Introduction
to Biology
Bui Hong Thuy, Ph.D.
School of Biotechnology,
International University
Email: bhthuy@hcmiu.edu.vn
1
Education
2002 – 2005:
Ph.D. in Life Science,
Kobe University, Kobe, Japan.
2000 – 2002:
MSc. in Reproductive Biology,
Kobe University, Kobe, Japan.
1987 – 1992: Received Honor Graduate in
Doctor Veterinary Medicine (DVM)
University of Agriculture & Forestry
Hochiminh City, Vietnam.
2
Past work positions
March 2009 – July 2013:
Associated Professor
Lab of Germ cell and Regenerative Biomedicine
Konkuk University, Seoul, Korea.
March 2008 – Feb. 2009:
Postdoctoral Research Scientist
Department of Animal Biotechnology
Konkuk University, Seoul, Korea.
April 2005 – Feb. 2008:
Postdoctoral Research Scientist
Laboratory for Genomic Reprogramming
Center for Developmental Biology,
RIKEN-Kobe Institute, Kobe, Japan.
3
Research topics
My research is focused on :
✓ Assisted Reproductive Technology (ART),
✓ Embryology, Cell reprogramming
✓ Embryonic stem (ES) cells
✓ Epigenetic reprogramming
✓ Female germ line stem cells
✓ Regenerative biomedicine
Present work position
Nov. 2013 – Present: Lecturer, School of
Biotechnology, International University
Ho Chi Minh National University
4
The questions of Developmental Biology ?
Fertilized egg
1 Cell
(Zygote)
Blastocyst
Trophectoderm
(TE) cells
Placenta
Inner cell
Mass (ICM)
Fetus
6,000,000,000 cells
(230 different
cell types)
5
2000-2002: MSc in Reproductive Biotechnology
2002-2005: Ph.D in Life Science
Kobe, Japan
6
2005-2008: Center for
Developmental Biology
Kobe-Japan
7
Members of Lab for Genomic
Reprogramming
RIKEN-CDB, KOBE, JAPAN
8
2008 – 2013: Department of Animal Biotechnology,
Konkuk University, Seoul, Korea
9
Members of Lab of Germ cell and
Regenerative Biomedicine
Konkuk University, Seoul, KOREA
10
Course overview
• Agenda:
– Theory class: Friday
• Assessments
– Midterm Exam: 40%
– Final Exam: 40%
– Assignments: 20%.
✓ Oral Presentation (by group) : 10%
✓ Group work: 5%
✓ Class participation : 5%
10th Edition -Campbell
Biology-Benjamin
Cummings (2013)
11
Requirement
❖ Be ON TIME 10:35 A.M- – every Friday
Read over the lecture and learn the glossary
and before attending class.
❖ Ask questions and answer questions.
❖ Contact Email: bhthuy@hcmiu.edu.vn
❖ Face book:
➢ https://www.facebook.com/thuy.bui.39545
❖ Office hours (for offline)
–Monday & Tuesday Afternoon 1-5 PM
– Room No. A1.713
– Walk-In Office By Appointment
12
Guide for Online Attendance
❖ Use school email for the attendance, personal
email is not allowed.
❖ URL to the form will be sent in the zoom
chatbox.
❖ Attendance form will be available for 15 minutes
from the time the lecturer send the link.
❖ Fake attendance or filling incorrect information
will be considered as “ABSENT”.
University regulations indicate that students may
be refused to take final assessment if they attend
less than 80% of scheduled classes
13
14
15
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Syllabus
Lecture 1: Introduction to Biology
Lecture 2: The Chemistry of Life (G1)
Lecture 3: The Cell 1 (G2)
Lecture 4: The Cell 2 (G3)
Lecture 5: Genetics 1 (G4)
Lecture 6: Genetics 2 (G5)
Lecture 7: Mechanisms of Evolution (G6)
Lecture 8: Biotechnology-Review
Mid-term exam
Lecture 9: The Evolutionary History of Biological Diversity 1 (G7)
Lecture 10: Animal Form and Function 1 (G8)
Lecture 11: Animal Form and Function 2 (G9)
Lecture 12: Plant Form and Function (G10)
Lecture 13: Ecology (G11)
Lecture 14: The Evolutionary History of Biological Diversity 2
Lecture 15: Review
16
Final exam
The Science of Biology
Bui Hong Thuy, Ph.D.
School of Biotechnology,
International University
Email: bhthuy@hcmiu.edu.vn
17
Outlines
⚫What is Biology?
⚫Cell: the basic unit of an organism
⚫Heritable information
⚫Internal and external interactions/regulation
⚫Unity and diversity
⚫Evolution
⚫Scientific inquiry
⚫Biology, technology and society
18
Introduction: The Scientific Study of Life
Biology: The study of life
Bio: Life
Logos: Study of
❖ Characteristics of living things
❖ Information transfer in living systems
❖ Diversity of Life / classification of
living systems
❖ Energy flow in living systems
❖ Scientific Method
19
❖ Characteristics of living things
I. Life is based on many structural levels
Levels of biological organization:
– Atoms
– Molecules
– Subcellular organelles
– Cells
– Tissues*
– Organs*
– Organ systems*
– Organism: May consist of a single cell or a
complex multicellular organism.
* Level of organization not found in all organisms
20
Levels of organization in the body
Oxygen, carbon, hydrogen, nitrogen.
96% of the total body chemistry
The stomach.
(Multi cells)
The digestive
system
Cells are the basic
units of life.
The whole body
21
The Chemical level: Various atoms and molecules
Atoms:
make up the body
Oxygen (O), Carbon (C), Hydrogen (H), Nitrogen (N)
Molecules:
Proteins, Carbohydrates, fats, nucleic acids, DNA etc…
The Cellular level: Cells are the basic units of life
Cells: cell Structure
Organisms: unicellular or multicellular
22
Levels of organization beyond organism:
• Population: Group of organisms of the same
species that interact with one another.
• Community: Several different populations living
together in same area (e.g.: lake, forest, jungle).
• Ecosystem: Interactions of community with nonliving environment (air, water, soil).
• Ecosphere: All ecosystems on planet earth.
Includes:
–
–
–
–
Biosphere: All biological communities on earth.
Atmosphere (air)
Hydrosphere (water)
Lithosphere (crust)
23
Common features of all organisms:
1. Cells: Basic structural and functional unit of life.
Genetic information contained in DNA.
2. Growth and Development:
• Growth: Occurs by an increase in cell size, cell
number, or both.
• Development: Changes that take place during
an organism’s life.
3. Energy use and metabolism:
• All organisms must take in and transform
energy to do work, to live.
• Metabolism: All chemical reactions and energy
transformations essential for growth,
maintenance, and reproduction.
24
4. Regulation
External environment may change, but internal
environment remains fairly constant.
– Homeostasis: Organisms constantly strive to maintain a
“steady state” (e.g.: constant body temperature or blood
pH) despite changes in the internal and external
environment.
– Metabolism is regulated by homeostatic mechanisms.
5. Movement:
• Internal movement: Characteristic of all life
• Locomotion: Self-propelled movement from
point A to point B. Not observed in all life
forms.
6. Respond to environmental stimuli:
Organisms respond to internal and external
changes (visual stimuli, temperature, light,
sound, pressure, etc.).
25
7. Order:
Organisms are highly organized, when
compared to nonliving environment.
8.Reproduction:
Organisms come from other organisms.
Reproduction may be sexual or
asexual.
9.Evolutionary adaptation:
Populations, not individuals, “evolve” or
change over many generations so they
can survive in a changing world.
26
Order
Response
to the
environment
Evolutionary
adaptation
Regulation
Energy
processing
Some properties of life
Reproduction
Growth and
development
27
❖ All living things are made up of cells
– The cell is the basic unit of life, both in structure
and function; it is living material bounded by a
membrane
– Cells come from and give rise to other cells
– Some organisms are unicellular; some are
multicellular
Neuron
Blood cells
Liver cell
28
Basic Cell Functions
1. Obtain nutrients and oxygen from surrounding
environment.
2. Performing chemical reactions that nutrients and
O2 to provide energy for the cell.
Food + O2 = CO2 + H2O + Energy
3. Eliminate carbon dioxide and other wastes to
surrounding environment.
4. Synthesizing proteins and other components
needed for cell structure, growth and cell
functions.
29
Basic Cell Functions
5. Control exchange of materials between cell
and its surrounding environment.
6. Sensing and responding to changes in
surrounding environment
7. Reproduction:
 In the case of most cells.
 Exception: Nerve cells and muscle cells lose their
ability to reproduce during their early development.
30
Nuclear
envelope
ENDOPLASMIC RETICULUM (ER)
Flagellum
Rough ER
NUCLEUS
Nucleolus
Smooth ER
Chromatin
Centrosome
Plasma
membrane
CYTOSKELETON:
Microfilaments
Intermediate
filaments
Microtubules
Ribosomes
Microvilli
Golgi
apparatus
Peroxisome
Mitochondrion
Lysosome
31
NUCLEUS
Nuclear envelope
Nucleolus
Chromatin
Rough endoplasmic
reticulum
Smooth endoplasmic
reticulum
Ribosomes
Central vacuole
Golgi
apparatus
Microfilaments
Intermediate
filaments
Microtubules
CYTOSKELETON
Mitochondrion
Peroxisome
Chloroplast
Plasma
membrane
Cell wall
Plasmodesmata
Wall of adjacent cell
32
Secretion process for proteins synthesized by ER
1
3
Rough ER
2
4
Rough ER
lumen
Secretory
vesicles
6
Golgi complex
5
Lysosome
7
Cytoplasm
33
Signa
l
Different cell types make different sets of proteins
CYTOPLASM
NUCLEUS
Chromatin
Chromatin
modification
DNA
mRNA in cytoplasm
Degradation
of mRNA
Gene available
for
transcription
Gene
Polypeptide
Transcription
RNA
Translation
Protein processing
Exon
Primary transcript
Intron
RNA processing
Tail
Cap
Degradation
of protein
Active
protein
Transport to cellular
destination
mRNA in
nucleus
Transport to
cytoplasm
CYTOPLAS
M
Cellular
function
34
Cell differentiation
Placenta
Trophectoderm
(TE) cells
8-cell
embryo
Fertilized
egg
Inner cell
Mass (ICM)
Blastocyst
Fetus
Pancreatic
islet cells
Pluripotent embryo
stem cells
(ES cells)
Bone
marrow
Nerve
cells
Heart
muscle
Blood
The DNAs of all differentiated cells are identical
35
35
Cell differentiation
Can divide
Can divide
Differentiation
Can divide
Pluripotent
stem cell
(Embryonic
stem cell)
Differentiation
Multipotent
stem cells
(Adult stem cell)
Differentiated cells
(muscle, nerve, skin,
fibroblast, etc)
36
The Science of Biology
❖ Characteristics of living things
❖ Information transfer in living
systems
❖ Diversity of Life / classification of
living systems
❖ Energy flow in living systems
❖ Scientific Method
37
Information transfer in
living systems
➢ Information must be transferred from one cell
generation to the next
➢ In multicellular organisms, information must also
be transferred from one generation to the next
38
➢Organisms pass on their DNA to the next
generation
➢Characteristics of each generation depend
upon DNA
Sperm cell
Nuclei
containing
DNA
Egg cell
Fertilized egg
with DNA from
both parents
Embryo’s cells with
copies of inherited DNA
Offspring with traits
inherited from
both parents
39
Organisms Contain an
Information System
➢Cells have an information
system made up of nucleic
acids – specifically: DNA
(deoxyribonucleic acid)
⚫
⚫
⚫
⚫
The information is encoded in
regions of DNA called genes, the
units of heredity
Genes are instructions that use a
special, unique code
Instructions are generally for the
production of specific proteins
The nucleic acid code is virtually
identical in all species
40
Chromatin Structure and DNA Packing
4141
Histone Modifications
❖ The histone code hypothesis proposes that specific
combinations of modifications help determine
chromatin configuration and influence transcription
NH3+
Nucleosome
P
DNA
-K9
S10-K14
Ac Me
Ac
-K18
Ac
H2B H2A
H4
H3
P
S28-
-K27 Me
DNA
H3
Octameric
histone core
42
Epigenetic Inheritance
➢ Although the chromatin modifications just discussed
do not alter DNA sequence, they may be passed to
future generations of cells
➢ The inheritance of traits transmitted by mechanisms
not directly involving the nucleotide sequence is called
Epigenetic Inheritance
In biology, the term Epigenetics refers to changes
in phenotype (appearance) or gene expression
caused by mechanisms other than changes in the
underlying DNA sequence, hence the name
epi- (Greek: over; above) -genetics.
43
Regulation of
Chromatin
Structure
➢ Histone acetylation,
acetyl groups are
attached to positively
charged lysines in
histone tails
➢ This process loosens
chromatin structure,
thereby promoting the
initiation of
transcription
Histone
tails
DNA
double helix
Amino
acids
available
for chemical
modification
(a) Histone tails protrude outward from a
nucleosome
Unacetylated histones
Acetylated histones
(b) Acetylation of histone tails promotes loose
chromatin structure that permits transcription
44
Application
Genetic Testing and Counseling
➢ Genetic counselors can provide information
to prospective parents concerned about a
family history for a specific disease
➢ Using family histories, genetic counselors
help couples determine the odds that their
children will have genetic disorders
➢ For a growing number of diseases, tests are
available that identify carriers and help define
the odds more accurately
Newborn Screening: Some genetic disorders
can be detected at birth by simple tests
45
PREIMPLANTATION
GENETIC DIAGNOSIS (PGD)
In Vitro fertilization
Pronuclei
Zygote (1-cell embryo)
8-cell embryos
2-cell embryos
4-cell embryos
Normal
Trysomy 21
chromosome 21
46
Tissues for Preimplantation Biopsy
Egg
Polar Body
Cleavage stage
Blastomere
Blastocyst
Trophectoderm
47
Fetal Testing
Amniotic fluid
withdrawn
Centrifugation
Fetus
Fetus
Placenta
Placenta
Uterus Cervix
Fluid
Fetal
cells
BioSeveral chemical
hours
tests
Several
weeks
Several
weeks Karyotyping
(a) Amniocentesis
Chorionic
villi
Several
hours
Suction tube
inserted
through
cervix
Fetal
cells
Several
hours
(b) Chorionic villus sampling (CVS)
48
The Science of Biology
❖ Characteristics of living things
❖ Information transfer in living
systems
❖ Diversity of Life / classification of
living systems
❖ Energy flow in living systems
❖ Scientific Method
49
Darwin’s theory: evolution occurs
by natural selection
➢ Survival of the Fittest: Individuals with
certain heritable adaptive characteristics
survive and reproduce at a higher rate than
other individuals.
➢ Natural selection increases the adaptation
of organisms to their environment over time.
➢ Speciation: If an environment changes over
time, natural selection may result in adaptation
to these new conditions and may give rise to
new species.
50
Species Genus Family Order
Class Phylum Kingdom Domain
Ursus americanus
(American black bear)
Ursus
Ursidae
Carnivora
Mammalia
Chordata
• Diversity of Life /
classification of
living systems
Animalia
Eukarya
51
(a) DOMAIN BACTERIA
The Three Domains of Life
(b) DOMAIN ARCHAEA
(c) DOMAIN EUKARYA
Kingdom Plantae
Protists
Kingdom Animalia
Kingdom Fungi
52
Domain
Eukarya
Domain bacteria
Domain Archaea
53
Reproductive Isolation =
Barriers to Interbreeding
➢
Reproductive isolation = means of preventing
gene flow between two species
–
➢
for a new species to evolve from an existing
(sexually reproducing) species, there must be a
reproductive isolating mechanism in place
Reproductive isolating mechanisms can be
classified as either prezygotic or postzygotic
–
prezygotic barriers – prevent fertilization (zygote
formation) between gametes from two species
–
postzygotic barriers – reproductive isolation after
fertilization has occurred
54
Reproductive Barriers
Between Species
Prezygotic Barriers
Habitat
Temporal
Isolation
Individuals
of
different
species
(a)
Isolation
(c)
(d)
Postzygotic Barriers
Behavioral Mechanical
Gametic
Isolation
Isolation
Isolation
Mating
attempt
(e)
(f)
Reduced
Reduced Hybrid
Hybrid Viability Fertility
Viable,
fertile
offspring
Fertilization
(g)
(h)
Hybrid
Breakdown
(i)
(l)
(j)
(b)
(k)
55
The Science of Biology
❖ Characteristics of living things
❖ Information transfer in living
systems
❖ Diversity of Life / classification of
living systems
❖ Energy flow in living systems
❖ Scientific Method
56
Living cells require energy from outside
sources
Light
energy
Photosynthesis
in chloroplasts
ECOSYSTEM
How do these leaves power the
work of life for the giant panda?
Organic + O
molecules 2
CO2 + H2O
Cellular respiration
in mitochondria
ATP
ATP powers most cellular work
Energy flow and chemical recycling
in ecosystems
Heat
energy
57
Life Depends on a Continuous
Input of Energy
Sunlight
• All life depends upon
energy
• Original source mostly
the sun
• Energy flows through
cells, organisms
• Energy flows through
ecosystems (the concept
of a food chain or food
web)
Ecosystem
Cycling
of
chemical
nutrients
Producers
(plants and other
photosynthetic
organisms)
Heat
Chemical
energy
Consumers
(such as
animals)
Heat
58
Energy is used:
❖To maintain existing cellular structures and
components (replacement of damaged or worn
out materials within the cell)
❖To produce materials to support growth,
development, and reproduction
❖To support:
–
–
–
Movement, either of cell itself or of materials into
and out of the cell
Signaling responses, such as hormone production
and perception, nerve impulses, etc.
Other forms of cell work, such as symbiotic
relationships with other organisms, defense against
pathogens
59
⚫Producers (autotrophs) manufacture their
own food from simple materials
• usually produce food by the process of
photosynthesis:
Carbon dioxide + Water + light energy
───> Carbohydrate (food) + Oxygen
60
⚫Energy is released from food mostly by
oxidative respiration
Carbohydrate (food) + Oxygen ───> Carbon
dioxide + Water + energy
⚫overall, producers use carbon dioxide and
water and release food and oxygen
61
Cellular Respiration
62
Fermentation and Aerobic
Respiration Compared
Glucose
CYTOSOL
Glycolysis
Pyruvate
O2 present:
No O2 present:
Aerobic cellular
Fermentation
respiration
MITOCHONDRION
Ethanol
or
lactate
Acetyl CoA
Citric
acid
cycle
63
The Science of Biology
❖ Characteristics of living things
❖ Information transfer in living
systems
❖ Diversity of Life / classification of
living systems
❖ Energy flow in living systems
❖ Scientific Method
64
SCIENCE AS A METHOD OF INVESTIGATION
Scientia (Latin): To know
Science is a systematic way of thinking, answering
questions, and solving problems.
Steps of scientific method:
1. Observations
2. Question
3. Hypothesis
4. Predictions
5. Test predictions (Experiments)
Results of experiments may:
– Support (but not prove) hypothesis
– Disprove hypothesis -----> Change hypothesis.
65
Observation
Questio
n
Hypothesis 1
Hypothesis 2
Hypothesis 3
Hypothesis 4
Hypothesis 5
SCIENCE AS A METHOD OF
INVESTIGATION
Experiment
Reject
hypotheses
1 and 4
Potential
hypotheses
66
Observation
Questio
n
Hypothesis 1
Hypothesis 2
Hypothesis 3
Hypothesis 4
Hypothesis 5
Potential
hypotheses
SCIENCE AS A METHOD OF
INVESTIGATION
Experiment
Hypothesis 5
Hypothesis 3
Hypothesis 2
Reject
hypotheses
1 and 4
Experiment
Reject
hypotheses
2 and 3
Remaining
possible
hypotheses
67
SCIENCE AS A METHOD OF
INVESTIGATION
Observation
Questio
n
Hypothesis 1
Hypothesis 2
Hypothesis 3
Hypothesis 4
Hypothesis 5
Potential
hypotheses
Experiment
Hypothesis 5
Hypothesis 3
Hypothesis 2
Remaining
possible
hypotheses
Reject
hypotheses
1 and 4
Experiment
Hypothesis 5
Reject
hypotheses
2 and 3
Last remaining
possible hypothesis
Predictions
Experiment 1
Experiment 2
Experiment 3
Predictions
confirmed
Experiment 4
68
The Scientific Method
➢Summarize existing observations (and
make new ones)
➢Formulate a hypothesis, a model that:
– Explains existing observations
– Makes testable predictions
– Can never be proven true, only supported or
disproved
➢Test the hypothesis (experiment)
69
The Scientific Method
➢ Learning biology is not just learning a set of
facts and concepts; you need to organize that
information
➢ Watch for the recurrence of certain themes that
come up repeatedly in biology (major examples
on next slides)
➢ In addition, an awareness of the process of
scientific inquiry and the application of science
(technology) are important aspects of any study
of biology
70
Levels of Biological Organization
The biosphere
Cells
Organs and
organ systems
10 µm
Cell
Ecosystems
Organelles
Communities
1 µm
Atoms
Tissues
50 µm
Molecules
Populations
Organisms
71
72
73
Themes
➢ The cell
➢ Information management
• heritable information
• regulation
• interaction with the environment
➢ Energy management
➢ Structure and function
➢ Unity and diversity
➢ Emergent properties
➢ Evolution – the core unifying theme that
explains much of the observations connected
with the other themes
74
Critical Thinking
in Biology
Bui Hong Thuy, Ph.D.
School of Biotechnology,
International University
Email: bhthuy@hcmiu.edu.vn
75
Critical Thinking is a Skill That
Carries You To Success
Four Aspects of Critical Thinking
➢1. Abstract thinking: Thinking past what your
senses tell you.
➢2. Creative thinking: Thinking “out of the box”
Innovating.
➢3. Systematic thinking: Organizing your
thoughts into logical steps.
➢4. Communicative thinking: Being precise in
giving your ideas to others.
76
CRITICAL THINKING:
What is Involved?
➢ Question: What is being asked?
➢ Purpose: Why do I want the answer?
➢ Point of view: Where do I stand to look at
the question?
➢ Information: What data to I have?
➢ Concepts: What ideas are involved?
➢ Inferences: What conclusion am I
drawing?
➢ Consequences: What are the implications
of my question?
77
After listening to a presentation,
which are the four criteria to
check the information?
➢ Clarity: Is the information clear?
➢ Accuracy: Are the data accurate?
➢ Relevancy: Is the information relevant
to my studies or works?
➢ Depth: Is the problem important?
78
After listening to a presentation,
how to summarize
what you just heard?
➢ What was the most Important Point?
➢ What was the most Puzzling or
Confusing Point?
➢ What are the New information or New
ideas?
➢ What are the most Challenging
Points?
79
Powerful Questions to Ask
(How to ask questions
without offending the teacher
or your friend)
80
The questions to ask when you
like to have more evidence
➢ Where is the source of your argument
➢ What are the author’s opinion which
support your argument ?
➢ Where did you find the author’s view of
point in the text?
➢ What additional evidence would you give if
someone has a doubt about your given
source?
81
The questions to ask when you
like to have more clarification
➢ Can you restate the word clearly?
➢ What’s a good example of what you are
talking about?
➢ What do you mean by that?
➢ Can you define the word that you just
used?
➢ Can you give a different illustration of your
point?
82
The question you ask when you
like to correlate the problem with
another
➢ Is there any connection between what you just
said and the thing you said before?
➢ How does your observation relate to what the
group decided last week?
➢ Does your idea oppose or support what we are
saying?
➢ How does that contribution add to what has
already been said?
83
Summary and
Synthesis Questions
➢ What are one or two particularly important
ideas that come from this discussion?
➢ What remains unresolved or debatable about
this topic?
➢ What do you understand better as a result of
today’s discussion?
➢ Based on our discussion today, what are the
topics for further discussion if we’re to
understand this issue more?
84
Questions To Encourage Ideas
➢ 1. What if…?
➢ 2. How can we improve…?
➢ 3. How will the Optimist Member and/or
the community benefit?
➢ 4. Are we forgetting anything?
➢ 5. What’s the next step?
➢
➢
➢
➢
➢
6. What can we do better…?
7. What do you think about…?
8. What should we add?
9. What should we eliminate?
10.What other ideas do you have...?
85
An Excellent Thinker is
➢ Thinking of and listing many ideas
(Fluency)
➢ Thinking from different perspectives
(Flexibility)
➢ Coming up with unique ideas
(Originality)
➢ Building upon an existing ideas, adding
details (Elaboration)
86