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Beadle and Tatum: bombarded bread mold with xrays, gave the bread mold minimal medium
supplemented with different intermediates in the arginine pathway; they determined the metabolic
pathway for arginine synthesis; one enzyme one gene (now known as one enzyme one polypeptide)
Garrod: analyzed urine and discovered alkaphenoturia (sp); discovered that an enzyme was missing in
the metabolic pathway, if it was it would turn urine dark, dark deposits in ears, eyes, along spine
What composes RNA, protein, DNA? RNA (made of U, A, C, G and a ribose sugar/phosphate backbone);
proteins made of amino acids with a specific R group, there are 20 different amino acids; DNA made of
deoxyribose sugar/phosphate backbone T, A, C, G)
What is a codon? Anticodon? Where are they found? Triplet code of nucleotides found on the mRNA
that codes for a specific amino acid; anticodon is the complementary nucleotide sequence that coincides
with a “specific” codon on the mRNA , it is attached to the tRNA that carries a specific amino acid
How do you interpret a codon wheel or chart?
What are the differences, if any, for the genetic code for organisms? Prokaryotes have circular DNA;
some of the codon sequences do not code for the same amino acid and can be substituted (most codons
code for the same amino acid but there can be subtle differences in this between organisms)
Mechanism for transcription in eukaryotic vs prokaryotic?
Eukaryotes require transcription factors that allow RNA polymerase to bind to the promoter
(TATA box); occurs in nucleus; have introns and exons; spliceosomes remove the introns; mRNA gets
processed to add 5’cap and poly A tail which helps it to get out of the nucleus; repressors can bind to
the activator and stop transcription, or an inducer can bind to the activator and start the pathway
Prokaryotes: happens in cytoplasm, has exons but no introns, no TATA box, no transcription factors,
RNA polymerase still binds to transcribe the DNA, mRNA not processed (no 5’cap or poly A tail) because
translated immediately;
Mechanisn for translation in eukaryotic vs prokaryotic? Both use ribosomes, both happen in cytoplasm,
See ribosomes, tRNA below
Primary transcript? The original mRNA transcript of the DNA before the introns are cut out, before the 5’
cap is added, and the 3’ poly A tail is added
Processed transcript? mRNA transcript that has had the introns removed by spliceosomes, the
spliceosomes splice the exons back together; 5’ cap is added (it is a modified guanine and 3 phosphates);
the Poly A tail is added to the 3’ end; the 5’ cap and poly A tail prevent degradation of the mRNA, helps
the mRNA to leave the nucleus, and helps the ribosome attach for translation
Alternative splicing? How multiple polypeptides can be made from the same mRNA transcript depending
on which introns are removed from the transcript
Introns? Exons? UTRs? Introns are noncoding regions that get removed from the primary transcript,
Exons are the coding regions of the nucleotide sequence; UTR noncoding region that remains in the
processed mRNA transcript thought to be regulatory
Ribosomal RNA? What is it made of? How does it work? Made of large subunit (RNA and proteins) and
small subunit (RNA); contains the E site, P site, A site; mRNA attaches to the mRNA site on the small
subunit of the ribosome; tRNA is brought to the mRNA by the aminoacyl synthetase and brings the
appropriate amino acid to the mRNA (matches the anticodon site on the tRNA to the codon site of the
mRNA); the tRNA is delivered to the A site (the enzyme is then released to get/charge another tRNA);
the tRNA then moves over to the P site and the amino acid it carries is attached to the growing
polpeptide chain; the tRNA is then moved to the E site and ejected from the ribosome to go off and be
charged again
Transfer RNA? How does its 3d shape occur? How does it work? Brings the appropriate amino acid to
the ribosome; usually RNA is linear, 3D shape occurs when the RNA folds back on itself and finds
complementary sequences and hydrogen bonds to itself; it has two binding sites- one site holds the
amino acid, the other site has the anticodon that will bind to the codon region of an mRNA in a
ribosome
mRNA? Messenger RNA, a complementary strand to DNA that is processed and allowed to leave the
nucleus of the cell
Where does transcription occur? Translation? In prokaryotes? In eukaryotes transcription occurs in the
nucleus, translation occurs in the cytoplasm; prokaryotes do not have a nucleus so
transcription/translation occurs simultaneously in the cytoplasm
DNA to mRNA to amino acid (be able to decode, transcribe and translate) see codon wheel above and
practice
Gatcatctgatc (DNA sequence)
Cuaguagacuag (RNA sequence)
Cua/gua/gac/uag establish reading frame
Look up codon on codon chart
Leu-val-asp-stop codon
Order of protein synthesis? DNA is transcribed to RNA; RNA is translated to protein
What does wobble mean and what does it allow? It allows for flexibility of the tRNA at the 3rd base of
the codon; it allows tRNA to bind to more than one codon and deliver the correct amino acid (there are
45 different tRNAs that can recognize 60 different codons)
What is a reading frame? The 3 nucleotides that are read to correctly create a codon
What can cause reading frame shifts? Deletions, insertions can cause reading frame shifts
What other types of mutations can occur? Base pair substitutions; missense, nonsense, silent mutations;
translocations, inversions
Operon model? An operon contains the operator, the promoter, the genes that are going to be
expressed, RNA polymerase; shows how DNA is transcribed in prokarytoes and some eukaryotes; RNA
polymerase attaches to the promoter, if no repressor the RNA polymerase will untwist the DNA and
creates RNA nucleotides, once the DNA is transcribed the RNA polymerase “pops off” of the DNA and
the transcription complex comes apart
Example: trp operon, lac operon
Lac operon: lac pathway is inducible operon that is always turned off but can be turned on by
allolactase (enzyme that inactivates the repressor by binding to the repressor and changes the shape of
the repressor so it can’t bind to the operator and allows the transcription pathway to continue)
repressible operon? The pathway is usually on but can be slowed/stopped by the repressor binding to
the operator
Inducible operon? Pathway is usually off but can be started by the repressor being inactivated
Regulatory genes? Genes that code for a protein, such as a repressor (or an enhancer) that controls the
transcription of another gene or group of genes
Promoter? A specific nucleotide sequence in the DNA that binds RNA polymerase, positioning it to start
transcribing RNA at the appropriate place
Repressor? A protein that inhibits gene transcription; in prokaryotes repressors bind to the DNA in or
near the promoter; in eukaryotes repressors can bind to the control elements within enhancers, to
activators, or to other proteins in a way that blocks activators from binding to DNA
Inducer? a specific small molecule that binds to a bacterial repressor protein and changes the
repressor’s shape so that it cannot bind to the operator thus switching the operon on.
Enhancer? A segment of eukaryotic DNA containing multiple control elements usually located far from
the gene whose transcription it regulates
Activators? Proteins that bind to certain mediator proteins and general transcription factors helping
them form an active transcription initiation complex on the promoter
Nonsense? When a point mutation changes the original codon to code for a stop codon; no polypeptide
can be made
Missense? a point mutation that changes an amino acid in the polypeptide chain
Silent? A point mutation that doesn’t alter the amino acid that is added to the chain (changes the codon
for the same amino acid)
How much of the genome codes for genes? What does the rest do? 1.5% actually codes for genes; used
to be considered “junk” but being found to code for regulatory aspects of protein synthesis
Epigenetics? How environmental factors can alter gene expression by affecting the condensing of
chromatin and how the transcription machinery can “fit” onto the chromatin to start transcription;
REMEMBER: DNA nucleotides can not be altered but the epigenome can; methy groups can attach and
condense the chromatin; if methyl groups are taken off the chromatin relaxes; addition of an acetyl
group does the opposite.
siRNA ? microRNA? siRNA (small interfering RNA) and microRNA (smaller than small siRNA) work the
same; they are sequences of RNA that attach to the mRNA and cause hairpin loops; if the microRNA or
siRNA are a perfect complement to the mRNA, the mRNA will be completely destroyed by the dicer
enzyme; if a siRNA/microRNA is a close match then translation is slowed down
totipotent? a cell that can still become any type of cell (stem cell)
Pluripotent? A cell that has been “determined” to be a certain type of cell but hasn’t started
differentiation
Determined? An “apprentice cell” that knows what type of cell it will be but hasn’t started to “change”
into that cell type
Differentiated? A cell that becomes specialized. A “master”cell
Transcription factors? Proteins that bind the promoter and enable RNA polymerase to bind (there are
atleast 1000 transcription factors that are specific for the particular sequences that code for specific
gene expression)
Egg polarity genes? Help to determine body plan; sets up anterior/posterior part of embryo and
dorsal/ventral axis (example was bicoid gene)
Homeotic genes? Control pattern formation in the late embryo; highly conserved sequence in a lot of
eukaryotes
Post transcriptional control? mRNA degradation by the removal of the poly A tail, the 5’ cap;
microRNA/siRNA slowing or stopping translation; primary transcript of mRNA can be alternatively
spliced to synthesize different proteins; regulatory protein can bind to the UTR region of the mRNA and
temporarily/permanently stop translation initiation