Bio 172 Exam 3

Sanger sequencing

(a) The incorporation of an incoming dideoxynucleotide stops the elongation of a new strand. (b) Dideoxynucleotides are incorporated into growing DNA strands, terminating their growth. (c) Separation of interrupted daughter strands by size shows where each terminator was incorporated and hence the identity of the corresponding nucleotide in the template strand.

chromatin remodling

(takes energy) chromatin remolding use ATP to move nucleose; opens up chromatin

During the extension step of PCR, DNA synthesis takes place in the...

-3'-5' direction on top strand, 5'-3' direction on the bottom strand -3'-5' direction on bottom strand, 5'-3' direction on the top strand -always in the 3'-5' direction -always in the 5'-3' direction (Correct)

which of the following mechanisms is used only in eukaryotes and not in prokaryotes?

-DNA binding proteins to specific DNA sequences to regulate transcription -several genes acting in the same pathway are transcribed as one polycistronic RNA -a small molecule binds to a protein to changed its formation and activity -regulation of chromatin structure by modifying histones (correct)

what are the three ways chromatin can be packaged

-DNA methylation -modification of histones -chromatin remodling

How is MPF deactivated?

-M-cyclin is ubiquitinated by an enzyme that is activated during anaphase of mitosis -the ubiquitin tag targets cyclin to the proteasome where it is destroyed -this is an example of negative feedback regulation: a process is slowed down by one of its products

required for recombinant DNA

-The donor fragment may be a protein coding gene, a regulatory part of a gene, or any DNA segment of interest -vector--sequence into which the donor fragment is to be inserted. MUST HAVE ABILITY TO BE MAINTAINED IN BACTERIAL CELLS

which of the following could be used as a cancer treatment?

-VEGF inhibitor (correct) -VEGF activators (increase angiogenesis) -activators of HIF (increase angiogenesis) -Activator of the VEGF receptor (increase angiogenesis)

which of the following would most likely contribute uncontrolled cell proliferation?

-a mutant Cdk that was active in the absence of its cyclin binding partner (correct) -a mutant cycling that cannot bind to its Cdk partner -constitutive expression of a cyclin (correct)

telomerase is

-a proto-oncogene (correct) -tumor suppressor -neither

post translational forms of regulation include:

-assisted folding of proteins -targeted destruction of proteins (proteasome degrades ubiquitin tagged proteins) chemical modification -chemical modification (phosphorylation) -protein transport (cytoplasm to nucleus)

shotgun sequencing

-cut genome into small fragments. sequence each fragment and assemble sequence -sequences small pieces of genomes which are assembled by a computer. the sequenced fragments do not originate from a particular gene or region but from sites scattered randomly across the chromosome

In comparing a nerve cell and a liver cell in the same person, you will find that these cells contain

-different chromosomes -different genes -different proteins (correct)

differences between Enzyme linked kinase and G protein signaling

-enzyme linked kinase--change in protein conformation by covalent addition of a phosphate (kinase) -change in protein conformation by non--covalent binding of GTP (G protein)

which of the following does not contribute to the large amount of noncoding DNA in eukaryotic genomes?

-exons that can be alternatively spliced -tandem repeats -transposable elements -polyploidy

specific miRNA controls the translation of the LIN-41 protein. What do you expect to see in cells that lack the gene encoding this microRNA?

-increased levels of LIN-41 RNA and increased levels of LIN-41 protein -decreased levels of LIN-41 RNA and decreased levels of LIN-41 protein -unchanged levels of LIN-41 RNA and increased levels of LIN-41 proteins (correct) -unchanged levels of LIN-41 RNA and decreased levels of LIN-41 proteins

cell cycle consist of

-interphase (non dividing) -M phase (dividing)

how does phosphorylation of a protein regulate its function?

-it causes a conformational change in the protein (correct) -it leads to protein degradation by the proteasome -it changed the amount of DNA in the cell -it initiates mutagenesis in the protein

steroid hormone signaling is an example of

-juxtacrine signaling -paracrine signaling -autocrine signaling -endocrine signaling (correct)

what will be the result of mutation that makes lacI unable to bind lactose? -lacZ and lacY will not be transcribed, regardless of lactose levels -lacZ and lacY will always be transcribed regardless of lactose levels -lacZ and lacY will be transcribed in the presence of lactose but not in the absence

-lacZ and lacY will not be transcribed, regardless of lactose levels

under which conditions does it make sense for E. coli to express B-galactosidase and Galactosidase permease? -lactose levels are low and glucose levels are low -lactose levels are low and glucose levels are high -lactose levels are high and glucose levels are low -lactose levels are high and glucose levels are high -both c and d

-lactose levels are high and glucose levels are low

Positive regulation of the activator is when

-low glucose and high levels of cAMP, RNA polymerase binds--high levels of transcription -high levels of glucose and low levels of CRP-cAMP--RNA polymerase cannot bind--low levels of transcription

other regulatory mutants do not express LacZ and LacY even in the presence of lactose...

-mutant activator protein -mutant binding site for the activator

which of the following mutations in Rb will promote cancer?

-mutation that prevents Rb from binding E2F (correct, loss of function) -mutation that prevents Rb phosphorylation -duplication of Rb gene -any mutation

Which one of the following is a difference between PCR and cellular DNA replication -DNA synthesis in the 3'-5' versus in the 5'-3' direction -need for primers -need for helices enzyme -need for nucleotides

-need for helices enzyme

what are the keys to PCR?

-need to have a sequence information to design primers -heat stable DNA polymerase (allows separation of double stranded DNA by heat without killing the enzyme)

what is the consequence for a cell in which p53 protein is mutated and cannot bind to DNA?

-no cell division will occur -cell division will only take place if DNA is undamaged -cell division will take place even if the DNA is damaged (correct)

what is the consequence for a cell in which Rb protein is mutated and cannot bind E2F?

-no cell division would occur -cell division will only take place if sufficient nutrients and social signals are present -cell division will take place even if there are not enough nutrients and social signals (correct)

what level of telomerase expression would you expect to see in many cancer cells/tumors?

-normal levels -higher than normal (correct) -lower than normal

gene expression in eukaryotes

-packaging: chromatin structures provides a mechanism of negative control in eukaryotes that does not exist in bacteria -complexity: transcriptional control is much more complex in eukaryotes than in bacteria -alternative splicing: primary transcripts in eukaryotes must be spliced and modified

what are the two explanations of C-value paradox?

-polyploidy (how many copies of genome we have, more than two paired sets of chromosomes) -noncoding DNA

DNA elements include

-promoter--region of DNA where RNA polymerase binds and begins transcription -enhancers and silencers--regulatory DNA elements bound by regulatory proteins

in comparing a muscle cell and a skin cell, you are likely to find the greatest difference in each cell's component of:

-promoters -silencers -enhancers -basal transcription factors -regulatory transcription factors

In comparing a muscle cell and a skin cell, you are likely to find the greatest differences in each cells content of:

-promoters -silencers -enhancers -basal transcription factors -regulatory transcription factors (correct)

what is the major difference between controlling translation by a regulatory protein bound to a specific RNA, versus phosphorylation of a ribosomal protein?

-regulatory proteins inhibit translation while phosphorylation of a ribosomal protein enhances translation -regulatory proteins enhance translation while phosphorylation of a ribosomal protein inhibits translation -a regulatory protein will control translation of one or a few proteins, phosphorylation of ribosomal protein will control translation of all proteins (correct)

what are the preparations a cell must make during interphase?

-replication of the DNA in the nucleus so that each daughter cell receives a copy of the genome -an increase in cell size so that each daughter cell receives sufficient amounts of cytoplasmic and membrane components to allow it to survive on its own

high glucose, low lactose

-repressor bound to operator -cAMP levels low -CRP not bound to CRP site -LacZ not transcribed

Low glucose, high lactose

-repressor not bound to activator -cAMP levels high -CRP bound to CRP site -LacZ transcribed

high glucose, high lactose

-repressor not bound to operator -cAMP levels low -CRP not bound to CRP site -LacZ not transcribed

siRNA

-second strand synthesis -cleavage into small fragments when leaves nuclear envelope -miRNA-RISC complex is not mismatched to mRNA -mRNA degradation--can chop up mRNA, inhibition of transcription

what are the properties of cancer cells?

-self sufficiency in growth signals (grow even if they don't receive signals) -insensitivity to antigrowth signals -evasion of apoptosis (resistant to cell suicide) -limitless replicative potential (divide forever) -tissue invasion and metastasis (spread of cancer) -sustained angiogenesis (growth of new blood vessels)

which of the following is not a function performed by a tumor suppressor gene?

-slowing cell division -repairing mutations -enforcing cell checkpoints -inhibiting apoptosis (correct) -inhibiting the action of oncogenes

why is it important that histone proteins are positively charged?

-so the negatively charged phosphate groups on DNA are attracted to them (correct) -so the positively charged phosphate groups on DNA are attracted to them -so the negatively charged deoxyribose sugars are attracted to them -so the positively charged deoxyribose sugars are attracted to them

if cytosol from a mitotic cell was heated to 94 degrees before injection into interphase cells, what would happen to the injected interphase cell?

-the injected cell would enter mitosis, because mitotic inhibitory factors would be denatured -the injected cell enter mitosis because DNA from the injected cell would be denatured -the injected cell would not enter mitosis because its DNA would be denatured -the injected cell would not enter mitosis because mitosis promoting factors from the mitotic cell would be denatured (correct) -the injected cell would enter mitosis because heat would have no effect on the outcome of the experiment

Praeder Willi syndrome patients inherit mutant allele from the father. The same mutation inherited from the mother causes no phenotype. Based on this information we can conclude that:

-the paternal allele of this gene is expressed (correct) -the maternal allele of this gene is expressed -both allele are expressed -neither allele is expressed

what would happen during cell division in animals if the cell was deficient in actin?

-the sister chromatids would not separate (mitosis) -the mitotic spindle would not form (mitosis) -the cell would not divide (correct) -the centromeres would remain unattached (mitosis)

A student cloned a piece of DNA into a plasmid, transformed bacteria with the plasmid, and plated the bacteria on agar plates. The next day the bacteria completely covered the agar, no individual colonies were seen. what could explain this result?

-the student forgot to add the appropriate antibiotic to their agar plates (correct) -the student did not use the proper restriction enzymes in their cloning procedure -the student forgot to use ligase -the cloning plasmid did not have an origin of replication

a mutant Arabidopsis thaliana, normal amount of MET-1 mRNA are produced but is shorter than normal, and there is no MET-1 protein made. Which of the following is a possible explanation?

-there is a mutation in a protein that binds to the 3' UTR of the MET-1 mRNA to regulate RNA stability -there is a mutation in the MET-1 gene in one of the sites recognized by the splice some, leading a change in splicing (correct) -there is mutation in the enzyme that would edit the MET-1 mRNA

When can gene expression be regulated?

-transcription (efficient but can be slow) -translation -posttranslational (fast but waste energy)

repetitive sequences in eukaryotes

-transposable elements 45% of the genome -short tandem repeats 3% of the genome

miRNA

-turns into hairpin structure and taken out of cytoplasm -leaves nuclear envelope and cleavage into small fragments -miRNA-RISC complex is mismatched to mRNA -inhibition of translation because cannot chop of mRNA

how do some mutants express lacZ and lacY even in the absence of lactose?

-type 1: mutant repressor protein -type 2: mutant operator (binding site for the repressor)

which of the following statements about receptor kinases is false?

-when receptor kinases are activated, they activate G proteins by phosphorylating them (correct because phosphorylate each other, not G protein) -a receptor kinase has an extracellular ligand binding domain, a transmembrane domain, and an intracellular enzymatic domain -in response to ligand binding, the receptor kinase dimerizes -a dimerized receptor kinases gets phosphorylated as part of the activation process

under what conditions does E. coli produce B-galactosidase?

1. Glucose only (NO) 2. Glucose + Lactose (NO) 3. Lactose only (YES)

process of transcriptional regulation in eukaryotes

1. Regulatory transcription factors bind with a DNA sequence called an enhancer 2. binding of regulatory transcription factors recruits the general transcription factors to the promoter of the gene 3. the general transcription factors recruit the components of the RNA polymerase complex and transcription takes place

requirements for PCR

1. Template DNA 2. DNA polymerase 3. All four deoxynucleotide triphosphates (A, T, G, C) 4. Two primers 5. Taq DNA polymerase 6. Buffer

what are some ways cancer can arise?

1. a cell behaves as if it has received a signal for cell division when in fact it hasn't 2. a tumor may form as the result of the overproduction of a signaling molecule 3. a tumor may form as the result of the production of an altered form of a signaling molecule

requirements for plasmid

1. an origin of replication 2. antibiotic resistant gene 3. a cloning site to insert DNA of interest

When can gene regulation occur?

1. at the level of chromosome itself 2. by controlling transcription or translation 3. after the protein is made

M cyclin-CDK complex

1. chromosomal proteins-->chromosome condensation 2. Nuclear laming-->initiate nuclear envelope breakdown 3. Microtubule associated proteins-->promote spindle formation 4. Ubiquitin-ligase-->leading to the degradation of M-cyclin-->MPF deactivation

what cancer causing gain of function mutations in proto-oncogenes cause the protein to be hyperactive?

1. deletion or point mutation in coding sequence 2. gene amplification 3. chromosome rearrangement

From a single gene, RNA editing can result in

1. different proteins in different cells 2. different proteins within the same cell

what is the purpose of mitosis and the cell cycle in eukaryotes?

1. growth 2. wound repair 3. asexual reproduction in unicellular organisms

signal transducers and activators of transcription (STATs)

1. inactive STAT protein is in the cytoplasm 2. activated by phosphorylation in response to an extracellular signal 3. activated STAT forms a dimer that translocates to nucleus 4. binds to enhancer and activates transcription

two types of signaling molecules and receptors

1. lipid soluble--molecule that can cross plasma membrane. Hydrophobic and intracellular receptor 2 lipid insoluble--molecule that cannot cross plasma membrane. Hydrophilic and cell surface receptor

what two events does the M phase consist of?

1. mitosis--separation of the chromosomes and two nuclei 2. cytokinesis--the division of the cell itself into two separate cells

replica plating to find mutants

1. plate mutagenized cells (ex. glucose present) 2. Copy onto second plate (ex. glucose present to lactose only) 3. Identify mutant colony (ex. lactose only)

steps in cell signaling

1. receptor activation--the signal binds to a receptor which is then activated 2. signal transduction--the signal is transmitted to the interior of the cell by a signal transduction pathway 3. response--the cell responds for example by activating an enzyme or turning on transcription of a gene 4. termination--the response is terminated so that new signals can be received

steps of gene activation

1. regulatory transcription factor binds to enhancer 2. recruitment of HATs and chromatin remodelers to open chromatin 3. assembly of general transcription factors at the promoter (1st) 4. recruitment of RNA polymerase (2nd) 5. transcription begins

illumina sequencing cycle 1

1. reversibly terminating dNTPs add one nucleotide 2. remove the terminating chemical group

Steps in signaling pathway

1. signal arrives and binds receptor 2. receptor changes conformation. Bound G protein replaces GDP with GTP 3. Active G protein binds to and activates effector protein (enzyme). Effector produces secondary messengers and triggers response 4. signaling molecule detaches. Receptor is inactivated 5. secondary messengers are degraded 6. G protein hydrolyzes GTP to GDP and its inactivated

what are the four essential elements to cellular communication?

1. signaling cell 2. signaling molecule 3. receptor protein 4. responding cell

Cell-to-Cell Communication

1. signaling cells release signaling molecules 2. receptors on or in another cell bind the signaling molecule 3. conformational change in the receptor changes its activity 4. the signal is sometimes transducer from one protein to another 5. response--the activity of the target cell changes 6. termination--signal is deactivated

Steps of signaling pathway of Ras

1. signals arrives and binds to receptor 2. receptor dimerizes and is phosphorylated 3. receptor binds Ras, Ras exchanges GDP to GTP and is activated 4. GTP bounds Ras activates a kinase and triggers a kinase cascade 5. a phosphorylation cascades results, each protein phosphorylating another until response is triggered

what are the steps of binary fission?

1. the circular bacterial DNA molecule is attached by proteins to the inner membrane 2. DNA replication begins at a specific location and proceeds bidirectionally around the circle 3. the newly synthesized DNA molecule is also attached to the inner membrane, near the attachment site of the initial molecule 4. as replication proceeds the cell elongates symmetrically around the midpoint separating the DNA attachment sites 5. cell division begins with the synthesis of new membrane and wall material at the midpoint

Steps for Binary Fission

1. the circular bacterial DNA molecule is attached to the inner membrane 2. DNA replication proceeds bidirectionally 3. the newly synthesized DNA molecule is also attached to the inner membrane 4. the cell elongates symmetrically around the midpoint, separating the DNA attachment sites 5. synthesis of new membrane and cell wall material at the midpoint. FtsZ protein forms a ring at the constriction 6. daughter cells separate

requirements of cell division

1. the two daughter cells must each receive the full complement of genetic material (DNA) present in the single parent cell 2. the parent cell must be large enough to divide in two 3. must contribute sufficient cytoplasmic components such as proteins, lipids, and other macromolecules to each daughter cell

How does CRISPR work?

1. transform a cell with a plasmid containing sequences that code for a CRISPR RNA as well as the CRISPR associated protein Cas9. RNA contains a region that can form a hairpin structure 2. When RNA undergoes base pairing with the target DNA, Cas9 cleaves the target DNA 3. an exonuclease widens gap in the target DNA 4. the editing template is used to repair the gap in the target DNA 5. the result is edited DNA with a target sequence

DNA that exists in the nuclei of your cells is present in _____ copies per cell, except for DNA in the X and Y chromosomes in males

2

Personal genome consists of DNA in ____ sets of chromosomes

2 sets. one inherited from each parent, plus a smaller mitochondrial genome inherited from mother

How many chromosomes do humans have?

23 chromosome pairs

dideoxynucleotide (chain terminator)

3' hydroxyl group is missing

how many strands of DNA can we find in a replicated chromosome?

4

In how many stages does mitosis occur?

5

in prokaryotic cells _____ percent of DNA sequences code for a product used by the cell

90

enhancer

A DNA segment containing multiple control elements that can recognize certain transcription factors that stimulate the transcription of nearby genes. Binds with a particular DNA sequence in or near a gene

TATA box

A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex.

allosteric effect

A change in the shape that alters its binding affinity for DNA of a protein as the result of binding of a molecule to a site other than the active site

Which of the following genes might be activated by E2F? A gene required for cytokinesis A gene needed for the transcription of MPF A gene needed for DNA replication A chromosome condensation gene A gene required to separate chromosomes at anaphase

A gene needed for DNA replication

chromatin remodling

A mechanism for epigenetic gene regulation by the alteration of chromatin structure.

G0 phase

A nondividing state occupied by cells that have left the cell cycle, sometimes reversibly.

What is meant by the term homologous chromosomes? A chromosome from one cell that is identical to a chromosome in another cell. A pair of identical chromosomes, each carrying the same DNA sequence. A pair of chromosomes, each carrying the same set of genes. The total number of chromosomes in a cell.

A pair of chromosomes, each carrying the same set of genes.

In negative regulation: A regulatory molecule (usually a protein) binds to the DNA near the gene in order to prevent transcription A regulatory molecule (usually a protein) binds to the DNA near the gene in order to for transcription to take place A regulatory DNA binds to an RNA molecule in order for transcription to take place A regulatory DNA binds to an RNA molecule in order to prevent transcription

A regulatory molecule (usually a protein) binds to the DNA near the gene in order to prevent transcription

In positive regulation: A regulatory molecule binds to the protein in order to prevent transcription of the mRNA corresponding to the bound protein A regulatory molecule binds to the protein in order to activate transcription of the mRNA corresponding to the bound protein A regulatory molecule (usually a protein) binds to the DNA near the gene in order for transcription to be prevented A regulatory molecule (usually protein) binds to the DNA near the gene in order for transcription to take place

A regulatory molecule (usually protein) binds to the DNA near the gene in order for transcription to take place

inducer

A small molecule that interacts with the repressor and prevents it from binding DNA (allosteric interaction)

Plasmid

A small ring of DNA that carries accessory genes separate from those of the bacterial chromosome

How can cancer cells ensure that oxygen levels remain high at the tumor site? Lack of oxygen is not a problem for tumor cells. Secreted factors will move towards red blood cells, capture the oxygen, and transport it back to the tumor site. A transcription factor activates synthesis of a secreted factor necessary for angiogenesis. Tumor cells will move towards areas of high oxygen concentration.

A transcription factor activates synthesis of a secreted factor necessary for angiogenesis.

growth factor

A type of signaling molecule that causes the responding cell to grow, divide, or differentiate

The figure below shows a primer annealed to a strand of DNA template to be used in a sequencing reaction. Unfortunately, some of the ingredients are missing. To the mix of template and primer, you add buffer, DNA polymerase and a mix of dATP, dCTP, dTTP, and ddGTP, but no other nucleotides (d=deoxy; dd=dideoxy). What will be the sequence of synthesized DNA in the 5' to 3' direction? ATC CAGTTAAG d. A range of synthesis products including A, AT, ATC, ATCG, ATCGT, ATCGTA etc A range of synthesis products including C, CA, CAG, CAGT, CAGTT, CAGTTA etc ATCG

ATCG

When does post-translational control take place? During transcription. After a protein is synthesized. As soon as the mRNA is transported out of the nucleus. When mRNAs bind to ribosome.

After a protein is synthesized.

Which of the following would not lead to a cell becoming cancerous? A cell that divides in an uncontrolled way. An overproduction of a growth signaling molecule. An antibody that binds to a receptor and prevents the receptor from binding to a growth signaling molecule. An increased quantity of the growth factor receptor molecule.

An antibody that binds to a receptor and prevents the receptor from binding to a growth signaling molecule.

DNA methylation patterns can be inherited from cell generation to the next because... An enzyme called DNA methyltransferase recognizes hemimethylated DNA and methylates the other strand All cytosines are methylated in eukaryotic DNA DNA polymerase can copy methylated DNA to produce another methylated copy During the production of gametes DNA methylation is erased

An enzyme called DNA methyltransferase recognizes hemimethylated DNA and methylates the other strand

what enzyme cleaves lactose, releasing glucose and galactose

B-galactosidase

what does cyclin activate?

CDK

what phosphorylates Rb?

CDK

Which of the following stays constant during the cell cycle? The amount of DNA in the nucleus Phosphorylation of CDK target genes Cdk activity levels Cyclin protein levels Cdk protein levels

Cdk protein levels

What is a key difference between cell signaling by a cell-surface receptor and cell signaling by an intracellular receptor? Cell-surface receptors bind to specific signaling molecules; intracellular receptors bind any signaling molecule. Cell-surface receptors bind polar signaling molecules; intracellular receptors bind nonpolar signaling molecules. Cell-surface receptors typically bind to signaling molecules that are smaller than those bound by intracellular receptors. Signaling molecules that bind to cell-surface receptors lead to cellular responses restricted to the cytoplasm; signaling molecules that bind to intracellular receptors lead to cellular responses restricted to the nucleus. None of the other answer options is correct.

Cell-surface receptors bind polar signaling molecules; intracellular receptors bind nonpolar signaling molecules.

Diagram summarizes E2F regulation by Rb. If there was a mutation in the Rb gene, such that it could not release E2F, you would expect Cells to be stuck in anaphase Cells to be stuck in G2 Cells to be stuck in G1 Cells to be stuck in M phase Cells to be stuck in S phase

Cells to be stuck in G1

If the p53 gene in cells is mutated (loss-of-function mutation), which of the following situations may occur? Cells are marked for apoptosis Cells cannot pass the G1/S checkpoint Cell cannot pass the metaphase checkpoint Cells with DNA damage may proliferate in an uncontrolled manner

Cells with DNA damage may proliferate in an uncontrolled manner

Which of the following is not an example of post-translational modification of a protein? Changing the mRNA codon sequence Adding a covalent functional groups such as a carbohydrate. Marking proteins for degradation. Phosphorylating proteins.

Changing the mRNA codon sequence

3. Metaphase

Chromosomes align in the center of the cell

homologous chromosomes

Chromosomes that have the same sequence of genes and the same structure

Which of the following is not considered translational control of protein synthesis? Controlling the primary protein sequence. Controlling the location of where a protein is synthesized. Controlling when a protein is synthesized. Controlling the rate of protein synthesis.

Controlling the primary protein sequence.

Which of the following is not considered translational control of protein synthesis? Controlling when a protein is synthesized. Controlling the rate of protein synthesis. Controlling the location of where a protein is synthesized. Controlling the primary protein sequence.

Controlling the primary protein sequence.

adenylyl cyclase

Converts ATP to cyclic AMP in response to an extracellular signal.

What is the difference between Sanger sequencing and PCR with regard to the materials needed to perform these reactions? -Primers are needed in PCR but not in Sanger sequencing. -DNA polymerase is needed in Sanger sequencing but not in PCR. -Dideoxynucleotides are needed in Sanger sequencing, but not in PCR. -DNA polymerase is needed in PCR but not in Sanger sequencing. -Primers are needed in Sanger sequencing but not in PCR.

Correct! Dideoxynucleotides are needed in Sanger sequencing, but not in PCR.

What would be the result in a cell if ubiquitin ligase was not phosphorylated by MPF? The cell would enter G0. The cell would not enter M phase The nuclear envelope would not break down Cyclin concentrations would remain high

Cyclin concentrations would remain high

regulatory transcription factors have

DNA binding domains and domains that can recruit co-regulators

hemi-methylated DNA

DNA from methylated DNA that is partially methylated

human genome

DNA in the chromosomes present in a sperm or egg

why is gene regulation in prokaryotes more simpler than in eukaryotes?

DNA is not packaged into nucleosomes, mRNA is not processed, and transcription and translation are not separated by a nuclear envelope

Which of the following is true of DNA methylation? DNA methylation is a chemical modification to the DNA which can influence gene expression DNA methylation blocks transcription by changing DNA nucleotide sequence Heavy methylation of DNA activates transcription Methyl groups when bound to the promoter, recruit RNA polymerase

DNA methylation is a chemical modification to the DNA which can influence gene expression

Which of the following is true of DNA methylation? DNA methylation is a chemical modification to the DNA which can influence gene expression Heavy methylation of DNA activates transcription DNA methylation blocks transcription by changing DNA nucleotide sequence Methyl groups when bound to the promoter, recruit RNA polymerase

DNA methylation is a chemical modification to the DNA which can influence gene expression

Which of the following is true regarding both animal cell division and bacterial cell division? Chromosome condensation occurs during prophase Microtubules or microtubule-like proteins play important roles during cytokinesis The nuclear envelope needs to break down prior to chromosome separation, and needs to be rebuilt afterwards DNA replication and separation of chromosomes are occurring simultaneously. DNA must be replicated so that cell division can occur

DNA must be replicated so that cell division can occur

Recombinant DNA

DNA produced by combining DNA from different sources. involves cutting DNA by restriction enzymes, isolating them by gel electrophoresis, and ligating them with enzymes used in DNA replication

Which of the following would NOT be different between your brain cells and your skin cells? The pattern of chromatin packing in the nuclear DNA The methylation patterns of the DNA The genes expressed in the two cells DNA sequences of enhancer elements

DNA sequences of enhancer elements

transposable elements

DNA sequences that can replicate and insert themselves into new positions in the genome. Have the potential to increase their copy number in the genome over time. essentially move from one location to another

One difference between DNA sequencing and PCR is: Primer(s) is/are needed for DNA sequencing, but not for PCR Primer(s) is/are needed for PCR, but not for DNA sequencing PCR uses dideoxy nucleotides, while DNA sequencing does not In PCR, new nucleotides are added to DNA strands made of deoxynucleotides, while in DNA sequencing new nucleotides are added to DNA strands made of dideoxynucleotides. DNA sequencing uses dideoxy nucleotides, while PCR does not

DNA sequencing uses dideoxy nucleotides, while PCR does not

what are the main players for positive regulation?

DNA, RNA polymerase complex, and a regulatory protein called a transcriptional activator

When several different cell cycle regulators fail, leading to both the overactivation of oncogenes and the loss of tumor suppressor activity, cancer will likely

Develop

what does Rb bind to and inactivate?

E2F (determine if we enter into S phase)

Muscle cells and nerve cells in a single organism owe their differences to Having different chromosomes Having different enhancer elements Using different genetic codes Expressing different genes

Expressing different genes

each receptor activates multiple

G proteins

Rb tumor supressor in what checkpoint?

G1

p53 tumor supressor in what checkpoint?

G1 and G2

When nutrients are suboptimal for cell growth and division, the cell cycle arrests. At which stage of the cell cycle/checkpoint would you predict this arrest to occur? It is not possible to answer with the information given. G1, G2, and the M checkpoints M checkpoint G1 checkpoint G2 checkpoint

G1 checkpoint

what is the DNA damage checkpoint?

G1 checkpoint. Pass this checkpoint if cell size is adequate, nutrients are sufficient, social signals (growth factors) are present, and DNA is undamaged

checkpoints in cell cycle

G1, G2, M -if the preparations for the next stage of the cell cycle are incomplete or if there is some kind of damage there are mechanisms that block the cyclin-CDK activity required for the next step, pausing cell division until preparations are complete or the damage is repaired

what checkpoint are proto-oncogenes involved in?

G1--promote cell division in a controlled manner

Which major checkpoint delays the cell cycle when DNA replication is incomplete? G1 checkpoint M checkpoint G1, G2, and the M checkpoints G2 checkpoint None of the checkpoints delays the cell cycle when DNA replication is incomplete.

G2 checkpoint

DNA replication checkpoint is the

G2 checkpoint. Pass this if chromosomes have replicated successfully and DNA is undamaged. This is negative regulation of MPF activation

Which pair includes a phase of the cell cycle and a cellular process that occurs during that phase? S phase, cell division G1 phase, DNA replication G2 phase, preparation for mitosis M phase, cell growth

G2 phase, preparation for mitosis

what else happens during termination?

GTP goes to GDP by hydrolysis (off position). without the active GTP, adenylyl cyclase cannot make cyclic AMP, signal comes to a halt. cAMP goes to AMP which no longer activates protein kinase A.

What is a tumor suppressor? Genes that encode proteins that function to inhibit cell division. Genes that allow the growth of only certain types of tumors. A specialized category of oncogenes. Genes that by-pass normal regulatory controls.

Genes that encode proteins that function to inhibit cell division.

Which of the following is NOT a DNA binding protein? regulatory transcription factors CRP the repressor LacI HDACs RNA polymerase

HDACs

The human genome contains many transposable elements, yet these elements rarely move from one location to another. Which of the following is NOT a likely explanation? Histone acetylation levels at transposable elements are high DNA methylation levels are high at transposable elements siRNAs target transposable elements for silencing The DNA of transposable elements in tightly packaged

Histone acetylation levels at transposable elements are high

sister chromatids

Identical copies of a chromosome; do not separate

What is the type of protein found on the surface of metastatic cancer cells that interacts with the basal lamina? receptor tyrosine kinases Cadhesins cyclins Integrins

Integrins

How does protein phosphorylation regulate protein function? It changes the amount of ATP in the cell. It causes a conformational change in the protein. It promotes protein cleavage. It initiates mutagenesis in the protein.

It causes a conformational change in the protein.

What is the function of the enzyme beta-galactosidase? It regulates transcription of the lacZ gene. It regulates transcription of the lacY gene. It cleaves lactose into glucose and galactose. It transports galactosidase into a cell.

It cleaves lactose into glucose and galactose. It transports galactosidase into a cell.

You are studying regulation of the SDC-2 gene by another gene called LET-34 in the eukaryote C. elegans. You find that in cells that lack the LET-34 gene (it is deleted), SDC-2 mRNA levels are unchanged, but protein levels are higher. What can you conclude about LET-34? It could be a miRNA gene or code for a protein that binds the 3' UTR of the SDC-2 mRNA It could be a miRNA gene It could be an siRNA gene It could code for a protein that binds to an enhancer of the SDC-2 gene. It could code for a protein that binds the 3' UTR of the SDC-2 mRNA.

It could be a miRNA gene or code for a protein that binds the 3' UTR of the SDC-2 mRNA

The final step in a DNA sequencing reaction is to run the fragments on a gel. What purpose does this serve? It terminates the sequencing reaction at particular bases. It provides the substrate for DNA polymerase. It separates DNA fragments generated during the sequencing reaction based on their size. It separates the dideoxynucleotides away from the standard deoxynucleotides.

It separates DNA fragments generated during the sequencing reaction based on their size.

Which of the following types of signaling depends on direct cell-cell contact? Autocrine Juxtacrine Paracrine Endocrine

Juxtacrine

if the phosphoprotein is the active form of the protein then

Kinase-->protein I----phosphatase positive regulation= ---> negative regulation= I---

if the phosphoprotein is the inactive form of the protein then

Kinase--I protein <----phosphatase

what happens when there is a mutation in operator, lactose present or absent?

LacI protein cannot bind to operator, RNA polymerase bind to promoter and transcription occurs

What is the spindle assembly checkpoint?

M (metaphase) checkpoint. Pass this checkpoint if all chromosomes are properly attached to the spindle apparatus

what are the two distinct phases of the cell cycle?

M phase and interphase

All of the following statements correctly describe MPF except MPF causes the cell to enter the S phase and begin DNA replication MPF has two subunits, a cyclin and a cyclin dependent kinase You Answered MPF is active during the M phase MPF triggers many events by phosphorylating other proteins

MPF causes the cell to enter the S phase and begin DNA replication

Difference between mitosis and meiosis

Meiosis has two rounds of genetic separation and cellular division while mitosis only has one of each. In meiosis homologous chromosomes separate leading to daughter cells that are not genetically identical. In mitosis the daughter cells are identical to the parent as well as to each other.

MAP kinase

Mitogen-activated protein kinase. Signaling molecule that is the final kinase in a three-kinase sequence called the MAP-kinase signaling module.

RTKs activate Ras. Ras can be mutated to promote uncontrolled cell growth. Which of the following mutations will convert Ras into an oncogene? A. A mutation that prevents Ras from binding to the RTK. B. A mutation that prevents Ras from converting its bound GTP to GDP. C. A mutation that prevents Ras from binding GDP or GTP. D. A deletion of the entire Ras gene.

Mutation that prevents Ras from converting to its bound GTP to GDP (gain of function)

One difference between PCR and DNA sequencing is There is more amplification of template DNA in sequencing as compared to PCR. Need for helicase PCR uses dideoxy nucleotides, while sequencing uses deoxy nucleotides DNA polymerase is needed in PCR, but not in sequencing Need for two primers versus one primer

Need for two primers versus one primer

are there introns in bacteria and archaea

No

is there a relationship between genome size and organismal complexity

No

5. Telophase

Nuclear envelope re-forms and chromosomes decondense

repetitive DNA

Nucleotide sequences, usually noncoding, that are present in many copies in a eukaryotic genome. The repeated units may be short and arranged tandemly (in series) or long and dispersed in the genome.

Which of the following is likely to be the same when comparing a neuron cell to a skin cell in the same organism The kind of regulatory transcription factors present Cell size Number of chromosomes in the nucleus Cell shape Expression levels of neuron-specific genes

Number of chromosomes in the nucleus

What protein is an example of a tumor suppressor?

P53

Which of the following is a function of MPF? Phosphorylation of microtubule associated proteins to prevent assembly of the mitotic spindle Phosphorylation of nuclear lamins that lead to reassembly of the nuclear envelope Phosphorylation of chromosomal proteins that lead to chromosome condensation Phosphorylation of M-cyclin to promote entry into mitosis Phosphorylation of a ubiquitin ligase to activate cyclin by ubiquitination

Phosphorylation of chromosomal proteins that lead to chromosome condensation

Plasmid

Plasmid

The M-cyclin/Cdk complex functions to do all of the following, except: Prepare the cell for DNA replication initiate chromosome condensation Initiate M-cyclin destruction. initiate nuclear envelope breakdown initiate spindle formation

Prepare the cell for DNA replication

One difference between cDNA and genomic DNA of the same gene is: U versus T bases Presence of STOP codons Presence of introns Presence of ATG start codon Presence of 5' cap

Presence of introns

which enzyme is used for reverse transcriptase?

RNA polymerase

which of the following enzymes can perform reverse transcription -DNA polymerase -RNA polymerase -telomerase -topoisomerase -both DNA and RNA polymerase

RNA polymerase

what happens to Ras in the absence of a signal?

Ras is bound to GDP and is inactive

what is the gatekeeper for the G1 checkpoint?

Rb

what must happen first before E2F can activate transcription of S phase genes?

Rb-Ph must release E2F

Which one of these is not an example of a post-translational event? Insertion of an integral membrane protein into the plasma membrane Protein folding Addition of a copper cofactor to an enzyme Removal of introns

Removal of introns

Scientists studied isolated cells at various stages of the cell cycle and found that some cells have 1.5 times more DNA than the parental cell. These cells were in which phase of the cycle? G1 S G0 G2

S

when does the duplication of chromosomes occur?

S phase

What would occur in a cell if Rb were in a constant phosphorylated state? The cell would not be able to enter S phase. S-phase genes would always be activated to some degree. E2F would always be bound to Rb. E2F would not be able to bind to DNA.

S-phase genes would always be activated to some degree.

paracrine signaling

Signal released from a cell has an effect on neighboring cells through diffusion

Which of the following immediately follows receptor activation in a signaling pathway? Response Signal activation Termination Signal transduction

Signal transduction

Which of the following immediately follows receptor activation in a signaling pathway? Signal activation Response Termination Signal transduction

Signal transduction

polycistronic RNA

Single bacterial RNA molecule that encodes more than one polypeptide chain; uncommon in eukaryotes.

4. Anaphase

Sister chromatids (which become individual chromosomes when the centromere splits) separate and travel to opposite pole

alternative splicing

Splicing of introns in a pre-mRNA that occurs in different ways, leading to different mRNAs that code for different proteins or protein isoforms. Increases the diversity of proteins.

Which statement describes the proper order of steps leading to regulation by miRNAs? Synthesis of hairpin miRNA precursor, formation of the RISC complex, cleavage of miRNA, inhibition of translation. Synthesis of hairpin miRNA precursor, formation of the RISC complex, inhibition of translation, cleavage of miRNA. Synthesis of hairpin miRNA precursor, cleavage of miRNA, formation of the RISC complex, inhibition of translation. Formation of the RISC complex, Synthesis of hairpin miRNA precursor, cleavage of miRNA, inhibition of translation.

Synthesis of hairpin miRNA precursor, cleavage of miRNA, formation of the RISC complex, inhibition of translation.

DNA editing

Techniques that allow researchers to "rewrite" the nucleotide sequence of DNA so that specific mutations can be introduced into genes.

renaturation

The base pairing of complementary single-stranded nucleic acids to form a duplex; also known as hybridization, it is the opposite of denaturation.

If p53 were mutated such that it was present in the nucleus at high levels at all time, what is the most likely outcome? Apoptosis would be inhibited. The cell would never enter the cell cycle. The cell would only be able to complete S and G2 phase. The cell cycle would speed up.

The cell would never enter the cell cycle.

When cytosol from a mitotic cell is injected into an interphase cell, the interphase cell enters mitosis. What would happen if the cytosol from the mitotic cell was first treated with DNase (an enzyme that degrades DNA) prior to injection into interphase cells? The injected cell would enter mitosis, because mitosis promoting factors would still be present The injected cell would enter mitosis, because mitosis inhibiting factors would be degraded You Answered The injected cell would NOT enter mitosis, because mitosis promoting factors would be degraded The injected cell would NOT enter mitosis, because mitosis inhibiting factors would still be present The injected cell would enter S phase to replace the degraded DNA

The injected cell would enter mitosis, because mitosis promoting factors would still be present

Where does the signal bind to the receptor? The regulatory site Away from the active site The active site The ligand binding site

The ligand binding site

You look at a cell under the microscope and see nicely condensed chromosomes in the nucleus. What would you expect to happen next? Chromosomes would be pulled to either side of the cell. Sister chromatids would align. The nuclear envelope would break down. The centromere would replicate.

The nuclear envelope would break down.

Which of the following is not a requirement for successful cell division? The parent cells must be in a quiescent state. The parent cell must have enough cytoplasmic components to contribute to the daughter cells. Each daughter cell must receive all equal genetic material. The parent cell must be large enough to divide into two.

The parent cells must be in a quiescent state.

sequence assembly

The short sequences are put together in the correct order to generate the long, continuous sequence of nucleotides in the DNA molecule present in each chromosome.

metastasis

The spread of cancer cells beyond their original site

Which of the following statements about enhancers is correct? They contain a unique base sequence called the TATA box They bind to general transcription factors to recruit RNA polymerase to the promoter They are found in a variety of locations in the DNA and are functional in any orientation They are located only in introns

They are found in a variety of locations in the DNA and are functional in any orientation

Proto-oncogenes

They are involved in cell division, but do not themselves cause cancer. Only when they are mutated do they have the potential to cause cancer.

Which of the following statements about G proteins is false? They must be active before the cell can make the second messenger cAMP They become activated when bound to GDP They can lead to activation of protein kinases They bind to and are regulated by guanine nucleotides

They become activated when bound to GDP

How do miRNAs regulate a specific mRNA? Through complementary base pairing with the mRNA. Through alternate splicing. By enhancing RNA editing. By inhibiting the spliceosome

Through complementary base pairing with the mRNA.

True or False: The 3' end of each primer must be oriented toward the region to be amplified so that when DNA polymerase extends the primer it creates a new DNA strand complementary to the targeted region

True

True or False: primers flank the specific region of DNA to be amplified

True

How many times does a metastatic cancer cell cross the capillary basal lamina? Once Four Twice Zero

Twice

How is a new cell wall formed in dividing plant cells? Actin and myosin filaments pull existing cell wall components to the center of the two newly formed cells. A new cell wall is pinched off from the existing cell wall. After two complete plasma membranes are formed, portions of the extracellular matrix polymerize to form a new cell wall. Vesicles originating from the Golgi apparatus are used to form a cell plate.

Vesicles originating from the Golgi apparatus are used to form a cell plate.

What is one way cancer can occur?

When cellular mechanisms that promote cell division are inappropriately activated or the normal checks on cell division are lost, cells may divide uncontrollably. The result can be cancer, a group of diseases characterized by rapid, uncontrolled cell division.

Which of the following is not a characteristic of benign tumors? Continuous cell division. You Answered Does not invade surrounding tissue. Rarely life threatening. Will break away from the main tumor.

Will break away from the main tumor.

CRISPR

a collection of DNA sequences that tells Cas9 exactly where to cut

Southern blotting

a labeled probe can be used to determine the size and number of DNA sequence of interest in a gel

Which one of the following would MOST likely contribute to uncontrolled cell proliferation (i.e., cancer)? a mutant CDK that was active in the absence of its cyclin binding partner a mutant enzyme needed for microtubule synthesis/polymerization a mutant DNA replication mechanism causing extra chromosome copies a mutant kinetochore protein that causes reduced microtubule attachment a mutant cyclin that cannot bind to its normal CDK binding partner

a mutant CDK that was active in the absence of its cyclin binding partner

what does Abl1 encode?

a nonreceptor tyrosine kinase. It is a proto-oncogene. BCR-ABL is a form of tyrosine that is always on

positive regulation

a regulatory molecule (usually a protein-activator) must bind to the DNA at a site near the gene in order for transcription to take place (turns gene on)

negative regulation

a regulatory molecule (usually a protein-repressor) must bind to the DNA at a site near the gene in order for transcription to be prevented (turns gene off)

An operator is: a protein encoded by the structural genes of an operon is a different name for the repressor protein a regulatory region in DNA; the binding site for the repressor a region of DNA consisting of an operon, the promoter, and the coding sequences for the structural genes

a regulatory region in DNA; the binding site for the repressor

how does cytokinesis work in animals?

a ring of actin and myosin filaments contracts inside the cell membrane, causing it to pinch inward and cleavage furrow

open reading frame (ORF)

a sequence of DNA or RNA that could be translated to give a polypeptide. consist of AUG and a STOP codon

virus

a small infectious agent that contains a nucleic acid genome packaged inside a protein coat called capsid

What is a miRNA? messenger RNA, will be translated into protein part of the ribosome part of the splicing machinery a small regulatory RNA that forms a hairpin structure

a small regulatory RNA that forms a hairpin structure

polymerase chain reaction (PCR)

a technique for making copies of DNA, which allows a targeted region of a DNA molecule to be replicated or amplified into as many copies as desired

sequence motif

a telltale sequence that indicates what types of function may be encoded in a particular region of the genome

open unmethylated

ability to currently replicate

decondensed chromatin allows RNA polymerase to

access DNA

histone acetylation

acetyl groups are attached to positively charged lysines in histone tails

Positive control by CRP

activates transcription when [cAMP] levels are high (resulting from low [glucose])

cAMP-CRP acts as an _____ to the operon

activator

A(n) ________________ is a small molecule that binds to repressors in prokaryotes. A(n) _______________ is a DNA sequence to which regulatory transcription factors bind in eukaryotes. activator, inducer inducer, activator inducer, enhancer activator, enhancer co-activator, activator

activator, enhancer

G protein bound to GTP

active

When LacI can bind to DNA

active

G1/S cyclin-CDK complex

active at the end of the G1 phase and is necessary for the cell to enter S phase. -promotes expression of histone proteins needed for packaging the newly replicated DNA strands

histone acetyl transferases (HATs)

add acetyl groups to positively charged lysine residues

DNA methyltransferase (DNMT)

adds methyl groups to cytosines

cAMP is an ____ activator of CRP binding

allosteric

Illumina sequencing

allows you to sequence millions of DNA fragments on a microscope slide

Post translational modification of proteins ...

alter function

RNA binding proteins that interact with splicesomes regulate

alternative splicing (determine if the exon is included)

RNA editing

alters nucleotide sequence of mRNA

C-Value paradox

amount of DNA in the body

If there was a mutation in your genome, such that the RISC protein could not be translated, you would expect your mRNA to be degraded upon transcription the sequence of your mRNA to be changed introns being translated into protein along with exons fewer proteins translated than usual an increase of LINE elements in your genome

an increase of LINE elements in your genome

step 2 of PCR amplification

annealing--when the solution is cooled, the two primers anneal to their complementary sequence on the strands of the template duplex

if damage is too much to repair, then p53 activates

apoptosis (cell suicide)

cyclin-dependent kinases (Cdks)

are always present within the cell (protein levels) but are active only when bound to the appropriate cyclin

Proto-oncogenes are genes that suppress cancer-causing genes. will suppress cancer when activated by a signaling molecule. are normal genes that, when mutated, have the potential to cause cancer. are genes that will cause cancer when an organism ages.

are normal genes that, when mutated, have the potential to cause cancer.

where do the microtubules attach to the chromosomes?

at their centromeres

what are promoter sequences bound by?

basal transcription complex (same for all genes)

when does damage DNA (p53) checkpoint occur?

before S phase

annealing

begins as soon as solution is cooled

G1 Phase

between the end of M phase and the start of S phase. specific regulatory proteins are made and activated. once activated the regulatory proteins promote the activity of enzymes that synthesize DNA. Time of preparation for S phase DNA synthesis

G2 Phase

between the end of S phase and start of M phase. both size and protein content of the fell increase in preparation for division. Time of preparation for M Phase mitosis and cytokinesis

how do prokaryotes divide?

binary fission

how do you prevent BCR-ABL from being active?

bind it with Gleevec

How do viruses reproduce?

bind to receptor proteins on cells of the host organism, enabling the viral genome to enter the cell.

One key regulator of the cell cycle is CDK. CDK is a protein that binds to cyclin to become activated is degraded after it is used is only active during mitosis fluctuates in concentration during various stages of the cell cycle

binds to cyclin to become activated

silencer

binds with regulatory transcription factors to repress transcription

in order to make sure donor DNA can be fused with vector DNA

both pieces are cut with the same restriction enzyme so they both have the same overhangs

what does chromatin looping do?

brings enhancers and promoters close to spatial proximity

describe one way chromatin is remodeled

by chemical modification of the histones around which DNA is wound

cAMP receptor protein (CRP) binds

cAMP

what happens to CRP-cAMP in the absence of glucose?

cAMP levels are high and cAMP binds to CRP, changing the shape of CRP so that it can bind at a site near the operator and stimulate binding of RNA polymerase to transcribe lacZ and lacY when lactose is present in the cell

what happens if glucose is present in the cell

cAMP levels are low, and the cAMP-CRP complex does not bind the lactose operon. Even in the present of lactose, the lactose operon is not transcribed to high levels

Histone modification: -is fixed, but this has no effect on whether genes are expressed. -is random; sometimes the lysines are modified and sometimes they are not, but the state is independent of the environment or cell type. -is fixed; once a histone is modified, it stays that way and the genes with which it is associated are turned on or off permanently. -can change over time in response to environmental cues, allowing genes to be turned on or off as needed. -can change over time in response to environmental cues, but this has no effect on gene expression.

can change over time in response to environmental cues, allowing genes to be turned on or off as needed.

Histone modification: can change over time in response to environmental cues, allowing genes to be turned on or off as needed. is random; sometimes the lysines are modified and sometimes they are not, but the state is independent of the environment or cell type. is fixed, but this has no effect on whether genes are expressed. can change over time in response to environmental cues, but this has no effect on gene expression. is fixed; once a histone is modified, it stays that way and the genes with which it is associated are turned on or off permanently.

can change over time in response to environmental cues, allowing genes to be turned on or off as needed.

Oncogene

cancer causing gene

haploid

cell one complete set of chromosomes

receptor tyrosine kinases

cell surface, when it is unbound it is inactive. -signal bound-dimerization autophosphorylation of receptor and receptor is activated

what happens when you inject cytoplasm of M-phase cell into interphase cell?

cell will enter mitosis

diploid

cell with two complete set of chromosomes

what do viruses use to hijack a cell?

cellular ATP

signal transduction can be thought of as a

chain reaction. Signal is often amplified at each step

DNA binding proteins package DNA into

chromatin

1. Prophase

chromosomes condense and become visible in the nucleus. Centromeres radiate microtubules and migrate to opposite poles

structural genes

code for the sequence of amino acids making up the primary structure of each protein

genomes also contain

coding sequences for RNAs that are not translated into protein, such as rRNA and tRNA

comparative genomics

compares similarities and differences in gene content, function, and organization among genomes of different organisms

protein coding genes

composed of different regions, including regulatory elements that specify when and where and RNA transcript is produced, noncoding introns that are removed from the RNA transcript during RNA processing, and protein coding eons that contain the codons that specify the amino acid sequence of a polypeptide chain

what is DNA methylation associated with?

condensed chromatin--inhibition of transcription

regulatory transcription factors

control the recruitment of general transcription factors

what happens under normal conditions when EGF binds to its receptors?

controlled division of cells

what do cyclins bind to and activate?

cyclin-dependent kinases

how does cytokinesis in plants?

cytoplasm is divided and form vesicles that are transported from the Golgi apparatus to the middle of the dividing cell along microtubules. These vesicles fuse to form a cell plate

step 1 of PCR amplification

denaturation--a solution containing double stranded DNA (template duplex) is heated to separate the DNA into two individual strands

transcription factors help

determine where the gene will be transcribed

what does multicellularity differentiation mean

different cells have different functions even though they have the same DNA

RNA splicing of transcripts

different proteins can be made from a single gene depending upon how the RNA transcript is spliced together

in eukaryotes when two cells are close together, how does the signal move?

diffusion

6. Cytokinesis

division of the cytoplasm to form two separate daughter cells; 2nd stage of cell division

some mutations only cause disease when inherited from either the mother or the father. Inheritance of the same mutation from the other parent ________

does not cause disease

gametes

egg and sperm

lacI

encodes for a repressor protein

regulatory transcription factors can bind to ______ to promote transcription or _____ to repress transcription

enhancer; silencer

kinase

enzyme that catalyzes the transfer of phosphate groups

restriction enzymes

enzyme that recognizes specific short nucleotide sequences in double stranded DNA and cleaves the DNA at these sites

open reading frame

example of sequence motif. a long string of nucleotides that if transcribed and processed into mRNA, would result in a set of codons for amino acids that does not contain a stop codon

step 3 of PCR amplification

extension--solution is heated to optimal temperature for DNA polymerase. DNA polymerase synthesizes new DNA strands (complementary to the template duplex strands) by extending primer in a 5' to 3' direction

All DNA sequences are transcribed into RNA. True False

false

where can transcription factors be located

far upstream of the gene, downstream of the gene, or in introns

chromatin remodeling to expose promoter region

gene activation

histone acetylation

gene activation

regulated expression

gene product made on demand; expression can be induced or repressed

DNA methylation

gene repression

HDAC activity

gene repression

lacZ

gene that codes for the enzyme B-galactosidase

lacY

gene that codes for the protein lactose permease

transgenic organsims/genetically modified organisms (GMOs)

genetically engineered organisms

short fragments move a _______ distance than larger fragments

greater

step 3 of plasmid cloning

grow more plasmid -only cells that have picked up a plasmid can grow in the presence of antibiotics -plasmid containing bacterial cells will grow in colonies

if DNA damage is moderate, then p53 will

halt the cell cycle to give cell time to repair DNA

What is responsible for pulling apart the double stranded DNA when running a PCR reaction? Taq polymerase Helicase DNA ligase Heat

heat

S cyclin-CDK function

helps complete DNA synthesis

S cyclin-CDK complex

helps initiate DNA synthesis -activates enzymes and other proteins necessary for DNA replication -prevents the replication proteins from reassembling at the same place and re-replicating the same DNA sequence

M-cyclin-CDK (MPF) function

helps prepare the cell for mitosis

Low O2 then

high HIF and VEGF is secreted so blood vessels grow (cancer causing)

what are microtubules made out of?

hollow tube formed from tubular dimers

the length of time a signaling molecule remains bound to its receptor depends on what?

how tightly the receptor holds on to it--binding affinity

personalized medicine

in which an individual's genome sequence, by revealing his or her disease susceptibilities and drug sensitivities, allows treatments to be tailored to that individual

when LacI cannot bind to DNA

inactive

lactose acts as an _______ of the lactose operon since it prevents binding of the repressor protein

inducer

Lactose ______ expression of B-galactosidase

induces

p53 levels in the nucleus rise then p53 acts as a transcription factor to turn on genes that

inhibit cell cycle or promote apoptosis

Glucose ______ production of B-galactosidase

inhibits

Heavy methylation of the CpG island...

inhibits transcription

GLD-1 is an RNA binding protein which binds to the 3' UTR of the MES-3 mRNA. If GLD-1 is not functional, MES-3 mRNA levels do not change, but MES-3 protein levels increase. The size of the MES-3 protein does not change, only its quantity. What is the function of GLD-1? promotes alternative splicing enhances mRNA degradation inhibits translation promotes translation promotes mRNA stability

inhibits translation

deamination of adenosine produces

inosine

step 1 of plasmid cloning

insert DNA of interest into plasmid -the restriction enzyme cuts the plasmid sometimes leaving sticky and blunt ends -ligase then binds the DNA to the plasmid

cDNA

intronless DNA copy of the gene

what happens when the signal binds to the receptor

it activates the receptor by causing a conformational change in the receptor

what happens when complementary DNA (cDNA) is made?

it can be used as a template in PCR

limitation of recombinant DNA

it can make use only of existing DNA sequences

what happens when a protein is phosphorylated by a kinase?

it is activated

what happens when Ras is bound to GTP?

it is active

A G-protein is active when it is bound to GTP it is bound to ADP it is bound to GDP it is bound to ATP

it is bound to GTP

what does active Ras do?

kinase cascade--activate growth promoting genes

what is a product of the LacI gene

lac repressor

what is the relationship between lactose and LacI gene?

lactose binding changes the conformation so that it can no longer bind to DNA. Lactose is an inducer

what happens if lactose is not present in the cell

lactose repressor binds to the lactose operator and prevents transcription even in the presence of the cAMP-CRP complex

signaling molecule is often referred to as

ligand

what type of hormones are steroid hormones?

lipid (hydrophobic) and intracellular

High O2, then

low HIF. VEGF not secreted so blood vessels don't grow (tumor suppressing)

how is Rb a tumor suppressor?

making sure E2F doesn't promote when its bound to Rb

short tandem repeats

microsatellitle--repeating sequence of 1-5 bases -repeat sequences are hyper variable (vary among individuals)

what does alternative splicing produce?

more than one mature mRNA form the same gene

Retrotransposons

move by means of an RNA intermediate. reverses flow of genetic information from DNA to RNA

lactose operon is an example of ___________ regulation by a repressor whose function is modulated by an inducer

negative

fragments of double stranded DNA are _____ charged so molecules move toward the positive pole of the electric field

negatively

histone methylation

neither gene activation or gene repression

are CDKs active when not bound to cyclin?

no

does transcription occur during mitosis?

no

what happens when there is a loss of function mutation in LacI, lactose present or absent?

no LacI made, RNA polymerase binds to promoter and transcription occurs

do prokaryotes undergo mitosis? do prokaryotes undergo cytokinesis?

no, yes

epigenetic inheritance

non-DNA sequence-based heritability

G protein bound to GDP

not active

unmethylated closed

not currently replicating but has the potential to in the future

methylated closed

not replicating and will not replicate in the future (G0 phase)

2. Prometaphase

nuclear envelope breaks down and the microtubules of the mitotic spindle attach to chromosomes

What happens in telophase? chromosomes attach to the mitotic spindle. nuclear envelopes re-form around newly segregated chromosomes. sister chromatids separate. the parent cell divides into two daughter cells.

nuclear envelopes re-form around newly segregated chromosomes.

RNA processing

occurs after transcription takes place 1. addition of a nucleotide cap to the 5' end 2. addition of poly A tail

constitutive expression

occurs continuously

To promote cancer, proto-oncogenes must be turned ________ and tumor suppressors must be turned ______. on; on off; on on; off off; off

on; off

recombinant DNA renaturation

once renaturation takes place, the ends of the donor fragment and the vector are covalently joined by DNA ligase

Fill in the blanks: _______________ promote cancer and __________________ block specific steps in the development of cancer. oncogenes, proto-oncogenes tumor suppressors, oncogenes oncogenes, tumor suppressors tumor suppressors, tumor suppressors

oncogenes, tumor suppressors

gel electrophoresis

one way to determine the actual size of a DNA fragment, a procedure in which DNA samples are inserted into slots or wells near the edge of a rectangular slab of porous material resembling agar, which is composed of a tangle of polymers that make it difficult for large molecules to pass through

when does E. coli preferentially utilize lactose?

only when glucose is depleted

histone acetylation

opens up chromatin

wild type LacI when no lactose present- LacI binds ______ and prevents _______ from binding to promoter

operator, RNA polymerase. Transcription doesn't occur

lacO

operator; binding site for the repressor protein

gene expression in prokaryotes

operons: coordinate control of transcription of multiple genes as a single polyscistronic mRNA occurs only in prokaryotes

when DNA is damaged by radiation a specific protein kinase is activated that phosphorylates a protein called

p53

what happens as p53 levels in the nucleus increase?

p53 acts as a transcription factor to turn on genes

When DNA is damaged, what protein is activated?

p53 blocking the export and degradation process

What happens when p53 is mutated?

p53 protein, which normally arrests cell division in response to DNA damage. When the p53 protein is mutated or its function is inhibited, the cell can divide before the DNA damage is repaired. The result is that cells continue to divide in the presence of damaged DNA, leading to the accumulation of mutations that promote cell division.

dimerization

partnering of two similar or identical molecules. activates the cytoplasmic kinase domains of the paired receptors, causing them to phosphorylate each other at multiple sites on their cytoplasmic tails

what does p53 do?

phosphorylated p53 acts as a transcription factor that turns on genes that inhibit cell cycle, giving the cell time to repair damaged DNA

what can prevent or slow translation?

phosphorylation of ribosomal proteins

many signaling molecules are ____ _____ that cannot pass through the hydrophobic core of the plasma membrane

polar proteins

why are eukaryotic genomes so large?

polyploidy--having more than two sets of chromosomes in the genome. 2 sets of 23 chromosomes giving us 43 chromosomes in total

how do we turn genes on and off?

positive and negative regulation

CRP-cAMP

positive regulator of lac operon (protein that activates gene expression upon binding DNA

Complete the following sentence: Acetylation of histones neutralizes the _____________ charges on histones, therefore phosphate groups on DNA are __________ attracted to them. positive, more negative, less negative, more positive, less

positive, less

in both prokaryotes and eukaryotes, transcription can be

positively or negatively regulated

what is a mutation of the Ras protein in cancer?

prevents Ras from converting its bound GTP too GDP. the protein remains locked in the active GTP bound states causing sustained activation of the MAP kinase pathway

when a repressor protein binds to DNA, it_______

prevents transcription of a gene

wild type LacI when lactose present-Lactose _____ LacI from binding to operator, _______ can bind to promoter

prevents, RNA polymerase. Transcription occurs

in the absence of lactose, the repressor protein binds to the operator and _______ transcription from taking place

prevents. The RNA polymerase complex is not recruited and transcription does not take place

genome annotation

process of attaching biological information to gene sequences

gene expression depends on

production or activation of different regulatory proteins

when an activator protein binds to DNA, it ______

promotes transcription of a gene

what does termination protect?

protects the cell from overreacting to existing signals and allows the cell to respond to new signals

capsid

protein coat surrounding a virus

integrin

protein that attaches a cell to extracellular molecules (have connections with connective tissue)

lactose permease

protein that transports lactose from the external medium into the cell

Cyclins

proteins are synthesized that active the kinases. Their levels rise and fall with each turn of the cell cycle. phosphorylate target proteins involved in promoting cell division

the life span of an mRNA is controlled by

proteins binding to the 3' UTR of mRNAs

Tumor suppressor

proteins whose normal activities inhibit cell division. Tumor suppressors act in opposition to proto-oncogenes.

gain of function mutation in ____ promotes cancer

protooncogene

palindromic

reading the same backwards and forwards

lacP

recruit the RNA polymerase complex and initiate transcription

when lactose is present in the cell, the repressor protein is unable to bind to the operator, RNA polymerase is ____ and transcription occurs

recruited

general transcription factors

recruited to the gene's promoter, which is the region of a gene where transcription is initiated

DNA methylation

recruits proteins that affect changes in chromatin structure, histone modification, and nucleosome positioning that RESTRICT access of transcription factors to gene promoters

operon

region of DNA consisting of the promoter, operator, and the coding sequence for structural genes. portion of DNA including s set of genes involved in a specific metabolic pathway -single regulatory protein -generates polycistronic RNA -repressor is the product of a separate regulatory gene -repressor binds to the operator and blocks RNA polymerase -allosteric regulation of repressor

Centromere

region where two sister chromatids are joined tightly together

G1/S cyclin-CDK function

regulates entry into S phase

what are enhancers and silencers bound by?

regulatory transcription factors (vary by gene) -can be located far from the gene, 5' to 3'

Taq polymerase

remains active at high temperatures

DNA methylation is _____ following cell divisions

remembered

histone dacetylases (HDACs)

remove acetyl groups (react with protein)

Negative control by lac repressor

represses transcription unless lactose is present (lactose inactivates repressor)

the lactose operon is negatively regulated by the _____ protein encoded by the lacI gene

repressor

the structural genes of the lactose operon are always expressed unless the operator is turned off by a regulatory molecule a ______

repressor

juxtacrine signaling

requires direct contact between the signaling and responding cell

sexual reproduction

results in offspring that receive genetic material from two parents

in polycistronic mRNA, each of the coding sequences is priced by a _________ so translation can be initiated

ribosome binding site

cyclic AMP is also known as a

second messenger

Transposons

segments of DNA that can move from one region of DNA to another

when the sequences of a sufficient number of short stretches of the genome have been obtained the next step is

sequence assembly

conserved

sequences that are similar in different organisms

telomeres

shortening of telomeres will arrest the cell cycle and may cause apoptosis (tumor suppressor)

endocrine signaling

signaling by means of molecules that travel through the bloodstream

in eukaryotes when two cells are far apart, how does the signal move?

signaling molecule is transported by circulatory system

second messenger

signaling molecules found inside cells that relay information to the next target in the signal transduction pathway. sends signal to the inside of the cell

autocrine signaling

signaling molecules may be released by a cell and then bind to receptors on the very same individual cell

gel electrophoresis separates the resulting DNA fragments according to their

size

rate of mitigation depends on

size not sequence

restriction enzymes produce

some produce a 5' overhang, others produce 3' overhang, and some cleave in the middle of their restriction site and leave blunt ends with no overhang

what doesn't an ORF contain

stop codon

histone tails

strings of amino acids that protrude from the histone proteins in the nucleosome

If there was a loss of function mutation in the gene that codes for E2F, you would expect the cell to be stuck in G1 stuck in the S phase stuck in the M phase stuck in G2

stuck in G1

If there was a loss of function mutation in the gene that codes for E2F, you would expect the cell to be stuck in the S phase stuck in G1 stuck in G2 stuck in the M phase

stuck in G1

In regulatory mutants proteins binding tp specific DNA sequences act as ______

switches

S phase

synthesis of DNA and does not immediately precedent or follow mitosis but is separate from it by two gap phases

what do CDKs phosphorylate?

target proteins involved in promoting cell division

Infection by the same virus

the DNA copy of the viral genome is transcribed to RNA that combines with a protein that has a DNA cleaving function

how do bacteria remember and defend themselves from past infections

the RNA serves as a guide to identify target DNA in the virus by complementary base pairing and the protein cleaves the target DNA

Tumor development involves... acquiring one mutation that turns the cell cancerous. no mutations. complete loss of all DNA from the cell. the accumulation of multiple mutations.

the accumulation of multiple mutations.

histone methylation

the addition of methyl groups to histones

what causes the protein's ability to bind to the repressor

the binding of the inducer to the repressor results in an allosteric change in repressor structure

Chromatin

the complex of DNA, RNA, and proteins making up chromosomes

where in the many steps of transcription initiation does regulation occur?

the first point at which transcription can be regulated is in the recruitment of the general transcriptional factors and components of the RNA polymerase complex

genome

the genetic material of a specified organism, cell, nucleus, organelle, or virus

an increase in gene dosage increases

the level of expression because each copy of the gene is regulated independently of other copies

what happens during M phase?

the parent cell divides into two daughter cells

what happens In cancerous cells when EGF binds to its receptors?

the presence of excess receptors heightens the response of the signaling pathway leading to abnormally high gene expression and excess cell division

tumor angiogenesis

the process of the formation of blood vessels within the tumor itself

catabolite repression

the product of the reaction inhibits making more enzyme (glucose inhibits production of B-galactosidase)

restriction site

the recognition of sequences the enzyme cleaves

transformation of recombinant DNA

the recombinant DNA is mixed with bacteria that have been chemically coaxed into a physiological state in which they take up DNA from outside the cell

Which one of the following is NOT a result of RNA editing? the production of different types of proteins from mRNA transcripts for the same gene within a single cell the deamination of cytosine to produce uracil the deamination of adenosine to produce inosine the recruitment of RNA polymerase following the binding of general transcription factors the production of differently edited mRNA transcripts from the same gene in different cell types

the recruitment of RNA polymerase following the binding of general transcription factors

ligand-binding site

the signaling molecule binds to a specific part of the receptor protein (nonviolent and highly specific)

what happens when general transcription factors are bound to the promoter?

the transcription factors recruit the components of the RNA polymerase complex (the enzyme complex that synthesizes the RNA transcript complementary to the template strand of DNA)

when glucose levels are high, what happens to cAMP levels?

they are low

how do eukaryotes divide?

they first divide the nucleus by mitosis then divide the cytoplasm into two daughter cells by cytokinesis

what if bacteria contain mutations that eliminate function of the lacZ or lacY gene?

those bacteria cannot utilize lactose as a source of energy

interphase

time between two successive M phases

what happens if regulatory transcription factors do not recruit the components of the transcription complex to the gene?

transcription does not occur

step 2 of plasmid cloning

transform plasmid into bacteria -genetic transformation--genetic alteration in a cell as a result of uptake and expression of foreign genetic material -increase permeability of bacterial cell membrane by chemical treatment or electrical shock

what is the poly A tail required for?

translation and RNA stability

what is the 5' cap required for?

translation initiation

what do LINEs represent?

transposable elements

CDK only active when cyclin levels are high

true

Recombinanat DNA technology can combine DNA from any two sources including different species

true

The donor fragment may be a protein coding gene, a regulatory part of a gene, or any DNA segment of interest

true

True or False: ORF by itself is enough to annotate the DNA segment as potentially protein coding

true

True or false: the concentration of the kinase subunit does not change during the cell cycle, but the concentration of cyclin changes during the cell cycle

true

at high temps, DNA polymerase enzymes from many species irreversibly lose both structure and function

true

true or false: DNA polymerase can only use DNA as a template

true

true or false: RNA must be processed before translation

true

true or false: if the activator does not bind to the DNA, the RNA polymerase cannot bind and transcription does not occur

true

true or false: if the repressor protein binds to the DNA, it inhibits recruitment of RNA polymerase, and transcription does not occur

true

true or false: in negative transcriptional regulation, the native state of the DNA allows the RNA polymerase complex to be recruited and transcription takes place (pg 452)

true

true or false: when the activator protein is present in a state that can interact with its binding site in the DNA, the RNA polymerase complex is recruited to the promoter of the gene and transcription takes place

true

true or false: without a functional product from lacY, lactose cannot enter the cell, and without a functional product from lacZ, lactose cannot be cleaved into its component sugars

true

loss of function mutation in ______ promote cancer

tumor supressor genes

what does each pair of homologous chromosomes represent?

two of the same type of chromosome both carrying the same set of genes

asexual reproduction

type of reproduction that occurs when offspring receive genetic material from a single parent

Epigenetics

typically involve changes not to the DNA sequence itself but to the manner in which the DNA is packaged. Often reversible and responsive to changes in the environment

where can the binding site for the promoter be located?

upstream, downstream, or overlapping with the promoter

deamination of cytosine produces

uracil

how do eukaryotes identify open reading frames

use cDNA sequences and then locate the gene in the genome sequence

what is the purpose of DNA sequencing?

used to determine the nucleotide sequence of an unknown stretch of DNA, nucleotide by nucleotide

when does E. coli preferentially utilize glucose?

when both glucose and lactose are present

dideoxynucleotide adding

whenever a dideoxynucleotide is incorporated into a growing daughter strand, there is no hydroxyl group to attack the incoming nucleotide and strand growth is stopped

Benign

which means that it is relatively slow growing and does not invade the surrounding tissue, or it may be malignant, which means that it grows rapidly and invades surrounding tissues

metastatic cells have reduced cell-cell adhesion

will become weaker as cancer cells break away