INTRODUCTION TO

BIOCHEMISTRY
CELL
1. Define and describe the different parts
of the cell
2. Describe the transport mechanism;
3. Differentiate hypertonic, hypotonic
and isotonic reactions in cell
The key to
every
biological
problem
must finally
be sought in
the cell, for
every living
organism is,
or at some
E.B. Wilson, 1925
 Cells are Us

Cilia on a protozoan Sperm meets egg

A person contains about 100 trillion cells. That’s
100,000,000,000,000
or 1 x 10 14
cells.200 different cell types in mammals.
There are about
Cells are tiny, measuring on
average about 0.002 cm (20
um) across. That’s about 1250
cells, “shoulder-to-shoulder”
per inch.

Red and white blood cells

above vessel-forming cells.
nerve cell
SIZE RANGE OF CELLS
PROKARYOTIC CELL
AND EUKARYOTIC
CELL
 The basic structural and
functional unit of every organism
is one of two types of cells:
Only prokaryotic
organisms of theor
domains Bacteria and
eukaryotic
Archaea consist of prokaryotic cells
Protists, fungi, animals, and plants all consist
of eukaryotic cells.
Both prokaryotic cell and eukaryotic cell
have
• Plasma membrane
• Semifluid substance called cytosol
• Chromosomes (carry genes)
 Fimbriae

Nucleoid

Ribosomes

Plasma
membrane
Bacterial
chromosome Cell wall

Capsule

0.5 m
(a) A typical Flagella (b) A thin section
rod-shaped through the
bacterium bacterium Bacillus
coagulans (TEM)

Prokaryotic cells are characterized by having no

nucleus, have DNA in an unbound region called the
nucleoid, have no membrane-bound organelles and
Eukaryotic cells are
characterized by
having DNA in a
nucleus that is
bounded by a
membranous
nuclear envelope,
membrane-bound
organelles, and
cytoplasm in the
region between the A eukaryotic cell
The Fundamental Units of Life
• All organisms are made of cells
• The cell is the simplest collection of
matter
that can be alive
• Cell structure is correlated to cellular
function
• All cells are related by their descent
from earlier cells
All organisms are made of
cells.
The cell is the simplest collection of matter that can be
FOUR MAJOR alive.
EPITHELIAL
TYPES OF CELLS
CELLS NERVE MUSCLE CONNECTIVE
CELLS
These CELLS
cells are These cells are
TISSUE
These cells specialized for specialized for
are tightly communication contraction. CELLS
attached to . They send They pull and
one another. These cells
signals from tug on bones
They cover provide
the brain to and tendons to
over the structural
muscles and produce
interior of strength to the
glands that motion. They
hollow body and also
control their also form the
organs, like defend against
functions. They thick outer
blood vessels foreign invaders
also receive walls of hollow
or digestive like bacteria.
sensory organs, like
organs, or Other cells
information blood vessels
else form the migrate into
from the skin, and digestive
surface of connective tissue
the eyes, and organs, and can
 Cell structure is correlated to cellular function.
The contents of the cell, or the structures of the cell, allow the
cell to be SPECIALIZED. Together with the cell's proteins,
they allow the cell to do specific things. They allow a cell to
act like a neuron or a bone cell or a skin cell.
The structure-function relationship describes a pattern
evident throughout biological systems. This relationship is
evident in proteins (protein structure determines its
function), nucleic acid (nucleic acid structure results in a
genetic code), anatomy (longer necked giraffes are more
functional
Specialized than
cells short neck
perform manygiraffes),
diverse as well as cells.
functions, from
digestion and excretion to message transmission and
oxygen distribution. The structure of each type of human
cell depends on what function it will perform. This
structure-function relationship can be extended to all
other organisms, from the largest whale to the smallest
The variability between cell function is related to the proteins expressed
in a particular type of cell. They do have many proteins in common, a
neuron is going to use select different proteins than muscle cell. A
direct relationship exists between the proteins expressed, the size and
shape of every cell and the tasks it needs to accomplish.

• Red blood cells are flat, round, and very small. Their small size
allows easy maneuverability through the capillaries, the
narrowest blood vessels, where oxygen is transferred into body
cells.
• Neurons have a long, thin cellular extension, allowing for very
quick and accurate communication and responses. The long
length allows a neuron to send electrical messages extremely
quickly.
• Skeletal muscle cells have an arrangement of linear protein
fibers. The elongated shape allows for muscle contraction.
 THE CELL STRUCTURE
FOUND IN BOTH
PLANT CELL
AND ANIMAL
CELL
• Nucleus
• Golgi Complex
• Mitochondrion
• Lyosomes
• Endoplasmic
Reticulum
• Cell Membrane
• Ribosomes
• Vacuoles
FOUND ONLY IN
PLANT CELL
• Chloroplasts
• Cell Wall
ROLE THAT CELL COMPONENTS PLAY IN MAKING
Major Divisions of the Eukaryotic Cell
 Organelles

Organelles are structures that enable the cell to live, grow and reproduce.

all cells have

organelles,
however not all
cells have
Nucleus • The Nucleus:
• The control center of the
cell Information Central
• Contains the cell’s DNA
•The nucleus contains most
of the cell’s genes and is
DNA usually the most
conspicuous organelle
•The nuclear envelope
encloses the nucleus,
separating it from the
Nucleolus cytoplasm
•The nuclear membrane is
Nuclear Membrane
a double membrane; each
Figure 6.9
1 m
Nucleus
Nucleolus

Chromatin

Nuclear envelope:
Inner membrane
Outer membrane
Nuclear pore

Rough ER
Pore
complex
Surface of nuclear
envelope Ribosome

Close-up
0.25 m

of nuclear Chromatin
envelope
1 m

Pore complexes (TEM)

Nuclear lamina (TEM)

Figure 6.9a
Nucleus
Nucleolus

Chromatin

Nuclear envelope:
Inner membrane
Outer membrane
Nuclear pore

Rough ER
Pore
complex
Ribosome

Close-up
of nuclear Chromatin
envelope
 • Pores regulate the entry and exit of molecules
from the nucleus
• The shape of the nucleus is maintained by the
nuclear lamina, which is composed of protein

© 2011 Pearson Education, Inc.

 • In the nucleus, DNA is organized into discrete
units called chromosomes
• Each chromosome is composed of a single DNA
molecule associated with proteins
• The DNA and proteins of chromosomes are
together called chromatin
• Chromatin condenses to form discrete
chromosomes as a cell prepares to divide
• The nucleolus is located within the nucleus and
is the site of ribosomal RNA (rRNA) synthesis

© 2011 Pearson Education, Inc.

Ribosome Mitochondrion
• Site where proteins are
•Power center of cell
made •Provides the energy
• Cell parts are made of the cell needs to
proteins
move, divide, etc.
Outer Membrane

Inner Membrane
Cell Membrane
• Outer layer of cell made of
phospholipids
• Allows nutrients into the cell
and wastes outside of the cell
Cell Membrane
Cytoplasm
• Cytoplasm a jelly-like
fluid contained in the cell
that holds the organelles.
The endomembrane system regulates
protein traffic and performs metabolic
functions in the cell
• Components of the endomembrane system
– Nuclear envelope
– Endoplasmic reticulum
– Golgi apparatus
– Lysosomes
– Vacuoles
– Plasma membrane (Cell membrane)
• These components are either continuous or
connected via transfer by vesicles
 Endoplasmic Reticulum
•Transportation system of cell
Nuclear Envelope•Rough ER- ribosomes attached
• Double-layered •Smooth ER- no ribosomes
membrane that •Substances move through tubular
encloses and connections from one place to
protects the another.
contents of the •The ER is responsibleEndoplasmic
for delivering
Reticulum
nucleus during proteins to different parts of the cell.
most of the cell's
lifecycle. .

Ribosomes
The Endoplasmic Reticulum: Biosynthetic
Factory
• The endoplasmic reticulum (ER) accounts for more than half
of the total membrane in many eukaryotic cells
• The ER membrane is continuous with the nuclear envelope
• There are two distinct regions of ER
– Smooth ER, which lacks ribosomes
Synthesizes lipids / Metabolizes carbohydrates
Detoxifies drugs and poisons / Stores calcium ions
– Rough ER, surface is studded with ribosomes
Has bound ribosomes, which secrete glycoproteins (proteins
covalently bonded to carbohydrates)
Distributes transport vesicles, proteins surrounded by
membranes
A membrane factory for the cell
 Smooth ER
Nuclear
envelope
Rough ER

ER lumen
Cisternae Transitional ER
Ribosomes
Transport vesicle
200 nm
Smooth ER Rough ER
 Golgi
Lysosome
• Complex
Packaging house of cell
• Packages, processes, and ships out the stuff
•Digests food particles and cell parts
the cell makes •Protects cell by digesting foreign
• They modify and package the proteins and invaders
lipids (that came from ER) and ship them
out of the cell. •Special vesicles that contain enzymes.
•When a cell engulfs a particle, the
lysosomes bump into it an pour enzymes
into it. Then the particle is digested by
the enzymes.
•Sometimes lysosomes break open and
pour out the enzymes into the cytoplasm.
This will kill the cell.
- this is why tadpoles lose their
tails
- this is why humans don’t have
webbed feet. The lysosomes kill the cells
that make up the tails and webbing. This
act is a theory on how we age.
Vacuole
• Stores water, food & wastes
• Vacuole is largest organelle in
plant cell
• Vacuoles that are full of water and
air, support the cell.
• When the water and air is lost, the
plants go limp.
• The pressure that the water uses to
keep the plant up right is called
Turgor pressure.
Cell Wall
•Stores water, food & wastes
•The strength of billions of cell
walls ill be able to make a tree stand
up tall and bear huge limbs.
•Cell walls are made up of a
material called cellulose.
•Cellulose is a material that is
intertwined together. It resembles a
blanket or even like hashbrown
potatoes all piled up.
•When the plant cells are stacked on
top of each other and next to each
other it looks like building blocks.
Cytosol
• Liquid found inside of
cells. It is the water-based
solution in which
organelles, proteins, and
other cell structures float.
• The cytosol of any cell is
a complex solution,
whose properties allow
the functions of life to
take place. Cytosol
contains proteins, amino
acids, mRNA, ribosomes,
sugars, ions, messenger
molecules, etc
 Cytoskeleton The cytoskeleton is a
Provides support in a cell. It is a
network of protein fibers supporting
network of fibers that
cell shape and anchoring organelles
within the cell.
organizes structures
and activities in the cell.
• The cytoskeleton is a network of
fibers extending throughout the
cytoplasm
• It organizes the cell’s structures
and activities, anchoring many
organelles
• It is composed of three types of
molecular structures
– Microtubules
– Microfilaments
10 m

– Intermediate filaments
 Roles of the
Cytoskeleton: Support ATP
Vesicle
Receptor for
and Motility motor protein
• The cytoskeleton helps to
support the cell and maintain
its shape Motor proteinMicrotubule
• It interacts with motor (ATP powered)of cytoskeleton
proteins to produce motility (a)
• Inside the cell, vesicles can Microtubule Vesicles 0.25 m
travel along “monorails”
provided by the cytoskeleton
• Recent evidence suggests
that the cytoskeleton may
help regulate biochemical
activities

(b)
Components of the Cytoskeleton
• Three main types of fibers make up the
cytoskeleton
– Microtubules are the thickest of the three
components of the cytoskeleton
– Microfilaments, also called actin filaments, are
the thinnest components
– Intermediate filaments are fibers with
diameters in a middle range
Table 6.1a

10 m

Column of tubulin dimers

25 nm

  Tubulin dimer
Table 6.1b

10 m

Actin subunit

7 nm
Table 6.1c

5 m

Keratin proteins
Fibrous subunit (keratins
coiled together)
812 nm
Centrosomes and
Centrioles
• In many cells, Centrosome Microtubule
microtubules grow
out from a Centrioles
centrosome near 0.25 m
the nucleus
• The centrosome is
a “microtubule-
organizing center” Longitudinal
section of
• In animal cells, one centriole

the centrosome
has a pair of
centrioles, each Microtubules Cross section
with nine triplets of the other centriole
Chloroplast
• Found only in plant cells
• Contains chlorophyll (makes
plants green)
• Where photosynthesis takes
place
• Plants don’t ingest food like
we do or animals do, they
have to make their own food.
• Chloroplasts uses the sun’s
light energy to make sugar.
The sugar is then used by the
mitochondria to make energy.
 OTHER PARTS OF A CELL
Cilia Flagella
Small hair-like protuberances on Long, whip-like filamentous protein
the outside of eukaryotic cells. structures found in bacteria, archaea, and
They are primarily responsible for eukaryotes, though they are most commonly
locomotion, either of the cell itself
or of fluids on the cell surface. 
found in bacteria. They are typically used to
propel a cell through liquid. 

• BACTERIA is a member of a large group of unicellular

microorganisms which have cell walls but lack
organelles and an organized nucleus, including some
that can cause disease.
• ARCHAEA is any of a group of single-celled prokaryotic
organisms whose cells lack a defined nucleus but have a
distinct molecular characterisitcs separating them from
bacteria and from plants and animals.

• EUKARYA is any group of organisms consisting of a cell

or cells in which the genetic material is DNA in the form
of chromosomes contained within a distinct nucleus.
DISEASES LINKED TO CELL AND CELL
PROCESSES
Patient #1: Jackie
Jackie was a healthy baby when she was first born, but after 4 months,
she had gained little weight. Her parents suspected something was
seriously wrong. Her head became disproportionally large for her face.
She experienced hair loss, and her skin became thin and wrinkled.
Jackie’s doctors told them that the condition was progeria which
occurs when the genetic material doesn’t have proper protection.
This disease is incredibly rare. It
affects only one in every 4-8
million births. It is caused by a
mutation in a gene called LMNA,
but is not hereditary. This disease
causes premature aging. People
with progeria have an average life
expectancy of 14 years and usually
die from heart disease related to
their “aging” body.
Patient #2: Fiona
Fiona is a freshmen in college. She is a good student who does her work on
weekdays and likes to party on the weekends with her friends. A few months ago,
Fiona developed a cough that wouldn’t to go away and worsened over time.
She has also had difficulty breathing over the past week or so. Her friends
encouraged her to see the doctor, so she finally made an appointment. The doctor
asked her whether or not she smoked cigarettes. Fiona responded that she started
smoking cigarettes (about 2 per day) her freshman year of high school.
The doctor decided it was necessary to take a
biopsy of the cells that line the bronchus
(passageway to the lungs). After several days,
the biopsy report has come back along with a
micrograph of the bronchial cells. Fiona's
cigarette smoking has badly damaged these
organelles which are responsible for mucous
and dirt moving up and out of her respiratory
system. What cell organelles have been
damaged?
Patients #3: Zeke and Morgan
Zeke and Morgan have lived in Vermont most of their lives. They are
both in their late 20's and recently married. They have been trying to
have their first child for a number of months but Morgan has been
unable to get pregnant. Zeke and Morgan decided to go to their family
physician to see if there may be something wrong. The physician
obtained a sample of Zeke's sperm cells
and had it sent to a lab for microscopic
analysis. After several days, the physician
received a micrograph of the sperm cells
and noted a structural defect in the
organelle responsible for cell movement.
Help determine the organelle responsible
for Zeke and Morgan's inability to
have a baby.
Patient #4: Trevor
Trevor is a 20-year old male who has suffered from repeated episodes
of hemolytic anemia. During these episodes, Trevor’s red blood cell
counts drop off dramatically due to rupturing of large numbers of cells
and the inability of his bone marrow to replace the ruptured cells fast
enough. When Trevor comes into a clinic for treatment, he is
diagnosed initially with a hereditary deficiency in the enzyme glucose-
6-phosphate dehydrogenase, but biochemical tests rule this out. An
examination of his blood reveals that many of his red blood cells have
an elliptical shape which leads to the
diagnosis of hereditary elliptocytosis. In this disorder,
structures within the red blood cells
alter the shape of the cell from the
normal biconcave, disc shape to an
elliptical shape, causing premature
damage and rupture of the cells.
Patient #5: Rosanna
Rosanna is a 39-year old woman who comes to visit an urban
New York City clinic. Despite rarely working out, she has a
very muscular build, suggesting a hypertrophy (enlargement)
of her muscles. She has suffered from bouts of extreme
muscle stiffness, especially in her legs, and often brought on
by cold weather throughout her life. Her father and paternal
grandmother also had these symptoms. After genetic
screening and biochemical tests, the doctors determine that
she is suffering from myotonia congenita, a
“channelopathy” involving a
malfunction of chloride
channels, which regulate the
movement of chloride ions
between the outside and
inside of the cell.
Patient #6: Harvey
Harvey was a perfectly happy baby with normal development until about
six months of age. He had learned to roll over and sit up for a few
seconds, but then was suddenly unable to do either of these things. He
stopped turning and smiling at his mother's voice as he had before, and
he did not seem as interested in his toys as he once was. Harvey’s
parents took him to the doctor because they were concerned about
these changes. It took exams by several specialists to diagnose
Harvey's Tay-Sachs disease. This disease has become very rare (fewer
than ten cases appear each year) in large part due to screening
programs in population groups known to have this inherited illness.
Harvey's parents were not among those ethnic groups most as risk.
Also, they had no idea that they both were carriers of the gene that
causes this very rare illness. A neurologist verified her hypothesis of
Tay-Sachs by looking into Harvey's eyes, where she saw the telltale
cherry red spot indicating the illness. There was a build up fatty material
on his nerve cells that his cells couldn’t break down. His nervous system
would continue
to fail, and he would be
paralyzed and unable to see or
hear by the time he died
before the age of four.
Patient #7: Kathy
Kathy is a fifteen-year-old soccer player at a nearby high school. She arrived
in the ER at 6:07 p.m. She was experiencing extreme muscle weakness and
loss of muscle coordination, particularly in her arms and legs! She told the
doctors that for the past few days, she had been extra tired with little energy to
do anything. The doctors decided to do some blood work which showed one
particular abnormality. Kathy’s glucose levels were rather high although she
was an athlete and did mention she usually ate carbohydrates the night before
a game. However, this explanation could be dismissed since she did not have a
game in the past week. The doctors agreed that
something else must be going on to cause such high
glucose levels (i.e. something was not breaking down these
sugar molecules). The doctors ordered for a muscle
biopsy to be performed. The doctors viewed the
tissue sample under the microscope, and saw that
the muscle fibers were ragged red which contained
mild accumulations of glycogen and decreased
activity for the enzyme cytochrome c oxidase.
Patient #8: Lucy and Jim
Lucy and Jim have been married for 5 years and have decided they
would like to try to have a child. However, a rare genetic disorder
runs in both or their families, so they decide to go to a genetic
counselor to determine the chances that their future child will be
affected. The disease achondrogenesis 1a affects the ability of
proteins necessary for bone and cartilage development to be
modified and packaged properly after
leaving the endoplasmic reticulum. The
results are devastating. Individuals with this
disorder are often stillborn or die soon after
birth from respiratory failure. Fortunately,
after doing a genetic screening, the genetic
counselor determined that while Jim is a
carrier for this autosomal recessive disorder,
Lucy is not. Therefore, if they do have a child,
it is unlikely that their child will be affected.
Patient #9: Vera
When Vera came home from her first day of kindergarten, she was very
upset. She always knew she was different, but she had never been around
this many new people who were staring and whispering. Vera was born
with Treacher Collins syndrome. She has it because there is a mutation
in her DNA that codes for the part of the cell responsible for assembling
proteins. Because these cells are unable to
make proteins, they undergo apoptosis
(programmed cell death). Doctors don’t
know why but this cell death occurs only in
the cells necessary for the development of
facial bones and tissues. Even though Vera
has had several plastic surgeries in her life
to make her appearance less affected by
the disease, she continues to have distinct
facial characteristics, such as
underdeveloped cheek bones, unusually
formed ears, and a very small jaw and chin.
Name of Organelle Picture Function Patient/Disease

Nuclear Envelope Double-layered membrane that encloses and Patient #1 Jackie

protects the contents of the nucleus during most of Progeria
the cell’s lifecycle

Cilia Small hair-like protuberances on the outside of Patient #2 Fiona

eukaryotic cells. They are primarily responsible for Cough from smoking/COPD
locomotion, either on the cell itself or of fluids on the
cell surface

Flagella Long, whip-like filamentous protein structures found Patient #3 Zeke and Morgan
in bacteria, archaea, and eukaryotes, though they Infertility/MMF
are typically used to propel a cell through liquid

Cytoskeleton Provides support in a cell. It is a network of protein Patient #4 Trevor

fibers supporting cell shape and anchoring Hereditary Elliptocytosis
organelles within the cell.

Plasma Membrane The border between the interior and exterior of a Patient #5 Rosanna
cell. It controls passage of various molecules – Myotonia Congenita
including sugars, amino acids, ions, and water – into
and out of the cell

Lysosome A vesicle that contains hydrolytic enzymes that can Patient #6 Harvey
break down many kinds of biomolecules Tay-Sachs

Mitochondria Rod-shaped organelles that can be considered the Patient #7 Kathy

power generators of the cell, converting oxygen and Decreased Cytochrome C
nutrients into adenosine triphosphate (ATP) Oxidase/Myopathy

Golgi Gathers simple molecules and combines them to Patient #8 Jim and Lucy
make molecules that are more complex. It then Achondrogenesis 1a
takes those big molecules, packages them in
vesicles, and either stores them for later use or
sends them out of the cell. It is also the organelle
that builds the lysosomes.

Ribosomes Link amino acids together in the order designated by Patient #9 Vera
the mRNA to create proteins, can be found floating Treacher Collins
free in the cytoplasm or attached to the endoplasmic
reticulum.
All cells are related by their descent from earlier cells.
All cells are related by their descent from earlier cells. However,
PRESENT
they have been modified in many0different ways during the long
evolutionary history of life on Earth. But although cells can differ
substantially from one another, they share common features.
1
It appears that life first
emerged at least 3.8
MULTICEL
billion years ago,
2 LULAR
approximately 750 million ORGANIS
years after Earth was MS
FIRST
formed. How life EUKARYOTE
3
originated and how the S
OXIDATIVE
first cell came into being METABOLIS
are matters of FIRST
M
4 PHOTOSYNT
CELLS
speculation, since these HESIS
events cannot be 4.
FORMATI
reproduced in the ON OF
6
EARTH