Chapter 17 Study Guide – Science Olympiad
By Julia Beamesderfer (2005)
The Connection Between Genes and Proteins
I.
Evidence for genes specifying proteins was first hypothesized by British physician Archibald
Garrod, who believed that genes dictate phenotypes through enzymes that catalyze specific
chemical processes within the cell
II.
Decades later, George Beadle and Edward Tatum tested this hypothesis with mutants of a bread
mold called Neurospora crassa.
A. Auxotrophs- The mutants of the bread mold could not survive on the minimal medium
(modest food requirements) that the wild types of the mold could, because they could not
synthesize certain necessary ingredients from the minimal medium
B. To pinpoint their metabolic defect, Beadle and Tatum put the mutants into vials of the
minimal medium plus single additional nutrients to pinpoint the ones that would aid the
mutants in surviving.
C. They discovered that the mutants needed the amino acid arginine to survive, and that there
were three precursors of arginine needed to produce it
D. From this three classes of mutants were discovered- those who only needed arginine, those
who needed its 1st precursor, or those who needed its 2nd precursor
E. From this it was concluded that each mutant type lacked a different enzyme
III.
One Gene—One Polypeptide Hypothesis
A. Since not all proteins are enzymes, and some proteins were made of multiple polypeptide
chains, the one gene-one enzyme hypothesis was altered to the above name
IV.
Quick Facts Regarding Transcription and Translation
A. RNA- chemically similar to DNA except it consists of a ribose sugar (instead of a
deoxyribose sugar) and the possible nitrogenous base of uracil U (rather than thymine T)
B. Transcription- synthesis of RNA under direction of DNA
C. Messenger RNA (mRNA)- a faithful transcript of the gene’s protein-building instructions
which carries genetic message from DNA to protein-synthesizing machinery
D. Translation- actual synthesis of polypeptide occurring under direction of mRNA. Also, cell
must translate base sequence of mRNA into amino acid sequence of a polypeptide
E. RNA Processing- the process which takes the initial RNA transcript (pre-mRNA or primary
transcript) and yields the finished mRNA
F. Triplet Code- since there are 20 amino acids and only 4 nitrogenous bases, it is necessary for
an amino acid to be coded by a triplet of nucleotide bases- yielding 64 possible codes. The
genetic instructions for a polypeptide chain are written in the DNA as a series of threenucleotide words.
G. Template Strand- the DNA strand that is transcribed during RNA transcription
H. Codons- mRNA base triplets EX- UGG is codon for amino acid tryptophan (Trp)
V.
The Genetic Code
A. In 1961 Marshall Nirenberg deciphered the first codon (UUU) by synthesizing an artificial
mRNA by linking uracil nucleotides. When he added the strand to amino acids, ribosomes,
and other components, he got a polypeptide containing a string of a single amino acid,
phenylaline.
B. Start Signal (AUG)- it was also discovered that AUG could serve as methionine (Met) as well
as functioning as initiation codon, to start translating mRNA with methionine.
C. Stop Signals (UAA, UAG, and UGA)- these three codons are not designated as amino acids,
but rather they mark the end of translation acting as termination codons.
D. Codon Redundancy- in many cases, codons that are synonyms for a certain amino acid differ
only in the third base of the triplet.
E. Because the genetic code is nearly universal, the RNA codon CCG, ex, is translated to amino
acid proline in all studied organisms, though there are a few exceptions
Transcription- the DNA-directed synthesis of RNA
I.
Initiation
A. Promoter- the region of DNA where RNA polymerase attaches and initiates transcription
1. RNA Polymerase- enzyme that pries DNA strands apart and hooks together RNA
nucleotides with base pairing along DNA template
2. The promoter determines where transcription starts and which DNA helix strand is used
as template
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Chapter 17 Study Guide – Science Olympiad
By Julia Beamesderfer (2005)
3. TATA Box- A crucial promoter DNA sequence used to form initiation complex
B. Transcription Factors- in eukaryotes, these proteins bind to the promoter and causes RNA
polymerase to bind to it
C. Transcription Initiation Complex- completed assembly of transcription factors and RNA
polymerase bound to the promoter
II.
Elongation of RNA Strand
A. RNA polymerase continues to move and untwist DNA, adding nucleotides to the 3’ end of the
growing RNA molecule
B. In its wake, DNA re-twists and RNA molecule peels away from its template
C. Several molecules of RNA polymerase can transcribe a single gene by following each other,
causing the growing strands to trail from each polymerase, helping to make protein in large
amounts
III.
Termination
A. Terminator- sequence that calls for termination of transcription
1. Transcribed terminator (RNA sequence) acts as actual termination signal
2. In eukaryotes, shortly after the polymerase has passed the termination signal, AAUAAA,
it cuts free from enzyme.
RNA Processing- the modifying of pre-mRNA by enzymes in a eukaryotic nucleus
I.
Alteration of mRNA Ends
A. 5’ End
1. 5’ Cap- during RNA processing the 5’ end of the pre-mRNA molecule is capped off with
a modified form of a guanine G nucleotide
2. Function
a. First, this helps protect the mRNA from degradation by hydrolygic enzymes
b. Second, after mRNA reaches cytoplasm, 5’ cap functions as part of an “attach here”
sign for ribosomes
B. 3’ End
1. Poly (A) Tail- this is added by an enzyme to the 3’ end of the pre-mRNA. It consists of
30 to 200 adenine nucleotides
2. Function
a. Inhibits degradation of the RNA
b. Helps ribosomes attach to it
c. Facilitates the export of mRNA from the nucleus
II.
RNA Splicing- the removal of a large portion of the pre-mRNA molecule
A. Introns- noncoding segments of nucleic acid that lie between coding regions
1. Importance
a. Maybe introns play regulatory roles in the cell
b. Domains- discrete structural and functional components (EX- active site, area where
protein attaches to membrane, etc.) that are thought to be coded by a split genes’
exons
c. Since exons are separated by intron DNA, frequency of recombination within a split
gene can be higher than for a gene lacking introns, since they increase opportunity
for crossing over between two alleles of a gene
B. Exons- the other regions that are eventually expressed, or translated into amino acid
sequences
C. Process
1. snRNPs- small nuclear ribonucleoproteins that recognize short nucleotide sequences at
the ends of introns, signaling RNA splicing
a. Composed of RNA (called small nuclear RNA, or snRNA) and protein molecules
2. Spliceosomes- consist of different snRNPs joined with additional proteins. Spliceosomes
interact with splice sites and cuts ends of introns to release them and then join the two
exons
D. Ribozymes- Sometimes primary transcripts are spliced by intron RNA itself (Ex- tetrahymena
protozoan use self-splicing
1. Proves that not all biological catalysts are proteins
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Chapter 17 Study Guide – Science Olympiad
By Julia Beamesderfer (2005)
The Synthesis of Proteins
I.
Transfer RNA (tRNA)- molecule which transfers amino acids from the cytoplasm to ribosome.
A. Cytoplasm is stocked with all 20 amino acids, gained by synthesizing them from other
compounds or taking them up from surrounding solution
B. tRNA molecules are not identical; each type of tRNA molecule links a particular mRNA
codon with a certain amino acid
C. When tRNA arrives at ribosome, one end bears the specific amino acid and the other has a
nucleotide triplet called an anticodon, which binds to complementary codon on mRNA.
D. Structure and Function
1. Made in nucleus and travels to cytoplasm where translation occurs
2. Consists of a single, short RNA strand (looking like a clover) with the anticodon on one
end and the 3’ end that is an attachment site for the amino acid.
E. Wobble- there are only 45 different tRNA molecules needed (instead of 61) because some can
recognize two or more different codons (due to the fact that the third base of the codon is not
strict.
1. When tRNAs have inosine I (a modified base) in the wobble position of a codon, it can
bond with U,C, or A
2. Explains why synonymous codons for a given amino acid can often differ in 3rd base
F. Aminoacyl-tRNA Synthetase- enzyme that joins amino acid to correct RNA.
1. There are 20 of these enzymes in a cell, one for each amino acid
2. It’s active site fits only certain combination of amino acid and tRNA
3. It attaches amino acid to tRNA, driven by hydrolysis of ATP
II.
Ribosomal RNA (rRNA)- the type of RNA which, along with proteins, constructs the ribosomal
subunits
A. Ribosomes consist of large subunit and small subunit
1. Each subunit is made in nucleus and sent to cytoplasm, where they join to form ribosome
when they attach to mRNA
B. Each ribosome has 3 binding sites
1. P Site (peptidyl-tRNA site)- holds the tRNA carrying the growing polypeptide chain
2. A Site (aminoacyl-tRNA site)- holds the tRNA carrying the next amino acid to be added
to the chain
3. E Site (exit site)- site where discharged tRNAs leave the ribosome
III.
Translation- Building a Polypeptide
A. Initiation- when mRNA, tRNA with amino acid, and two ribosome subunits are joined
1. Small ribosomal subunit attaches to leader segment (5’ end) of mRNA.
2. Then initiation codon, AUG, signals start of translation (initiator tRNA carrying amino
acid Met attaches to the initiation codon)
3. Large ribosomal subunit is added, completing translation initiation complex.
4. Initiation Factors- required to bring all components together, by use of GTP molecule
5. Results- initiator tRNA sits in the P site of the ribosome, and vacant A site is ready for
the next aminoacyl tRNA.
B. Elongation- amino acids are added one by one to the first amino acid, involving elongation
factors
1. Codon Recognition- mRNA codon in the A site of ribosome bonds with incoming tRNA
molecule (which carries appropriate amino acid)
a. Requires energy from GTP
2. Peptide Bond Formation- an rRNA molecule catalyzes formation of peptide bond that
joins the polypeptide chain from the P site to the new amino acid in the A site
3. Translocation1. tRNA in the A site is translocated to the P site (bonds remain, the mRNA moves
along with it and brings the next codon into the A site)
2. tRNA in the P site moves to the E site and leaves the ribosome.
3. Requires energy from GTP
4. Ribosome moves along the mRNA in direction of 5’ to 3’, and they move relative to
each other
C. Termination
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Chapter 17 Study Guide – Science Olympiad
By Julia Beamesderfer (2005)
1.
Elongation continues until a stop codon (UAA, UAG, or UGA) reaches the A site of a
ribosome
2. Release factor- protein that binds to stop codon in A site and causes addition of water
molecule instead of amino acid to polypeptide chain, and frees polypeptide from
ribosome.
D. Polyribosomes- when a string of ribosomes trails along a single mRNA strand to produce
polypeptides more efficiently
IV.
From Polypeptide to Functional Protein
A. During and after synthesis, a polypeptide chain coils and folds spontaneously forming a
functional protein of specific conformation
B. Posttranslational Modifications- steps that may be required before a protein can begins
functioning
1. Certain amino acids may be chemically modified by attaching sugars, lipids, phosphate
groups, etc.
2. Enzymes may remove one or more amino acids from the leading (amino) end of the
polypeptide chain
3. A single chain may be enzymatically cleaved into two or more pieces
4. Two or more polypeptides may join to become subunits of a protein with quaternary
structure
V.
Signal Peptides- since there are free (cytosol) ribosomes and bound ribosomes (attached to ER),
bound ribosomes and secretory ribosomes are marked by signal peptides, targeting them to the ER
A. Signal peptides are short sequences of amino acids near the leading end of a polypeptide
B. Signal-Recognition Particle (SRP)- protein-RNA complex that recognize signal peptides
when they emerge from a ribosome and brings them to a receptor protein on the ER
membrane
C. Once attached to the ER membrane, protein synthesis continues, signal peptide is removed by
an enzyme, and secretory proteins are released into the cisternal space of ER via a protein
pore and a membrane protein remains embedded in ER membrane
D. Other signal peptides target polypeptides to other organelles in the cell, but translation is
completed before they are translocated.
Prokaryotes (Bacteria) Vs. Eukaryotes
I.
Differences
A. Contain different RNA polymerases; eukaryotes’ depend on transcription factors
B. Transcription is terminated differently
C. Slightly different ribosomes
D. Cell organization
1. Prokaryotic cell assures a streamlined operation, simultaneously transcribing and
translating the same gene
2. Eukaryotic cell’s nuclear envelope segregates transcription from translation and provides
compartment for extensive RNA processing
E. Eukaryotes have complicated mechanisms for targeting proteins to the appropriate cellular
compartment.
Mutations- changes in the genetic material of a cell or virus
I.
Large Scale Mutations- chromosomal rearrangements that affect long segments of DNA (previous
.
chapters
II.
Point Mutations- chemical changes in just one or a few pairs in a single gene
A. Genetic Disorder- if a mutation has an adverse effect on the phenotype of a human or other
animal
B. Two Main Types
1. Base-Pair Substitution- the replacement of one nucleotide and its partner in the
complementary DNA strand with another pair of nucleotides
a. Silent Substitutions- due to the redundancy of the genetic code, a change in a base
pair may transform one codon into another that has the same amino acid
b. Other changes of a single nucleotide pair may switch an amino acid but have little
effect on the protein if the new amino acid has similar properties
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Chapter 17 Study Guide – Science Olympiad
By Julia Beamesderfer (2005)
c.
III.
Some alterations of a single amino acid in a crucial area of a protein will
significantly alter protein activity
d. Missense Mutations- when the altered codon still codes for an amino acid and still
makes sense, although it’s incorrect
e. Nonsense Mutation- alterations that change an amino acid codon to a stop signal,
usually leading to a nonfunctional protein
2. Insertions and Deletions- additions or losses of one or more nucleotide pairs in a gene
a. These have disastrous effects because mRNA is read as a series of nucleotide
triplets, and an insertion or deletion that is not a multiple of three would throw
everything off
b. Frameshift Mutation- when number of inserted or deleted nucleotides is not a
multiple of three; almost certainly producing non-functional protein
Mutagens- physical and chemical agents that interact with DNA to cause mutations
A. In 1920 Hermann Muller discovered that X-rays caused an increased frequency in genetic
changes
B. Base Analogues- chemicals similar to normal DNA bases but pair incorrectly during DNA
replication
C. Other mutagens insert themselves in DNA and distort double helix.
D. Ames Test- method to test the mutagenic activity of different chemicals, developed by Bruce
Ames
1. Uses colonies of bacteria with mutations rendering them unable to synthesize amino acid
histidine.
2. When suspected mutagenic chemical is added to culture, the only bacteria that will form
colonies are those who have undergone a back-mutation to restore histidine-producing
ability
3. Therefor, the number of colonies that grow increases measure of strength of mutagen
4. Ames test is often used to screen chemicals to identify those that cause cancer, because
most cancer-causing chemicals, or carcinogens, are mutagenic.
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