AP Biology Chapter 16

What makes up the backbone of DNA?

sugar-phosphate

How many layers of bases are there in the DNA ladder?

ten

What are the two chemical components of chromosomes?

DNA and protein

What are the two DNA polymerases that are used in E. Coli?

DNA pol III, and DNA pol I

How do DNA polymerases "proofread" DNA?

During DNA replication, they proofread each nucleotide against its template as soon as it is added to the growing strand. Upon finding an incorrectly paired nucleotide, the polymerase removes the nucleotide and then resumes synthesis.

How far apart are the bases stacked apart?

0.34 nm

Steps of DNA replication

1. Helicase unwinds the parental double helix 2. Molecules of single-strand binding protein stabilize the unwound template strands 3. The leading strand is synthesized continuously in the 5'-->3' direction by DNA pol III 4. Primase begins synthesis of the RNA primer for the fifth Okazaki fragment 5. DNA pol III is completing synthesis of the fourth fragment. When it reaches the RNA primer on the third fragment, it will dissociate, move to the replication fork, and add DNA nucleotides to the 3' end of the fifth fragment primer 6. DNA pol I removes the primer from the 5' end of the second fragment, replacing it with the DNA nucleotides that it adds one by one to the 3' end of the third fragment. The replacement of the last RNA nucleotide with DNA leaves the sugar-phosphate backbone with a free 3' end 7. DNA ligase bonds the 3' end of the second fragment to the 5' end of the first fragment

List the three components of a nucleotide.

1. nitrogenous bases 2. deoxyribose 3. phosphate group

Transformation

A change in genotype and phenotype due to the assimilation of of external DNA by a cell.

Okazaki fragments

A short segment of DNA synthesized away from the replication fork on a template strand during DNA replication, many of which are joined together to make up the lagging strand of newly synthesized DNA.

How does a virus reproduce?

A virus must infect a cell and take over it's metabolic machinery.

What are the pairs of nitrogenous bases? Why do they pair like this?

Adenine with thymine and guanine with cytosine; this occurs because adenine and guanine are purine meaning they have two organic rings and in contrast cytosine and thymine are pyrimidines meaning they have a single ring. Thus purines are about twice as wide a pyrimidines. By pairing a purine with a pyrimidine it allows for a uniform diameter. Moreover, adenine can form two hydrogen bonds with thymine and only thymine, and guanine can form three hydrogen bonds with only cytosine.

Telomerase

An enzyme that catalyzes the lengthening of telomeres in eukaryotic germ cells, thus restoring their original length and compensating for the shortening that occurs during DNA replication. It is not active in human somatic cells, but it is in germ cells.

What does antiparallel mean and what is it's significance when talking about DNA?

Antiparallel means that the subunits run in opposite directions to each other; DNA's double helix runs antiparallel

Bacterial chromosome vs. eukaryotic chromosome

Bacterial chromosome is one double-stranded, circular DNA molecule that is associated with a small amount of protein. A eukaryotic chromosome consists of one linear DNA molecule associated with a large amount of protein.

How does the antiparallel arrangement of the double helix affect replication?

Because of their structure, DNA polymerases can add nucleotides only to the free 3' end of a primer or growing DNA strand, never to the 5' end. Thus, a new DNA strand can elongate only in the 5''--> 3' direction. Along one template strand, DNA pol III can synthesize a complementary strand continuously by elongating the new DNA in the mandatory 5'-->3' direction. DNA pol III simply nestles in the replication fork on that template strand and continuously adds nucleotides to the new complementary strand as the fork progresses. The DNA strand made by this process is called the LEADING STRAND. Only one primer is required for DNA pol III to synthesize the leading strand. To elongate the other new strand of DNA in the mandatory 5'-->3' direction, DNA pol III must work along the other template strand in the direction away from the replication fork. The DNA strand elongating in this direction is called the LAGGING STRAND. In contrast, the leading strand which elongates continuously, the lagging strand is synthesized discontinuously, as a series of segments.

Why did researchers originally think that protein was the genetic material?

Biochemists had identified them as a class of macromolecules with great heterogeneity and specificity of function, which are essential requirements for the heredity material.

Thymine dimers

Cause the DNA buckle and interfere with DNA replication.

Explain the origin of replication in E. Coli.

E. Coli is circular and has a single origin. Proteins that initiate DNA replication recognize this sequence and attach to the DNA, separating the two strands and opening up a replication "bubble". Replication of DNA then proceeds in both directions until the entire molecule is copied.

Dispersive Model

Each strand of both daughter molecules contains a mixture of old and newly synthesized DNA.

DNA Polymerases

Enzymes that catalyze the synthesis of new DNA by adding nucleotides to a preexisting chain.

Chromatin

Eukaryotic DNA is precisely combined with a large amount of protein. This complex of DNA and protein is called chromatin and it fits in the nucleus.

Explain origin of replication in eukaryotic cells.

Eukaryotic cells may have hundreds or even a few thousand replication origins. Multiple replication bubbles form and eventually fuse, thus speeding up the copying of the very long DNA molecules. DNA replication proceeds in both directions from each origin. At each end of the replication bubble is a REPLICATION FORK, a Y-shaped region where the parental strands of DNA are being unwound. Several kinds of proteins participate in the unwinding. HELICASES are enzymes that untwist the double helix at the replication forks, separating the two parental strands and making them available as template strands. After parental strand separation, SINGLE-STRAND BINDING PROTEINS bind to the unpaired DNA strands, stabilizing them. The untwisting of the double helix causes tighter twisting and strain ahead of the replication fork. TOPOISOMERASE helps relieve this strain by breaking, swiveling, and rejoining DNA strands. The unwound sections of parental DNA strands are now available to serve as templates for the synthesis of new complementary DNA strands. However, the enzymes that synthesize DNA cannot initiate the synthesis of a polynucleotide; they can only add nucleotides to the end of an already existing chain that is base-paired with the template strand. The initial nucleotide chain that is produced during DNA synthesis is actually a short stretch of RNA, not DNA. This RNA strand is called a PRIMER, and is synthesized by the enzyme PRIMASE. Primase starts an RNA chain from a single RNA nucleotide, adding RNA nucleotides one at a time, using the parental DNA strand as a template. The completed primer is thus base-paired to the template strand. The new DNA strand will start from the 3' end of the RNA primer.

Telomeres

Eukaryotic chromosomal DNA molecules have these special nucleotide sequences at their ends to help the genes of eukaryotes from being eroded away during successive rounds of DNA replication. Telomeres don't contain genes, instead they contain multiple repetitions of one short nucleotide sequence. They also contain specific proteins that prevent the staggered ends of the daughter molecule from activating the cell's systems for monitoring DNA damage.

How often does the helix make a turn?

Every 3.4 nm.

What role did Rosalind Franklin play in establishing that DNA had a double helix shape?

Franklin produced an X-ray diffraction image of DNA that Watson saw. Watson was able to deduce that DNA was helical in shape but he was also able to approximate the width of the helix and the spacing of the nitrogenous bases along it. The width of the helix suggested that it was made up of two strands. The presence of two strands accounts for the term DOUBLE HELIX.

Experiments of Erwin Chargaff

He analyzed the base composition of of DNA from a number of different organisms. In 1950, he reported that the base combination of DNA varies from one species to another. This evidence of molecular diversity, made DNA a more credible candidate for the genetic material. He also noticed a peculiar regularity in the ratios of nucleotide bases within a single species. In the DNA of each species that he studied, the number of adenines approximately equaled the number of thymines, and the number of guanines approximately equaled the number of cytosines. These equivalences became known as the CHARGAFF RULES. The basis of these rules remained unexplained until the discovery of the double helix.

Summary of Griffith's experiment

He studied two strains of Streptococcus pneumoniae. Bacteria of the smooth strain can cause pneumonia in mice; they are pathogenic because they have a capsule that protects them from an animal's defense system. Bacteria of the rough strain lack a capsule and are nonpathogenic. To test for the trait of pathogenicity, Griffith injected mice with Living smooth cells (control), Living rough cells (control), heat-killed smooth cells (control), and mixture of heat-killed smooth and living rough cells. The mice that receive the living smooth cells and the mixture both die. Griffith concluded that the living rough bacteria had transformed into pathogenic smooth bacteria by an unknown, heritable substance from the dead smooth cells that allowed the rough cells to make capsules.

Summarize Hershey and Chase's experiment.

Hershey and Chase used radioactive sulfur and phosphorus to trace the fates of protein and DNA, respectively, of T2 phages that infected bacterial cells. They wanted to see which of these molecules entered and could reprogram the cells to make more phages. Steps of the experiment: 1. Mixed radioactively labeled phages with bacteria. The phages infected the bacterial cells. 2. Agitated the mixture in a blender to free phage parts outside the bacteria from the cells. 3. Centrifuged the mixture so that bacteria formed a pellet at the bottom of the test tube; free phages and phage parts, which are lighter, remained suspended in the liquid. 4. Measured the radioactivity in the pellet and the liquid. In the experiment there were two phages, phage 1 the phages were grown with radioactive sulfur which was incorporated into phage protein (pink) and phage 2 the phages were grown with radioactive phosphorus which was incorporated into phage DNA (blue). In batch 1, radioactivity remained outside the cells and in batch 2 radioactivity was found inside the cells. Bacterial cells with radioactive phage DNA released new phages with some radioactive phosphorous. In conclusion, phage DNA entered bacterial cells, but phage proteins did not. Hershey and Chase concluded that DNA, not protein, functions as the genetic material of phage T2.

Heterochromatin

Interphase chromatin that is visible as irregular clumps with a light microscope

Who built the first model of DNA?

James Watson and Francis Crick

DNA Ligase

Joins 3' end of DNA that replaces primer to rest of leading strand and joins Okazaki fragments of lagging strand.

Euchromatin

Less compacted and more dispersed chromatin.

What is the composition of a virus?

Little more than DNA enclosed by a protective coat, which is often much simpler than protein.

Incorrectly paired nucleotides after replication

Maintenance of the genetic information encoded in DNA requires frequent repair of various kinds of damage to existing DNA. DNA molecules are constantly subjected to potentially harmful chemical and physical agents. Each cell continuously monitors and repairs its genetic material.

Mismatch pair

Mismatched nucleotides sometimes evade proofreading by a DNA polymerase. In this case, enzymes removes and replace incorrectly paired nucleotides that have resulted from replication errors.

Explain the role that DNA pol III has on E. Coli.

Most DNA polymerases require a primer and a DNA template strand, along which complementary DNA nucleotides line up. DNA pol III adds a DNA nucleotides to the RNA primer and then continues adding DNA nucleotides, complementary to the parental DNA template strand, to the growing end of the new DNA strand. Each nucleotides added to a growing DNA strand comes from a nucleoside triphosphate which is a nucleoside with three phosphate groups--similar to ATP. The main difference between ATP and dATP (the nucleoside triphosphate that supplies an adenine nucleotide to DNA) is the sugar component which is deoxyribose in the building block of DNA, but ribose in ATP. Like ATP, the nucleoside triphosphates used for DNA synthesis are chemically reactive, partly because their triphosphate tails have an unstable cluster of negative charge. As each monomer joins the growing end of a DNA strand, two phosphate groups are lost as a molecule of pyrophosphate. Subsequent hydrolysis of the pyrophosphate to two molecules of inorganic phosphate is a coupled exergonic reaction that helps drive the polymerization reaction,

What did Oswald Avery determine to be the transforming factor?

Oswald Avery, a bacteriologist, did a 14 year research study devoted to finding out what caused the transformation to occur in Griffith's experiment. He focused on three main candidates: DNA, RNA, and protein. He broke open the heat-killed pathogenic bacteria and extracted the cellular contents. In separate samples, he used specific treatments that inactivated each of the three types of molecules. He then tested each treated sample for its ability to transform live nonpathogenic bacteria. Only when DNA was allowed to remain active did transformation occur. In 1944, Avery and his colleagues Maclyn McCarty and Colin MacLeod announced that the transforming agent was DNA. People doubted this because they believed protein was still a better candidate for being the genetic material, they weren't convinced that the genes of bacteria would be similar in composition and function to those of more complex organisms, and there was still not that much to be known about DNA.

What experiment did Alfred Hershey and Martha Chase conduct?

Performed experiments to show that DNA is the genetic material of a phage known as T2. This is one of the many phages that infect E. Coli, a bacterium that normally lives in the intestines of mammals. At the time, biologists already knew that that T2 was composed of DNA and protein, like other phages. They also knew that the T2 phage could quickly turn an E. Coli cell into a T2-producing factory that released many copies when the cell ruptured. Somehow T2 could reprogram its host cell to produce viruses. But it was unknown which viral compound--protein or DNA-- was responsible? Hershey and Chase attempted to answer this question through experimentation.

DNA pol I

Removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides.

Histones

Responsible for the first level of DNA packing in chromatin. It is a small protein with a high proportion of positively charged amino acids that binds to the positively charged amino acids that binds to the negatively charged DNA.

Origins of replication

Site where the replication of DNA molecules begins, consisting of a specific sequence of nucleotides.

How was additional evidence collected to support that DNA was the genetic material?

Studies of viruses that infect bacteria. These viruses are called BACTERIOPHAGES or PHAGES.

Frederick Griffith's studies of Streptococcus pneumoniae

The discovery of the genetic role of DNA can be traced back to this experiment. Griffith's attempted to develop a vaccine against pneumonia by studying Streptococcus pneomoniae that causes pneumonia in mammals. He had two strains of the bacteria, one pathogenic (disease-causing) and one nonpathogenic (harmless). He found through his studies that the pathogenic bacteria was killed with heat and when he mixed the cell remains with living bacteria of the nonpathogenic strain, some of the living cells became pathogenic. The newly acquired trait of pathogenicity was inherited by all the descendants of the transformed bacteria. Clearly some chemical component of of the dead pathogenic cells caused this heritable change, although the identity of the substance was not known. He referred to this phenomenon as transformation.

Conservative model

The two parental strands reassociate after acting as templates for new strands, thus restoring the parental double helix.

Semiconservative model

The two strands of the parental molecule separate, and each functions as a template for synthesis of a new, complementary strand.

Replicating the ends of DNA molecules

There is no way to replicate the 5' ends of daughter DNA strands. As a result, repeated rounds of repetition produce shorter and shorter DNA molecules with uneven ends. The shortening of DNA does not occur in most prokaryotes because their DNA is circular and therefore has no ends.

Explain Meselson and Stahl's experiment.

They cultured E. Coli for several generations in a medium containing nucleotide precursors labeled with a heavy isotope of nitrogen. The scientists then transferred the bacteria to a medium with a lighter nitrogen isotope. Two DNA samples were taken from this flask, one at 20 minutes and one at 40 minutes, after the first and second replications, respectively. They could distinguish DNA of different densities by centrifuging DNA extracted from the bacteria. In conclusion, the first replication in the lighter isotope produced a band of hybrid DNA. This result eliminated the conservative model. The second replication produced both light and hybrid DNA, a result that refuted the dispersive model and supported the semiconservative model. They therefore concluded that DNA replication is semiconservative.

How do most cellular systems for repairing incorrectly paired nucleotides work?

They often use a mechanism that takes advantage of the base-paired structure of DNA. Often, a segment of the strand containing the damage is cut out by a DNA cutting enzyme--NUCLEASE--and the resulting gap is then filled in with nucleotides, using the undamaged strand as a template. The enzymes involved in filling the gap are DNA polymerase and DNA ligase. One such repair system is the nucleotide excision repair.

How did Watson and Crick's model provide the basis for Chargaff's rules?

Wherever one strand of a DNA molecule has an A, the partner strand has a T. And a G in one strand is always paired with a C in the complementary strand. Therefore, in the DNA of any organism, the amount of adenine equals the amount of thymine, and the amount of guanine equals the amount of cytosine.

Nucleoid

Within a bacterium certain proteins cause the chromosome to coil and "supercoil", densely packing it so that it fills only part of the cell. It is called a nucleoid and isn't bound by a membrane.

What are the "rungs" of the DNA ladder?

nitrogenous bases