AP Biology

Chapter 19.

Control of Eukaryotic Genome

AP Biology

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?

AP Biology

Prokaryote vs. eukaryote genomeProkaryotes

small size of genomecircular molecule of naked DNA

DNA is readily available to RNA polymerasecontrol of transcription by regulatory proteins

operon systemmost of DNA codes for protein or RNA

no introns, small amount of non-coding DNAregulatory sequences: promoters, operators

AP Biology

Prokaryote vs. eukaryote genomeEukaryotes

much greater size of genomehow does all that DNA fit into nucleus?

DNA packaged in chromatin fibersregulates access to DNA by RNA polymerase

cell specializationneed to turn on & off large numbers of genes

most of DNA does not code for protein97% “junk DNA” in humans

AP Biology

Points of controlThe control of gene expression can occur at any step in the pathway from gene to functional protein

unpacking DNAtranscriptionmRNA processingmRNA transport

out of nucleusthrough cytoplasmprotection from degradation

translationprotein processingprotein degradation

AP Biology

Why turn genes on & off?Specialization

each cell of a multicellular eukaryote expresses only a small fraction of its genes

Developmentdifferent genes needed at different points in life cycle of an organism

afterwards need to be turned off permanentlyResponding to organism’s needs

homeostasiscells of multicellular organisms must continually turn certain genes on & off in response to signals from their external & internal environment

AP Biology

DNA packingHow do you fit all that DNA into nucleus?

DNA coiling & folding

double helixnucleosomeschromatin fiberlooped domainschromosome

from DNA double helix to condensed chromosome

AP Biology

Nucleosomes“Beads on a string”

1st level of DNA packinghistone proteins

8 protein moleculesmany positively charged amino acids

arginine & lysinebind tightly to negatively charged DNA

DNA packing movie

8 histone molecules

http://bio.kimunity.com, http://www.WDinteractive.com/file://localhost/Users/kfoglia/Kim's%20NEW%20WORK/Half%20Hollow%20Hills/%20Campbell%20CDs/BIOLOGY6eCIPLchapters18-28/ImageLibrary18-28/19-EukaryoticGenomes/19-01-DNAPacking.mov

AP Biology

DNA packingDegree of packing of DNA regulates transcription

tightly packed = no transcription= genes turned off

darker DNA (H) = tightly packedlighter DNA (E) = loosely packed

AP Biology

DNA methylationMethylation of DNA blocks transcription factors

no transcription = genes turned offattachment of methyl groups (–CH3) to cytosine

C = cytosinenearly permanent inactivation of genes

ex. inactivated mammalian X chromosome

AP Biology

Histone acetylationAcetylation of histones unwinds DNA

loosely packed = transcription= genes turned on

attachment of acetyl groups (–COCH3) to histonesconformational change in histone proteinstranscription factors have easier access to genes

AP Biology

Transcription initiationControl regions on DNA

promoternearby control sequence on DNAbinding of RNA polymerase & transcription factors“base” rate of transcription

enhancersdistant control sequences on DNAbinding of activator proteins“enhanced” rate (high level) of transcription

AP Biology

Model for Enhancer action

Enhancer DNA sequences distant control sequences

Activator proteinsbind to enhancer sequence & stimulates transcription

Silencer proteinsbind to enhancer sequence & block gene transcription

Turning on Gene movie

http://bio.kimunity.com, http://www.WDinteractive.com/file://localhost/Users/kfoglia/Kim's%20NEW%20WORK/Half%20Hollow%20Hills/%20Campbell%20CDs/BIOLOGY6eCIPLchapters18-28/ImageLibrary18-28/19-EukaryoticGenomes/19-09-TurningOnAGene.mov

AP Biology

Post-transcriptional controlAlternative RNA splicing

variable processing of exons creates a family of proteins

AP Biology

Regulation of mRNA degradationLife span of mRNA determines pattern of protein synthesis

mRNA can last from hours to weeks

RNA processing movie

http://bio.kimunity.com, http://www.WDinteractive.com/file://localhost/Users/kfoglia/Kim's%20NEW%20WORK/Half%20Hollow%20Hills/%20Campbell%20CDs/BIOLOGY6eCIPLchapters18-28/ImageLibrary18-28/19-EukaryoticGenomes/19-08-RNAprocessing.mov

AP Biology

RNA interferenceSmall RNAs (sRNA)

short segments of RNA (21-28 bases)bind to mRNAcreate sections of double-stranded mRNA“death” tag for mRNA

triggers degradation of mRNA

cause gene “silencing”even though post-transcriptional control, still turns off a genesiRNA

NEW!

AP Biology

RNA interferenceSmall RNAs

double-stranded RNAsRNA + mRNA

mRNA

mRNA degraded

functionally turns gene off

Hottestnew topicin biology

AP Biology

Control of translationBlock initiation stage

regulatory proteins attach to 5’ end of mRNA

prevent attachment of ribosomal subunits & initiator tRNAblock translation of mRNA to protein

Control of translation movie

http://bio.kimunity.com, http://www.WDinteractive.com/file://localhost/Users/kfoglia/Kim's%20NEW%20WORK/Half%20Hollow%20Hills/%20Campbell%20CDs/BIOLOGY6eCIPLchapters18-28/ImageLibrary18-28/19-EukaryoticGenomes/19-10-ControlOfTranslation.mov

AP Biology

Protein processing & degradationProtein processing

folding, cleaving, adding sugar groups, targeting for transport

Protein degradationubiquitin taggingproteosome degradation

Protein processing movie

http://bio.kimunity.com, http://www.WDinteractive.com/file://localhost/Users/kfoglia/Kim's%20NEW%20WORK/Half%20Hollow%20Hills/%20Campbell%20CDs/BIOLOGY6eCIPLchapters18-28/ImageLibrary18-28/19-EukaryoticGenomes/19-12-ProteinProcessing.mov

AP Biology

Ubiquitin“Death tag”

mark unwanted proteins with a label 76 amino acid polypeptide, ubiquitinlabeled proteins are broken down rapidly in "waste disposers"

proteasomes

1980s | 2004

Aaron CiechanoverIsrael

Avram HershkoIsrael

Irwin RoseUC Riverside

AP Biology

ProteasomeProtein-degrading “machine”

cell’s waste disposercan breakdown all proteins into 7-9 amino acid fragments

play Nobel animation

AP Biology

transcription

1

mRNA processing2 mRNA transport out of nucleus3

translation5

mRNA transportin cytoplasm

4

1. transcription -DNA packing-transcription factors

2. mRNA processing-splicing

3. mRNA transportout of nucleus

-breakdown by sRNA

4. mRNA transport in cytoplasm

-protection by 3’ cap & poly-A tail

5. translation-factors which block start of translation

6. post-translation-protein processing-protein degradation-ubiquitin proteasome

6post- translation

AP Biology

Any Questions??

AP Biology

1

23

5 4

6

AP Biology

Structure of the Eukaryotic Genome

AP Biology

How many genes?Genes

only ~3% of human genomeprotein-coding sequences

1% of human genomenon-protein coding genes

2% of human genometRNAribosomal RNAssiRNAs

AP Biology

What about the rest of the DNA?Non-coding DNA sequences

regulatory sequencespromoters, enhancersterminators

“junk” DNAintronsrepetitive DNA

centromerestelomerestandem & interspersed repeats

transposons & retrotransposonsAlu in humans

AP Biology

Repetitive DNARepetitive DNA & other non-coding sequences account for most of eukaryotic DNA

AP Biology

Genetic disorders of repeatsFragile X syndrome

most common form of inherited mental retardationdefect in X chromosome

mutation of FMR1 gene causing many repeats of CGG triplet in promoter region

200+ copiesnormal = 6-40 CGG repeats

FMR1 gene not expressed & protein (FMRP) not produced

function of FMR1 protein unknown binds RNA

AP Biology

Fragile X syndromeThe more triplet repeats there are on the X chromosome, the more severely affected the individual will be

mutation causes increased number of repeats (expansion) with each generation

AP Biology

Huntington’s DiseaseRare autosomal dominant degenerative neurological disease

1st described in 1872 by Dr. Huntingtonmost common in white Europeans1st symptoms at age 30-50

death comes ~12 years after onsetMutation on chromosome 4

CAG repeats40-100+ copiesnormal = 11-30 CAG repeatsCAG codes for glutamine amino acid

AP Biology

Huntington’s diseaseAbnormal (huntingtin) protein produced

chain of charged glutamines in proteinbonds tightly to brain protein, HAP-1

Woody Guthrie

AP Biology

Families of genesHuman globin gene family

evolved from duplication of common ancestral globin gene

Different versions are expressed at different times in development allowing hemoglobin to function throughout life of developing animal

AP Biology

Hemoglobindifferential expression of different beta globin genes ensures important physiological changes during human development

AP Biology

Interspersed repetitive DNARepetitive DNA is spread throughout genome

interspersed repetitive DNA make up 25-40% of mammalian genomein humans, at least 5% of genome is made of a family of similar sequences called, Alu elements

300 bases longAlu is an example of a "jumping gene" –a transposon DNA sequence that "reproduces" by copying itself & inserting into new chromosome locations

AP Biology

Rearrangements in the genomeTransposons

transposable genetic elementpiece of DNA that can move from one location to another in 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 oth. 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.

AP Biology

TransposonsInsertion 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

AP Biology

TransposonsBarbara McClintock

discovered 1st transposons in Zeamays (corn) in 1947

1947|1983

AP Biology

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

Any Questions??

AP Biology

Aaaaah…Structure-Function

yet again!

Chapter 19.The BIG Questions…Prokaryote vs. eukaryote genomeProkaryote vs. eukaryote genomePoints of controlWhy turn genes on & off?DNA packingNucleosomes DNA packingDNA methylationHistone acetylationTranscription initiationModel for Enhancer actionPost-transcriptional controlRegulation of mRNA degradationRNA interferenceRNA interferenceControl of translationProtein processing & degradationUbiquitinProteasome Slide Number 22Any Questions??Slide Number 24Structure of the �Eukaryotic GenomeHow many genes?What about the rest of the DNA?Repetitive DNAGenetic disorders of repeatsFragile X syndromeHuntington’s DiseaseHuntington’s diseaseFamilies of genesHemoglobinInterspersed repetitive DNARearrangements in the genomeTransposonsTransposonsSlide Number 39Retrotransposons Any Questions??Slide Number 42