The Cell

The basic unit of life

 Cells
• Smallest living unit
• Most are microscopic
 Discovery of Cells
• Robert Hooke (mid-1600s)
– Observed sliver of cork
– Saw “row of empty boxes”
– Coined the term cell
Cell History

• Robert Brown
– discovered the nucleus in
1833.
• Matthias Schleiden
– German Botanist Matthias
Schleiden
– 1838
– ALL PLANTS "ARE
COMPOSED OF CELLS".
• Theodor Schwann
– Also in 1838,
– discovered that animals
were made of cells
 Cell History

• Rudolf Virchow
– 1855, German Physician
– " THAT CELLS ONLY COME FROM OTHER CELLS".
• His statement debunked "Theory of
Spontaneous Generation" 
 Cell Theory
• The COMBINED
work of Schleiden,
Schwann, and
Virchow make up
the modern CELL
THEORY.
 The Cell Theory states that:
1. All living things are composed of a cell or
cells.

2. Cells are the basic unit of life.

3. All cells come from preexisting cells.

Cell Size
 Characteristics of All Cells
• A surrounding membrane
• Protoplasm – cell contents in thick fluid
• Organelles – structures for cell function
• Control center with DNA
 Cell Types

• Prokaryotic

• Eukaryotic
 Prokaryotes and Eukaryotes, continued
Prokaryotes Eukaryotes

Single cell Single or multi cell

No nucleus Nucleus

No organelles Organelles

One piece of circular DNA Chromosomes

No mRNA post Exons/Introns splicing

transcriptional modification
 Prokaryotic Cells
• First cell type on earth
• Cell type of Bacteria and Archaea
 Prokaryotic Cells
• No membrane bound nucleus
• Nucleoid = region of DNA concentration
• Organelles not bound by membranes
EUKARYOTIC CELLS

Two Kinds:
Plant and Animal
 Eukaryotic Cells
• Nucleus bound by membrane
• Include fungi, protists, plant,
and animal cells
• Possess many organelles

Protozoan
Eukaryotic Example
Section 7-2

Smooth endoplasmic
Vacuole reticulum
Ribosome
(free)
Chloroplast
Ribosome
(attached)
Cell
Membrane
Nuclear
Cell wall envelope

Nucleolus

Golgi
apparatus Nucleus

Mitochondrion Rough endoplasmic reticulum

Plant Cell
The Nucleus

• Brain of Cell
• Bordered by a porous
membrane - nuclear envelope.
• Contains thin fibers of DNA
and protein called Chromatin.
• Rod Shaped Chromosomes
• Contains a small round
nucleolus
– produces ribosomal RNA which
makes ribosomes.
Ribosomes
• Small non-membrane
bound organelles.
• Contain two sub units
• Site of protein synthesis.
• Protein factory of the cell
• Either free floating or
attached to the Endoplasmic
Reticulum.
Endoplasmic Reticulum
• Complex network of
transport channels.
• Two types:
1. Smooth- ribosome free
and functions in poison
detoxification.
2. Rough - contains
ribosomes and releases
newly made protein from
the cell.
 Rough Endoplasmic Reticulum
• Ribosomes attached to surface
– Manufacture protiens
– Not all ribosomes attached to rough ER
• May modify proteins from ribosomes
 Smooth Endoplasmic Reticulum
• No attached ribosomes
• Has enzymes that help build molecules
– Carbohydrates
– Lipids
 Golgi Apparatus
• A series of flattened
sacs that modifies,
packages, stores, and
transports materials
out of the cell.
• Works with the
ribosomes and
Endoplasmic
Reticulum.
Lysosomes
• Recycling Center
– Recycle cellular debris
• Membrane bound
organelle containing a
variety of enzymes.
• Internal pH is 5.
• Help digest food particles
inside or out side the cell.
 Centrioles

• Found only in animal cells

• Paired organelles found
together near the
nucleus, at right angles to
each other.
• Role in building cilia and
flagella
• Play a role in cellular
reproduction
 Cytoskeleton

Cell membrane

Endoplasmic
reticulum

Microtubule

Microfilament

Ribosomes Mitochondrion
 Cytoskeleton

• Framework of the cell

• Contains small microfilaments and larger
microtubules.
• They support the cell, giving it its shape and
help with the movement of its organelles.
 Mitochondrion

• Double Membranous
• It’s the size of a bacterium
• Contains its own DNA;
mDNA
• Produces high energy
compound ATP
The Chloroplast
• Double membrane
• Center section contains
grana
• Thylakoid (coins) make up
the grana.
• Stroma - gel-like material
surrounding grana
• Found in plants and algae.
 The Vacuole

• Sacs that help in food

digestion or helping
the cell maintain its
water balance.
• Found mostly in plants
and protists.
 Cell Wall

• Extra structure surrounding its plasma

membrane in plants, algae, fungi, and
bacteria.
• Cellulose – Plants
• Chitin – Fungi
• Peptidoglycan - Bacteria
Section1: What is Life made of?
• All living things are made of Cells
– Prokaryote, Eukaryote
• Cell Signaling
• What is Inside the cell: From DNA, to RNA, to
Proteins
 More Terminology
• The genome is an organism’s complete set of DNA.
– a bacteria contains about 600,000 DNA base pairs
– human and mouse genomes have some 3 billion.
• human genome has 24 distinct chromosomes.
– Each chromosome contains many genes.
• Gene
– basic physical and functional units of heredity.
– specific sequences of DNA bases that encode
instructions on how to make proteins.
• Proteins
– Make up the cellular structure
– large, complex molecules made up of smaller subunits
called amino acids.
 All Life depends on 3 critical molecules
• DNAs
– Hold information on how cell works
• RNAs
– Act to transfer short pieces of information to different parts of
cell
– Provide templates to synthesize into protein
• Proteins
– Form enzymes that send signals to other cells and regulate gene
activity
– Form body’s major components (e.g. hair, skin, etc.)
 Discovery of DNA
• DNA Sequences
– Chargaff and Vischer, 1949
• DNA consisting of A, T, G, C
– Adenine, Guanine, Cytosine, Thymine
– Chargaff Rule
• Noticing #A#T and #G#C
– A “strange but possibly meaningless”
phenomenon.
• Wow!! A Double Helix
1 Biologist
– Watson and Crick, Nature, April 25, 1953
1 Physics Ph.D. Student
– 900 words
Nobel Prize

– Rich, 1973 Crick Watson

• Structural biologist at MIT.
• DNA’s structure in atomic resolution.
 Watson & Crick – “…the secret of life”
• Watson: a zoologist, Crick: a physicist

• “In 1947 Crick knew no biology and practically

no organic chemistry or crystallography..” –
www.nobel.se

• Applying Chagraff’s rules and the X-ray image

from Rosalind Franklin, they constructed a
“tinkertoy” model showing the double helix
Watson & Crick with DNA model
• Their 1953 Nature paper: “It has not escaped
our notice that the specific pairing we have
postulated immediately suggests a possible
copying mechanism for the genetic material.”

Rosalind Franklin with X-ray image of DNA

 DNA: The Basis of Life
• Humans have about 3 billion base pairs.
– How do you package it into a cell?
– How does the cell know where in the
highly packed DNA where to start
transcription?
• Special regulatory sequences
– DNA size does not mean more complex
• Complexity of DNA
– Eukaryotic genomes consist of variable
amounts of DNA
• Single Copy or Unique DNA
• Highly Repetitive DNA
DNA, continued
• DNA has a double helix
structure which
composed of
– sugar molecule
– phosphate group
– and a base (A,C,G,T)

• DNA always reads from 5’

end to 3’ end for
transcription replication
5’ ATTTAGGCC 3’
3’ TAAATCCGG 5’
DNA, RNA, and the Flow of Information

Replication

Transcription Translation
 DNA, continued
• DNA has a double helix structure. However, it
is not symmetric. It has a “forward” and
“backward” direction. The ends are labeled 5’
and 3’ after the Carbon atoms in the sugar
component.
5’ AATCGCAAT 3’
3’ TTAGCGTTA 5’
DNA always reads 5’ to 3’ for transcription
replication
 DNA Components
• Nitrogenous Base:
N is important for hydrogen bonding between bases
A – adenine with T – thymine (double H-bond)
C – cytosine with G – guanine (triple H-bond)

• Sugar:
Ribose (5 carbon)
Base covalently bonds with 1’ carbon
Phosphate covalently bonds with 5’ carbon
Normal ribose (OH on 2’ carbon) – RNA
deoxyribose (H on 2’ carbon) – DNA
dideoxyribose (H on 2’ & 3’ carbon) – used in DNA sequencing

• Phosphate:
negatively charged
 Double helix of DNA

• The double helix of DNA has these features:

– Concentration of adenine (A) is equal to thymine (T)
– Concentration of cytidine (C) is equal to guanine (G).
– Watson-Crick base-pairing A will only base-pair with T, and C with G
• base-pairs of G and C contain three H-bonds,
• Base-pairs of A and T contain two H-bonds.
• G-C base-pairs are more stable than A-T base-pairs
– Two polynucleotide strands wound around each other.
– The backbone of each consists of alternating deoxyribose and
phosphate groups
Double helix of DNA
• Central Dogma
(DNARNAprotein) The
paradigm that DNA directs
its transcription to RNA,
which is then translated
into a protein.
• Transcription
(DNARNA) The process
which transfers genetic
information from the DNA
to the RNA.
• Translation
(RNAprotein) The
process of transforming
RNA to protein as specified
by the genetic code.
 Central Dogma of Biology

The information for making proteins is stored in DNA. There is a

process (transcription and translation) by which DNA is converted to
protein. By understanding this process and how it is regulated we
can make predictions and models of cells.

Assembly

Protein
Sequence
Sequence analysis Analysis
Gene Finding
 Transcription
• The process of making
RNA from DNA
• Catalyzed by
“transcriptase” enzyme
• Needs a promoter region
to begin transcription.
• ~50 base pairs/second in
bacteria, but multiple
transcriptions can occur
simultaneously

http://ghs.gresham.k12.or.us/science/ps/sci/ibbio/chem/nucleic/chpt15/transcription.gif
 DNA  RNA: Transcription
• DNA gets transcribed by a protein
known as RNA-polymerase
• This process builds a chain of
bases that will become mRNA
• RNA and DNA are similar, except
that RNA is single stranded and
thus less stable than DNA
– Also, in RNA, the base uracil (U) is
used instead of thymine (T), the DNA
counterpart
 Central Dogma Revisited
Transcription Splicing
DNA hnRNA mRNA
Nucleus Spliceosome

Translation
protein
Ribosome in Cytoplasm
• Base Pairing Rule: A and T or U is held together by 2
hydrogen bonds and G and C is held together by 3
hydrogen bonds.
• Note: Some mRNA stays as RNA (ie tRNA,rRNA).
Splicing
The Central Dogma (cont’d)
 RNA  Protein: Translation
• Ribosomes and transfer-RNAs (tRNA) run along the
length of the newly synthesized mRNA, decoding one
codon at a time to build a growing chain of amino acids
(“peptide”)
– The tRNAs have anti-codons, which complimentarily match the
codons of mRNA to know what protein gets added next
• But first, in eukaryotes, a phenomenon called splicing
occurs
– Introns are non-protein coding regions of the mRNA; exons are
the coding regions
– Introns are removed from the mRNA during splicing so that a
functional, valid protein can form
 Translation
• The process of going from
RNA to polypeptide.
• Three base pairs of RNA
(called a codon)
correspond to one amino
acid based on a fixed
table.
• Always starts with
Methionine and ends
with a stop codon
 Translation, continued
• Catalyzed by Ribosome
• Using two different sites,
the Ribosome continually
binds tRNA, joins the
amino acids together and
moves to the next
location along the mRNA
• ~10 codons/second, but
multiple translations can
occur simultaneously

http://wong.scripps.edu/PIX/ribosome.jpg
Life Science

Genetics
 Genetics The study of
heredity, how traits are passed from parent to
offspring

or
x =
or
 The study of heredity started
with the work of Gregor Mendel and his
pea plant garden

Mendel was an Austrian Monk that lived

in the mid 1800’s
Mendel noted that the size of pea
plants varied. He cross-bred these
pea plants to find some surprising
results.
Mendel’s cross between tall pea plants yielded all
tall pea plants. His cross between small pea plants
yielded all small pea plants.

X = X =

Mendels’ cross between tall pea plants and small pea

plants yielded all tall pea plants.

x =
Mendel then crossed these second generation tall pea
plants and ended up with 1 out 4 being small.

x =
Mendel’s work led him to the understanding
that traits such as plant height are carried in
pairs of information not by single sets of
information.

-Carrying the information are chromosomes.

-Chromosomes are made up of sections
called genes. -
Genes are made up of DNA
 DNA
D.N.A. - Deoxyribonucleic Acid
Molecule made of:
1. Deoxy Sugar
2. Combination of four nitrogen bases
Either: a. Guanine
b. Cytocine
c. Thymine
d. Adenine

The sum total of combinations that these

four bases are capable of creating are
greater than all the stars visible in the night
time sky
 DNA

• Nitrogen bases pair up

– Cytosine & Guanine
– Thymine & Adenine
• Pairing creates a ladder shape
• Angle of bonds creates a twist

Ladder and Twist produces the famous

“Double Helix”
 DNA
Nucleus
Cell
• DNA resides in all cells
DNA
– Inside the nucleus
• Each strand forms a chromosome
 DNA
DNA is found in all living cells
– It controls all functions inside a
cell
– It stores all the genetic
information for an entire living
organism
– Single cell like an amoeba
– Multi cell like a human
 Genetics
Small sections of DNA are responsible for a
“trait”. These small sections are called
“Genes”.
– Gene - A segment of DNA that codes for a specific
trait
– Trait - A characteristic an organism can
pass on to it’s offspring through DNA

Gene
 Genetics

Hair color is a perfect example of a

trait

What color hair

should their children
have?
Prince Charming Snow White
is blond has dark hair
 Genetics
There are three basic kinds of genes:
– Dominant - A gene that is always expressed and
hides others
– Recessive - A gene that is only expressed when a
dominant gene isn’t present
– Codominant - Genes that work together to
produce a third trait
 Genetics

Dominant and Recessive Genes

Widows Peak
• A dominant gene will always mask a
recessive gene.
• A “widows peak” is dominant, not
having a widows peak is recessive.
• If one parent contributes a gene for a
widows peak, and the other parent
doesn’t, the off- spring will have a
widows peak.
 Genetics

Punnet Square - A tool we use for predicting

the traits of an offspring
– Letters are used as symbols to designate genes
– Capital letters are used for dominant genes
– Lower case letters are used for
recessive genes
– Genes always exist in pairs
 Genetics

A Widows Peak, dominant, would be symbolized

with a capital “W”, while no widows peak,
recessive, would be symbolized with a
lower case “w”.

Father - No Widows Peak - w

Mother - Has a Widows Peak - W

 Genetics

All organisms have two copies of each gene, one

contributed by the father, the other contributed
by the mother.

Homozygous - Two copies of the same gene

Heterozygous - Two different genes
 Genetics

For the widows peak:

WW - has a widows peak Homozygous dominant

Ww - has a widows peak Heterozygous
ww - no widows peak Homozygous recessive
 Genetics
Since Herman has no widows peak, he must be
“ww”, since Lilly has a widows peak she could
be either “WW” or “Ww”

Definitely ww Homozygous
recessive
Either Ww Heterozygous
or WW Homozygous dominant
 Genetics
We can use a “Punnet Square” to determine
what pairs of genes Lilly has

• A Punnet Square
begins with a box 2 x 2
Assume Lilly is heterozygous
Ww • One gene is called an
“allele”
Assume Herman is homoozygous W w • One parents pair is
recessive split into alleles on top,
ww the other along the side
w Ww ww
• Each allele is crossed
with the other allele to
w Ww ww predict the traits of the
offspring
 Genetics
Notice that when Lilly is crossed with Herman,
we would predict that half the offspring
would be “Ww”, the other half would be
“ww”

Half “Ww”, Heterozygous, and will have a

widows peak W w

Half “ww”, Homozygous, and will not

w Ww ww
have a widows peak
w Ww ww
 Genetics
Another possibility is that Lilly might be
“WW”, homozygous dominant.

Assume Lilly is homozygous

dominant
WW
Assume Herman is homoozygous W W
ww Notice that all the
w Ww Ww offspring are
heterozygous and will
have a widows peak
w Ww Ww
 Genetics
So which is true? Is Lilly homozygous dominant
(WW) or is she heterozygous (Ww)?

W w W W

w Ww ww w Ww Ww

w Ww ww w Ww Ww
 Genetics

If Lilly were heterozygous, If Lilly were homozygous, all

then 1/2 of their offspring of their children will have a
should have a widows peak, widows peak
1
/2 shouldn’t

W w W W

w Ww ww w Ww Ww

w Ww ww w Ww Ww
 Genetics

Recall that Herman and Lilly had another

offspring, Marylin. She had no widows peak,
therefore, Lilly must be heterozygous.
 Genetics
So, back to the original question. What color
hair will the offspring of Prince Charming and
Snow White have?
 Genetics
Hair color is different from widows peak, no
color is truly dominant.
– Brown and blond are the two, true traits
– Homozygous conditions produce either brown or
blond hair
– Heterozygous conditions produce red hair
 Genetics
For Snow White to have brown hair she must
be homozygous dominant, “BB”, a blond
Prince Charmin must be homozygous
recessive, “bb”.

B B

b Bb Bb

b Bb Bb
 Genetics

All the offspring from Prince Charming and

Snow White will therefore be heterozygous,
“Bb”, and since hair color is codominant…..
all their children will have red hair.

+
Cell Division
(Meiosis)

1. A process of cell
division where the
number of chromasomes
is cut in half
2. Occurs in gonads 3. Makes gametes
(testes, ovaries, stamens, (sperm, ova, pollen, etc)
etc)
CHROMOSOMAL MUTATION
 What Are Mutations?

• Changes in the
nucleotide sequence of
DNA
• May occur in somatic
cells (aren’t passed to
offspring)
• May occur in gametes
(eggs & sperm) and be
passed to offspring
 Are Mutations Helpful or Harmful?

• Mutations happen
regularly
• Almost all mutations are
neutral
• Chemicals & UV
radiation cause
mutations
• Many mutations are
repaired by enzymes
 Are Mutations Helpful or Harmful?

• Some type of skin

cancers and leukemia
result from somatic
mutations
• Some mutations may
improve an organism’s
survival (beneficial)
 Types of Mutations

• Genomic: abnormal chromosome number

(monosomy, polysomy, aneuploidy)
• Chromosomal: abnormal chromosome
structure
• Gene: DNA sequence changes in specific
genes
 Chromosome Morphology

• Telomere: chromosome ends

• Centromere: site of spindle
attachment
– Constriction of the
metaphase chromosome at
the centromere defines two
arms
• Nucleosome: DNA double
helix wrapped around
histone proteins
 Chromosome Morphology

Telomere
Short
arm (p)
Centromere Arm

Long
arm (q)
Telomere

Metacentric Submetacentric Acrocentric

Cancer: A Genetic Disease

Mutations in genes that control cell

growth and division are responsible
for cancer.
(cell proliferation and differentiation)

Carcinogens  DNA mutations

© John Wiley & Sons, Inc.

 Cancer
• Cancers arise when critical genes are mutated, causing
unregulated proliferation of cells.

• These rapidly dividing cells pile up on top of each other to

form a tumor.

• When cells detach from the tumor and invade surrounding

tissues, the tumor is malignant and may form secondary
tumors at other locations in a process called metastasis.

• A tumor whose cells do not invade surrounding tissues is

benign.
Tumor – is a condition where there is abnormal cellular growth thus
forming a lesion or in most cases, a lump in some part of your body.

Benign tumor – grows in confined area

Malignant tumor – capable of invading surrounding tissues

Cancer – degenerative disease with a cellular condition where there is uncontrolled

growing mass of cells capable of invading neighboring tissues and spreading via body fluids to
other parts of the body.
Named for site of origin

Carcinomas – epithelial cells; cover external & internal body

surfaces (90%)

Sarcomas – supporting tissue; bone, cartilage, fat, connective

tissue, pancreas, Liver.

Lymphoma & leukemias – blood & lymphatic tissue

(leukemia reserved for cancers that reside in bloodstream
not as solid tissue)
Comparison of Normal and Tumor Growth in the Epithelium of the Skin

Location/distribution
 Oncogenes
• Oncogene: “onco” (cancer) gene

• 1989 Nobel Prize in Medicine or Physiology:

The Discovery of the Cellular Origin of
Retroviral Oncogenes
– J. Michael Bishop (UCSF)
– Harold Varmus (UCSF)
Oncogenes are genes whose presence can contribute to
uncontrolled cell proliferation and cancer.

Oncogenes can arise inside cells in two fundamentally

different ways.

1. A mechanism involves the participation of viruses

that introduce oncogenes into the cells they infect.

2. A series of mechanisms that convert normal cellular

genes into oncogenes, often as a result of exposure to
carcinogenic agents.
 Cellular oncogenes arise from Proto-
oncogenes
Proto-oncogenes are normal cellular genes
- can be converted into oncogenes
- contribute to the regulation of cell proliferation and
survival
The mutations of proto-oncogenes can cause cancer.
- gain-of-function mutations can induce tumor
formation

Cellular oncogenes were initially detected

in gene transferred experiment
Transfection with tumor cell DNA
The DNA of bladder cancer cells contains genetic
information, not present in normal DNA, that is capable of
causing cancer (early 1980s, Robert Weinberg and Geoffrey Cooper) .
 RAS oncogene was the first
human oncogene to be
identified.
- DNA sequence is related to v-
ras oncogene
- ras ---> ”rat sarcoma”
 RAS proto-oncogene
produces a protein involved in a
normal pathway for stimulating
cell proliferation.

 Oncogenes cannot always be

detected using DNA transfection
techniques.

Inducing cancer by DNA transfection.

Kleinsmith LJ. Principles of cancer biology.

Pearson International Edition. Benjamin
Cummings, San Francisco. 2006. p.37.
Two approaches to identifying oncogenes
• Exposure of
noncancerous cells to
tumor DNA in culture
– Human tumor DNA to
transform normal mouse
cells
– Human DNA isolated
from transformants
 The mechanisms by which cellular oncogenes arise can be grouped
into 5 basic categories:
1. point mutation
2. gene amplification
3. chromosomal translocation
4. DNA rearrangement
5. insertional mutagenesis

Mechanism 1: Point mutations can convert proto-

oncogenes into oncogenes

Kleinsmith LJ. Principles of cancer biology. Pearson International Edition. Benjamin Cummings, San Francisco. 2006. p.160.
Mechanism 2: Gene Amplification can convert proto-
oncogenes into oncogenes

 DNA located in a specific chromosomal region is replicated

numerous time in succession.
----> creating dozens, hundreds, or thousands of copies of the same
stretch of DNA.

 Chromosome regions containing amplified genes often exhibit a

distinctive, abnormal appearance that can be recognized when
chromosomes are examined by light microscopy.
----> homogeneously staining regions (HSRs) and double minutes
(DMs).
 Appearance of chromosome regions containing Amplified DNA

Kleinsmith LJ. Principles of cancer biology. Pearson International Edition.

Benjamin Cummings, San Francisco. 2006. p.161.

 Gene amplification typically yields oncogenes that produce normal

proteins but in excessive quantities.
 Members of MYC gene family, MYC, MYCL, and MYCN, are among
the most commonly encountered oncogenes to arise by gene
amplification in human cancers.
MYC ----> detected in cancers of the breast, ovary, uterine cervix,
lung, and esophagus.
MYCN ----> detected in neuroblastoma
Mechanism 3: Chromosomal translocation can convert
proto-oncogenes into oncogenes
 A piece of one chromosome is broken off and moved to another
chromosome.
 Chromosomal translocations contribute to cancer development by;
1) fusing two gene together to form an oncogene coding for a
fusion protein
BCR= Breakpoint cluster region
ABL= Abelson murine leukemia
viral oncogene homolog

Tyrosine Kinase activity 

---> Philadelphia chromosome is associated with 90% of all cases

of chronic myelogenous leukemia (CML).
2) activating the expression of a proto-oncogene by placing it
near a highly active gene

Highly active
antibody genes

---> Burkitt’s lymphoma; the entire MYC proto-oncogene is moved

from chromosome 8 to 14.

Mechanism 4: Local DNA rearrangements can convert
proto-oncogenes into oncogenes
 DNA rearrangements disrupt the expression or structure of a proto-
oncogene located in that region.
 Types of DNA rearrangements;
1) Deletion
2) Insertion
3) Transposition
4) Inversion

 DNA rearrangements are frequently detected in human tumor cells,

especially in certain types of cancer.
----> thyroid cancers (nearly 50%)
Mechanism 5: Insertional mutagenesis can convert
proto-oncogenes into oncogenes
 Retrovirus randomly inserts its genes near a proto-oncogene.
 The retroviral LTRs may stimulate transcription of the proto-
oncogene and trigger overproduction of a normal cellular protein that
can contribute to cancer development.
Summary: Cellular oncogenes arise from proto-
oncogenes by mechanisms that alter gene structure or
expression.
ALCOHOL AND CANCER

127
 Health Effect
• Cardiovascular Disease
• Cancers (upper aerodigestive tract cancer, HCC, colorectal cancer and breast
cancer)
• Obesity
• Diabetes
• Birth defect
• Breastfeeding
• Aging
• Alcohol abuse and dependence
• Hepatic effect (Alcohol-related liver disease, included cirrhosis and alcoholic
hepatitis )
• Genetic and related effects
• Injury/Accident
• Total mortality

128
 Global Mortality Burden (deaths in thousands) Attributable to Alcohol by
Major Disease Categories – 2000

Eur Addict Res 2003;9:157–164

Global Burden of Disease Attributable to Alcohol
Jürgen Rehma, Robin Room, Maristela Monteiro, Gerhard Gmel, Kathryn Graham, Nina Rehn, Christopher T. Sempos, David
129
Jernigan
 Global burden of disease (DALYs in thousands) attributable to alcohol by
major disease categories – 2000

Eur Addict Res 2003;9:157–164

Global Burden of Disease Attributable to Alcohol
Jürgen Rehma, Robin Room, Maristela Monteiro, Gerhard Gmel, Kathryn Graham, Nina Rehn, Christopher T. Sempos, David
130
Jernigan
 Alcohol and Cancer
• Nearly 100 years ago, Lamy noticed an increased incidence of esophageal
cancer in absinth drinkers (Lamy, 1910).
• Since then, extensive epidemiological data has accumulated which identified
alcohol as a major risk factor for cancer
• Furthermore, substantial epidemiological evidence accrued over the past 50
years has shown that alcohol contributes to the development of these cancers.
• In 1988, IARC concluded that there is sufficient evidence that alcohol beverage
are carcinogenic in humans.
• Nevertheless, the mechanisms underlying alcohol-related cancer development
remain largely unclear.

131
 9 Possible Mechanisms How Alcohol Intake Increase Cancer Risk

According to Blot et al (1992)

1. Contain congeners and other contaminants that may be

carcinogenic
2. Generated metabolites that are carcinogenic to humans
3. Act as solvent, increasing penetration of other carcinogens
into target tissue
4. Reduce intake and bioavailability of nutrition
5. Inhibit the detoxification of carcinogenic compounds
6. Catalyze the metabolic activation of some compounds into
carcinogens
7. Affect hormonal status
8. Increase cellular exposure to oxidants
9. Suppress immune function

132
 Alcohol Metabolism

Source: Klaassen,CD (1998) Casarett & Doull's Toxicology: The basic science of poisons, fifth edition

133
Modern Genetic Technology
(Polymerase Chain Reaction)
• PCR, polymerase chain reaction, is an in-vitro
technique for amplification of a region of DNA
whose sequence is known or which lies
between two regions of known sequence
• Before PCR, DNA of interest could only be
amplified by over-expression in cells and this
with limited yield
 Purpose of PCR
• Amplify specific nucleic acids in vitro (“Xeroxing”
DNA)
• PCR will allow a short stretch of DNA (usually fewer
than 3000 base pairs) to be amplified to about a
million fold
• This amplified sample then allows for size
determination and nucleotide sequencing
• Introduced in 1985 by Kary Mullis
• Millions of copies of a segment of DNA can be made
within a few hours.
• 1966, Thomas Brock discovers Thermus
Aquaticus, a thermostable bacteria in the
hot springs of Yellowstone National Park
• 1983, Kary Mullis postulated the concept of
PCR ( Nobel Prize in 1993)
• 1985, Saiki publishes the first application of
PCR ( beta-Globin)
• 1985, Cetus Corp. Scientists isolate
Thermostable Taq Polymerase (from
T.Aquaticus), which revolutionized PCR
• Separation: Double Stranded DNA is denatured by
heat into single strands.
• Short Primers for DNA replication are added to the
mixture.
• DNA polymerase catalyzes the production of
complementary new strands.
• Copying The process is repeated for each new strand
created
• All three steps are carried out in the same vial but at
different temperatures
 Step 1: Separation
• Combine Target Sequence, DNA primers template,
dNTPs, TAQ Polymerase
• Target Sequence: Usually fewer than 3000 bp
– Identified by a specific pair of DNA primers- usually
oligonucleotides that are about 20 nucleotides
• Heat to 95 degrees Celsius to separate strands (for
0.5-2 minutes)
– Longer times increase denaturation but decrease enzyme
and template
 Magnesium as a Cofactor
• Stabilizes the reaction between:
– oligonucleotides and template DNA
– DNA Polymerase and template DNA
 Heat Denatures DNA by uncoiling the
Double Helix strands.
 Step 2: Priming
• Decrease temperature by 15-25 degrees
• Primers anneal to the end of the strand
• 0.5-2 minutes
• Shorter time increases specificity but
decreases yield
• Requires knowledge of the base sequences of
the 3’ - end
 Selecting a Primer
• Primer length
• Melting Temperature (Tm)
• Specificity
• Complementary Primer Sequences
• G/C content and Polypyrimidine (T, C) or polypurine (A,
G) stretches
• 3’-end Sequence
• Single-stranded DNA
 Step 3: Polymerization

• Since the Taq polymerase works best at

around 75 degrees C (the temperature of
the hot springs where the bacterium was
discovered), the temperature of the vial is
raised to 72-75 Degrees Celsius
• The DNA polymerase recognizes the primer
and makes a complementary copy of the
template which is now single stranded.
• Approximately 150 nucleotides/sec
 PCR Applications
• Detection of infectious diseases
• Detection of variations and mutations in genes
• Detection of diseases from the past
• PCR and the law
Detection of infectious diseases

- AIDS Virus
- Otitis Media-middle ear infection
- Lyme Disease-joint inflammation from tick bites
- Detect 3 sexually transmitted diseases in one
swab-herpes, papillomarvirus, chlamydia
 Detection of Variations and Mutations in
Genes
• Detects people with inherited disorders
• Lets us know who carries deleterious
variations (mutations)
• Direct way of distinguishing among the
confusion of different mutations in a single
gene. Ex: Duchenne muscular dystrophy
• Track presence or absence of DNA
abnormalities characteristic to cancer
 Detection of diseases from the past
• Presidential candidate Humphreys-had cancer
• John Dalton-was colored blind and realized
that this was the case because he lacked a
gene for one of the three photopigments,
which caused him to be color blind
 PCR and the Law
• DNA fingerprinting
– Can multiply small amounts of DNA found in blood
samples, hair, semen, and other body fluids
• Proving innocence of those already convicted
– Kirk Bloodsworth-wrongly accused of raping and
murdering a nine year old. Using PCR, he was proved
innocent and released from prison in 1993