Ch 13 Molecular Basis of Inheritance 2017 - KEY PDF

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AP Biology Ch 13 KEY: The Molecular Basis of Inheritance Key Concepts: 1. DNA is the genetic material. 2. Many Proteins work together in DNA Replication and repair. 3. A Chromosome consists of a DNA Molecule packed together with Proteins (histones). 4. Understanding DNA structure and replication makes Genetic Engineering possible. CH 13: 5. Nucleic Acids are unique molecules due to their ability to direct their own replication 6. o o o o

In this chapter you will learn: How scientists deduced that DNA was the genetic material How DNA is replicated (copied) How cells repair DNA How DNA is packed w/proteins to form a chromosome.

7. TH Morgan et al. group showed that Genes exist as parts of chromosomes. After that, the two components of chromosomes that became candidates as “the” genetic material were DNA and Proteins. Understandably, proteins were the frontrunners as they were identified as a class of macromolecules with great heterogeneity and specificity (essential characteristics for hereditary material). Nucleic acids seemed too uniform…but, this was incorrect. 8. The view of Protein’s role gradually changed as the role of DNA in heredity was worked out in studies of Bacteria and the Viruses (bacteriophages) that infect them 9. Concept 13.1: Discuss the experiments of the following scientists and how their experiments gave evidence as DNA as the genetic material. Scientist

Year

Frederick Griffith 1928

Experiment (description)

Evidence gained

Inject mice with different forms of pneumonia -Smooth=deadly -Rough=non-deadly -Heat killed Smooth -Heat killed smooth & living Rough

Molecules from the dead Smooth cells can transform the Rough bacteria into the Smooth form. Assimilated the DNA

Heat killed pathogenic bacteria mixed with non-pathogenic in experimental group

Something (DNA) was taken up by the non-deadly that allowed it to transform into deadly.

Non-pathogenic became deadly due to change in genotype = change in phenotype

Oswald Avery & Collin MacLeod 1944

Hershey and Chase 1952

Purified parts of deadly cells and tried to transform living bacteria. Blender Exp: Radioactively label protein with sulfur (S) in Batch 1 and radioactively label DNA with Phosphorous (P) in Batch 2. Only (P) made it into the cell. Experiment: McGraw Hill

Only DNA could transform bacteria, therefore DNA was THE genetic material of organisms.

DNA is the genetic material of the T2 phage Confirmed that DNA and NOT protein is the genetic material DNA plays a role in the infection process of the E. coli Exp. Campbell

Erwin Chargaff 1947

Analyzed the base composition of DNA from many different organisms (species)

Nitrogenous Base Pairing A = T C = G Chargaff’s rules

Maurice Wilkins and Rosalind Franklin

1953

Used X-ray diffraction crystallography to discover the double helix structure of DNA Used the images of diffracted x-rays through DNA fibers

DNA is a double helix -Helical pattern -Width of the Helix - Spacing of the bases -Two strands -External Sugar/Phosphate backbone -Bases internalized -One full turn every 3.4nm

James Watson and Francis Crick

1953

Took everyone’s work listed above and then put it all together and made a model for the structure of DNA.

Working model for the structure of DNA. Constructed the antiparallel strands of the double helix

Model based on Xrays of Frankiln/Wilkins and Chargaff’s rules

10. Franklin had concluded that the sugar-phosphate backbones were on the outside of the DNA molecule. This arrangement was appealing as it put the negatively charged Phosphates facing the aqueous environment. Meanwhile the relatively hydrophobic Nitrogenous bases were hidden in the interior. 11. Watson’s constructed model had 2 sugar-phosphate backbones running in an Anti-parallel direction/fashion; meaning that their nucleotide subunits ran in Opposite directions. 12. What two reasons did Watson and Crick give that they believed that the purine adenine paired with the pyrimadine thymine and that the purine guanine paired with the pyrimidine cytosine? 1. Due to the width of the double helix (consistent with the x-ray data – 2 nm) one purine had to pair with one pyrimidine – one double ringed base with a single ring base. A & G are purines with 2 rings while C & T are pyrimidines with 1 ring. 2. Each base has side groups that can form hydrogen bonds with its appropriate partner. Adenine can form 2 hydrogen bonds with thymine and guanine can form 3 hydrogen bonds with cytosine 13. How were Chargaff’s rules explained through the discovery of the double helix? His data is on p257

Chargaff rules stated that in any one species, there were not equal amounts of the 4 different nitrogen bases. Instead, the 4 bases existed in correlated ratios. Specifically, if cytosine existed in a certain proportion, then guanine existed in approximately the same proportion. Likewise with adenine and thymine respectively. The discovery of the double helix demonstrated that adenine paired thymine and guanine paired with cytosine (explaining the ratios). 14. The sequence of bases - holds the genetic code and can be varied in countless ways. 15. Watson and Crick published their findings in a ONE PAGE ARTICLE in the journal Nature in 1953(year). Awarded a Nobel Prize in 1962! (article attached to this packet) 16. The beauty of the proposed double helix model was that it suggested the basic mechanism of

its own replication (due to the complimentary base pairing/arrangement).

More 13.1 (and Chapter 3.6 review): What do you know about DNA Structure? 17. The monomers of DNA are called Nucleotides. 18. Each of these monomers is made up of a Nitrogenous Base (one of four), a Deoxyribose sugar (pentose) and one to three Phosphates. 19. The four different nitrogenous bases of DNA are: http://www.biology-pages.info/B/BasePairing.html a) Adenine b) Guanine c) Thymine d) Cytosine (Label the four nitrogenous bases to the right )

20. Pyrimidines - are bases with six-membered carbon rings (circle the bases above that fall into this category) 21. Purines- are bases with a six-membered carbon ring fused to a five-membered carbon ring (put a square around the bases above that fall into this category)

The Structure of DNA and the “Double Helix”: 22. Nitrogen Bases makes up the “rungs” of the double helix 23. Deoxyribose and Phosphate groups make up the backbone of the double helix. 24. One nucleotide is connected to other nucleotides by chemical bonds: A) hydrogen bonds between bases B) phosphodiester linkages along the DNA backbone 25. This functional group is seen at the 31 end of the DNA molecule: Hydroxyl -OH 26. This functional group is seen at the 51 end of the DNA molecule: Phosphate -PO4

27. Review the structure of DNA by labeling the following diagrams

Phosphate

Complementary bases

PDE bond

nucleotide Label the diagrams above with the terms given below -phosphate, cytosine, guanine, adenine, thymine, nucleotide, hydrogen bond, complimentary bases, deoxyribose, nucleotide, phosphodiester bond You can clearly see the antiparallel nature od

DNA looking at the paired nucleotides in squares above Label the diagrams above with the terms given below: -Distance between nucleotides, 3-prime and 5-prime ends Look at the diagram: Why can/do we say that the two strands are antiparallel? Antiparallel means parallel but running in opposite directions. This term is used to describe the opposite orientation of the strands of a DNA molecule. It helps to focus on the O in the deoxyribose sugar molecules on opposite sides of the molecule to see the fact that the nucleotides are certainly running in the opposite direction. It is also apparent at an open 31 or 51 end as it will line up with a 51 or 31 end respectively (across the helix). Think Carbons: please explain the use of the terms 5-prime and 3-prime in regards to DNA/sugar structure. The 5' and 3' mean "five prime" and "three prime", which indicate the carbon numbers of the sugar molecule. 5' specifies the 5th carbon in the deoxyribose ring, counting clockwise from the oxygen molecule, and 3' specifies the 3rd carbon in the ring. The 5' carbon has a phosphate group attached to it and the 3' carbon a hydroxyl group. This asymmetry gives a DNA strand a "direction".

DNA REPLICATION http://www.dnatube.com/video/29698/DNA-replication-schematic-view Replication FlyOver 13.2: 28. Watson and Crick wrote: “It has NOT escaped our notice the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” 29. How many complementary strands exist in the parent molecule? Two

30. “We imagine that prior to duplication the Hydrogen bonds are broken, and the two chain unwinds ad separate.” 31. “Each chain then acts as a template for the formation on to itself of a new companion chain, so that eventually we shall have Two Pairs of chains, where we only had One before. Moreover, the Sequenceof the pairs of bases will have been Duplicated exactly.” Overview of DNA Replication (Campbell) 32. The Semiconservative model is the supported model of how DNA replication occurs where each parental strand acts as a template for a new strand. After one replication, half of each new DNA molecule is parental and half is brand new (made of complementary nucelotides/bases).

33. In a favorable environment, an E. Coli bacterial/prokaryotic cell can copy all of its 4.6 million nucleotide pairs and divide to form two identical daughter cells in about an hour. It takes one of your eukaryotic cells a few hours to copy its DNA (6 billion nucleotide pairs).

Use Figure 13.13 34. Explain the Meselson-Stahl experiment & Explain what information they gained from their work. Meselson-Stahl Experiment (Campbell)

M and S grew Bacteria for several generations on a medium containing 15N (heavy). All of the DNA produced by these bacteria contained the heavy 15N. Then they transferred the bacteria to a new medium containing only 14N (light). Therefore, the entire new DNA produced by the bacteria used the light 14N. They allowed one sample of bacteria to reproduce for 20 min., which required the bacteria to replicate its DNA once. They allowed another sample of bacteria to reproduce for 40 min., which required the bacteria to replicate its DNA twice. Then they extracted the DNA from each sample, centrifuged the DNA, and compared the results to what would be expected if DNA replicated according to the conservative model, semiconservative model, and the dispersive model. They discovered that DNA replication occurred according to the semi-conservative model. 35. In prokaryotes there is one chromosome and it is circular (4.6 million bases) . It has one origin of replication. Where the chromosome opens a replication “bubble” forms (TWO REPLICATION FORKS). Label the diagram below.

36. In eukaryotic cells there are multiple origins of replication so that replication can occur at a faster rate (46 chromosomes, 6 billion bases). Label the diagram below:

37. The Replication fork is the location at which the DNA strands elongate.

“DNA Replication Machine” As a process, A Closer Look DNA Replication (Campbell) Enzymes in Replication (Campbell) 1. To begin, unwind and unzip the parent strands 2. The replication of DNA begins at special sites called the origin of replication. 3. The 2 strands of DNA unwind and unzip using the enzyme helicase 4. The strands are kept from reforming hydrogen bonds by single strand binding proteins 5. Topoisomerase is an enzyme that helps relieve the strain on the double helix created by the untwisting. 6.

Primase provides an RNA Primer ( 5-10 nucleotides long) for the beginning of the new strand of DNA. This is because DNA Polymerase needs guidance/initiation.

Label the Basics:

7. Each half of the double helix is used as a Template strand to make a new strand. This is able to occur due to complementary base pairing (making two of the original). 8. DNA Polymerase is the enzyme that synthesizes new DNA chains from the existing template. 

Two kinds of these play a significant role in E. coli DNA replication: DNA Polymerase I and DNA Polymerase III



In eukaryotes at least 11 have been discovered

9. In prokaryotes replication occurs at about 500 nucleotides /sec, whereas in humans it is 50 nucleotides/sec. 10. The energy needed to build the strand of DNA comes from nucleotide triphosphates. A pyrophosphate is released as the phosphodiester bond is formed between nucleotides. 11. DNA strands are considered to be antiparallel which means that the strands of DNA run counter to each other. (5’ end of one strand is bound to the 3’ end of its complimentary strand) Label the Process/Parts:

12. Define what is meant by 51 and 31 and how does this relate to the direction a DNA template is read versus the direction a new strand is built? The sugar and phosphate backbones of the strands of DNA run in opposite directions. At the 5’ end of one strand the phosphate group is attached to the 5’ carbon of the sugar and at the 3’ end a hydroxyl group extends from the 3’ carbon of the terminal sugar. This is important because a new strand of DNA can only be built from 5’  3’ (which means the template DNA is copied from 3’  5’). DNA polymerase works in a 5' to 3' direction, that is, it adds nucleotides to the 3' end of the molecule (the -OH group), thus advancing (elongating/polymerizing) in that direction.

13. One strand continues to replicate from 51 to 31 , this strand is called the:

Leading Strand

14. The second strand called the Lagging Strand is made piece by piece (Okazaki fragments) as DNA polymerase III moves down the helix. 15. DNA polymerase I kicks out the primer and adds DNA nucleotides. 16. These fragments are bound together by the enzyme DNA Ligase to form a continuous strand.

Label the “Lagging” Diagram Carefully:

The Big Picture – Label all the parts below & Know This!

Fancy & Fantastic: Replication Overviews http://www.dnatube.com/video/5921/Detailed-explanation-of-DNA-replication-mechanism http://www.dnatube.com/video/2335/Video-for-DNA-Replication DNA REPLICATION (Bioflix)

DNA Profreading & Repairing DNA 1. In the final DNA strand 1 error occur per 10 billion nucleotides However, 1 in 100,000 actually occurs during replication. Proofreading is a gud thing.  2. DNA Polymerase II does the initial proofreading. If one is missed mismatch repair occurs. 3. Post replication repair is carried out by multiple enzymes (in humans 130 have been identified). 4. Nucleotide Excision repair uses nucleases to excise out the mutation and then DNA Polymerase and Ligase to fill in the new correct bases. An example of damage that is repaired is a Thymine Dimer.

5. What is the evolutionary significance of the mistakes that can occur during DNA replication? Be sure to discuss the genotypic and phenotypic implications. Trick Question: Are mutations bad?

6. Telomeres are composed of multiple repeats (TTAGGG in humans). These repeats help to protect DNA from erosion and loss through successive rounds of DNA replication.

7. Telomerase is an enzyme that restores shortened strands of DNA. This is done by adding RNA which acts as a template for a new telomere segment. http://www.dnatube.com/video/6886/Telomere-Replication-Science-video

Telomere Video

13.3 A Chromosome consists of a DNA molecule packed with Proteins Bacterial Chromosomes: The genome is a One , double stranded, circular DNA molecule with small amounts of

Protein 4.6 million nucleotide pairs

4,400 genes

This is 100 times more DNA than is typically found in a virus but 1/100th as much DNA as in a human somatic (body) cell. Fits into a dense region called a Nucleoid with no membrane Eukaryotic Chromosomes Single linear double helix (existing in 46 total chromosomes in humans)

1.5 x 108 nucleotide base pairs Chromatin is the combination/packing of DNA & large amounts of Protein in eukaryotic cells.

Define Histone: Proteins found in eukaryotic cell nuclei that package and order DNA into units called nucleosomes. Histones are the primary protein components of chromatin. DNA winds around the histone. Without histones DNA is exceedingly long. Histones also play a role in gene regulation/expression. https://www.dnalc.org/resources/3d/07-how-dna-is-packaged-basic.html DNA Packaging Define Nucleosome: A nucleosome is a section of DNA that is wrapped around a core of histone proteins. Inside the nucleus, DNA forms a complex with proteins called chromatin, which allows the DNA to be condensed into a smaller volume. When the chromatin is extended and viewed under a microscope, the structure resembles beads on a string. Each of these tiny beads is a called a nucleosome and has a diameter of approximately 11 nm. The nucleosome is the fundamental subunit of chromatin. Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones, which are known as a histone octamer. Each histone octamer is composed of two copies each of the histone proteins H2A, H2B, H3, and H4. The chain of nucleosomes is then compacted further and forms a highly organized complex of DNA and protein called a chromosome. (Scitable by Nature)

During Interphase centromeres, telomeres, and some chromosomal regions exist in a highly condensed state called Heterochromatin.(inaccessible)

Euchromatin is the part of a chromosome during Interphase that is loosely packed. A chromosome is a dynamic structure that is condensed, loosened, modified, and remodeled as necessary.

SOME STUDY IMAGES:

1.

1.

____________ bonds hold the DNA complementary base strands together. a. Phosphodiester b. Hydrogen c. Covalent d. Peptide e. Ionic

B

2.

The DNA double helix is built (written) in the A a. 5’ to 3’ direction b. 3’ to 5’ direction c. 3’ to 3’ direction d. 5’ to 5’ direction

3.

If thymine makes up 40% of the bases in a DNA double helix, what percent of the bases are guanine? E a. 80% b. 60% c. 40% d. 20% e. 10%

4.

Which of the following nitrogenous bases are purines? MARK ALL THAT APPLY a. Guanine b. Adenine c. Cytosine d. Thymine

5.

DNA _________ is responsible for joining the gaps in the Okazaki fragments. a. Primase b. Helicase c. Polymerase d. Ligase

6.

Refer to the strand on the top of the drawing. Which number points to the 3’ end of the molecule? a. 1 b. 2 c. 3 d. 4

7.

Arrange the steps of DNA replication on the lagging strand in order with the earliest steps first. 1. DNA ligase links segments 2. Okazaki fragments form 3. Enzymes unwind the DNA double helix 4. DNA polymerase attaches to the nucleotides 5. Enzymes add short RNA primers a) 1, 2, 3, 4, 5 b) 2, 4, 3, 1, 5 c) 3, 5, 4, 2, 1 d) 4, 5, 1, 2, 3 e) 5, 4, 3, 1, 2

8.

In DNA replication, the enzyme __________ breaks the bonds which hold the complementary base strands together. C a. Gyrase b. Primase c. Helicase d. Single-stranded binding proteins

A&B

D

A

C

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