The Plant Genome

The Plant Genome - Chapter 1, pgs 20-24

Outline

• Nucleus

• Dna packaging

• Central dogma

• Shout out to At

• Mendels’s genes

• Mutations

• Transposons

The Nucleus

• Chloroplast and mitochondria have their own sets of DNA

• Holds the DNA for the cell and shouts it out to the rest of the cell

• Surrounded by outer nuclear envelope

  • Dotted with nuclear pores= 

    • selective channels 

    • Made of nucleoporin proteins

  • Proteins destined for the nucleus have a nuclear localization signal (amino acid tag) on them that allows them access

• Chromosomes: DNA and associated proteins

• DNA is organized/

  •  wound around histones forming nucleosomes

    • Double helix wound around histones connected with linker dna

      • Linker dna is more accessible

  • Nucleosomes are condensed into a chromatin fiber

  • Chromatin fibers form looped domains

  • Looped domains form condensed chromatin

  • Sections of condensed chromatin form one little slot of a chromatid

    • Euchromatin the transcriptionall active form of chromatin/ available

    • Heterochromatin is unavailable/ hard to get to about 10% of the dna in the nucleaus 

CENTRAL DOGMA of MOLECULAR BIO

Step 1. The Expo

• Transcription 

  • RNA polymerase finds in the genome the message to be expressed and makes a copy of it

• The menu at a restaurant is like the genome and the order reader is rna polymerase

Step 2. The Sous/ Line Cooks

• Processing

  • Ribosomes send the message to make polypeptides

    • Some are coded to go to specific places 

    • Protein synth happens on ribosomes that are attached to the rough ER

• There are many line cooks making different components of your dish (Transfer RNAs) but the sous is the one who is overseeing the whole process(Ribosomes)

• Every 3 base sequences code for a specific protein/ chain of amino acids

Step 3. The runners

• Vesicles

• Proteins are completed and shuttled off to go where it is needed

  • Those proteins are a direct manifestation of the original section of dna 

• All of this is happening in therought  E.R and then like slide into transport vesicles that are cut off and then move

Thank you Arabidopsis thaliana for being the plant model organism 

• It is easy to mess with its genome > full genome sequence was published in 2000. 

Gregor Mendel - Founder of Genetics

• Born a peasant in 1822, entered a monastery in 1843, went to the uni of Vienna and studied math and botany

• First experiments reported in 1865 but largely ignored until after his death

  • Studied well-researched suited materials

  • Carefully designed experiments

  • Collected large amounts of data

  • Employed mathematical analysis

• His main question was the prevailing notion of Prevailing notion (prevailing until like 1900)

  • “Essences” blend together to create different gene expression

  • The issue was that that doesn’t like actually happen> eye color 

• Studied 7 characteristics 

  • Flower Position, flower color, stem length, pea shape, pea color, pod shape, and pod color

• Experiemental Rationale: mendel observed that tall peas had tall offspring

  • What would happen if he prevented one flower from pollinating itself, and fertilized it with the pollen from a different flower, from a different plant. 

    • Pollination and Fertilization (a quick review on perfect flowers)

1. Pollen develops in anthers

2. Eggs develop in the ovules of the ovary

3. Pollination - pollen to stigma

4. Pollen grain forms a single-cell pollen tube

5. Fertilization - pollen tube makes it to the ovule and combines with the egg and sometimes with the polar nuclei 

• His process

  • Crossed the pollen from a true breeding for yellow peas to a True breeding for green peas

    • The results were all the peas were yellow

  • Started to use the idea of dominant vs recessive

MONOHYBRID CROSS

• Start with two pure-breeding homozygous parental lines

• Purple = dominant WW

• White = recessive ww

  • After one generation the dominant is over represented then a cross between Ww and WW leads to a 1:2:1 genotype ratio or a 3:1 phenotypic ratio

MENDELS PRINCIPLES

• Principle of segregation

  • Individuals carry pairs of genes for each trait and these pairs separate during meiosis

• Principle of

  • D

• Linkage discovered in 1905

  • If two genes are located close together on a chromosome, they will not segregate independently

    • Both alleles come as a package deal/ Homologous reconbination

    • Present problems in plant breeding when a favorable trait is linked to an unvavorable trait

    • Linkage maps can be used to determine positions of genes along chromosomes

• Peas are Selfish - self pollinate

  • Stigma and anthers are completely enclosed by petals

  • Pea flowers dont open until after pollination and fertilization

  • To cross-pollinate, the self pollination process must be stopped 

• Mendel prevented this by cutting off the immature stamens 

  • Took pollen from another plants mature pollen and dusted the carpel with pollen

MUTATIONS

• Chance changes in a gene

• Originally figured out by Hugo de Vries in 1901 while studying primrose

  • Patterns of heredity were generally well ordered and predictable

  • Occasionally, a characteristics would appear that wasn’t in line with its parent lines

    • Hypothesized that new charactistsc are the phenotypic expression of a change

• Types of mutations

  • Gene-level

    • Point mutation: one or a few nucleotides are altered

      • Insertations, deletions, inversions, substitutions,

  • Chromosome-level

    • Entire segments can be altered via the same above mentioned ways

    • Entire chromosomes can also be added or lost

    • Translocation can happen

• THEY ARE GOOD SOMETIMES

  • Mutations happen all the time, unfavorable ones disappear, favorable ones are selected and cultivated for desirable qualities

  • Mutations in eukaryotes occur spontaneously at a rate of 1 mutant gene per locus(zip code in genome)  per 200,000 cell divisions

    • Pretty often

  • Provide the raw materials for change in evolution

    • Different from genetic modification its on a molecular level

Transposons

• First characterisized by Barbara McClintock in the 1940s and won a nobel prize in 1983

  • Did a lot of work at MU woo but ended up leaving bc conditions were not great for a woman in genetics in the 40s

• Large proportion of eukaryotic genome is composed of transposons: repetitive elements that duplicate and move independently

  • Known as jumping genes

  • Transposition results in position effects