Bio 212: Biology of Plants

Bio 212: Biology of Plants Introduction: How would these people have taught a plant course? •Carl Linnaeus •Gregor Mendel •Melvin Calvin, Andrew Benson or James Bassham Now: modern plant biology (What Bio 212 it is and isn’t) (Home work: read interview with Gloria Coruzzi, p. 668, Campbell , 5th ed, on modern plant biology)

Unit 1: A. Intro: What is a Plant? 1. Seems to be a stupid question. You can identify a plant, right?

a. characteristics of all plts your opinion……… b. critique of your characters

2. my characteristics a. cellulose CW b. mostly sexual repro with alternation of generations c. mostly PS d. mostly rooted into substrate and therefore stationary e. mostly diploid or polyploid f. true vacuole g. mostly multicelled eukaryotes

3. The angiosperm plant body has only 4 organs (animals have many more) A. roots B. ______ C. leaves D. _______

4. Intro to the Angiosperm plant body A. roots 1) absorb and conduct water upwards 2) can conduct organic compounds up and down 3) can store C as ________________ 4) ____________ 5) can form associations with fungi for better abs (mycorrhizal relationships) or bacteria ( N2 fixation)

B. shoots 1) can conduct water upwards (in the xylem) 2) can conduct organic compounds up and down (in the phloem) 3) forms the main support organs for holding plt up 4) occasionally can be PS 5) can store C

C. leaves 1) main collector of _________ for PS 2) main organ of PS 3) water evaporation (transpiration) 4) ____ _________ through the stomata

D. reproductive organs (flowers) 1) site of fertilization (pollination) 2) site of growth of zygote and surrounding tissues into embryo, seed and fruit

5. where did plants come from? A. discussion of evolutionary lineage of plants/move to land/symbiosis (overhead of fig1.1 of plt physiol, Taiz & Zeiger) (overhead of fig. 29.3 (cd29.1) of Campbell, p. 549)

Unit 2: plant cells A. intro 1. Plt cells have char that are shared with all cells (quick review) 2. Plts also have organelles that are unique to plt cells a. chloroplasts b. tonoplast c. peroxisome (different function in plts than other cells) 3. Plt cells communicate a. all cells do this including plts b. best examples are in human cells

B. Organelle Review 1. Nucleus a. double nuclear memb. contiguous with rER 1) allows nuc. memb. to be pulled back into ER during mitosis b. space between nuclear memb's is _________________ with rER space

1. Review of nucleus (cont.) c. nuclear pores dot the surface (& regulate what moves in and out) 1) allows transport of stuff out •rRNA •mRNA •tRNA •cell signal molecules

1. Review of nucleus (cont.) 2) allows transport of stuff into nucleus •polymerase and other enzymes •second messenger molecules 3) keeps some stuff in the nucleus •chromosomes •histone proteins •transcriptions factors, etc.

1. Review of nucleus (cont.) d. nuclear lamina: protein scaffold that support nuc. memb. e. part of endomemb. system

1. Review of nucleus (cont.) f. functions of nucleus 1) _________: retains/protects chromosomes from reactive chemicals of cytoplasm 2) site of nuclear transcription and regulation of transc. 3) site of DNA repl./storage 4) site of mitosis (& cytokinesis) 5) nuclear transport

2. Endoplasmic Reticulum a. system of memb. channels and sacs b. part of endomemb. system c. 2 types of ER 1) rER (50% of total memb.) a) directly attached to nucleus b) has ribosomes c) pancake-like morphology

1) rER (cont) d) functions of rER 1. translation of processed mRNA (surface) 2. modification of proteins (lumen) 3. _____________ of lipids (lumen)

2. Endoplasmic Reticulum (cont) 2) sER (which is much of the rest of memb) a) attached to rER and more peripheral b) no ________________ c) more tubular in form d) functions (1) transport of proteins to Golgi via transport vesicles that bud off sER (surface) (2) modification of proteins: add __________ grps, carbohydrates, cleave into smaller peptides, form 3˚ structures (lumen) 3. provides spaces for rxn's that require environments different than that in ______________ (lumen)

3. Golgi a. stack of memb. bound sacs b. cis face receives transport vesicles with proteins for modification and sorting c. trans face forms vesicles containing modified proteins for transport to plasma memb. or form lysosomes d. part of endomemb. system

4. vesicles a. many types b. memb. bound c. bud from the •ER (_____________vesicles) •plasma memb (_______________) •Golgi (most others) d. guided to destination by snare proteins of the vesicle membrane

e. examples of vesicles (cont) 1) lysosome: Golgi derived, sacs of digestive enzymes in cytoplasm, combine with endosomes or aging organelles to destroy and recycle 2) endosome: invaginated from plasma memb. to bring in by endocytosis (RME), specific compounds or things to be destroyed for food or safety of the cell (e.g. WBC's and bacteria) (Q: can plt cells carry out phagocytosis? pinocytosis?) 3) secretory vesicles: Golgi derived, carry protein hormones, enzymes, or other signal chems to be secreted outside the cell by exocytosis. 4) transport vesicles: within the cytoplasm

5. mitochondria a. site of •Krebs cycle (____________) •ETS (inner memb) which makes chemiosmotic potential (intermemb. space) •ATPase to use to make ATP b. double memb. bound sacs c. many scattered in the cytoplasm d. contains it own chromosomes, ribosomes e. endosymbiosis origin

6. cytoskeleton a. at least 3 separate proteins make up scaffolds and have many different functions b. actin: pushes out pm allowing ameboid movement, maintains or changes cellular shape c. microtubules: flagella, cilia, highways for organelle & vacuolar movement inside cell, chromosome movement in mitosis d. Intermediatefilaments: nuclear lamina, cell shape e. all are very important in cellular functions

C. Organelles specific to plt cells 1. Chloroplasts : cover in PS section 2. Tonoplast membrane of central vacuole a. by far largest organelle in living plt cells b. pushes most of other organelles to periphery of cell c. bilayer memb. sac d. part of endomemb. system

2. Tonoplast membrane (cont) 5. functionally complex and functions are still being working out: dynamic storage site a. main storage site for _______ in cell (necessary since the plant cant move when it rains) b. plts can use the internal pressure of water (tugor pressure) to put pressure on cw during growth (hydrostatic jack) c. storage for dissolved ions (K+ Cl- Na+, etc)

2. Tonoplast membrane/central vacuole (cont) function (cont) d. storage site for proteins or metabolic by-products that would be destructive in cytoplasm e. storage site for pigments other than chlorophyll (which is in chloroplast)

3. Plt cell wall a. CW’s found in all cells (except animal cells) but are multiphyletic b. in plts CW’s are thick and complex and made of layers of cellulose fibers (beta 1,4-glucose) and proteins c. multiple layers are at angles to each other (like a layers in plywood)

3. Plt cell wall (cont) d. middle lamella is sticky carbo layer between 1o cw of adjacent cells: holds cells together e. thick 2o cw of cellulose is laid down later in 2o growth f. func. 1) gives cell shape 2) rigidity 3) physical protection 4) retains cm intact under high hydrostatic pressure

4. Peroxisome a. specialized metabolic compartment b. found in most cells but functions vary widely c. variety of oxidizing reactions occur here EM micrograph of part of a peroxisome

4. Peroxisome (cont) d. functions 1) catabolize fatty acids by beta-oxidation to make acetate (Co-A) for energy 2) also can anabolize f.a. into sugars in fat storing seeds (=glyoxysome)

4. Peroxisome (cont) d. functions (cont) 3) detox. functions a) breakdown alcohols in liver b) breakdown other toxic compounds in plants (often done by adding e- (and H+) to toxic chem’s to make H2O2 , which is poisonous. H2O2 must be sequestered and then broken down by peroxidase in this cellular compartment)

And remember: all of these organelles must talk to each other and function together if the cell is to function correctly and survive.

Unit 3: Enzymes and Proteins A. Review of Proteins 1. Composed of Amino acids (aa) a) individual aa have different properties b) therefore aa’s give these diff properties to the proteins that contain them.

1. Amino acids (cont) c) examples •some are polar or nonpolar •some kink the protein (proline) •some are neg. or pos. charged •some can H bond •some can ionically bond to other aa (charged aa) •some can covalently bond with other aa (those with a sulfhydryl grp like cysteine)

2. protein complexity a. 1˚ structure: the linear sequence of aa’s in a protein 1) linked by peptide bonds (condensation synthesis of amine and carboxyl grps of adj. aa's) 2) remember that proteins have linear directionality just like DNA does. a) There is an amine end and a carboxyl end and therefore NH2-gly-glu-arg-leu-val-COOH is not the same as NH2-val-leu-arg-glu-gly- COOH. 3) protein size usually between 50 and 2000 aa’s long

b. 2˚ structure: 2 types are common 1) alpha helix a) H bond interactions between closely placed aa (ketone O and amine H) b) regular and repeating: throws strand into a uniform helix c) precludes certain aa which "kink" the strand (e.g. Proline) d) alpha helix make that region of protein more "linear"

2) ßeta pleated sheet a) caused by H bonds between aa’s in •two different proteins OR •two diff regions of the same protein b) often Beta sheet is regular and repeating as well: throws protein strand into a lampshade or accordion shape and H bonds ties the 2 beta stands together

2) ßeta pleated sheet (cont)c) one protein often has regions of a-helix and b-sheet

3) 3˚ structure a) very important in determining 3-D structure of the protein b) caused by 1)Hydrophobic/philic interactions between far apart aa’s 2) polar/nonpolar interactions between far apart aa’s 3) ionic bonds interactions between far apart ionic aa’s 4) covalent bonds (cys-cys) between far apart sulfur containing aa’s (disulfide bridge)

3) 3˚ structure (cont) c) effects of 3˚ structure on proteins (1) The 3 ˚ interactions bend protein strand on itself (2) gives overall 3-D shape, which mostly will be the lowest energy conformation (3) Makes loops and has the effect of making the protein globular and possibly forming pockets in the protein (these can be active sites or allosteric sites in enzymes) (4) this shape is a balance of torque that the various interactions induce and the stress of bending the molecule (like folding up a piece of flat paper, it will pop open unless held)

4) 4˚ structure: Many proteins (e.g. hemoglobin) have multiple protein subunits. Subunits are translated separately and then assembled into the holoprotein (in Golgi or sER).

5) Prosthetic groups a) many proteins (e.g. hemoglobin) have prosthetic grps (ions, sugars or lipids) that are covalently bonded to the protein. Often these prosthetic grps are important in the func. of the protein. b) e.g. Fe, Cu, Mg, and other metal ions are often bonded to proteins at active sites and perform enzymatic reactions. c) All prosthetic grps are added after translation.

3. Native conformation a. The shape of the protein is a balance of torque that the various interactions induce and the stress of bending the molecule (like folding up a piece of flat paper, it will pop open unless held). b. The native conformation will be a balance of the induced twisting and the structural stress caused by the twisting

4. More on protein structure and function a. reactive sites on enzymes 1) 3˚ confers a globular shape on many proteins. 2) This also leads to pockets and cavities in these proteins 3) pockets or grooves are often active sites or regulatory sites (e.g. allosteric site)

4. More on protein structure and function(cont) b. characteristics of an active site 1) cavity has a specific shape •determined by 1˚-3˚interactions •basis of enzyme's specificity 2) cavity fits a specific molecule(s). 3) fit is determined by the shape of the cavity and the molecule

b. characteristics of an active site (cont) 4) Some of the aa’s of the active site are often are bound to a prosthetic group 5) Prosthetic group usually has a metal ion, that binds reversibly to a _______________ and catalyze a change in the subst. 6) active site provides a micro-environment for the specific reaction to take place

c. How the active site interacts with substrate: a model for enzyme activity in lock and key or induced fit enzymes (1) majority of aa’s of the active site are predominantly non-polar, generally excluding water unless it is a substrate (2) active site may also have some aa’s that make the site acidic. Acidic groups interact with subst. to destabilize certain bonds OR (3) active site may have a few aa’s which are polar that are strategically placed to hold prosthetic grp. Prosthetic grp induces electrical instability in a certain bonds in substrate OR (4) active site may have a few aa’s which are polar. These aa’s are strategically placed to interact with subst. and produce physical instability in certain bonds substrate (2, 3 or 4 can get the subst. to a transitional state so that it can transform into a product)

d. example of Carbonic Anhydrase active site (draw) 1) rxn: H2O + CO2 -> HCO3- + H+ (makes HCO3-, part of carbonate buffer system of mammal blood) 2) active site must fit H2O AND CO2 together. 3) the active site has 3 his residues (polar) coordinately bonded to Zn+2 at bottom of a deep cleft.

Bio 212: Biology of Plants