Genetics Chapter 23

Technique application Place the technique with its most appropriate use. Assay levels of protein : Compare DNA and Protein sequences : Study protein function : Find DNA sequences bound by Protein : Determine changes in RNA expression : Determine identity of a protein :

2-D gel eletrophoresis BLAST Functional protein microarray ChIP chip assay DNA microarray Mass spectometry

A ________ microarray is a slide with many DNA sequences spotted on it. To compare gene expression between two cells _________ is isolated from each cell type. When mRNA is used to direct the synthesis of DNA, the resulting DNA is called ____________. cDNA from two cell types can be differentially labeled and ____________ to the microarray. DNA microarrays can be used to look for insertions or deletions if labeled ______________ DNA is used.

DNA mRNA cDNA hybridized genomic

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

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.

Two dimensional gel electrophoresis separates proteins based on size alone. During isoelectric focusing proteins are separated by the pH at which they have a net neutral charge. SDS coats the proteins to give them a net positive charge. SDS allows proteins to separate based on molecular mass. Two dimensional electrophoresis allows proteins that differ by one charged amino acid to be separated.

False True False True True

Amino acids from a hypothetical cell surface receptor from Homo sapiens are compared to the same cell surface receptor in other species using the BLAST program. The following results are obtained. Place the labels in the correct column. H. sapiens YWEDPGGGTCYFSTNQVHKFTSSR P. catodon YWEDPGYGTCYFPTNQVEKFTSSR M. mulatta YWEDPGGGTCYFSTNQVHKFTSSR F. cattus YWEEPGGGTCYFSTNQVEKFTSSA C. cristata YWEEPGYGTCYFPTNQVEKFTDSA

Predicted to have the highest E value: C. cristata Predicted to have the lowest E value: M. mulatta Predicted to have an E value between highest and lowest: P. catodon F. cattus

A multiple sequence alignment is shown for a protease that is highly conserved among species. What amino acid do you predict is essential for function of the protease? Dots are indicative of gaps where the sequences do not line up. Species 1 WEDSSNQLRKEWWYFPGCCNQTTSAALLPGE Species 2 WEDSSNQ..............WYFPGCCNQTTSAALLPGE Species 3 WEDSSNQLRKEWWYFPGCCNQTTSAAL......... Species 4 WCCSSNQLRKEWWYLGGCCNFSSSSSLLPGE Species 5 GED........QLRKEWVCFP.............QTTSARRLPGE Species 6 WEDSSNQLRKEWWYFPGCCNQTTSAAGGPGE

Q in position 7

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

Single-stranded cDNA

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

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

cDNA

Chromatin immunoprecipitation involves __________.

chemical cross linking of DNA to protein

A _____________ is a collection of computer files stored in one place. An example of a nucleotide database is _____________ . An example of a protein motif database is _____________ . 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 _________________ .

database Genbank Prosite annotated

A protein microarray that can demonstrate protein-to-protein interactions is the ____________________. A protein microarray that can determine protein expression levels is the __________________. In an antibody microarray _______________ to specific proteins are spotted onto the chip. In a functional protein array the _________________ whose function is to be tested are spotted onto the chip.

functional protein microarray antibody microarray antibodies proteins

The BLAST program starts with a protein or DNA sequence and then locates ________________ sequences within a database. 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 _____________ . The better the match the ____________ the E value. If there is a 100% match between the sequence used for searching and a sequence in the database the E value would be ________ .

homologous E value lower 0

Genes derived from the same ancestral gene. Two homologous genes found in different species. Two or more homologous genes found in the same organism. Two or more paralogs in a single organism.

homologous genes orthologs paralogs gene family

A gene knockout means that the gene has been altered in a way that ______________ its function. Gene knockouts may be created by using transposable elements to _____________ into a gene. Knockout mice can also be created using ____________ technology. 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. Gene knockouts are useful as many disease and syndromes are the result of __________ that inactivate genes.

inactivates insert CRISPR-Cas loss-of-function mutations

DNA microarrays contain __________.

single-stranded DNA

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

some mRNAs are alternatively spliced