revision – AP Biology

the blueprint of life [11]: DNA replication 1

DNA replication

Definition: the process of copying a parental DNA molecule to form two daughter DNA molecules.

Introduction to DNA replication

DNA replication is essential for cell proliferation, i.e. mitosis, meiosis.
DNA replication is a complex endeavor involving a series of enzyme activities.→see “DNA polymerases”
DNA replication is performed in a semiconservative and semidiscontinuous mode.→see “DNA replication is semi-conservative”
DNA replication has 3 stages: initiation, elongation and termination.→next section
DNA replication is tightly regulated, involving various protein-protein, protein-DNA interactions.
DNA replication of prokaryote and eukaryote shares similar features, but is distinctive in details.

Chemical Reaction of DNA replication

Essentials

1. Substrate: deoxynucleoside triphosphates(dNTPs)
2. Template: a primer-template junction

DNA is synthesized by extending the 3’ end of the primer (free 3’-OH is required)

– RNA primer or priming from a nick in DNA

3. Enzymes: DNA polymerases etc

4. Energy supply: Hydrolysis of pyrophosphate (PPi) is the driving force for DNA synthesis

5. Ions involved: Mg++ or Zn++

DNA polymerases

DNA polymerase I
- Pol I was the first enzyme discovered with polymerase activity, and it is also the best characterized one.
- Although abundant in cells (400/cell), Pol I is NOT the primary enzyme involved with bacterial DNA replication.
- Main functions of Pol I: (1) Fill any gaps in the new DNA that result from the removal of the RNA primer by its 5’ -3’ polymerase activity; (2) Remove a new mispaired base by proofreading (校读)3’-5’ exonuclease (外切酶) activity. (3)Remove the RNA primer by its 5’-3’ exonuclease activity

The 3′–>5′ exonuclease activity intrinsic to several DNA polymerases plays a primary role in genetic stability; it acts as a first line of defense in correcting DNA polymerase errors. A mismatched basepair at the primer terminus is the preferred substrate for the exonuclease activity over a correct basepair. (source)

DNA polymerase III
- The primary polymerase in DNA replication, although lower in abundance (15/cell)than pol →referred to as “replicase”
- functions: (1) 5’→3’ polymerase activity; (2) 3’→5’ exonuclease activity – proofreading
- Catalytic efficiency: much higher than pol I→High processivity and polymerization rate
- A multi-unit complex: “holoenzyme” (全酶)

DNA replication is semi-conservative

Bet you all have learned it in high school, and the famous experiment by Meselson and Stahl. We still need to go over the points again as they are essentially important for what we will learn next.

The key to the mechanism of DNA replication is the fact that each strand of the DNA double helix carries the same information-their base sequences are complementary (we talked about this in THE BLUEPRINT OF LIFE [2]: PRIMARY AND SECONDARY STRUCTURE OF DNA).

During replication, the two parental strands separate and each acts as a template (that’s right, the template for DNA replication is DNA itself!)to direct the enzyme-catalyzed synthesis of a new complementary daughter strand with the normal base-pairing rules (A-T, C-G)

This semi-conservative mechanism was demonstrated experimentally in 1958 by Meselson and Stahl.

Hypotheses:

In the experiment:

E. coli cells were grown for several generations in presence of the stable heavy isotope ¹⁵N so that their DNA became fully density labeled (both strands are ¹⁵N labeled: ¹⁵N/¹⁵N)

The cells were then transferred to medium containing only normal ¹⁴N and, after each cell division, DNA was prepared from a sample of the cells and analyzed on a CsCI gradient using the technique of equilibrium (isopycnic) density gradient centrifugation, which separates molecules according to differences in buoyant density.

After the first cell division, when the DNA had replicated once, it was all of hybrid density, in a position on the gradient half way between fully labled (¹⁵N /¹⁵N )and fully light (¹⁴N/¹⁴N). After the second generation in ¹⁴N, half of the DNA was hybrid density and half fully light.

Thus, two of the hypotheses were denied, left us with the semi-conservative mechanism.

After each subsequent generation, the proportion of ¹⁴N/¹⁴N increased, while some DNA of hybrid density persisted. Thus the semi-conservative mode of DNA replication is confirmed: each daughter molecule contains one parental strand and one newly-synthesized strand.

Genetics [10] reproduction 3: Meiosis 2

Last section we gave a general introduction of meiosis in terms of chromosome behaviors.

In this section, we will deal with two other respects of meiosis. First, a specific description of meiosis in animals; second, we will mention a situation when meiosis goes wrong.

Meiosis in animals

is found only in ovaries (卵巢)and testes(曲细精管), and even in these tissues is restricted to cells that are destined to form gametes(the germline).

Despite the fact that the mechanisms of gametogenesis differ somewhat between organisms,the steps involved in gametogenesis in mammals are relatively similar.

In male gametogenesis (spermgenesis).

precursors of germ cells go through many rounds of mitotic divisions in order to maintain a pool of spermatogonia(plural of spermatogonium 精原细胞).↓

Spermatogonia subsequently differentiate into primary spermatocytes(based on what you learned in high school. guess what this word mean? : D ). It is in these cells that meiosis takes place.↓

After meiosis I, these cells are referred to as secondary spermatocytes. These are haploid. The products of the second meiotic division are spermatids. ↓

Spermatids differentiate into motile spermatozoa with rounded or elongate head and a long posterior flagellum.(The final activation of spermatozoa takes place after copulation/sexual intercourse)

Without cytoplasm and many subcelluar organelles, the sperm is light and fast (almost all its weight concentrated in its head, where stored the key of a potential life, nuclei. ).

In female mammals, the pattern of oogenesis is superficially similar.

Here oogonia(plural of oogonium, 卵原细胞) go through mitotic divisions before differentiating into primary oocytes. These then undergo meiosis.↓

Both daughter cells of the primary oocytes are haploid but differ greatly in size. The larger daughter cell is the secondary oozyte, the smaller the first polar body. The two cells remain attached. Both undergo a second meiotic division.↓

The secondary oocyte undergoes an unequal division producing a large ovum and a small secondary polar body. The first polar body divides into two secondary polar bodies.

Only the ovum, which contains almost all the cytoplasm, will transmit genes into the next generation.

The first meiotic division is only completed at ovulation(the discharge of a mature ovum from the ovary), and the second occurs after fertilization.

Little known: In human females, primary oocytes can be held in meiotic arrest for up to 45 years. This may be important in the increased frequency of aneuploid births observed in older mothers.

Production of aneuploid gametes

The major cause of anueploidy(the situation of having or being a chromosome number that is not an exact multiple of the usually haploid number) is aberrant chromosome behavior at meiosis. In other words, it’s the failure of chromosmes to segregate properly(known as nondisjunction)

At anaphase I, if two homologous chromosomes move to the same pole, first division nondisjunction occurs. In this case, of the 4 cells arsing from meiosis, two will be disomic(contain two copies of the chromosome) and two nullisomic (contain no copy of the chromosome.

At anaphase II, if the chromatids in a cell remain together, division nondisjunction occurs. The resulting tetrad will contain two normal cells, one nullisomic, and one disomic.

Aneuploidy also arises due to nondisjunction at an early mitosis in the embryo, resulting in two populations of cytogenetically different cells in the individual, which is known as a mosaic.

MOSAIC (GENETICS)"Heterochromia iridum and iridus" image from simple.wikipedia.org — MOSAIC (GENETICS)”Heterochromia iridum and iridus” image from simple.wikipedia.org

Mosaic is common in Turners syndrome.

↑Turner syndrome or Ullrich–Turner syndrome is a chromosomal abnormality in which all or part of one of the sex chromosomes is absent or has other abnormalities . In some cases, the chromosome is missing in some cells but not others, a condition referred to as mosaicism or “Turner mosaicism”.

Occurring in 1 in 2000– 1 in 5000 phenotypic females, the syndrome manifests itself in a number of ways. There are characteristic physical abnormalities which affect many but not all people with Turner syndrome, such as short stature,swelling, broad chest, low hairline, low-set ears, and webbed necks. Girls with Turner syndrome typically experience gonadal dysfunction (non-working ovaries), which results in amenorrhea (absence of menstrual cycle) and sterility. Concurrent health concerns may also be present, including congenital heart disease, hypothyroidism (reduced hormone secretion by the thyroid), diabetes, vision problems, hearing concerns, and many autoimmune diseases.Finally, a specific pattern of cognitive deficits is often observed, with particular difficulties in visuospatial, mathematical, and memory areas.

Turner syndrome is named after Henry Turner, the endocrinologist who first described it in 1938.（wikipedia）

the blueprint of life [10]: eukaryotic structure of DNA 3

let’s go over the terms again. Make sure you all know what they mean.

•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

Sister chromotid 姐妹染色单体;
mitotic spindle 纺锤体
spindle microtubule纺锤丝

• Centromere: 中心粒; Telomere: 端粒

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The familiar picture of a chromosome is actually that of the most highly condensed state at mitosis(which we reviewed in the blueprint of life [8]: eukaryotic structure of DNA 1(chromatin structure)).

As the daughter chromosomes are pulled apart by the mitotic spindle at cell division, the fragile centimeters-long chromosomal DNA would certainly be sheared by the forces generated, were it not in this highly compact state.

picture above is from Instant Notes in Molecular Biology

As we can see from the picture, the chromosomal loops fan out from a central scaffold or nuclear matrix region consisting of protein(which we talked about last section). One possibility is that consecutive loops may trace a helical path along the length of the chromosome.
The centromere is the constricted region where the two sister chromatids are joined in the metaphase chromosome. This is the site of assembly of the kinetochore, a protein complex which attaches to the microtubules of the mitotic spindle.

(The microtubules act to separate the chromotids at anaphase)

The DNA of the centromere has been shown in yeast to consist merely of a short AT-rich sequence of 88 bp, flanked by two very short conserved regions, although in mammalian cells, centromeres seem to consist of rather longer sequences, and are flanked by a large quantity of repeated DNA, known as satellite DNA.

Telomeres are specialized DNA sequence that form the ends of the linear DNA molecules of the eukaryotic chromosomes. A telomoere consists of up to hundreds of copies of a short repeated sequence(5′-TTAGGG-3′ in humans), which is synthesized by the enzyme telomerase in a mechanism independent of normal DNA replication.

The telomeric DNA forms a special secondary structure, the function of which is to protect the ends of the chromosome proper from degradation.(Independent synthesis of the telomere acts to counteract the gradual shortening of the chromosome resulting from the inability of normal replication to copy the very end of a linear DNA molecule—we will talk about this when reaching DNA replication)

Interphase chromosome

In interphase(S phase, to be exact), the genes on the chromosomes are being transcribed and DNA replication takes place. During this time, the chromosmes adopt a much more diffuse structure and cannot be visualized individually. It is believed, however, that the chromosomal loops are still present, attached to the nuclear matrix.

Genetics [9] Reproduction 2: Meiosis

During the process of reducing the number of chromosomes by half, the combination of alleles are rearranged to give recombinant gametes. Two distinct processes are involved. These are independent assortment of chromosomes and crossing-over.

Meiosis involves twosuccessive divisions, resulting in producing four cells, each containing half the number of chromosomes of the mother cell. There is NO replication between the two divisions.

We call the two divisions meiosis I and meiosis II, as in Chinese 减数第一次分裂 and 减数第二次分裂. Here we will introduce more of meiosis than meets in high school textbooks.

Meiosis I

meiosis I is divided into prophase, metaphase, anaphase and telophase. Although they have the same names as the four phases in typical mitosis, behavior of chromosomes in these four phases in meiosis is very different from that in mitosis.

In prophase each chromosome pairs with its homolog (copy of the same chromosome inherited from the other parent). The paired chromosomes are called bivalents. Each pair is held together by chiasmata(plural of chiasma). The exchange of genetic material is known as crossing-over.

A chiasma (plural: chiasmata), in genetics, is thought to be the point where two homologous non-sisterchromatids exchange genetic material during chromosomal crossover during meiosis (sister chromatids also form chiasmata between each other, but because their genetic material is identical, it does not cause any change in the resulting daughter cells). (from wikipedia)

Prophase of meiosis is subdivided into five stages: leptotene, zygotene, pachytene, diplotene, and diakinesis.
In leptotene(literal translation:thin threads), the chromatin is seen to condense into very long thin strands, that appear tangled in the nucleus. As prophase proceeds chromosomes become shorter and thicker.
At zygotene(literal translation: yoked/linked threads), homologous chromosomes are seen as partially paired structures. They are still very elongated at this stage and chromosome pairs may overlap or interwine.
By patchytene(thick threads), pairing is complete, though it still isn’t possible identify clearly the individual chromatids in each bivalent.
As the homologous chromosomes begin to separate, transition from patchytene to diplotene(double threads) occurs.

This process begins at the centromeres and the bivalents are seen to be held together by chiasma.

The nuclear membrane and the nucleolus breaks down.

The four chromatids in each bivalent become identifiable and individual chiasma clearly to be identified.

Chromosomes carrying on condensing, the cell moves into diakinesis(moving apart), the final subdivision of prophase I.

The scheme below shows the five stages in prophase in a simple way:

At metaphase I the nuclear envelope breaks down, the bivalents lie across the equator of the cell with their centromeres attached to the microtbules←similar to the spindle in mitosis.

The dynamic action of the spindle causes one member of each homologous cell to move to the opposite poles of the cell.

↑WHY wouldn’t the action of the spindle tear apart the sister chromatids?

BECAUSE at metaphase the sister chromatids are held together by proteins called cohesions, which holds chiasmata in place and so holds the chromosomes together.

At anaphase I the cohesions in the chromosome arms are cut, allowing the homologs to separate.

In telophase I, two neclei form around the segregating chromosomes and a degree of chromosome decondensation is observed.

Meiosis II

The process of meiosis II closely resembles that of the typical mitosis.

In prophase II the chromosomes are seen to recondense within the two nuclei. At metaphase II, the nuclear membrane breaks down and chromosoms rearranged at the equator , the centromere splits and…At anaphase II and telophase II,the initial dipliod cell has divided into four…we already knew these in high school.

What we didn’t know in high school is that each of the four haploid cells has a different genotype. And in many instances the group of four haploid cells may remain together and is known as a tetrad.

SUMMARY OF MEIOSIS

Genetics [8]：reproduction 1

Reproduction takes place by one of two methods, asexual or sexual.

Asexual reproduction involves the production of a new individual(s) from cells or tissues of a pre-existing organism. This process is common in plants and in many microorganisms. It can involve simple binary fission(splitting into two) in unicelluar microbes or the production of specialized asexual spores(孢子).

NATURAL VEGETATIVE PROPAGATION. New plants grow from parts of the parent. (image from: leavingbio.net)

These processes may be exploited for commercial purposes as in the vegetative propagation of plants. More recently it has been possible to regenerate whole organisms from a single cell. This was first shown in carrots and frogs, but it has now been reported in mammals, and by implication, is possible in all mammals including humans.

Asexually reproduced organisms are genetically identical to the individual from which they were derived. A group of such genetically identical organisms is known as a clone.

Here I found an article at Buzzle , thinking it may help us learn more about animal cloning: http://www.buzzle.com/articles/animal-cloning/. Below is an excerpt of that article.

1, The Process of Animal Cloning
Initial attempts at artificially induced Animal Cloning were done using developing embryonic cells.

The DNA nucleus was extracted from an embryonic cell and implanted into an unfertilized egg, from which the existing nucleus had already been removed. The process of fertilization was simulated by giving an electric shock or by some chemical treatment method. The cells that developed from this artificially induced union were then implanted into host mothers.

The cloned animal that resulted had a genetic make-up identical to the genetic make-up of the original cell←the embryonic cell that contributes the DNA nucleus.

Since Dolly, of course, it is now possible to create clones from non-embryonic cells.

Now animal cloning can be done both for reproductive and non-reproductive or therapeutic purposes. In the second case, cloning is done to produce stem cells or other such cells that can be used for therapeutic purposes, for example, for healing or recreating damaged organs; the intention is not to duplicate the whole organism.

2. Ethics of Animal Cloning
While most scientists consider the process of animal cloning as a major break through and see many beneficial possibilities in it, many people are uncomfortable with the idea, considering it to be 'against nature' and ethically damning, particularly in the instance of cloning human beings.

The truth is that most of the general public are not aware of the exact details involved in cloning and as a result there are a lot of misconceptions about the entire matter.

In recent times, there have been a spurt of new laws banning or regulating cloning around the world. In some countries, animal cloning is allowed, but not human cloning. Some advocacy groups are seeking to ban therapeutic cloning, even if this could potentially save people from many debilitating illnesses.

3. Points against Animal Cloning
In a large percentage of cases, the cloning process fails in the course of pregnancy or some sort of birth defects occur, for example, as in a recent case, a calf born with two faces. Sometimes the defects manifest themselves later and kill the clone.

4. Points for Animal Cloning
On the favorable side with successful animal cloning - particularly cloning from an adult animal - you know exactly how your clone is going to turn out. This becomes especially useful when the whole intention behind cloning is to save a certain endangered species from becoming totally extinct.←for more info, please see http://www.buzzle.com/articles/cloning-extinct-animals.html

That this is possible was shown by cloning an Indian Gaur in 2001. The cloned Gaur, Noah, died of complications not related to the cloning procedure.

Speaking of saving extinct animals, I couldn’t help but think of Jurassic Park. Although in the movies looks like cloning extinct animals brings threat to humans, or maybe it truly would in reality, the idea of cloning them remains magically attractive to me. Especially, would the biodiversity allow, cloning those who became extinct because of our hunting.

What’s your idea?

Before I lead you off the topic, let’s go back and talk about Sexual reproduction, which differs from asexual reproduction, in that it involves fusion of cells (gametes←we knew in high school as配子), one derived form each parent, to form a zygote. The genetic processes involved in the production of gametes allow for some genetic changes in offspring.

The production of gametes is referred to as gametogenesis. This may be a complex process, involving sexual differentiation and the production of highly differentiated male and female gametes, or in lower eukaryotes identical cells may fuse–isogamy.

isogamy , in biology, a condition in which the sexual cells, or gametes, are of the same form and size and are usually indistinguishable from each other. Many algae and some fungi have isogamous gametes. In most sexual reproduction, as in mammals for example, the ovum is quite larger and of different appearance than the sperm cell. This condition is called anisogamy. (infoplease.com)

Whatever the biology of the process, one fact is obvious: gametogenesis must involve a halving of the chromosome number, otherwise each succeeding generation would have double the chromosome number of its parents.←That’s why, sexual reproduction is limited to species that are diploid or have a period of their life cycle in the diploid state.

Halving of chromosome numbers is achieved in a specialized form of cell division, meiosis(←we learned in high school as减数分裂), which is only observed in gametogenesis.

We will talk about meiosis more detailedly next section.

the blueprint of life [7]: prokaryotic chromosome structure of DNA

First, let’s make sure the anatomy of prokaryotes are familiar to us:

Prokaryotes are the simplest living cells, typically 1~10μm in diameter, and are found in all environmental niches from the guts of the animals to acidic hot springs.

They are bounded by a cell (plasma)membrane comprising a lipid bilayer, in which are embeded proteins that allow the exit and entry of small molecules.
Most prokaryotes also have a rigid cell wall outside the plasma membrane, which prevents the cell from swelling or shrinking in environments where osmolarity differs significantly from that inside the cell.
Sometimes the cell wall is surrounded by an (often) polysaccharide envelope called capsule.
The cell interior (cytoplasm or cytosol) usually contains a single, circular chromosome compacted into a nucleoid and attached to the membrane.
There are no distinct subcelluar organelles in prokaryotes as in eukaryotes(except for the ribosomes核糖体).
The surface of a prokaryote may carry pili, which allow the prokaryote to attach to other cells and surfaces. Some prokaryotes also carry flagella, whose rotating motion allows the cell to swim.

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To talk about prokaryotic chromosome structure, we use E. coli (大肠杆菌)as the example.

E. coli chromosome contains a single supercoiled circular DNA molecule of length 4.6 million bp.
E. coli chromosome is highly folded: 1500 µm of DNA length versus ~1 µm of cell size, forming a structure called the nucleoid.
The nucleoid has a very high DNA concentration, perhaps 30~50 mg/ml, as well as containing all the proteins associated with DNA, such as polyerases, repressors(a protein that is determined by a regulatory gene, binds to a genetic operator, and inhibits the initiation of transcription of messenger RNA), etc.

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DNA domains (loops)

Remember this famous electron micrograph of an E. coli cell we showed before? The cell was carefully lysed, all the proteins removed and then, it was spread on an EM grid to reveal all of its DNA.

Several of such experiments revealed one level of organization of the nucleoid.

The DNA consists of 50~100 domains or loops, about 50~100 kb in size (kb: kilobase, a unit of measure of the length of a nucleic-acid chain that equals one thousand base pairs).
The ends of the loops are constrained by binding to a structure which probably consists of proteins attached to part of the cell membrane.
Not known whether the loops are static or dynamic, but one model suggests that the DNA may spool(wind) through sites of polyerase or other enzymic action at the base of the loops.

E coli DNA instant notes

image above is from”Instant Notes in Molecular Biology”

Supercoiling of the genome

The E. coli chromosome as a whole is negatively supercoiled, although there is some evidence that indicates individual domains may be supercoiled independently. Electron micrographs indicate that some domains may not be supercoiled, perhaps because the DNA has become broken in one strand, where other domains clearly do contain supercoils.

The domains may be topologically independent. There is, however, no real biochemical evidence for major differences in the level of supercoiling in different regions of the chromosome in vivo

DNA-binding proteins

The looped DNA domains of the chromosome are constrained further by inter-action with a number of DNA-binding proteins.

The most abundant of these are protein HU, a small basic (+charged) dimeric protein, which binds DNA non-specifically by the wrapping of the DNA aorund the protein.

And H-NS (formerly known as the protein H1), a monomeric neutral protein, which also binds DNA non-specifically in terms of sequence, but seems to have a preference for regions of DNA which are intrinsically bent.

These proteins are sometimes known as histone-like proteins, and have the effect of compacting the DNA, which is essential for the packaging of the DNA into the nucleoid, and of stabilizing and constraining the supercoiling of the chromosome.

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.

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.

Mendel’s Genetics [4]: examples of mutiple alleles

All the examples used in last classes have employed genes with only two alternative alleles. But the majority of genes exist in several different forms, multiple alleles. This is caused by the mutations of bases at different sites within the same gene, thus affecting different amino acids in the encoded protein.

examples of multiple-allele traits/diseases:

the human β-globin gene where a specific mutation at one site of the gene results in an allele responsible for the hereditary syndrome sickle cell (picture)anaemia, while mutations at several other sited sites in the gene cause a different syndrome, β-thalassemia(beta地中海贫血),
A SICKLE CELL,image from the Internet

Beta-thalassemia, inherited blood disorder caused by reduced or absent synthesis of the beta chains of hemoglobin, resulting in variable phenotypes ranging from severe anemia to clinically asymptomatic individuals.

Although they are alterations of the same gene, the changes are to different codons(a specific sequence of three consecutive nucleotides that is part of the genetic code and that specifies a particular amino acid in a protein or starts or stops protein synthesis). The resulting proteins have variant beta-globins with discrete differences in amino acid sequence and so behave differently.

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In rabbits, multiple alleles of one gene are responsible for a number of different coat color phenotypes.

Here we go, a little confusing but, interesting:

There are four members of the allelic series: agouti, chinchilla, Himalayan and albino. When homozygous, each series produces a distinct coat pattern. When heterozygous, there is a clear pattern of dominance. Agouti is dominant over all the alleles, chinchilla is dominant over Himalayan and albino, while Himalayan is dominant over albino, which fails to produce any pigment and hence is recessive to the others…Hope your mind is still clear!

1, Agouti rabbit: the wild rabbit.

genetics 4 an agouti rabbit — AN AGOUTI RABBIT, image form the Internet

If you blow into the fur of an Agouti rabbit, you will see “bandings” of different colors along the shaft of the hair, being blue, black, tan, fawn. The Agouti also has light tan coloring around the nostrils and at the back of the neck. The belly is cream.(http://rabbit.wikia.com/wiki/Agouti)

2, Chinchilla rabbit: soft, grey fur.

genetics 4 A five-week-old Chinchilla rabbit — A FIVE-WEEK-OLD CHINCHILLA RABBIT, image from the Internet

Chinchilla Rabbits originated in France and were bred to standard by M. J. Dybowski. They were introduced to the United States in 1919. (wikipedia)

3. Himalayan rabbit: white body with colored points, recognized colors are black, blue, chocolate and lilac.

A HIMALAYAN RABBIT, image from the Internet

red eyes; posed stretched out, body to be 3.5 head lengths. They are the ancestors of Californians, one of the most common meat rabbits.(wikipedia: Himalayan_rabbit)

4. Albino rabbit: completely white since it’s missing the melanin which determines the color of their skin, eyes, and fur.

genetics 4 albino rabbits — AN ALBINO RABBIT, image from the Internet

Not all white rabbits are albinos, so you’ll need to check their eyes. If their eyes are red or pink and their hair is totally white, they would be considered an albino. They are not rare.

An albino rabbit may not have the greatest eyesight due to their lack of eye pigment. Since their eyesight is not the best, they should be caged or kept inside since they may not be able to see predators.(http://www.ask.com/question/albino-rabbits)

Having seen so much about rabbits, hope you haven’t forgotten what we were doing before those cute bunnies. We were learning about examples of multiple alleles of one gene.

the human ABO blood group system.

(all form wikipedia: ABO blood group system:)

The ABO blood type is controlled by a single gene (the ABO gene) with three types of alleles inferred from classical genetics: i, I^A, and I^B. The gene encodes a glycosyltransferase— an enzyme that modifies the carbohydrate content of the red blood cell antigens.

The I^A allele gives type A, I^B gives type B, and i gives type O.

Both I^A and I^B are dominant over i, so only ii people have type O blood. Individuals with I^AI^A or I^Ai have type A blood, and individuals with I^BI^B or I^Bi have type B.

I^AI^B people have both phenotypes, because A and B express a special dominance relationship: codominance(we talked about it last class), which means that type A and B parents can have an AB child.

A type A and a type B couple can also have a type O child if they are both heterozygous (I^Bi,I^Ai)

Hope your mind is still clear!

NOTE: the concept of multiple alleles of one gene is totally different from multiple-gene inheritance.

A polygene, multiple factor, multiple gene inheritance, or quantitative gene is a group of, non-allelic, genes that together influence a phenotypic trait.