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!

1 2

3

6

5

1 & 2. _________________

- ____________________

- ____________________

3 & 4. _________________

- ____________________

- ____________________

- ____________________

- ____________________

5. _________________

- ____________________

____________________

6 & 7. _________________

- ____________________

- ____________________

7

4

4

Gene Regulation