G

T
A

AP Biology

A
C

G
T

T
C

Macromolecules: Nucleic Acids

Examples:

RNA (ribonucleic acid)

single helix

DNA (deoxyribonucleic acid)

double helix

Structure:

AP Biology

monomers = nucleotides

DNA

RNA

Nucleotides
3 parts
nitrogen base (C-N ring)
pentose sugar (5C)

ribose in RNA
deoxyribose in DNA

phosphate (PO4) group

Are nucleic acids

charged molecules?

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Nitrogen base
Im the
A,T,C,G or U
part!

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)

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Purine = AG
Pure silver!

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

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Copying DNA
Replication

2 strands of DNA helix are

complementary
have one, can rebuild the

whole

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Learning Check
Use the pipe cleaners and beads to
build a DNA model that follows
Chargaffs rules of base pairing

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But how is DNA copied?

Replication of DNA

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base pairing suggests

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

Models of DNA Replication

Alternative models

become experimental predictions

conservative

P
1

2
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Can you design

a nifty experiment
to verify?

semiconservative

dispersive

Semiconservative replication

1958

Meselson & Stahl

label parent nucleotides in DNA strands with
heavy nitrogen = 15N
label new nucleotides with lighter isotope = 14N

parent

15

N/15N

N parent
strands
15

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replication

Semiconservative replication
Make predictions

1958

N strands replicated in 14N medium

1st round of replication- middle
2nd round- middle and top
15

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DNA Replication
Origin(s) of replication

specific sequence of
nucleotides recognized by
replication enzymes

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Bidirectional Synthesis
In prokaryotes, the circular DNA is
opened up, and synthesis occurs in both
directions

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Replication forks
In eukaryotes, the linear DNA has
many replication forks

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Replication: 1st step

Unwind DNA

Helicase
unwinds part of DNA helix
creates replication fork

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DNA Replication Issues

1. DNA strands must be
unwound during replication
Single stranded binding
proteins (SSB)

prevent immediate
reformation of the double
helix

Topoisomerases

untying the knots that

form

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Replication: 2nd step

Build daughter DNA
strand

DNA
Polymerase III
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add new
complementary
bases
DNA Polymerase III
But
Wheres the
Were missing
ENERGY
something!
for the bonding!
What?

Energy of Replication
Where does energy for bonding usually come
from?
We come
with our own
energy!

You
remember
ATP!
Are there
other ways
to get energy
out of it?

energy

TTP
GTP
ATP
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modified nucleotide

And we
leave behind a
nucleotide!

TMP
GMP
ADP
AMP

Energy of Replication
The nucleotides arrive as nucleosides

DNA bases with PPP

P-P-P = energy for bonding

DNA bases arrive with their own energy source

for bonding
bonded by enzyme: DNA Polymerase

ATP
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GTP

TTP

CTP

Replication
Adding bases

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energy
DNA
Polymerase III

can only add

nucleotides to
3 end of the
growing DNA strand

B.Y.O. ENERGY!
The energy rules
the process

Initiation
DNA polymerase III can only elongate
the 3 end of new DNA strands. It needs
help to get replication started.
Primase will be the first to add a
complementary RNA primer,
creating a 3 end for DNA
Polymerase III to bind and start
adding DNA nucleotides.
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24

Initiation
DNA polymerase I then comes when a
new strand meets a primer to replace
the RNA nucleotides with DNA
nucleotides

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25

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Replication Continues
DNA polymerase can add
nucleotides only at the 3
end

Replication is continuous
on one strand with DNA
polymerase nestled in
the replication fork.
Leading Strand

discontinuous on the
other

Lagging strand

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Okazaki fragments
Synthesis of the leading strand is

continuous-As the replication fork opens up,

new strand is elongated

The lagging strand (discontinuous) is

synthesized in pieces called Okazaki

fragments
Finally, Ligase comes to bond the DNA
fragments together- like the glue of DNA

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AP Biology

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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Replication- Create a diagram that shows how the

following components interact with each other

Lagging strand
Helicase
DNA polymerase 1
DNA polymerase 3
RNA primase
Okazaki fragments

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Replication fork
RNA primer
Leading strand
DNA ligase

Replication Issues
4. 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.

2.

3.

4.

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DNA strands must be unwound during

replication
A new DNA strand can only elongate in the 5
3 direction
DNA polymerase cannot initiate synthesis and
can only add nucleotides to end of an existing
chain
Presence of RNA primer on the 5 ends of
daughter DNA leading strand leaves a gap of
uncopied DNA