Gene and DNA structure. Dr Saeb Aliwaini

Transcription

1 Gene and DNA structure Dr Saeb Aliwaini 2016

2 DNA during cell cycle

3 Cell cycle for different cell types

4 Molecular Biology - "Study of the synthesis, structure, and function of macromolecules (DNA, RNA, and protein) and their roles in cells and organisms"

5 Gene Gene is a segment of DNA containing the information for a single polypeptide or RNA molecule, including transcribed but non-coding regions. Alleles are Alternate forms of the same gene Genome: the whole of the genetic information of an organism.

6 Primary structure Nucleic acids are long chains or polymer of repeating subunits, called nucleotides. Nucleotide is composed of three parts: - a five-carbon sugar, - a phosphate group, - And a base.

7 Primes are used in the numbering of the ring positions in the sugars to differentiate them from the ring positions of the bases. Hydrogen and carbon atoms are usually omitted for clarity.

8 Sugars: - RNA contains a pentose (five-carbon) sugar called ribose. - DNA contain the sugar deoxyribose. - Both sugars have an oxygen as a member of the five-member ring. - The 5 -carbon is outside the ring. - Sugars differ only in the presence or absence ( deoxy ) of an oxygen in the 2 position.(2 -hydroxyl group)

9 Nitrogenous bases Nitrogen-containing molecules having the chemical properties of a base (a substance that accepts an H + ion or proton in solution). - Purines which have a double carbon nitrogen ring structure; these are called adenine (A) and guanine (G) - Pyrimidine which have a single ring structure; thymine (T), cytosine (C), and uracil (U) - (T) is found in DNA only, while (U) is specific for RNA

10 Chargaff s rules: - [A]=[T] conc - [G]=[C] conc - And purine bases equals that of the pyrimidine bases ([A]+[G]=[T]+[C]) - percent G+C, differs among species but is constant in all cells of an organism within a species. The G+C content can vary from 22 to 73%, depending on the organism.

11 The phosphate functional group (PO 4 ) gives DNA and RNA the property of an acid (a substance that releases an H + ion or proton in solution) nucleic acid. esters linking give stabilization after the phosphodiester bond is formed, one oxygen atom of the phosphate group is still negatively ionized The negatively charged phosphates are extremely insoluble in lipids. How does this help?

12

13 Nucleosides and nucleotides Each base is chemically linked to one molecule of sugar at the 1 -carbon of the sugar.(nucleoside) a phosphate group is also attached to the 5 -carbon of the same sugar. (a nucleotide) Nucleotides are joined (polymerized) by condensation reactions to form a chain.

14 The hydroxyl group on the 3 -carbon of a sugar of one nucleotide forms an ester bond to the phosphate of another nucleotide, eliminating a molecule of water. Linked by 3 to 5 phosphodiester bonds between adjacent nucleotides

15 Phospho-' refers to the element phosphorus, '-di-' means two, and '-ester' refers to a specific type of chemical bond that includes a single atom bound to two oxygen atoms So, a phosphodiester bond is a phosphorus atom involved in two ester bonds Phosphate is a very simple molecule made up of a phosphorus atom bonded to four oxygen atoms

16 Significance of 5 and 3 This 5 3 directionality of a nucleic acid strand is an extremely important property of the molecule. By convention, a DNA sequence is written with the 5 end to the left, and the 3 end to the right.

17 The number of base pairs (bp) is used as a measure of length of a doublestranded DNA. kilobase pair (kb or kbp) OR (Mb or Mbp) (usually less than 50 bases) called oligonucleotides. Single or Double strand! This lecture will focus on DNA. Various chemical forces drive the formation of the DNA double helix. These include hydrogen bonds between the bases and base stacking by hydrophobic interactions.

18 Hydrogen bonds Between the nitrogenous bases on opposite strands of the interwound DNA chains.

19

20 Hydrogen bonds are very weak bonds that involve the sharing of a hydrogen between two electronegative atoms, such as oxygen and nitrogen. The hydrogen bonding between bases is referred to as Watson Crick or complementary base pairing. adenine (A) normally pairs with thymine (T) by two hydrogen bonds, and guanine (G) pairs with cytosine (C) by three hydrogen bonds.

21 G-T is possible, but if G-C to G-T There are proofreading mechanisms and DNA repair mechanisms that recognize non Watson Crick base pairs and correct the majority of mistakes G-U base pairing is stable, and is of importance in RNA structure and RNA protein interactions

22 Base stacking provides chemical stability to the DNA double helix The nitrogenous bases are hydrophobic nonpolar. Once the bases are attached to a sugar and a phosphate to form a nucleotide, they become soluble in water, but even so their insolubility still places strong constraints on the overall conformation of DNA in solution. The paired, relatively flat bases tend to stack on top of one another by means of a helical twist

23 A double-stranded DNA molecule thus has a hydrophobic core composed of stacked bases, the sugars and phosphates are soluble in water they orient towards the outside of the helix.

24 Structure of the Watson Crick DNA double helix polarity in each strand (5 3 ) of the DNA double helix: one end of a DNA strand will have a 5 -phosphate and the other end will have a 3 -hydroxyl group Watson and Crick found that hydrogen bonding could only occur if the polarity of the two strands ran in opposite directions The DNA double helix is also referred to as double-stranded DNA (dsdna) or duplex DNA to distinguish it from the single-stranded DNA (ssdna) found in some viruses

25 The sugar phosphate backbone is not equally spaced and results in what are called the major and minor grooves of DNA. Two grooves of different width a wider major groove and a more narrow minor groove that spiral around the outer surface of the double helix. The major groove carries a message (the base sequence of the DNA) in a form that can be read by DNA-binding proteins. most transcription factors (proteins involved in regulating gene expression) bind DNA in the major groove.

26 DNA can undergo reversible strand separation During DNA replication and transcription, the strands of the helix must separate transiently and reversibly. This equals denaturation in Vitro = unwinding Heating lead to broken hydrogen bonds, whereas the phosphodiester bonds remain intact. As DNA denatures, its absorption of UV light increases, a phenomenon known as hyperchromicity. The temperature at which half the bases in a double-stranded DNA sample have denatured is denoted the melting temperature (Tm)

27

28

29 The G+C content of a DNA molecule has a significant effect on its Tm because GC base pair has three hydrogen bonds

30 The melting temperature also depends on the salt concentration: in low salt, a given DNA will melt at a lower temperature than in a higher salt concentration. This is because DNA is a polyanionic molecule. The salt "shields" the negative charges on each phosphate. When the charges are NOT shielded, the electrostatic repulsion makes it energetically more favorable to separate the strands.

31 Also high ph or organic solvents such as formamide disrupt the hydrogen bonding between DNA strands and promote denaturation. When heated solutions of denatured DNA are slowly cooled, single strands often meet their complementary strands and form a new double helix. This is called renaturation or annealing.