Genetic Code Chapter 17: page 306-309

Mutations Chapter 17: page 322-325

Transposons Chapter 19: page 360-361

Mutations

The Genetic Code is Universal

All living things use the same 4 bases

All living things use the same code: codons code for the same amino acid no matter what the organism

The Genetic Code is Redundant64 different

codons on mRNABut only 20

different amino acids

Conclusion?

More than one codon can code for the same amino acid.

Fig. 17.4

The Genetic Code is Redundant64 different codons

on mRNABut only 45

different tRNA molecules

Conclusion?

Some tRNAs recognize more than one codon.

Wobble Hypothesis

Base pairing rules are flexible in the wobble position

Wobble position: third base of the mRNA codon and its corresponding tRNA anticodon

Fig. 17.4

Inosine in the wobble positionInosine:

a modified form of adenine that is found in tRNA (anticodon)

can form H bonds with U, C, or A on the mRNA

From http://bio.winona.msus.edu/berg/ChemStructures/Inos-ade.gif

Inosine

Adenosine

Inosine in the wobble positionExample: tRNA anticodon CGI Can bind to codons

GCU, GCC and GCA All result in the

addition of the amino acid alanine

Fig. 17.4

Reading the Genetic Code

Characteristics of the CodeDegenerate / Redundant

There are 64 codons, but only 20 amino acids

The same amino acid may be coded by more than one codon

E.g. GCU and GCC both specify alanineNo ambiguity

Each codon only specifies one amino acid

Marshall Nirenberg (1961) Deciphered first codon Awarded Nobel Prize in

1968 for the interpretation of the genetic code

Discovery Channel 100 Greatest Discoveries – History of Genetics (Nirenberg @ 25:25-28:49) http://www.youtube.com/watch?v=0qgMd0obEkc

http://profiles.nlm.nih.gov/ps/access/JJBBWR.jpghttp://upload.wikimedia.org/wikipedia/commons/thumb/1/10/Marshall_Nirenberg_performing_experiment.jpg/481px-Marshall_Nirenberg_performing_experiment.jpg

Nirenberg’s Experiment

Synthesized artificial mRNA with identical RNA nucleotidesE.g. UUUUUUUUUUUUUUUThus only 1 type of codon (e.g. UUU)Resulted only in one type of amino acid in

the polypeptide (e.g. phenylalanine)Repeated with other nucleotidesOther techniques used to decode mixed

triplets

Tutorial: Reading the Genetic Code http://learn.genetics.utah.edu/units/basics/transcribe/

Mutation

a change in the genetic material of an organism

genetic disorder or hereditary disease: harmful mutations in gametes that are passed onto the next generation

Origin/Cause of Mutation

Spontaneous: errors in the genetic machinery during DNA

replicationdue to enzymes

Induced: arising from exposure to mutagenic agents

Transposable elements:errors during recombination (crossing over)transposons

Mutagen

a substance that can cause mutations Physical mutagen

Radiation, UV light, x-raysChemical mutagen

Base analogues: chemical similar to normal DNA bases but

pair incorrectly during DNA replication e.g. used in a drug for treating HIV

Distort DNA helix interfering with replication e.g. ethidium bromide, used in gel

electrophoresis for visualizing DNAChanging pairing properties in bases

Effect of Mutations

Affects 3 levels: RNA codons:

Point mutation Frameshift mutation

Amino acid sequence on polypeptide: Missense Nonsense Silent

Protein function Negative Positive Neutral

Types of Mutations

Point mutationsFrameshift mutationsChromosomal mutations

Point Mutations: Substitution

a small change in a DNA basepair where one nucleotide is replaced with another

Frameshift Mutation:Insertion & Deletion Reading frame: triplet grouping (codons) of a

genetic message Frameshift mutation: number of nucleotides

added/lost is not a multiple of 3 thus altering the reading frame Insertion: addition of one or more nucleotide pairs

in a gene Deletion: loss of one of more nucleotide pairs in a

gene

No frameshift: number of nucleotides added/lost is a multiple of 3 Leads to extra or missing amino acid

Fig. 17.24

Frameshift Mutations

Frameshift deletion

Frameshift insertion

No frameshift

Effects of mutations on polypeptide

Missense mutation: altered codon codes for a different amino acid May or may not have an effect on protein function

Nonsense mutation: changes an amino acid codon into a stop codon Results in truncated protein. Most are digested by

the cell. often lethal at the embryonic stage

Silent mutation: altered codon codes for same amino acid No effect on protein function

Fig. 17.24Fig. 17.4

Missense Mutation

Example: Sickle Cell AnemiaSubstitution missense: A T changes

amino acid glutamine to valine

Fig. 17.24Fig. 17.4

Nonsense Mutation

Fig. 17.24Fig. 17.4

Silent Mutation

Wild Type: Two men sat and had hot teaMutationsTwo men Sat and had hot teaTwo men sat and had hot seaTwo me. Two men sat and had hot tte aTwo mes ata ndh adh ott ea

SilentMissenseNonsense

Frameshift InsertionFrameshift Deletion

Point/Frameshift Mutation Summary

Types Missense effect

Nonsense effect

Silent

Point Mutation

Substitution

Frameshift Insertion or

Deletion

No Frameshift Insertion or

Deletion

Point/Frameshift Mutation Summary

Types Missense effect

Nonsense effect

Silent

Point Mutation

Substitution

Frameshift Insertion or

Deletion

extensive

No Frameshift Insertion or

Deletion

(extra or

missing amino acid)

Effect of mutation on protein function / organism Negative mutations

Changes protein function to make it detrimental to the organism

From missense or nonsense mutations Example: most molecular biological research is related to

this idea Positive mutations

Changes protein function to benefit the organism From missense mutations Example: back mutations / reversions that restore original

sequence Example: antibiotic resistance

Neutral mutations Silent mutations: no change in amino acid Sometimes missense: change in amino acid without

changing protein function Example: mutations in introns doesn’t affect expressed

protein

HW Question

The genetic code is redundant but not ambiguous. Explain what that means.

MaCS Enrichment

The topic of transposons is for MaCS enrichment only

Transposons

DNA segments that naturally move around the genomeTransposable elementsMobile genetic elements

Transposons

Barbara McClintock was awarded the Nobel Prize in 1983 for her discovery of transposons in maize (corn)

Discovery Channel 100 Greatest Discoveries – History of Genetics (McClintock @ 11:18-16:10) http://www.youtube.com/watch?v=0qgMd0obEkc

http://profiles.nlm.nih.gov/ps/access/LLBBQQ.jpg

Transposon in humans

Almost half the human genome consists of transposons:Retrotransposons accounting 42% DNA transposons (most if not all are

inactive) accounting for 2-3% Reference: http://www.nature.com/nature/journal/v409/n6822/full/409860a0.html

No known function. Junk DNA.

Types of Bacterial TransposonsInsertion sequenceComposite transposon

Insertion Sequence

Simplest type of bacterial transposon Consists only of DNA needed for the act of

transposition Transposon contains:

gene for transposaseTransposase: enzyme that catalyzes movement

of transposon Inverted repeats

at ends of transposons where transposase binds

Fig 18.16

Insertion Sequence EffectCan cause mutations when they land in

DNA region that regulates gene expression or the coding region of a gene

Mutation due to insertion sequence is rare (1 in 10 million generations)

No known benefit

Composite Transposon

Longer transposon and more complexContain genes other than transposase Beneficial in bacterial reproduction

confer antibiotic resistance

Fig 18.18

Mechanism of TranspositionDNA transposon

Transposition by cut-and-paste mechanism

Transposition by replicative mechanismRetrotransposon

Transposition by an RNA intermediateUses reverse transcriptase

Animation

Transposons “Shifting Segments of the Genome” http://highered.mcgraw-hill.com/sites/dl/free/

0072556781/192785/anim0039.swf

Simple Transposition (cut-and-paste) http://highered.mcgraw-hill.com/sites/0072995246/

student_view0/chapter23/simple_transposition.html

Mechanism of Transposition: Replicative http://highered.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?

it=swf::535::535::/sites/dl/free/0072437316/120082/bio36.swf::Mechanism%20of%20Transposition

http://www.chrisdellavedova.com/wp-content/uploads/2008/01/transposons1.jpg

Mechanism of Cut-and-Paste Transposition

Transposase bind to both inverted repeats and target site

Cut out transposonCut open the target

siteJoin transposon to

target siteReseal DNA

Mechanism of Replicative Transposition

transposon replicated at original site

copy inserts into new site

original transposon still at original site

Retrotransposon

Transposons that transpose through an RNA intermediate

Abundant in plants (e.g. maize = corn)

Mechanism of Retrotransposon Movement

http://www.bio.miami.edu/~cmallery/150/gene/c7.19.16b.transposon.jpg

Mechanism of Retrotransposon Movement1. Retrotransposon RNA produced during

transcription2. Translation of RNA makes:

Reverse transcriptase: enzyme that converts RNA DNA

Enzymes that catalyze insertion of retrotransposon into target site

3. Retrotransposon DNA synthesized by reverse transcriptase action on RNA

4. DNA inserted into target site