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DNA Structure & Replication 1 2 DNA • DNA is often called the blueprint of life. • In simple terms, DNA contains the instructions for making proteins within the cell. 3 Why do we study DNA? We study DNA for many reasons, e.g., • its central importance to all life on Earth, • medical benefits such as cures for diseases, • better food crops. 4 Chromosomes and DNA • Our genes are on our chromosomes. • Chromosomes are made up of a chemical called DNA. 5 The Shape of the Molecule • DNA is a very long polymer. • The basic shape is like a twisted ladder or zipper. • This is called a double helix. 6 The Double Helix Molecule • Discovered by James Watson & Francis Crick • The DNA double helix has two strands twisted together. 7 One Strand of DNA • The backbone of the molecule is alternating phosphates and deoxyribose sugar • The teeth are nitrogenous bases. phosphate deoxyribose bases 8 Nucleotides O O -P O O O O -P O O One deoxyribose together with its phosphate and base make a nucleotide. O O -P O O Nitrogenous base O Phosphate C C C O Deoxyribose 9 One Strand of DNA nucleotide • One strand of DNA is a polymer of nucleotides. • One strand of DNA has many millions of nucleotides. 10 Four nitrogenous bases DNA has four different bases: C • Thymine T • Adenine A • Guanine G • Cytosine 11 Two Stranded DNA • Remember, DNA has two strands that fit together something like a zipper. • The teeth are the nitrogenous bases but why do they stick together? 12 C N N C N N C C C O • The bases attract each other because of hydrogen bonds. • Hydrogen bonds are weak but there are millions and millions of them in a single molecule of DNA. • The bonds between cytosine and guanine are shown here with dotted lines N Hydrogen Bonds N C N C C O 13 C N Hydrogen Bonds, cont. • When making hydrogen bonds, cytosine always pairs up with guanine • Adenine always pairs up with thymine • Adenine is bonded to thymine here N O O C C C C N C 14 Chargaff’s Rule: • Adenine and Thymine always join together A T • Cytosine and Guanine always join together C G 15 DNA by the Numbers • Each cell has about 2 m of DNA. • The average human has 75 trillion cells. • The average human has enough DNA to go from the earth to the sun more than 400 times. • DNA has a diameter of only 0.000000002 m. The earth is 150 billion m or 93 million miles from the sun. 16 DNA Replication 17 Replication Facts • DNA has to be copied before a cell divides • DNA is copied during the S or synthesis phase of interphase • New cells will need identical DNA strands 18 Synthesis Phase (S phase) • S phase during interphase of the cell cycle • Nucleus of eukaryotes S DNA replication takes place in the S phase. phase G1 interphase G2 Mitosis -prophase -metaphase -anaphase -telophase 19 DNA Replication • Begins at Origins of Replication • Two strands open forming Replication Forks (Y-shaped region) • New strands grow at the forks 5’ Parental DNA Molecule 3’ 3’ Replication Fork 20 5’ DNA Replication • As the 2 DNA strands open at the origin, Replication Bubbles form • Prokaryotes (bacteria) have a single bubble • Eukaryotic chromosomes have MANY bubbles Bubbles Bubbles 21 DNA Replication • Enzyme Helicase unwinds and separates the 2 DNA strands by breaking the weak hydrogen bonds 22 Question: • What would be the complementary DNA strand for the following DNA sequence? DNA 5’-CGTATG-3’ 23 Answer: DNA 5’-CGTATG-3’ DNA 3’-GCATAC-5’ 24 25 PROTEIN SYNTHESIS 26 DNA and Genes DNA • DNA contains genes, sequences of nucleotide bases • These Genes code for polypeptides (proteins) • Proteins are used to build cells and do much of the work inside cells Genes & Proteins Proteins are made of amino acids linked together by peptide bonds 20 different amino acids exist 29 Amino Acid Structure 30 Polypeptides • Amino acid chains are called polypeptides 31 DNA Begins the Process • DNA is found inside the nucleus • Proteins, however, are made in the cytoplasm of cells by organelles called ribosomes • Ribosomes may be free in the cytosol or attached to the surface of rough ER 32 Starting with DNA • DNA ‘s code must be copied and taken to the cytosol • In the cytoplasm, this code must be read so amino acids can be assembled to make polypeptides (proteins) • This process is called PROTEIN SYNTHESIS 33 RNA Roles of RNA and DNA • DNA is the MASTER PLAN • RNA is the BLUEPRINT of the Master Plan 35 RNA Differs from DNA • RNA has a sugar ribose DNA has a sugar deoxyribose 36 Other Differences • • RNA contains the base uracil (U) DNA has thymine (T) RNA molecule is single-stranded DNA is doublestranded DNA 37 Structure of RNA 38 . Three Types of RNA • Messenger RNA (mRNA) copies DNA’s code & carries the genetic information to the ribosomes • Ribosomal RNA (rRNA), along with protein, makes up the ribosomes • Transfer RNA (tRNA) transfers amino acids to the ribosomes where proteins are synthesized 39 Messenger RNA • Long Straight chain of Nucleotides • Made in the Nucleus • Copies DNA & leaves through nuclear pores • Contains the Nitrogen Bases A, G, C, U ( no T ) 40 Messenger RNA (mRNA) • Carries the information for a specific protein • Made up of 500 to 1000 nucleotides long • Sequence of 3 bases called codon • AUG – methionine or start codon • UAA, UAG, or UGA – stop 41 codons Ribosomal RNA (rRNA) • rRNA is a single strand 100 to 3000 nucleotides long • Globular in shape • Made inside the nucleus of a cell • Associates with proteins to form ribosomes • Site of protein Synthesis 42 The Genetic Code • A codon designates an amino acid • An amino acid may have more than one codon • There are 20 amino acids, but 64 possible codons • Some codons tell the ribosome to stop translating 43 The Genetic Code •Use the code by reading from the center to the outside •Example: AUG codes for Methionine 44 Name the Amino Acids • • • • • GGG? UCA? CAU? GCA? AAA? 45 Remember the Complementary Bases On DNA: A-T C-G On RNA: A-U C-G 46 Transfer RNA (tRNA) • Clover-leaf shape • Single stranded molecule with attachment site at one end for an amino acid • Opposite end has three nucleotide bases called the anticodon 47 Transfer RNA amino acid attachment site U A C anticodon 48 Codons and Anticodons • The 3 bases of an anticodon are complementary to the 3 bases of a codon • Example: Codon ACU Anticodon UGA UGA ACU 49 Transcription and Translation Pathway to Making a Protein DNA mRNA tRNA (ribosomes) Protein 51 Protein Synthesis The production or synthesis of polypeptide chains (proteins) Two phases: Transcription & Translation mRNA must be processed before it leaves the nucleus of eukaryotic cells 52 DNA RNA Protein Nuclear membrane DNA Transcription Eukaryotic Cell Pre-mRNA RNA Processing mRNA Ribosome Translation Protein 53 54 Transcription • The process of copying the sequence of one strand of DNA, the template strand • mRNA copies the template strand • Requires the enzyme RNA Polymerase 55 Template Strand 56 Question: What would be the complementary RNA strand for the following DNA sequence? DNA 5’-GCGTATG-3’ 57 Answer: • DNA 5’-GCGTATG-3’ • RNA 3’-CGCAUAC-5’ 58 Transcription • During transcription, RNA polymerase binds to DNA and separates the DNA strands • RNA Polymerase then uses one strand of DNA as a template to assemble nucleotides into RNA 59 Transcription • Promoters are regions on DNA that show where RNA Polymerase must bind to begin the Transcription of RNA • Called the TATA box • Specific base sequences act as signals to stop • Called the termination signal 60 RNA Polymerase 61 mRNA Processing • After the DNA is transcribed into RNA, editing must be done to the nucleotide chain to make the RNA functional • Introns, non-functional segments of DNA are snipped out of the chain 62 mRNA Editing • Exons, segments of DNA that code for proteins, are then rejoined by the enzyme ligase • A guanine triphosphate cap is added to the 5’ end of the newly copied mRNA • A poly A tail is added to the 3’ end of the RNA • The newly processed mRNA can then leave the nucleus 63 Result of Transcription CAP New Transcript Tail 64 mRNA Transcript •mRNA leaves the nucleus through its pores and goes to the ribosomes 65 66 67 Translation • Translation is the process of decoding the mRNA into a polypeptide chain • Ribosomes read mRNA three bases or 1 codon at a time and construct the proteins 68 Transcription Translation 69 Ribosomes • Made of a large and small subunit • Composed of rRNA (40%) and proteins (60%) • Have two sites for tRNA attachment --- P and A 70 Step 1- Initiation • mRNA transcript start codon AUG attaches to the small ribosomal subunit • Small subunit attaches to large ribosomal subunit mRNA transcript 71 Ribosomes Large subunit P Site A Site mRNA Small subunit A U G C U A C U U C G 72 Step 2 - Elongation • As ribosome moves, two tRNA with their amino acids move into site A and P of the ribosome • Peptide bonds join the amino acids Initiation aa1 aa2 2-tRNA 1-tRNA anticodon hydrogen bonds U A C A U G codon G A U C U A C U U C G A mRNA 74 Elongation peptide bond aa1 aa3 aa2 3-tRNA 1-tRNA anticodon hydrogen bonds U A C A U G codon 2-tRNA G A A G A U C U A C U U C G A mRNA 75 aa1 peptide bond aa3 aa2 1-tRNA 3-tRNA U A C (leaves) 2-tRNA A U G G A A G A U C U A C U U C G A mRNA Ribosomes move over one codon 76 aa1 peptide bonds aa4 aa2 aa3 4-tRNA 2-tRNA A U G 3-tRNA G C U G A U G A A C U A C U U C G A A C U mRNA 77 aa1 peptide bonds aa4 aa2 aa3 2-tRNA 4-tRNA G A U (leaves) 3-tRNA A U G G C U G A A C U A C U U C G A A C U mRNA Ribosomes move over one codon 78 aa1 peptide bonds aa5 aa2 aa3 aa4 5-tRNA U G A 3-tRNA 4-tRNA G A A G C U G C U A C U U C G A A C U mRNA 79 peptide bonds aa1 aa5 aa2 aa3 aa4 5-tRNA U G A 3-tRNA G A A 4-tRNA G C U G C U A C U U C G A A C U mRNA Ribosomes move over one codon 80 aa4 aa5 Termination aa199 aa3 primary structure aa2 of a protein aa200 aa1 200-tRNA A C U terminator or stop codon C A U G U U U A G mRNA 81 End Product –The Protein! • The end products of protein synthesis is a primary structure of a protein • A sequence of amino acid bonded together by peptide bonds aa2 aa1 aa3 aa4 aa5 aa199 aa200 82 83 Messenger RNA (mRNA) start codon mRNA A U G G G C U C C A U C G G C G C A U A A codon 1 protein codon 2 methionine glycine codon 3 serine codon 4 isoleucine codon 5 glycine codon 6 alanine codon 7 stop codon Primary structure of a protein aa1 aa2 aa3 peptide bonds aa4 aa5 aa6 84 Protein Synthesis 85