Plant biology and genetics background Information

Gene

A gene is a functional unit of a DNA sequence. Typically, genes are transcribed into mRNA which is then translated into a protein. Genes typically contain a promoter region, a coding region, and a terminator region. The promoter region contains RNA polymerase binding sites and often has a role in regulating the expression of the gene. The coding region of the gene is the part that codes for polypeptide chain that makes up the protein, if a protein is the gene product. The coding region is made up of codons. Each codon is three nucleotides long and corresponds to one of the twenty amino acids. The terminator region can have a regulatory role for gene expression, but is not always required.

Locus

A locus is the location on a chromosome at which a gene for a trait resides.

Allele

An allele is a variant of a gene. If there is a gene for eye color, there might an allele that leads to blue eyes and a different allele that leads to brown eyes.

DNA

DNA stands for deoxyribonucleic acid. A strand of DNA is a polymer, or chain, of nucleotides. Each nucleotide contains three parts, a five carbon sugar, a phosphate group, and a base. The base is typically adenine, guanine, cytosine, or thymine. DNA can be single stranded, but is typically double stranded in an anti-parallel fashion. The opposing strands of DNA will base pair with each other with adenine matching thymine and guanine matching cytosine. DNA is stable and is the primary means of storing hereditary information.

RNA

RNA stands for ribonucleic acid. It is similar to DNA, but is less stable and can have several functions within a cell. mRNA, or messenger RNA, is the RNA message that is produced when a gene is transcribed. An mRNA sequence is then translated to produce a protein. RNA contains for bases like DNA, except the base uracil takes the place of thymine in RNA. Other types of RNA include siRNA (important for gene regulation / silencing), tRNA (important for codon recognition during translation), and rRNA (part of the ribosome, important for translation).

Protein

Proteins have many functions within a cell and are responsible for much of the cellular metabolism and structure. Proteins comprised of one or more precisely folded chains of aminoacids and may contain other modifications, such as glycosylation. Proteins with catalytic activity are called enzymes. Enzymes catalyze reactions by lowering the activation energy needed for a reaction to occur. This catalytic activity is essential for cell metabolism. Proteins can also act to regulate gene expression, facilitate cell to cell communication, or play a structural role in a cell.

Transcription

Transcription is the process by which RNA is synthesized from a complementary strand of DNA. RNA polymerases are the principle enzyme responsible for this process, though many proteins and this is a carefully regulated process.

Translation

Translation is the process by which a polypeptide chain is produced using a mRNA sequence as a template. Each codon, or three nucleotide sequence, on an mRNA codes for one amino acid, as specified by the nearly-universal genetic code. The ribosome is the primary catalytic unit responsible for translation. tRNAs recognize individual codons and bring in the correct amino acid to extend the polypeptide chain. The polypeptide chain folds to form the protein, which may undergo further post-translational modifications.

Intron

An intron is an intervening sequence of non-coding DNA within the coding region of a gene. Introns are only present in eukaryotes. Before translation, introns are removed from the mRNA sequence.

Exon

An exon is a coding DNA sequence withing the coding region of a gene. Exons are separated by introns. Exons can sometimes be spliced together in different ways to lead to the production of distinct protein products from a single gene.

Mendelian inheritance

In classic diploid mendelian inheritance, alleles segregate during meosis and the offspring inherits one allele for each gene from each parent. In the simplest case, a trait is controlled by the allele composition at a single gene locus and the alleles are either fully dominant or fully recessive. A Punnett square is a common and simple method to predict the genotypes and phenotypes of the progeny of a cross.

Dominant allele

An allele is dominant if one copy of the allele (out of two alleles present in a diploid organism) is sufficient to cause the phenotype associated with that allele. This is in contrast to a recessive allele, which requires that both alleles are present for the phenotype to be expressed.

Recessive allele

A recessive allele is an allele that is masked by a dominant allele – both alleles in a diploid organism must be recessive for the recessive phenotype to be displayed.

Genotype

The genotype is the allelic makeup of an organism.

Phenotype

The phenotype is the observable trait displayed by an organism.

RNA silencing

RNA silencing is a process by which RNA is degraded within a cell prior to being translated. Anti-sense RNA, an overly abundant amount of sense RNA can lead to RNA silencing. RNA silencing is a way of regulating the expression of genes and may help to protect plants and animals from viruses and transposons.

Traditional breeding

Traditional breeding techniques can be used to incorporate a desirable trait into a production variety of a crop species. Traditional breeding relies upon the genetic diversity that exists in a species. For example, suppose that production tomato species are susceptible to a particular virus but it is known that a wild variety of tomato is immune. The wild tomato can be crossed with production tomato. Hopefully, some or all of the offspring will be resistant to the virus. However, these offspring will likely lack many of the desirable traits of the production variety. Therefore, the resistant offspring are crossed back to the production variety for several generations until a resistant and desirable plant is obtained. This approach will not work if the desirable trait is not present in a variety that can reproduce with the production variety.

Transformation

The term transformation is generally used to refer to the introduction of foreign DNA into an organism. For plants, the creation of a stable transformant line typically means that a piece of foreign DNA has been integrated into the host genome Agrobacterium and biolistics are two common methods used for plants. Heat shock and electroporation and methods commonly used for other organisms. Because transformation events are usually rare (in relation to the total number of host cells) a marker gene is typically used to select for transformants.

Marker gene

Marker genes are typically used to select for cells/organisms that have been successfully transformed. The organism of interest in transformed with both a marker gene and a gene of interest at the same time and the marker gene is used to select for organism that have likely received both genes. Marker genes often confer the ability for an organism to survive on a selective media, though they can also lead to a color change or some other easily selectable trait. Common examples are resistance genes for antibiotics or herbicides or GUS for a color change.

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