In This Lesson:
Unit 5
DNA Structure
and Replication
(Lesson 1 of 3)
Today is Thursday,
November 19th, 2015
Pre-Class:
Today we start DNA. Tell me everything you
know about it. You must write this down (the
more scientific, the better).
(But write down everything you can)
What are the names of all the DNA bases
we’ve learned so far?
Also, today is our Strawberry Lab. It’s in the
turn-in box – go get a copy! Also get a small
paper towel.
www.savagechickens.com
Today’s Agenda
•
•
•
•
•
Strawberry DNA Extraction
Where we are and where we’ve been
Challenge Questions
DNA Structure
DNA Replication
– As in, what happened in S phase.
• DNA Pickup Line?
• Where is this (all) in my book?
– Pages 182 and following…
By the end of this lesson…
• You should be able to identify the detailed
structures of DNA.
• You should be able to describe the process
by which DNA copies itself.
Orientation
• First, we studied atoms.
• Atoms make up all matter.
• Some of this matter is considered organic,
and is organized into four major groups.
• Life-supporting organic matter has nonliving functions, like diffusion and osmosis.
Orientation
• Diffusion and osmosis help living things
carry on life and undergo respiration.
• Life’s smallest unit is the cell.
• There are prokaryotes and eukaryotes, and
they all have different organelles.
• Even among eukaryotes, there are plant
cells and there are animal cells.
Orientation
• All cells, however, need to grow and
reproduce.
• For body cells (also known as somatic
cells), growth occurs through mitosis.
• Mitosis is a process in which the genetic
material (DNA) is copied and the nucleus
(and right after, the cell) divides.
Orientation
• Sex cells (or gametes), use the process of
meiosis.
• The chromosomes in your cells are made of
DNA, which makes you who you are.
• Today we will begin learning about how
DNA copies and how it “codes” for
proteins, which is the molecular basis for
genetics.
Challenge Questions
• To the whiteboards!
Introducing DNA
• Video: DNA Introduction
• Video: TED – Judith Hauck – The Twisting
Tale of DNA
DNA’s Discovery
• Discovered by Friedrich
Miescher in 1869.
– Noticed something in
pus in discarded
surgical bandages.
– Called it “nuclein,” but
other than a guess
didn’t know it had any
role in heredity.
http://upload.wikimedia.org/wikipedia/commons/b/bc/Friedrich_Miescher.jpg
Johann Friedrich Miescher
DNA’s Discovery
James Watson
Francis Crick
And all
three were
exploiting
the work
of…
Rosalind Franklin
With
some
big
help
from…
&
Maurice Wilkins
• DNA’s structure was discovered in 1953 by:
http://sciencecomm.wikispaces.com/file/view/3441067.jpg/96607078/3441067.jpg
http://www.nobelprize.org/nobel_prizes/medicine/laureates/1962/watson.jpg
http://www.nobelprize.org/nobel_prizes/medicine/laureates/1962/wilkins.jpg
http://www.floridahumanist.org/images/FrancisHarryComptonCrick.jpg
DNA Overview Video
• Video: DNA Overview
DNA
• The big important statement:
– DNA in a long strand and wrapped around proteins
is called chromatin. When condensed, a piece of
chromatin is called a chromosome.
– Segments of the DNA strand are called genes.
These genes tell the cell what proteins to make,
which determine your traits.
• Genes are like chapters in the book of DNA.
• Each cell has the whole book, but depending on their
jobs, the cells read different chapters.
DNA and Review
• DNA is a nucleic acid, a
long string of nucleotides.
• DNA takes the shape of a
double-helix.
• There are four kinds of
nucleotides:
–
–
–
–
http://ghr.nlm.nih.gov/handbook/illustrations/dnastructure.jpg
Adenine
Cytosine
Guanine
Thymine
Nucleotide Review
• Each nucleotide has a:
– Sugar molecule with 5-carbons (pentose)
• Deoxyribose in DNA
• Ribose in RNA
– Phosphate group
• Phosphorous-based molecule
– Nitrogenous base (makes the nucleotide unique)
•
•
•
•
Adenine
Thymine
Cytosine
Guanine
Nucleotide Structure Review
Guanine
Adenine
Cytosine
Thymine
http://www.biologyjunction.com/images/nucleotide1.jpg
Nucleotide Structure Review
• More “scientific”
Nucleotides and Nucleosides
• Just so you know, you’ll occasionally hear
of a nucleoside.
• The only difference between a nucleoside
and a nucleotide is that a nucleoside is just
a sugar and nitrogenous base – no
phosphate group.
DNA
• Surrounding the base pairs and
forming the sides of the “ladder” is
a sugar-phosphate backbone.
• The backbone is made of a sugar
(deoxyribose) and a phosphate
group, alternating and in reverse
order from the other strand.
– Backbone is linked by phosphodiester
bonds.
– The end of DNA with the phosphate
on top is the 5’ (“five prime”) end.
– The other end of the backbone is the
3’ (“three prime”) end.
http://ghr.nlm.nih.gov/handbook/illustrations/dnastructure.jpg
3’ and 5’? Huh?
• 3’ and 5’ get their names from
the pentose sugar’s carbon
atoms.
• Each carbon in pentose is
numbered and has a specific
job in the formation of DNA.
– Carbon 1 = base attachment
– Carbon 2 = oxygen (ribose) or
not (deoxyribose)?
– Carbon 3 = another nucleotide
attachment
– Carbon 4 = completes ring
– Carbon 5 = phosphate
attachment
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Pentose.gif
http://www.synapses.co.uk/genetics/pentose1.gif
DNA
• DNA stands for
Deoxyribonucleic Acid.
• By hydrogen bonds,
cytosine bonds to guanine
and adenine to thymine.
• A↔T
• C↔G
http://ghr.nlm.nih.gov/handbook/illustrations/dnastructure.jpg
Base Pairs
• (Held together by hydrogen bonds)
• How can we remember this?
Deoxyribose
Adenine
---H---
Thymine
Deoxyribose
DNA Unwound (Basic)
P
P
Deoxyribose
Cytosine
---H---
Guanine
Deoxyribose
P
P
Deoxyribose
Thymine
---H---
Adenine
Deoxyribose
5’
3’
---H---
Guanine
Cytosine
PD Bond
Deoxyribose
Deoxyribose
DNA Unwound
(Advanced)
P
P
---H---
Thymine
PD Bond
Adenine
Deoxyribose
Deoxyribose
PD Bond
P
P
PD Bond
---H---
Adenine
Thymine
Deoxyribose
Deoxyribose
5’
P
3’
Complementary Base Pairs
• Video: Complementary Base Pairs
DNA Worksheet
• Try problems 1 and 2 on your DNA
worksheet.
1:
1:
AC
TG
2: G A A G G C G T T
DNA
• Adenine and guanine are
purines and have a doublering structure.
• Cytosine and thymine are
pyrimidines and have a
single-ring structure.
• A purine always bonds to a
pyrimidine.
• How can we remember this
one?
Chargaff’s Rule
• Little side note here:
– Austrian chemist Erwin Chargaff proposed that
the amount of purines in a cell equal the
amount of pyrimidines.
– Makes sense!
– Video!
– Exclamation point?
Chargaff’s Rule Sample Question
• A DNA molecule is 40% guanine. By percent,
how much thymine is in the molecule?
• 10%
• If it’s 40% guanine, it’s 40% cytosine.
• That’s 80% total, so 20% is left to be split
between adenine and thymine.
• The molecule thus must be 10% adenine and 10%
thymine.
DNA Worksheet
• Try problems 3, 4, and 5 on your worksheet.
3: T T G C A A G T C
4:
5. Always three rings (keeps the same width).
DNA Worksheet
• Try problems 6 and 7 on your worksheet.
6: Sugar/Phosphate Backbone
7: A ↔ T, C ↔ G
7: Purines – 2 rings, Pyrimidines – 1 ring
DNA Replication
• There comes a time in (almost) every DNA
molecule’s life when it needs to be replicated
(copied).
– That time would be S phase.
• Here’s the general process:
– Unwind the double-helix.
– Break the hydrogen bonds (“unzip” the DNA).
– Use enzymes to replace base pairs on each side.
Looks like this… [IMPORTANT]
Note that even
though there
are two
strands
forming down
here, each is
only “half”
new.
The “old”
strand is
sometimes
known as the
template
strand
because it’s a
model for the
new one.
Looks like this… [IMPORTANT]
http://online.santarosa.edu/homepage/cgalt/BIO10-Stuff/Ch10-Protein_Synthesis/DNA-Replication-Animation.gif
DNA Replication - Schematic
• Video: DNA Replication – Schematic
Time for a Game!
• In this game, you will be practicing the
process of replication.
• Don’t mess up the base pairs!
• You’ll also use the DNA you make to figure
out which organism it comes from.
• http://nobelprize.org/educational/medicine
/dna_double_helix/dnahelix.html
Adding some names…
• In that activity, we matched DNA bases to
one another. Ts were with As, Gs with Cs.
• Because they go together, we call these
pairings complementary.
– “The complementary base of G is C.”
Enzymes
• The role we played – breaking the DNA “ladder”
and replaced missing base pairs – is a role played by
enzymes in the human body.
• There are four main enzymes – here are the first
two:
1. DNA Helicase
• Unzips the DNA double-helix (breaks H-bonds).
• The points at which Helicase has opened the DNA strand are
called replication forks.
2. DNA Polymerase
• Adds complementary base pairs.
DNA Helicase Animation
http://gifsoup.com/view/1504259/dna-helicase.html
DNA Replication – Molecular
• Video: DNA Replication – Molecular
Deoxyribose
Adenine
Deoxyribose
Thymine
Replication
P
P
P apart
PDNA Polymerase makes
DNA move
DNAnew
Helicase
breaks
H-bonds
Strands
P
---H---
Deoxyribose
P
Thymine
Thymine
P
Deoxyribose
Deoxyribose
Guanine
Adenine
DeoxyH
ribose
Thymine
Deoxyribose
P
Cytosine
Deoxyribose
H
P
---H---
Guanine
Cytosine
Deoxyribose
DeoxyH
ribose
H
H
P
---H---
Adenine
Adenine
Deoxyribose
DeoxyH
ribose
The Replication Caveat
• As it turns out, DNA Polymerase can only
work from the 5’ end to the 3’ end.
• This means that one side of the DNA strand
can be made continuously.
– The leading strand.
• The other side of the DNA must be made in
pieces.
– The lagging strand.
Replication Bubble
Notice that though
Helicase can move in
both directions,
Polymerase can only
read from 3’ to 5’ on
the template strand.
As a result, one new
strand is built
continuously from 5’
to 3’, but one is built
from 3’ to 5’ in pieces.
http://www.svusd.org/hp_images/1752/D23456-Replication%20Bubble.jpg
Replication Videos
• Video: Honors – DNA Replication
• Video: Honors – DNA Replication 2
Additional Replication
Vocabulary
• The pieces of the new strand are called Okazaki
Fragments.
• Okazaki Fragments are started by RNA Primase, an
enzyme that lays the foundation for them to be
built.
• At the end, Okazaki Fragments are linked (annealed)
by DNA Ligase, another enzyme.
• While all this is happening, the cell has placed
single-stranded binding proteins (or SSBs or SSBPs)
onto the exposed nitrogenous bases to prevent the
DNA from “re-zipping-up.”
Putting It All Together
http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit6/genetics/DNA/DNArep/images/lag.gif
What We Know About DNA
• We always hear that DNA is the genetic material of
the cell, or the command center, or what is
responsible for you. Whatever. What exactly does
that mean?
• DNA helps the cell “decide” which proteins to make.
– The proteins are different for everyone.
– That’s why your DNA makes you unique
• And why we can use DNA to test potential criminals.
Time for a Flowchart
• Find some room in your notebooks.
Guiding Question
• How can one person have two different eye
colors?
• Your questions? What do you want to
know?
Time for a Gizmo
• It’s called Building DNA, and that’s just
what you’ll be doing.
• As usual, you’ll need a second window
open for Quia:
– Building DNA Gizmo
• [Log-in Instructions]
Exit Ticket (Part One)
• What are the full names of the four
nitrogenous bases in DNA?
• Which are purines, which are pyrimidines?
• Which bases pair to which?
Exit Ticket (Part Deux)
• Which enzyme “unzips” the DNA double
helix?
• Which enzyme places new nucleotides to
complete the base pairs?