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Chapter 1

Introduction: What do life sciences study?


Fundamentals in Biology (2014-2015)
Dr. Ibis KC Cheng

Textbook:
Lehninger Principles of Biochemistry; DL Nelson (Sixth Edition)
Chapter 1: The Foundations of Biochemistry
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Overview
Five Kingdoms
The Cell Concept
Prokaryotic Cells
Eukaryotic cells
Functions of Organelles
Bioenergetics

Life Science
Life Science (Biology) is devoted to the study of
living organisms.
Microbiology

Anatomy

Virology (viruses)

(gross structure)

Bacteriology (bacteria)

Physiology

(gross function)

Mycology (fungi)

Botany

Histology

(plants)

(tissue)

Zoology

Cell biology

(animals)

(cells)
Genetics

(inheritance)
Branches of Biology

Biochemistry and
Molecular Biology
(molecules)

Five Kingdoms
All cellular organisms fall into two natural groups, known as
prokaryotes and eukaryotes.
The terms prokaryote and eukaryotes refer to differences in the
location of the DNA (the genetic material).
Prokaryotes
The DNA is not enclosed by nuclear membranes and lies free in
the cytoplasm.
The cells therefore lack of true nuclei.
Eukaryotes
Do contain true nuclei.
Evolved from prokaryotes.

Five Kingdoms
Five kingdoms include the prokaryotae and four eukaryotae
kingdoms.

Living organism

Prokaryotae

e.g.
Bacteria

Viruses

Eukaryotae

Protocitista

Fungi

not cellular

Plantae

Animalia
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Five kingdoms
One group of organisms that does not fit neatly
into any classification scheme is the viruses.
Viruses are extremely small particles consisting
only of a piece of genetic material (DNA or RNA)
in a protective coat of protein.

Hepatitis B virus
(HBV)

They do not have a cellular structure.


They can only reproduce by invading living cells.

Bacteriophage

Influenza virus

Human immunodeficiency virus


(HIV)

Hepatitis C virus
(HCV)

Human Papilloma virus


(HPV)
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The Cell concept


One of the most important concepts in biology is that the basic
unit of structure and function in living organisms is the cell.
Cells as seen with the light microscope.

The Cell Concept


The size of the cells bears no relationship to the size of the
organism.
An elephant and a flea have cells of about the same size
The elephant just has more cells than the flea
Why is such uniformity in cell size maintained?

The Cell Concept


The surface area to
volume ratio for an
object of a given
shape depends on its
size.

The Cell Concept


The complex chemical processes in a cell and the large
molecules that participate in them require a significant
volume.
The cell must also exchange substances with its surroundings
to support the active metabolism within the cell that require
a significant surface area.
Too large a cell will not have enough surface for this exchange
to occur.

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The Cell concept


A cell can be thought of as a
bag of chemicals which is
capable of surviving and
replicating itself.
Without a barrier between the
bag and the environment, the
chemicals would mix freely
and the differences could not
be maintained. Life could not
exist.
The barrier which surrounds
all living cells is known as a cell
membrane.
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The Cell concept


Cell membrane

It is made by phospholipid bilayer.


It allows the cell to maintain a
constant internal environment.

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The Cell concept


Cell membrane (cont)

It is selectively
permeable controlling
exchange between the
cell and its
environment.
It can communicate
with adjacent cells
and receive
extracellular signaling.

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The Cell concept


Cytoplasm
The living material between the
nucleus and the cell surface
membrane is known as cytoplasm.
This contains a variety of organelles.
An organelle is a distinct part of a cell
which has a particular structure and
function.

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Prokaryotic Cells
They are the most ancient group of organisms, having appeared
about 3500 million years ago.
The smallest organisms with a cellular structure.
Typical example: Escherichia coli (E. coli) - Rod-shaped bacterium

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Prokaryotic Cells

~ 0.5m, diameter
~ 1.5 m long

Surrounded by a plasma
membrane and usually by
a strong and rigid cell wall
which is made up of
polysaccharide chains.
The cytoplasm is not
divided into
compartments.

Nucleoid region
Ribosomes
Cytosol
Plasma membrane
Periplasmic space
Cell wall

Outer membrane
Pili

Flagella

E. coli cell

~~

The genetic information is in form of one or more DNA molecules


that freely exist in the cytosol.

The total DNA is much less than that of a eukaryotic cell.


The surface of a prokaryotic cell may carry pili (for attaching to
other cells) and flagella (for swimming).

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Eukaryotic Cells
Most eukaryotic cells are larger than prokaryotic ones.

They are compartmentalized.


Specialized functions are carried out in organelles.
Animal Cells
Plant Cells

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Eukaryotic Cells
Animal cell

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Eukaryotic Cells
Plant cell

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Prokaryotes and Eukaryotes

Comparison of Prokaryotic and Eukaryotic Cells

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Evolution of Eukaryotes
Mitochondria

Chloroplast

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Organelles in Eukaryotic cells


Nucleus

Surrounded by nuclear envelop of two membranes that is


perforated by nuclear pores.
Nuclear pores allow exchange of substances between the nucleus
and the cytoplasm. E.g. messenger RNA (mRNA)
The nucleolus appears as a rounded, darkly stained structure in
nucleus. Its function is to make ribosomes for protein synthesis.
Nucleolus
Nuclear
envelop

Chromatins
Nuclear pores

Chromosome

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Organelles in Eukaryotic cells


Nucleus (cont)
Deeply staining material
known as chromatin is
the loosely coiled form
of chromosomes.
Chromosomes contain
DNA associated with
basic protein called
histone.

Chromatin and condensed chromosome

DNA is wound around the histones which from bead-like structures


called nucleosomes.
Chromosomes appear as thread-like structures just before nuclear
division.
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Organelles in Eukaryotic cells


Nucleus (cont)

DNA is the genetic material


for controlling the cells
activities.
Nuclear division is the basis
of cell replication (DNA can
replicate itself), and hence
reproduction (new cells can
form).

Cell division (mitosis)


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Organelles in Eukaryotic cells


Mitochondrion
Surrounded by an envelop
of two membranes.
The inner membrane being
folded to from cristae.
Contains a matrix with a few
ribosomes, a circular DNA
molecule.
It is the powerhouse of cells
providing energy in the form
of ATP from oxidative
respiration.
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Organelles in Eukaryotic cells


Endoplasmic reticulum (ER)

A system of flattened, folded


membrane-bound structure.
It is continuous with the outer
membrane of the nuclear
envelope.
If ribosomes are found on its
surface it is called rough ER and
transports proteins made by the
ribosomes through the sac.

Smooth ER (no ribosomes) is a


site of lipid and steroid
synthesis.

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Organelles in Eukaryotic cells


Ribosomes

Attached to the surface ER or


free in cytoplasm.
Inside the mitochondria and
chloroplasts.
Consist of a large and a small
subunit.

They are made of roughly equal


parts of protein and RNA
(ribosomal RNA, rRNA).
They are used in protein
synthesis.
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Organelles in Eukaryotic cells


Ribosomes (cont)
Protein synthesis (Translation)

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Organelles in Eukaryotic cells


Golgi apparatus

Flattened membrane-bound
chambers.
It is continuously formed at one end
of the stack and budded off as
vesicles at the other.
Internal processing system

Modifies proteins from ER


Internal transport system

Transport the materials to other


parts of the cell or to the cell
surface membrane for secretion.
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Organelles in Eukaryotic cells


Golgi apparatus (cont)
Makes lysosomes.
Lysosomes contain many digestive enzymes to get rid of old
organelles, digest bacteria, autolysis (self-digestion).

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Organelles in Eukaryotic cells

Pieces of the ER bud off around proteins, form vesicles and deliver these proteins to the Golgi

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Organelles in Eukaryotic cells


Microfilaments and microtubules
They are cytoskeleton providing the cell with shape, strength,
and movement (cell motility).

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Organelles in Eukaryotic cells (Plant)


Cell wall

Outside the cell membrane.


Cell wall

It is rigid because it consists of cellulose


microfibrils.
It provides mechanical support and
protection.
It prevents osmotic bursting of the cell.

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Organelles in Eukaryotic cells (Plant)


Cell wall (cont)

It contains pores containing fine threads known as


plasmodesmata which link the cytoplasm of neighboring cells
through the cell walls.

Plasmodesmata
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Organelles in Eukaryotic cells (Plant)


Chloroplast

Present in photosynthetic eukaryotes.


It is surrounded by an envelop of two
membranes.

Contains a gel-like stroma through which


runs a system of stacked membranes
called grana where starch is stored.
The stroma also contains ribosomes, a
circular DNA molecule.
Photosynthesis takes place there,
producing sugars from carbon dioxide
and water using light energy trapped by
chlorophyll.

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Biological Molecules
Biochemistry is the study of the chemicals
of living organisms.
Living creatures are composed mainly of a
very few elements, principally carbon (C),
hydrogen (H), oxygen (O) and nitrogen (N).
These elements are important to life
because of their strong tendencies to form
covalent bonds.
A second tier of essential elements
includes sulphur (S) and phosphorus (P).
Sulphur: constituent of proteins.
Phosphorus: energy metabolism (ATP) and
the structure of nucleic acids (DNA and RNA).

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Bioenergetics
A living cell is a dynamic structure.

It GROWS, MOVES, SYNTHESIZES complex macromolecules


(Proteins, Carbohydrates, Lipids and Nucleic acids) and
SHUTTLES substances in and out between compartments.
All of these activities requires ENERGY.
Energy has an ability to do work or bring
about change.
Plants gather energy from sunlight while
animals use the energy stored in plants
or other animals.
Bioenergetics is a quantitative analysis of
how organisms gain and use energy.
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Bioenergetics
First law of Thermodynamics

Energy cannot be created nor can it be destroyed.


The quantity of energy remains the same.
It can be transformed from one form into another, but the
total amount of energy in the universe remains constant.

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Bioenergetics
Second law of Thermodynamics
Systems of molecules have a natural tendency to randomization.

The degree of randomness or disorder of a system is called


entropy (S).
The entropy of an isolated system will tend to increase to a
maximum value.

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Bioenergetics
Every biological system is open to exchange energy and matter
with its environment.
Both energy and entropy
changes will take place in
many reactions.
Both are important in
determining the direction
of thermodynamically
favorable processes.

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Bioenergetics
The total (internal) energy is called enthalpy (H).
The useable energy is called Gibbs free energy (G).

The unusable energy is entropy (S), a measure of the disorder of


the system.
The Gibbs free energy is defined as:

For favorable reaction: DG < 0 (Spontaneous, exergonic)


Decrease in DH (-ve)
Increase in DS (+ve)

For unfavorable reaction: DG > 0 (Not spontaneous, endergonic)41

Bioenergetics - Metabolism
Exergonic reaction
G products < G reactants
Reaction will
proceed.
spontaneously
Free energy is
released.
Endergonic reaction
G product > G reactants
Free energy is
required or
consumed.
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Bioenergetics - Examples

?G?

?G?
?G?

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Bioenergetics - Metabolism
Functions of ATP
Provision of energy in macromolecules synthesis.
Transporting substances across the plasma membrane.
Motility, muscle contraction, beating flagella.
Structure of ATP

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Bioenergetics - Metabolism

ATP

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Bioenergetics - Metabolism

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Bioenergetics - Metabolism
The free energy released by the exergonic reaction can be
used to drive the endergonic reaction.
Coupled reactions

(Endergonic)

(Exergonic)

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