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Unit 4
- CHAPTER 16: CONTROL OF GENE EXPRESSION
- CONTROL OF GENE EXPRESSION
- PROKARYOTES
- regulate gene expression in
response to their environment
- OPERONS
- REPRESSION (makes product)
- if product is available,
enzymes are not needed
- trp OPERON
- genes associated with the
amino acid TRYPTOPHAN
- coding region has 5 ENZYMES
- coding region has 5 ENZYMES
- REPRESSOR binds to
OPERATOR when
- TRYPTOPHAN is present
- tryptophan binds to repressor
and changes its shape
- so it CAN BIND to operator
- so it CAN BIND to operator
- tryptophan binds to repressor
and changes its shape
- TRYPTOPHAN is present
- genes associated with the
amino acid TRYPTOPHAN
- trp OPERON
- if product is available,
enzymes are not needed
- INDUCTION (makes enzyme)
- made in response
to substrate
- lac OPERON
- REPRESSOR binds to
OPERATOR when
- ALLOLACTOSE is NOT present
- allolactose binds to repressor
and changes its shape
- so it CANNOT BIND to operator
- so it CANNOT BIND to operator
- allolactose binds to repressor
and changes its shape
- ALLOLACTOSE is NOT present
- GLUCOSE REPRESSION
- bacterium prefer glucose, and
want to break it down first
- (easier to do)
- (easier to do)
- they break down lactose when
there is no more glucose
- high levels of glucose = low levels of cAMP
- low levels of glucose = high levels of cAMP
- high levels of cAMP enables cAMP
to bind to CAP to form complex
- high levels of cAMP enables cAMP
to bind to CAP to form complex
- enzymes are NOT needed
if glucose is present
- low levels of glucose = high levels of cAMP
- bacterium prefer glucose, and
want to break it down first
- REPRESSOR binds to
OPERATOR when
- lac OPERON
- made in response
to substrate
- 2 regions:
- regulatory region
- controls whether coding
region is transcribed or not
- PROMOTER
- GENE
- CAP-BINDING SITE
- PROMOTER
- OPERATOR
- REPRESSOR
- repressor may bind to operator to STOP
- CONFORMATIONAL CHANGE
- shape of repressor changes
- shape of repressor changes
- repressor may bind to operator to STOP
- REPRESSOR
- RNA polymerase attaches to promoter
- OPERATOR
- binding site for catabolite activator protein
- helps RNA polymerase bind to promoter
- cAMP binds to site to form complex
- PROMOTER
- gene for repressor protein
- CAP-BINDING SITE
- promoter for repressor gene
- GENE
- controls whether coding
region is transcribed or not
- coding region
- code for
enzymes
- GENES
- code for
enzymes
- regulatory region
- REPRESSION (makes product)
- regulate gene expression in
response to their environment
- EUKARYOTES
- regulate gene expression to
maintain homeostasis
- TRANSCRIPTION
FACTORS
- important for RNA to bind
- GENERAL
- helps bind RNA
polymerase
- promoters
- helps bind RNA
polymerase
- SPECIFIC
- increases level of transcription;
makes process better;
enhances
- activator binds to
enhancer, forms loop
- increases level of transcription;
makes process better;
enhances
- important for RNA to bind
- regulate gene expression to
maintain homeostasis
- PROKARYOTES
- GENE REGULATION
- REGULATORY PROTEINS
regulate gene expression
- proteins bind to specific
sequences of DNA
- regulatory proteins possess
DNA-binding MOTIFS
- DNA-BINDING MOTIFS
- regions of regulatory
proteins which bind to DNA
- regions of regulatory
proteins which bind to DNA
- DNA-BINDING MOTIFS
- proteins bind to specific
sequences of DNA
- REGULATORY PROTEINS
regulate gene expression
- POSTTRANSCRIPTIONAL REGULATION
- gene expression regulated after transcription
- ALTERNATIVE SPLICING
- introns spliced out
of pre-mRNA
- introns spliced out
of pre-mRNA
- RNA EDITING
- chemical modifications
- NOT A MUTATION: not in genome, in RNA
- chemical modifications
- ALTERNATIVE SPLICING
- gene expression regulated after transcription
- CONTROL OF GENE EXPRESSION
- CHAPTER 19: CELLULAR MECHANISMS OF DEVELOPMENT
- PROCESS OF DEVELOPMENT
- CELL DIFFERENTATION
- CELL DIVISION
- EMBRYOGENESIS
- Development of embryo; before birth
- series of mitotic division after
fertilization to increase amount
of cells
- series of mitotic division after
fertilization to increase amount
of cells
- Development of embryo; before birth
- EMBRYOGENESIS
- PATTERN FORMATION
- MORPHOGENESIS
- MORPH : SHAPE
- GENESIS : PRODUCE
- ANIMALS REGULATE
- number, timing, and orientation of cell division
- growth and expansion
- growth and expansion
- number, timing, and orientation of cell division
- MORPH : SHAPE
- first more cells need to be made
- cells adopt fate based on location
- cells adopt fate based on location
- MORPHOGENESIS
- all cells within an individual
organism are the same; they all have
the same DNA (genetic information)
- CELL DETERMINATION
- molecular decision to become a
particular type of cell
- cells already know what type of
cell they will become
- acquires positional label that
reflects its location in the
embryo; whats around cell may
influence cell
- CELLS BECOME COMMITTED
- CELLS BECOME COMMITTED
- acquires positional label that
reflects its location in the
embryo; whats around cell may
influence cell
- cells already know what type of
cell they will become
- DETERMINATION takes
place in STAGES
- molecular decision to become a
particular type of cell
- CELL DETERMINATION
- CELL DIVISION
- CELL DIFFERENTATION
- STEM CELLS
- PLURIPOTENT
- TOTIPOTENT
- MULTIPOTENT
- UNIPOTENT
- UNIPOTENT
- TOTIPOTENT
- PLURIPOTENT
- PROCESS OF DEVELOPMENT
- CHAPTER 17: BIOTECHNOLOGY
- RESTRICTION ENDONUCLEASES
- RECOMBINANT DNA
- single DNA molecule made
from two different sources
- single DNA molecule made
from two different sources
- GEL ELECTROPHORESIS
- separates DNA fragments by size
- MOLECULAR CLONING W/ VECTORS
- VECTOR
- carries something from
one place to another
- carries something from
one place to another
- REVERSE TRANSCRIPTASE
- DNA LIBRARIES
- collection of DNA molecules that can
be MAINTAINED and REPLICATED in a
HOST ORGANISM
- DNA inserted into PLASMID then
inserted into BACTERIA
- DNA inserted into PLASMID then
inserted into BACTERIA
- CLONING VECTORS NEED:
- a sequence that allows replication in host organism
- a selectable marker
- sequences that allow DNA fragments to be added
- sequences that allow DNA fragments to be added
- a selectable marker
- a sequence that allows replication in host organism
- cDNA LIBRARIES
- POLYMERASE CHAIN REACTION (PCR)
- mimics DNA REPLICATION to produces
MILLIONS of COPIES of a DNA sequence
- allows amplification via PRIMERS
- 3 STEPS in PCR
- DENATURATION
- ANNEALING OF PRIMERS
- DNA SYNTHESIS
- DNA polymerase attaches to primer, synthesizes DNA
- 72
- DNA polymerase attaches to primer, synthesizes DNA
- RNA PRIMERS BIND to DNA fragment
- 55
- PRIMERS
ADDED
- PRIMERS
ADDED
- DNA SYNTHESIS
- HEAT SEPARATES 2 strand DNA into SINGLE strand DNA
- 95
- ANNEALING OF PRIMERS
- put into THERMAL CYCLER
- DENATURATION
- REVERSE TRANSCRIPTION PCR (RT-PCR)
- PCR is performed on cDNA made from RNA
- REVERSE TRANSCRIPTION to make cDNA
- cDNA is then used in PCR
- cDNA is then used in PCR
- QUANTITATIVE (RT-PCR)
- involves isolating mRNA, converting to cDNA using RT,
then using PCR to amplify specific cDNAs
- then amount of DNA produced is measured in real time
- dyes added to DNA to be visualized
- dyes added to DNA to be visualized
- then amount of DNA produced is measured in real time
- involves isolating mRNA, converting to cDNA using RT,
then using PCR to amplify specific cDNAs
- DNA FINGERPRINTING
- can identify individual with small
amount of tissue or body fluids
- can identify individual with small
amount of tissue or body fluids
- PCR is performed on cDNA made from RNA
- mimics DNA REPLICATION to produces
MILLIONS of COPIES of a DNA sequence
- collection of DNA molecules that can
be MAINTAINED and REPLICATED in a
HOST ORGANISM
- viruses use REVERSE TRANSCRIPTASE to use RNA to make DNA
- BACTERIA DO NOT CUT INTRONS OUT
- BACTERIA DO NOT CUT INTRONS OUT
- DNA LIBRARIES
- bacteria have 1 circlular chromosome
- PLASMID
- not essential for survival;
bonus material
- not essential for survival;
bonus material
- PLASMID
- can insert DNA into PLASMID into BACTERIA
- VECTOR
- GEL is either AGAROSE or POLYACRYLAMIDE
- GEL is submersed in BUFFER
- BUFFER carries ELECTRICAL CURRENT
- WELLS at NEGATIVE end, DNA moves to POSITIVE end
- DNA is NEGATIVEly charged
- LARGER DNA fragments move SLOWER
- SMALLER DNA fragments move FASTER
- DNA visualized using fluorescent dye
- DNA is cut from GEL, PURIFIED, and used to RECOMBINE RNA
- SMALLER DNA fragments move FASTER
- DNA is NEGATIVEly charged
- WELLS at NEGATIVE end, DNA moves to POSITIVE end
- BUFFER carries ELECTRICAL CURRENT
- GEL is submersed in BUFFER
- separates DNA fragments by size
- enzymes that cleave DNA
at different spots
- CLEAVE: break, cut
- enzyme cuts DNA at
prescribed locations
- which INACTIVATES GENETIC INFO
- which INACTIVATES GENETIC INFO
- CLEAVE: break, cut
- used by BACTERIA to fight off VIRUSES
- used in GENOME MAPPING
- 3 TYPES OF RESTRICTION ENDONUCLEASES
- type I and type III cleave w/
less precision, not used in
manipulating DNA
- TYPE II
- recognizes specific DNA sequences
- most are PALINDROMES
- a PALINDROME is word/phrase
that reads the same in forward
or reverse
- a PALINDROME is word/phrase
that reads the same in forward
or reverse
- DNA sequence is 4-12 bases
- most are PALINDROMES
- results in STICKY or BLUNT ends
- STICKY ENDS are better
- insertion DNA also needs to have
STICKY end, that is complementary
- insertion DNA also needs to have
STICKY end, that is complementary
- can be joined
- STICKY ENDS are better
- recognizes specific DNA sequences
- EcoRI always cleaves the
sequence 5-GAATTC-3
- type I and type III cleave w/
less precision, not used in
manipulating DNA
- RECOMBINANT DNA
- DNA LIGASE
- enzyme DNA LIGASE joins strands,
FORMS phosphodiesters, FORMS
back bone
- DNA ligase joins DNA fragments cut by restriction endonucleases and purified using an agarose gel
- DNA ligase also joins okazaki
fragments on lagging strand in
replication
- enzyme DNA LIGASE joins strands,
FORMS phosphodiesters, FORMS
back bone
- RESTRICTION ENDONUCLEASES
- DNA ---> DNA (REPLICATION) ---> RNA (TRANSCRIPTION) ---> PROTEIN (TRANSLATION)
- RNA --> DNA
- RNA --> DNA
- CHAPTER 18: GENOMICS
- MAPPING GENOMES
- GENETIC MAP
- show relative location of
GENES ON CHROMOSOMES,
and they use genetic
markers in order to do
so, look at RELATIVE
POSITION of markers
- show relative location of
GENES ON CHROMOSOMES,
and they use genetic
markers in order to do
so, look at RELATIVE
POSITION of markers
- PHYSICAL MAP
- actual DNA SEQUENCE ON
GENOME, map of entire
genome using markers,
shows ABSOLUTE
POSITION of markers
- 3 TYPES of PHYSICAL MAPS
- RESTRICTION MAPS
- CHROMOSOME MAPS
- use fluorescent
stains/dye that produce
patterns of bands on
chromosome
- use fluorescent
stains/dye that produce
patterns of bands on
chromosome
- SEQUENCE TAGGED SITE MAPS (STS MAPS)
- uses unique short-stretches of genomic
DNA, can be amplified by PCR, then
analyzed, pieced back together
- uses unique short-stretches of genomic
DNA, can be amplified by PCR, then
analyzed, pieced back together
- useful for small genomes,
genomes from organelles or viral
genomes; NOT human genomes
- DNA cut w/ RESTRICTION ENZYMES
(which cut at specific location)
- use ELECTROPHOREISIS to arrange
DNA fragments by size
- PATTERN ANALYZED
- fragments put BACK TOGETHER based
on SIZE and OVERLAP ---> CONTIG
- CONTIG is a contiguous segment of the genome
- CONTIG is a contiguous segment of the genome
- fragments put BACK TOGETHER based
on SIZE and OVERLAP ---> CONTIG
- PATTERN ANALYZED
- use ELECTROPHOREISIS to arrange
DNA fragments by size
- DNA cut w/ RESTRICTION ENZYMES
(which cut at specific location)
- CHROMOSOME MAPS
- RESTRICTION MAPS
- SEQUENCING GENOMES
- ULTIMATE physical map is BASE-PAIR
SEQUENCE of entire genome
- DIDEOXY TERMINATOR SEQUENCING
- use DIDEOXYNUCLEOTIDE CHAIN TERMINATORS
- there is NO HYDROXYL GROUP at 2
and 3 carbon in 5-carbon sugar
- another nucleotide can NOT BIND because of this
- this where DNA nucleotide ENDS
- this where DNA nucleotide ENDS
- A, T, C, and G tagged w/ different colored fluorescent DYE
(each), fragments ANALYZED, fragments SEPARATED by
length, detector READS sequence
- another nucleotide can NOT BIND because of this
- there is NO HYDROXYL GROUP at 2
and 3 carbon in 5-carbon sugar
- use DIDEOXYNUCLEOTIDE CHAIN TERMINATORS
- NEXT-GENERATION SEQUENCING (NGS)
- cost decreased significantly over time
- FEATURES:
- you can sequence DNA w/out constructing genomic
library by CONVENTIONAL CLONING
- you can carry out MILLIONS of
sequencing reactions at the SAME TIME
- also sequencing reaction can occur in solution;
be read directly (NO ELECTROPHORESIS)
- you can sequence DNA w/out constructing genomic
library by CONVENTIONAL CLONING
- CHALLENGES:
- produce LESS info
- read length is SHORT
- need MORE computing power
- ERROR PRONE if longer reads are done
- produce LESS info
- cost decreased significantly over time
- ULTIMATE physical map is BASE-PAIR
SEQUENCE of entire genome
- actual DNA SEQUENCE ON
GENOME, map of entire
genome using markers,
shows ABSOLUTE
POSITION of markers
- GENETIC MAP
- THE HUMAN GENOME PROJECT
- originated in 1991
- GOAL: to sequence entire human genome
- uses shotgun sequencing
- CHARACTERIZING GENOMES
- found fewer genes than
expected; expected 100,000,
there is actually 20,000
- COMPLEXITY OF AN ORGANISM IS NOT NECESSARILY RELATED TO ITS GENE NUMBER OR GENOME SIZE
- COMPLEXITY OF AN ORGANISM IS NOT NECESSARILY RELATED TO ITS GENE NUMBER OR GENOME SIZE
- PRODUCED REFERENCE SEQUENCE
- 1000 GENOME PROJECT
- looked at 1000 individuals from
26 populations, identified 80
million genetic variants
- looked at 1000 individuals from
26 populations, identified 80
million genetic variants
- 1000 GENOME PROJECT
- found fewer genes than
expected; expected 100,000,
there is actually 20,000
- BIOINFORMATICS
- computer programs to search for genes, and to assemble/compare genomes
- math; modeling
- math; modeling
- COMPARATIVE GENOMICS
- compare genomes
- SYNTENY refers to conserved arrangements of
DNA segments in related genomes
- relate function to other organisms
- relate function to other organisms
- compare genomes
- PROTEOMICS
- PROTEOME: all of proteins that are
produced from genome
- proteins are MORE DIFFICULT
to study because...
- POSTTRANSLATIONAL MODIFICATIONS
- ALTERNATIVE SPLICING
- there are modifications that
happen to proteins that do
NOT reflect sequence of DNA
- ALTERNATIVE SPLICING
- POSTTRANSLATIONAL MODIFICATIONS
- PROTEOME: all of proteins that are
produced from genome
- computer programs to search for genes, and to assemble/compare genomes
- GENOMICS CAN HELP TO IDENTIFY AND TREAT DISEASE
- identify genetic abnormalities
- identify victims by their remains
- tracing bacteria/viruses used in bioterrorism
- ETHICAL ISSUES
- GENE PATENTS
- identify genetic abnormalities
- THE HUMAN GENOME; THE GENOGRAPHIC JOURNEY
- DNA is able to trace back to earliest days of our species
- typos happen as DNA is passed on from generation to generation
- mtDNA; maternal; mitochondrial DNA comes from mother
- takes cells 8 HOURS to copy genome
- takes cells 8 HOURS to copy genome
- mtDNA; maternal; mitochondrial DNA comes from mother
- typos happen as DNA is passed on from generation to generation
- many ppl have AFRICAN ORIGIN
- recent common ancestor from 60,000 years ago
- patterns of human migration
- patterns of human migration
- recent common ancestor from 60,000 years ago
- sampled 1,000 populations, over 500,000 participants
- DNA is able to trace back to earliest days of our species
- originated in 1991
- MAPPING GENOMES
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