BI213: Exam 1 Part II (Lectures 6-8)

to use antibodies to isolate (and detect) a protein from lysed cells or mixture of proteins

What is the function of immunoprecipitation?

- mixture of radiolabeled proteins is incubated with antibody against protein of interest

- the antibody binds to the specific protein

- collect antigen-antibody complexes by incubation with beads that bind to the antibody

- proteins are dissociated by boiling

- gel electrophoreses, protein will migrate down gel

- expose to film to detect the radio-labeled protein

Describe the process of immunoprecipitation.

detection of protein-protein interaction

What is the purpose of co-immunoprecipitation (co-IP)?

- cell nucleus contains two proteins of interest

- nuclear extraction

- add antibody directed against one of the proteins of interest

- add antibody binding beads

- immunoprecipiate the protiens of interest

- wash and collect immunopreciptated proteins

- Western blot (with Antibody #2) analysis of immunoprecipitated protein of intest

Describe the process of co-IP.

overexpress a protein that may change the cellular function

studies of gene expression, protein localization, and short term activity

What can the introduction of DNA into animal cells allow for?

liposomes (lipid vesicles)

What does transfection use?

viruses harboring clones genes

What does infection use?

- introduce DNA plasmid into cultured animal cells

- high fraction of cells take up and transiently express plasmid DNA

- selection in drug containing medium

- only stably transformed cells form colonies

- stably transformed cells contain plasmid sequences integrated into chromosomal DNA (will be transcribed and translated into protein)

Describe the process of introducing DNA into animal cells?

1) How do mutations in specific sequences affect gene function

2) Does mutant protein product cause a phenotype

What questions does mutagenesis help answer?

- after cloning, scientists often want to mutate gene of interest using mutagenesis

- denature and hybridize with mutagenic oligonucleotide

- DNA synthesis and ligase

- plasmid containing mismatched base at site of mutation

- isolate plasmids after replication

- introduce DNA into culture animal cells

Describe the process of mutagenesis with synthetic oligonucleotides

Yes, not just in cloned genes!

Can we study the function of cloned genes in animals?

10%

What percent of injected embryos integrate the plasmid into their chromosomes

random sites throughout the genome - not at site of normal gene

Where does integration of genes occur?

- microinject plasmid DNA into pronucleus of fertilized egg

- let culture in a dish, circular plasmid gents integrated by repair enzymes

- transfer embryos to foster mothers, multiple generations

Describe the production of transgenic mice

the cloned gene could be normal or mutant (normal version is still there) which can cause problems for analysis

What is a problem with the normal production of transgenic mice

the gene is replaced with mutant (no normal gene is produced)

What is different about homologous recombination in comparison to the normal transgenic production?

- embryonic stem cells carry normal copies of gene on both chromosomes

- undergoes homologous recombination with inactive mutant copy of gene

- ES cell carrying one mutated and one normal gene copy

- ES cell is injected into blastocyst and transfer to foster mother

- offspring carrying one mutated and one normal copy gene

- continue mating until some offspring carry two copies of mutated gene

Describe the production of mutant mice by homologous recombination in ES cells.

less than 1%

How effective is homologous recombination in ES cells?

a naturally occurring defense mechanism discovered in bacteria to cut a viral genome - where the bacteria express RNA complementary to foreign (guide RNAs) and the enzyme Cas9 cuts the DNA

can be used as a much more efficient and effective method in mutating a genome (20-30%)

also has therapeutic applications

What is CRISPR/Cas? What can it be applied to do?

- Cell carrying normal copy of gene is exposed to Cas9 with 2 nuclease cleavage sights

- guide RNA binds to RNA complementary to direct Cas9 where to cut

- target DNA is cleaved - Double stranded break (DSB occurs)

- non-homologous end ligated, bases that were cleaved are lost

Describe how CRISPR can be used to cut out a segment of DNA.

Yes, mutated specific mutation introduced into the target gene and homologous recombination occurs at the cleavage site

Can CRISPR be used to insert a mutated copy of a gene?

analyzing gene function by blocking gene expression in cultured cells

before CRIPSR

What is gene expression inhibition by antisense RNA or DNA used for?

When was this method developed?

single stranded sequence that is complementary to mRNA or DNA

What is antisense DNA or RNA?

antisense RNA or DNA hybridizes to normal mRNA; blocking protein synthesis

double stranded RNA prevents protein translation

How does gene expression blocking by antisense RNA or DNA occur?

RNA intereference (RNAi)

What is the most generally-used powerful method for blocking gene function?

microRNAs (miRNAs)

What does endogenous RNAi involve?

Yes, all cells synthesize antisense RNA and the cell can produce small RNAs that fine tune its own expression levels (although scientists didn't know this occurred naturally at first)

Does RNAi occur naturally?

- Double stranded RNA (70-90 bp) is cleaved by Dicer

- siRNA (21-23 bp) is associated with RISC (unwinds siRNA)

- pairing with target mRNA occurs, RISC/siRNA is recycled

- mRNA is cleaved

Describe the process of RNAi

QUANTITATIVE understanding of the integrated dynamic behavior of complex biology systems and processes

What is the goal of systems biology?

bioinformatics and systems biology

What answers the question: What do we do with the information found in complete genome sequencing?

systems biology

What do large-scale experimental approaches (genome wide- studies) form the basis of?

traditional biology

What uses single gene and protein experiments to understand individual molecules and pathways?

systems biology

What uses genome and proteome wide experiments to understand integrate cell processes?

functional genomics

What is a genome-wide functional analysis?

screening for any cellular property testable in high throughput format (ex: changes in gene expression, cell signaling cell morphology, etc.)

What does genome-wide RNAi screening allow for?

- each well in an assay contains siRNA against an individual gene

- inoculate with cells

- incubate and allow for cell growth

- well in which siRNA blocked cell growth or viability will appear differently/not grow

Describe the genome-wide RNAi screening for cell growth and viability

which genes are involved in survival and growth

What questions does a genome-wide RNA screen answer?

increased

How have genome sizes changed over evolutionary time?

1) Structure of genes (intergenic DNA)

2) Introns - intragenic DNA

3) Repetitive sequences

4) Gene duplications and pseudogenes

What are the components of DNA in higher eukaryotes?

sequences between genes that play a very important role in gene regulation

What is intergenic DNA?

regulatory RNAs

What are many intergenic DNA strands transcribed into?

RNA sequences that code for proteins

What are exons?

RNA sequences that get transcribed but get spliced out before translation

What are introns?

introns - within a gene - DNA sequences that do not code for an amino acid

What is intragenic DNA?

adenovirus mRNA

What were used in the identification of introns?

- adenovirus mRNA was hybridized to DNA

- using microscopy and biochemical techniques, they found that there were unmatched areas/ some DNA strands were missing in the RNA

How were introns discovered?

untranslated regions; usually found in first and last exons

What are UTRs? Where are they usually found?

untranslated regions, Start Codon, translated regions

What does the first exon have?

UTRs, translated, stop codon

What does the last exon have?

ENCYclopedia Of DNA Elements, database showing the number of bases

What is the ENCODE database?

coding sequence < total exon sequence < intron sequence

Are there more base pairs in the total exon sequence or intron sequence or codon sequence?

10

How many exons are in the average human genome?

88%; none

What percentage of the bacterial genome is protein-coding sequence? What percent is intron sequence?

1.2%; 35%

What percentage of the human genome is protein coding sequences? What percent is intron sequence?

regulatory roles - transcription and alternative splicing

What important role do introns play?

non-coding RNA; they are spliced

What do some introns encode? What happens to most of them?

evolution

How did introns become a part of eukaryotic genes?

when one gene produces more than one mature RNA with different combinations of exons

What are alternative transcripts?

several thousand

How many mRNAs per gene can there be for human pre-mRNAs

sequential order (Exon 1, Exon 2)

While the exons in each alternative transcript varies, what order are they always in?

introns

What are enzymes in alternative splicing code based on?

alternative splicing

How does the cell make slight changes/fine tune in protein functions

simple-sequence repeats

What type of repetitive sequences make up approximately 10% of the genome?

simple-sequence repeats

What make up hundreds to thousands of repeats that emerged as a part of genome evolution and relate to chromosomes' higher order organization (eg: ACAAACT)

55%

What fraction of the genome do transposons make up?

transposons

What are single units repeats that have a gene structure (5' end, 3' end and coding sequence) and are scattered throughout the genes?

genome structure; viral integration

What do transposons help with? How did they emerge?

1) transcription into mature mRNA

2) reverse transcriptase produces retrotransposon DNA

3) Integration into chromosomal DNA - two copies

millions of years

How did retrotransposons end up in the chromosome? How long did this take?

- enzyme to copy itself - will not code for the virus again because the sequence was mutated and integrated

What do retrotransposons produce?

evolutionary role in gene rearrangements and regulation of gene expression (not necessarily on purpose)

What are the roles of transposable elements?

- transfer of DNA sequence by unequal cross-over or DNA replication error

- reverse transcription: processed pseudogenes

What are some methods for duplication of segments of DNA?

approximately 11,000

How many pseudogens are in the human genome?

non-functional gene copies that have acquired many mutations (do not produce protein)

What are pseudogens?

unequal crossing over leads to multiple copies of a gene (embryonic, psuedogenes, fetal and adult)

How do gene families emerge?

gene replication of processed pseudogenes own genome, using its own reverse transcriptase

What is gene duplication by reverse transcription?

- transcription

- splicing

- reverse transcription and integration into new chromosomal site on host genome

- adds mechanisms to prevent transcription (doesn't have transcription coding sequences and some are in regulatory regions)

- results in processed pseudogene (double stranded DNA identical to mRNA)

How are processed pseudogenes formed?

processed

Are most pseudogenes processed or unprocessed?

- growth factor genes is transcribed and spliced

- mRNA is reverse transcribed and integrated into genome

- double stranded copy is inserted into retrotransposon resulting in abnormal growth factor gene expression

How are retrogenes that determine short legs in dog breeds transposed?

processed pseudogene integrated into retrotransposon, leading to abnormal expression

What is a retrogene?

1986

When was the launch of the human genome initiative?

2001 - dideoxy sequencing

When was the first human genome sequencing drafted? What was used?

2012

When were thousands of individual genomes sequenced (ENCODE)

No, approximately all vertebrates have the same number of genes

Do some vertebrates have more genes than others?

90%

What percent of genes are common to human, mouse, and rat

99%

What percent of chimpanzees and human genomes are identical?

2 yards

About how many yards long would all the DNA in a human cell be?

23; 16

How many chromosomes do humans have? How many chromosomes do yeast have?

histones

What coils/packages double stranded DNA?

4; 2

How many types of histone are there? How many of each are present in a histone octameter?

lysine and arginine make up a large percentage and they are positively charged, which attracts them to the negatively charged DNA

Why do histones bind to DNA?

147 base pairs of DNA wrapped around a histone octamer

What is a nucleosome core particle?

DNA associated with histones

What is chromatin

- extracted DNA from lysed cell and viewed with electron microscopy, saw 10 mm fibers, digested with nuclease, gel electrophoresed

- saw there were evenly separated by 200 bp

How were nucleosomes discovered?

basic repeating subunit of 200 base pairs; fundamental pieces of fibers

What is a nucleosome

linker histone HI

What does the nucleosome core particle NOT contain?

heterochromatin

What is highly condensed inactive chromatin that is located in the periphery of the nucleus and nucleolus associated?

euchromatin

What is transcriptionally active; less condensed chromatin?

light grey

How does euchromatin show up on electron microscopy?

darker/black spots

How does heterochromatin show up on microscopy?

centromeres and telomeres

What are two important structures in chromatin condensation during mitosis?