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Genes and How They Work. Chapter 15. 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

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the nature of genes
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.

the nature of genes3
The Nature of Genes

Evidence for the function of genes came from studying fungus.

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
the nature of genes4
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.
the nature of genes6
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.

the nature of genes7
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.

the genetic code
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.

the genetic code11
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
the genetic code12
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.

the genetic code14
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.

gene expression overview
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

gene expression overview16
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
gene expression overview17
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
gene expression overview18
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

gene expression overview19
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

prokaryotic transcription
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
prokaryotic transcription22
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
prokaryotic transcription23
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
prokaryotic transcription25
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

eukaryotic transcription
Eukaryotic Transcription

RNA polymerase Itranscribes rRNA.

RNA polymerase II transcribes mRNA and some snRNA.

RNA polymerase IIItranscribes tRNA and some other small RNAs.

Each RNA polymerase recognizes its own promoter.

eukaryotic transcription29
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
slide30

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)
slide31

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
trna and ribosomes
tRNA and Ribosomes

tRNAmolecules carry amino acids to the ribosome for incorporation into a polypeptide

  • aminoacyl-tRNA synthetasesadd amino acids to the acceptor arm of tRNA
  • the anticodon loop contains 3 nucleotides complementary to mRNA codons
trna and ribosomes35
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
trna and ribosomes37
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

translation
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

translation40
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
translation43
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.

translation44
Translation

Elongation continues until the ribosome encounters a stop codon.

Stop codons are recognized by release factors which release the polypeptide from the ribosome.

translation46
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.

translation47
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.

mutation altered genes
Mutation: Altered Genes

Point mutations alter a single base.

  • base substitution mutations – substitute one base for another
    • transitionsor transversions
    • also called missense mutations
  • nonsense mutations – create stop codon
  • frameshift mutations – caused by insertion or deletion of a single base
mutation altered genes51
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
mutation altered genes52
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
mutation altered genes54
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.