1. Define the following terms and
utilize these terms in an appropriate context:
anticodon
codon
consensus sequence
exon
intron
messenger RNA promoter
ribosome
transcription
translation
wobble hypothesis
enhancer
primer
up mutation
down mutation
2. Describe in general the two main functions of DNA.
3. Explain and illustrate with diagrams how mRNA synthesis occurs.
4. Explain and illustrate with diagrams the location and "anatomy" of a ribosome.
5. Describe the arrangement of nucleotide
bases in a tRNA molecule, and the basic
functions of the two "ends" of the molecule.
6. Given the tRNA anticodon, and
a mRNA code chart, determine which activated
amino acid would become attached to that
particular tRNA molecule.
7. Outline, using diagrams, the attachment
of the proper amino acid-tRNA combination
to the initiator codon of a mRNA strand
at the P-site of a 40S ribosome particle.
8. Outline translation of the genetic
code by listing in their proper sequence the events
which must occur, starting with amino
acid activation and ending with the release of the
completed polypeptide.
9. Explain that the genetic code,
stored in DNA, is transferred to RNa, where it is
used to direct the synthesis of polypeptide
chains.
10. Explain what is meant by the
descriptions of the genetic code being, degenerate,
unambiguous, nonoverlapping, and comma-free.
11. Describe the observed pattern
of degeneracy in the code involving only the third
letter of a triplet series, leading to
the proposal of the Wobble Hypothesis.
12. Define and differentiate between transcription and translation.
13. Relate transcription and translation-
RNA and protein biosynthesis, respectively-
are fundamental processes essential to
the expression of genetic information.
14. Illustrate the fact that the
processes of transcription and translation are more complex
in eukaryotes than in prokaryotes.
15. Contrast the roles of tRNA and
mRNA during translation and list all enzymes that
participate in the transcription and translation
process.
16. Differentiate between the locations and roles of the codon and anticodon.
17. If given a sequence of DNA sense
strand:
-predict the mRNA sequence it will generate.
-using the mRNA codon sequence and the
coding dictionary, predict the corresponding
polypeptide sequence as determined
by the tRNA anticodons.
18. If given a sequence of a short
wild-type protein as well as various mutant forms of the
protein:
-using the coding dictionary construct
a potential mRNA sequence
-describe the general type of mutation
in each case
-indicate the specific base-pair change
that occurred for each mutation, assuming these
mutations resulted from single
base-pair changes.
Resources: Text Chapter 12 and 13,
Cartoon Guide pgs. 129-157
Synthesis of RNA and Protein: Transcription and Translation
Clear that proteins are end products of many genes -gene expression
Problem:
How is DNA, a nucleic acid, able to specify a protein (How is info transferred?)
How can DNA, confined to the nucleus, synthesize protein in the cytoplasm?
DNA copied in small pieces and removed from nucleus--> RNA
Transcription- process by which RNA molecules are synthesized on DNA template. (mRNA)
Translation-
RNA sequence, written in genetic code, translates code into polypeptide
chains.
tRNA- transfer RNA- serve as adaptors between codons of mRNA and amino
acids
specified by them.
Codon/Anticodon
-rely on base-pairing affinities between complementary base
-transcribe one (sense strand) strand of DNA
-triplet codon (3 base sequence on mRNA) pairs with anticodon triplet of
tRNA
-A.A.'s assembled at ribosome
Garrod-relationship between inheritance and metabolic disease, "inborn
errors of
metabolism"
Beadle & Tatum- one gene, one enzyme
Pauling & Itano- revised to one gene, one polypeptide
Central Dogma
(rigidly held principle or doctrine)- DNA serves as a template for
its
own replication and for transcription
of complementary RNA.
RNA- RiboNucleic Acid
1. single stranded
2. ribose sugar instead of deoxyribose
3. pyrimidine bases uracil rather than thymine.
Transcription:
RNA synthesis
Info flow from DNA ---> protein suggests:
1. since DNA in nucleus and protein synthesis is in cytoplasm. . . DNA
does
not participate in protein synthesis (Eukaryote)
Concept that RNA is intermediate suggests:
2. RNA synthesized in nucleus (Eukaryotes) where DNA is found & is
chemically
similar to DNA
3. following its synthesis, most RNA migrates to cytoplasm
4. amount of RNA generally proportional to amount of protein in a cell.
General features of RNA synthesis
(copied from the segment of DNA that constitutes
a gene)
1. Precursors
ATP, adenosine triphosphate (Adenine)
UTP, uridine triphosphate (Uracil)
CTP, cytidine triphosphate (Cytosine)
GTP, guanosine triphosphate (Guanine)
Differ from DNA only in sugar and uracil replaces thymine
2. Formation of RNA, sugar-phosphate bond between nucleotides 5'--> 3',
same as
DNA except RNA polymerase used. (if assembly in 5'--> 3' then how
does it read,
transcribe, the DNA? 3' --> 5'
3. Sequence of bases on RNA determined by sequence on DNA.
*difference between DNA polymerase and RNA polymerase is that RNA polymerase
is able to initiate chain growth without primer
*in any particular region of DNA only one strand serves as a template for
RNA
sense vs. missense (nonsense)
-Promoter recognition RNA polymerase binds to DNA within a base sequence
from 20-200 bases called a promoter
many promoters have been isolated, sequence variation corresponds to different
strangths of promoters.
2 consensus sequences (bases most often observed) most often observed at
a
specific position
*Pribnow box, -10 box, TATA box
*-35 box
Located "upstream" from start of transcription
More closely promoter elements resemble consensus, the stronger the promoter.
In Eukaryotes, enhancers interact w/ promoters to determine level of transcription
down mutation- destroy matches w/ consensus sequence, weaken promoter
up mutation- improves match w/ concensus sequence, strengthens promoter.
-Chain initiation
RNA polymerase initiates synthesis at consensus site, first nucleotide
triphosphate
placed at this site and synthesis begins in 5' --> 3' direction
-Chain elongation
RNA polymerase moves along DNA adding nucleotides.
*remember, only one of the 2 DNA strands transcribed
-Chain termination
chain terminating sequence UAA, UGA, UAG
inverted repeats, symmetrical about center, would read the same if rotated 180o
Hair pins- symmetrical about center and is self complementary, can pair to form hairpin
mRNA- Transcribes
DNA
-template strand of each gene corresponds to only one of the DNA strands
-which DNA strand differs from gene to gene
*Not all mRNA molecules transcribed from same DNA strand
mRNA processing
1. Translation rarely starts exactly at one end of RNA and proceeds to
the other end.
2. Section of untranslated RNA called leader, in some cases contains regulatory
sequences.
3. Coding sequence - specifies polypeptide chain, typical coding sequence
500- 3000 bases long, depends on # of amino acids in chain
4. "Cap"- terminal group necessary for ribosomes to bind with mRNA to begin
protein synthesis
5. Poly-A tail aids mRNA stability
6. Initiation codon- AUG (methionine)
7. Stop codons UAA, UAG, UGA; no tRNA exists to bind to these, interupts
elongation
8. Editing- excision of introns (junk)
Translation- translation of mRNA
code into amino acid sequence
A. rRNA- ribosomes, located in cytoplasm, endoplasmic retic. composed of
RNA and
protein (formed by DNA!)
1. 2 subunits (Svedberg units) 60s particle and 40s particle (s refers
to sedimentary
rates in a centrifuge)
P site- polypeptide, holds elongating chain
A site- Amino acid, accepts incoming amino acids
B. tRNA- transfer RNA, contains paired and unpaired bases
-one end is anticodon (matches complementary mRNA codon)
-other end is attached to a specific Amino acid
Anticodon- pairs with mRNA codon
tRNA responsible for translating mRNA into a specific amino acid sequence
(polypeptide ---> protein)
C. Amino Acids (20 naturally occurring)
peptide formation
D. translation takes place at ribosome
40s unit contains Psite and Asite
1. small subunit recognizes "cap" and initiator codon AUG
-initiator tRNA (w/ anticodon UAC) attaches to initiator
-large subunit attaches, translation begins
2. elongation- tRNA w/ attached polypeptide chain is at Psite
-new tRNA w/ new AA arrives at Asite
--translocation: new AA ataches to chain, ribosome moves down
3. mRNA translated until ribosome encounters stop codon
4. polysome- more than one ribosome working to make protein
The Genetic Code
-triplet, codons (code
words) direct insertion of single amino acids to polypeptide chain
General features:
1. code is in linear form derived from DNA
2. each "word" within mRNA contains 3 letters, thus code is triplet: each
group of
3 nucleotides (codon) codes for one amino acid.
-if one nucleotide ---> one AA, then only 4 AA's
-if two nucleotides ---> 42, only 16 AA's
-if three nucleotides ---> 43 = 64, plenty to code for 20 *tRNA contains
anticodon
3. code is unambiguous, each triplet specifies only one AA
4. code is degenerate, more than one triplet specifies for a given
AA (this is the case
for 18 of the 20AAs)
5. code contains "start" (AUG) and "stop" (UAA, UGA, UAG)
6. code is commaless, no internal punctuation. Once translation
begins, each
three nucleotides are read in turn.
7. code is nonoverlapping, once translation begins any single nucleotide
is part of
only one triplet
8. code is universal, with only minor exceptions, single coding
dictionary is used by
viruses, pro and eukaryotes.
Deciphering the code:
Crick and others ---> Frame shift mutations
insertions- induce changes (mutants)
deletions- reversions to wild type
Change and restoration of original reading frame
Marshall, Nirenberg- RNA homopolymers
poly U ---> phenyalanine
poly C
poly G
poly A etc
poly UG (RNA heteropolymers)
Complete code pg 238
Degeneracy- most often first two letters are common for triplets of any amino acid
Wobble
hypothesis
-first two more important than the third
-less specific hydrogen bonding required for third
-wobble would allow single tRNA species to pair w/ more than one triplet
in mRNA
-codes degeneracy would allow this to occur w/o changing amino acids
Comparing coding assignments it appears that U at position #3 of tRNA may
pair
w/ A or G at #3 spot in mRNA
-applying "wobble" rules, minimum of 30 tRNA needed
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