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Please pick up ch.12 notes: cut out and glue into your notebooks, thank you Glue new ch.12 notes into notebooks Lecture/Notes on section 1 Foldable Vocabulary Cards DNA video No homework tonight 12–1 DNA Griffith and Transformation Griffith’s Experiment Transformation Avery and DNA The Hershey-Chase Experiment Bacteriophages Radioactive Markers The Structure of DNA Chargaff’s Rules X-Ray Evidence The Double Helix How do genes work? What are they made of, and how do they determine the characteristics of organisms? Are genes single molecules, or are they longer structures made up of many molecules? In the middle of the 1900s, questions like these were on the minds of biologists everywhere. To truly understand genetics, biologists first had to discover the chemical nature of the gene. If the structures that carry genetic information could be identified, it might be possible to understand how genes control the inherited characteristics of living things. In 1928, British scientist Frederick Griffith was trying to figure out how bacteria make people sick. Griffith had isolated two slightly different strains, or types, of pneumonia bacteria from mice. The disease-causing strain of bacteria grew into smooth colonies on culture plates, whereas the harmless strain produced colonies with rough edges. The differences in appearance made the two strains easy to distinguish. When Griffith injected mice with the disease-causing strain of bacteria, the mice developed pneumonia and died. When mice were injected with the harmless strain, they didn’t get sick at all. Griffith wondered if the disease-causing bacteria might produce a poison. To find out, he took a culture of these cells, heated the bacteria to kill them, and injected the heat-killed bacteria into mice. The mice survived, suggesting that the cause of pneumonia was not a chemical poison released by the disease-causing bacteria. Griffith’s next experiment produced an amazing result. He mixed his heat-killed, disease-causing bacteria with live, harmless ones and injected the mixture into mice. By themselves, neither should have made the mice sick. But to Griffith’s amazement, the mice developed pneumonia and many died. When he examined the lungs of the mice, he found them filled with the disease-causing bacteria. Somehow the heat-killed bacteria had passed their disease-causing ability to the harmless strain. Griffith called this process transformation because one strain of bacteria (the harmless strain) had apparently been changed into another (the disease-causing strain). Heat-killed, disease-causing bacteria (smooth colonies) Disease-causing bacteria (smooth colonies) Harmless bacteria Heat-killed, disease(rough colonies) causing bacteria (smooth colonies) Dies of pneumonia Lives Lives Control (no growth) Harmless bacteria (rough colonies) Dies of pneumonia Live, disease-causing bacteria (smooth colonies) In 1944, a group of scientists led by Canadian biologist Oswald Avery at the Rockefeller Institute in New York decided to repeat Griffith’s work. They did so to determine which molecule in the heat-killed bacteria was most important for transformation. Avery and his colleagues made an extract, or juice, from the heat-killed bacteria. They then carefully treated the extract with enzymes that destroyed proteins, lipids, and carbohydrates. Transformation still occurred. Obviously these molecules were not responsible for the transformation. If they had been, transformation would not have occurred, because the molecules would have been destroyed by the enzymes. Avery and the other scientists repeated the experiment, this time using enzymes that would break down DNA. When they destroyed the nucleic acid DNA in the extract, transformation did not occur. Avery and other scientists discovered that DNA is the nucleic acid that stores and transmits the genetic information from one generation of an organism to the next. Bacteriophage with phosphorus-32 in DNA Phage infects bacterium Radioactivity inside bacterium Bacteriophage with sulfur-35 in protein coat Phage infects bacterium No radioactivity inside bacterium Bacteriophage with phosphorus-32 in DNA Phage infects bacterium Radioactivity inside bacterium Bacteriophage with sulfur-35 in protein coat Phage infects bacterium No radioactivity inside bacterium Bacteriophage with phosphorus-32 in DNA Phage infects bacterium Radioactivity inside bacterium Bacteriophage with sulfur-35 in protein coat Phage infects bacterium No radioactivity inside bacterium 1952: Two American scientists, Alfred Hershey and Martha Chase, studied viruses- nonliving particles smaller than a cell that can infect living organisms. A virus that infects and kills bacteria is known as a bacteriophage; composed of a DNA or RNA core and a protein coat. Hershey and Chase reasoned that if they could determine which part of the virus—the protein coat or the DNA core—entered the infected cell, they would learn whether genes were made of protein or DNA. To do this, they grew viruses in cultures containing radioactive isotopes of phosphorus-32 (32P) and sulfur35 (35S). The radioactive substances could be used as markers. If 35S was found in the bacteria, it would mean that the viruses’ protein had been injected into the bacteria. If 32P was found in the bacteria, then it was the DNA that had been injected. All the radioactivity in the bacteria was from phosphorus (32P), the marker found in DNA. Hershey and Chase concluded that the genetic material of the bacteriophage was DNA, not protein. Fold a piece of your notebook paper toward the spiral. Cut top part into 3 equal sections. Label the outside of the 3 sections with the 3 Scientists. Write the experiment they did and what their conclusion was on the inside paper. 5 minutes 3 Functions of DNA: Genes carry information from one generation to the next. They had to put that information to work by determining the heritable characteristics of organisms. Genes had to be easily copied. DNA is a long molecule made up of subunits called nucleotides. Each nucleotide is made up of 3 parts: a 5-carbon sugar called deoxyribose, a phosphate group, and a nitrogen base. There are 4 kinds of nitrogenous bases in DNA. Two of the nitrogenous bases, adenine (A) and guanine (G), belong to a group of compounds known as purines. The remaining two bases, cytosine (C) and thymine (T), are known as pyrimidines. Purines have two rings, and pyrimidines have one ring. The backbone of a DNA chain is formed by sugar and phosphate groups of each nucleotide. The nitrogenous bases stick out sideways from the chain. The nucleotides can be joined together in any order, meaning that any sequence of bases is possible. Chargaff’s Rule: Erwin Chargaff, an American biochemist, had discovered that the percentages of guanine [G] and cytosine [C] bases are almost equal in any sample of DNA. The same thing is true for the other two nucleotides, adenine [A] and thymine [T]. 1950: A British scientist named Rosalind Franklin began to study DNA. She used a technique called X-ray diffraction to get a picture of the structure of a DNA molecule. By itself, Franklin’s X-ray pattern doesn’t reveal the structure of DNA. The X-shaped pattern in the image does shows that there are 2 strands in DNA that are twisted around each other, a shape known as a helix. At the same time that Franklin was continuing her research, Francis Crick, a British physicist, and James Watson, an American biologist, were trying to understand the structure of DNA by building three-dimensional models of the molecule. 1953: Watson was shown a copy of Franklin’s remarkable X-ray pattern and reported the pattern’s clues to Crick. Within a few weeks, Watson & Crick figured out the final structure of DNA: a two stranded double helix. Watson & Crick discovered that hydrogen bonds could form between certain nitrogenous bases and provide just enough force to hold the two strands together. Hydrogen bonds can form only between certain base pairs— adenine & thymine and guanine & cytosine. Once they saw this, it explained Chargaff’s rules. A = T and G = C. Nucleotide Hydrogen bonds Sugar-phosphate backbone Key Adenine (A) Thymine (T) Cytosine (C) Guanine (G) Please spend 2 minutes writing a summary about what we have learned from ch.12 section 1. In your groups, write the definition in your own words, and add an example and/or a picture. DNA Structure Chargaff’s Rule 3 Functions of DNA Rosalind Franklin Griffith Watson & Crick Avery Purine & Pyrimidine Hershey-Chase 3 minutes Play DVD 16min. HHMI video Please pick up 1 warm-up card per pair Glue in new notes for 12-2 also! Warm-up cards from section 1 Lecture/Notes on section 2 Vocabulary Cards DNA Replication Activity 12–2 Chromosomes & DNA Replication DNA and Chromosomes DNA Length Chromosome Structure DNA Replication Duplicating DNA How Replication Occurs Prokaryotic cells do not have a nucleus, instead, their DNA is located in the cytoplasm and consists of a single circular chromosome of genetic information. Eukaryotes have 1,000 times more DNA than prokaryotes! Eukaryotic DNA is found in the nucleus and forms into many chromosomes. Humans have 46 chromosomes, fruit flies have 8, and trees have 22. DNA Length: the single chromosome of a prokaryotic E. coli bacteria contains 4 million base pairs (letters), and is about 1.6mm long. DNA has to be tightly folded to fit inside of a tiny cell. Eukaryotic DNA contains 30 million base pairs, and is 10x longer than a bacteria's chromosome. Eukaryotic chromosomes contain both DNA and proteins (histones) that help it to stick together as tightly packed nucleosome coils. Chromosome Structure of Eukaryotes Chromosome Nucleosome DNA double helix Coils Supercoils Histones DNA stands are complementary, meaning that each side matches the other: chargaff’s rule, so DNA can be easily copied by following the base pairing rule. Before cells divide (mitosis) their DNA must be duplicated in a process called DNA Replication. DNA Replication: the DNA molecule separates into 2 stands, then produces 2 new complementary strands following the rules of base pairing. Each strand of the double helix of DNA serves as a template/model for the new stands. DNA replication is carried out by enzymes. Remember that enzymes help speed up reactions and are very specific (lock & key). The enzyme Helicase unzips a molecule of DNA first by breaking the hydrogen bonds between the base pairs. Each strand serves as a template for the attachment of complementary bases. The enzyme DNA Polymerase adds new base pairs to the new DNA stand, and also proofreads to make sure it is adding the correct bases to make a perfect copy. Original strand New strand DNA polymerase Growth DNA polymerase Growth Replication fork Replication fork New strand Original strand Nitrogenous bases Each DNA molecule resulting from replication has 1 original strand and 1 new stand. Example: a strand that is TACGTT produces a complementary stand with bases ATGCAA. Please spend 2 minutes writing a summary about what we have learned from ch.12 section 2. In your groups, write the definition in your own words, and add an example or a picture. Prokaryotic Chromosome Eukaryotic Chromosomes DNA Replication Mitosis Helicase DNA Polymerase In pairs: Pick up 1 DNA Replication Packet Read through the first page together, then follow the directions on the second page. Take turns with different steps. When finished, each person glues ½ of the replicated copy of DNA into their notebook. Homework: answer the 6 questions at the end 30 minutes Please pick up 1 card EACH Glue in the diagram for today’s notes. Notes on 12-3 Foldable Transcription/Translation Practice 12-3 Summary Videos Snork DNA Activity Homework due next class. 12–3 RNA and Protein Synthesis The Structure of RNA Types of RNA Transcription RNA Editing The Genetic Code Translation The double helix structure of DNA shows how easily it can be replicated, but it doesn't explain how a gene works to give us genic information. Genes are coded DNA instructions that control the production of proteins within the cell. The first step in decoding these genetic messages is to copy part of the nucleotide (base pair) sequence from DNA into RNA. The RNA molecules are then used to make proteins. RNA, like DNA, consists of a long chain of nucleotides. Remember, nucleotides are made of 3 parts: a 5-carbon sugar, a phosphate, and a nitrogen base. Three differences between RNA and DNA: RNA contains the sugar “ribose”, where DNA contains the sugar “deoxyribose”. RNA is a single stand, and DNA is a double strand. RNA contains the bases A,C, G, U; and DNA contains the bases A, C, G, T. You can think of RNA as a disposable copy of a segment of DNA that is only used as 1 time instructions for a single gene. There are 3 types of RNA that help with protein synthesis: mRNA (messenger RNA = the single stand of code) rRNA (ribosomal RNA = what ribosomes are made of) tRNA (transfer RNA = brings amino acids to the ribosome in the order of the mRNA code) rRNA mRNA tRNA RNA can be Messenger RNA also called Ribosomal RNA which functions to mRNA Carry instructions also called which functions to rRNA Combine with proteins from to to make up DNA Ribosome Ribosomes Transfer RNA also called which functions to tRNA Bring amino acids to ribosome Fold paper in ½ towards the bottom of your notebook. Cut 2 vertical sections to make 3 areas to write: Outside: list & draw the 3 types of RNA. Inside: Describe what their job and location. Adenine (DNA and RNA) Cystosine (DNA and RNA) Guanine(DNA and RNA) Thymine (DNA only) Uracil (RNA only) RNA polymerase DNA RNA A process in the nucleus, where mRNA is made by copying part of the nucleotide sequence (a gene) in DNA. Transcription requires an enzyme called RNA Polymerase (acts just like DNA Polymerase by adding RNA nucleotides: A, U, G, C). How does RNA Polymerase know where to start? There is a region on DNA known as a Promoter, which signals where to bind and start transcription. Like a writer’s first draft of a paper, RNA molecules require editing before they are ready to leave the nucleus and make protein. There are 2 main parts to mRNA: Introns: “in between” pieces that are not needed. Exons: “exactly” the genes to be read to make protein. The introns get cut out and we are left with only exons in our mRNA strand. It can now leave the nucleus and go to a ribosome to be read. Proteins are made by joining amino acids together into chains called polypeptides. There are 20 different types of amino acids. By reading the nucleotide sequence of mRNA, we can “translate” the letters into amino acids, and join them together one after another to make a protein. We read 3 mRNA letters at a time to make 1 amino acid: each set of 3 letters is called a Codon. Ex: UCGCACGGU would be read as: UCG-CAC-GGU, and would make the amino acids: serine-histidine-glycine Because there are 4 nucleotide bases in RNA (A, U, G, C), there are 64 possible codons combinations. Some amino acids can be made from more than 1 codon. All proteins start with the amino acid Methionine - AUG. All proteins end with a “stop” codon (multiple codons). The process of making proteins from mRNA, occurs at the ribosome. In the first step we edited the mRNA into exons only, then it left the nucleus and went to a ribosome. At the ribosome, we know that the mRNA gets read and 1 amino acid is attached after reading a codon (3 letters). So how does the amino acid get there? The tRNA molecule has an anticodon (3 complementary letters to the mRNA codon) on one side, and a specific amino acid on the other side. Nucleus Messenger RNA Messenger RNA is transcribed in the nucleus. Phenylalanine tRNA Lysine mRNA Transfer RNA Methionine The mRNA then enters the cytoplasm and attaches to a ribosome. Translation begins at AUG, the start codon. Each tRNA has an anticodon whose bases are complementary to a codon on the mRNA strand. Ribosome mRNA Start codon The Polypeptide “Assembly Line” The ribosome joins the two amino acids, Then their tRNA floats away, allowing the ribosome to bind to another tRNA. The ribosome moves along the mRNA, binding new tRNA molecules and amino acids. Lysine Growing polypeptide chain Ribosome tRNA tRNA mRNA Completing the Polypeptide mRNA Ribosome Translation direction The process continues until the ribosome reaches a stop codon. The result is a polypeptide chain = protein. Transcribe your DNA into mRNA, then translate into codons and anticodons to determine the amino acids. Glue into your notebook when finished. Please spend 2 minutes writing a summary in your notes about what we learned from section 3. Please study the processes of: Transcription and Translation. Be familiar with: DNA mRNA Protein Vocabulary: codon, anticodon, polypeptide, intron, exon, 3 types of RNA. You are given a Snork’s mRNA sequence, your job is to determine the Snork’s traits that are coded for in the genes you read by Translating them into Amino Acids. After determining the traits, draw your Snork! Be creative, use colors, show Ms. Lutz when you’re finished. Choose 1 for homework: Snicker Snork Snuffle Snork Snapple Snork Snoopy Snork In your groups: write the definition in your own words, and add an example and picture. 3 types of RNA Transcription RNA Polymerase & Promoter Introns & Exons Translation Amino Acids (# number) 4 minutes Pin to board when finished! Please close and put away your notebook. Have a pencil out! Hand in quiz to your block’s bin when done. Pick up and glue in notes for 12-4 & 12-5 Please pick up 1 card EACH! Warm-up: pick up 1 card each please Pick up graded quizzes Notes on 12-4 and 12-5 2 short video clips Unit 5 Review Packet 12–4 Mutations Gene Mutations Chromosome Mutations Every now and then cells make mistakes in copying their own DNA - inserting an incorrect base or sometimes even skipping a base as the new strand is put together. These mistakes are called mutations. Mutations are changes in the DNA sequence that affect genetic information. Gene mutations result from changes in a single nucleotide base. Chromosomal mutations involve changes in whole chromosomes. Substitution Insertion Deletion 2 Types of gene mutations: Point Mutations result in the substitution of a base Frameshift Mutations result in the insertion or deletion of a base, causing different amino acids to be made. Deletion Duplication Inversion Translocation 4 types of chromosome mutations: Deletion, duplication, inversion, translocation. This is NOT in your notes. Please spend the next 2 minutes writing a summary in your notes about what we learned from section 4. 12–5 Gene Regulation Prokaryotic & Eukaryotic Gene Regulation Gene Enhancement Regulation and Development Regulatory sites Promoter (RNA polymerase binding site) Start transcription DNA strand Stop transcription As we’ve seen, there is a promoter to one side of the gene. But what are the “regulatory sites” next to the promoter? These are places where other proteins can regulate transcription. The actions of these proteins help to determine whether a gene is turned on or off. Only some of the genes in a cell are expressed at any given time. An expressed gene is a gene that is transcribed into RNA (turned on/being used). How does the cell determine which genes will be expressed and which will remain off? Molecular biologists have found that certain DNA sequences serve as promoters (binding sites for RNA polymerase). Others serve as start and stop signals for transcription. Cells are filled with DNA-binding proteins that attach to specific DNA sequences and help to regulate gene expression (turn on/off). Lac operon genes are found in certain bacteria and help the bacteria to use lactose as food. If lactose is present the lac operon will turn the gene on as RNA Polymerase binds to the promoter. After the lactose food is used up, the gene is turned off by a Repressor Protein binding to the operon. Repressor proteins stop gene transcription by twisting the DNA strand so that RNA Polymerase cannot read it. The lac operon turns on when lactose is present because the DNA strand will straighten out, causing the repressor protein to fall off. RNA polymerase attaches to the promoter and can easily read the straight DNA strand. Unlike prokaryotes, eukaryotic genes do not contain operons to regulate gene expression, instead, they have a short nucleotide sequence of –TATA- for a start site. The TATA Box helps position where RNA polymerase needs to bind to begin transcription. Short DNA Promoter sequences are found just before the TATA box to help position it correctly. There are special proteins that bind to enhancer sequences of a gene that help to regulate gene expression in several ways: Many proteins can bind to different enhancer sequences at the same time = more efficient. Some proteins enhance transcription by opening up tightly coiled chromatin. Help attract RNA polymerase to begin transcription. Video Gene regulation in eukaryotes is more complex than in prokaryotes because: Cell specialization requires genetic specialization. All eukaryotic cells carry the entire genetic code, each type of cell performs a different function in a different part of the body. Hox genes control the differentiation of cells and tissues of developing embryos. Animals share many common patterns of development because we all share the same bases (ATGC) but have different numbers and arrangements of chromosomes. Example: Fruit flies can grow legs on their head if the hox gene is tampered with during development. In humans the hox gene acts similar to fruit fly’s. Please write definition in your own words, add a picture and an example. ALL group members work on card together, we will go over responses after posting to card board. Mutations Gene Regulation Lac Operon TATA Box Gene Enhancement Hox Genes Please spend the next 2 minutes writing a summary about what we learned from section 5. Hox Genes Video Unit 5 Review Packet will be due the day of the test: B-day the test is Friday 2/13 A-day the test is Tuesday 2/17 Next class we will spend the entire block reviewing ch.12 material.