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AA

A

A

TC

G

CG

TG

C

T

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Macromolecules: Nucleic Acids Examples:

RNA (ribonucleic acid) single helix

DNA (deoxyribonucleic acid) double helix

Structure: monomers = nucleotides

RNADNA

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Nucleotides 3 parts

nitrogen base (C-N ring) pentose sugar (5C)

ribose in RNA deoxyribose in DNA

phosphate (PO4) group

Are nucleic acidscharged molecules?

Nitrogen baseI’m the

A,T,C,G or Upart!

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Types of nucleotides 2 types of nucleotides

different nitrogen bases purines

double ring N base adenine (A) guanine (G)

pyrimidines single ring N base cytosine (C) thymine (T) uracil (U)

Purine = AGPure silver!

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Nucleic polymer Backbone

sugar to PO4 bond phosphodiester bond

new base added to sugar of previous base

polymer grows in one direction N bases hang off the

sugar-phosphate backbone

Dangling bases?Why is this important?

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Pairing of nucleotides Nucleotides bond between

DNA strands H bonds purine :: pyrimidine A :: T

2 H bonds G :: C

3 H bonds

Matching bases?Why is this important?

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DNA molecule Double helix

H bonds between bases join the 2 strands A :: T C :: G

H bonds?Why is this important?

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Copying DNA Replication

2 strands of DNA helix are complementary have one, can build other have one, can rebuild the

whole

Matching halves?Why is this

a good system?

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When does a cell copy DNA? When in the life of a cell does DNA have

to be copied? cell reproduction

mitosis gamete production

meiosis

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Learning Check Use the candy and instructions to build

a DNA model that follows Chargaff’s rules of base pairing

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But how is DNA copied? Replication of DNA

base pairing suggests that it will allow each side to serve as a template for a new strand

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Models of DNA Replication Alternative models

become experimental predictions

conservative semiconservative

Can you designa nifty experiment

to verify?

dispersive

1

2

P

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Semiconservative replication Meselson & Stahl

label “parent” nucleotides in DNA strands with heavy nitrogen = 15N

label new nucleotides with lighter isotope = 14N

1958

parent replicationMake predictions…

15N parent strands

15N/15N

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Semiconservative replication Make predictions…

15N strands replicated in 14N medium 1st round of replication? 2nd round?

1958

where should the bands be?

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Franklin Stahl

Matthew Meselson

Matthew Meselson Franklin Stahl

Meselson & Stahl

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DNA Replication Origin(s) of replication

specific sequence of nucleotides recognized by replication enzymes

Prokaryotes – Single sequence Bidirectional Synthesis

Replication proceeds in both directions

Eukaryotes – hundreds/thousands of origin sites

per chromosome Replication forks

Bubbles elongate as DNA is replicated and eventually fuse

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Bidirectional Synthesis In prokaryotes, the circular DNA is opened

up, and synthesis occurs in both directions

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In eukaryotes, the linear DNA has many replication forks

Replication forks

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Learning Check Break the toothpicks at the center of

your models and replicate your DNA strand You should end up with 2 complete

strands of DNA

Keep in mind Chargaff’s rules and Meselson & Stahl’s semi-conservative model

Animation

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Replication- Create a diagram that shows how the following components interact with each other (15 min)

Lagging strand Helicase DNA polymerase Single stranded

binding protein Topoisomerase

Replication fork RNA primer Leading strand DNA ligase RNA primase Okazaki fragments

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DNA Replication Issues1. DNA strands must be

unwound during replication DNA helicase

unwinds the strands Single stranded binding

proteins (SSB) prevent immediate

reformation of the double helix

Topoisomerases “untying” the knots that

form

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Replication Issues2. A new DNA strand can

only elongate in the 5’ 3’ direction

DNA polymerase can add only at the 3’ end

Replication is continuous on one strand Leading Strand

discontinuous on the other Lagging strand Okazaki fragments

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Okazaki fragments

Synthesis of the leading strand is continuous

The lagging strand (discontinuous) is synthesized in pieces called Okazaki fragments

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Replication Issues3. DNA polymerase cannot initiate

synthesis because it can only add nucleotides to end of an existing chain

Requires a “primer” to get the chain started

RNA Primase can start an RNA chain from a single

template strand DNA polymerase can begin its chain

after a few RNA nucleotides have been added

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Summary At the replication fork, the leading strand is

copied continuously into the fork from a single primer

Lagging strand is copied away from the fork in short okazaki fragments, each requiring a new primer

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Learning Check

1. What is the purpose of DNA replication?

2. How is the new strand ensured to be identical to the original strand?

3. How is replication on one side of the strand different from the other side?

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Replication Issues4. Presence of RNA primer

on the 5’ ends of daughter DNA leading strand leaves a gap of uncopied DNA

Repeated rounds of replication produce shorter and shorter DNA molecules

Telomeres protect genes from being

eroded through multiple rounds of DNA replication

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Telomeres Ends of eukaryotic

chromosomes, the telomeres, have special nucleotide sequences Humans - this sequence is

typically TTAGGG, repeated 100 - 1,000 times

Telomerase adds a short molecule of RNA as a template to extend the 3’ end

Room for primase & DNA pol to extend 5’ end

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Summary Explain how the cell overcomes each of the

following issues in DNA replication

1. DNA strands must be unwound during replication

2. A new DNA strand can only elongate in the 5’ 3’ direction

3. DNA polymerase cannot initiate synthesis and can only add nucleotides to end of an existing chain

4. Presence of RNA primer on the 5’ ends of daughter DNA leading strand leaves a gap of uncopied DNA