Topics Concept 5.5: Nucleic Acids: What are the parts of a nucleotide? Compare RNA and DNA. Understand how DNA is polymerized (5’ to 3’). How does DNA.

Topics Concept 5.5: Nucleic Acids: What are the parts of a nucleotide? Compare RNA and DNA. Understand how DNA is polymerized (5’ to 3’). How does DNA carry information? Concept 12.1: What is the relationship between a chromosome and DNA? Why do cells divide? Why do chromosomes replicate? Concept 16.2: What did the Messelsohn-Stahl experiment tell us? Explain semiconservative. Why does replication cause a leading and lagging strand? Concept 17.1: How does information in a gene result in a protein being made? Describe the steps and know how to transcribe RNA and translate to an amino acid sequence. Concept 17.5: Compare different types of mutations. What is the difference in their effect on an organism. Why could cause a mutation to be bad/good/or neither? Concept 20.2: How does gel electrophoresis help us study mutations? Essential Knowledge 3.a.1: DNA is the primary source of heritable information 3.a.3: The chromosomal basis of inheritance provides an understanding of the pattern of transmission of genes from parent to offspring 3.c.1: Changes in genotype can result in changes in phenotype

Unit 6: DNA Big Idea: Organisms store information as DNA tightly coiled into chromosomes. In order for information in DNA to encode our traits, information must be transcribed (DNA→RNA) and translated (RNA→protein). Changes in information can result in changes in organisms.

Warm-UP: 1. What is DNA? 2. What do you know about the structure of DNA? 3. How is more DNA made? 4. Why is more DNA made? Warm-UP: 1. What is DNA? 2. What do you know about the structure of DNA? 3. How is more DNA made? 4. Why is more DNA made? Homework for tonight: 10 Key Ideas, Concept 5.5 Homework DUE 10/10 (next Tuesday): Modeling Cell Respiration

DNA Models: Cut out the 16 nucleotides for your group. Arrange them as they would be arranged in DNA. Some key characteristics: DNA is double stranded purines always bond with pyrimidines adenine always bonds with thymine (2 hydrogen bonding sites) cytosine always bonds with guanine (3 hydrogen bonding sites) the sugar of one nucleotide is bonded to the phosphate of the next nucleotide. one strand of DNA is antiparallel to the other strand Labels: nucleotide deoxyribose phosphate base the type of base (C, T, G, or A) the carbons of deoxyribose (1’, 2’, 3’, 4’, 5’) purine or pyrimidine

Model Analysis: 1.How does this model compare to real DNA? 2.Where on your model is the information for making your traits? 3.How could this molecule vary so that you can be different than your neighbor? Before you leave, divy up the nucleotides so each person gets at least 4 nucleotides. TAPE a model of DNA into your notebook as reference.

Warm-UP: In Hershey and Chase’s experiment, they FIRST gave a virus radioactively labeled proteins then infected a bacteria with the virus. The bacteria then showed no radioactively labeled proteins. They then repeated their experiment, this time giving the virus radioactively labeled DNA.The bacteria DID show it contained radioactively labeled DNA. Which question does this experiment best answer? a.Is DNA or protein the heritable information for an organism? b.Are viruses capable of infecting bacteria? c.Do bacteria have DNA? d.How long can a bacteriophage’s DNA infect its host cell? Homework for tonight: 10 Key Ideas, Concept 16.2 Homework DUE 10/10/2030 (or next Tuesday): Modeling Cell Respiration

Noteworthy Scientists Avery-MacLeod-McCarty: DNA causes bacteria to transform (be “permanently different) rather than protein Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Information is stored as DNA tightly coiled into chromosomes.

DNA: A polymer of nucleotides sugar + phosphate = “backbone” “information”= base (adenine, guanine, cytosine, thymine) base: purines: adenine, guanine pyrimidines: thymine, cytosine base complementarity: A-T: 2 hydrogen bonds C-G: 3 hydrogen bonds double helix two-strands twisted antiparallel nucleotides “point” in opposite directions 5’  3’ 3’  5’ only can be made 5’  3’

Information is stored as DNA tightly coiled into chromosomes. DNA: A polymer of nucleotides sugar + phosphate = “backbone” “information”= base (adenine, guanine, cytosine, thymine) base: purines: adenine, guanine pyrimidines: thymine, cytosine base complementarity: A-T: 2 hydrogen bonds C-G: 3 hydrogen bonds double helix two-strands twisted antiparallel nucleotides “point” in opposite directions 5’  3’ 3’  5’ only can be made 5’  3’

Information is stored as DNA tightly coiled into chromosomes. DNA Replication: making more DNA for: growth repair tricky: antiparallel: enzymes are substrate specific, so DNA only can be: made 5’  3’ read 3’  5’

Information is stored as DNA tightly coiled into chromosomes. DNA Replication: making more DNA for: growth repair tricky: antiparallel: enzymes are substrate specific, so DNA only can be: made 5’  3’ read 3’  5’ Step 1: Helicase breaks the hydrogen bonds

Information is stored as DNA tightly coiled into chromosomes. DNA Replication: making more DNA for: growth repair tricky: antiparallel: enzymes are substrate specific, so DNA only can be: made 5’  3’ read 3’  5’ Step 1: Helicase breaks the hydrogen bonds Step 2: DNA Polymerase I uses the base pairing rules to bring in the correct nucleotide

Information is stored as DNA tightly coiled into chromosomes. DNA Replication: making more DNA for: growth repair tricky: antiparallel: enzymes are substrate specific, so DNA only can be: made 5’  3’ read 3’  5’ Step 1: Helicase breaks the hydrogen bonds Step 2: DNA Polymerase I uses the base pairing rules to bring in the correct nucleotide http://www.dnalc.org/resources/3d/04-mechanism-of-replication-advanced.html

Information is stored as DNA tightly coiled into chromosomes.

DNA Replication: making more DNA for: growth repair tricky: antiparallel: enzymes are substrate specific, so DNA only can be: made 5’  3’ read 3’  5’ Problem: The “Lagging Strand” DNA polymerase add nucleotides only to the free 3  end of a growing strand Here, the leading strand is being made continuously. BUT WHAT ABOUT THE OTHER HALF!!! The lagging strand is “stuck”.

Information is stored as DNA tightly coiled into chromosomes. DNA Replication: making more DNA for: growth repair tricky: antiparallel: enzymes are substrate specific, so DNA only can be: made 5’  3’ read 3’  5’ Problem: The “Lagging Strand” DNA polymerase add nucleotides only to the free 3  end of a growing strand Here, the leading strand is being made continuously. BUT WHAT ABOUT THE OTHER HALF!!! The lagging strand is “stuck”.

Fig. 16-16b1 Template strand 5 5 3 3 DNA Replication: making more DNA for: growth repair tricky: antiparallel: enzymes are substrate specific, so DNA only can be: made 5’  3’ read 3’  5’ Solution: The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase DNA polymerase must work in the direction away from the replication fork. Information is stored as DNA tightly coiled into chromosomes.

Fig. 16-16b2 Template strand 5 5 3 3 RNA primer 3 5 5 3 1 Information is stored as DNA tightly coiled into chromosomes. DNA Replication: making more DNA for: growth repair tricky: antiparallel: enzymes are substrate specific, so DNA only can be: made 5’  3’ read 3’  5’ Solution: The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase DNA polymerase must work in the direction away from the replication fork.

Fig. 16-16b3 Template strand 5 5 3 3 RNA primer 3 5 5 3 1 1 3 3 5 5 Okazaki fragment Information is stored as DNA tightly coiled into chromosomes. DNA Replication: making more DNA for: growth repair tricky: antiparallel: enzymes are substrate specific, so DNA only can be: made 5’  3’ read 3’  5’ Solution: The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase DNA polymerase must work in the direction away from the replication fork.

Fig. 16-16b4 Template strand 5 5 3 3 RNA primer 3 5 5 3 1 1 3 3 5 5 Okazaki fragment 1 2 3 3 5 5 Information is stored as DNA tightly coiled into chromosomes. DNA Replication: making more DNA for: growth repair tricky: antiparallel: enzymes are substrate specific, so DNA only can be: made 5’  3’ read 3’  5’ Solution: The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase DNA polymerase must work in the direction away from the replication fork.

Fig. 16-16b5 Template strand 5 5 3 3 RNA primer 3 5 5 3 1 1 3 3 5 5 Okazaki fragment 1 2 3 3 5 5 1 2 3 3 5 5 Information is stored as DNA tightly coiled into chromosomes. DNA Replication: making more DNA for: growth repair tricky: antiparallel: enzymes are substrate specific, so DNA only can be: made 5’  3’ read 3’  5’ Solution: The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase DNA polymerase must work in the direction away from the replication fork.

Fig. 16-16b6 Template strand 5 5 3 3 RNA primer 3 5 5 3 1 1 3 3 5 5 Okazaki fragment 1 2 3 3 5 5 1 2 3 3 5 5 1 2 5 5 3 3 Overall direction of replication Information is stored as DNA tightly coiled into chromosomes. DNA Replication: making more DNA for: growth repair tricky: antiparallel: enzymes are substrate specific, so DNA only can be: made 5’  3’ read 3’  5’ Solution: The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase DNA polymerase must work in the direction away from the replication fork.

Drawings of DNA Replication Labels: DNA polymerase, helicase, ligase, sugar, phosphate, deoxyribose, nitrogenous base, hydrogen bond, nucleotide, A, G, C, T, 5’ end, 3’ end, leading strand, lagging strand, Okazaki fragments Ideas you need to show: DNA is made semiconservatively DNA is antiparallel and only made 5’  3’ the leading strand is made differently than the lagging strand Questions: 1.What are the roles of the different enzymes in Replication? 2.What problems do the limitations of the enzymes pose (ie Polymerase only makes DNA 5’  3’)? 3.Why is more DNA made? How does that help organisms?

Warm-UP: When DNA replicates, each strand of the original DNA molecule is used as a template for the synthesis of a second, complementary strand. Which of the following figures most accurately illustrates enzyme-mediated synthesis of new DNA at a replication fork? AP Test Money DUE: 3/6 Remember, the 2 nd semester Final Exam will be an AP test (the week before the official AP test); you might as well take the official test too! Homework DUE: 2/10 Modeling Cell Respiration Homework for tonight: 10 Key Ideas 17.1

Gallery Walk: Drawings of DNA Replication Gallery Walk: Drawings of DNA Replication Compare: Notice similarities and differences between your model and 2 others Analysis: 1.Describe how: a.DNA is made semiconservatively b.the leading strand is made differently than the lagging strand 2.What are the roles of the different enzymes in Replication? 3.What problems do the limitations of the enzymes pose (ie Polymerase only makes DNA 5’  3’)?

Fig. 16-9-1 A T G C TA TA G C CONCEPT MAP ligase helicase DNA Polymerase I DNA Polymerase III primase antiparallel primer template lagging strand single strand binding protein made: 5’  3’ read: 3’  5’ Okazaki fragments leading strand semiconservative http://www.mcb.harvard.edu/losick/images/trombonefinald.swf

Information is stored as DNA tightly coiled into chromosomes. Chromosomes: tightly coiled DNA histones: proteins that cause DNA to coil

Fig. 16-21a DNA double helix (2 nm in diameter) Nucleosome (10 nm in diameter) Histones Histone tail H1 DNA, the double helixHistones Nucleosomes, or “beads on a string” (10-nm fiber) Information is stored as DNA tightly coiled into chromosomes.

Fig. 16-20 1 µm Information is stored as DNA tightly coiled into chromosomes.

Warm-Up: 1.Given ½ the DNA shown, determine the other ½. 2.DNA is in the nucleus. Proteins are built in the cytoplasm. Crick hypothesized there must be a “go between” molecule. Why does this make sense? Warm-Up: 1.Given ½ the DNA shown, determine the other ½. 2.DNA is in the nucleus. Proteins are built in the cytoplasm. Crick hypothesized there must be a “go between” molecule. Why does this make sense? DNA nonsense strand Do now DNA sense strand ATG GTG CAC CTG AGT CCT GAG GAG AAG TCT mRNA tRNA’s amino acid sequence In order for information in DNA to encode our traits, information must be transcribed (DNA→RNA) and translated (RNA→protein). Leave blank for now

In order for information in DNA to encode our traits, information must be transcribed (DNA→RNA) and translated (RNA→protein).

KEY TERMS: transcription translation mRNA tRNA ribosome DNA nucleus cytoplasm codon anticodon amino acid polypeptide protein

STEP 1: transcription: in the nucleus DNA sense strand: – the gene – template for ordering the sequence of nucleotides in an mRNA transcript. mRNA synthesized using rules: – T complements A – A complements U – G complements C – C complements G STEP 2: translation: at ribosomes in the cytoplasm codons: decoded into a sequence of amino acids tRNA molecules, containing the anticodon, transfers the correct amino acids to the polymerizing polypeptide In order for information in DNA to encode our traits, information must be transcribed (DNA→RNA) and translated (RNA→protein).

Transcription http://m.youtube.com/watch?v=WsofH466lqk Translation http://m.youtube.com/watch?v=5bLEDd-PSTQ

Modeling Gene Expression Go to pHet: https://phet.colorado.edu/en/simulation/gene- expression-basicshttps://phet.colorado.edu/en/simulation/gene- expression-basics Analysis: 1.sadf

Mutations in DNA: 1.Substitution: a nucleotide is different, which causes one of the following: a.silent: no affect on amino acids b.missense: one amino acid different c.nonsense: many amino acids missing 2.Insertion/Deletion: a nucleotide is added or deleted, which causes one of the following: a.frameshift: one amino acid missing b.frameshift: all amino acids different c.frameshift: many amino acids missing Changes in information can result in changes in organisms.

WHITEBOARD: Types of Mutations WHITEBOARD: Normal (wild-type): Copy the chart below and determine the amino acid sequence Mutation: Repeat, but change the DNA so that one of the following happens: 1.Substitution: a nucleotide is different, which causes one of the following: a.silent: no affect on amino acids b.missense: one amino acid different c.nonsense: many amino acids missing 2.Insertion/Deletion: a nucleotide is added or deleted, which causes one of the following: a.frameshift: one amino acid missing b.frameshift: all amino acids different c.frameshift: many amino acids missing DNA nonsense DNA sense TAC GAG CTC CTG TGT CCT GCG GAG AAG ATT mRNA tRNA’s amino acid sequence

WHITEBOARD: Gallery WalkWHITEBOARD: Compare: Create a Venn Diagram with 3 circles Notice similarities and differences between your group’s mutation and 2 others Analysis: 1.Why do some mutations cause no change, others cause small changes, and some cause large changes? 2.Is it possible for a single nucleotide deletion to cause more change than for 3 nucleotide deletions? Explain. 3.What is the role of DNA in affecting changes in organisms?

LAB: Gel Electrophoresis Part 1: Enzyme Digest of DNA 1.Obtain 5 clear microtubes. Label them C, 1, 2, 3, S 2.Use the table to add the correct reagents to each microtube. Spin microtubes to mix reagents. Do not reuse tips. Use aseptic techniques sterlize hands and table often close tip box; do not touch tips 3.Tape your 5 microtubes together. Label your tape with your name. 4.Place all 5 microtubes in 37C water bath overnight.

Pipetting 1.To draw your desired volume into your tip: a.1 st stop b.Into the solution c.Release d.Out of the solution 2. To eject your desired volume into your microtube: a.Eject: to the 2 nd stop b.Perfection?: TOUCH the drop to “unstick” the last bit REMINDERS a.No double dipping b.Close tip box lids c.Keep your hands, breath, etc. to yourself d.Sterilize everything: before, during, and after e.Small volumes DO NOT equal no volume: Use a microcentrifuge!

Add to tubeControlChild 1Child 2Child 3Sue sd H 2 O (flask) 10.0ul8.0ul buffer 2.0ul React 2 (orange) 2.0ul React 3 (blue) 2.0ul React 3 (blue) 2.0ul React 2 (orange) 2.0ul React 2 (orange) enzyme (purple) 3ul4ul Child 1’s DNA (green) 1ul Child 2’s DNA (pink) 1ul Child 3’s DNA (yellow) 1ul Sue’s DNA (clear) 1ul

LAB: Gel Electrophoresis Part 2: Electrophoresis of DNA Fragments 1.Retrieve your 5 clear microtubes from the water bath. Spin microtubes so that all of your liquid is at the bottom of your microtube. 2.Add 3ul of sample loading buffer. Spin microtubes to mix reagents. Do not reuse tips. Use aseptic techniques sterlize hands and table often close tip box; do not touch tips 3.Load wells: 15ul each. 4.Record which sample is in each well. 5.Plug in and turn on power. Run for at least 30 min at 100 volts. 6.Unplug and place in staining tray. Mr. Jones will stain for viewing tomorrow.

ControlChild 1Child 2Child 3Sue Yesterday’s Product 15ul Sample Loading Buffer 3ul

Fig. 20-3-1 Restriction site DNA Sticky end Restriction enzyme cuts sugar-phosphate backbones. 5353 3535 1

http://learn.genetics.utah.edu/content/labs/ gel/

LAB: Gel Electrophoresis Part 3: Analysis 1.Retrieve your stained gel. 2.Place it on the light source. 3.Using an acetate sheet and a sharpie, draw your gel results. 4.Answer the analysis questions and come to a conclusion. Did any of Sue’s kids get unlucky?

Topics Concept 5.5: Nucleic Acids: What are the parts of a nucleotide? Compare RNA and DNA. Understand how DNA is polymerized (5’ to 3’). How does DNA.

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Topics Concept 5.5: Nucleic Acids: What are the parts of a nucleotide? Compare RNA and DNA. Understand how DNA is polymerized (5’ to 3’). How does DNA.

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Presentation on theme: "Topics Concept 5.5: Nucleic Acids: What are the parts of a nucleotide? Compare RNA and DNA. Understand how DNA is polymerized (5’ to 3’). How does DNA."— Presentation transcript:

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