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1/28/2016 Performance Expectations (by the end of Unit 3, Part 1 you should be able to…) DNA, RNA, and Protein Synthesis Performance Expectations (by the end of Unit 3, you should be able to…) • HS-LS3-1: Ask questions to clarify relationships about the role of DNA and chromosomes in coding the instructions for characteristic traits passed from parents to offspring. (All organisms have DNA. If the structure of DNA is universal, how come you don’t look like a fish, or a monkey? What does inheritance mean (not the kind where you get money)? ) Where is DNA? • DNA is located in the nucleus of cells. • All cells in a person’s body have the same DNA and the same genes. • Genes are sequences located in the DNA that code for specific characteristics. • HS-LS1-1: Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins which carry out the essential functions of life through systems of specialized cells. (Proteins carry out the essential functions of life – remember enzymes?! How do proteins get made in the first place? DNA provides the blueprints, or recipes for proteins, so we’ll look at the structure of DNA, look at RNA and then study the process of making proteins.) What is DNA? • DNA (deoxyribonucleic acid) is a molecule that carries most of the genetic instructions used in the development, functioning and reproduction of all known living organisms and many viruses. • DNA stores biological information – it’s a blueprint for life processes. QOD 1/19/2016 • What is the function of DNA? (deoxyribonucleic acid) • The “expression” of the genes differs between cells. For example, a liver cell will make different proteins than a skin cell. • No QOD sheets. Write in your notes template. 1 1/28/2016 1/19/2016 Assignment • You are reading Chapter 10 in the textbook and taking notes (outline). • You’ll complete the Reading Guide worksheet tomorrow using notes only. • Write what you need – I won’t be checking for complete sentences, spelling errors, etc. • Don’t copy the paragraphs – summarize! • Once you complete the Reading Guide and I have checked it, you will have the opportunity to correct it for your grade – but only if you make a good faith effort the first time. QOD 1/20/2016 • What is the shape of DNA? Include this in your outline…. • What was Rosalind Franklin’s role in establishing the structure of DNA? • What’s the monomer of a nucleic acid? • What are the steps of DNA replication? What’s a replication fork? • How does RNA differ from DNA? • What are the steps of protein synthesis? QOD 1/21/2016 • What are the base pairing rules in DNA? No QOD sheets. Write in your notes template. History of DNA History of DNA An overview of the many experiments conducted in the 20th century to further our understanding of the role and function of DNA. • 1928- Fredrick Griffith ▫ He found that when harmless bacteria are mixed with dead harmful bacteria, the harmless bacteria will absorb the genetic material of the harmful and become harmful themselves. ▫ The transfer of genetic (hereditary) material from one cell to another is called transformation. 2 1/28/2016 Two strains of Streptococcus pneumoniae bacteria, one virulent and one not. The heat killed S strain released a hereditary factor that transfers the disease-causing ability to the harmless cells. History of DNA • 1940s- Oswald Avery and colleagues ▫ Avery wanted to know what caused the transformation in Griffith’s experiment DNA, RNA, or protein. Used enzymes to each of the molecules in heat killed S cells. Separately mixed each type with live R cells. The cells missing DNA did not transform the R cells into S cells. They concluded DNA was the cause of transformation. ▫ In other words, they found if harmless bacteria took in harmful bacteria’s DNA, the harmless became harmful. Discovery of DNA • 1952- Alfred Hershey and Martha Chase ▫ Wanted to test whether DNA or protein was the genetic material that viruses pass on when they infect an organism. ▫ They used viruses that infect bacteria (called bacteriophages) ▫ They radioactively labeled the DNA and the protein (this allowed them to trace the path of each). ▫ They found DNA was injected into the bacteria to infect it, not protein. So DNA was the genetic material in viruses. Hershey and Chase Discovery of DNA • 1953- James Watson, Francis Crick, Rosalind Franklin, and Maurice Wilkins and the structure of DNA. ▫ Franklin and Wilkins discover DNA is helical by use of X-ray diffraction. ▫ Watson and Crick obtain Franklin’s photograph without permission. ▫ Using the photograph and other information, Watson and Crick build a model of DNA and determine it is a double helix. ▫ Watson, Crick and Wilkins went on to win the Nobel Prize in 1962. 3 1/28/2016 DNA Structure • DNA is a double helix. Structure of DNA • Remember that there are four macromolecules (the molecules of life): carbohydrates, lipids, proteins and nucleic acids • Nucleic acids are polymers. (DNA is a polymer.) • The monomer of a nucleic acid is a nucleotide. ▫ Monomers: small units that make up larger units called polymers. One strand of DNA is a long polymer of nucleotides. One strand of DNA has many millions of nucleotides! phosphate deoxyribose bases DNA Structure • Nucleotides (the monomers of DNA) have 3 parts: 1.Nitrogenous base (there are 4 kinds) 2.Phosphate Group 3.5 carbon sugar called deoxyribose DNA Structure – Parts of Nucleotides • Nitrogenous bases: ▫ Contain nitrogen and is a base ▫ Purines- (double ringed) Adenine (A) Guanine (G) ▫ Pyrimadines- (single ringed) Cytosine (C) Thymine (T) nucleotide 4 1/28/2016 Hydrogen Bonding • A purine (A or G) will easily form a hydrogen bond with a pyrimidine (T or C). This is because of their structure and the availability of bonding sites. • Hydrogen bonds are weak but there are millions and millions of them in a single molecule of DNA. DNA Structure • If DNA was a spiral staircase… ▫ The alternating sugar and phosphates would be the hand rails. ▫ The bases would be the steps. ▫ But, they would be weak steps as they are only held together by hydrogen bonds. DNA Structure • Base pairing rules in DNA: ▫ ▫ ▫ ▫ Hydrogen bonds form between specific pairs. Adenine ALWAYS pairs with Thymine. Cytosine ALWAYS pairs with Guanine. These pairs (A-T and C-G) are called complementary base pairs. ▫ Each complimentary pair contains one single and one double ringed base DNA Structure • DNA is made up of 2 straight chains of nucleotides • The bases on each of those chains are attracted to each other and form hydrogen bonds. • The force of thousands or millions of hydrogen bonds keeps the two strands of DNA held tightly together. DNA Structure • Since the sugar-phosphate “hand rails” of DNA never change, we often simplify DNA into the letters of the nitrogenous bases. • For example, this DNA strand can be simplified to… TGAC ACTG DNA Structure • Because of the base pairing rules, one strand of DNA is complementary to the other strand (otherwise they would not stick together!) ▫ The order of the nitrogenous bases on DNA is called its base sequence ▫ So if one strand has a base sequence of TGCC, the other strand will have ACGG. 5 1/28/2016 Let’s Practice • Write the complimentary strand for… “The Double Helix” Video • http://www.hhmi.org/biointeractive/doublehelix TGACCGAT ACTGGCTA TGGCCAATATA ACCGGTTATAT “The Double Helix” Video Questions 1. 2. What are the chemical components of a DNA molecule? (There are three.) How are the instructions for the traits of an organism determined? a. The proportions of A, T, C and G in DNA molecules. b. The order of nucleotides in DNA molecules. c. The length of DNA molecules. 3. The two strands of a DNA molecule are held together by hydrogen bonds between the ___________. 4. In the 1950s when Watson and Crick were working on their model of DNA, many scientists did not think that DNA carried the genetic code. a. What was the other type of molecule that some scientists thought might carry genetic information? b. Why did this other type of molecule seem a likely candidate? 5. The following table is a sample of the data Erwin Chargaff published in 1952. Which of the following observations can be supported by the data in the table? a. All organisms contain about the same amounts of adenine and thymine in their DNA. b. The proportions of adenine + thymine and guanine + cytosine are the same in all organisms. c. Larger organisms have greater amounts of each nitrogenous base than smaller organisms have. d. The total length of DNA molecules in all organisms in about the same. 6. In one or two sentences, explain how these observations helped Watson and Crick build their mode of DNA. 7. Why do you think the proportions of nitrogenous bases in the DNA of two different human tissues (thymus and sperm) are about the same? 8. The image shows the famous photo B51 taken in May 1952 by Rosalind Franklin and her student Raymond Gosling. This x -ray diffraction pattern provided information about the positions of atoms in a DNA molecule. Proportions of Nitrogenous Bases in the DNA of Different Organisms Organism Tissue %Adenine %Guanine %Cytosine %Thymine Yeast 31.3 18.7 17.1 32.9 Sea urchin Sperm 32.8 17.7 18.4 32.1 Rat Bone marrow 28.6 21.4 21.5 28.4 Human Thymus 30.9 19.9 19.8 29.4 Human Sperm 30.3 19.5 19.9 30.3 a. What is the clue in this photo that revealed DNA is a helix? b. Measurements revealed that the distance between the two strands was always equal. Explain how this information helped Watson and Crick build a successful model of DNA. c. Was this information consistent with the data obtained by Chargaff? Why or why not? QOD 1/25/16 • What are the three parts of a nucleotide? 6 1/28/2016 Why would DNA need to replicate? • Approximately 2 trillion cells are produced by an adult human body every day. • All cells come from the division of preexisting cells. • Remember, all cells in a person’s body have the same DNA. DNA Replication • DNA Replication is the process by which DNA is copied in a cell before the cell divides. DNA Replication DNA Replication • First, enzymes called helicases separate the two strands of DNA. ▫ Helicases break hydrogen bonds. ▫ The Y-shaped region formed as bonds are broken is called the replication fork. DNA Replication • Next, enzymes called DNA polymerases add complimentary nucleotides to the separated strands of DNA. ▫ Nucleotides are found floating freely in the nucleus. ▫ The addition of new nucleotides occurs in opposite directions on each strand (one toward the replication fork and one away from it). 7 1/28/2016 DNA Replication • Replication of DNA proceeds in opposite directions on each strand. • On one strand, DNA replicates in the direction of the replication fork. • On the other strand, short fragments are replicated in the reverse direction. DNA Replication • On the strand that is moving away from the replication fork, DNA polymerase synthesizes a short fragment at a time and connects them into a strand at the ends. • These fragments are called Okazaki Fragments, after the scientist who discovered them. DNA Replication – Why do strands go in opposite directions? • When two strands of DNA bind together, they line up in opposite directions (remember, each nucleotide is paired with its partner). • One end is called the 5’ (five prime) end and one end is called the 3’ (three prime) end. • This refers to the five carbon sugars in DNA. Each carbon is assigned a number. Carbons assigned the number five and carbons assigned the number three are at different ends. • DNA polymerase can replicate DNA only in the direction of 5’ to 3’. DNA Replication • Several replication forks form on the DNA strand and the process continues until all of the DNA has been replicated. ▫ If only one was formed it would take too long to replicate DNA (53 days for humans!!) • When replication is finished, there are two DNA molecules. Each has one old strand and one new strand. 8 1/28/2016 DNA Replication • Replication is usually very accurate. ▫ There is only about one error for every BILLION nucleotides added! ▫ The reason is that DNA polymerases also “proofread” the DNA and fix any errors during replication. DNA Replication • If an error does occur, it results in a different nucleotide sequence in the new DNA strands. ▫ This is called a mutation. ▫ A change in even one nucleotide can be very harmful to an organism (for reasons we will see later). ▫ Some mutations can affect the growth of cells, causing growth to accelerate, which results in cancer. ▫ Changes can be good- mutations sometimes lead to adaptations and therefore evolution. QOD DNA Replication Animation • http://www.hhmi.org/biointeractive/dnareplication-basic-detail • What’s wrong with this statement? Given the DNA strand 5’ AAT CGC AGC 3’ the complementary strand is 5’ TTA GCG TCG 3’ Genetic Code Genetic Code • DNA is the “code” for hereditary characteristics. • The genetic code is how organisms store hereditary information and translate it into amino acids (the monomers, or building blocks, of proteins). 9 1/28/2016 Genetic Code • DNA codes for all of the body’s proteins (such as enzymes). ▫ Genes are sequences located in the DNA that code for specific characteristics. ▫ For example, the code (or gene) for the production of the protein melanin is in your DNA and creates your hair and skin color. ▫ The code or recipe for all of the enzymes that help you digest your food is located in your DNA. The Human Genome • A genome is the complete genetic content of an organism. • We now know the human genome. ▫ Biologists have deciphered 3.2 billion base pairs in the 46 human chromosomes. The human genome is so large it would take 10 years to read the base sequences. ▫ These sequences code for about 30-40,000 genes. ▫ We are still researching which sequences code for which genes. Genetic Code • The “code” or “recipe” within DNA cannot be read directly. ▫ DNA cannot leave the nucleus and proteins are made in the cytoplasm of cells. ▫ So the code is transcribed (copied) and translated (turned into something useful) by ribonucleic acid (RNA). Genetic Code • Remember, proteins make us who we are. ▫ They are responsible for chemical reactions occurring in us (enzymes) and for the hereditary characteristics that we have (such as eye color). ▫ The building blocks (or monomers) of proteins are amino acids. ▫ DNA holds the recipe for the amino acid sequence of all the proteins we need to make. Protein Synthesis • RNA directs protein synthesis, which is the making of proteins from DNA. 10 1/28/2016 DNA vs RNA • Both are made of nucleotides. • Both are involved in protein synthesis. • DNA has the sugar deoxyribose, while RNA has the sugar ribose. • RNA uses the nitrogenous base uracil instead of thymine (used in DNA). • RNA is single stranded, while DNA is double stranded. • RNA is usually MUCH shorter than DNA. Protein Synthesis Video • http://vegas.pbslearningmedia.org/resource/nv ra.sci.prosynth/protein-synthesis/ RNA • There are several types of RNA involved in protein synthesis. RNA ▫ Messenger RNA (mRNA) – carries the genetic instructions from the DNA to the ribosomes. DNA is in the nucleus. Ribosomes are in the cytoplasm. RNA ▫ Ribosomal RNA (rRNA) – part of the ribosome The function of ribosomes in the cell is to make proteins. 11 1/28/2016 RNA ▫ Transfer RNA (tRNA) – transfers the amino acids to the ribosomes to make proteins Protein Synthesis We’ve got the blueprints and the tools – now what? • DNA is the blueprint used for constructing proteins, and RNA is the guide. • The process of developing the guide from the blueprint is called transcription. Protein Synthesis: Transcription (RNA synthesis) • Step 1: Transcription (to re-write) • DNA is too large to go from the nucleus to the cytoplasm, so only pieces of DNA are copied into RNA. This RNA then travels from the nucleus to the cytoplasm. Protein Synthesis Transcription ▫ An enzyme called RNA polymerase binds to a gene’s promoter region. A promoter is just a specific nucleotide sequence where the RNA polymerase can attach. ▫ The RNA attaches to the RNA polymerase and the DNA begins to uncoil. 12 1/28/2016 Protein Synthesis Transcription • The RNA polymerase adds complimentary nucleotides resulting in a straight chain RNA molecule. ▫ The DNA code determines which bases will be added (A with U, T with A, and G with C). ▫ For example: if the DNA code for a gene is ATCCGTT, then the RNA will be UAGGCAA. ▫ Remember, RNA does not have thymine, it has uracil!! Protein Synthesis Transcription • The copying of DNA continues until the RNA polymerase reaches a termination signal. ▫ That is a specific sequence of nucleotides that tells the RNA polymerase to “STOP” and release the RNA and DNA. ▫ The RNA is mRNA, because it is the messenger of the “code” from the DNA to the ribosomes. Transcription – Trimming the transcribed mRNA. • Once the mRNA is completed, it gets “trimmed”, or spliced. • Introns are parts of genes that are noncoding – they do not code for proteins. • Exons are parts of genes that code for proteins. • Genes have introns and exons, side by side. • During the process of RNA splicing, introns are removed and exons joined to form a contiguous coding sequence. This "mature" mRNA is ready for translation. Protein Synthesis Protein synthesis: Translation • Step 2: Translation (to make useful) • The RNA is then made into something useful, like assembling amino acids into proteins in the ribosome. Translation • Once the newly made mRNA leaves the nucleus it attaches to a ribosome at the promoter region. • Ribosomes will “read” 3 nucleotides in the RNA code at a time. ▫ These 3 nucleotides are called codons. ▫ Each codon codes for an amino acid, a START signal, or a STOP signal. messenger RNA 13 1/28/2016 Protein Synthesis - Translation Protein Synthesis - Translation • For example, the sequence AUG codes for the amino acid methionine and means START (it is the only one that means start). ▫ ALL mRNA molecules start with AUG, otherwise, they would not have a start region for protein synthesis. • The RNA is translated into amino acids, which are put together to form proteins (or polypeptides). • The translation occurs with the help of tRNA, which carries the amino acids. Protein Synthesis - Protein Synthesis - Translation • When the ribosome reads the start sequence (AUG), a tRNA molecule comes along with the anticodon. ▫ The anticodon is the complementary sequence, UAC. ▫ The complementary bases bond with each other and the amino acid methionine begins the protein synthesis within the ribosome. ▫ tRNA transfers amino acids to the ribosome. Codon Chart Translation • There are only 20 amino acids. • Most amino acids have more than one codon. ▫ For example, Leucine’s codons are UUA, UUG, CUU, CUC, CUA, and CUG. • But each codon codes for ONLY 1 amino acid. ▫ For example, CUU only codes for Leucine and nothing else. Protein Synthesis - Translation • After the start sequence, the ribosome moves to the next codon. ▫ Let’s say the next codon is GUC. ▫ Now a tRNA that has the anticodon CAG would attach to the ribosome and it would carry the amino acid valine. ▫ The amino acid valine would attach to the methionine from before (now we have a dipeptide)! 14 1/28/2016 Protein Synthesis - Translation • This process continues and the polypeptide grows until the STOP codon is reached. ▫ UAA, UAG, and UGA are the only stop codons. ▫ The protein, ribosome and all RNA is released to perform other needed functions. • How do I keep the steps of protein synthesis straight? • Alphabetical order (transcription, then translation) Protein Synthesis - Overview • Amino acids are listed by their CODON!!! ▫ The three nucleotide sequence on the mRNA. DNA mRNA tRNA A U A T A U G C G C G C Protein Synthesis - Overview Protein Synthesis - Overview •This is an mRNA strand- figure out the original DNA code. A→T U→A C↔G mRNA Strand: AUG/ACG/GAG/CUU/CGG/AGC/ UAG Protein Synthesis - Overview •Now figure out the anticodons (found on the tRNA). DNA Strand: TAC/TGC/CTC/GAA/GCC/TCG/A TC 15 1/28/2016 Protein Synthesis - Overview A→U U→A C↔G mRNA Strand: AUG/ACG/GAG/CUU/CGG/AGC/ UAG tRNA Strand: UAC/UGC/CUC/GAA/GCC/UCG/A UC Protein Synthesis - Overview • Now use the CODON chart to figure out the amino acid sequence. • Remember to use the codons from the mRNA to determine amino acid sequence. Protein Synthesis - Overview •1 - UAC •2 - UGC •3 - CUC •4 - GAA •5 - GCC •6 - UCG •7 - AUC Protein Synthesis - Overview •1 – Methionine (start) •2 - Threonine •3 – Glutamic Acid •4 - Leucine •5 - Arginine •6 - Serine •7 - STOP Let’s Break the Genetic Code 1. Start with DNA: TACTAGCTAACC 2. Write the complimentary strand for mRNA AUGAUCGAUUGG 3. Identify the codons on the mRNA AUG-AUC-GAU-UGG 4. Identify the anticodons on the tRNA UAC-UAG-CUA-ACC 5. Identify the amino acid sequence from the mRNA Met - Iso - Asp - stop Mutations 16 1/28/2016 Genetic Mutations Genetic Mutations • Any change in the DNA sequence is called a mutation. ▫ Mutations can effect body cells. • Not all mutations are bad. Example = CANCER ▫ Mutations can effect reproductive cells. These are called germline mutations and can be passed from parent to child. If a child inherits a germline mutation from his or her parents, every cell in their body will have this error in their DNA. Germline mutations are responsible for inherited genetic disorders. Genetic Mutations • Types of DNA mutations: ▫ Point ▫ Frameshift ▫ Inversion • Some mutations result in characteristics that give the organism a greater chance of survival. • Example: Sickle cell anemia (deflated look of red blood cells) is caused by a mutation, however it is beneficial to people in Africa who often contract malaria – the parasite can no longer attach to their red blood cells, therefore they aren't affected Point mutations • Occurs when a single base changes. Types: ▫ Silent mutation- no amino acid change ▫ Missense- changes amino acid that is coded ▫ Nonsense- changes sequence to a stop codon Frameshift Mutation • A single base pair in DNA is deleted or added. • It changes everything “downstream” – after the base pair. • This type of mutation can make the DNA meaningless and often results in a shortened protein. Inversion • In an inversion mutation, an entire section of DNA is reversed. • A small inversion may involve only a few bases within a gene, while longer inversions involve large regions of a chromosome containing several genes. 17 1/28/2016 Causes of Mutations Examples ▫ THE DOG BIT THE CAT. ▫ THE DOB ITT HEC AT. ▫ THE DOG BIT THE CAT. ▫ THE DOG BIT THE CAR. ▫ The fat cat ate the wee rat. ▫ The fat tar eew eht eta tac. • Frameshift • Point • Inversion • Spontaneous: ▫ Mistake in base pairing during DNA replication • Mutagen – agent that causes DNA change ▫ High energy radiation X rays ▫ Chemicals Dioxins, asbestos, benzene, cyanide, formaldehyde ▫ High temperatures 18