Bio 122 Study Guide Chapter 16: The Molecular Basis of Inheritance

Three conclusions from X-ray pictures of DNA:

- Two nucleotide polymers in one DNA molecule - Uniform width along the entire length of the DNA molecule - Twisted into a helix (double helix since there are two polymers)

Chromatin allows DNA to perform the following functions:

- package DNA (levels of structure) - transcription - replication

Watson and Crick proposed a semi-conservative model for DNA replication. Semi-conservative replication involves the following steps:

- the two strands must separate, breaking the base pair bonds - single nucleotides base-pair to each "old" strand, one at a time - the nucleotides get added in the 5' to 3' direction - as new nucleotides get added, they are covalently linked together. semiconservative model: 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.

Nucleotides are covalently added ONE WAY. New nucleotides are only added to the

3' side of a nucleic acid.

Level 2 of chromatin structure is the

30 nm chromatin fiber. Nucleosomes get twisted into a 30 nm chromatin fiber.

The sequence of bases along a DNA polymer is unique for each gene. The sequence is read from

5' to 3', similar to how English is read from left to right.

A sample of double-stranded DNA contains 42% cytosine. Approximately what percent of the nucleotides in this sample will be thymine? A) 8% B) 16% C) 42% D) 58%

A

Chromatin is necessary for all of the following functions EXCEPT A) base-pairing B) replication C) packing DNA into nuclei E) transcription

A

DNA strands are antiparallel. Which of the following statements defines "antiparallel"? A) A 5' to 3' DNA strand is paired with the 3' to 5' DNA strand. B) One DNA strand contains bases that complement the bases in the opposite strand. C) The double helix structure of DNA creates nonparallel strands. D) Hydrogen bonds between base pairs cause DNA strands to cross.

A

During DNA replication, the leading strand is synthesized continuously, whereas the lagging strand is synthesized as Okazaki fragments. Why is this so? A) DNA synthesis can take place only in the 5' to 3' direction. B) DNA polymerases can bind to only one strand at a time. C) There are thousands of origins of replication on the lagging strand but only one on the leading strand.

A

In a DNA double helix an adenine of one strand always pairs with a(n) _____ of the complementary strand, and a guanine of one strand always pairs with a(n) _____ of the complementary strand. A) thymine ... cytosine B) cytosine ... thymine C) guanine ... adenine D) uracil ... cytosine E) cytosine ... uracil

A

Telomere shortening puts a limit on the number of times a cell can divide. Research has shown that telomerase can extend the life span of cultured human cells. Which of the following best explains the effect of telomerase on cellular aging? A) Telomerase can eliminate telomere shortening and slows aging. B) Telomerase shortens telomeres, which delays cellular aging. C) Telomerase would have no effect on cellular aging. D) Telomerase will speed up the rate of cell proliferation.

A

The replication fork is the place where A) the two strands are separated. B) replication ends. C) replication begins. D) the chromosome ends.

A

The sequence of nucleotides below is present at a DNA location where the chain opens to form a replication fork:3' C C T A G G C T G C A A T C C 5'An RNA primer is formed starting at the underlined T (T) of the template. Which of the following represents the primer sequence? A) 5' A C G U U A G G 3' B) 5' A C G T T A G G 3' C) 5' A G C C T A G G 3' D) 5' A G C C U A G G 3'

A

The strands of DNA differ in that [read each answer carefully] A) new leading strand DNA is synthesized continuously in the 5′→3′ direction, while new lagging strand DNA is synthesized as short DNA fragments in the 5′→3′ direction. B) the leading strand template requires an RNA primer, whereas the lagging strand template does not. C) new leading strand DNA is synthesized by adding nucleotides to the 3' end of the growing strand, and new lagging strand DNA is synthesized by adding nucleotides to the 5' end. D) new lagging strand DNA is synthesized continuously, whereas new leading strand DNA is synthesized in short fragments that are ultimately get connected.

A

True or false? Single-stranded DNA molecules are said to be antiparallel when they are lined up next to each other but oriented in opposite directions. A) True B) False

A

What is the role of DNA polymerase during DNA synthesis? A) DNA polymerase is the enzyme that catalyzes the addition of a nucleotide onto the 3' end of a growing DNA strand. B) DNA polymerase removes inorganic phosphate from the template strand of DNA to catalyze the polymerization reaction. C) DNA polymerase catalyzes the synthesis of the template strand of DNA. D) DNA polymerase provides the free energy to catalyze the endergonic addition of a nucleotide onto the 3' end of a growing DNA strand.

A

Which of the following characteristics of DNA allows it to carry a vast amount of hereditary information? A) sequence of bases B) complementary pairing of bases C) phosphate-sugar backbones D) antiparallel orientation

A

Which of the following statements about DNA synthesis is true? A) Primers are short sequences that allow the initiation of DNA synthesis. B) As DNA polymerase moves along the template strand, each new nucleotide provides a 5' hydroxyl group for the next reaction to occur. C) Nucleotides are added in a random fashion to single-stranded DNA. D) DNA polymerase adds dNTP monomers in the 3' to 5' direction.

A

Which of the following statements about Okazaki fragments in E. coli is true? A) They are formed on the lagging strand of DNA. B) They are sealed together by the action of helicase. C) They are synthesized in the 3' to 5' direction. D) They are usually 50 to 500 bases long.

A

Transformation

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

Lagging strand

A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.

DNA ligase

A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3' end of a new DNA fragment to the 5' end of a growing chain.

Virus

A little more than DNA (or sometimes RNA) enclosed by a protective coat, which is often simply protein. To produce more viruses, a virus must infect a cell and take over the cell's metabolic machinery.

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.

Nucleotide excision repair

A repair system that removes and then correctly replaces a damaged segment of DNA using the undamaged strand as a guide.

Bacterophage

A virus that infects bacteria; also called a phage.

As a result of its involvement in a chemical reaction, an enzyme A) is uncharged by the reactants or products B) receives functional groups from reactants, allowing them to become products C) donates electrons to its reactants, turning them into products D) donates amino acid R groups to its reactants, turning them into products

A. An enzyme is a macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed or changed by the reaction. An enzyme catalyzes a reaction by lowering the Ea barrier, enabling the reactant molecules to absorb enough energy to reach the transition state. Enzymes emerge from the reaction in their original form, having neither donated nor received matter or energy from the reactants.

During mitosis, centromeres separate and chromatids become individual chromosomes during which phase? A) anaphase B) telophase C) prometaphase D) metaphase

A. During prophase and prometaphase, the duplicated chromosomes become condensed. During metaphase, the duplicated chromosomes are all aligned at the metaphase plate, a plane that is equidistant between the spindle's two poles. Anaphase is the phase where the two sister chromatids of each pair separate and each chromatid become an independent chromosome. This is followed by telophase, during which two daughter nuclei form in the cell, the nucleoli reappear, and the chromosomes become less condensed. transformation

Addition of a nucleotide onto a DNA strand is an endergonic reaction. What provides the energy to drive the reaction? A) Release of pyrophosphate from the incoming nucleotide, and then hydrolysis of the pyrophosphate to inorganic phosphate B) The dehydration reaction between the 5'-phosphate of the incoming nucleotide and the 3'-OH of the growing strand of DNA C) Complementary bases on the template and the incoming nucleotide are attracted to each other, releasing free energy. D) Binding of the pre-existing new strand, the template strand, and the incoming nucleotide to the active site of the DNA polymerase

A. Each deoxyribonucleotide enters the reaction as a triphosphate, and hydrolysis of the phosphates releases the free energy needed for the nucleotide to bind to the growing strand.

A phosphorescent red strain of bacteria is heat-killed and mixed with a living, colorless strain. Further observations of the mixture show that some of the living cells are now red. Which of the following observations would provide the best evidence that red color is a heritable trait? A) after a few generations there are no more colorless cells, all cells are red B) as the living cells divide the number of red cells increases C) especially bright red color in some members of the living strain D) when the heat-killed and living cells are mixed there is a decrease in the overall amount of red color

B

Given a template strand of 3'-ATGCTTGGACA-5' and a partially-made complementary strand containing only 5'-TAC-3', what would be the sequence of the new strand of DNA (including the 5'-TAC-3') if the only additional nucleotides available to DNA polymerase were those containing the bases G, A, and C? A) 5'-TAC-3'; All four nucleotides are required for DNA polymerase to function. B) 5'-TACGAACC-3' C) 3'-TACGAACCTGT-5' D) 5'-GAACC-3'

B

In his work with pneumonia-causing bacteria and mice, Griffith found that A) the protein coat from pathogenic cells was able to transform nonpathogenic cells. B) some substance from pathogenic cells was transferred to nonpathogenic cells, making them pathogenic. C) the polysaccharide coat of bacteria caused pneumonia. D) heat-killed pathogenic cells caused pneumonia

B

Replication in prokaryotes differs from replication in eukaryotes due to which of the following reasons? [read each answer carefully] A) Prokaryotes have telomeres, and eukaryotes do not. B) Prokaryotic chromosomes have a single origin of replication, whereas eukaryotic chromosomes have many. C) Prokaryotes replicate DNA in the 5' to 3' direction, eukaryotes replicate DNA in the 3' to 5' direction. D) Prokaryotes produce short DNA molecules on the lagging strand, but eukaryotes do not.

B

What catalyzes DNA synthesis? A) Replication fork B) DNA polymerase C) Primer D) dNTPs

B

Which of the following enzymes is important for relieving the tension in a helix as it unwinds during DNA synthesis? A) Ligase B) Topoisomerase C) Single-strand binding proteins D) Helicase

B

Which of the following statements accurately describes the structure of a eukaryotic chromosome? A) It has different numbers of genes in different cell types of an organism. B) It is a single linear molecule of double-stranded DNA plus proteins. C) It is constructed as a series of nucleosomes wrapped around two DNA molecules. D) It is composed of a single strand of DNA.

B

Which of the following statements describes the process of transformation in bacteria? A) A strand of DNA is created from an RNA molecule. B) External DNA is taken into a cell, becoming part of the cell's genome. C) Bacterial cells are infected by a phage DNA molecule. D) A strand of RNA is created from a DNA molecule.

B

Single-strain binding protein

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

A sample of double-stranded DNA contains 28% thymine. Approximately what percent of the nucleotides in this sample will be guanine? A) 16% B) 8% C) 22% D) 72%

C

An old DNA strand is used as a _____ for the assembly of a new DNA strand. A) model B) primer C) template D) complement E) source of nucleotides

C

Frederick Griffith heat-killed a culture of pathogenic bacteria. He split the sample and injected half of it into mice. The mice lived. He then mixed the other half with a living, nonpathogenic bacteria strain and injected the mixture into mice. The mice died. These results best support which of the following conclusions. A) the initial heat treatment was unsuccessful B) non-pathogenic bacteria were transformed by pathogenic capsule proteins C) a substance had been transferred from pathogenic to nonpathogenic bacteria D) splitting the culture revived the pathogenic bacteria

C

In a nucleosome, the DNA is wrapped around A) ribosomes. B) other DNA to form a rope-like structure. C) histone proteins. D) DNA polymerase molecules.

C

In the replication of DNA, a phosphodiester bond is formed between a phosphate group of the nucleotide being added and ________ of the last nucleotide in the polymer. A) the 2' H B) the 5' ATP C) the 3' OH D) a nitrogen from the nitrogen-containing base

C

Nucleotides are added to a growing DNA strand as nucleoside triphosphates. What is the significance of this fact? A) Nucleoside triphosphates are more abundant in the cell than nucleotides. B) Nucleoside triphosphates are more easily transported in the cell than are nucleotides. C) Hydrolysis of the two phosphate groups (P-Pi) and DNA polymerization are a coupled exergonic reaction.

C

The synthesis of a new strand begins with the synthesis of a(n) _____. A) poly(A) tail B) single-strand binding protein C) RNA primer complementary to a preexisting DNA strand D) Okazaki fragment E) short pieces of DNA

C

What are telomeres? A) the sites of origin of DNA replication B) the structures that hold two sister chromatids together C) the ends of linear chromosomes D) enzymes that elongate the DNA strand during replication

C

What is the function of helicase in DNA replication? A) it adds nucleotides to the new strand in the 5′ to 3′ direction B) it joins together Okazaki fragments C) it untwists the double helix and separates the two DNA strands D) it relieves strain from twisting of the double helix as it is unwound E) it checks for errors in the newly synthesized DNA strand

C

Which of these is a difference between a DNA and an RNA molecule? A) DNA contains five-carbon sugars, whereas RNA contains six-carbon sugars. B) DNA contains nitrogenous bases, whereas RNA contains phosphate groups. C) DNA is usually double-stranded, whereas RNA is usually single-stranded. D) DNA contains uracil, whereas RNA contains thymine. E) DNA is a polymer composed of nucleotides, whereas RNA is a polymer composed of nucleic acids.

C

Which part of a deoxynucleoside triphosphate (dNTP) molecule provides the energy for DNA synthesis? A) Sugar B) Free 3' hydroxyl (-OH) group C) Phosphate groups D) Base

C

The two strands of a DNA double helix are held together by ______ between pairs of nitrogenous bases. A) disulfide (S-S) bonds B) covalent bonds C) hydrogen bonds D) ionic bonds

C. DNA molecules have two polynucleotides, or "strands", that wind around an imaginary axis, forming a double helix. The sugar-phosphate backbones are on the outside of the helix, and the nitrogenous bases are paired in the interior of the helix. The two strains of DNA are held together by hydrogen bonds between the paired bases.

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 the base pairing rules; they will then be polymerized by enzymes into new complementary strands.

A hydroxyl is present at the 3' end of the growing DNA strand. What is at the 5' end? A) a nitrogenous base B) a deoxyribose C) a ribose D) a phosphate group

D

Griffith's experiments with S. pneumoniae were significant because they showed that traits could be transferred from one organism to another. What else did he find that was significant? A) protein could not be the genetic material heat kills bacteria B) a virus made the bacteria pathogenic C) DNA was the genetic material D) the transferred traits were heritable

D

In DNA polymerization, a phosphodiester bond is formed between a phosphate group of the nucleotide being added and which of the following atoms or molecules of the last nucleotide in the polymer? A) the 5' phosphate B) C6 C) a nitrogen from the nitrogen-containing base D) the 3' OH

D

In his pneumococcus transformation experiments, what did Griffith observe? "pathogenic" means "disease-causing" A) Mice infected with a pathogenic strain of bacteria can spread the infection to other mice. B) Infecting mice with nonpathogenic strains of bacteria makes them resistant to pathogenic strains. C) Mutant mice were resistant to bacterial infections. D) Mixing a heat-killed pathogenic strain of bacteria with a live nonpathogenic strain can convert some of the living cells into the pathogenic form.

D

The Watson and Crick model of the DNA molecule explains how DNA can carry a vast amount of hereditary information. Which part of the DNA structure carries the information? A) the 5' and 3' ends of each nucleotide B) the twisting of two DNA polymers into a double helix C) phosphate-sugar backbone D) the sequence of bases

D

The action of helicase creates _____. A) primers and DNA fragments B) DNA fragments and replication bubbles C) primers and replication bubbles D) replication forks and replication bubbles E) DNA fragments and replication forks

D

Which of the following enzymes creates a primer for DNA polymerase? A) Ligase B) Helicase C) Topoisomerase D) Primase

D

During ______ of the cell cycle, the cell grows and replicates both its organelles and its chromosomes. A) mitosis B) prophase C) cytokinesis D) interphase

D. Interphase can be divided into three phases: G1 phase, S phase, and G2 phase. During all three phases of interphase, a cell grows by producing proteins and cytoplasmic organelles. Duplication of the chromosomes, crucial for eventual division of the cell, occurs entirely during the S phase of interphase. Cell division occurs during the M phase, which can be divided into two stages: mitosis and cytokinesis.

What is the genetic material?

DNA and RNA. Must be capable of - Replication - Storage of information - Expression of information - - Rare but permanent changes (mutations)

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.

Cytosine (C) makes up 30% of the nucleotides in a sample of DNA from an organism. Approximately what percentage of the nucleotides in this sample will be thymine (T)? A) 30% B) 60% C) 40% D) 70% E) 20%

E

The first step in the replication of DNA is catalyzed by _____. A) primase B) DNA polymerase C) ligase D) single-strand binding protein E) helicase

E

After DNA replication is completed, _____. A) each new DNA double helix consists of two new strands B) there are four double helices C) one DNA double helix consists of two old strands and one DNA double helix consists of two new strands D) each of the four DNA strands consists of some old strand parts and some new strand parts E) each new DNA double helix consists of one old DNA strand and one new DNA strand

E. DNA replication is semiconservative.

Why is the new DNA strand complementary to the 3' to 5' strands assembled in short segments? A) the replication forks block the formation of longer strands B) only short DNA sequences can extend off the RNA primers C) it is more efficient than assembling complete new strands D) DNA polymerase can assemble DNA only in the 3' to 5' direction E) DNA polymerase can assemble DNA only in the 5' to 3' direction

E. Since DNA polymerase can assemble DNA only in the 5' to 3' direction, the new strand complementary to the 3' to 5' strand must be assembled either in short 5' to 3' segments, which are later joined together by ligase, or be assembled continuously.

What does it mean when we say that the two DNA strands in the double helix are antiparallel? What would an end of the double helix look like if the strands were parallel?

Each strand in the double helix has polarity; the end with a phosphate group on the 5' carbon of the sugar is called the 5' end, and the end with an —OH group on the 3' carbon of the sugar is called the 3' end. The two strands run in opposite directions, one running 5' → 3' and the other alongside it running 3' → 5'. Thus, each end of the molecule has both a 5' and a 3' end, one on each strand of the double helix. This arrangement is called antiparallel. If the strands were parallel, they would both run 5' → 3' in the same direction, so an end of the molecule would have either two 5 ends or two 3 ends.

What protects the genes of linear eukaryotic chromosomes from being eroded away during successive rounds of DNA replication?

Eukaryotic chromosomal DNA molecules have special nucleotide sequences called telomeres at their ends. Telomeres do not contain genes; instead, the DNA typically consists of multiple repetitions of one short nucleotide sequence.

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

In order to tell which end is the 5' end, you need to know which end has a phosphate group on the 5' carbon (the 5' end) and/or which end has an —OH group on the 3' carbon (the 3 end).

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.

Compare DNA replication on the leading and lagging strands, including similarities and differences.

On both the leading and lagging strands, DNA polymerase adds onto the 3' end of an RNA primer synthesized by primase, synthesizing DNA in the 5' → 3' direction. Because the parental strands are antiparallel, however, only on the leading strand does synthesis proceed continuously into the replication fork. The lagging strand is synthesized bit by bit in the direction away from the fork as a series of shorter Okazaki fragments, which are later joined together by DNA ligase. Each fragment is initiated by synthesis of an RNA primer by primase as soon as a given stretch of single-stranded template strand is opened up. Although both strands are synthesized at the same rate, synthesis of the lagging strand is delayed because initiation of each fragment begins only when sufficient template strand is available.

How do the two ends of a DNA strand differ in structure?

One end, the 5'' end, has a phosphate group, which is attached to the 5'' carbon of the sugar, the one that is not in the ring. The other end, the 3'' end, has an —OH group attached to the 3'' carbon of the sugar; this carbon is in the ring.

What was the Griffith experiment?

Pneumonia was caused by different strains of pneumococcus bacteria. His job: study the different strains, and figure out ways to treat people who were sick from each strain (at the time that involved giving each strain to horses, then taking serum from the horses and injecting the horse serum it into people). He identified the strains by growing them in petri dishes and injecting them in mice. Each strain of pneumococcus came in two forms: the harmless form and the form the will kill you. Griffith's experiments with Streptococcus pneumoniae show that dead cells can transfer genetic (heritable) information to live cells, in a process called transformation.

DNA pol I

Removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides added to 3' end of the adjacent fragment.

How does euchromatin differ from heterochromatin in structure and function?

The 10-nm fiber of euchromatin is less compacted during interphase than in mitosis and is accessible to the cellular proteins responsible for gene expression. In contrast, the 10-nm fiber of heterochromatin is relatively compacted (densely arranged) during interphase, and genes in heterochromatin are largely inaccessible to proteins necessary for gene expression.

Describe the levels of chromatin packing you'd expect to see in an interphase nucleus.

The chromatin in an interphase nucleus is present as the 10-nm fiber, either fairly loosely arranged in euchromatin or more densely arranged in heterochromatin (such as at the centromeres and telomeres). The euchromatin is also subdivided into larger compartments and smaller looped domains. This organization may reflect differences in gene expression occurring in these regions.

Leading strand

The new complementary strand synthesized continuously along the template strand toward the replication fork in the mandatory 5' to 3' direction. Only one primer is required for DNA pol III to synthesize the entire leading strand.

Interphase chromosomes appear to be attached to the nuclear lamina and perhaps also the nuclear matrix. Describe these 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 a nuclear matrix, a framework of protein fibers extending throughout the nuclear interior.

Describe the bonds that hold together the nucleotides in one DNA strand. Then compare them with the bonds that hold the two DNA strands together.

The nucleotides in a single DNA strand are held together by covalent bonds between an oxygen on the 3 carbon of one nucleotide and the phosphate group on the 5 carbon of the next nucleotide in the chain. Instead of covalent bonds, the bonds that hold the two strands together are hydrogen bonds between a nitrogenous base on one strand and the complementary nitrogenous base on the other strand. (Hydrogen bonds are weaker than covalent bonds, but there are so many hydrogen bonds in a DNA double helix that, together, they are enough to hold the two strands together.)

DNA pol III

Using parental DNA as a template synthesizes a new DNA strand by adding nucleotides to an RNA primer or a pre-existing DNA strand.

Most DNA polymerases require

a primer and a DNA template strand, along which complementary DNA nucleotides are lined up, one by one. In E. coli, DNA polymerase III (abbreviated DNA pol III) adds a DNA nucleotide to the RNA primer and then continues adding DNA nucleotides, which are complementary to the parental DNA template strand, to the growing end of the new DNA strand.

In order for DNA polymerase to synthesize a complete new strand of DNA, it requires

a template to determine the order of bases on the new strand, a 3'-OH end to add more nucleotides onto, and the full set of four kinds of nucleotides (A,C,T,G) if they are needed to complement the template strand.

Enzymes called DNA polymerases catalyze the synthesis of new DNA by

adding nucleotides to the 3' end of a preexisting chain. In E. coli, there are several DNA polymerases, but two of them appear to play the major roles in DNA replication: DNA polymerase III and DNA polymerase I. The situation in eukaryotes is more complicated, with at least 11 different DNA polymerases discovered so far, although the general principles are the same.

But because of the shape of the molecule, the only way they can face each other along the entire length of DNA is by being

antiparallel and twisting into a helix. Antiparallel means the 5' and 3' ends are opposite for each polymer.

In ​interphase cells stained for light microscopy, the chromatin usually appears

as a diffuse mass within the nucleus, with some denser clumps, including in regions of centromeres and telomeres.

The lagging strand is made in segments, each with its own RNA primer. DNA pol III adds nucleotides to the 3' end of the lagging strand so that it elongates

away from the replication fork.

In the cell, eukaryotic DNA is precisely combined with a large amount of protein. The exact way in which this complex of DNA and protein, called

chromatin, fits into the nucleus has long been debated. DNA by itself cannot do anything. DNA needs to be combined with proteins in order to do anything. DNA and proteins combine in a special way and form chromatin.

Primase starts a

complementary RNA chain with a single RNA nucleotide and adds RNA nucleotides one at a time, using the parental DNA strand as a template. The completed primer, generally five to ten nucleotides long, is thus base-paired to the template strand. The new DNA strand will start from the 3′ end of the RNA primer.

In contrast to the leading strand, which elongates continuously, the lagging strand is synthesized

discontinuously, as a series of segments. These segments of the lagging strand are called Okazaki fragments, after Reiji Okazaki, the Japanese scientist who discovered them.

Each of your somatic cells has 46 DNA molecules in its nucleus, one long

double-helical molecule per chromosome. In all, that represents about 6 billion nucleotide pairs, or over 1,000 times more DNA than is found in most bacterial cells.

The less compacted, more dispersed interphase chromatin is called

euchromatin ("true chromatin") to distinguish it from the more compacted, denser-appearing heterochromatin.

DNA Polymerase needs a short stretch of double-stranded nucleic acid to

get started. All cells use a short stretch of RNA base-paired to the template DNA. The RNA is called an RNA primer. The RNA primer is a short stretch of RNA nucleotides complementary to the DNA.

Because heterochromatin is so compacted, it is largely

inaccessible to the proteins responsible for transcribing the genetic information, a crucial early step in gene expression. In contrast, the looser packing of euchromatin makes its DNA accessible to those proteins, and the genes present in euchromatin are available for transcription.

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 DNA nucleotides to the end of an already existing chain that is base-paired with the template strand. Replication can only start if there is an RNA primer on the template strand.

DNA Polymerase cannot replicate the DNA at the end of the lagging strand. Every time the DNA is replicated,

it gets shorter and shorter. Since the end region is the telomere, the telomeres get shorter and shorter.

Synthesis of the leading strand and synthesis of the lagging strand occur concurrently and at the same rate. The lagging strand is so named because

its synthesis is delayed slightly relative to synthesis of the leading strand; each new fragment of the lagging strand cannot be started until enough template has been exposed at the replication fork.

Mutations can change the phenotype of an organism. And if they occur in germ cells, which give rise to gametes,

mutations can be passed on from generation to generation. The vast majority of such changes either have no effect or are harmful, but a very small percentage can be beneficial. In either case, mutations are the original source of the variation on which natural selection operates during evolution and are ultimately responsible for the appearance of new species.

Level 1 of chromatin structure is the

nucleosome. one nucleosome: approximately two twists of DNA, wrapped around a "hockey puck" made of 8 histone proteins. Histones are responsible for during DNA on and off.

Nucleic acids are polymers of

nucleotides joined by phosphodiester bonds.

As a cell prepares for mitosis, its chromatin becomes

organized into loops and coils, eventually condensing into a characteristic number of short, thick metaphase chromosomes that are distinguishable from each other with the light microscope.

The replication of chromosomal DNA begins at particular sites called,

origins of replication, short stretches of DNA that have a specific sequence of nucleotides.

Mismatched nucleotides sometimes evade proofreading by a DNA polymerase. In mismatch repair,

other enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors.

An initial nucleotide chain that can be used as a pre-existing chain is produced during DNA synthesis; this is actually a short stretch of RNA, not DNA. The RNA chain is called a

primer and is synthesized by the enzyme primase.

Adenine and guanine are

purines, nitrogenous bases with two organic rings, while cytosine and thymine are nitrogenous bases called pyrimidines, which have a single ring. Pairing a purine with a pyrimidine is the only combination that results in a uniform diameter for the double helix.

After the parental strands separate, single-strand binding proteins bind to the unpaired DNA strands, keeping them from

re-pairing. The untwisting of the double helix causes tighter twisting and strain ahead of the replication fork.

Topoisomerase is an enzyme that helps

relieve strain in the double helix ahead of the replication fork by breaking, swiveling, and rejoining DNA strands.

At each end of a 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.

The E. coli chromosome, like many other bacterial chromosomes, 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. In contrast to a bacterial chromosome, a eukaryotic chromosome 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. As in bacteria, eukaryotic DNA replication proceeds in both directions from each origin.

DNA Polymerase needs to make new DNA on both template strands

simultaneously. That is because DNA Polymerase follows the replication fork. It can only make new DNA after helicase opens up the two DNA strands. But the strands are antiparallel, so while the new DNA on one strand gets made in the right direction, the other new DNA strand is GOING THE WRONG WAY.

Telomeres have two protective functions. First,

specific proteins associated with telomeric DNA prevent the staggered ends of the daughter molecule from activating the cell's systems for monitoring DNA damage. (Staggered ends of a DNA molecule, which often result from double-strand breaks, can trigger signal transduction pathways leading to cell cycle arrest or cell death.) Second, telomeric DNA acts as a kind of buffer zone that provides some protection against the organism's genes shortening, somewhat like how the plastic-wrapped ends of a shoelace slow down its unraveling. Telomeres do not prevent the erosion of genes near the ends of chromosomes; they merely postpone it.

Most cellular systems for repairing incorrectly paired nucleotides, whether they are due to DNA damage or to replication errors, use a mechanism that

takes advantage of the base-paired structure of DNA. In many cases, a segment of the strand containing the damage is cut out (excised) by a DNA-cutting enzyme—a 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 a DNA polymerase and DNA ligase.

Immortal cells (germ cells, stem cells, and cancer cells) have a special enzyme called

telomerase. Telomerase copies the DNA at the ends of chromosomes (at the telomeres). • In cells that have telomerase, the chromosomes do not get shorter when the cell divides.

Telomeres become shorter during every round of replication. Thus, as expected,

telomeric DNA tends to be shorter in dividing somatic cells of older individuals and in cultured cells that have divided many times. It has been proposed that shortening of telomeres is somehow connected to the aging process of certain tissues and even to aging of the organism as a whole.

The two strands of DNA in a double helix are antiparallel, meaning

that they are oriented in opposite directions to each other, like the two sides of a divided street. Therefore, the two new strands formed during DNA replication must also be antiparallel to their template strands.

DNA Polymerase can only make new DNA in

the 5' to 3' direction.

Completion of replication requires replacing the RNA primers with DNA. First,

the RNA primers are removed. Then, new DNA is made in place of the primers. Then, gaps in the DNA are sealed.

During DNA replication, many DNA polymerases proofread each nucleotide against its template as soon as it is covalently bonded to the growing strand. Upon finding an incorrectly paired nucleotide,

the polymerase removes the nucleotide and then resumes synthesis. (This action is similar to fixing a texting error by deleting the wrong letter and then entering the correct one.)

The error rate after proofreading and repair is extremely low, but rare mistakes do slip through. Once a mismatched nucleotide pair is replicated,

the sequence change is permanent in the daughter molecule that has the incorrect nucleotide as well as in any subsequent copies.

An enzyme called telomerase catalyzes the lengthening of telomeres in eukaryotic germ cells, thus restoring

their original length and compensating for the shortening that occurs during DNA replication. This enzyme contains its own RNA molecule that it uses as a template to artificially "extend" the leading strand, allowing the lagging strand to maintain a given length. Telomerase is not active in most human somatic cells, but its activity varies from tissue to tissue. The activity of telomerase in germ cells results in telomeres of maximum length in the zygote.

Early on, biologists assumed that interphase chromatin was a tangled mass in the nucleus, like a bowl of spaghetti, but

this is far from the case. Although an interphase chromosome lacks an obvious scaffold, there are proteins that further organize the 10-nm fiber into larger compartments and smaller looped domains. Some of the looped domains appear to be attached to the nuclear lamina, on the inside of the nuclear envelope, and perhaps also to fibers of the nuclear matrix. These attachments may help organize regions of chromatin where genes are active. The chromatin of each chromosome occupies a specific restricted area within the interphase nucleus, and the chromatin fibers of different chromosomes do not appear to be entangled.

The leading strand is made continuously from a single RNA primer located at the origin of replication. DNA pol III adds nucleotides to the 3' end of the leading strand so that it elongates

toward the replication fork.

Helicases are enzymes that

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

DNA replication often creates knots, since

unwinding the double helix in one place causes over winding in another place. Topoisomerases release the kinks in the overwound region.