topics concept 5.5: nucleic acids: what are the parts of a nucleotide? compare rna and 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?

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

• Franklin: produced a picture of the DNA molecule

• Watson and Crick: built a model of the molecule

Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings


• Avery-MacLeod-McCarty: DNA causes bacteria to transform (be “permanently different) rather than protein



• Hershey and Chase: proved DNA was the “heritable” molecule, not protein


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’


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’





• made 5’ 3’• read 3’ 5’

Step 1: Helicase breaks the hydrogen bonds





• made 5’ 3’• read 3’ 5’


Step 2: DNA Polymerase I uses the base pairing rules to bring in the correct nucleotide





• made 5’ 3’• read 3’ 5’


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







• made 5’ 3’• read 3’ 5’

Problem: The “Lagging Strand”• DNA polymerase add nucleotides only

to the free 3end 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

53

3




• 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. 16-16b2

Template strand

5

53

3

RNA primer 3 5

5

3

1





• made 5’ 3’• read 3’ 5’




Fig. 16-16b3

Template strand

5

53

3

RNA primer 3 5

5

3

1

1

3

35

5

Okazaki fragment





• made 5’ 3’• read 3’ 5’




Fig. 16-16b4

Template strand

5

53

3

RNA primer 3 5

5

3

1

1

3

35

5

Okazaki fragment

12

3

3

5

5





• made 5’ 3’• read 3’ 5’




Fig. 16-16b5

Template strand

5

53

3

RNA primer 3 5

5

3

1

1

3

35

5

Okazaki fragment

12

3

3

5

5

12

3

3

5

5





• made 5’ 3’• read 3’ 5’




Fig. 16-16b6

Template strand

5

53

3

RNA primer 3 5

5

3

1

1

3

35

5

Okazaki fragment

12

3

3

5

5

12

3

3

5

5

12

5

5

3

3

Overall direction of replication





• made 5’ 3’• read 3’ 5’




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: 3/6Remember, the 2nd 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: 2/10Modeling Cell Respiration

Homework for tonight: 10 Key Ideas 17.1

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 semiconservativelyb. the leading strand is made differently than the

lagging strand2. 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

GC

T A

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

http://www.mcb.harvard.edu/losick/images/trombonefinald.swf


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 tailH1

DNA, the double helix Histones Nucleosomes, or “beads on a string” (10-nm fiber)


Fig. 16-20

1 µm


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 nowDNA sense strand ATG GTG CAC CTG AGT CCT GAG GAG AAG TCTmRNAtRNA’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

KEY TERMS:

transcriptiontranslationmRNAtRNAribosomeDNAnucleuscytoplasmcodonanticodonamino acidpolypeptideprotein

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



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



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

http://m.youtube.com/watch?v=WsofH466lqk

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

Modeling Gene Expression

Go to pHet: https://phet.colorado.edu/en/simulation/gene-expression-basics

Analysis:1. sadf

https://phet.colorado.edu/en/simulation/gene-expression-basics

https://phet.colorado.edu/en/simulation/gene-expression-basics

Mutations in DNA:1. Substitution: a nucleotide is different,

which causes one of the following:a. silent: no affect on amino acidsb. missense: one amino acid

differentc. nonsense: many amino acids

missing2. Insertion/Deletion: a nucleotide is

added or deleted, which causes one of the following:

a. frameshift: one amino acid missingb. frameshift: all amino acids

differentc. frameshift: many amino acids

missing

Changes in information can result in changes in organisms.

Changes in information can result in changes in organisms.

WHITEBOARD:Types of Mutations

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 acidsb. missense: one amino acid differentc. 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 missingb. frameshift: all amino acids differentc. frameshift: many amino acids missing

DNA nonsense

DNA sense TAC GAG CTC CTG TGT CCT GCG GAG AAG ATTmRNA

tRNA’s

amino acid sequence

WHITEBOARD: Gallery Walk

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, S2. 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.

Pipetting1. To draw your desired volume into your tip:

a. 1st stopb. Into the solutionc. Released. Out of the solution

2. To eject your desired volume into your microtube:e. Eject: to the 2nd stopf. Perfection?: TOUCH the drop to “unstick” the last bit

REMINDERSg. No double dippingh. Close tip box lidsi. Keep your hands, breath, etc. to yourselfj. Sterilize everything: before, during, and afterk. Small volumes DO NOT equal no volume: Use a microcentrifuge!

Add to tube Control Child 1 Child 2 Child 3 Sue

sd H2O (flask)

10.0ul 8.0ul 8.0ul 8.0ul 8.0ul

buffer2.0ul

React 2 (orange)

2.0ulReact 3 (blue)

2.0ulReact 3 (blue)

2.0ulReact 2 (orange)

2.0ul React 2 (orange)

enzyme (purple) 3ul 4ul 4ul 4ul 4ul

Child 1’s DNA

(green)1ul

Child 2’s DNA (pink) 1ul

Child 3’s DNA

(yellow)1ul

Sue’s DNA (clear) 1ul


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.

Control Child 1 Child 2 Child 3 Sue

Yesterday’s Product

15ul 15ul 15ul 15ul 15ul

Sample Loading Buffer

3ul 3ul 3ul 3ul 3ul

Fig. 20-3-1Restriction site

DNA

Sticky end

Restriction enzymecuts sugar-phosphatebackbones.

53

35

1

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





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....

Documents

structure of dna

dna models

dna big idea

topics concept

key ideas

phenotype slide

organisms store information

key characteristics