Lecture 008s1 part 1
Protein Synthesis, Genetic Code, Mutation and Gene Exp, Gen of Chloroplasts & Mito
1. PROTEIN SYNTHESIS, GENETIC CODE, EFFECTS OF MUTATION ON GENE EXPRESSION,
GENETICS OF CHLOROPLASTS AND MITOCHONDRIA
a. Aminoacyl-tRNA synthetase (red) recognizes a particular tRNA (blue) and will couple to the
corresponding amino acid (not shown).
b. Answer the question: How do genes express themselves? ______________________________
____________________________________________________________________________
c. Who is the translator? _________________________________
d. Four essential concepts to consider with gene expression:
i. __________________________ _________ _____________________ is the key to the
transfer of information from DNA to RNA to protein.
ii. ________________________(directionality) help to guide the mechanism of gene
expression.
iii. Gene expression will require the input of ________________________ and machinery in
the form of ____________________________________________________
______________________________________________________.
iv. Recognition that mutations change _________________ ________________________
or obstruct the flow of its expression all of which greatly affect ___________________.
2. PROTEINS AND PHENOTYPE
a. Have sequence mapcompare to genetic codei.d. which are genes Phenotype
b. Answer questions:
c. How was the genetic code (triplet nucleotide repeats or codons) established as
d. the basic unit that relates DNA to protein?
e. Are sequences of nucleotides colinear with sequences of amino acids?
f. What is the significance of the reading frame?
g. Which codons are associated with which amino acids?
h. Why do geneticists use mutations to provide evidence for the genetic code?
i. Do all organisms use the same genetic code?
3. DNA  RNA PROTEIN
a. How DNA is copied from generation to generation: _____________________________
b. How RNA is synthesized from specific regions of DNA: ____________________________
c. The synthesis of a polypeptide directed by the RNA sequence___________________________
4. DNA  RNA PROTEIN
a. TERMS TO KNOW or REVIEW:
b. Gene expression: the process by which a gene’s information is converted into RNA and then (for
protein-coding genes) into a polypeptide.
c. RNA: ribonucleic acid – a polymer of ribonucleotides found in the nucleus and cytoplasm of
cells; it plays an important role in protein synthesis. There are several classes of RNA molecules
including messenger RNA (mRNA) transfer RNA (tRNA), ribosomal RNA (rRNA), and other
small RNA’s, each serving a different purpose (for example – a ribozyme).
d. Transcription: the conversion of DNA-encoded information to its RNA-encoded equivalent.
e. Translation: the process in which the codons carried by mRNA direct the synthesis of
polypeptides from amino acids according to the genetic code.
f. Transcript: the produce of transcription, a specified fragment of RNA.
g. Messenger RNA (mRNA): RNA that serve as a template for protein synthesis. A molecule of
RNA that undergoes processing to become an mRNA in eukaryotes.
h. Ribosomes: cytoplasmic structures composed of ribosomal RNA (rRNA) and protein; the site of
protein synthesis.
5. DNA  RNA  PROTEIN DOES NOT EXPLAIN THE BEHAVIOR OF ALL GENES
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Beavers
Lecture 008s1 part 1
Protein Synthesis, Genetic Code, Mutation and Gene Exp, Gen of Chloroplasts & Mito
a.
b.
c.
d.
e.
Two types of RNA: Messenger RNA (mRNA) and Functional RNA
Functional RNA’s are active as RNA’s – never translated into proteins.
FUNCTIONAL RNA’s make up the largest fraction of total cellular RNA.
TERMS TO KNOW or REVIEW:
Ribosomal RNA (rRNA)
i. Ribosomal RNA (rRNA): RNA components of ribosomes.
ii. Nucleolus: a large, sphere-shaped organelle visible in the nucleus of interphase
eukaryotic cells with a light microscope; formed by the nucleolar organizer. The nucleoli
play a key role in the manufacture of ribosomes.
iii. Nucleolar organizer: clusters of rRNA genes on long loops of DNA within a nucleolus.
f. Transfer RNA (tRNA): small RNA adapter molecules that place specific amino acids at the
correct positions in a growing polypeptide chain.
6. THE GENETIC CODE
a. Genetic code: the sequence of nucleotides, coded in triplets (codons) along the mRNA that
determines the sequence of amino acids in protein synthesis.
b. The genetic code is made up of triplet codons
i. Codon: nucleotide triplet that represents a particular __________________ _________
to be inserted in a specific position in the growing amino acid chain during translation.
Codons can be either in the mRNA or in the DNA from which the RNA is transcribed.
ii. What is the language used in the genetic code? _________________
iii. The code shows the 5’  3’ sequence of the three nucleotides in each mRNA codon: The
first nucleotide is at the 5’ end of the codon. Example: CUA (Leu), C is the 5’ end of the
codon.
7. COLINEARITY OF GENE AND PROTEIN
a. COLINEARITY: The correspondence between the location of a mutant site within a gene and
the location of an amino acid substitution within the polypeptide translated from that gene.
b. 1963: Colinearity demonstrated in the laboratory of Charles Yanofsky of Stanford University
using point mutations (changes in only one nucleotide pair) and purified mutant proteins.
c. Yanofsky was the FIRST to compare maps of mutations within a gene to the particular
_______________ _______________ ____________________________ that resulted.
d. What is an auxotrophic mutant? ____________________________________________
e. What did Yanofsky discover?
i. The order of nucleotides in a gene corresponds to the order of amino acids in the
polypeptide.
ii. He provided evidence that a codon is composed of more than one nucleotide:
1. A single codon must contain two or more base pairs/nucleotides.
a. He found that recombination could occur between two mutations that
changed the identity of the same amino acid, producing a wild-type.
b. Because the smallest possible unit of recombination is the base pair.
c. Two mutations capable of recombination in the same codon (because they
affect the same amino acid) must be in different nearby nucleotides.
d. Therefore, a codon must contain more than one nucleotide.
e. (See mutation in glycine position #211 – one mutation, #23 changed the
amino acid to an arginine, the other changed it to a glutamic acid at THE
SAME POSITION.)
iii. Each mutation alters the identity of one amino acid; therefore, each nucleotide is part of
one codon.
1. Point mutations change only a single nucleotide pair.
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Beavers
Lecture 008s1 part 1
Protein Synthesis, Genetic Code, Mutation and Gene Exp, Gen of Chloroplasts & Mito
2. Point mutations consistently altered ONLY ONE AMINO ACID in a polypeptide.
3. Each nucleotide in a gene must influence the identity of only a single amino acid.
8. NONOVERLAPPING TRIPLET CODONS HAVE A DEFINED READING FRAME
a. In 1955, Crick and Brenner demonstrated that codons consist of 3 nucleotides with a defined
start point in the gene that would establish a reading frame.
b. Intragenic suppression: the restoration of gene function by one mutation canceling another in the
same gene.
c. What is a reading frame? The partitioning of groups of 3 nucleotides from a fixed starting point
such that the sequential interpretation of each succeeding triplet generates the correct order of
amino acids in the polypeptide chain.
9. CRACKING THE CODE
i. Discovery of RNA.
ii. Synthesizing polypeptides in a test tube.
iii. The production of synthetic mRNA’s.
iv. 1961, Nirenberg & Matthaei mixed synthetic mRNA with the protein-synthesizing
machinery of E. coli and watched a protein formed!
v. What did they see formed from this first synthetic strand of RNA?
vi. 5’-UUUUUUUUUUUUUUU-3’
b. What is meant by a degenerate code or a redundant code?
c. Degeneracy: a property of the genetic code in which several different codons can specify the
same amino acid.
d. STOP CODON or NONSENSE CODONS: the three stop codons that terminate translation. UAA,
UAG, UGA. These can lead to nonsense mutations that terminate protein synthesis and truncate
the protein.
e. INITIATION CODON: nucleotide triplet that marks the precise spot in the nucleotide sequence
of an mRNA where the code for a particular polypeptide begins. AUG which codes for
methionine often serves in this position.
10. POLARITIES
a. Only one strand of the DNA double stranded molecule serves as the template strand for mRNA.
b. RNA-like DNA strand same polarity and sequence of RNA.
c. Polypeptide polarity: The 5’ to 3’ direction in an mRNA corresponds to the N-terminus to Cterminus direction in the polypeptide.
d. Template strand (also called the antisense strand or the noncoding strand): the strand of the
double helix that is complementary to both the RNA-like DNA strand and the mRNA.
e. RNA-like strand (also called the sense strand or the coding strand): strand of a double-helical
DNA molecule that has the same nucleotide sequence as the RNA (except for the substitution of
T for U) and that is complementary to the template strand.
11. GENETIC CODE IS NEARLY UNIVERSAL
12. REVERSE TRANSCRIPTION DEVIATES FROM DNA  RNA  PROTEIN
a. HIV is a retrovirus: viruses that hold their genetic information in a single strand of RNA (2
identical copies) and carry the enzyme reverse transcriptase to convert that RNA into DNA
within a host cell.
b. REVERSE TRANSCRIPTASE: an RNA dependent DNA polymerase that synthesizes DNA
strands complementary to an RNA template. Therefore, the product of reverse transcriptase is a
cDNA molecule.
Transcription, (in our text: section 8.2 pages 256-264) was covered in your prior biology class and will not be reviewed. We
will look at alternative splicing pages 264-265.We will look at HIV and reverse transcription.
13. ALTERNATIVE RNA SPLICING
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Beavers
Lecture 008s1 part 1
Protein Synthesis, Genetic Code, Mutation and Gene Exp, Gen of Chloroplasts & Mito
a. Alternative RNA splicing: production of different mature mRNA’s from the same primary
transcript by joining different combinations of exons.
b. Alternative splicing that produces two different mRNA’s.
c. Trans-splicing combines exons from different genes.
Translation section 8.3 (pgs 265 – 272), Differences in gene expression, section 8.4 (pages 272-274) and Comprehensive example
section 8.5 (pages 274-275) contain information that should have been part of your previous biology class and will not be reviewed.
14. HOW MUTATIONS IN A GENE CAN AFFECT GENE EXPRESSION
a. REVIEW:
b. Silent mutations: mutations without effects on phenotype; usually denotes point mutations that
change one of the three bases in a codon but that do not change the identity of the specified
amino acid because of the degeneracy of the genetic code.
c. Missense mutations: changes in the nucleotide sequence of a gene that change the identity of an
amino acid in the polypeptide encoded by that gene.
i. Conservative if substitution has chemical properties similar to the one it replaces.
ii. Nonconservative if the substitution of the amino acid has very different chemical
properties that are likely to have a more notable consequence.
d. Nonsense mutations: mutational changes in which a codon for an amino acid is altered to a stop
codon, resulting in the formation of a truncated protein.
e. Frameshift mutations: insertions or deletions of base pairs that alter the grouping of nucleotides
into codons which in turn alters the reading frame.
15. MUTATIONS OUTSIDE OF THE CODING REGION
a. EXAMPLES:
b. Change in sequence of promoter.
c. Change in sequence of ribosome binding site.
d. Altered splice sites.
e. Loss of stop codons.
16. IT’S ALL ABOUT DOSAGE!
a. Loss-of-function mutation: DNA mutation that reduces or abolishes the activity of a gene; most
(but not all!) loss of function alleles are recessive.
b. Null (or amorphic) mutations: mutations that abolish the function of a protein encoded by the
wild-type allele. Such mutations either prevent synthesis of the protein or promote synthesis of a
protein incapable of carrying out any function.
c. Hypomorphic mutation: produces either less of a protein or a protein with a weak but detectable
function.
17. INCOMPLETE DOMINANCE: When a phenotype varies continuously with levels of protein function.
18. WHY SOME MUTANT ALLELES ARE DOMINANT
a. Haploinsufficiency: a rare form of dominance in which an individual heterozygous for a wildtype allele and a null allele shows an abnormal phenotype because the level of gene expression is
not enough to produce a normal phenotype.
b. Dominant negative mutation: (or antimorphic) alleles that block the activity of wild-type alleles
of the same gene, causing a loss of function even in heterozygotes.
c. Gain-of-function mutation: rare mutations that enhance a gene’s function or confer a new activity
on the gene’s product.
d. Hypermorphic mutation: produces an allele generating either more protein than the wild-type
allele or the same amount of a more efficient protein. If excess protein activity alters phenotype,
the Hypermorphic allele is dominant.
e. Ectopic expression: gene expression that occurs outside the cell or tissue where the gene is
normally expressed.
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