Chapter 24 Genetics

The technique of RNA sequencing: 1) ____ RNA from a sample of cells 2) ____ the RNAs into small _____ 3) ____ short oligonucleotide ____ to the ____of the RNAs 4) Synthesize ____ via ____ transcriptase PCR, using the RNAs as ____. This means the PCR primers are now _____ to the linkers. 5) _____ the cDNAs using next generation sequencing technology 6) Using computer technology, ____ the cDNA sequences along the _____ sequence

1) Isolate 2) break , fragments 3) Attach , linkers , ends 4) cDNAs , reverse , templates , complementary 5) Sequence 6) align , cDNA , genomic

The technique of RNA sequencing: 1) Isolate ____ from a sample of cells 2) Break the ____ into ____ fragments 3) Attach ____ _____ linkers to the ends of the ____ 4) Synthesize cDNAs via _____ ____ ____ , using the ____ as templates. The PCR ____ are complementary to the ____. 5) Sequence the ____ using next generation sequencing technology 6) Using ____ technology, align the ____ sequences along the genomic _____

1) RNA 2) RNAs , small 3) short oligonucleotide , RNAs 4) reverse transcriptase PCR , RNAs , primers , linkers 5) cDNAs 6) computer , cDNA , sequence

In humans, ____ paralogous genes are functionally expressed

9

BLAST stands for _____ _____ ____ ____ _____.

Basic Local Alignment Search Tool

Making a ____ ____ involves spotting technologies that are quite similar to the way that an inkjet printer works

DNA microarray

Researchers have developed an exciting technology called _____ ______ , aka _____ _____ , which make it possible to monitor thousands of genes simultaneously

DNA microarrays, gene chips

_____ examines the functional roles of the proteins that a species can make

Proteomics

In ____ sequencing, transcriptomes are the set of all ____ molecules, including ____ and ____-____ ____ , that are transcribed in one cell or a population of cells

RNA , RNA , mRNAs , non-coding RNAs

In two-dimensional gel electrophoresis, spots present only in abnormal cells are very common in ____ cells.

cancer

In eukaryotes, the _____ coding sequences may be _____ by ____

chromosomal , interrupted , introns

The actual size of the proteome is _____ to determine

difficult

In _____ , the chromosomal coding sequences may be interrupted by introns

eukaryotes

The entire collection of a species' proteins is its ____.

proteome

In humans, the globin family contains several _____ that are not expressed and a ____ gene

pseudogenes , myoglobin

DNA microarrays are fragments that are made _____

synthetically

A computer program can translate a genomic DNA sequence in all ___ reading frames, seeking to locate a ____ open reading frame.

3 , long

In a ____ sequence, the reading of codons could begin with the first, second or third _____ , which are called reading frame 1, 2 , and 3, respectively.

DNA , nucleotides

The ____ ____ represents the number of times that the match or a better one would be expected to occur purely by random chance in the entire database

E-value (expected value)

_____ data can provide important information about the proteome, as: 1) DNA microarrays ____ the genes that are transcribed under a given set of conditions, and.... 2) Gene homology studies between species can be used to predict protein ____ and/or ___

Genomic 1) reveal , genes 2) structure , function

_____ genetic sequences can identify conserved sites that are functionally important

Homologous

_____ is a powerful tool for predicting the function of genetic sequences

Homology

_____ _____ gel electrophoresis is a ____ technique that can distinguish hundreds or even thousands of different _____ in a cell ____

Two-dimensional , separation , proteins , extract

The identification of a stop codon for a particular gene is an example of a) sequence recognition. b) pattern recognition. c) both a and b. d) none of the above

a) sequence recognition.

The technique of tandem mass spectrometry is used to determine a) the amino acid sequence of a peptide fragment. b) the nucleotide sequence of a segment of RNA. c) the nucleotide sequence of a segment of DNA. d) the number of genes in a species' genome.

a) the amino acid sequence of a peptide fragment.

A gene knockout is a gene a) whose function has been inactivated. b) that has been transferred to a different species. c) that has been moved to a new location in the genome. d) that has been eliminated from a species during evolution.

a) whose function has been inactivated.

In two-dimensional gel electrophoresis, spots present only in ____ cells are very common in cancer cells.

abnormal

On a DNA microarray, the DNA fragments can be either ____ by PCR and then spotted on the ____ , or synthesized ____ on the microarray itself

amplified , microarray , directly

The purpose of a ChIP-chip assay is to determine a) the expression levels of particular genes in the genome. b) the sites in a genome where a particular protein binds. c) the amount of a specific protein that is made in a given cell type. d) any of the above.

b) the sites in a genome where a particular protein binds.

The E-value represents the number of times that the match or a ____ one would be _____ to occur purely by ____ chance in the entire database

better , expected , random

For the method of RNA sequencing (RNA-Seq), which of the following is the correct order of steps? a) Isolate RNAs, synthesize cDNAs, fragment RNAs, sequence cDNAs, align cDNA sequences b) Synthesize cDNAs, sequence cDNAs, isolate RNAs, fragment RNAs, align cDNA sequences c) Isolate RNAs, fragment RNAs, synthesize cDNAs, sequence cDNAs, align cDNA sequences d) Synthesize cDNAs, isolate RNAs, fragment RNAs, sequence cDNAs, align cDNA sequences

c) Isolate RNAs, fragment RNAs, synthesize cDNAs, sequence cDNAs, align cDNA sequences

The BLAST program begins with a particular genetic sequence and a) translates it into an amino acid sequence. b) determines if it contains one or more genes. c) identifies homologs within a database. d) does all of the above.

c) identifies homologs within a database.

A DNA microarray is a slide that is dotted with a) mRNAs from a sample of cells. b) fluorescently labeled cDNA. c) known sequences of DNA. d) known cellular proteins.

c) known sequences of DNA.

A _____ _____ is a site that is identical or similar across multiple species.

conserved site

Cells respond to environmental changes via the _____ ____ of their genes

coordinate regulation

Mass spectrometry can be used to identify protein ____ ____.

covalent modifications

During two-dimensional gel electrophoresis, proteins are separated based on a) their net charge at a given pH. b) their mass. c) their ability to bind to a specific resin. d) both a and b

d) both a and b

Homologous genes a) are derived from the same ancestral gene. b) are likely to carry out the same or similar functions. c) have similar DNA sequences. d) exhibit all of the above features.

d) exhibit all of the above features.

Homology is powerful tool for predicting the ____ of genetic sequences

function

In general, there is a strong correlation between homology and ____.

function

Two-dimensional ____ _____ is used to separate a mixture of different _____

gel electrophoresis , proteins

A ____ ____ consists of two or more copies of homologous genes within the genome of a single organism

gene family

The proteome is much larger than the _____ because of _____ processes, including: 1) ___ ____ 2) ____ ____ 3) _____ _____ _____ These processes all ____ the number of potential proteins in the ____.

genome , cellular 1) Alternative splicing 2) RNA editing 3) Postranslational covalent modification increase , proteome

Microarrays make it possible to study the expression of the whole _____ under different _____ conditions

genome , environmental

Sequencing and analysis of an entire ____ can identify all the ____ that a given species contains

genome , genes

The composition of hemoglobin changes during the course of ____.

growth

Each ____ protein is composed of two a-chains and two b-chains

hemoglobin

Once a DNA microarray has been made, it is used as a ______ tool

hybridization

In postranslational covalent modification, ____ changes, such as proteolytic processing and the attachment of prosthetic groups, sugars or lipids may be necessary to _____ a functional _____.

irreversible , produce , protein

In prokaryotes, ____ open reading frames are contained within the ____ gene sequences

long , chromosomal

On a DNA microarray, the DNA ____ can be either amplified by ____ and then spotted on the microarray, or synthesized directly on the _____ itself

microarray , PCR , microarray

A DNA _____ is a small silica, glass or plastic slide that is ____ with many ____ of DNA

microarray , dotted , sequences

The conserved site approach was first shown when two scientists demonstrated that whale ____ and human __-____ have similar sequences, and since then, this approach has been used to compare more than two genetic sequences.

myogloban , B-hemoglobin

An open reading frame (ORF) is a _____ sequence that does not contain any ____ codons

nucleotide , stop

An open ____ ____ is a nucleotide sequence that does not contain any stop codons

open reading frame (ORF)

Two sequences with genes in two species that are homologous to each other are called ______ , and are derived from the same _____ gene.

orthologs , ancestral

Two homologous genes that are found in different species are termed ____ , while two homologous genes found in a single organism are termed ____.

orthologs , paralogs

Two-dimensional gel electrophoresis involves two different electophoresis experiments, where the first separates by ____ /____ interactions, or _____ point, and the second separates by ____

pH/charge , isoelectric , size

To determine a Gene sequence from a peptide sequence, you must: 1) Determine the possible _____ sequences that would encode the ____ in question 2) Using software, the ____ sequences would be used as a ____ sequence to scan the entire genome sequence 3) The program would ____ the actual gene in the genome 4) The gene sequence, in turn, can be used to predict the _____ ____ sequence of the entire protein

peptide 1) codon , peptide 2) codon , query 3) locate 4) amino acid

In postranslational covalent modification, reversible changes, such as _____ , ____ , and ____ , transiently affect the function of the ____

phosphorylation , acetylation, methylation , protein

Sequences of DNA in a DNA microarray will act as ____ to identify genes that are transcribed.

probes

In ____ , long open reading frames are contained within the chromosomal gene sequences

prokaryotes

In postranslational covalent modification, irreversible changes, such as ____ processing and the ____ of ____ groups, ____ or ____ may be necessary to produce a _____ protein.

proteolytic , attachment of prosthetic groups , sugars , lipids , functional

Genomic data can provide important information about the ____ , as 1) _____ ____ reveal the genes that are transcribed under a given set of conditions, and... 2) ____ ____ studies between species can be used to ____ protein structure and/or function

proteome 1) DNA microarrays 2) Gene homology , predict

Any given cell of a multicellular organism will produce only a subset of the proteins in its ____ , and the resulting subset depends on ____ type, ____ of ____ , and _____ ____

proteome , cell , stage of development , environmental conditions

Basic local alignment search tool, or BLAST, is the relationship between the ____ sequence and each ____ sequence, and is given an E-Value (expected value).

query , matching

One way to locate coding regions within a DNA sequence is to examine translational ____ ____.

reading frames

In postranslational covalent modification, ____ changes, such as phosphorylation, acetylation, and methylation, transiently affect the ____ of the protein

reversible , function

Proteomics examines the functional ____ of the ____ that a species can make

roles , protein

Two-dimensional gel electrophoresis is used to ____ a ____ of different proteins

separate , mixture

Each ____ in a DNA microarray corresponds to a known gene.

sequence

Comparing the _____ of the hemoglobin chains can give insight into their structure and ____.

sequences , function

A DNA microarray is a small ____ , glass or plastic ___ that is dotted with many sequences of _____.

silica, slide , DNA

A reading frame could proceed from right to left, so therefore, ____ reading frames are possible in a newly discovered sequence

six

Alternative _____ , RNA _____ , and postranslational ____ ____ are cellular processes that all increase the number of potential _____ in the proteome.

splicing , editing , covalent modification , proteins

A single DNA microarray slide contains tens of thousands of different ____ in an area the size of a postage stamp, and the relative location of each ____ is known

spots , spot

Bioinformatics are useful when the user does not know where the ____ codon is located or the _____ of the coding sequence.

start , direction

In two-dimensional gel electrophoresis, spots where proteins which are very abundant in a cell type may be important for that cells _____ or _____.

structure , function

Researchers have developed an exciting technology called DNA microarrays , aka gene chips, which make it possible to monitor _____ of genes ______

thousands, simultaneously

RNA-Sequencing has several important applications in comparing _____

transcriptomes

In RNA sequencing, _____ are the sets of all RNA molecules, including mRNAs and non-coding RNAs, that are _____ in one cell or a population of cells

transcriptomes , transcribed

A conserved site approach that has been used to compare more than ____ genetic sequences produces a ____ ____ ____

two , multiple sequence alignment

Each hemoglobin protein is composed of ___ a-chains and ___ b-chains

two , two