Smart Book 23

Which factors influence the amount of a specific protein that will be found in a cell?

- Rate of degradation (turnover) of the protein - Level of mRNA produced from the gene - Rate of mRNA translation

Gene knockout collections in mice, in which each strain has one or more of its genes knocked out, are useful for ______.

- understanding how protein products of genes participate in cellular pathways - determining the function of the knocked out gene - studying inherited human diseases

Arrange the steps of the chromatin immunoprecipitation technique in order, starting with the first step at the top of the list.

1. Add formaldehyde to cross-link the protein to the DNA. Lyse cells. Sonicate the DNA into small pieces. 2. Add antibodies (linked to beads) that recognize the protein of interest. Subject the sample to centrifugation. 3. Collect complexes in pellet. 4. Add chemical that breaks the crosslinks to remove the protein. 5. Conduct PCR using primers to a specific region. If DNA is amplified, the protein was bound to the DNA region that is flanked by the primers.

True or false: The functions of proteins encoded by homologous genes are usually similar to one another.

True

Most genes ______.

encode proteins

The majority of an organism's genes encode ____.

proteins

A DNA microarray contains ______ on a ______ silica, glass or plastic slide.

tens of thousands of different DNA sequences; small

The human genome has about ______ genes.

22,000

Which technique allows genome-wide analysis of gene expression?

DNA microarrays

BLAST is a ______.

computer program that can locate homologous sequences within a large database

The field of ____ genomics aims to understand the roles of genetic (DNA, RNA, and amino acid) sequences in a given species.

functional

The technology that enables the expression of thousands of genes to be studied simultaneously is called a DNA ____.

microarray

The complete set of proteins that a given cell or organism synthesizes is called its ____.

proteome

Researchers in the field of ______ study the interplay among the entire set of proteins produced by a cell.

proteomics

The study of the functions and interactions of a cell's proteins is termed ____.

proteomics

Which of the following processes account for the larger size of the proteome relative to the genome?

Alternative splicing Posttranslational covalent modifications RNA editing

How can bioinformatics be used to identify the function of a new gene?

By finding a homologous gene whose mechanism of activity is known

The transcriptome is the set of all ______ produced in one cell or a population of cells.

RNA molecules

Complementary DNAs are derived from mRNA molecules. ____-____ is a method for sequencing these complementary DNAs using next-generation sequencing methods.

RNA sequencing

In a DNA microarray experiment, a high fluorescence intensity in one spot means that ______ at that location.

a large amount of cDNA in the sample hybridized to the DNA

Newer computer programs can compare several protein regions and sensibly put in gaps. This produces a ______.

multiple-sequence alignment

True or false: Conserved sites within a polypeptide are more likely to be functionally important than non-conserved sites.

True

A site within a polypeptide that is identical across multiple species is called a ____ site.

conserved

RNA-Seq is a method used to ______.

sequence complementary DNAs derived from RNAs

Which of the following statements about the human genome is true?

It has approximately 22,000 genes, but only a subset of those genes are expressed in any given cell.

What is the goal of functional genomics?

To understand the roles of genetic sequences in a given species

A computer program called BLAST can be used to identify homology between two DNA or protein sequences. BLAST stands for basic ____ ____ ____ tool.

basic local alignment search tool

The collection, storage, and analysis of DNA, RNA, and protein sequences is called ______.

bioinformatics

In the technique of chromatin immunoprecipitation, the formaldehyde serves to ______.

cross-link the protein to the DNA

Homologous genes are those ______.

derived from the same ancestral gene and so have similar sequences

The proteome refers to the ______.

entire collection of proteins made by a given organism

A gene ____ consists of multiple paralogs within the genome of a species.

family

The set of all RNA molecules that are transcribed in one cell or a population of cells is called the ____.

transcriptome

Homologous genes encode proteins that carry out ______.

similar functions

Each spot in a DNA microarray contains ______ DNA from ______ gene(s).

single-stranded; a specific

Which of the following statements about alternative splicing is true?

It is usually cell-specific and related to environmental conditions.

The phenomenon of ____ ____ typically produces many different proteins from the same pre-mRNA.

alternative splicing

Chromatin immunoprecipitation (ChIP) is a technique that is used to ______.

analyze DNA-protein interactions

A gene family is comprised of ______.

two or more paralogs within the genome of a single species

Two bacteria are likely to have similar DNA sequences if they ______.

are evolutionarily closely related to one another

Genes that are derived from the same ancestral gene are called ____ genes.

homologous

A method called chromatin ____ (ChIP) can be used to determine whether proteins can bind to a particular region of DNA.

immunoprecipitation

A gene that has been altered in a way that inactivates its function is called a gene

knockout

Using mice, geneticists can produce gene ____ involving two or more genes to better understand how the protein products of those genes contribute to a complex trait.

knockout

This figure depicts a(n) ____-____ ____ among members of the globin gene family in humans.

multiple-sequence alignment

Arrange the steps of a microarray experiment in order, starting with the earliest on top.

1. RNA is isolated from cells and used to make labeled cDNA 2. Labeled cDNA is layered onto a DNA microarray 3. Microarray is washed with a buffer to remove unbound cDNAs 4. Microarray is placed in a microscopy device called a laser scanner 5. Fluorescence intensity of spots is quantified and used to estimate cDNA amount

The proteome is typically much larger than the genome. This is due to three main phenomena: (1) ____ splicing; (2) RNA ____ ; and (3) ____ covalent modification.

alternative, editing, posttranslational

The field that uses computers, mathematical tools, and statistical techniques to record, store, and study biological information is known as ____.

bioinformatics

A gene that has been changed such that the normal function is altered is called a ______.

gene knockout

Organisms that have a close evolutionary relationship tend to have ______.

genes with similar DNA sequences

Bioinformatics can help to identify the function of a newly determined gene by identifying a(n) ____ gene whose function is known.

homologous

The levels of a specific protein found in a cell depend on the amounts of ____ produced by transcription, the rate of mRNA ____ to synthesize the protein, and the ____ rate for the protein.

mRNA, translation, turnover