Ch 18 Gene Regulation. HOMEWORK MONDAY Read and outline 18.1 We are not covering this in notes. Be...
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Transcript of Ch 18 Gene Regulation. HOMEWORK MONDAY Read and outline 18.1 We are not covering this in notes. Be...
HOMEWORK MONDAY
Read and outline 18.1 We are not covering this in notes. Be thorough! Make note of any questions you may have for when we go
over this Tuesday in class. Answer concept check 18.1 Due TUESDAY 3-11
TUESDAY Read and outline 18.3
We are not covering this in notes. Be thorough! Make note of any questions you may have for when we go
over this Wednesday in class. Answer concept check 18.3 Due WEDNESDAY 3-12
WEDNESDAYWEDNESDAY Read and outline 19.2 and 19.5Read and outline 19.2 and 19.5 Concept check for these sectionsConcept check for these sections Due THURSDAYDue THURSDAY
Gene Regulation in Bacteria Cells vary amount of specific enzymes by _______________
gene transcription turn genes on or turn genes ______ Turn genes on example:
if bacterium encounters new sugar (energy source), like lactose, then it needs to start making enzymes used to _______________ lactose
Turn genes off example: if bacterium has enough tryptophan then it
_______________ need to make enzymes used to _______________ tryptophan
REGULATING
OFF
DIGEST
DOESN’TBUILD
Bacteria group genes together Operon
Genes grouped together with related _______________. Example: all enzymes in a metabolic pathway
Promoter = __________________ binding site Single promoter controls _______________of all genes in
operon Transcribed as one unit & a _________ mRNA is made
Operator = DNA binding site of _______________ protein
FUNCTIONS
RNA POLYMERASE
TRANSCRIPTION
SINGLEREPRESSOR
Operon Model When gene is turned
ON: Polymerase binds to
_______________ Gene is
_______________ Operon:
Operator, promoter & genes they control: serve as a ______________ for gene regulation
When gene is turned off: Repressor binds to ___________ site Blocks RNA Polymerase
Diagram
PROMOTER
TRANSCRIBED
MODEL
OPERATOR
How can genes be turned off? _______________protein
binds to DNA at operator site _______________RNA polymerase blocks _______________
REPRESSOR
BLOCKINGTRANSCRIPTION
trp operon 1 trp operon 2 (Watch half only) (Watch half only)trp operon 3
LINKSLINKS
choose narrated Boring Man 1 Boring Man 2Boring Man 2
Control of Eukaryotic Genes Evolution of Gene Regulation
Prokaryotes Single-celled Evolved to grow & divide _______________ Must respond quickly to changes in _________
environment exploit _______________ resources
Gene regulation turn genes on & off rapidly
flexibility & _________________ _______ levels of enzymes for synthesis & digestion
RAPIDLYEXTERNAL
TRANSIENT
REVERSABILITYADJUST
Eukaryotes Multicellular Evolved to maintain constant _______________ conditions
while facing changing external conditions __________________
Regulate body as a whole _______________& development
Specialization Turn on & off large number of genes
Must coordinate the body as a _______________ rather than serve the needs of individual cells
INTERNAL
HOMEOSTASIS
GROWTH
WHOLE
Pg 365 fig 19.5
On a separate piece of paper, please compare/contrast the trp operon and the lac operon.
Pg 370 fig 19.10
On the same sheet of paper from yesterday, please describe 4 different ways eukaryotic genes are controlled.
Understanding and Manipulating Genomes Recombinant DNA (do not confuse with recombinants in genetics)
Definition- DNA in which nucleotide sequences from two __________________ sources (__________) are combined in vitro into the same DNA molecule.
Basis of genetic __________________ Def: manipulation of genes for ______________ purposes Examples: Protein products such as __________________
and blood-clotting factors, much more. Biotechnology- manipulation of ______________ or their
components to make useful __________________. Ex: microbes used to make wine and cheese, ___________
breeding (exploiting naturally occurring mutations of genetic recombination.)
DIFFERENT SPECIES
ENGINEERINGPRACTICAL
HORMONES (HGH)
ORGANISMSPRODUCTS
SELECTIVE
DNA Cloning Problems with DNA
DNA molecules are very ________. Genes occupy only a small portion of DNA (others are
__________________ nucleotides) Gene may be only 1/__________________ of a
chromosome. Gene __________________- method to prepare well-defined
gene-________ pieces of DNA in __________________copies.
LONG
NON-CODING100,000
CLONINGSIZED MULTIPLE
Cloning and Applications Common approach of DNA cloning uses bacteria (E. coli) and
their __________________. Plasmids- small circular DNA molecules that _____________
separate from bacterial chromosomes Plasmids are first __________________ from bacterial
cells Foreign DNA is then ______________ into the plasmid. Resulting plasmid is __________________ to bacterial cell
producing a __________________bacterium It can then reproduce to form a ____________. Clone of cells contains __________________copies of
the gene.
PLASMIDSREPLICATE
ISOLATEDINSERTED
RETURNEDRECOMBINANT
CLONEMULTIPLE
Cloned genes are useful: To make many copies of a particular _________. To produce a __________________ product
Copies of cloned genes can be isolated for __________________ or to give an organism a new __________________capability.
Ex. Pest __________________ can be transferred into plants of different species. (Potato famine)
__________________ such as human growth hormone can be harvested from bacterial ___________ carrying the cloned gene for a protein.
Why is DNA cloning valuable Protein-coding genes are very ________- 1 ppm, so the ability
to clone such rare fragments can make something rare more ___________________.
GENEPROTEIN
RESEARCHMETABOLIC
RESISTANCE
PROTEINSCULTURES
RARE
AVAILABLE
Restriction Enzymes Definition- restriction _______________ protect the bacterial
cell against intruding DNA and work by ________ foreign DNA (restriction).
ENDONUCLEASESCUTTING
How they work: Restriction enzymes are ________________ and recognize
a particular DNA sequence (restriction site). They then cut both DNA strands at specific ________
within the restriction site. DNA of bacterial cell is __________________ from cell’s
own restriction enzymes by adding _______________ (_____) groups to adenines or cytosines within sequences recognized by enzyme.
SPECIFIC
POINTS
PROTECTEDMETHYL
CH3
More details about restriction enzymes Most sites are __________________: nucleotides are
identical when read from 5’3’ direction. Ex: 5’GAATTC 3’
Most recognize sequences of 4-8 __________________. Restriction __________________- pieces of DNA cut by
restriction enzymes. Same restriction enzymes result in _______________
fragments. Useful restriction enzymes ___________ sugar-phosphate
backbones in both DNA strands in a ______________ way. Resulting double stranded fragments have at least one
single stranded end- __________________
SYMMETRICAL
NUCLEOTIDESFRAGMENTS
SAME
CLEAVE
STAGGERED
STICKY END
Sticky ends can form hydrogen-bonded __________________ with complementary sticky ends on ___________ DNA molecules cut with the same enzyme.
DNA ____________ can permanently bind the two fragments by forming a covalent bond between the sugar-phosphate backbone.
BASE PAIRSOTHER
LIGASE
Restriction enzyme animation
Cloning Eukaryotic Gene in Bacterial Plasmid Original plasmid is a cloning __________________- DNA
molecule can carry foreign DNA into a cell and __________________ there.
Cloning vectors can be isolated, manipulated to form __________________ plasmids by insertion of foreign DNA in vitro, and then __________________into bacterial cells.
Cells reproduce rapidly and __________________ foreign DNA carried.
plasmid vectorplasmid vector
VECTOR
REPLICATES
RECOMBINANTREINTRODUCED
MULTIPLY
Producing Clones of Cells not boring man boring man Human genomic DNA is isolated and vector from bacterial
plasmid is isolated. Plasmid carries two genes: ampR (E.coli resistant to
__________________) and lacZ (encodes B-galactosidase which hydrolyzes __________________). lacZ gene contains a single copy of restriction site.
Both plasmid and human DNA are ___________ by the same restriction enzyme producing sticky ends. Plasmid is cut once while human DNA is cut at __________________ fragments.
The human DNA and plasmid fragments are __________________ which allows base pairing between __________________ sticky ends. DNA ligase is then added __________________ plasmid and human DNA fragments.
AMPICILLINLACTOSE
DIGESTED
MANY
MIXEDCOMPLEMENTARYJOINING
Resulting plasmids can be recombinant (contain __________________ DNA), be a combination of two plasmids, or a ____________________version of the original plasmid.
DNA resulting from step c is then mixed with bacteria with a __________________ in lacZ gene making them unable to __________________ lactose.
Cells take up foreign DNA by __________________. Some cells acquire a recombinant plasmid with gene of
interest and others acquire plasmid with _________ gene. Cloning step: bacteria are plated on ______________(nutrient
medium) containing ampicillin and X-gal. This allows us to identify clones of cells
__________________with recombinant plasmid.
HUMANNONRECOMBINANT
MUTATIONHYDROLYZE
TRANSFORMATION
ANOTHERAGAR
TRANSFORMED
How to recognize clones carrying recombinant plasmids Only cells with plasmid will reproduce since they have ampR
gene allowing __________________to ampicillin in the medium and will __________________.
Once clone contains 105 cells it can be seen as a _________________ on the agar.
__________________of colonies allows us to determine colonies of bacteria with recombinant plasmids from those with nonrecombinant plasmids.
Colonies with nonrecombinant plasmids with intact lacZ are __________________ because they produce B-galactosidase which hydrolyzes X-gal and produces a __________________ product.
Colonies with recombinant plasmids will be white because there is no __________________B-galactosidase.
RESISTANCEDIVIDE
COLONYCOLOR
BLUE
BLUE
FUNCTIONAL
Identifying Clones Carrying Gene of Interest Look for the Gene Itself
Nucleic Acid __________________- DNA of the gene is detected by ability to base-pair with complementary sequence on __________________ nucleic acid molecule.
If a part of the nucleotide sequence of the gene of interest is known, a nucleic acid ______________ can be used.
Nucleic acid probe- a short complementary molecule of __________________________ nucleic acid (DNA or RNA).
Example: sequence of DNA on gene of interest: 5’ GGCTAACT 3’
HYBRIDIZATION
ANOTHER
PROBE
SINGLE STRANDED
Probe molecules are labeled with __________________ isotopes so that it can be tracked.
The probe molecules will hydrogen bond to the complementary part of the __________________ gene.
Heat or chemicals are used to __________________the cells’ DNA to make it single stranded and able to base pair with the probe.
RADIOACTIVE
DESIREDDENATURE
Example Filter paper is pressed against the plate
__________________ cells to the filter. The filter is treated to break cells and
__________________ DNA. Radioactive probe molecules are __________________
with the filter and allows it to base pair with complementary DNA.
Filter paper is laid under film while exposing __________________ areas.
Colonies carrying gene of interest have been _________.
TRANSFERRING
DENATUREINCUBATED
RADIOACTIVE
LOCATED
Cloned Genes in DNA Libraries Genomic _________- set of thousands of DNA ____________
from a genome, each carried by a plasmid, phage, or other vector. Advantage of phages over plasmids is that phages can carry a
_________ DNA segment. Complementary DNA(___________) Library Only represents ____________ of a genome- genes that were
____________ into mRNA. Start with mRNA extracted from cells, reverse
__________________ (RT) is used to make single stranded _______ from _______, then DNA polymerase will complete the second strand of DNA.
LIBRARY SEGMENTS
LARGERcDNA
PARTTRANSCRIBED
TRANSCRIPTASEDNA mRNA
Use of DNA libraries Genomic library use
Want to clone a gene but unsure in what cell ______ it is expressed or _________ to obtain cell type.
Interested in _______________ sequences or introns of a gene.
cDNA use interested in _______________ sequence of genes Studying genes responsible for specialized
_______________ of cell types Changes in _______________ of gene _______________
TYPEUNABLEREGULATORY
CODING
FUNCTIONSPATTERNS EXPRESSION
Cloning and Expressing Eukaryotic Genes Having cloned eukaryotic gene function in a bacterial host can be
difficult due to the _______________ of gene expression in prokaryotes and eukaryotes.
Expression vector- cloning vector that contains a highly active _______________ promoter upstream of a restriction site where eukaryotic gene can be inserted in the correct _______________ frame.
Bacterial host recognizes the promoter and ___________ to express the foreign gene.
Expression vectors allow _______________of eukaryotic proteins in bacterial cells.
DIFFERENCES
PROKARYOTIC
READINGCONTINUES
SYNTHESIS
Another problem can result when _______________are present in eukaryotic genes and can be solved by using ______ (only exons).
Yeast Artificial Chromosomes (_________) Yeast cells are single-celled fungi that are easy to grow and
have _______________. YACs _______________eukaryotic chromosome with foreign
DNA. YACs act and divide ___________ in mitosis and can carry
_______________ DNA segment than plasmid vectors. Electroporation
Brief electrical pulse applied to a solution containing cells creating brief holes in their ________________________ allowing DNA to enter.
INTRONScDNA
YACs
PLASMIDSCOMBINE
NORMALLYLONGER
PLASMA MEMBRANES
Polymerase Chain Reaction (PCR) When DNA is ________ or impure, PCR can be used to make
copies. A specific target segment with one or many DNA molecules is
_______________ many times in a test tube. PCR can make billions of copies of a target segment of DNA in a
few _______________, much faster than the _______________it would take to obtain the same number of copies by screening a DNA library for a clone.
Procedure (1 cycle) The reaction mixture is heated to _______________the DNA
strands It is cooled to allow _______________ to anneal (hydrogen
bond) to strands Heat stable DNA polymerase _______________ primers in
5’3’ direction.
SCARCE
COPIED
HOURSDAYS
DENATURE
PRIMERS
EXTENDS
PCR is also very specific. Very small amounts of DNA can be used and it can be
partially _______________. By the end of the third cycle, one-fourth of the molecules are
_______________ to the target segment Each successive cycle, the number of identical pieces will
_________, soon outnumbering all other DNA molecules. Limitations: cannot _______________ gene cloning in cells when
__________ amounts of a gene are desired. Errors can limit number of good copies made.
Impact on biotechnology DNA from 40,000 year old ___________________ DNA from fingerprints, blood, tissue, or semen at _______
scenes DNA from single ____________ cells for prenatal diagnosis
of genetic disorders
DEGRADED
IDENTICAL
DOUBLESUBSTITUTE
LARGE
WOOLY MAMMOTHCRIME
EMBRYONIC
Restriction Fragment Analysis- detects _______________ in nucleotide sequence of DNA Gel Electrophoresis
Uses a gel as a tool to separate nucleic acids or proteins based on ______, electrical charge, and other physical ____________. (Figure 20.8).
Nucleic acids carry _______________ charges on phosphate groups and travel toward positive electrode.
Longer molecules are __________ more than shorter molecules which allows separation of DNA fragments by __________.
Gel electrophoresis separates a mixture of linear DNA molecules into ________, each consisting of DNA molecules that have the same length.
Band created reflects the restriction enzyme used and starting molecule.
DIFFERENCES
SIZE PROPERTIES
NEGATIVE
IMPEDEDLENGTH
BANDS
Uses: Provides a way to prepare pure sample of individual
_______________. Useful for _______________ two different DNA molecules
Example: two alleles for a gene will be cut at different sites and will display different mixtures of ___________.
Sickle Cell disease (figure 20.9) Southern blotting
__________ gel electrophoresis and nucleic acid hybridization
Reveals not only whether a particular sequence is present but also the _____ of the restriction fragments that contain the sequence.
FRAGMENTSCOMPARING
FRAGMENTS
COMBINES
SIZE
Example: three people: normal, heterozygous carrier, homozygous person for sickle cell disease. (p.395 Fig 20.10)
Electrophoresis of DNA contains _______________ bands to distinguish the three.
By use of southern blotting, we can _______________ bands that include parts of B-globin gene.
Probe will be complementary to B-globin gene and will ____________ to B-globin gene.
When film is laid over the paper, radioactivity can be seen which allows the mutant alleles to be _____.
TOO MANY
DETECT
BIND
SEEN
Restriction Fragment Length Polymorphisms (__________) Differences in restriction sites on homologous
chromosomes resulting in different restriction fragment _______________.
RFLP can serve as a genetic marker for a locus in the _______________.
RFLPs can be ___________ and analyzed by southern blotting.
RFLPs can serve as genetic __________ for making linkage maps.
Frequency which two RFLP markers are inherited is a measure of ___________ of two loci on a chromosome.
RFLPs
PATTERNS
GENOMEDETECTED
MARKERS
CLOSENESS
Mapping Genomes Human Genome Project
Project that aimed to map the human genome starting in _____. The nucleotide sequence of the majority of DNA in each
human chromosome was obtained by ___________. Three Stages: 1. Genetic (_________) mapping. 2. Physical
mapping. 3. DNA _______________ Genetic (linkage mapping)
_______________ provides the number of chromosome and overall banding pattern.
Some genes were already located by fluorescence in situ hybridization (FISH).
Using cytogenetic maps, a linkage map was constructed by ordering genetic _______________ (_______________, simple sequence DNA, etc.)
1990
2003LINKAGE
SEQUENCING
KARYOTYPE
MARKERSRFLPs
Physical Mapping Distances _______________ markers are expressed in
physical measure (number of __________________ along DNA).
Physical map is made by cutting DNA of each chromosome into a number of restriction _______________ and determining original _______________ of fragments in chromosomal DNA.
Make fragments that overlap and use probes to find _______________ to determine sequence.
First cloning vector is a YAC or bacterial artificial chromosome (BAC).
Once long fragments are _______________, they are cut into smaller pieces, cloned and then _______________ again.
BETWEENBASE PAIRS
FRAGMENTSORDER
OVERLAPS
ORDERED
SEQUENCED
DNA sequencing Goal is to determine the _______________ sequence of
each chromosome. If many copies of a DNA fragment up to _______ base
pairs is available, the sequence can be determined by a sequencing ______________.
Chain-termination method could not be used for _______________ chromosome.
NUCLEOTIDE
MACHINE
HUMAN
800
Venter’s idea (Whole-genome _________ approach)- ________ genetic mapping and physical mapping stages
Cut DNA from many copies of entire chromosome into fragments _______________ enough for sequencing.
Clone fragments in _______________. Sequence each _______________. Use computer software to _______________the
fragments into one sequence. How does the approach to genome mapping used in the Human
Genome Project differ from shotgun approach?
SHOTGUNSKIP
SHORTVECTORS
FRAGMENTASSEMBLE
Differential Gene Expression Cell _________________ (_________________)
Different cells result as a result of gene ____________ and not from differences in cell’s ________________.
Differentiation occurs during _________________as specific genes are turned on and off by regulatory mechanisms.
DIFFERENTIATION SPECIALIZATIONEXPRESSION
GENOMESDEVELOPMENT
Evidence of Genomic _________________: Plants All cells have the same genes. Question: What happens to ___________ after cell
differentiation? Do skin cells contain _________________ genes that
specify eye color (or anything else) or is it permanently inactive or gone completely?
_________________ cells: the ability to _________________ and then divide to give rise to ______ the specialized cell types in an organism.
Carrot Plant Experiment: Differentiated cells were taken from the ___________ of a
carrot plant. These cells were placed into a culture medium where they
were allowed to grow into normal adult plants. Each of the plants was _________________ to the parent.
EQUIVALENCE
GENES
FUNCTIONING
TOTIPOTENTDEDIFFERENTIATE ALL
ROOTS
IDENTICAL
Cloning Definition: using one or more somatic cells from a
multicellular organism to make an individual that is _________________ identical. Each individual made this way is a ___________.
Evidence of Genomic Equivalence: Animals Nuclear _________________: Scientists removed the
____________ of an unfertilized egg cell or zygote and replaced it with the nucleus of a ________________ cell.
GENETICALLYCLONE
TRANSPLANTATIONNUCLEUS
DIFFERENTIATED
Researchers used tadpoles in order to do this and used a variety of differentiated cells.
The ______________ the donor was, the more likely it would develop into tadpoles (higher __________ potency).
Less differentiated cells worked ___________ than fully differentiated cells.
Conclusions Something in the nucleus does _____________ as animal
cells differentiate. Nuclear potency is _________________ as cell
differentiation progresses. Scientists agree that nuclei of most differentiated animal
cells have _____ the genes required for making the entire _________________.
YOUNGERNUCLEAR
BETTER
CHANGE
RESTRICTED
ALLORGANISM
Cloning of Mammals (adults) Dolly (1997-2003)- Lamb cloned from an _____________
sheep by nuclear transplantation Procedure
Cultured mammary glands in nutrient-poor medium (semi-___________) causing a stop of the _________________ and resulting in __________________.
These cells were then _____________ with sheep egg cells that had their nuclei removed.
The resulting diploid cells divided to form early embryos which were implanted in the uterus of a surrogate ________. Out of several hundred implanted embryos, Dolly was born.
ADULT
STARVED CELLDEDIFFERENTIATION
FUSED
MOTHER
Dolly’s DNA was _________________to that of the donor nucleus DNA.
Death of Dolly Dolly suffered from a lung disease that is seen in much older
sheep and was ____________. Some believe that her cells were “________” than normal
sheep. Other cloning: mice, cats, cows, horses, pigs. “All twins are clones, but not all clones are twins.” Example:
__________ Cat- calico cat Implications:
IDENTICAL
EUTHANIZEDOLDER
COPY
South Korea 2004: Human Cloning? Nuclear transplantation occurred and eggs were stimulated to
____________ and some reached the ____________ stage (early embryonic stage), they were _______ allowed to develop beyond this stage.
Ethics of cloning. ___________ with animal cloning
Only a small _________________ of cloned embryos develop to birth
Cloned animals exhibit various _____________ Cloned mice are prone to obesity, pneumonia, liver failure
and early _________.
DIVIDE BLASTOCYSTNOT
PROBLEMSPERCENTAGE
DEFECTS
DEATH
Low efficiency of cloning and high incidence of _________________. DNA in embryonic cells from cloned embryos have more
______________ groups than DNA in equivalent cells from ______________ embryos This suggests that reprogramming is not always
________________ DNA methylation helps gene ______________ and
the misplacement of these methyl groups may interfere with pattern of gene expression needed for _______________ embryonic development.
ABNORMALITIES
METHYLUNCLONED
COMPLETEREGULATION
NORMAL
Stem Cells of Animals Stem cell- relatively _________________ cell that can
reproduce itself and under appropriate conditions, differentiate into _________________ cells of one or more types.
Stem cells are able to _________________their own cells and can generate cells that can have _________ differentiation pathways.
Many animal embryos have _________________ stem cells which can result in differentiated cells of any type.
Stem cells can be isolated at the ______________ stage (blastocyst in humans).
In culture, embryonic stem cells _________________ indefinitely and can differentiate into specialized cells depending on the _________________ they are in.
UNSPECIALIZED
SPECIALIZEDREPLENISH
VARYING
TOTIPOTENT
BLASTULA
REPRODUCE
CULTURE
Adults also have a variety of stem cells that can replace __________________ specialized cells as needed.
Adult stem cells are considered _________________ as they are able to give rise to multiple but not ________ cell types. Blood marrow stem cells can give rise to all the kinds of
__________ cells and stem cells in the intestinal wall can regenerate the various cells forming the lining of the ______________.
Adult _____________ stem cells continue to produce certain kinds of nerve cells.
Adults have a very ______________ amount of stem cells. Scientists are learning how to identify, isolate adult stem cells
from tissues and have been able to ________ these cells in culture. In the right culture conditions, we have been able to have
these cells _________________ into specialized cells.
NONREPRODUCINGPLURIPOTENT
ALL
BLOOD
INTESTINEBRAIN
SMALL
GROW
DIFFERENTIATE
What does the future hold? The more research and information we gain, we can apply
these _________________. Goal: supply _______ to _______ damaged or diseased
organs. Examples:
Insulin-producing ____________ cells for diabetics Specific brain cells for people with _________________
or Huntington’s. Currently, embryonic stem cells are more ____________
than adult stem cells. Ethics and politics discussion.
MEDICALLYCELLS REPAIR
PANCREATICPARKINSON’S
PROMISING
Now, stem cells are gathered from patients undergoing _________________ treatment or from long-term cell cultures with cells isolated from _________________ embryos.
Embryo cloning _________________cloning- the main goal of cloning to
produce embryonic stem cells to treat __________. Is it ok to clone humans? Is it ok to clone embryos for
therapeutic reasons?
INFERTILITYDONATED
THERAPEUTICDISEASE