Biology Lecture Exam 2 Review

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					Biology Lecture Exam 2 Review

9/22/07 Lecture Notes Continued

      2) fluidity –
           a) phospholipid movement
              (1) lateral movement
                   (a) 10x per second
              (2) flip-flopping (from one phospholipid layer to the other)
                   (a) rare – approx. once per month
           b) membrane fluidity
              (1) unsaturated hydrocarbon tails with kinks in them
              (2) viscous when it is saturated hydrocarbon tails
           c) cholesterol
               (1) reduces fluidity at moderate temperatures by reducing phospholipid movement
               (2) hinders solidification at low temperatures by disrupting packing of phospholipids

9/29/07 Lecture Notes

    B. Membrane Transport
       1. Passive transport – simple diffusion across a membrane with no energy investment
          a. Diffusion – tendency for molecules to diffuse from a region of high concentration
          to low concentration
             1) concentration gradient – the increase or decrease of density of substances in an area.
                  a) substances move down their concentration gradient
                  b) molecular movement occurs until equilibrium is reached
             2) molecules that diffuse freely across membrane (few but important)
                  a) oxygen
                  b) carbon dioxide
                  c) lipids and nonpolar molecules
                  d) water
          b. Osmosis – diffusion of water across a membrane
             1) moves down its concentration gradient, from high to low
             2) fewer molecules present if molecules dissolved in water
                  a) solute – anything dissolved in water
                  b) solvent – water, in this case
                  c) solution – a liquid that is a homogenous mixture of 2 or more substances
                  d) tonicity – the ability of a solution to cause a cell to gain or lose water
             3) Solutions based on solutes/water concentration
                  a) hypertonic – more solutes/less water
                  b) hypotonic – less solutes/more water
                  c) isotonic – same concentration of solutes and water

           4) Water balance problems
               a) animal cells
                  (1) hypertonic solution outside the cell – causes water to leave the cell; the cell may
                  shrivel and die (called crenation)
                  (2) hypotonic solution outside the cell – causes water to enter the cell; the cell may take
                  up so much water that it bursts
                  (3) isotonic solution outside the cell – optimal solution; the plasma is isotonic to the red
                  blood cells being transported in it
            b) plant cells
               (1) hypertonic solution outside the cell – causes water to leave the cell; the cell may
               shrivel and die (called plasmolysis)
               (2) hypotonic solution outside the cell – water still enters cell; however, the cell will not
               burst because the plant cell wall prevents excess water buildup
                    (a) this condition is termed turgid and is ideal for a plant
               (3) isotonic solution outside the cell – plant becomes flaccid and may wilt
     5) Water balance critical for survival
            a) protists such as Paramecium, which live in a hypotonic environment, have a contractile
               vacuole that takes up excess water and expels it to keep it from bursting.
               (1) osmoregulation – the control of water balance
            b) the human kidney keeps the bloodstream isotonic to the fluid that surrounds the body
            c) contact lens solution is isotonic
            d) pouring salt on a slug will kill it (changing its water balance)
  c. facilitated diffusion
     1) molecules are facilitated or helped across membrane
     2) process is carried out by transport proteins from pores or tunnels through
     which molecules can travel
     3) molecules still follow the rules of diffusion
     4) Molecules that enter via facilitated diffusion:
            a) glucose
            b) amino acids
            c) water (moves faster across the membrane this way)
               (1) aquaporins – the transport proteins for water

2. Active Transport – requires a transport protein and energy
   a. moves molecules up their concentration gradient (low to high)
      1) process
           a) solute binding – solute binds to a specific binding site
           b) phosphorylation – transport proteins use ATP energy to transport the solute molecules
           c) transport – causes transport protein to change shape and release the solute molecule on
              the other side
           d) protein reversion – phosphate detaches from the transport protein and returns to its
              original shape

  b. movement of large molecules
     1) exocytosis
          a) moves material out of cell
          b) example: proteins
     2) endocytosis
          a) uptake of material into the cell
          b) types
             (1) phagocytosis – (cell-eating) the uptake of solid material into the cell
                 (a) examples: amoeba takes up food in this manner; white blood cells take in bacteria
                 this way
             (2) pinocytosis – (cell-drinking) uptake of fluids
             (3) receptor mediated cytosis – only one particular type of molecule is taken up
                 (a) cholesterol is taken up this way; found in regions of the membrane called coat
                 proteins (a fuzzy layer on the cytoplasmic side)
       3) medical applications
           a) hypercholesterolemia (high cholesterol) – results from no functional LDL
           (low density lipoprotein) receptors or few LDL receptors; a factor in
           development of atherosclerosis (hardening of the arteries)
           b) desirable cholesterol levels
              (1) total cholesterol should be less than 200mg/dL
              (2) LDL (“bad” cholesterol) less than 100mg/dL
              (3) triglycerides less than 150mg/dL
              (4) HDL (high density lipoprotein or “good” cholesterol) more than 40mg/dL

C. Energy – the capacity to do work
   1. types of energy
      a. kinetic energy
         1) actually doing work – moving matter
         2) example: riding a bicycle
      b. potential energy
         1) stored energy that can be used later
         2) example: cyclist at the top of a hill
         3) chemical energy: potential energy stored in chemical bonds; runs the chemical
         reactions of cellular metabolism
   2. energy transformations
      a. energy conversion is essential to life
         1) plants convert solar energy to chemical energy (sugars)
         2) humans convert chemical energy in food to kinetic energy
      b. thermodynamics – the study of energy transformations
         1) 1st law of thermodynamics – energy cannot be created or destroyed, only
         converted to different forms.
         2) 2nd law of thermodynamics – the universe is becoming more and more
               a) entropy – the amount of disorder in a system.
               b) energy conversion also converts some energy to heat
      c. chemical reactions
         1) types
               a) endergonic reaction – requires energy input
                  (1) photosynthesis – a series of endergonic reactions
                      (a) CO2 + H2O  sugars
               b) exergonic reaction – release of energy
                  (1) reactants have energy stored in bonds, and when broken, energy is released.
                  (2) wood burns – heat is released
                  (3) cellular respiration
         2) cellular metabolism – the sum of exergonic and endergonic reactions
         3) energy coupling – the release of energy from exergonic reactions to drive
         endergonic reactions
    d. ATP (adenosine triphosphate)
       1) provides the chemical energy for cellular metabolism
            a) energy released by exergonic reactions is stored in ATP
            b) ATP is then used to run endergonic reactions
            c) hydrolysis – an endergonic reaction
                (1) the covalent bond is broken by the addition of water and a third phosphate is
                (2) ATP becomes ADP (adenosine diphosphate)
                (3) energy is released
            d) phosphorylation – an exergonic reaction in which a phosphate from ATP
            is transferred to another molecule
       2) ATP nucleotide is composed of:
            a) the nitrogenous base adenine
            b) the sugar ribose
            c) 3 phosphate groups
       3) cellular work
            a) types of work
                (1) mechanical – examples:
                    (a) beating of cilia
                    (b) contraction of muscle cells
                    (c) movement of chromosomes
                (2) transport, i.e. the pumping of substances across the plasma membrane
                (3) chemical, i.e. the synthesis of polymers
       4) how ATP powers types of cellular work
            a) mechanical – ATP phosphorylates motor proteins
            b) transport – ATP phosphorylates transport proteins
            c) chemical – ATP phosphorylates key reactants

D. Enzymes
  1. Energy of activation – an energy barrier that must be overcome for a reaction to
  take place
     a. examples:
        1) the energy to break a bond
        2) the energy to bring molecules together
        3) the energy to change the shape of a molecule
     b. Mexican jumping bean – this is not an actual bean that can jump, but rather a
     bug has crawled inside the bean and is making it appear as though it’s jumping by
     moving inside it. The bug is exceeding the bean’s “energy of activation” in a sense by
     having enough energy to move the bean.
  2. Enzymes do:
     a. lower the energy of activation required for a reaction to take place
     b. without enzymes, chemical reactions in cells would progress so slowly that cells would die
  3. Enzymes do not:
     a. add energy to the reaction
     b. become one of the reactants
     c. become one of the products
     d. get used up by the reaction
4. Catalytic Cycle of an Enzyme
   a. terms
      1) substrate – specific reactant upon which the enzyme reacts
      2) active site – region on the enzyme which binds with the substrate (usually, a pocket or groove
      on the surface of the enzyme)
      3) induced fit – may strain substrate bonds to place in position for reaction to take place
   b. cycle example
      1) components of the cycle
           a) an enzyme (e.g. sucrase)
           b) a substrate (e.g. sucrose)
           c) products, e.g. glucose and fructose
      2) cycle
           a) enzyme has an empty active site
           b) sucrose binds to the active site
           c) this binding causes the enzyme to change shape slightly
           d) changed shape produces a better or induced fit
           e) reaction occurs
           f) sucrose is broken down into glucose and fructose
           g) enzyme releases products
           h) the enzyme is available for another reaction
5. Enzyme Activity
   a. factors that affect activity
      1) temperature change
           a) can denature an enzyme and make it non-functional
           b) most human enzymes are functional between 35-40°C
           c) bacteria in hot springs have enzymes that function best at high temperatures
      2) high salt concentration
           a) disrupts the chemical bonds, which lowers enzyme activity
      3) pH level change
           a) can denature enzymes
           b) most enzymes function best in a pH range of 6-8
           c) exception: enzymes in the stomach work best at a pH of 2
           d) acid precipitation may affect aquatic organisms by affecting their enzymes
      4) cofactors or coenzymes (organic molecules)
           a) may be needed to help the enzyme work
           b) may be single atoms such as zinc or iron
           c) may be small molecules like vitamins
6. Enzyme Inhibitors
   a. block enzyme reactions
   b. types of enzyme inhibitors:
      1) competitive inhibitor
           a) binds to an active site on the enzyme so that substrate cannot bind to it
           b) substrate and inhibitor “compete” for active site
      2) non-competitive inhibitors
           a) bind to a place on the enzyme other than an active site
           b) changes the enzyme’s shape and keeps the enzyme from binding to the substrate
             3) Examples of enzyme inhibitors
                   a) malathion (insecticide) – shuts down nervous system of insect, killing it
                   b) cyanide – inhibits an enzyme necessary for the production of ATP
                   c) penicillin – inhibits an enzyme in bacteria which creates their cell walls
                   d) AZT- used to treat AIDS infections; protease inhibitors which target viral enzymes
                   e) aspirin – inhibits an enzyme that is necessary for synthesis of prostaglandins which cause
       7. Regulation of Enzyme Activity
          a. allosteric enzymes oscillate from active to inactive forms
          b. allosteric regulation – any case in which a protein function at one site is affected by the binding
             of a molecule at another site
             1) types of allosteric regulation:
                   a) allosteric inhibitor – binds at the regulatory site, stabilizes inactive form
                   b) allosteric activator – binds at the regulatory site, stabilizes active form
                   c) cooperativity – substrate molecule binds to active site, locks all subunits into an active
                   d) feedback inhibition – metabolic pathway is switched off by binding an end product to an
                      enzyme that functions earlier in the pathway

Lecture Notes 10/6/07

VI. Photosynthesis
     A. Photosynthetic Organisms (also called autotrophs or self-feeders)
        1. includes:
           a. plants
           b. some bacteria
           c. some algae
        2. Effects on the planet
           a. oxygen production
              1) photosynthetic organisms release oxygen
           b. food production
              1) photosynthetic organisms convert CO2 and H2O with minerals using solar (light) energy into
              2) all living things depend on photosynthetic organisms for food (energy)
     B. Site of photosynthesis in plants
        1. Anatomy of the leaf
           a. epidermis – the outer layer of cells
           b. stomata – small pores within the epidermis
              1) allows CO2 to enter and exit the leaf
           c. mesophyll – tissue, the primary location of photosynthesis in the plant
              1) types of mesophyll
                    a) palisade mesophyll
                        (1) vertical cells in the upper portion of the leaf
                        (2) appear tight together in leaf
                    b) spongy mesophyll
                        (1) somewhat circular cells in the bottom portion of the leaf
                        (2) loose arrangement allows for gaseous exchange
         2) Chloroplasts concentrated in the mesophyll cells
               a) anatomy of the chloroplast
                  (1) outer membrane – separates chloroplast from cytoplasm
                  (2) inner membrane – encloses two parts:
                       (a) stroma – a thick fluid where sugars are made from CO2 and H2O minerals
                       (b) thylakoids – suspended in the stroma; appear as stacks called grana; chlorophyll
                           molecules are embedded in the thylakoid membrane
               b) photosynthetic pigments in chloroplasts
                  (1) absorb different wavelengths of visible light (only visible light used in photosynthesis;
                       shorter wavelengths = higher energy; violet – 400nm and red – 700nm)
                  (2) types of photosynthetic pigments: (all of these pigments are present during
                       photosynthesis and all absorb different wavelengths)
                       (a) chlorophyll A – most abundant pigment
                       (b) chlorophyll B – energy absorbed is transferred to chlorophyll A
                       (c) caratenoids – some provided photoprotection which absorbs and dissipates
                          excessive light energy that would (a) damage the chlorophyll and (b) interact with
                          oxygen to form reactive molecules dangerous to the cell
                          photoprotection – prevents “bleaching” of the chlorophyll
                       (d) xanthophylls – appear yellow
C. Photosystem – reaction center surrounded by a light harvesting complex
   1. Components of a photosystem
      a. light harvesting complex (surrounds reaction center) – light (solar) energy is absorbed and
         transferred from one pigment molecule to another
      b. reaction center – consists of:
         1) 2 special chlorophyll A molecules that
               a) receive energy from the pigment molecules in the light harvesting complex
               b) boost 1 electron to a higher energy level
         2) primary electron acceptor – picks up the excited electron and passes it to the electron
            transport chain
   2. Types of photosystems and their electron transport chains (light reactions)
      a. photosystem II
         1) pigment molecules absorb and transfer solar (light) energy
         2) light excites electron chlorophyll P680
         3) excited electron is captured by the primary electron acceptor
         4) electron from the splitting of H2O replaces this excited electron
         5) O2 is released
         6) photoexcited electron (captured by the primary electron acceptor) is passed to the electron
            transport chain on the way to photosystem I
      b. electron transport chain (from photosystem II to photosystem I)
         1) consists of
               a) plastoquinone (Pq) – electron carrier
               b) cytochrome – iron-containing protein
               c) plastocyanin (Pc) – protein
         2) provides energy for ATP synthesis and a replacement electron for P700
      c. photosystem I
         1) pigment molecules absorb solar energy
         2) light excites electron of chlorophyll P700
         3) excited electron captured by primary electron acceptor
         4) electron from the electron transport chain (long chain from PII) replaces the excited electron
            from P700
         5) photoexcited electron from P700 (captured by primary electron acceptor) then passes to a
            short electron transport chain where it forms NADPH from NADP+.
      d. short electron transport chain
         1) electrons pass through ferrodoxin (Fd), a protein
         2) enzyme NADP+ reductase transfers electrons from ferrodoxin to NADP+ to form NADPH (two
            electrons required)
   3. ATP synthesis
      a. electron transport chains in the thylakoid membrane provide energy
      b. this energy pumps H+ ions from the stroma to the interior of the thylakoid membrane
      c. result is stroma with low H+ concentration, thylakoid space with high H+ concentration
      d. energy of the H+ concentration gradient is used to create ATP
         1) created by the flow of H+ from the interior of the thylakoid membrane through the stroma
         2) then flows through ATP synthase complexes (called chemiosmotic production)
D. Calvin cycle (dark reactions)
   1. occur in the stroma
   2. a food making process, like a sugar factory
   2. Steps in the Calvin cycle
      a. carbon fixation
         1) the enzyme rubisco (RuBP caboxylase) combines with CO2 and RuBP (ribulose biphosphate)
         2) 2 molecules of 3-phosphoglycerate acid are formed from each CO2 molecule
      b. reduction
         1) requires ATP and NADPH
         2) G3P (glyceraldehyde-3-phosphate), an energy-rich sugar, is produced
      c. release of one molecule of G3P
      d. regeneration of RuBP
         1) uses ATP
         2) reconfigures 5 G3P molecules to form RuBP
E. Summary of photosynthesis
   1. Summary equation: 6 CO2 + 12 H2O + solar energy, pigments and enzymes yields C6H12O6 + 6
      H2O + 6 O2 (glucose, water and oxygen)
   2. Photosynthesis is a series of endergonic reactions
      a. solar energy runs the reactions
      b. reactants: CO2 and H2O
      c. products: high-energy molecule (glucose plus new H2O and O2)
   3. Stages of photosynthesis
      a. light reactions
         1) solar energy (ATP and NADPH) is converted to chemical energy
         2) O2 is a byproduct
         3) reactions take place in the thylakoid membrane
         4) because these reactions require the input of light energy and they occur in the presence of
            light, they are called light reactions
      b. Calvin cycle (dark reactions)
         1) chemical energy from ATP and NADPH is used to produce glucose
         2) reactions take place in the stroma
         3) these reactions do not require light, so called dark reactions
    F. Evolutionary plant adaptations to conserve water needed for photosynthesis
       1. Calvin cycle
          a. requires constant input of CO2 through stomata
          b. these open stomata allow water to diffuse out of the plant
          c. plants may lose up to 95% of their water through the open stomata
       2. types of plants (water conserving adaptations)
          a. C3 plants (from 3-PGA – 1st organic product formed)
             1) gets CO2 directly from air
             2) keeps stomata open except on hot, dry days
             3) photorespiration occurs on hot, dry day when stomata are closed
                  a) CO2 levels in the leaf increase
                  b) O2 levels increase for a period of time
                  c) rubisco can bind to O2 when CO2 is scarce
                  d) no sugar is produced and growth is slowed
             4) plant examples: rice, wheat, soy beans
          b. C4 plants (from 4 carbon compound formed 1st)

Bonus questions: (Know the spelling of all of these answers!)
6. The opposite ends of the Golgi apparatus are referred to as the cis face and the trans face.
1. Gaucher disease is caused by the deficiency of what enzyme? glucocerebrosidase
2. What term refers to the binding of a regulatory molecule to an enzyme at one site, which then affects
protein function at another site? allosteric regulation

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