The Science of Biology 1

Instructor: Đoàn Thị Phương Thùy, PhD.

Email: thuy.doanvn@gmail.com
 Outlines
§  Lecture 1: Studying life (Chapter 1,2)
§  Lecture 2: Cells: the working unit of life (Chapter 5)
§  Lecture 3: Cell membranes (Chapter 6)
§  Lecture 4: Cell signaling and communication (Chapter 7)
§  Lecture 5: Energy, enzymes and metabolism (Chapter 8)
§  Lecture 6: Pathways that harvest chemical energy (Chapter 9)
§  (Midterm exam)
§  Lecture 7: Photosynthesis (chapter 10)
§  Lecture 8: The cell cycles and cell division (Chapter 11)
§  Lecture 9: Inheritance, genes, the role of DNA in Heredity (Chapter 12, 13)
§  Lecture 10: Gene expression (Chapter 14)
References
Sadava et al, Life: The Science of Biology, 9th edition.

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Grading

- Discussions: 30%
- Quizzes: 20%
- Final exam: 50%

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Chapter 1.1: Studying life
1.  What is biology?
2.  Three domains of life
3.  Biology and applications?
 1.1 What is biology?
§  Biology: The scientific study of living things
§  Living organisms:
-  Consist of one or more cells

-  Contain genetic information

-  Use genetic information to reproduce

-  Are genetically related and have evolved

-  Convert molecules obtained into new biological molecules

-  Extract energy from environment and use it to do biological work

-  Can regulate their internal environment

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1.1 Cells are the basic unit of life
§  Unicellular organisms

§  Multicellular organisms

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I.1 Cells are the basic unit of life
§  Robert Hook (1653)

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1.1 Cells are the basic unit of life
§  Cell theory by Matthias Schleiden and Theodor
Schwan (1838)
§  Cells are the basic structural and physiological
units of all living organisms
§  Cells are both distinct entities and building
block of more complex organisms

Question: Does living things arise spontaneously

from non living materials?

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1.1 Cells are the basic unit of life
§  Cell theory and Louis Pasteur experiments (1859)

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1.1 Cells are the basic unit of life
§  Cell theory and Louis Pasteur experiments (1859)

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1.1 Cells are the basic unit of life
§  Cell theory and Louis Pasteur experiments (1859)
1)  Cells are the basic structural and physiological units of
all living organisms
2)  Cells are both distinct entities and building block of
more complex organisms
3)  All cells come from preexisting cells
4)  All cells are similar in chemical composition
5)  Most of the chemical reactions of life occur in aqueous
solution within cells
6)  Complete sets of genetic information are replicated and
passed on during cell division
7)  Viruses lack cellular structure but remain dependent on
cellular organisms.
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1.1 Discoveries in biology can be
generalized
§  Model systems

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 1.1 Genetic language of cells
§  DNA: the genetic information that is passed from
parent to daughter cells.
Consists of repeating subunits—nucleotides
§  Genome: sum total of all the DNA in the cell.
All cells in a multicellular organism
have the same genome.
§  Gene: a specific segment of DNA
molecule—contains information for making proteins
§  Mutations are alterations in the nucleotide sequence.

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 1.1 Gene expression in multicellular
organisms: cellular differentiation
§  In multicellular organisms
Different cells have different
functions and form different
structure à different type of
cells in an organism must
express different part of the
genome.

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 1.1 Gene expression in multicellular
organisms: cellular differentiation
§  Tissues: a group of many
cells with similar and
coordinated functions
§  Organs: combine several
tissues that function together
§  Population: a group of
many organism of the same
species
§  Community: a group of
many population of many
different species
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1.2 There domains of life

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 1.2 Energy pathways of organisms
§  Autotrophs:
Organisms capable
of photosynthesis or
chemosynthesis
§  Heterotrophs:
Require a source of
molecules synthesized
by other organisms

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1.3 Biology and applications

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Chapter 1.2: Small molecules

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Contents
§  Atoms and periodic table
§  Electrons
§  Electron configurations and chemical activities

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2. Periodic table of the elements

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2. Periodic table of the Elements

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2.1 Atoms
§  Atom is the building block of all matter.
§  An atom consist of three types of particles
Name Charge
Electron -1
Neutron 0
Proton +1

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 2.1 Atoms

§  In an electrically neutral atom:

•  Number of protons = number of electrons

•  The atomic number = number of protons

The number of protons identifies the elements/chemical

identity
§  The electrical activity of an atom determines by
•  The number of electron

•  The motion of electrons

The number of electrons determine how atoms will interact

2.2. Electrons - 3D orbitals
2.2 Electrons - 3D orbitals

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2.2 Electron configurations
 2.2 Valence electrons
§  Valence electrons

•  The electrons locate in

the outermost electron shell

•  Participate in the formation of a

chemical bond

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Exercise
Write electron configurations of
a. Carbon (C, 6)
b. Sodium (Na, 11)
c. Hydrogen (H, 1)
d. Helium (He, 2)
e. Oxygen (O, 8)
g. Chlorine (Cl,17)
h. Nitrogen (N, 7)

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Exercise
Write orbital configurations of
a. Carbon (C, 6)
b. Sodium (Na, 11)
c. Hydrogen (H, 1)
d. Helium (He, 2)
e. Oxygen (O, 8)
g. Chlorine (Cl,17)
h. Nitrogen (N, 7)

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2.3. Electron configuration and
chemical reaction

§  Chemical reactions involve changes in the distribution

of electrons between atoms.
§  Reactive atoms have unpaired electrons.
§  Atoms can share electrons, or loose or gain electrons,
resulting in atoms bonded together to form molecules.
2.4 Electronegativities
§  Electronegativity: the attractive force that an atomic
nucleus exerts on electrons
§  Electronegativity depends on
•  The number of protons
•  The distance between the nucleus and electrons.
2.5 Chemical bonds
§  Chemical bond: attractive force that links atoms
together to form molecules

•  Covalent bonds
•  Ionic bonds
 Ionic bonds
§  Ions: electrically charged particles
— when atoms loose or gain
electrons
•  Cations —positive

•  Anions — negative

§  Ionic bonds: are formed by the

electrical attraction of positive and
negative ions.
Covalent bonds
§  Covalent bonds:
Atoms share one or more pairs of electrons, so that the
outer shells are filled.
Covalent bond in H2 molecule
Covalent bonds in methane (CH4)
Exercise
Define molecules with covalent bonds and molecules
with ionic bonds
a.  HCl
b.  CaCl2
c.  CH3COONa
d.  CH3CH2COOH
e.  NH3
f.  AlCl3
g.  CH4
h.  FeCl3
i.  Cu(OH)2
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j.  K2S
Covalent bonds
§  Nonpolar covalent bond
when two atoms have similar
electronegativity à electrons
shared equally

§  Polar covalent bond

the electrons are drawn to the
nucleus with more electronegativity
à electrons not shared equally.
Covalent bonds
Single bond- Sharing one pair of electrons
C-H

Double bond – Sharing two pairs of electrons

C=C
Triple bonds – Sharing three pairs of electrons
N=N
Covalent bonds
 2.7 Functional groups
§  Responsible for the characteristic chemical reactions of
a molecule
§  Participate in chemical reactions

Common functional groups

a. Hydroxyl: ROH
b. Carboxyl: RCOOH
c. Aldehyde: RCHO
d. Keto: R-CO-R’
e. Amino: RNH2, R2 NH, R3 N
f. Sulhydryl: RSH
g. Phosphate: RPO42-
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Functional group with Oxygen and
Sulfur

R= hydrocarbon

R’=hydrocarbon
(giống hoặc không
giống R)
Functional group with Nitrogen
Functional group with Phosphorus
2.8 Condensation vs. Hydrolysis
§  Condensation
Form covalent bond
between monomers and
release a H2O molecule
in the process

§  Hydrolysis
Break covalent bond
between monomers by the
addition of a H2O molecule
2.9 Water molecule

§  H2O is a polar molecule

2.10 Hydrogen bonds
§  Hydrogen bonds:
The attraction between the positive charge hydrogen (δ
+) and another negative charge atom (δ–)
Exercise
Find molecules those can form hydrogen bonds.
The electronegativity of atoms as following
H: 2.1, C: 2.5, N: 3.0, O: 3.5, F: 4.0,
a. H2O
b. NH3
c. HF
d. H2O2
e. CH3OH
f. CH3COOH
g. CH3NH2
h. CH4 51
2.11 Energy of chemical bonds
2.11 Water molecules
2.12 Polarity of molecules
§  Hydrophilic molecule
Can form hydrogen bonds with water molecules

§  Hydrophobic molecule
Can’t form hydrogen bonds with water molecules

§  van der Waals forces:

The attractive forces between hydrophobic molecules
Exercise
§  Các phân tử sau có thể tạo liên kết hydro với phân tử
khác không? Tính số lượng liên kết hydro mỗi phân
tử có thể tạo (nếu có)?

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Discussion

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Discussion
What makes water so important for life?