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AP Biology
Eukaryotic Gene
Control
The BIG Questions…
How are genes turned on & off in eukaryotes?
How do cells with the same genes differentiate to perform completely different, specialized functions?
Evolution of gene regulation
Prokaryotes
single-celled
evolved to grow & divide rapidly
must respond quickly to changes in external environment exploit transient resources
Gene regulation
turn genes on & off rapidly flexibility & reversibility
adjust levels of enzymes for synthesis & digestion
Evolution of gene regulation
Eukaryotes
multicellular
evolved to maintain constant internal conditions while facing changing external conditions homeostasis
regulate body as a whole growth & development
long term processes
specialization turn on & off large number of genes
must coordinate the body as a whole rather than serve the needs of individual cells
Points of control
The control of gene
expression can occur at any
step in the pathway from
gene to functional protein
1. packing/unpacking DNA
2. transcription
3. mRNA processing
4. mRNA transport
5. translation
6. protein processing
7. protein degradation
How do you fit all
that DNA into
nucleus?
DNA coiling &
folding
double helix
nucleosomes
chromatin fiber
looped
domains
chromosome
from DNA double helix to
condensed chromosome
1. DNA packing
Nucleosomes
“Beads on a string”
1st level of DNA packing
histone proteins
8 protein molecules
positively charged amino acids
bind tightly to negatively charged DNA
DNA packing movie
8 histone
molecules
file://localhost/Users/kfoglia/Kim's%20NEW%20WORK/Half%20Hollow%20Hills/%20Campbell%20CDs/BIOLOGY6eCIPLchapters18-28/ImageLibrary18-28/19-EukaryoticGenomes/19-01-DNAPacking.mov
DNA packing as gene control
Degree of packing of DNA regulates transcription
tightly wrapped around histones
no transcription
genes turned off heterochromatin
darker DNA (H) = tightly packed
euchromatin
lighter DNA (E) = loosely packed
H E
So, which one
can be transcribed?
DNA methylation Methylation of DNA blocks transcription factors
no transcription
genes turned off
attachment of methyl groups (–CH3) to cytosine C = cytosine
nearly permanent inactivation of genes ex. inactivated mammalian X chromosome = Barr body
Modifications on chromatin can be passed on to
future generations
Unlike DNA mutations, these changes to
chromatin can be reversed (de-methylation of
DNA)
Explains differences between identical twins
Epigenetic imprinting silences the imprinted
genes
Epigenetic Inheritance
Histone acetylation
Acetylation of histones unwinds DNA
loosely wrapped around histones
enables transcription
genes turned on
attachment of acetyl groups (–COCH3) to histones
conformational change in histone proteins
transcription factors have easier access to genes
2. Transcription initiation
Control regions on DNA
promoter nearby control sequence on DNA
binding of RNA polymerase & transcription factors
“base” rate of transcription
enhancer distant control
sequences on DNA
binding of activator proteins
“enhanced” rate (high level) of transcription
Model for Enhancer action
Enhancer DNA sequences
distant control sequences
Activator proteins
bind to enhancer sequence & stimulates transcription
Silencer proteins
bind to enhancer sequence & block gene transcription
Turning on Gene movie
file://localhost/Users/kfoglia/Kim's%20NEW%20WORK/Half%20Hollow%20Hills/%20Campbell%20CDs/BIOLOGY6eCIPLchapters18-28/ImageLibrary18-28/19-EukaryoticGenomes/19-09-TurningOnAGene.movhttps://www.youtube.com/watch?v=vi-zWoobt_Q&index=29&list=PLSy2IqrL3nn9etf2mmBU3OOGYxlRH1BNN
Transcription complex
Enhancer
ActivatorActivator
Activator
Coactivator
RNA polymerase II
A
B F E
HTFIID
Core promoterand initiation complex
Activator Proteins• regulatory proteins bind to DNA at
distant enhancer sites• increase the rate of transcription
Enhancer Sitesregulatory sites on DNA distant from gene
Initiation Complex at Promoter Site binding site of RNA polymerase
3. Post-transcriptional control
Alternative RNA splicing
variable processing of exons creates a
family of proteins
4. Regulation of mRNA degradation
Life span of mRNA determines amount
of protein synthesis
mRNA can last from hours to weeks
RNA 5’ and PolyA processing and RNA splicing video
file://localhost/Users/kfoglia/Kim's%20NEW%20WORK/Half%20Hollow%20Hills/%20Campbell%20CDs/BIOLOGY6eCIPLchapters18-28/ImageLibrary18-28/19-EukaryoticGenomes/19-08-RNAprocessing.movhttps://www.youtube.com/watch?v=YjWuVrzvZYAhttps://www.youtube.com/watch?v=FVuAwBGw_pQ&t=5s
RNA interference Small interfering RNAs (siRNA)
short segments of RNA (21-28 bases)
bind to mRNA
create sections of double-stranded mRNA
“death” tag for mRNA
triggers degradation of mRNA
cause gene “silencing”
post-transcriptional control
turns off gene = no protein produced
siRNA
Action
of
siRNA
siRNA
double-stranded
miRNA + siRNA
mRNA degradedfunctionally
turns gene off
mRNA for translation
breakdownenzyme(RISC)
dicerenzyme
RNA interference 1990s | 2006
Andrew Fire
Stanford
Craig Mello
U Mass
“for their discovery of
RNA interference —
gene silencing by
double-stranded RNA”
Another video,
I love videos
https://www.youtube.com/watch?v=cK-OGB1_ELE
5. Control of translation
Block initiation of translation stage
regulatory proteins attach to 5' end of mRNA
prevent attachment of ribosomal subunits &
initiator tRNA
block translation of mRNA to protein
Control of
translation video
/Users/kfoglia/Kim's NEW WORK/Half Hollow Hills/ Campbell CDs/BIOLOGY6eCIPLchapters18-28/ImageLibrary18-28/19-EukaryoticGenomes/19-10-ControlOfTranslation.movhttps://www.youtube.com/watch?v=TfYf_rPWUdY
6-7. Protein processing & degradation
Protein processing
folding, cleaving, adding sugar groups, targeting for transport
Protein degradation
ubiquitin tagging
proteasome degradation
Ubiquitin
“Death tag”
mark unwanted proteins with a label
76 amino acid polypeptide, ubiquitin
labeled proteins are broken down
rapidly in "waste disposers"
proteasomes
1980s | 2004
Aaron Ciechanover
Israel
Avram Hershko
Israel
Irwin Rose
UC Riverside
Proteasome
Protein-degrading “machine”
cell’s waste disposer
breaks down any proteins
into 7-9 amino acid fragments
cellular recycling
Proteins labeled for
Destruction
https://www.nobelprize.org/nobel_prizes/chemistry/laureates/2004/popular.html
initiation of transcription
1
mRNA splicing
2
mRNA protection3
initiation of translation
6
mRNAprocessing
5
1 & 2. transcription
- DNA packing
- transcription factors
3 & 4. post-transcription
- mRNA processing
- splicing
- 5’ cap & poly-A tail
- breakdown by siRNA
5. translation
- block start of
translation
6 & 7. post-translation
- protein processing
- protein degradation
7 protein processing & degradation
4
4
Gene Regulation
AP Biology
19.5 – DUPLICATIONS,
REARRANGEMENTS, AND
MUTATIONS OF DNA
CONTRIBUTE TO GENOME
EVOLUTION
Families of Genes Human globin gene family
Evolved form duplication of common
ancestral globin gene
Different versions are expressed at
different times in development allowing
hemoglobin to function throughout life
of the developing animal
Evolution occurred long ago, all
vertebrates have multiple globin genes
and most mammals have the same set
of globin genes.
Different versions of each globin
subunit are expresses at different times
in development, allowing hemoglobin
to function effectively in the changing
environment of the developing animal.
Interspersed repetitive DNA
Repetitive DNA is spread throughout the genome
Makes up 25 – 40% of the mammalian genome
In humans, at least 5% of genome is made of a
family of similar sequences called Alu
elements.
300 bases long, Alu is an example of a
“Jumping gene”
A transposon DNA sequence that
reproduces itself & inserts into new
chromosome locations
Rearrangements in the genome
Transposons:
Transposible (movable) genetic element
A piece of DNA that can move form one
location to another in a cell’s genome
One gene of an insertion sequence codes for
transposase, which catalyzes the transposon’s
movement. The inverted repeats, about 20 to 40
nucleotide pairs long, are backward, upside-down
versions of each other.
In transposition, transposase molecules bind to
the inverted repeats & catalyze the cutting &
resealing of DNA required for insertion of the
transposon at a target site.
Peto’s Paradox
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060950/
AP Biology
Transposons
Insertion of
transposon
sequence in new
position in genome insertion sequences
cause mutations when
they happen to land
within the coding
sequence of a gene or
within a DNA region
that regulates gene
expression
Transposons 1947/1983
Barbara McClintock
discovered 1st
transposons in Zea
mays (corn) in 1947
She found that
transposons were
responsible for a
variety of types of gene
mutations, usually
insertions deletions
and translocations
AP Biology
RetrotransposonsTransposons actually make up over 50% of the
corn (maize) genome & 10% of the human genome
Most of these
transposons are
retrotransposons,
transposable
elements that
move within a
genome by means
of RNA
intermediate,
transcript of the
retrotransposon
DNA
AP Biology
Turn your
Question Genes on!
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Gene Regulation