SQ3 63-75

67. c) Describe how, in simplest terms, cell cycle control illustrates different ways of controlling protein function, with examples of 1-synthesis, 2-allosteric and 3-phosphorylation/dephosphorylation control.

1.Control by regulating protein synthesis: cyclins are made and degraded on a repeating schedule. 2.allosteric: cyclins allosterically activate Cdks 3.phosphorylation/dephosphorylation control: Cdks phosphorylate proteins that participate in the next phase of the cycle.

68. ♥ e) Describe each of the labels used in the experiment, including what was labeled.

35S, radioactive sulfur, was used to label the proteins in the phage. And 32P, radioactive phosphorus, was used to label the DNA in the phage.

♥64. a) What is a conditional mutant?

A conditional mutant is an organism that displays a wild type phenotype under permissive conditions, but under restrictive conditions displays a mutant phenotype.

69. ♥b) What is the source of information for semi-conservative replication?

A parent/template strand of DNA is used to synthesize a new strand using complementary base pairing.

63. ♥d) What kinds of assays/tests or measurements could you make to determine which of two sets of (synchronized) cells is in G1 and which is in G2?

A possible test is to determine the amount (concentration) of DNA within the cell. If it is normal then it is still in the G1 phase, if it has doubled then it is in G2.

74. ♥a) In cellular replication, exactly what is a primer?

A short strand of RNA with a free 3' hydroxyl end that is based pair to the DNA template.

74. d) In general molecular biology (including biotechnology), what is a primer, and where and how is it made?

A synthetically made short nucleic acid strand. It is made without a template.

72. ♥e) What is the term that is used to describe the relationship between complementary nucleic acid strands, besides complementary?

Antiparallel

63 ♥b) What ranges of cell cycle length are found in various mammalian cells?

Anywhere between 8 hours to 3 days for dividing cells, although, in adults especially, there are cells that stop dividing completely.

65. ♥ c) What are the main conditions the cell checks for before passing the M (spindle-assembly) checkpoint? What happens if the cell "passes" the M checkpoint?

At the metaphase/anaphase border, it checks for correct chromosome attachment to the spindle fibers. If it passes then it can finish mitosis.

72. ♥d) Why does one end of double-stranded DNA (two strands) have one strand labeled 5' and the other labeled 3'?

Because the complementary strands run/pair in opposite directions.

71. c) From the origin, which direction does replication proceed (with respect to the chromosome) and on which strand(s)?

Bi-directional, continues replicating in both directions from the origin within the double strand

65.♥ a) What are the main conditions the cell checks for before passing the S/G1 checkpoint? What happens if the cell "passes" the S/G1 checkpoint?

Conditions include: enough nutrients and space for other cells, Intact/healthy DNA, Some cells:presence of growth factor. If the cell passes the checkpoint then it can start S-phase (DNA replication)

65. ♥b) What are the main conditions the cell checks for before passing the G2 checkpoint? What happens if the cell "passes" the G2 checkpoint?

Conditions of the G2 checkpoint include: DNA replication is complete ,intact/healthy DNA. If the cell passes the checkpoint then it can start mitosis.

68. f) In culture A the label was found in the cell pellet, and in culture B the label was found in the supernatant. What was the difference between the phage in cultures A and B, and what was the significance of these results?

Culture A the DNA was labeled with radioactive phosphorus, in Culture B protein was labeled with Radioactive sulfur. The existence of the radioactivity in the pellet from culture A means that DNA was injected into the cell, meaning it is the genetic material.

67. b) Explain how cells arrest in G1 if they have DNA damage.

DNA damage in G1 causes an increase in both the concentration and activity of a protein called p53, which is a transcription regulator that activates the transcription of a gene encoding a Cdk inhibitor protein --- p21. The p21 protein will inhibit G1-Cdk, preventing them from driving the cell into S phase, giving the cell time to repair the DNA damage.

73. d) What is DNA ligase and what is its function?

DNA ligase is a specialized enzyme that ties fragments of DNA together (sealing a gap in one strand)

73. Answer the following questions about replication at the biochemical level. ♥a) In what direction (biochemically—at the level of the polynucleotide chain) does DNA polymerase "read" a template strand, and in what direction (biochemically) does DNA polymerase synthesize DNA?

DNA polymerase "reads" from 3' → 5' while it synthesizes DNA from 5' → 3'.

74. c) Where and how is the cellular primer made?

DNA primase creates the RNA primer along the DNA template.

69. You should be able to identify deoxyribose, purines, pyrimidines, and nucleotides, and make correct H-bonds between G-C and A-T base pairs. ♥ a) Draw out the process of semi-conservative replication of DNA, showing at least three phases. Describe the process by labeling your drawing.

Draw Elsewhere

70. b,c,d,e

Draw elsewhere

73. b) Draw out your answer to a), including template strand and new strand.

Draw elsewhere

63. ♥c) What is meant by G0 phase?

G0 is the phase that cells which no longer divide go into. It perpetually exists in a G1 state.

67. a) Name each protein in the complex needed to pass the S/G1 checkpoint,and describe the function of each protein, explaining how the cell moves on from the S/G1 checkpoint.

G1-cyclinis the allosteric effector that activates G1-CdK. G1-Cdk phosphorylate are the proteins that trigger DNA replication.

63. ♥a) What is the most variable part of the cell cycle?

G1.

73. ♥c) If a new strand of DNA is being extended, which of its ends is being added to, the 5' or 3'?

It adds to the 3' end.

75. ♥d) What additional use do the authors of ecb4 suggest telomerase provides by its work (this is discussed at the very end of the section)?

It can help the cell to recognize if there is a damage such as DNA accidentally breaking in chromosomes.

64. ♥b) When is it important or absolutely necessary to use conditional mutants to study a cellular function?

It's necessary when the mutation is lethal, especially if it is lethal quickly. A conditional mutant allows you to study function while it is alive. Survival functions.

66. ♥c) Name each protein in the complex needed to pass the G2 checkpoint, and describe the function of each protein, explaining how the cell moves on from the G2 checkpoint.

M-cyclin activates M-Cdk (cyclin-dependent kinase) as the allosteric activator of M-Cdk. M-Cdk phosphorylate proteins that participate in/carry out the mitosis.

75. Read about telomeres in ecb4 page 209 (bottom)-211 (top). ♥a) Why do prokaryotes NOT have the problem that eukaryotes have?

Prokaryotes have circular DNA molecules as chromosomes, so the last fragments of the lagging strand can be finished by running into each other around the circle.

75. ♥c) In simple terms, what does telomerase do?

Telomerase provides a mechanism that can complete replication of the lagging strand ends by adding multiple copies of the same short DNA sequence to the template strand, meaning it can be completed by conventional DNA replication.

72. ♥ c) What group is free at the 5' end of a strand, and what group is free at the 3' end?

The 5' end has a free phosphate group and the 3' end has a free OH group

66. b) What checkpoint(s) does MPF pass the cell through?

The G2 and M checkpoints.

68. d) Explain why a blender was used before centrifuging/pelleting cells.

The blender was used to separate any outside material from the surface of the bacteria before centrifugation. If you didnt do this first then the rest of the materials from the phage would pellet with the injected cells.

75. ♥b) In simple terms, what is the problem for eukaryotes (e.g. what does the last part of Figure 6- 21 show)?

The ends of the lagging strand can't be completed, because the last fragment can't replace its RNA with DNA.

73. ♥e) Explain why bidirectional replication on both strands away from the origin poses a problem, and describe how the solution includes a "lagging" strand. It is not necessary to mention the enzymes involved.

The issue is, while it replicates bidirectionally, it only synthesized from 5' → 3'. To solve this, on the lagging strand that would be "backwards" DNA is replicated in segments, then those segments are "tied" together by DNA ligase. This means replication is slightly slower on the lagging strand.

72. ♥b) In diagrams of DNA, what do the numbers 5' and 3' refer to?

The numbers refer to the carbons of the deoxyribose.

68. Hershey and Chase used T2 bacteriophage infection of E. coli in their experiment. ♥a) What was Hershey and Chase's hypothesis, and what was the alternative hypothesis?

Their hypothesis was that DNA is the genetic material for the cell. The alternative was that protein was the genetic material.

♥70. In the Meselson-Stahl density labeling experiment, the starting DNA was pure 15N: ♥a) What was Meselson and Stahl's hypothesis, and what were the alternative hypotheses?

Their hypothesis was that DNA synthesis was semi-conservative, or alternatively is completely conservative or dispersive.

71. a) Where on a chromosome does replication begin? What exactly does that site refer to?

They begin replication at a specific DNA sequence (recognized by the proteins that start DNA replication) referred to as the origin point. There are several in Euk. and only one in prok.

74. b) Why do cells need a primer?

They need a primer because DNA cannot put the first nucleotide onto a strand.

69. ♥c) What would be the source of information for conservative or dispersive replication?

They would require a separate and complex protein or enzyme to remember the sequence needed to construct an identical new strand

71. b) Read ecb4 page 199. Explain why origins are "A-T rich."

This is because A-T are held together by fewer bonds than their G-C counterpart, making them easier to break apart.

64. ♥c) What is the phenotype of a conditional lethal mutant under permissive conditions? What is its phenotype under restrictive conditions?

Under permissive conditions, a conditional mutant will function identically to it's non mutated wild type counterpart (has wild-type phenotype). Under restrictive conditions it will die.

68. c) What was the experimental basis for investigating b)?

When centrifuged, whatever entered the cell would pellet with it.

72. ♥a) Name the activated monomeris for replication.

dNTPs

68. ♥b) What was the basic premise of the experiment?

the genetic material must enter cells to direct phage replication

66. a) Describe the specific molecular make-up of MPF.

♥MPF is made up of two proteins mitotic Cdk (M-Cdk) and Mitotic cyclin (M-Cyclin)