MCB 102 Part III: Molecular Biology

minor base

5-methylctidine is an example of a ___ ___; it is not pprominent, but is definitely present and helps with regulation.

linear, circular

Agrobacterium tumefaciens is a perfect counterexample to how bacteria always have circular chromosomes. While this may be the case, this bacterium actually has one _____ and one ___ chromosome.

inverted repeats, transposase

An insetion sequence is something that has ___ ___ are the ends and in the middle, it has an enzyme, which is usually known as _____.

circularized

As low doses, bacteriophages can lysogenize the host. After their DNA is injected into the host, it is actually _____, and then it becomes an episome/plasmid.

3.6, 7,

As you remember from Jeremy's section, the alpha helix shows a turn every ___ amino acid residues. . In a lucine zipper, you have a leucine residue every ____ residues, and this forms a straight line along the hydrophobic surface. The leucine lines can line up among one another and this helps with the protein-protein interaction.

primer

Aside from a template that tells the DNA synthesis what it needs to start, the DNA polymerase also needs a ___, which is a strand segment with a free 3' hydroxyl group in which the next nucleotide can be added. The free 3' end of the primer is called the primer terminus.

poly A tail

At the 3' end, most eukaryotic mRNAs have a string of 80 to 250 a residues making up the __ __ ___, which serves as a binding site for one or more specific proteins. Many prokaryotes may also have these tails, but they accelerate the decay of mRNA rather than protecting it from degradation.

fill this out

Can you go over the role that the helicase II, excinuclease I, and SSB have in mismatch repair?

DNA

Acetylation is needed when something needs to be transcribed. This is because when you acetylate the lysine residues, you decrease the histone's affinity for ___.

RNA polymerase

CRP-cAMP positively recruits RNA polymerase. It basically bends the DNA in such a manner that ___ _____ can more readily recognize the promoter.

b, c, b

After DNAA causes the AT region to open up, the ___ and ___ interact to form a comple and DNAA interacts with this complex to load ___ onto the unwound DNA.

mRNA

After IF3 and IF1 bind to the 30S subunit and prevent it from recombining witht eh 50S subunit, you get binding of the ____.

fire

After M phase, the M phase CDK activity has declined and in the next G1, the components of the pre replication complex can _____. Thus, this basically says that once an origin has fired, it cannot fire again until a new pre replication complex is established.

dna polymerase

After cutting at the region where the unmethylated GATC was, the other half of the DNA with the wrong genetic material is cleaved with helicase II, exinuclease I, SSB. After this, ___ ______ fills in the rest of the DNA wand it will be A-OKAY.

P-TEFb, carboxy terminal domain

After formtaion of the preinitiation complex, elongation factors _-____ (phosphorylating transcription elongation factor b) When this is recruited, you get phosphorylation of the ___ ___ ___ oh RNA polymerase II

ATP

After loading DnaB followed by loading of the sliding clamp, interaction of teh sliding clamp with DNAA stimulated ___ hydrolysis.

muth

After mutS finds the place on the new strand with the mismatch ___ nicks the DNA 5' to the umethylated GATC.

UvrC

After the UVrA2B binds to the site where a bad thing has occurred (nucleotide excision repair). the UvrA subunits get replaced by ____ and that with the original UvrB does the cutting out

ATP

After the clamp attaches to the DNA and the clamp loader is released by the hydrolysis of ___, the DNA polymerase then attaches.

cleavage and polyadenylation specific factor (CPSF)

After the endonuclease cuts the RNA after the polyadenylation signal sequence, you get the polyadenylatio signal sequence being recognized by ___ ___ ___ ___ ___

F, E, H

After the initial recruitment of TFIID, you then get TFIIB, which stabilizing the TFIID. Then you get addition of TFII_ and RNA polymerase II; this transcription factor helps Pol II find its spot on the DNA promoter. After this, TFII_ comes in and Then TFII_. This creates the pre-initiation complex in eukaryotes (closed complex)

oriT, re-ligated

After the plasmid is completely transferred over to the femal ecell (in conjugation, recall how you only transfer one strand of DNA), and that one strand is then replicated to form a ds entitiy. After formation of that double stranded entity, you have finished replication, so you cut the DNA at ___, and afterwards, the DNA in both cells in __-_____ and the two cells separate.

DNA replication

After the ssDNA is pushed into the recipient cell, the process of ___ ____ converts the ssDNA to dsDNA. After this completion, you actually end up getting. the conversion of the female cell into the male cell.

B. F,

After you get binding of TFIID and specifically, TBP binding, TFII_ comes in and binds to the DNA on either side of TBP. After this, you then get simultaneous arrival of TFII_ (the whole goal of this TF is to target RNA polymerase to its promoter) and RNA polymerase II and those stick to the domain as well.

restriction endonucleases, methylated

Chromosomal DNA and resident plasmid DNA within the actual bacterium is usually protected from the ___ ___ because both of those are ______ at the right sites.

processivity, B

DNA polymerase III has a much smaller ____ than one would expect. Howevever, the increase is brought about by the addition of __ subunits, four od which complete the DNA polymerase III Enzyme.

DNA polymerase delta, DNA polymerase epsilon, DNA polymerase alpha

DNA polymerase III in prokaryotes is to ____ __ ___ in humans. DNA polmyerase I is to ___ ___ ___ in humans. Primase in bacteria is to ___ ___ ___ in humans.

I, 5, 3

DNA polymerase __ has a _'-_' exonuclease activity, something that is not common at all among all polymerases. However, this property helps it replace segments of DNA or RNA that are simply not supposed to belong.

II

DNA polymerase __ is involved mostly in DNA proofreading, but not the one that replaces the primers.

epsilon

DNA polymerase ___ is analogous to DNA polymearse I in prokaryotes.

delta

DNA polymerase ___ is analogous to DNA polymerase III in pprokaryotes.

III

DNA polymerase ___ is much more complex than the 4 other polymerases in the bacterial cell because it has 13 subunits (9 of them are unique).

III, 10

DNA polymerase ___ is the principal replication enzyme involved in E. coli. This polymerase, unlike I, has more than __ subunits (I just has 1, and II has 7)

cruciforms

DNA under winding also provides the necessary energy to facilitated the formation of _____ from the different palindromic sequences that might be presence.

ATP

DNAA can only bind to its initiator regions if it is bound to___ as well.

DNAC

DNAB (in bacteria, which is also known as helicase) binds to the DNA with the help of ____ (again, this is in bacteria only)

6, lagging, 5, 3

DNAB helicase is made from _ identical subunits, is attached to the ___ strand and goes _'->_'.

MutS, MutL

Defects in mismach repair lead to hereditary cnacer that affects 1/200 people. The cancer results from a defect in the genes that encode protein that are highly homologous to ___ and ___ from E. coli.

cancer

Defectsin mismatch repair can cause ____ in humans.

primase, polymerase

Dna polymerase A in humans is made of a ____ subunit that is used to synthesize an RNA primer, and a ____ subunit that is used to add a stretch of 20 nucleotides to that primer

DNA poly I (this is DNA poly III is very processive, wherease DNA poly was PROGRESSIVE, and this is slow)

Do you have more DNA poly III or DNA poly I?

G, Tu

EF-__ is also known as translocase It looks the same as EF-___ complexed with tRNA because they both ust be in the same place at the same time.

G

EF-___ is also known as translocase and itgoes to teh A site and just pushes it forward.

telomerase

Elizabeth blackburn and carol greider found ____, and they ssay they did to see if that was the case was adding in a triphosphate substrate, and they predicted that if DNA was being added on, then only certain triphosphates would be incorporated, and that is indeed what they found.

H3, H4

Histones __ and ___ are nearly identical in ammino acid sequence among all eukaryotes.

separating

However, instead of supercoiling, if you did have underwinding, you can also accomodate the strain by just ___ the two DNA strands over a distance of 10bp. However, because coiling the axis of the DNA requires less energythan breaking the H bonds, you usually get supercoiling.

polyadenylation

In eukaryotic organisms, the RNA polymerase actually tends to go well beyond the cleavage and ____ signal sequence prior to actually terminating. The termination, however, has not even been defined yet.

single strand

In conjugation, a __ ___of the DS F DNA is transferred and then DNA replication restored the complementary strands in both the host and recipient.

eukaryote, prokaryote

In eIF, the e usually signals ____, but if it is not present, then you can assume that the initiation factor is relvant for ___.

activators

In eukaryotes, ____ bind to genes at sites called enhancers. They help determine which gene will be turned on and they speed the rate of transcription.

negative, positive

In eukaryotes, dna base pairs (146) going around the histone octomer introduces a ___ supercoil, which leads to a ___ supercoil due to conservation of the linking number. However, topoisomerase fixes the positive supercoil, adn you get an overall decrease in linking number

A (D also acceptable)

In eukaryotes, the TATA binding protein is also known as transcription factor II_, and it helps bind to the TATA box. This is then bound by transcription factor IIB, and the rest is then bound by TF IIF and Pol II., After this, TFIIE and TF IIH bind and you get complete formation of the closed complex.

g, 40, shine-delgarno

In eukaryotes, there is an initiation ocmplex with loads of eIFs. The eIF4_ binds to both the cap binding protein (eIF4e) and the polyA binding protein. This helps create a loop of the mRNA and then, the complex basically just guides the __S ribosomal subunit to teh first AUG codon to initiate protein synthesis. In this case, the difference is that there is no ___-____ sequence for the ribosome to recognize.

15, 14

In the messelson and stahl experiemnt, we started by growing the DNA in the N-___ medium and then we switched it to the N-___ medium. The difference can be noted via density centrifugation

rolling circle DNA replication

In the original host cell of conjugation, you have __ ___ __ ___, and this is basically since you transfer one single strand of DNA, you need to remake it, and it is literally being remade as it is being lost.

cyclobutane thymine dimer,

In the presence of UV, adjacent thymine residues turn into __ ___ ___, and this causes a bend in the DNA that prevents it from being transcribed or replicated.

3

In the tRNA, the __' end is longer than the _' end (we're judging from the top).

different

Incompatibility of replication. Plasmids fall into ~ 26 compatibility groups. Only plasmids from ____ compatibility groups will be maintained in a particular host.

newer

Mismatch repair usually gets on the ___ strand and just goes down and checks for mistakes

glucocorticoid elements

Metallothionein removes toxic heavy metals from the cell, and it can be induced by metals such as cadmium or ______ elements.

telomerase

Mice have extremely long telomeres, and we are not as fortunate. In this case, we do need the enzyme ____ to work properly if we want to live a healthy life.

GC

Microorganisms exposed to ultraviolet light generally have a higher ___ content because that helps geenrate fewer thymine dimers

beta

PCNA (proliferating cell nuclear antigen) has a function analogous to that of ____ subunit of DNA polymerase in prokaryotes because it helps DNA polymerase delta stay on task.

transcription

Protein/protein interactions between the transcription factors and RNA polymerase II activates ___ in eukaryotes.

rrna, trna, mrna

RNA hairpin sare imrpotant for the correct structure and stability of ___, ___ and most ____.

RNA synthesis

RNA hairpins can regulate __ ___ by causing RNA polymerase puasing and termination.

ribosomal binding

RNA hairpins can regulate ___ ___ by hiding or exposing ribosomal binding sites on mRNA>

double stranded, single stranded

RNA tertiary structure is determined by a mix of ___ ___ and ___ ___ regions.

3, 5, 6

RNA polymerase lacks _'-_' exonuclease activity, which means that it cannot proofread. However, it also has __ subunits (if you include sigma factor)

3, hydroxyl, pyrophosphate

RNA polymerase works by the same mechanism in elongation as DNA polymerase. The __' ____ atttacks the phosphate of the incoming nucletide and diaplaces _____, whose hydrolysis drives the reaction.

autoradiography

Radioactivity in a sample can expose photographic film. The film can then be developed with developer and fixer. The exposed film is called an autoradiogram.

10.5

Related moelcule of DNA = ___ base pairs/turn. There is no tension if this exists.

negatively

Removal of the histone core makes the DNA ____ supercoiled

complexity

Renaturation of DNA depends on its ____. For exmaple, for viral DNA, the renaturation is fast and complete, whereas in human dna (which is 3.2 million kb instead of 10 kb), it is slow and only partial.

restriction enzymes

Restriction endonnucleases are more commonly known as ___ ___ in the lab.

specific sites

Restriction endonucleases are really important in the lab because they can help cut the DNA at ___ ___, which you can then analyze.

defective

Somatic mutations can also be the consequence of ___ DNA repair. In this case, you try to fix something that is wrong, and that eventually is what kills you.

base-pairing

Specificity of the relationship between the mRNA and the tRNA is determined by __-____.

clamp loader

The ATP binding to the ___ ___ leads to a confomational change that allows this substance to bind to the clamp.

proofreading

The 3'-5' exonuclease activity is also known as ____ for DNA polymerase III. This is present in most DNA polymerases.

phosphate, hydroxyl

The 5' end has no nucleotide at the 5' position and that is where the free ___ is! (for 3' it is a ___).

degeneracy

The ___ of the genetic code is not universa. Methionine can only be made one way, whereas leucine can be made in 6 ways.

wobble

The ___ phenomenon is actually good because if all three bases engaged in strong W-C pairing, the tRNAs would dissociate too slowl for it to matter.

EF-Tu-tRNA, EF-G

The ___-___-____ and __-__ have the same shape because they must fit into teh same site on the ribosome. The first one is involved in adding in a new aminoacyl tRNA to its correct position, nad the latter is used in the process of translocation.

shine-degarno

The ___-____ sequence is completmentary to teh 3' end of the 16S rRNA that is part of the 30S subunit. This binding essentially ends up positioning the ribosome.

sixth, sigma 70

The ____ subunit on RNA polymerase determines where it will bind. The most common form of this subunit is the one that is named ___ __. There are six overall subunits to RNA polymerase

enhancers

The additional regulatory sequence sin eukaryotes are referred to as ____ and in yeast, they are upstream activator sequences.

U2

The adenosine buldge that occurs at the place within the intron in the spliceosomal mechanism occurs because ___ is paired to that site and makes the A pop out (this eventually goes on to become the nucleophile)

2, 3, 2, 3

The amino acid is added to the tRNA but it attacks ATP first, displaces the PP, and then the _' or _' OH on the 3' end of the tRNA attacks the amino acid and displaces it. Thus, you can get a _'- amino acyl tRNA or you can geta _' aminoacyl tRNA, but bothar ein equilibrium .

mutations, repair systems, oncogenes

The cancer that is caused by DNA damage is usally from ____. In particular, these can come from various different sources: DNA ___ ___, tumor suppressor genes, and ___, which alter the regulation of the cell cycle.

Amino acid + tRNA + ATP (MG2+ cofactor) -> aminoacyl-tRNA + AMP + 2P

The equation for going from tRNA to charged tRNA is:

3, 5, ,5, 3

The eukaroytic helicase opens from _'->_'. wheras the prokaryotic helicase opens _'-> _'.

n-formylmethionine, methionine

The first result inserted in all polypeptides is _-____ (in prokaryotes) or ___ (in eukaryotes)

antibiotic resistant bacteria

The hospital, for obvious reasons is one of the hotspots for teh creation of ___ ___ ____

A

The incoming amino acid to be added sits in the __ site of the ribosome.

CRISPR

The initial start of CRISPRs came from the bioinformatics sector, where they saw that there were regions in bacterial DNA where you had regions of palindromic repeats with distinct DNA strands in the middle. So there were clusters of regularly interspaces short palindromic repeats, or ________

10, 13

The length of a primer for DNA replciation is usually between ___ and ___ nucleotides.

writhe, twist

The linking number is broken down into the ___ and the ___. The former is thought of as a measure of the coiling of the helix axis and the latter is a way ot determining the loca twisting or spatial relationship of neighboring base pairs.

3, I (ionitosole)

The maximum number of codons that one tRNA can bind to is __, and that is if it has ____ as its first nucleotide on the anticodon.

g1, regulated

The pre-replication complex forms in ___, and the firing of this preassembled complex is where eukaryotic DNA replciation is most ____.

plasmids

The presence of ___ allow pseudomonas to grow on a wide variety of foods, including many toxic wastes. Specifically, pseudomonas can live on over 100 different carbon sources, and an grow on things that other things would deem as toxic. This is simply because it has so many plasmids that essentially nothing is toxic to it anymore.

splicing

The process of _____ and transcription are coupled in eukaryotes, and they tend to occur at the same time.

initiation, elongation, termination

The process of replication, transcription and translation all involves the three common stages of __, ___, and ___.

transposons

The reason why barbara mcclintock got an idea of the presence of _____ was because she notice that certain genetic elements were not following the normal rules of genetics that were proposed by mendel.

specific, efficient

The reason why it is advantageous to require lots of trnascription factors is simply because it is better to have positive regulation because it is more ___ and ___.

antiparallel, 5', 3'

The reason why lagging strand synthesis is so complicated is because of the ____ nature of the DNA, and the fact that DNA polymerase must always go from __ to ___.

telomeres

The repetitive ends for humans are in the form of AGGGTT at the 5' end. And these repeats are referred to as ____.

upstream

The repressor of the lac operon is transcribed from its own promoter ____ of the actual lac operon.

reverse transcriptase

The telomerase enzyme contains a __ ___ subunit and an RNA that is complementary to the telomeric DNA.

lysogenic phage

The thing that is responsible for making a toxin in diphtheria is a ___ ___, and toxin is called diphteria toxin.

elongation, elongation factors (EFs)

The third stage of protein synthesis sis called ___. And the factors taht it uses are aoften referred to as ___ ___.

negative

The tight wrapping of DNA around the histone core requires the removeal of about one helical turn in the DNA, and thus, you get a ___ supercoil.

photolyase

The way that we can get rid of thymine dimers is via: DNA ___ binds to thymine dimers in the dark. Then in the light (370

nucleosome

There are 2 copies of the H2A, H2B, H3, and H4 histones that all come together with DNA to form the ____.

mRNA, tRNA, GTP, protein synthesis factors, ribosomes

There are 5 things that are needed for protein synthesis. What are they?

H2A, H2B, H3, H4

There are 8 histones in a nucleosome and there ar 2 __, 2__, 2___, and 2 ___

6

There are ___ overall subunits that make up RNA polymerase holoenzyme (2 identical alpha, beta 1, beta 2, omega, and transient sigma)

circular, telomere

There are different ways to solve the telomere problem, and one way to do it is with a ____ chromosome or just have lots of shit at the end of the chromosome that we don't need, and that is called a ____.

self splicing

There are four groups of slicing introns. The GRoups I and II are important because they are __-___

H1

There are more __ histones in regions that are turned off.

a, b, z

There are three forms of DNA and they are the __ form and __ and ___ forms.

S, M

There are two cyclins. One for the __ phase, and one for the __ phase.

conjugative, non-conjugative

There are two mains groups of plasmids and that is: ___ and ___-____ plasmids.

proofreading, polymerization

There are two things that any polymerase can do. One of these actvities is referred to as _____ and the other is ____. Both happen at separate active sites in the peptide.

anticodon

Transfer rNAs base-pair with mRNA codons at a three base pair sequence on the tRNA known as an ___

topoisomers

Two forms of circular DNA that differ only in a topological property such as linking number are referred to as ____

thymine dimer

UV is infamous for cuasing ___ ___

primer

Unlike DNA synthesis, RNA polymerase cannot extend a _____.

3, 5, proofreading

Virtually all DNA polymerases have a _'-_' exonulcease activity that checks each nucleotide after it is added. This is referred to as ______

methylated

Viruses or plasmid DNA invading a cells with a restriction system will be destroyed (and this i sbecause the DNA will not be ____ at the corret sites).

beta

Watson and Crick determine the ___ form of DNA.

10 billion

We have an error for 1 in every ____ _____ base pairs.

adenine

We learned that GATC methylation is something that helps determine what is the new and old strand. Within that sequence of 4 nucleotides, the ___ is the one that is actually methylated (if and when that does happen)

7-methylguanosine

What is the name of the species that is added to the 5' end of eukaryotic mRNA?

3', 5'

What part of the mRNA is most susceptible to RNase activity?

leading strand

What strand of DNA is elongated by telomerase?

cyclin, cyclin

When CDk is activated by ___, it goes and phosphorylates all needed for mitosis. However, within mtiosis, ____ is degraded readily, and this is why something in G1 can't just reenter the S phase, unless something physically gives it the cyclin .

10.5

When DNA is in the relaxed state, you have ___bp per turn, but the moment it is anything different from this, you will get supercoiling.

enhancer

When bound by the appropriate regulatory proteins, an ____ increases transcription at nearby promoters regardless of its orientation in DNA.

DNA binding proteins

___ ___ ___ can act as repressor or co-repressors. They can also act as activators. These are also known as trasncription factors.

chromatin remodeling factor (another way to get around the nucleosome barriers in eukaryotes)

___ ___ ___ can move the DNA around and allow transcription to happen. This is something that affects how tightly nucleosomes bind to DNA.

replication protein A

___ ___ ___ is a eukaryotic single stranded DNA binding protein equivalent in function to teh E. coli single stranded binding protein.

nucleotide excision repair

___ ___ ___ is really good for removing thymine dimer or just anything that has caused a buldge to happen.

basal factors

___ ___ are basically things in eukaryotes that respond to injunctions from activators. They position the RNA polymerase II at the start of the protein coding region and send the enzyme on its way.

zinc fingers

___ ___ are more common in eukaryotes than in prokaryotes.

DNA photolyase, FADH2

___ ___ binds to thymine dimers in the dark, and then, in the light, at 370 nm, the enzmye breaks cyclobutane bonds. The cofactor for this enzyme is ___.

living cells, dead cells

___ ___ can repair DNA, but __ ___ cannot.

hammerhead ribozymes

___ ___ can specifically target mRNAs for degradation.

thymine dimers

___ ___ covalent bonds between two adjacent thymines on the SAME strand. Can't easily be broken. Will have a horribly time trying to copy this. You might even get cancer.

polyadeylate polymerase

___ ___ does not require templates, but it does require the cleaved mRNA at the point of AAUAAA to work well.

insertion sequence

___ ___ is a short DNA sequence that acts as a simple trnasposable element. They are small relative to other transpoabe elements and they only code for proteins implicated in transposition activity.

leucine zipper

___ ___ is an amphipathic alpha helix with a series of hydrophobic amino acid residues concnetrated on one side, with teh hydrophobic surface forming the area of contact between the two polypeptides of a dimer.

linking number, supercoiled

___ ___ is equal to the number of twists + rhythes (if this number is anything other than 0, then the DNA is ___

sigma factor

___ ___ is important for recognition of bacterial promoters, which are sites of DNA binding by RNA polymerase.

cell growth

___ ___ is the largest area of molecule biology.

mismatch repair, older ,newer

___ ___ is when you have a change in the nucleotides that are binding to one another and not like an explcit change in the structure. In this case, it is difficult to determine which strand was originally right. AKA what do I believe, and the thing that helps out here, is the presence of the ___ group because that is on the older strand, and if you are the cell, you assume that the mutation happened in the ___ strand.

linking number

___ ___: another topological characteristic. Ths is a property because it does not vary as long as both DA strands remain intact. In practicality, for two strand of dna, this tells us the number of times that one pieces through the other's surface.

origin recognition complexes

___ ____ ___ binds to and regulates origin firing in eukaryotes. It is a complex of 6 proteins that are conserved in eukaryotes. Its subunit has ATPase activity like DNAA

processive synthesis

___ ____ allows efificent synthesis of the genome. This basiclly refers to the fact that once the polymerase gets on ,it stays on.

inverted repeats

___ ____ are also known as palindromes.

antisense nucleotides (form of translational regulation)

___ ____ can bind to teh mRNA and cause it to maket he site not recognizable for the ribosome (if it messes with teh ribosomal binding site), or its binding can target the RNA for degradation.

antisense oligodeoxynucleotides

___ ____ can hybridize to mRNAs and target it for degradation by RNase H.

modified bases

___ ____ help preserve the structure of the tRNA and protect it from digestion by RNases.

DNA replication

___ ____ tends to be regulated at initiation.

topoisomerases

___ also removes the supercoils generated by replication

H1

Transcriptionally active chromatin tends to be deficient in histone __ , which binds to the linker DNA between nucleosome partciles.

acetylation, deacetylation

___ and ___ of lysine residues on histones tends to change histone affinity for DNA by making them more/less basic. These changes and also activate or inactivate transcription.

helicases, topoisomerases

___ are enzymes that create topological stress in dna tructure by unwinding them. However, _____ solves this strain problem in many ways.

checkpoints

___ are just ways that the cell cycle is regulated. They assume that all essential reactions are carried out corectly before progression form one phase to teh next.

histones

___ are small basic proteins that are modified. Modification at one sit ecan influence modification at another.

plasmids

___ are usually circular in nature, but this is not always true. For exmaple, the lyme disease bacterium has 12 linear ___ and 9 circular ____.

transposons, antibiotic resistance

___ asrise form two insertion sequences elements that flank DNA. The capturned chromosomal gene tends to be a gene for __ ___ or something else that is important.

methylated.

___ bases can silence gene expression when present in a regulatory region of a gene.

ORC

___ binds really strongly to autonomously replicating seqences in the yeast genome. In humans and otehr species, this protein complex regulates initiation but is not bound at psecific DNA. Rather, specific chromatic structure seems to dictate binding sites rather than a particular sequence.

ATP

___ bound to DANA multimerizes to allow origin unwinding.

bacteria

___ can kill people really quickly.

DNase

___ cuts at random, except where the DNA is protected

exonuclease

___ degrade nucleic acids form one end of the molecule. Many operate in only the only in the 5' -> 3' direction.

enhancers

___ do not have a fixed location with respect to the promoter. IFyou deleted a region very far from the initiation site, and got 0 activity and then you ran into this. Additionally, flipping the sequence around also does not do anything. This overall sequence was called an ___ because it enahnces the signal. BOTCHAN NAMED THIS!

lederberg

___ got the nobel prize in 1958 for discovering genetic exchange in bacteria.

helicase

___ has a 6 membered ring structure, and it loads on double strands, but moves on single strands.

crick

___ has the idea that amino acids would bind to an adaptor molecule and correspond to a specific series of nucleotides.

photolyase

___ is a great enzyme because it can literally reverse the entire reaction that causes thymine dimers in the first place!

DNAG

___ is also known as primase, and it is used in RNA primer syntehsis. (prokaryotes)

RNA

___ is rapidly degraded at high pH.

dam

___ methylase methylates DNA at the N6 position of all adenines within 5' GATC sequences. This helps with the differentiation between the template and new strand.

telomeres

___ prevent the ends of chromosomes from being fused to other chromosomes by repair enzymes.

topoisomerases

___ remove supercoils that are generated by replication and transcription

cancer

___ usually develops as the result of the accumulation of many mutations.

heat, OH-, urea

___, ____ or ___ disrupt the hydrogen bonding of the bases in DNA and help disrupt its structure.

LINES-1

___-_ is an example of a transposable element that is found in humans. IT strands for long interspersed nuclear elements.

Cdc-6, cdt-1

___-__ and ___-_ are two important proteins that help regulate the formation of the pre initiation complex in the G1 phase of eukaryotes. However, when they leave, is when you get firing.

non-processive synthesis

___-___ _____ refers to teh fact that the polmyerase will come onto the strand, then dissociate, then reassociate, then dissociate, etc. This generates short elongateion productss (distribution synthesis)

non-conjugative

___-___ plasmids are usually small, andabout 3-10 kb. There are actually loards of these (about 20-200 per cell), and furthermore, it also have various drug resistance genes. Usually these genes have proteins that inactivate antibiotics.

origin recognition complexes

____ ___ ___ regulate cell cycle events and transitions. So the reason that the G1 cell went straight into S was because hte S had the cyclin ad that bound to teh CDk and activated it. However, in the G2 has no use for the cyclin, and thus, nothing happened there.

hyperchromic shift

____ ___ is the idea that denatured dna absorbs more UV light than native dna. (specifically denatured absorbs 37% more light)

Alternative splicing

____ ____ is a way to include different exons as a part of the final mRNA that makes the protein.

primary

a newly synthesized RNA molecule is called a ____ transcript.

3,10

a non-conjugative bacterial plasmid usually have about 3-10 kb and this usually represents about _-_ genes.

left

a positive supercoil is ___ handed.

open reading frame

a reading grame without a temrination codon among 50 or more codons is referred to as an ___ ___ ___, and long sequences of these USUALLY CORRESPOND TO GENES ENCODING PROTEINS.

10.5

a relaxed DNA molecule has ___ base pairs per turn.

origin

a sinlge complex of four to 5 dnaA proteins bind to four 9 bp repeats in the ____ (of replciaton) .

autoradiography

a technique using X-ray film to visualize molecules or fragments of molecules that have been radioactively labeled.

DNA gyrase, type II

a topoisomerase in e coli is ___ ____ and it changes the way that the strands are wound around one another. There are two types. The one in this question is a ___ __

inactivated

after initiation, ORC, Cdc6, cdt1 are all ____ and remain that way throughout the cell cycle, until the M-phase CDK activity decreases in the M phase.

degradation

after splicing, what is the eventual fate of the intron?

GTP, signal sequence, endoplasmic reticulum

after the GTP bound SRP gets to its receptor on the ER, it then delivers the peptide to a peptide translocation complex, and after this the SRP dissociates from the ribosome - accompanied by hydrolysis of ___ in both the SRP and SRP receotptor. The elongation now proceeds as normla but the peptide goes into teh ER until the complete protein has been synthesized. After this the __ ___ is removed by a peptidase and the ribosome dissociates. The important part is the that protein ended up int eh __ ___

open

after the RNA polymerase binds to the promoter site, it can create a transcription bubble and an ____ complex. This complex has a long half life, and it can remain in this position for almost 3 days.

Lk = Tw + Wr (the left side must be an integer, but the right side need not be integers).

determine the linking number as a function of twist and writhe (Lk, Tw, and wr, respectively)

sequences

different sigma factors recognize different ____ of nucleotides at the -35 and -10 regions.

-35, -10

different sigma factors recognize different consensus sequences at __ and ___ upstream of the promoter.

thymine, GC

dimerization often tends to happen when you are exposed to UV light, and specifically, it tends to happen to the nucleotide that is ____. Thus, the organisms that tend to be exposed to a lot of UV light tend to have a lot of ___ content. And now we know the answer to the question! We don't want to make thymine dimers.

alpha

dna polymerase __ in eukaryotes is analogous to primase, but it has no 3'->5' exonuclease activity, which is what makes it less than ideal.

primase

dna polymerase a has the function that is the same as __ (which is DNAg) in prokaryotes.

endoplasmic reticulum

after the SRP has bound to teh signal sequence, the GTP-bound STP directs teh ribosome and incomplete polypeptide to GTP bound STP receptors on the cytosolic face of the ___ ____.

topoisomerase

after you finish replicated, ___ is required to separate the replicated chromosomes.

sticky end cuts (blunt end cuts)

after you react DNA with restriction endonucleases, what you end up with are referred to as ___ ___ ____.

carboxy terminal domain

all three of the capping enzymes and the 5' end of the transcript itself is associated to the ___ __ ___ of RNA polymerase until the cap is finally made.

aminoacyl-tRNAs, aminoacyl-tRNA synthetase

amino acids, in translation, are attached to tRNAs, and they are rferred to as ___-___, and the enzymes that catalized this reaction are known as ___-___ ____.

amino acid, tRNA

amino acyl tRNA synthetases need to not only differentiate for a specific ____ ___, but also for a specific ___ as well.

operon

an ____ includes genes that are linked and cotranscribed from the same promoter. However, the genes are all translated separately because each has its own ribosomal binding site.

sigma

an example of a specificity factor that alters the specificity of RNA polymerase for a given promoter or a set of promoters is known as the ___ factor.

primer

another aspect of polymerase is that it needs an initial ____, which is a strand segment with a free 3' hydroxyl to which nucleotides can be added. This is called the perimer terminus.

physiological conditions (recall how an increase in temperature can cause an increase in the sigma factor related to heat shock genes)

another factor that determines whether a promoter will be good or bad are ___ ___ like high or low temperature or salt.

helix turn helix

another important protein-protein interaction motiff aside from the leucine zipper is the __-___-___ motiff. IF two proteins have this, they can interact

palindromes

certain DNA sequences can adopt unusual structures. In particular, there are things called ____, and if they occur on dfferent strands, then they can form hairpins.

reading frames

changing the reading frame completely changes the amino acid sequence of the protein. So ___ ___ usually do not overlap, but sometimes they do.

strong acid

chargaff ran DNA on a gel and got four spots, but how did he totally break down the DNA? What did he use?

DNA, protein

chromosomes are made of ___ + ____

end, telomeres

ciruclar DNA gets it nice because there is no problem at the ___, but linear DNA, it is not the same thing and that might be why we age. They are called ___

anticodon

codons in mRNA are recognized by tRNA using the ____ loop.

codons

codons recognized by very abundant ___ are more hihgly expressed.

crp-camp

compared to the consensus sequence, the promoter for RNA polymerase is relatively weakly, and thus, it needs further activation. this further activation comes in the form of __-___ complex.

cyclins, cyclin

cyclin dependent kinases are activated by binding of specific ___ at different stages of the cell cycle. However, after each cycle, the ___ is destoyed.

cytidylate

cytidine + phosphate

cytidine

cytosine + sugar = ____

endonucleases

degrade nucleic acid at internal sites andmakes smaller and smaller frafgments

exonucleases

degrade nucleic acids from one end of the molecule.

decrease

denaturation causes a ___ in viscosity of DNA.

covalent, hydrogen, decrease

denaturation of DNA involves the breaking of ___ bonds, not ___ bonds. Additionally, because the two strands are apart form one another now, they actually cause a ____ in viscosity.

hyperchromic shift

denauted DNA absorbs more UV ligth that native DNA. 37% more, and this is the ___ ___.

high

deoxyribose makes DNAmuch more stable at ___ pH. It is alkali labile - even at ph =9.

base (DNA base)

It has been show, however, that a protein can reocognize DNA in more than one way, and thus, there is no simple amino-acid - ___ code.

profitable

It is also not "___" for drug companies to devleop new antibiotics. Most of the need is in poor third world countries, so we only have a handful of antibiotics in the pipeline.

B-galactosidase, lactose permease

It is important to remember that even when the repressor is bound to the operator in the lac operon, there are still times when it can dissociate for a bit. thus, even when the repressor is bound, you still get basal levels of production of _-____ and ___ ____ within the cell (first two parts of the lac operon)

old, new

during replication, the old and new nucleosomes are segregated so that both daughter molecules receive some of the ___ and some of the ___.

H

during synthesis of the first 60-70 nucleotide of RNA, the TFIIE falls off and then TFII_falls off.

eukaryotic initiation factor

eIF4g is the intitiation factor that ___ ___ ____ 4g.

loops

enhancers have their effect on DNA by making ____. This is how enhancers can influence promoters even though their position is so variable.

-10

errors happens 10^-(__). This is ebcause of specificivty of base pairing (10^-5), proofreading, and mistmatch repair (10^-3).

activator

eukaryotic RNA poolymerase has little or no intrinsic activity for the promoter. Instead, almost all initiation is dependent on the action of multiple ____ proteins. This is because the DNA, within the complex structure of chromatin will remain essentially silent, unless otherwise turned on, and thus, that it why it is dependet on activators. Thus, Repressors that bind to DNA to preclude access to RNA would simply be redundant.

3, 5, 5, 3, identical, different

eukaryotic helicase goes from __' to ___'. On the other hand, bacterial helicase goes from __' to __'. On the other hand, bacterial helicase has 6 ___ sudunits, and eukaryotic helcase has 6 ___ subunits,

leading, lagging

eukaryotic helicase moves on the ____ stranding, wheras the prokaryotic helicase moves on the ____ strand.

mRNA

eukaryotic proteins are made at about the same rate as ____.

transposable elements

eukaryotic tranposons are very abundant, and thus, they play a huge role in the diversity. Retroviruses are also specifically ___ ___ that insert their cNA into the chromosome at certain parts of their life cycle. Thus, retroviruses are a frequent source of spontaneous mutation

slower, more

even though eukaryotic machiery is ___ than prokaryotic machinery for DNA replciation, it is a-okay because there are ____ origins of replication to compensate.

cyclin dependent kinase

even though the firing in most of the parts of the eukaryotic genome is mediated by __ ___ ___, it must be kept in mind that each of the origins must fire only once, and that not all origins are activated at the same time, and the firing of late origins must not affect firing of early origins.

cell growth, DNA replication, cell division

for cells to continuously divide, they need to have ___ ___, ___ ___, and ___ ___. The second part is actually regualted by the initiation step of the process.

bacteria

topoisomerase 7 does the untangling of the two DNA strands after the ___ have finished replication. You can design antibiotics against this because this has little or no affect on our DNA, but it sure does affect bacteria!

breakage, rejoining

topological properties are changed only by ____ and ___ of the backbone of one or both DNA strands.

promoter

transcription initiation is regulated by proteins that bind to or near ___ regions.

alternate sigma factors.

transcription is controlled in a number of ways. For one thing, you have ___ ___ ___ that recognize specific promoter sequences.

true

true/false: the CAP protein is the same as the CRP protein?

metastasize

tumors are most dangerous when they ___ in the blood.

does

type II topoisomerase (does/doesn't) use ATP. DNA Gyrase is an exmaple of this.

break

type II topoisomerases make a double stranded ___.

proofread

unlike DNA polymerase, RNA polymerase lacks a 3' -> 5' exonuclease active site, which means that it cannot ______. This is also why the error rate of transcription is greater than it is for replication. This is because a mistake in the RNA of a cell is of less consequence to the ecell than a mistake in the permanent information stored in the DNA.

uridine

uracil + sugar = ____

uridylate

uridine + phosphate

major

usually DNA-protein interactions happen in the ___ groove because it permits discrimination between different base pairs.

2'

usually, the first and second nucleotides adjacent to the end of the mRNA also get methylated, but it is one the __ hydroxyls of the ribose.

exon shuffling

various combinations of exons may have been lost, reshuffled, etc. Changes in the sequence due to changes in exons is ____ _ __

3.4

vertically stacked bases inside the double helix are exactly ___ A apart.

largest

vibrio cholerae is the winner for the ___ number of sigma factors.

B

watson and crick discovered _ form of DNA.

260

we can quantify DNA by its UV color and absorance at ___ nm.

DNAA, unwinding

for ecoli, what happens at initiation is that _____ binds to the intiatior site. When the DNAA binds to the site, it causes the DNA to bend (superhlical tension). The superhelical tension allows local ___ of the AT-rich region.

1

for prokaryotes, if you have one stop codon, then you can stop a protein synthesis and then if you have another one, that'll help you start another protein (this is how operons work), butin eukaryotes, the RNA usually can only code for __ protein.

3, 1

for prokaryotes, there are __ release factors, and they are named accordingly, but in eukaroyes, there is only ___ release factor and it is eRF and it recognizes all three stop codons.

sliding clamp

for the lagging strand in prokaryotes, you often need a new ___ ___ for each new RNA primer that work past, and this is because you have to loop back on it.

universal

for the most part, the genetic code is _____. The only exception includes some protozoa, and mitochondria that tend to have their own tRNAs and display a few difference in the use of the code.

3', third, 5', first

for wobble, the nucleotide on the _' end of the codon (aka the __ nucleotide is flexible), whereas in the anticodon, it is the nucleotide on the _' end (aka the ___ nucleotide is flexible)

ATP

form where does hliecase get its energy to unwind the strands?

two

formation of each aminoacyl-tRNA uses __ high energy phosphate groups.

ATP (it moves its rotor at 6000 RPM)

helicase gets its energy from _____.

DNAB (protein)

helicase is also known as ___

ATP

helicase separates the two strands of DNA and gets the energy to do so from ____. The action of helicase induces stress, which is relieved by ____, and the separated strands themselves are separated by ___-____ ____.

lagging

helicase usually resides on __ strand of the DNA in prokaryotes and the single strain binding proteins tend ot be behind it.

30

higher order compaction is expected among DNA because it wouldn't be expected to fold in the nulceus otherwise. one form of this is the __ nm fiber.

evolutionary diversity.

higher organisms are though to make up a tiny portion of ____ ____.

H1, H2A, H2B, H3, H4

histone __ binds to the linker DNA, wheras histones __, __, __, ___ (2 of eahc) are involved in making the entire nucleosome.

chromatin

histones also have variant forms because certain amino acid side chains are modified by methylaton, ADP-ribosylation, phosphorylation, glycoslyation and acetylation. These changes affect the overally property of the histone, and more importantly, the ____.

basic

histones are really ___ (and thus, they have residues like lysine, or arginine, etc), and this is because DNA is negatively charged, and these residues help it be positively charged.

AT

histones do not bind randomly to DNA. Rather they tend to position themselves at places whether there is a local abundance of ____ base pairs. This might be because the tight wrapping of DNA around nucleosome's histone core requires compression of the minor groove of the helix at this points, and AT make this more likely.

1/256

how frequent is a GATC sequence, in general (give fraction)

4

how many ATP (equivalents; 2 are usually in the form of ATP and other 2 in GTP) are needed to bring one amino acid into a peptide?

2

how many ATP are needed to correct for a mistake in protein synthesis?

3

how many RNA polymerases do eukaryotes have?

1, F positive, F negative

how many copies of the f plasmid can be present in agiven bacterium - regardles of whether it is freee or integrated? FYI; bacteria that posses a copy are called _-_____ bacteria, and things without one are called _-___ bacteria.

4 (space (x, y, z, time)

how many dimensions of separation are there between transcription and translation in eukaryotes?

5 (U1, U2, U4, U5, U6)

how many small nuclear RNAs are there within each snmall neuealr ribonucleoprotein?

45

humans carry around a lot of transposable DNA. In fact, it is the weight that is equivalent to a big mac and fries. This is because ___% of our DNA is transposable DNA.

phosphotransferase transport system

if glucose is present, then it is often brought into the cell via the ___ ___ ___ as glucose 6 phosphate. This involves a long phosphate transfer pathway. However, if glucose is not presnet, then the phosphate is transferred to adenylate cyclase, which activates it and that creates CAMP from ATP. This increases the amount of cAMP in the cell. This is where the association between glucose and cAMP comes from. When glucose is high in the cell cAMP is low because adenylate cyclase is off, but when glucose is low, cAMP is high because adenylate cyclase is on!

cells.

if we inhibit topoisomerase (ciprofloxacin) in different organisms, we get destruction of ___.

committed

if you pick any cell, the moment that you are past teh regulation step, you are ___. You can't stop. You will finsih!

negatively

if you removed the histone core, then the DNA would be ____ supercoiled.

arrested, apoptosis

if your chromosomes ever get too short, the cells will be ___ in growth and ___ will be induced.

bubonic plague

in 1348, the ___ ___ killed about 1/4 people in europe, and the organism that caused this was called yersinia pestis, which is often carried by flees, rodents and other vectors.

10, 3.6, 2.4

in B DNA, one turn of the helix is ___ base pairs, and it is ___ nm in length and ___ nm wide.

newer

in DNA, the thing that is not methylated is the one that is ____.

reading frame

in E. coli, DNA polymerase IIIt thao and gamma subunits are simply created from the same gene, but the ____ ___ frame that is used is simply different.

cut, paste

in ___ and ____ transposition, what you get is the transposon literally moving from one site to another. In this case, transposase will bind to the transposons inverted repeats. This will form a circle, which will lead to a cut in the DNA, and then, the DNA will be interted into another place.

helical turns

in a closed circular DNA molecule, the number of helical turns cannot be changed without transiently breaking one of the DNA strands. Thus, the number of ___ ___ in a dna molecule provides a precise definition of supercoiling.

aminoacyl, peptidyl, exit (APE)

in a full prokaryote ribosome, or any ribosome, there are three sites, the ____ site, the ___ site, and the ___ site. Both the 30S and the 50S subunits contribute to the characteristics of the A and P sites, but the E site is largest confined to teh 50S subunit.

146, 54

in a histone, ___ bp go around the histone core of the nucleosome and __ bp serve as linker DNA.

splicing

in a process called ____ within eukaryotes, the introns are removed fro mthe primary primary transcript of the RNA and exons are joined to form a continuous sequence.

helicase

in bacteria, DNAA is responsible for binding to the 9 base pair regions, and rotating. This rotaraction pulls apart the 13 bp repeats, and allos DNAB, which is known as ____ to do its thing.

transcription, translation, 5, 3, mRNA

in bacteria, _____ and ____ are closely cloupled. mRNAs are synthesized and translated in the same _'=_' direction. The situation is different in eukaroyets, where the ___ must leave teh nucleus before it can be translated.

F plasmid

in bacterial conjugation, the thing that is literally transferred from one cell to another is one single ___ ______. And the way it gets form one cell to the other is through a pore complex that is also plasmid encoded.

adenine, thymine

in both bacteria and eukaryotes specific proteins bind to origins and regulate their firing. However, in prokaryotes, the sites that are usually going to be origins are usually the ones that are rich in __-___ nucleotides.

topoisomerase IA, topoisomerase III

in circular chromosomes, topoisomerases are requires to separate the replicated chromosomes. they are first treated with ____ ___, and then with ___ ____, and this results in two independent plasmids.

plasmid encoded

in conjugation, you actually get teh transfer of a single strand of DNA from the male cell to the female, adn the replication machinery fills inthe rest. However, usually, the transfer of DNA occurs through a pore complex, and the way the pore complex is __-_____ (aka this is what encodes for it)

release factors, 1, 2, 3

in prokaryotes, there are three ___ ___ (aka termination factors) that bind when you come to a stop codon. RF_ and RF_ bind to or near the A site, but the RF_ binds elsewhere

simultaneously

in prokaryotes, transcription and translation occur ____

origin of replication

in some eukaryotes, it seems that there is no specific sequence that determines the ___ _____ ___. RAther, the site of initiation is usually determined by

IF-2,

in step II of the initiation process, you get a GTP bound __-_, complexed with teh tRNA carrying formylemthionine (prokaryotes)

II

in type ___ topoisomerase, what you get is a strand package mechanism. In this case, you literally cut the DNA stands in 2 places and squeeze one over the other.

GTP

in what form is the energy that is needed for protein synthesis coming form >

bends

initially, after the TAT binding protein binds to teh TAT box, it ___ the DNA.

transposase

insertion sequence elements encode an enzyme that is called ____.

helicase, sliding clamp

intitially you have bidning of DNaA to teh intiatior site, and that opens up the AT region and allows DNAb to bind. This is laso known as ____. However, the loading of DNAb also means you need to load the ___ ___, and interaction between this substance and DNAa causes DNAa to dissociate from the origin, and now, helicase takes over.

hairpin

inverted repeats allow for the formation of a ____ structure. Usually, this is after the two strands that have the inverted repeats ahve been denatured. Thereafter, they fold back on themselves.

No (either strand of the DNA can serve as a template)

is there always a distinact template and coding strand? AKA is the watson (5' -> 3') or crick (3'-> 5') always the template strand?

mismatch repair

lynch syndrome is basically also known as hereditary nonpolyposis colorectal cacner and it is usually from a defect in ___ ___

histone acetyltransferases

lysine residues on histones tend to be acetylated or deacetylated by ____ _____

30

mRNA is threaded through the center of the ribsosome on the surface of the __S subunit. (for prokaryotes)

rare

mRNA molecules containing ___ codons are expressed poorly.

processing

mRNA, tRNA, and rRNAs all undergo ____, in which the DNA is post-transcriptionally modified.

cloning

molecular ___ is a set of experimental methods in molecular biology that are used to assemble recombinant DNA molecule and to direct their replication within host organisms.

G1,

most of the cell growth happens in the ___ phase

aminoacyl-tRNA synthetase

most of the proofreading in the charging of the tRNA takes place with the _____-___ ____, where oth the correct amino acid and the correct TRNA need o join.

origin

most of the regulation for DNA occurs when the ___ of replication is first opening up. Then from there, you can load on the helicase, which will open up the DNA and allow replication to proceed.

pre-proteins

most proteins are made as __-____ and require some sort of post-translational modiciations.

chapterones

most proteins require folding corrections by _____. Others may require other covalent modifications.

telomerase

mutations cause cancer. In this case, one of the first things that is needed for cancer is induction of ___, which is usually on in development, but not during other times.

oncogenes

mutations that can happen in ____ can be really bad because they are usually very involved in the regulation of the cell cycle.

decrease

mutations that result in a shift away from the consensus sequence in prokaryotes generally leads to a ___ in promoter function

codon usage, ribosome binding site, availability of the AUG codon

name 3 mechanisms of translational regulation

150, 15, 50 nm

native DNA is usually double stranded and stiff. It has a persistence length of ___ nucleotides, which is __ turns, and is ___ long.

right handed

negative supercoils tend to be represented by ___ ___ super helices

300, 900 (since each amino acid is coded for by 3 nucleotides)

on average, the rate of protein synthesis is ___ aa/20 seconds, and this amounts to ___ nucleotides/20 seconds.

5' cap, first and second

on top of methylating the __-_____ that is added to the 5' end to create a 5' cap, there is also methylation of the ___ and ___ nucleotides to the cap. The methyl groups are form _-______.

termination factors, 30, 50

once a termination codon occupies teh ribosomal A site, three __ ___ or release factors (RF-1, RF-2, RF-3_contribute to teh hydrolysis of teh terminal peptidyl tRNA bond and release of teh free polypeptide and the release of the free tRNA from the P site. The release factor also leads to dissociation of the 70S ribosome into its ___S and ___S suubunits.

DNA polymerase I

once an okazaki fragment has been completed, its RNA primer is removed and replaced with DNA via ___ ___ ___, and the remaining nick is sealed by DNA ___.

sigma factor

once the first 8-9 nulceotides are synthesized, you get release of the ___ ___.

RNase

one advantage of RNA hairpins is the fact that they can actually stabilize RNA and block clevage by _____.

enol

one important thing to remember is that all the nucleotides you see that have ketones in them can equally also be in the ___ form.

energy sources, coenzymes, regulation

one main function of nucleotides aside from DNA is that they are often great ___ ___ and also, adenine nucleotides are components of many enzyme ___ (NADPH). And lastly, some nucleotide moieties are also really relevant in terms of ____ (thin cAMP_

codon usage

one of the mechanisms of translational regulation is by ___ ___, where codons recognized by very abundant tRNAs are more highly expressed. Conversely, mRNA molecules containing rare codons are expressed poorly.

Mg2+

one of the metal cofactors for RNA polymerase is ____

incompatibility of replication

one of the reasons that bacteria in nature don't have every possible plasmid is because they have ___ ___ ____. This basically means that there are 26 classes of plasmids, and only plasmids from different groups are maintained at particular levels.

infidelity (screw up)

one of the ways that you can get somatic mutation in the dna that can lead to cancer is _____ in DNA replication In this case, something goes wrong with the DNA replication, and you automatically get screwed, but this needs to happen a lot over time to be significant.

ribonucleotide triphosphates

one thing that is different among replication and transcription is that instead of incorporating deoxyribonucleotide triphosphates, you are incorporating ______ ____ , which has a ribose as the sugar

10

one turn of DNA has how many nucleotides

10.5, 3.6, 2.4, right

one turn of the B form of DNA is __ bases, and ___ nm in legnth, and ___ nm in width. It is ___ handed.

10, 3.4, 34

one turn of the helix has ___ nucleotides and because there are ___ between base pairs per turn, you get a repeat turn distance of ___.

regulatory proteins

other factors that influence whether a promoter will be bad or good include ___ __ (aka transcription factors - which can be repressors, activators, or specificity factors, like sigma factor)

inverted repeats, hairpin

palindromes that are on opposite strands are referred to as ___ __ and they can form ___ stucturs.

genetic recombination

palindromic sequences are also good because they induce regions of instability in the DNA, and that ends up leads to ___ ____ (aka palindromes tend to be the regions where there is crossing over).

protein, nucleic acid

partially unwound dna is not stable unless the DNA is bound to to a ____ or _____ ____.

proofreading

people do not know what we have RNA primers, but one hypothesis is that when we replace them with DNA, it provides another ___ mechanism, and that helps keep the error rate low.

xeroderma pigmentosum

people who have a mutation in the excision repair could get a disease called ___ ____, in which the skin is EXTREMELY sensitive to sunlight (up to 1000x more than normal), and skin cancer usually develops on the arms and neck, and most pateients die from cancer before the age of 30 :(.

removing

photolyases are often involved in direct repair, which means that they repair the DNA without ____ a base or nucleotide.

delta, epsilon, III

polymerase _ and __ are involved in replication. On the other hand, dona polymerase ___ in e coli is involved in the same thing,

epsilon, delta

polymerase ____ works on the leading strand and polymerase ___ works on the lagging strand. The two polymerases tend to be involved with eukaryotes.

catalysis

polymerase resemables a right ahnd and ___ occurs in the palm domain and two metal ions bind to the 3' end.

left handed

positive supercoils tend to be represented by ___ ____ super helices (left handed or right handed?)

spliced

precurosor mRNAs are ___ to remove sequences not meant to be translated.

bases, hydrophobic, resonance

properties of nucleotides includes the fact that they are ___ in solution, that they are __ _molecules and that they are planar and show ____.

autoradiogram.

radioactivity in a sample can exposre photographic film, and the film can then be developed with developer and fixer. The exposed filed is called an ____

15

rate of protein syntehsis is __ amino acids/ second.

overlap

reading frames usually do not ___, but sometimes they do. This is usually not good because changing the reading frame will completely change the amino acid sequence. The HIV virus engages in this sort of reading, so it really makes it error-prone, which is exactly what it wants.

histones

regulation of transcription can also occur by methylating, acetylating, changing charge or shape of ___, which are not the direct genetic carriers, but definitely do play a role in how readily the genetic material can be accessed.

DNA sequences

regulatory proteins like transcription factors usually bind to specific ___ ___. Their binding to these sequences is usually 10^4 to 10^6 times greater than any other sequence.

origin, bi-directionally

replication begins at an ____ and usually proceeds __-_____.

5, 3, primer, origin, two, opposite

replication goes in the _' to __' direction only, and it requires a ___ and it begins at the ___, and ___ forks per oriins that move in __ directions.

single strand binding protein

replication protein A is analogous to ___ ___ ___ ___ in prokaryotes. It paves the way open for DNA polymerase.

plasmids

small autonomously replicating DNA units present in bacteria (and yeast) in addition to their genetic DNA.

same

some phages, in the lysogenic phase, produce an enzyme that modifies the bacteria host surface. The purpose of this is to prevent other phages from infecting the ___ host.

glycosylated

some proteins are ___ or modified in other ways to target them to subcellular locations.

proteolysis

some proteins undergo significant ___ to activate them at teh time and place needed.

processing

sometimes one mRNA can be ___ differently in eukaryotes to get two different proteins.

copy, paste

sometimes the reason that some organisms are bigger in terms of DNA is because the work by the ___ and ____ mechanism of moving transposons

zinc fingers.

sp1 is a general transcription factor that binds to a GC box, and it does so by using ___ ____. Additionally, since it is a transcription factor, it also make a stable complex with the polymerase.

reverse transcriptase

telmoerase has a ___ ___ subunit and an RNA comlementary to teh telomeric DNA>

DNA

telmoeres prevent loss of informational ___ from chromosome ends during replication.

reverse transcriptase (it carries its own RNA with it and basically uses that to make the repetitive elements at the ends of the linear chromosome)

telomerase is a ___ ___ enzyme because it copies RNA and makes DNA.

70

the 50S and 30S come together to make a __S ribsoomes and now it is totally functional because it has the mRNA, the fMettRNA and it is offitically ready to go!

primer

the 60-100 bases that are lost from the chormosome ends every time that DNA is replcated. Of the 60-100 relationships, you get30-70, you anticipate to finish with the last primer, and 30 for the ___ itself.

28, 3.4

the A form of DNA is __A per turn, whereas B is __nm.

eukaryotes

the AUG is nearest to the 5' end in ___ is what counts as the start codon.

right

the DNA is arranged in a ___ handed helix.

sigmoidal, right,

the DNA melting curve is ___ in shape, and the GC is shifted more to the __.

3, 5, 5, 3

the DNA polymerase III in ecoli has _' to __' exonuclcease activity, wherease DNA polymerase (has _ to __' activity.

ten billion

the DNA polymerase makes one miskake for every __ ___ base pair per division. This is partly attributed to three main reasons. The first reason is that DNA polymerase relies on the specificity of base pairing to select incoming base. The second reason is that, even if the inccorect base is added, it can be removed by 3' -> 5' exonuclease activity, which adds on another 10^2. Lastly, DNA repair can provide an additional 10^ 3. So (10^5 x 10^2 x 10^3 - 10^

replisome

the E coli ____ refers tot eh entire complex that helps pull through with replication. It is a group of 20 or more different enzymes adn proteins each performing a different task.

A

the EF-Ts, GTP complex is needed to bind to the aminoacyl tRNA and that allows it to bind to the _ site of the ribosome in eukaryotes.

constant, different

the GC contant is ___ WITHIN organisms, but ___ BETWEEN organisms.

hairpin (importance of inverted repeats)

the RNA that is transcribed from DNA is also important because it can form ____ that regulate many functions.

II

the U1, U2, U4, and U5 snRNA are made from RNA polymerase __.

tm

the _ is the temperature at which DNA is half unwound.

n-terminal, n-formyl

the _-____ ends of proteins are also alwys modified. In fact, prokaryotic proteins always have the _-____ group removed from the N-terminal methionine.

signal recognition particle, EF-G

the __ ___ __ binds to teh signal sequence and blocks __-__ from its binding site. This prevents translocation and this is why the protein no longer gets longer when the singla recognition partcile binds.

excision repair system

the __ ___ ___ can also repair thymine dimers. In this case, the first step is that the change is first reocgnized and the DNA is opened up.

tata binding protein, coding

the __ ___ ___ is a part of teh transcription factor IID comlpex, and it is something that binds to the TATA box, which is located on the ____ strand.

signal recognition particle

the __ ___ ___ is something that binds ot teh signal sequence as it emerges form the ribosome. The ___ ___ ___ then binds to GTP and halts eloncation of teh polypeptide when it is about 70 amino acid long and the signal sequence has completely emerged from the ribosome.

signal sequence, signal peptidase

the __ ___ is usually removed after passage through teh membrane by an enzyme called a ___ ___

a, b, right, z,

the __ and ___ form are ___ handed, and the __ form is not.

G2,

the __ phase prepares the cell for mitosis.

U1, U5,

the __ snRNA is complementary to the 5' consensus sequence, and the __ snRNA is complementary tot he 3' splicejunction. This is relative to all the introns that are related to the splicesomal mechanism.

5 cap

the __' ___ helps protect mRNA form ribonucleuases and it binds to a specific cap-binding complex of proteins and participatesin initiating translation

3, 5

the __' and __' ends of RNA are the ones that are most vulnerable to RNAse activity.

R-factor

the __-_____ plasmids are plasmids that encode proteins that inactivate antibiotics by either degrading the antibiotic (the B-lactamase and penicillin), modifying the antibiotic (basically changing its structure so that it is no longer active), or just expressing a pump that pumps the antibitoitic out of the cell before it can act (pump efflux)

carboxy terminal domain

the ___ ___ ___ in RNA polymerase II has a repeating section of amino acids and they have loads of repeating subunits within various ortanisms. The sequence is YSPTSPS and S2 and S5 tend to be phosphorylated.

TATA binding protein, 100

the ___ ___ ___ is part of transcription factors IID's domain and it binds to both DNA and other transcription factors. When it does bind to the DNA, it bends the DNA about ___ degrees.

signal recognition particle

the ___ ___ ____ blocks EF-G from its spot, and this stops translocation.

sliding clamp

the ___ ___ allows the DNA polymerase to stay on and if it were not there, then DNA polymerase would stay on for a little bit and then fall off.

signal sequence.

the ___ ___ directs a protein to its appropriate location in the cell and for many proteins, it is removed during transport or after the protein has reached its final destination.

consensus sequence

the ___ ___ is the most frequent sequence from many genes. For sigma 70, this involves an optimal sequence from the -35 region and the -10 region. However, for other sigma factors, the sequences can be found in different places and different nucleotides.

lysogenic phage, toxic shock syndrome

staphylococcus aureus harbors a ____ ____ which produces a toxin that is responsible for __ ___ ___, and the toxin is induced by low Mg2+ that is associated with the use of highly adorbent tampons.

nonsense, UAA, UAG, UGA

stop codons are also referred to as ____ codons, and they include three main codons, which are __, ___, and ____.

topoisomerases

strand separation creates topological stress in the helical DNA structure, and this is relieved by ____, and the separated strands are stabilized by DNA binding proteins.

compact

supercoiled DNA molecules are more ____ than relaxed dna molecules, and thus, they tend to migrate more rapidly during gel electrophoresis.

true

t/f: The initiator binding site is right next to the AT rich DNA elements. The initiator binds to it, and this causes the AT-rich region to open up.

true

t/f: The spliceosome works as the mRNA is being transcribed. Both things are happening concurrently. Thus as it is being tracribed, things are being cut out of the transcript.

true

t/f: in John Cairn's experiment, he made E. coli dna radioactive by growing cellsin a medium containing thymididine labeled tritium. When the DNA was carefully isolated, spread and overlaid with photographic emulsion for several weeks, the radioactive thymidine residues generated tracks of silver grains in the emulsion, producing an image of the dna molecule.

true

t/f: three types of regulatory proteins regulate transcription initiation: specificity facotrs alter the specificity with which RNA polymerase binds to a given protmoer, repressors impede access or RNA polymerase to the promoter and activators increase access.

true

t/f: when we did not have the great tools that we have today, we used simple systems, and that was what DAvid Zusman talked about.

true

t/fL when an amino aid is sepcified by several different codons, the codons that differ in either of the first two bases require different tRNAs

75

tRNA in prokaryotes are betwen 73-93 nucletoides long. In botchan's lecture, however ,he said, they were about ___ nucleotides long.

ds, hairpins

tRNA is about 50% __ (ds/ss), which means that it forms ____

hyperchromic shift

the ___ effect is basically the fact that close interaction between stacked bases decreases the absorbtion of UV light of DNA. Thus, as denaturation of a ds nucleic acid progresses, you get an increase in absorance.

5', 5'

the ___ end has no nulceotide at the ___ position. The same thing follows at the 3 end.

z

the ___ form of DNA tends to be a radical departure from watson and crick's b form. The most prominent characteristic of this form is that it is in the left handed form.

wobble

the ___ hypothesis is that teh first two bases of an mRNA codon always form strong WAtson-CRick base pairs with the corresponding bases of teh rNA anticodon and confer most of the coding specificity.

ribosome

the ___ is the machine used for translating the coded information. It contains boththe structure for holding components together as well as many of the enzymatic activities.

nuclear

the ___ membrane separares the transcription from translation .

U2, 2

the ___ snRNA binds to teh RNA and this activates the __' hydroxyl on the adenine.

zinc finger (usually eukaryotes)

the ___-____ motiff is commonly found in transcription factors.

shine-delgarno

the ___-____ sequence is what is used to get the ribosome positioned. This sequence is located about 10 bases upstream of the start codon.

helix turn helix

the ____ ___ ____ motiff is when you have 20 amino acids in two short alpha helical segments, each 7-9 amino acids residues ong separated by a beta turn. This structure is usually not stable by itself; it is simply the reactive portion of a somewhat alrger DNA binding domain.

coding

the ____ strand is identical in base sequence to RNA transcribed from the gene except that U replaces T

leading

the ____ strand of DNA is elongated by telomeras.

lactose

the _____ operon includes the gene for B-galactosidase, galactoside permease, and thiogalactoside transacetylase. The last enzyme is involved in removing toxic galactosides from the cell.

promoter

the _____ site in bacteria extends from -70 to +30. These numbers are basically 70 bp before the transcription start site to about 30 bp after it.

tautomeric

the active site of DNA polymerase can actually reject base pairs that do not lead to a shape that is common, such as AT, and CG. However, mistakes can still occur because a base can be in its ____ form, allowing it to hydrogen bond with an incorrect partner.

base interactions,

the addition of nucleotides by DNA polymerase has a delta G that is equal to approximately 0. This is ebcause the phosphodiester bond is formed at the expense of a somehwat less stable phosphate anhydride. However, noncalvent ___ ___ seem to provide additional stabilization.

UAG

the amber stop codon is ___ __ __.

3

the amino acid is attached to the __' end of the tRNA.

3'

the amino acid is eventually going to end up attached to the __' hydroxyl of the last nucleotide in the tRNA's (on h

2, 3

the amino acid is usually added on to teh _' or _' hydroxyl of the last base on the tRNA. The two are in equilibrium and it doesn't really matter. Specifically,

lysine, arginine

the amino acids ____ and ____ are really prevalent in histones because they help counteract the negatively charged DNA molecule - which is due to the phosphodiester backbone.

2, IF-2

the are _ tRNAs for methionine in prokaryotes. And the cell knowns to take the fmet one when it is bound the factor ___-_, which is only present during initiation.

reduced

the autoradiography in john carn's experiment worked by basically _____ Ag+. This then made the silven darker, so you can see exactly where the dna was.

processivity

the average number of nucleotides added before the polymerase dissociates is referred to as its _____________

processivity

the average number of nucleotides that are added before the DNA polymerase dissociated from the template is defined as its ____.

regulatory proteins

the basal rate of transcription initiation at nonhousekeeping kenes is also determiend by the promoter sequence, but expression of these genes is further modulated by ___ ___. These things often work by enhancing or inhibiting the interaction between RNA polymerase and the DNA promoter region.

hydrogen bonded, hydrophobic effect

the base pairs are __ ___ to one another and on the top and bottom, they stabilized by the ___ ___ (which includes van der waals contacts).

eight

the bead of each nucleosoem contains ___ histone molecules.

ATP

the binding of ___ causes helicase to move and change configuration.

operators

the binding sites that repressors bind to in DNA are often referred to as ____

transcription, 17

the bubble that is made to start transcription is known as the ____ bubble and it is abut ____ base pairs long.

U2

the buldged adenosine is a direct conseqeunce of the __ snRNA binding to the site, adn this frees up the adenine to be a nucleophile.

50, 30

the catalysis within the __S subunit fo rthe prokaryotes, and the decoding and proofreading happens in the __S.

new

the cell assumes the that __ DNA is likely to have the error.

sigma factors

the cell can use different ___ ___ to determine where binding occurs within the DNA. This also determines what genes are expressed and which ones are not.

open, DNA polymerase

the clamp loader binds to the clamp in the ___ state. It tehn allows the clamp to bind to the DNA. This then leads to teh loading of DNA polymerase to teh 3'OH. Once the clamp binds to teh DNA, the 3' end of the primer enters the clamp loader. After this, ATP is hydrolyzed and the clamp loader is released. From this, the clamp recruits the ___ _____.

ATP

the clamp loader is active and it opens up the sliding clamp and puts it on the dna when it is bound to ___, but when it is not, ti basically goes away and the sliding clamp stays on.

supercoiling

the coiling of a coil

aminoacyl tRNA, elongation factors, GTP

the process of elongation requires teh inittiation complex, ___ ___, __ ___ (which facilitates the entire process), and __ _(energy source)

1

the process of termination actually uses up __ GTP molecule. This is because the release factor usually binds with a GTP and that gets hyydrolyzed to also release the polypeptide.

2, 50, 30, 70

the prokaryotic ribosome has __ subunits and they include the __S and the ___S, which come together to form the __S .

70

the promoter in the LAC operon is srecognized by the sigma ___ factor. However, the sequence is not perfectly lined up, and thus, it often requires activation by CRP-cAMP.

3, 5

the proofreading activity refers to a _' to _' exocnuclease activity.

ribosome

the protein folding is literally occurring s the protein is coming out of the ____.

n, c

the protein is usually synthesized from the _-terminus to the _-terminus

mediator

the proteins that bind to enahcncer sequences in eukaryotes often need a ___ protein to mediate ineratcts between it and the RNA polymase/pre-intiation complex.

DnaA

the rate limiting step is usually when Dnaa-ATP is ydrolyze to DnaA-ADP, and this essentially causes ____ to dissociate from the origin.

prokaryotes, eukaryotes

the rate of DNA polymerase is much faster in ___ rather than ___ because the machinery is not as good int he latter.

1000, 50, origins of replication

the rate of DNA synthesis in prokaryotes is ___ nucleotides per second, but for eukaryotes, it is ___ nucleotides per second. It is 1/20th of that observed in e. coli. This is okay because there are multiple ___ ____ ____.

15, 300

the rate of portein syntehsis is about __ amino acids per second, which is an average of __ amino acids per 20 seconds. This is relatively slow and implies that it takes a lot of time to make proteins.

260

the reason why single strand absorbs better at ___ nm for DNA is becuase base stacking interferes with UC absorbtion, and thus, loss of the secondary structure removes this hindrance and thus, you get an increase in absorbace.

first

the reason why the third base is least specific is because it pairs only loosely with its coresponding base in the anticodn, which binds to the codon via its ___ base pair.

F

this transcription factors (TFII__ helps RNA polymerase find its promoter). It is recruited after you have TFIID, and TFIIB already present on the promoter.

thymidylate

thymidine + phosphate

thymidine

thymine + sugar = ____

AT rich

to facilitate unwinding, the DNAA needs to be bound to ___. The circular nature of DNAA allows it to cause tension, and this is what allows the unwinding to occursin the ___ ___ regions.

exonuclease

DNA polymerase I has ____ activity (in e colit)

1, 10

DNA polymerase I in E coli has _ protein subunit, whereas III has __.

U1, U2, U5

** ___ snRNA is complementary to the 5' consensus sequence, ___ snRNA complementary to the branch site, and ___ snRNA is complementary to the 3' splice junction

15, 45

**Eukaryotic proteins are made at about the same rate as mRNA and that is becuase they add __ amin acids/ second aka __bp/second.

epsilon, delta

**Polymerase ____ in eukaryotes in on the leading strand, and polymerase ____ is on the laggin strand.

P-TEFb (phosphorylating transcription elongation factor B- NOT TFIIH like in textbook)

**The factor responsible for phosphorylating the carboxy terminal domain is _-____

R-factor

**_-____ plasmids are those that have enzymes that encode proteins that can inactivate antibiotics.

translation

**___ is targetted by antibiotics than any other process in the cell.

leading, 3, 5, lagging, 5, 3

**eukaryotic helicase is on the ___ strand and goes _' - _'. prokaryotic helicase is on the ____ strand and goes _'-_'

mismatch repair, nucleotide excision repair

**lynch syndrome is because of a mutation in the ___ ___ system, whereas xeroderma pigmentosa is a mistake in the ___ ___ ___ system.

N-formyl, N-terminal

**most proteins are made as pre-proteins. After they are made,ALL prokaryotic proteins have the _-__ group removed from the N-terminal methionine, and about half proteins ahve the _-____ methionine removed all together.

cyclin,

**the diffusable factor was ___, not CDK.

long polymers, nucleotide bases, 5 carbon sugar residues and phosphodiester backbone

4 similarities between DNA and RNA.

codon

A ___ is a tripler of nucleotides that codes for a specific amino acid. The processof translation happens in such a way that these codons are read in a sucessive nonoverlapping fashion

conjugative

A ______ plamid is large and about 50-100 kb (all of which code for about 100 genes). There are usually only 1-2 of these per cell, and they usually contain captured chromcomsome genes, and they encode for conjugation functions.

polyadenylation signal sequence, cleavage and polyadenylation specific fact

AAUAAA is known as the ___ ___ ___ and it is reocgnized by ___ and ____ ____ ___.

positive

ANother reason why it is advantageous to have ___ regulation (aka why are so many transcription factors needed) within humans is because it reduces the chances for random DNA sequence, which could be present in high numbers, to be inappropriately turned on. Just think about it: if you need several proteins binding for an active complex to form, this vastly reduces the probability that a random occurrence will be transcribed.

DnaA

ATP binding and hydrolysis regulates ___ binding

true

Also within chromatin are various nonhistone proteins, some of which help maintain chromsome structure and others that help resulate expression of specific genes.

2

Althgouh only one codon exists for mthionine, there are __ tRNAs for it. One is exclusively for methionine at the start site, but teh other is for methionine within the protein chain.

adenosine

An ____ is part of the branch site that is located at about 40 nucleotides from the 3' splice sites. And the mechanism is involved in how the intron is taken out of the DNA. The nucleotide is actually within the intron, and ti cuts out the 5' end, and the 3' is then cut by the newly formed OH.

DNA

Ancient DNA is badly damaged and fragmented, and it is very difficult to sequence. This supports the notion that ___ tends to pick up bad mutations over time as it is exposed to natural environmental conditions.

mRNA processing

Another advantage of hairpins is the fact that really long hairpins can actually trigger ___ ___ (microRNAs actually arise from clevage of long hairpins).

primers

Another difference between replication and transcription is that RNA polymerases do not require ____, which is yet another hint that there was an RNA world before a DNA world.

pump, pump out (pump efflux)

Another method of drug resistance that bacteria can have it through actually synthesizing a ____, which can then be sued to __ ___ the antibiotic bbefore it can act in the cell.

growth rates

Another reason that bacteria in nature don't hae every possible plasmid is because of ___ ____, which are slowed by the burden and maintenance that it requires to have such a large number of products. So one of the reasons a cell does not contain all of the plasmids is because it would really slow down its growth!

widespread

Another reason that transposable elements work is because they are simply just _____ (aka we have loads of them in different places)

processive

Another similarity among RNA and DNA polymerase is that both of the enzymes are highly ____, which means that they can stay on their templates for long periods of times.

bacteriophage

Another thing that can act as a vector for the transfer and redistribution of cloned/captured bacterial genes is a _____ (think transduction!)

enzymatic modification

Another way that you can have somatic mutations is through ___ ____ in DNA. This is related to the epigenetics sector of molecular DNA.

SOS

Another way to repair damaged DNA is by cutting out the damaged DNA and replacing it by guessing, which is commonly referred to as ____ repair.

excise, new (and better)

Another way to replace DNA is to ___ the damaged DNA and to replace it with a ___ template. (some what like a cut and paste)

major groove

CRP can't bind into the ___ ____ of DNA unless camp is bound to it because when cAMP is bound, you get a change in conformation such that binding is more easy.

2

Base pairing between the U2 snRNA and mRNA brnach site activates the _' OH of the free adenine

male, female, male

BEfore DNA conjugation, you have one ___ cell and another ___ cell. After DNA conjugation, you have 2 ___ cells.

origin of replication

Bacteria and eukaryotic replication initiates at ___ ___ ___, and the process of replication proceeds bidirectionally.

clustered regularly interspaced short palindromic repeats

Bacteria can establish immunity to a previous phage or plasmid invasion using CRISPR, which stands for:

infection

Bacteria conjugation can either be seen as a bit of romance or infection. Which one did Zusman is more indicative of the relatonship.

anthrax, 2, plasmid copy number

Bcillus anthracis causes the disease _____, and this bacterium is literally harmless unless it contains ____ different plasmids. The laethality of the bacterium depends on the __ ___ ___, which has to do with the balance between positive and negative regulation. A high number indicates a more relaxed regulation, having 01-100s per cell, wherease low is stringent 1-2/cell.

RNA polymerases (And they have them)

Because chloroplasts and mitochondria have their own genomes, they also need their own ___ ____ for making their own mRNA transcripts.

cAMP, cAMP

CRP binds most avidly to the DNA in the lac operon when ___ is present. In the presence of glucose the production of ____ is inhibited, and that is why CRP does not readily bind.

3, 2

CG have ___ hydrogen bonds, whereas AT have __.

11.1, 10.8

CG is __A, and AT is __A APART from one another. form literally one side to the other.

cleavage and polyadenylation specific factor

CPSF stands for __ __ ___ ___ __. This is what recognizes the polyadenylation sequence after the endonuclease cuts at that region. It basically, from then onwards, serves as a place for poly A permerase to bind and start making the poly A tail.

true

Childhood experiences, abuse, or drug addiction may result in changed methylation of histone proteins or of DNA. These changes can be maintain over many cell divisions or even inherited.

cancer, xeroderma pigmentosum

Clearly, excision repair is important in preventing mutation and ___. If you look at a graph, people who do not have excision repair often get ___ ___, and once someone gets that, they are MUCH more likely to get non-melanoma skin cancer.

botulin toxin

Clostridium botulinum harbors a ___ ___ that makes botulin toxin.

lyssogenic phage

Corynbacterium diptheria harbors a ____ ___which produces diphtheria toxin,. When the bacteria are cured of the phage, no toxin is produced.

secondary structures

Coupling of transcription and translation allows RNA ___ ___ to control transcription by termination of a leader transcript.

1, monomeric

DNA polymerase I has _ subunit and thus, it is referred to as a ____ protein

3', 5' exonuclease

DNA polymerase I has __-___ ___ activity. Note that all polymerases have 3' -> 5' exonuclease activity, but this is NOT the same thing.

FADH2

DNA photolyase tends to have two different cofactors. One is folate, and the other is ____, and that is something that just helps the enzyme absorb light ot carry out its function.

repair systems

DNA ___ ___ attempt to fix damaged DNA, but before we adress that, we need to relaize that oxidative damage, exposure to radiation (UV, cosmic, radioacitivty), and spontaneous depurination are the three main things that affect our DNA. Living cells can usually repain damaged DNA, but dead cells cannot.

primase

DNA ___ synthesizes a primer that is anywhere in between 10-13 nuceltoides long.

footprinting

DNA _________ is a technique that is derieved from priciples used in DNA sequences, and it identifies the DNA sequences bound by a particular protein.

ribose, deoxyribose, ribose

DNA contains deoxyribose instead of ribose because ___ makes sugar phosphate backbones reaction and because the 2' adn 3' positions can both be involved in phosphodiester bones. The __ is much more stabble. ____ more reactive in base because it can cyclize.

promoter, template

DNA plays two roles in transcription. The first is that it acts as the ____, which is the site where RNA polymase brind, and it also acts as the ___, which species the nucleotides that need to be incorporated.

primase

DNA polymerase A has enzymatic activity in eukaryotes, and it is analogous to ___ in bacteria.

double strands, single strands

DNA helicase bind to ___ ___, but it moves on ___ ___, and it has a 6 membered ring structure.

relaxed, supercoiling

DNA is ___ when there is no form of structural strain, and wen there is a strain, you get ____.

15, 150

DNA is usually only straight if it is less than __ turns. This eans that the persistance length of DNA is ___ nucleotides (since 10 bp/turn for B form)

nucleotide excision repair

DNA lesions that cuase large distortions in the helical structure of DNA are generally repaired by the ____-____ _____

dark, light, FADH2

DNA photolyase tends to bind thymine dimers in the ____, and it breaks these dimers when it is in the ___ (specifically 370nm). The cofactor is ____.

III

DNA polymerase ____ has the highest processivity and also polymerization rate (greater than 500,000 BP, and 250-1000 bp/sec). (The other two, starting with the lower have processivities of 3-200, and 1500- whereas polmerization was 16-20, and 40)

template

DNA polymerase adds complementary sequences to the original two ___ strands

exonuclease

DNA polymerase also has ___ mechanisms, and this can also be referred to as a 3' -> 5' exonuclease activity.

5', 3', primer, 2, opposite

DNA polymerase goes in the __- to ___ direction only. It also requires a ___ and it being at the origin. One origin usually hae ___ replication forks that move in ___ directions.

template

DNA polymerase requires a ____, which is basically the fact that C always pairs with G and that A always bonds with T. Provided chemical basis for semiconservative replication.

template (NOT the same thing as a primer)

DNA polymerases require a ___ to do their job propertly, and this also guides the polymerization. This is basically the idea that the polymerase knows what to put next because of what is located on this __.

alpha

DNA precipitates out of solution in the __ form.

coordinated,

DNA replication and cell divison needs to be _____ because if it is not, you get mistakes

semi-conservative

DNA replication is ____-______, which means that each DNA strand serves as a template for teh synthesis of a new strand.

initiation

DNA replication is regulated at ____. In eukaryotes, DNA replication is controlled by the cell cycle regulation.

nucleosomes

DNA s packaged into _____

relaxed

DNA supercoilding is usually a manifestation of structural strain. When there is no net bending of the DNA axis upon itself, the DNA is said to be in a ___ state.

positively, efficient

DNA transcription in eukaryotes is ____ regulated. This is because all we need to do is turn on the parts of the DNA that we want expressed. This is simply more ____ because most of the genes are already inactive, due to the complex histone nature, and then, all we need is specific TFs that will activate the parts we want to activate.

antibiotic, modify,

Drug resistance usually involves enzymes that can degrade the ___, for example B-lactamase degrades penicillin. Another mechanism is to ___ the antibiotic so that it is no longer active. This is what neomycin phosphotransferase does to kenamycin. It phosphorylates kenamycin so that it just doesn't work.

conjugative, non-conjugative

Drug resistant genes are often found in what types of plasmids?

elongation factors

During the elongation phase in eukaryotes, the activity of the RNA polymerase is greatly enhanced by ___ ___, which suppress pausing during transcription and also coordinate interactions between protein complexes involved in post transcriptional processing of RNAs

histones

Eukaryotic DNA is also covered with ___ (nucleosomes), and that is another problem that might prevent RNA polymerase from finding promoters.

sigma

Eukaryotic RNA polymerase does not have specific ____ factors, and that means that it can't bind to specific sequences. Instead, if must bind to transcription factors.

histones

Eukaryotic chromosomes has ___ and this prevents the RNA polymerase from readily finding the promoter sequence.

E, P

Eukaryotic ribosomes have no __ site; the uncharged tRNAs are expelled directly from the _ site.

low

Even though the number of transposons is high, they overally frequency of transposition is rather ___, and it is anywhere in between 10^-5 to 10^-7 per generation. This is because, as previously mentioned, transpositions can cause lots of mutations and you really don't

mutations.

Excision repair is important in preventing _____, which are the things that tend to lead to cancer (though there are some that are from viruses)

methionine

FOR PROKARYOTES, A special methionyl-tRNA is used to initiate protein synthesis. This is made in two successive steps. First, you have the addition of just plain old ____ to the tRNA.From there, you have a transformylase that transfers a formyl group onto it.

tRNA

FOR PROKARYOTES, WHAT TYPE OF RNA undergoes the most type of processing?

antibiotic resistance

Farms are one of the biggest hotspots of antibiotic resistance because farmers known that if you add antibiotics to animal feeds, then they will get fatter and bigger. This is exactly what they want because it helps them get the most bang for their buck. However, this is bad because it increases ____ _____.

antibiotics

Feedlots and farms select for drug-resistant bacteria because tons of _____ are fed to cattle taht so that they will gain weight more quickly.

endonuclease

For addition of the poly A tail, an ____ cuts the mRNA about 10-30 nucleotides from the end site. Then from there, you get a fere 3' OH, wehre A residues are immediately added by polyadenylate polymerase.

aminoacyl-tRNA synthetase

For amino acid with 2+ tRNAs, the same __-__ __ usually binds it to the two different tRNA.

polyadenylation signal sequence, polyA polymerase, polyA binding protein

For the 3' end, there is a ____ _____ ____ that is recognized by the cleavage and polyadenylation specific factor. Then, this cleaves about 30 nucleotides later. The specific factor leaves, and the end if polyadenylated by ___ _____. The newly formed poly A tail binds to the ____ ___ ____.

A, C, U, G

For the wobble hypothesis: when the FIRST base pair of the ANTICODON (which binds to the third base pair of the CODON) is an _ or _, the binding is speciic, and when it is _ or _, it is less specific. And of course, if it __, it is the LEAST specific because it can bind to A, C, OR U.

1.1

From Cairn's autoradiography, he found that the E. coli chromosome was molecule that was ___mm long.

circular

From Cairn's autoradiography, he was also able to reason that the E.coli DNA is _____

4700

From cairn's autoradiography, he was also able to conclude that the DNA was ____ kb.

lactose, cAMP

Glucose tends to inhibit the transcription of the ____ operon. This is because when glucose is added, it inhibits the production of __, which then cannot bind to cAMP receptor protein, which can't positively activate the promoter.

high

Good promoters have a ___ affinity for the RNA polymerase, whereas bad promoters do not

2 (You go to AMP + PP, and the latter hydrolyzes too)

How many high energy phosphate bonds are ultimately expended for each amino acid molecule that i activated?

1, 3, dissociate, 30

IF_ and IF_ bind to the 70S ribosome and cause it to ___. Afterwards, the remain stuck to the __S subunit.

inducer, substrate

IPTG was an ____, but not a ____ of the lactose operon, which was something that the experimenters wanted.

transposase, inverted repeats

IS elements encode an enzyme called ___ that recognize the ___ ___ at their ends and catalyzes their transposition. This is one of the biggest reasons that insertion sequences can move to different places in the DNA.

processive, clamp

IT is important realize that not all polymerases are the same as DNA polymerase III or polymerase epsilon and delta in eukaryotes. This means that not all enzymes are ____ and not all have a ___.

pilus

If the F plasmid is present in an organism, then it also will most likely have a ___, which it can use to bind to other things that don't have the F factor. Then when it binds, it starts bringing the pilus back.

lysogenis phage

If there is anything that produces a toxin, then it tends to be produced from a ___ ___.

nuclease

If xeroderma pigmentosa was a result of a mutation in the nuclease involved in excision repair, then you can cure it using a suntan lotion that has a repair ____.

n-1

If you have n amino acids in a peptide, how many GTPs will you use in translocation?

thao, gamma

In Ecoli, using one reading frame, will result in an earlierstop codon, so you get the ___ subunit, but, on the other hand, using another reading frame will give you a longer protein, and that is the ___ subunit. Both are subunits are of DNA polymerase.

reaction

In a helix turn helix, there is one helix and that is the ____ helix because it usually ocntains many of the amino acids that interact with the DNA in a sequence specific way. When bound to the DNA, this helix is position in or nearly in the major groove.

N-terminal

In about half of E.coli proteins, the _-____ methionine is removed as well.

replication

In bacteria, DNA polymerase III and the polymerase delta and esilon are used for ____ and thus, they are processive enzymes.

gain of function, loss of function

In cancer, one of the conditions is that you need to have induction of telomerase. From there,you need to have ___ ___ ____ mutations,which makes you more susceptible. Another thing you need to have is ___ ___ ___ mutations, which mutation in things that are known as tumor suppressor genes.

endonuclease

In mismatch repair MUTH is an ____ because it cuts the DNA 5' to the unmethylated GATC.

endonuclease, helicase II, I, DNA ligase

In nucleotide excision repair, what you get is, initially, a trimer recognizes the lesion and unwinds the DNA. then you get the replacement of the two UvrAs in teh intial trimer replaced by UvRC, and now the protein is a dimer, and this dimer (UvrBC - an ____) cuts the DNA strand containing the lesion on both sides of the damage. The oligonucleotide is then removed by ___ __, and the gap is filled by DNA polymerase _ and sealed by __ ___.

methionyl-tRNA, formyl

In prokaryotes, a special ___-____ is usually used to initiate protein synthesis. The ___ gorup is attained directly from N-formyltetrahydrofolate.

circular, linear

In prokaryotes, most of the bacteria have ____ chromosomes, but there are many exceptions with ____ chromosomes

formyl

In prokaryotes, the ___ group is added after the tRNA is charged with teh methionine.

If-2

In prokaryotes, the transcription factor __-_ comes in bound to the formyl methioine tRNA

4-5

In starting replication, you have about ___ (still prsent in one complex) DNAA protein molecules that are all bound to ATP that bind to four 9bp repeats. the DNA is wound aroudn this complex. Then, the three A_T rich 13 bp are dentured sequentially

nucleotide excision repair

In the ___-___ ___, an enzyme hydrolyzes thw two phosphodiester bonds on either side of the distortion caused by the lesion.

hemophilia

In the case of ___, a LINE-1 sequence from chromosome 22 has inserted into the gene for factor VIII, which is a gene that is required for blood clotting on teh X-chromosome.

recognizes, unwinds

In the excision repair system, the UvrA2B ___ the lesion and ____ the dna.

antibiotic resistance, resistant

In the future, it will be really difficult to fight bacteria and that is because of ___ ___ and how the overuse of antibiotics has selected for organism that are _____.

U1, U2

In the intiial spicesomal mechanism, the ___ binds to teh 5' end and then __ binds to the center. Then the remaining snRNPs come in and make this an active spliceosome, in which U1 and U4 are released and the intron can evnetually be released.

helicase II, excinuclease I, SSB (single strand binding protein DNA)

Initially, in mismathc repair, you get detection of a mismatch on a new strand, and then, the metH knicks the DNA in a specific manner. Specifically, MutH nicks the 5' end with the unmethylated GATC region. However, it is still attached, so the rest is removed via the aid of ____ __, ___ _, and ____.

transcription

Initiation of ____ is a crucilal regulation point for both prokaryotic and eukaryotic gene expression

yes, no

Is ATP required for the assembly of the spliceosome? What about for the actual clevage-ligation reactions that occur?

Yes (hell we can't even come close to analyzing the really old DNA)

Is it true that there are problems with current methods used to analyze DNA?

bidirectional

John Karin's experiment showed that the DNA replication that occurred at a fork was ___, which is why the radioactivity that it had would fade away gradually in both directions.

G1, S, G1, G2

Johnson and johnson did an experiment, and they fused cells from different stages of the cel cycle and determined if fusion causes a nonreplicating cell to enter the S phase. This works with the cells in ___, but not in the ___. So they ocncluded that the S phase cell releasing something that dirve __ into S. On the other hand, the __ cell is resistant to the S-phase promoting factor.

bacterial conjugation,

Joshua lederberg discovered ___ ____.

D (with TBP), B, F (RNA), E, H

Just name the order of the 5 transcription factors needed to make the pre=initiation complex in eukaryotes

replicating, inserting

LINES-1 is a tranposable element that we have in our body and it is present is really high amounts. Most of it is present in fragments throughout the genome, but very few are active. NEvetheless, it is these few that are responsible for ____ and ____ themselves elsewhere.

15

LINES-1 is an example of a transposable element that is found in humans. IT is 6.5 kb long, and present in about 5,0000 fulll length copies and 500,000 truncated copies, which represents about __% of our DNA. However, almost all of the LINES-1 transposons are inactive, mutated, and nonfunctional, very few overall are active. Very rarely, LINES-1 replicates and inserts elsewhere.

leucine zipper, helix loop helix

Like DNA binding motiffs, the structural motiffs that mediate protein-protein interacts tend to fall within on of a few common categories: ___ ____ and the basic ___ __ __.

leading, 3, 5

MCM helicase, which is what is found in eukaryotes, is made of 6 DIFFERENT subunits, is found on the ___ strand and goes in the _' -> _' direction.

metals, glucocorticoid

MEtallothionein removes toxic heavy metals from the cell and it is induced by ___ or ____ hormones.

translation

Many antibiotics work by inhibiting bacterial ____.

resistant

Many of the deaths in the hostpial are due to bacteria that literally are ____ to the drug that we give and that is much sad :(.

antibiotics

Many of the durg resistant genes that are inserted into transposons tend to work by creating proteins that inactivate _____.

humans, natural selection.

Molecular cloning has been taking place for millionso f years as a part of natural genetic exchange. CLoning was not invented by ___, instead it was estbalished by ___ ___.

hydrogen bonds

Most of the protein-DNA interactions that occur are usually in the form of ____ ___ in the major groove. This is also possible in the minor groove, but discrimination among the DNA bases is not readily possible.

lysogenic, lytic

Most of the time phage lambda is in the ____ cycle, but if there is something bad that happens to the host, then that detroys the repressor protein, and this cause entrance into the ____ cycle.

mismatch repair, e coli

MutS, MutL, and MutH are all proteins involved in DNA ___ ___, but specifically within __ ____. We do not have these proteins, btu we jsut have something else that is very homologous.

recombination

One way to remove bad DNA is by replacing the damaged dna via ____ and using undamaged DNA as a template.

200

Nucleases, such as DNase, which break up the DNA into several base pairs always tend to make it into fragements of about ___ base pairs, reglecting the regular repeating structure of the nucleosome.

octomer

Nucleosome particles contain DNA coiled around a histone ____

compact, transcription, negatively

Nucleosomes help ___ DNA, regulate ___, and cause DNA to be ___ supercoiled.

denature

OH, urea or heat can __ DNA. You can see this by a change in abs at 260 nm.

6, origin recognition complex

ORC is a complex of __ proteins that are conserved in eukaryotes and it have ATPase activity like DNAA. IT basically regulates intiiation because it binds nad this causes sueprcoiling, which leads to the creation of the origin of replication. ORC stands for ___ ____ ____.

poly A binding protein, exonucleases

Once the poly A tail is made, it binds to ___ __ ___ ___, which is a protein that binds to the 3' end of the mRNA and protects the 3' end from ____ in the cell.

bubonic plague

Once you are infected by yersinia pestis, you get the ___ ___ and will probably die in 2-4 days.

MCM

Once you have binding of the origin recognition complex, you get binding of Cdt1, and cdc 6, and that activates the complex, and makes it more likely to recruit ____, which is the DNA helicase for eukaryotes

lyme disease

One exception of a bacterium that does not have circular chromosomes is borrelia burgdorferi, which causes ___ ___. This organism has 1 linear chromosome, 12 linear plasminds and 9 circular plasmids.

mitochondrial DNA, free radicles

One of the biggest signs of aging is when there is damage to the _____ ___. This is because this is the site of oxidative phosphorylation and there is no recombinational repair. Additionally, whenever only some electrons are transferred to teh oxygen instead of all of them, you also get formation of ___ ___.

feedback repression

One of the mechanisms of control includes the translational repression, which includes___ ___, which is basically when the protein accumulates in the cell, it goes back and binds to its own mRNA and prevents further translation (negative feedback much?)

3, 5 (this is commonly what is referred to as proofreading)

One of the things that keeps the error rate low is the _'-_' exonuclease activity of ALL DNA polymerases (so use the one that is more common)

enzyme

One of the ways that DNA is repaired is that the damage is directly reversed with the use of an ____.

multi-subunit (restriction enzymes)

One reason why palindrominc DNA is important is because it is often involved in the binding of ___-____ proteins

planar, planar, pucker

PYRIMIDINES are ___ molecues and purines are nearly very ___ with a slightly ___.

Barbara McClintock

People were like damn transposons are hella legit because these genetic elements can move to other locations on the chromosome. However, they didnt realize that ___ ___ had already published how these entities worked, ad because of this, she won the nobel prize.

mutation

People who have a mutation in the excision repair tend to not live very long because there is not way of escaping ____ in the body, and thus, you're bound to get cancer.

99, 1, repressor (this protein tends to be destroyed by some thing that is changed in the environment)

Phage lambda is a bacteriophage, and it goes into the ___ cycle __% of the time and it goes into the lytic cycle __% of the time. In the lysogenic cycle, the phage lambda is integrated into the host chromosome and the expression of lytic genes is prevented by a ____ protein.

introns

Phillip Sharp and Richard Roberts independently discovered that many genes for polypeptide in eukaryotes are interrupted by noncoding sequences caled ___

survival

Plasmids usually contain additional genes that are not present in the organism's genome that still play a role in the ____ of the organism.

replicate, extra genes, drug resistance

Plasmids, viruses, and transposons are all natural vectors for cloning genetic material. This is because they ___ inside of cells, can acommodate __ ___, and frequently encode __ ___ genes that can provide a means for selection in nature and in the laboratory.

clone (insert)

Plasmids, viruses, and transposons are often used to _____ genes.

hairpins

RAN transcribed from DNA can makes things called ___, which cna then help with regulation, stability and structure. These things are involved with rRNA, tRNA, and some mRNAs.

sigma factors

REMEMBER that eukaryotic RNA polymerases do not have a ___ ____ and thus, they cannot bind to specific sequences and find particular promoters.

pre-replication

REgulation of initiation in eukaryotes occurs in two stages. The first stage is the __-____ complex. In this stage, you have binding of the origin replication complex to the DNA.

hairpins

RNA ___ regulate ribsomal binding by hiding the start codon, and also RNA synthesis by causing RNA polymerase and termination. Very long hairpins can trigger processing.

nucleolus

RNA polymerase I is found in the ___, and there are about 40,000/celll and it has about 50-70% activity.

sigma

RNA polymerase II does not recognize specific sequences in the DNA because it does not have a ___ factor like its analog in prokaryotes.

12

RNA polymerase II is central to transcription in eukaryotes, and it has ___ subunits. Some of them are analogous to the 2 a, B, and B prime subunits present within bacteria.

nucleoplasm (nucleus is okay)

RNA polymerase II is found in the ____ (whichis just in the nucleus) and there are 40,000/cell and its activity is 20-40%.

transcription factors

RNA polymerase II requires an array of other proteins called ___ ___ in order to form the active transcription complex. The general ___ ___ required at every pol II promoter arae usually designated TFII, with an additional modifier, and they are conserved throughout eukaryotes.

nucleoplasm (nucleus is okay)

RNA polymerase III is also found in the ___ (much like RNA polymerase II) and there are 20,000 copies/cell and the activity is about 10%

I

RNA polymerase _ in eukaryotes is responsible for syntehsis of only one type of RNA, which is pre-ribsomal RNA.

II

RNA polymerase __ is responsible for synthesis of mRNA and some specialized RNAs.

termination

RNA polymerase ____ is not precise in eukaryotes, and the precursor RNA is cut following a AAUAAA sequence by an endonuclease.

III

RNA polymerase ____ is responsible for making tRNAs and 5S rRNA and other small specialized RNAs.

promoter

RNA polymerase binds to specieis sequences in DNA referred to as ____. The duplex DNA is important for this very reason. It serves as a ____ site for the RNA binding, and it is also a template for the RNA to be made.

consensus sequences

RNA polymerase contains different sigma factors that recognize different ___ ____.

positive, negative, topoisomerases

RNA polymerase generates a wave of ___ supercoils ahead of teh transcription bubble, and ___ superocils behind. This has been observed both in vitro and in vivo. The problems are solved by _____

5, sixth

RNA polymerase has __ core subunits and another subunit (with is the sixth) that transiently binds to the core. This is that ____ subunit and it directs the RNA polymerase to the place where it should bind.

toxins

Some phages encode ___ that assist in the virulence of the host.

true

TRUE/FALSE? Both the leading and lagging strand in DNA are made from one DNA polymerase III

polyadenylation

Splcing occurs while transcription is in progress and it is followed by clevage and ____.

GU, AG

Spliceosomal introns always have the same consensus sequence at intron-exon junctions. At the 5' end of the intro, there is a ___ and at the 3' end there is an ___.

transcription

Splicing via the spliceosomal mechanism happens while ____ is happening in eukaroyes.

D

TFII_ is the first general transcription factor to bind to the promoter. Theymade a mutation within the TATA box, and saw that, instead of starting at one place, transcription started everywhere in eukaryotes.this showed that the sequence of the TATA box was specific for beginning transcription.

F

TFII_ remains associated with RNA polymerase II throughout elongation and the activity during this part is also greatly enhanced by elongation factors.

adenine, thymine

Strand melting usually happens in sequences that are rich in ___ and ___.

H

TFII_, which is the last protein that was recruited in the process of forming the pre-initiation complex has both helicase and kinase activities.

H

TFII__ can also help fix mistakes and helps recruit the machinery for nucleotide excision repain if RNA poly III halts at the site of a lesion

excision repair enzyme

Supplying the missing __ ___ ___ reduces mutations and cancer frequencies for people who had xeroderma pigmentosa, which was a direct result of not have the nuclease involved in excision repair

False (not quite yet)

T/F: Resaerchers can examine the structure of DNA binding protein and infer the DNA sequence to which it binds.

False (not true, it is possible that some things can have linear chromosomes)

T/F: all plasmids are circular in shape.

true

T/F: the structure of RNA and DNA polymerase are structurally very similar.

true

T/f: IT is very difficult to analyze old DNA because it is hard to recover, is largely degraded and fragmented, is clinically altered, and frequently contaminated with much more recent undegraded DNA.

True

T/f: Most transposons are mutated and can only transpose as a larger group.

true

T/f: Within the zinc finger, the zinc itself does not interact with teh DNA, rather the coordination of zinc with the amino acid residues stabilizes this small structural motif.

TATA binding protein associated factors (TBP associated factors)

TAFs stands for:

kinase, helicase

TFIIH has both ___ and ___ activities.

UAG, UAA, UGA

THREE CODONS do not correspond to any amino acid because they cause ___. These codons are:

pcna

The B clamp in eukaryotes is callde _____ (this is basically just the beta clamp in humans)

repair system

The DNA ___ ___ is something that is super helpful because, even after the DNA polymerase has carried out its function, we can get this system working to out benefit.

histones, nucleosomes

The DNA in chromsomes is very tightly associated with proteins called ____, which package and order the DNA into structual units called ____.

R-factor (plasmid)

The E coli conjugated with yersinia and transmitted the _-___ when they were both in the digestive tract of the flea, which is the vector for the yersinia. This is crazy because yersinia by itself was already bad enough and now we need a better way to kill it off.

superocoiled loops, negative supercoiling

The E. coli DNA is organized in ____ ___. In particular, it is ___ ___ becuase the supercoiling is due to the underwinding of the DNA.

plasmids

The ___ have one origin of replication because they need to still replicate. Additioally, it also usually cuases circular DNA, and it has DNA sequences that control its replication, and you also have additional genes that are epxressed and affect the host.

helicase

The MCM(2-7) is just another name for the eukaryotic ____

semi conservative

The Messelson and stahl experiment is the one that showed that DNA replication is ___ ___

A-T

The Origins of replication tend to be in places that have large amounts of __-___ pairs. The opening then causes DNaC to board the dna B protein onto the unwound region.

DNA, transcription factors

The TATA binding protein can bind to both ___ and ___ ____, which is needed because the TFIID that it is part of has loads of TAFs (TBP associated factors)

D

The TATA binding protein is a part fo the transcription factor II_ domain. The II refers to RNApolymerase II. The other proteins in this complex are knwon as TAFs, which are TBP associated factors

50

The TRNAs bind to the __S subunit of the bacterial ribosome.

endonuclease

The UvrBC that cuts teh DNA strands containing the lesion on both sides of the damage is an example of an _____.

first two

The __ ___ letters of a codon are usually the determinants of specificity.

replication factor C

The ___ ___ ___ is analogous to teh gamma complex of the bacteiral clamp loader.

specificity

The core RNA polymerase (which is the 2 identical alpha, beta 1, beta 2, and omega), can still theoretically carry out the synthesis of RNA, but the rate of synthesis is 1/50 th the rate of the holoenzyme. Additionally, the ____ of the polymerase is lost because it just start transcribing anywhere (which makes sense because it has no sigma factor)

F factor

The creation of the pillus is clearly defined entirely by the _-___ becuase without it, you don't even get formation of the pilus.

R-factor, conjugation, transposon

The development of drug resistance through the conjugation of the _-____ plasmid is not good. This confers multiple drug resistances, including to mercury, solfonamid, streptomycin, chloamphenol, fusidici acid, tetracycline, and many more. And this is crazy because all of these genes are on ONE plasmid, and thus, they can be readily transmitted by ____ or by ___ mediated recombination.

C, B, B, helicase

The dnaA binds to an initiator site that is away from the AT region. In this case, the bind of DnaA happens in a ciruclar fashion, which increases the supercoiling, and this increase causes the AT region to open up. After it opens up, the DNA_ loads the DNA_ onto the dNA and then it disassmbles. Recall that hte DNA_ stays on and it plays the role of ____ essentially.

telomeres,

The ends of lienar eukaryotic chromosomes contain ___, which are short repetitive DNA segments.

looping

The enhancers are recognized by specific transcription factors and thoe factors interact with other factors and the DNA, and this leads to the DNA ____ that is often observed.

unidirectional

The one mistake that John Cairn made from his autoradiography was that hethought teh DNA was replicated in a ____ manner from a fixed origin (THIS WAS WRONG).

origin firing

The second step of the regulation of initiation is ___ ___, and this happens after the MCM (eukaryotic helicase) has been recruited. Now, there is activation by the S-phase Cdk and DDK, which causes the loss of Cdt1, and cdc6, which essentially just activates the activity of the helicase.

polyadenylation signal

The sequence AAUAAA in eukaryotic mrna is known as the ___ ____. IT not only signals cutting of the mRNA right after that region, but it also signals another enzyme to add something ^__^.

antiparallel

The sequence that is formed by the tRNA and RNA duplex is (parallel or antiparallel)

16s rrna

The shien delgarno sequence on the mRNA interacts with teh __ ___ of the 30S ribosomal subunit.

stable

The sites of integrations for transposons tend to be relatively ____, and that once the transposon moves to another site, it can just stay there.

carboxy terminal domain

The somponents of splicing apparatus appear to be tethered to the __ __ ___ of RNA polymerase II.

touch

The squirrels in lake tahoe have fleas that are infected with yersinia, and thus, it is in your best interest to NOT __ the squirrels.

RNA polymerase

The structures of prokaryotic and eukaryotic ___ ____ are similar to one another, which implies evolutionary relatedness.

linking number (increase super coils/writhes, then you get decrease in turns)

The superhelical tension that is created by DNA A causes the opening of the AT regions. This is all linked back to the ____ properties of cirular DNA.

CRP (CAP)

Things that are mutants in the cAMP receptor protein gene cannot make the ___ protein. This protein, when activated by cAMP, is a transcription factors necessary for the expression of catabolite repressible genes (

superhelical density (specific linking difference)

This is the number of turns removed or added divded by the number present in the original DNA. This is basically helping us come up with a quantity that is independent of the length of DNA.

underwinding

This si the fact that the DNA has FEWER helica turns than would be expected for the B form. This will lead to more bp/turn than expected and this causes supercoiling. This is the most common type of supercoiling.

chromatin remodeling factor

This will effect how tightly nucleosomes bind to DNA as the polymerase goes down and unravels the DNA, and tries to get around the histones.

redundant

Three nucleotides define a codon, but the gnetic code is ____ (degenerate)

cleavage and polyadenylation specific factor

To what protein does the poly A polymerase bind prior to starting to make the poly A tail?

IS, DNA

Transposons tend to work by transposing as individual ___ elements or as a larger group containing both IS elements and the ___ that is flanked in between (which can include various antibiotic resistance genes - most of which work by encoding proteins that inactiviate the antibody).

methylated

Usually at CpG sequences some of the C residues tend to be ____, which can silence generegulation when present in a regulatory region of the gene.

opened, 8

When the RNA polymerase binds, to form an open complex about 14-17 bp of the DNA are _____ - forming the overall transcripton bubble. The RNA-DNA hybrid that forms is about _ base pairs long before the RNA can just live by itself.

phorphorylated, dephosphorylated

When the carboxy terminal domain is ____ by pTEFb, it activates the RNA polymerase and it mvoes and when it is ____, you get termination.

mirror repeats

When the inverted repeats (aka the palindrome) occur on the same strand, they are ___ ___ and they can't form hairpins.

oriT

When the plasmid is completely transferred over to the female cell and the DNA replication within that cell is completed, the DNA is cut at ___

lytic, lytic

When the repressor protein that was intiially inhibiting the expression of the ____ genes is destroyed, the bacteriophage DNA enters the ____ cycle. n this case, the phage DNA comes out of the host DNA and circularizes. After this, the phage DNA is replicated, and the phage proteins are made and assembled. Thereafter, the host is lysed.

high GC content is for organisms that tend to be in lots of UV light. (because it will decrease the liklihood of dimerization).

Why do some organisms have high GC content and others dont?

2A, 2B, 1

Within a nucleosome, the H3 and H4 histones, which make up half of the overall histones are nearly identical across organisms, which suggests strict conservation of function. On the other hand, histones H_ _, H _ _ and H_ do not should as much similarity.

R-factor (plasmid)

Yersinia, which causes the bubonic plague, has recently reemerged and seems to be multi-drug resistant. HOWDIDTHISHAPPEN? it seems like E coli conjugated with yersinia to tranmit the _-______ This happened while they were both in the digestive tract o the flea.

single strain binding protein, replication protein A-3 subunits

___ ___ ___ ___ pave teh way for polymerase becuase it stabilizes the strains that may be forming. This is in bacteria. But the eukaryotic equivalent is alled ___ ___ _-_ ____

excision repair

Zeroderma pigmentosum is a genetic disease that affect 1/250000 people and it is when someone has a mutation in the __ ____ pathway. Here, skin is 1000x more sensitive to sunlight, and skin cancer usually devleops on the arms and nexk. he pateints usually die form cancer before the age of 30.

a-amanitin

_-____ disrupts RNA polymerase II function and at higher concentrations, it disrupts RNA polymerase III. Neither polymerase nor bacterial RNA polymerase is sensitive to this poison that is also foudn in mushrooms.

a aminitin

_-_____ is a poison that inhibits polymerase I and III. The only cure is a liver transplant and if you don't get it within a few days, you are screwed. (For RNA polymerase I, the amount needed is 1 ug/ml, and III it is 10 ug/ml)

S-adenosylmethionine

_-_____ is used as a methyl group donor in DNA systems and helps modify the different nucleotides.

anthrax

__ (the disease) is yet another example of useful genes that were cloned by natural selection and are transmissible.

single stranded binding proteins

__ ___ __ ___ in bacteria help pave the wave for bacteria.

insertion sequence

__ ___ elements encode an enzymes, which is called transposase.

lynch syndrome

__ ___ is basically also known as hereditary nonpolyposis colorectal cacner and it is usually from a defect in mismatch repair

feedback repression

__ ___, in which the protein goes back to bind to its own mRNA when it becomes too prevalent, is really prevalent in ribosomal proteins.

RNA polymerase, DNA polymerase

__ _____ structure is conserved from prokaryotes and eukaryotes, but the ___ ____ is completely different. Thus, the first must have evolved, but the latter definitely evolved independently in the two groups.

EF-G, EF-Tu-tRNA

__-_ mimics the structure of __-__-___, which is the initial structure/factor that is used to bind to the A site. The binding can then displace the peptidyl RNA and help with translation.

CRP-cAMP

__-___ binds to a site near the lac promoter and the RNA polymerase binds to the promote. The firs thing bends the DNA in such a way that it is better for RNA polymerase to bind to the DNA.

type II topoisomerase

___ __ ___ break both dna strands and change Lk in increments of 2.

replication protein A3

___ __ ___ is the major eukaryotic, single strand specific DNA binding protein. It constists of three subunits and it regulates access of proteins to DNA.

type I topoisomerase

___ __ _____ act by transiently beraking one of the two dna srands and passing the unborken strand through the break and rejoining the broken ends. It changes the Lk in increments of 1.

replication factor C

___ ___ ___ , in eukaryotes is identical to teh clamp loader for PCNA (which is the clamp).

single strand binding proteins

___ ___ ___ ___ bind to single stranded DNA and stabilize it.

single stranded binding proteins, replication protein A

___ ___ ___ ___ in bacteria and __ ___ __ (3 subunits) in eukaryotes repgulate access of proteins to DNA and signal damage. They pave the wave for polymerase and stabilize single strands.

yersinia pestis, 2, 4

____ ____ is the pathogen that causes the bubonic plague. It invades the lymph nodes (which causes them to swell, and they are called buboes) The blood vessels then break and cause internal bleeding. The dried blood under the skin causes teh skin to turn black, which is why you get black death. the whole process: from fever to pain to death takes about _-_ days.

mismatch repair

____ ____ relies directly on DAM methylase to methylate the adenine within GATC sequences. Once that happens, the system can tell the old from the new, and this allows it to repair DNA up to 1000 bp from any hemimethylated GATC sequence.

DNA ligase

____ ___catalyzes the formation of a phosphodiester bond between a 3' hydroxyl and a 5' phosphate at their ends

archaea

____ actually have intron whereas bacteria do not. And the introns they do have are group I, group II, and group 4, but they don't have the spliceosomal introns because they are cleave

cdc6, cdt1, MCM

____ and ___ are two important proteins that are used in the pre replicaton formation complex in the eukaryotes. These two things play a big role in recruiting the ___ (whcih is the eukaryotic helicase)

enhancers

____ are DNA sites that are distant from the promoter in eukaryotes and that enhances communication between core and proximal proteins. A large mediate protein is needed to mediate the interactions.

polysomes

____ are knwon as a fiber of adjcent ribosomes that translate a mRNA repeatedly. This allows the highly efficient use of the mRNA>

enhancers

____ are sequences of DNA that are requried for transcription, but do nothave a fixed location with respect to the promoter (only in eukaryotes)

checkpoints, S

____ assure that all essential reactions are carried out correctly before progressing from one phase to the next. The one that we are essentially interested for cell cycle progression is the __ phase checkpoint.

RNAi

____ can specifically target mRNAs for degradation.

chromatin, histones, nucleosomes

____ consists of fibers ocntaining protein and DNA in approximately equal masses, along with small amount of RNA. The DNA in chromatin is tightly associated with proteins called ____, which package andorder the DNA into structural units called ____.

snRNAs

____ facilitate recognition of the splice junction in the spliceosomal mechanism of intron removal .

coactivators

____ in eukaryotes are adaptor molecules that integrate signals from activators and repressors and relay the information to the basal factors, which are bound to the RNA polymerase.

repressors

____ in eukaryotes bind to selected sets of genes at sites known as silencers. They interfere with functioning of activators (both in prokaryotes and eukaryotes) and thus, slow transcription

DNAB

____ in prokaryotes unwinds the DNA. It is the helicase equivalent.

tetracycline

____ inhibit protein synthesis in bacteria by blocking the A site on teh ribosome, which prvents the binding of amino acyl tRNAs.

trna

____ is about 50% double stranded (jsut goes to show the importance of palmindromic sequences and how it can allow nucleic acids to be double stranded).

puromycin

____ is an antibiotic that actually a competitive inhibitor becuase it looks very similar to an aminoacyl tRNA. Thus, it binds to the ribosomal A site, IT creates a peptide bond, but can't undergo translocation, so what you get is dissociation and premature termination of the peptide.

puromycin, A

____ is an antibiotic that binds to teh __ site ob bacterial ribosomes and causes premature termination. This is because it undergoes the reaction catalyzed by the peptidyl transferase, but

heterochromatin, euchromatin

____ is generally more condensed than the rest of the chromatin. This is transcriptionally inactive. The less consdensed chromatin is called ____.

DNAC

____ is needed for DNAB binding at the origin.

epigenetics

____ is the study of heritable changes that are not cause dby changes in DNA sequence.

coactivators, basal factors

____ often get messages from the activators, and they tend to send the message to __ __, which essentially posiiton the RNA polymerase for transcription in eukaryotes.

telomeres

____ prevent loss of informaitonal DNA from chromsomes ends during replication.

distributive

____ synthesis is the opposite ove processive synthesis. In this, you get on, do shit for a while, and then fall off, and repeat.

Khorana (not Nirenburg)

____ was the scientist who knew how to synthesize polyribonucleotides with defined, repeating sequences of two to four bases.

enhancers

____ work by making loops. They are recognized by specific transcription factors.

plasmids, viruses, transposons, replicate, extra genes, drug resistance

____, ___ and ___ are alll natural vectors that can be used to clone genetic material because they can ___ inside of cells. They are all small and can accomodate __ ___. They frequently encode ___ ___ genes that can provide a means for selection in nature and in the lab.

RNA, DNA

____, not ____ is rapidly degraded at high pH because of the differences in sugars.

tRNA

____- this is needed for protein synthesis and often is charged with the appropriate amino acids to be incorporated into proteins.

initiation

_____ IS THE only stage in DNA replication that is thought to be regulated.

nucleosomes, 70

_____ are successively packed into higher order structures. The DNA that wraps around DNA is about __ A in length.

eIF4G (eukaryotic initiation factor 4G), 40S (because eukaryotes), 5

_____ binds both the Cap binding protein and the polyA binding protein. This complex guides the ___ ribosomal subunit to teh first AUG codon from the _' end. The complex causes mRNA to be circular and stabilizes the RNA and facilitates ribosome recycling.

topoisomerases.

_____ catalyze changes in linking number of DNA. They are also known as enzymes that increase or decrease the extent of DNA underwinding.

RNA, DNA

_____ duplexes are much more stable than ____ duplexes and the reasoning for this is not yet known.

termination

_____ happens when you reaech one of the three stop codons.

methylation, acetylation

_____ has to do with chromosomal inactivation and ____ has to do with chromosomal activation.

activators, repressors

_____ increase the ability of RNA polymerase to do its job, wherease ____ decrease it.

hemophilia

_____ is a result of a transposon. This is because the LINES-1 transposon that is present on chromosome 22 basically inserts itself in the middle of the gene for factor 8 that is present in the X-chromosome. This inactivates the factor 8 gene, and thus, it inhibits the entire production of that protein, which is what leads to the diseased state of ____.

supercoiling

_____ is important because it helps us get all that genetic material into the nucleus in an effective manner

photolyase

_____ use energy fom light to reverse damaged that might have originally been caused by UV light.

endonuclease

______ can begin to degrade at a specific internal sites in a nucleic acid strand or molecule, reducing it to smaller and smaller fragment.

type I

a ___ __ toposiomerase only creates one distinct break in the DNA.

GTP, translocation, 4

a ___ is also cleaved in the first elongation step and nother during the ___, and thus on average (if we take into conideration the GTP -> GMP) thtat occurs in making the aminoacyl tRNA, it is the hydrolysis of __ NTPs to NDPs required for the formation of each peptide bond.

chelate

a ___ is often defiend as a metal bound in a ring structure.

3, 1, 2, replication

a bacterium like E. coli has __ DNA polymerases. _ and ___ are involved in proof reading, whereas the third one is involved with the atual ___ part.

consensus

a change by just one base pair in the ____ regions that are located at -35, and -10 can drastically decrease the ability with which RNA polymerase inds to the promoter

adenosine

adenine + sugar = ____

adenylate

adenosine + phosphate

AUG, prokaryote

another mechanism of translational regulation is the availability of the __ codon. This is because base pairing within the mRNA may partially blocok or completely block the ribsoome binding site or the start codon. The gene can then only be translated when the secondary strcuture of RNA is disrupted - which might happen when adjacent gene is translated (clearly, we are assuming the organism under examination is a ___ because we usually have on gene, one transcript.

translational repression

another mechanism of translational regulation is via ___ ___ , where some genes have a feedback system to regulate teh amounts of proteins that are syntehsized.

antisense nucleotides

another mechanism of translational repression is via binding of __ ___ where anti sense RNA or oligo-deoxynucleotides are complementary to mRNA. The bind to teh ribosomal binding site and makes it unavaible for translation. It can also bind and target the RNA for degradation.

small non-coding RNA (this can lead to gene silencing because the non coding RNA binds and makes the site unavailble for translation)

another method of gene regulation is via binding of __ ____-___ ____, and this word similarly to the antisense nucleotides, except this is a noncoding RNA and it just binds and prevents ribosome from binding - making it unavailable for trnalsation. The only difference between this and the antisense nucleotides is that this is exclusively RNA.

horizontal gene transfer

another purpose for transposable elements is that they are a mechanism for ___ ___ _____ from one genetic element (like a plasmid or vector) to another genetic eleemnt (like another plasmid or vector)

gene regulation

another purpose of transposons is that they can alter ___ ____. In other words, genes can move out of one place and into another and this either take it from a strong promoter to a weaker one or vice versa

A, C, U

another reason for the wobble is the fact that the tRNA has the nucleotide hypoxanthine (inosinate), and this can base pair with ___, ___ or ____ on the actual coding strand itself, which lends lots of flexibility - at least in the last base pair.

ribsomal binding site

another translational regulatory mechanism is via the ___ ___ __. In this case, a strong ribosomal binding site on the mRNA will lead to more frequent initiation.

mutagen

another way that you can get somatic mutations that lead to cancer is if you have ___ exposure. This is anything including UV or something in the

yes (this is basically called epigenetic)

are chromatin modification propagated through cell divisions?

DNA polymerase I

arthur kornerbg simplified adn purified ___ ___ __, which was one of four distinct DNA polymerases in the E coli lcell.

hydrogen bonding, base stacking interactions

aside from the phosphodiester bonds, there are two forces that hold the DNA duplex together: the __ __ between complementary base pairs and the __ ___ __, which are non specific, but are also themajor contributors to the stability of the double helix.

AMP, GMP, UMP, TMP, CMP

at 260, ____ absorbs the most, and then you have ___, and then ___, and then ___ and then ___. (ATP, UMP, CMP, TMP, GMP)

restriction endonucleases

bacteria have ___ _____ that cut DNA at particular sites if it is unmethylated

single, multiple

bacteria have a ___ origin while eukaryotes have ___ origins.

methylated, unmethylated, restriction endonucleases

bacteria protect themselvesby encoding enzymes that ____ DNA at specific sites. Then they cut DNA at these sites if it is ____. This action is carried out by ___ ________.

oeprons

bacteria regulate genes by having similar ones on the same transcript. All the genes are under one promoter. The gene cluster and promter plus additional sequences that function together in regulation are known as _____

phage, lytic

bacteria that are harboring lysogenic phages express some ___ genes. For example a repressor is expressed that prevents entrance into the ___cycle.

identical, different

bacterial helicase has 6 ___ subunits (DNAB helicase), and eukaryotic helicase has ___ subunits (MCM helicase)

260

bases absorb strongly in the ___ nm region.

phosphorylation, acetylation, methylation

basic amino acids of the histones can be modified to solve the issue of nucleosome barriers during transcription. For example, they can undergo ___, ____, and _____. There are also chromatin remodeling factors that can hel pthe polymerase.

delayed

because of checkpoints, S phase progression cna be ____ in order to repair damage or talled replication forks.

bind

binding of CRP-cAMP induces a severe bend in the DNA that helps RNA polymerase ____ the promoter.

50, 30

binding of initiation factor 1 and 3 causes dissociation of the ribosome into the __S and ___S subunits in prokaryotes.

messelson, stahl

botchan said that the most beautiful experiment ever was the one done by ___ and ___.

DNA polymerase III

both the leading and lagging strand in prokaryotes are made by a single, asymmetric ____ ___ ___.

true

buldges in DNA can be target for repair enzyme systems. T/F?

cAMP

by itself CRP cannot change its alpha helices to bind into adjacent section of the major groove of the DNA; however, when it binds to ___, it changes conformation such that the CRP can fit in perfectly into the DNA.

activates

cAMP ____ CRP because its binding changes the conformation such that its a-helices can fit into adjacent sections of the major groove of the dna.

glucose, glucose, lactose

cAMP is low in the cell when ____ is present. Thus, to induce the lac operon heavily, you need both a lowered concentration of _____ (To increase the amount of camp) and an increased production of ___ (to decrease the repressor)

positive

cAMP receptor protein is also known as CAP, and it is a ____ regulatory element because its presence increases the rate of transcription in the operon.

supercoiling, supercoiling, underwinding

generally, we're supposed to have 10.5 bp/turn,and let's say we have 84 bp. Then we expect about 8 turns. Now, let's say on of those turns were removed, now you have fewer turns, and this means you have 84/7 = 12 np/turn, which is different from the ideal 10. Thus, you are going to get ___. In particular, it will be ____ due to ___ because the helix has FEWER helical turns than would be expected for a the B form structure.

guanosine

guanine + sugar = ____

guanylate

guanosine + phosphate

shorter, longer (strand separation is unfavorable over short distances, but become more favorable as the the amount of bases you need to separate increases).

having supercoiling is much more favorable than having strand separation for however many turns. This is because, over ___ regions, it much more favorable to only have supercoiling. IF you want to consider strand separation, that becomes more prominent only for _____ DNA and higher levels of unwinding.

peptide bond

in elongation, after you have an amino acyl tRNA in the P and A site, you get ___ ___ formation. In this case, the amino acid in the _ site acts as a nucleophile and displaces the tRNA in the p site. The nitrogen is the nucleophile and the COO-R group is teh electrophile.

5' cap

in eukaryotes what happens to teh 5' end of the mRNA? In other words, what is added to it?

epsilon

in eukaryotes, DNA polymerase __ is responsible for replcaing the primers of okazaki fragments on the lagging strand.

phosphorylated

in eukaryotes, RNA polymerase II will start transcription when its carboxy terminal domain is ____

DNAC

in eukaryotes, the CDC6, and CDT1 proteins have a role comparable to that of bacterial ____ protein because it helps load on MCM helicase near replication origin.

pribnow

in eukaryotes, the TATA box is analogous to the ___ box in prokayotes.

cap binding protein

in eukaryotes, the eI4E is also known as __ ___ ___, because it literally attached to the 5' cap and allows the eukarytic initiation complex to go forward from there.

methionine, n-formyl methionine

in eukaryotes, the first amino acid added to a chain is usually _____, whereas in prokaryotes, it is _____

linear, circular, circular,

in eukaryotes, the nuclear chromosomes are ___, the mitochondrial chromosomes are ____, and the chloroplast chromosomes are _____.

leading strand, lagging stand

in eukaryotes, the polymerase e is often associated with teh ___ ___ and polmyerase d is associated with ___ ___

DNA polymerase, DNA polymerase a

in eukaryotes, the primase is actually a ___ ___ (which is effing sick!) Specifically, it is __ ___ ___, and the primers are extended by DNA polymerase gamma (which carries out both leading and laging strand synthesis in a complex comparable to the dimeric bacteria DNA polymerase III; it also forms a circular clamp, but with another portein)

cap biding protein, polyA binding protein

in eukaryotes, the process of starting translation is slightly different from what it is in prokaryotes. Firstly, at the 5' end, the mRNA message is bonding to eIF4E, which is also known as the __ ___ ___, and at the 3' end, the mRNA message is bound to the ___ ___ ___,. This basically ties mRNA into a loop.

coding strand

in eukaryotes, the so called TAT box is on the ____ ____ and is usually around -31--26 region.

space, time

in eukaryotes, transcription and translation are separated in ___ and ___.

dephosphorylated

in eukaryotes, transcription is terminated when the carboxy terminal domain is _____ and then it can be recycled and used to initiate a new transcript.

3' poly A tail

in eukaryotes, what is the number of the thing that is added to the 3' end?

methylated

in eukaryotic cells about 5% of cytidine reisudes in DNA are ____. This is most common at CpG sequences and varies by molecular region in lage eukaryotic dna molecules. This increases the tendency to assume the Z form and also inhibits transposon activity.

UvrA, UvrC,

in excision repair, you initially get breaking of the lesion with UvrA2B, which is a dimer, and then you get replacement of the ____ subunits with ____. From there, you get the new UvrBC dimer cut the lesions on both sides of the damage.

rrna

in general, peptide bond formation is catalzyed by ___ (general class of rnas)

transposons

in lysogenic phase, some phages harbor ___ that confer drug resistance to the host. The reason why these genes seem beneficial to the host is because they are. The virus wants the host to live so it can mooch off it.

muts, muth, mutl

in mismatch repair, ___ is the protein that scans the new DNA for a mismatch, ___ is the protein that HUNTS for the unmethylated GATC, and ___ is the protein that hold the former two together.

mutS, mutL

in mismatch replair, ___ and ___ form a complex at the place where there ar emismathced base pairs. Then, the mutH binds to mutL and GATC (methylated). Once this complex is made mut H has an endonuclease activity that it can use to cut out the mistake on the older strand (Where the GATC is not methylated)

I, III

in nucleotide excision repair, DNA polymerase ___ is the one that fills in the gap, but in mismatch repair, it is DNA polymerase ____. (both apply for e coli only)

dna polymerase I, dna polymerase epsilon

in nucleotide excision repair, let's say you have a thymine dimer, then enzyme cuts out around it, and the gap is filled in with ___ __ __ in e coli and ___ ___ ___ in humans. The enzyme that does the cutting is made up of smaller subunits called: UvrA2B (which is means 2 Uvra and one UVrB)

LIGHT YEAR'S, exonuclease

in one year, you tend to transcribe about a ___ ___ worth of DNA. The ___ activity of DNA is the one that adds on a 10^2 additional accuracy to its current ability.

unmodified

in prokaryotes the mrna is usually ____ and is translated immediately by the ribosomes.

primase, primers

in prokaryotes, DNAG is also known as ____ and it sets down ____ needed to start elongation.

shine dalgarno sequence, 5

in prokaryotes, the AUG nearested to the ___ ____ ___ is the start codon, where in prokaryotes, the AUG nearest the __' end is the start codon because the intitaition complex starts moving from that end.

DNA polymerase III

in prokaryotes, the leading and lagging strand are both produces by a single ___ ___ ___, which is how the leading and lagging strand work together.

formyl

in prokaryotes, the starting methionine is dffierentiated by the methionine that is within the chain by the attachment of a ___ group.

RNA polymerase

in transcription, the helicase function is taken over by ___ _____.

topoisomerases ( 2 of the tpye I, and 1 of the type II), IA, IB,

in supercoiling, there are three types of ____. In the type __, you basically have a cleave and pass mechanism. In the type ___ topoisomerase, you have a cleave and rotate mechanism. In type ___ topoisomerase, you actually have a cleave and pass mechanism.

shine-delgarno

in terms of initiation of translation, the ___-____ sequence is relavant mostly in prokaryotes. Nothing else. For eukaryotes, the initiating AUG is detected within the mRNA not by its proximity to a ___-____ like sequence, but by a scanning prpocess until the first AUG is encountered from the 5' end.

footprint

in the DNA ____ anaylsis, the footprint is usually where there are missing bands, which indicates that that's where DNAase was unable to cut.

NTPs

in the DNA footpring, the way that you make sure that the RNA polymerase is stuck at the promter is by holding back the _____.

zinc finger

in the ___ ___ motiff, you have about 30 amino acid residues that form an elongated loop held together at the base by a single __ ions which is coordinated to four of the residues in the loop (usually four Cys, or two cys, or two his)

zinc finger

in the ___ ___ motifff of protein-DNA interactions, you actually get chelation of the Zinc ion with either 4 cystiene residues or 2 cysteines and 2 histidine.

cAMP, activator

in the absence of glucose, enzyme III of the phosphotransferase system transfers a phosphate onto adenylate cyclase, which activates it, and this creates more ___, which can join with CRP to create an activated complex and bind to the lac operon and act as an ____.

H

in the carboxy terminal domain, the phosphorylation happens via TFII_, which also has a helicase function

hliecases, supercoils, topoisomerase

in the case of DNA replication, if you take on the role of ___, then you willl slowly start to get ______, and this will need to be fixed by ___.

earlier, later

in the cell cycle, some of the things tend to fire ____ while other things tend ot fire ___. The ORIs happen in g1, and we don't know why come things fire early or later - it is an unsolved problem.

60, 100

in the end problem of the replication, what you get is a loss of about _-___ bases at the ends every time that DNA is replicated.

translocation

in the final step of the elongation process is called ____, where the ribsome moves one codon toward the 3' end of teh mRNA.

30, 50, 30

in the first step of initition, IF1 and IF3 bind to the ribosome and this causes dissociation of the 70S ribosome into its __S and __S parts. The inititation factors remain stuck to the __S subunit.

aminoacyl tRNA, aminoacyl-tRNA-EF-Tu-GTP

in the first step of the elongation cycle, the incoming ___ -___ binds to a complex GTP bound Elongation factor-Tu. So you get a compelx of ____-__-__-__-___

repressor

in the lac operon, the LacI portion encodes the lac ____ and the Lac Z, y, and A encodes the structural genes of tthe operon.

hydrophobic, DNA

in the leucine zipper, the alpha helices are held together by ____ interactions, mostly between the leucine sidechains. The basc protein side regions are usually the ones the end up interacting with the __

2, 1, 3 (steps 1 and 3 are incorporation of a new aminoacyl tRNA and translocation)

in the overall process of elongation, which takes 3 steps, there is a usage of _ GTP(s), and they occur in step _ and step _.

amino

in the peptide bond formation, the ___ group of the amino acyl tRNA in A-site nucleophilically displaces the tRNA of the peptidyl tRNA in the P-site.

inducible

in the presence of an incudcer, there is a 1000 fold increase in enzyme. In other words, B-galactosidase is _______.

primer, lagging strand

in the presence of telomerase. you only add to the leading strand, and thus, after the leading strand has gone on for enough, a new ___ is synthesized and used for __ ____ synthesis.

translocation, a, p

in the process of ____ within elongation, you get movement of the peptidyl tRNA from the _ site to the _ site. The uncharged tRNA is now in the E site. Once it is there, it just normally leaves.

GTP

in the process of adding on amino acids to teh growing peptide chain, you actually get hydrolysis of two ___ (hydrolyzed to GDP + P). Ribosome moves from codon to codon along the mRNA toward the 3' end.

GTP,

in the process of elongation, one ___ is used in the process of getting a new aminoacyl tRNA to bind and another is used in the process of ____.

GTP

in the process of eongation, you initially have a complex of aminoacyl-tRNA-EF-Tu-GTP , and from there, you ge hydrolysis of teh ___ , and the Ef-Tu-GDP complex is released

30, mRNA, tRNA< formylmethionine

in the second step of the process of initiation of translaton you get the _S subunit binding to the ___ and the ___(for the ______) IN PROKARYOTES.

U1, U2, U5, U4, U6

in the spliceosome assembly, you have the first step as the __ snRNP binding to the 5' junction site, next a ___ snRNP binds to the branch point within the intron, and lastly, after completion of the 3' junction site, the __ snRNP binds. Then __/___ join the complex.

50, GTP, GDP, P

in the third step of the initiation of translation of prokaryotes, you get combination with the __S ribosomal subunit, and simultaneously you also get hydrolysis of the ___ that was attached to the IF2 in the stpe II. The resulting __ and _ are released from the complex and the three initiation factors depart from the ribosome from this point.

H

in the transcription complex initiation, the TFII_ has helicase activity, and it is also the last transcription factor to bind, so nbd.

protein sequence alignments, clamp

it is important to know that there are a large number of DNA polymerases and that tehy are group into families based on ___ ___ ___. Furthermore, not all are processive, and thus, do not need a ___. Some can help with repair and recombination!

prokaryotes, eukaryotes

it is important to remember that whenever sigma factors are mentioned, they are usually in relation to ____, not ____.

archaea, eubacteria

it is not right to say that prokaryotes do not have introns. This is because ___ do have introns and ___ do not have intros.

2.4 nm, 1.1 mm

john cairns had a problem becuase DNA was too skinny to be seen without the EM ___ wide, and it was too long to be seen with the EM ____ long. So his solution was to make DNA look really fat and then visualize it with a LM. He pasted many fields together so an entire molecule could be reconstrcuted

unidirectional, circular

john carin believed in ____ replicatication from a fixed origin. This was incorrect. But he also figured out e coli chromosome was ___ and 4700 kb, and 1.1 mm long, so not a total loser (jk love you)

200 (there are 200 twists and 0 supercoils)

let's say that we have a genome that is made of 2,000 bases, and that you have 10 bases/turn. Assuming you are in the relaxed state, what is the linking number of this?

cancer

linear ends to the chromosme are a real problem! Telomerase is only active in a developing fetus,cancer cells, and thus, if we can inhibit telomerase, we can treat ___. This is also one of the reasons why the length of telomeres can affect your life expectancy.

twists, writhes

linking number = ___ + ____

weak

many eukaryotic DNA-binding proteins contain zinc fingers. They interaction of a single zinc finger with DNA is usually __ and many DNA binding proteins have multiple zinc fingers that substantially enhance binding by interacting simultaneoulsy with DNA.

inactive, active

mathylation is usually associated with transcriptionally ____ genes, and acetylation is associated with transcriptionally ___ genes.

signal sequence, n-terminal

membrane proteins usually contains a __ ___ (about 20 amino acid sequence that facilitates transport of teh protein through the protein). This sequence is usually near the __-___ end of the protein.

ancient bacteria

mitochondria and chloroplasts are through to be derieved from engulfment of ____ _____.

active, rRNA

nucleosomes are entirely absent in regions that are very __ in transcription, such as ____ genes.

DNA

nucleosomes much be removed from the ___ to allow for open complex formation.

start

nucleotides are numbered from the transcription ___ site. Positive numbers to the right and negative numbers to the left.

260

nuleotides, because of their resoance absorb UC light and they have a peak around ____ nm.

translation

of all the antibiotics, the process that is affected the most is the process of ____.

false (do not require ATP

of the four groups of introns, I and II are self splicing and require ATP.

excision repair enzyme

scientists used liposomes filled with ___ ___ ___ on people who had xeroderma pigmentosa, and patients shouwed 11/3 fewer cancers than controls after treatment!

initiation

single origins in bacteria at a unique site on the chromosome allows regulation at ____.

antibiotic resistance, larger, smaller, conjugation

the conjugative plasmid and non-conjugative plasmid are similar in that they both can contain genes that confer ___ _____. However, conjugative plasmids are usually ___ (smaller/larger), and present in ___ (higher, smaller) quantities. The main difference, however, is that the former codes for ____ functions, wherease the latter is not.

apoenzyme, holoenzyme

the core RNA polymerase enzyme with only about 5 subunits (2 alpha, 2 beta, and an omega) is an ____, but once sigma factor comes it, the entire enzyme becomes the ____

DNA A

the crucial compoentnet in the initiation process is the ___ _ protein

third

the degenceacy of teh genetic code is usually in the __ base pair - a phenomenon often known as wobble.

chromatin assembly factor 1

the deposition of new nucleotides is carried forward by ___ ___ ___ _ during replication.

R-factor, bacteria

the development of a plasmid that is resistant to LOTS of different antibiotics is present in the __-____, which can be transmitted via the process of transposons and conjugation. This is only one of the reasons why ____ are such ridiculous pathogens.

sliding clamp (beta clamp)

the difference betwen DNA poly III and I is that the III have a ___ ___. The I does not have this, so it falls off.

cyclin dependent kinase

the diffusable factor in Johnson's experiments ended up being a __ __ ___ and this is what regulates the firing of initiation in eukaryotes (the rate limiting step)

pilus

the donor cell produces the ___ in conjugation. From there, the ___ attaches to teh recipient cell and brings the two cells together. Here the memrbane fuse, and the plasmid is nicked and a single strand of DNA is transferred to the recipient cell. Then, the strands are filled back in, and you get a new F plasmid in both cells!

GTP

the energy source for protein synthesis is ___

B-galactosidase

the enzyme _-____ breaks the B-galactoside bond that is present in lactose, which breaks it up into glucose and galactose.

aminoactyl-tRNA synthetase

the enzyme ___-__ ____ joins the amino acid to teh tRNA.

cut, DNA

the enzyme ____ is used to break DNA in specific regions. This is good but it needs to be used such that there is an average of one ___ per ___ molecule

peptidyl transferase

the enzyme that catalyzes peptide bond formation is known as ___ ____, and it was never known what protein specifically did it. But later, they realized that this was actually catalyzed by rRNA of the ribosome.

hemi-methylated, methylase

the enzyme that is responsible for methylating the new strands after replication (which technically exist in a ___-_____ state for a while) is called a ____.

guanylyl transferase, 5, 5

the enzyme that puts teh 7 methyl guanosince on the 5' end is called ___ ____ (you need a GTP for this doe), and it's unique because its a ___' to ___' linkage.

60, 40, 80

the eukaryotic ribsome has a __S subunit with a __S subunit to make a combined ribosome equal to __S

diffusable factor

the experiments of Johnson and Johnson basically told us that there must indeed be a __ ___ that is helping determien teh cell cycle.

degenerate

the fact that an amino acid can be coded for by more than one codon implies that the genetic code is ____. This does not suggest that teh code i flawed.

major groove, minor goove

the fact that the two sugar phosphate backbones are not exactly opposite to one anotehr means that there is a __ ___ and a ___ __.

64, 20

the fact that there are ___ possible triplets, but only __ amino acids is what suggests the the genetic code is degenerate.

specificity,3', 5', DNA repair

the fidelity of DNA is due to three main reasons. the firs tmain reason is that the DNA polymerase enzyme relies on the ___ of base pairing to select incoming nucleotide (10^5), and thesecond is that, if the incorrect base is added, it can be removed by the __-___ exonuclease activity (adds on another 10^2), and the third one is that you have an additional sense of security via ____ ______.

P

the first formylmethionine that attaches to the ribosome attaches at the __ site.

mutations

the frequency of transpositions are low because these tend to create _____, which can kill!

natural selection

the genes that confer antibiotic resistance are just some of the the genes that are cloned onto plasmids via ___ ___.

redundant (degenerate okay)

the genetic code is _____

mRNA

the genetic code was cracked using artifical ___ templates.

lower

the higher the amount of AT base pairs in the DNA, the ___ its melting point. Thus, careful determination of the melting point of a DNA sepcimen can yield an estimate of its base composition.

zinc finger

the human gene hairless encodes a ___ ___ transcription factor in the brain the the skin. IF this is mutated, then you will get complete absence of hair follicles.

repressor

the inducer binds to the ____, and causes it to fall off the DNA. On the other hand, the repressor binds to the DNA

allolactose (binds to the repressor and causes it to dissociate off)

the inducer in the lac operon is the _____, which is an isomer of lactose.

AUG, methionine

the initiation codon, in ALL cells tends to be ___, and it codes for ___

30, mRNA, formylmethionine, GTP, 50 , Mg(2+)

the intiation of polypeptide synthesis in bacteria requires: ___S subunit, the ___ coding fo rthe polypeptide to be made, the initiating tRNA (which actually binds to the amino acid _____), a set of three initiation factors (IF1, IF2, IF3), ___ (energy source, the __S ribosomal subinit, and __(cofactor)

lariot

the introns that are released in the splicesomal method are usually in the shape of a _____.

spliceosomal introns, spliceosome.

the introns that we learned about in class are the _____ ____ because their removal occurs within and is catalyzed by a large protein complex called a ____

muli-subunit

the inverted repeats are really good places for ___-___ proteins to bind, like restriction endonucleases.

DNA loop

the lac repressor binds to the main operator site about the transcription start site and another operator (there are two others and it binds to one. In lecture, this is the one that is at +410). AFter binding to both sites, the repressor forms a ___ ___ which prevents RNA polymerase from transcribing the operon.

tetramer

the lac repressor is a ____ (decribe the number of subunits it has as a protein)

negative, positive

the lac repressor is a ____ regulatory element with respect to lactose and the cAMP receptor protein is a ___ regulatory element responsive to glucose levels.

operator, Z

the lac repressor works by binding to the first and second ____ regions. This literally loops out the lac __ gene which codes for beta galactosidase.

2, 4

the lactose operon has how many transcriptional start sites? translational?

protein, rRNA

the large and small subunits of the ribosomes are made of two main things. What are they?

carboxy terminal domain

the largest subunit of DNA polymerase II has an unusual feature and that is a long carboxy terminal tail that has many repeats of the amino acid sequence: YSPTSPS. This is known as the ___ ___ ___

continuously, discontinuously

the leading strand is created _____, whereas the lagging strand is made ____

single, multiple

the leading strand requires the use of ___ primer whereas the lagging strand requirres the use of?

integer

the linking number is always an ___ and it is broken down into two sub components called the writhe and twist, as a means of determining the local twisting.

right handed helix, left handed helix

the linking number is defined as + for strainds that are interwound in a ___-___ ___, and negative for things in a __-___ ___.

writhes, twists

the linking number is the number of ___ + _____ (which occur when the double strands cross over one another)

true

the loci in CRIPR seems to be related to phage DNA, and they thought it might protect the bacteria for so many time.

AT

the lower the ___ content that DNA has, the less likely you are to have adjacent thymines. This makes them less vulnerable to dimerization.

5, 3

the mRNA is translated in the __'-___' direction

30

the mRNA is usually boudn to the __S subunit of the bacterial ribosome.

F plasmid

the male bacterium in conjugation is the one thathas the __ ____, and the female does not have this.

helix turn helix (CAP, CRP also utilizes this domain, and so does the TRP repressor)

the mechanism by which the lac repressor binds to the DNA is via the ___ ___ ____ motif.

II, lariot

the mechanism that the spliceosome uses to cut out the intron is very similar to the one used by the group __ introns, where there is a buldged A and its hydroxy attacks the 5' end. This then cuts out one end, but not the empty OH attacks the U, so you get formation of a ___

N-methyladenine

the methylated adeniene in the GATC is called _-_____ (the 6th nitrogen, specifically)

e coli

the methylation of the GATC sequences helps differentiate old from new in _ ____, but hte mechanism by which we tell old from new in higher order organisms remains to be worked out.

EF-G

the movement of the ribosome requires the factor known as __-___, which is an important elongation factor. The enrgy for trnaslatiocation comes from the energy in a molecule of ___.

timer, 2, 1

the mutation that happens in the dna that is attempted to be fixed with the excision repair is fixed initially with a protein that is abbreviated UvrA2B, and this is a ___ that has _ UvrA and __ UvrB subunits.

epigenetics

this is the inheritance of gene expression states that are not encoded in the DNA - the stat can change without changing the sequence.

basic

the nucleotide bases are ___ in solution and can take on a proton

stack

the nucletotide bases tend to ___ on top of one naother. TTis involves a combinatior of van der waals forces dipole/dipole interactions between the bases. it also helps minimize the contact of the bases with water.

UAA

the ochre stop codon is ___ __ __

methylated adenine

the older DNA strand, in mismatch repair, tends to label the older DNA strand with a ___ ___ within GATC.

helicase II

the oligonucleotide that is initially cut out from the nucleotide excision repair is initially cut by uvrBC. after it is cut, the oligonucleotide is removed by ___ __.

UGA

the opal stop codon is __ __ __

CRP-cAMP

the open complex of RNA polymerase and the promer does not form readily unless the ___-____ is present to facilitate transcription.

2, Z

the operator binds to __ sites, and this loops out the lac __ gene.

sequence, chromatin structure

the origin of replication in bacteria is determiend by ____, but in eukaryotes, they are determined by ___ ____.

hemimethylated (and it can't get re-reprlicated until it has been completely methylated again. this is how regulation)

the origin of replication often tends to be methylated. However, after replication, the DNA is __-___, and the parents strands ahve the original methylation present, but the newly synthesized strands do not.

protein

the overall error rate of protein syntehsis is one mistake for every 10^4 amino acids. This is not nearly as low as DNA replication because flaws in a protein can be overcome by simply degrading the ____. This is enough to ensure that most proteins contain no mistakes and that thelarge amount of energy needed to make a protein is not waster.

two-fold, rotational

the palindromes in dna have __-___ ___ symmetry.

energy source, 23S rRNA

the peptide bond formation happens in the absence of an ___ ____ because it is catalyzed by the ___ _____.

23S rRNA

the peptidyl transferase, which was the activity that was referring to the thing that catalyzes formation of the peptide bond, is actually catalyzed by __ ___.

conjugation

the plasmids in yeast (pseduomonas) were just so great that they could be used to degrade lots of of odd things. This includes things like camphor, naphthalene, octance, salicylate, etc. So we then used this to our advtange because we basically cloned on specific genes into plasmids via natural selection. Then , as the palmids were transferred from one organism to another via ___, you can slowly get a population that digests things that might be harmful to anything else. This inlcudes oil and was how the oil spill was dealt with.

poly A binding protein

the poly A tail binds to the ___ __ ___ __ This tail is also required for binding the ribosomes and initiation protein synthesis.

g1, cdk

the pre replication complex assembles in the ___ phase of the cell cycle, adn initiation is activated by the presence of the activated S-phase _____

G1, CDK-cyclin

the pre replication complex formation is the first step of DNA replication firing in the eukaryotes. IT happens in the ___ phase and can only happen without _____ complex.

branching

the presence of ribose as a sugar in RNA instead of deoxyribose is bad because it increases reactivity. It also makes it more likely that ____ can occur since both the 2' and 3' hydroxyl can be involved in pshophodiester bonds.

DNase

the presence of the enzyme _____ in footprinting is what cuts up the DNA at literally every possible site.

UV

the problem is that ___ light causes the bases to dimerize, and this distorts the structure of DNA.

antibiotic resistance, transmissible

the problem of ___ ___ is now widespread. There are some bacteria that are literally resistant to everything. Hell, there are some that are resistant to drugs taht are not even released for public use yet. And the worst part is, many of the resistance genes are ____.

helicase, exonuclease, single stranded binding protein

the process of DNA digestion of something that is not correctly entered via mistamtch repair involves Mut S, MutL, and mut H. Once the complex is formed, the DNA is digested with the aid of ____ II, ___ I, and __ ___ ___ ___ (this is in ecoli, which is why this is mentioned)

redundant, amino acid (this isalso goes to show that if something lived in an area with loads of UV light, it would try to pick a codon that did not have an T or A)

the reason why we can have such a large variation in GC is because the genetic code is ___ and thus, mutations in the third nulceotide may not change the ___ ___ the codon is coding for.

Mg(2+)

the reason why we need to always include ___ when we're wokig with DNA is because it is an important cofactor. Specifically, it tends to add stabiization for the negatively charged backbone.

GTP, formylmethionine

the second step of the intiation of translation of prokaryotes requires 1 ___, because this is bound ot the transcription factor IF2 and needed for the third step. The IF2 is also complexed with the tRNA for ____, which is the first amino acid added in prokaryotes.

RNA

the seqeunce that telomerase consistently adds so is AGGGTT and that is to the 5' of DNA, and it does this by using ____ as a template.

pribnow box

the sigma 70 consensus seuqence is called the ___ ___

expressed

the sigma factor is very important in regulating the specificity of which genes are _____. For example, sigma 70 is for regular genes, sigma 32 is for heat shock genes, sigma 54 is for nitrogen related genes, sigma 28 is for flagella and chemotaxis, etc.

pribnow

the sigma factor on RNA polymerase recognizes two sequences. One of them is at -35 and the other one is at -10 and the one at -10 is called the ____ box.

spontaneous mutation

the significance of transposable elements is that they are a major source of ____ ____.

two trimers, three dimers

the sliding clamp in bacteria is made of __ ___ (called B sliding clamp, whereas in eukaryotes it is __ ___ (called PCNA). This is a closed circle, and it needs to be opened to bind to DNA and it tethers polymerase to DNA.

three dimers, two trimers

the sliding clamp is ___ ___ in eukaryotes, and in prokaryotes, it is ___ ___, but it is conserved for both eukaryotes and prokaryotes. IT basically tethers polymerase to teh DNA and it is a closed circle, but it must be opened to do its job.

4

the sliding clamp that is made for DNA polymerase III is made from __ B subunits. These subunits associate in pairs to form donut shaped structures that encircle the DNA and act as a clamp.

telomeres

the solution for eukaryotes to the end replication problem is that their ends contain ___, which are short repetitive DNA segments.

small nuclear ribonuclearproteins (snRNPs)

the splceosome is made up of specialized RNA protein compelxes, which are referred to as __ ___ ___ ___

small nuclear RNAs

the splicesosome is made up of small nuelcuear riboproteins called snRNPs. Within them, there are a class of eukaryotic RNAs that are about 100-200 nucleotides long known as __ ___ ___

sliding clamp

the stability for DNA polymerase that participates in replication is provided by the __ ___.

van der waals

the stacking between bases relies on ___ ___ ___ interactions.

DNA topoisomerase (II or I = depends)

the strain that is induced on DNA because of the DNAb activity is often relieved by ____ ____ in front of the helicases activity.

5, 3, 3, 5

the strand that goes _' to _' form left to right is the watson strand, but _' to _' is crick and this is also left to right.

template, coding

the strand that is copied during transcription is called the ___ strand, and the one that is not copied is called the ___ strand.

right hand

the structure of DNA polymerase resembles that of a ____ __. The catalysis occurs in the palm domain the two metal ions coordinate at the 3' end and incoming nucleotide.

identical, 6, helicase

the subunits of DNAb are ____, and there are __ of them, and DNAb is another name for the protein ___.

positive supercoiling

the super coiling that takes place as a result of overwinding is called ___ _____.

negative supercoiling

the super coiling that takes place as a result of underwinding is called ____ ____.

75

the t RNA is about __ nucleotides long and half of them are involved in h bonding to one another to make double stranded RNA.

TFIID

the tata binding protein (TBP) + tata binding protein associated facotrs (TAFs) = ____ (abbreviation)

leading strand, lagging strand

the telomerase mechanism literally only adds to the ___ ___, and as it does this, the process of making -__ ___ also continues because, once the extension gets long enough, you put down primer, and follow it as you normally do.

UvrA2B

the term excinulcease is used to describe _____, which represents the three subunits of proteins that are used to

males, F-plasmid, pilus

the thing about conjugation that is slightly odd is that after it actually happens, both the parties are ____ becuase both of them have the __-____, and this factor actually ends up coding for the ____ That is then used to make more!

chromatin assembly factor I

the thing that adds in new nucleosomes in dna replication is called ___ ___ ___ __. (CAF1)

codon, first, anticodon

the third base on the ____ and the ____ base on the ____ pair rather loosely with one another, and this causes the wobble phenomenon.

wobble

the third base on the mRNA and the first base on the tRNA pair rather loosely with one another, and this causes the _____ phenomenon.

arg, leu, ser

the three amino acids that has 6 codons coding for them are:

home, hospitals, farms

the three main places that antibiotic resistance tends to happen the most are: ___, ___ and ___

oxidative damage, radiation (UV, cosmic, radioacitivty), and spontaneous depurination

the three main things that dmage the DNA include:

UAA, UAG, UGA

the three stop codons include: ___ , __, and ___

D

the transcription factor IIA, is also known as transcription factor II_ or TATA binding protein (TBP). This then binds to the TATA binding region. This then recruits TFIIB, and TFIIF with polymerase II. After this TFIIE and TF IIH join. TFII_ has helicase activity, which actually causes the closed complex to become open and unwinds the DNA.

B

the two __ subunits of E coli polymerase III form a circular clamp that surrounds the DNA. This increases processivity to greater than 500,000 by preventing its dissociation from the DNA.

RNA polymerase

the two large subunits of RNA polymerase II show extensive homology to each other and to the B' subunit of the prokaryotic ________ _________.

ribose, deoxyribose, uracil, thymine

the two maindiferent betweenDNA and RNA respective: ___ instead of ____ as the sugar, and ___ instead of ___ as the base.

topology

the understanding of DNA supercoiling is faciliated by ____, in whcih the properties of an object do not change under continuous deformation.

origin

the unwinding of the ___ is the regulatory step of the process of replication

bending

the way that the TATA binding protein changes the shape of DNA by bending it 100 degrees is the first sign that DNA itself was not a rigid rod.Showed that you can get higher order ____ to get functions you want.

Tm

the___ is known as the temperature at which the DNA is half unwound. And because DNA rich in GC melts at a high temperature than AT, you can estimate the average GC content of DNA from Tm.

3, 2, lacZ

there are __ operator binding sites, but only __ get used to loop out lac Z. One is right after the promoter and hte other is right after_____.

spontaneous depurinations

there are about 10,000 ___ ____ events/cell/day

200, 140

there are about ____ bp for each repetition of histones, and of this, ___ are wrapped around the histone and the rest are linked DNA

lysine, arginine

there are large amounts of ___ and ___ in histones becuase they are largely basic molecules.

modified bases

there are loads of ____ ___ that are present in tRNA. This helps preserve its unusual structure and protects its degradation from RNAase.

mutation

there are some cancers that are actually based on viruses, such as HPV. However, most are based on the fact that there was some inherent ____ that cause out of control growth.

aminoacyl-tRNA, peptide bond, translocation

there are three steps involved in elongation: initially, you have binding of an incoming ___-___ and next you have ___ ___ formation, and lastly, you have ____.

n, n-2

there are usually two alternatives. You can have either 2 negative supercoils with ___ turns of the helix or you can have closed, circular DNA with no supercoils, ____ turns and a loclly unwound region that takes up the space of the 2 turns.

splicing

there is a coordation between transcription and _____ within eukaryotes. Well, it technically has to be eukaryotes because prokaryotes (except archae) don't do this process.

pribnow

there is an important region where RNA polymerase binds at the -10 region and that is known as the ____ box for prokaryotes (related to the TATA box for eukaryotes)

episomes

these are genetic elements inside bacterial cells that can replicate independently of the host or by integrating into the chromosome.

protein synthesis factors

these are proteins or enzymes which are needed for protein synthesis, but are not actually part of the ribosome and do not co-purify with it.

intra chromosomal recombination

this is the hardest for you to remember, but plaindromic sequences allow for __ ___ ____. aka the recombiantion that helps repair the y chromosome.

proofreading

we think that we might have RNA primers because it provides us with an extra ____ step (at least that's what we thing. evolution is the best tinkerer, and no better solution emerged).

tRNA

what RNA molecule bridges the gap between mRNA and protein?

prevents loss of information from chromosome ends, prevents end of chromosomes form being fused to other chromosomes by repair enzymes, and when we run out, their lack arrests growth and apoptosis.

what are the benefits of telomeres?

binding of multi-subunit proteins, formation of hairpins, intrachromosomal recombination

what are the three functions of inverted repeats?

pentose sugar, phosphate group(s), and nitrogenous base

what are the three things that a nucleotide has?

SAM (S-adenosylmethionine)

what donates the methyl groups that are added to the guanosine, and the first and second nulceotides adjuacent to the end?

conjugative (30-100kb, whereas non-conjugative is 3-10kb)

what is bigger: conjugative or non-conjugative plasmids?

RNA polymerase I

what is the most active RNA polymerase in eukaryotes?

5, 5

what kind of phosphodiester linkage is prevalent in the 5' cap? __'-__'.

helix turn helix

what motiff does cAP/CRP use to bind to the promoter? the lac repressor does this as well.

Cys (all four), His (or 2 cys with 2 his)

what two amino acids help chelate the zinc in the zinc finger motiff?

good

when CRP-cAMP binds to DNA, it causes the DNA to bend, and this turns a bad promoter, which it actually is because it does not match the consensus sequence of sigma 70 very well. into a ___ promoter.

ATP

when DNAA binds to the DNA, it forms a helical filament, and this is what cuases the bubble to form. To let DNAB leave the complex that it is initially in with DNA C, the original DNAC moelcule hydrolyzes ____.

closed, open

when RNA polymerase binds to the DS DNA at the promoter site, there is a ____ complex, and an ____ complex The former is when the bound DNA is intact and partially unwowund near the -10 sequence and the latter is when the bound DNA is intact

charged,

when an amino acid is added on to the tRNA< the tRNA is said to be ____.

adenine, thymine

when chargaff ran the bases on the gel ___ migrated the least (because it has the highest mass) and ___ migrated the arther.

ss

when does chargaff's rule not apply? (ds or ss?)

absent

when glucose and lactose are present, the lac operon is off. This is ebcause of cAMP and cAMP receptor protein (CRP - aka CAP). This is a homodimer with binding sites for DNA and cAMP. However, this only binds to the lactose operon when glucose is ___, and this stimulates RNA transcription 50 fold!

arrest, apoptosis

when telomeres are too short, they cause the growth to ____ and then undergo ____.

female cell

when the pilus binds to the ____ ____, then it starts to extract and head back toward the place where it came from.

inhibition, apoptosis

when there simply are not enough telomeres left, and not neough telomerase to extend it, we induce ___ of growth and ___ (programmed cell death)

cya, crp

when they looked for mutants to understand the catbolite repression in the lac operon, they found ___ mutants and ___ mutants. The first ones were mutated in the adenylate cyclase genes (which means they could not make cAMP) and the second ones were mutated in the gene that makes cAMP receptor protein

200

when they used an endonuclease to cut the DNA they always got base pairs in multiples of ___, which suggest that the basic nucleosome subunit included this many base pairs. They basically did this by cleaving with endonuclease, labeling the DNA with ethidium bromide against a ladder and seeing what is what size.

buldge

when you put an A with a G, you get a ___ in the DNA, and this signals to teh DNA that it is made a mistake. So it uses its 3'-5' exonuclease activity to replace it.

bubbles, AT,

when you start heating dna to denature it, the first thing you'll get are called ____ and they occur in regions have are rrich in ___ base pairs Often times, DNA replication starts in sites like these.

nucleus, nucleus, cytoplasm

where does splicing occur in eukaryotes? what about transcription? translational?

efficiency (aka bacteria with small genomes can often grow more quickly than those with large genomes- so there is a tradeoff between having all these plamids and actually living a goodlife)

why are some carbon source utilization genes maintained on plasmids while others are not?

open

with CRP-cAMP, RNA polymerase and no repressor, you get formation of the ____ complex, which permits transcription to start.

sigma factor

without the ___ ___, the RNA polymerase moves at 1/50 of its original speed and loses its specifictit

negative supercoil, supercoil

wrapping DNA around histones is an example of a ___ ___, which, if you have to conserve the linking number, will lead to a positive ___ elsewhere in the molecule.

nuclease

xeroderma pigementosa is a result of a mutation in the ____ involved in excision repair.

DNA-protein, protein-protein

zinc fingers and helix turn helix are both structural motifs for ___-_____ interactions. On the other hand, however, there are also ___-____ interactions that are needed,