BIOL425 17 Fall
CH 1 introduction
Plants : Primary production
“What drives life is: a little current kept up by the sunshine” (Szentgyorgyi)
Botany: Greek word originated from “to feed”
Not only food but oxygen, fuel, fiber, medicines, etc even the money (dollar bills)
Origin of life, Evolution of life forms,
Local events or pan-spermia?
Experimental evidence: accumulation of chemical building blocks of life in the Miller
experiments (artificial ancient atmosphere and conditions)
-Meteorites, comets contain organic compounds➔messengers?
First: protenoid microspheres
Later: Autotrophic, heterotrophic life forms,
-conquering the Earth by photoautotrophic organisms,(Cyanobacterium like).
-environmental changes, free oxygen,
Fast evolution: survival then heterotrophic life forms because of the possibility of
respiration.
First prokaryotes were Anaerobic !!!!!! Dramatic change to aerobic conditions because
of photosynthetic O2 release and accumulation in the atmosphere
Eukaryotic cells: nucleus and organelles
Colonization of land by plants:
First adaptations to rocky costs
Problem : how to provide continuous water flow and positive water balance,
-Structural adaptation: root, vascular system in the stem, cuticle on the leaves.
-Stomata for gas exchange, Vascular system: Xylem and Phloem
Basic anatomy of a vascular plant: root, stem, leaf, tissues and organs
Communities:
Biomes(living components) ecosystems (with nonliving environment)
Major biomes e.g.: Deciduous forest, tundra, taiga, tropical rainforest, desert, savanna,
Human impact:
Agriculture, initiated the development of plant sciences, domesticated plants 5,000-
10,000 years ago
Such as plant taxonomy, systematics, morphology, anatomy, physiology, genetics,
genomics, genetic engineering, ecology, etnobotanics and many others.
Plant sciences are challenged by over-population, pollution, global warming ( fossil C
burning, CO2 emmition..
Response: fast development of plant genetic engineering technologies for plant
protection, increased yield, better quality, phytoremediation abilities, increased utilization
of renewable resources.
CH2: MOLECULAR COMPOSITION OF PLANT CELLS:
Organic molecules: C-C-C bonds,
Originated from CO2 fixation: Plants, Algae, bacteria (photo and chemo autotrophics)
-Carbohydrates:
Sugars, monosaccharides, disaccharides, polysaccharides
-Building blocks: monosaccarides: hydrophilic
-transported: disaccharides (sucrose)
-polysaccharides:
Energy storage: starch, glycogen, fructans etc.
Structural components:, cellulose, hemicellulose, chitin, pectic acid.
-Lipids: triglycerides: hydrophobic, stores energy, fats and oils.
Phospholipids:
– membrane components,
-saturation level, fluidity➔ temperature adaptations.
-steroids: (membrane components and hormones) classified as lipids:
physiological effects and membrane temperature adaptations
-waxes, suberin, cutin: waterproofing the plants compartments
-Proteins: Building blocks are amino acids (20),
hydrophobic, hydrophilic, uncharged or charged +/-
Hydrogen bonds: secondary structures alpha helix, beta sheats, globular of
fibrous.
Tertiary structures self assembly or molecular chaperones. disulfide bridges
Structural or catalytic functions
Nucleic acids: Nucleotide building blocks,
– deoxyribose of ribose the sugar component
-Phospho-sugar backbone with bases,
– TAGC : DNA UACG: RNA
types: nDNA, cpDNA mtDNA
rRNA, e.g. 16S 23S bacterial , 18S 25S cytoplasmic
mRNA, tRNA, snRNA, iRNA or micro RNA (regulatory functions)
Secondary metabolites:
Alkaloids: Nicotine, morphine, cocaine, caffeine, THC, atropine, codeine,
Terpennoids: made of from isoprene units (C5H8), mono- di- and tetraterpenes
Essential oils, taxol, rubber, Gibberrelines (plant hormone)
Phenolics: Flavonoids, anthocyanins, tannins, lignins salicylic acid (aspirin) SA:
SAR, systemic acquired resistance.
CH 3
Plant Cells, cell cycle
–Robert Hook used the word “CELL” the first time (using microscope), fixed the light
source,
Plant cell has internal compartments: organelles with specific functions(e.g. chloroplast,
mitochondria, vacuole, nucleus)
-Inside of the cell membrane (plasmalemma) and outside of the nucleus: cytoplasm
-Cytosol: semi-fluid matrix
-Protoplast: the membrane surrounded cell
-Membranes are selectively permeable barriers (active, passive transport) not only
outside, (organelles and internal network, compartmentalization)
-Nucleus: envelope/pores, chromatin, chromosomes,
-cytoplasmic connection by internal membrane system
-Internal membrane system: rough-ER, => smooth ER,=> Golgi (dictyosome)=>
plasmalemma => secretory vesicles (transport direction)
-Oil bodies: are not true organelles, arise from ER, (lipid synthesis)
-Plasmodesmata: intercellular connection, size selectivity and specific transport.
-Vacuoles: membrane surrounded, (tonoplast) internal dump site for storage, processing
and turgor regulation
-Ribosomes: free or attached to the RER (different protein modification and targeting)
Chloroplasts: energy conversion (light=>Physical (H+/chemical
ATP/NADPH=>chemical C-C-C)
-independent protein synthesis, DNA replication, tRNA-s, and transcription
-fine structure grana, stoma, thylakoid membranes,
– biochemical factory as well!!! Fatty acid and aromatic amino acid biosynthesis
– Proplastid-chloroplast-chromoplast-amyloplast
Mitochondrion: energy conversion chemical to chemical
-independent protein synthesis, DNA replication, tRNA-s, and transcription
-double membrane, cristae,
-intimate interaction with the chloroplast
Origin of the above organelles: -endo-symbiotic events: from an aerobic and from a
photosynthetic bacterium
Peroxisomes: associated with photorespiration no DNA< RNA, ribosomes
Glyoxysomes: Lipid degradation ➔ sugar (gluconeogenesis)
Cytoskeleton: actine filament,
microtubule ( tubulin alpha, beta)
intermediate filaments,
They direct cell expansion, cell division, chromosome movements, channels
Cell wall:
-Primary (mainly cellulose, interpenetrated by a matrix of non-cellulosic molecules: such
as other polysaccharides (hemicellulose) and structural proteins (extensin)
Pectins cements together contiguous cells (middle lamella)
Secondary wall: different, deposited from inside, lignin)
Pits: bordered and simple: thin primary and no secondary wall: plasmadesmata-
connection.
Reproduction of the cell
Cell division: two daughter cells
Prokaryotic cell division: binary fission
Eukaryotic cell division:
Mitosis (nuclear division) and Cytokinesis (cell division)
Cell cycle: Universal, (M-G1-S-G2-M) except the checkpoint are hormone regulated
G1➔S auxin dependent; G2➔M Cytokinin dependent (Auxin/Cytokinin ratio)
Interphase can be long or short, arrest can be in G1 or in G2
Apical meristems: initials and sister cells
Mitochondrion and plastids independently divide (semiautonomous) DNA synthesis
Cell division in plants: is very different because of the large vacuole and the cell wall.
Nucleus has to move into center position➔ cytoplasmic strands has to be formed
A cytoplasmic plane (continuum) has to be formed where the division can occur
Microtubules and actin filaments arranged in that plane there, forming the
phragmosome
Mitosis is completed along the cell plane of phragmosome
Phragmoplast is formed from the microtubules after the chromosomes separated
and the cell plate formation is initiated (vesicle traffic, membranes, cell wall
material) until the separating cell wall is completed, (However continuously
connected with plasmodesmata, never separated )
Cell division: two daughter cells
Prokaryotic cell division: binary fission
Eukaryotic cell division: Mitosis (nuclear division) and Cytokinesis (cell division)
Cell cycle: Universal, (M-G1-S-G2-M) except the checkpoint are hormone regulated
G1➔S auxin dependent; G2➔M Cytokinin dependent (Auxin/Cytokinin ratio)
Interphase can be long or short, arrest can be in G1 or in G2
Apical meristems: initials and sister cells
Mitochondrion and plastids are independently divide (semiautonomous)
Phragmoplast is formed from the microtubules after the chromosomes separated and the
cell plate formation is initiated (vesicle traffic, membranes, cell wall material)
until the separating cell wall is completed, (continuously connected with
plasmodesmata)
Chapter 4: The movement of substances into and out of the cells
Membranes separate cells from the surroundings
-Mission impossible: separating and connecting, isolating and transporting
–Structure is the key:
-Fluid mosaic model: with transmembrane, integral and peripheral proteins
-Phospholipids and sterols plus glycoproteins and glycolipids, lectins
(Nuclear envelops, ER, Golgi, tonoplast, thylakoid, mt cristae, etc.)
–Movement of water and solutes:
-Water moves passively along water potential gradient, diffusion,
-Osmosis is a special case of diffusion (driving force is the same!!!)
-osmosis and osmotic potential, measurements
-Water potential has a concentration, a pressure and a gravitational component
Cells and diffusion:
Turgor pressure, plasmolysis, wilting
Transport of solutes across membranes: transporters (transport proteins)
-Passive transport: simple diffusion, facilitated diffusion
(Carrier and channel proteins mediate it)
-Aquaporins are for water transport.
–Co-transport: Symporters and antiporters when the transfer is coupled
-Active transport: energy is required directly (ATP) or indirectly (H+pumping)
Some of the cotransport is secondary active (coupled with the previously
pumped H+ transport)
-Vesicle mediated transport:
– Phagocytosis, pinocytosis, receptor mediated endocytosis
-Cell to cell communication:
Signal transduction pathways: chemical messengers
-Target(cell), receptor, second messengers and more downstream components of
the signal transduction pathways
-Reception-transduction-induction
–Plasmodesmata:
Cell to cell transport and communication (symplastic pathway)
–not only a “hole” complex structure, hundreds of proteins, diverse function
-Exclusion limits and the exceptions
-Active recognition of certain molecular complexes, virus movement proteins
Chapter 5: The Flow of Energy
Energy is capacity to do work. Cells carry out various types of work
Life on Earth is solar-powered however less than 1% is captured by photosynthesis
Energy flow in biological systems: Sun➔photosynthesis➔Carbohydrates➔respiration
-Laws of Thermodynamics:
– I. Total energy (in a closed system) is constant, cannot be destroyed or
created only changed from one form to another.
Energy forms: potential energy, (e.g. positional) chemical, physical, thermal,
electrical
–II. Energy conversions are not perfect, some energy lost as heat, entropy
(disorder) is increasing. Spontaneous processes are exergonic (downhill)
dG=dH-TdS
-Maintaining life requires steady input of energy➔open and closed systems
– Oxidation (decreases organization level)-Reduction (increases organization level)
–Enzymes: Activation energy: energy required to move out from a stability pocket
-Catalyst: gets around the activation energy, by an alternative reaction, does not really
lower it.
-Active site: binds specific substrate, focuses energy there, or activation (e. g. ATP)
-Induced fit hypothesis
-cofactors: contribute specific functions for the enzyme reactions (e. g electron)
-Metabolic pathways:
-There can be an arrangement of enzymes of the same pathway (no accumulation
of a product (feed back inhibition))
– can be segregated in different compartments depending on the need metabolic
channeling
– Isoenzymes: same function, different genes (tissue specificity)
-Regulation of enzyme activity
-Gene expression is regulated on different levels: (transcription, post
transcription, translation, post translation/enzyme activity level)
temperature, pH, ion concentrations
– Regulatory enzymes (respond to signals)
– Allosteric enzymes: active site, effector site
– Feedback inhibition
Energy factor: ATP
-Energy rich P-P-P bonds, the 3rd PO43- energy is used
-ATP synthase and ATP-ase
-Coupled reactions
-Phosphatases, kinases
Chapter 6. Respiration
-Complete breakdown of organic molecules to CO2 and H2O.
-Oxidation: loss of electrons
-1M Glucose= 686kcal~36ATP
Main steps:
Glycolysis, ➔ Krebs- Szentgyorgyi (Citric acid, TCA ) cycle ➔ Electron transport
chain (In the presence of O2, regulated by O2 by the NAD+ regeneration in ETC)
Glycolysis ➔Fermentation (absence of oxygen, producing ethanol + CO2 or lactate)
-Glycolysis:
Glucose to pyruvate (+4 H atom + 2ATP net)
-Pyruvate: key intermediate in cellular energy metabolism enters the mitochondrion
matrix➔Further oxidation: CO2 loss, plus more NADH+H ➔ Acetyl CoA
Krebs Cycle:
Acetyl group is further oxidized (other names: K-S C or TCA cycle or C4AC)
Result: Oxaloacetate + 2CO2 + CoA + ATP + 3NADH+H + FADH2
Electron transport chain:
Reducing equivalents donated their electrons to the METC (RETC).
