pGLO and bacterial genomics
Warm Up (2-1-16)
• What do you know about DNA and how it is
replicated?
• Try to be as specific as possible.
Outline
•
•
•
•
Objectives
Read chapter 16
notes
DNA background information
Objectives
• IWBAT identify what DNA is and explain the
discovery of the structure of DNA
DNA review
• DNA
– Deoxyribonucleic acid
– Found in the nucleus in eukaryotes
– Genetic code
– Allows for organisms to replicate and reproduce
Biology 2 ch. 16 notes
• DNA is the genetic material
– The Search for genetic material
• Originally thought that protein was the genetic material
• Wasn’t consistent with microorganisms (bacteria / viruses)
• 1928 – Frederick Griffith – key player in finding DNA
–
–
–
–
Streptococcus pneumoniae
R strain was harmless
S strain was pathogenic
Mixed heat-killed S strain with live R strain and injected mice
» Mouse died
» Recovered pathogenic strain from the mouse =
transformation!! (we’ll touch on this more later!)
Ch. 16 notes
• 1944 – Oswald Avery, Maclyn McCarty and Colin
MacLeod said DNA transformed
– Many were skeptical
• Proteins were considered better candidates for genetic material
• Also a belief that the genes of bacteria could not be similar in
composition and function to those of more complex organisms
• Viruses:
– DNA (sometimes RNA) enclosed by protective coat of
protein
– Replication:
• Infect a host cell and take over metabolic machinery
• Bacteriophages – viruses that specifically infect bacteria (phages)
• 1952 – Alfred Hershey and Martha Chase
– Showed that DNA was the genetic material of the
phage T2
– Found that when bacteria had been infected with T2
phages that contained radiolabeled proteins, most of
the radioactivity was in the pellet with the bacteria
– Concluded that the injected DNA of the phage
provides the genetic info that makes the infected cells
produce new viral DNA and proteins to assemble into
new viruses
• Circumstantial evidence for DNA being the
genetic material
– Cells double the amount of DNA in a cell prior to
mitosis then distribute DNA evenly amongst
daughter cells
– Observation that diploid sets of chromosomes
have twice as much DNA as haploid sets in
gametes of the same organism
• 1947 Erwin Chargaff developed rules based on a survey of DNA
composition
– Knew that DNA was a polymer of nucleotides consisting of nitrogenous
base, deoxyribose, and phosphate group
– Bases could be adenine, thymine, guanine, or cytosine
• Noted that DNA composition varied amongst different species
• In any species all four bases are found but not necessarily equal
ratios
• Chargaff’s rules
– In all organisms %A’s = %T’s (bases)
– In all organisms %C’s = %G’s (bases)
• **PROOF! Human DNA 30.9% adenine, 29.4% thymine, 19.9%
guanine and 19.8% cytosine
• Watson and Crick
– Discovered the double helix by building models to conform
with X-ray data
• 1950s – hunt was on to find a 3D structure of DNA
– Scientists researching – Linus Pauling, Maurice Wilkins,
Rosalind Franklin
• Wilkins and Franklin used x-ray crystallography to study
DNA structure
– James Watson learned that DNA was helical in shape
– Watson and Francis Crick began to work on a model with
two strands – double helix
• Placed sugar-phosphate chains on the outside and nitrogenous
bases on the inside
– This put the hydrophobic nitrogenous bases in the molecule’s interior
• Sugar-phosphate chains are like the sides of a rope ladder
• April 1953 Watson and Crick published a paper in
Nature reportin their double helix model of DNA
Warm Up (2-2-16)
• Identify the four nitrogenous bases that are
present in a double helix molecule of DNA
Outline
•
•
•
•
Objectives
Read chapter 16
Notes
DNA background information
Objectives
• IWBAT identify what DNA is and explain the
discovery of the structure of DNA
16.2 Notes
Warm Up (2-3-16)
• Briefly explain the discovery of the double
helix structure of DNA and that DNA was the
genetic material. Try to include as many
scientists as possible.
Outline
•
•
•
•
Objectives
Read chapter 16
Notes
DNA background information
Objectives
• IWBAT identify what DNA is and explain the
discovery of the structure of DNA
16.3 Notes
Warm Up (2-4-16)
• Try and match the following strand of
nitrogenous bases with their pairs.
• ATTCAGCA
• TGACGCCTA
Outline
•
•
•
•
Objectives
Read chapter 16
Notes
DNA background information
Objectives
• IWBAT identify what DNA is and explain the
discovery of the structure of DNA
16.4 Notes
Warm Up (2-5-16)
• Explain the process of DNA replication. Be as
specific as possible
Outline
•
•
•
•
Objectives
Read chapter 16
Notes
DNA background information
Objectives
• IWBAT identify what DNA is and explain the
discovery of the structure of DNA
16.4 Notes
Warm Up (2-18-15)
• Explain the process of transcription and
translation and how these processes occur.
Outline
• Objectives
• DNA transformation practice
Objectives
• IWBAT model DNA transformation and
demonstrate how a section of DNA is spliced
by transposons in order for new information
to be inserted into the DNA.
Chapter 8 Notes
• McDougal Littell Biology Book
• Stephen Nowicki
KEY CONCEPT
DNA structure is the same in all organisms.
DNA is composed of four types of
nucleotides.
• DNA is made up of a long chain of nucleotides.
• Each nucleotide has three parts.
– a phosphate group
– a deoxyribose sugar
– a nitrogen-containing base
phosphate group
deoxyribose (sugar)
nitrogen-containing
base
• The nitrogen containing bases are the only difference in
the four nucleotides.
Watson and Crick determined the threedimensional structure of DNA by building
models.
• They realized that DNA is
a double helix that is
made up of a sugarphosphate backbone on
the outside with bases
on the inside.
• Watson and Crick’s discovery built on the work of Rosalind
Franklin and Erwin Chargaff.
– Franklin’s x-ray images suggested that DNA was a
double helix of even width.
– Chargaff’s rules stated that A=T and C=G.
Nucleotides always pair in the same way.
• The base-pairing rules show
how nucleotides always pair
up in DNA.
– A pairs with T
– C pairs with G
• Because a pyrimidine
(single ring) pairs with a
purine (double ring), the
helix has a uniform width.
G
A
C
T
• The backbone is connected by covalent bonds.
• The bases are connected by hydrogen bonds.
hydrogen bond
covalent bond
KEY CONCEPT
DNA replication copies the genetic information of a
cell.
Replication copies the genetic
information.
• A single strand of DNA serves as a template for a new
strand.
• The rules of base pairing direct
replication.
• DNA is replicated during the
S (synthesis) stage of the
cell cycle.
• Each body cell gets a
complete set of
identical DNA.
Proteins carry out the process of
replication.
DNA serves only as a template.
•
• Enzymes and other proteins do the actual work
of replication.
– Enzymes unzip the double helix.
– Free-floating nucleotides form hydrogen bonds
with the template strand.
nucleotide
The DNA molecule unzips
in both directions.
– DNA polymerase enzymes bond the nucleotides
together to form the double helix.
– Polymerase enzymes form covalent bonds between
nucleotides in the new strand.
new strand
nucleotide
DNA polymerase
• Two new molecules of DNA are formed, each with an
original strand and a newly formed strand.
• DNA replication is semiconservative.
original strand
Two molecules of DNA
new strand
Replication is fast and accurate.
• DNA replication starts at many points in eukaryotic
chromosomes.
There are many origins of replication in eukaryotic chromosomes.
• DNA polymerases can find and correct errors.
KEY CONCEPT
Transcription converts a gene into a single-stranded
RNA molecule.
RNA carries DNA’s instructions.
• The central dogma
states that
information flows in
one direction from
DNA to RNA to
proteins.
•
The central dogma includes three processes.
– Replication
– Transcription
– Translation
• RNA is a link between
DNA and proteins.
replication
transcription
translation
• RNA differs from DNA in three major ways.
– RNA has a ribose sugar.
– RNA has uracil instead of thymine.
– RNA is a single-stranded structure.
Transcription makes three types of RNA.
• Transcription copies DNA to make a strand of RNA.
• Transcription is catalyzed by RNA polymerase.
– RNA polymerase and other proteins form a
transcription complex.
– The transcription complex recognizes the start of
a gene and unwinds a segment of it.
start site
transcription complex
nucleotides
– Nucleotides pair with one strand of the DNA.
– RNA polymerase bonds the nucleotides together.
– The DNA helix winds again as the gene is transcribed.
DNA
RNA polymerase
moves along the DNA
– The RNA strand detaches from the DNA once the gene
is transcribed.
RNA
• Transcription makes three types of RNA.
– Messenger RNA (mRNA) carries the message that will
be translated to form a protein.
– Ribosomal RNA (rRNA) forms part of ribosomes where
proteins are made.
– Transfer RNA (tRNA) brings amino acids from the
cytoplasm to a ribosome.
The transcription process is similar to
replication.
• Transcription and replication both involve complex
enzymes and complementary base pairing.
• The two processes have different end results.
– Replication copies
all the DNA;
transcription copies
a gene.
– Replication makes
one copy;
transcription can
make many copies.
one
gene
growing RNA strands
DNA
KEY CONCEPT
Translation converts an mRNA message into a
polypeptide, or protein.
Amino acids are coded by mRNA base
sequences.
• Translation converts mRNA messages into polypeptides.
• A codon is a sequence of three nucleotides that codes for
an amino acid.
codon for
methionine (Met)
codon for
leucine (Leu)
• The genetic code matches each codon to its amino acid or
function.
The genetic code matches each RNA codon with its amino acid or function.
– three stop
codons
– one start
codon,
codes for
methionine
• A change in the order in which codons are read changes
the resulting protein.
• Regardless of the organism, codons code for the same
amino acid.
•
Amino acids are linked to become a
protein.
An anticodon is a set of three nucleotides that is
complementary to an mRNA codon.
• An anticodon is carried by a tRNA.
• Ribosomes consist of two subunits.
– The large subunit has three binding sites for tRNA.
– The small subunit binds to mRNA.
• For translation to begin, tRNA binds to a start codon and
signals the ribosome to assemble.
– A complementary tRNA molecule binds to the exposed
codon, bringing its amino acid close to the first amino
acid.
– The ribosome helps form a polypeptide bond between
the amino acids.
– The ribosome pulls the mRNA strand the length of one
codon.
– The now empty tRNA molecule exits the ribosome.
– A complementary tRNA molecule binds to the next
exposed codon.
– Once the stop codon is reached, the ribosome
releases the protein and disassembles.
KEY CONCEPT
Gene expression is carefully regulated in both
prokaryotic and eukaryotic cells.
Prokaryotic cells turn genes on and off by
controlling transcription.
• A promotor is a DNA segment that allows a gene to
be transcribed.
• An operator is a part of DNA that turns a gene “on”
or ”off.”
• An operon includes a promoter, an operator, and
one or more structural genes that code for all the
proteins needed to do a job.
– Operons are most common in prokaryotes.
– The lac operon was one of the first examples of gene
regulation to be discovered.
– The lac operon has three genes that code for enzymes
that break down lactose.
• The lac operon acts like a switch.
– The lac operon is “off” when lactose is not present.
– The lac operon is “on” when lactose is present.
Eukaryotes regulate gene expression at
• Different sets of many
genes arepoints.
expressed in different
types of cells.
• Transcription is controlled by regulatory DNA
sequences and protein transcription factors.
• Transcription is controlled by regulatory DNA sequences
and protein transcription factors.
– Most eukaryotes have a TATA box promoter.
– Enhancers and silencers speed up or slow down the rate
of transcription.
– Each gene has a unique combination of regulatory
sequences.
Warm Up (2-19-15)
• Does all DNA code for specific genes? If not,
what is the importance of the noncoding
sequence?
Outline
• Objectives
• Gene notes
• DNA notes
Objectives
• Students will be able to explain the
importance of gene sequencing and why the
splicing of DNA can be so beneficial.
Warm Up (2-20-15)
• Explain the difference between introns and
exons and explain what process involves the
removal of introns from an RNA sequence
Outline
• Objectives
• Chapter 8 notes – DNA replication,
transcription, and translation
Objectives
• Students will be able to explain mRNA
processing and explain the alignment of genes
on a strand of DNA and RNA
• Students will be able to identify which genes
are coding sequences and which genes are
noncoding sequences.
• RNA processing is also an important part of gene regulation
in eukaryotes.
• mRNA processing includes three major steps.
• mRNA processing includes three major steps.
– Introns are removed and exons are spliced together.
– A cap is added.
– A tail is added.
KEY CONCEPT
Mutations are changes in DNA that may or may not
affect phenotype.
Some mutations affect a single gene,
while others affect an entire
chromosome.
• A mutation is a change in an organism’s DNA.
• Many kinds of mutations can occur, especially during
replication.
• A point mutation substitutes one nucleotide for another.
mutated
base
• Many kinds of mutations can occur, especially during
replication.
– A frameshift mutation inserts or deletes a nucleotide in
the DNA sequence.
• Chromosomal mutations affect many genes.
• Chromosomal mutations may occur during crossing over
– Chromosomal mutations affect many genes.
– Gene duplication results from unequal crossing over.
• Translocation results from the exchange of DNA segments
between nonhomologous chromosomes.
Mutations may or may not affect
phenotype.
• Chromosomal mutations tend to have a big effect.
• Some gene mutations change phenotype.
– A mutation may cause a premature stop codon.
– A mutation may change protein shape or the active site.
– A mutation may change gene regulation.
blockage
no blockage
• Some gene mutations do not affect phenotype.
– A mutation may be silent.
– A mutation may occur in a noncoding region.
– A mutation may not affect protein folding or the active
site.
• Mutations in body cells do not affect offspring.
• Mutations in sex cells can be harmful or beneficial to
offspring.
• Natural selection often removes mutant alleles from a
population when they are less adaptive.
•
Mutations can be caused by several
Replication errors canfactors.
cause
mutations.
• Mutagens, such as UV ray and
chemicals, can cause mutations.
• Some cancer drugs use
mutagenic properties to kill
cancer cells.
Warm Up (2-23-15)
• What is the importance of being able to splice
out genes within the DNA?
Outline
• Objectives
• DNA replication video
• DNA manipulatives
Objectives
• Students will explain the importance of DNA
replication
• Students will identify the steps that must
occur in order for DNA replication to happen
DNA Replication Video
• https://www.youtube.com/watch?v=27TxKoF
U2Nw
– Binary fission, asexual reproduction
DNA manipulatives
• http://www.dnai.org/b/index.html
Interesting article
• http://www.nature.com/scitable/topicpage/di
scovery-of-dna-structure-and-functionwatson-397
DNA Transformation Background
• http://www.dnalc.org/resources/animations/t
ransformation1.html
Warm Up (2-24-15)
• Explain what the process is of splicing a gene.
Can the DNA be cut anywhere? Be specific.
Outline
• Objectives
• Chapter 9 notes – biology book
Objectives
• Students will explain the process of DNA
fingerprinting
• Students will identify how DNA can be used in
modern technology
KEY CONCEPT
Biotechnology relies on cutting DNA at specific
places.
Scientists use several techniques to
manipulate DNA.
• Chemicals, computers, and bacteria are used to work
with DNA.
• Scientists use these tools in genetics research and
biotechnology.
Restriction enzymes cut DNA.
• Restriction enzymes act as “molecular scissors.”
– come from various types of bacteria
– allow scientists to more easily study and manipulate
genes
– cut DNA at a specific nucleotide sequence called a
restriction site
• Different restriction enzymes cut DNA in different
ways.
– each enzyme has a different restriction site
– some cut straight across and leave “blunt ends”
– some make staggered cuts and leave “sticky ends”
Restriction maps show the lengths of
DNA fragments.
• Gel electrophoresis is used to separate DNA
fragments by size.
– A DNA sample is cut with restriction enzymes.
– Electrical current pulls DNA fragments through a gel.
– Smaller fragments move faster and travel farther
than larger fragments.
– Fragments of different
sizes appear as bands
on the gel.
• A restriction map shows the lengths of DNA fragments
between restriction sites.
– only indicate size, not
DNA sequence
– useful in genetic
engineering
– used to study
mutations
KEY CONCEPT
DNA fingerprints identify people at the molecular
level.
A DNA fingerprint is a type of restriction
map.
• DNA fingerprints are based on parts of an individual’s
DNA that can by used for identification.
–
–
–
–
based on noncoding regions of DNA
noncoding regions have repeating DNA sequences
number of repeats differs between people
banding pattern on a gel is a DNA fingerprint
DNA fingerprinting is used for
identification.
• DNA fingerprinting depends on the probability
of a match.
– Many people have the
same number of
repeats in a certain
region of DNA.
– The probability that two
people share identical
numbers of repeats in
several locations is
very small.
(mother) (child 1) (child 2) (father)
– Individual probabilities are multiplied to find the
overall probability of two DNA fingerprints randomly
matching.
1 x 1 x 1 =
1
= 1 chance in 5.4 million people
500 90 120
5,400,000
– Several regions of DNA are
used to make DNA fingerprints.
• DNA fingerprinting is used in several ways.
– evidence in criminal
cases
– paternity tests
– immigration requests
– studying biodiversity
– tracking genetically
modified crops
KEY CONCEPT
DNA sequences of organisms can be changed.
Entire organisms can be cloned.
• A clone is a genetically identical copy of a gene or of
an organism.
• Cloning occurs in nature.
– bacteria (binary fission)
– some plants (from roots)
– some simple animals (budding, regeneration)
• Mammals can be cloned through a process called nuclear
transfer.
– nucleus is removed from an egg cell
– nucleus of a cell from the animal to be cloned is
implanted in the egg
• Cloning has potential benefits.
– organs for transplant into humans
– save endangered species
• Cloning raises concerns.
– low success rate
– clones “imperfect” and less healthy than original animal
– decreased biodiversity
New genes can be added to an
organism’s DNA.
• Genetic engineering involves changing an organism’s
DNA to give it new traits.
• Genetic engineering is based on the use of
recombinant DNA.
• Recombinant DNA contains genes from more than
one organism.
(bacterial DNA)
• Bacterial plasmids are often used to make
recombinant DNA.
– plasmids are loops of
DNA in bacteria
– restriction enzymes cut
plasmid and foreign DNA
– foreign gene inserted into
plasmid
Genetic engineering produces organisms
with new traits.
• A transgenic organism has one or more genes from
another organism inserted into its genome.
• Transgenic bacteria can be used to produce human
proteins.
– gene inserted into plasmid
– plasmid inserted into bacteria
– bacteria express the gene
• Transgenic plants are common in agriculture.
– transgenic bacteria
infect a plant
– plant expresses
foreign gene
– many crops are now
genetically modified
(GM)
• Transgenic animals are used to study diseases and
gene functions.
– transgenic mice used to study development and
disease
– gene knockout mice used to study gene function
• Scientists have concerns about some uses of genetic
engineering.
– possible long-term health effects of eating GM foods
– possible effects of GM plants on ecosystems and
biodiversity
Boundless Microbiology notes
• Transcription, Translation, Transformation
• https://www.boundless.com/microbiology/tex
tbooks/boundless-microbiologytextbook/microbial-genetics-7/genetictransfer-in-prokaryotes-81/bacterialtransformation-442-6842/
Warm Up (2-25-15)
• What are some thoughts that you have on the
manipulation of DNA.
• Think of some advantages as well as some
disadvantages that could occur because of
these modern advances.
Outline
• Objectives
• Gene Splicing interactive
Objectives
• Students will be able to practice splicing out
DNA from specific sequences of DNA using the
simulation.
DNA manipulatives
• http://www.dnai.org/b/index.html
Gene Splicing Interactive
• http://www.biotechnologyonline.gov.au/popu
ps/int_splicing.html
Warm Up (2-26-15)
• Write down what you can remember about
DNA replication, transcription, and translation.
Outline
• Objectives
• DNA replication, transcription, translation quiz
• Bacterial DNA information
Objectives
• Students will identify the different stages in
DNA replication
• Students will describe the processes involved
in DNA replication
• Students will demonstrate mastery of the
processes of DNA transcription and translation
and replication.
Quiz - DNA
•
•
•
•
Replication
Transcription
Translation
http://www.proprofs.com/quizschool/quizshow.php?title=bio-3-examtranslation-dna-replication-transciption&q=1
Bacterial DNA notes and structure
• Chapter 18 biology