test 5 bio 6

morphogen gradient hypothesis

, in which gradients of substances called morphogens establish an embryo's axes and other features of its form

copy-number variants

- loci where some individuals have one or multiple copies of a gene or genetic regions

lowest

Humans and other mammals have the ___ gene density, or number of genes, in a given length of DNA

lytic cycle

Is a phage replicative cycle that culminates in the death of the host cell Produces new phages and lyses (breaks open) the host's cell wall, releasing the progeny viruses

transcription regulation

The regulation of transcription initiation factors such as enhancers are part of

regulatory gene,

The repressor is the product of a separate ______, located some distance from the operon itself

RNA polymerase

The repressor prevents gene transcription by binding to the operator and blocking

two repeat sequences

When a phage infects a bacterial cell that has the CRISPR-Cas system, the phage DNA is integrated between

denaturation

Which of these is not used to make a recombinant DNA?

electroporation

applying a brief electrical pulse to create temporary holes in plasma membranes to introduce recombinant DNA into eukaryotic cells

Stem cells

are relatively unspecialized cells that can both reproduce indefinitely and, under certain conditions, differentiate into one or more specialized cell types

plasmids

are small, circular DNA molecules that replicate separately from the bacterial chromosome

MicroRNAs (miRNAs)

are small, single-stranded RNA molecules that can bind complementary sequences in mRNA, cause degradation of the target mRNA or sometimes block its translation

homeobox genes

code for a domain that allows a protein to bind to DNA and to function as a transcription regulator

multigene families

collections of two or more identical or very similar genes

DNA microarray assays

compare patterns of gene expression in different tissues at different times or under different conditions

DNA microarray assays

compare patterns of gene expression in different tissues at different times or under different conditions, a DNA chip is usually used

Stanley

confirmed this latter hypothesis by crystallizing the infectious particle, now known as tobacco mosaic virus (TMV)

genome evolution

consequence of duplication, rearrangement and mutation of DNA

eggs cytoplasm

contains RNA, proteins, and other substances that are distributed unevenly in the unfertilized egg

annealing

cool to allow primers to form hydrogen bonds with ends of sequence.

control elements and transcription factors

critical to the precise regulation of gene expression in different cell types

cyclic AMP (cAMP)

crp is activated by binding with ____, which allows crp to attach to the promoter of the lac operon and increases the affinity of rna polymerase

bacterial enzymes

cut DNA molecules at specific DNA sequences called restriction sites

pseudogenes

ingle copy former genes that have accumulated mutations and are nonfunctional

repressors

inhibiting expression of a particular gene in several different ways

mediator proteins

interact with general transcription factors at the promoter This helps assemble and position the preinitiation complex

determination

irreversibly commits a cell to becoming a particular cell type; precedes differentiation

cell differentiation

is marked by the production of tissue-specific proteins

pattern formation

is the development of a spatial organization of tissues and organs; begins with the establishment of the major axes

genetic engineering

is the direct manipulation of genes for practical purposes

gene therapy

is the introduction of genes into an afflicted individual for therapeutic purposes and may be useful for treating disorders traceable to a single defective gene

viral envelope

is usually derived from the host cell's plasma membrane as the viral capsids exit

retroviruses

is usually derived from the host cell's plasma membrane as the viral capsids exit; HIV

DNA methylation

the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species

bioinformatics

the application of computational methods to the storage and analysis of biological data

proto-oncogenes

the corresponding normal cellular genes that are responsible for normal cell growth and division

proteome

the entire set of proteins expressed by a cell or group of cells

differential gene expression,

the expression of different genes by cells with the same genome

Nondisjunction

the mechanism contributes to polyploidy

positional information

the molecular cues that control pattern formation, tells a cell its location relative to the body axes and to neighboring cells

nuclear transplantation

the nucleus of an unfertilized egg cell or zygote is replaced with the nucleus of a differentiated cell

cell differentiation

the process by which cells become specialized in structure and function

capsid

the protein shell that encloses the viral genome

genomics

the study of whole sets of genes and their interactions

obligate intracellular parasites

they can replicate only within a host cell

RNA polymerase

transcribes the proviral DNA into RNA molecules

hox genes

Homeotic genes in animals

viral envelopes

(derived from membranes of host cells) surround the capsids of influenza viruses and many other viruses found in animals.; contain a combination of viral and host cell molecules

miRNA and siRNA

22 nucleotides long

piRNA

24-31 nucleotides

Horizontal transmission

= viruses enter through damaged cell walls

long noncoding RNA

>200 nucleotides

simple sequence dna

A DNA sequence that contains many copies of tandemly repeated short sequences. common in centromeres and telomeres

corepressor

A ______is a molecule that cooperates with a repressor protein to switch an operon off For example, E. coli can synthesize the amino acid tryptophan when it has insufficient tryptophan (

operon

A cluster of functionally related genes can be coordinately controlled by a single "on-off switch"

dna sequencing

A gene's complete nucleotide sequence can be determined using a process called

virulent phage

A phage that reproduces only by the lytic cycle

cloning vector

A plasmid used to clone a foreign gene is called a

activator

A protein that binds to DNA and stimulates transcription of a specific gene.

restriction fragments

A restriction enzyme usually makes many cuts, yielding _____

short tandem repeats (STRs)

A series of repeating units of 2 to 5 nucleotides

noncoding RNAs (ncRNAs)

A significant fraction of the genome may be transcribed into

ncrnas

A significant fraction of the genome may be transcribed into noncoding RNAs

denaturation, annealing and extension

A three-step cycle ____,_____,______ brings about a chain reaction that produces an exponentially growing population of identical DNA molecules

selective degradation

After translation, polypeptides undergo processing, including cleavage, and chemical modifications The length of time each protein functions is regulated by

A

Based on the diagram below, which DNA fragment is the largest?

rna processing

Alternative RNA splicing occurs during

operon

An ______is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control

morphological complexity

An increase in the number of miRNAs in a species may have allowed _____ to increase over evolutionary time

lac operon

An inducible operon is one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription

introns, exons

Another problem with eukaryotic gene expression in bacteria is the presence of ____ in most eukaryotic genes Researchers can avoid this problem by using cDNA, complementary to the mRNA, which contains only ____

cytoplasmic determinants

As the zygote divides by mitosis, cells contain different ______, which lead to different gene expression

one active oncogene

At the DNA level, a cancerous cell is usually characterized by at least ______ and the mutation of several tumor-suppressor genes

crispr-cas

Both bacteria and archaea can protect themselves from viral infection with the _________ ____system

histone acetylation and dna methylation

Can condense chromatin Can cause long-term inactivation of genes in cellular differentiation. E.g. genomic imprinting

ubiquitin, proteasomes

Cells mark proteins for degradation by attaching ____ to them This mark is recognized by ____, which recognize and degrade the proteins

metagenomics

DNA from a group of species in an environmental sample is sequenced

extension

DNA polymerase adds nucleotides to the 3' of each primer

phage DNA

Every time the host divides, it copies the _____ and passes the copies to daughter cells

specific transcription factors

For genes that are not expressed all the time, high levels of transcription depend on the presence of another set of factors

restriction enzymes

Foreign DNA can be identified as such and cut up by cellular enzymes called

RNA interference (RNAi)

Gene expression can also be silenced using; Synthetic double-stranded RNA molecules matching the sequence of a particular gene are used to break down or block the gene's mRNA

heterochromatin

Genes within highly packed ____ are usually not expressed

ssRNA; serves as template for DNA synthesis.

HIV belongs to this virus type:

chromatin modification

Histone acetylation and DNA methylation are examples of

true

In addition to homeotic genes, many other developmental genes are highly conserved from species to species

alu elements

In primates, a large portion of transposable element-related DNA ( usually about 300 nucleotides long) consists of a family of similar sequences. Many are transcribed into RNA molecules; some are thought to help regulate gene expression.

synthesis

In sequencing by _____, many DNA fragments are copied

crispr-cas system

It is based on sequences called clustered regularly interspaced short palindromic repeats, Each "spacer" sequence between the repeats corresponds to DNA from a phage that had infected the cell

membranous envelope

Many viruses that infect animals have a

p53 gene

Mutations in the ____ prevent suppression of the cell cycle which damages cells dna. normal gene prevents cell from passing on mutation, activates miRNA expression that inhibits cell cycle, turn on genes involved with dna repair, and activates suicide genes

BRCA1 or BRCA2

Mutations in the _____ gene are found in at least half of inherited breast cancers, and tests using DNA sequencing can detect these mutations

genbank

NCBI database of sequences

crispr cas proteins

Nuclease proteins interact with the CRISPR region; these are called C, they can also identify and cut phage dna

untranslated region (UTR)

Nucleotide sequences that influence the life span of mRNA in eukaryotes reside in the _____ at the 3′ end of the molecule

temperate phage

Phages that use both the lytic and lysogenic cycles

mobile genetic elements

Plasmids, transposons, and viruses are all m

true

Prions are infectious proteins that appear to cause degenerative brain diseases in animals.

regulation of translation

Regulation of translation initiation factors is involved in

negative gene regulation

Repressible and inducible operons are examples of

Recombinant DNA

Researchers can insert DNA into a plasmid to produce a __________ molecule, which contains DNA from two different sources; results in cloning of the plasmid including the foreign DNA

complementary DNA (cDNA)

Reverse transcriptase is added to mRNA to make _____ which serves as a template for PCR amplification of the gene of interest

systems biology

Scientist have begun to compile catalogs of genes and proteins and have begun to focus on their functional integration in biological systems. This approach is called

Alu elements

Short interspersed elements; are transcribed into RNA molecules; some are thought to help regulate gene expression

Small interfering RNAs (siRNAs)

Similar to miRNAs in size and function, but are specific to a particular target

cellular nucleic acid

Since viruses can replicate only within cells, they probably evolved as bits of

activator

Some operons are also subject to positive control through a stimulatory protein. This protein is considered as an

Nusslein-Volhard and Wieschaus

Studied segment formation -created mutants, conducted breeding experiments, and looked for corresponding genes

Gene editing

The CRISPR-Cas9 system avoids the complications of using viral vectors to deliver gene therapy

mRNA, genomes

The RNA molecules function both as ___ for synthesis of viral proteins and as ___ for new virus particles released from the cell

methylated

The bacterium's own DNA is protected from the restriction enzymes by being

RNA interference (RNAi)

The blocking of gene expression by siRNAs is called

extension

The cloning a eukaryotic gene in a bacterial plasmid does not include

whole-genome shotgun approach

The cloning and sequencing of fragments of randomly cut DNA followed by assembly into a single continuous sequence

nucleic acid hybridization

The complementarity of the two DNA strands is the basis for_______________, the base pairing of one strand of nucleic acid to the complementary sequence on another strand

protein-mediated bending

The currently accepted model suggests that ______ of the DNA brings the bound activators into contact with a group of mediator proteins

genetic engineering

The direct manipulation of genes is called

line-1

The human genome also contains many sequences of a type of retrotransposon (6,500 base pairs). Transcription of these is crucial for embryo development

gene annotation

The identification of protein-coding genes within DNA sequences in a database

epigenetic inheritance

The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence

regulatory proteins

The initiation of translation of selected mRNAs can be blocked by _____ that bind to sequences or structures of the mRNA

prophage

The integrated viral DNA

Taq polymerase

The key to PCR is an unusual, heat-stable DNA polymerase called

exons

The lowest percentage of human genome is

mRNAs

The most straightforward way to discover which genes are expressed in certain cells is to identify the ___ being made

sticky end

The most useful restriction enzymes cut DNA in a staggered way, producing fragments with at least one single-stranded end called a

repressor

The operon can be switched off by a protein ________

Induction

The other major source of developmental information is the environment around the cell, especially signals from nearby embryonic cells; signal molecules from embryonic cells cause changes in nearby target cells; induces differentiation of specialized cell types

Morphogenesis

The physical processes that give an organism its shape constitute _______

ACGT

The sticky end of the DNA restriction fragment shown here will pair with a DNA restriction fragment with the sticky end _____.

systems approach

The study of expression of thousands of genes at one time constitutes a

operator

The switch is a segment of DNA called an ________usually positioned within the promoter

provirus

The viral DNA that is integrated into the host genome is called a _______; remains a permanent resident of the host cell

p53

This gene encodes for a transcription factor that promotes the synthesis of cell cycle-inhibiting proteins.

ras

This is a proto-oncogene.

gene cloning

This production of multiple copies of a single gene is a type of DNA cloning

Roadmap Epigenomics Project

This project is used to characterize the epigenetic features of the genome (the epigenome

trp operon

This repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription.

gel electrophoresis

This technique uses a gel made of a polymer to separate a mixture of nucleic acids or proteins based on size, charge, or other physical properties

expression

To overcome differences in promoters and other DNA control sequences, scientists usually employ an _________vector, a cloning vector that contains a highly active bacterial promoter

dna cloning

To work directly with specific genes, scientists prepare well-defined DNA segments in multiple identical copies by a process called

true

Trp operon is responsible for the synthesis of tryptophan. So when tryptophan is present, repressor is active and the operon is turned off.

corepressor

Tryptophan

lysosomes

Viruses may damage or kill cells by causing the release of hydrolytic enzymes from

bacteriophages

Viruses that infect bacteria

restriction enzyme, ligase

Which enzyme is used to create this DNA? Click all that are apply.

mutation, gene amplification, translocation, transposition, epigenetic change

Which of these can turn proto-oncogenes into oncogenes?

RNA sequencing

With rapid and inexpensive sequencing methods, researchers can now just sequence cDNA samples from different tissues or embryonic stages to determine the gene expression differences between them. This approach is called; RNAs are isolated, cut into short, similar-sized fragments, converted into cDNAs, and sequenced

Activator proteins

____ in the nucleus recognize specific control elements and promote simultaneous transcription of the genes

MyoD

a "master regulatory gene" that encodes a transcription factor that commits the cell to becoming skeletal muscle

homeobox

a DNA sequence within a homeotic gene that regulates development in animals

Ras protein

a G protein that relays a signal from a growth factor receptor on the cell surface

host range

a limited number of host cells that it can infect

line-1

a low rate of transposition and may have effects on gene expression, transposons may play roles in the diversity of neuronal cell types

bicoid gene

a maternal effect gene that affects the front half of the body

CRISPR-Cas9 system

a powerful new technique for gene editing in living cells and organisms

activator

a protein that binds to an enhancer and stimulates transcription of a gene

true

ac operon is responsible for the synthesis of enzymes that break down lactose.

histone acetylation,

acetyl groups are attached to an amino acid in a histone tail. This appears to open up the chromatin structure, thereby promoting the initiation of transcription

activator

active crp

inducer

allolactose

proteomics

an approach to studying large sets of proteins and their properties

Lysozyme

an enzyme that helps protect animals against bacterial infection

DNA ligase

an enzyme that seals the bonds between restriction fragments

genetic profile

an individual's unique set of genetic markers

Viral glycoproteins

bind to specific receptor molecules on the surface of a host cell

polymerase chain reaction (PCR)

can produce many copies of a specific target segment of DNA

Small ncRNAs

can regulate gene expression at multiple steps and in many ways

Alternative RNA splicing

can significantly expand the repertoire of a eukaryotic genome It is a proposed explanation for the surprisingly low number of genes in the human genome

environmental signals

can trigger the virus genome to exit the bacterial chromosome and switch to the lytic mode

oncogenes

cancer-causing genes in some types of viruses

pluripotent

capable of differentiating into many different cell types

prions

cause disease in plants and animals, respectively

totipotent

cell can generate a completed new organism

myoblasts

cells determined to form muscle cells and produce large amounts of musclespecific proteins

whole-genome shotgun approach

cloning and sequencing of fragments of randomly cut DNA followed by assembly into a single continuous sequence

alternative RNA splicing

different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns (

Lewis

discovered homeotic genes, which control pattern formation in the late embryo, larva, and adult stages

Prions

e infectious proteins that appear to cause degenerative brain diseases in animals, incorrectly folded proteins, can be transmitted in food, act slowly, and are virtually indestructible

Maternal effect gene

encode cytoplasmic determinants that initially establish the axes of the body of Drosophila

General transcription factors

essential for the transcription of all protein-coding genes

genome-wide association studies

est for genetic markers, sequences that vary among individuals

Sanger Sequencing:

first automated procedure was based on a technique called dideoxy or chain termination sequencing, developed by Frederick Sanger

RNA viruses

have an unusually high rate of mutation

bacteria defend against phasges

having mutation that can not be recognized by virus., using restriction enzymes. using the CRISPR-Cas system, DNA replication

gene annotation

he identification of protein-coding genes within DNA sequences in a database

denaturation

heat briefly separate DNA strands

tryptophan

in trp operons, repressor is only active in the presense of corepressor ____

piwi-interacting RNAs (piRNAs)

induce formation of heterochromatin, blocking the expression of parasitic DNA elements in the genome known as transposons , help to reestablish appropriate methylation patterns during gamete formation in many animal species

dna technology

main techniques for sequencing and manipulating DNA

cytoplasmic determinants

maternal substances in the egg that influence early development

viral genomes

may consist of either double- or single-stranded DNA or double- or single-stranded RNA; either single linear or circular molecule

transposons

move by means of a DNA intermediate and require a transposase enzyme

retrotransposons

move by means of an RNA intermediate, using a reverse transcriptase

tumor suppressor genes

normally inhibit cell division

mRNA can be detected by nucleic acid hybridization with complementary molecules These complementary molecules, of either DNA or RNA are ____

nucleic acid probes

copy number variants

one or multiple copies of a gene or genetic regions at loci in some humans

inducible operon

one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription

repressible operon

one that is usually on; binding of a repressor to the operator shuts off transcription E.g. the trp operon

repetitive dna

present in multiple copies in the genome

capsomeres

protein subunits that make up capsids

inducer

r inactivates the repressor to turn the lac operon on

Long noncoding RNAs (lncRNAs)

range from 200 to hundreds of thousands of nucleotides in length

exon duplication and shuffling

rearrangements of parts of genes due to meiotic errors

biotechnology

refers to the manipulation of organisms or their components to make useful products

Tumor-suppressor proteins

repair damaged DNA control cell adhesion act in cell-signaling pathways that inhibit the cell cycle

lysogenic cycle

replicates the phage genome without destroying the host; The viral DNA molecule is incorporated into the host cell's chromosome

rna polymerase

requires the assistance of transcription factors to initiate transcription

adenovirus

respiratory illness

Differential gene expression

results from genes being regulated differently in each cell type

a-lactalbumin

s a nonenzymatic protein that plays a role in milk production in mammals

reverse transcriptase polymerase chain reaction

s useful for comparing amounts of specific mRNAs in several samples at the same time

control elements,

segments of noncoding DNA that serve as binding sites for transcription factors that help regulate transcription

SNPs (single nucleotide polymorphisms)

single nucleotide variants, are among the most useful genetic markers; those that are found frequently associated with a particular inherited disorder alert researcher to the most likely location for the diseasecausing gene.

micrornas

small, single-stranded RNA molecules that can bind complementary sequences in mRNA

in vitro mutagenesis

specific mutations are introduced into a cloned gene, altering or destroying its function. When the mutated gene is returned to the cell, the normal gene's function might be determined by examining the mutant's phenotype

transposable elements

stretches of DNA that can move from one location to another within the genome

blast

the NCBI software allows users to search for DNA sequence, predicted protein sequence and common regions of amino acids in a protein

in situ hybridization

use fluorescent dyes attached to probes to identify the location of specific mRNAs in place in the intact organism

n situ hybridization

uses fluorescent dyes attached to probes to identify the location of specific mRNAs in place in the intact organism

Repressible enzymes

usually function in anabolic pathways; their synthesis is repressed by high levels of the end product

Inducible enzymes

usually function in catabolic pathways; their synthesis is induced by a chemical signal

short tandem repeat

variations in the number of repeats of specific DNA sequences

virus

very small infectious particle consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope

Vertical transmission

viral infection inheriting the virus from a parent

globin genes

which code for oxygen-binding proteins

Next-generation sequencing (NGS)

which method uses a dideoxy chain termination?