8/14/2019 VI. Gene Function.docx

1/20

PROTEIN SYNTHESIS

Table of Contents

One-gene-one-protein|The structure of hemoglobin|Viruses contain DNA

RNA links the information in DNA to the sequence of amino acids in protein

Transcription: making an RNA copy of a DNA sequence|The Genetic Code

Protein Synthesis|Mutations redefined|Links

One-gene-one-protein |Back to Top

During the 1930s, despite great advances, geneticists had several frustrating questions

yet to answer:

What exactly are genes?

How do they work?

What produces the unique phenotype associated with a specific allele?

Answers from physics, chemistry, and the study of infectious disease gave rise to the

field of molecular biology. Biochemical reactions are controlled byenzymes,and

often are organized into chains of reactions known asmetabolic pathways.Loss ofactivity in a single enzyme can inactivate an entire pathway.

Archibald Garrod, in 1902, first proposed the relationship through his study of

alkaptonuria and its association with large quantities "alkapton". He reasoned

unaffected individuals metabolized "alkapton" (now called homogentistic acid) to

other products so it would not buildup in the urine. Garrod suspected a blockage of the

pathway to break this chemical down, and proposed that condition as "an inborn error

of metabolism". He also discovered alkaptonuria was inherited as a recessive

Mendelian trait.

George Beadle and Edward Tatum during the late 1930s and early 1940s established

the connection Garrod suspected between genes and metabolism. They used X rays to

cause mutations in strains of the moldNeurospora. These mutations affected a single

genes and single enzymes in specific metabolic pathways. Beadle and Tatum

proposed the "one gene one enzyme hypothesis" for which they won the Nobel Prize

in 1958.

http://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#One-gene-one-proteinhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#One-gene-one-proteinhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#The%20structure%20of%20hemoglobinhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#The%20structure%20of%20hemoglobinhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#The%20structure%20of%20hemoglobinhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Viruses%20contain%20DNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Viruses%20contain%20DNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Viruses%20contain%20DNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#RNA%20links%20the%20informationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#RNA%20links%20the%20informationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Transcription:%20making%20an%20RNA%20cohttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Transcription:%20making%20an%20RNA%20cohttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#The%20Genetic%20Codehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#The%20Genetic%20Codehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#The%20Genetic%20Codehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Protein%20Synthesishttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Protein%20Synthesishttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Mutations%20redefinedhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Mutations%20redefinedhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Mutations%20redefinedhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Linkshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Linkshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Linkshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossE.html#enzymeshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossE.html#enzymeshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossE.html#enzymeshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossM.html#metabolic%20pathwayhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossM.html#metabolic%20pathwayhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossM.html#metabolic%20pathwayhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossM.html#metabolic%20pathwayhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossE.html#enzymeshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Linkshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Mutations%20redefinedhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Protein%20Synthesishttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#The%20Genetic%20Codehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Transcription:%20making%20an%20RNA%20cohttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#RNA%20links%20the%20informationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Viruses%20contain%20DNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#The%20structure%20of%20hemoglobinhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#One-gene-one-protein

8/14/2019 VI. Gene Function.docx

2/20

Since the chemical reactions occurring in the body are mediated by enzymes, and

since enzymes are proteins and thus heritable traits, there must be a relationship

between the gene and proteins. George Beadle, during the 1940s, proposed that

mutant eye colors inDrosophilawas caused by a change in one protein in a

biosynthetic pathway.

In 1941 Beadle and coworker Edward L. Tatum decided to examine step by step the

chemical reactions in a pathway. They usedNeurospora crassaas an experimental

organism. It had a short life-cycle and was easily grown. Since it ishaploidfor much

of its life cycle, mutations would be immediately expressed. The meiotic products

could be easily inspected. Chromosome mapping studies on the organism facilitated

their work.Neurosporacan be grown on a minimal medium, and it's nutrition could

be studied by its ability to metabolize sugars and other chemicals the scientist could

add or delete from the mixture of the medium. It was able to synthesize all of the

amino acids and other chemicals needed for it to grow, thus mutants in synthetic

pathways would easily show up. X-rays induced mutations inNeurospora, and the

mutated spores were placed on growth media enriched with all essential amino acids.

Crossing the mutated fungi with non-mutated forms produced spores which were then

grown on media supplying only one of the 20 essential amino acids. If a spore lacked

the ability to synthesize a particular amino acid, such as Pro (proline), it would only

grow if the Proline was in the growth medium. Biosynthesis of amino acids (the

building blocks of proteins) is a complex process with many chemical reactions

mediated by enzymes, which if mutated would shut down the pathway, resulting in

no-growth. Beadle and Tatum proposed the "one gene one enzyme"theory. One gene

codes for the production of one protein. "One gene one enzyme" has since been

modified to "one gene one polypeptide"since many proteins (such as hemoglobin) are

made of more than one polypeptide.

http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossH.html#haploidhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossH.html#haploidhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossH.html#haploidhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossO.html#%22one%20gene,%20one%20enzyme%20hypothesihttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossO.html#%22one%20gene,%20one%20enzyme%20hypothesihttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossO.html#%22one%20gene,%20one%20polypeptide%20hypohttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossO.html#%22one%20gene,%20one%20polypeptide%20hypohttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossO.html#%22one%20gene,%20one%20polypeptide%20hypohttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossO.html#%22one%20gene,%20one%20enzyme%20hypothesihttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossH.html#haploid

8/14/2019 VI. Gene Function.docx

3/20

8/14/2019 VI. Gene Function.docx

4/20

The Beadle and Tatum experiment that suggested the one gene one enzyme

hypothesis. Images from Purves et al., Life: The Science of Biology, 4th Edition, by

Sinauer Associates (www.sinauer.com)and WH Freeman (www.whfreeman.com),

used with permission.

The Structure of Hemoglobin |Back to Top

Linus Pauling used electrophoresis to separatehemoglobinmolecules. Sickle-cell

anemia (h) is a recessive allele in which a defective hemoglobin is made, ultimately

causing pain and death to those individuals homozygous recessive for the trait.

Pauling reasoned that if Beadle and Tatum were correct, there should be a slight (but

detectable) difference between the structure of a normal (HH) and sickle cell (hh)

hemoglobin due to genetic differences. Heterozygotes (Hh, also sampled by Pauling)

make both normal and "sickle cell" hemoglobins. Later, Vernon Ingram discovered

that the normal and sickle-cell hemoglobins differ by only 1 (out of a total of

300)amino acids.

Viruses Contain DNA |Back to Top

The coats of viruses act asantigens,initiating an antigen-specificantibodyresponse.

Remember that vaccines work by either prompting the immune system to make

antibodies or by supplying antibodies. If a virus (or anything else for that matter)

mutates its antigens, the immune system is forever playing catch-up.

http://www.sinauer.com/http://www.sinauer.com/http://www.sinauer.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossH.html#hemoglobinhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossH.html#hemoglobinhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossH.html#hemoglobinhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#amino%20acidshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#amino%20acidshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#amino%20acidshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#antigenshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#antigenshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#antigenshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#antibodieshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#antibodieshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#antibodieshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#antibodieshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#antigenshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#amino%20acidshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossH.html#hemoglobinhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www.whfreeman.com/http://www.sinauer.com/

8/14/2019 VI. Gene Function.docx

5/20

RNA Links the Information in DNA to the Sequence of Amino Acids in Protein

|Back to Top

Ribonucleic acid (RNA)was discovered after DNA. DNA, with exceptions in

chloroplasts and mitochondria, is restricted to the nucleus (in eukaryotes,

thenucleoidregion in prokaryotes). RNA occurs in the nucleus as well as in thecytoplasm (also remember that it occurs as part of theribosomesthat line the rough

endoplasmic reticulum).

Scientists for some time had suspected such a link between DNA and proteins. Cells

of developing embryos contain high levels of RNA. Rapidly growingE. colihas half

its mass as ribosomes. Ribosomes are 2/3 RNA (a type of RNA known asribosomal

RNAor rRNA) and 1/3 protein. RNA is synthesized from viral DNA in an infected

cell before protein synthesis begins. Some viruses, for example Tobacco Mosaic Virus

(TMV) have RNA in place of DNA. If RNA extracted from a virus was injected into a

host cell the cell began to make new viruses. Clearly RNA was involved in proteinsynthesis.

Crick's central dogma. Information flow (with the exception ofreverse transcription)

is from DNA to RNA via the process oftranscription,and thence to protein

viatranslation.Transcription is the making of an RNA molecule off a DNA template.

Translation is the construction of anamino acid sequence(polypeptide) from an RNA

molecule. Although originally called dogma, this idea has been tested repeatedly with

almost no exceptions to the rule being found (saveretroviruses).

http://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribonucleic%20acid%20(RNA)http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribonucleic%20acid%20(RNA)http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossN.html#nucleoidhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossN.html#nucleoidhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossN.html#nucleoidhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomeshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomeshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomeshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomal%20RNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomal%20RNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomal%20RNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomal%20RNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#reverse%20transcriptionhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#reverse%20transcriptionhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#reverse%20transcriptionhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#transcriptionhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#transcriptionhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#transcriptionhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#translationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#translationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#translationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#amino%20acid%20sequencehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#amino%20acid%20sequencehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#amino%20acid%20sequencehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#retroviruseshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#retroviruseshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#retroviruseshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#retroviruseshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#amino%20acid%20sequencehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#translationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#transcriptionhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#reverse%20transcriptionhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomal%20RNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomal%20RNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomeshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossN.html#nucleoidhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribonucleic%20acid%20(RNA)http://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contents

8/14/2019 VI. Gene Function.docx

6/20

The central dogma. Image from Purves et al., Life: The Science of Biology, 4th

Edition, by Sinauer Associates (www.sinauer.com)and WH Freeman

(www.whfreeman.com), used with permission.

The blue-background graphics throughout this chapter are from the University of

Illinois'DNA and Protein Synthesissite.

Messenger RNA (mRNA)is the blueprint for construction of a protein.Ribosomal

RNA(rRNA) is the construction site where the protein is made.Transfer RNA

(tRNA)is the truck delivering the proper amino acid to the site at the right time.

RNA has ribose sugar instead of deoxyribose sugar. The baseuracil(U) replaces

thymine (T) in RNA. Most RNA is single stranded, although tRNA will form a

"cloverleaf" structure due tocomplementarybase pairing.

http://www.sinauer.com/http://www.sinauer.com/http://www.sinauer.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.life.uiuc.edu/bio100/lessons/dna_and_protein_synthesis.htmlhttp://www.life.uiuc.edu/bio100/lessons/dna_and_protein_synthesis.htmlhttp://www.life.uiuc.edu/bio100/lessons/dna_and_protein_synthesis.htmlhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossM.html#messenger%20RNA%20(mRNA)http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossM.html#messenger%20RNA%20(mRNA)http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomal%20RNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomal%20RNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomal%20RNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomal%20RNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#transfer%20RNAs%20(tRNAs)http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#transfer%20RNAs%20(tRNAs)http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#transfer%20RNAs%20(tRNAs)http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#transfer%20RNAs%20(tRNAs)http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossU.html#uracilhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossU.html#uracilhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossU.html#uracilhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossC.html#complementary%20nucleotideshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossC.html#complementary%20nucleotideshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossC.html#complementary%20nucleotideshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossU.html#uracilhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#transfer%20RNAs%20(tRNAs)http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#transfer%20RNAs%20(tRNAs)http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomal%20RNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#ribosomal%20RNAhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossM.html#messenger%20RNA%20(mRNA)http://www.life.uiuc.edu/bio100/lessons/dna_and_protein_synthesis.htmlhttp://www.whfreeman.com/http://www.sinauer.com/

8/14/2019 VI. Gene Function.docx

7/20

Transcription: making an RNA copy of a DNA sequence |Back to Top

RNA polymeraseopens the part of the DNA to be transcribed. Only one strand of

DNA (thetemplate strand)is transcribed. RNA nucleotides are available in the region

of the chromatin (this process only occurs during Interphase) and are linked together

similar to the DNA process.

The Genetic Code: Translation of RNA code into protein |Back to Top

The code consists of at least three bases, according to astronomer George Gamow. To

code for the 20 essential amino acids agenetic codemust consist of at least a 3-base

set (triplet) of the 4 bases. If one considers the possibilities of arranging four things 3

at a time (4X4X4), we get 64 possible code words, or codons (a 3-base sequence on

the mRNA that codes for either a specific amino acid or a control word).

The genetic code was broken by Marshall Nirenberg and Heinrich Matthaei, a decade

after Watson and Crick's work. Nirenberg discovered that RNA, regardless of its

source organism, could initiate protein synthesis when combined with contents of

broken E. coli cells. By adding poly-U to each of 20 test-tubes (each tube having a

different "tagged" amino acid) Nirenberg and Matthaei were able to determine that the

codon UUU (the only one in poly-U) coded for the amino acid phenylalanine.

http://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#RNA%20polymerasehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#RNA%20polymerasehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#template%20strandhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#template%20strandhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#template%20strandhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossG.html#genetic%20codehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossG.html#genetic%20codehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossG.html#genetic%20codehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossG.html#genetic%20codehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossT.html#template%20strandhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossR.html#RNA%20polymerasehttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contents

8/14/2019 VI. Gene Function.docx

8/20

Steps in breaking the genetic code: the deciphering of a poly-U mRNA. Image from

Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates

(www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Likewise, an artificial mRNA consisting of alternating A and C bases would code for

alternating amino acids histidine and threonine. Gradually, a complete listing of the

genetic code codons was developed.

http://www.sinauer.com/http://www.sinauer.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.sinauer.com/

8/14/2019 VI. Gene Function.docx

9/20

Deciphering the code: poly CA. Image from Purves et al., Life: The Science of

Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman

(www.whfreeman.com), used with permission.

The genetic code consists of 61 amino-acid coding codons and three termination

codons, which stop the process of translation. The genetic code is thus redundant(degenerate in the sense of having multiple states amounting to the same thing), with,

for example, glycine coded for by GGU, GGC, GGA, and GGG codons. If a codon is

mutated, say from GGU to CGU, is the same amino acid specified?

The genetic code. Image from Purves et al., Life: The Science of Biology, 4th Edition,

by Sinauer Associates (www.sinauer.com)and WH Freeman (www.whfreeman.com),

used with permission.

Protein Synthesis |Back to Top

Prokaryotic gene regulation differs from eukaryotic regulation, but since prokaryotes

are much easier to work with, we focus on prokaryotes at this point.Promotersaresequences of DNA that are the start signals for the transcription of mRNA.

Terminators are the stop signals. mRNA molecules are long (500- 10,000

nucleotides).

Ribosomes are the organelle (in all cells) where proteins are synthesized. They consist

of two-thirds rRNA and one-third protein. Ribosomes consist of a small (inE. coli,

http://www.sinauer.com/http://www.sinauer.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.sinauer.com/http://www.sinauer.com/http://www.sinauer.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossPQ.html#promoterhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossPQ.html#promoterhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossPQ.html#promoterhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossPQ.html#promoterhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www.whfreeman.com/http://www.sinauer.com/http://www.whfreeman.com/http://www.sinauer.com/

8/14/2019 VI. Gene Function.docx

10/20

30S) and larger (50S) subunits. The length of rRNA differs in each. The 30S unit has

16S rRNA and 21 different proteins. The 50S subunit consists of 5S and 23S rRNA

and 34 different proteins. The smaller subunit has a binding site for the mRNA. The

larger subunit has two binding sites for tRNA.

Subunits of a ribosome. Image from Purves et al., Life: The Science of Biology, 4th

Edition, by Sinauer Associates (www.sinauer.com)and WH Freeman

(www.whfreeman.com), used with permission.

Transfer RNA (tRNA) is basically cloverleaf-shaped. tRNA carries the proper amino

acid to the ribosome when the codons call for them. At the top of the large loop arethree bases, theanticodon,which is the complement of thecodon.There are 61

different tRNAs, each having a different binding site for the amino acid and a

different anticodon. For the codon UUU, the complementary anticodon is AAA.

Amino acid linkage to the proper tRNA is controlled by the aminoacyl-tRNA

synthetases. Energy for binding the amino acid to tRNA comes from ATP conversion

to adenosine monophosphate (AMP).

http://www.sinauer.com/http://www.sinauer.com/http://www.sinauer.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#anticodonhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#anticodonhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossC.html#codonhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossC.html#codonhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossC.html#codonhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossC.html#codonhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossA.html#anticodonhttp://www.whfreeman.com/http://www.sinauer.com/

8/14/2019 VI. Gene Function.docx

11/20

Two models of tRNA. Image from Purves et al., Life: The Science of Biology, 4th

Edition, by Sinauer Associates (www.sinauer.com)and WH Freeman

(www.whfreeman.com), used with permission.

Translation is the process of converting the mRNA codon sequences into an amino

acid sequence. Theinitiator codon(AUG) codes for the amino acid N-formylmethionine (f-Met). No transcription occurs without the AUG codon. f-Met is

always the first amino acid in a polypeptide chain, although frequently it is removed

after translation. The intitator tRNA/mRNA/small ribosomal unit is called the

initiation complex. The larger subunit attaches to the initiation complex. After

theinitiationphase the message gets longer during theelongationphase.

http://www.sinauer.com/http://www.sinauer.com/http://www.sinauer.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossI.html#initiation%20codon%20(AUG)http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossI.html#initiation%20codon%20(AUG)http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossI.html#initiation%20codon%20(AUG)http://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossI.html#initiationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossI.html#initiationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossI.html#initiationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossE.html#elongationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossE.html#elongationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossE.html#elongationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossE.html#elongationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossI.html#initiationhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/BioBookglossI.html#initiation%20codon%20(AUG)http://www.whfreeman.com/http://www.sinauer.com/

8/14/2019 VI. Gene Function.docx

12/20

Translation. Image from Purves et al., Life: The Science of Biology, 4th Edition, by

Sinauer Associates (www.sinauer.com)and WH Freeman (www.whfreeman.com),

used with permission.

New tRNAs bring their amino acids to the open binding site on the ribosome/mRNA

complex, forming a peptide bond between the amino acids. The complex then shifts

along the mRNA to the next triplet, opening the A site. The new tRNA enters at the A

site. When the codon in the A site is a termination codon, a releasing factor binds to

the site, stopping translation and releasing the ribosomal complex and mRNA.

http://www.sinauer.com/http://www.sinauer.com/http://www.sinauer.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.sinauer.com/

8/14/2019 VI. Gene Function.docx

13/20

Termination. Image from Purves et al., Life: The Science of Biology, 4th Edition, by

Sinauer Associates (www.sinauer.com)and WH Freeman (www.whfreeman.com),

used with permission.

Often many ribosomes will read the same message, a structure known as a polysome

forms. In this way a cell may rapidly make many proteins.

http://www.sinauer.com/http://www.sinauer.com/http://www.sinauer.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.sinauer.com/

8/14/2019 VI. Gene Function.docx

14/20

Many ribosomes translating the same message, a polysome. Image from Purves et

al., Life: The Science of Biology, 4th Edition, by Sinauer Associates

(www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

The illustration below is from Genentech's Access Excellence site, which may be

reeached by clickinghere.The drawing is availableathttp://www.gene.com/ae/AB/GG/protein_synthesis.html

Mutations Redefined |Back to Top

We earlier defined mutations as any change in the DNA. We now can refine that

definition: a mutation is a change in the DNA base sequence that results in a change

of amino acid(s) in the polypeptide coded for by that gene. Alleles are alternate

sequences of DNA bases (genes), and thus at the molecular level the products of

alleles differ (often by only a single amino acid, which can have a ripple effect on an

organism by changing ). Addition, deletion, or addition of nucleotides can alter the

http://www.sinauer.com/http://www.sinauer.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.whfreeman.com/http://www.gene.com/ae/http://www.gene.com/ae/http://www.gene.com/ae/http://www.gene.com/ae/AB/GG/protein_synthesis.htmlhttp://www.gene.com/ae/AB/GG/protein_synthesis.htmlhttp://www.gene.com/ae/AB/GG/protein_synthesis.htmlhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www.gene.com/ae/AB/GG/protein_synthesis.htmlhttp://www.gene.com/ae/http://www.whfreeman.com/http://www.sinauer.com/

8/14/2019 VI. Gene Function.docx

15/20

polypeptide. Point mutations are the result of the substitution of a single base. Frame-

shift mutations occur when the reading frame of the gene is shifted by addition or

deletion of one or more bases. With the exception of mitochondria, all organisms use

the same genetic code. Powerful evidence for the common ancestry of all living

things.

Links |Back to Top

The Genetic Code

The genetic code consists of 64 triplets ofnucleotides.

These triplets are called codons.With three exceptions,

each codon encodes for one of the 20amino acidsused

in the synthesis of proteins. That produces someredundancy in the code: most of the amino acids being

encoded by more than one codon.

One codon, AUGserves two related functions:

it signals the start oftranslation

it codes for the incorporation of the amino acidmethionine(Met) into the

growing polypeptide chain

The genetic code can be expressed as either RNA codons or DNA codons. RNAcodons occur inmessenger RNA(mRNA) and are the codons that are actually "read"

during the synthesis of polypeptides (the process calledtranslation). But each mRNA

molecule acquires its sequence of nucleotides bytranscriptionfrom the corresponding

gene. Because DNA sequencing has become so rapid and because most genes are now

being discovered at the level of DNA before they are discovered as mRNA or as a

protein product, it is extremely useful to have a table of codons expressed as DNA. So

here are both.

Note that for each table, the left-hand column gives the first nucleotide of the codon,

the 4 middle columns give the second nucleotide, and the last column gives the third

nucleotide.

The RNA CodonsSecond nucleotide

Index to this page

The RNA Codons

The DNA Codons

Codon Bias Exceptions to the Code

http://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contentshttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/N/Nucleotides.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/N/Nucleotides.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/N/Nucleotides.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/AminoAcids.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/AminoAcids.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/AminoAcids.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Cys_met.gifhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Cys_met.gifhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Cys_met.gifhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.html#mRNAhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.html#mRNAhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.html#mRNAhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html#rna_codonshttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html#rna_codonshttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html#The_DNA_Codonshttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html#The_DNA_Codonshttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html#CodonBiashttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html#CodonBiashttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html#Exceptionshttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html#Exceptionshttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html#Exceptionshttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html#CodonBiashttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html#The_DNA_Codonshttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html#rna_codonshttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.html#mRNAhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Cys_met.gifhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/AminoAcids.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/N/Nucleotides.htmlhttp://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookprotsyn.html#Table%20of%20Contents

8/14/2019 VI. Gene Function.docx

16/20

U C A G

U

UUU Phenylalanine(Phe) UCU Serine(Ser) UAU Tyrosine(Tyr) UGU Cysteine(Cys) U

UUC Phe UCC Ser UAC Tyr UGC Cys C

UUA Leucine(Leu) UCA Ser UAA STOP UGA STOP A

UUG Leu UCG Ser UAG STOP UGG Tryptophan(Trp) G

C

CUU Leucine(Leu) CCU Proline(Pro) CAU Histidine(His) CGU Arginine(Arg) U

CUC Leu CCC Pro CAC His CGC Arg C

CUA Leu CCA Pro CAA Glutamine(Gln) CGA Arg A

CUG Leu CCG Pro CAG Gln CGG Arg G

A

AUU Isoleucine(Ile) ACU Threonine(Thr) AAU Asparagine(Asn) AGU Serine(Ser) U

AUC Ile ACC Thr AAC Asn AGC Ser C

AUA Ile ACA Thr AAA Lysine(Lys) AGA Arginine(Arg) A

AUG Methionine(Met)

or START

ACG Thr AAG Lys AGG Arg G

G

GUU ValineVal GCU Alanine(Ala)GAU Aspartic

acid(Asp)GGU Glycine(Gly) U

GUC (Val) GCC Ala GAC Asp GGC Gly C

GUA Val GCA AlaGAA Glutamic

acid(Glu)GGA Gly A

GUG Val GCG Ala GAG Glu GGG Gly G

The DNA Codons

These are the codons as they are read on thesense(5' to 3') strand of DNA. Except that

the nucleotide thymidine (T) is found in place of uridine (U), they read the same as

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/SenseStrand.pnghttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/SenseStrand.pnghttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/SenseStrand.pnghttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/SenseStrand.png

8/14/2019 VI. Gene Function.docx

17/20

RNA codons. However, mRNA is actually synthesized using theantisense strand of

DNA(3' to 5') as the template. [Discussion]

This table could well be called the Rosetta Stone of life.

The Genetic Code (DNA)

TTT Phe TCT Ser TAT Tyr TGT Cys

TTC Phe TCC Ser TAC Tyr TGC Cys

TTA Leu TCA Ser TAA STOP TGA STOP

TTG Leu TCG Ser TAG STOP TGG Trp

CTT Leu CCT Pro CAT His CGT Arg

CTC Leu CCC Pro CAC His CGC Arg

CTA Leu CCA Pro CAA Gln CGA Arg

CTG Leu CCG Pro CAG Gln CGG Arg

ATT Ile ACT Thr AAT Asn AGT Ser

ATC Ile ACC Thr AAC Asn AGC Ser

ATA Ile ACA Thr AAA Lys AGA Arg

ATG Met* ACG Thr AAG Lys AGG Arg

GTT Val GCT Ala GAT Asp GGT Gly

GTC Val GCC Ala GAC Asp GGC Gly

GTA Val GCA Ala GAA Glu GGA Gly

GTG Val GCG Ala GAG Glu GGG Gly

*When within gene; at beginning of gene, ATG signals start of translation.

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/SenseStrand.pnghttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/SenseStrand.pnghttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/SenseStrand.pnghttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/SenseStrand.pnghttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/SenseStrand.pnghttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/SenseStrand.png

8/14/2019 VI. Gene Function.docx

18/20

Codon Bias

All but two of the amino acids (Met and Trp) can be encoded by from 2 to 6 different

codons. However, the genome of most organisms reveals that certain codons are

preferred over others. In humans, for example, alanine is encoded by GCC four times

as often as by GCG. This probably reflects a greatertranslationefficiency by the

translation apparatus (e.g., ribosomes) for certain codons over their synonyms. [More]

Exceptions to the CodeThe genetic code is almostuniversal. The same codons are assigned to the same

amino acids and to the same START and STOP signals in the vast majority of genes in

animals, plants, and microorganisms. However, some exceptions have been found.

Most of these involve assigning one or two of the three STOP codons to an amino

acid instead.

Mitochondrial genes

When mitochondrial mRNA from animals or microorganisms (but not from plants) is

placed in a test tube with the cytosolic protein-synthesizing machinery (amino acids,

enzymes, tRNAs, ribosomes) it fails to be translated into a protein.

The reason: these mitochondria use UGA to encode tryptophan (Trp) rather than as a

chain terminator. When translated by cytosolic machinery, synthesis stops where Trp

should have been inserted.

In addition, most

animal mitochondria use AUA for methionine not isoleucine and

all vertebrate mitochondria use AGA and AGG as chain terminators.

Yeast mitochondria assign all codons beginning with CU to threonine instead

of leucine (which is still encoded by UUA and UUG as it is in cytosolic mRNA).

Plant mitochondria use the universal code, and this has permittedangiospermsto

transfer mitochondrial genes to their nucleus with great ease.

Link to discussion of mitochondrial genes.

Nuclear genes

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html#CodonBiashttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html#CodonBiashttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html#CodonBiashttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Plants.html#Angiospermshttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Plants.html#Angiospermshttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Plants.html#Angiospermshttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Endosymbiosis.html#The_Mitochondrial_Genomehttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Endosymbiosis.html#The_Mitochondrial_Genomehttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Plants.html#Angiospermshttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html#CodonBiashttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html

8/14/2019 VI. Gene Function.docx

19/20

Violations of the universal code are far rarer for nuclear genes.

A few unicellular eukaryotes have been found that use one or two (of their three)

STOP codons for amino acids instead.

Nonstandard Amino Acids

The vast majority of proteins are assembled from the 20 amino acids listed above even

though some of these may be chemically altered, e.g. by phosphorylation, at a later

time.

However, two cases have been found where an amino acid that is not one of the

standard 20 is inserted by a tRNAinto the growing polypeptide.

selenocysteine. This amino acid is encoded by UGA. UGA is still used as achain terminator, but thetranslation machineryis able to discriminate when a

UGA codon should be used for selenocysteine rather than STOP. This codon

usage has been found in certainArchaea,eubacteria,and animals (humans

synthesize 25 different proteins containing selenium).

pyrrolysine. In several species of Archaea and bacteria, this amino acid is

encoded by UAG. How the translation machinery knows when it encounters

UAG whether to insert a tRNA with pyrrolysine or to stop translation is not yet

known.

Prokaryotes and the Operon Model

Prokaryotes are sensitive to their environment, and their genetic activity is controlled by specific proteins

that interact directly with their DNA to quickly adjust to environmental changes. Genetic expressionis the

process where genotypes coded in the genes are exhibited by the phenotypes of the individuals. The

DNA is copied by the RNA and then synthesized into protein. The process of transcription, which is the

synthesis of RNA from a DNA template, is where the regulation of the gene expression is most likely to

occur. The default setting for prokaryotes appears to allow for the continual synthesis of protein to occur,

whereas in eukaryotes the system is normally off until activated.

An operon is a self-regulating series of genes that work in concert. An operon includes a special segment

of genes that are regulators of the protein synthesis, but do not code for protein, called the promoter and

operator. These segments overlap, and their interaction determines whether the process will start and

when it will stop. RNA polymerase must create RNA by moving along the chromosome and reading the

genes in the process of transcription.

RNA polymerase first attaches to the promoter segment, which signals the beginning of a particular DNA

sequence. If not blocked, it passes over the operator and reaches the protein-producing genes where it

creates the mRNA that instructs the ribosomes to create the desired protein. This process continues until

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Archaea.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Archaea.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Archaea.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Eubacteria.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Eubacteria.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Eubacteria.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Eubacteria.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Archaea.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html

8/14/2019 VI. Gene Function.docx

20/20

the system is blocked by repressor proteins. Repressors bind with the operator and prevent RNA

polymerase from proceeding to create mRNA by prohibiting access to the remainder of the protein-

producing genes. As long as the repressor is binding with the operator, no proteins are made. However,

when an induceris present, it binds with the repressor, causing the repressor to change shape and

release from the operator. When this happens, the RNA polymerase can proceed with transcription, and

protein synthesis begins and continues until another repressor binds with the operator. Refer to the

illustration Transcription regulation.

Transcription regulation.

The lacoperon model is probably the most studied and well known. In bacteria, such as E. coli, three

genes are part of an operon that code for three separate enzymes needed for the breakdown of lactose, a

simple sugar. A regulatory gene, located before the operon, continually makes repressor proteins that

bind with the operator and prohibit the function of RNA polymerase. The system therefore remains off

until a flood of lactose molecules binds with all available repressors and prevents their attachment to the

operator. When the operator is free, the production of the enzyme to break down lactose continues until

enough of the lactose molecules are broken down to then release repressors to recombine with the

operator to stop production of the enzymes.

Two additional types of operons exist that operate in the same way except for the function of the operator.

The trpoperon differs because the repressor is active only when bonded to a specific molecule. For the

remainder of the time, it remains unbonded and inactive in the absence of that molecule. Finally, in a

positive twist, activatorsare used by a third type of operon to bond directly with the DNA, which allows the

RNA polymerase to work more efficiently. Absent the activators, RNA polymerase proceeds at a slow

rate.

Read more:Inheritance: Regulation of Gene Expression in Prokaryotes and Eukaryotes |Infoplease.comhttp://www.infoplease.com/cig/biology/regulation-gene-expression-prokaryotes-

eukaryotes.html#ixzz2jZ1b9cuX

http://www.infoplease.com/cig/biology/regulation-gene-expression-prokaryotes-eukaryotes.html#ixzz2jZ1b9cuXhttp://www.infoplease.com/cig/biology/regulation-gene-expression-prokaryotes-eukaryotes.html#ixzz2jZ1b9cuXhttp://www.infoplease.com/cig/biology/regulation-gene-expression-prokaryotes-eukaryotes.html#ixzz2jZ1b9cuXhttp://www.infoplease.com/cig/biology/regulation-gene-expression-prokaryotes-eukaryotes.html#ixzz2jZ1b9cuXhttp://www.infoplease.com/cig/biology/regulation-gene-expression-prokaryotes-eukaryotes.html#ixzz2jZ1b9cuXhttp://www.infoplease.com/cig/biology/regulation-gene-expression-prokaryotes-eukaryotes.html#ixzz2jZ1b9cuXhttp://www.infoplease.com/cig/biology/regulation-gene-expression-prokaryotes-eukaryotes.html#ixzz2jZ1b9cuXhttp://www.infoplease.com/cig/biology/regulation-gene-expression-prokaryotes-eukaryotes.html#ixzz2jZ1b9cuXhttp://www.infoplease.com/cig/biology/regulation-gene-expression-prokaryotes-eukaryotes.html#ixzz2jZ1b9cuXhttp://www.infoplease.com/cig/biology/regulation-gene-expression-prokaryotes-eukaryotes.html#ixzz2jZ1b9cuXhttp://www.infoplease.com/cig/biology/regulation-gene-expression-prokaryotes-eukaryotes.html#ixzz2jZ1b9cuX