1 The traditional definitions imply that functional and structural - - PDF document

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A primer on the structure and function of genes What is the definition of a gene?

GENE: the genetic element which is transmitted from parent to offspring during the process of reproduction that influences hereditary traits.

• Beadle and Tatum (1941): one gene, one-enzyme hypothesis
• one-gene, one-polypeptide hypothesis

GENE: is the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the codon region (leader and trailer) as well as intervening sequences (introns) between individual coding segments (exons). [Note this is also the definition of a cistron.]

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The traditional definitions imply that functional and structural diversity arises via local changes in the DNA sequence Important motivation for private backing of human genome sequencing Human Genome Project (HGP) and the definition of a gene

~13,000 Fruit fly ~19,000 Nematode ~30,000 Mouse ~30,000 Human Number of genes Genome

HGP:

• many genes encode more than one protein
• much functional divergence between humans, chimpanzee, and mice due to

changes in gene regulation (Clark et al. 2003)

• We should reconsider our definition of a gene if we want to define it according

to its function

• genome-function relationship is more complex than we (some) had thought

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What is a gene? 1. a unit of inheritance 2. a location on a chromosome 3. a sequence of base pairs 4. a transcriptional unit 5. a determinant of phenotype They are all correct. Types of genes: 1. Protein-coding genes 2. Regulatory signal genes 3. RNA encoding genes

RNA start DNA Introns

Exon 1 Exon 2 Exon 3

Regulatory Signals

• 220

+2400 Poly-A addition site

1. Protein coding genes

• This type easily fits the modern definitions, in that they transcribe a

messenger RNA (mRNA) that is used as a template for making a polypeptide.

• These genes are sometimes called structural genes
• We can see the problems with defining a gene as a segment of DNA

involved in producing a polypeptide chain, as this differs among eukaryotes, prokaryotes and virus’s.

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Consider alternative splicing in eukaryotes: One definition of a gene: a segment of DNA that encodes a polypeptide How many genes?

• 2. Regulatory signal genes. These are elements or motifs of DNA that are not

transcribed, and serve as signals to regulate the processing of the DNA molecule. The prominent types of such genes are:

• Replicator signals: These signal the initiation or termination of DNA replication.
• Telomeres: These are repeats of specific DNA sequences found at the ends of eukaryotic

chromosomes.

• Segregator signals: These determine the specific sites at which the segregation machinery of the

cell attaches to the chromosomes for the process of mitosis and meiosis.

• Recombination signals: The sequence element that provides a recognition site for a recombination

enzyme.

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• 3. RNA encoding genes. In contrast to mRNA of protein coding genes,

the final product of the RNA gene is only transcribed RNA. RNA molecules specified by such genes fold into complex structures that associate with proteins to form a sort of “chemical machine”. i. Transfer RNA (tRNA) ii. Ribosoaml RNA (rRNA) iii. Small nuclear RNA (snRNA) iv. Others: (snaRNA, microRNA, gRNA)

A primer on the structure and function of proteins

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Protein is derived from the Greek “proteios”, for “of first rank” (Jöns J. Berzelius, 1838) Examples of protein functionality:

• Enzymatic catalysis
• Transport and Storage
• Motion
• Signaling and communication
• Immunity
• Control of gene expression

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Polypeptides are built by using the peptide bond 20 amino acids are defined by 20 unique R-group side-chains

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D E M I CS-S A S CS-H G N Q V L P T R K H Y F W Polar Aromatic Aliphatic Negative Charged Hydrophobic Positive Small Tiny

Overlapping physiochemical properties of amino acids The structural hierarchy of a protein can be described at four levels

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Prosthetic group: any small, non polypeptide, molecule that is tightly bound to a protein

• essential role in protein function
• influence 3D fold
• ex: Heme molecular of haemoglobin.

Globin fold > 800 million years old

• association can be covalent or non-

covalent

• not all proteins have prosthetic groups

Post-translational modifications: covalent modifications that affect the structure and function of proteins

• Disulphide bridges
• Polypeptide cleavage
• Modification of amino acid side chains
• Addition of carbohydrates
• Addition of lipids

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Enzymes convert preproinsulin into insulin:

• 1. Preproinsulin is cleaved by an enzyme almost immediately after the chain of 108 amino acids is

synthesized.

• 2. Proinsulin is folded in such a way that the state of lowest free energy at this point is the one in

which the disulfide bridges can be formed.

• 3. Lastly, enzymes remove the C-chain to produce the insulin. By utilizing intermediate stages, the

cell is able to form a stable conformation (insulin) that is not the one with the lowest free energy.

The native conformation of insulin is NOT the one with the lowest free energy

Note: Free energy is a measure of the potential energy of a biological reaction. Free energy determines the direction of the reaction, with the reaction going in the direction of lower free energy.

Protein functionality derives from 3D conformation:

1. Recognize and bind variety of molecules: i. Heme ii. Other native proteins iii. Foreign proteins iv. RNA and DNA v. Etc.

e.g., regulatory proteins binding directly with DNA

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Protein functionality derives from 3D conformation:

• 2. Complimentary

surfaces or clefts:

i. Very precise 3D surfaces ii. Side chain interactions via physiochemical properties of side- chains

Protein functionality derives from 3D conformation:

• 3. Precise orientation =

increased catalytic power: i. Reaction rate increased > 1 million fold by enzymes ii.

• ptimal distance

iii.

• ptimal orientation

iv. Charged R-groups important in reactions

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Protein functionality derives from 3D conformation:

• 3. Proteins transmit

molecular signals: i. Allosteric control ii. Conformational changes iii. Hg uses this to “perceive” changes in its environment

30,000 protein-coding genes of mice and men:

• 1. Effect of mutations in active sites, etc.
• 2. Mix and match regulatory elements
• 3. Alternative splicing of exons
• 4. Post-translational modifications