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Chapter 17
Neurospora

Auxotrophy
Enzyme
Mutant
Transcription
Translation

RNA polymerase

Nascent RNA
Primary transcript
mRNA

rRNA
tRNA

snRNA
siRNA
miRNA
Ribosome
Genetic Code

RNA processing
RNA splicing
Spliceosome
5’cap

A bread mold that Beadle and Tatum used to identify the enzymes in the
metabolic pathway that corresponded to genes which had been mutated
and were no longer working
...

The inability to synthesize a particular organic compound required for
growth
A protein that catalyzes a reaction by lowering the activation energy
required to start a reaction
...

Copying a DNA template strand onto a complementary mRNA transcript
using RNA polymerase (purpose: to make protein coded by certain genes)
Translating processed RNA into a polypeptide by a ribosome and tRNA;
involves adding an amino acid carried by tRNA (identified by aminoayl tRNA
synthetase) to the A site of the ribosome, then translocated to the P site by
the large subunit, and then exited through the E site in the large subunit of
the ribosome to make a protein
...
Pries DNA strands apart (exposing about 20 at a time)
...
RNA polymerase II is one of 3 types of RNA polymerase in
the nucleus, and it is used to transcribe mRNA that is translated into
protein
...

The original copy of nucleotide bases prior to further processing and caps
(in nucleus)
Messenger RNA; complementary to the template DNA strand and
transported into the cytoplasm for translation, allowing for expression of
genes encoding proteins that will be used by the cell
Ribosomal RNA; used for catalyzing reactions and forming the structure of
the ribosome (makes up majority of cell RNA)
The translator in translation; identifies with 1-3 amino acids using
synthetase and adds to the growing polypeptide by placing them at the P
site of a ribosome during translation

Made of large and small subunits; used in translation; lives in rough ER;
made in nucleosome
A combination of 3 nucleotide bases (a triplet or codon) and the amino
acids that each one corresponds to
...

The addition of the 5’ cap, then the 3’ cap
...

Removal of introns by the spliceosome
Cleaves intron sections and connects the exons on either side
A modified Guanine molecule added to 5’ end of mRNA for processing

Poly-A tail
Polyadenylation
Intron
Exon
SNRNP
Open reading frame
5’UTR
3’UTR
codon
Anticodon
Aminoacyl tRNA
synthetase
central dogma
reading frame
Transgenic animal
Promoter

TATA box
Transcription factor
Wobble

A site
P site
E site
SRP
SRP RNA
Tay Sachs Disease
Sickle Cell Anemia

Silent Mutation
Missense Mutation
Nonsense Mutation
Frameshift Mutation

Mutagen

A long chain of 50-250 adenine bases added after the 5’ cap to the 3’ end of
the mRNA being processed
AAUAA sequences that triggers the release of the mRNA strand before
release into cytoplasm
...

A non-coding section of mRNA that is taken out before translation
A coding section of mRNA that gets translated into protein
The start codon until the stop codon
Follows the 5’ cap and precedes the start codon
...

A triplet of nucleotides on either strand of DNA that do NOT overlap and act
as genetic instructions for polypeptide chains
A triplet of nucleotides corresponding to the mRNA codon
An enzyme that identifies the correct amino acid to add to the growing
polypeptide chain in translation
DNA – RNA – protein (Francis Crick, 1956)
The correct grouping of nucleotide bases on an mRNA strand; they must be
read 5’ to 3’ and in groups of 3
...

The sequence on DNA that makes up the binding place for RNA Polymerase
II to begin transcription
...

Example: TATA box
A crucial promoter for RNA transcription
Proteins that help RNA polymerase attach BY BINDING TO THE PROMOTER
The 3rd nucleotide in the CODON is less important because it does not
usually change the amino acid the codon associates with
...
These
are almost always BAD and often result in a stop codon being placed where
there wasn’t one before, and that will result in an incomplete protein
Anything that causes a mutation

Ames Test

A test with bacteria to tell how mutagenic a chemical is; you get lots of
colonies if it is very mutagenic, only a few if it is fairly mutagenic, and none
if it isn’t mutangenic
...
What organism did Beadle and Tatum use in their research? What made it so amenable to their
research aims? Why did some of their mutants grow with some substances while others didn’t? What
did this tell them about the relationship between genes and enzymes?
Neurospora crassa, a type of bread mold
...
After bombarding the neurospora with x-rays to mutate the
genetic information, they created mutants that were defective for a certain enzyme within the
metabolic pathway
...
The enzyme that catalyzed the production of that supplement was the one that was
defective; adding the supplement allowed the rest of the pathway to continue
...
They proved that by
altering genes they would also alter enzymes, which would then alter phenotype
...
What is the central dogma of molecular biology? What exceptions does it have that we studied in
class?
DNA to RNA to protein
...

3
...
We need triplet codons
in order to get the 64 possible combinations that form 20 amino acids in order for us to create proteins
based on our genetic information
...

The 3 stop codons are UAA, UGA, and UAG, which do not add amino acids but instead tell tRNA to add a
water molecule to a growing polypeptide chain in order to trigger its release from the ribosome
...
You should be able to spot an open reading frame within a nucleic acid and be able to translate it into
protein given the genetic code
...
How were mononucleotides, dinucleotides, and trinucleotides used to decipher the genetic code?

6
...
What does
that say about the genetic code?
The genetic code is generally UNIVERSAL; meaning that genes can be inserted into a different species
and still produce the protein that they would have produced in the original species
...
What are the stages of eukaryotic transcription? What is the enzyme that carries it out? In which
direction does this enzyme function? How does the enzyme know which nucleotide to put where? From
where does the energy for polymerization come? What differences are there between prokaryotic and
eukaryotic transcription?
mRNA is transcribed, then it is processed, both in the nucleus
...
Then it is transported to cytoplasm for translation
...
The primary
difference between prokaryotic and eukaryotic transcription is the separation of transcription and
translation in eukaryotes that isn’t present in prokaryotes
...
What is a promoter? What is the relationship between promoters and transcription factors? Where
does RNA synthesis begin? Where does it end?
The promoter is a sequence on the DNA that 1) determines the template strand and 2) acts as a binding
spot for RNA Pol II, allowing it to initiate transcription with the help of transcription factors (which bind
to the promoter to help the polymerase attach)
...
The STOP signal is the
polyadenylation sequence (AAUAAA) in the pre-mRNA which signals proteins to bind immediately
...
When the enzymes
catch up to the polymerase, it disassociates
...
What is the RNA called when it is first made? What modifications are done to it to make it into an
mRNA? What are the functions of these modifications?
It is called pre-mRNA, or the Primary Transcript
...
The 3’ and 5’ caps at both ends have
multiple functions; 1
...
2
...
3
...

10
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What is the difference between an intron and an exon? Which is left in the mRNA? Which is cut out?

12
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What is the relationship between exons and protein domains?

14
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What is a stem loop structure in an RNA? How is one formed? Do they have biological functions?

16
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What is an aminoacyl tRNA synthase? How many are there? What do they do, and how do they do
it? What is their function in protein synthesis?

18
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How is translation initiated? What factors must be present for this to occur? Which codon always
initiates translation? Which amino acid does it encode?

20
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How many ribosomes translate a given mRNA? What are the differences between prokaryotic and
eukaryotic transcription and translation?

22
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What is the difference between a silent and a missense mutation? What is the causative mutation in
sickle cell anemia? Why does this mutation cause this disease?

24
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What is a mutation? What agents can cause them? What is the Ames test and how does it work?
What is the relationship between mutagens and carcinogens? Are all carcinogens mutagenic?

Chapter 18
Structural gene
Operon
Operator
Repressor
Promoter
Polysistronic
cAMP
CAP protein
Histone
Nucleosome
Acetylation
Heterochromatin
Euchromatin
Cytosine
Methylation
Epigenetics
Enhancer
Proximal control

Gene that codes for a protein
A set of linked structural genes
A sequence between the promoter and structural genes (operon) where
regulatory proteins can bind; such as a repressor
...
They bind to
the promoter in order to allow RNA Pol II to attach and begin
transcription at the START POINT
...
They can have MORE THAN
ONE OF EACH DOMAIN
...
proteins
...


Oncogene

Proto-oncogene
Tumor suppressor
Growth factor
Growth Factor receptor
Translocation
Gene amplification
Ras
P53
Rb
Metastasis
Polyp
Adenoma
Malignant

A cancerous version of a proto-oncogene usually resulting from a
mutation that either changes the function of a protein or increases the
production of a protein
...
What is an operon? What is the advantage to bacteria of organizing its genes into operons?
It is a set of linked structural genes that usually code for enzymes in a metabolic pathway
...

2
...
What is a repressor protein? What does it do? Is the gene for the repressor for an operon located
within the operon, or remotely? Is the repressor made in response to nutrients, or is it made all the
time?
A repressor protein in allosterically controlled & always produced at low levels even though it may be
inactive; when active and bound to the operator, transcription is off
...
What is tryptophan, and what kind of molecule is it? What is it to the E
...
) What does a cell want to do if it has none? What if it has plenty?
Tryptophan is built in an anabolic pathway when there is none present in the cell
...


5
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An active repressor stops expression of the genes for that protein
so that it doesn’t make more than it needs to
...

6
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Coli cell? What does the cell do when it has
none, and what does it do when it has plenty?
Lactose is metabolically broken down by the E
...
When there is
no lactose, the repressor is bound and inactivates the operon because it doesn’t need to digest it
...
When glucose is not present, cAMP levels are raised, and with
cAMP there is the CAP regulator protein
...

7
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The active repressor binds to the operator in the presence of
lactose and stops expression of the lac operon genes
...

8
...
When glucose is
very low, cylic AMP increases along with CAP which can bind to the lac operon and increase expression
...
What is a histone? How many are in a nucleosome? How do these appear in an electron micrograph?
It is a positively charged protein that is associated with chromosomes in the nucleus to form chromatin
...
8 histones make up a nucleosome, which is a
complex of DNA wrapped around the histone proteins with their N-terminus tails sticking outward
...

10
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Genes in a heterochromatic state might
be on the x-chromosome, inactivated due to X-inactivation
...
What would the effect of acetylation be on a histone protein? How would such a modification affect
the interaction between a histone protein and the DNA? What would the effect be on transcription?
What other sort of modifications are carried out on histone proteins, and what is their effect on
transcription? What is the effect of DNA methylation on transcription? Is DNA methylation heritable?

12
...

13
...
Promoters
are located upstream of operons and a proximal control elements
...
How can genes be transcribed in some cells and not others?

15
...
This lets a different combination of genes be
expressed in translation, while using the same portion of DNA during the initial transcription phase
...
What is ubiquitin? How can ubiquitin be used to control protein stability?
It is a signal that binds to a protein and tags it for degradation by a proteasome
...
What are siRNAs and miRNAs? How are they similar? How are they different? How are they created
and what do they do?
siRNA = small interfering, and miRNA = microRNA
...
What are master control genes and what are their functions during embryonic development? Can
you name any examples? How does myoD activate a muscle cell developmental program?

19
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20
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They also have a smaller genome and reproduce frequently
...
What is bicoid? What does it do? What happens to the drosophila larva when it is absent? What
experiments revealed its function? How does the inheritance of bicoid differ from other genes and why?
Bicoid is a maternal effect gene, and also a morphogen
...
To test
hypothesis, scientists injected pure bicoid mRNA into various regions of early embryos and the protein
resulting from it caused anterior structures to form at the injection sites
...
If inserted, it will cause the anterior structure wherever it is
placed
...
When the
mother is homozygous recessive for mutant bcd, all the offspring will be mutant with posterior ends on
both sides because the mutant bicoid gene is placed in the egg
...

22
...
Translocation/Transposition of DNA {gene moves to new locus}


Leads to over-production of growth factor



Cancer cells frequently contain chromosomes that have trans-located fragments from one
chromosome to another



If a trans-located proto-oncogene ends up near an especially active promoter, or another control
element, its transcription may increase, making it an oncogene

2
...
Point mutations {in control element or in proto-oncogene itself}


In control element - leads to over production of growth factor



In gene – leads to hyperactive or degradation-resistant protein



May occur in promoter or enhancer that controls proto-onc



Causes increase in expression of proto-oncogene



May occur in the coding sequence of the proto-oncogene



Changes gene’s product to a protein that is more active or more resistant to degradation than
normal protein

23
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What is the normal function of tumor suppressor genes? What happens to them that can cause
cancer? Name two & give functions of at least one
...
They can act as repressors for
cell division, so when they’re altered and inactivated, they can no longer stop cell division and allow
cancer to form
...

25
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How do anti-cancer treatments work? Name one way tumor cells can become resistant to anticancer
agents
...
Tumor cells often mutate and become resistant
to treatment because they are very unstable
...
Name ten reasons why you should either not start smoking or stop smoking right away
...
Tobacco is addictive
...
Tobacco smoke is highly mutagenic
...
It irritates your lungs
...
If
you stop, circulation around your lungs will improve and debris will clear but lung function cannot be
restored to what it was before EVER AGAIN
...
You will smell bad
...


Chapter 19

Virus
Bacteriophage
Prion

Viroid
Host range

Capsid
Capsomere
Glycoprotein

Envelope
Lytic phage

Temperate phage
Lysogenic
Prophage

Restriction enzyme

Retrovirus

Reverse transcriptase
Provirus
Vaccine
Polio
Small pox
Influenza
Ganciclovir
Inflammation
HIV

Very small, simple genomes – obligate intracellular parasites
...
NOT LIVING
...

A virus that infects bacterial cells; has a double-stranded DNA genome
...
It
is a misfolded version of a normal brain protein that is indestructible and
has an incubation period of 10+ years
...

There are types of viruses for all different species, but not every virus
infects every organism
...

Proteins surrounding the genetic material of a virus
Subunits that produce viral capsid proteins
Enable virus to bind to protein receptors (white blood cells, for a
retrovirus)
Protein on the outside of a viral envelope; proteins are made by host
ribosome and sugar is added by the cell enzymes in the ER & Golgi
Complex
...
Bacteria
double in 20 min, so the viral replication rapidly outpaces bacterial
replication
A phage that has a lytic cycle and a lysogenic cycle
When a virus incorporates its own DNA into the host cell and keeps the
majority of its genome turned off
Viral DNA incorporated into host genome
...
Has a repressor that inactivates most
of the viral genes to keep from initiating lytic cycle
...
Digest unmodified (unmethylated) DNA bacterial DNA is modified, so it is protected
...
A restriction enzyme is normally 6-8 nucleotides long and
is the same backwards in forwards; may have sticky ends or clean ends
...
It integrates it’s own DNA
(provirus) into the host chromosome PERMANENTLY
...


1
...

2
...

3
...
How do lytic phages differ from temperate phages? How is a lysogenic life cycle carried out? What is
the function of the prophage? What causes it to switch from a lysogenic to a lytic cycle?
Lytic phages always destroy the host cell in releasing newly made copies of the virus
...

A prophage allows the viral DNA to be copied by host cell mechanisms and uses a repressor to keep the
other viral genes inactive so as to not lyse the cell
...

5
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They
also have restriction enzymes that digest unmodified DNA, which leaves the bacterial DNA alone since it
is methylated (modified)
...
How are DNA viruses similar to bacteriophages? How are they different?
They use similar infection methods
...
How do retroviruses differ from the other viruses we’ve examined? How might they interfere with
normal gene expression?
They start with RNA and make DNA from it, using reverse transcriptase
...
What are the components of the HIV virus, the causative agent behind AIDS? How does it carry out its
life cycle?
2 identical single-stranded RNA molecules + 2 molecules of reverse transcriptase that enter the cell
...

9
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10
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Where did viruses come from? Are there extant nucleic acid species that might hold clues to viral
origins?
Transposons and plasmids are believed to be the mobile genetic material that viruses evolved from
...
Why are viral diseases so different from one another? What generates the majority of the
symptoms?
They affect different parts of the body and the strains are ever-changing
...
How did AIDS rise from an obscure tropical disease to a worldwide epidemic? What factors aided its
spread?
It came from a small population and grew and spread quickly
...

14
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What is a viroid? What organisms do they infect?
Viroids are the smallest form of a virus with genomes only a couple of hundred nucleotides long
...

16
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How are prion diseases spread? How
do prions replicate? Are there genetic forms of spongiform encephalopathy?
A prion in a mutated version of a protein that converts normal proteins into being mutant
...
Used by bacteria to
digest unmethylated DNA (like that of viruses)
...
There are
hundreds of different kinds of restriction enzymes
...

A 4-8 nucleotide sequence that a restriction enzyme can bind to and
separate
Same forwards and backwards
Method used to separate genetic fragments by size, electrical charge, or
other properties
...

Bacteria; used to contain defense enzymes
Comes from genes in resistance plasmids inside of bacteria
Used to make recombinant DNA by catalyzing covalent bonds between
the sticky ends of fragments cut up by restriction enzymes
A collection of genes in a genome within cloned bacterium using
recombinant plasmids
...

A library of a genome with a gene per bacteria culture using
recombinant plasmids made from mRNA using RT in order to get only
the EXPRESSED genes in a tissue sample
...

Base pairing of one strand to the complementary sequence on a strand
from another nucleic acid molecule
combines transfer of electrophoresis-separated DNA fragments to a
filter membrane and subsequent fragment detection by probe
hybridization
...
The first
automated procedure for sequencing
...
(SANGER)
This is still used for SMALL SCALE sequencing
...
Utilizes a heat-resistant
polymerase called taq polymerase
...
Number of strands doubles per cycle
...


Microarray

Fluorescein
Rhodamine
Reproductive Cloning

Nuclear transfer
Therapeutic Cloning
Stem cell
Committed cell
Differentiated cell
Self renewal
Intestinal crypt
Haematopoetic stem cell
Stromal stem cell
Embryonic stem cell
Pluripotent
Totipotent
Adult stem cells

Gene Therapy
Induced pluripotency

A tool with little wells where each cDNA fragment goes
...
It is read
by a computer
...

Cloning for the purpose of fixing damaged organs/tissue in people
A cell that can become multiple or any types of cells; is NOT committed
One that
A cell that
Used by stem cells to regenerate themselves
A place in the intestine where stem cells are kept
Found in bone marrow cells; capabale of becoming any type of blood
cell
A stem cell in the stroma of a plant
A totipotent cell that is found in embryos and important for
development of all tissues
A cell that can become many types of cells
A cell that can be come any type of cell
are less well characterized- their full potential is not yet known (but
they could provide a non-controversial solution to avoid the ethical
issues that arise when human embryos are involved)
The processing of inserting corrected genetic information to cure
disease
Un-differentiating a cell so that it can become many types of cells

1
...
Their function in
bacteria is to digest unmodified DNA in defense to viruses
...

2
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3
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Migration has to do with polarity; positive end is at
the bottom and negative at the top
...
What is a plasmid? Why do they replicate autonomously in bacterial cells? Do they convey any
benefits to the bacteria?
They are separate from the bacteria chromosome, and contain defense genes for a bacterial cell to use
against things like antibiotics
...
How can DNA ligase be used to recombine DNA?
It catalyzes the covalent hydrogen bonds between two complementary sticky ends of fragments that
were cut by the same restriction enzyme and makes the bond permanent to create a recombined DNA
molecule
...
What is a genomic library? How is one made? What purpose does it serve?

7
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How is a hybridization carried out? How would one use hybridization to find genes?

9
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10
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This is the first
automated technique which allows sequencing of LARGE GENOMES
...
What are the steps of the polymerase chain reaction? How much DNA is made per cycle? How much
DNA can be amplified? Why is a heat stable DNA polymerase employed? How would one use PCR to
examine gene expression?

12
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13
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Animals were difficult because an
embryo has to be formed before you can get stem cells, and the fertilization and growth of the embryo
doesn’t work every time
...
In vertebrate cloning, how do embryonic nuclei compare to those from adults? Why might this be?
They’re less methylated, for one thing
...
What was the first cloned mammal? How was it created? What happened to it?
Dolly was created by taking a nucleus from one sheep and implanting it into the de-nucleated egg of a
donor sheep
...
She died at age 6 from a lung disease normally only found in much older
sheep
...
Why might one want to clone a person? Why would this be a really bad idea?
For fertility or for organs; it wouldn’t be humane to harvest organs from a person, even a clone, and for
fertility there are always differences or things that go wrong in cloning so the child could be extremely
“messed up”
...
What is therapeutic cloning? How might this further the cause of medicine?
It is used for a medical purpose, like replacing damaged tissue and has to do more with cloning a certain
cell type than a whole individual
...
What are stem cells? How do they differ from committed and differentiated cells? Name six types of
stem cells
...
What is so special about embryonic stem cells? Where do they come from? What do they do?
They come from embryos during the blastocyst stage and are totipotent; meaning they can easily be
differentiated into any type of cell
...
Is there a way to turn somatic cells (the majority in your body) into stem cells?

Yes, they can turn keratinocytes (skin cells) into stem cells
...
They’re
approach began with cloning (in plasmids) and sequencing DNA
fragments randomly cut from DNA with powerful programs to put
together overlapping short sequences into one continuous sequence
...
Weakness is short, repetitive
sequences
...

Move within a genome by means of DNA intermediates
...
They use transposase,
an enzyme that the transposon encodes
...

Most transposable elements are of this type
...
Leave copy behind
...
To insert, RNA is made into DNA by
RT and another enzyme catalyzes insertion of the reverse-transcribed
DNA
...
May be up to 500 nucleotides long
...

Two alleles with different lengths or the same; used in crime
investigations
...
More active in
cells of DEVELOPING BRAIN, maybe contributing to the diversity of
neurons
...


1
...
How does one obtain a cytogenetic map? What about a linkage map? How do these two differ?
3
...
How was a physical map of the human genome assembled and how did this lead to the sequence of
the human genome?
5
...
Craig Ventner differ?
6
...
How big is your genome? How many genes are in it?
8
...
What is alternative splicing? How might that contribute to the complexity of our genome?
10
...
What
evidence exists that it isn’t just junk?
11
...
What is in your genome? How much genomic sequence is repeats versus exons?
13
...
How might a transposable element alter the genome within a single cell? How might it change gene
expression?
15
...
What is a multigene family? Name two
...
What is a pseudogene? How are they formed? What are their defining characteristics?

18 How can meiotic nondisjunction contribute to genomic evolution?
19
...
What is a homeobox? What can clusters of homeobox genes tell us about evolution?
21
...
How can duplications, deletions, inversions, and translocations create new proteins?



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