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The Structure and Function of Large Biomolecules, But animals must carry…

- - - - In addition to forming polymers, some monomers have their own functions
  - - - 2 molecules covalently bonded w/ loss of small molecule
        
        If the small molecule is water: dehydration/condensation rxn)
        
        One molecule provides -H, the other provides -OH
        
        Rxn is repeated as monomers are added to the chain —> lengthen the polymer
    - - Hydrolysis (reverse of condensation rxn)
        
        Bond between monomers is broken by addition of water; -H attaches to one group, -OH attaches to another
- - - - Eg glucose
        
        has 2 diff structures when gluc forms a ring
        
        Alpha configuration: -OH groups positioned above the plane of the ring
        
        Beta configuration: -OH group positioned below the ring
    - - Carbonyl group
        
        C=O, exists in either the form of ketone or aldehyde
      - Multiple -OH groups
    - - Location of carbonyl group
        
        Aldose (aldehyde sugar) eg glucose —> carbonyl group at end of skeleton (i.e carbon 1)
        
        Ketose (ketone sugar) eg fructose —> carbonyl group w/in carbon skeleton (i.e any other carbon atom except carbon 1)
      - Size of carbon skeleton (3 to 7 carbons long)
        
        Hexoses (6 carbons) eg gluc, fruct
        
        Trioses (3 carbons) eg glyceraldehyde & dihydroxyacetone (both are initial breakdown pdts of gluc)
        
        Pentoses (5 carbons) eg ribose (component of RNA) & ribulose (intermediate of P-synthesis)
      - Placement of parts arranged spatially around asymmetric carbons
        
        Asymmetric carbon is a carbon attached to 4 diff atoms/groups of atoms
        
        Eg gluc and galact differ in placement of parts around one asymmetric carbon
    - - Energy source (resporatory substrate) to produce ATP
      - Monomers for disaccharide and polysaccharide synthesis
      - Raw material for synthesis of other organic molecules
    - - Monosaccharides may exist as linear (open-chain) or ring structures, which exist in a dynamic equilibrium in the cell
        
        Ring structure is the more predominant form because it is energetically more stable
        
        Eg: gluc ring form is created when the oxygen on carbon 5 links with the carbon with carbonyl group (carbon 1) and transfers its hydrogen to the carbonym oxygen to create a hydroxyl group
        
        Anomeric carbon is formed (carbon that is bonded to 2 oxygen atoms)
        
        The -OH group bonded to the anomeric carbon (eg carbon 1 in gluc) can assume 2 configurations
        
        Lying below plane of ring (alpha form of carb molecule)
        
        1 more item...
        
        Lying above plane of ring (beta form)
        
        1 more item...
        
        The ring structure is the form incoporated into di- and polysaccharides
  - - - Hydrolysis, one molecule of water id added via: incubation with dilute acid at 100C (i.e acid hydrolysis) or incubation w an enz
    - - Surcrose (gluc+fruct); maltose (gluc+gluc); lactose (gluc+galact)
      - Glycosidic bonds: C-O-C
  - - - Structure and function of polysaccharide is determined by its monosaccharides and the position of its glycosidic bonds
    - - Plants: starch
        
        Stored as starch grains in chloroplasts or w/in specialised plastids for starch storange known as amolyplasts
        
        2 kinds
        
        Amylose
        
        Simplest form; unbranced/straight chain str.
        
        Joined by 1-4 glycosidic bonds
        
        Forms a compact helical structure; 6 units per turn in the helix
        
        Amylopectin
        
        more complex form; branched str.
        
        (1,4) bonds between 2 gluc units in the straight chain
        
        (1,6) bonds at the branch points
        
        more branched=more available to digestive enz
        
        Extensive branching causes it to be highly compact - can contain up to twice as many gluc residues as amylose
        
        Branch points occur at every 12 - 30 residues and average branch length is between 24 - 30 residues
        
        All gluc monomers are in the alpha-configuration
        
        Allows certain starch molecules to be largely helical —> function of effectively storing units
      - Animals: glycogen
        
        Extensively branched: more free ends available for breakdown by enz
        
        Breakdown of glycogen stored as cytoplasmic granules in liver and skeletal muscle cells
        
        In liver, it is used as a source of gluc to maintain blood sugar levels
        
        In muscle, it serves as a fuel source to generate ATP for muscle contraction
        
        Alpha (1,4) and alpha (1,6) bonds
        
        More compact than amylopectin, alpha(1,6) bonds occur every 8-12 units
      - Anomeric carbon is involved in glycosidic bond formation, leaving very few free anomeric hydroxyl groups —> starch and glycogen are unreactive and chemically stable
      - Starch and glycogen are large molecules —> insoluble —> does not affect w.p in cells
      - Starch and glycogen have several 100s-1000s of gluc monomers —> large store of carbon (respiratory substrate)
    - - Cellulose
        
        Polymer of beta-gluc with 1-4 glycosidic bonds, up to 10000 molecules
        
        All gluc are in beta confirguration, making every monomer “upside down” with respect to its neighbours
        
        Enz that hydrolyse alpha linkages cannot hydrolyse beta linkages due to diff shapes; few organisms possess cellulase enz that can digest beta linkages in cellulose (amylase can only digest alpha 1,4)
        
        Eg humans, cellulose passes through digestive tract to be egested in faeces
        
        The cellulose abrades the wall of digistive tract —> simulate mucus secretion —> aids in smooth passage of food
        
        Can digest: eg cows and termites have protists in their gut to digest cellulose in food, fungi can digest cellulose from soil
        
        Cellulose is straight-chained and never branched; some -OH groups on gluc monomers are free to hydrogen-bond with the -OH of other celluose molecules lying parallel to it
        
        These parallel cellulose molecules held together by H-bonds are called microfibris: high tensile strength for structural support
        
        Microfibrils associate with other non-cellulose polysaccharies to form macrofibrils in cell wall —> further increases tensile strength
        
        Cellulose fibres laid down in diff orientations in diff layers —> cell wall can ithstand forces exerted in all directions
        
        Unbranched structure fits its function of providing strength/support for plant
        
        Fully permeable to water and solutes
      - Chitin (not in syllabus)
        
        Used by anthropods to build exoskeleton, exoskeleton is made up of chitin embedded in a layer of proteins; chitin is leathery and flexible at first, it becomes hard when:
        
        The proteins are chemically linked to e/o (eg in insects)
        
        Encrusted with calcium carbonate (eg in crabs)
        
        Also found in fungi cell walls
        
        Similar to cellulose, with beta-linkages, but glucse monomer of chitin has a nitrogen-containing attachment
- - - - Typiclally an additional small charged/polar molecule is also linked to the phosphate group
      - Hydrophilic head = glycerol + phosphate (+ additional small molecule if have)
      - Hydrophibic tails = 2 FA
        
        When phospholipids are aded to water they self-assemble into a bilayer to shield their hydrophobic tails from water
  - - - steroids are differenciated by the particular chem groups that attach to the rings
    - - In vertebrates it is synthesized in the liver and obtained form diet
      - Common component of animal cell memb; precursor for other steroids to be synthesized eg vertebrate sex hormones
  - - - Glycerol is an alcohol; each of its 3 carbons have a -OH groups
      - FA has a long carbon skeleton, usually 16-18 carbon atoms in length
        
        Carbon at the end of the skeleton is part of the carboxyl group (hence fatty acid)
        
        Rest of skeleton consists of a hydrophobic chain
    - - Flexibility allows them to pack tgt tightly
    - - Nearly every C=C occuring naturally is a cis double bond, which creates a kink in the hydrocarbon chain
        
        Kinks prevent molucules from packing close enough tgt to solidify
    - - 1g of fats stores 3x as much energy as 1g of polysaccharides
        
        Ok for plants to have bulky energy storage (starch) since they are immobile
- - - - At the centre of the AA is an alpha carbon atom, bonded to: amino group; carboxyl group; H atom; variable R group
        
        R groups (aka side chain) may be as simple as a H atom, or it may be a cabon skeleton with various functional groups attached
        
        Phys and chem properties of side chains determine the unique characteristics of the particular AA, affectiong its functional role in the pp
      - All AAs used in proteins are L enantiomers
        
        Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images and cannot be superimposed on e/o (like L and R hands)
    - - Nonpolar side chains (hydrophobic)
        
        Glycine (Gly/G); Alanine (Ala/A); Valine (Val/V); Leucine (Leu/L); Isoleucine (Ile/I); Methionine (Met/M); Phenylalanine (Phe/F); Tryptophan (Trp/W); Proline (Pro/P)
      - Polar side chains (hydrophilic)
        
        Serine (Ser/S); Threonine (Thr/T); Cysteine (Cys/C); Tyrosine (Tyr/Y); Asparagine (Asn/N); Glutamine (Gln/Q)
        
        Cycteine is only weakly polar —> sometimes classified as nonpolar AA
      - Electrically charged side chains (hydrophilic)
        
        Acidic
        
        Aspartic acid (Asp/D); Glutamic acid (Glu/E)
        
        Acidic AAs have side chais that are generally -ve in charge due to carboxyl groups which dissociates/ionises at cellular pH
        
        Basic
        
        Lysine (Lys/K); Arginine (Arg/R); Histidine (His/H)
        
        Basic AAs have side chains that are generally +ve in charge
        
        The terms acidic and basic only refer to the side chains because all AAs as monomers have carboxyl (acidic) and amino groups (basic)
  - - - Repeat this process to form a polypeptide
        
        repeating sequence is called a pp backbone; R groups extend from it
        
        the kind and sequence of the side chains, which determines how a pp folds and hence the protein’s final structure and chem characteristics
  - - - Sequence of AAs, determined by inherited genetic info
    - - Formed by hydrgogen bonds between repeating constituents of pp backbone (not side chains)
        
        between oxygen atoms (partial -ve charge) and hydrogen atoms attached to the nitrogens (partial +ve charge)
        
        Individual bonds are weak but because they are repeated many times over a relatively long region of backbone they can support particular shapes
      - Alpha helix
        
        Delicate coil held tgt by h-bonds between every fourth AA
      - Beta pleated sheet
        
        2 of more segments of pp (known as beta strands) lying parallel side by side connected by h-bonds
    - - superimposed on 2ndary str; 2ndary str involves interactions btwn backbone constituents but 3rtiary str is the overall shape of pp resulting from interactions btwn side chains of AAs
      - Hydrophobic interaction
        
        as pp folds into its functional shape, AAs with hydrophobic/nonpolar side chains usually end up in clusters at core of protein, out of contact with water (hydrophibic int. caused by exclusion of nonolar subst. by water)
        
        Once nonpolar side chains are close tgt, held tgt by Van der Waals interactions
        
        What are V.d.W interactions?
        
        A molecule with nonpolar covalent bonds may have +ve and -ve charges; electrons are not always evenly distributed, at any instant they may accumulate in one part of the molecule
        
        Hence ever-changing regions of +ve and -ve charge enables all atoms and molecules to stick to e/o
        
        Individually weak and only occur when molecules are close tgt, but have strong cumulative effect
      - Hydrogen bonds btwn polar side chains and ionic bonds between charged side chains also stabilize tertiary str
      - disulfide bridges (covalent bond)
        
        2 cysteine monomers (they have sulfhydryl -SH groups) are brought tgt, sulfurs bond tgt
        
        Disulfide bridge -S-S- rivets part of the prot tgt
  - - - prot transferred from aqueous soln to nonpolar solvent (eg ether, chloroform)
        
        Pp chain refolds so hydrophobic region faces outwards to solvent (unlike normal hydrophobic interaction)
      - Chemicals that disrupt 2nd/3rd structure
        
        Eg disrupt h-bonds, ionic bonds, disulfide bridges
    - - proving that information about shape is intrinsic to prot’s primary str (sequence of AAs determine prot shape; denaturation does not change AA sequence)
      - Might not alw be the case (eg fried egg does not turn back to liquid when placed into fridge)
  - - - Eg digestive enz
    - - Eg: antibodies inactivate and help destroy virus and bact
    - - Eg: casein (in milk) —> major source of AA for baby mallams; plants have storage prot. In seeds; ovlbumin (in egg white) used as AA source for developing embryo
    - - Eg: haemoglobin (iron-containing prot of vertebrae blood) tpts o2 from lungs to rest of body; channel and carrier prot across cell memb
    - - Eg: insulin and glucagon
    - - Eg: receptor prot (on dendrite i.e the end branches of a dendron) in memb of nerve cell detect signalling molecules released by other nerve cells
    - - Eg: motor prot called dyenins are responsible for undulations of cilia and flagella; actin and myosin proteins responsible for the contraction of muscles
    - - Eg: keratin (prot in hair, horns, feathers other skin appendages); silk fibres (cocoons and spiderwebs); collagen and elastin proteins provide fibrous framework in animal connective tissues
- - - - Pentose sugar
        
        DNA: deoxyribose
        
        Difference: DNA lacks one oxygen atom on the second carbon in the ring
        
        RNA: ribose
      - Nitrogenous base
        
        Each base has 1-2 rings that include N atoms
        
        They are called bases because the nitrogen tends to take up. H+ from solution hence acting as bases
        
        Pyrimidine: 1 six-membered ring of C and N atoms (cytosine, thymine, uracil)
        
        Purine: larger, six-membered ring fused to a five-membered ring (adenine, guanine)
    - - Beginning monomer has 3 phosphate groups, 2 are lost during polymerisation
        
        One to three phosphate groups are attached to the 5’ carbon of the ring
  - - - Results in a repeating pattern of sugar-phosphate units —> sugar-phosphate backbone (n-bases are not part of backbone, but attached along it)
    - - 5’ end has a phosphate attached to a 5’ carbon
        
        A poly-n.t has built-in directionality along its backbone —> from 5’ to 3’
      - 3’ end has hydroxyl group on 3’ carbon
  - - - 2 poly-n.t strands, wound around imaginary axis, form dbl helix; 2 strands in antiparallel 5’ to 3’ direction
        
        Strands held tgt by H bonds between n bases on interior of helix; A forms 2 H bonds with. T, C forms 3 H bonds with G
        
        One long DNA dbl helix in a eukaryotic chromosome includes many genes, each one a particular segment of the dbl stranded molecule, which codes for a specific pp
        
        2 strands are complimentary
        
        Hence it is possible to generate 2 identical copies of each DNA molecule in a cell that is preparing to divide (DNA structure fits function of transmitting genetic info when a cell reproduces)
    - - Exists as single strands
        
        Complimentary base pairing can still occur between regions of 2 RNA molecules or between 2 stretches of n.t in same RNA
        
        Base pairing in RNA makes 3D shape that is necessary for function
        
        Eg: tRNA (brings AA to ribo during pp synthesis)
        
        ~80 n.t long; functional shape is from base pairing between n.t where complementary stretches run antiparallel to e/o