Nucleic Acids: Structure and Function

Transcription

1 ucleic Acids: Structure and Function

2 Components of ucleotides The building blocks (monomers) of the nucleic acids are called nucleotides. ucleotides are made up of: phosphoric acid, a pentose sugar, and heterocyclic nitrogenous bases: P - P - - 3P4,Phosphoric Acid P4 3-,Phosphate

3 The pentose sugar found in DA is 2-deoxy-D-ribose; that found in RA is D-ribose. C 2 C 2 The bases found in DA are C 2 adenine cytosine guanine thymine The bases found in RA are 2 2 adenine cytosine guanine uracil 2

4 Biosynthesis of ucleotides The net result of nucleotide biosynthesis can be represented as two dehydration reactions: 2 Dehydrations 2 P C P C 2 ucleotide

5 ucleotide umbering 2 P C ote that primed numbers are used for substituents on the sugar ring and unprimed numbers are used for substituents on the heterocyclic ring.

6 ucleotide omenclature ucleotides derived from ribose are called ribonucleotides; those from deoxyribose are called deoxyribonucleotides. ucleotide names are usually abbreviated: Deoxy- becomes: d- eterocyclic base names become: A, C, G, T, U 5 -Monophosphate becomes: MP 2 2 P - - C 2 AMP - P - C 2 dcmp

7 ucleic Acid Formation from ucleotides The assembly of nucleotides into polynucleotides, or nucleic acids, can be thought of as a dehydration reaction between the 3 - of one nucleotide and the phosphate group of a second nucleotide to form a phosphodiester group. Dehydration P C P C P C 2 - P C 2 By convention, nucleotide sequences are named in the 5 one 5 -end and one 3 -end). 3 direction (a nucleic acid has There may be a phosphate group attached at the 5 -end of the chain or at the 3 -end.

8 Polynucleotides

9 The Three-Dimensional Structure of DA The three-dimensional structure of DA was first deduced by James Watson and Francis Crick in 1953, on the basis of two key pieces of data:! Chargoff rules:! moles of A = moles of T and!!!!! moles of C = moles of G!!!!!!! for the DA of any species.!!!!!! The percentage of A+T or C+G!!!!!! varied from species to species.!! DA x-ray diffraction photographs obtained by!!!! Maurice Wilkins and Rosalind Franklin.

10 The three-dimensional structure of DA is called the double helix. In the double helix, two strands of DA coil about each other, running in opposite directions. The deoxy-sugars and phosphate groups are located on the outside of the helix and the heterocyclic bases are stacked on top of each other on the inside of the helix.

11 Base Pairing The heterocyclic bases are stacked in pairs, each A across from a T (a), and each C across from a G (b). The pairs of bases are held together by hydrogen bonds: two for an AT base pair, and three for a CG base pair. Sugar Phosphate Backbone Sugar Phosphate Backbone Sugar Phosphate Backbone Sugar Phosphate Backbone

12 Illustrating Base Pairing with Electrostatic Diagrams

13 The two deoxynucleotide strands in DA are complementary to each other: the sequence of bases on the 5 3 strand and the 3 5 strand are always matched: AT, TA, CG, or GC. ydrophobic interactions between the stacked base pairs also contribute significant stability to the double helix.

14 DA in the Cell DA strands have molecular masses estimated to be from a few billion to 100 billion. The human genome contains 23 pairs of chromosomes containing 3.2 billion base pairs. Each DA molecule is compacted by folding about a structure called a nucleosome core. Each nucleosome core consists of two pairs each of four different proteins called histones. Each DA molecule wraps around the nucleosome cores to form a chain of nucleosomes, each containing base pairs. The chain of nucleosomes is coiled to higher and higher levels to form a compact, highly supercoiled chromatin fiber.

15

16

17 An Artists Conception of DA

18 Structure of RA Ribonucleic acids exist as single-stranded molecules. Several types of RA exist: Messenger RA - carries genetic information from DA to the site of protein synthesis (the ribosome) Transfer RA - helps in decoding genetic information by carrying specific amino acids to the ribosome Ribosomal RA - forms structural component of the ribosome Catalytic RAs - catalyze transformations of other RAs

19 Ribonucleic acids exist as single-stranded molecules but have extensive secondary and tertiary structure. An good example are the transfer RA s.

20 Artist s Rendition of Transfer RA s

21 Ribosomal RA Secondary Structure

22 Information Flow from DA to Protein The Central Dogma of Molecular Biology Replication is the copying of DA in the course of cell division. Transcription is the synthesis of RA from DA. Translation is the synthesis of polypeptides through the combined efforts of rra, mra, and tra. Approximately 2% of the nucleotides in DA result in the formation of polypeptides. These regions in the DA are called coding regions. The remaining 98% of the nucleotides do not appear to have any function and are called junk DA.

23 Replication, Transcription, and Translation

24 Replication uman cell division is extremely complex and takes a little less than one day. Approximately one third of this time is involved in replicating DA. Replication of DA is carried out with an error level of less than 1 wrong nucleotide per 10 billion. This extreme accuracy preserves the genetic integrity from generation to generation. DA replication involves: A replication bubble, with two replication forks. Several Enzymes, including:! Unwinding Enzyme! DA polymerase for continuos replication! DA ligase for discontinuous replication! Exo- and Endonucleases - to correct errors

25 Semiconservative Replication Replication proceeds simultaneously at thousands of replication bubbles along each DA strand. Replication of an entire DA strand requires approximately 10 minutes. A single parent DA duplex molecule is transformed into two daughter DA duplexes, each containing one strand of the parent DA and one newly synthesized DA strand. This form of DA replication is termed semiconservative.

26 Basic Model of Replication

27 Replication at the Molecular Level

28 Replication: The Big Picture

29 Transcription Transcription is the synthesis of rra, tra, and mra, using the nucleotide sequence information from DA. The RA is synthesized as a complementary copy of one of the two DA single strands (template strand), in a process similar to DA synthesis. The template strand in a transcription bubble is read by RA polymerase, starting at an initiation site and ending at a termination site. The error rate of RA polymerase is less than 1 base in 10,000, much higher than for DA polymerase.

30 Transcription: The Big Picture

31 Introns and Exons After its initial synthesis, an RA molecule is called primary transcript RA (ptra). ptra is subsequently modified by posttranscriptional processing to form m-, r-, and t-ra s. Some posttranscription processing occurs in the nucleus and some in the cytoplasm. An important part of posttranscriptional processing is the deletion of non-coding RA segments (introns), and splicing together the coding segments (exons).

32 Repressors and Inducers nly a fraction of the DA in the coding regions of any one cell is actually expressed (~2%). Repressor proteins turn off DA synthesis coding for proteins not needed in a particular cell type. Inducer proteins turn on DA synthesis for required proteins. ote: The biinding of some inducer and repressor proteins to DA is influenced through alteration of their three - dimensional structure by interactions with hormone molecules.

33 Translation is the process of polypeptide synthesis, mediated by rra, mra, and tra. Translation Translation occurs in the cytoplasm at structures called ribosomes (which contain rra). mra binds to a ribosome and provides the genetic message which specifies a particular polypeptide sequence. tra molecules carrying attached α-amino acids supply the amino acids to be polymerized into the peptide.

34 Translation: The Big Picture

35 Ribosomes consist of two subunits, one large and one small, and are composed of rra (60%) and protein (mostly enzymes required for protein synthesis).

36 Translation: tra synthesis Each amino acid is attached to a tra molecule by an enzyme molecule called an aminoacyl-tra synthetase. This enzyme has recognition sites for both the amino acid and the corresponding tra.

37 Translation: tra synthesis

38 Translation at the Molecular Level

39 Translation at Multiple Sites

40 Translation at Multiple Sites

41 Expansion of the Central Dogma DA-Directed-DA-Polymerase RA-Directed- DA-Polymerase DA-Directed-RA-Polymerase RA-Directed-RA-Polymerase

42 Restriction Endonucleases - Clues from Bacteriophages

43 Restriction Endonucleases - Specificity

44 Restriction Endonucleases - ow Bacteria Protect Themselves

45

46

47