Bio Exam 4 - Final
genes
A cell does not and cannot express all of its ____ all of the time
kinases
A common type of posttranslational modification is catalyzed by ________.
sequence a DNA fragment
A laboratory might use dideoxyribonucleotides to _____.
proteins in the cell will include lysine instead of phenylalanine at amino acid positions specified by the codon UUU
A mutant bacterial cell has a defective aminoacyl-tRNA synthetase that attaches a lysine to tRNAs with the anticodon AAA instead of the normal phenylalanine. The consequence of this for the cell will be that ____
Proteins in the cell will include lysine instead of phenylalanine at amino acid positions specified by the codon UUU
A mutant bacterial cell has a defective aminoacyl-tRNA synthetase that attaches a lysine to tRNAs with the anticodon AAA instead of the normal phenylalanine. What will be the consequence of this for the cell?
nonsense mutation
A mutation that results in premature termination of translation ____
AAA
A particular triplet of bases in the template strand of a coding sequence of DNA is AAA. The anticodon on the tRNA that binds the corresponding mRNA codon is ________.
retrovirus
A virus consisting of a single strand of RNA, which is transcribed into complementary DNA, is a _____.
Methanine
AUG codes for ___
The lac operon would be transcribed continuously.
According to the lac operon model proposed by Jacob and Monod, what is predicted to occur if the operator is removed from the operon?
histone acetylation
Acetyl groups added to lysine residues on histone tailes
genes that code for regulatory proteins
Although the expression of most genes is tightly regulated, some genes are expressed at roughly constant rates. What genes would you predict to be constitutively (constantly) expressed?
always produce β-galactosidase
An E. coli cell without a functional lacI gene is expected to __
duplication and divergence of genes
Arise from unequal crossing over or replication mistakes, lead to new genes or gene families
catabolite activator protein
CAP =
viral
CRISPR contains ___ DNA which is stored in memory and shared to the repeats
RNA processing
CRISPR goes from double stranded DNA to transcribed pre-crRNA to ____ and thus forming mature cr-RNAs
Codons are a nearly universal language among all organisms.
Codons are three-base sequences that specify the addition of a single amino acid. How do eukaryotic codons and prokaryotic codons compare?
nucleosome
DNA + histones
storage
DNA = information ___
DNA recombination
DNA cloning is also known as ___
more plasmid/large amounts of gene products
DNA cloning results in _____
genomes
DNA fingerprinting identifies individuals based on unique features of their ___
PCR, gel electrophoresis
DNA fingerprinting starts with using ___ to amplify a region of STRs, and then comparing the lengths using ____
nucleus, transcribed, translated
DNA is found in the ___ which is ___ into mRNA and then ___ into a protein
methyltransferases
DNA methylation catalyzes by DNA _____
condensing
DNA methylation leads to ____ of chromatin
dideoxy sequencing
DNA replication using fluorescently labeled dideoxy-nucleoside triphosphates (ddNTPs)
transposable elements (transposons)
DNA segments that can move from one place to another within the genome
chain termination, Sanger sequencing
Dideoxy sequencing is also known as ____
A site
During elongation, which site in the ribosome represents the location where a codon is being read?
Apoptosis
During metamorphosis, a tadpole's tail is reduced in size by the process of ________.
lactose
E. coli can use ___ when glucose is depleted
code for transcription regulatory factors
Gap genes, segment-polarity genes, and homeotic genes all _____.
regulatory transcription factors
Gap genes, segment-polarity genes, and homeotic genes all code for ____
any other part of the body
Genes in your brains cells can code for genes in ____
repairing
Genome editing depend on two mechanisms for _____ double strand breaks in DNA
histone acetyltransferases
HATS =
add
HATs ___ acetyl groups
histone deacetylases
HDACs =
remove
HDACs ____ acetyl groups
choosing a plasmid with a single restriction site, design a gene with matching restriction sites near its ends
How are recognition sites identified?
antiparallel and complementary
How do the codon and anticodon relate?
insertion of external DNA into a cell
How do we describe transformation in bacteria?
A stop codon is reached
How does termination of translation take place?
the human genome would likely contain many more genes
If alternative splicing did NOT occur, then ________.
the stem or the root of the prized plant
If each plant cell is a genetic equivalent of another cell in the same plant, then a horticulturalist could produce a clone of a prize-winning plant by harvesting a cell from ________.
5' ACU 3'
If the sequence of a codon is 5' AGU 3', then the anticodon on the corresponding tRNA would be
have turned off or slowed down the process of transcription
If you were to observe the activity of methylated DNA, you would expect it to _____.
The mutant will show low levels of gene expression.
Imagine that you've isolated a yeast mutant that contains histones resistant to acetylation. What phenotype do you predict for this mutant?
low levels of gene expression
Imagine that you've isolated a yeast mutant that contains histones resistant to acetylation. What phenotype do you predict for this mutant?
sigma
In E. coli, if RNA polymerase is missing ________, then transcription initiation would not occur at the appropriate initiation sites.
incorporates the entire template molecule in the product
In comparing DNA replication with RNA transcription in the same eukaryotic cell, only DNA replication _____.
bind to other proteins or to the TATA box
In eukaryotes, general transcription factors ________
off through their association in nucleosomes
In eukaryotes, the normal or default state is that genes are turned _____.
transcription factors
In eukaryotic cells, transcription cannot begin until several ____ have bound to the promoter
3
In eukaryotic transcription ____ RNA polymerases are used for each type of RNA
SNPs where one allele is found more often in persons with a particular disorder than in healthy controls
In large-scale, genome-wide association studies in humans we look for ________.
a regulatory protein binds to DNA and shuts down transcription
In negative control, a gene is switched off when ____
a plasmid used to transfer DNA into a living cell
In recombinant DNA methods, the term "vector" can refer to ________.
more
In the lac operon, a mutation in the operator that prevents repressor binding will cause ____ expression of the lac operon when lactose is absent
not bound
In the lac operon, the repressor inhibits transcription when the repressor is _____ to the inducer
starts, builds, ends
Initiation ____ transcription, elongation ___ RNA, and termination ___ transcription
there are introns
It is more difficult to identify eukaryotic genes than prokaryotic genes because in eukaryotes ________.
DNA methylation
Methyl groups add to C nucleotides
inducer
Most repressor proteins are allosteric. What binds with the repressor to alter its conformation?
express different genes
Muscle cells differ from nerve cells mainly because they
Z
No B galactosidase is lac___
Y
No galactoside permease is lac___
the base that would have come next in the sequence
Once every possible length is generated in dideoxy sequencing, what does each end with?
proofreading
Pfu DNA polymerase is less error prone due to ____ ability
3, 1, 2, 5, 4
Put the following events of bacterial transcription in chronological order. 1. Sigma binds to the promoter region. 2. The double helix of DNA is unwound, breaking hydrogen bonds between complementary strands. 3. Sigma binds to RNA polymerase. 4. Sigma is released. 5. Transcription begins.
1, 2, 3, 5, 4
Put the following events of elongation in prokaryotic translation in chronological order. 1. Binding of mRNA with small ribosomal subunit 2. Recognition of initiation codon 3. Complementary base pairing between initiator codon and anticodon of initiator tRNA 4. Base pairing of the mRNA codon following the initiator codon with its complementary tRNA 5. Attachment of the large subunit
5'--->3'
RNA is built in what direction?
out of the nucleus
RNA processing doesn't happen in prokaryotes because it doesn't have to travel ____ into the cytoplasm
pre-mRNA, mature mRNA
RNA processing in eukaryotes goes from DNA to ___ to ____
bacteria
RNA processing is rare in ____
eukaryotes
RNA processing occurs in many steps in ____
enzyme for replication
RNA replicase is an _____
termination
RNAP transcribes a ____ signal that results in mRNA folding into a hairpin structure
holoenzyme
RNAP whole enzyme
tRNA
Release factor proteins must have a similar structure to what other molecule?
RNA polymerase
Ribosomes translate mRNA as it is being synthesized by ____
repair
SOS response - negative control, induces transcription of 40 genes that initiate DNA ____
large size of eukaryotic genomes and the large amount of eukaryotic repetitive DNA
Sequencing eukaryotic genomes is more difficult than sequencing genomes of bacteria or archaea because of the ________.
The viral genome has genes coding for enzymes needed for its own reproduction
Some human viruses require a type of replication that humans do not normally have. For example, humans normally do not have the ability to convert RNA into DNA. How can these types of viruses infect humans, when human cells cannot perform a particular role that the virus requires?
pre-mRNA
Step 1 in RNA splicing: snRNPs are small nuclear ribonucleoproteins bind to the _____
spliceosome
Step 2 in RNA splicing: snRNPs assemble to form the _____
cleavage
Step 3 in RNA splicing: the 5' end of the intron is cut, and the intron forms a loop structure, snRNAs (ribozymes) perform the _____
loop
Step 4 in RNA splicing: the 3' end of the intron is cut releasing the _____
he embryos would show no development of posterior regions.
Suppose the protein specified by bicoid was injected into Drosophila embryos so that a high concentration was present everywhere in the embryo. What might be the result of such an experiment?
homeotic genes
Suppose you found several Drosophila mutants that possessed additional legs growing out of their head segments. The probable mutation would be found in ________.
hairpin
Termination of transcription in bacteria occurs when a _______ forms in the RNA transcript and separates from the RNA polymerase.
anterior structures would form in both ends of the embryo
The bicoid gene product is normally localized to the anterior end of the embryo. If large amounts of the product were injected into the posterior end as well, what would occur?
Anterior structures would form in both ends of the embryo.
The bicoid gene product is normally localized to the anterior end of the embryo. If large amounts of the product were injected into the posterior end as well, which of the following would occur?
A gene from an organism can theoretically be expressed by any other organism.
The genetic code is essentially the same for all organisms. From this, one can logically assume...
alternative splicing
The human genome contains ~20,000 protein-coding genes, but >80,000 proteins have been identified. What could help to explain this discrepancy?
cannot be predicted
The human genome size is ~6 billion base pairs, and the size of the genome of yeast (a single-celled eukaryote), is ~12 million base pairs. Therefore, the genome size for another eukaryotic, single-celled organism, an amoeba...
posttranscriptional modification removes the introns
The mRNA is smaller than the length of the DNA that codes for it because ________
missense mutation
The mutation resulting in sickle cell disease changes one base pair of DNA so that a codon now codes for a different amino acid, making it an example of a ________.
are at considerable distances from the promoter; promoter-proximal elements are close to the promoter
The primary difference between enhancers and promoter-proximal elements is that enhancers _____.
5' AAC UUC GAC GGA 3'
The template strand of DNA has a sequence of 5' AAC TTC GAC GGA 3'. What would be the sequence of the anticodons that would be responsible for translation of this sequence?
the rules for base pairing between the third base of a codon and tRNA are flexible
There are 61 mRNA codons that specify an amino acid, but only 45 tRNAs. This is best explained by the fact that
It cannot bind to the inducer
There is a mutation in the repressor that results in a molecule known as a super-repressor because it represses the lac operon permanently. Which of these would characterize such a mutant?
repressor
To turn on the operon a lactose inducer binds to the ____
infection
ToxR - positive control, stimulates transcription when a bacterium encounters the human gut, allowing ____
5' ---> 3'
Transcription builds RNA in what direction?
RNA polymerase (RNAP)
Transcription is carried out by _____
mRNA, tRNA, ribosomes, and GTP
Translation directly involves _____
copy themselves
Viruses use the host cell to _____ and make viral proteins
The viral genome has genes coding for enzymes needed for its own reproduction.
Viruses use the host's machinery to make copies of themselves. However, some human viruses require a type of replication that humans do not normally have. For example, humans normally do not have the ability to convert RNA into DNA. How can these types of viruses infect humans, when human cells cannot perform a particular role that the virus requires?
1. Add a gene to a plasmid 2. Force bacteria to take up plasmid from the environment 3. Produce and harvest the product
What are the 3 basic steps to DNA cloning?
1. addition of 5' cap on mRNA 2. splicing to produce mRNA 3. addition of 3' poly A tail on mRNA
What are the 3 main steps in RNA processing of eukaryotes?
A - entrance P - holding new chain E - exit
What are the 3 sites of a ribosome and what are they for?
The number of repeats varies widely from person to person or animal to animal.
What characteristic of short tandem repeats (STRs) DNA makes it useful for DNA fingerprinting?
genetic material composed of nucleic acid
What characteristics, structures, or processes is common to bacteria and viruses?
More than one codon can specify the addition of the same amino acid
What does it mean when we say the genetic code is redundant?
The sequence of the ends of DNA to be amplified
What information is critical to the success of polymerase chain reaction (PCR) itself?
he discovery of RNA viruses that synthesize DNA using reverse transcriptase
What is an exception to the central dogma?
Denature DNA; anneal primers; and extend primers.
What is in the correct order for one cycle of polymerase chain reaction (PCR)?
the small subunit of the ribosome recognizing and attaching to the 5' cap of mRNA
What is the first event to take place in translation in eukaryotes?
It uses viral RNA as a template for DNA synthesis.
What is the function of reverse transcriptase in retroviruses?
Enveloped viruses have a phospholipid membrane outside their capsid, whereas nonenveloped viruses do not have a phospholipid membrane
What is the main structural difference between enveloped and nonenveloped viruses?
It incorporates the entire template molecule in the product
What is true for DNA replication, but NOT for transcription?
it incorporates the entire template molecule in the product
What is true for DNA replication, but NOT for transcription?
hydrogen
What type of bonding is responsible for maintaining the shape of the tRNA molecule
a deletion of two nucleotides
What type of mutation, resulting in an error in the mRNA just after the AUG start of translation, is likely to have the most serious effect on the polypeptide product?
alternative splicing
What types of gene expression regulation occurs in eukaryotes but not in prokaryotes?
no 3' OH for the next base to attach
When a ddNTP is incorporated during DNA synthesis, elongation is stopped because?
A
When ribosomes shift codons which opens up site ___
continue
When sigma is released, transcription can ___
two types of daughter cells: a stem cell and a determined cell
When stem cells exhibit the property of self-renewal, they produce ________
the phosphate bonds in the nucleotide triphosphates that serve as substrates
Which molecule or reaction supplies the energy for polymerization of nucleotides in the process of transcription?
alternative forms of RNA splicing
Which of the following allows more than one type of protein to be produced from one gene? alternative forms of nucleosomes alternative forms of RNA splicing alternative forms of chromatin remodeling control of the frequency of translation initiation
genetic material composed of nucleic acids
Which of the following characteristics, structures, or processes is common to both bacteria and viruses?
Allosteric regulation of a repressor
Which of the following is an aspect of BOTH the trp operon and the lac operon
post-translational control
Which of the following levels of gene expression allows the most rapid response to environmental change?
Concurrent transcription and translation
Which of the following occurs in prokaryotes but not in eukaryotes? Concurrent transcription and translation Translation in the absence of a ribosome Posttranscriptional splicing Gene regulation
an RNA-based lysogenic virus
Which of the following viruses would most likely have reverse transcriptase? an RNA-based lytic virus a DNA-based lytic virus an RNA-based lysogenic virus a DNA-based lysogenic virus
Ribozymes may function in RNA splicing
Which one of the following statements about RNA processing is TRUE? Exons are cut out before mRNA leaves the nucleus. RNA splicing can be catalyzed by tRNA. A primary transcript is often much shorter than the final RNA molecule that leaves the nucleus. Ribozymes may function in RNA splicing.
Histones are positively charged, and DNA is negatively charged.
Why do histones bind tightly to DNA?
It might substitute a different amino acid in the active site.
Why might a point mutation in DNA make a difference in the level of a protein's activity?
This virus has a negative-sense genome.
You have isolated a newly discovered virus and are attempting to characterize it. You begin with its genome. You first isolate the virion-producing mRNA from cultured cells infected with the virus. When you compare this mRNA to the viral genome, you find that they are complementary. What does this tell you?
signals
___ can induce division, differentiation, movement, shape changes, or cell death
AUG
___ is the start codon
point
___ mutation alters the sequence of one or more small number of base pairs
karyotypes
___ reveal chromosome mutations
noneveloped
___ viruses commonly rely on endocytosis
lactose
____ binding to the repressor releases the repressor from DNA
chromosome
____ mutations change the structure or number of chromosomes
assembly, mediator
____ of proteins, other transcriptional activators bind to the exposed DNA, DNA is looped and activators bind to ____
UAA, UAG, UGA
_____ are the stop codon
cell division
a chromosome is only present while a cell is undergoing ___
sequences
a core promoter is responsible for different ___
codon
a group of three DNA bases that specifies a particular amino acid
mediator
a large protein complex that interacts with many regulatory transcription factors and recruits RNA polymerase for transcription
vector
a plasmid used to make copies of a foreign DNA sequence
protein folding
a post translational modification that is determined by the amino acid sequence, can occur spontaneously, guided and accelerated by molecular chaperones
chemical modifications
a post translational modification within the rough ER and Golgi, can be phosphorylation/glycosylation/activation/etc.
3
a ribosome has ___ binding sites
exons
a spliced transcript contains only ____
introns, exons
a template strand of DNA has ___ and ___
helicase
a thermostable enzyme is used in place of ___ since it is more efficient
thermostable enzyme
able to withstand high temperatures used to denature double-stranded DNA
decondensed
acetylation leads to _____ chromatin
vaccine
activates immune response
frameshift
addition or deletion of a nucleotide
induced pluripotent stem cells (IPS)
adult stem cells altered to be more like ES cells, can be differentiated to help with injury or disease (stem cell therapy)
committed
adult stem cells are ____ to only become limited cell types
genetic equivalence
all cells of an organism contain the same DNA and thus the same genes
constitutively
all of the time
ribosomes
all viruses utilize host ____ for translation
wobble hypothesis
allows one tRNA to read more than one codon
proteins
alternative splicing cuts pre-mRNA into different ___ and can alter the overall total
eukaryotes
alternative splicing only occurs in ____
nucleotides
amino acids cannot easily interact with ___
nucleotides
amino acids cannot easily interact with ____
A site
aminoacyl tRNA
forensics
amplify DNA from blood or hair to match individuals in paternity, crimes, natural disasters, etc.
CCA
an amino acid ends in ____
galactoside permease
an enzyme that trans ports lactose into a cell
B-galactosidase
an enzyme the breaks down lactose
genetic equivalence
an example of ____ is plants because you can remove any part like a branch, stem, or roots and cells will reform these parts
virus
an obligate intracellular parasite
tRNA
anticodon - binds specific ___
mRNA
anticodon binds to ____ codon
epigenetics
any mechanism of inheritance due to something other than changes in DNA sequences
deconstruct
apoptosis can help to ___ malfunctioning cells
no
are viruses alive?
exponential
as we repeat the cycle of PCR we are amplifying DNA as ___ increase
-10, -35
bacteria promoter contains ____ and ___ boxes
viral
bacteria store fragments of ___ DNA in their genome
sigma
bacteria uses ____ factors
restriction endonucleases
bacterial enzymes that cut DNA at specific base sequences
cytoplasmic determinant
bicoid gene is an example of a ______
general transcription factors
bind to core promoter to initiate transcription in many genes
regulatory transcription factors
bind to enhancers, silencers, promoter-proximal elements
core promoter
binding site for RNA polymerase
repressor
binds to DNA and shuts down transcription
activator
binds to DNA and triggers transcription
shotgun sequencing
breaking a genome into large chunks then comparing to a reference genome
viral envelope
budding uses the cell exterior as part of its ____ when it buds off of the host cell
noneveloped
bursting is typical in _____ viruses
low
cAMP is only produced when glucose concentration is ___
amino acids
catalytic - binds specific ____
aminoacyl tRNA synthetases
catalyze addition of amino acids to tRNAs
controlled
cell division is highly _____ by location, timing, and extent
differentiated
cell has a clear cut identity
committed
cell is following a particular path of specialization; weak and easily reverse
determined
cell is locked into becoming a particular cell type (not yet full specialized)
other cell types
cells that don't receive the inducing signals will differentiate into ____
developmental pathway
cells that receive the inducing signal will follow one distinct ______
differential gene expression
cells with the same genome express different sets of genes
missense mutation
change in nucleotide sequence that changes the amino acid specified by a codon
silent mutation
change in nucleotide sequence that does not change the amino acid specified by a codon
nonsense mutation
change in nucleotide sequence that results in an early stop codon
aminoacyl tRNA
charged tRNA
gene expression
chromatin is altered during ___
octamer
chromatin is assembled into an ___
protease
cleave polypeptides into functional proteins
promoter-proximal elements
close to promoter, allow coordinated regulation of genes of the same types
mRNA
codes for specific proteins delivered to cells
non-overlapping
codons are read one after another
universal
codons code for the same amino acids in all organisms
genome wide association studies
compare many genomes to identify variable sequences of DNA that are associated with a particular trait
chromatic remodeling, RNA processing, mRNA stability
compared to prokaryotes, what additional levels or control do eukaryotes have?
development biology
considers the mechanisms and patterns of how organisms develop from a single cell into a multicellular adult
I
constant expression of lacZ and lacY is lac__
endonuclease
crRNA with the help of another RNA (tracrRNA) binds to an _____ called Cas
splicing
cutting out introns
interior
cytoplasmic determinants are ____ development of cell differentiation
2 different types
cytoplasmic determinants cause one cell to divide into ___
part
cytoplasmic determinants effects ___ of a cell
OH groups
ddNTPs don't have ___
redundant
degeneracy, most amino acids are coded for by multiple codons
obligate
depend entirely on a host cell to replicate
antiviral drugs
designed to target specific viruses at specific stages of infection
differential gene expression
different cells use the same set of genes in different ways to become specialized
cell, tissues, activity
differential gene expression creates different ____ types, arranges cells into ____, and coordinates ___
different combinations
during RNA processing, splicing can create ______ of exons
made accessible
during chromatin remodeling, genes must be ____
bind
during chromatin remodeling, transcriptional activators ____ to enhancers, recruit chromatin remodeling complexes or HATS
life spans/stabilities
during mRNA stability, different mRNAs can have different ___
bind to a receptor
during uncoating, viruses ____
unambiguous
each codon codes for one one amino acid
pluripotent
embryonic stem cells are not committed
hox genes
encode transcription factors that trigger the development of specific body parts
lytic cycle
ending with the lysis of a bacterial host cell
passed on to offspring
epigenetic patterns can be _____
environment
epigenetic patterns can be altered by ____
above
epigenome means _____ the genome
short tandem repeats
eukaryotes contain ____ know as STRs
TATA
eukaryotes contain only ____ box
TATA binding protein (TBP)
eukaryotes have a _____ instead of sigma
more DNA, larger cells
eukaryotes require more complex regulation because
pattern formation
events that determine the spatial organization of cells in an embryo
genetic equivalence
every cell has the information to make any other cell in the organism
cloning
evidence of genetic equivalence in animals is ___
exposed
exposure of promoter and regulatory sequences, a region of DNA is _____, including the promoter, promoter-proximal element, and other enhancers
enhancers
far from promoter, bound by activator proteins to begin or increase transcription
silencers
far from promoter, bound by repressor proteins to shut down transcription
subunit
fragments of viral genes, proteins, or carbs
lactose
galactoside permease and B galactosidase are only produced in high levels when ___ is present
vary/change
gene expression is not just on/off, it can ___
research
gene expression studies, sequencing, cloning, classifying organisms, etc.
virus
gene therapy uses a ___ as a vector to infect a cell and deliver genes
multiple transcription factors
general transcription factors are in eukaryotic transcription, _____ are required to initiate transcription
regulatory transcription factors
genes code for ______ which tell it what genes to turn on for specific parts
exons
genes that are expressed =
introns
genes that intervene =
exons
genes that remain part of mRNA
volume
glucose and cAMP are ____ controls
galactoside permease
glucose inhibits the activity of _____
complementary, rejoin
having a "sticky end" means the two ends are ___ and can specifically ___
low
high glucose = ____ lactose
low
high glucose = low cAMP = ___ transcription of lac operon
transcription
high glucose with low lactose has no ___
low/no
high methylation near promoters = ____ transcription
replaces/fixes
homology-directed repair _____ a gene that is broken
two binding sites
how are amino acids attached to tRNAs?
genome and virion morphology, nature of host species, and how it replicates within the host
how are viruses classified?
DNA ligase
how do we "glue" the pieces of the plasmid and gene together?
antibiotic resistance
how do we select only bacteria that contains plasmid?
checkpoints, signaling from other cells, mitosis promoting factor
how is cell division controlled?
3, each produces a different class of RNA (tRNA, mRNA, rRNA)
how many RNA polymerases are in eukaryotes?
20, one for each specific amino acid
how many different synthetases are there are why?
40-45
how many tRNAs are there?
one
how many types of RNA polymerases are in bacteria?
pattern of expression
hox genes location on the chromosome match the ____
medical field
identify bacterial and viral pathogens, monitor the course of infections, diagnose cancer
differentiate in other cell types
if a cell does not receive a cell determinant will ____
Cas
if the crRNA finds and pairs with viral DNA, then ___ enzyme cuts the viral DNA to remove the virus
TATA box
in Eukaryotic cells, transcription has diverse promoters, ____ is rare
off
in a negative control, the default state is ___
latency
in animal cells, the delay of replicative growth is called ___
lysogeny
in bacterial cells, the delay of replicative growth is called ___
allosteric regulation
in both lac operons and trp operons, there is ____ of the repressor because it is a negative relationship
separated
in eukaryotic cells, transcription and translation are ___
on
in negative control when lactose is present inside the cell, the lac operon is ___
off
in negative control, the lactose is absent inside the cell and the lac operon is ___
blocks
in negative control, the repressor is bound to DNA operator and ____ transcription
trascription
in negative control, when the lactose is bound to the repressor, it releases from the DNA and ___ occurs
sigma, hairpin
in prokaryotes, ____ recognizes and ____ terminates
increases
in prokaryotes, as gene size increases, number of genes _____
operator
in the on negative control, the repressor cannot bind to the ___
transformation
incorporation of external DNA into a cell
lactose
inducer exclusion prevents ___ from entering the cell
exterior
induction are ____ development of cell differentiation
path
induction causes the one cell to differentiate along a different ____
whole
induction effects ___ of a cell
antibiotic resistance
insert gene to grow in antibiotic, kills off genes without the desired plasmid
noncoding
introns are ___ so they can be cut out
genealogy
investigate a person's ancestry
taq polymerase
isolated from the heat-tolerant bacterium Thermus aquaticus
inactivated
killed version of the viurs
repressor
lacI codes for ____ protein
regulation
lacI is responsible for ____ of other genes
metabolism
lacZ, lacY code for enzymes involved in ____
on/off
lactose is the _____ switch
chromatin remodeling complexes
large enzyme complex that uses ATP to reshape chromatin
poly (A) tail
long chain of A's added to 3' end
unpaired
loops in the tRNA secondary structure consist of ___ bases
deletion
loss of a segment of a chromosome
high
low glucose = ___ lactose
cAMP
low glucose = high CAP production = ___ transcription
lactose
low glucose allows more ___ into the cell
increased
low methylation near promoters = ___ transcription
carrier
mRNA = information ___
transcribed
mRNA is _____ to codons
anticodon strand
mRNA is translated to ____
shorter
mRNA that is translated is significantly ___ than the DNA from which it is transcribed in eukaryotes
ribonucleoprotein
made of protein and rRNA
genetic marker
many alleles differ by a single nucleotide known as a ____
viral DNA fragments and repeats
mature crRNA is broken up into what?
cofactor
metal ion that helps with reactions
ribozymes
modifications to the central dogma, 1. RNA molecules the do not code for proteins are called ____
reverse
modifications to the central dogma, 2. ____ transcriptase is an enzyme that makes DNA from RNA and is used by many viruses
5' cap
modified GTP added to the 5' end
cytoplasmic determinants
molecules that are asymmetrically located in the cytoplasm of a cell
Pfu DNA polymerase
more common enzyme used in PCR
maternal effect genes
morphogens are known as ____ because the mother deposits into the embryo
eukaryotic
multiple methods of termination are in ____ transcription
transcription
negative control prevents ____
inactivates
nonhomologous end joining ___ a gene by sticking 2 pieces of DNA together
general transcription factors
not involved much in regulation
complementary base pairs
once the gene is inserted into the plasmid, the sticky ends on the plasmid and gene pair up in ______
detaches
once transcription begins, sigma ___
homeotic mutations
one body part substituted in place of another
induction
one cell receives a signal that another doesn't
genetic regulatory cascade
one initially activated gene turns on the expression of other regulatory genes, which in turn trigger the expression of yet more regulatory genes
one enzyme
one-gene, one-enzyme hypothesis says that each gene contains the information encoded to make ___
5'--->3'
palindromic sequences are the same ___ on top and bottom
ambisense
part of genome is + and part is -
increase cell permeability, break the cell wall
plasmid is taken up by bacteria after we temporarily ____
neutral
point mutation can be beneficial, deleterious, ___
nucleicacids
polymerase means building ____
binding
positive control helps ____
activated proteins
post translational control does not translate proteins to ___
introns, exons
pre-mRNA contains ___ and _____
bicoid gene
produced at anterior region and diffuses toward posterior, creates a concentration gradient
DNA cloning
producing many copies of a DNA sequence of interest
chain reaction
products serving as templates for the next reaction
operons
prokaryotes organize genes into ____
transcription factors
proteins that bind to DNA and are involved in the process of transcription
ribozyme
rRNA catalyzes peptide bond formation
core promoter, promoter proximal elements, enhancers, silencers
regulatory sequences specific to eukaryotes:
allosteric
relating to or denoting the alteration of the activity of a protein through the binding of an effector molecule at a specific site.
tRNA
release factors are similar to ____ in shape
any known
replace crRNA with ____ sequence that's complementary to what you want to attack, then combine the crRNA and tracrRNA into one piece is how you edit a genome
undifferentiated cells
replace worn-out or damaged cells, create white blood cells
gene therapy
replacing defective copies of a gene with a normal allele to treat or prevent disease
operator
repressor binds to the ____ to prevent transcription
enzymes
restriction endonucleases are ___
palindromic
restriction endonucleases cut ___ sequences
viral infections
restriction enzymes and cas9 both help bacteria fight ____
RNA, DNA
reverse transcriptase takes you from ___ to ____
introns
sections that are removed from mRNA
duplication
segment of a chromosome is duplicated
translocation
segments of a chromosome are detached and joined to a different chromosome
inversion
segments of a chromosome are detached, flipped, and rejoined
controlled together
separate genes or operons with the same regulatory sequences that are ____
negative sense (-ssRNA)
sequence is complementary to mRNA, must be copied before being translated
positive sense (+ssRNA)
sequence matches the mRNA, directly read by ribosomes to synthesize proteins
operon
set of coordinately regulated bacterial genes that are transcribed together into one mRNA
morphogens
set up body axes
single guide RNA
sgRNA
promoter
short sequence of DNA where proteins bind to initiate transcription
STRs
short, repeated DNA sequences that vary in repeat number between individuals
functional
sigma + core enzyme is fully ___
RNAP
sigma factors are detachable subunit of ___
sticky ends
single stranded bases on a fragment cut by restriction enzymes
inducer
small molecule that triggers transcription
plasmid
small, circular DNA molecule common in many bacterial cells
cut out
snRNAs loop introns together to be ____
RNA replicase
some RNA require ____ and enzyme for replication
constitutively
some genes are transcribed _____ (all of the time)
stem
some methods of gene therapy use ____ cells
regulatory transcription factors
specific for different types of cells
toxoid
specific toxins (proteins) of the virus
RNA replicase
synthesize RNA from RNA
recycled
tRNA is ___ after translation
E site
tRNA that will exit
P site
tRNA with growing polypeptide attached
aminoacyl tRNA
tRNA+amino acid
poly(A) signal
termination downstream of a long stretch of A nucleotides
attachment
the 3' is the ____ site for amino acids
cytoplasm
the Poly(A)tail helps to get the DNA strand into the ____
-30
the TATA box is around ____
nucleosomes
the beads on a string reference is about ____
histones
the chromatin structure has DNA wrapped around proteins called ___
mammary-cell donor
the cloned animal will be genetically identical to ___
on
the default state of trp negative control is ___
single nucleotide polymorphism
the differing nucleotide base pair is called a ___
CCA
the end of amino acids end in the ___ codon
biotechnology
the engineering of genes, cells, and organisms for research
start site, +1
the first base RNAP reads and builds from
codon
the genetic code is found in a ____ table
stepwise
the growth pattern of viruses in ____ which is faster than exponential
pause, mRNA
the hairpin causes RNAP to ____ allowing the release of ___
off
the lac operon is ___ until needed
not used
the most condensed DNA is ____
length
the number of STRs and thus the overall ____ of the repeat region differ widely between individuals making it a quick way to match DNA samples to individuals
recognition site
the place where restriction endonucleases cut DNA
polymerase
the promoter of lac operon binds _____ to start transcription
plasmid and gene
the recognition sites have the same sequence in the ____
no correlation
the relationship between gene size and number of genes in eukaryotes is...
direct correlation
the relationship between gene size and number of genes in prokaryotes is...
restriction sites, sticky ends
the restriction enzyme cuts the DNA at each of the _____ and the ___ result on both the plasmid and gene
large subunit
the ribosome structure that contains tRNA binding sites, and peptide bond formation occurs
small subunit
the ribosome structure that holds mRNA is ?
mature mRNA
the same gene can yield more than one _____
alternative splicing
the same primary transcription can be spliced in different ways
gene expression
the set of processes converting information in DNA into a functional product
gene expression
the set of processes that convert information in DNA into a product
connected
the sticky ends are complementary to the gene becomes _____ to the plasmid
amino acids
the stop codons do not code for ___
antiparallel
the template strand and new strand are ____
opposite/reverse,
the template strand is ___ of the non template strand
mRNA
the template strand is translated to _____
backwards
the template strand of DNA is read ______
anticodon
the template strand of DNA matches the ____ strand
wobble base
the third base that differs for the same amino acid is called the ____
on
the trp operon is ____ until it isn't
negative
the trp operon is the alternative ____ control
3rd, match
the wobble hypothesis says that bases in the ____ position of codons/anticodons can bind in ways that do not ___ watson-crick base pairing
mRNA
the wobble pair is on the ____
apoptosis
tightly-controlled self destruction
operons
to control gene expression, ___ are used to only work in favorable conditions and thus separate desired cells from undesired
target
to edit a genome, Cas will cut dsDNA at a specific ____ sequence
genetics
to learn if prospective parents have alleles associated with serious illness
repressor, DNA
to turn off the operon trp (co repressor) binds to the ____, the repressor changes shape and is now able to bind ____
proteins
transcription ----> translation -----> ____ -----> phenotypes
primer
transcription does not require a ____
nucleus
transcription happens in the ___
reading the DNA template, writing the RNA
transcription is ____ while translation is ____
lactose
transcription is always happening whether _____ is present or not
absent
transcription only needs to happen when trp is ___
template
transcription requires a ____ for base pairing
template
transcription uses the ___ strand
mRNA
transcriptional control does not transcript DNA to ___
foreign
transformation is putting ____ DNA into a cell
cytoplasm
translation happens in the ____
codons
translation uses ____ of the transcribed strand
proteins
translational control does not translate mRNA to ____
anabolic
trp is a negative control of an ___ pathway
stem cells
undifferentiated cells
self-renewal
undifferentiated cells maintain population by ___
+1
upstream refers to being up from ___
transcription
uses DNA template to make an RNA molecule with a complementary sequence
translation
uses information in mRNA to synthesize protein
uncoating
viral capsid is removed, and the genome is released
single stranded or double stranded
viral genomes can be linear or circular, DNA or RNA, and ___
endocytosis
virions enter cell via _____, acidification causes viral proteins to change shape, promoting release
bursting
virus exit that does destroy the host cell
budding
virus exit that does not destroy the host cell
replicative growth
viruses infect host cells via __
high
we add a ___ concentration of primers to ensure binding to the template DNA
live attenuated
weakened form of the virus
chromatic remodling, RNA processing
what additional levels occur inside the nucleus?
mRNA stability
what additional levels occur outside the nucleus?
cytoplasmic determinants and induction
what are 2 mechanisms of cell differentiation?
RNA molecules that don't code for proteins and reverse transctiptase
what are 2 modifications to the central dogma?
heat shock, electric shock
what are 2 ways to break the cell wall and increase permeability?
only requires small amounts of template DNA (sensitive), can make billions of copies in a short amount of time (fast), it is cheap and pretty simple
what are some advantages of PCR?
Galactoside permease, B-galactosidase
what are the 2 enzymes used in lactose metabolism?
1. enables ribosome to bind to mRNA and be translated 2. protects mRNA from degradation by ribonucleases (RNases)
what are the 2 functions of the cap and tail?
budding, bursting
what are the 2 mechanisms for a virus to exit a cell?
transcription, translation
what are the 2 steps of the central dogma of molecular biology?
small subunit, large subunit
what are the 2 structures of a ribosome?
genetic material (DNA/RNA) and protein shell (capsid)
what are the 2 things all viruses contain?
nonhomologous end joining, homology-directed repair
what are the 2 ways to repair a break in DNA?
directly interfere with it/replication or activate an immune response
what are the 2 ways to treat a viral infection?
anterior/posterior, dorsal/ventral, left/right
what are the 3 body axes?
1. initiation 2. elongation 3. termination
what are the 3 overall steps of transcription
initiation, elongation, termination
what are the 3 ribosomal translation steps?
denaturation, annealing, extension
what are the 3 stages of PCR?
committed, determined, differentiated
what are the 3 stages of cell differentiation?
1. incoming aminoacyl tRNA enters A site 2. amino acid in P site is transferred to amino acid in A site 3. translocation, ribosome moves down one codon, tRNAs shift sites
what are the 3 steps of translation elongation?
1. mRNA binds to small subunit at the ribosome binding site 2. initiator aminoacyl tRNA binds to start codon 3. large subunit binds; first tRNA in P site
what are the 3 steps of translation initiation?
1. protein release factor binds to stop codon, breaks the polypeptide from tRNA 2. polypeptide and tRNAs are released 3. ribosome subunits separate
what are the 3 steps translation termination?
rRNA, mRNA, tRNA
what are the 3 types of RNA?
dsDNA, ssDNA, dsRNA, ssRNA
what are the 4 options of viral genomes?
1. Build reaction w/many dNTPs and a few labeled ddNTPs 2. During DNA synthesis each strand ends w/labeled ddNTP 3. Eventually a labeled strand of every possible length is generated 4. Separate fragments by length using electrophoresis and read fluorescence output on a machine
what are the 4 steps of dideoxy sequencing?
1. cell division 2. cell signaling 3. cell differentiation 4. cells move, expand, or contract in certain directions 5. programmed cell death
what are the 5 stages of the essential developmental processes
template DNA, Mg2+, buffer, dNTPs, primers, enzyme
what are the 6 components of PCR?
1. enter host cell 2. viral genome is transcribed to make proteins 3. replication 4. particles assemble inside host 5. particles exit to exterior 6. free virions are transmitted to new host cell
what are the six phases of the viral growth cycle?
2
what are the two binding sites of an amino acid and tRNA?
negative control, positive control
what are the two ways transcription can be regulated?
body part substitution
what can happen to an organism when hox gene expression is altered?
building blocks of DNA
what do dNTPs do in PCR
heat resistant DNA polymerase
what do enzymes do in PCR
short oligonucleotides that flank the target
what do primers do in PCR
clustered regularly interspaced short palindromic repeats
what does CRISPR stand for?
cofactor for polymerase
what does Mg2+ do in PCR
provide optimal conditions for the reaction
what does a buffer do in PCR
exponential increase of a targeted region of DNA
what does a polymerase chain reaction result in?
there is less reaction with the new neutral charge since DNA is negatively charged
what does covering up the positive charge on lysine do for DNA?
piece of DNA you want to amplify
what does template DNA do in PCR
large, TATA box
what does the promoter structure appear like in eukaryotes?
RNAP moves along the DNA continuously downstream
what happens during transcription elongation?
sigma+RNAP bind to the promoter, RNAP opens the DNA and begins transcription, sigma is released allowing RNAP to continue transcribing
what happens during transcription initiation?
a termination signal is transcribed and folds into a hairpin structure, the hairpin causes the release of RNA from RNAP
what happens during transcription termination?
repeats
what is CRISPR named for?
1. condensation state of chromatin determines where and if transcription can occur 2. cells of different types have different patterns of DNA methylation and histone acetylation 3. certain genes are active at different times
what is a summary of chromatin remodeling?
phospholipids
what is a virus envelope made of?
transcription factors
what is it in the cell that causes differential gene expression?
must have knowledge of target DNA sequence in order to design primers in complementary pairs
what is one limitation of PCR?
Cas
what is the CRISPR enzyme used for bacterial defense?
Cas
what is the CRISPR enzyme used for genome editing?
alternative splicing
what is the RNA processing control?
It attaches to an amino acid
what is the function of the ACC sequence at the 3' end?
It base pairs with a codon of mRNA.
what is the function of the AGU on the loop of the tRNA?
apoptosis
what is the predominant mechanism in animals to program cell death?
recombinant DNA
what is the product of cloning?
35 and 10 box
what is the promoter structure of bacteria?
Primers bind to template DNA (60 C)
what occurs during annealing?
DNA strand separate due to high temperatures (95 C)
what occurs during denaturation?
polymerase active, extend DNA from primer (72 C)
what occurs during extension?
the process repeats, and the polypeptide chain extends while the ribosome moves along the mRNA
what occurs during translation elongation?
1.5%
what percent of the human genome is protein coding?
sigma
what protein associates with the promoter in bacteria?
many general transcription factors
what protein associates with the promoter in eukaryotes?
chromatin remodeling complexes
what slides nucleosomes or knocks histones off the DNA?
replicative growth
when a virus delays ____ it will become incorporated into the host's genome
virion
when a virus is outside of a host cell it is called a ___
Mediator, transcription
when an RNA polymerase binds to core promoter, the general and regulatory transcription factors assemble on the ____, RNAP binds to the core promoter, and ____ begins
CAP
when bound to cAMP (second messenger), binds to DNA to increase transcription
DNA
when lactose binds to a repressor it changes shape and can no longer bind to ____
conservative
when multiple codons code for the same amino acid, usually only the third base differs
enzyme
when you break one gene, you break a specific ___
reverse transcriptase
when you go backwards through the central dogma you use ____
about 50% of an average genome consists of repeated sequences that can have mistakes, unequal crossing over, or movement
why are eukaryotic genomes so complex?
it covers up the positive charge on lysine with a neutral charge
why does the chromatin structure make sense?
no start codon, no ribosome binding site
why is pre-crRNA not translated?
transcriptional control
why type of control is most efficient (saves energy)?
