DNA Structure and Replication
Review

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Click here if you’d like to review part 1: DNA Discovery and Structure
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Click here if you’d like to jump to part 2: DNA
Replication
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Part 1: DNA Discovery and Structure

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Observed that in DNA molecules:
% A = % T
% C = % G

What was Rosalind Franklin’s contribution to the discovery of DNA’s structure?
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1 st to recognize helix shape of DNA using x-ray diffraction (aka x-ray crystallography)

What was Maurice Wilkins’s role in the race for the double helix?
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Worked with Franklin
Shared her photo with Watson and Crick

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Put it all together!
Came up with a model of DNA’s structure (the double helix) and proposed how DNA replicated

DNA is a polymer made of repeating monomers. What are the monomers of DNA?
 nucleotides

What are the three parts of a nucleotide
(n.t.)?
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Sugar (deoxyribose)
Phosphate
Nitrogen base

In every DNA nucleotide, which two parts are the same? Which part may differ?
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Same – deoxyribose and phosphate
Different - base

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 adenine (A) thymine (T) cytosine (C) guanine (G)

In a nucleotide, how are the carbon atoms in the deoxyribose numbered?
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Find the oxygen in the ring of the deoxyribose.
Move clockwise to the first C atom. This is the 1’ (one prime) carbon
Continue moving clockwise numbering the carbons: 2’, 3’, and 4’
The 5’ C is the carbon outside of the ring

The four DNA bases are divided into two groups. What are the groups and what’s the difference between the two?
Purines
Two ring structure
Pyrimidines
1 ring strucure

Which two bases are purines? Which two are pyrimidines?
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Purines = A and G
Pyrimidines = T and C

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Double helix

In a DNA molecule, which parts of the nucleotides are on the outside and which part faces the center?
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Sugars and phosphates alternate on the outside making up the “backbone”
Bases face the inside

What type of bond connects one nucleotide to its neighbors in one strand of the DNA
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Covalent
The 5’ phosphate group of one nucleotide bonds to the 3’ end of its neighbor by a covalent bond new covalent bond

A DNA molecule is double stranded. It’s made of two polynucleotide strands held together by what type of bonds?
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Hydrogen bonds!
Remember, covalent bonds are shown with solid lines but H bonds are shown with dashed lines
Covalent bonds in backbone holding one n.t. to the next
H bonds down the center of the molecule

What ensures that the backbone of the DNA stays parallel?
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Purines always pair with pyrimidines
Purine - always pairs with Pyrimidine
A
G
T
C
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The chart above shows the base-pairing rules in DNA!

What are those base pairing rules again?
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A always pairs with T
C always pairs with G

How many H bonds occur between each base pair?
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3 between C and G
2 between A and T

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If a molecule of DNA is 34% cytosine, determine the percentages of the remaining bases.
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34% G (because % C = % G)
16% A and 16% T
Bases must add up to 100%
34% G + 34% C + X = 100%
X = 32% BUT that must be divided evenly between the remaining two bases (A and T)
32/2 = 16; so 16% A and 16% T

What are the 3 enzymes involved in DNA replication? Give their names and functions.
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DNA helicase – unwinds and “unzips” the double helix
DNA polymerase – builds the new DNA polymer
DNA ligase – seals gaps left behind in DNA after RNA primers are removed

2.
3.
What are the 3 basic steps of replication?
1.
Helicase separates the strands by breaking H bonds between bases
RNA primers anneal (attach)
DNA polymerase adds new complementary bases to build new strands

What do we call the region the is opened by the DNA helicase?
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Replication bubble

The replication bubble is made of 2
__________________ that move in opposite directions.
 replication forks

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 a short segment of RNA complementary to the DNA starting point for DNA polymerase

Where are the nucleotides being added to build new DNA found?
 floating in the nucleus

We call each original DNA strand a
“template” strand. Why?
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Each original strand must serve as a pattern for DNA polymerase to build new complementary strands.
Original strands are in blue
The resulting two
DNA molecules are identical to the original one
Each original strand serves as a template to build new complementary strands shown in red

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Two double stranded DNA molecules identical to the orignal

DNA replication is semi-conservative. What does that mean?
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Each new double stranded DNA is
1 original strand + 1 new complementary strand

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The strands are parallel BUT they run in opposite directions
One strands runs 5’ → 3’
The complementary strand runs 3’ → 5’

How are the two ends of the polynucleotide chains different?
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One end has a phosphate group – it’s the 5’ end
One end has a hydroxyl group on the deoxyribose – it’s the 3’ end
See the next slide!

5’ end has the phosphate group of the nt hanging off
3’ end has a deoxyribose sugar with a hydroxyl group on the 3’ carbon
Notice how in this complementary strand, the nucleotides are upside down so that the 5’ and 3’ ends are opposite of the other strand

In which direction does DNA polymerase read? In which direction does it work?
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DNA pol reads 3’ → 5’ meaning that it looks at the strand running 3’ → 5’ in the same direction as the replication fork so it knows which bases to add
DNA pol works 5’ → 3’ meaning that it builds a new strand that is 5’ → 3’ complementary to the strand that it’s reading
Since the two DNA strands are antiparallel and DNA pol can only work 5’ → 3’ replication happens differently on the two DNA strands

Replication on the leading strand is pretty basic. What are the steps?
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Helicase unwinds/unzips DNA
RNA primers anneal
DNA pol reads the 3’ → 5’ template following the replication fork
DNA pol builds a new complementary strand 5’ → 3’

Because DNA pol can work nonstop on the leading strand, we say replication on that strand is ________________.
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Continuous or contiguous

Just a reminder… on the lagging strand,
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After helicase unwinds/unzips the DNA, RNA primers still anneal
DNA pol still reads 3’ → 5’ and builds a new strand 5’ →
3’

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What is the difference in replication on the
See how the leading strand lagging strand?
runs 3’ to 5’ toward the replication fork and a new 5’ to 3’ strand is made continuously?
DNA pol moves away from the replication fork so that it’s reading 3’
→ 5’ and working
There is one RNA primer needed on the leading strand, but it isn’t shown above in green
5’ → 3’
Bases are added in short stretches called Okazaki fragments
On the lagging strand, DNA is built away from the fork in the
5’ to 3’ direction.
Several RNA primers are needed and they’re shown in green.

Because replication happens in fragments on the lagging strand, we refer to replication on that strand as being __________.
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Discontinuous or discontigous

What are the DNA fragments on the lagging strand called?
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Okazaki fragments

What happens to RNA primers once replication is complete?
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Primers must be removed and replaced with DNA nt

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After RNA primers are removed and replaced with DNA nt, ligase seals the “nicks” or gaps left behind in the DNA backbone

How is DNA replication different in prokaryotes and eukaryotes?
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Prokaryotic replication has only one origin of replication
(one replication bubble)
Eukaryotic replication has multiple origins and multiple replication bubbles
See the next two slides for diagrams!

Prokaryotic: 1 bubble with 2 forks that move in opposite directions around the circular chromosome until that meet at the other side and replication is complete

Eukaryotic: 1 DNA strand has multiple replication bubbles each with two forks that move away from each other; replication bubbles eventually merge as they grow; this speeds up replication! Without multiple bubbles, it would take about 1 month for our DNA to replicate instead of 1 hour!

How accurate is DNA replication before repair?
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About 1/10000 bases are paired incorrectly

What do we call the repair that happens after replication?
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Mismatch and excision repair

After repair, the error rate goes down to
_______?
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1/1000000000 bases (the human genome is 3.2 billion bp, so there may be only 3 mistakes after repair!!!)

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Can be random/spontaneous
Chemicals
UV radiation

What do we call changes in the nt sequence?
 mutations

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No – most are. Some are silent – no effect. Some may actually be beneficial.
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That’s the end of the review! Click here if you’d like to go back to the beginning.