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12-3 Notes: Protein Synthesis
Proteins are the links between genotype and phenotype

Sir Archibald Garrod (1909) – hypothesized that some diseases are inborn and inheritable

Beadle and Tatum postulated that “one gene codes for one enzyme”
o This was later expanded to be “one gene one polypeptide chain”

Based on B & T’s research, Linus Pauling investigated the structure of hemoglobin

Performed gel electrophoresis on different hemoglobin genotypes (normal, sickle cell,
and carriers)
o Results proved that differences were in the genes
TWO MAIN PARTS OF PROTEIN SYNTHESIS
Transcription = synthesis of mRNA using DNA as a template

A gene’s unique nucleotide sequence is transcribed from DNA to a complementary
nucleotide sequence in messenger RNA (mRNA)

Occurs in the nucleus or nucleoid region
Translation = synthesis of a polypeptide, which occurs under the direction of messenger RNA

Occurs on ribosomes
RNA: The Connection between DNA and Proteins
RNA = ribonucleic acid

Cells making lots of protein (ex. pancreas) have higher RNA levels

Structure:
o Sugar = ribose
o Four N-bases = A, C, G, and uracil (U) instead of T
o Single-stranded

3 Kinds exist:
o Messenger RNA (mRNA) = carries the message for how to build a gene’s protein
from the DNA to a ribosome, where it is built
o Transfer RNA (tRNA) = brings amino acids to the ribosome and puts them in the
correct order, according the mRNA’s directions
o Ribosomal RNA (rRNA) = together with some proteins, makes up the ribosome
The Central Dogma Theory
Information in cells only goes one way: genotype  phenotype
That is:
DNA  RNA  protein
The Genetic Code
20 amino acids exist, but there are only 4 different nucleotides to code for them
Gamow:
if each nucleotide = 1 a.a., maximum of 4 a.a. are possible
If 2 nucleotides = 1 a.a. = 4 x 4 = 16 a.a. possible
If 3 nucleotides = 1 a.a. = 4 x 4 x 4 = 64 a.a. possible
So code is a triplet code
Codon = set of three mRNA nucleotides
Nirenberg and Matthaei Exp/ Deciphers the Code
Realized the code is universal to all living things

Transferring RNA from one organism to another results in the same polypeptide chain
Created artificial RNA by putting together chains of RNA nucleotides

Set up 20 test tubes with E. coli extracts

Each tube had 1 radioactive a.a. and 19 normal ones

Added poly-U to each tube

1 tube – phenylalanine – built radioactive polypeptide chains of phe
o Therefore, UUU = phenylalanine

Repeated experiment with all different combinations to determine the code

64 Combinations are possible
o 61 make a.a.  only 20 a.a. exist, so code is “degenerate” (repetitious)
o 3 “STOP” codons
12-4 Notes: Transcription
Transcription occurs in three stages: Initiation, Elongation, and Termination
Specific DNA nucleotide sequences mark where transcription of a gene begins (promoter) and ends
(terminator). These initiation and termination sequences plus the nucleotides in between (the gene) are
called a transcription unit.
INITIATION

RNA Polymerase bind and initiate transcription

Promoter = region of DNA where RNA polymerase binds to begin transcription
o
Is upstream from the gene to be made into a protein
o
In eukaryotes, RNA polymerases cannot recognize the promoter without the help of certain
proteins called transcription factors

TATA Box = a short nucleotide sequence at the promoter which is rich in thymine (T) and adenine
(A) and is usually located about 25 nucleotides upstream from the initiation site

When active RNA polymerase binds to the promoter, the enzyme unzips the two DNA strands at the
initiation site and transcription begins
ELONGATION

RNA polymerase moves along the DNA and performs two functions:
1. It untwists and opens a short segment of DNA (about 10 bases long)

Only one strand is the actual template for base-pairing with the RNA nucleotides
2. It links incoming RNA nucleotides to the 3’end of the elongating strand

Therefore, RNA grows one nucleotide at a time in the 5’  3’ direction

mRNA grows at about 30 to 60 nucleotides per second
As the strand elongates:
1) It peels away from the DNA template
2) The DNA behind it re-forms its DNA-DNA double helix by H-bonding
Following in series, several molecules of RNA polymerase can transcribe the same gene, which allows the
cell to produce particular proteins in large amounts
TERMINATION

Transcription proceeds until RNA polymerase transcribes a DNA sequence called a terminator

Prokaryotic mRNA is ready for translation as soon as it leaves the DNA template.

Eukaryotic mRNA, however, must be processed before it leaves the nucleus and becomes
functional.
Eukaryotic Cells Modify mRNA After Transcription
Pre-mRNA = primary transcript that will be processed to functional mRNA
1) 5’ Cap = modified guanine nucleotide (guanosine triphosphate = GTP) that is added to the 5’ end of
mRNA shortly after transcription begins
- Protects the growing mRNA from degradation by hydrolytic enzymes
- Helps small ribosomal subunits recognize the attachment site on mRNA’s 5’ end
2) Poly-A Tail = Sequence of about 50-100 adenine (A) nucleotides added to the 3’ end of mRNA before it
exits the nucleus

May inhibit degradation of mRNA in the cytoplasm

May facilitate attachment to the small ribosomal subunit

May regulate protein synthesis by facilitation mRNA’s export from the nucleus to the
cytoplasm

Is not attached directly to the stop codon, but to an untranslated trailer segment of mRNA

Trailer Sequence = noncoding (untranslated) sequence of mRNA from the stop codon to the
poly (A) tail
3) “Split Genes” – Roberts and Sharp (1977) – must also be dealt with during the processing of eukaryotic
mRNA

Introns = noncoding (“interrupting”) sequences in DNA that intervene between coding sequences
and are initially transcribed, but not translated because they are excised (cut out) from the transcript
before the mature mRNA strand leaves the nucleus

Exons = coding sequences of the mRNA that are translated into an actual protein

RNA Splicing = process that removes introns and joins exons from eukaryotic pre-mRNA
- Results in an mRNA with a continuous coding sequence

Small nuclear ribonucleoproteins (snRNPs) = complexes of proteins and small nuclear RNAs that are
found only in the nucleus; some participate in RNA splicing
- Referred to as “snurps” (also referred to as snRNAs)

Ribozymes = RNA molecules that can catalyze reactions by breaking and forming covalent bonds and
are NOT proteins

Spliceosomes = a large molecular complex that catalyzes RNA splicing reactions
- Made of snRNPs and other proteins
Why Introns?

May play a regulatory role in the cell

May control gene activity
o
Some introns give rise to microRNAs (miRNAs) = small moecules that bind with mRNA and
block translation from happening

Splicing process itself may help regulate the moving of mRNA to the cytoplasm

May allow a single gene to direct the synthesis of different proteins
o
Alternative mRNA Splicing = using different exons depending on environmental variables


Ex. Immunoglobulin Genes (for antibody production)
Play an important role in the evolution of protein diversity by increasing the probability that
recombination of exons will occur between alleles  that is, the more introns a chromosome carries,
the higher the crossing over frequencies are