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  • This is DNA.

  • This is the molecule we use to store our genetic information.

  • DNA contains the instructions needed for an organism to develop, survive and reproduce.

  • If you want to understand how DNA works, the first step is to learn about its structure.

  • The structure of a molecule determines its function, so making sense of the structure

  • is essential for you to understand HOW DNA can do its job.

  • In April of 1953, James Watson and Francis Crick changed the world of biology forever

  • with a landmark paper published in the journal Nature.

  • It was just one page long.

  • They reported they had determined the structure of DNA was an antiparallel double-helix.

  • How did Watson & Crick figure this out?

  • They didn’t do experiments.

  • Instead, they built models out of tin and wire that matched measurements derived from

  • other scientists, including biochemical data from Erwin Chargaff, and X-Ray diffraction

  • data obtained by Maurice Wilkins, Rosalind Franklin and Raymond Gosling, under the direction

  • of John Randall.

  • You may have tried making your own DNA molecule using a chemistry molecular modeling kit.

  • Today were building models of DNA using a 3D printing pen.

  • MorphPen was kind enough to send a 3D printing pen to Socratica for us to test out, so of

  • course we are making DNA with it.

  • Obviously.

  • You can make whatever you want with YOUR 3D pen.

  • Single-stranded DNA is a polymer of nucleotides, made up of repeating units of sugar, phosphate,

  • and nitrogenous base.

  • In double-stranded DNA, two polynucleotides are attached at their complementary bases,

  • zipping the two strands together with hydrogen bonds.

  • Keep in mind, most DNA molecules are very, VERY long - thousands or even millions of

  • base-pairs long.

  • Were going to just make a very short stretch of double-stranded DNA as an illustration.

  • DNA looks like a twisted ladder.

  • The sides of the ladder are made of sugars and phosphate groups.

  • These repeat over and over.

  • Sugar - phosphate. Sugar - phosphate.

  • This is the backbone of DNA.

  • Let’s first make a backbone, using our 3D pen.

  • Were actually going to need two of these, one for each side of the ladder.

  • Now, let’s look at the rungs of the ladder, which is really the business end of DNA.

  • Theserungsof the DNA ladder are made of 4 different kinds of nitrogenous bases:

  • Guanine, Adenine, Thymine, and Cytosine.

  • Abbreviated GATC.

  • The order of these bases is how information is stored in DNA.

  • Think of it like the order of letters in a word, and the order of words in a sentence.

  • Guanine always pairs with Cytosine

  • Adenine always pairs with Thymine.

  • These are known as Chargaff’s Rules, in honour of Erwin Chargaff who determined this

  • biochemically.

  • Notice that there are 3 hydrogen bonds holding G and C together, while there are 2 hydrogen

  • bonds holding A and T together.

  • Let’s take a closer look at these components.

  • The 5 carbon sugar in DNA is deoxyribose.

  • Deoxy, meaning it’s missing an oxygen compared to regular ribose.

  • The phosphate group looks like this.

  • This is where it attaches to deoxyribose.

  • These phosphate groups are acidic.

  • Think of them like little acidic flags hanging off the structure.

  • This is what gives DNA its acidic nature when in solution in water.

  • Now about thosenitrogenous bases.”

  • They are called that because they are literally basic, as opposed to acidic, and they all

  • contain nitrogen.

  • Two of them, Adenine and Guanine look like this, with two fused rings.

  • These bases are called purines.

  • The other two, Cytosine and Thymine, look like this, with only one ring.

  • These bases are called pyrimidines.

  • Since Adenine always pairs with Thymine, and Guanine always pairs with Cytosine, you can

  • also say that a purine always pairs with a pyrimidine.

  • One unit, or monomer of the DNA polymer is called a nucleotide.

  • This is one sugar, one phosphate, and one nitrogenous base.

  • In the case of DNA, they are also calleddeoxyribonucleotides,” as opposed to in RNA where they are called

  • ribonucleotides,” because they contain ribose instead of deoxyribose.

  • Nucleotides are joined together by covalent bonds.

  • The phosphate group of one nucleotide is linked to the hydroxyl group on the sugar of the

  • next nucleotide.

  • These are known as phosphodiester linkages.

  • Here’s a technical note.

  • Biochemists have a particular way of labeling the atoms in DNA, so they know what part of

  • the structure they are referring to.

  • This is an important shorthand, so you can just say something is happening at C5, for

  • example, rather than having to point it out on a diagram.

  • They start with labeling the skeleton - the atoms in the ring area - of the nitrogenous

  • base.

  • You can see here, these atoms labeled 1-6, or over here, labeled 1-9.

  • Then, to label the skeleton of the sugar, they don’t want to use the same numbers

  • that they used for the base, because that would be confusing, so they label them

  • 1’, 2’, 3’, 4’ and 5’.

  • The 5’ Carbon is this one that sticks up from the ring.

  • This is where the notation 5’ to 3’ comes from.

  • You may have heard that phraseDNA runs in the 5’ to 3’ direction.”

  • That’s talking about one of the two strands.

  • You can see the sides of the ladder run in opposite directions - remember, it’s an

  • ANTIPARALLEL double helix.

  • On one end of a DNA strand, there’s a Phosphate group attached to the 5’ carbon, and the

  • other end of that strand has an -OH group on the 3’ carbon.

  • We say this side runs in the 5’ to 3’ direction, because of the labeling of the

  • atoms.

  • The other side of the ladder runs in the 3’ to 5’ direction.

  • This is going to be important to remember later when we study how information is stored

  • in DNA.

  • One side is the coding strand, or sense strand, the 5’ to 3’ side.

  • The other side is called the anticoding strand, or antisense strand.

  • Because of complementary pairing, if we know the sequence of one strand, we know the sequence

  • of the other strand.

  • It’s kind of like a photograph and the photographic negative.

  • Watson and Crick, rather cheekily, said at the end of their paper that the structure

  • of DNA suggested a mechanism of replication, and they were right.

  • But well talk about DNA replication another day.

  • That’s a very long, complicated, and serious story.

  • Back to the DNA structure.

  • Remember we said Watson & Crick were guided by X-ray Diffraction data.

  • That’s how they knew the spacing of the components of DNA.

  • Their physical model had to match the values derived from the X-ray photographs from Gosling,

  • Franklin, and Wilkins.

  • This is what they determined:

  • The radius of DNA is 1 nm.

  • This is what you get if G pairs with C and A pairs with T. So this also satisfied Chargaff’s Rules.

  • If you don’t pair G with C and A with T, you get a strand that is either too fat or

  • too skinny to match the X-ray diffraction data.

  • The two polynucleotide strands wrap around a central axis to form a right-handed helix.

  • The helix makes 1 full turn every 3.4 nm.

  • And there is a 0.34 nm distance between nitrogenous bases.

  • This means there are 10 layers of base pairs or rungs, per turn of the helix.

  • Notice that there are two different kinds of grooves made as a result of the twisting

  • of the helix.

  • In one groove, the backbones are far apart, and that’s known as the major groove.

  • Then we see here, where the backbones are close together, and that’s called the minor groove.

  • This plays a significant functional role because there are specific DNA binding proteins that

  • will only bind at certain locations - and some of them bind to the minor groove, and

  • others bind only at the major groove.

  • Now that you know all about the structure of DNA, youll be prepared to learn about

  • its function.

  • I have to tell you, this is a huge subject.

  • Really, there’s an entire field of biology devoted to the function of DNA and other biological

  • molecules, called molecular biology.

  • I personally am a molecular biologist, so I plan on guiding you through that study.

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  • Thanks for watching.

This is DNA.

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B2 dna phosphate strand helix structure ladder

What is DNA Structure? How to Make a Double Helix with a 3D Pen | Biology | Biochemistry

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    林宜悉 posted on 2020/03/06
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