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Issues in Biotechnology:
The Way We Work With Life
Dr. Albert P. Kausch
life edu.org
OnCampus Live
BCH 190, MIC 190, AFS 190, NRS 190, PLS 190
OnLine BCH 190
A Sweeping General Survey on Life and Biotechnology
A Public Access College Course
The University of Rhode Island
Issues in Biotechnology:
Biotechnology, Our Society and Our Future
Issues in Biotechnology:
The Way We Work With Life
Dr. Albert Kausch
Kimberly Nelson
BCH 190
Section I. The Mechanics of DNA: What is Life
Section II. The Applications of Biotechnology
A Sweeping General Survey on Life and Biotechnology
A Public Access College Course
The University of Rhode Islandlife edu.org
Issues in Biotechnology:
The Way We Work With Life
Dr. Albert P. Kausch
life edu.org
The Mechanics of DNA: What is Life?
7. Gene Expression, Development
8. The Genomics Revolution
A Sweeping General Survey on Life and Biotechnology
The University of Rhode Island
Gene expression and the genomics revolution
Lectures 7 & 8
Issues in Biotechnology:
The Way We Work With Life
Dr. Albert P. Kausch
life edu.org
The Mechanics of DNA: What is Life?
8. The Genomics Revolution
A Sweeping General Survey on Life and Biotechnology
The University of Rhode Island
The Genomics Revolution
Lecture 8
First Draft of the
Human Genome
February 15 2001
‘The accomplishment of
landing on the moon
pales in significance
compared with the
recent advances in DNAbased biotechnology’
What's a genome?
A genome is all the DNA in an organism, including its genes. Genes
carry information for making all the proteins required by all
organisms.
Our understanding
of the evolutionary
relationships
among species is
made more
accurate through
analysis and
comparison of the
DNA sequences in
their genomes
Genomic Technologies
• Genome Sequencing
• Measuring mRNA levels
• Measuring and Characterizing Proteins
Genomic Technologies
• Genomics
• Transcriptomics
• Proteomics
Comparative Genomics
Issues in Biotechnology
The entire genomic sequences are now known for many species of
bacteria, fungi, insects, plants and animals, including humans
and chimpanzees. This vast amount of information has been
published and is in the public domain. The genome databases
aligned and the similarities and relations can be examined.
Individual gene sequences can be searched to find striking
similarities between species. These types of analyses have shown
that humans are 98% similar in DNA sequence to the
chimpanzee; 88% similar to mice and about 33% similar to the
genes of a rice plant. This type of analysis is called:
(A) Transgenic analysis
(B) Comparative genomics
(C) Mutational analysis
(D) Functional genomics
(E) DNA gold mining
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DNA Sequencing
Using dideoxy nucleotide bases
together with DNA polymerase the
ddbase will cause the DNA
synthesis to stop at that base and
label it. The labeled base is then
detected by gel electrophoresis and
autoradiography
Dideoxy labelled fragments are separated
by gel electrophoresis and detected by
autoradiography (the old days) or by
fluorescent dyes. Automated
high-throughput sequencing is now
conducted by robots and mega computers
allowing genome sequencing (Celera)
China’s Sequencing
Powerhouse Comes of Age
With new sequencing centers in Europe and the United States, BGI hopes its growing clout
will help deliver the benefits promised by genomics—and revenue to pay off a mounting debt
Illumina
HySeq
454
How the 454 System works
Attach DNA fragments to beads
The system relies on fixing nebulized and adapter-ligated DNA
fragments to small DNA-capture beads in a water-in-oil emulsion.
Amplify the DNA
The DNA fixed to these beads is then amplified by PCR.
Place beads in microscopic wells
Each DNA-bound bead is placed into a ~44 μm well on a
PicoTiterPlate, which is a fiber optic chip. A mix of enzymes such as
polymerase, ATP sulfurylase, and luciferase are also packed into the
well. The PicoTiterPlate is then placed into the GS-FLX for
sequencing.
Add nucleotides
At this stage, the four nucleotides (TAGC) are washed in series over
the PicoTiterPlate. During the nucleotide flow, each of the hundreds
of thousands of beads with millions of copies of DNA is sequenced in
parallel.
If a nucleotide complementary to the template strand is flowed into a
well, the polymerase extends the existing DNA strand by adding
nucleotide(s). Addition of one (or more) nucleotide(s) results in a
reaction that generates a light signal
Read the light signal from each well
The light signals are recorded by the CCD digital camera in the
instrument. This technique is an example of pyrosequencing. The
signal strength is proportional to the number of nucleotides, for
example, homopolymer stretches, incorporated in a single nucleotide
flow. However, the signal strength for homopolymer stretches is linear
up to eight consecutive nucleotides; signal fall-off is rapid after a
stretch of more than eight identical nucleotides.
Pharmacogenomics
Personalized
Medicine
&
The
Composition
of Humans
The Role of Pharmacogenomics
Pharmacogenomics is the study of how an individual's genetic inheritance
affects the body's response to drugs.
Personalized Medicine: Based on patients’ DNA sequence
Sequencing and analysis of the human genome's six billion base pairs
Drug Metabolism: Based on individual
genomics
A drug that might be good for you might not do anything for
someone else
A drug that might be good for someone else might kill you
Disease Predisposition
Disease Diagnosis
See more on this in the next lecture…
The Role of Pharmacogenomics
Pharmacogenomics is the study of how an individual's genetic inheritance
affects the body's response to drugs.
Personalized Medicine: Based on patients’ DNA sequence
The Ultimate Genetic Test
Radoje Drmanac SCIENCE VOL 336 1 June 2012 pp1110-1111
Encoded in the DNA sequence of our
individual genome is the genetic program
to build, maintain, and adapt all our
tissues and their functions.
Each human genome contains 200,000
coding elements (exons) and millions of
regulatory elements defining complex
signaling and regulatory networks.
CB Lowe et al SCIENCE 333, 1019 (2011)
See more on this in the next lecture…
Southern Blot Analysis
Detection of Specific DNA
Sequences
DNA Isolation
Southern Blot Analysis: Detection of
known DNA sequences that have
been separated by gel electrophoresis
and bound to a nitrocellulose filter.
Issues in Biotechnology
A ‘Southern blot’ is used for
(A) sequencing the individual amino acids of specific
proteins
(B) detection of proteins using antibodies as in a home
pregnancy test
(C) detection of specific DNA sequences
(D) detection of specific RNA sequences
(E) Detecting DNA in confederate soldiers from the Civil
war in the US
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Northern Blot Analysis
Detection of Specific RNA
Sequences
Western Blot Analysis
Detection of Specific Proteins
The Immune System:
What happens when humans are invaded
The Immune System:
Antibodies are proteins encoded by genes
Antibodies
versatile protein molecules capable of recognizing
foreign proteins
Fv
Antigen
Binding
Site
VH
CH1
VL
CH2
Fc
Ancillary
functions
Antigen/pathogen specificity
CH3
Effector functions:
•Neutralization/blocking effects
•Complement fixation
•Agglutination
The B cell receptor
Ag
Ag
b a
a
b
Production of Hybridomas
and Monoclonal Antibodies
Monoclonal
antibodies are a
homogeneous
population of
antibodies that are
specific to their
antigen.
Western Blot Analysis
Detection of specific
proteins
proteins are separated
by gel electrophoresis
separated proteins are
transferred to a filter
antibodies recognize
proteins and are detected
with specific dyes
Issues in Biotechnology
A ‘Western blot’ is used for
(A) detection of proteins using antibodies as in a home
pregnancy test
(B) detection of specific RNA sequences
(C) sequencing the individual amino acids of specific
proteins
(D) detection of specific DNA sequences
(E) detection of antibodies
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Applications of monoclonal antibodies
ELISA
Enzyme Linked
Immunosorbent Assay
Home Pregnancy Testan antibody test specific to
human chorionic
gonadotropin HCG is
captured and detected with
a color enzyme developed
product
19. The technologies useful for the analysis of biological
compounds were essential to the development of
biotechnology and its applications. A ‘Southern blot’ is
used for
(A) sequencing the individual amino acids of specific
proteins
(B) detection of proteins using antibodies as in a home
pregnancy test
(C) detection of specific DNA sequences
(D) detection of specific RNA sequences
(E) the most important diagnostic used in determining the
forensic results of a crime scene
20. What is pharmacogenomics?
(A) Name given to researchers at large pharmaceutical companies
who are mining the genetics of indigenous peoples.
(B) Name given to the recent class of genetically engineered
drugs
(C) Specialized pharmacies, which sell genetically manipulated
foods like BT corn.
(D) Name given to the study of genetic variation that results in
disease susceptibilities and the differences in response to
medications between people.
(E) A recent biotech start-up company specializing in
homeopathic medicine
21. A National discussion had developed about the teaching
in public schools of an alternative explanation, to
evolution, for biological diversity called Intelligent
Design. This idea suggests that that the world ecology
and biology is so complex that this infers that there
must be a creator much the same way that the
complexity of a watch infers a watchmaker. Intelligent
Design:
A. Is a theory that is well supported by scientific evidence
B. Is currently a well-established, evidence-based alternative to theories of
natural selection
C. Is not currently a well-established, evidence- based alternative to
theories of evolution by natural selection
D. Has been determined by the Supreme Court as material that should be
taught in public schools along with other theories of origin including
all world wide mythologies and religions.
E. There is insufficient information about evolution
22. The entire genomic sequences are now known for many
species of bacteria, fungi, insects, plants and animals,
including humans and chimpanzees. This vast amount of
information has been published and is in the public
domain. The genome databases aligned and the similarities
and relations can be examined. Individual gene sequences
can be searched to find striking similarities between
species. These types of analyses have shown that humans
are 98% similar in DNA sequence to the chimpanzee; 88%
similar to mice and about 33% similar to the genes of a
rice plant. This type of analysis is called:
(A) Transgenic analysis
(B) Comparative genomics
(C) Mutational analysis
(D) Functional genomics
(E) DNA gold mining
23. The flow of information is one characteristic of life.
The flow of biological information in life is studied using
various techniques in biotechnology. A ‘Northern blot’ is
used for
(A) detection of specific DNA sequences
(B) detection of specific RNA sequences
(C) detection of proteins using antibodies as in a home
pregnancy test
(D) sequencing the individual amino acids of specific
proteins
(E) determining the effects of arctic global warming
24. The code in DNA that we call a ‘gene’ is the code for
a protein. Each specific gene therefore as a specific code
for a specific protein. Different proteins can be
distinguished from each other by
(A) their ATP molecules
(B) the ribosomes that make them
(C) the type of sugar molecules they generate
(D) their amino acid sequence
(E) PCR analysis
25. Proteins are molecules made from sequences of a
number of:
(A) twenty donuts
(B) twenty amino acids
(C) infinite different amino acids
(D) four different ribonucleic acids
(E) DNA triple helices
26. The ‘cloning’ of plants was demonstrated by Steward
in 1958 at Cornell Univ. showing that plants could be
grown back from a single cell. This ability is called
“totipotency” and like the more recent examples of
animal cloning, demonstrates
(A) that all biological scientists are unethical and fraudulent
(B) that all of the DNA that codes for an entire organism is
in every cell of that organism
(C) Steward must have belonged to the group that calls
themselves the ‘Raeliens’
(D) the necessity to ban all types cloning
(E) the basis of intelligent design
27. Each gene codes for a messenger RNA that when
translated produces a protein that was encoded by the
sequences of bases in the DNA of its gene. A ‘Western
blot’ is used for
(A) detection of proteins using antibodies as in a home
pregnancy test
(B) detection of specific RNA sequences
(C) sequencing the individual amino acids of specific
proteins
(D) detection of specific DNA sequences
(E) detection of nuclear weapons of mass destruction
28. Humans have about 3 billion base pairs of DNA.
Some of these sequences code for proteins and are called
genes. In humans, genes make up ______ of the DNA.
(A) about 75%
(B) 100%
(C) less than 5%
(D) about 10%
(E) about 50%
Hint: (see your text chapter 5...)
29. Our understanding of the evolutionary relationships
among species is made more accurate through analysis
and comparison of their DNA Different organisms have
various amounts of DNA. Organismal complexity does
not correlate with the amount of DNA. The full set of an
individual organism’s DNA is called its:
(A) complement.
(B) genome.
(C) nucleosome.
(D) nucleotide.
(E) chromosome.
Hint: (see your text chapter 5...)
30. Molecular techniques are often the ‘unsung’ heroes of
biotechnology. Without the advancements in techniques
over the past two decades, many of the applications of
biotechnology would not be possible. Also, many of the
observations of modern biology would not be possible.
The polymerase chain reaction (PCR):
(A) makes it possible to create huge numbers of copies of
tiny pieces of DNA.
(B) enables researchers to determine the sequence of a
complementary strand of DNA when they have only singlestranded DNA.
(C) utilizes RNA polymerase to build strands of DNA.
(D) can create messenger RNA molecules from small pieces
of DNA.
(E) All of the answers are correct.