DNAThe Universal Code of Life

• To which class of biological molecules does DNA belong?

• What are the monomers of DNA?

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DNA is a:

1 2 3 4 5

2%9%

0%

90%

0%

1. Carbohydrate2. Protein3. Lipid4. Nucleic Acid5. Depends on the

organism

The monomers of DNA are:

1 2 3 4 5

2% 0% 0%

98%

0%

1. Sugars2. Amino acids3. Fatty acids4. Nucleotides5. Depends on the

organism

Early History• 1869: Friederich Mieschner

isolates “nuclein” from nuclei of cells. His student Richard Altman later renames the substance “nucleic acid.”

• Mid 1800s: Biochemists identify two distinct nucleic acids.

• 1929: Phoebus Levine identifies four distinct bases in DNA.

Heredity as a Science• Genetics arose as a new science in

the late 19th and early 20th centuries, spurred by questions raised by Darwin’s On the Origin of Species:

• Are there patterns to inheritance?

• Are traits handed on intact (particle theory) or blended together in each generation (blending theory)?

Mendel’s Answers

• Gregor Mendel’s work was rediscovered in 1900, answering both questions:

• Inheritance of many traits follows predictable patterns.

• Traits are handed on intact via some kind of particle: “elementen.”

Hereditary Molecule?

• Question in the 20th century: What is the hereditary molecule?

• Cell nucleus associated with inheritance.

• Both proteins and nucleic acids are in the nucleus. Which contains information coding for traits?

Protein or DNA?

• Linus Pauling favored protein: DNA has only four bases, protein has over 20 amino acids. Seemed like protein could store more information.

• Others favored DNA, which is found only in the nucleus.

Frederick Griffith

• In 1928, Frederick Griffith carried out experiments on pneumonia bacteria, trying to create a vaccine against pneumonia. Among his findings were early clues about hereditary factors.

LivingR-strain

LivingS-strain

Heat-killedS-strain

Living Rstrain,heat-killed S-strain

Bacterial strain(s) injected into mouse Results Conclusions

R-strain does notnot causepneumonia.

S-strain causespneumonia.

Heat-killed S-strain does notcause pneumonia.

A substance fromheat-killed S-straincan transform theharmless R-straininto a deadlyS-strain.

Mouse contractspneumonia, dies.

Mouse remainshealthy.

Mouse remainshealthy.

Mouse contractspneumonia, dies.

Griffith’s Experiment

Why were living S-strain bacteria recovered from dead mice injected with dead S-strain and live R-

strain bacteria?

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Oswald Avery

• Avery learned of Griffith’s experiment and thought it might hold a clue to the identity of the hereditary molecule.

• Avery isolated carbohydrates, proteins, lipids, and nucleic acids from the bacteria to discover which, if any, would transform the non-virulent R-strain bacteria.

Of the substances isolated and tested, only DNA from killed S-strain bacteria transformed R-strain

bacteria.

Hershey & Chase• Early 1950’s: Alfred

Hershey and Martha Chase used the bacteriophage virus in another series of experiments to identify the hereditary material.

• Bacteriophages, like other viruses, contain both protein and DNA, but are non-living.

DNA

tail

head

Protein coat

Bacteriophage

1 Phage attachesto bacterium.

2 Phage injects itsDNA intobacterium.

3 Phage DNAis replicated.

4 Phage partssynthesized, usingbacterial metabolism.

5 Completephages assembled.

6 Bacterial walldestroyed; phagereleased.

Results: Bacteria areradioactive; phage coats are not.

5 Measure radioactivity of phagecoats and bacteria.

1 Label phages with P32 or S35.

2 Infect bacteria withlabeled phages; phages injectgenetic material into bacteria.

3 Whirl in blender to break offphage coats from bacteria.

4 Centrifuge to separate phage coats(low density: stay in liquid)from bacteria (high density:sink to bottom as a “pellet”)

Results: Phage coats areradioactive; bacteria are not.

Radioactive sulfur (S35)Radioactive phosphorus (P32)

RadioactiveDNA (blue)

Radioactiveprotein(yellow)

Conclusion: Infected bacteria are labeled with radioactive phosphorus but not with radioactive sulfur,supporting the hypothesis that the genetic material of bacteriophages is DNA, not protein.

Radio-tagged DNA Radio-tagged Protein

These early experiments showed that DNA is the hereditary molecule

because:

1 2 3

7%0%

93%1. Only DNA could

break down proteins.

2. Only DNA caused changes in hereditary traits.

3. Only bacteria and viruses have DNA.

DNA Structure?

• While many research teams were trying to discover the hereditary molecule, other researchers were working to discover the nature of DNA.

Erwin Chargaff

• Chargaff took apart DNA into its component nucleotides and studied the proportions.

• Found consistent ratios between certain nucleotides.

In DNA, Chargaff consistently found equal amounts of adenine compared with thymine, and equal amounts of

cytosine compared with guanine.

Did that mean the bases were always

paired?

If a strand of DNA is 30% adenine, how much thymine does it have?

1 2 3 4

2% 2%

95%

2%

1. 15%2. 20%3. 30%4. Impossible to

predict

If a strand of DNA is 30% adenine, how much cytosine does it have?

1 2 3 4

9%

17%12%

62%

1. 15%2. 20%3. 30%4. Impossible to

predict

Franklin and Wilkins

• Rosalind Franklin worked in Maurice Wilkins’ lab in the late 1940s, using X-ray crystalography to find clues about the structure of DNA.

• Franklin’s images were the first to suggest a helical structure.

The X-shape on the radiograph was characteristic of helical molecules. Franklin also measured distances

between bases and other dimensions using her images.

Watson and Crick• James Watson and Francis Crick

worked at the same time as Franklin and Wilkins.

• Applying Chargaff’s rule, they concluded that A pairs with T, C with G.

• Used their knowledge of molecular geometry to try to discover the structure of DNA.

• Wilkins consulted with Watson and Crick. Without Franklin’s knowledge, he handed them several of Franklin’s X-ray images.

• Watson immediately recognized their significance, though he’d criticized Franklin’s work earlier.

By adding Franklin’s data to their own (without her permission!), Watson and Crick assembled

the first plausible model of DNA and published an article on the structure of DNA in 1953.

DNA Structure

DNA contains four bases. RNA also has four bases, but has uracil instead of thymine.

As Chargaff’s work suggested, Adenine always pairs across the DNA ladder with Thymine, while Cytosine

always pairs with Guanine.

How many H-bonds?

How many H-bonds?

How many rings?

How many rings?

5’ end

3’ end

1’

2’3’

4’

5’1 2

345

6

Nucleotides are 3-dimensional, with an orientation that affects the shape of the entire nucleic acid.

5’ end

3’ end

1’

2’3’

4’

5’

1 23

456

789

1’

2’3’

4’

5’ 1 23

456

The 3’ end of one nucleotide binds with

the 5’ end of the next nucleotide in

the chain.

5’end

3’end

3’ end

5’end

Two chains of DNA nucleotides are held together

by hydrogen bonds between

the bases of each strand.

Notice that the strands run in

opposite directions. They are

antiparallel.

free phosphate

free sugar

The 3-dimensional shape of the nucleotides creates

the helical structure of DNA.

The sugar in the backbone of DNA is:

1 2 3 4

16%

3%

62%

19%

1. Glucose2. Ribose3. Deoxyribose4. Lactose

In the DNA double helix, adenine always matches thymine because:

1 2 3 4

0% 0%

11%

89%1. Adenine is polar and thymine is nonpolar.

2. Both can form two hydrogen bonds with each other.

3. Both are single-ring bases.

4. Wrong! Adenine always matches adenine.

• Suppose that one side of a DNA double-helix reads:

A T A A C A G T T A G C A G G

According to the base-pairing rule, what is the sequence of bases on the other side of the DNA double-helix?

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Label the four bases in this diagram.

(Look back several slides for a hint.)

Circle one complete nucleotide on

each side. (Hint: look back several

slides to see which carbon on the sugar

attaches to the phosphate.)

T

T

A

A

G C

C G

DNA Replication

• When cells divide, the two resulting daughter cells must have exactly the same DNA as the original cell.

• Therefore, before cell division happens, the cell must replicate (copy) its DNA.

replication forks

replication bubbles

DNA

DNA helicase

The enzyme DNA helicase “unzips” DNA by breaking hydrogen bonds holding the two strands

together.

“Unzipping” occurs at multiple points on the DNA strand.

replication forks

DNA helicase

DNApolymerase #2

DNApolymerase #1

5′

3′

5′

3′

continuous

synthesis

discontinuoussynthesis

Within each replication bubble, the enzyme DNA polymerase builds a new strand of DNA, using the

original strands as templates.

DNApolymerase #2

DNApolymerase #1

5′

3′5′

3′

continuous

synthesis

discontinuoussynthesis

5′3′

5′3′

3′

5′continuous synthesis

discontinuous synthesis

DNApolymerase #2leaves

DNApolymerase #3

DNA polymerase #1continues alongparental DNA strand

Because DNA polymerase always travels from the 3’ to the 5’ end of DNA, one polymerase is always

moving away from the replication fork

5′3′

5′3′

3′

5′continuous synthesis

discontinuous synthesis

DNApolymerase #2leaves

DNApolymerase #3

DNA polymerase #1continues alongparental DNA strand

5′3′

5′3′

3′

5′ DNApolymerase #3leaves

DNApolymerase #4

3′

5′

DNA ligase joinsdaughter DNA strandstogether.

Multiple DNA polymerase molecules are required for the strand where discontinuous replication is

happening.

How does DNA polymerase “know” which bases to use when replicating?

Remember Chargaff’s rule: A and T always

match, C and G always match.

Practice DNA base-pair matching:http://learn.genetics.utah.edu/content/begin/dna/builddna

• Suppose a segment of a DNA double-helix reads:

A G T C A A T G CT C A G T T A C G

After replication, what will the two resulting DNA double-helices read?

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The enzyme that “unzips” DNA is:

1 2 3

33% 33%33%

1. DNA polymerase

2. Helicase3. Ligase

The enzyme that “pastes” in new bases during replication is:

1 2 3

33% 33%33%

1. DNA polymerase

2. Helicase3. Ligase

The enzyme that mends gaps in the sugar-phosphate backbone is:

1 2 3

33% 33%33%

1. DNA polymerase

2. Helicase3. Ligase

• Helicase, DNA polymerase, and ligase are enzymes. To which class of biological molecules do enzymes belong?

• Where are the instructions for making DNA polymerase found?

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Mutations

• Though many enzymes patrol your DNA, looking for replication errors, some errors do creep in.

• Most cells with a DNA error will die. A few may turn cancerous.

• If mutated cells are sex cells, the mutation can be passed on and will affect all cells in the offspring.

• Mutations may be harmful, helpful, or neutral.

• Harmful mutations result in genetic disease or death.

• Helpful mutations increase evolutionary “fitness” (i.e. having offspring).

• Neutral mutations neither help nor harm at the present.

original DNA sequence

Nucleotide substitution

nucleotide pair changed from A–T to T–A

substitution

Silent mutation: still codes for the same

amino acid.

Missense mutation: codes for a different

amino acid, which may or may not affect the

final protein.

Nonsense mutation: codes for a “stop” in the middle

of the sequence, producing a useless

protein.

Examples:

• Sickle-cell anemia is caused by a missense mutation due to a nucleotide substitution.

• Duschenne’s Muscular Dystrophy is caused by a nonsense mutation in a gene for a critical enzyme.

• Lactose persistence may be caused by a single nucleotide substitution.

original DNA sequence

T–A nucleotide pairinserted

Insertion mutation

Example: Huntington’s disease, a loss of neural function in middle-age, is caused by a string of

insertions.

Deletion mutation

C–G nucleotide pairdeleted

original DNA sequence

Example: a 32-base-pair deletion in the gene for a

certain cell membrane receptor protein causes

resistance to HIV.

original DNA sequences

DNA segment inverted

Inversion

breaks

Example: an inversion mutation is responsible

for one form of hemophilia.

original DNA sequences

break

Translocation

break DNAsegmentsSwitched

Examples: Several forms of leukemia, lymphoma and possibly schizophrenia are

caused by translocation mutations.

What causes mutations?

http://learn.genetics.utah.edu/archive/sloozeworm/mutationbg.html

Recap• DNA is a nucleic acid which

contains coded hereditary information.

• The base-pairing rule helps the information in DNA accurate.

• All cells in the body have the same DNA containing the same information. DNA must be replicated before cell division.