2. Secondary structure of DNA—stabilized partial structure formed by polymers of nucleotide
Professor Dong: First, please familiarize yourselves with Chargaff’s Rule:
A+G=T+C & G+T=A+C
↓↓
A=T & G=C
(Chargaff’s Rule)
(Based on analysis of the chemical composition of duplex DNA in the early 1950s, E. Chargaff deduced these rules about the amounts of different nucleotides in DNA.)
Professor: The secondary structure of DNA is a partial structure formed by polymers of nucleotide. The structure is referred to as the double-helix structure.
Two separate chains of DNA are wound around each other, each following a helical (coiling) path, resulting in a right-handed double helix structure.
In 1953, Watson and Click proposed the DNA double-helix structure based on Chargaff’s Rule and DNA Crystallography and X-ray diffraction images of DNA structure by Wilkins and Franklin. (Rosalind Franklin, who was not that well-known as Watson, Click and Wilkins but apparently played a equally significant role in the discovery of the structure.The whole was later nominated Nobel Prize but her, is that even fair?)
—————————————————————————
The backbone of duplex DNA is a serious of phosphodiester group (the covalent linkage of a phosphate group between the 5′-hydroxyl of one sugar and the 3′-hydroxyl of the next, that is , repeats of P-sugar unit) linked by phosphodiester bond.
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The strands are joined noncovalently by hydrogen bonding between the bases on opposite strands, to form base pairs.
There are around 10 base pairs per turn in the DNA double-helix. The two strands are oriented in opposite directions in terms of their 5’to3′ direction(the nucleotides in one strand is opposite to their direction in the other strand).
More crucially, the two strands are complementary in terms of sequence. The bases hydrogen-bond to each other as purine-pyrimidine pairs which have very similar geometry and dimensions.
A–T: 2 H-bonds ; C–G: 3 H-bonds
5’- A T G T C -3’
¦¦ ¦¦ ¦¦¦ ¦¦ ¦¦¦
3’- T A C A G -5’
Thus, the sequence of one strand uniquely specifies the sequence of the other, with all that which implies for the mechanism of replication of DNA and its transcription to RNA.
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Professor Dong added:
Between the backbone stands run the major and minor grooves.
In a detailed analysis of DNA structure, there are two types of grooves that can be seen; the major groove has the nitrogen and oxygen atoms of the base pairs pointing inward toward the helical axis, while in the minor groove,the nitrogen and oxygen atoms point outwards;
Shown by prof.Dong, MAJOR GROOVE A-TShown by prof.Dong, MAJOR GROOVE G-C
Major Groove Minor Groove
Depth: 8.5 Å Depth: 7.5 Å
Width: 11.7 Å Width: 5.7 Å
Å
Definition: Symbol for Ångström, a unit equal to 0.1 nanometer, mainly used in expressing sizes of atoms, lengths of chemical bonds, and wavelengths of electromagnetic radiation.
Professor: The major groove is more dependent on base composition. and major grooves and minor grooves are also recognition and binding sites for certain protein factors, and are involved in the regulation of gene expression.
——————————————————————————
slide shown by Prof.Dong
Professor: Summary of “Double Helix” Model (B-DNA):
DNA is important because it is the genetic material ←contain all the info for the synthesis and functioning of a living form duplicate and passes through to the next generation.
Hearing this Annie questioned herself: DNA is not the genetic for ALL viruses. RNA “blueprints” for the rest of the viruses. Virus, though not even having a cell structure, is a form of life. So why not be fair, and say the blueprint of life are DNA and RNA?
Professor Dong continued,
Proofs:
Bacterial Transformation Experiment
—Griffith, 1928
Professor: So what is the transforming principle?
Annie: It could be a cool type of enzyme that moved the toxic part of S strain onto R strain…
Professor: Well, Enzyme did help a lot in the experiment we’ll talk about later, but it is not the hero of the story.
Annie: So what’s the story?
Professor:
—Avery et al., 1944
slide shown by Prof. Dong ,AVERY REPEATED GRIFFITH’S EXPERIMENT WITH MODIFICATION
Only DNA is responsible for the transformation.
Annie thought: Well, there still existed possibilities that DNA and some other things that were not sugar, lipid or protein cooperated to complete the transformation… The “other things” also contributed to the transformation but could not complete it without DNA? In this case DNA is not the only one that is responsible,
T2 Bacteriophage Infection (Blender Experiment)
—Hershey &Chase, 1952
Experiment 1
Experiment 2
Radioactive labeling of proteins and DNA
The professor continued. So now let’s go deeper and see the chemical composition of DNA.
A 5-carbon sugar , hand in hand with base group and phosphorous group, thought Annie.
It’s not that simple as you learned in high school, said the professor. We need to know the chemical composition of the base group, deoxyribon and phosphorous group as well.
slide shown by Prof. Dong,SUGAR GROUP
Professor:
slide shown by Prof. Dong,BASE GROUPS
Annie thought: Pyrimid-ine, Could it have anything to do with the Pyramid in Egypt?
The professor was explaining the structure and Annie didn’t interrupt him with her question.
Any character (trait) which can be shown to be inherited, such as eye color, leaf shape or an inherited disease, such a cystic fibrosis, is referred to as a phenotype.
Description: A fly may be described as having a red-eyed phenotype. A child may be described as displaying the cystic fibrosis phenotype.
Genotype
The pattern of genes that are responsible for a particular phenotype in a individual is referred to as genotype.
Dominance
In hybrids between two individuals displaying different phenotypes, only one phenotype may be observed. This phenotype is referred to as the dominant trait and the un-shown one the recessive.
For instance, if the wife has wide eyes while the husband has small eyes, and their little girl has wide eyes, then the wide eyes are dominant to small eyes.
Pure-breeding lines
Organisms which have been inbred for many generations in which a certain phenotype remain the same.Pedigree breeds of dogs or cats are commonplace examples of pure-breeding lines.
A puppy from two purebred dogs of the same breed, for example, will exhibit the traits of its parents, and not the traits of all breeds in the subject breed’s ancestry.
Homozygous: Individuals with two identical copies of a gene.
“True breeding (pure-breedind) organisms are always homozygous for the traits that are to be held constant.”
Heterozygous: Individuals with two different copies of the gene.
Mendel made a cross between two pure-breeding lines of pea plants, one of which had violet petals and the other white petals. The hybrids produced in this cross were referred to as the F1 (first filial) generation.
In Mendel’s experiment, the ratio of violet pedals and white ones in the second filial were very close to 3 to 1, which applied to the theoretic reasoning shown above.
He did many other experiments focusing on different types of genotypes of the pea plants and the results were shockingly similar. The hidden phenotype in the first filial reappeared in the second filial and the ratio of the dominant to the recessive phenotype were all close to 3 to 1.
The 3:1 ratio is referred to as the monohybrid ratio and is the basis for all patterns of inheritance in higher organisms.
One simple extension of the 3:1 phenotype ratio is a 1:1 ratio, produced when a heterozygous F1 individual is crossed to the homozygous-recessive parent. The process is known as testcross.
Testcross is useful in any condition when it is necessary to determine whether an individual is heterozygous or homozygous. Conceivable that if F2 all have dominant phenotype, then the tested parent is homozygous-dominant; if F2 have a 1:1 ratio of dominant and recessive phenotype, then the tested parent is heterozygous.
Here I found a great page story-telling Mendel’s Genetics.Can’t be more suitable as a revision of what we learned about genetics and inheritance in high school. >>Mendel’s Genetics
I believe by reading the link page you have remembered the principles of Mendel’s Genetics. We’ll summarize these principles again in next posts.
While Mendel’s research was with plants, the basic underlying principles of heredity that he discovered also apply to people and other animals because the mechanisms of heredity are essentially the same for all complex life forms.”
It must be a cliche to summarize the success factors of Mendel’s experiments, but it has to be done, for many of the factors are still important for today’s experimentalists.
Firstly, before the experiment,Mendel spent a long time observing different traits of the peas and decided which traits he was going to focus on in the after experiments. He was prepared, had anticipation and, perhaps already held some hypothesis of what was going to happen.
Then it was the choice of his “lab-rats”. As the link page says,”Mendel picked common garden pea plants for the focus of his research because they can be grown easily in large numbers and their reproduction can be manipulated. ” Based on a large number of offspring, the resulting statistics can be assumed as very close to theoretic statistics. In this case, it’s way more convenient to study the traits of these peas than those of some fragile and rare pole plants.
More important, “pea plants have both male and female reproductive organs. As a result, they can either self-pollinate themselves or cross-pollinate with another plant. In his experiments, Mendel was able to selectively cross-pollinate purebred plants with particular traits and observe the outcome over many generations. This was the basis for his conclusions about the nature of genetic inheritance.”
Reproductive
structures of
flowers
the picture is from http://anthro.palomar.edu
Last but not least, Mendel was a pioneer in applying Math(Statistics) to experiment analysis. He rounded the ratio of numbers of different traits to a whole number and discovered the astonishing similarity of all the results.
In high school that’s all the factors, but actually there’s more. For one, Mendel succeeded because all the genes that controlled traits he picked to observe happened to be on different chromosomes. Otherwise, the phenomena of “linkage” would have appeared (which we’ll talk about later)and he should never have had such a groundbreaking discovery.
![the blueprint of life [2]: primary and secondary structure of DNA](https://apbiology.cn/wp-content/uploads/sites/8/2013/07/dna2.jpg)
![the blueprint of life[1]](https://apbiology.cn/wp-content/uploads/sites/8/2013/06/Science-Human-Gene.jpg)
![Mendel’s Genetics[2]: The monohybrid cross](https://apbiology.cn/wp-content/uploads/sites/8/2013/07/genetics2.png)
