Cell And Molecular Exam 2

Front 1

Why was protein thought to be the genetic material?

Back 1

Researchers first learned that chromosomes contained both DNA and protein - they just werent sure which of these components encoded the organism's genetic information. Biologists in the 1940s had difficulty accepting DNA as the genetic material due to its simple structure of only a long polyer composed of only 4 types of nucleotide subunits, which are chemically very similar.

Front 2

What early evidence was there that DNA was the genetic material?

Back 2

Researchers learned that chromosomes contain both protein and DNA. In the early 1950s, DNA was examined by X-ray diffraction analysis, showing a 3D atomic structure of DNA. The DNA appeared as two strands wound into a helix. The double stranded helix of DNA was important in that it provided immediate suggestion on how DNA could encode the instructions necessary for life, and how these instructions could be copied and passed along when cells divide.

Front 3

Why was the genetic material called "Transforming Activity?"

Back 3

Fred Griffith performed an experiment using Strep. pneumoniae and mice. Living S strain killed mouse, living R strain allowed the mouse to live. Heated living S strain, mouse lived. Heated living S strain combined with living R strain, mouse died. This showed that the harmless R strain of S. pneumoniae could be transformed into the pathogenic strain. That is why the genetic material was called "transforming activity."

Front 4

Describe or draw the structure of a nucleotide. Know the structure of its three components.

Back 4

Front 5

Draw or describe each of the 4 nucleotides

Back 5

Front 6

Draw or describe a base pair

Back 6

A bulkier two ring base, a purine, is paired with a single ring base, a pyrimidine. [Complementary base pairing] Phosphate, sugar, and base pair for each nucleotide

Front 7

What are the major and minor grooves of DNA?

Back 7

The wider groove is called the major groove and the smaller one is the minor groove.

Front 8

What is chromatin? Euchromatin? And Heterochromatin?

Back 8

Chromatin is the complex of both classes of protein [histones and nonhistone chromosomal proteins] with nuclear DNA.

Euchromatin are the rest of the interphase chromatin where heterochromatin arent.

Heterochromatin is the most highly condensed form of interphase chromatin. They typically make up about 10% of interphase chromatin. In mammals, heterochromatin are concentrated around the centromere region and in the telomeres at the ends of chromosomes.

Front 9

What are the three levels of chromatin (DNA) structure? What structural features does each of these levels include?

Back 9

Primary = naked DNA that you hardly find in nature

Second level = beads on a string

Third level = 30-100 meter fiber structure

Front 10

What is a histone?

Back 10

One class, out of two, of the proteins that bind to DNA to form eukaryotic chromosomes. Histones are present in large quantities, and their total mass in chromosomes is about equal to that of the DNA itself. Histones are responsible for the first and most fundamental level of chromatin packing, the nucleosome

Front 11

What are the structural components of a nucleosome?

Back 11

An individual nucleosome core particle consists of a complex of eight histone proteins and a stretch of double stranded DNA, 147 nucleotide pairs long, that winds around this histone octomer.

Front 12

Be able to draw schematically the structure of the histones and DNA in a nucleosome

Back 12

Front 13

What are the five classes of histones found in nucleosomes?

Back 13

H1/H5, H2A, H2B, H3, H4

H2A, H2B, H3, and H4 are considered core histones

H1 and H5 are considered linker histones which helps to pull nucleosomes together and pack them into a more compact chromatin fiber.

Front 14

Which histones are found in the core nucleosome, and how do they interact?

Back 14

H2A, H2B, H3, H4

These four histones make up the octamer and are relatively small proteins, with high proportion of positively charged amino acids (lysine and argenine). The positive charges help the histones bind tightly to the negatively charged sugar-phosphate backbone of DNA. These electrostatic interactions explain why DNA of any sequence can bind to a histone octamer. The histones in the core also have a long, unstructured N-terminal amino acid "tail" that extend out from the nucleosome core particle. These histone tails are subject to several types of reversible, covalent chemical modifications that control many aspects of chromatin structure.

Front 15

How does the DNA interact with the histones in the nucleosome?

Back 15

--

Front 16

What is the length of DNA found in a core nucleosome?

Back 16

The nucleosome core particle consists of approx. 146 base pairs of DNA

Front 17

What is the 30 nm fiber structure of chromatin?

Back 17

Multiple histones wrap into a 30 nm fiber consisting of nucleosome arrays in their most compact form (heterochromatin).

Front 18

What is the function of histone H1 in the 30 nm fiber structures?

Back 18

With addition of H1, the beads on a string structure in turn coils into a 30 nm diameter helical structure known as the 30 nm fiber

Front 19

What is the central dogma of molecular biology? Which are "2-way streets," which are not?

Back 19

The central dogma is the flow of genetic information in cells from DNA to RNA to protein. All cells express their genetic information in this way

Front 20

What are the primary structure differences between RNA and DNA?

Back 20

RNA contains the sugar ribose vs DNA which contains the sugar deoxyribose [has an additional -OH group]. r

RNA contains the base Uracil vs DNA which contains Thymine

Front 21

What is meant by the DNA double helix being "anti-parallel?"

Back 21

DNA has two strands that run in opposite directions.

Front 22

Be able to draw the short form nomenclature of a nucleic acid molecule

Back 22

--

Front 23

Why is the double-helical structure of DNA excellent for a mechanism of DNA replication?

Back 23

Each strand of a double helix contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand. Each strand can therefore serve as a template strand for the synthesis of a new complementary strand. Thus, the genetic information can be accurately copied.

Front 24

Describe a typical replication origin

Back 24

The process of DNA synthesis is begun by initiator proteins that bind to specific DNA sequences called replication origins. The initiator proteins pry the two strands apart, breaking the hydrogen bonds between the bases . The exposed single strands form a bubble called the replication origin which serve as templates for copying DNA

Front 25

What are the number and components of a bacterial origin of replication?

Back 25

In simple cells such as bacteria or yeast, replication origins span approx. 100 nucleotide pairs. They are composed of DNA sequences that attract the initiator proteins and are especially easy to open.

A bacterial genome has a single replication origin.

Front 26

How are eukaryotic origins of replication organized?

Back 26

--

Front 27

Describe a replication fork its direction and speed?

Back 27

DNA molecules in the process of being replicated contian Y-shaped junctions called replication forks. Two replication forks are formed at each replication origin. At each fork, a replication machine moves along the DNA, opening up the two strands of the double helix and using each strand as a template to make a new daughter strand. The two fork move away from the origin in opposite directions unzipping the double helix and replicating the DNA as they go, hence the term bidirectional. The forks move very quickly - at about 1000 nucleotide pairs per second in bacteria and 100 nucleotide pairs per second in humans.

Front 28

What is an asymmetrical replication fork?

Back 28

At each replication fork, one new DNA strand is being made on a template that runs in one direction (3' to 5'), whereas the other new strand is being made on the template that runs in opposite direction (5' to 3'). Therefore, the replication fork is assymetrical.

Front 29

What are the differences between the leading and lagging strands during replication?

Back 29

The DNA strand that appears to grow in the incorrect 3' to 5' direction is actually made discontinuously, in successive, separate, small pieces. This strand is called the lagging strand because the backstitching creates a slight delay in the process.

The other strand is synthesized continuously, the leading strand.

Front 30

What does 3'->5' mean? What does 5'-3' mean?

Back 30

3' and 5' indicate the carbon numbers in the DNAs sugar backbone. The assymetry gives DNA a "direction."

Front 31

Describe the chemistry of DNA synthesis?

Back 31

DNA synthesis starts at a specific place on a chromosome called the origin. One daughter strand is initiated at an origin on one parental strand and another is initiated at another origin on the opposite parental strand. Replication of both strands is initiated at one origin.

Front 32

Replication proceeds at replication forks in E. coli in a semi-discontinuous manner.

What does semi-discontinuous mean?

Back 32

Semidiscontinuesmeans one template molecule is replicated continuously and the otherdiscontinuously. The property is that the DNA polymerase can only go from 5’ to3’. Because the DNA is complementary, the polymerase adds the nucleotides fromthe 3’ end to the 5’ but moves in the 5’ to the 3’ end. Priming problem of anokazaki fragment, is the DNA polymerase can only synthesize if there is a primer.So the primase makes and RNA primer. The RNA primer is a god solutions becausethe DNA polymerase does not make mistakes so the RNA primer can be recognizedby not being a DNA primer so it can be removed later. The nuclease removes the primer. The ligaseremoves the nicks.trs6S)

Front 33

Replication proceeds at replication forks in E. coli in a semi-discontinuous manner.

What property of DNA polymerases results in the need for semi-discontinuous synthesis?

Back 33

See previous

Front 34

Replication proceeds at replication forks in E. coli in a semi-discontinuous manner.

What is an okazaki fragment?

Back 34

When a strand is being made discontinuously, small pieces are separating from the strand. These small pieces are called okazaki fragments which are later joined together to form a continuous new strand.

Front 35

Replication proceeds at replication forks in E. coli in a semi-discontinuous manner.

What is the "priming problem" for synthesis of an okazaki fragment?

Back 35

--

Front 36

Replication proceeds at replication forks in E. coli in a semi-discontinuous manner.

Why is an RNA primer a good solution to the priming problem?

Back 36

--

Front 37

Discuss DNA replication proofreading

Back 37

DNA polymerase is self-correcting - it has two special processes that help the accuracy of this idea. First, the enzyme carefully monitors the base-pairing between each incoming nucleotide and the template strand. Only when the match is correct does DNA polymerase catalyze the nucleotide-addition reaction. Second, when DNA polymerase makes a rare mistake and adds the wrong nucleotide, it can correct the error through an activity called proofreading. This process occurs during DNA synthesis. The polymerase will clip off the mispaired nucleotide and try again. Proofreading is carried out by nuclease that cleaves the phosphdiester backbone. This is why DNA polymerase must polymerize in the 5' to 3' direction.

Front 38

Describe the general properties of DNA polymerase

Back 38

Self-correcting

Polymerizes nucleotides to the DNA strand

3'-5' exonuclease

Can only polymerize in 5' to 3' direction

Can only add nucleotides, not start a new DNA strand

Keeps mutation rate low

Front 39

What is semi conservative DNA replication? Why is this an important feature of DNA replication?

Back 39

Each parent strand serves as a template for the synthesis of a new daughter strand. The first round of replication would produce two hybrid molecules, each containing one strand from the original parent in addition to one newly synthesized strand

Front 40

What are primases used for in replication? What do they synthesize?

Front 41

How are okazaki fragments resolved into a continuous lagging strand?

Back 41

--

Front 42

What is a DNA helicase? Discuss the structure of helicases

Back 42

DNA helicase unzips the DNA during DNA replication

DNA helicase sits at the front of the replication machine where it uses the energy of ATP hydrolysis to propel itself forward, pryign apart the double strand helix as it speeds along the DNA

Front 43

How does DNA polymerase move and stay connected to the DNA?

Back 43

An additional replication protein called a sliding clamp keeps DNA polymerase firmly attached to the template while it is synthesizing new strands of DNA. If left on their own, DNA polymerases would synthesize only a short string of nucleotides before falling off the strand.

On the lagging strand, the clamp has to detach each time the polymerase completes an okazaki fragment

Front 44

Describe how the replication machine is assembled? How does it move?

Back 44

(Helicase energy)

Front 45

Describe a typical telomere

Back 45

Long repetitive nucleotide sequence at the end of their chromosomes which are incorporated into structures called telomeres. These sequences attract an enzymes called telomerase to the chromosome ends. Using an RNA template that is part of the enzyme itself, telomerase extends the ends of the replicating lagging strand by adding multiple copies of the same short DNA sequence to the the template strand. This extended template allows replication of the lagging strand to be completed by conventional DNA replication.

Front 46

What is a "mis-match"?

Back 46

Mismatch pair is a backup to the proofreading abilities of DNA replication. Mismatch pair is dedicated to correcting the errors missed by proofreading. DNA mismatch repairs 99% of these errors. A complex of mismatch repair proteins recognize a DNA mismatch, remove a portion of the DNA strand containing the error, then resynthesize the missing DNA. This repair system corrects the sequence.

These play an important role in preventing cancer.

Front 47

What is depurination and deamination?

Back 47

Depurination and Deamination are the most frequent chemical reaactions known to create serious DNA damage in cells.

Depurination removes a purine base from a nucleotide, giving rise to lesions that resemble missing teeth. [G or A = purines]

Deamination is the spontaneous reaction of an amino group from a cytosine in DNA to produce the base uracil.

Front 48

What are the three most common types of damage that happen to DNA?

Back 48

Depurination

Deamination

Oxidative damage to nucleotides

Front 49

Why is the presence of uracil in DNA bad?

Back 49

Could lead to substitution of one nucleotide pair for another as a result of incorrect base-pairing during replication or to deletion of one or more nucleotide pairs in the daughter strand after DNA replication. Some damage could also stall the DNA replication machinery at the site of the damage

Front 50

What is the recognition or strand specificity problem in DNA repair? How have cells solved this problem?

Front 51

What are the three basic steps in base excision repair?

Back 51

1. The damaged DNA is recognized and removed. These involved nucleases, which cleave the covalent bonds that join the damaged nucleotides to the rest of the DNA strand, leaving a small gap on one strand of the DNA double helix in the region.

2. A repair DNA polymerase binds to the 3'-hydroxyl end of the cut DNA strand. It then fills in the gap by making a complementary copy of the information stored in the undamaged strand. Repair DNA polymerases synthesize DNA strands in the same way.

3. Wen the repair DNA polymerase has filled in the gap, a break remains in the sugar-phosphate backbone of the repaired strand. This nick in the helix is sealed by DNA ligase.

Front 52

What is homologous recombination?

Back 52

If a double stranded break occurs shortly after a stretch of DNA has been replicated, the undamaged double helix can readily serve as a template to guide the repair of the broken DNA: info on the undamaged strand of the intact double helix is used to repair the complementary broken strand in the other. [Two identical nucleotide sequences outside the broken region]

Front 53

Describe a holliday junction

Back 53

The DNA crossover idea, looks like an X or a + with the replication bubble in the center

Front 54

What is bacterial transposable element? Why are they called "hopping genes"?

Back 54

--

Front 55

What are the main differences between replication and transcription?

Back 55

Transcription is the process of expressing one of its many thousands of genes by copying the nucleotide sequence of that gene into RNA.

RNA uses ribonucleotides vs deoxyribose in DNA and RNA also contains Uracil instead of Thyamine in DNA. RNA is also single stranded so it can fold up into a variety of shapes.

Unlike a newly formed DNA strand, the RNA strand does not remain hydrogen bonded to the DNA template strand. Instead, just behind the region where the ribonucleotides are being added, the RNA chain is displaced and the DNA helix reforms. Also, because RNAs are copied from only a limited region of DNA, RNAs are much shorted than DNA molecules.

Front 56

What are ribonucleotides? How do they differ from deoxynucleotides?

Back 56

Ribonucleotides are sugars that contain ribose rather than deoxyribose; Ribose has an additional -OH group in comparison

Front 57

Describe a generic RNA polymerase

Back 57

RNA polymerase links the ribonucleotides to the growing RNA chain. They catalyze the formation of phosphodiester bonds that link the nucleotides together to form the sugar phoshate backbone of the RNA chain. The RNA polymerase moves stepwise along the DNA, unwinding the DNA helix just ahead to expose a new region of the template strand for complementary base pairing.

Can start an RNA chain without a primer.

Front 58

How does bacterial transcription work?

Back 58

Sigma factor recognizes the promoter region. Then RNA polymerase determines which strand should be used for transcription. Then RNA polymerase polymerizes the strand for complementary base pairing with incoming ribonucleotides.

Front 59

Describe a typical bacterial promoter?

Back 59

A promoter contains a specific sequence of nuleotides that lies immediately upstream of the starting point for RNA synthesis. Each promoter has a certain polarity: it contains two different nucleotide sequences upstream of the transcriptional start site that position the RNA polymerase, ensuring that it binds to the promoter in only one orientation

Front 60

What is a sigma factor?

Back 60

Subunit of RNA polymerase

Responsible for recognizing the promoter sequence on the DNA. Each base presents unique features to the outside of the double helix, allowing the sigma factor to find the promoter sequence without having to separate the entwined DNA strands.

Front 61

What is the main function of a sigma factor?

Back 61

Responsible for recognizing the promoter sequence on the DNA.

Front 62

RNA polymerase transcribes from both strands. How is the transcript organized?

Front 63

- Eukaryotes have a more complex transcription machinery. Give a general overview ofthe steps involved in transcription and RNA processing

Back 63

RNA polymerase 2 cannot initiate transcription on its own. General transcription factors assemble on the promoter, where they position the RNA polymerase and pull apart the DNA double helix to expose the template strand, allowing the polymerase to begin transcription. The general transcription factors bond to a segment of the DNA which is mostly made up of Ts and As, TATA box. Other factors bind to the general transcription factor to form the general transcription complex. When RNA polymerase 2 finishing transcribing a gene it is released from the DNA

Front 64

What are he main differences between bacterial and eukaryotic transcription?

Back 64

1) Bacteria contain a single RNA polymerase whereas, Euks contain RNA Polymerase 1, 2, and 3. RNA polymerase 1 and 3 transcribe genes encoding tRNA and rRNA. RNA polymerase 2 transcribes the vast majority of eukaryotic genes, including those that encode proteins and miRNAs.

2) Bacteria RNA polymerase can initiate transcription on its own, eukaryotic RNA polymerases require the assistance of a large set of accesory proteins (general transcription factors)

3) Transcription in Euks have mechanisms that control its initiation which are much more complicated and elaborate that Bacteria.

4) Eukaryotic transcription initiation must consider packing the DNA into nucleosomes and more compact forms of chromatin structure

Front 65

What type of role does the compartmentalization (e.g., RNA is produced in the nucleus but translated in the cytoplasm) play in all of this?

Back 65

It allows splicing and processing of the RNA

Front 66

Why are eukaryotic mRNAs capped? How does capping function?

Back 66

RNA capping modifies the 5' end of the RNA transcipt, the end that is synthesized first. The RNA is capped by the addition of an atypical nucleotide - a guanine nucleotide bearing a methyl group. The capping occurs after RNA polymerse 2 has produced about 25 nucleotides of RNA, long before it has completed transcribing a whole gene.

Front 67

What is a lariat in RNA splicing?

Back 67

RNA splicing is where introns are removed from the newly synthesized RNA and the exons are stitched together.

The special sequences to be spliced are found at or near each end of the intron. A slicing machine cuts out the intron in the form of a "lariat" structure formed by the reaction of the "A" nucleotide, joining the two exons together into a continuous coding sequence. The lariat looks like a lasso.

Front 68

Describe snRNPs

Back 68

Small nuclear RNAs (snRNPs) are packaged with additional proteins to form small nuclear ribonucleoproteins. The snRNPs recognize splice-site sequences through complementary base pairing between their RNA components and the sequences in the pre-mRNA, and they also participate in the chemistry of splicing.

Front 69

Describe a spliceosome

Back 69

The large assembly of RNA and protein molecules that carries out RNA splicing in the nucleus.

Asplisosome is where an intron gets removed. SnRPs have RNA inside their proteincomplexes. There are 3 SnRPs, U1, U3 and U5? One recognizes the splicing on oneside and he second, recognizes an internal sequences of an intron. The thirdcuts the intron sequences and draws the introns together. Lariot, lasso….

Front 70

Describe some of the actions that take place at the nuclear pore when transporting“export-ready” mRNA.

Back 70

Transport of mRNAs to the cytosol from the nucleus is highly selective: only correctly processed mRNAs are exported. This selective transport is mediated by nuclear pore complexes. To be "export ready," an mRNA molecule must be bound to an appropriate set of proteins, each of which recogizes different parts of a mature mRNA moelcule. These proteins include poly-A-binding proteins, a cap-binding complex, and proteins that bind to mRNAs that have been appropriately spliced.

Front 71

For the RNA sequence below indicate the amino acids that are encoded in all threereading frames. If you were told that this segment of RNA was in the middle of an mRNA thatencoded a large protein would you know which reading frame was used to make the protein?How so?AGUCUAGGCCACUGA

Back 71

The answer is yes. How? It is a messenger RNA sequencebecause it has Us in it. The right reading frame: AGUCUA = first reading frame,GUCUA = second reading frame, UCUA = 3rd reading frame. If it has a stop codon, its at the end.

Front 72

- Define the genetic code and discuss its redundancy

Back 72

The rules by which the nucleotide sequence of a gene, through an intermediary mRNA molecule, is translated into the amino acid sequence of a protein.

Redundant by: several different codons can specify a single amino acid

Front 73

Describe the structure of a typical tRNA and highlight its function as a molecular adaptor

Back 73

The translation of mRNA into protein depends on adaptor molecules that can recognize and bind to a codon at one site on their surface and to an amino acid at another site. These adaptors consist of a set of smal RNA molecules called tRNAs.

Four segments of the folded tRNA are double helical, producing a molecule that looks like a cloverleaf.

Front 74

- What is a “wobble” position in the genetic code?

Back 74

Some tRNAs are constructed so that they require accurate base pairing only at the first two positions of the codon and can tolerate a mismatch (or wobble) at the third position.

Front 75

What enzyme couples the tRNA to the correct amino acid?

Back 75

Aminoacyl-tRNA synthetases; recognition and attachment of the correct amino acid depends on this enzyme

Front 76

Why are there only 20 aminoacyl-tRNA-synthases coupling as many as 48 (humans)different tRNAs?

Back 76

There is a different synthetase enzyme for each amino acid. Each synthetase enzymes recognizes specific nucleotides in both anticodon and the amino-acid-accepting arm of the correct tRNA

Front 77

Describe the molecular composition of a ribosome

Back 77

A large complex made from dozen of small proteins (the ribosomal proteins) and several crucial RNA molecules called rRNAs

Front 78

How is an mRNA molecule translated?

Back 78

The mRNA message is decoded by ribosomes.

1) A charged tRNA carrying the next amino acid to be added to the polypeptide chain binds to the vacant A site on the ribosome by forming base pairs with the mRNA codon that is exposed there.

2) The carboxyl end of the polypeptide chain is uncoupled from the tRNA at the P site and joined by a peptide bond to the free amino group of the amino acid linked to the tRNA at the A site. This reaction is catalyzed by and enzymatic site in the large subunit.

3) A shift of the large subunit relative to the small subunit moves the two tRNAs into the E and P sites of the large subunit.

4) The small subunit moves exactly three nucleotides along the mRNA molecule,bringing it back to its original position relative to the large subunit. This movement ejects the spent tRNA and resets the ribosome with an empty A site sot that the next charged tRNA molecule can bind.

Front 79

How does a ribosome select the reading frame?

Back 79

Only the appropriate tRNA molecules can base pair with each codon, this codon determines the specific amino acid added. The A and P sites are close together so that their two tRNAs are forced to form base pairs with codons that are contiguous, with no stray bases in between. This positioning of the tRNAs ensures that the correct reading frame will be preserved throughout the synthesis of the protein

Front 80

How is translation initiated in eukaryotes?

Back 80

With a start codon, AUG, and an initiator tRNA which always carries the amino acid methionine. Thus newly made proteins all have methionine as the first amino acid at their N terminal end (synthesized first).

The small ribosomal unit must first find the 5' cap present in all eukaryotic mRNAs. An intiator tRNA is first loaded into the P site along with translation initiator factors. The small ribosomal unit will move forward along the mRNA searching for the first AUG. When this AUG is found, the tRNA is bound to the P site already so protein synthesis is ready to begin with addition of the next charged tRNA to the A site

Front 81

How is translation initiated in bacteria?

Back 81

Different because there is no 5' cap for the small ribosomal unit to bind to. Instead, they contain specific ribosome-binding sequences that are located a few nucleotides upstream of the AUGs at which translation will be begin. A prokaryotic ribosome can readily bind directly to a start codon that lies in the interior of an mRNA

Front 82

How is translation terminated?

Back 82

It is signaled by the presence of stop codons in the mRNA. They are not recognized by the tRNA and do not specify with an amino acid, instead signal to the ribosome to stop translation. Release factors bind to any stop codon that reaches the A site on the ribosome; this binding alters the activity of the peptidyl transferase in the ribosome, causing it to catalyze the additon of a water molecule instead of an amino acid to the peptidyl-tRNA.

Front 83

What is an operon?

Back 83

a unit made up of linked genes that is thought to regulate other genes responsible for protein synthesis.

Front 84

What are "regulatory DNA sequences" found in operons?

Back 84

Used to switch gene on or off. Simple (switch) or complex (microprossesor)

Front 85

What are structural genes? What are gene regulatory proteins?

Back 85

Anything other than regulatory DNA sequences.

Front 86

What does "negatively-acting" mean? What is the outcome of a repressor?

Back 86

Negative control involves the binding of a repressor to the operator to prevent transcription

Front 87

What does “positively-acting” mean? What is the outcome of an activator?

Back 87

with positive control, an activator protein stimulates transcription by binding to DNA

Front 88

What is "constitutive expression" of a gene?

Back 88

unregulated gene expression where gene is continuously being transcribed instead of when only being needed.

Front 89

What is an inducer? What is a repressor?

Back 89

repressor- a repressor is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator. A DNA-binding repressor blocks the attachment of RNA polymerase to the promoter, thus preventing transcription of the genes into messengerRNA. inducer- is a molecule that starts gene expression. An inducer can bind to repressors or activators.

Front 90

Describe the regulatory switch of the operon that manufactures tryptophan in E. coli

Back 90

When there is an abundance tryptophan its repressor binds to the operator and blocks access of RNA polymerase to the promoter and prevents transcription.-The repressor can bind to DNA only if it has also bound several molecules to tryptophan. When there is a low concentration of tryptophan and the repressor no longer binds DNA and the tryptophan operon is transcribed.

Front 91

Describe the dual nature of the regulatory switch that controls the lactose operon in E. coli.

Back 91

The Lac repressor- shuts off operon in absence of lactose. Cap activator- Switches on genes that allow cell to utilize all sources of Carbon- including lactose. Wasteful if no lactose present so lac repressor actviated to conserve.

Front 92

Why does eukaryotic RNA polymerase II require general transcription factors to initiatetranscription?

Back 92

The RNA polymerase 2 only starts transcription after phosphorylation.

Front 93

whyy is eukaryotic RNA polymerase II phosphorylated?

Back 93

in order to disengage it from the transcription factors and release it from the transcription initiation complex so it can continue transcription

Front 94

Describe how gene activation can occur at a distance of up to several thousand base pairsin eukaryotic promoters?

Back 94

Enhancers: short regions of DNA that enhance transcription levels of genes in a gene cluster. They do not have to be close to the gene of interest. The DNA acts as a tether, causing a protein bound to an enhancer even thousands of nucleotide pairs away to interact with the protein in the vicinity of the promoter.

Front 95

Describe one of the simplest genetic mechanisms, which allow daughter cells to“remember” what kind of cells they are supposed to be

Back 95

Using a positive feedback loop, a key transcription regulator activates transcription of its own gene in addition to that of other cell-type-specific genes.