Week 4 – 9/13-9/17Week 4 – 9/13-9/17 DNA bases. Divided into two groups:Purines = A and G (double ringed of 6 and 5 C’s, N9 will link to sugar)Pyrimidines are cytosine and thymine. CUT the Py. (single rings of 6 C’s, and 2 N’s. N1 will link to the sugar)Each base exists in alternative tautomeric states in equilibriumwith each other. Formation of the nucleotides in DNA:• Condensation reactions join deoxyribose, phosphoric acid, and a base to form each deoxynucleoside monophosphate.- Nucleotide consists of a phosphate joined to a sugar (2’-deoxyribose) to which a base is attached. ‘ = position on sugar, not baseOccurs through condensation reaction, H20 removed between 1’ carbon of the sugar andthe base’s N9 to form a glycosidic bond. Sugar + base alone = nucleoside. Link phosphate to 2’deocyribose by removing water from phosphate and 5’ C ofsugar to create a phosphoester bond. Addingthis phosphate on makes the nucleoside a nucleotide. -H-bond donors and H-bond acceptors must be properly positioned for compatible base-pairing.- Base pairing occurs in an antiparallel orientation. Double helix held together by weak, noncovalent bonds b/w bases. Adenine on one chain is paired with Thymine on other, likewise with g and c. Two strands have same helical geometry, but base pairing holds them together with the opposite polarity. -A and T match up so that an H-bond can form between the exocyclic amino group at C6 on adenine and the carbonyl at C4 in thymine. Another can form b/w N1 of A and N3 of T.-N1 of guanine and N3 of cytosine, and the carbonyl at C6 of G and the Nh2 at C4 of cytosine form H-bonds. Exocyclic NH2 at C2 on guanine can H-bond with carbonyl on C2 of C. So has 3 H-bonds. -No matter the pairings, the distance between the sugar attachment points are the same. -All four base pairs are accommodated w/in same arrangement w/o any distortion of overall structure of DNA. Class: Bases have to be close together and lined up just right in order for H-bonds to occur. If they are shifted, then H-bonds can’t form. B/w C and G there are three H-bonds. B/w A and T there are 2. So C and G ratio in DNA = higher, then it is more stable. Always purine pairing with pyrimidine. If pairing occurs incorrectly, we can’t form ydrogen bonds. That’s why we have to stick with AT and CGbase pairing. Structure of DNA: • The distances between the two DNA backbone strands ismaintained constant.• The two DNA strands are in an antiparallel orientation.• The 5’ end has a phosphate group and the 3’ end has ahydroxyl group.• Nucleotides are joined to each other in polynucleotidechains through the 3’-OH of 2’deoxyribose of onenucleotide and the phosphate attached to the 5’-OH ofanother nucleotide. This is a phosphodiester linkage,phosphoryl group b/w nucleotides has on sugar attachedto it at 3’OH and the other at the 5’methyl. Theselinkages create the repeating sugar-phosphate backboneas well as an inherent polarity. • Class: These two strains are held at a constant distance. 2tsraight lines held together by H-bonds. Backbone =sugar, phosphate, sugar, phosphate, etc. connected by phosphodiester bonds on theoutside with bases on the inside. That makes our double stranded DNA. DNA Helix Forms:• The B form (or something very similar to it) isthe most common form in the cell.• The A- and B-forms are right-handed helices,while the Z-form is a left-handed helix.• Z-DNA is favored by alternating G and Csequence, and unwound DNA. • These DNA molecules form double helixes.Depending on condition for DNA, it can exist inthree different types of helical forms – A, B, andZ types.• B form is the typical one that everyone talksabout – standard form. Each helical turn is 34Angstroms, and they are right hand turns.• A form is slightly shorter and fatter – it is alsoright handed. It exists when the DNA double helixis being opened up for transcription. If you lookfor the cross section, B form is looser, A form ismore compact. • Z form is a left handed helix, unlike A and B. Ontop of that, it is slightly skinner. It exists in highsalt concentrations. No one knows its biologicalsignificance.DNA Double Helix Structure:• Two anti-parallele strands.• About 10 bases per turn of the helix in the mostcommon form of DNA• H-bonding and hydrophobic (base-stacking)interactions hold the two strands together.• Looking at B form. • Another interaction that makes DNA go into double helical form– base stacking. Hydrophobic interactions b/w the bases on thesame DNA strand cause it to get into its most stable form. Hasten base pairs per helical turn. Length of turn = 34 Angstroms.Each base pair is 3.4 angstroms then. Diameter of double helixis twenty angstroms. • Size difference allows for protein-DNA interactions. Proteinscan stick part of domain or motif into protein sturcture. • There is a major and minor groove on the surface of the helixthat is an important site of interaction for many regulatoryproteins.• If you turn DNA, get different gaps in between the twobackbones. Named the major groove and minor groove.• In major groove, much more of the atoms of bases areexposed than in the minor groove. Basically, we havebigger, smaller, bigger, smaller, alternating surfaces.Major and minor grooves are where the proteins willinteract with DNA. • In the major groove, all four base-pairingscan be distinguished.• In the minor groove, only two of the fourbase-pairings are clearly distinguished.- That is how a sequence specific DNAinteraction occurs. Only the proper H-bonding isallowed for sequence specific binding. Thisinteraction happens b/w protein and major grooveof DNA molecule.-Recognition and interaction b/w DNA nd proteinis initiated in the major groove. Denaturation and Renaturation of DNA- Annealing of longer complementary stretches of DNA will be favored over shorter ones. - Held together by h-bonds b/w two strands, can be denatured. Denaturation happens by separating the two strands. Often by heat in test tubes. In cells, seapration is carried out by enzymes. Once denatured, if you lower the temperature, the will renature. During renaturation, how do they know how to line up exactly? Their maybe local annealing that is not perfect, but if other pieces are longer, they are more stable so over time they wlll eventually line back up perfectly. -It starts purely by chance, if there are complementary sequences they will start annealing, forming local