BIOCHEM SHEET (8) Made by: rahmeh Alsukkar corrected by: date : 11-10

Transcription

1 BIOCHEM SHEET (8) Made by: rahmeh Alsukkar corrected by: date :

2 Note: Thursday it is a revision lecture slide 3 ( 5:11 min ) *nucleic acid is a monomer of DNA *nucleotide composed of :1-nitroenous base 2-phosphate group 3-sugar * Pyrimidine and purine are the essential bases for the DNA and RNA structure ** largest name has smallest structure and vice. ** Punctuation is important - pyrimidine starts from N 1 and it is clockwise, purine starts from the left N atom which is numb 1 and anticlockwise. slide 4,5,6 7 ** there are the modified nucleosides : Fig. 9-1, p.216 Fig. 9-2a, p.216 2

3 -Hypoxanthine is like Guanine but have H instead of N2H on C#2 -N6-Dimethyladenine different from Adenine it have H3C-N-CH3 instead of NH2 on C#6 Fig. 9-2b, p methylcytosine different from cytosine on C#5 it have CH3 instead of H -5,6-Dihydrouracil different from Uracil it has CH2 instead of CH of C#5 & 6 Fig. 9-2c, p.216 found in RNA because it is oxidized * Note:- - Β-glycosidic btw sugar + base. - phosphodiester btw sugar + phosphate.(the backbone) - H.bond btw 2 strands. (btw bases) horizontal - van der walls btw bases vertical * يرتبط cis sugar ب ذرة كرون رقم 1 مع N في base 3

4 * nucleoside + phosphate nucleotide. - in most biological nucleotide, the phosphate is attached to the 5 th carbon of the sugar Ex. Adenosine 5- (nucleoside) triphosphate (ATP) C #5 In sugar (or linkage) * nucleoside of RNA :- 1- adenosine 2- guanosine 3- cytidine 4- uridine * nucleoside of DNA :- 1- deoxyadenosine 2- deoxyguanosine 3- deoxycytidine 4- deoxythymidine * 5 contain phosphate * 3 contain sugar 5 3 * strand polynucleotide 2 strand antiparallel run in opposite directions * G-C is stronger than A-T for pictures go back to slide 8,9,10,11,12 ** Suffixes : OH alcohols, CHO aldehydes,cooh carboxyl acids. deoxy=without oxygen *deoxy forms are found in DNA like guanisine 5-monophosphate RNA deoxyguanisine 5-monophosphate DNA *Uridine 5-monophosphate only found in RNA and cant have a deoxy form *thymidine must be with prefix deoxy because it is usually found only in DNA so you must say (Deoxythymine 5-monoophosphate) only 4

5 Slide 14 (16:51) *structure of DNA ** they Discover that the nitrogen bases are inside the DNA attach with sugar then phosphate group ** phosphate group + sugar found outside the DNA. *the backbone of DNA composed of sugar & phosphate group\while nitrogenous base are found inside *inside DNA is hydrophobic region ** DNA and RNA are negatively charged due to the presence of negatively phosphate group in the outside. ** DNA is a double strands two chains and they are antiparallel (the first chain starts from the 3'- terminus and end in 5'-terminus whereas the second chain it is the opposite (opposite direction). *the two strands connected by non-covalent bonds *DNA stores genetic information *RNA transcribes information ** A specific enzyme attached to the negatively charged region in the DNA and RNA. *components of nucleic acid: 1-sugar -DNA deoxyribose sugar -RNA ribose sugar they are a pentose sugars(have 5 carbons) *in C #2 ribose has OH group but deoxyribose has H *deoxy stabilize DNA (more resistant to hydrolysis) 5

6 Slide 15 Fig. 9-5, p.219 ** the bond which links two sugars with gather called 3'-5'-phosphodiester bonds. slide 16 Fig. 9-6, p.219 ** the bases Associated with each other by a hydrogen bonds ; for example : the adenine "A" associated with thymine "T" in double hydrogen bond whereas cytosine "C" associated with guanine "G" in 3 hydrogen bonds 6

7 ** increasing the number of triple bond between the C and G make the structure stronger. ** in the termination of poly peptide replication, the double bonds between T and A increase to make the structure weaker then the mrna can separate from DNA. The 3-dimensional double helix structure of DNA, correctly elucidated by James Watson and Francis Crick. Complementary bases are held together as a pair by hydrogen bonds Fig. 9-7, p.221 slide 17,18,19 **Å = angstrom " length unit" the length must be equal 11 Å to promote the bases to arrange above each other in a compact structure. Adenine ==Thymine (A=T) makes 2 H-bonds (1-3 N-H & 6-4 H-O) length 11 A Guanine===Cytosine (G=C) make 3 H-bonds (2-2 (H-O) 1-3 (H-N) 6-4 (O-H)) *the length is 11 A Slide 20 -watson & creik won the noble prize in 1962 slide 21 (22:44 min ) ** there is three types of DNA : B-form,a-form, and z-form ; the differ from each other in length, width, and direction either left or right. 7

8 Three different conformations of the DNA double helix. (A) A-DNA is a short, wide, right-handed helix. (B) B-DNA, the structure proposed by Watson and Crick, is the most common conformation in most living cells. (C) Z-DNA, is a left-handed helix unlike A- and B-DNA, is a left-handed helix. Slide 22 ** left and right handed forms are a mirror images. Fig. 9-10, p.224 Slide 23 (24:16 min ) ** There is a z-form within B-form of the DNA الن ال DNA ملفوف على نفسه 8

9 Fig. 9-11, p.225 Slide 24,25 large and minor groove is important because the enzymes will make attached in this region " splitting" Fig. 9-12, p.225 Fig. 9-13, p.225 9

10 Template strand Slide 26 ** in the replication there is template strand and coding strand. ** New RNA similar to coding strand Coding strand RNA slide 27,28 (25:46 min) p.226 ** the origin form is the relaxed form Rotation clockwise(right-handed) positive supercoil Rotation counterclockwise(left-handed) negative supercoil. Fig. 9-14a, p

11 Fig. 9-14b, p.227 slide 29 the previous form important for replication ; there is an enzyme "DNA gyrase" that separate the double strands from each other **in the eukaryotic DNA replication occur in multiple sites so it must converted the double strands into circles to doing replication in each circle then associated together,whereas in the prokaryotic " circular DNA " in one site only Fig. 9-15, p.228 slide 30 DNA is supercoiled and inside it there is a histones "which contain positive a.a such as: argnine,and 11

12 histidines " note : التفاف ال histones ليكون ب very small space DNAحول ال Fig. 9-16, p.229 slide 31,32 (28:58 min ) ** because it composed of a poly peptide it is affected by temperature **denaturation of protein loose its function, whereas denaturation of DNA due increase temp separating the double strands ** if the DNA cooling down the strands retain to link with gather (renaturation). *neuclosomes: structural unit of eukaryotic chromosome, consisting of a length of DNA coiled around a core of histone *histone positive A.A wrapped to attach small nuclei Fig. 9-17, p

13 Fig. 9-18, p.231 slide 33 (30:29 min ) ** the protein which form in the end of process may be enzyme,receptor, and so on. Fig. 9-19, p.231 slide 34 ** in the prokaryotic the genes arrange beside each other so synthesize of mrna (transcription) and translation occur at the same time. 13

14 Fig. 9-20a, p.232 slide 35 ** in the eukaryotic transcription is complication due to the presence of introns between genes and much than exons ** Exon gene given a specific adjective such as : eye color, hair color,etc. ** the different between prokaryotic and eukaryotic in the replication is due to the presence of hematonucleos and cytoplasm in the eukaryotic ; )حيث يخرج ال mrna من النواه الى ال cytoplasm وحدوث ال ) translate slide 36 (33:15) Fig. 9-20b, p

15 **the numb of universal code is coding sequence, 3 a.a including initial code. **there is more than 56 type of trna ; ممكن يكون لل a.a اكثر من. coding sequence **mrna synthesis in nucleus and then exit to cytoplasm. Table 9-1, p.233 slide 39 (35:14 min ) **transfer RNA the only one contains double strands and it is contain hydrogen bond and modified bases too. **mrna it is a single strands Fig. 9-21, p

16 slide 38,39, 40, 41 **pseudouridine is common in trna. Fig. 9-22a, p.233 slide 42,43 **Ribosome is a protein inside it there is a ribosomal RNA. **Ribosome composed of two subunits ;large"50s" and small "30s" not addition together **small and large subunit called "centrifuged units Fig. 9-25, p