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biology chap 4-5 (chapter 5 (lipids -not generally considered…

- - - - monosaccharides -multiple of CH2O
        
        can be classified by
        
        location of carbonyl group -aldose or ketose
        
        size of carbon skeleton (3-7)
        
        5 and 6 carbon sugars tend to form rings
        
        how parts are arranged around asymetric carbon
        
        glucose and galactose differ only by placement
        
        used by cells for
        
        fuel
        
        turned into other organic molecules
        
        for example glucose: C6H12O6
      - disaccharides -two monosaccharides with glycosidic linkage
        
        for example maltose (malt sugar) is formed by two glucoses
        
        and sucrose (table sugar) is formed by a glucose and a fructose
        
        plants transport carbohydrates in the form of sucrose
        
        and lactose is glucose and galactose
        
        lactose intolerant people don't have the enzymes necessary to break it down
    - - storage
        
        starch -made of glucose monomers
        
        amylose -a simple, unbranched starch
        
        amylopectin -a complex starch with many branches
        
        glycogen -a polysaccharide stored in the liver and muscle cells of animals, used for energy when sugar is low
      - structural
        
        cellulose -a polysaccharide made of glucose monomers used for cell walls in plant cells
        
        the glucose monomers are shaped differently from the monomers used in starch. their hydroxyl groups are on the other side of the glucose molecule, causing cellulose to be straight and never branched
        
        very few animals can digest cellulose
        
        termites and cows have bacteria in their guts that can convert it into other compounds
        
        some fungus can also digest cellulose
        
        chitin -also made of a different kind of glucose
        
        used by arthropods to build their exoskeletons
  - - - structure
        
        not actually a polymer, but assembled from smaller molecules
        
        triacylglycerol
        
        1glycerol -an alcohol with three carbons each bearing a hydroxyl group
        
        3 fatty acids -16 or 18 carbons long with hydrogens, this nonpolar tail is why fats are hydrophobic
        
        bonded together by a dehydration reaction
      - saturation
        
        unsaturated -one or more double bonds
        
        double bonds cause kinks, creating a bent molecule
        
        because they cannot pack as tightly they a re liquid at room temperature
        
        saturated -no double bonds, as many hydrogens as possible
        
        no double bonds so straight
        
        pack tightly and a re liquid at room temperature
        
        hydrogenated oil -products like margarine or peanut butter are artificially saturated
        
        trans fats -artificially unsaturated
      - uses
        
        compact energy storage for animals in adipose cells
        
        also cushions vital organs
    - - structure
        
        head -hydrophilic
        
        phosphate
        
        glycerol
        
        any of a variety of molecules such as choline
        
        tail -hydrophobic
        
        two fatty acids
        
        one with a kink due to double bonds
      - when in water they group together with the hydrophobic tail pushed to the inside and the hydrophilic heads on the outside
        
        because of this they are used for the walls of cells and organelles
        
        in a way, all life depends on phospholipids
    - - for example, cholesterol
        
        used in cell membranes
        
        synthesized into sex hormones
        
        obtained from diet and produced by liver
  - - - amino acids
        
        a carbon bonded to
        
        an amino group
        
        a carboxyl group
        
        a hydrogen
        
        and an "R" group
        
        different R groups make different amino acids
        
        different amino acids -there are 20
        
        nonpolar, hydrophobic
        
        isoleucine
        
        methionine
        
        leucine
        
        phenylalanine
        
        valine
        
        tryptophan
        
        glycine
        
        alanine
        
        proline
        
        polar, hydrophilic
        
        tyrosine
        
        asparagine
        
        cysteine
        
        glutamine
        
        threonine
        
        acidic
        
        aspartic
        
        glutamic
        
        serine
        
        basic
        
        arginine
        
        histidine
        
        lysine
      - four levels of structure
        
        tertiary -overall shape of a peptide
        
        caused by
        
        hydrophobic interactions
        
        nonpolar amino acids are pushed to the middle by water and van der waals interactions hold them together
        
        hydrogen bonds
        
        disulfide bridges
        
        between the sulfers of cystein monomers
        
        quaternary
        
        more than one polypeptide chain fit together
        
        for example, hemoglobin (fromred blood cells) is made of two of two kinds of polypeptide subunits
        
        secondary
        
        caused by hydrogen bonds between atoms of amino acids
        
        alpha helix -caused by bonding in every fourth amino acid
        
        transthyretin has only one alpha helix section
        
        alpha keratin (in hair) is made mostly of alpha helix
        
        beta pleated sheet
        
        segment connected of a polypeptide chain lying side by side
        
        primary
        
        in a dehydration reaction, peptide bonds link the amino acids
        
        the resulting chain are called polypeptides
        
        the order of polypeptides determines protein structure
        
        for example, transthyretin is made of 4 chains of 127 amino acids
        
        to try to produce one of these by chance would be one in 20^127
        
        thankfully their order is not up to chance but inherited genetic information (DNA)
      - just a slight change can alterr a protein's structure
        
        for example, the substitution of valene for glutamic acid in the hemoglobin can cause a red blood cell to have a sickle shape
        
        this causes clogs in blood vessels
      - biochemists have found the order of many proteins but still don't know how they're folded
        
        misfolded proteins can cause serious problems
        
        scientists use x-ray crystallography to build 3d models of proteins
        
        some structures are difficult to determine because their stuctures are indistinct and changing
      - denaturation -a protein unfolded and no longer usefu
        
        can be caused byl
        
        exposure to chemicals that disrupt any of the bonds
        
        excessive heat
        
        changed to a nonpolar solvent
    - - movement
        
        actin and myosin proteins contract muscles
      - defense
        
        antibodies help destroy viruses and bacteria
      - hormones -coordination of organisms activities
        
        insulin regulates blood sugar
      - transport of substances
        
        hemoglobins in blood cells transport oxygen
        
        other proteins transport molecules across membranes
      - storage of amino acids
        
        Ovalbumin in egg white stores amino acids for the embryo
        
        casein in milk stores amino acids for baby animals
        
        plants have storage proteins in their seeds
      - receptor proteins -response of cell to chemical stimuli
        
        receptors on the membranes of nerve cells detect signals
      - enzymes -acceleration of chemical reactions
      - support
        
        collagen in animal connective tissues
        
        keratin in hair, horns, feathers and other
  - - - structure
        
        backbone
        
        sugar
        
        phosphate
        
        nitrogenous base
        
        cytosine
        
        thymine
        
        adenine
        
        guanine
        
        two backbones attach to each other with matching nitrogenous bases
        
        thymine to adenine
        
        cytosine to guanine
    - - structure
        
        RNA has only one backbone
        
        and uracil instead of thymine
    - - given an evolutionary view of life these can be stretched to reflect similar heritage between species
        
        for example the beta polypeptide in human homoglobin and the hemoglobin peptides of other vertabrates
  - - - from 1980 to the early 2000's the entire human genome was sequenced
      - bioinformatics -use of computer software to deal with vast amounts of information
    - - proteomics -analysis of large sets of proteins
      - genomics -analyzing sets of genes or comparing genomes of different species
  - - - dehydration reaction -two monomers are bonded with a loss of water. one monomer contributes OH and the other contributes H
        
        this is how polymers are made
      - hydrolysis -water breakage, water breaks the bond between monomers by adding hydrogen to one and OH to another
        
        for example, hydrolysis breaks down organic molecules too large to enter cells during digestion
    - - different very long sequences of these cause different structures of macromolecules
- - - - 1828 Freidrich Wohler synthesized urea out of ammonium and cyanate
        
        organic chemistry was defined as the study of all carbon compounds
  - - - how bonds with carbon are formed
        
        carbon has six electrons, two in its inner shell and four on its outer. It either gives away 4 electrons or takes 4 in order to achieve 8 valence electrons
        
        this causes carbon to be able to participate in 4 bonds at once
        
        carbon compounds are three dimensional
        
        when carbon is involved in 4 bonds it tends to take the shape of a tetrahedron
        
        when two carbons are bonded to each other and three other atoms they tend to take the shape of two intersecting tetrahedrons
        
        when carbons are double bonded, the shape of the compound remains flat
        
        carbon's most frequent bonding partners are H, O, and N
        
        examples
        
        CO2, carbon dioxide, is a carbon double bonded to two oxygens
        
        O=C=O
        
        CO(NH2)2 , Urea, has a carbon in the center with an oxygen and two NH2's bonded to it
    - - hydrocarbons -organic molecules consisting only of hydrogen and carbon
        
        not common in living organisms by themselves, but used in other organic molecules
        
        for example, in the tail of fats
        
        they can be broken down to release a lot of energy
        
        gasoline in cars
        
        fats store fuel for plants and animals
        
        they are generally nonpolar and hydrophobic
      - isomers -compounds with the same number of atoms but different structures causing different properties
        
        cis-trans isomers --same covalent bonds but different spatial arrangements
        
        when carbons are double bonded to each other and other atoms different variations are possible
        
        two given atoms could be on the same side of the bond in one isomer and on different sides of the bond in another
        
        enantiomers -mirror images
        
        when a carbon is asymetric between 4 atoms or groups of atoms, there are two different ways they can be arranged
        
        for example, Methamphetamine can be a highly addictive drug or a treatment for congestion
        
        structural isomers -different arrangements of covalent bonds between atoms
        
        for example, C5H12 can have a straight spine or a branching one. there are 18 variations
  - - - Amino -Amine, can pick up H+
        
        glycine -an amino acid
      - Sulfhydryl -Thiol, two can stabilize protein structure, causes straightness or curliness in hair
        
        cystiene -an amino acid
      - Carboxyl -carboxylic acid or organic acid, can donate H+
        
        acetic acid -gives vinegar its sour taste
      - Phosphate -organic phosphate, can contribute negative charge, causes molecules to react with water and release energy
        
        glycerol phosphate -takes part in chemical reactions in cells
        
        atp is made of adenosine and 3 phosphate groups. it can release energy when breaking off a phosphate, so it is used to store energy
      - Carbonyl -Ketone or aldehyde,
        
        acetone -the simplest ketone, propanol -an aldehide
      - Methyl -methylated compound, effects the expression of genes, effects the shape of sex hormones
        
        5-methylcytosine - a dna modified by methyl
      - Hydroxyl group -alcohol, polar, helps dissolve sugars
        
        ethanol -an alcohol in alcoholic beverages