Lipids.ppt by ert554898

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									Lipids & Biological Membranes

Biological   membranes      that    define    the
boundaries of cells are composed largely of lipid
molecules, which form a permeability barrier
allowing only certain molecules to enter the cell.
Lipids are one of the four important classes of
biomolecules that have a variety of structural
and functional roles.



               Harini Chandra
    Master Layout (Part 1)
1
    This animation consists of 4 parts:
    Part 1 – Fatty acids
    Part 2 – Membrane lipids
    Part 3 – Proteins in membrane structures
    Part 4 – Properties of cell membranes
                                                                              b
                                                                  w
2                                     w                                       3        2   1



                                                                                       a

                                                                       Fatty acid –
                                  w-3 double
3     Degree of
                                  bond
                                                                       general structure

                                                  Chain length
      unsaturation




4


5
    Source: Biochemistry by Lubert Stryer, 5th & 6th edition (ebook)
    Definitions of the components:
1   Part 1 – Fatty acids
    1. Fatty acid: Fatty acids, more simply known as fats, are the key components of
    lipids that play an important role in signal transduction pathways and as structural
    elements of membranes. They are long hydrophobic chains of different lengths that
2   possess a carboxylate group at one end. Most naturally occuring fatty acids have an
    even number of carbon atoms with varying degrees of unsaturation.
    2. Degree of unsaturation: The number of double bonds present in a fatty acid
    chain defines its degree of unsaturation.
    3. Chain length: The total number of carbon atoms present in a fatty acid chain is its
    chain length.
3   4. w-carbon: Fatty acids are numbered starting from their carboxyl group with the
    second and third carbon atoms being known as the a and b carbons. The carbon
    atom that is furthest away from the carboxylate group, at the distal end of the chain
    is known as the w carbon.


4


5
    Part 1, Step 1:
1    Fatty acids – general structure
                                                                                                        w
                               b
            w

                                       2
2                              3               1
                                                                      Degree of
                                                                                                    w-3 double
                                                                                                    bond
                                                                      unsaturation
     w-carbon                           a                                                                           Chain length

                                            Carboxylate




3
                                            group (C1)
                Saturated fatty acid
                                                           Short chain length &
                                                         increased unsaturation
                                                            enhance fluidity &
                                                          decrease MP of fatty
                                                                  acids.                        Unsaturated fatty acid




4   Action        Description of the action                                               Audio Narration
     As         (Please redraw all figures.)                     Fatty acids are long hydrophobic chains of carbon atoms
                                                                 having different lengths and a carboxylate group at one end.
     shown in   First show the figure on the left appearing      Fatty acids that do not contain any double bonds are said to be
     animatio   with its labels from the right end to the left   saturated while those possessing one or more double bonds in
                in parts as depicted in the animation.           their structure are unsaturated. Most naturally occuring fatty
     n.                                                          acids have an even number of carbon atoms with varying
                Next, show the figure on the right with the
                                                                 degrees of unsaturation. The carboxylate group is numbered as
                labels appearing after the figure.
5                                                                one and the last carbon atom that is furthest away from the
                                                                 carboxylate group is known as the omega carbon.


    Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
    Part 1, Step 2:
1        Fatty acids - nomenclature                                                              Systematic name is derived by
                                                                                                 replacing the final ‘e’ of the parent
                                                                                                 hydrocarbon with ‘oic’/’oate’. For eg.
                                                                                                 C16 fatty acid is hexadecanoate
                                                                                                 (parent hydrocarbon is hexadecane).
     Palmitic acid (C16, saturated)
2   16           14         12
                                         10             8               6           4            2
                                                                                                         1
           15         13          11           9                7               5            3



    Oleic acid (C18, monounsaturated)



3   18
            17
                         Double bonds referred to by cis/trans- ∆-
                         number at which the double bond is
                      15 located in superscript.
                                 13
                                                                   4

                                                                             6
                                                                                        5
                                                                                                 3
                                                                                                     2       1




                                                                                                             18:1 indicative of 18 carbon
                                                                                                             atoms with 1 double bond.
                 16                           11
                           14                               9               7
                                                   10               8                       Systematic name: cis-∆9-octadecenoate
                                       12
4
    Action Description of the action                                                                 Audio Narration
     As           (Please redraw all figures.)                          The fatty acid names are derived from their corresponding parent
     shown        First show the figure on top followed by              hydrocarbons by replacing the ‘e’ at the end with ‘oic’ or ‘oate’. A
                  the green callour located above it. Next              saturated fatty acid with 16 carbon atoms, for instance, is known
     in
                  show the figure below followed by the                 as hexadecanoate. If there is one double bond, then it become
     animati      two text boxes and then the violet callout            deceneoate with the position of the double bond being indicated
     on.
5                 shown.                                                as a superscript after a delta symbol. For instance, a 18 carbon
                                                                        fatty acid with one double bond is known as ocatadecenoate while
                                                                        with two double bonds, it is known as octadecadienoate.

    Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
    Master Layout (Part 2)
    This animation consists of 4 parts:


1   Part 1 – Fatty acids
    Part 2 – Membrane lipids
    Part 3 – Proteins in membrane structures
    Part 4 – Properties of cell membranes



2                                                                            Cholesterol
              Fatty acid

                                               Sugar unit



3
                      Glycolipids


                                                                  G

4                                                Fatty
                                                 acid
                                                                  L
                                                                  Y
                                                                  C
                                                 Fatty            E
                                                 acid             R         Phosphate      Alcohol
                                                                  O
                                                                  L


5                                                                      Phospholipids

          Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
     Definitions of the components:
1    Part 2 – Membrane lipids
    1. Lipids: These are water insoluble biomolecules that readily dissolve in organic
    solvents like chloroform and have a wide range of biological functions. They are
    important components of membranes, serve as fuel reserves and signalling molecules.
    Three important membrane lipids include phospholipids, glycolipids and cholesterol.
2   2. Phospholipid: Phospholipids are composed of four components – fatty acids, a
    platform to which the fatty acid is attached, phosphate residue and an alcohol attached to
    the phosphate. The platform to which the fatty acids are linked is commonly glycerol but
    in some cases, a more complex alcohol known as sphingosine may also be present.
    Phospholipids containing glycerol are known as phosphoglycerides, with two OH groups
    of glycerol being esterified with the carboxylate groups of fatty acids. The fatty acid
3   chains form the hydrophobic tail while the remaining components constitute the
    hydrophilic head group.
    3. Glycolipid: Lipids that have a sugar component in them are known as glycolipids.
    They are made up of a sphingosine backbone with the amino group acylated by a fatty
    acid and one or more sugar residues attached to the primary hydroxyl group. The
    simplest glycolipid is known as cerebroside which contains either glucose or galactose as
    its sugar residue.
4   4. Cholesterol: Cholesterol is a steroid molecule whose structure is significantly different
    from that of phospholipids and glycolipids. Cholesterol is found in varying quantities in
    animal membranes but is not present in prokaryotes. It is composed of a hydrocarbon
    chain linked to one end and a hydroxyl group at the other end.


5
1
  Part 2, Step 1:
     Membrane lipids - phospholipids
                               G
         Fatty                 L
         acid                  Y
                               C
         Fatty                 E
         acid                                                                                             Phosphatidate
2                              R
                               O
                                          Phosphate                   Alcohol                      (Diacylglycerol 3-phosphate)
                               L
                                                                                                         Glycerol
                                                                                                         backbone
                                                                                                                             Phosphate
                                                     Fatty acids                                                             group


3                  Shorthand depiction


                                                                         Ester
      Hydrophobic tail                          Polar head               linkage
                                                group

4    Action           Description of the action                                                        Audio Narration
     As shown in   (Please redraw all figures.)                                    Phospholipids are composed of four components – fatty acids, a
                   First show the coloured block diagram structures on left top.   platform to which the fatty acid is attached, phosphate residue
     animation.    First the blue rectangle must appear followed by the two ovals and an alcohol attached to the phosphate. The platform to which
                   and then the green rectangle and finally the violet             the fatty acids are linked may be glycerol or sphingosine.
                   parallelogram. Next, the structure on bottom right must appear. Phospholipids containing glycerol are known as
                   First the central region must appear marked ‘glycerol
                                                                                   phosphoglycerides, with two OH groups of glycerol being
                   backbone’. Next, the groups on the left marked ‘fatty acids’
                                                                                   esterified with the carboxylate groups of fatty acids. The simplest
5                  must appear followed by the pink group on the right. The green
                   box must then highlight the region as indicated with the
                                                                                   phospholipid, phosphatidate, is made up of only the phosphate
                   corresponding label. The figure on bottom left must then appear group and fatty acids attached to the glycerol backbone.
                   with the labels.
    Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
1
  Part 2, Step 2:
     Common phosphoglycerides



                                              Glycerol
                                              backbone

2                 Fatty acids




3                                                  Phosphatidyl ethanolamine
                                                   Phosphatidyl serine
                                                   Phosphatidyl choline
                                                   Phosphatidyl inositol
                                                   Diphosphatidyl glycerol
                                                   (cardiolipin)


4     Action Description of the action                                              Audio Narration
      As shown      (Please redraw all figures.)               The important phophoglycerides found in membranes
      in            First show the blue and green parts of the are derived from phosphatidate by esterification of the
      animation     structure with their labels. Next, the red phosphate group with the hydroxyl group of various
      .             groups must appear sequentially one after
                                                               alcohols. The most commonly observed
                    another with their corresponding names
                    appearing below as shown in animation. phosphoglycerides include phosphatidyl serine, choline,
5                   (The red groups are layered one over       ethanolamine, inositol and diphosphatidyl glycerol, also
                    another – watch in slide show mode only) known as cardiolipin.

    Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
1
  Part 2, Step 3:
      Phospholipids - sphingomyelin




2                                     Sphingosine



                                   Fatty acid




3                                                                                 Choline




                                                   Sphingomyelin

4    Action        Description of the action                                        Audio Narration
      As shown     (Please redraw all figures.)            Sphingosine is another amino alcohol backbone that serves
      in           First show the figure on top with its   as a platform for attachment of fatty acids and alcohols.
      animation.   label followed by the figure below      Sphingomyelin, derived from sphingosine , consists of a
                   with its labels as shown.
                                                           fatty acid linked to the amino group via an amide bond and a
                                                           choline moiety attached to the primary hydroxyl group via a
5                                                          phosphate group.


    Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
1
  Part 2, Step 4:
     Membrane lipids - glycolipids

          Fatty acid


                                              Sugar
2        SPHINGOSINE
                                            residue(s)




3
                                               Cerebroside
4    Action        Description of the action                                          Audio Narration
      As shown    (Please redraw all figures.)                     Lipids that have a sugar component in them are
      in          First show the box diagrams shown on top         known as glycolipids. They are made up of a
      animation   left. The green rectangle must appear first      sphingosine backbone with the amino group acylated
      .           follwed by the blue parallelogram and then
                  the brown oval. Next show the structure
                                                                   by a fatty acid and one or more sugar residues
                  below in which the blue region must appear       attached to the primary hydroxyl group. The simplest
5                 first followed by the green region and finally
                  the pink labeled box.
                                                                   glycolipid is known as cerebroside which contains
                                                                   either glucose or galactose as its sugar residue.

    Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
1
  Part 2, Step 5:
     Membrane lipids - cholesterol




2                                                                              Alkyl side chain




3                        Polar head group            A       B
                                                                 C      D

                                                                     Steroid nucleus




4    Action        Description of the action                                              Audio Narration
      As shown     (Please redraw all figures.)                  Another group of structural membrane lipids is the sterols,
      in           Show the appearance of the structure          found in most eukaryotic cells. The steroid nucleus consists of
      animation.   above. First ring A must appear followed      four fused rings that are oriented in a planar manner.
                   by ring B, then ring C and then ring D. All   Cholesterol is an amphipathic molecule with a polar hydroxyl
                   the other groups attached at the various      head group and a non-polar steroid nucleus and hydrocarbon
                   positions must appear after all four rings    side chain. In addition to having a structural role in
5                  have appeared.                                membranes, sterols are precursors for several products such
                                                                 as steroid hormones and bile acids.

    Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
1
  Part 2, Step 6:
                                                                                                            Micellar
     Membrane formation by phosphoglycerides
                                                                                                            arrangement

                 Polar head group            Hydrogen
    Hydrophobic tail                         bonding,
                                             electrostatic
                                             attraction
2                                                                                                               Hydrophobic,
                                                                                                                Van der Waals
                                                                                                                interactions




3             Random orientation

                                                                             Bilayer arrangement
4    Action        Description of the action                                                Audio Narration
      As shown     (Please redraw all figures.)                   The amphipathic nature of the phosphoglyceride molecules consisting
      in           First show the green structures oriented       of a polar head group and a hydrophobic tail enables them to
      animation.   randomly. Next they must be surrounded by      rearrange themselves in an aqueous environment. When they come
                                                                  in contact with aqueous surroundings, they can either reorient to form
                   water (blue clouds). When this happens, the
                                                                  a micellar structure or a bilayer arrangement. In these arrangements,
                   green structures must reorient themselves in   the polar head groups are in contact with water by means of hydrogen
                   the two arrangements shown on the right
5                  after the arrows. The arrows and green
                   ovals with the text must then appear.
                                                                  bonding while the hydrophobic tails interact with each other through
                                                                  hydrophobic and Van der Waals interactions. The lipid bilayer
                                                                  arrangement is more favoured for phospholipids and glycolipids.

    Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
    Master Layout (Part 3)
       This animation consists of 4 parts:


1      Part 1 – Fatty acids
       Part 2 – Membrane lipids
       Part 3 – Proteins in membrane structures
       Part 4 – Properties of cell membranes

                                                                   Glycoprotein
2                Glycolipid
                                              Outside

                                                Integral protein




3                                                                                 Lipid
                                                                                  bilayer



     Phospholipids

4                                               Sterol



                                              Inside
         Peripheral
         protein

5
    Source: Biochemistry by A.L.Lehninger, 4th edition (ebook)
    Definitions of the components:
1   Part 3 – Proteins in membrane structures
    1. Lipid bilayer: The flat membrane sheets that form a barrier around cells consisting of
    two layers of lipid molecules is known as the lipid bilayer. The hydrophobic tail regions
    are sequestered within the bilayer, away from the aqueous environment while the polar
2   heads face outward and interact with the surrounding molecules. The bilayer is also
    embedded with proteins that perform specific functions for the cell.
    2. Integral proteins: Those proteins that span the membrane and are embedded within
    the lipid bilayer are known as integral proteins. They interact extensively with the
    hydrophobic chains of lipids and cannot be easily dissociated from the membrane.
    3. Peripheral proteins: Peripheral membrane proteins, however, are only bound to the
3   membrane surfaces by means of electrostatic and hydrogen bond interactions with the
    polar head groups of the lipids. They can be easily dissociated from the membrane with
    mild agents such as salts, acids or alkali since they are not embedded within it.
    4. Glycoprotein: Carbohydrate groups are often covalently attached to proteins to form
    glycoproteins. The sugar residues are typically attached to the amide nitrogen atom of the
    aspargine side chain or to the oxygen atom of the serine or threonine side chain. These
4   glycoproteins are components of cell membranes and have a variety of functions in cell
    adhesion processes.




5
1
  Part 3, Step 1:
     Integral proteins - Bacteriorhodopsin

                                                                               Amino acid sequence of membrane protein

                                                       AQITGRPEWIWLALGTALMGLGTLYFLVKGM
                                                       GVSDPDAKKFYAITTLVPAIAFTMYLSMLLGY
2                                                      GLTMVPFGGEQNPIYWARYADWLFTTPLLLL
                                                       DLALLVDADQ G TI LALVGAD GIM IGTGLV GAL
                                                       TK VYS YR F V W WAI S TAAM LYI LYV LF F G F T S K




3
                                                       AESMRPEVASTFKVLRNVTVVLWSAYVVVW
                                                       LIGSEGAGIVPLNIETLLFMVLDVSAKVGFGL
                                                       I LLR S RAI F G EAEAPE PSAD GAAAT S

                                                                          Residues of the 7 membrane-spanning helices
       Membrane spanning a-helices                                        (largely non-polar)
                                                                          Charged residues
4    Action Description of the action                                                             Audio Narration
     As shown (Please redraw all figures.)                       Bacteriorhodopsin is an archaeal integral membrane protein that
     in         First show the figure on the left. The red       plays a role in energy transduction, using light energy for the
     animation. box must then appear which must be               transport of protons from inside to outside the cell. It is made of seven
                   zoomed into to show the figure on the right   membrane-spanning alpha helices that are oriented perpendicular to
                   with the highlighted regions as depicted      the plane of the membrane. Determination of the amino acid
                   along with all the labels and the key shown   sequence of this protein revealed that most of the residues within the

5                  below.                                        membrane are non-polar, thereby allowing favorable interactions with
                                                                 the lipid hydrocarbon chains. Very few charged residues were found
                                                                 in the structure.

    Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
    Part 3, Step 2:
1    Integral proteins – Porins                                                                                          --
                                                                                                                          -


       Hydrogen bonded b-strands

     Amino acid sequence of porin from
2    Rhodopseudomonas blastica



                                                                                                                              Hydrogen
        Hydrophobic


3
                                                                                                                              bonds
        residues (on
        surface of
        structure)

       Hydrophilic
       residues
       (buried inside)

4    Action Description of the action                                                            Audio Narration
     As shown in (Please redraw all figures.)                   Porins are another class of integral membrane proteins that form channels
     animation. First show the structure on top with its label. within the membrane. They are composed entirely of b-strands with
                 Then show the dotted arrows and the figure     essentially no alpha helices in their structure. These beta strands are
                 on right top. The brown circles must appear    hydrogen bonded to each other to form a beta sheet which folds to form a
                 and pass through the blue cylinder. This must hollow cylindrical structure. The folding occurs such that the polar amino
                 happen continuously throughout this            acid residues line the inside of the cylinder, thereby making it hydrophilic.

5                animation. Simultaneously, the green box       This allows the channel to be filled with water and also allows passage of
                 must appear and this region must be zoomed small ions and charged molecules. The non-polar residues facing outside
                 into and the figure below must be shown with interact hydrophobically with the lipid chains of the membrane.
                 its labels and the key on the left.
    Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
1
  Part 3, Step 3:
     Peripheral proteins
                                  Acid/alkali added –
                                  change in pH                      Dissociation

                        Integral proteins


2
                                                                            Peripheral membrane proteins




3                                                    Dissociation



4     Action          Description of the action                                           Audio Narration
      As shown in (Please redraw all figures.)                      Peripheral membrane proteins are attached to either
      animation. First show the figure in the middle with the       the outside or inside surface of the membrane via
                    yellow and blue shapes labeled a-e. Next
                    show the blue cloud appearing on the blue       electrostatic and hydrogen bond interactions with
                    shapes with the corresponding label. The blue   either the lipid heads of the membrane or with other
                    shapes, d & e, must then dissociate from the
                                                                    integral proteins. These polar interactions can be
5                   figure as shown.
                                                                    easily disrupted by addition of acids or alkali which
                                                                    modify the pH or by addition of salts.

    Source: Biochemistry by A.L.Lehninger, 4th edition (ebook)
1
  Part 3, Step 4:
      Prediction of transmembrane helices – Hydropathy index                                                       Each amino acid is associated
                                                                                                                   with a free energy change for
                                                                                                                   its transfer from a hydrophobic
                                                                                                                   to aqueous environment.

                                                                                                                                   Threshold value for
2                                                                                                                                  helix detection




                                                                                        Hydropathy index, kJ/mol
                    ~ 20 amino


3                   acid residues
                                          ~ 30 Ao

                      Free energy calculations are made for
                      transfer of every 20 amino acid residues
                      (i.e. 1-20, 2-21, 3-22 etc.) from
                      hydrophobic to aqueous environment.
                      This is plotted as a hydropathy plot.                                                          First amino acid residue in window
4
      Action Description of the action                                                                                  Audio Narration
       As         (Please redraw all figures.)               It is possible to predict transmembrane helix regions of a protein by calculating the free
       shown in   First show the long chain like structure   energy changes associated with the transfer of residues from a hydrophobic to aqueous
       animatio                                              environment. The width of a membrane is typically around 30Ao, which can fit
                  shown in the centre with the labels.       approximately 20 amino acid residues. Therefore the free energy change for
       n.         Next show the dialogue box on the          hypothetical alpha helices formed every 20 residues, from residue1 to 20, 2 to 21, 3 to
                  right top followed by the dialogue box     22 and so on are calculated until the end of the sequence is reached. These free energy

5                 at the bottom. Once this is shown, the
                  graph on the right must appear with
                                                             changes are plotted against the first amino acid residue of every 20-residue window ito
                                                             obtain a hydropathy plot. A peak above 84 kJ/mol is indicative of a likely membrane
                                                             spanning helix. This, however does not detect membrane spanning b sheets.
                  the arrow mark and text box.
    Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
    Master Layout (Part 4)
       This animation consists of 4 parts:


1
                                                                                               Bleach
       Part 1 – Fatty acids
       Part 2 – Membrane lipids




                                                                      Fluorescence intensity
       Part 3 – Proteins in membrane structures
       Part 4 – Properties of cell membranes
       Fluorescence Recovery After Photobleaching (FRAP)


2                                  Bleach
                                                           Recovery                                     Recovery


                                                                                                    Time




3       Lateral diffusion
                                         Very fast
                                            1 mm/s




4     Transverse diffusion
      (flip-flop)                       Very slow
                                         t1/2 in
                                         days



5
    Source: Biochemistry by A.L.Lehninger, 4th edition (ebook)
    Definitions of the components:
1   Part 4 – Properties of cell membranes
    1. Fluorescence Recovery After Photobleaching (FRAP) : This is a technique by which
    a cell surface component is first labelled by means of a fluorescent molecule and a small
    region of the cell surface is viewed by means of fluorescence microscopy. The fluorescent
2   molecules in the region being viewed are destroyed by a laser pulse, a process known as
    bleaching. Once this occurs, the time required for fluorescence to reappear in this region
    is plotted against the fluorescence intensity. This helps in understanding the movement of
    molecules across the cell surface.
    2. Lateral diffusion: The process by which membrane components move laterally from
    one region to another in the same plane. This is a quick process and takes place in a
    matter of microseconds. Proteins exhibit varying degrees of lateral mobility, with some
3   being as mobile as lipids and others being almost immobile.
    3. Transverse diffusion (flip-flop): This is a process by which molecules in the
    membrane transition from one surface of the membrane to the other. The time required
    for transverse diffusion is significantly more than that for lateral diffusion and can be
    measured by electron spin resonance techniques. This process is made quicker by the
    enzyme ‘flippase’.
4   4. Fluid Mosaic Model: The overall organization and properties of biological membranes
    were proposed by Jonathan Singer and Garth Nicolson in 1972 as the Fluid Mosaic
    Model. They proposed that membranes are two-dimensional solutions of oriented lipids
    and globular proteins, with the lipids serving as a “solvent” for integral membrane proteins
    and functioning as a permeability barrier. They also hypothesized that membrane proteins
    undergo lateral diffusion freely but not transverse diffusion.

5
1
  Part 4, Step 1:
       Lateral diffusion of membrane components - FRAP
                                                                                                                                      Bleach




                                                                                                             Fluorescence intensity
                                                                           Laser
2
                                                                                                                                               Recovery
                                                              Bleaching
                      Recovery
                                                                                                                                           Time
                                                              Region being viewed through


3                        Cell surface components labelled
                         with fluorescent molecule
                                                              microscope




4   Action           Description of the action                                                          Audio Narration
    As shown     (Please redraw all figures.)                                                   Lateral diffusion of membrane components can be proved
    in           First show the blue figure with the green spots on it and the                  using fluorescence recovery after photobleaching
                 corresponding labels. Followed by the red box and its label. Next, show        technique. A cell surface component is first labelled by
    animation.   the ‘laser’ and its light falling on the green spot at the bottom. Once this   means of a fluorescent molecule and a small region of the
                 happens, the green spot must change color to grey and the label
                                                                                                cell surface is viewed by means of fluorescence
                 ‘bleaching’ must appear. Then the laser must be removed and the grey
                                                                                                microscopy. The fluorescent molecules in the region being
                 spot should move down and disappear and simultaneously the green spot

5                on top must move into the red box as shown in animation. When
                 bleaching occurs, the downward slope of the graph must be shown and
                 when the green spot on top enters the red box, the upward curve must be
                                                                                                viewed are destroyed by a laser pulse, a process known as
                                                                                                bleaching. Fluorescence however reappears in the region
                                                                                                after a certain time that is dependent on the diffusion
                 shown to appear.                                                               coefficient of the molecules.
     Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
    Part 4, Step 2:
1    Lateral diffusion Vs Transverse diffusion



      Lateral diffusion
                                                 Very fast


2                                                 1 mm/s
                                                                                                    Flippase




    Transverse diffusion



3
                                                Very slow                                                   Very fast
    (flip-flop)
                                                 t1/2 in                                                     t1/2 in
                                                 days                                                        seconds




4    Action Description of the action                                                              Audio Narration
     As shown in (Please redraw all figures.)                                               The Fluid Mosaic model explains the lateral
     animation. First show the green figures on top with the title ‘lateral diffusion’. The diffusion of membrane components but not the
                 blue shape must move as indicated by the arrow and reach the               transverse diffusion. Lateral diffusion is a rapid
                 position indicated on the right. This must occur quickly. Next show the process taking place in the range of microseconds.
                 figure on left bottom with the title ‘transverse diffusion’. The blue      However, transverse diffusion, also known as the
                 shape alone must flip very slowly in the direction indicated by the        ‘flip flop’ reaction takes place very slowly over a

5                arrow to reach the position shown on the right. Next, the brown oval       period of several hours. This reaction is facilitated
                 must appear with its label. When this happens, the flipping must take by the enzyme flippase, which carries out transverse
                 place quickly in the same way as the previous diagram.                     diffusion in the time range of few seconds.

    Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
1
  Part 4, Step 3:
     Factors determining membrane fluidity
                                                                                                             Length of fatty
                                                                                                               acyl chain –
             Presence of                                                                                      longer chain,
             cholesterol                                                                                        higher Tm
              – greater




                                                Fluid-like
             cholesterol,
2             higher Tm




3                                               Solid-like
                                                                    Tm

                                                               Temperature                                   Degree of
                                                                                                           unsaturation –
                                                                                                           Saturated fatty
                                                                                                           acids increase
                                                                                                                 Tm
4    Action Description of the action                                                             Audio Narration
     As shown in (Please redraw all figures.)                  The fluidity of any biological membrane is dependent on the properties of the
     animation. The graph must appear gradually. As the        fatty acid chains present in it. Transition of the membrane from a rigid state to
                  graph is appearing in the centre, the text   a fluid state occurs abruptly as the temperature is increased and crosses the
                  around it must appear sequentially as        melting temperature, Tm. This melting temperature is a function of the length
                  shown.                                       of fatty acyl chains present and their degree of unsaturation. Increase in
                                                               length of fatty acyl chain increases the Tm while increase in the degree of

5                                                              unsaturation decreases the Tm. In other words, greater number of double
                                                               bonds disrupts the packing order achieved by saturated fatty acids thereby
                                                               decreasing the Tm. In animals, the cholesterol content is another regulator of
                                                               fluidity. Greater the amount of the bulky steroid, higher is the Tm.
    Source: Biochemistry by Lubert Stryer, 6th edition (ebook)
1   Interactivity option 1:Step No: 1
     Membrane lipids are useful for designing lipid vesicles known as liposomes, which consist of
     small aqueous compartments surrounded by a lipid bilayer. These liposomes are increasingly
     being used as drug delivery systems in hydrophobic environments. Shown below is an
     example for formation of a glycine-containing liposome. Click on the green phospholipid layer
     to view liposome formation and then answer the question below.
2     Glycine in water




                                Sonication                                 Gel filtration

3

     Phospholipid
4    (Click here)

     Interacativity Type       Options                                                  Results
                           (Please redraw all figures.)       When the user clicks on the green layer, the animation must be
     Click to view         User must click on the green       shown. The green layer shown at the bottom must gradually form
     experiment & then     layer at the bottom of the first   green circles as shown in the middle panel and must surround a few
                                                              red dots. Once this happens, the arrow saying ‘gel filtration’ must be
     choose the correct    figure to view the animation



5
                                                              shown and the red dots must disappear leaving only the green
     answer.               after which the question with
                                                              circles enclosing the red circles. The user must then answer the
                           4 options must appear and
                                                              question shown in the next slide. Correct answer is C. If user gets it
                           user must be allowed to            right, ‘correct answer’ must be displayed otherwise ‘wrong answer’
                           choose any 1 option.               must be displayed.
1   Interactivity option 1:Step No: 1
     What property of membrane lipids allows them to form such liposome vesicles?




     A) Their low melting temperature
2
     B) The presence of cholesterol



     C) Their self-sealing nature
3
     D) The presence of glycerol in the phospholipids




4
     Interacativity Type       Options                                                  Results
                           (Please redraw all figures.)       When the user clicks on the green layer, the animation must be
     Click to view         User must click on the green       shown. The green layer shown at the bottom must gradually form
     experiment & then     layer at the bottom of the first   green circles as shown in the middle panel and must surround a few
                                                              red dots. Once this happens, the arrow saying ‘gel filtration’ must be
     choose the correct    figure to view the animation



5
                                                              shown and the red dots must disappear leaving only the green
     answer.               after which the question with
                                                              circles enclosing the red circles. The user must then answer the
                           4 options must appear and
                                                              question shown in the next slide. Correct answer is C. If user gets it
                           user must be allowed to            right, ‘correct answer’ must be displayed otherwise ‘wrong answer’
                           choose any 1 option.               must be displayed.
1       Questionnaire
    1. How many double bonds would be present in a fatty acid having the systematic name
       “all-cis-∆9, ∆12, ∆15-Octadecatrienoate”?

    Answers: a) 1 b) 2 c) 3 d) 4
2
    2. Which of the following is a saturated fatty acid with 18 carbon atoms?

    Answers: a) cis- ∆9-Octadecenoate b) Octadecanoate        c) Eicosanoate
      d) Tetradecanoate
3   3. Which of the following components is not present in Phosphatidyl inositol?

    Answers: a) Sphingosine b) Glycerol c) Phosphate d) Inositol

    4. If the degree of unsaturation of fatty acyl chains increases, what happens to the Tm?


4   Answers: a) Tm increases b) Tm remains same c) Tm decreases d) None of the above

    5. The threshold value of hydropathy index for detection of alpha helices is?

    Answers: a) -22 kJ/mol b) +22 kJ/mol c) +67 kJ/mol d) +84 kJ/mol

5
              Links for further reading
                                      Books:
          Biochemistry by Stryer et al., 6th edition
   Biochemistry by A.L.Lehninger et al., 4th edition
         Biochemistry by Voet & Voet, 3rd edition
                             Research papers:
Singer, S. J. & Nicolson, G. L. The Fluid Mosaic Model of the Structure of Cell Membranes.
                              Science 1972, 175 (4023), 720-731.

								
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