1 Nucleic Acids DNA & RNA

2 What do they do ? Dictate amino-acid sequence in proteinsGive information to chromosomes, which is then passed from parent to offspring

3 The 4th type of macromolecules The chemical link between generations What are they ? The 4th type of macromolecules The chemical link between generations The source of genetic information in chromosomes

4 The central dogma of molecular biology.

5 28.11 Nucleic Acids and HeredityProcesses in the transfer of genetic information: Replication: identical copies of DNA are made Transcription: genetic messages are read and carried out of the cell nucleus to the ribosomes, where protein synthesis occurs. Translation: genetic messages are decoded to make proteins. Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003

6 The nucleus contains the cell’s DNA (genome) RNA is synthesized in the nucleus and exported to the cytoplasm Nucleus Cytoplasm DNA RNA (mRNA) Proteins replication transcription translation The nucleus contains the cell’s DNA, which makes up the genome. The nucleus is surrounded by a nuclear envelope, two membrane bilayers Molecules come into and out of the nucleus through nuclear pores The inside of the nucleus is called the nucleoplasm. Chromatin is the name given to DNA complexed with proteins (histones) The nucleolus is a region where the DNA is concentrated for replication

7 Two types of Nucleotides (depending on the sugar they contain)1- Ribonucleic acids (RNA) The pentose sugar is Ribose (has a hydroxyl group in the 3rd carbon---OH) 2- Deoxyribonucleic acids (DNA) The pentose sugar is Deoxyribose (has just an hydrogen in the same place--- H) Deoxy = “minus oxygen”

8 Definitions Nucleic acids are polymers of nucleotidesNucleotides are carbon ring structures containing nitrogen linked to a 5-carbon sugar (a ribose) 5-carbon sugar is either a ribose or a deoxy-ribose making the nucleotide either a ribonucleotide or a deoxyribonucleotide In eukaryotic cells nucleic acids are either: Deoxyribose nucleic acids (DNA) Ribose nucleic acids (RNA) Messenger RNA (mRNA) Transfer RNA (tRNA) Ribosomal RNA (tRNA)

9 Nucleic Acid Function DNAGenetic material - sequence of nucleotides encodes different amino acids RNA Involved in the transcription/translation of genetic material (DNA) Genetic material of some viruses

10 Nucleotide Structure Despite the complexity and diversity of life the structure of DNA is dependent on only 4 different nucleotides Diversity is dependent on the nucleotide sequence All nucleotides are 2 ring structures composed of: 5-carbon sugar : b-D-ribose (RNA) b-D-deoxyribose (DNA) Base Purine Pyrimidine Phosphate group A nucleotide WITHOUT a phosphate group is a NUCLEOSIDE

11 NUCLEIC ACIDS (DNA and RNA) NotesDNA – Deoxyribonucleic Acid DNA controls all living processes including production of new cells – cell division DNA carries the genetic code – stores and transmits genetic information from one generation to the next Chromosomes are made of DNA DNA is located in the nucleus of the cell

12 Nucleotides and NucleosidesNitrogeneous base Pentose Phosphate Nucleoside = Nucleobase =

13 What are they made of ? Simple units called nucleotides, connected in long chains Nucleotides have 3 parts: 1- 5-Carbon sugar (pentose) 2- Nitrogen containing base (made of C, H and N) 3- A phosphate group ( P ) The P groups make the links that unite the sugars (hence a “sugar-phosphate backbone”

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15 Nucleic Acids Nucleic acids are molecules that store information for cellular growth and reproduction There are two types of nucleic acids: - deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) These are polymers consisting of long chains of monomers called nucleotides A nucleotide consists of a nitrogenous base, a pentose sugar and a phosphate group:

16 Nucleic Acids DNA and RNA are nucleic acids, long, thread-like polymers made up of a linear array of monomers called nucleotides All nucleotides contain three components: 1. A nitrogen heterocyclic base 2. A pentose sugar 3. A phosphate residue

17 Chemical Structure of DNA vs RNARibonucleotides have a 2’-OH Deoxyribonucleotides have a 2’-H

18 Pentose Sugars There are two related pentose sugars:- RNA contains ribose - DNA contains deoxyribose The sugars have their carbon atoms numbered with primes to distinguish them from the nitrogen bases

19 Nucleotide Structure - 4Base-Sugar-PO42- N 5 6 1 2 3 4 P O O C 5’ 1’ 4’ 3’ 2’ OH Monophosphate

20 Nucleotide Function Building blocks for DNA and RNA Intracellular source of energy - Adenosine triphosphate (ATP) Second messengers - Involved in intracellular signaling (e.g. cyclic adenosine monophosphate [cAMP]) Intracellular signaling switches (e.g. G-proteins)

21 Nucleotide Structure - 4Phosphate Groups Phosphate groups are what makes a nucleoside a nucleotide Phosphate groups are essential for nucleotide polymerization Basic structure: P O X

22 Nucleotide Structure - 4Phosphate Groups Number of phosphate groups determines nomenclature Monophosphate e.g. AMP P O CH2 Free = inorganic phosphate (Pi) Diphosphate e.g. ADP P O CH2 Free = Pyro- phosphate (PPi)

23 Nucleotide Structure - 4Phosphate Groups Triphosphate e.g. ATP P O CH2 No Free form exists

24 It is the order of these base pairs that determines genetic makeupOne phosphate + one sugar + one base = one nucleotide Nucleotides are the building blocks of DNA – thus, each strand of DNA is a string of nucleotides

25 Sanger dideoxy sequencing incorporates dideoxy nucleotides, preventing further synthesis of the DNA strand

26 base（purine、pyrimdine）+ribose（deoxyribosN-glycosyl linkage nucleoside+phosphate phosphoester linkage nucleotide phosphodiester linkage nucleic acid

27 FIGURE 8-1a Structure of nucleotidesFIGURE 8-1a Structure of nucleotides. (a) General structure showing the numbering convention for the pentose ring. This is a ribonucleotide. In deoxyribonucleotides the —OH group on the 2′ carbon (in red) is replaced with —H.

28 Nucleotide Structure - 1Sugars O HOCH2 OH Generic Ribose Structure Ribose O HOCH2 5’ 1’ 4’ 3’ 2’ O HOCH2 OH H N.B. Carbons are given numberings as a prime Deoxyribose

29 Purine and Pyrimidine Pyrimidine contains two pyridine-like nitrogens in a six- membered aromatic ring Purine has 4 N’s in a fused-ring structure. Three are basic like pyridine-like and one is like that in pyrrole Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003

30 Nucleotide Structure - 2Bases - Purines N H NH2 Adenine A N 1 2 3 4 5 6 7 8 9 N H O NH2 G Guanine

31 FIGURE 8-2 (part 1) Major purine and pyrimidine bases of nucleic acidsFIGURE 8-2 (part 1) Major purine and pyrimidine bases of nucleic acids. Some of the common names of these bases reflect the circumstances of their discovery. Guanine, for example, was first isolated from guano (bird manure), and thymine was first isolated from thymus tissue.

32 Nucleotide Structure - 3Bases - Pyrimidines NH N O T H H3C Thymine N 5 6 1 2 3 4 C N NH2 O H Cytosine

33 FIGURE 8-2 (part 2) Major purine and pyrimidine bases of nucleic acidsFIGURE 8-2 (part 2) Major purine and pyrimidine bases of nucleic acids. Some of the common names of these bases reflect the circumstances of their discovery. Guanine, for example, was first isolated from guano (bird manure), and thymine was first isolated from thymus tissue.

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35 Nitrogen Bases The nitrogen bases in nucleotides consist of two general types: - purines: adenine (A) and guanine (G) - pyrimidines: cytosine (C), thymine (T) and Uracil (U)

36 Nucleotide Structure - 4Bases - Pyrimidines Thymine is found ONLY in DNA. In RNA, thymine is replaced by uracil Uracil and Thymine are structurally similar Uracil NH N O U H N 5 6 1 2 3 4

37 Nucleosides and NucleotidesA nucleoside consists of a nitrogen base linked by a glycosidic bond to C1’ of a ribose or deoxyribose Nucleosides are named by changing the the nitrogen base ending to -osine for purines and –idine for pyrimidines A nucleotide is a nucleoside that forms a phosphate ester with the C5’ OH group of ribose or deoxyribose Nucleotides are named using the name of the nucleoside followed by 5’-monophosphate

38 Names of Nucleosides and Nucleotides

39 AMP, ADP and ATP Additional phosphate groups can be added to the nucleoside 5’- monophosphates to form diphosphates and triphosphates ATP is the major energy source for cellular activity

40 1 DNA The illustration is a ‘model’ of the double helix forming part of a DNA molecule (Slide 14)

41 Watson Crick Died in 2004

42 DNA stands for deoxyribose nucleic acid2 DNA stands for deoxyribose nucleic acid This chemical substance is present in the nucleus of all cells in all living organisms DNA controls all the chemical changes which take place in cells The kind of cell which is formed, (muscle, blood, nerve etc) is controlled by DNA

43 DNA is a very large molecule made up of a long chain of sub-unitsDNA molecule 3 DNA is a very large molecule made up of a long chain of sub-units The sub-units are called nucleotides Each nucleotide is made up of a sugar called deoxyribose a phosphate group -PO4 and an organic base

44 28.8 Nucleic Acids and NucleotidesDeoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are the chemical carriers of genetic information Nucleic acids are biopolymers made of nucleotides, aldopentoses linked to a purine or pyrimidine and a phosphate Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003

45 Heterocycles in DNA and RNAAdenine, guanine, cytosine and thymine are in DNA RNA contains uracil rather than thymine Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003

46 Deoxyribonucleotides found in DNAdA dG dT dC

47 The Deoxyribonucleotides

48 Hydrogen Bonding InteractionsTwo bases can hydrogen bond to form a base pair For monomers, large number of base pairs is possible In polynucleotide, only few possibilities exist Watson-Crick base pairs predominate in double- stranded DNA A pairs with T C pairs with G Purine pairs with pyrimidine

49 In RNA: AMP、CMP、GMP、TMP In DNA: dAMP、dCMP、dGMP 、dUMP一、the building block molecule of nucleic acid--nucleotide In RNA: AMP、CMP、GMP、TMP In DNA: dAMP、dCMP、dGMP 、dUMP

50 Functions of Nucleotides and Nucleic AcidsNucleotide Functions: Energy for metabolism (ATP) Enzyme cofactors (NAD+) Signal transduction (cAMP) Nucleic Acid Functions: Storage of genetic info (DNA) Transmission of genetic info (mRNA) Processing of genetic information (ribozymes) Protein synthesis (tRNA and rRNA)

51 3’terminal 5’terminal Nucleotide residues phosphodiester bridge二、the linkage ---- phosphodiester bridge 3’terminal 5’terminal Nucleotide residues

52 DNA Nucleotides Composition (3 parts):1- Deoxyribose sugar (no O in 3rd carbon) 2- Phosphate group 3- One of 4 types of bases (all containing nitrogen): - Adenine - Thymine (Only in DNA) - Cytosine - Guanine

53 28.10 Base Pairing in DNA: The Watson–Crick ModelIn 1953 Watson and Crick noted that DNA consists of two polynucleotide strands, running in opposite directions and coiled around each other in a double helix Strands are held together by hydrogen bonds between specific pairs of bases Adenine (A) and thymine (T) form strong hydrogen bonds to each other but not to C or G (G) and cytosine (C) form strong hydrogen bonds to each other but not to A or T Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003

54 The Difference in the StrandsThe strands of DNA are complementary because of H- bonding Whenever a G occurs in one strand, a C occurs opposite it in the other strand When an A occurs in one strand, a T occurs in the other Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003

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56 Primary Structure of Nucleic AcidsThe primary structure of a nucleic acid is the nucleotide sequence The nucleotides in nucleic acids are joined by phosphodiester bonds The 3’-OH group of the sugar in one nucleotide forms an ester bond to the phosphate group on the 5’-carbon of the sugar of the next nucleotide

57 Generalized Structure of DNA

58 Reading Primary StructureA nucleic acid polymer has a free 5’-phosphate group at one end and a free 3’-OH group at the other end The sequence is read from the free 5’-end using the letters of the bases This example reads 5’—A—C—G—T—3’

59 Example of DNA Primary StructureIn DNA, A, C, G, and T are linked by 3’-5’ ester bonds between deoxyribose and phosphate

60 Nucleic Acid StructurePolymerization Nucleotide Sugar Phosphate “backbone”

61 FIGURE 8-7 Phosphodiester linkages in the covalent backbone of DNA and RNA. The phosphodiester bonds (one of which is shaded in the DNA) link successive nucleotide units. The backbone of alternating pentose and phosphate groups in both types of nucleic acid is highly polar. The 5′ end of the macromolecule lacks a nucleotide at the 5′ position, and the 3′ end lacks a nucleotide at the 3′ position.

62 A typical sequence is written as TAGGCTDescribing a Sequence Chain is described from 5 end, identifying the bases in order of occurrence, using the abbreviations A for adenosine, G for guanosine, C for cytidine, and T for thymine (or U for uracil in RNA) A typical sequence is written as TAGGCT Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003

63 Properties of a DNA double helixThe strands of DNA are antiparallel The strands are complimentary There are Hydrogen bond forces There are base stacking interactions There are 10 base pairs per turn

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65 The Double Helix (DNA) Structural model:Model proposed by Watson & Crick, 1953 Two sugar-phosphate strands, next to each other, but running in opposite directions. Specific Hydrogen bonds occur among bases from one chain to the other: A---T , C---G Due to this specificity, a certain base on one strand indicates a certain base in the other. The 2 strands intertwine, forming a double- helix that winds around a central axis

66 Untwisted it looks like this:The sides of the ladder are: P = phosphate S = sugar molecule The steps of the ladder are C, G, T, A = nitrogenous bases (Nitrogenous means containing the element nitrogen.) A = Adenine T = Thymine A always pairs with T in DNA C = Cytosine G = Guanine C always pairs with G in DNA Untwisted it looks like this: (Apples are Tasty) (Cookies are Good) Nucleotide

67 Secondary Structure: DNA Double HelixIn DNA there are two strands of nucleotides that wind together in a double helix - the strands run in opposite directions - the bases are are arranged in step-like pairs - the base pairs are held together by hydrogen bonding The pairing of the bases from the two strands is very specific The complimentary base pairs are A-T and G-C - two hydrogen bonds form between A and T - three hydrogen bonds form between G and C Each pair consists of a purine and a pyrimidine, so they are the same width, keeping the two strands at equal distances from each other

68 Model of DNA: The model was developed by Watson and Crick in 1953. They received a nobel prize in 1962 for their work. The model looks like a twisted ladder – double helix.

69 Nucleic Acid Structure“Base Pairing” DNA base-pairing is antiparallel i.e. 5’ - 3’ (l-r) on top : 5’ - 3’ (r-l) on T A G C 3’ 5’

70 Discovering the structure of DNAErwin Chargaff – ( ) Columbia University, NY Investigated the composition of DNA His findings by 1950 strongly suggested the base-pairings of A-T & G-C Met with Watson and Crick in 1952 and shared his findings “Chargaff’s rule” A = T & C = G

71 Nucleic Acid StructureThe double helix First determined by Watson & Crick in 1953 Most energy favorable conformation for double stranded DNA to form Shape and size is uniform for all life (i.e. DNA is identical) Without anti-parallel base pairing this conformation could not exist Structure consists of “major” grooves and “minor” grooves Major grooves are critical for binding proteins that regulate DNA function

72 Present in all living cells Contains all the informationDiscovering the structure of DNA DNA = Deoxyribose nucleic acid Present in all living cells Contains all the information Nucleotides: a subunit that consists of: a sugar (deoxyribose) a phosphate and one nitrogen base – 4 different bases Adenine (A) and Thymine (T) Guanine (G) and Cytosine (C)

73 The paired strands are coiled into a spiral called13 The paired strands are coiled into a spiral called A DOUBLE HELIX

74 17 The strands separate PO4 PO4

75 Nucleic Acid Structure“Base Pairing” RNA [normally] exists as a single stranded polymer DNA exists as a double stranded polymer DNA double strand is created by hydrogen bonds between nucleotides Nucleotides always bind to complementary nucleotides A T (2 H-bonds) C G (3 H-bonds)

76 G A T T A C A C T A A T G T Practice DNA Base Pairs“Gattaca” is a science fiction movie starring Uma Thurman, Ethan Hawke, and Jude Law

77 Nucleic Acid StructureThe double helix Minor Groove Major Groove

78 Before a cell divides, the DNA strands unwind and separatereplication 16 Before a cell divides, the DNA strands unwind and separate Each strand makes a new partner by adding the appropriate nucleotides The result is that there are now two double-stranded DNA molecules in the nucleus So that when the cell divides, each nucleus contains identical DNA This process is called replication

79 STEP 1 Hydrogen bonds between base pairs are broken by the enzyme Helicase and DNA molecule unzips DNA molecule separates into complementary halves

80 Complementarity of DNA strandsTwo chains differ in sequence (sequence is read from 5’ to 3’) Two chains are complementary Two chains run antiparallel

81 FIGURE 8-11 Hydrogen-bonding patterns in the base pairs defined by Watson and Crick. Here as elsewhere, hydrogen bonds are represented by three blue lines.

82 Nucleic Acid Structure“Base Pairing”

83 Nucleic Acid StructurePolymerization 5’ 3’ Sugar Phosphate “backbone” T A G C Bases TAGCAC 5’ 3’

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85 Nucleic Acid StructurePolymerization P S N C P S N C Phosphodiesterase P (PPi) + P S N C

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87 DNA Replication Cell division involving mitosis produces 2 daughter cells that are genetically identical to each other and genetically identical to the parent cell Remember that for this to happen, DNA in the parent cell must be replicated (copied) before the cell divides – this process occurs during Interphase in the cell cycle

88 STEP 2 Nucleotides match up with complementary bases Free nucleotides abundant in nucleus

89 STEP 3 New Strand Original StrandNucleotides are linked into 2 new strands of DNA by the enzyme, polymerase—DNA polymerase also proofreads for copying errors New Strand Original Strand

90 Mutations occur when copying errors cause a change in the sequence of DNA nucleotide bases

91 FIGURE 8-14 Complementarity of strands in the DNA double helixFIGURE 8-14 Complementarity of strands in the DNA double helix. The complementary antiparallel strands of DNA follow the pairing rules proposed by Watson and Crick. The base-paired antiparallel strands differ in base composition: the left strand has the composition A3 T2 G1 C3; the right, A2 T3 G3 C1. They also differ in sequence when each chain is read in the 5′→3′ direction. Note the base equivalences: A = T and G = C in the duplex.

92 Diagram Examples of DNA Replication:(You could see DNA replication represented different ways.)

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95 Storage of DNA In eukaryotic cells (animals, plants, fungi) DNA is stored in the nucleus, which is separated from the rest of the cell by a semipermeable membrane The DNA is only organized into chromosomes during cell replication Between replications, the DNA is stored in a compact ball called chromatin, and is wrapped around proteins called histones to form nucleosomes

96 DNA Replication When a eukaryotic cell divides, the process is called mitosis - the cell splits into two identical daughter cells - the DNA must be replicated so that each daughter cell has a copy DNA replication involves several processes: - first, the DNA must be unwound, separating the two strands - the single strands then act as templates for synthesis of the new strands, which are complimentary in sequence - bases are added one at a time until two new DNA strands that exactly duplicate the original DNA are produced The process is called semi-conservative replication because one strand of each daughter DNA comes from the parent DNA and one strand is new The energy for the synthesis comes from hydrolysis of phosphate groups as the phosphodiester bonds form between the bases

97 FIGURE 8-15 Replication of DNA as suggested by Watson and CrickFIGURE 8-15 Replication of DNA as suggested by Watson and Crick. The preexisting or "parent" strands become separated, and each is the template for biosynthesis of a complementary "daughter" strand (in pink).

98 Figure 5-14 Schematic representation of the strand separation in duplex DNA resulting from its heat denaturation. Page 90

99 Direction of ReplicationThe enzyme helicase unwinds several sections of parent DNA At each open DNA section, called a replication fork, DNA polymerase catalyzes the formation of 5’-3’ester bonds of the leading strand The lagging strand, which grows in the 3’-5’ direction, is synthesized in short sections called Okazaki fragments The Okazaki fragments are joined by DNA ligase to give a single 3’-5’ DNA strand

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101 RNA Nucleotides Composition ( 3 parts):1- Ribose sugar (with O in 3rd carbon) 2- Phosphate group 3- One of 4 types of bases (all containing nitrogen): - Adenine - Uracyl (only in RNA) - Cytosine - Guanine

102 Ribonucleic Acid (RNA)RNA is much more abundant than DNA There are several important differences between RNA and DNA: - the pentose sugar in RNA is ribose, in DNA it’s deoxyribose - in RNA, uracil replaces the base thymine (U pairs with A) - RNA is single stranded while DNA is double stranded - RNA molecules are much smaller than DNA molecules There are three main types of RNA: - ribosomal (rRNA), messenger (mRNA) and transfer (tRNA)

103 Types of RNA

104 Its sequence is copied from genetic DNA Messenger RNA (mRNA) Its sequence is copied from genetic DNA It travels to ribsosomes, small granular particles in the cytoplasm of a cell where protein synthesis takes place Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003

105 Ribosomes are a complex of proteins and rRNA Ribosomal RNA (rRNA) Ribosomes are a complex of proteins and rRNA The synthesis of proteins from amino acids and ATP occurs in the ribosome The rRNA provides both structure and catalysis Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003

106 There is a specific tRNA for each amino acid Transfer RNA (tRNA) Transports amino acids to the ribosomes where they are joined together to make proteins There is a specific tRNA for each amino acid Recognition of the tRNA at the anti- codon communicates which amino acid is attached Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003

107 Transfer RNA Transfer RNA translates the genetic code from the messenger RNA and brings specific amino acids to the ribosome for protein synthesis Each amino acid is recognized by one or more specific tRNA tRNA has a tertiary structure that is L-shaped - one end attaches to the amino acid and the other binds to the mRNA by a 3-base complimentary sequence

108 Ribosomal RNA and Messenger RNARibosomes are the sites of protein synthesis - they consist of ribosomal DNA (65%) and proteins (35%) - they have two subunits, a large one and a small one Messenger RNA carries the genetic code to the ribosomes - they are strands of RNA that are complementary to the DNA of the gene for the protein to be synthesized

109 How DNA Works 1- DNA stores genetic information in segments called genes 2- The DNA code is in Triplet Codons (short sequences of 3 nucleotides each) 3- Certain codons are translated by the cell into certain Amino acids. 4. Thus, the sequence of nucleotides in DNA indicate a sequence of Amino acids in a protein.

110 Transcription ProcessSeveral turns of the DNA double helix unwind, exposing the bases of the two strands Ribonucleotides line up in the proper order by hydrogen bonding to their complementary bases on DNA Bonds form in the 5  3 direction, Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003

111 RNA—Ribonucleic Acid RNA is a messenger that allows the instruction of DNA to be delivered to the rest of the cell RNA is different than DNA: The sugar in RNA is ribose; the sugar in DNA is deoxyribose RNA is a single strand of nucleotides; DNA is a double strand of nucleotides RNA has Uracil (U) instead of Thymine (T) which is in DNA RNA is found inside and outside of the nucleus; DNA is found only inside the nucleus

112 Transcription of RNA from DNAOnly one of the two DNA strands is transcribed into mRNA The strand that contains the gene is the coding or sense strand The strand that gets transcribed is the template or antisense strand The RNA molecule produced during transcription is a copy of the coding strand (with U in place of T) Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003

113 Example of RNA Primary StructureIn RNA, A, C, G, and U are linked by 3’-5’ ester bonds between ribose and phosphate

114 The Parts of Transfer RNAThere are 61 different tRNAs, one for each of the 61 codons that specifies an amino acid tRNA has ribonucleotides and is bonded to a specific amino acid by an ester linkage through the 3 hydroxyl on ribose at the 3 end of the tRNA Each tRNA has a segment called an anticodon, a sequence of three ribonucleotides complementary to the codon sequence

115 Protein Synthesis The two main processes involved in protein synthesis are - the formation of mRNA from DNA (transcription) - the conversion by tRNA to protein at the ribosome (translation) Transcription takes place in the nucleus, while translation takes place in the cytoplasm Genetic information is transcribed to form mRNA much the same way it is replicated during cell division

116 RNA Polymerase During transcription, RNA polymerase moves along the DNA template in the 3’-5’direction to synthesize the corresponding mRNA The mRNA is released at the termination point

117 Processing of mRNA Genes in the DNA of eukaryotes contain exons that code for proteins along with introns that do not Because the initial mRNA, called a pre-RNA, includes the noncoding introns, it must be processed before it can be read by the tRNA While the mRNA is still in the nucleus, the introns are removed from the pre-RNA The exons that remain are joined to form the mRNA that leaves the nucleus with the information for the synthesis of protein

118 Removing Introns from mRNA

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122 Transcription Several steps occur during transcription:- a section of DNA containing the gene unwinds - one strand of DNA is copied starting at the initiation point, which has the sequence TATAAA - an mRNA is synthesized using complementary base pairing with uracil (U) replacing thymine (T) - the newly formed mRNA moves out of the nucleus to ribosomes in the cytoplasm and the DNA re-winds

123 The Structure of tRNA Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003

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125 Regulation of TranscriptionA specific mRNA is synthesized when the cell requires a particular protein The synthesis is regulated at the transcription level: - feedback control, where the end products speed up or slow the synthesis of mRNA - enzyme induction, where a high level of a reactant induces the transcription process to provide the necessary enzymes for that reactant Regulation of transcription in eukaryotes is complicated and we will not study it here

126 The Ribonucleotides

127 The Genetic Code The genetic code is found in the sequence of nucleotides in mRNA that is translated from the DNA A codon is a triplet of bases along the mRNA that codes for a particular amino acid Each of the 20 amino acids needed to build a protein has at least 2 codons There are also codons that signal the “start” and “end” of a polypeptide chain The amino acid sequence of a protein can be determined by reading the triplets in the DNA sequence that are complementary to the codons of the mRNA, or directly from the mRNA sequence The entire DNA sequence of several organisms, including humans, have been determined, however, - only primary structure can be determined this way - doesn’t give tertiary structure or protein function

128 The sequence of bases in DNA forms theGenetic code 1 19 The sequence of bases in DNA forms the Genetic Code A group of three bases (a triplet) controls the production of a particular amino acid in the cytoplasm of the cell The different amino acids and the order in which they are joined up determines the sort of protein being produced

129 Valine Alanine Codes for Codes for 21 Cytosine Adenine ThymineCoding 21 For example Cytosine Adenine Valine Codes for Thymine Cytosine (C) Alanine Codes for Guanine (G) Adenine (A)

130 This is known as the triplet code22 This is known as the triplet code Each triplet codes for a specific amino acid CGA - CAA - CCA - CCA - GCT - GGG - GAG - CCA - Ala Val Gly Gly Arg Pro Leu Gly The amino acids are joined together in the correct sequence to make part of a protein Although the DNA in the nucleus specifies the amino acids and their sequence, it is in the cytoplasm that the protein build-up takes place. The DNA of the nucleus makes a single strand of messenger RNA (ribo-nucleic acid) which leaves the nucleus and builds up the protein in the cytoplasm. The RNA code is complementary, but not identical, to the nuclear DNA. Text books usually give the coding for the RNA but in this presentation it is for the DNA itself Ala Val Gly Gly Arg Pro Leu Gly

131 mRNA Codons and Associated Amino Acids

132 Reading the Genetic CodeSuppose we want to determine the amino acids coded for in the following section of a mRNA 5’—CCU —AGC—GGA—CUU—3’ According to the genetic code, the amino acids for these codons are: CCU = Proline AGC = Serine GGA = Glycine CUU = Leucine The mRNA section codes for the amino acid sequence of Pro—Ser—Gly—Leu

133 Translation and tRNA ActivationOnce the DNA has been transcribed to mRNA, the codons must be tranlated to the amino acid sequence of the protein The first step in translation is activation of the tRNA Each tRNA has a triplet called an anticodon that complements a codon on mRNA A synthetase uses ATP hydrolysis to attach an amino acid to a specific tRNA

134 Initiation and TranslocationInitiation of protein synthesis occurs when a mRNA attaches to a ribosome On the mRNA, the start codon (AUG) binds to a tRNA with methionine The second codon attaches to a tRNA with the next amino acid A peptide bond forms between the adjacent amino acids at the first and second codons The first tRNA detaches from the ribosome and the ribosome shifts to the adjacent codon on the mRNA (this process is called translocation) A third codon can now attach where the second one was before translocation

135 Termination After a polypeptide with all the amino acids for a protein is synthesized, the ribosome reaches the the “stop” codon: UGA, UAA, or UAG There is no tRNA with an anticodon for the “stop” codons Therefore, protein synthesis ends (termination) The polypeptide is released from the ribosome and the protein can take on it’s 3-D structure (some proteins begin folding while still being synthesized, while others do not fold up until after being released from the ribosome)

136 The proteins build the cell structuresDNA and enzymes 23 The proteins build the cell structures They also make enzymes The DNA controls which enzymes are made and the enzymes determine what reactions take place The structures and reactions in the cell determine what sort of a cell it is and what its function is So DNA exerts its control through the enzymes

137 Such a sequence forms a geneGenes 24 A sequence of triplets in the DNA molecule may code for a complete protein Such a sequence forms a gene There may be a thousand or more bases in one gene

138 FIGURE 8-16b Structural variation in DNAFIGURE 8-16b Structural variation in DNA. (b) For purine bases in nucleotides, only two conformations with respect to the attached ribose units are sterically permitted, anti or syn. Pyrimidines generally occur in the anti conformation.

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140 Conformation around N-Glycosidic BondRelatively free rotation can occur around the N-glycosidic bond in free nucleotides The torsion angle about the N-glycosidic bond (N-C1') is denoted by the symbol c The sequence of atoms chosen to define this angle is O4'- C1'-N9-C4 for purine, and O4'-C1'-N1-C2 for pyrimidine derivatives Angle near 0corresponds to syn conformation Angle near 180 corresponds to anti conformation Anti conformation is found in normal B-DNA

141 FIGURE 8-10 Absorption spectra of the common nucleotidesFIGURE 8-10 Absorption spectra of the common nucleotides. The spectra are shown as the variation in molar extinction coefficient with wavelength. The molar extinction coefficients at 260 nm and pH 7.0 (ε260) are listed in the table. The spectra of corresponding ribonucleotides and deoxyribonucleotides, as well as the nucleosides, are essentially identical. For mixtures of nucleotides, a wavelength of 260 nm (dashed vertical line) is used for absorption measurements.

142 Replication of Genetic CodeStrand separation occurs first Each strand serves as a template for the synthesis of a new strand Synthesis is catalyzed by enzymes known as DNA polymerases Newly made DNA molecule has one daughter strand and one parent strand. “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material” Watson and Crick, in their Nature paper,1953

143 Messenger RNA: Code Carrier for the Sequence of ProteinsIs synthesized using DNA template Contains ribose instead of deoxyribose Contains uracil instead of thymine One mRNA may code for more than one protein

144 FIGURE 8-21 Bacterial mRNAFIGURE 8-21 Bacterial mRNA. Schematic diagrams show (a) monocistronic and (b) polycistronic mRNAs of bacteria. Red segments represent RNA coding for a gene product; gray segments represent noncoding RNA. In the polycistronic transcript, noncoding RNA separates the three genes.

145 Factors Affecting DNA DenaturationThe midpoint of melting (Tm) depends on base composition high CG increases Tm Tm depends on DNA length Longer DNA has higher Tm Important for short DNA Tm depends on pH and ionic strength High salt increases Tm