Introduction to Biophotonics
生醫光子學導論
Chapter 2: Basic biology
孫家偉 Chia-Wei Sun
交通大學光電工程學系
Optics in biological tissue
An understanding of the propagation of
light in biological tissue is essential for
the use of light for medical diagnosis
and therapy. Light propagation in tissue
is complicated by multiple scattering
effects. Numerous models that predict
fluence rates in tissue, or reflection and
transmission of light by tissue have
been developed.
Optics in biological tissue
The accuracy of these models
ultimately depends upon how well the
optical properties of the tissue are
known. Optical parameters are
obtained by converting measurements
of observable quantities (e.g.,
reflection) into parameters which
characterize light propagation in tissue.
The conversion process is based on a
particular theory of light transport in
tissue.
Hierarchical structure of biological
systems
All living creatures are made up of cells. They
exist in a wide variety of forms, from single cell in
free-living organisms to those in complex
biological organisms. Despite the great diversity
exhibited by living systems, all biological systems,
amazingly, are composed of the same types of
chemical molecules and utilize similar principles
in replication, metabolism, and, in higher
organisms, the ability to organize at the cell
levels. Even at the most elemental cellular level,
microorganisms exhibit a large range of length
scale, from viruses measuring 20–200 nm to a
eukaryotic cell measuring 10–100 mm.
Hierarchical structure of biological
peptides 胜肽
polysaccharide 多醣類
systems
nucleotide 核 酸
ribose 核酸糖
磷酯
Biological systems are essentially anphospholipid
assembly
of
molecules where water, amino acids,
carbohydrates (sugar), fatty acids, and ions
account for 75–80% of the matter in cells. The
remainder of the cell mass is accounted for by
macromolecules, also called polymers (or
biopolymers in the present case), which include
peptides/proteins (formed from amino acids),
polysaccharides (formed from sugars), DNA
(deoxyribonucleic acid, formed from nucleotide
bases and deoxyribose sugar), RNA (ribonucleic
acid, formed from nucleotide bases and ribose
sugar), and phospholipids (formed from fatty
acids).
Hierarchical structure of biological
prokaryotic 原核的
eukaryotic 真核的
systems
These macromolecular polymers organize to form
cells. To contain these molecules, a
semipermeable membrane (phospholipid bilayer)
surrounds them to form a cell. Prokaryotic cells
(bacteria) are cells with little internal structure and
no defined nucleus. Eukaryotic cells have a
significantly more complex internal architecture
including a defined, membrane-bound nucleus.
The smallest organized particle is a virus. The
smallest self-replicating cells are bacteria.
Eukaryotic cells, for the most part, organize to
form complex living organisms.
Hierarchical structure of biological
systems
Small molecules:
Amino acids
Nucleic acids
Water
Lipids
Ions
Polymerization of nucleic acids to form DNA and
RNA, and polymerization of amino acids to form
protein
Virus
Size scale: 20–200 nm
Structure: Single- or doublestranded RNA or DNA
Function: Infectious but not
self-replicating
Prokaryotic cells: Bacteria
Size scale: ~1–10 mm
Structure: Single-cell
organism consisting of
single closed compartment
that lacks a defined nucleus
Function: Free-living and
self-replicating
Eukaryotic cells: Animal/
plant cells
Size scale: ~10–100 mm
Structure: Complex structure
surrounded by a lipid
membrane, contains an
organized nuclear structure
Function: Self-replicating
and able to assemble to form
tissues
Hierarchical Buildup of a Living Organism
Cells
Cell differentiation and association
Tissues
Organization to perform a function
Organs
Integration of various functions
Organism
Structural components of
amembrane
cell細胞膜
plasma
cytoplasm 細胞原漿
cytosol 細胞漿液
organelle 胞器
chromosome 染色體
Plasma membrane, which defines the outer
boundary of a cell. This is present in all cells.
Cell wall, which exists in the prokaryotic cells as
well as in the eukaryotic cells of plants but not
animals.
Cytoplasm, which represents everything within a
cell, except the nucleus.
Cytosol, which is the fluid of the cytoplasm.
Organelle, which is the name used for a
subcellular compartment in a cell where a specific
cellular function takes place.
Nucleus, which contains the chromosomes
(genetic information).
Comparison between prokaryotic cell and
eukaryotic cell
Prokaryotic cell
Eukaryotic cell
Comparison between prokaryotic cell and
eukaryotic cell
peptidoglycan 胜糖
It is readily seen that the prokaryotic cell, or
bacteria, has a much less complex internal
structure compared to the eukaryotic cell.
In addition, a complex outer wall structure
exists in most bacteria and is composed of
unique outer membrane and inner
membrane structures between which are
sandwiched a rigid unique polysaccharide
cell wall. This wall consists of a
macromolecule known as peptidoglycan
that enables an organism to survive in
changing environments.
Plasma membrane
alkyl 烴基
This forms a semipermeable outer boundary of
both prokaryotic and eukaryotic cells. This outer
membrane, about 4–5 nm thick, is a continuous
sheet of a double layer (bilayer) of long-chain
molecules called phospholipids. A phospholipid
molecule has a long tail of alkyl chain, which is
hydrophobic (repels water), and a hydrophilic
head (likes water) which carries a charge (and is
thus ionic). Phospholipid molecules
spontaneously orient (or self-organize) to form a
bilayer in which the hydrophobic tails are pointed
inwards (shying away from the outer aqueous
environment). The hydrophilic, ionic head groups
are in the exterior and are thus in contact with the
surrounding aqueous environment.
Plasma membrane
Phospholipid membrane bilayer structure
Plasma membrane
The membrane derives its rigidity by inclusion of
cholesterol molecules, which are interdispersed in
the phospholipid bilayer. Also embedded are
membrane proteins (receptors, pores, and
enzymes) that are important for a number of cell
activities including communication between the
intracellular and extracellular environments. The
plasma membrane controls the transport of food,
water, nutrients, and ions such as Na+, K+, and
Ca2+ (through so-called ion channels) to and from
the cell as well as signals (cell signaling)
necessary for proper cell function.
Cytoplasm
Cytoplasm represents everything enclosed by the
plasma membrane, with the exclusion of the
nucleus. It is present in all cells where metabolic
reactions occur. It consists mainly of a viscous
fluid medium that includes salts, sugars, lipids,
vitamins, nucleotides, amino acids, RNA, and
proteins which contain the protein filaments, actin
microfilaments, microtubules, and intermediate
filaments. These filaments function in animal and
plant cells to provide structural stability and
contribute to cell movement.
Cytoplasm
Many of the functions for cell growth,
metabolism, and replication are carried out
within the cytoplasm. The cytoplasm
performs the functions of energy production
through metabolic reactions, biosynthetic
processes, and photosynthesis in plants.
The cytoplasm is also the storage place of
energy within the cell. Cytosol, a subset of
cytoplasm, refers only to the protein-rich
fluid environment, excluding the organelles.
Cytoskeleton
The cytoskeleton structure, located just under the
membrane, is a network of fibers composed of
proteins, called protein filaments. This structure is
connected to other organelles. In animal cells, it is
often organized from an area near the nucleus.
These arrays of protein filaments perform a variety
of functions:
Establish the cell shape
Provide mechanical strength to the cell
Perform muscle contraction
Control changes in cell shape and thus produce
locomotion
Provide chromosome separation in mitosis and meiosis
Facilitate intracellular transport of organelles
Nucleus
The nucleus is often called the control center of
the cell. It is the largest organelle in the cell,
usually spherical with a diameter of 4–10 µm, and
is separated from the cytoplasm by an envelope
consisting of an inner and an outer membrane. All
eukaryotic cells have a nucleus. The nucleus
contains DNA distributed among structures called
chromosomes, which determine the genetic
makeup of the organism. The chromosomal DNA
is packaged into chromatin fibers by association
with an equal mass of histone proteins. The
nucleus contains openings (100 nm across) in its
envelope called nuclear pores, which allow the
nuclear contents to communicate with the cytosol.
Nucleus
Nucleus
ribosome 核酸醣小體
The inside of the nucleus also contains
another organelle called a nucleolus, which
is a crescent-shaped structure that
produces ribosomes by forming RNA and
packaging it with ribosomal protein. The
nucleus is the site of replication of DNA and
transcription into RNA. In a eukaryotic cell,
the nucleus and the ribosomes work
together to synthesize proteins.
Mitochondria
chloroplast 葉綠質小粒
Mitochondria are large organelles, globular in
shape (almost like fat sausages), which are 0.5–
1.5 µm wide and 3–10 µm long. They occupy
about 20% of the cytoplasmic volume.
Mitochondria serve as the engine of a cell. They
are self-replicating energy factories that harness
energy found in chemical bonds through a
process known as respiration, where oxygen is
consumed in the production of this energy. This
energy is then stored in phosphate bonds. In
plants, the counterpart of mitochondria is the
chloroplast, which utilizes a different mechanism,
photosynthesis, to harness energy for the
synthesis of high-energy phosphate bonds.
Mitochondria
http://en.wikipedia.org/wiki/Mitochondrion
Golgi apparatus
This organelle is named after Camillo Golgi, who
described it. It consists of stacked, flattened
membrane sacs or vesicles, which are like
shipping and receiving departments because they
are involved in modifying, sorting, and packaging
proteins for secretion or delivery to other
organelles or for secretion outside of the cell.
There are numerous membrane-bound vesicles
(<50nm) around the Golgi apparatus, which are
thought to carry materials between the Golgi
apparatus and different compartments of the cell.
Various types of cells
Cells come in many shapes, sizes, and
compositions. The human body is made up
of over 200 different types of cells, some of
which are living cells. The human body also
consists of nonliving matter such as hair,
fingernails, and hard parts of bone and
teeth, which are also made of cells. These
cell variations are produced by cell
differentiation. Also, different types of cells
assemble together to form multicellular
tissues or organisms.
Epithelial cells
ciliated 有纖毛的
mucus 黏液
secretory 分泌的
exocrine 外分泌
gastric juice 胃液
endocrine 內分泌
Epithelial cells form sheets, called epithelia, which
line the inner and outer surfaces of the body.
absorptive cells
have numerous hair-like microvilli projecting from their surface
to increase the absorption area,
ciliated cells
move substances such as mucus over the epithelial sheet
secretory cells
form exocrine glands that secrete tears, mucus, and gastric
juices
endocrine glands
secrete hormones into the blood
mucosal cells
protect tissues from invasive microorganisms, dirt, and debris.
Epithelial cells
http://en.wikipedia.org/wiki/Epithelium
Blood cells
These cells are contained in blood. These
cells comprise about 45% of the blood’s
volume and are suspended in a blood plasma,
which is a colloidal (small, suspendable
particle) suspension of proteins in an
electrolyte solution containing mainly NaCl.
The three different types of blood cells are
erythrocytes
commonly known as red blood cells; often abbreviated as
RBC
leucocytes
commonly known as white blood cells
thrombocytes
also known as platelets
Blood cells
http://en.wikipedia.org/wiki/Red_blood_cell
Blood cells
Erythrocytes or red blood cells are very small
cells, 7–9 µm in diameter, with a biconcave,
discotic shape. They usually have no
nucleus. One cubic centimeter of blood
contains about 5 billion erythrocytes, the
actual number depending on a number of
factors such as age, gender, and health.
They contain an oxygen-binding protein
called hemoglobin and thus perform the
important function of transporting O2 and
CO2.
Blood cells
lymphocyte 淋巴球
neutrophil 啫中性白血球
Leucocytes or white blood cells provide protection
against infection. They exist in a ratio of one
white blood cell for about every 1000 red blood
cells. They are usually larger than red blood cells.
There are a number of different types of
leucocytes, including
lymphocytes, which are responsible for immune
responses (the two kinds of lymphocytes are T cells,
which are responsible for cell-mediated immunity, and
B cells, which produce antibodies)
macrophages and neutrophils, which move to sites of
infection where they ingest bacteria and debris.
Platelets are organelles devoid of a nucleus and 2–5
µm in diameter (smaller than red blood cells). They
produce specific substances for blood coagulation.
Muscle cells
These specialized cells form muscle tissues
such as skeletal muscles to move joints,
cardiac muscles to produce heartbeat, and
smooth muscle tissues found around the
internal organs and large blood vessels.
Muscle cells produce mechanical force by
their contraction and relaxation.
http://en.wikipedia.org/wiki/Muscle
Neurons
Neurons are cells specializing in
communication. The brain and spinal cord, for
example, are composed of a network of
neurons that extend out from the spinal cord
into the body.
http://en.wikipedia.org/wiki/Neurons
Sensory cells
These cells form the
sensory organs such
as
hair cells of the inner
ear, which act as
detectors of sound
retina, where rod cells
specialize in responding
to light. The rod cells
contain a photosensitive
region consisting of lightsensitive pigments
(chromophores) called
rhodopsin.
http://en.wikipedia.org/wiki/Hair_cell
http://en.wikipedia.org/wiki/Retina
Germ cells
haploid 半染色體
gamete 配子
Germ cells are haploids (cells containing one
member or a copy of each pair of chromosome).
The two types of germ cells specialized for sexual
fusion, also called gametes, are
a larger, nonmotile (nonmoving) cell called the
egg (or ovum) from a female
a small, motile cell referred to as sperm (or
spermatozoon) from a male. A sperm fuses
with an egg to form a new diploid organism
(containing both chromosomes).
Bacteria are another example of haploid cells.
Stem cells
Stem cells can be thought of as blank cells
that have yet to become specialized
(differentiated), giving them the
characteristics of a particular type of cell
such as the ones described above. Stem
cells thus have the ability to become any
type of cell to form any type of tissue
(bone, muscle, nerve, etc.).
Stem cells
The three different types of stem cells are
embryonic stem cells
come from embryos
embryonic germ cells
come from testes
adult stem cells
come from bone marrow
這是受精後5~6天的人類細胞，稱為
胚囊。剝開囊胚取出的內部細胞圖
（圖中紅色突出部份），可用來製造
胚胎幹細胞。(取自科學人)
Stem cells
Embryonic stem cells are classified as
pluripotent because they can become any
type of cell. Adult stem cells, on the other
hand, are multipotent in that they are
already somewhat specialized. The
pluripotent type (which are in the early
stage of specialization after several cell
divisions) are more useful than the adult
stem cells. However, recent research
suggests that multipotent adult stem cells
can have pluripotent capability.
Stem cells
Stem cells can provide a solution in regard
to curing diseases caused by cell failure
and repairing tissues that do not repair by
themselves by allowing one to produce
appropriate cells and grow needed tissues.
Some of the diseases for which stem cell
research is projected to benefit are heart
damage, spinal cord injuries, Parkinson’s
disease, leukemia, and diabetes.
Nucleic acids
purine 嘌呤
pyrimidine 嘧啶
Nucleic acids exist in a cell in two forms: (i)
deoxyribonucleic acids (DNA) and (ii)
ribonucleic acids (RNA). Both forms consist
of three chemical building blocks
nitrogen-containing ring compounds that are
either purine or pyrimidine bases
sugar (either deoxyribose for DNA or ribose for
RNA)
phosphate
Nucleic acids
The four bases constituting DNA are
adenine (A), guanine (G), thymine (T), and
cytosine (C). In the case of RNA, the base
thymine (T) is replaced by another base,
uracil (U).
胞嘧啶（C）、鳥嘌呤（G）、腺嘌呤
（A）、胸腺嘧啶（T，通常為DNA專有）
和尿嘧啶（U，通常為RNA專有）。
Nucleic acids
Nucleic acids
The constituent sugars are ribose for RNA and 2-deoxyribose for
DNA.
Proteins
Proteins are formed during a
polymerization process that links amino
acids. Only 20 different amino acids form a
vast array of proteins capable of highly
diverse tasks. The functional nature of each
of these amino acids resides in the sidechain group (R group). The amino acids
link together by a peptide bond formed by
condensation of the amino group of one
amino acid with the carboxylic group of
another.
Proteins
Three possible representations of the three-dimensional structure of
the protein triose phosphate isomerase(磷酸丙糖異構酶). Left: allatom representation colored by atom type. Middle: simplified
representation illustrating the backbone conformation, colored by
secondary structure. Right: Solvent-accessible surface representation
colored by residue type.
http://en.wikipedia.org/wiki/Protein
Tissue
A tissue is a multicellular bioassembly in which
cells specialized to perform a particular task
contact tightly and interact specifically with each
other. The functions of many types of cells within
tissues are coordinated, which collectively allows
an organism to perform a very diverse set of
functions such as its ability to move, metabolize,
reproduce, and conduct other essential functions.
There are more than 200 distinguishable kinds of
differentiated cells that organize to form a variety
of tissues in the human body.
Tissue
Epithelial tissues
Epithelial tissues form the surface of the
skin and line all the cavities, tubes, and
free surfaces of the body. They are made of
closely packed epithelial cells arranged in
flat sheets. They function as the boundaries
between cells and a cavity or space. They
perform the function of protecting the
underlying tissues, as in the case of skin.
Muscle tissues
Skeletal muscle
Smooth muscle
Cardiac muscle
Connective tissues
The cells of connective tissues are embedded in
the extracellular materials. Examples of
supporting connective tissues are cartilage and
bone. Examples of binding connective tissues are
tendons and ligaments. Another type is fibrous
connective tissues, which are distributed
throughout the body and serve as a packing and
binding material for most of the organs.
http://en.wikipedia.org/wiki/Connective_tissue
Nerve tissues
These tissues are composed primarily of
nerve cells (neurons). They specialize in
the conduction of nerve impulses.
http://en.wikipedia.org/wiki/Nervous_tissue
Tumors
Understanding the molecular basis of cancer
growth is of great significance to society.
This understanding can perhaps lead to the
prevention, early detection, and cure of
cancer. Tumor is a general term used to
describe aberrations in normal cellular
behavior. Tumors differ from their normal
counterparts in growth control, morphology,
cell-to-cell interactions, membrane
properties, cytoskeletal structure, protein
secretion, and gene expression. Tumors can
either be benign or malignant (neoplasms).
Tumors
oncogene 致癌基因
Neoplasms multiply rapidly even in the absence
of any growth-promoting factors, which are
required for proliferation of normal cells.
Furthermore, neoplastic cells are resistant to
signals that program normal cell death
(apoptosis). One process by which normal cells
can transition to tumor cells is known as
transformation. In this process, any foreign genetic
material that causes cancer and has been
incorporated into the chromosome is activated by
factors in a process that is not yet clearly
understood. These “oncogenes” interfere with
normal regulatory processes, resulting in loss of
replicative control in the cell.
Tumors
metastasis 轉移
Tumors that remain localized are called benign. In the
case of a benign tumor, the tumor cells resemble and
function like the normal cells. The benign tumors pose
little threat to life and can be removed without affecting
any normal functions of a tissue.
Tumors in which the cells exhibit rapidly growing features
and possess a high nucleus-to-cytoplasm ratio are called
malignant tumors, neoplasms, or cancers. They often do not
remain localized and they may invade the surrounding
tissues. Neoplastic cells spread through the body’s
circulatory system and establish secondary areas of
growth. This behavior is called metastasis. Metastatic cells
also break their contacts with other cells, thus creating a
degeneration of the tissue function.