Homework Chapter 23

If there is a 100% match between the sequence used for searching and a sequence in the database the E value would be -- .

0

Assay lvls of protein

2-D gel electrophoresis

compare dna and protein sequences

BLAST

Knockout mice can also be created using -- technology.

CRISPR-Cas

find dna sequences bound by protein

ChIP chip assay

A -- microarray is a slide with many DNA sequences spotted on it.

DNA

determine changes in rna expression

DNA microarray

You have created a mouse that has a homozygous knockout for your gene of interest. What techniques could you use to show that the gene is no longer expressed? (Check all that apply.)

DNA microarray, Antibody microarray, RNA-Seq, 2-D gel electrophoresis Any of these techniques aside from chromatin immunoprecipitation could be used to show that the gene you knocked out is no longer expressed. Chromatin immunoprecipitation is used to find DNA sequences which are bound by certain proteins. Both RNA-Seq and DNA microarrays could be used to determine if an RNA transcript was present from your knockout gene. 2-D gel electrophoresis and an antibody microarray could be used to confirm that the protein of interest is not being made.

You are carrying out a chromatin immunopreciptation experiment. At the step where you are supposed to add the antibody to your protein of interest, you accidentally add a mixture of antibodies that someone was storing in the lab. What will your results show?

DNA will still be isolated, but it will correspond to DNA that was bound by any protein recognized by the antibody mixture. The ChIP assay will still isolate DNA, but instead of being DNA bound by just one protein, it will contain DNA bound by any of the proteins to which there was an antibody in the antibody mixture.

The value that represents the number of times that the match or a better match would be expected to be found by random chance in an entire database is known as the -- .

E value

1. Two dimensional gel electrophoresis separates proteins based on size alone.

False

3. SDS coats the proteins to give them a net positive charge.

False

study protein function

Functional protein microarray

An example of a nucleotide database is -- .

Genbank

determine identity of a protein

Mass spectometry

An example of a protein motif database is -- .

Prosite

In the microarray procedure, what molecule is labeled with a fluorescent tag?

Single-stranded cDNA

2. During isoelectric focusing proteins are separated by the pH at which they have a net neutral charge.

True

4. SDS allows proteins to separate based on molecular mass.

True

5. Two dimensional electrophoresis allows proteins that differ by one charged amino acid to be separated.

True

True or False: DNA microarrays are used to study patterns of gene expression.

True

True or False: DNA microarrays may be used to study how a cell responds to specific environmental conditions.

True

You are studying a transcription factor. You have identified the DNA sequence to which it binds through a ChIP-chip experiment. You now wish to find other genes whose transcription is controlled by this transcription factor. What approach should you take?

Use a computer program to search by signal Since you have already identified the DNA sequence to which the transcription factor binds, it makes sense to take a search by signal approach. In this approach, you would use a computer program to search for genes that are flanked by the DNA sequence to which the transcription factor binds. This sequence is likely to be the promoter.

If the files in the database include additional information such as the name of the organism from which the sequence was obtained the database is said to be -- .

annotated

In an antibody microarray -- to specific proteins are spotted onto the chip.

antibodies

A protein microarray that can determine protein expression levels is the --.

antibody microarray

To use a microarray, mRNA from cells of interest are first converted to __________.

cDNA

When mRNA is used to direct the synthesis of DNA, the resulting DNA is called --.

cDNA

Chromatin immunoprecipitation involves __________.

chemical cross linking of DNA to protein The DNA sequence is being isolated by CHIP for analysis, not the protein.

A -- is a collection of computer files stored in one place.

database

A protein microarray that can demonstrate protein-to-protein interactions is the --.

functional protein microarray

4. Two or more paralogs in a single organism.

gene family

DNA microarrays can be used to look for insertions or deletions if labeled -- DNA is used.

genomic

The BLAST program starts with a protein or DNA sequence and then locates -- sequences within a database.

homologous

1. Genes derived from the same ancestral gene.

homologous genes

cDNA from two cell types can be differentially labeled and -- to the microarray.

hybridized

A gene knockout means that the gene has been altered in a way that -- its function.

inactivates

Gene knockouts may be created by using transposable elements to -- into a gene.

insert

The goal of the Knockout Mouse Project and other large-scale mouse knockout efforts is to create at least one -- mutation in each of the protein encoding genes in the mouse genome.

loss-of-function

The better the match the -- the E value.

lower

To compare gene expression between two cells -- is isolated from each cell type.

mRNA

Gene knockouts are useful as many disease and syndromes are the result of -- that inactivate genes.

mutations

2. Two homologous genes found in different species.

orthologs

3. Two or more homologous genes found in the same organism.

paralogs

In a functional protein array the -- whose function is to be tested are spotted onto the chip.

proteins

DNA microarrays contain __________.

single-stranded DNA

One reason the proteome is larger than the genome is __________.

some mRNAs are alternatively spliced