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 time has
been, a cell.
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 1014 cells.
There are about 200 different cell types in mammals.
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:
prokaryotic or eukaryotic
Only organisms of the domains Bacteria and 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)
• Ribosomes (make proteins)
 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 have cytoplasm bound by the plasma membrane
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 plasma
membrane and nucleus.
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 alive.
FOUR MAJOR TYPES OF CELLS
EPITHELIAL NERVE CELLS MUSCLE CELLS CONNECTIVE
CELLS These cells are These cells are
TISSUE
These cells are specialized for specialized for
tightly attached communication. contraction. They CELLS
to one another. They send signals pull and tug on
They cover over These cells provide
from the brain to bones and tendons
the interior of structural strength to
muscles and glands to produce motion.
hollow organs, the body and also
that control their They also form the
like blood defend against foreign
functions. They also thick outer walls of
vessels or invaders like bacteria.
receive sensory hollow organs, like
digestive Other cells migrate
information from blood vessels and
organs, or else into connective tissue
the skin, the eyes, digestive organs,
form the from the bloodstream
and the ears, and and can contract to
surface of to fight diseases.
send this regulate the
things, like the information to the diameter of these
skin. brain. hollow organs.
 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 than short neck giraffes), as well as cells.
Specialized cells perform many diverse 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 bacteria.
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.
• Sperm cells are the only human cell with flagella. This is because of their need to
"swim" long distances to reach an egg for fertilization.
 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 AND MOVING PROTEINS
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 membrane
covered organelles.
Nucleus • The Nucleus:
• The control center of Information Central
the cell
• Contains the cell’s DNA •The nucleus contains most of the
cell’s genes and is usually the most
DNA conspicuous organelle
•The nuclear envelope encloses
the nucleus, separating it from the
cytoplasm
•The nuclear membrane is a
Nucleolus double membrane; each membrane
consists of a lipid bilayer
Nuclear Membrane
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
•Power center of cell
• Site where proteins •Provides the energy the
are made cell needs to move, divide,
• Cell parts are made etc.
of proteins Outer Membrane

Inner Membrane
Cell Membrane Cytoplasm
• Outer layer of cell made of • Cytoplasm a jelly-like fluid
phospholipids contained in the cell that holds the
• Allows nutrients into the cell organelles.
and wastes outside of the cell

Cell Membrane
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 connections
encloses and protects from one place to another.
the contents of the •The ER is responsible for delivering proteins to
nucleus during most of different parts of the cell. Endoplasmic Reticulum
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 Complex
• Packaging house of cell
• Packages, processes, and
ships out the stuff the cell
makes
• They modify and package
the proteins and lipids (that
came from ER) and ship
them out of the cell.
Lysosome
•Digests food particles and cell parts
•Protects cell by digesting foreign invaders
•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 Cell Wall
• Stores water, food & wastes •Stores water, food & wastes
• Vacuole is largest organelle in plant cell •The strength of billions of cell walls ill be able
to make a tree stand up tall and bear huge
• Vacuoles that are full of water and air,
limbs.
support the cell. •Cell walls are made up of a material called
• When the water and air is lost, the plants cellulose.
go limp. •Cellulose is a material that is intertwined
• The pressure that the water uses to together. It resembles a blanket or even like
keep the plant up right is called Turgor hashbrown potatoes all piled up.
pressure. •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,
 Cytoskeleton
Provides support in a cell. It is
a network of protein fibers
supporting cell shape and
anchoring organelles within
the cell.
The cytoskeleton is a network
of fibers that 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
10 m
– Microfilaments
– Intermediate filaments
 Roles of the Cytoskeleton: Vesicle
Support and Motility ATP
Receptor for
motor protein
• The cytoskeleton helps to
support the cell and maintain
its shape Motor proteinMicrotubule
(ATP powered)of cytoskeleton
• It interacts with motor (a)
proteins to produce motility Microtubule Vesicles 0.25 m
• Inside the cell, vesicles can
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 centrosome Centrioles
near the nucleus 0.25 m
• The centrosome is a
“microtubule-
organizing center”
Longitudinal
• In animal cells, the section of
centrosome has a pair one centriole
of centrioles, each
with nine triplets of
microtubules arranged Microtubules Cross section
in a ring 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 the outside of eukaryotic
cells. They are primarily
responsible for locomotion,
either of the cell itself or of
fluids on the cell surface.
Long, whip-like filamentous protein structures
found in bacteria, archaea, and eukaryotes,
though they are most commonly 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 cell. Patient #5 Rosanna
It controls passage of various molecules – including Myotonia Congenita
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, they have
PRESENT
0
been modified in many different ways during the long evolutionary
history of life on Earth. But although cells can differ substantially from
one another, they share
1
common features.
It appears that life first emerged at
least 3.8 billion years ago,
MULTICELLULAR
approximately 750 million years
2 ORGANISMS
after Earth was formed. How life
originated and how the first cell
FIRST EUKARYOTES
came into being are matters of OXIDATIVE
3
speculation, since these events METABOLISM
PHOTOSYNTHESIS
cannot be reproduced in the
laboratory. Nonetheless, several FIRST CELLS
4
types of experiments provide
important evidence bearing on 4.6 FORMATION OF
some steps of the process. EARTH