1. Replication, transcription, translation and expression of nucleic acid

2. Central dogma of molecular biology translation transcription replication DNARNAPROTEIN Solid arrow indicate types of information transfers that occur in cells. DNA directs its own replication to produce new DNA molecule; DNA is transcribes into RNA; RNA is translated into protein. The dashed lines represent information transfers that occur in certain organisms. Describe the flow of genetic information from DNA through RNA and eventually to protein

3. Information Flow DNA RNA Protein Replication: DNA duplicates itself Transcription: RNA is made on a DNA template Translation: Protein is synthesized from AAs and the three RNAs. Reverse Transcription: RNA directs synthesis of DNA RNA replication: RNA replicates itself

4. DNA replication DNA replication is an anabolic polymerization process, that allows a cell to pass copies of its genome to its descendants. DNA replication is an anabolic polymerization process, that allows a cell to pass copies of its genome to its descendants. Must occur before every cell division Must occur before every cell division After two strands of DNA separate, each serves as template for the synthesis of a complementary strand. After two strands of DNA separate, each serves as template for the synthesis of a complementary strand. Biologists say that DNA replication is semiconservative replication because each daughter DNA molecule is composed of one original strand and one new strand. Biologists say that DNA replication is semiconservative replication because each daughter DNA molecule is composed of one original strand and one new strand.

5. PRINCIPAL OF DNA REPLICATION

6. c) Synthesis of lagging strand DNA REPLICATION PROCESS

7. Initial Processes in DNA Replication DNA replication begins at a specific sequence of nucleotides called an origin. DNA replication begins at a specific sequence of nucleotides called an origin. First, a cell removes chromosomal proteins, exposing the DNA helix. First, a cell removes chromosomal proteins, exposing the DNA helix. Next, an enzyme called DNA helicase locally "unzips/unwind" the DNA molecule by breaking the hydrogen bonds between complementary nucleotide bases, which exposes the bases in a replication fork. Other protein molecules stabilize the single strands so that they do not rejoin while replication proceeds Next, an enzyme called DNA helicase locally "unzips/unwind" the DNA molecule by breaking the hydrogen bonds between complementary nucleotide bases, which exposes the bases in a replication fork. Other protein molecules stabilize the single strands so that they do not rejoin while replication proceeds

8. After helicase untwists and separates the strands, a molecule of an enzyme called DNA polymerase III binds to each strand. After helicase untwists and separates the strands, a molecule of an enzyme called DNA polymerase III binds to each strand. DNA polymerases III replicate DNA in only one direction - 5' to 3' - like a jeweler stringing pearls to make a necklace, adding them one at a time, always moving from one end of the string to the other. DNA polymerases III replicate DNA in only one direction - 5' to 3' - like a jeweler stringing pearls to make a necklace, adding them one at a time, always moving from one end of the string to the other. Because the two original (template) strands are antiparallel cells synthesize new strands in two different ways: Because the two original (template) strands are antiparallel cells synthesize new strands in two different ways: 1) One new strand, called the leading strand, is synthesized continuously as a single long chain of nucleotides. 2)The other new strand, called the lagging strand, is synthesized in short segments that are later joined.

10. Synthesis of the Leading Strand A cell synthesizes a leading strand toward the replication fork in the following series of five steps 1) An enzyme called primase synthesizes a short RNA molecule that is complementary to the template DNA strand. This RNA primer provides the 3' hydroxyl group required by DNA polymerase. 2) Triphosphate deoxyribonucleotides form hydrogen bonds with their complements in the parental strand. Adenine nucleotides bind to thymine nucleotides, and guanine nucleotides bind to cytosine nucleotides. 3) Using the energy in the high-energy bonds of the triphosphate deoxyribonucleotides, DNA polymerase III covalently joins them one at a time by dehydration synthesis to the leading strand.

11. 4) DNA polymerase III also performs a proofreading function. About 1 out of every 100,000 nucleotides is mismatched with its template; for instance, a guanine might become incorrectly paired with a thymine. DNA polymerase III recognizes most such errors and removes the incorrect nucleotides before proceeding with synthesis. This role, known as the proofreading exonuclease function, acts like the delete key on a keyboard, removing the most recent error. DNA polymerase III recognizes most such errors and removes the incorrect nucleotides before proceeding with synthesis. This role, known as the proofreading exonuclease function, acts like the delete key on a keyboard, removing the most recent error. Because of this proofreading exonuclease function, only about one error remains for every ten billion (10 10 ) base pairs replicated. Because of this proofreading exonuclease function, only about one error remains for every ten billion (10 10 ) base pairs replicated. 5) Another DNA polymerase - DNA polymerase I - ­replaces the RNA primer with DNA. Note that researchers named DNA polymerase enzymes in the order of their discovery, not the order of their actions.

12. Synthesis of the Lagging Strand The steps in the synthesis of a lagging strand are as follows : The steps in the synthesis of a lagging strand are as follows : As with the leading strand, primase synthesizes RNA primers. As with the leading strand, primase synthesizes RNA primers. Nucleotides pair up with their complements in the template-adenine with thyamine, and cytosine with guanine. Nucleotides pair up with their complements in the template-adenine with thyamine, and cytosine with guanine.

13. DNA polymerase III joins neighboring nucleotides and proofreads. In contrast to synthesis of the leading strand, however, the lagging strand is synthesized in discontinuous segments called Okazaki fragments. Each Okazaki fragment requires a new RNA primer and consists of 1000 to 2000 nucleotides. DNA polymerase III joins neighboring nucleotides and proofreads. In contrast to synthesis of the leading strand, however, the lagging strand is synthesized in discontinuous segments called Okazaki fragments. Each Okazaki fragment requires a new RNA primer and consists of 1000 to 2000 nucleotides. DNA polymerase I replaces the RNA primers of Okazaki fragments with DNA and further proofreads the daughter strand. DNA polymerase I replaces the RNA primers of Okazaki fragments with DNA and further proofreads the daughter strand. DNA ligase seals the gaps between adjacent Okazaki fragments to form a continuous DNA strand. DNA ligase seals the gaps between adjacent Okazaki fragments to form a continuous DNA strand.

14. Transcription TRANSCRIPTION is the synthesis of RNA under the direction of DNA TRANSCRIPTION is the synthesis of RNA under the direction of DNA DNA strand provide a template for assembling a sequence of RNA nucleotides DNA strand provide a template for assembling a sequence of RNA nucleotides The resulting RNA molecule is the transcript of the gene’s protein-building instruction The resulting RNA molecule is the transcript of the gene’s protein-building instruction Called mRNA (messenger RNA) – carry genetic message from DNA Called mRNA (messenger RNA) – carry genetic message from DNA

15. TRANSCRIPTION Cells transcribe four main types of RNA from DNA : Cells transcribe four main types of RNA from DNA : RNA primer molecules for DNA polymerase to use during DNA replication RNA primer molecules for DNA polymerase to use during DNA replication messenger RNA (mRNA) molecules, which carry genetic information from chromosomes to ribosomes messenger RNA (mRNA) molecules, which carry genetic information from chromosomes to ribosomes ribosomal RNA (rRNA) molecules, which combine with ribosomal polypeptides to form ribosomes-the organelles that synthesize polypeptides ribosomal RNA (rRNA) molecules, which combine with ribosomal polypeptides to form ribosomes-the organelles that synthesize polypeptides transfer RNA (tRNA) molecules, which deliver amino acids to the ribosomes transfer RNA (tRNA) molecules, which deliver amino acids to the ribosomes

16. The stages of transcription 1) Initiation 2) Chain elongation 3) termination

18. Initiation of Transcription RNA polymerases - the enzymes that synthesize RNA RNA polymerases - the enzymes that synthesize RNA RNA polymerase bind to specific nucleotide sequences called promoter - include the transcription startpoint (the nucleotides where RNA synthesis begin) RNA polymerase bind to specific nucleotide sequences called promoter - include the transcription startpoint (the nucleotides where RNA synthesis begin)

19. Initiation of Transcription Once it bind to the promoter sequence, RNA polymerase unwinds and unzips the DNA molecule in the promoter region Once it bind to the promoter sequence, RNA polymerase unwinds and unzips the DNA molecule in the promoter region After unzip, RNA polymerase initiate RNA synthesis at the promoter on the template strand After unzip, RNA polymerase initiate RNA synthesis at the promoter on the template strand

20. Elongation of the RNA Transcript As RNA polymerase moves along the DNA, it continues to untwist the double helix for pairing with RNA nucleotides As RNA polymerase moves along the DNA, it continues to untwist the double helix for pairing with RNA nucleotides The enzyme add nucleotides to the 3’ end of the growing RNA molecule as it continues along the double helix The enzyme add nucleotides to the 3’ end of the growing RNA molecule as it continues along the double helix

21. Elongation of the RNA Transcript In the wake of transcription, the DNA strands re-form the double helix and the new RNA molecule peels away from its DNA template In the wake of transcription, the DNA strands re-form the double helix and the new RNA molecule peels away from its DNA template

22. Termination of Transcription Transcription proceeds until shortly after the RNA polymerase transcribes a DNA sequence called a terminator Transcription proceeds until shortly after the RNA polymerase transcribes a DNA sequence called a terminator Terminator = sequence of nucleotides along the DNA, that signal the end of transcription unit Terminator = sequence of nucleotides along the DNA, that signal the end of transcription unit After the RNA is released, the polymerase dissociate from the DNA After the RNA is released, the polymerase dissociate from the DNA

23. TRANSLATION Translation is the process whereby ribosomes use the genetic information of nucleotide sequences to synthesize polypeptides composed of specific amino acid sequences.

25. In translation process, cell interprets a genetic message and builds a protein Message = is a series of codons along an mRNA molecule Interpreter = transfer RNA (tRNA) tRNA = transfer amino acids from cytoplasm’s amino acid pool to ribosome The ribosome adds each amino acid brought to it by tRNA to the growing end of a polypeptide chain

26. As a tRNA molecule arrives at a ribosome, it bears a specific amino acid at one end. At the other end is a nucleotide triplet called an anticodon, which binds according to base-pairing rules to a complementary codon on mRNA.

27. How do ribosomes interpret the nucleotide sequence of mRNA to determine the correct order in which to assemble amino acids?

28. The genetic code Is a coding dictionary that specifies a meaning for a base sequence the genetic code define as triplets of mRNA nucleotides called codons that code for specific amino acids. 64 possible arrangements - more than enough to specify 21 amino acids.

29. 61 codons specify amino acids and 3 codons -UAA, UAG, and UGA-to stop translating UGA codes for the 21st amino acid, selenocysteine. Codon AUG also has a dual function, acting as both a start signal and coding for an amino acid – methionine.

31. AUG = start codon

33. Mutations of Genes: Types of mutation Mutations range from large changes in an organism's genome, such as the loss or gain of an entire chromosome, to the most common type of mutation - point mutations - in which just one nucleotide base pair is affected. Mutations range from large changes in an organism's genome, such as the loss or gain of an entire chromosome, to the most common type of mutation - point mutations - in which just one nucleotide base pair is affected. Mutations include base pair insertions, deletions, and substitutions. Mutations include base pair insertions, deletions, and substitutions.

34. Effects of Mutations Some base-pair substitutions produce silent mutations because the substitution does not change the amino acid sequence because of the redundancy of the genetic code. Some base-pair substitutions produce silent mutations because the substitution does not change the amino acid sequence because of the redundancy of the genetic code. For example, when the DNA triplet AAA " is changed to AAG, the mRNA codon will be changed from UUU to UUC; however, because both codons specify the amino acid phenylalanine, there is no change in the phenotype - the mutation is silent because it affects the genotype only. For example, when the DNA triplet AAA " is changed to AAG, the mRNA codon will be changed from UUU to UUC; however, because both codons specify the amino acid phenylalanine, there is no change in the phenotype - the mutation is silent because it affects the genotype only.

35. Of greater concern are substitutions that change a codon for one amino acid into a codon for a different amino acid. Of greater concern are substitutions that change a codon for one amino acid into a codon for a different amino acid. A change in a nucleotide sequence resulting in a codon that specifies a different amino acid is called a missense mutation; what gets transcribed and translated makes sense, but not the right sense. A change in a nucleotide sequence resulting in a codon that specifies a different amino acid is called a missense mutation; what gets transcribed and translated makes sense, but not the right sense. The effect of missense mutations depends on where in the protein the different amino acid occurs. The effect of missense mutations depends on where in the protein the different amino acid occurs. When the different amino is in a critical region of a protein, the protein becomes nonfunctional; however, when the different amino acid is in a less important region, the mutation has no adverse effect. When the different amino is in a critical region of a protein, the protein becomes nonfunctional; however, when the different amino acid is in a less important region, the mutation has no adverse effect.

36. A third type of mutation occurs when a base-pair substitution changes an amino acid codon into a stop codon. A third type of mutation occurs when a base-pair substitution changes an amino acid codon into a stop codon. This is called a nonsense mutation. Nearly all nonsense mutations result in nonfunctional proteins. This is called a nonsense mutation. Nearly all nonsense mutations result in nonfunctional proteins.

37. Frameshift mutations (that is, insertions or deletions) typically result in drastic missense and nonsense mutations, except when the insertion or deletion is very close to the end of a gene Frameshift mutations (that is, insertions or deletions) typically result in drastic missense and nonsense mutations, except when the insertion or deletion is very close to the end of a gene