Download Gene Duplication

GENE DUPLICATION: SOMETIMES MUTATIONS ARE A GOOD THING – STUDENT HANDOUT
Background Refresher:
1. Through the processes of transcription and translation, cells make ________________, which are
made up of folded strings of __________________.
2. There are two basic categories of proteins. Name them and briefly describe what they do.
a.
b.
3. A segment of DNA that codes for a protein or a trait is called a _______________.
4. If almost all of the cells in a human body contain the exact same sequence of DNA, how is it
possible to have different types of cells that have very different jobs (e.g. nerve cells, muscle cells,
liver cells, eye cells, etc.)? In other words, what do the cells do differently from each other in order
to perform their different jobs?
5. We know that one gene can have many forms (alleles). For example, the gene for flower color
may have red, white, or yellow alleles. What is the name of the process that caused these different
alleles to be formed in the first place?
6. This process is very important because it is what causes individuals to be different. Explain how
this individual variation is important regarding the formation of adaptations.
Gene Duplication
Sometimes, a gene (which codes for a protein) is duplicated and both copies are kept in the DNA. If
both copies of the gene work, then both can be transcribed and translated to make extra amount of
the protein.
7. One way that genes are duplicated is from unequal crossing over. You should remember what
normal (or equal) crossing over is. What is it and when does it occur?
Gametes
Figure 1. Unequal
crossing over occurs
when one
chromosome of a
homologous pair
keeps more DNA than
it gives to the other
chromosome.
Gene Duplication
This chromosome has two
copies of the original gene.
Page 1
Figure 2. Genes can move from one chromosome of a homologous pair to another chromosome of a
different homologous pair. This is called translocation. Notice how one of the extra copies of the
gene moved from the larger chromosome to the smaller one.
Gametes
This gamete has two copies of the gene,
but they are on different chromosomes
When an organism has two copies of a gene, the first copy usually stays the same (and does its
important job), but the second copy may change (mutate). If the mutated gene helps the organism
survive better than before the duplication, then it is an adaptation. This is sometimes called
“Duplicate and Diverge.” The gene duplicates and then their functions diverge (by mutating).
It turns out that 38% percent of human DNA exists as a result of gene duplication!
Case Study #1 – Eye pigments
Pigments are proteins that are sensitive to certain
wavelengths (colors) of light. Your retina contains
four different light-sensitive pigments (rhodopsin,
blue, red, and green pigments). The gene that codes
for rhodopsin is the original eye-pigment gene. It
is found on chromosome #4. All the other eyepigment genes were duplicated from this original
one. This pigment is found in the rods of the retina, is
sensitive to the middle wavelengths of visible light,
and only works in dimly lit situations. The gene that
codes for the blue-sensitive pigment (and lets you
see the color blue) is found on chromosome #7. The
genes that code for the red and green-sensitive
pigments are both on the X-chromosome.
Figure 3. This figure shows the wavelengths of
light each eye pigment absorbs.
BLUE PIGMENT
GREEN PIGMENT
RHODOPSIN
RED PIGMENT
8. Fill in the following Table1 which compares the genes for eye-pigments.
Table 1. Location and functions of the eye-pigment genes
Eye-pigment
Chromosome where gene is
located
Rhodopsin
Blue
Red
Green
Gene Duplication
Page 2
Wavelength of light that it
absorbs best
Use the information provided to fill in the
phylogenetic tree (Figure 4) that shows how the
eye pigments are related to each other. There
are two equally good answers.
Table 2. This table shows the percent
DIFFERENCES in amino acids among the eyepigment proteins.
Rhodopsin
9.
Red
Pigment
Green
Pigment
RHODOPSIN
Blue
Pigment
Figure 4. Phylogenetic Tree of
eye pigments
Rhodopsin
---
60%
60%
60%
Blue Pigment
---
---
60%
60%
Red Pigment
---
---
---
4%
Green Pigment
---
---
---
---
10. Use what you know about how genes duplicate and move (translocate) to fill in the chart below.
a. Fill in the names of the pigments and which chromosomes they are found on.
b. In the boxes above or below each of the arrows fill in the mechanisms that probably
made and/or moved the new gene.
•
GD = “gene duplication”
•
T = “transposition”
There are two equally good answers.
Gene:
Gene:Rhodopsin
Chromosome #:
Chromosome #: 4
Gene:
Gene:
Chromosome #:
Chromosome #:
11. What is an adaptation?
12. Explain how these new eye-pigment genes are adaptations.
Gene Duplication
Page 3
13. Fill in the Table 3 to explain how a new eye-pigment adaptation could be formed.
Table 3. Steps to developing new eye pigments.
Steps to getting an adaptation
How humans developed new eyepigments
1. More offspring are produced than can survive
and reproduce.
2. Because of gene duplication and further
mutation (divergence), members of a
population may have different genes.
3. Selective pressures are present.
4. Individuals with the genes that give them the
most favorable traits are more likely to survive
and pass those genes on to their offspring.
14. It turns out that some people have two working copies of the green eye-pigment gene (the green
eye-pigment gene has duplicated again!). Over time, what do you think might happen to this
second copy of the gene?
Case Study #2: Antifreeze in Fish
Sometimes a gene duplication results in a protein that can do something totally new (this is called a
novel function). Arctic cod (Boreodadus saida) live in the freezing cold waters of the arctic. The
average temperature of this water would freeze most fish (because they are ectothermic or “coldblooded”). This would kill them because, when animals freeze, ice crystals grow inside of their bodies.
These ice crystals slice cells and tissues apart. However, the arctic cod makes an antifreeze protein
that prevents ice crystals from growing. The antifreeze protein is made in the cod’s liver and is
released into its bloodstream.
Just how did the arctic cod develop such a nifty adaptation? Well, it turns out that the gene that codes
for the antifreeze protein is very similar to a gene that is used to make a digestive enzyme in the
pancreas. Researchers figured out that the gene for the digestive enzyme duplicated and that the
second gene mutated into one that produced the antifreeze protein. The newer antifreeze
protein is made in the liver and released into the bloodstream.
15. List two ways the new gene is different from the original one.
a.
b.
Gene Duplication
Page 4
16. Fill in Table 3 to explain how the arctic cod could have developed such a cool adaptation. Be
specific with regards to how the genetic variation arose.
Table 3. Steps to developing antifreeze proteins.
Steps to getting an
adaptation
How the arctic cod
developed antifreeze
proteins
Figure 6. A phylogenetic tree of
the orders of fish
1.
2.
3.
4.
Well, it turns out that arctic cod are not the only fish to have
developed an antifreeze gene. A group of fish, called the
Notothenoids, that live on the other side of the planet (around
Antarctica) have also developed an antifreeze gene. Not only
that, but their gene also resulted from the replication of a
digestive enzyme gene.
Figure 5. Distribution of arctic cod and the notothenoids.
Arctic cod (Boreogadus saida)
Notothenoid species
http://ww© The Exploratorium, www.exploratorium.edu
Table 4. Classification of Arctic Cod and Notothenoids
Arctic Cod
Notothenoids
Kingdom
Animalia
Animalia
Phylum
Chordata
Chordata
Class
Actinopterygii
Actinopterygii
Order
Gadiformes
Perciformes
17. Look at the phylogenetic tree of the orders of fish (Figure 6) and the classification of the arctic
cod and notothenoids (Table 4). Use them to explain whether you think fish antifreeze formed
only one time or more than one time in the history of these organisms. Hint: highlight the
orders of fish that make antifreeze.
Gene Duplication
Page 5
Case Study #3: Snake Venom
Snakes are a group of reptiles that are closely related to lizards. Unlike most lizards, snakes do not
have legs. Furthermore, they are strictly carnivorous and must swallow their prey whole (they cannot
rip their food apart or chew it). As you can imagine, catching a live animal without being able to use
arms/legs can be quite dangerous for any predator.
18. Primitive or early forms of snakes, like boas and pythons, do not produce venom. How do you
think they kill or subdue their prey?
19. Many modern groups of snakes produce venom, which contains toxic proteins that kill and/or
subdue their prey. Explain how this is an adaptation.
Originally, scientists assumed that these venomous proteins were ones that were already in the
saliva. Over time, these proteins were thought to have become more toxic as the snakes were relying
on them more and more to subdue their prey.
Researchers have only recently started to study the genes that code for the venomous proteins, and
the explanation is not quite that simple. So far, they have identified 24 different toxic proteins in the
venom. Of these proteins, only two were originally produced in the salivary glands (which then
developed into venom glands) and became more toxic because of selective pressures. The
remaining 22 proteins were products of gene duplication. In other words, the original proteins
have other jobs in the snakes’ bodies. The genes that code for these proteins duplicated. These
duplicated genes then accumulated mutations that enabled them to be made in the salivary (venom)
glands. These particular proteins do things that make them quite dangerous if injected directly into
one’s blood stream.
Figure 7. Venom Gland.
Figure 8. Garter snake eating a toxic newt
Figure 9. Location of where some of the venomous proteins originated.
URETERS
TESTES
KIDNEYS
LARGE INTESTINE
SMALL INTESTINE
SPERM DUCT
Gene Duplication
SPLEEN GALLBLADDER
STOMACH
PANCREAS
Page 6
HEART
LIVER
LUNG
TRACHEA
THYROID GLAND
BRAIN
VENOM GLAND
ESOPHAGUS
20. Look at Table 5. It gives the name of some of the original proteins and what they do. Fill in the
missing explanations of how these proteins would help kill or subdue prey if injected directly into
their body.
Table 5. Examples of proteins are now made in the venom glands of some snakes.
Name of modified
protein (venom
protein)
Where the
original protein
is made
What the original
protein does
How the modified protein (venom) helps
kill or subdue prey when injected into
bloodstream
Acetylcholinesterase
Muscles
Helped control
muscle
contractions
Disrupts nerve impulses causing heart and
respiratory failure of the prey.
BNP
Heart
Relaxes muscles
around heart
Blood pressure drops dramatically.
L-amino oxidase
Immune tissues
Causes cells to
burst open
Lectin
Throughout
body
Makes blood clot
ADAM
Sperm ducts,
colon, lung,
lymph node,
thymus
Tissue decay
Note: these are only a sample of the 24 venom proteins that have been identified.
So far, studies suggest that all venomous snakes make the same toxic proteins in their venom
glands. Some snakes are less poisonous than others (e.g. garter snakes). This difference is because
they either make a smaller amount of the toxic proteins, or they inject less into their prey.
21. Look at Figure 10 (Phylogenetic Tree of Major Snake Groups). Does it appear that the evolution
of snake venom occurred one time or more than one time? Explain your answer. (Hint: highlight
all of the snake groups that can make venom.)
Figure 10. Phylogenetic Tree of Major Snake Groups
Scolecophidia (incl. Blind snakes) NF, NV
Henophidia (incl. Boas and pythons) NF, NV
Viperidae (incl. Vipers and rattlesnakes) FF, V
Homalopsinae (incl. Stout-bodied water snakes) some species RF and MV
Colubrinae (incl. Bullsnakes, kingsnakes, brown tree snakes) some species RF and MV
Natricinae (incl. Water snakes and garter snakes) NF, some species MV
Xenodontinae (incl. Hognosed snake) some species RF and MV
Atractaspidae (incl. Mole viper and burrowing asp) FF, V
Elapidae (incl. Cobras, coral snakes, and sea snakes) FF, V
Note:
NF = “no fangs”, RF = “rear fangs”, FF = “front fangs”
NV = “non-venomous”, MV = “mildly venomous”, V= “venomous”
22. In your own words, describe the “take-home message” of this lesson. Think about what all of
these case studies have in common.
Gene Duplication
Page 7