Chapter 19: Control of Gene Expression in Eukaryotes

Which of the following is most critical for the association between histones and DNA? 1. There are at least five different histone proteins in every eukaryote. 2. Histones are synthesized in the cytoplasm. 3. Histones are positively charged. 4. Histones are highly conserved (that is, histones are very similar in every eukaryote)

3. Histones are positively charged.

In eukaryotes, the first step in the control of gene expression is ______. 1. chromatin remodeling 2. RNA processing 3. mRNA stability control 4. transcription

1. chromatin remodeling

Which statement best characterizes DNA wrapped around histones?

DNA wrapped around histones are not transcribed and are protected from degradation by nucleases

example of a promoter sequence in eukaryotes?

TATA box

what do nucleosomes do?

allow for the compaction of DNA

enhancers and silencers can be far from the gene they regulate

also unique to the gene they regulate also specific to eukaryotes enhancers-sequences to which proteins bind to promote transcription silencers- sequences to which proteins bind to stop transcription

Splicing the same primary mRNA in different ways is known as...

alternative splicing

Why can one DNA sequence produce many different proteins?

alternative splicing

what part of transcription regulation uses splicesomes?

alternative splicing

What binds to the promoter-proximal region?

an activator/regulatory transcription protein

in RNA interference, the hairpin structure is finished being processed into single stranded miRNA in the...

cytoplasm

how come smooth and striated muscle cells have different proteins but have the same genes?

each express different genes/proteins based on alternative splicing patterns

regulatory sequences found far from the promoter that activate transcription are?

enhancers

RNA interference

eukaryotes can regulate stability of mRNA unstable RNA could be subject to degradation situations where mRNA is produced but not needed (enviornmental changes)

evolution of RNA interference

evolved as a defense mechanism towards viruses viruses store their genetic information in double strands this acts as a defense mechanism for the bacteria and triggers this RNA interference

cells react to their environment

express different genes at different times. all of our cells have the same DNA but different genes are expressed in different cells based on their function

alternative splicing

generate several mature mRNAs from a single transcript splicing involve splicesomes remove introns (intervening sequences from primary RNA) also remove certain exons as well SPLICING INTRONS IS SPECIFIC TO EUKARYOTES, IT DOES NOT OCCUR IN PROKARYOTES BC PROKARYOTES DO NOT PRODUCE INTRONS spliceosomes can be used for selective retention of certain exons or the disregarding of others within the same RNA sequence

during RNA interference, the mRNA strand...

gets cut and will not produce a protein

what physically blocks the core promoters to prevent initiation?

histones

Does bacteria have alt splicing, condensation of chromosomes or RNA interference?

no

what protein can recruit chromatin remodeling proteins?

regulatory transcription factors

What are proto-oncogenes?

when mutated they become oncogenes, which drive the cell thro the cell cycle and promote cancer (unregulated cell division)

what would happen if condensed chromatin was exposed to DNAseI?

would not degrade/be cut up bc DNAse I cannot access the DNA to cut it

do introns and exons both serve as a template for transcription

yes, the entire thing serves as a template for transcription. the introns are later spliced out

what protein adds acetyl groups to histones?

HAT-histone acetyl transferase

Chromatin

DNA and proteins (histone) mixed UNIQUE TO EUKARYOTES chromatin can be remodeled its state impacts whether or not a gene is transcribed proteins bind to DNA and dictates whether or not transcription happens

properties of DNA

DNA is flexible, which allows for it to bend so the proteins can reach the enhancers that are far away and the PPE and the promoter

why do DNA and histones associate?

DNA is negatively charged and histones are positively charged

differences between transcriptional control in bacteria and eukaryotes?

DNA packaging- big in eukaryotes, not bacteria eukaryotes-more proteins/more complex both rely on post transcriptional control though

transcription regulation in terms of eukaryotes

Promoter (TATA box) DNA sequence (where general transcription factors and RAN polymerase bind) low specificity Promoter proximal elements DNA sequence (where regulatory transcription factors bind) close to the promoter high specificity enhancer DNA sequence (where reg trans factors bind) doesn't have to be far from the gene high specificity silencers also a DNA sequence to which reg trans factors bind doesn't have to be far from gene high specificity general transcription factors protein binds to regulatory transcription/mediator complex also binds to RNA polymerase bind to promoters low specificity regulatory transcription factors protein binds to PPE/enahncers/silencers also bind to mediator complex high specificity

what are histones?

Proteins associated with DNA to form chromatin.

the life span of an mRNA molecule can be controlled by...

RISC complex

what does a mediator do in transcription?

bridges regulatory transcription factors, general transcription factors and RNA polymerase. it also delivers a signal to RNA polymerase to start transcription

RNA interference process

causes degradation of target mRNA with a specific sequence (nucleus) 1. transcription of the microRNA gene by RNA polymerase 2. formation of a hairpin structure with a loop on the end (internal complementarity) (precursor miRNA) (cytoplasm) 3. exported to cytoplasm and processed further (loop is cut off) 4. miRNA becomes single stranded. one of the strands binds to RISC and guides it to its target mRNA (complementary base pairing between target mRNA and miRNA) 5. miRNA binds comp to target mRNA 6. RISC then cuts the target DNA, rendering it nonfunctional

how do miRNA interfere with translation?

complementary base pair to a target mRNA and either cut it using RISC or interfere with its translation

Chromatin condensation and de-condensation (proteins used)

condensed chromatin can be opened using HAT (histone acetyl transferase) DNA is negatively charged while histones are postively charged. that is why they attract one another. by adding methyl groups (negatively charged) to the histones, you reduce the attraction between the histones and the DNA, thus making it more relaxed and open and subject to transcription to close the open DNA, use HDAC (histone de-acetylase) which remove the acetyl groups and thus restore the attraction between DNA and histones, making the chromatin more condensed

What is the default state of DNA in eukaryotes vs prokaryotes?

default state of transcription in eukaryotes-off in prokaryotes-on

post translation controls?

destroying proteins/altering their function (ex:ubiquitin tagging and destruction using proteasomes)

once the mRNA is produce, it is considered to be immature

needs to be modified before it is used as a template for translation processing steps are used as a method of gene regulation (making multiple different proteins from one mRNA)

normal vs alt splicing

normal-removal of all the introns and keep all of the exons alt splicing-removal of all the introns and some exons as well to produce different mature mRNAS since alt splicing can occur, there are many more proteins than genes that code for proteins

Chicken blood cells experiment

ovalbumin gene which is not normally expressed and beta globin gene which is normally expressed incubate with DNAse I the ovalbumin gene was not cut (condensed state bc not normally expressed in chickens) the beta globin gene was cut (open state bc normally expressed) easier for DNAse I to make contact with open rather than closed DNA

translational and post-translational control

prokaryotes and eukaryotes

where does RNA polymerase bind to during transcription?

promoter

What does RNA polymerase bind to to start transcription in eukaryotes?

promoter sequence

what does p53 activate within a cell?

reg trans factor that activates gene that induce apoptosis in cells with extensive damage that cannot be repaired. also activated genes that fix damage to cells

what happens in the cytoplasm in RNA interference?

single strand miRNA binds to RISC and then that compl base pairs to target mRNA and RISC cuts it

p53

transcription regulator that prevent cancer (transcribed in response to DNA damage and regulated at a transcriptional level) p53 proteins pauses the cell cycle until it can repair the damage done (cells will not divide until damage is repaired) activates gene important for cell cycle arrest (worst case scenario, activates proteins required for cell death (apoptosis)) better to kill of the cell than to let it continue damaged through the cell cycle

proteins that stop/slow the cell cycle when conditions are unfavorable are called?

tumor suppressors (p53 is a tumor suppressor)

The product of the p53 gene _____. 1. slows down the rate of DNA replication by interfering with the binding of DNA polymerase 2. inhibits the cell cycle 3. causes cells to reduce expression of genes involved in DNA repair 4. allows cells to pass on mutations due to DNA damage

2. inhibits the cell cycle

Which statements about the regulation of transcription initiation in these genes are true? Select all that apply. fantasian gene has enhancers ABC and imaginin gene as enhancers CDE 1. Control elements C, D, and E are distal control elements for the imaginin gene. 2. Both the fantasin gene and the imaginin gene will be transcribed at high levels whenever general transcription factors are present in the cell. 3. Control elements A, B, and C are proximal control elements for the fantasin gene. 4. The imaginin gene will be transcribed at a high level when repressors specific for the imaginin gene are present in the cell. 5. Both the fantasin gene and the imaginin gene will be transcribed at high levels when activators specific for control elements A, B, C, D, and E are present in the cell. 6. The fantasin gene will be transcribed at a high level when activators specific for control elements A, B, and C are present in the cell. 7. The fantasin gene and the imaginin gene have identical enhancers.

1, 5 and 6 are true

Which statements about the modification of chromatin structure in eukaryotes are true? Select all that apply. 1.Acetylation of histone tails in chromatin allows access to DNA for transcription. 2. DNA is not transcribed when chromatin is packaged tightly in a condensed form. 3. Acetylation of histone tails is a reversible process. 4. Methylation of histone tails in chromatin can promote condensation of the chromatin. 5. Some forms of chromatin modification can be passed on to future generations of cells. 6. Deacetylation of histone tails in chromatin loosens the association between nucleosomes and DNA.

1-5 are correct

How does a microRNA recognize a specific target mRNA? 1. A microRNA can recognize a specific target whenever it can form complementary base pairs with the target. 2. A microRNA can recognize a specific target by biding to the hairpin-containing precursor on the target. 3. A microRNA can recognize a specific target by binding to the TATA box of the target. 4. A microRNA can recognize a specific target due to different RISC proteins binding it to the target.

1. A microRNA can recognize a specific target whenever it can form complementary base pairs with the target.

Compare and contrast general transcription factors and sigma. What do they have in common? 1. Both are proteins that must bind with the promoter before RNA polymerase can initiate transcription. 2. Both are parts of the holoenzyme that must bind with the promoter before RNA polymerase can initiate transcription. 3. Both are proteins that must bind with the TATA box before RNA polymerase can initiate transcription. 4. Both are proteins that must bind with the operator before RNA polymerase can initiate transcription.

1. Both are proteins that must bind with the promoter before RNARNA polymerase can initiate transcription.

Why does chromatin remodeling have to be the first step in gene activation? 1. Eukaryotic DNA can be highly packaged in condensed chromatin and inaccessible to transcription factors and RNA Polymerase. 2. Eukaryotic DNA can be highly packaged in "open" chromatin (nucleosomes) and inaccessible to transcription factors and RNA Polymerase. 3. Eukaryotic and bacterial DNA can be highly packaged in condensed chromatin and inaccessible to regulatory proteins and RNA Polymerase. 4. Eukaryotic DNA can be highly packaged in condensed chromatin and inaccessible to spliceosomes.

1. Eukaryotic DNA can be highly packaged in condensed chromatin and inaccessible to transcription factors and RNA Polymerase. not option 3 because regulatory transcription factors can still bind to condensed chromatin

Individuals who inherit mutations in p53 would be expected to have what symptoms? See Section 19.6 (Page) . 1. Higher likelihood of developing various types of cancer 2. No symptoms, unless the patient is exposed to abnormally high UV radiation 3. A tendency to sunburn 4. Higher ability to tan when exposed to sunlight

1. Higher likelihood of developing various types of cancer

What is alternative splicing? 1. folding that leads to proteins with alternative conformations 2. mRNA processing that leads to different combinations of exons being spliced together 3. actions by regulatory proteins that lead to changes in the life span of an mRNA 4. phosphorylation that leads to different types of post-translational regulation

2. mRNA processing that leads to different combinations of exons being spliced together

During the process of RNA interference, the double stranded miRNA precursor is separated by which of the following? 1. RISC helicase activity 2. DNA helicase 3. RISC polymerase 4. RNA helicase

1. RISC helicase activity

How do miRNA recognize a particular target mRNA? 1. The miRNA sequence is complementary to the mRNA sequence so they base pair. 2. The RNA processing complexes edit the miRNA base pair sequence by changing the identity of bases so it can base pair with the target mRNA. 3. The binding of miRNA complex to RISC alters the RISC complex so these proteins bind directly to the mRNA. 4. The miRNA and mRNA have the same sequence so they base pair.

1. The miRNA sequence is complementary to the mRNA sequence so they base pair.

Which of the following statements about enhancers is correct? 1. They are found in a variety of locations and are functional in any orientation. 2. They are located only in introns. 3. They are located only in 5'-flanking regions. 4. They contain a unique base sequence called a TATA box.

1. They are found in a variety of locations and are functional in any orientation

Imagine that you've discovered a regulatory sequence thousands of base pairs away from the promoter and that when this sequence is lost due to mutation, levels of gene expression decrease sharply. This sequence is most likely ______. 1. an enhancer 2. a promoter 3. a silencer 4. a promoter-proximal element

1. an enhancer

In a nucleosome, the DNA is wrapped around _____. 1. histones 2. satellite DNA 3. ribosomes 4. a thymine dimer 5. polymerase molecules Submit

1. histones

The functioning of enhancers is an example of _____. 1. transcriptional control of gene expression 2. a post-transcriptional mechanism to regulate mRNA 3. post-translational control that activates certain proteins 4. a eukaryotic equivalent of prokaryotic promoter functioning 5. the stimulation of translation by initiation factors

1. transcriptional control of gene expression

Why is RNA interference aptly named? See Section 19.4 (Page) . 1. The function of RISC complex is prevented when it binds to miRNA. 2. Both the miRNA that does the interfering and the mRNA that is destroyed are RNA. 3. The function of RNA polymerase is prevented when it binds to miRNA. 4. The RISC complex is cleaved when it binds mRNA.

2. Both the miRNA that does the interfering and the mRNA that is destroyed are RNA.

Which choice is utilized by eukaryotes to control their gene expression that is NOT used in bacteria? 1. Control of chromatin remodeling 2. Control of both RNA splicing and chromatin remodeling 3. Transcriptional control 4. Control of chromatin remodeling, RNA splicing, and transcription 5. Control of RNA splicing

2. Control of both RNA splicing and chromatin remodeling

Alternative RNA splicing ________. 1. is due to the presence or absence of particular snRNPs 2. can allow the production of proteins of different sizes and functions from a single mRNA 3. can allow the production of similar proteins from different genesis a mechanism for increasing the rate of transcription 4. increases the rate of transcription

2. can allow the production of proteins of different sizes and functions from a single mRNA

Compare and contrast promoter-proximal elements and the operator of the laclac operon. What do they have in common? 1. Both are regulatory sites in mRNA located close to the cap. 2. Both are regulatory sites in mRNA located close to the poly(AA) signal. 3. Both are regulatory sites in DNA located close to the promoter. 4. Both are regulatory sites in DNA located close to the transcription termination codon.

3. Both are regulatory sites in DNA located close to the promoter

Compare and contrast enhancers and the E. coli CAP binding site. What do they have in common? 1. Both are sites in DNA where basal transcription factors bind. 2. Both are sites in DNA where tumor suppressor binds. 3. Both are sites in DNA where regulatory proteins bind. 4. Both are sites in DNADNA where RNARNA polymerase binds.

3. Both are sites in DNA where regulatory proteins bind.

If cells of an individual contain the same set of genes, how do these cells become different from each other during development? 1. Different cell type-specific regulatory elements in DNA are selectively lost during development. 2. Different cell type-specific regulatory elements in DNA are created during development. 3. Differences in extracellular signals received by each cell lead to differences in the types of regulatory proteins present in each cell. 4. Differences develop in promoter sequences that lead to different signals being produced by each type of cell.

3. Differences in extracellular signals received by each cell lead to differences in the types of regulatory proteins present in each cell.

Why do histones bind tightly to DNA? 1.. Histones are negatively charged, and DNA is positively charged. 2. Histones are covalently linked to the DNA. 3. Histones are positively charged, and DNA is negatively charged. 4. Both histones and DNA are strongly hydrophobic. 5. Histones are highly hydrophobic, and DNA is hydrophilic.

3. Histones are positively charged, and DNA is negatively charged.

Proto-oncogenes can change into oncogenes that cause cancer. Which of the following best explains the presence of these potential time bombs in eukaryotic cells? 1. Proto-oncogenes are genetic "junk." 2. Proto-oncogenes first arose from viral infections. 3. Proto-oncogenes normally help regulate cell division. 4. Cells produce proto-oncogenes as they age. 5. Proto-oncogenes are mutant versions of normal genes.

3. Proto-oncogenes normally help regulate cell division.

Which of the following is involved in the first step of initiating transcription? 1. mediator 2. histone acetyltransferase 3. TATA binding protein 4. RNA polymerase II

3. TAT binding protein

Which statement is most accurate concerning how gene expression in eukaryotes compares with that in bacteria? 1. The tight packaging of eukaryotic DNA provides a mechanism of positive control nonexistent in bacteria. 2. Coordinated control of functionally related genes by a single promoter is common in both. 3. The number of proteins that control transcription is much greater in eukaryotes. 4. Proteins that control transcription perform fundamentally different roles in eukaryotes versus prokaryotes.

3. The number of proteins that control transcription is much greater in eukaryotes.

Which of the following is most likely to have a small protein called ubiquitin attached to it? 1. a regulatory protein that requires sugar residues to function properly 2. a cell surface protein that requires transport from the ER 3. a cyclin protein, which usually acts in G1, in a cell that is in G2 4. an mRNA leaving the nucleus to be translated 5. an mRNA produced by an egg cell that will be retained until after fertilization

3. a cyclin protein, which usually acts in G1, in a cell that is in G2

The addition of acetyl groups to histones is associated with ______. View Available Hint(s) 1. chromatin decondensation and low levels of gene expression 2. chromatin condensation and low levels of gene expression 3. chromatin decondensation and higher levels of gene expression 4. chromosome condensation and high levels of gene expression

3. chromatin decondensation and higher levels of gene expression

Gene expression can be altered more easily at the level of post-transcriptional processing in eukaryotes than in prokaryotes because _____. 1. eukaryotic mRNAs get 5' caps and 3' tails 2. prokaryotic genes are expressed as mRNA, which is more stable in the cell 3. eukaryotic exons may be spliced in alternative patterns 4. prokaryotes use ribosomes of different structure and size

3. eukaryotic exons may be spliced in alternative patterns

The predominant mechanism driving cellular differentiation is the difference in gene _____. 1. sequences 2. order 3. expression 4. replication

3. expression

How can the 2 meters of DNA found in a typical human cell be packed into a nucleus that is only a few micrometers in diameter? 1. the DNA molecules are normally single stranded 2. Eukaryotic nuclei are expandable and enlarge to accommodate the long DNA molecules 4. DNA is associated tightly with histone proteins in the nucleosome, which pack the DNA compactly

4

_____ bind(s) to DNA enhancer regions. 1. RNA polymerase 2. Promoters 3. Introns 4. Activators 5. Exons

4. Activators

Which of the following statements about the DNA in one of your brain cells is TRUE? 1. Most of the DNA codes for protein. 2. Each gene lies immediately adjacent to an enhancer. 3. All of the genes of the genome are likely to be transcribed. 4. It is the same as the DNA in one of your heart cells. 5. Many related genes are transcribed from a single promoter.

4. It is the same as the DNA in one of your heart cells.

Tropomyosin is a protein found in both skeletal and smooth muscle, but the mRNA produced in each of these is different in composition even though they are transcribed from the same gene. This observation is explained by a mechanism in eukaryotic cells known as _______. View Available Hint(s) 1. post-translational modification 2. alternative expression 3. RNA silencing 4. alternative splicing

4. alternative splicing

Predict how a drug that inhibits histone deacetylase will alter gene expression. 1. chromatin would stay condensed; transcription would stop; amount of protein would decrease 2. chromatin would stay condensed; transcription would be prolonged; amount of protein would increase 3. chromatin would stay decondensed; transcription would stop; amount of protein would decrease 4. chromatin would stay decondensed; transcription would be prolonged; amount of protein would increase

4. chromatin would stay decondensed; transcription would be prolonged; amount of protein would increase

Muscle cells differ from nerve cells mainly because they _____. 1. have unique ribosomes 2. contain different genes 3. have different chromosomes 4. express different genes 5. use different genetic codes

4. express different genes

Differential gene expression is the result of different cells containing different ______. 1. nucleosomes 2. regulatory sequences 3. genes 4. regulatory proteins

4. regulatory proteins

What is chromatin? 1. the histone-containing protein core of the nucleosome 2. the 30-nmnm fiber 3. the histone and non-histone proteins in eukaryotic nuclei 4. the complex of DNA and proteins found in the nucleus

4. the complex of DNA and proteins found in the nucleus

Which of these directly bind(s) to the promoter? 1. enhancer 2. promoter 3. RNA polymerase 4. general transcription factors 5. 3 and 4

5. 3 and 4

Use this information to answer the question(s) below.A researcher found a method she could use to manipulate and quantify phosphorylation and methylation in embryonic cells in culture.In one set of experiments she succeeded in increasing acetlylation of histone tails. Which of the following results would she most likely see? 1. inactivation of the selected genes 2. decreased binding of transcription factors 3. activation of histone tails for enzymatic function 4. increased chromatin condensation 5. decreased chromatin condensation

5. decreased chromatin condensation

The reason for differences in the sets of proteins expressed in a nerve and a pancreatic cell of the same individual is that nerve and pancreatic cells contain different _____. 1. promoters 2. genes 3. promoter-proximal elements 4 regulatory sequences 5. sets of regulatory proteins

5. sets of regulatory proteins

different ways in which gene expression is controlled

in the nucleus 1. chromatin remodeling-"open" vs "closed" DNA 2. transcription- primary transcript and pre-mRNA 3. RNA processing- addition of a 5' G cap or a 3' PolyA tail. production of mature mRNA cytoplasm. RNA interference 4. mRNA stability- can be degraded if unstable or not needed anymore 5. translation- add a protein to ribosome or phosphorylate it, etc 6. post translational control- folding with molecular chaperones, transport, activation, degradation eukaryotes have more options at their disposal

How does chromatin condense

a. nucleosome structure- composed of 8 histones wrapped around 2x with DNA. Also, an H1 protein holds the complex together. between each nucleosome is linker DNA (no proteins) that connects the nucleosomes. b. then the nucleosomes coil around one another and form a 30nm fiber c. finally the chromosome winds up in its most condensed form (the form in which it takes during cell division)

enhancers are where ___ bind while silencers are where ____ bind.

activators bind to enhancers and repressors bind to silencers

RISC exists in all eukaryotes

as well as a double stranded kickback system because of evolution

regulatory transcription factors in terms of chromatin state

can bind to closed chromatin (find enhancers on closed chromatin) recruit chromatin remodelers like HAT to make the chromatin decondensed HAT opens DNA and now the gene can be transcribed lets all of the other proteins and RNA polymerase attach to the DNA and transcribe the gene

examples of post translational modification

chaperone proteins help protein achieve correct folding covalent addition of a group peptide complexes with other polypeptide molecules

What are two mechanisms used to turn off genes in eukaryotic cells?

chromatin in condensed, silencers bind to proteins

list the steps of transcription initiation in the proper order?

chromatin remodeling, exposure of promoter and regulatory sequences in the DNA, proteins assemble and then proteins contact the core promoter. RNA polymerase binds to promoter and transcription ensues

what is responsible for the formation of specialized cell types and arranging them into tissue?

differential gene expression

eukaryotes vs prokaryotes (promoters)

eukaryotes TATA box how TATA-binding proteins can recognize the promoter and recruit other proteins like RNA polymerase to join there prokaryotes sigma binds to promoter while already attached to RNA polymerase -10, -35 box for recognition both promoter is where RNA polymerase must go to start transcription and has recognizable sequences

Which statement best describes a eukaryotic promoter?

found close to the promoter, upstream, contains a TATA box, it is a DNA sequence to which regulatory transcription factors bind

How do different cells express different genes?

the expression of genes is regulated and turned on/off by signal pathways activated by molecules secreted by nearby/distant cells

LC- the function of miRNA? how are bacteria and eukaryotes similar? why do humans have more proteins than genes?

guide RISC to target mRNA to be destroyed the protein binds to DNA sequence neat target gene and prevents its expression alternative splicing

tropomyosin gene

has exons and introns interspersed throughout it alternative splicing produces more than one type of mature RNA mRNA produced in skeletal muscle different than the mRNA produced in smooth muscle they contain the same RNA but produce different mature mRNAs bc they have a different function both have all of their introns spliced, and may even share some of the exons that are present, but they wind up having a few different exons present skeletal might have 1,3,4,5,6,7,8,9,10,11 and 12 but exclude 2, 13 and 14 smooth might have 1,2,,4,5,6,7,8,9,10,13,4 but exclude 3,11 and 12 since splicesomes can choose what they keep and what they disregard, multiple different mRNAs can arise from the same primary transcript

invitro DNAse I incubation experiment

have condensed chromatin and de condensed chromatin the condensed chromatin has a lot of proteins, while the open chromatin does not have any after treatment with DNAse I, the condensed chromatin remained the same while the open chromatin was cut into little bits DNAse I can only cut open DNA, it cannot access condensed chromatin bc it is wound up too tightly this is used to determine the state of a gene when it is being transcribed (open) vs when it is not (condensed)

p53 and cancer

in about 1/2 cancerous tumors, p53 not functional. DNA damaged and continues through the cell cycle, causing cancer p53 usually causes the promotion of transcription of genes that promote cell arrest

control in eukaryotes vs prokaryotes

prokaryotes chromatin remodeling- less packaging of DNA remodeling not a major issue regarding gene expression transcription- positive and negative control by regulatory proteins that act at sites close to the promoter sigma interacts with promoter lac operon RNA processing- rare mRNA stability-rarely used for control translation-regulatory proteins bind to mRNAs and ribosomes and affect translation rate post translational control-folding, chemical modifications, protein activity eukaryotes chromatin remodeling- extensive packaging of DNA decondensed for transcription to begin transcription-positive and negative control by regulatory proteins that act at sites close to/far from the promoter transcription factors interact with the core promoter and regulatory sequences mediator required RNA process-extensive. splicing, alt splicing, addition of cap and tail mRNA stability-RNA interference translation-same as prokaryotes post translational control-same as prokaryotes. also have ubiquitin tagging for degradation of a protein

The primary difference between enhancers and promoter-proximal elements is that enhancers _____. 1.enhance transcription; promoter-proximal elements inhibit transcription 2. are DNA sequences; promoter-proximal elements are proteins 3. are transcription factors; promoter-proximal elements are DNA sequences 4. are part of the promoter; promoter-proximal elements are regulatory sequences distinct from the promoter 5. are at considerable distances from the promoter; promoter-proximal elements are close to the promoter

proximal elements are close to the promoter

Define enhancer

regions of DNA far from the promoter that activates transcription

proteins that regulate transcription in eukaryotes

regulatory transcription factors. they could also be called activators. they bind to the PPE and enhancers. they then recruit the mediator complex, which attaches itself to all of the regulatory transcription factors this whole complex then recruits the general transcription factors. they bind to the promoter as well and recruit RNA polymerase to bind to the promoter and start transcription general transcription factors will not bind to the regulatory transcription factors and mediatory complex if that whole thing is not properly created

What do histone deacetylases do?

remove acetyl groups from histones, restoring full attraction between histones and DNA, causing it to condense and for transcription to stop

Inhibitors of initiation of transcription?

repressors/silencers

what process is critical to protein formation (starts with a s)

splicing because forms mature RNA

splicing is not gene regulation but alternative splicing is

splicing happens all the time regardless of the gene, but alt splicing causes the production of different mRNA transcripts

Promoter proximal elements also regulate expression of genes

they are near the promoter and unlike the promoter which has a more general sequence (ex: TAT box), the PPE is specific to the gene it regulates PPE is where proteins bind to both eukaryotes and prokaryotes have promoters to which RNA polymerase must bind in order to transcribe the desired gene in the correct spot, but only eukaryotes have the PPE

why did bacteria never evolve spliceosomes

they don't have introns to be spliced out

What is chromatin?

tightly coiled DNA-protein complex

eukaryotes can also tag a protein for degradation

ubiquitin tagging addition (covalently) of a ubiquitin tag this causes proteasomes to come and destroy the tagged protein (cut it into bits) can use this to degrade cyclin to control the cell cycle (mitosis isn't being promoted when it shouldn't be)