Download DNA Replication, Transcription, and Translation

Genetics, DNA, Replication, Transcription, and Translation
Objectives:
•Describe the structure of DNA and chromosomes.
•List the 5 bases and the 2 categories they belong to.
•Discuss the processes of replication, transcription, and translation.
•Research/Investigate chromosome structure and genetic composition.
•Analyze the roles of mRNA, tRNA, and rRNA.
•Explain protein structure/folding.
•Predict the implications nutrient deficiencies might have on any of the above
processes or structures.
•Describe the types of genetic mutations possible.
•Evaluate the pros and cons of current genetic technology
Vocabulary:
nucleotide * purine * pyrimidine * replication * replication forks * uracil *
antiparallelism * histone * dimers * transcription * translation * codon *
ribosomes * point mutation * promoter * anticodon * mRNA * tRNA * rRNA *
genes * introns * exons * junk genes * methionine * R groups * complement *
polypeptide * conformation * disulfide bonds * mutagen * carcinogen *
substitution * deletion * insertion * frameshift * translocation * nonsense
mutation * transposons * jumping genes * inversion * trisomy * monosomy *
genetic engineering * GMO * restriction enzymes * electrophoresis *
nondisjunction
DNA (deoxyribonucleic acid) consists of monomer nucleotides
made of a 5 carbon sugar (deoxyribose), a nitrogenous base, and
phosphate. The nitrogenous base can be either a double carbon and
nitrogen ring called a purine or a single carbon and nitrogen ring called
a pyrimidine. Adenine and guanine are purines and thymine and
cytosine are pyrimidines. Adenine always binds to its complementary
base, thymine, and guanine always binds to its complement, (partner)
cytosine, via hydrogen bonds. These form the “rungs” of the DNA
double helix “ladder”. The “rungs” are bound to deoxyribose on each
side. Completing the sides of the ladder are phosphates. These
alternate with the deoxyribose sugars.
Chromosome Structure:
PO4
PO4
Sugar -- purine * * pyrimidine -- Sugar
PO4
PO4
(**hydrogen bonds)
Before a cell can divide, the DNA containing chromatin needs to
double. This doubling process is called replication. For replication to
proceed, the double helix of DNA strands must unwind (break hydrogen
bonds between complementary base pairs) in many locations at once.
These unzipped areas are called replication forks.
Each DNA strand of the double helix has a 5’ (5 prime) and a 3’
end. The two DNA strands align in opposite directions. This head to
tail alignment is called antiparallelism. Additional bases to form the
new DNA strand are added from the 5’ end toward the 3’ direction.
When replication is complete, 2 complete double helixes of DNA exist
BUT each one contains 1 old strand and 1 new strand of DNA.
It is only after replication that chromatin can condense around
histone proteins to form chromosomes and complete the cell cycle.
Unfortunately, if copying errors were made and not caught by
proofreading polymerases, mutations can occur. Thymine dimers are
the most common cause. This happens when 2 adjacent thymines on
the same strand covalently bind to each other causing a kink. This
makes it easier to insert the wrong base in the new DNA strand.
Transcription
Since DNA can’t leave the nucleus, its information for protein
synthesis has to be carried to the ribosomes (site of protein synthesis)
in the cytoplasm by RNA (same basic structure as DNA but with a 5
carbon ribose sugar instead of deoxyribose).
To do this, DNA unzips and nucleotides form the RNA complement
to the DNA template. This process is called transcription. Only a
single strand of RNA is formed. This RNA is called messenger RNA
(mRNA) because it carries DNA’s message for protein synthesis. RNA
will not normally contain thymine bases. Instead, every adenine on the
DNA will be paired with a uracil base (pyrimidine) on the RNA strand.
So, RNA can contain A, U, C, and G, but not T. A combination of a 3
base triplet on RNA that codes for an amino acid is called a codon.
Only DNA sequences that code for amino acids or RNA parts (genes)
need to reach the ribosomes. These sections of DNA are called exons.
However, DNA contains many “non-gene” sequences too. These are
called introns. When DNA is transcribed, the introns are cut away and
the exons are re-assembled into mRNA.
At one time, introns were considered genetic “junk”, or “junk genes”.
Today we realize these segments probably control the when, where,
etc. of DNA replication and transcription.
The cell knows where to start the transcription process because a
promoter region on DNA attracts the transcription factors and RNA
polymerase. There are many different factors controlling transcription.
Some of these factors contain nutrients such as zinc, the amino acid
leucine, etc. So, a deficiency in a particular nutrient could stop the
transcription of information for an important protein. And, proteins are
what give us our shape (morphology) and appearance (phenotype), so
a missing or abnormal protein could cause disease or mutations.
Finally, the cell knows when to stop transcribing DNA when a
sequence of bases called the “terminator” region is reached. Imagine
what might happen if the terminator region was not correctly replicated
or read during transcription. Fortunately, our bodies have many
“proofreading” enzymes doing their best to make sure all goes well.
Protein Synthesis
The mRNA exits the nucleus and travels to the ribosomes (site of
protein synthesis). Some ribosomes are attached to endoplasmic
reticulum and will make mostly proteins for export out of the cell. Other
ribosomes are loose in the cell and make proteins likely to stay in the
cell and be used for growth, repair, etc.
The ribosomes are composed of a protein sub-unit and an RNA subunit called ribosomal RNA (rRNA). It is at the ribosomes that mRNA
will be translated. Translation is the process where mRNA is read in
order to synthesize a new protein.
mRNA contains triplets of nitrogenous bases. Each triplet codes for
an amino acid (except the “stop” triplet). These triplets are called
codons. The first mRNA codon is usually “AUG”. It signals the transfer
RNA (tRNA) to start translation by bringing the amino acid “methionine”.
tRNA carries amino acids to the ribosome to form a polypeptide. tRNA
has anti-codons that are the triplet complement to the mRNA codons.
Polypeptides are long chains of amino acids that individually, or in
combination, become a protein. Proteins are very complex and can
fold into a 3 dimensional shape, called its conformation. The simplest
“chain” of amino acids is called the “primary” conformation. Some
folding occurs due to hydrogen bonds between non-adjacent carboxyl
and amino groups (due to their polarity). This is called the secondary
structure. Then more folding occurs as ionic bonds form between the
side groups (R-groups) of the amino acids and as disulfide bonds form
between sulfurs. This is the final, tertiary structure of individual
polypeptides and many proteins. However, sometimes individual
polypeptides must bond together to make a functional protein. For
example, 4 polypeptide chains interact to make the blood protein
hemoglobin. This interaction creates the quaternary structure of some
proteins.
Mutations
There are several copying errors that can be made during replication
or transcription. Occasionally, these are induced by environmental
hazards like ultraviolet light, X-rays, chemical exposure, etc. Anything
that can cause a mutation is called a mutagen. (“Teratogens” is also
used and refers to substances that cause structural birth defects.)
Some mutations can actually be beneficial. However, if exposure to a
mutagen causes cancer, the mutagen is known as a carcinogen.
When a single base is incorrectly complemented, inserted or deleted,
in a gene, it is called a point mutation. When the wrong base is
substituted for the correct complement (Ex: an “A” partners with a “C”
instead of a “T”), it’s called substitution. If this codes for a different
amino acid than normally found here, it is sometimes called a missense
mutation. When a complementary base is left out in the copying
process, it’s a deletion. And, when an extra base is put in, it’s an
addition. Usually, a substitution is the least serious because it
sometimes allows the same amino acid to form or the new amino acid
has little effect on the overall function of the protein formed. If the
substitution causes the codon to read “stop”, it’s a “nonsense mutation”.
Additions or deletions are usually VERY serious problems for protein
synthesis. That’s because they cause a reading frameshift mutation.
Remember, each triplet (codon) of bases codes for a different amino
acid. Think of these as words in a sentence. Ex:
The Cat And Dog Ran.
If I insert an “A” in the middle of “The”, the new triplets are read as . . .
Tah Eca Tan Ddo Gra . . .
If I delete the “H” from “The” in the original codon string, I get . . .
Tec Ata Ndd Ogr An . . .
A substitution is usually far less traumatic. Ex: Substitute “A” for “e” in
“The” from the original triplet string.
Tha Cat And Dog Ran
HOWEVER, in sickle cell anemia only one base is wrong due to a
substitution that caused valine (CAC at the DNA level - complements to
GUG on mRNA)) to replace glutamic acid (CTC on DNA, but GAG on
mRNA). Valine is a polar amino acid, that causes hemoglobin to fold
incorrectly.
Chromosomal mutations can also occur. Pieces of chromosome can
break off and be lost (deletion) in the copying process. They can break
off and reconnect to a nonhomologous chromosome (Ex: break off
chromosome #1 and reattach to chromosome #3). This is called
translocation. There are certain genes (about 10% of them) in humans
that fairly easily move to different chromosome locations. These are
called “transposons” or “jumping genes”.
Occasionally, a piece of chromosome breaks off and reattaches
upside down to the same chromosome. This is called an “inversion”.
And, of course, nondisjunction of chromosomes can cause trisomy (3
copies of a chromosome in the genome) or monosomy (a single
chromosome, no homolog).
Gene Technology
Genetic engineering involves cutting genes from one organism and
splicing them into the genes of another. The combination DNA from
the 2 organisms is called recombinant DNA. In order to create
recombinant DNA, enzyme “knives” (restriction enzymes) that
recognize certain base sequences are used to cut them away from the
rest of the DNA.
Once the selected DNA is isolated, it must be inserted into the DNA of the
second organism. Very often a virus is used because these can easily enter
cells. Bacterial plasmids (DNA rings) also work in some cases.
Genetic engineering has been used to cheaply make insulin and other
human hormones using human DNA inserted in bacteria. It has also
been used in plants to make crops resistant to herbicides used to kill
weeds in the fields As a result, GMO {genetically modified organisms}
soybeans are more heavily sprayed than ever! It has also been used to
insert the gene for BT (bacillus thurengis?) in corn to kill corn borers
BUT it kills other caterpillars too! So, its use is quite controversial.
Gene splicing has also been used in vaccine production. For example,
the vaccine for Hepatitis B involves splicing a gene from the virus with a
fungus. Similar crosses are being used in plants to create rice, for
example, that makes beta-carotene in levels similar to a carrot.
Unfortunately, these combinations can cause allergic reactions that
might not occur to the single organism’s DNA. Once these crosses are
made, they are in the gene pool to stay and will be carried in future
generations. So, if you are allergic to carrots, but not rice, GMO rice
using carrot genes may now also cause an allergic reaction in you.
In order to see gene sequences of nitrogenous bases, we can use
gel electrophoresis. This allows us to take pieces of the human
genome and display them as bands based on their molecular weight
and their attraction to an electric current. The same technique can be
used on other polar/charged molecules as well.