Bio Exam 4 - Final

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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)?


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