Bio 1 Ch. 16 Molecular Basis of Heredity

What is bacteriophage and how does it behave when it enters a host cell?

A bacteriophage is a virus that infects a bacteria, also known as phages. Once attached to a host cell the virus injects its DNA(OR RNA) into th cell.

What is meant by the term transformation?

A change in genotype and phenotype due to the assimilation of external DNA by a cell. When the external DNA is from a member of a different species, transfomation results in horizontal gene transfer. This means that bacteria can change genetically by incorporating hereditary material from other living or dead individuals.

Describe the structure of a nucleosome, the basic unit of DNA packing in eukaryotic cells .

A nucleosome is made up of eight histone proteins, two each of four different types, around which DNA is wound. Linker DNA runs from one nucleosome to the next.

What is a nucleotide?

A nucleotide is the building block of a nucleic acid.

excision repair

A repair system that removes and then correctly replaces a damaged segment of DNA using the undamaged strand as a guide. Excision repair enzymes also fixes any damage to DNA caused by chemicals, UV, etc.

What is a "replication bubble"?

A replication bubble is where DNA replication starts. This is where DNA strands seperate and open. Replication of DNA is then proceeded in both directions until the entire molecule is copied.

What is a replication fork, and how many replication forks are there per replication bubble?

A replication fork is a y-shaped region on a replicating DNA molecule where the parental strands are being unwound and new strands are being synthesized. In eukaryotic chromosomes: unwinding and replication begin in several places at once. Whereas in bacteria, DNA in a ring, unwinding beins in one place.

What is a primer?

A short polynucleotide with a free 3' end, bound by complementary base pairing to the template strand and elongated with DNA nucleotides during DNA replication.

In analyzing the number of different bases in a DNA sample, which results would be consistent with the base-pairing rules?

A+G=C+T

RNA polymerase

An enzyme that links ribonucleotides into growing RNA chain during transcription, based on complementary binding to nucleotides on a DNA template strand. RNA polymerases can start a polynucleotide strand.

Describe the experiments of Avery et al. with Streptococcus pneumoniae transformation and explain how they showed that the hereditary material was contained in DNA and not RNA or protein.

Avey, MacLeod and McCarty took heat-kill virulent Streptococcus and removed lipids and carbs. This then left the proteins, DNA, and RNA. They then divided it into three samples that used enzymes that would digest protein in one, RNA in the second, and DNA in the third. They then incubated each sample with live, non-virulent Streptococcus. This was to see which would transform into virulent strains. Their results were that live bacteria transformed by S-strain extract, except for those without DNA. This concludes that DNA carries the hereditary material.

single stranded DNA binding proteins

Bind to and stabilizes single-stranded DNA until it is used as a template.

What role does complementary base pairing play in the replication of DNA?

Complementary base pairing ensures that the two daughter molecules are exact copies of the parental molecule. When the two strands of the parental molecule separate, each serves as a template on which nucleotides are arranged, by base-pairing rules, into new complementary strands.

A biochemist isolates, purifies, and combines in the test tube a variety of molecules needed for DNA replication. When she adds some DNA to the mixture, replication occurs, but each DNA molecule consist of normal strand paired with numerous segments of DNA a few hundred nucleotides long. What has she probably left out of the mixture?

DNA Ligase.

Identify two major functions of DNA pol III in DNA replication.

DNA pol III covalently adds nucleotides to new DNA strands and proofreads each added nucleotide for correct base pairing.

What is the basis for the difference in how the leading and lagging strands of DNA molecules are synthesized?

DNA polymerase can join new nucleotides only to the 3' end of a pre-existing strand, and the strands are antiparallel.

How are RNA polymerases and DNA polymerases different in this regard?

DNA polymerase synthesizes a DNA strand and used in DNA replication while RNA polymerase is used during transcription to synthesize the mRNA strand. In contrast with the DNA polymerase, RNA polymerase do not necessarily require the so called primer to start the process and they actually ave no proofreading systems.

What two properties, one structural and one functional, distinguished heterochromatin from euchromatin?

Euchromatin is chromatin that becomes less compacted during interphase and is accessible to the cellular machinery responsible for gene activity. Heterochromatin, on the other hand, remains quite condensed during interphase and contains genes that are largely inaccessible to this machinery.

Describe the work of Griffith with Streptococcus pneumonia and explain how it demonstrated bacterial transformation.

Griffith studied two strains of the bacterium Streptococcus pneumoniae. The S strain can cause pneumonia in mice; it is pathogenic because the cells have an outer capsule thaat protects them from an animals immune system. Cells of the R strain lack a capsule and are nonpathogenic. To test for the trait of pathogenicity, Griffith injected mice with the two strains. The conclusion was that the living R bacteria had been transformed into pathogenic S bacteria by unknown , heritable substance from the dead S cells that enabled the R cells to make capsules.

Griffith was trying to develop a vaccine for S. pneumonia when he was surprised to discover the phenomenon of bacterial transformation Based on his results, what result was he expecting in forth panel? Explain.

He expected that the mouse injected with the mixture of heat-killed S-cells and living R-cells would survive, since neither type of cell alone would kill the mouse.

In what major way(s) is heredity in bacteria different from heredity in eukaryotes?

Heredity in bacteria is very differen from heredity in eukaryotes, because bacteria have no formal sexual reproduction but they have diverse ways of exchanging genetic material. Most bacteria are unicellular, so cell division is their form of reproduction. Therefore they have faster generation time.

Describe the experiments of Hershey & Chase using bacteriophage. Explain why they used radioactively labeled phosphorus and sulfur. What was the outcome? What was the significance of their results?

Hershey and Chase usked radioactive sulfur and phosphorous to trace the fates of proteins and DNA, repectively, of T2 pahges that infected bacterial cells. they wanted to see which of these molecules entered the cells and could reprogram them to make more phages. When proteines were labeled (batch 1), radioactivity remained outside the cells, but when DNA was labeled (batch 2), radioactivity was found inside the cells. Cells containing radioactive phage DNA released new phages with somes radioactive phosphorus. They concluded that Phage DNA entered bacterial cells, but phage proteins did not. They concluded that DNA, not protein, functions as the genetic material.

In a nucleosome, the DNA is wrapped around

Histones

mismatch repair

In mismatching repair, other enzymes remove and replace incorrectly paired nucleotides that have resulted isom replication errors. Mismatch repair enzymes double-check replication, and recognizes and fixes mismatches that DNA polymerase missed. This improves accuracy to less than 1 mismatch per billion.

What is the relationship between DNA replication and the S-phase of the cell cycle?

In the cell cycle, DNA synthesis occurs during the S-phase, between the G1 and G2 phases of interphase. DNA replication is therefore complete before the mitotic phase begins.

topoisomerase

Is an enzyme that helps relieve this strain by breaking, swiveling, and rejoining DNA strands.

DNA proofreading

Is where the DNA polymerase backs up and removes wrng nucleotides, and inserts the correct one. This then improves accuracy to 1/10,000,000. mismatches.

Describe the steps involved in replication of the leading and the lagging strands, explaining the roles of DNA polymerase, RNA polymerase, and ligase. What are Okazaki fragments?

Leading strand- 1. after RNA primer is made, DNA pol III starts to synthesize the leading strand. 2. The leading strand is elongated continuously in the 5'-3' direction as the fork progresses. Lagging Strand- 1. primase joins RNA nuleotides into primer. 2. DNA pol III adds DNA nucleotides to the primer, forming, Okazaki fragment 1. 3. After reaching the next RNA primer to the right, DNA pol III detaches. 4. fragment 2 is primed. Then DNA pol III adds DNA nucleotides, detaching when it reaches the fragment 1 primer. 5. DNA pol I replaces the RNA with DNA, adding nucleotides to the 3' end of the fragment 1 (and later of fragment 2). 6. DNA ligase forms a bond between the newest DNA and the DNA of fragment 1. 7. The lagging strand in this region is now complete. Okazaki Fragments- a short segment of DNA synthesized away from the replication fork on a template strand during DNA replication. Many such segments are joined together to make up the lagging strand of newly synthesized DNA.

What is it about DNA polymerase that makes a primer necessary for DNA polymerization?

Most DNA polymerase requires a primer and a DNA template strand, along which complementary DNA nucleotides are lined up. The DNA polymerase then removes primer of previous segment, and replaces it with DNA nucleotides.

The spontaneous loss of amino groups from adenine in DNA results in Hypoxanthine, an uncommon base, opposite thymine. What combination of proteins could repair such damage?

Nuclease, DNA polymerase, DNA ligase.

To which end of the DNA strand are new nucleotides added?

Nucleotides must be added to the 3' end (strand grows in 5'-3' direction).

In what form must nucleotides be in order to be polymerized?

Nucleotides must have a primer and a template: nucleoic acid starter segment with exposed 3' end. DNA polymerase cannot start a strand; can only add on to one already started.

How does replication on the two strands differ, and why must that be the case?

Only one primer is required for DNA pol III to synthesize the entire leading strand. To elongate the other new strand fo DNA pol III must work along the other template in the direction away from the replication fork. The DNA strand elongating in this direction is the lagging strand. In contrast to the leading strand, which elongates continuously, the lagging strand elongates discontinuously, as a series of segments. Only one primer is required for the leading strand, the lagging strands must be primed seperately.

What is primase and what does it do?

Primase is an enzymes that joins RNA nucleotides to make a primer during DNA replication, using the parental DNA strand as a template. primase synthesizes an RNA primer at 5' end of leading strand and at 5' end of each fragment of lagging strand.

How do prokaryotes and eukaryotes differ in regard to replication bubbles?

Prokaryotes have circular DNA, meaning that one replication bubble will start the DNA replication process and continue until both ends of the replication fork meet. This creating two daughter DNA molecules. In eukaryotes on the other hand, their DNA is linear, and much larger than that of prokaryotes. This means that multiple replication bubbles start the DNA replication process. The bubbles expand as replication proceeds in both directions. Eventually, the bubbles fuse and synthesis of the daughter strands are complete.

Explain what it means to say that replication of DNA is semi-conservative

Semiconservative is the type of DNA replication in which the replicated double helix consists of one old strand, derived from the parental molecule, and one newly made strand. (New molecules conserve half of original)

If the DNA pol I in a given cell were nonfunctional, how would that affect the synthesis of a leading strand?

Synthesis of the leading strand is inherited by an RNA primer, which must be removed and replaced with DNA, a task that could not be performed if the cell's DNA pol I were non-functional. A functional DNA pol I would replace the RNA primer of the leading strand with DNA nucleotides. The nucleotides would be added onto the 3' end of the first fragment of the upper lagging strand.

In general, what sort of cells have telomerase, and what sort don't? Do bacteria have telomeres and telomerases? Explain why or why not.

Telemerase is in the human germ cells., thus restoring their original lenghts and compensating for the shortening of DNA replication. Telomerase is not active in most human somatic cells, but its activation varies from tissue to tissue. Telomeres and Telomerase is not present in bacteria cells because during their DNA replication process their DNA remains the same, and there is no need of shortening beause of their circular DNA.

What is telomerase and how does it function?

Telomerase is the enzyme responsible for adding telomers to the ends of the chormosomes. Telomerase has a single-stranded RNA segment, which serves as a template for a single-stranded DNA. Telomerase has built-in RNA template complementary to telomere sequence. This telemerase can often cause cancer when inapproproately activiated.

What is a template and what function does it have in the replication of DNA? Explain the role of hydrogen bonding in this process.

The DNA strand that provides the pattern, or template, for ordering, by complementary base pairing, the sequence of nucleotides in an RNA transcription. The role of hydrogen bonding in this process is the two bases bonding. When an incoming nucleotide arrives it bonds to the base of the template strand.

Explain why the end of a lagging strand isn't replicated. What happens to the unreplicated ends?

The lagging strand end remains unreplicated, because there is no place for the primer upstrem. The primer is removed but cannot be replaced with DNA because there is no 3' end available for DNA polymerase. The unreplicated ends are then snipped off. The chromosomes are then shortened.

Explain what is meant by leading and lagging strand, making reference to the replication fork.

The leading strand is the new complementary DNA strand synthesized continuously along the template strand toward the replication in the mandoatory 5'-3' direction. The lagging strand on the other hand is a discontinuously synthesized DNA strand that elongates by eans of Okazaki fragments, each synthesized in a 5'-3' direction away from the replication fork.

Interphase chromosomes appear to be attached to the nuclear lamina and perhaps also the nuclear matrix. Describe the two structures.

The nuclear lamina is a netlike array of protein filaments that provides mechanical support just inside the nuclear envelope and thus maintains the shape of the nucleus. Considerable evidence also supports the existence of nuclear matrix, a framework of protein fibers extending throughout the nuclear interior.

How are nucleotides linked together to make a nucleic acid? Be sure you know which are the 3' and 5' carbons of a nucleotide and can tell the 3' and 5' ends of a polynucleotide chain.

The phosphate group of one nucleotide is attached to the sugar of the next by a cocalent bond, forming a "backbone" of alternating phosphate and sugars from which the bases project. A polynucleotide strand has directionality, from the 5' end (phosphate group) to the 3' end (with the -OH group of the sugar). 5' and 3' refer to the numbers assigned to te carbons in the sugar ring.

Describe the orientation of the two strands of a DNA molecule relative to each other. What term is used for this? What holds the two strands to each other?

The two strands of the DNA molecule run in opposite directions (antiparallel). They are held to each other by hydrogen bonds joined by the paired nitrogenous bases.

Given a polynucleotide sequence such as GAATTC, explain what further information you would need in order to identify which is the 5' end.

You cant tell which end is the 5' end. You need to know which end has a phosphate group on the 5' carbon or which end has an -OH group on the 3' carbon.

Helicase

an enzyme that untwist the double helix at the replication forks, separating the two parental strands and making them available as template strands.

The elongation of the leading strand during DNA synthesis

depends on the action of DNA polymerase

Name the three component parts of a nucleotide

five-carbon sugar covalently bonded to a nitrogenous base and one to three phosphate groups.

DNA polymerase

is an enzyme that catalyzes the synthesis of new DNA by adding nucleotides to the 3' end of a pre-existing chain.

What are telomeres?

is the tandomly repetitive DNA at the end of a eukaryotic chromosome's DNA molecule. Telomers protect the organisms genes from being eroded during successive rounds of replication.

E. coli cells grown on 15N medium are transferred to 14N medium and allowed to grow for two more generations. DNA extracted from these cells is centrifuged. What density distribution of DNA would you expect in this experiment?

one low-density and one intermediate-density band

In his work with pneumonia-causing bacteria and mice, Griffith found that

some substance from pathogenic cells were transferred to nonpathogenic cells, making the pathogenic.