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Botany Exam 1, Major building block of cellulose that distinguishes from…

- - - - Last Universal Common Ancestor
    - - Arose in a prebiotice soup containing most of necessary molecules
        
        Suggest spontaneously formed
      - Growth and energy supply available
      - Early floating living world
      - Membrane bubbles
        
        Containing information molecule
        
        Perform limited number of metabolic reactions
        
        Able to divide
        
        Able to interact
        
        Able to fuse
      - Fuse and share genomes and metabolic reactions
    - - Simple experiment
      - Dry and wet cycles
      - DNA + lipids
      - Sandwich to lipid vesicle with DNA inside
    - - Phospholipid
      - Micelle
      - Covered with protective wall in some organisms
      - Embedded proteins
      - Facilitate metabolism
        
        Receptors for functions such as self identity
  - - - Evidence of eukaryotic cells ~ 2.7 bya
      - Geologically stable biomarker made predominately by eukaryotes (cholesterol)
    - - Continuous connected membrane
      - Forming multiple organelles
        
        Plasma membrane
        
        Golgi body
        
        endoplasmic reticulum
        
        Nuclear envelope
    - - Microfilaments
        
        Important for vesicle movement near membrane
        
        Actin
      - Intermediate filaments
        
        More permanent, fix things in place
        
        Dimers to tetramers
      - Microtubules
        
        Trackway for long-range movement of transport vesicles
        
        Alpha and Bets-tubulin
  - - - Has own circular DNA
      - Similar in size to bacteria
      - Self-replicate binary fission (independent of nucleus)
      - Can only be made from preexisting ones
      - Ribisomes similar in size to bacteria
      - Double membrane
  - - - Outer membrane
      - Inner membrane
        
        Folded areas are cristae
        
        Location of oxidative phosphorylation
      - Matrix
        
        Internal solution
        
        Location of the citric acid cycle
    - - Chloroplasts: typically green plastids used for photosynthesis
        
        Outer membrane
        
        Inner membrane
        
        Grana
        
        Stack of thylakoids
        
        Thylakoid reactions with proteins embedded in thylakoid
        
        Stromal reactions within aqueous storm
      - Etioplasts are the precursors of chloroplasts
      - Chromoplasts: colored plastids for pigment synthesis and storage
      - Leukoplasts: coloured plastids for monterpene synthesis
      - Amyloplasts: for starch storage
      - Elaioplasts: for storing fat
      - Proteinoplasts: for storing and modifying protein
      - inheritance
        
        mainly from egg parent
        
        gymnosperms from sperm parent
  - - - Layer of additional protection
      - Create turgor pressure along with large central vacuole
      - Composed primarily of cellulose, hemicellulose, and pectin
      - Remains somewhat flexible to permit growth
    - - Made of glucose monomers
      - Beta 1,4 glucose bonds
      - Through dehydration synthesis
      - Hydrogen bonds make cellulose extremely strong
      - Very few organisms have the capacity to break/ digest cellulose
      - Fiber in our diets
    - - Chitin
        
        Insect exoskeleton
      - Keratin
        
        Hair
        
        Fingernails
- - - - A suggestion that metabolism may have predated biological macromolecules
      - Hydrogen sulfide reacts with iron monosulfide to form pyrite
        
        Yield energy
        
        Yield chemical reducing power (hydrogen)
    - - Early branches
      - Hyperthermophilic prokaryotes
      - Do not use oxygen during metabolism
      - Most die in presence of oxygen
    - - Move electrons around
      - Electron movement provides impetus for energy production
      - Redox reactions
        
        OIL RIG
        
        Oxidation Is a Loss
        
        Reduction Is a Gain
    - - Present very early in the formation of life
      - Nicotinamide adenine dinucleotide
      - Electron carrier
        
        Picks up electrons, becomes reduced, drops them off somewhere else and becomes oxidized
      - Move back an forth
        
        Oxidation and reduction
        
        Move electrons around in cell
      - Strong reducing agent
    - - Through electron transport chain
      - Primarily generates ATP
      - Energy from inorganic molecules
        
        Circulation of electrons
        
        Circulation of protons
        
        Synthesis of ATP
    - - Adding phosphate group to ADP
      - Create high-energy bond
      - Primary energy courier in all living cells
      - Light-driven electron flow linked to existing machinery for making ATP
        
        Photophosphorylation
  - - - Energy is stored (two ATP per glucose)
      - Reducing equivalents are formed (two NADH per glucose)
    - - Net Products
        
        2 ATP
        
        2 Pyruvate
    - - Uses up 2 ATP
      - Produces 4 ATP
      - Begins with glucose as the substrate
      - Ends with pyruvate as the product
    - - Each important in other biosynthetic pathways
      - Pyruvate is the final product
        
        Fermentation
        
        The salvage pathway
        
        NADH recycled to NADH+
        
        Leads to lactic acid or ethanol
        
        Aerobic respiration
  - - - Likely began with chemosynthesizmers
      - Living around ancient volcanic vents
      - Variation among bacteria on how sugars are synthesized
      - Only organisms which can use an external energy source able to manufacture own carbohydrate fuel
      - Standardized in later lineages
        
        Described by the Calvin-Berson-Bassham cycle
        
        form used by plants
    - - Reductive citric acid cycle
      - Some bacteria use to synthesize C compounds
      - Some steps can be catalyzed by minerals through photochemistry
      - Precursor to stromal reactions of photosynthesis in plants
    - - Energy required to drive the creation of sugars
      - Chemosynthesizers use of oxidation of energy-rich inorganic molecules
      - Plants use sunlight
      - Glycolysis requires 2 ATP to get the reaction going
    - - Basic sugar that many organisms use for energy
      - Different models for the same molecule
        
        C6H12O6
        
        Alpha Glucose
        
        Isomer: energy storage
        
        Beta Glucose #
        
        Isomer: structure
        
        Starch
        
        Amylose
        
        Alpha bonds 1, 4
        
        Angular
        
        Amylopectin
        
        Alpha bonds 1, 6
        
        Linear
- - - - Glycolysis
      - Pyruvate oxidation
      - Citric acid cycle
      - Oxidative phosphorylation
  - - - Electrons stripped from pyruvate and given to NADH+
      - Carbon dioxide breaks off C3 to C2 forming Acetyl coenzyme A
        
        Acetyl CoA (C2) joins to C4 to form Citrate (C6)
    - - Coupled to break off of CO2
  - - - NAD+ oxidizing agent, accepting electrons
      - NADH is the reduced form and can give up electrons
      - Stronger proton motive force that FADH2
      - Can be converted to NADP
      - Vitamin niacin helps to build
    - - Strong oxidizing agent
      - FAD is reduced to FADH2
      - Weaker proton motive force compared to NADH
      - Vitamin B2 riboflavin base for construction
    - - Proton motive force
      - Trapped protons creates a battery
      - Only way down concentration gradient Is through
      - Special protein complex
        
        ATP synthase
        
        Catalyzes formation of ATP from ADP + P
        
        Brilliant example of a molecular machine
        
        Driven by energy from electrochemical gradient
        
        Across membranes
        
        Mitochondrial cristae
        
        Prokaryotic cell membranes
        
        Plant thylakoid membranes
        
        Drive synthesis of ATP
    - - Builds up the proton motive force
      - Regenerates electron carriers
      - Mitochondrial ETC consists of 4 large protein complexes
    - - Electrons dropped off by NADH and FADH2
      - Electrons pass through ETC
      - Protons are pumped across
      - Oxygen is final electron acceptor
      - Chemiosmotic electrochemical gradient runs ATP synthase
      - Driving production of ATP
- - - - First identifiable algae ~ 1.6 bya
      - First land plants before 600 mya
      - Seed plants ~ 350 mya
      - Flowering plants ~ 150 mya
    - - Major new forms seem to appear suddenly
      - Various Reasons
        
        Intermediate forms did not fossilize
        
        Very few fossils with limited distribution
    - - Multicellular photosynthetic organisms that live on land (generally)
      - History of plant life
      - Familiar features emerged over millions of years
        
        Origin of photosynthesis
        
        Plant cell
        
        Transition to land
        
        Diversity
    - - Common core of molecular features
      - Life's principal energy currency = ATP
      - A common genetic code = DNA & RNA
      - Molecular machinery for transcribing DNA to RNA
      - Machinery to translate RNA messages to proteins
        
        Structure
        
        Regulation
    - - Nested design give rise to taxonomic groupings
      - Evolutionary divergence from common ancestors under the influence of natural selection
    - - Based on similarity of ribosomes (RNA + proteins)
      - History of life microbial
      - Eukarya evolved after after bacteria and archaea were already around
    - - Give clues as to descent
      - Fossils
      - Biological molecules
      - Environmental isotopes
    - - 99% C12
      - C14 decays so not generally used to time
      - C13 discriminated against by photosynthesis
      - Living organisms enriched in C12 compared to environment
      - Evidence of photosynthesis in very old rocks
      - Carbon-12 and 13 are more talked about with isotopes
      - Carbon-14 is radioactive and less likely
      - Carbon-12 and 13 can be used to determine when photosynthesis started in rocks
      - In a heterotroph eater (mainly plants), their carbon-12 is like that found in plants
      - Isotope: an atom with a different number of neutrons
        
        The fewer neutrons, the lighter the atom will be
        
        The more neutrons, the heavier the atom will be
      - C12 is the most common carbon atom
    - - Evidence of organic microbial mats
      - Stromatolite like structures
        
        Stromatolite: bacterial mats that have built up over time
      - Isotopic signature suggests photosynthesis
      - It is thought that photosynthesis started about 3.5 bya in rocks, way before plants ever existed
  - - - Chemical reactions could have made life possible
      - Early scientists thought that ammonia and methane were most abundant
    - - Stanley miller (1953)
      - Gases thought to be relevant to early atmosphere
      - Later experiments showed that reducing atmosphere necessary (4H:1C) & absence of oxygen
      - When a molecule is oxidized, it loses electrons
    - - Life can come from chemistry
    - - Simple enough to form by physical processes
      - Sufficiently complicated to lay evolutionary groundwork for living cells
      - self-replicating
      - Direct synthesis of other compounds
      - Trajectory eventuallyindependent of physical processes
      - Synthesize molecules needed for growth
      - Tapping chemical/solar energy to fuel workings
    - - Early conditions not quite right to leap right into RNA
      - PNA can direct formation of RNA complement; thus, RNA could hav replaced it as a precursor
    - - RNA information-rich molecule
      - Form by self organization
      - Catalyze its own replication
      - As life matured, evolution introduced division of labor
        
        DNA provided more stable library
        
        Proteins took over most catalytic functions
      - RNA stands can be used to detect things in ancient times as DNA can be used
    - - Simple beginnings based on naturally occurring molecules
      - Biological freedom from physical process as biosynthetic pathways evolved
      - Complex biochemistry
        
        Natural selection
        
        Gene duplication
        
        Lateral transfer
        
        The transfer of genes not between parents and offspring but between different individuals
        
        Occurs a lot in bacteria
        
        Plays a major role in complexity & specialization seen today