Plant Biology 2D03 - midterm 1

four major event's in the development of life + when

1. first appearance of life (3.8 bya)

2. appearance of O2 in photosynthesis (3.5 bya)

3. appearance of eukaryotic organisms (2.7 bya)

4. multicellularity (1.25 bya)

why life was originally unable to develop on earth

no ozone layer for protection + constantly bombarded with celestial bodies

first evidence of photosynthesis

key enzyme in photosynthesis robisco prefers C12 over C13, the ratio between C12 and C13 can tell us how old a compound is

evidence of appearance of O2 in photosynthesis

iron rust

stromatolite fossils

hardened layers of a gel-like substance used to protect stromatolites from UV rays

evidence of appearance of eukaryotic organisms

molecular marker "-terols"

2 endosymbiotic events creating eukaryotes

1. non-photosynthetic; host cell eats proteobacterium and DNA enters nucleus

2. photosynthetic; same as non-photosynthetic except cell eats cyanobacteria

evolution of land plants + when

470 mya; green algae found in small pools that dried up seasonally so needed to adapt

adaptations for survival on land

1. waxy cuticles to prevent water loss

2. water transport system that goes against gravity

3. desiccation (dry tolerant) spores

what caused larger land plants

new vascular system developed lignin that thickened cell walls and provided mechanical support for plants' xylem

how did less CO2 in the atmosphere affect land plants

leaves grew bigger (more stomata) to absorb more CO2 and sunlight, also essential for flow of vascular system

definition of seed

zygote formed as a result of fertilization; develops into an embryo within a plants' protective endosporin

five types of seeds

gymnosperms:

1. cycads

2. ginkgos

3. conifers

4. angiosperms (most dominant)

2 generations in the plant life cycle

1. gametophyte: haploid sexual generation

2. sporophyte : diploid asexual generation

seed plant life cycle

angiosperms and gymnosperms; large sporophyte and small gametophytes

byrophytes life cycle

visible gametophyte generation with small parasitic sporophyte

3 unique features of angiosperms

1. flowers

2. seeds have endosperm

3. xylem

3 types of angiosperms

1. monocot

2. dicots (eudicots)

3. magnolids

monocot seedlings (# of cotyledons + vein arrangement + example)

1 cotyledons, parallel arrangement of veins, grass

eudicot seedlings (# of cotyledons + vein arrangement)

2 cotyledons, net arrangement of veins

3 different genomes of a plant cell + ploidy

1. nuclear, diploid

2. plastid, haploid

3. mitochondrial

2 nuclear genome traits

1. similar to other eukaryotes in terms of chromosome structure, replication (meiosis and mitosis) and expression (translation and transcription)

2. # of haploid chromosomes and DNA content (# of base pairs) vary across species

arabidopsis

first eukaryotic genome fully sequenced

number of plant genomes fully sequenced

49

transposons function + classes

mobile genetic element

Class I: retrotransposons

Class II: DNA transposons

steps of retrotransposon transposition

1. retrotransposon is transcribed and translated

2. RT (reverse transcriptase) makes cDNA

3. transposase binds LTRs (long terminal repeats) and integrates cDNA randomly

4. replicative: process makes 2 transposons

steps of how DNA transposons work

1. transposase recognizes repeated sequences at ends of transposons

2. transposase cuts and pastes transposon randomly into new site

3. leaves a copy of the repeated sequence at original site

4. non-replicative

consequences of transposon movement

1. insertion into a gene

2. insertion into a regulatory region

3. insertion follwed by excision; which may cause reversion to wild-type phenotype but not if a footprint is left behind

result: random mutations, deleterious and rarely advantageous

why have transposons in the genome?

adaptive advantage and genetic diversity via recombination

polyploidy

combination of 2 or more complete sets of chromosomes resulting in a larger genome

autoploidy

variation provided by addition of gene copies

alloploidy

variation increased by contribution of genomic info from each parent

consequences of polyploidy

formation of new species, increased seed plant and floral biodiversity

gene duplication cause + consequences

unequal crossing over during meiosis; one gene can be inactivated by mutation or epigenetic mechanisms, over time genes may acquire different functions from the ancestral gene

epigenetic

change in DNA function without changing DNA sequence by methylation & chromatin modifications

orthologs

genes that diverge from same ancestral gene after species separate

paralogs

genes that are duplicated in a single species

synteny

order of genes that is conserved between closely related species but less conserved in distantly related species as more time for chromosomal rearrangements to occur

5 tools for discovery of gene function

1. forward genetics + map-based cloning + sequencing

2. expression profiling using microarrays or RNA-seq

3. reverse genetics

4. overexpress gene of interest

5. disrupt gene of interest

steps of forward genetics

1. randomly mutagenize organisms using raditation, chemical mutagens or insertions by transposons

2. screen for mutagen phenotype of interest

3. find genes required for pathway of interest

4. map mutant phenotype to a region of genome

5. sequence region and compare to wild-type

6. identify mutant gene

expression profiling function

examine expression of all genes in a plant at a particular time or in response to a certain stress to give clues about gene function

steps of expression profiling

1. extract mRNA from tissues (represents genes being expressed at specific time)

2. convert mRNA to cDNA using fluorescently nucleotides

3. hybridize flourescent cDNA onto the microarray (has spot DNA probes)

4. scan slide with laser to measure fluorescent DNA that hybridized to particular spots

reverse genetics function

gene sequence known, need to discover function

overexpress gene of interest

creating an overabundant mutant and observing it's phenotype

disrupt function of gene of interest

knock out or reduce expression of gene and observe phenotype

endoreduplication

DNA replication without nuclear or cell division (S phase promoted, mitosis inhibited)

evidence of endoreduplication + example

measured DNA in various plant tissues (1C= mass of DNA present in haploid genome)

in arabidosis leaves 25% are diploid (2C) and 75% are polyploid with 1-4 rounds of endoreduplication

2 reasons for endoreduplication

1. for cells that produce lots of proteins (more genes available to transcribe and translate)

2. required for normal growth in arabidosis (positive correlation between plant growth and # of genes)

primary cell wall function

dictates plant cell shape, withstands outward pressure of water on plasma membrane, flexible so allows cells to expand

primary cell wall composition

composed of microfibrils embedded in a matrix of pectins and cross-linking glycans

primary cell wall synthesis

by cellulose synthase complex (a multisubunit enzyme embedded in plasma membrane)

cellulose synthase gene mutants

CESA 1 & 3 mutant causes death as seedlings, 6 is viable with bulging phenotype, 2, 5, 6 & 9 is redundant, 4, 7, 8 synthesizes secondary cell wall

how is cell wall flexible

cellulose polymers and microfibrils hels together by hydrogen bonds between hydroxyl groups and pectins form an amorphous network around microfibrils and glycans

cell expansion

constrained by microfibrils and directed by microtubules

microtubule

hollow cylinder made from the protein tubulin

3 functions of vacuoles

1. storage (waste products of cellular metabolism, toxic compounds from the environment, enzymes, pigments)

2. tugor pressure (water)

3. cell expansion

tugor pressure

water entering vacuole from an area of high water concentration to low concentration

lignin function

most important component of secondary cell wall, cross-links microfibrils in secondary cell walls

lignification of xylem

after secondary wall is formed, xylem cells die and forms a strong rigid pipe for water

vascular cambium

meristematic stem cells that give rise to phloem (outer) and xylem (inner)

refinery

any facility that converts raw materials into product of value

biofuels

fuels derived from biological carbin fixation

bioethanol

chemical digestion of plant material to get cellulose, then fermentation of cellulose (no way to get at carbon locked up in lignin)

Biodiesel

oil obstained from chemically treated oilcrops (canola, soybean, palm), agae, urban and farm plant waste, used vegetable cooking oils

3 benefits of biofuels

1. reduced greenhouse gas emissions

2. non-toxic and biodegradeable

3. renewable energy

problems with biofuel

non economically viable, need to be produced in large areas causing no gains in CO2 sequestration

switchgrass benefits

1. already used as a biofuel

2. native grass adapted to much of NA

2. needs little fertilizer

5. perrenial

6. harvested and stored like hay

7. creates wildlife habitat

challenges of switchgrass

1. potential pest issues in monocultures

2. must be grown next to bioethanol refinery

3. refinery needs constant fuel so needs to coordinate use of corn and weat in fall with switchgrass in spring

benefits microalgae as biofuel

1. microscopic

2. quick doubling

3. high oil content

4. no compromise of food production

challenges of microalgae as biofuel

1. low light penetration requires ponds to be shallow and large in area

2. open system easily contaminated

3. only viable in suitable climates