Question

1. Examine the DNA sequence shown below. How many possible reading frames does this piece of DNA have? Explain where they are. Which one can be used and how do you know?

5'-AGTCGA TCGAACGGTCA TCG-3' 3'-TCAGCTAGCTTGCCAGTAGC-5'

2. What feature of eukaryotes makes annotation more difficult?

3. Describe the process whereby DNA is transferred from Agrobacterium to plants.

Answer 1

A double-stranded DNA molecule has six reading frames. Both strands are read in the 5′→3′ direction. Each strand has three reading frames, depending on which nucleotide is chosen as the starting position. The key to the success of ORF scanning is the frequency with which termination codons appear in the DNA sequence.there are actually six reading frames: three on the positive strand, and three (which are read in the reverse direction) on the negative strand.

most DNA is found in a compartment within the cell called a nucleus. It is known as nuclear DNA. In addition to nuclear DNA, a small amount of DNA in humans and other complex organisms can also be found in the mitochondria. This DNA is called mitochondrial DNA (mtDNA).DNA is found in nearly all living cells. However, its exact location within a cell depends on whether that cell possesses a special membrane-bound organelle called a nucleus. Organisms composed of cells that contain nuclei are classified as eukaryotes, whereas organisms composed of cells that lack nuclei are classified as prokaryotes. In eukaryotes, DNA is housed within the nucleus, but in prokaryotes, DNA is located directly within the cellular cytoplasm, as there is no nucleus available.

Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes.

• a membrane-bound nucleus.
• numerous membrane-bound organelles (including the endoplasmic reticulum, Golgi apparatus, chloroplasts, and mitochondria)
• several rod-shaped chromosomes.

Eukaryotes contain organelles surrounded by a membrane like a nucleus and mitochondria. They also have ribosomes, cytoplasm, cell membrane, cell walls, and cilia/flagella.The unique about the DNA of eukaryotes are the DNA of eukaryotes is surrounded by a nucleus and is a double helix or twisted ladder.

The genomes of most eukaryotes are larger and more complex than those of prokaryotes. This larger size of eukaryotic genomes is not inherently surprising, since one would expect to find more genes in organisms that are more complex. However, the genome size of many eukaryotes does not appear to be related to genetic complexity. For example, the genomes of salamanders and lilies contain more than ten times the amount of DNA that is in the human genome, yet these organisms are clearly not ten times more complex than humans.his apparent paradox was resolved by the discovery that the genomes of most eukaryotic cells contain not only functional genes but also large amounts of DNA sequences that do not code for proteins. The difference in the sizes of the salamander and human genomes thus reflects larger amounts of non-coding DNA, rather than more genes, in the genome of the salamander. The presence of large amounts of noncoding sequences is a general property of the genomes of complex eukaryotes.

Genetic transformation of host plants by Agrobacterium tumefaciens and related species represents a unique model for natural horizontal gene transfer. Almost five decades of studying the molecular interactions between Agrobacterium and its host cells have yielded countless fundamental insights into bacterial and plant biology, even though several steps of the DNA transfer process remain poorly understood. Agrobacterium spp. may utilize different pathways for transferring DNA, which likely reflects the very wide host range of Agrobacterium. Furthermore, closely related bacterial species, such as rhizobia, are able to transfer DNA to host plant cells when they are provided with Agrobacterium DNA transfer machinery and T-DNA. Homologs of Agrobacterium virulence genes are found in many bacterial genomes, but only one non-Agrobacterium bacterial strain, Rhizobium etli CFN42, harbors a complete set of virulence genes and can mediate plant genetic transformation when carrying a T-DNA-containing plasmid.

Pathways of DNA Transfer to Plants from Agrobacterium

Step 1: Virulence Induction and Generation of Single-Stranded T-DNA

Step 2: Export of the T-DNA and Effector Proteins and Cell-to-Cell Interactions

Step 3: Entry and Subcellular Sorting of T-DNA and Effector Proteins in the Host Cell

Step 4: T-DNA Integration in the Host Chromosomal DNA