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DNA structure

Page history last edited by Charles Forstbauer 14 years, 2 months ago

Closed 1/14/10

Totaled 1/10/10 Mr F

Totaled 1/5 /10 Mr F

Totaled 12/22 Mr F 

Totaled 12/10 Mr F

Who Discovered DNA and its proporties?

         Griffith: 1928

  • Mouse experiment
  • He injected rough strain into mouse which had no effect
  • He injected the smooth strain which killed the mouse
  • He heat killed the smooth strain and then injected it into the mouse with no negetive result
  • Then he mixed the rough strain (which did not kill the mouse), and the heat killed smooth strain (which did not kill the mouse) together and injected it into the mouse. This mixture killed the mouse. This mixture killed the mouse becuase bacteria can assimilate external genetic material and transform the genetics from the heat killed strain to the rough strain which made the mixture dangerous for the mouse.

 

          Avery: 1943

  • Avery proved that neucleic acid transforms not protiens
  • Proved that DNA is a material in which genes and protiens are made

 

          Chargaff: 1950

  • Found DNA is composed of four different bases -- ratio of purines (2x rings) to pyriroids) to pyrimidines (1x ring) = 1
  • The ratio of A to T is around 1, and the ratio of C to G is about 1
  • Ratios of A to T, and of G to C is different for differnet species of animals

 

 

- Chargaff in short

     - ratio of nucleotuide bases 1:1 (A=T; C=G)

Nucleotides: nitrogenous base (thymine, adenine, cytosine, guanine) sugar deoxyribose; phosphate group

 

This is a diagram of a nucleotide and i found it nice and simple to understand.

 

 

-Watson and Crick

     - strands are complimentary; nucleotides line up on template accordinfg to base pair rules

 

 

  

 

          This is a really good image of DNA  structure.  It shows the A and T   along with the   C and G.  This shows how there is an equal amount of the pairs because they are in pairs and not single.  That is why there is an equal amount of C and G    and    A and T. 

 

This Video below is a really good quick summary of the DNA structure. It brakes down the parts of the DNA and explains them and then puts them together. I found this gradual build-up process helpful.

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Here is another great video about the structure of DNA. It is also incredibly informative and presented in a simple way so it is easy to understand. I found it very helpful.

 

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This video has basic review on the purpose and history of dna

 

The Loretto Chapel:

The story goes that in 1873, a chapel was being constructed in Santa Fe, New Mexico. The chapel was designed by french architect Antoine Mouly, in the gothic revival style. However the architect proved unable to finish the project, as he died suddenly, leaving the upstairs choir loft inaccessible to the public and churchgoers. The church understandably needed a way to get up there, and the rest of the story is disputed. Religious people from the area claim that a man came on a donkey and offered his help for free, so long as no one watched him while he was working. The result however, is definite. He constructed a Double Helix Spiral Staircase, without a single nail, screw, or drop of glue.

 http://upload.wikimedia.org/wikipedia/commons/a/a4/Loretto_Chapel_Miraculous_staircase.jpg

Whether or not you believe the religious aspect of the story or not, it was still a feat in carpentry and a first glimpse at the inner workings of DNA, decades before its time.

 

 

 

There are two types of bases found in DNA: Purines and Pyrimidines.

Purines consist of: Adenine and Guanine, shown below.

Pyrimidines consist of: Cytosine and Thymine, shown below.

 

The double ring always attaches to a single ring and are held together by hydrogen bonds

A-T = 2 hydrogen bonds

C-G = 3 hydrogen bonds 

  

Illustration of the double helical structure of the DNA molecule.

The structure of DNA is illustrated by a right handed double helix, with about 10 nucleotide pairs per helical turn. Each spiral strand, composed of a sugar phosphate backbone and attached bases, is connected to a complementary strand by hydrogen bonding (non- covalent) between paired bases, adenine (A) with thymine (T) and guanine (G) with cytosine (C).

Adenine and thymine are connected by two hydrogen bonds (non-covalent) while guanine and cytosine are connected by three.

This structure was first described by James Watson and Francis Crick in 1953

 

DNA Double Helix

DNA is a normally double stranded macromolecule. Two polynucleotide chains, held together by weak thermodynamic forces, form a DNA molecule.

Structure of DNA Double Helix

Features of the DNA Double Helix

  • Two DNA strands form a helical spiral, winding around a helix axis in a right-handed spiral
  • The two polynucleotide chains run in opposite directions
  • The sugar-phosphate backbones of the two DNA strands wind around the helix axis like the railing of a sprial staircase
  • The bases of the individual nucleotides are on the inside of the helix, stacked on top of each other like the steps of a spiral staircase.

Base Pairs

In molecular biology, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). In the canonical Watson-Crick base pairing, adenine (A) forms a base pair with thymine (T), as does guanine (G) with cytosine (C) in DNA. In RNA, thymine is replaced by uracil (U). Non-Watson-Crick base pairing with alternate hydrogen bonding patterns also occur, especially in RNA; common such patterns are Hoogsteen base pairs. Pairing is also the mechanism by which codons on messenger RNA molecules are recognized by anticodons on transfer RNA during protein translation. Some DNA- or RNA-binding enzymes can recognize specific base pairing patterns that identify particular regulatory regions of genes. The size of an individual gene or an organism's entire genome is often measured in base pairs because DNA is usually double-stranded. Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands (with the exception of non-coding single-stranded regions of telomeres). The haploid human genome (23 chromosomes) is estimated to be about 3 billion base pairs long and to contain 20,000–25,000 distinct genes.

 

Within the DNA double helix, A forms 2 hydrogen bonds with T on the opposite strand, and G forms 3 hyrdorgen bonds with C on the opposite strand.  

 

 

This video is a little boring but it helps a lot with the understanding of the DNA structure!!

 

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Important Facts about the DNA- The Double Helix

 

- Full Name for DNA= Deoxyribonubleic Acid

- Gene= A segment of DNA that codes for specific trait

- Chromosomes are located in the nucleus

- DNA is found in the mitochondria and the chloroplasts

- The sugar deoxyribose is found in DNA

- The sugar ribose is found in RNA

- DNA is made up of repeating unites called nucleotides

- Even though all the DNA in your cells is the same, cells have different functions because the cell can turn off genes

- DNA tells how to build the organism

 

DNA Backbone

  • The deoxribose sugar of DNA backbone has 5 carbons and 3 oxygens
  • The carbons are numbered 1,2,3,4,5
  • The hydroxyl groups on the 5 and 3 carbons link to the phosphate groups from the backbone
  • The backbone is a polymer with an alternating sugar phosphate sequence

 

This site is an interactive activity where you can interact by zipping and unzipping DNA

 

This is incorrectly placed. It should be in DNA replication  Mr F 12/10 

So while one side goes from 5' to 3', the other complementary strand will only go the other way.  So short strands of 5' to 3' will be added at a time, going the opposite direction.  These are called Okazaki fragments. However, there are still gaps in between each short strand, and as said earlier, Ligase is an enzyme that is used to connect phosphate with sugar, and will be used to fill in the gap between the strands or any other gaps in the strands. This diagram shows the part Ligase takes in the bonding and replication (in the bigger scheme of things) of DNA. 

The above image also shows the role of energy in the bonding. The energy for the bonding usually comes from the phosphates themselves, and it carries its own energy in the form of ATP's bonds will break, resulting in the release of energy, and will become either ADP or AMP(Adenacine Monophosphate) depending on how many phosphates it gives up. Also, it will leave behind a nucleotide, with a sugar, a phosphate, and a base at the end. ATP is based on nucleic acid-this is very important to know. Every base has one of these, so for Thymine, it will be TTP, TDP, and TMP. For Cytosine, it will be CTP, CDP, and CMP, and finally for Guanine, we'll have GTP, GDP, and GMP.  DNA bases have their own energy source, and the bonding is completed with DNA polymerase III.

 

 

Nucleotides: vs. Nucleosides:

Nucleotides contain one or more phosphates, while Nucleosides do not contain any phosphates.

A nucleotide consists of:

  • A BASE (adenine, cytosine, guanine, thymine)
  • A SUGAR (that is part of the backbone of dna)
  • A PHOSPHORUS (that is part of the backbone of dna)

    A,C,G,T can all loose their phosphoruses. When 2 of these 3 are lost, the A/C/G/ or T is joined onto the new DNA daughter strand (in replication), with the energy it has gained from shedding 2 phosphoruses. It then becomes a nucleotide.

A nucleoside consists of:

     A nucleobase that is bound to a ribose through beta-glycosidic linkage. They can also be used produce nucleotides. You are able to create more of an abundancy of nucleosides by digesting more nucleic acids in your diet. Examples of these nucleosides are cytidine, uridine, adenosine, gaunosine, thymidine, and inosine 

 

 

This is a picture of the structure of DNA when it is being replicated. You can clearly see how the new strand is being wound around the old strand while the parent strand of DNA is still in place. The ends of each strand are labled so you can tell which direction they are growing in and which side would be fragmented.

 

 

The diagram above shows the 4 nitrogen bases that together make up DNA. Adenine and Thymine are a pair as Guanine and Cytosine are also a pair. when ever there is of these bases on the chain, you will find the corresponding pair connected to it. also the "backbone" of the DNA helix is made up of Phosphate chains connected together.

DNA is composed of four nitrogenous bases:

                            Adenine (A), Guanine (G), Thymine (T), Cytosine (C).

            This Diagram shows how each nitrogen base only links together with its corresponding base. So adenin and thymine will only go together while guanine and cystosine will only link together.

                     The purines, A and G, pair up with pyrimidines, T and C,

                            of another strand by hydrogen bonding.  This A-T and

           

 

 

After they built the first model of DNA in together, Watson and Crick went their seperate ways. One had a research laboratory in California, and the other had one in Long Island. Watson created the "sequential hypothesis," in which DNA codes RNA which codes protein. Not to be outdone, Crick named the same thing "central dogma," but his terminology was incorrect because it suggested that it happened absolutely all the time. Instead of T, A's base pair in RNA is Uracil (U). 

 

DNA is found just in the nucleous, while RNA is found in both the nucleous and the cytoplasm. Transcription is the process by which DNA is copied from DNA to RNA to proteins. It creates Messenger RNA, known as mRNA. It has four stages: Initiation, Elongation, Termination, and RNA processing.

 

Initiation is the first stage of the process of transcription. Initiation occurs at the promoter region, (the TATA box). DNA is opened by heliocase in order to form a repliacation eye. The DNA proceeds to attatch itself the the RNA polymerase.

 

The second stage of transformation is called elongation. In this stage, ATP activates RNA polymerase, and RNA nucleotides are added. U is used instead of T. DNA reads 3 to 5, while RNA builds 5 to 3. The RNA seperates from the DNA template. The DNA reforms behind the RNA polymerase.  

 

The third stage is termination. In this stage, termination is stopped, as well as transcription. All factors and enzymes are released at this point. The RNA is release as messenger RNA (mRNA). The transcription unit is the DNA strand from the promoter region to termination. 

 

The final stage is called RNA processing. The 5' end is capped for protection from enzymes. The 3' end has a poly A tail added of 100-200 Adenines for further protection and recognition. The introns, which are non coding pieces that are cut out, or possibly old codes, are removed.

 

DNA vs RNA

 

DNA:

-2 strand double helix

-deoxyribose sugar

-stable

-long stands

-A + T

- C + G

 

RNA:

 

-single strand

-ribose sugar

-less stable

-generally shorter chains

- A + U

- C + G

 

Above is an illustration of how the DN

A is structured. The deoxyribose sugar and phosphase groups of the nucleotides bond togeth

 

http://www.sumanasinc.com/webcontent/animations/content/DNA_structure.html 

^Copy and paste this website into your URL.

This site is very simplistic and is easily understood.  

linear fashion, with the nitrogen bases sticking out. Two chains of nucleotides are then linked together by

 

Specific Info About DNA 

 

Deoxyribonucleic acid (DNA) is a nucleic that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints or a recipe, or a code, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.

 

DNA is a long polymer made from repeating units called nucleotides The DNA chain is 22 to 26 Angstroms wide (2.2 to 2.6 nanometers), and one nucleotide unit is 3.3 Å (0.33 nm) long. Although each individual repeating unit is very small, DNA polymers can be very large molecules containing millions of nucleotides. For instance, the largest human chromosome, chromosome number 1, is approximately 220 million base pairs long.

 

Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.

 

Within cells, DNA is organized into long structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication.Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.

 

In living organisms, DNA does not usually exist as a single molecule, but instead as a pair of molecules that are held tightly together. These two long strands entwine like vines, in the shape of a double helix. The nucleotide repeats contain both the segment of the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand in the helix. A base linked to a sugar is called a nucleoside and a base linked to a sugar and one or more phosphate groups is called a nucleotide. If multiple nucleotides are linked together, as in DNA, this polymer is called a polynucleotide.

 

The backbone of the DNA strand is made from alternating phosphate and sugar residues. The sugar in DNA is 2-deoxyribose, which is a pentose (five-carbon) sugar. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. These asymmetric bonds mean a strand of DNA has a direction. In a double helix the direction of the nucleotides in one strand is opposite to their direction in the other strand: the strands are antiparallel. The asymmetric ends of DNA strands are called the 5' (five prime) and 3' (three prime) ends, with the 5' end having a terminal phosphate group and the 3' end a terminal hydroxyl group. One major difference between DNA and RNA is the sugar, with the 2-deoxyribose in DNA being replaced by the alternative pentose sugar ribose in RNA.

 

The DNA double helix is stabilized by hydrogen bonds between the bases attached to the two strands. The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T). These four bases are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate.

These bases are classified into two types; adenine and guanine are fused five- and six-membered heterocyclic compounds called purines, while cytosine and thymine are six-membered rings called pyrimidines. A fifth pyrimidine base, called uracil (U), usually takes the place of thymine in RNA and differs from thymine by lacking a methyl group on its ring. Uracil is not usually found in DNA, occurring only as a breakdown product of cytosine. In addition to RNA and DNA, a large number of artificial nucleic acid analogues have also been created to study the proprieties of nucleic acids, or for use in biotechnology.

 

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This video is kind of long, but really informative.  It gives a great explanation of how chromosomes are formed.  It also touches on what histones are, which I was unclear of before watching this.  Aside from this, this video really explains the whole structure in depth.

 

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I found this video to be helpful because the speaker talks slow and relates what they are saying to a picture.  The video has good visuals.

Comments (1)

Charles Forstbauer said

at 2:03 pm on Dec 7, 2009

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