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34449625
Unit 4
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Biology Mind Map on Unit 4, created by dumb himbo on 11/11/2021.
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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
REPRESSOR binds to OPERATOR when
TRYPTOPHAN is present
tryptophan binds to repressor and changes its shape
so it CAN BIND to operator
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
GLUCOSE REPRESSION
bacterium prefer glucose, and want to break it down first
(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
enzymes are NOT needed if glucose is present
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
RNA polymerase attaches to promoter
binding site for catabolite activator protein
helps RNA polymerase bind to promoter
cAMP binds to site to form complex
gene for repressor protein
promoter for repressor gene
coding region
code for enzymes
GENES
EUKARYOTES
regulate gene expression to maintain homeostasis
TRANSCRIPTION FACTORS
important for RNA to bind
GENERAL
helps bind RNA polymerase
promoters
SPECIFIC
increases level of transcription; makes process better; enhances
activator binds to enhancer, forms loop
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
POSTTRANSCRIPTIONAL REGULATION
gene expression regulated after transcription
ALTERNATIVE SPLICING
introns spliced out of pre-mRNA
RNA EDITING
chemical modifications
NOT A MUTATION: not in genome, in RNA
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
PATTERN FORMATION
MORPHOGENESIS
MORPH : SHAPE
GENESIS : PRODUCE
ANIMALS REGULATE
number, timing, and orientation of cell division
growth and expansion
first more cells need to be made
cells adopt fate based on location
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
DETERMINATION takes place in STAGES
STEM CELLS
PLURIPOTENT
TOTIPOTENT
MULTIPOTENT
UNIPOTENT
CHAPTER 17: BIOTECHNOLOGY
RESTRICTION ENDONUCLEASES
RECOMBINANT DNA
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
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
CLONING VECTORS NEED:
a sequence that allows replication in host organism
a selectable marker
sequences that allow DNA fragments to be added
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
RNA PRIMERS BIND to DNA fragment
55
PRIMERS ADDED
HEAT SEPARATES 2 strand DNA into SINGLE strand DNA
95
put into THERMAL CYCLER
REVERSE TRANSCRIPTION PCR (RT-PCR)
PCR is performed on cDNA made from RNA
REVERSE TRANSCRIPTION to make cDNA
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
DNA FINGERPRINTING
can identify individual with small amount of tissue or body fluids
viruses use REVERSE TRANSCRIPTASE to use RNA to make DNA
BACTERIA DO NOT CUT INTRONS OUT
bacteria have 1 circlular chromosome
PLASMID
not essential for survival; bonus material
can insert DNA into PLASMID into BACTERIA
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
enzymes that cleave DNA at different spots
CLEAVE: break, cut
enzyme cuts DNA at prescribed locations
which INACTIVATES GENETIC INFO
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
DNA sequence is 4-12 bases
results in STICKY or BLUNT ends
STICKY ENDS are better
insertion DNA also needs to have STICKY end, that is complementary
can be joined
EcoRI always cleaves the sequence 5-GAATTC-3
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
DNA ---> DNA (REPLICATION) ---> RNA (TRANSCRIPTION) ---> PROTEIN (TRANSLATION)
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
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
SEQUENCE TAGGED SITE MAPS (STS MAPS)
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
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
A, T, C, and G tagged w/ different colored fluorescent DYE (each), fragments ANALYZED, fragments SEPARATED by length, detector READS sequence
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)
CHALLENGES:
produce LESS info
read length is SHORT
need MORE computing power
ERROR PRONE if longer reads are done
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
PRODUCED REFERENCE SEQUENCE
1000 GENOME PROJECT
looked at 1000 individuals from 26 populations, identified 80 million genetic variants
BIOINFORMATICS
computer programs to search for genes, and to assemble/compare genomes
math; modeling
COMPARATIVE GENOMICS
compare genomes
SYNTENY refers to conserved arrangements of DNA segments in related genomes
relate function to other organisms
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
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
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
many ppl have AFRICAN ORIGIN
recent common ancestor from 60,000 years ago
patterns of human migration
sampled 1,000 populations, over 500,000 participants
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