1. Genes and How They Work
Chapter 15

2. The Nature of Genes
Early ideas to explain how genes work came from studying human diseases.
Archibald Garrod studied alkaptonuria, 1902
Garrod recognized that the disease is inherited via a recessive allele
Garrod proposed that patients with the disease lacked a particular enzyme
These ideas connected genes to enzymes.

3. The Nature of Genes
Evidence for the function of genes came from studying fungus amongus.
George Beadle and Edward Tatum, 1941
studied Neurospora crassa
used X-rays to damage the DNA in cells of Neurospora
looked for cells with a new (mutant) phenotype caused by the damaged DNA

4. The Nature of Genes
Beadle and Tatum looked for fungal cells lacking specific enzymes.
The enzymes were required for the biochemical pathway producing the amino acid arginine.
They identified mutants deficient in each enzyme of the pathway.

6. The Nature of Genes
Beadle and Tatum proposed that each enzyme of the arginine pathway was encoded by a separate gene.
They proposed the one gene – one enzyme hypothesis.
Today we know this as the one gene – one polypeptide hypothesis.

7. The Nature of Genes
The central dogma of molecular biology states that information flows in one direction:
DNA RNA protein
Transcription is the flow of information from DNA to RNA.
Translation is the flow of information from RNA to protein.

9. The Genetic Code
Deciphering the genetic code required determining how 4 nucleotides (A, T, G, C) could encode more than 20 amino acids.
Francis Crick and Sydney Brenner determined that the DNA is read in sets of 3 nucleotides for each amino acid.

11. The Genetic Code
codon: set of 3 nucleotides that specifies a particular amino acid
reading frame: the series of nucleotides read in sets of 3 (codon)
only 1 reading frame is correct for encoding the correct sequence of amino acids

12. The Genetic Code
Marshall Nirenberg identified the codons that specify each amino acid.
RNA molecules of only 1 nucleotide and of specific 3-base sequences were used to determine the amino acid encoded by each codon.
The amino acids encoded by all 64 possible codons were determined.

14. The Genetic Code
stop codons: 3 codons (UUA, UGA, UAG) in the genetic code used to terminate translation
start codon: the codon (AUG) used to signify the start of translation
The remainder of the code is degenerate meaning that some amino acids are specified by more than one codon.

15. Gene Expression Overview
template strand: strand of the DNA double helix used to make RNA
coding strand: strand of DNA that is complementary to the template strand
RNA polymerase: the enzyme that synthesizes RNA from the DNA template

16. Gene Expression Overview
Transcription proceeds through:
initiation – RNA polymerase identifies where to begin transcription
elongation – RNA nucleotides are added to the 3’ end of the new RNA
termination – RNA polymerase stops transcription when it encounters terminators in the DNA sequence

17. Gene Expression Overview
Translation proceeds through
initiation – mRNA, tRNA, and ribosome come together
elongation – tRNAs bring amino acids to the ribosome for incorporation into the polypeptide
termination – ribosome encounters a stop codon and releases polypeptide

18. Gene Expression Overview
Gene expression requires the participation of multiple types of RNA:
messenger RNA (mRNA) carries the information from DNA that encodes proteins
ribosomal RNA (rRNA) is a structural component of the ribosome
transfer RNA (tRNA) carries amino acids to the ribosome for translation

19. Gene Expression Overview
Gene expression requires the participation of multiple types of RNA:
small nuclear RNA (snRNA) are involved in processing pre-mRNA
signal recognition particle (SRP) is composed of protein and RNA and involved in directing mRNA to the RER
micro-RNA (miRNA) are very small and their role is not clear yet

20. Prokaryotic Transcription
Prokaryotic cells contain a single type of RNA polymerase found in 2 forms:
core polymerase is capable of RNA elongation but not initiation
holoenzyme is composed of the core enzyme and the sigma factor which is required for transcription initiation

22. Prokaryotic Transcription
A transcriptional unit extends from the promoter to the terminator.
The promoter is composed of
a DNA sequence for the binding of RNA polymerase
the start site (+1) – the first base to be transcribed

23. Prokaryotic Transcription
During elongation, the transcription bubble moves down the DNA template at a rate of 50 nucleotides/sec.
The transcription bubble consists of
RNA polymerase
DNA template
growing RNA transcript

25. Prokaryotic Transcription
Transcription stops when the transcription bubble encounters terminator sequences
this often includes a series of A-T base pairs
In prokaryotes, transcription and translation are often coupled – occurring at the same time

28. Eukaryotic Transcription
RNA polymerase I transcribes rRNA.
RNA polymerase II transcribes mRNA and some snRNA.
RNA polymerase III transcribes tRNA and some other small RNAs.
Each RNA polymerase recognizes its own promoter.

29. Eukaryotic Transcription
Initiation of transcription of mRNA requires a series of transcription factors
transcription factors – proteins that act to bind RNA polymerase to the promoter and initiate transcription

30. Eukaryotic pre-mRNA Splicing
In eukaryotes, the primary transcript must be modified by:
addition of a 5’ cap
addition of a 3’ poly-A tail
removal of non-coding sequences (introns)

31. Eukaryotic pre-mRNA Splicing
The spliceosome is the organelle responsible for removing introns and splicing exons together.
Small ribonucleoprotein particles (snRNPs) within the spliceosome recognize the intron-exon boundaries
introns – non-coding sequences
exons – sequences that will be translated

32. tRNA and Ribosomes
tRNA molecules carry amino acids to the ribosome for incorporation into a polypeptide
aminoacyl-tRNA synthetases add amino acids to the acceptor arm of tRNA
the anticodon loop contains 3 nucleotides complementary to mRNA codons

38. tRNA and Ribosomes The ribosome has multiple tRNA binding sites:
P site – binds the tRNA attached to the growing peptide chain
A site – binds the tRNA carrying the next amino acid
E site – binds the tRNA that carried the last amino acid

40. tRNA and Ribosomes The ribosome has two primary functions:
decode the mRNA
form peptide bonds
peptidyl transferase is the enzymatic component of the ribosome which forms peptide bonds between amino acids

41. Translation
In prokaryotes, initiation of translation requires the formation of the initiation complex including
an initiator tRNA charged with N-formylmethionine
the small ribosomal subunit
mRNA strand
The ribosome binding sequence of mRNA is complementary to part of rRNA

43. Translation
Elongation of translation involves the addition of amino acids
a charged tRNA binds to the A site if its anticodon is complementary to the codon at the A site
peptidyl transferase forms a peptide bond
the ribosome moves down the mRNA in a 5’ to 3’ direction

46. Translation There are fewer tRNAs than codons.
Wobble pairing allows less stringent pairing between the 3’ base of the codon and the 5’ base of the anticodon.
This allows fewer tRNAs to accommodate all codons.

47. Translation
Elongation continues until the ribosome encounters a stop codon.
Stop codons are recognized by release factors which release the polypeptide from the ribosome.

49. Translation
In eukaryotes, translation may occur on ribosomes in the cytoplasm or on ribosomes of the RER.
Signal sequences at the beginning of the polypeptide sequence bind to the signal recognition particle (SRP)
The signal sequence and SRP are recognized by RER receptor proteins.

50. Translation The signal sequence/SRP holds the ribosome on the RER.
As the polypeptide is synthesized it passes through a pore into the interior of the endoplasmic reticulum.

52. Mutation: Altered Genes
Point mutations alter a single base.
base substitution mutations – substitute one base for another
transitions or transversions
also called missense mutations
nonsense mutations – create stop codon
frameshift mutations – caused by insertion or deletion of a single base

55. Mutation: Altered Genes
triplet repeat expansion mutations involve a sequence of 3 DNA nucleotides that are repeated many times
triplet repeats are associated with some human genetic diseases
the abnormal allele causing the disease contains these repeats whereas the normal allele does not

56. Mutation: Altered Genes
Chromosomal mutations change the structure of a chromosome.
deletions – part of chromosome is lost
duplication – part of chromosome is copied
inversion – part of chromosome in reverse order
translocation – part of chromosome is moved to a new location

59. Mutation: Altered Genes
Too much genetic change (mutation) can be harmful to the individual.
However, genetic variation (caused by mutation) is necessary for evolutionary change of the species.