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Genes Are DNA 1 Ex Biochem c1-genes DNA 1.1 Introduction Figure 1.2 2 Ex Biochem c1-genes DNA 1.5 Polynucleotide Chains Nitrogenous Bases 鹼基Linked to a Sugar–Phosphate Backbone A nucleoside consists of a purine or pyrimidine base linked to position 1 of a pentose sugar. 3 Ex Biochem c1-genes DNA Transfection DNA can enter eukaryotic cells and produce functional proteins Become part of the genome DNA can also be introduced into eggs by microinjection Become part of the genome 4 Ex Biochem c1-genes DNA Nucleic acid structure Positions on the ribose ring are described with a prime (′) to distinguish them. The difference between DNA and RNA is in the group at the 2′ position of the sugar. A nucleotide consists of a nucleoside linked to a phosphate group on either the 5′ or 3′ position of the (deoxy)ribose. Successive (deoxy)ribose residues of a polynucleotide chain are joined by a phosphate group DNA has a deoxyribose sugar (2′–H) RNA has a ribose sugar (2′–OH) Between the 3′ position of one sugar and the 5′ position of the next sugar One end of the chain (left) has a free 5′ end The other end has a free 3′ end 5 Ex Biochem c1-genes DNA Nucleosides Nucleoside: a compound that consists of Dribose 核糖or 2-deoxy-D-ribose 去氧核糖 bonded to a nucleobase by a -N-glycosidic bond uracil O HN -D-riboside O 5' H OCH2 4' H 1 N O H 3' H 2' HO OH Uridine a -N-glycosidic bond 1' H anomeric carbon 6 Ex Biochem c1-genes DNA Nucleotide Nucleotide: a nucleoside in which a molecule of phosphoric acid is esterified with an -OH of the monosaccharide, most commonly either the 3’-OH or the 5’-OH N H2 N O - 5' O - H H N O O-P- O-CH2 3' H 1' H HO OH Adenos ine 5'-monophosphate (5'-AMP) N N 7 Ex Biochem c1-genes DNA Nucleotides Deoxythymidine 3’-monophosphate (3’dTMP) O CH3 HN 5' HOCH2 O O H H H 3' O H - O P O - O N 1' H 8 Ex Biochem c1-genes DNA DNA Structure O phosphorylated 5' end CH3 HN O 5' O-P- O-CH2 O H H O O O O H 1' N HN H 2' H N N H 2N 5' O= P O N O - CH2 O H 1' H H free 3' end 3' H 2' OH H 9 Ex Biochem c1-genes DNA Pyrimidine/Purine Bases 3 4 N 2 N 5 N 6 O 1 1 N 2 N N 8 N 4 3 Purine N9 H N N O H Thymine (T) (DNA and some RNA) H Uracil (U) (in RNA) O N N HN N N H2 7 5 O O CH3 HN H Cytosine (C) (DNA and some RNA) Pyrimidine 6 O N H2 N H Adenine (A) (DNA and RNA) N HN H 2N N N H Guanine (G) (DNA and RNA) 10 Ex Biochem c1-genes DNA Other Bases Several “unusual” bases occur, principally but not exclusively, in transfer RNAs H3 C O N HN N N H Hypoxanthine N CH3 N H2 N N N H N 6 -Dimethyladenine CH3 N N O O N H 5-Methylcytosine HN O N H 5,6-Dihyrouracil 11 Ex Biochem c1-genes DNA Figure 1.07: A polynucleotide has a repeating structure. 12 Ex Biochem c1-genes DNA DNA Structure Writing a DNA strand an abbreviated notation dA dC dG OH 3' P 5' dT P 3' P P 5' even more abbreviated notations: pdApdCpdGpdT, or pdACGT, or ACGT 13 Ex Biochem c1-genes DNA 1.6 DNA Is a Double Helix The B-form of DNA is a double helix consisting of two polynucleotide chains that run antiparallel. The nitrogenous bases of each chain are flat purine or pyrimidine rings They face inward They pair with one another by hydrogen bonding to form A-T or G-C pairs only 14 Ex Biochem c1-genes DNA Figure 1.08: The double helix has constant width. 15 Ex Biochem c1-genes DNA Figure 1.09: Flat base pairs connect the DNA strands. 16 Ex Biochem c1-genes DNA The diameter of the double helix is 20 Å There is a complete turn every 34 Å Ten base pairs per turn The double helix forms: a major (wide) groove a minor (narrow) groove Figure 1.10 17 Ex Biochem c1-genes DNA DNA double helix 18 1.7 DNA Replication Is Semiconservative Ex Biochem c1-genes DNA The Meselson–Stahl experiment used density labeling to prove that: 19 The single polynucleotide strand is the unit of DNA that is conserved during replication Each strand of a DNA duplex acts as a template 模版 to synthesize a daughter strand. Ex Biochem c1-genes DNA DNA replication is semiconservative Figure 1.11: Base pairing accounts for specificity of replication. 20 Ex Biochem c1-genes DNA Semiconservative Replication 21 Ex Biochem c1-genes DNA Enzymes The enzymes that synthesize DNA are called DNA polymerases (DNA聚合脢) The enzymes that synthesize RNA are called RNA polymerases Nucleases are enzymes that degrade nucleic acids They include DNAases and RNAases They can be divided into endonucleases and exonucleases. 22 Ex Biochem c1-genes DNA Figure 1.14: Endonucleases attack internal bonds. Figure 1.15: Exonucleases nibble from the ends. 23 Ex Biochem c1-genes DNA 1.9 Genetic Information Can Be Provided by DNA or RNA Cellular genes are DNA Figure 1.16 Viruses and viroids may have genomes of RNA DNA is converted into RNA by transcription 24 RNA may be converted into DNA by reverse transcription The translation of RNA into protein is unidirectional. Ex Biochem c1-genes DNA Figure 1.18: Genomes vary greatly in size. 25 Ex Biochem c1-genes DNA 1.10 Nucleic Acids Hybridize by Base Pairing Heating causes the two strands of a DNA duplex to separate. The Tm is the midpoint of the temperature range for denaturation. Complementary single strands can renature when the temperature is reduced. Denaturation and renaturation/hybridization 雜交 can occur with the combinations: DNA–DNA DNA–RNA RNA–RNA They can be intermolecular or intramolecular 26 Ex Biochem c1-genes DNA Figure 1.20: DNA can be denatured and renatured. 27 1.11 Mutations Change the Sequence of DNA Ex Biochem c1-genes DNA All mutations 突變 consist of changes in the sequence of DNA. Mutations may: occur spontaneously be induced by mutagens Figure 1.22 28 Ex Biochem c1-genes DNA 1.12 Mutations May Affect Single Base Pairs or Longer Sequences A point mutation changes a single base pair. Point mutations can be caused by: the chemical conversion of one base into another mistakes that occur during replication Insertions are the most common type of mutation They result from the movement of transposable elements 29 Ex Biochem c1-genes DNA Figure 1.23 A transition replaces a G-C base pair with an A-T base pair or vice versa. Figure 1.24 30 Ex Biochem c1-genes DNA 1.13 The Effects of Mutations Can Be Reversed Forward mutations inactivate a gene Back mutations (or revertants) reverse their effects Insertions can revert by deletion of the inserted material 31 Deletions cannot revert Suppression occurs when a mutation in a second gene bypasses the effect of mutation in the first gene. Figure 1.25