Protein Synthesis

Text Ref: Pg 117 - 127

http://www.youtube.com/watch?v=suN-sV0cT6c

From DNA to RNA to Protein
http://www.youtube.com/watch?v=itsb2SqR-R0

DNA is used to build three types of RNA

1) mRNA - Messenger RNA
Function:

2) tRNA - Transfer RNA
Function:

3) rRNA - Ribosomal RNA
Function:


Protein Synthesis
2 Processes are needed to complete protein synthesis

1) Transcription Using DNA to Make mRNA
Occurs in the nucleus
Genes are segments of DNA which carry the code (set of instructions) for the creation of
messenger RNA (mRNA)
STEPS:
1. RNA polymerase binds to a section of DNA called a promoter site that has the base
sequence TATA and is called the TATA box
2. Beginning at the TATA box RNA polymerase unwinds a section of DNA
3. RNA polymerase attaches complementary RNA nucleotides (C,G,A,U) found floating
around in the nucleus to the DNA nucleotides
4. RNA polymerase forms phosphodiester bonds between the sugar of one nucleotide and
the phosphate of another in the complementary strand to form mRNA
5. Once complete, the new mRNA un-zips itself off of the DNA template strand and
leaves the nucleus to enter the cytoplasm where it will be used to make proteins
DNA is an important biological molecule which holds all of lifes instructions, however it has some
limitations. DNA does serve as a template for its own replication; however it is confined to the
nucleus of a cell. Protein synthesis occurs in the cytoplasm of the cell, and therefore DNA itself
cannot directly manufacture the proteins our cells need. DNA can be used as a template to make
RNA; a molecule which is capable of leaving the nucleus and synthesizing proteins in the cytoplasm
with the help of ribosomes.
RNA reads the genetic code in a gene (a segment of DNA) and specifies the sequence of amino acids
in a polypeptide. In this way genes control the structure and metabolism of the cell.

Steps Involved in the Transcription of mRNA















2) Translation Translating mRNA to Make Proteins

Occurs in the cytoplasm of a cell
mRNA is read in 3-letter words called codons, therefore it is often referred to as a
triplet code
Each codon codes for a specific amino acid e.g. AGC codes for the amino acid serine
There are 20 common amino acids which are the building blocks of all proteins
within the body




2. RNA polymerase then
unwinds a section of
DNA.
3. RNA polymerase reads the
DNA template strand and
attaches complementary RNA
bases (C,G,A,U) found floating
around in the nucleus to the
DNA nucleotides.
4. RNA polymerase joins the
new RNA nucleotides to form
a single strand of mRNA.
5. Once complete, the new mRNA un-zips itself off of the DNA
template strand and leaves the nucleus to enter the cytoplasm
where it will be used to make proteins. The DNA molecule simply
rewinds itself until it is needed again.
http://www.youtube.com/watch?v=ztPkv7wc3yU&feature=related
https://www.youtube.com/watch?v=AGzsgTMgSog




1. RNA polymerase binds to
the TATA box on a DNA
strand the promoter (start)
region for the synthesis of a
new mRNA molecule.


Translation has 3 steps:
1) Initiation
2) Elongation
3) Termination
http://www.youtube.com/watch?NR=1&v=5bLEDd-PSTQ&feature=endscreen

1. Initiation Assembly of the ribosome & Beginning of Protein Synthesis

The beginning of protein synthesis is initiated or begins when a small ribosomal subunit
made from ribosomal RNA (rRNA) attaches to a START codon (AUG) on mRNA
Next, a transfer RNA molecule (tRNA) carrying the matching anti-codon (UAC) and its
corresponding amino acid, bonds with the start codon
Finally, a large ribosomal subunit also made from rRNA joins to the small subunit to
form a complete ribosome

2. Elongation Formation of the polypeptide chain one amino acid at a time

The first tRNA then passes its amino acid onto the incoming tRNA
Peptide bonds join the 2 amino acids together to form a dipeptide, the beginning of a
polypeptide chain.
The empty tRNA then detaches itself from the mRNA and goes back into the cytoplasm to
bond onto another amino acid
The ribosome then shifts over to the next mRNA codon so that it can receive a new
incoming tRNA-amino acid complex that matches the next codon
This process repeats over and over until a polypeptide chain is formed (primary protein
structure).













3. Termination

A ribosome will continue to build a polypeptide chain until it reaches a terminator
(STOP) codon on the mRNA (see amino acid table for some examples)
Once protein synthesis is complete, the ribosome, mRNA, and tRNA molecules are
broken down and recycled back into the cytoplasm until they are needed again












As the R-groups on the amino acids on the newly released polypeptide chain begin
to interact with one another, they fold into their secondary and tertiary structure
If the amino acids of more than one polypeptide chain begin to interact and form bonds, a
quaternary protein results


Genetic Mutations


Frameshift Mutations
1) Deletion Mutations
On a DNA molecule a single nitrogenous base is left out in base pairing
As a result, the reading frame, for all codons on the mRNA transcribed from this
mutated DNA, from the point of the mutation onward is changed
e.g THE CAT ATE THE RAT

If the letter C is deleted the reading frame is shifted, and the codons are no longer
the same
THE ATA TET HER AT

Due to a single nucleotide deletion, our sentence i.e. gene no longer makes sense.
Tay Sachs disease and cystic fibrosis is caused by this type of mutation





Most genetic mutations occur when the nucleotide sequence in a DNA molecule is altered during
DNA replication. Because DNA is used as a set of instructions by mRNA for the synthesis of all
proteins within the body, changes in a single nucleotide within a DNA molecule have the potential to
produce partially or completely non-functional proteins.
To function correctly, each cell depends on thousands of proteins to function in the right places at
the right times. When a mutation alters a protein that plays a critical role in the body, a medical
condition can result. A condition caused by mutations in one or more genes is called a genetic
disorder. Some mutations alter a gene's DNA base sequence but do not change the function of the
protein made by the gene. Approximately 70% of genetic mutations have damaging effects, and the
remainder has no apparent effect on an individual.
If a mutation is present in a germ cell, it can give rise to offspring that carries the mutation in all of
its cells. This is the case in hereditary diseases. On the other hand, a mutation can occur in a
somatic cell (body cell) of an organism. Such mutations will be present in all descendants of this cell,
and certain mutations can cause the cell to become malignant, and thus cause cancer.
Often, gene mutations that could cause a genetic disorder are repaired by the DNA repair system of
the cell. Each cell has a number of pathways through which enzymes recognize and repair mistakes
in DNA. Because DNA can be damaged or mutated in many ways, the process of DNA repair is an
important way in which the body protects itself from disease.
2) Addition Mutations
Occur when an extra nitrogenous base is inserted during base pairing. Again, the
reading frame is shifted and the set of triplet codons on the resulting mRNA would be incorrect
from the point of the addition on.

Eg. CCU CGU AAG add A CCU CAG UAA G


Point Mutations

1) Silent Mutations
There is NO HARM when the codon created by the point mutation codes for the same
amino acid as the original codon
E.g. If a U was mistakenly replaced by a C the protein is unaffected because both
codons still code for the amino acid cysteine:

UGU (cysteine) UGC (cysteine)
Silent mutations do not affect the final 3-D structure of a protein and therefore have
no effect on its function


2) Nonsense Mutations
When a codon that codes for an amino acid is changed to be a STOP or termination
codon

E.g. If the C in is changed to a G you would get a STOP codon.
UAC (tyrosine) UAG (STOP codon)

If a STOP codon occurs before the end of a polypeptide chain, the polypeptide chain
will be too short and the protein will not be able to function





Homeostatic Imbalance
Duchenne Muscular Dystrophy (DMD) is a debilitating disease caused when the protein
dystrophin, an important structural component within muscle tissue that provides membrane
stability, is too short and unable to function correctly.
This happens when an amino acid in dystrophins polypeptide chain is mistakenly replaced by a STOP
codon. The STOP codon terminates the formation of dystrophins polypeptide chain before it is
finished.
As a result people with this disease experience rapid progression of muscle degeneration, eventually
leading to loss in control over movement, paralysis, and eventually a premature death.

3) Missense Mutations

When the change in one amino acid affects the final shape (tertiary or quaternary
structure) of a protein
A change in a single amino acid along a polypeptide chain as a result of a point
mutation can be enough to render a protein non-functional because it will no longer
have the 3-D shape it needs to function

E.g. UGU (cysteine) UGG (tryptophan)




Causes of Genetic Mutations

Mutagens are environmental influences that cause genetic mutations.
E.g. Radiation (ultraviolet, X-rays)
E.g. Organic Chemicals (cigarette smoke, pesticides, artificial food additives)

Homeostatic Imbalance
Sickle-cell anemia is a life-long disease where hemoglobin, a protein found in the blood that
functions to carry oxygen, has an abnormal rigid sickle shape. Normally, hemoglobin is a
quaternary protein that has a shape similar to a biconcave disc. By simply changing the sixth
amino acid in one of hemoglobins polypeptide chains red blood cells are distorted into a sickle
shape. Their abnormal shape makes them stack up inside of cells and they clog small vessels.
This causes hemorrhaging and leads to pain in internal organs and joints. People with sickle cell
disease have an average life expectancy of less than 50 years.