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DNA and Protein Synthesis California Standards 4 and 5 The Components and Structure of DNA • The Components and Structure of DNA •DNA is made up of nucleotides. The Components and Structure of DNA • A nucleotide is a monomer of nucleic acids made up of – a five-carbon sugar called deoxyribose –a phosphate group –a nitrogenous base • There are four kinds of bases in in DNA: •adenine •guanine •cytosine •thymine • The backbone of a DNA chain is formed by sugar and phosphate groups of each nucleotide. • The nucleotides can be joined together in any order. –X-Ray Evidence •Rosalind Franklin used X-ray diffraction to get information about the structure of DNA. •She aimed an X-ray beam at concentrated DNA samples and recorded the scattering pattern of the X-rays on film. • The Double Helix –Using clues from Franklin’s photograph and research from other scientists, James Watson and Francis Crick were able to build a physical model that explained how DNA carried information and could be copied. • The Double Helix Watson and Crick's model of DNA was a double helix, in which two strands were wound around each other, like a twisted ladder. • DNA Double Helix The Components and Structure of DNA • Watson and Crick discovered that hydrogen bonds can form only between certain base pairs—adenine and thymine, and guanine and cytosine. A-T, G-C • This principle is called base pairing. A T G C Review Questions A. What are the three parts of a nucleotide? B. What are the four bases and how to they attach together C. What is the shape of DNA 12–1 – DNA is a long molecule made of monomers called A. nucleotides. B. purines. C. pyrimidines. D. sugars. 12–1 – In DNA, the following base pairs occur: A. A with C, and G with T. B. A with T, and C with G. C. A with G, and C with T. D. A with T, and C with T. DNA Replication • DNA Replication •For a cell to reproduce, it must make a copy of its DNA so each cell has a complete copy of the information •The process of making a copy of the DNA is called DNA Replication DNA Replication • During DNA replication, the DNA molecule separates into two strands. Each strand, side, of the DNA chain has all the same information as the other strand, side. A-T-T-G-A-C-C-G-G-T-C-A-A-T T-A-A-C-T-G-G-C-C-A-G-T-T-A A-T-T-G-A-C-C-G-G-T-C-A-A-T TA A C TGG C CA G TTA AT T G AC C G GT C AAT T-A-A-C-T-G-G-C-C-A-G-T-T-A • Each strand of the double helix of DNA serves as a template for the new strand. • This form of replication is called semiconservative replication. –How Replication Occurs •DNA replication is carried out by enzymes, called Helicase, that “unzip” a molecule of DNA. •Hydrogen bonds between base pairs are broken and the two strands of DNA unwind. • The principal enzyme involved in DNA replication is DNA polymerase. • DNA polymerase joins individual nucleotides to produce a DNA molecule and then “proofreads” each new DNA strand. DNA Replication • DNA Replication •In most prokaryotes, DNA replication begins at a single point and continues in two directions. • In eukaryotic chromosomes, DNA replication occurs at hundreds of places. Replication proceeds in both directions until each chromosome is completely copied. • The sites where separation and replication occur are called replication forks • Replication can begin in the middle of the DNA chain. • The two chains unzip to form a replication bubble. • The two chains unzip until both chains have be separated and copied. DNA Replication New Strand Original strand Nitrogen Bases Growth Growth Replication Fork Replication Fork DNA Polymerase • As the replication bubble expands, one of the new DNA chains is replicated in a single continuous strand. • This is the “leading” strand. • The opposite strand, being formed in the opposite direction is the “lagging” strand. • It is formed in many small fragments that are ultimately attached together by an enzyme called DNA Ligase • DNA ligase attaches all DNA fragments together into a single complete chain. Review Questions a. What is semiconservative replication? b. What does DNA Polymerase, DNA Ligase and Helicase do? 12–2 – The first step in DNA replication is A. producing two new strands. B. separating the strands. C. producing DNA polymerase. D. correctly pairing bases. – A DNA molecule separates, and the sequence GCGAATTCG occurs in one strand. What is the base sequence on the other strand? A. GCGAATTCG B. CGCTTAAGC C. TATCCGGAT D. GATGGCCAG – In addition to carrying out the replication of DNA, the enzyme DNA polymerase also functions to A. unzip the DNA molecule. B. regulate the time copying occurs in the cell cycle. C. “proofread” the new copies to minimize the number of mistakes. D. wrap the new strands onto histone proteins. 12-3 RNA and Protein Synthesis RNA Function • Genes are coded DNA instructions that control the production of proteins. • Genetic messages can be decoded by copying part of the nucleotide sequence from DNA into RNA. • RNA contains coded information for making proteins. The Structure of RNA • The Structure of RNA •RNA consists of a long chain of nucleotides. •Each nucleotide is made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base. • There are three main differences between RNA and DNA: •The sugar in RNA is ribose instead of deoxyribose. •RNA is generally singlestranded. •RNA contains uracil in place of thymine. Deoxyribose Ribose HOCH2 HO HOCH2 HO OH H OH OH DNA RNA –What are the three main types of RNA? Types of RNA • Types of RNA –There are three main types of RNA: •messenger RNA •ribosomal RNA •transfer RNA • Messenger RNA (mRNA) carries copies of instructions for assembling amino acids into proteins. Ribosome Ribosomal RNA • Ribosomes are made up of proteins and ribosomal RNA (rRNA). • During protein construction, transfer RNA (tRNA) transfers each amino acid to the ribosome. Amino acid Transfer RNA Transcription –What is transcription? Transcription RNA RNA polymerase DNA •Transcription is when a section of DNA is copied by an enzyme to make a duplicate copy. The copy is made out of RNA. •Transcription requires the enzyme RNA polymerase. –During transcription, RNA polymerase binds to DNA and separates the DNA strands. –RNA polymerase then uses one strand of DNA as a template from which nucleotides are assembled into a strand of RNA. • RNA polymerase binds only to regions of DNA known as promoters. • Promoters are signals in DNA that indicate to the enzyme where to attach to make RNA. Transcription RNA RNA polymerase DNA RNA Editing •The DNA of eukaryotic genes contains sequences of nucleotides, called introns, that are not involved in coding for proteins. •The DNA sequences that code for proteins are called exons. •When RNA molecules are formed, introns and exons are copied from DNA. RNA Editing • The introns are cut out of RNA molecules. • The exons are the spliced together to form mRNA. Exon Intron DNA Pre-mRNA mRNA Cap Tail The Genetic Code •The genetic code is the “language” of mRNA instructions. •The code is written using four “letters” (the bases: A, U, C, and G). • A codon consists of three consecutive nucleotides on mRNA that specify a particular amino acid. •Each codon specifies a particular amino acid that is to be placed on the polypeptide chain. •Some amino acids can be specified by more than one codon. •There is one codon AUG that can either specify the amino acid methionine or serve as a “start” codon for protein synthesis. •There are three “stop” codons that do not code for any amino acid. These “stop” codons signify the end of a polypeptide. Translation –What is translation? –Translation is the decoding of an mRNA message into a polypeptide chain (protein). –Translation takes place on ribosomes. –During translation, the cell uses information from messenger RNA to produce proteins. •Messenger RNA is transcribed in the nucleus, and then enters the cytoplasm where it attaches to a ribosome. Nucleus mRNA • Translation begins when an mRNA molecule attaches to a ribosome. • As each codon of the mRNA molecule moves through the ribosome, the proper amino acid is brought into the ribosome by tRNA. • In the ribosome, the amino acid is transferred to the growing polypeptide chain. • Each tRNA molecule carries only one kind of amino acid. • In addition to an amino acid, each tRNA molecule has three unpaired bases. • These bases, called the anticodon, are complementary to one mRNA codon. •The ribosome binds new tRNA molecules and amino acids as it moves along the mRNA. Phenylalanine Methionine Ribosome mRNA Start codon Lysine tRNA • Peptide bonds form between the amino acids creating a polypeptide chain Peptide Bond Lysine tRNA Translation direction mRNA Ribosome The process continues until the ribosome reaches a stop codon. Polypeptide Ribosome tRNA mRNA The Roles of RNA and DNA •The cell uses the DNA “Recipe Book” (genes) to prepare mRNA “Recipe” (copy). The DNA stays in the nucleus. •The mRNA molecules go to the protein building sites in the cytoplasm—the ribosomes. • The sequence of bases in DNA (gene) is used as a template for mRNA. • The codons of mRNA specify the sequence of amino acids in a protein that is assembled at the ribosome. Codon Codon Codon Single strand of DNA Codon Codon Codon mRNA Alanine Arginine Leucine Amino acids within a polypeptide Protein Synthesis 1. DNA is copied to make mRNA in the nucleus 2. Ribosomes attach to the mRNA in the cytoplasm 3. tRNA brings Amino Acids to the ribosomes to make Proteins DNA→mRNA→Ribosome→Protein Genes and Proteins • Genes contain instructions for assembling proteins. • The different genes in DNA cause different proteins to be produced. • Each type of cell in the body produces different proteins that allow the cell to do specific jobs. 12–3 – The sequence that protein synthesis occurs? A. mRNA, DNA, Ribosome, protein B. DNA, Ribosome, mRNA, Protein C. Ribosome, DNA, protein, mRNA D. DNA, mRNA, Ribosome, Protein 12–3 – A base that is present in RNA but NOT in DNA is A. thymine. B. uracil. C. cytosine. D. adenine. 12–3 – The nucleic acid responsible for bringing individual amino acids to the ribosome is A. transfer RNA. B. DNA. C. messenger RNA. D. ribosomal RNA. 12–3 – A regions of a DNA molecule that codes for a polypeptide (protein) A. introns. B. exons. C. promoters. D. codons. 12–3 – A codon typically carries sufficient information to specify a(an) A. single base pair in RNA. B. single amino acid. C. entire protein. D. single base pair in DNA. Mutations –Mutations are changes in the genetic material. Kinds of Mutations •Mutations that produce changes in a single gene are known as gene mutations. •Mutations that produce changes in whole chromosomes are known as chromosomal mutations. •Gene mutations involving a change in one or a few nucleotides are known as point mutations because they occur at a single point in the DNA sequence. •Point mutations include substitutions, insertions, and deletions. • Substitutions usually affect no more than a single amino acid. • The effects of insertions or deletions are more dramatic. • The addition or deletion of a nucleotide causes a shift in the grouping of codons. • Changes like these are called frameshift mutations. • Frameshift mutations may change every amino acid that follows the point of the mutation. • Frameshift mutations can alter a protein so much that it is unable to perform its normal functions. • In an insertion, an extra base is inserted into a base sequence. • In a deletion, the loss of a single base is deleted and the reading frame is shifted. – A mutation that affects every amino acid following an insertion or deletion is called a(an) A. frameshift mutation. B. point mutation. C. chromosomal mutation. D. inversion. – The type of point mutation that usually affects only a single amino acid is called A. a deletion. B. a frameshift mutation. C. an insertion. D. a substitution. Manipulating DNA The Tools of Molecular Biology How do scientists make changes to DNA? –Scientists use their knowledge of the structure of DNA and its chemical properties to study and change DNA molecules. –Scientists use different techniques to: •extract DNA from cells •cut DNA into smaller pieces •identify the sequence of bases in a DNA molecule •make unlimited copies of DNA •In genetic engineering, biologists make changes in the DNA code of a living organism. –DNA Extraction •DNA can be extracted from most cells by a simple chemical procedure. •The cells are opened and the DNA is separated from the other cell parts. –Cutting DNA •Most DNA molecules are too large to be analyzed, so biologists cut them into smaller fragments using restriction enzymes. –Each restriction enzyme cuts DNA at a specific sequence of nucleotides. Recognition sequences DNA sequence Restriction enzyme EcoR I cuts the DNA into fragments Sticky end • A restriction enzyme will cut a DNA sequence only if it matches the sequence precisely. • The locations where the enzyme opens the DNA are called sticky ends. Using the DNA Sequence –Cutting and Pasting •Short sequences of DNA can be assembled using DNA synthesizers. •“Synthetic” sequences can be joined to “natural” sequences using enzymes that splice DNA together. Using the DNA Sequence • These enzymes also make it possible to take a gene from one organism and attach it to the DNA of another organism. • Such DNA molecules are sometimes called recombinant DNA. Separating DNA • In gel electrophoresis, DNA fragments travel through a gel, a porous material. • The shorter lengths travel faster than the longer lengths. • Gel electrophoresis can be used to compare the DNA of different organisms or different individuals. Longer fragments Shorter fragments Gel Electrophoresis Making Copies • Polymerase chain reaction (PCR) is a technique that allows biologists to make copies of genes. • A biologist adds short pieces of DNA that are complementary to portions of the sequence. Using the DNA Sequence • DNA is heated to separate its two strands • DNA polymerase starts making copies of the region between the primers two separated strands Polymerase Chain Reaction (PCR) DNA heated to separate strands DNA polymerase adds complementary strand DNA fragment to be copied PCR cycles 1 DNA copies 1 2 2 3 4 4 8 5 etc. 16 etc. Transforming Bacteria • Bacteria can be given human DNA so the bacteria will make human proteins. • Human insulin is common example. Transforming Bacteria • Foreign DNA is first joined to a small, circular DNA molecule found in bacteria. • These rings are known as plasmids. • Using restriction enzymes, human DNA is cut, and inserted in the bacteria plasmid. Transforming Bacteria Recombinant DNA Gene for human growth hormone Gene for human growth hormone Human Cell Bacterial chromosome Sticky ends DNA recombination DNA insertion Bacteria cell Plasmid Bacteria cell containing gene for human growth hormone Transforming Plant Cells • To help improve the quality of many crops, plants receive recombinant DNA for a variety of genes. • Plants receive genes that make them resistant to herbicides and pesticides. 13-3 – Which types of cells have plasmids? A. bacteria only. B. plant cells only. C. plant, animal, and bacterial cells. D. animal cells only. 13-2 – Restriction enzymes are used to A. extract DNA. B. cut DNA. C. separate DNA. D. replicate DNA. • 13-2 A particular restriction enzyme is used to A. cut up DNA in random locations. B. cut DNA at a specific nucleotide sequence. C. extract DNA from cells. D. separate negatively charged DNA molecules. 13-2 – During gel electrophoresis, DNA fragments become separated because A. multiple copies of DNA are made. B. recombinant DNA is formed. C. DNA molecules are negatively charged. D. smaller DNA molecules move faster than larger fragments. 13-2 – Which technique is used to make many copies of DNA in a short period of time? A. Restriction enzymes. B. Gel electrophorysis. C. Recombinant DNA D. Polymerase Chain Reaction (PCR)