to environmental influences and learning

https://tribune.com.pk/story/908871/centenarian-men-are-healthier-than-women/
 TWIN STUDIES – EPIGENETIC HINTS
Identical twin are genetic carbon copies

Their DNA is the same

Identical twins become increasingly different over time

Any differences between twins are due to their environments,

not genetics

http://www.sciencemuseum.org.uk/visitmuseum_OLD/encode/twins.aspx http://www.cbc.ca/news/health/identical-twins-differences-focus-of-epigenetics-studies-1.2849795

http://learn.genetics.utah.edu/content/epigenetics/twins/
 TWIN STUDIES – EPIGENETIC HINTS

http://learn.genetics.utah.edu/content/epigenetics/twins/

http://necessaryfacts.blogspot.ca/2013/12/epigenetics.html
GENES OR ENVIRONMENT?

Koonin and Wolf, 2009

GENE REGULATION

Jaenisch R, Bird A., Nat Genet, 2003

 The Cellular Basis of Life

Introduction to Biology

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1. Hierarchy of the Living World

2. Evolution, Unity, and Diversity

3. Science is a Process

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 Biology – the study of life

Covers research from submicroscopic molecules to the

global distribution of biological communities.

Studies not only living organisms but also ancestral life

forms stretching back nearly four billion years.

Because of new discoveries, biology is in continuous state of

flux.

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 Hierarchical Order of Life

Each level of biological structure builds itself on the level

below

Biology is studied on different levels:

- cellular biology;
- molecular biology;
- genetics;
- physiology;
- organism behaviour;
- ecology and environmental studies;
- paleontology.

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The Study of Life Reveals Common
Themes
• Biology is a subject of enormous scope

• There are five unifying themes

• Organization
• Information
• Energy and matter
• Interactions
• Evolution
New Properties Emerge at Each Level in
the Biological Hierarchy
• Life can be studied at different levels, from molecules to entire
living planet

• Study of life can therefore be divided into different levels of

biological organization through a strategy called reductionism

• Reductionism refers to reducing complex systems to simpler

components that are more manageable to study
Levels of organisation beyond the
individual organism
Population Localized group of organisms belonging to
the same species

Community Populations of species living in the same

area

Ecosystem An energy-processing system of

community interactions that include abiotic
environmental factors such as soil and
water
Biomes Large scale communities classified by
predominant vegetation type and distinctive
combinations of plants and animals
Biosphere The sum of all the planet’s ecosytems
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Levels of Biological Organization
Figure 1.3 Exploring Levels of Biological Organization.
The Power and Limitations of
Reductionism
• Reductionism - reduction of complex systems to simpler
components

• Powerful strategy in biology, as the study of individual

components is more manageable

• For example, studying molecular structure of DNA helps to

understand chemical basis of biological inheritance
Emergent Properties
• Emergent properties emerge from the arrangement and
interaction of parts within a system

• Novel properties emerge at each level that are absent from the
preceding one

• photosynthesis only occurs in chloroplasts, not in a test tube

containing chlorophyll and other chloroplast components

• atoms of molecule are able to interact with each other to

certain extent but not able to perform any specific function
within the cell.
Systems Biology
• Understanding biology requires a balance of reductionism with
the study of emergent properties

• Emergent properties are explored using systems biology, which

studies interactions among parts of a biological system

• Systems biology constructs models for dynamic behaviour of

biological systems

• Systems biology can be used to study life at all levels.

Cells are an organism’s basic units

All organisms consist of cells

Robert Hooke in 1665 – first described and named cells from

oak tree (30x)

Anton van Leeuwenhoek discovered a microbial world in

droplets of pound water.

Mattias Schleiden and Theodor Schwann (1839) called cells

“units of life” – cell theory.

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The Cell: an Organism’s Basic Unit
of Structure and Function
• The cell is the lowest level of organization that can perform all
activities required for life

• Cell theory developed in 1800’s states that,

• All living organisms are made of cells

• Actions of all organisms are based on the functioning of

cells.
Forms of Cells
• All cells
• Are enclosed by a membrane
• Use DNA as their genetic information

• Eukaryotic cell has membrane-enclosed organelles

• Largest is usually the nucleus

• Prokaryotic cell is simpler, usually smaller, and does not contain

membrane-enclosed organelles
Types of Cells
Contrasting eukaryotic and prokaryotic cells in size and
complexity.
 Eukaryotic versus prokaryotic cells

The cells of microorganisms commonly called bacteria (and

archaea) are prokaryotic.
All other forms of life are composed of eukaryotic cells.

Major differences

•The presence of nucleus;

•Internal membrane – subdivision into many different
organelles in eukaryotes;
•Separation of the genetic material – DNA into nucleus in
eukaryotes.

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The Continuity of Life Is Based on
Heritable Information in the Form of DNA
• Ability of cells to divide is basis of all reproduction, growth, and
repair of multicellular organisms
Figure 1.5 A lung cell from a newt divides into two smaller cells
that will grow and divide again.
DNA is the Genetic Material
• Each chromosome has one long DNA molecule with hundreds
or thousands of genes

• Genes encode information for building the molecules

synthesized within cells

• Genes themselves have many structural components

 DNA is the basis for continuity of life
The units of inheritance that transmit information from
parents to offspring are called genes

Each DNA molecule is made up of two long chains each

composed of four different building blocks called
nucleotides.

The linear sequence of these four nucleotides encode

the precise information in a gene, the unit of inheritance
from parent to offspring.

All forms of life use essentially the same genetic code.

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DNA Structure and Function
• DNA is inherited by offspring from their parents
• DNA controls the development and maintenance of organisms

Figure 1.6 Inherited DNA directs development of an organism.

DNA Structure and Function
Figure 1.7 DNA: The genetic material.

Each DNA molecule is

made of two long
chains arranged in a
double helix

Each chain is made up

of four kinds of
chemical building
blocks called
nucleotides that are
nicknamed A, G, C and
T
Gene Expression
• Genes indirectly control protein production
• DNA is transcribed into RNA, which is then translated into a
protein
• Protein is the key player in the cell involved in building,
maintaining and performing activities
• Gene expression - process of converting information from gene
to cellular product
Gene Expression
Figure 1.8 Gene expression: The transfer of information from a
gene results in a functional protein.
Genomics: Large-Scale Analysis of
DNA Sequences
• An organism’s genome is its entire set of genetic instructions

• The genomes of humans and many other organisms have

been sequenced
• Genomics is the study of whole sets of genes within and
between species
• Proteomics is the study of all the proteins encoded by the
genome (called proteomes)
Genomics
• Genomics approach depends on
• “High-throughput” technology, which yields enormous
amounts of data
• Bioinformatics, which is the use of computational tools to
process a large volume of data
• Collaboration between interdisciplinary research teams
Evolution, Unity, and Diversity
Diversity: 1.9 mln species are identified and named by
biologists

290 000 52 000 100 000

plants vertebrates fungi

Thousands of newly identified species are added to the list

each year.
Estimates for total diversity of life range from about 10 mln
to 100 mln species.

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Grouping Species: The Basic Idea
• Taxonomy - branch of biology that names and classifies species
into groups of increasing breadth
• Domains, followed by kingdoms, are the broadest units of
classification
• Organisms are divided into three domains

• Domain Bacteria 

 Prokaryotic organisms
• Domain Archaea 


• Domain Eukarya –Eukaryotic organisms

 Three Domains and Five Kingdoms
Domain Bacteria
Domain Eukarya

Domain Archaea

Protista Plantae
Unicellular Carry out
Prokaryota eukaryotes Fungi photosynthesis Animalia
and simple
All prokaryotic multicellular Defined by Multicellular
organisms, relatives nutritional mode, eukaryotes
including they absorb that ingest
Bacteria and nutrients after other
Archaea decomposing organisms
organic material
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The Three Domains of Life
• Most prokaryotes are single-celled and microscopic
Figure 1.13a,b The three domains of life.
The Three Domains of Life
• Domain Eukarya includes all eukaryotic organisms
Figure 1.13c The three domains of life.
Domain Eukarya
• Domain Eukarya includes four subgroups
• Kingdom Plantae, which produce their own food by
photosynthesis
• Kingdom Fungi, which absorb nutrients
• Kingdom Animalia, which ingest other organisms as food
• Protists (now split into several kingdoms) are mostly single-
celled, and the most abundant eukaryotes
Unity in the Diversity of Life
• A striking unity underlies the diversity of life; for example
• DNA is the universal genetic language common to all
organisms
• Unity is evident in many features of cell structure
Evolution, Unity, and Diversity
The unity in the diversity of life forms at the lower levels
of organisation.

It is evident from:

A universal genetic code.

Similar metabolic pathways (e.g., glycolysis)

Similarities of cell structure (e.g., flagella of

protozoans and mammalian sperm cells)

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Unity in the Diversity of Life
• Example of unity underlying the diversity of life: the
architecture of cilia in eukaryotes.
Figure 1.14 An example of unity underlying the diversity of life:
the architecture of cilia in eukaryotes.
Taxonomy – naming and classifying diverse species
Kingdom Animalia

Phylum
Chordata
Class
Mammalia
Order
Carnivora
Family
Felidae
Genus
Panthera
Species Pink
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panthera
 Figure 1.14
Species Genus Family Order Class Phylum Kingdom Domain

Ursus americanus
(American black bear)

Ursus

Ursidae

Carnivora

Mammalia

Chordata

Animalia

Eukarya
The Origin of Species (1859, Charles Darvin)
Evolution is one of the unifying biological topics
Life evolves (via process of “descent with
modification”):

- every species has an ancestor;

- similar species (dogs and wolfs) have common early

ancestor since they have branched recently;

- through very early ancestors all mammals are also

related

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The Origin of Species (1859, Charles Darvin)
Darvin synthesised the concept of natural selection
(mechanism of evolutionary change) from:

Observation 1: Individual variation. Individuals in a

population of any species vary in many heritable
traits.

Observation 2: Struggle for existence. The produced

offspring is far bigger than environment can support.

INFERENCE: Differential reproductive success. Those

individuals with traits best suited to the local environment
leave larger number of surviving fertile offspring.
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Structure and function are correlated

There is a relationship between an organism’s structure

and how it works. Form fits function.

Biological structure gives clues about what it does

and how it works.

Knowing a structure’s function gives insights about

its construction.

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Life Requires the Transfer and
Transformation of Energy and Matter
• The input of energy from the sun and the transformation of
energy from one form to another make life possible
• When organisms use energy to perform work, some energy is
lost to the surroundings as heat
• Energy flows through an ecosystem, usually enters as light and
exits as heat
• Therefore, energy flows through an ecosystem in one
direction
Energy Flow in an Ecosystem
• Living organisms transform energy from one form to another

Figure 1.9 Energy flow and chemical cycling.

 Sunlight

Leaves absorb
light energy from Leaves take in
the sun. carbon dioxide
CO2 from the air
and release
oxygen.

O2

Cycling
of
chemical
nutrients

Leaves fall to Water and Animals eat

the ground and minerals in leaves and fruit
are decomposed the soil are from the tree.
by organisms taken up by
that return the tree
minerals to the through
soil. its roots.
 A
Negative
feedback
Enzyme 1

D Enzyme 2
Excess D
blocks a step. D
D C

Enzyme 3

(a) Negative feedback

Life Requires the Transfer and
Transformation of Energy and Matter
• The input of energy from the sun and the transformation of
energy from one form to another make life possible
• When organisms use energy to perform work, some energy is
lost to the surroundings as heat
• Energy flows through an ecosystem, usually enters as light and
exits as heat
• Therefore, energy flows through an ecosystem in one
direction
Energy Flow in an Ecosystem
• Living organisms transform energy from one form to another

Figure 1.9 Energy flow and chemical cycling.

 W

Enzyme 4

X
Positive
feedback +
Enzyme 5

Excess Z Z Y
stimulates a Z
step.
Z Enzyme 6

(b) Positive feedback

 Science as a Process
Science is a process of getting knowledge
Create a hypothesis – test it – prove it
Good scientists are people who:

•Ask questions about nature and believe those questions

are answerable.

•Are curious, observant, and passionate in their quest for

discovery.

•Are creative, imaginative, and initiative.

•Are generally skeptics.

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Science is a way of knowing
Scientific method is a process which outlines a series of
steps used to answer questions

•Is not a rigid procedure.

•Based on the conviction that natural phenomena

have natural causes.

•Requires evidence to logically solve problems

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Characteristics of useful hypotheses
Hypothetico-deductive thinking

Hypotheses are possible causes.

Hypotheses reflect past experience with similar questions.

Multiple hypotheses should be proposed whenever possible.

Hypotheses can be eliminated, but not confirmed with

absolute certainty.

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No control – no experiment

In a controlled experiment – control group is the group in

which all variables are held constant.

Controls are necessary basis for comparison with the

experimental group, which has been exposed to a single
treatment variable.

Setting up the best controls is a key element of good

experimental design

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 Hypothesis
Test =
experiment or
observations
Support Reject
hypothesis hypothesis
Reject (may be true)

Test Modify or abandon

repeatedly hypothesis
Accept
Verify

Hypothesis becomes
theory
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 READING:
CHAPTER 1

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