All – 第 3 页 – AP Biology

the blueprint of life [6]: Chromosomal Structure of DNA 1

vocabulary

•Nucleus: 细胞核; Nucleolus: 核仁; Nucleoid: 类核

• Mitosis: 有丝分裂; Meiosis: 减数分裂

Interphase: 分裂间期; Prophase: 分裂前期; Metaphase: 分裂中期; Anaphase: 分裂后期; Telophase: 分裂末期

• Histone: 组蛋白

• Nucleosome: 核小体

•Chromosome: 染色体; Chromatin: 染色质; eu- 真染色质; hetero- 异染色质

• Centromere: 中心粒; Telomere: 端粒

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WHAT is chromosome:

Structure containing the genes of a cell and made of a single DNA molecule and its associated proteins.

CHROMOSOMES OF EUKARYOTES, shown by prof. Dong

HOW long is DNA in an chromosome
HOW LONG IS DNA, shown by prof. Dong.

→A chromosome is too long to fit into a cell without compaction.

WHY is DNA packed into chromosomes

Chromosome is a compact form of the DNA that readily fits inside the cell
To protect DNA from damage
DNA in a chromosome can be transmitted efficiently to both daughter cells during cell division
Chromosome confers an overall organization to each molecule of DNA, which regulates gene expression as well as recombination

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Diversity of chromosomes

in terms of:

Shape: circular or linear
Number: species-specific

eg. -fruitfly 8; -human 46; -horse 64; -dog 78; -chicken 78

-maize 20; -rice 24; -wheat 42

Copy number: haploid单倍体, diploid双倍体, polyploid 多倍体

Overall structure: highly different between prokaryotes 原核生物and eukaryotes真核生物

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Next section we will first talk about prokaryotic chromosome structure of DNA.

Flight Behavior: What Is The Use of Saving A Planet That Has No Soul Left In It?

World consumption of paper has grown 400 percent in the last 40 years. Now nearly 4 billion trees or 35 percent of the total trees cut around the world are used in paper industries on every continent.(source)

For the trees’ sake, please please please please use e-books!

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Flight Behavior by Barbara Kingsolver
Pages: 448
Release Date: November 6, 2012
Publisher: Harper
Genre: Literary Fiction

A novel you wouldn’t put down once opening the first page.

Barbara wrote with close attention to language and intelligent arrangement of plot. Only having read the first chapter, you would never get right what the novel is really about.

Generally, the 2012 novel focuses on the interactions between humans and the natural environmental they are living in, which leads to a core topic of today’s environmental situation:climate change. But not like what we read in Science, where climate change is drawn in a scientific way. No logical reasoning, non data analysis, climate change in Flight Behavior is lyrically written, tragic, sad, forcing innocent monarch butterflies abandon their hometown (also original wintering habitat) and flew all the way to a small town in southern U.S for survival.

Family matters, communities, scientists, butterflies, climate change, meanings of life, faith…

No more spoilers, hope you enjoy this book and after reading it, would see more respects in environmental conservation.

Illustrations of wild animals [insect 7 Homoptera 2]

同翅目 HOMOPTERA

角蝉科 Membracidae

1. 黑圆角蝉Gargara genistae

2. 小截角蝉 Truncatocornum parvum

沫蝉科 Cercopidae

1. 斑带丽沫蝉Cosmoscarta bispecularis

2. 东方丽沫蝉 Cosmoscarta heros

3. 紫胸丽沫蝉Cosmoscarta exultans

4. 象沫蝉 Philagra sp.

白纹象沫蝉Philagra aibinotata

6. 尖胸沫蝉Aphrophora sp.

蜡蝉科 Fulgoridae

1. 斑衣蜡蝉Lycirma delicatula

2. 雪白粒脉蜡蝉 Nisia atrovenosa

Mendel’s Genetics [6]: Examples of epistasis

In Mendel’s dihybrid cross, each gene locus(the position of a gene along a chromosome, often used to refer to the gene itself.) had an independent effect on a single phenotype. Thus, the R and r alleles affected only the shape of the seed and had no influence on seed color, while the Y and y alleles affected only seed color and had no influence on seed shape. In this case, there were two separate genes that coded for two separate characteristics.

But what happens when two different loci affect the same characteristic? For instance, what if both of the loci in Mendel’s experiment affected seed color?

Let’s begin with a relatively simple example.

example (1) 9:3:3:1→9:7

enzyme A serves to convert white substrate in an unnamed plant to white product; enzyme B synthesizes purple pigment and converts the white product to purple product.

In this case, If BOTH A & B exist, purple product is yielded;

If ONLY A OR B exists, synthesis of purple pigment cannot be completed, and purple product won’t be produced;

If NEITHER ENZYME exist, purple pigment, surely, cannot be synthesized, and purple product won’t be produced.

Based on the info above, the dihybrid F2 generation looks like this:

When the situation gets a little bit more complicated:

example (2) 9:3:3:1→9:3:4

enzyme A serves in the synthesis of red pigment and converts white substrate in an unnamed plant to red product; enzyme B synthesizes purple pigment and converts the red product to purple product.

In this case, If BOTH A & B exist, purple product is yielded;

If ONLY A exists, synthesis of red pigment can be completed but synthesis of purple pigment cannot, and red product will be produced;

If NEITHER ENZYME exist or ONLY B exists, surely, neither red or purple pigment, can be synthesized, and the the yield will be white.

Based on the info above, the dihybrid F2 generation looks like this:

A more complex situation:

example (3): 9:3:3:1→12:3:1

Here two enzymes compete for the same substrate. Enzyme A converts the substrate to a purple product, and enzyme B to a red product. BUT enzyme A has much higher affinity for the substrate than enzyme B. The difference in affinity is so marked that enzyme B can only work effectively without the presence of enzyme A

SO as long as enzyme A is present, the yield is be purple; only when enzyme B exists without enzyme A would the yield be red; and only when neither B or A exists would the yield be white.

Based on the info above, the dihybrid F2 generation looks like this:

[F2] purple: red: white=12: 3: 1

The three examples above lead us to a new concept: Epistasis.

Sometimes genes can mask each other’s presence or combine to produce an entirely new trait. Epistasis describes how gene interactions can affect phenotypes.

In a strict sense, 12: 3: 1 is the only ratio which was originally referred to as epistasis, because the presence of enzyme A can completely make the genotype of the B gene. But the term is now used wherever genes interact to alter the expected ratios.

There are several other variations of the 9:3:3:1 ratio caused by interaction between the gene products, including 9:6:1, 15:1, and 13:3.

In every case the ratios are derived by summing together the four phenotype classes 9, 3, 3, or 1 of the basic ratio.

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For more examples and explanations of the Epistasis, see Epistasis and Its Effects on Phenotype | Learn Science at Scitable

The blueprint of life [5]: spectroscopic and thermal properties of DNA

UV absorption

DNA absorbs UV light due to the conjugated aromatic nature of the bases; the sugar-phosphate backbone does not contribute appreciably(perceptibly/measurably) to absorption.

The wavelength of maximum absorption of light by both DNA and RNA is 260 nm, which is conveniently distinct from the λmax of protein(280 nm).

The absorption properties of DNA can be used for detection, quantitation and assessment of property.

Hypochromicity

UV absorption at 260nm is greatest for isolated nucleotides, intermediate for single-stranded DNA(ssDNA) or RNA, and least for double-stranded DNA(dsDNA)

The classical term for the change in absorbance is hypochromicity. For example, dsDNA is hypochromic (from the Greek for ‘less colored‘) relative to ss DNA, which is hypochromic relative to isolated nucleotides.

Thermodynamics of DNA

Denaturation: the transition of macromolecule from the native state to the denatured state. For DNA, under denaturing conditions (heating or high pH), double helix is separated to generate single-stranded form.

Melting Temperature(Tm): the temperature at which the rise in A260(absorbance at 260nm) is half complete during denaturation.

Factors that affect the Tm

1. G+C content: the higher G+C content, the higher Tm.

2. Ionic strength: The Tm increases as the cation (+) concentration increases. like Na+, K+ or Mg2+.

3. High pH or Agents that disrupt H-bonds or interfere with base stacking: formamide (甲酰胺)or urea (尿素)will decrease the Tm.

4. The imperfect hybridization between related but not completely complementary strands will reduce the Tm, about 1 °C for each percent mismatch.

The process of denaturation can be observed conveniently by the increase in absorbance as double-stranded nucleic acids are converted to single strands

Renaturation: Process of a macromolecule returning to its native 3-D structure. For DNA this involves the two strands of denatured DNA basepairing to restore the nature form of dsDNA. Also known as reannealing (重退火).

Requirements for renaturation:

1. Proper salt concentration: neutralize electrostatic repulsion

2. Proper reannealing temperature: 20-25℃ below Tm

Determinants for renaturation efficiency

(DNA renatures on cooling, but will form fully double-stranded native DNA only if the cooling is sufficiently slow to allow the complementary strands to anneal.)

1. Extent of base matching and

2. copy of matching regions

Thus, repetitive DNA renatures faster than single copy DNA

RENATURATION CURVES FOR E.COLI &MOUSE DNA, shown by prof. Dong

Mendel’s Genetics [5]: The dihybrid cross

Last sections we discussed inheritance where only a single gene was involved. The 3:1 ratio is the basic Mendelian ratio and everything that follows depends upon it.

The obvious next step is to look at a situation where the inheritance of two different inherited characters are studied at the same time, a dihybrid cross.

Again, we learn dihybrid cross by experiments. Let’s see what Mendel did:

He crossed two pure-bred starins of pea plants, one producing only round yellow seeds and the other only wrinkled green seeds.Round seeds are dominant over wrinkled ones; yellow seeds are dominant over green ones. Both phenotypes are determined by one single gene.

(Why did Mendel use the seed characteristics as his focus of study instead of other traits of the pea plants? )

A cross between the two parents produced a F1 generation that consisted only of round yellow seeds. Self-fertilization of F1 yielded F2 generation, the seeds of which showing considerable diversity.

Four different phenotypes could be identified. Of 556 seeds analyzed, Mendel found 315 round yellow seeds, 108 round green seeds, 101 wrinkled yellow seeds and 32 round green seeds. Close to a ratio of 9: 3: 3: 1, which is referred to as the dihybrid ratio.

dihybrid cross — THE 9:3:3:1 IN MENDEL’S EXPERIMENTS, image from Instant Notes in Genetics

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Interestingly, if we only focus on the round/wrinkled phenotype, the ratio of round seeds and wrinkled seeds is 3:1. the monohybrid ratio. Similarly, if we only focus on the yellow/green phenotype, the ratio of yellow seeds and green seeds is the monohybrid ratio as well. Just as we said “The 3:1 ratio is the basic Mendelian ratio and everything that follows depends upon it”

Now I want to introduce a little bit mathematics into this section. Let’s see what happens when we use polynomial multiplication to explain the relationship between 9: 3: 3: 1 and 3:1:

(yellow: green)× (round: wrinkled)

= (yellow·round): (yellow·wrinkled): (green·round): (green·wrinkled)

known: yellow: green=3:1; round: wrinkled=3:1

SO: (yellow: green)×(round: wrinkled)=(3:1)×(3:1)

=(3×3):(3×1):(1×3):(1×1)=9:3:3:1

Therefore, (yellow·round): (yellow·wrinkled): (green·round): (green·wrinkled)=9:3:3:1
Does this reasoning inspire you? What happens when it comes to a tri-hybrid ratio?

(3:1)×(3:1)×(3:1)=

(3×3×3):(3×3×1):(3×1×3):(3×1×1):(1×3×3):(1×3×1):(1×1×3):(1×1×1)

=27 : 9 : 9 : 9 : 3 : 3 : 3 : 1

See? Quite easy. The ratios for the three groups of phenotypes are simply multiplied across, and the 27 : 9 : 9 : 9 : 3 : 3 : 3 : 1 ratio is obtained.

SO what happens when it comes to tetra-hybrid, penta-, hex-? What happens when it comes to n-hybrid?

I’m sure the answer is easy for you now, make the n phenotypes multiplied across, and the expected ratio is obtained. In plain mathematics, (3:1)^n

——————————————————————————-As noted before the 3:1 ratio can be distorted by factors such as incomplete dominance or lethal alleles. These also affect the 9:3:3:1 ratio, but other factors can also modify this ratio.

The two different genes must not act on the same character. For instance, if the proteins encoded by the two genes are involved in the same biochemical pathway then the ratios of phenotypes resulting from the genotypes will be altered.
If the two genes lie close together on the same chromosome, linkage happens and the ratio won’t be 9:3:3:1 either, as we mentioned in Review of Mendel’s Genetics, the very beginning of our Genetics study.

Testcross

As with the monohybrid cross, it is also possible to conduct a testcross with F1 generation of the dihybrid cross.

Illustrations of wild animals [insect 6 Homoptera 1]

同翅目 HOMOPTERA

Order Hemiptera
suborder Heteroptera *	Bugs
suborder Homoptera *	Cicadas, Hoppers, Psyllids, Whiteflies, Aphids, and Scale insects

Most people tend to call anything with lots of legs a “bug.” However, to an entomologist, a “bug” is one of the 35,000 or so species of the order Hemiptera.

Hemiptera means “half wing” and refers to the fact that part of the first pair of wings is toughened and hard, while the rest of the first pair and the second pair are membranous. Hemipterans also have modified piercing and sucking mouthparts; some suck plant juices and are plant pests, while others can bite painfully.

A possibly paraphyletic group of insects known as the Homoptera is sometimes included within the Hemiptera, even though they lack the toughened areas on the first pair of wings.

Some entomologists group both Hemiptera and Homoptera within the group Heteroptera; others use the name Heteroptera for what we have called the Hemiptera and use Hemiptera for the Heteroptera.

Confused? So are we. Anyway, the Homoptera have the dubious distinction of being probably the most destructive insects of all. They include aphids, leafhoppers, cicadas, and scale insects: 45,000 species in all.

↑Quoted from University of California Museum Paleontology>arthropoda>uniramia>hemiptera

Hemiptera

Suborder Homoptera

Leafhoppers, Planthoppers, Treehoppers, Cicadas, Aphids, Psyllids, Whiteflies, Scale Insects

The name Homoptera, derived from the Greek “homo-“meaning uniform and “ptera” meaning wings, refers to the uniform texture of the front wings.

Classification & Distribution

Hemimetabola

incomplete development (egg, nymph, adult)

Hemipteroid

closely related to Thysanoptera and Psocoptera

Distribution: Abundant worldwide. All species are terrestrial herbivores.

	North America	Worldwide
Number of Families	38	60
Number of Species	6359	>32,000

Physical Features

Adults:

Antennae slender or bristle-like
Proboscis short, arising near lower back margin of head
Front wings, when present, uniform in texture; at rest, wings fold tent-like over the abdomen
Tarsi 1- to 3-segmented

Immatures:

Structurally similar to adults
Always lacking wings

Major Families

Cicadidae (Cicadas) — Nymphs live underground where they feed on the roots of trees and shrubs. Adults are the largest members of the Homoptera. Males produce loud songs to attract a mate.
Cicadellidae (Leafhoppers) — This is the largest family of Homoptera and includes many pests of cultivated plants. Leafhoppers are important carriers of plant diseases — especially mycoplasmas.
Membracidae (Treehoppers) — Ecologically similar to leafhoppers, these insects have a large pronotum that extends over most of the body. They often resemble thorns or small twigs.
Cercopidae (Spittlebugs or Froghoppers) — Nymphs live on plant stems and produce a frothy defensive secretion around themselves. Adults are similar to leafhoppers in size and general appearance.
Fulgoridae (Planthoppers) — This is one of eleven families classified as planthoppers (superfamily Fulgoroidea). These insects are ecologically similar to leafhoppers and treehoppers. Many species are oddly shaped and cryptically colored.
Psyllidae (Psyllids or Jumping Plant Lice) — Small, aphid-like insects with 3-segmented beaks and 10 segmented antennae. Many species are covered with a woolly layer of wax.
Aleyrodidae (Whiteflies) — Body and wings of adults are covered with a white powdery wax. Nymphs attach to the undersides of leaves and become immobile, resembling scale insects.
Aphididae (Aphids, Plantlice) — Second largest family in the suborder Homptera. Many of these insects are pests of cultivated plants. Aphids are considered the most important carriers of viral plant diseases.
Coccidae (Soft Scale insects) — This is one of 17 families that make up the superfamily Coccoidea (scale insects and mealybugs). Most species are sedentary during most of their life cycle and secreate a protective covering over their bodies. These insects are among the most common pests of cultivated plants.

====================================================↑Quoted from the General Entomology course at North Carolina State University >Resource Library > Compendium > Homoptera (© 2009 by John R. Meyer; Last Updated: 8 April 2009)

>Learn more about homoptera (www.insectsexplained.com)

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蝉科 Cicadidae

1. 草蝉 Mogannia sp.

2. 绿草蝉 Mogannia hebes

3. 蒙古寒蝉 Meimuna mongocica

4. 螗蝉Tanna japonensis

5. 鸣鸣蝉 Oncotympana maculaticollis

6. 蟪蛄Platypleura kaempferi

叶蝉科 Cicadellidae

1. 丽叶蝉 Calodia sp.

2. 华凹大叶蝉 Bothrogonia sinica

3. 条大叶蝉Atkinsoniella

4. 显脉叶蝉Paramesus sp.

5. 槽胫叶蝉Drabescus sp.

6. 窗耳叶蝉Ledra auditura

7. 隐纹大叶蝉Tettigoniella thalia

8. 横脊叶蝉Evacanthus sp.

9.白边拟大叶蝉Ishidaella albomarginata

Illustrations of wild animals [insect 5 Hemiptera]

半翅目 HEMIPTERA

Most people tend to call anything with lots of legs a “bug.” However, to an entomologist, a “bug” is one of the 35,000 or so species of the order Hemiptera.

A possibly paraphyletic group of insects known as the Homoptera is sometimes included within the Hemiptera, even though they lack the toughened areas on the first pair of wings.

Some entomologists group both Hemiptera and Homoptera within the group Heteroptera; others use the name Heteroptera for what we have called the Hemiptera and use Hemiptera for the Heteroptera.

↑Quoted from University of California Museum Paleontology>arthropoda>uniramia>hemiptera

Hemiptera(/heteroptera)
Suborder Heteroptera (/hemiptera)

True Bugs

The name Heteroptera, derived from the Greek “hetero-“em> meaning different and “ptera” meaning wings, refers to the fact that the texture of the front wings is different near the base (leathery) than at the apex (membranous).

Classification & Distribution

Hemimetabola
- incomplete development (egg, nymph, adult)
Orthopteroid
- closely related to Thysanoptera and Psocoptera
Distribution: Abundant worldwide. Found in most terrestrial and freshwater habitats.

North America
Worldwide

Number of Families
40

73

Number of Species
3587

>50,000
Life History & Ecology

Members of the suborder Heteroptera are known as “true bugs”.

They have very distinctive front wings, called hemelytra, in which the basal half is leathery and the apical half is membranous. At rest, these wings cross over one another to lie flat along the insect’s back.

These insects also have elongate, piercing-sucking mouthparts which arise from the ventral (hypognathous) or anterior (prognathous) part of the head capsule.

The mandibles and maxillae are long and thread-like, interlocking with one another to form a flexible feeding tube (proboscis) that is no more than 0.1 mm in diameter yet contains both a food channel and a salivary channel. These stylets are enclosed within a protective sheath (the labium) that shortens or retracts during feeding.

The Heteroptera include a diverse assemblage of insects that have become adapted to a broad range of habitats — terrestrial, aquatic and semi-aquatic.

Terrestrial species are often associated with plants. They feed in vascular tissues or on the nutrients stored within seeds. Other species live as scavengers in the soil or underground in caves or ant nests. Still others are predators on a variety of small arthropods. A few species even feed on the blood of vertebrates.

Bed bugs, and other members of the family Cimicidae, live exclusively as ectoparasites on birds and mammals (including humans). Aquatic Heteroptera can be found on the surface of both fresh and salt water, near shorelines, or beneath the water surface in nearly all freshwater habitats. With only a few exceptions, these insects are predators of other aquatic organisms.

Physical Features

Adults:

Antennae slender with 4-5 segments
Proboscis 3-4 segmented, arising from front of head and curving below body when not in use
Pronotum usually large, trapezoidal or rounded
Triangular scutellum present behind pronotum
Front wings with basal half leathery and apical half membranous (hemelytra). Wings lie flat on the back at rest, forming an “X”.
Tarsi 2- or 3-segmented

Immatures:

Structurally similar to adults
Always lacking wings

Major Families

The three largest families of Heteroptera are:
- - Miridae (Plant Bugs) — Most species feed on plants, but some are predaceous. This family includes numerous pests such as the tarnished plant bug (Lygus lineolaris).
  - Lygaeidae (Seed Bugs) — Most species are seed feeders, a few are predatory. This family includes the chinch bug, Blissus leucopterus a pest of small grains, and the bigeyed bug, Geocoris bullatis, a beneficial predator.
  - Pentatomidae (Stink Bugs) — Shield-shaped body with large, triangular scutellum. Most species are herbivores, some are predators. All have scent glands which can produce an unpleasant odor.
Other families of terrestrial herbivores include:
- - Tingidae (lace bugs)
  - Coreidae (squash bugs and leaffooted bugs)
  - Alydidae (broadheaded bugs)
  - Rhopalidae (scentless plant bugs)
  - Berytidae (stilt bugs)
Other families of terrestrial predators include:
- - Reduviidae (assassin bugs)
  - Phymatidae (ambush bugs)
  - Nabidae (damsel bugs)
  - Anthocoridae (minute pirate bugs)
The major families of aquatic predators include:
- - Corixidae (water boatmen)
  - Gerridae (water striders)
  - Nepidae (water scorpions)
  - Belostomatidae (giant water bugs)
  - Naucoridae (creeping water bugs)
  - Notonectidae (backswimmers)
Bug Bytes
- Two families of Heteroptera are ectoparasites. The Cimicidae (bed bugs) live on birds and mammals (including humans). The Polyctenidae (bat bugs) live on bats.
- Water striders in the genus Halobates (family Gerridae) are the only insects that are truly marine. They live on the surface of the Pacific Ocean.
- Unlike other insects, male bedbugs do not place their sperm directly in the female’s reproductive tract. Instead, they puncture her abdomen and inject the sperm into her body cavity. The sperm swim to the ovaries where they fertilize the eggs. This unusual type of reproductive behavior is appropriately known as “traumatic insemination”.
- Some members of the family Largidae resemble ants. They live as social parasites in ant nests, mimicking the ants’ behavior to get food

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>Learn more about heteroptera (www.insectsexplained.com)

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蝽科 Pentatomidae

1. 全蝽Homalogonia sp.

2.双峰疣蝽 Cazira verrucosa

3. 庐山珀蝽Plautia lushanica

4.弯角蝽Lelia decem punctata

5. 斑须蝽 Dolycoris baccarum

6.梭蝽Megarrhamphus sp.

7. 绿岱蝽 Dalpada amaragdina

8. 金绿曼蝽Menida metalica

9. 谷蝽Gonopsis affinis

10. 麻皮蝽Erthesns fullo

盲蝽科 Miridae

1. 中黑苜蓿盲蝽 Adelphocoris situralis

2. 后丽盲蝽 Apolygus sp.

3. 斑胸树丽盲蝽Lygocoris pronotalis

长蝽科 Lygaeidae

1. 小长蝽Nysius ericae

2. 红脊长蝽 Tropidothorax elegans

盾蝽科 Scutelleridae

1. 金绿宽盾蝽Poecilocoris lewisi

2.斜纹宽盾蝽 Poecilocoris dissimilis

The blueprint of life [4]: Tertiary Structure of DNA

Finally, we come to the last part of the molecular structure of DNA.

4. Tertiary Structure of DNA – superhelix structure

Advanced folding and intertwining of DNA molecules over the secondary structure .

DNA topology

1. Linear DNA:

Commonly seen in eukaryotes,
with extreme length,
complementary sequence
included in the chromatin (the combination or complex of DNA and proteins that make up the contents of the nucleus of a cell)
interacting with other cellular components.

2. Circular DNA:

(DNA frequently occurs in nature as closed-circular molecules, where the two single strands are each circular and linked together. The number of links is known as the linking number(Lk).)

Usually seen in prokaryotes, e.g. plasmid (质粒), circular bacterial chromosomes and many viral DNA molecules
cccDNA (covalently closed circular DNA) → supercoiled or Relaxed; ncDNA (nicked circular DNA): a nick (缺刻)formed by breaking one phosphodiester bond
two complementary single strands are each joined into circles, 5′ to 3′, and are twisted around one another by the helical path of DNA.
The molecule has no free ends and the two single strands are linked together a number of times corresponding to the number of double-helical turns in the molecule.

cccDNA Topology

Supercoiled DNA

Negative superhelix: natural status of cccDNA with less intra- molecular tension (underwound effect)

Positive superhelix: unnatural status with higher tension (overwound effect)

Relaxed circular DNA: intermediate between negative superhelix and positive superhelix

Topological Equation of cccDNA

L = T + W

L=Linking number=total number of times one strand of the double helix links the other

T=Twisting number= the number of times one strand completely wraps around the other strand

W=Writhing number= the number of times that the long axis of the double helical DNA crosses over itself in 3-D space

Features

1. The linking number of a closed-circular DNA is a topological property, that is one which cannot be changed without breaking one or both of the DNA backbones. (A molecule of a given linking number is known as a topoisomer. Topoisomers differ only in their linking number)

2. Twisting number

For B DNA, T>0(10 bp per turn)

For A DNA, T>0(10.5 bp per turn)

For Z DNA, T<0 (12 bp per turn)

3. Writhing number

Relaxed: W=0

Negative supercoils: W<0

Positive supercoils: W >0

TWIST &WRITHE, from Instant Notes in Molecular Biology(3rd edition)

Topoisomerases (enzymes used to regulate the level of supercoiling of DNA molecules)

To alter the linking number of DNA, the enzymes must transiently break one or both stands. There are two classes of topoisomerases:

Type I Topoisomerase nick one strand of the DNA, changing 1 Linking-number at a time(+/-1 Lk)

Type II Topoisomerase, which requires the hydroloysis of ATP, break two strands of DNA, changing 2 Linking-number at a time(+/-2Lk); also able to unlink DNA molecules.

Most topoisomerases reduce the level of positive or negative supercoiling, that is, they operate in the energetically favorable direction. (However, DNA gyrase, a bacterial type II enzyme, uses the energy of ATP hydrolysis to introduce negative supercoiling into hence removing positive supercoiling generated during replication.)

Topoisomerases are essential enzymes in all organisms; they are involved in replication, recombination and transcription.

Both type I and II enzymes are the target of anti-tumor agents in humans.

DNA superhelix

Biological significance of Superhelix:

DNA packing:

Eg.

This is a famous electron micrograph of an E. coli cell that has been carefully lysed, then all the proteins were removed, and it was spread on an EM grid to reveal all of its DNA.

DNA functioning:

Negative supercoils serve as a store of free energy that aids in processes requiring strand separation, such as DNA replication and transcription; Strand separation can be accomplished more easily in negatively supercoiled DNA than in relaxed DNA.

1. DNA in cells is negatively supercoiled;

2.(-)supercoiling introduced by a topoisomerase II (gyrase 促旋酶) in prokaryotes and by nucleosome (核小体)in eukaryotes

3.Cruciform or bubble structures introduced by (-) supercoiling are potential protein-binding sites

vocabulary

Diversity of chromosomes

同翅目 HOMOPTERA

角蝉科 Membracidae

沫蝉科 Cercopidae

蜡蝉科 Fulgoridae

Let’s begin with a relatively simple example.

When the situation gets a little bit more complicated:

A more complex situation:

The three examples above lead us to a new concept: Epistasis.

UV absorption

Thermodynamics of DNA

同翅目 HOMOPTERA

Adults:

Immatures:

Major Families

蝉科 Cicadidae

叶蝉科 Cicadellidae

半翅目 HEMIPTERA

Classification & Distribution

Life History & Ecology

Physical Features

Adults:

Immatures:

Major Families

蝽科 Pentatomidae

长蝽科 Lygaeidae

盾蝽科 Scutelleridae

DNA topology

DNA superhelix

Thermodynamics of DNA