chmi 2227 - e.r. gauthier, ph.d. 1 chmi 2227e biochemistry i gene expression

CHMI 2227 - E.R. Gauthier, Ph.D. 1

CHMI 2227EBiochemistry I

Gene expression


Nature of the gene Genes are discrete regions of a DNA

molecule

Genes are permanent fixtures of your DNA;

Every single cell in your body (every 100 trillion [i.e. 10-15 cells] of them) has the exact, same DNA, the exact, same set of genes.

Genes have « encoding » property: The order of the nucleotide bases in a

given gene (their sequence) has meaning;

For example: the order of nucleotide bases in the myoglobin gene has all the required information to make the myoglobin protein.


SpeciesGenome size

Number of genes

Humans

2.9 billion base pairs

20,000-25,000

Drosophila (Drosophila melanogaster)

120 million base pairs

13,601

Yeast(Saccharomyces cerevisiae)


6, 275

Nematode (Caenorhabditis elegans)


19,000

E. coli

4.1 million base pairs

4,800

Arabidopsis (Arabidopsis thaliana)


25,000


Nature of the gene But: chimps,

humans and even worms have the SAME NUMBER OF GENES…

Moreover, most of these genes are SHARED between these three species…

What the %$#@?


Nature of the gene Genes can be turned on or

off (i.e. regulated): Temporally: e.g. during

development;

Spatially: e.g. turned on in the brain/ turned off in the liver.

Timing and location (i.e. regulation) of gene expression is more important than the actual number of genes.

Different homeotic (Hox) genes (colors) are turned on (expressed) at specific time during development and lead to the formation of specific body structures.


What happens when gene expression is screwed-up?

Homeotic genes are responsible for the development of discrete regions of the body: Antp (antennapedia) specifies the formation

of legs wings/thorax (flies) / thorax (humans) Dfd (deformed) specifies the formation of the

head (flies)/neck (humans)

If the Antp gene is expressed in the same cells as Dfd, legs will grow on the head of the fly. That’s what happens in flies bearing the Antennapedia mutation.

Antennapediamutation

Normal fly


Central dogma of molecular biology


Transcription: turning on a gene Each gene is preceded by a stretch of DNA called the promoter;

The promoter has DNA sequences that allow the recruitment of a distinct set of proteins called transcription factors;

These transcription factors help to recruit RNA polymerase, the enzyme which catalyses the synthesis of an RNA molecule complementary and antiparallel to one of the DNA strands of the gene (the template strand).

Promoter

Transcriptionfactors


Promoters Two major sequences are found in bacterial promoters:

TATA box (aka Pribnow box): Centered 10 bp away from the transcription initiation site (denoted

+1 below); Directly binds RNA pol Tells the RNA pol where to start transcription

-35 box: Centered 35 bp away from the transcription initiation site Directly binds RNA pol Helps to stabilize the binding of RNA pol to the promoter


Promoters Variations in the nucleotide sequence of

the promoter are responsible for changes in the timing of gene expression;


Transcription


Transcription

(5’ 3’)Messenger RNA

(mRNA) is antiparallel to template strand

Complementarity


mRNAs are modified in eukaryotes


mRNAs are modified in eukaryotes

Introns: part of the gene which is transcribed but NOT found in the mRNA.Exons: part of the gene which ends up in the mRNA after transcription.

In bacteria, the mRNA is nice and ready to make proteins (i.e. being translated) as soon as it is produced;

In eukaryotes, the mRNA needs to be further processed before it can be translated: Removal of introns splicing

Addition of a non-coded GTP nucleotide at the 5’ end of the mRNA capping

Addition of 50-200 non-coded adenosine residues at the 3’end of the mRNA polyadenylation

Export of the mRNA out of the nucleus and into the cytoplasm (because translation ONLY occurs in the cytoplasm).


mRNAs are translated into proteins During translation, the nucleotide

sequence of the mRNA is read and decoded into an amino acid sequence.


Translation

To translate an mRNA into a protein, the following ingredients are needed:

mRNA template Amino acids Transfer RNA (tRNA):

adaptor between amino acid and mRNA In charge of converting the nucleotide sequence code into

an amino acid sequence. Ribosomes:

organelles directing the translation process.


Transfer RNA (tRNA)

Short RNA molecule (between 73 and 95 nucleotides long);

Has two major features: The acceptor arm: where a specific amino

acid is covalently coupled;

The anticodon arm: has a 3-nucleotide sequence: the anticodon The anticodon base pairs with a

complementary and antiparallel, 3 nucleotide sequence on the mRNA: the codon;

The genetic code is the relationship between the sequence of a codon with a specific amino acid.


The genetic code Each tRNA is bound to a unique, specific amino

acid;

The nature of this amino acid depends on the sequence of the anticodon;

Since the anticodon on the tRNA base pairs with the codon on the mRNA, there is a relationship between the sequence of the codon on the mRNA and the amino acid bound to the tRNA: this relationship is the GENETIC CODE.

Thus, in this example, the mRNA codon 5’UGU3’ codes for the amino acid Cys.

The genetic code is (almost) universal: the meaning of each codon is (pretty much) the same whatever organism is studied.

5’ 3’

3’ 5’AU

mRNA


The genetic code


Translation Translation is the phenomenon whereby the mRNA code (i.e. the

sequence of codons) is decoded into an amino acid sequence;

Translation involves three major steps: Initiation: recognition of the translation starting point by the ribosome

and a special tRNA;

Elongation: successive binding of tRNAs to the ribosome; formation of a peptide bond between an incoming amino acid and the

growing polypeptide chain; translocation of the ribosome to decode the next codon;

Termination: One of three « stop » codons reaches the ribosome The ribosome is dissociated, freeing the mRNA and the completed

polypeptide;


Translation - Initiation

The initiation codon is ALWAYS AUG Methionine

fMET = N-formyl methionine

http://biology.unm.edu/ccouncil/Biology_124/Images/RNAtranslation.jpeg


Translation - Elongation

Peptide bond: synthesized by the « peptidyl transferase » enzyme on the large ribosomal subunit

Translocation

http://biology.unm.edu/ccouncil/Biology_124/Images/RNAtranslation.jpeg


Translation - Termination

Three « Stop » codons exist: UGA; UAA, UAGhttp://biology.unm.edu/ccouncil/Biology_124/Images/RNAtranslation.jpeg


Protein folding

Change in cell behavior

Change in organism

Adaptation to environment

Cue from environment (hormones, temperature, etc)

http://www.contexo.info/DNA_Basics/images/gene_expression.gif

Protein function

chmi 2227 - e.r. gauthier, ph.d. 1 chmi 2227e biochemistry i gene expression

Documents

myoglobin gene

antp gene

given gene

geneeach gene

homeotic genes

set of genes

timing of gene expressionchmi

regulation of gene expression