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Cells (Cells Theory: (All cells are either; Prokaryotes or Eukaryotes…

- - - - Prokaryotic cells are only found in bacteria,
        everything else has Eukaryote cells
      - No Nucleus
        
        DNA is 'free floating'
        
        No membrane bound organells
      - They have their hereditary information
        in one large (long) molecule of DNA
        
        they have only one chromosome
    - - has a true Nucleus ( = enclosed in a membrane)
        
        has a variety of membrane bound organelles
        
        more complex cells
      - Animals, Plants, Protozoa & Fungi
        all have Eukaryote cells
      - They have their hereditary information
        stored in multiple chromosomes surrounded by
        a Nuclear envelope made up of two membranes
        
        it is stored in the nucleus, in multiple chromosomes
- - - - Chlorophyll:
        
        Gives plants their 'green' colour
        
        Enables the plant to perform photosynthesis
      - Nucleus
        
        contains most of the cells DNA (chromosomes)
        
        controls all metabolic activity of the cell
        
        carries inherited patterns for a cell
        from one generation to the next
        
        controls cell division
        
        contains nucleoplasm
      - Nucleolus
        
        Dense body consisting of RNA & proteins
        
        Ribosomes are ensembled here
      - Nuclear envelope / membrane
        
        structure:
        
        Double layered membrane that envelopes
        the contents of the nucleus
        
        Outer membrane is continuous with / connects
        to the membrane of the rough ER
        
        Like the rough ER, it has Ribosomes attached to the surface
        
        function:
        
        In order for the cells to function properly there is a continuous amount of traffic that must cross through the nuclear envelope / membrane -
        
        RNA (Ribonucleic acid = half the DNA double helix) & Robosomal sub units
  - - - a Cell Wall
        
        main function = prevents the cell form rupturing when the water pressure inside the cell is greater than outside the cell
        also...
        
        maintains the cells shape
        
        provides an anchorage place for the flagella
        
        the cell wall of bacteria are more rigid & complex
        than a plant cell wall
      - Flagella
        
        = a long appendage of the bacteria that moves / propels it
        
        not all bacteria have flagella, but those
        that do are said to be Motile
        
        Motile = Bacteria that have the ability to move on their own
        (advantage = enable the bacteria to move towards favorable conditions & away from unfavorable / adverse conditions)
- - - - wax cuticle:
        leaves have a protective top waxy layer = to prevent damage and water loss
      - Upper epidermis:
        the next layer is transparent
        ... so it can let light through to the palisade cells
      - Palisade cells
        
        The palisade cells have the most chloroplasts
        
        they are at the top of the leaf to catch
        as much sunlight as possible
      - Mesophyll
        The Mesophyll layer has some cells with chloroplasts,
        ... but also lots of space for CO2
      - Stroma
        = holes in the bottom layers of the leaf where CO2 pass through
        
        controlled by the guard cells to limit water loss
    - - Chloroplasts are large oval organelles
        
        they are located in in Palisade & Mesophyll cells in leaves
        (& in cells on the outer layers of green stems)
      - structure:
        
        Inside the the Chloroplasts there are flat membranes
        = Thylakoids
        ... these are arranged in stacks called Grana
        (1 stack = Granum)
        
        ...Inside the Thylokoid membranes there is Chlorophyll
        
        ... Inbetween the Grana stacks there is
        a fluid Matrix called Stroma
    - - There are 2 chemical pathways that make up photosynthesis
        ... these 2 pathways** take raw materials (H2O & CO2)
        & rearrange them**
        ... then they join together to make Glucose
        (and a waste product of Oxygen)
      - Photosynthesis requires:
        
        Solar energy / light from the sun
        
        Chlorophyll
        
        Enzymes
      - Overall word equation:
        Carbon Dioxide + Water = Glucose + Oxygen
      - The 2 chemical pathways:
        
        2nd Chemical pathway:
        (The Calvin Cycle)
        
        = A light independent reaction
        
        Happens in the Stroma
        
        Hydrogen (from the 1st pathway), and CO2
        go into a complex biochemical cycle with lots of rearrangement
        ...until glucose forms as the final product
        
        Glucose is used for:
        
        Respiration
        
        Stored as starch
        
        Used to make cellulose, fats & Amino Acids
        
        The 1st Chemical pathway:
        
        = a light dependent reaction
        
        Happens in the Thylokoid membranes of Chloroplasts
        
        Firstly:
        Chlorophyll is a pigment that can absorb light (In the thylokoids)
        
        Electrons in the Chlorophyll are 'excited' by solar energy ... these high energy electrons are passed along a chain of molecules
        ... & the energy is used to make ATP
        ... the electrons are then returned to the Chlorophyll
        
        Secondly:
        Water is split into hydrogen & oxygen ...
        
        Oxygen is not needed so it is released as a gas
        
        Hydrogen is transferred by a carrier molecules
        into the 2nd pathway
    - - 3 factors can affects
        the Rate pf photosynthesis
        
        Temperature
        
        Increasing Temp. = increasing rate of photosynthesis
        up to the optimum rate
        Optimum rate = fastest rate
        
        If temp. is too high or low
        = the enzymes denature
        = photosynthesis stops
        
        Light intensity
        
        Bright light intensity
        = increase rate of photosynthesis up to a maximum
        
        Above the maximum, there will be no further effect
        when light intensity increases.
        this is either because:
        
        light absorbing pigments are saturated
        
        temperature of CO2 concentration are limiting the Calvin cycle (witch is a light independent reaction)
        
        CO2 concentration
        
        CO2 concentration
        = increases the rate o photosynthesis to a maximum
        
        After maximum, no further increase will occur
        because the Calvin cycle is saturated
        (or by limiting the temp. or light intensity)
      - other (minor) factors that influence the rate:
        
        Water
        = stroma close to reduse water loss
        
        Mineral ions
        = magnesium in chlorophyll molecules in the chloroplast cells
        
        Wavelength of light
        = green is not absorbed but all other light is
        (hence leaves are green as the green light
        reflects off them into our eyes)
        = blue and red light cause the pigment to be the most active
      - The rate is determined by what is needed for the process;
        
        Enzymes
        
        Light
        
        CO2
        
        H2O
        
        Temperature
        
        The rate is measured by either the amount of...
        
        O2 produced
        
        CO2 used up
  - - - stages = I.P.M.A.T.C.
      - I = Interphase
        =chromosomes replicate to form 2 sister chromatids
        held together by a centromere
        (this isn't technically part of mitosis,
        but another part of cell cycle)
      - P = Prophase
        
        The Chromatids shorten & thicken
        
        Nuclear membrane disappears
        
        Spindle fibers develop
      - M = Metaphase
        = spindle fibers help Christmastides line up at the equator
      - A = Anaphase = Centromer split & individual chromatides **move towards 'poles**' pulled by spindle fibers
      - T = Telophase = At the poles, new nuclear membranes form around each group of chromatidss and
        the plasma membrane begins to constrict
      - C = cytokineses = cytoplasm devides in two and
        2 separate cells are formed
      - = Cell division into 2 identical daughter cells
        
        Every cell needs its own complete copy of DNA
        (witch are formed during the synthesis phase)
        
        For growth, repair & reconstruction of old or worn out cells
    - - Each cell needs its own copy of DNA,
        ...so DNA needs to be able to make copies of itself
        = Self replication
      - Steps:
        
        Replication has a series of steps all controlled
        by enzymes & all requiring energy from ATP
        
        1 - Double helix unwinds
        2 - the weak hydrogen bonds are broken
        by the enzyme 'helicase' (unzipping)
        3 - New pre-made nucleotides assemble opposite each strand
        & use energy (ATP) to join together,
        using the enzyme 'polymerase'
        4 - Two identical DNA molecules are formed
        & they rewind into the twisted double helix
      - The Complementary base pairing mechanism
        is how DNA replicates (C-G) (T-A)
      - DNA replication = Semi- conservative
        
        There are 2 identical DNA molecules made, but...
        ...each half of the original DNA strand gets a new copy of itself
        ... so each of the 2 cells will end up with a double helix, where one strand is new and one strand is the original
        
        This is done as it is quicker and safer as it is
        less likely to make a mistake
        
        Many sections are copied at once because it is faster
        
        leading strand = copied directly along the whole strand
        
        lagging strand = copied in sections & then joined
      - While chromosomes are long unraveling threads,
        they condense into smaller shapes for mitosis
    - - Cell cycle consists of 4 stages:
        G1, S, G2, M
      - Interphase
        
        Interphase is the stages:
        G1,G2 and S
        
        G1 = 1st Gap phase
        
        The cell...
        
        Performs its function (job)
        
        Rows in size
        
        makes what it will need for DNA replication
        
        S = Synthesis Phase
        
        the cell copies DNA, chromosomes are duplicated
        (DNA replication)
        
        G2 = 2nd Gap phase
        
        The cell....
        
        Grows more in size
        
        Performs its function (job)
        
        Makes what it needs for mitosis
        
        Cells spend **90% of their
        time in the Interphase**
      - M = Mitosis
        
        Makes new duplicated cells for
        growth & repair & replacement
        
        The previously duplicated DNA devides into 2 new cells
        & then the cytoplasm devides (Cytokineses)
    - - = For Growth, repair, & replacement
      - Cell division is most rapid during growth,
        not everyday life
      - cells also replace themselves when they are worn out
        
        different cell types divide at different rates
        depending on how easily they were out
    - - DNA = Deoxyribose Nucleic Acid
      - It is a large molecule
        
        In the form of chromosomes it carries the 'genetic code' (information to make everything happen)
      - It is arranged in a twisted double helix
        (has 2 connected strands twisted together)
        
        The 2 sides are strongly bonded together
        
        Made of alternating sugar & phosphate groups
        
        The 2 strands of DNA run anti-parallel (upside down)
        to each other
      - Nucleotide
        
        = 1 phosphate + 1 sugar +1 base
        
        Bases
        
        Adenine (A) --- Thymine (T) = 2 hydrogen bonds
        Cytosine (C) --- Guanine (G) = 3 hydrogen bonds
        
        The bases are held together by weak hydrogen bonds
        (they only bond to the corresponding base
        due to their specific chemical structure)
  - - - For any chemical reaction, molecules must collide & collide with sufficient energy (activation energy), and correct orientation, so that the chemical bonds can change and a reaction occur
      - enzymes can hep ensure correct orientation,
        by correcting the position of molecules
        ...as well as decreasing the amount of activation energy required
      - Activation energy = the amount of energy a reaction must overcome in order to occur
        
        enzymes lower the activation energy by destabilizing bonds in the substance they are more reactive
    - - Catabolic
        
        = Breaks down large molecules into smaller pieces
        ( - By separating substances)
      - Anabolic
        
        = Makes larger molecules out of smaller molecules
        ( - By joining things together)
    - - (Enzymes are specific - they only catalyse one kind of reaction)
        
        they are usually named after the substance they act upon
        
        often have the suffix "-ase"
      - While substrates change during the reaction by becoming products. enzymes aren't used up or broken down in the reaction
        ... they can catalyses reactions many, many times
        (before they eventually break down/ denature)
    - - Enzymes = proteins that act
        as biological Catalysts
        
        A Catalyst = something that speeds up a
        reaction without being used up in the reaction itself
    - - Amino Acids:
        
        Amino acids are joined together with peptide bonds
        forming a polypeptide chain
        
        Depending on the different sequence of Amino Acids,
        this determines the different enzymes
        ... hence determines the specific shape the enzyme folds into
        
        the shape of an Enzyme = determines its function
        
        Shape:**
        
        Certain Amino acids within the polypeptide chain will
        interact with each other & can form either ...
        - Hydrogen bonds
        - Di-sulfide bridges
        
        These two kinds of bonds are between sections of the enzyme and hold it together in the specific shape
        ... this is what gives the enzyme its 3D structure
      - the Active site:
        
        The most important part of an enzymes structure
        
        = The area on the enzyme where the chemicals
        involved in the reaction, bind together
        
        The shape of an Active site is very specific
        ... it corresponds of the shape of the substrate
        that bonds to it
        
        substrates = the chemicals that bond to the enzymes active site (what is actually reacting)
        
        An Enzyme can only catalyses one kind of reaction
        ... they are highly specific because of the unique shape of the active site
    - - PH:
        
        Enzymes will denature at either too low or too high PH
        
        different enzymes have different optimum PH's
      - Concentration
        
        Substrate concentration:
        
        Rate of reaction will increase as substrate concentration increases
        ... until all enzymes are 'saturated'
        the point where the reaction stops = the point of saturation
        
        a saturated solution = when there are no left over enzymes to catalyse the reaction
        (when there are no free reactants left to react)
        
        Enzyme concentration:
        
        Rate of reaction will keep increasing as
        numbers of enzymes increase
        (so long as there is unlimited substrate)
        
        if the substrate 'runs out', then then increasing enzyme numbers won't increase the rate of reaction any further.
      - Temperature
        
        the higher the temperature = the faster the enzymes can catalyse a reaction
        ... because the particles move faster & collide more often
        
        However above 40 - 45 degrees, enzymes will denature
        ... & there is a sudden drop in reaction rate
        
        (enzymes can still work at lower temperatures but the reaction is just slowed down, however they will denature at a too higher temperature)
        
        Optimal temperature = when the reaction rate is the fastest
      - Enzyme shape is maintained by weak hydrogen bonds,
        these can be broken by a number of things (e.g. high temperatures)
        ... broken bonds changes the shape of the enzyme = this is called Denaturing
        
        When an enzyme denatures it can no longer perform its function and catalyse the reactions and longer, it is 'dead'
    - - = many enzymes need
        another molecule to assist them
        = they complete 'empty spaces' on the the active site
        in order to make it functional
      - they can be organic ions or inorganic ions
    - - = prevent enzymes from catalyzing reactions
        (they 'stop' reactions)
      - inhibitors can be:
        
        Reversible or Irreversible
        
        Competitive or Non-Competitive
        
        Competitive inhibitors
        
        = Compete with a substance to bind to the active site
        ... this means that if they win, the substrate can't bind
        to the active site as the inhibitor is already there
        
        They tend to be irreversible and are therefore poisons
        
        Non - Competitive inhibitors
        
        = Bind to a different part of the enzyme (not the active site)
        ... this alters the shape of the Enzyme and its Active site
        ... therefore binding of the substrate to the active site
        is no longer possible
        
        - usually reversible (temporary)
        
        this can be used by cells as a way of controlling rate of reaction
  - - - Respiration occurs in the mitochondria of cells,
        in All organisms, All the time
      - Mitochondria = The 'powerhouse' of the cell
      - In cells that require a lot of energy...
        
        there are more mitochondria
        
        & more Cristae (membrane folds) within these mitochondria.
      - they....
        
        Are elongated oval shape
        
        Have inner membranes that are in fold called Cristae
        (these provide large surface area for the reactions)
        
        The space in between the Cristae = the Matrix
        (this has many enzymes and a gel)
      - All animal cells have more mitochondria than Plant cells...
        (this is because usually they have a higher energy demand)
        
        Animal cells that have particularly high energy demands:
        
        muscle
        
        heart
        
        sperm
        
        liver
        
        kidneys
        (basically any cell that 'moves')
        these cells can have up to 1000 mitochondria within the one cell!
      - Respiration is the process of breaking down glucose of from ATP (heat is a bi-product)
        
        ATP = the energy molecule of all living organisms
        = it fuels all the reactions of thee cell(s)
        some of theses reactions include:
        
        Active transport
        
        Making molecules (amino acids/ proteins, etc.)
        
        Movement (muscle contractions, cilia, etc.)
    - - Aerobic
        (with oxygen)
        
        Requires oxygen for the complete breakdown of;
        glucose = CO2 + Oxygen
        
        It has 3 steps:
        1- Glycolysis
        2- Krebs Cycle
        3- Electron transfer Chain
        
        Krebs Cycle:
        
        ( aka; the citric acid cycle)
        
        ocures in the matrix
        
        Pyruvate produced in step one (Glycolysis) now goes into
        a complete Biochemical pathway
        & extensive rearrangement changes
        
        Pyruvate = CO2 + H
        
        H = is picked up by the 'carrier' molecules &
        taken to the last step
        
        CO2 = A Waste product
        = diffuses out of the mitochondria and then out of the cell
        
        Electron Transfer Chain:
        
        (aka; Hydrogen transfer chain / Respiratory chain)
        
        Occurs in the Cristae
        (inner membrane of mitochondria)
        
        H = H+
        
        H atom becomes H+ ion, as an electron is removed
        
        the high energy electrons are passed along a chain of molecules along/ of the Cristae...
        = as they bounce along, there energy is used to change ADP to ATP...
        = at the end of respiration the electrons are returned to the H+ ions
        when they combine with O2 atoms to create H2O
        (O2 + H+ = H2O)
        
        This stage makes most of the ATP for the cell
        (in total) one molecule of glucose = 38 ATP molecules
        36 from 3rd step
        2 from 1st step
        
        Glycolysis:
        
        Occurs in the cytoplasm
        
        (splits the glucose )
        Glucose = 2 pyruvate molecules
        C6H12O3 = 2C3H4O3
        
        2ATP are made
        
        38 ATP overall
      - Anaerobic
        (without oxygen)
        
        Only requires glucose (no oxygen)
        
        Only stage one occures (Glycolysis)...
        so only 2 ATP are made (overall) from each Glucose
        (requires a lot less ATP than Aerobic respiration)
        
        ( happens in prolonged exercise)
        
        Glucose = Pyruvate = lactic acid + 2 ATP
        
        Some small organisms (e.g. yeast and bacteria)...
        Use Anaerobic respiration as their whole way of life
        
        although it only makes 2 ATP, this is enough for these organisms
        
        e.g. (in yeast)
        Pyruvate molecules broken down to Ethanol + CO2
        
        this process is fermentation (Ethanol = an Alcohol)
    - - ATP = Adenosine Tri Phosphate
        = made by adding a phosphate
        (has a higher energy band than ADP)
      - ADP = Adenosine Di Phosphate
        = only has 2 P's
        = high energy bond
        (but less energy than ATP)
      - when a cell needs energy the (ATP) higher energy bond
        is broken witch releases energy
        ATP to ADP
    - - Overall Word equation:
        Glucose + oxygen = Carbon Dioxide + water + 38 ATP + Heat
      - Overall Formula equation:
        C6H12O6 + 6O2 = 6CO2 + 6H2O + 38ATP + Heat
    - - Affected by;
        
        Temperature
        
        Energy demands
      - The rate increases until...
        the temp. increases to the optimum temp. for enzymes
        (37 degrees for humans)
        Too high above optimum temp. = The Enzymes denature
        
        reaction stops
        
        organism dies
      - Energy demands:
        
        As the Demands of the cell increases
        = The Rate of respiration increases
        (e.g. muscle cell demands increase when exercising)
        
        Amount of O2 required & hence amount of Co produced
        = breathing rate increases to compensate,
        = so respiration has an increased rate
  - - - All cells have a very thin
        boundary between the cell and its environment
        
        this maintains the different concentrations
        of substances within the cell
      - It is made of Phospholipids
        = A bi-layer (2 layers)
      - The phosphate heads = water loving = Hydrophilic
        The Lipid tails = water hating = Hydrophobic
      - The membrane is fluid, so it can reassemble itself
      - The membrane around the cells ...
        = same kind of membrane around the organelles
        (membrane bound organelles)
      - Cell membrane = Semi-permeable
        = some things can get thorough and others can't
        (only small non-charged things can get though,
        big or charged things can't get through)
    - - Active
        
        Requires energy
        (as the particles are moving against
        the concentration gradient)
        
        Types of active transport:
        
        Ion pumps
        
        Anything that goes against
        the concentration gradient
        
        Bulk transport (simple)
        
        Ion pumps
        
        = Specific carrier/transport proteins in the plasma membrane
        that carries out active transport
        
        Harness the energy of ATP...
        to pump molecules / ions from low to high concentration
        
        Bulk Transport
        
        Moving large 'amounts' by folding membranes called Cytosis
        
        Exoocytosis = Adds to the cell membrane
        Endocytosis = Uses up some cell membrane
        
        Pinocytosis = 'cell drinking' = fluids
        Phagocytosis = 'cell eating' = Solids
        
        ENERGY is needed
        (as in all active transport)
        
        The membrane is constantly being altered
        (added to or taken away from)...
        this is to allow 'things' in and out
      - Passive
        
        doesn't require energy
        
        Types of passive transport:
        
        Diffusion
        
        Facilitated diffusion
        
        Osmosis
        
        Facilitated diffusion:
        
        Needed for large molecules & charged molecules that are moving with the concentration gradient
        
        The process uses large Proteins that go right through the membrane as a pathways for the particle to travel
        
        = these are called Chanel proteins or Carrier proteins
        (& they are specific to molecules)
        
        Osmosis:
        
        Osmosis is a special class of diffusion
        as it only diffuses water
        
        = The movement of water across a semi-permeable membrane
        
        From an area of high concentration to low concentration
        (as with all passive transport)
        
        Hypotonic = low Tonicity = few H2O particles = Dilute = High water potential / concentration
        Hyertonic = high Tonicity = Lots of H2O particles = Concentrated = Low water potential / concentration
        Isotonic = Same tonicity in and our of the cell
        
        Diffusion
        
        Definition:
        The Random movement of particles,
        resulting in a net Movement of a substance from an
        area of high concentration to an area of low concentration, until the concentrations become the same (Equilibrium)
        
        The difference in concentrations between 2 areas
        = The Concentration Gradient
        
        Moving with the gradient = High to Low (Passive transport)
        
        Moving Against the gradient = Low to high (Active transport)
        
        Moving from a high to low concentration gradient
        = moving down the concentration gradient
        
        Diffusion is faster if...
        
        The gradient (difference) is greater
        
        Smaller particles
        
        Higher temperature
        
        H2O, O2 & CO2; all diffuse freely across a membrane
        with a concentration gradient
    - - Cell size and shape relates to its need for diffusion
      - Cells need to be small (volume) in order to diffuse substances both in & out of the cell
      - When cells grow their volume increases at a
        faster rate than their surface area
        (cytoplasm / organals grow at a faster rate than the membrane)
      - Surface area = Squared (x2)
        Volume = Cubed (X3)
      - When there is less membrane and more distance to
        the center of the cell, the cells compensate by either;
        
        Dividing
        
        Being long
        
        being Bioconcave
        
        Having Villi
      - The greater the Surface Area to volume ration
        = transport/ diffusion is more effective