Chapter 10 - Gene Expression
I.
How are genes and proteins related?
A. The key point of DNA is that information for information’s sake does not produce the reactions of life. Information must be processed.
B. DNA is organized in units called genes, sequences that generally encode a single protein product.
C. Summarized as “one gene, one protein” axiom in modern biology
D. DNA is the permanent copy of information in the cell and as such is manipulated the least, for this reason all information processing is done through a carrier molecule of RNA, ribonucleic acid.
E. There are three types of RNA
1. rRNA: ribosomal RNA, structural RNA sequences that form part of the structure for the ribosome.
2. tRNA: transfer RNA, structural RNA that serve as the translation bridge between nuclear sequence and amino acid sequence (discussed more in Section III).
3. mRNA: messenger RNA, complementary sequence of DNA codes that can be interpreted as protein sequences (more in section II & III).
F. The central dogma for information flow in modern biology is concisely written as follows:
DNA ----transcription----> RNA ----translation----> Proteins
II. Transcription
A. Transcription: the process of making complementary copies of DNA sequences in RNA for the purpose of utilizing information encoded in the DNA.
B. The process of transcription is accomplished with the enzyme RNA polymerase, and proceeds in three steps.
1. Intitiation: A special sequence (the promoter) on the DNA, preceding a gene, which triggers the attachment and activity of RNA polymerase.
2. Elongation: Similar to the process of replication the polymerase enzyme proceeds down the sequence constructing a 5’ à 3’ complementary copy in RNA instead of DNA.
a.
One caveat to remember, RNA sequences do not have thymine (T), but
instead have uracil (U), so the base pairing rules are A:U and C:G.
3. Termination: A second special sequence (termination sequence) triggers the polymerase the quit and detaches the new RNA strand.
C. Transcription is accomplished in the nucleus of the eukaryotic cell and the cytoplasm of the prokaryotic cell.
III. Translation
A. Translation: the process of converting a linear sequence of nucleic acids (encoded in RNA) into a linear sequence of amino acids.
B. Messenger RNA (mRNA) is the molecule that is actively translated, having been produced by transcription.
C. The site of protein production is the ribosome, which is a complex structure formed from rRNA and proteins.
D. The RNA sequence is divided into “words” of three nucleotide “letters” called codons.
E. The ribosome is looking for a specific codon to trigger attachment to the mRNA, this codon is called the start codon and has the sequence “AUG”
F. Codons form the “language” of the protein translation.
1. If one looks at all possible 3 letter combinations of four nucleotides, you get 64 possible combinations.
2. Each possible combination codes for a specific amino acid (or action), and this code is consistent across all life forms.
3. The genetic code is outlined in Table 10-3.
G. The ribosome attaches to the mRNA sequence at the start codon and proceeds down the sequence translating every codon into its accompanying amino acid, linking that new amino acid by a peptide bond to the proceeding translated chain. (Figure 10-6)
H. Realize that the start codon sets the “frame” for the remainder of the sequence (i.e. which sets of three are translated), and the frame starts at the first start codon (which may not be the very beginning of an mRNA).
I. Termination of translation is determined when the ribosome reaches a nonsense codon, a codon that encodes a STOP and no amino acid.
J. Translation is accomplished from the 5’ end of the mRNA.
5’- G C G A U G | C C C | G G A | U G G | U A A – 3’
MET PRO GLY TRP STOP
IV. Gene Regulation and Mutation
A. Genes are regulated through a variety of mechanisms, but most often they are regulated at the level of transcription.
B. As each individual gene can result in multiple mRNA copies and each mRNA can result in multiple proteins the effect is called amplification.
C. Genes are typically described as constitutive (always on), repressible (default: on, can be turned off), inducible (default: off, can be turned on).
D. In some cases whole chromosomes can be turned off, as in the case of Barr Bodies, where one X chromosome in each cell of a woman is turned off at random.
E. Mutation: a change to the base sequence of the DNA that is inherited.
1. Single base mutations – a change, deletion, or insertion of a single base pair.
5’- G C G A U G | C C C | G G A | U G G | U A A – 3’
MET PRO GLY TRP STOP
5’- G C G A U G | A C C | G G A | U G G | U A A – 3’
MET THR GLY TRP STOP (missense)
5’- G C G A U G | C C C | G G A | U A A | U A A – 3’
MET PRO GLY STOP (nonsense)
5’- G C G A U G | C C G | G A U | G G U | A A – 3’
MET PRO ASP GLY (frame-shift)
a. Missense Mutation – results in a change of amino acid encoded.
b. Nonesense Mutation – results in a premature STOP codon
c. Frame-Shift Mutation – results in a shift in frame for the translation.
d. Neutral Mutation (AKA Silent Mutation) – results in no change to the encoded protein.