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?