Bio 212 Chapter 2-3

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haleygreenbean
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195748
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Bio 212 Chapter 2-3
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2013-02-05 15:05:37
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basic chem types molecules
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basic chem., carbs, lipids, proteins, nucleic acids
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  1. Hydrophilic
    •  ionic and polar
    • covalent molecules that will dissolve in water

    ·       “water-loving” 
  2. Hydrophobic
    • molecules such as C-C and C-H bonds in which are nonpolar
    • and do NOT attract H2O molecules

    ·       “water –fearing”

    ·       Does NOT readily dissolve in water
  3. Amphipathic
    •  molecules w/both polar/ionized and nonpolar
    • regions at different sites
  4. Micelles:
    : spheres of amphipathic molecules

    • · Polar ends orient towards surface attracted to surrounding
    • H2O molecules

    ·   Non-p interior (minimizes n-p and H2O interaction)
  5. heat of vaporization
    • heat required to vaporize 1
    • mol of any substance at its boiling point

    2. very high due to presence of H bonds
  6. heat of fusion
    • amount of heat energy that
    • must be withdrawn or released from a substance to change from liquid to solid
  7. Hydrolysis
    reaction when water is used to break apart another molecule

    • · process when polymer
    • is broken down into monomers

    • · water molecule added
    • back per monomer released
  8. condensation rxn
    2 or more molecules combining to form 1 larger molecule with the loss of a small molecule
  9. dehydration reaction
    • common reaction used to build larger molecules in living organisms
    • · Type of condensation rxn

    • ·  molecule of water is
    • lost

    • · links monomers to
    • form polymers
  10. cohesion
    phenomenon of water attracting each other

    · Due to H bonding

    ·  Aids in movement of water thru vessels of plants
  11. adhesion
    ability of water to attract to a surface that is not electrically neutral

    ·  Why water acts as a lubricant
  12. surface tension
    measure of attraction between molecules at surface of liquid 
  13. Importance of Acids and Bases
    1. Shapes and f(x)s of molecules

    2.  Rates of chem. Reactions

    3.  Ability of 2 molecules to bind to each other

    4. Ability of ions or molecules to dissolve in water
  14. Acids
    when certain substances release h ions (so h ion concentration increases)

    Ex/ HCl -> H+ + Cl- (chloride ion)
  15. Bases
    absorbs h ions in solution

    Releases OH- ions

    • Ex/
    • NaOH -> Na+ + OH

    Lowers H concentrations bc increase of oh ions increases probability of H+ ions to rebond w/ OH to create water
  16. pH=
    - log(base 10) [H+]
  17. buffer
    composed of a weak acid and it

    · helps to keep a constant pH

    · EX/ water (is neutral) is [H+][OH-] = [10^-7M][10^-7M] so OH- in a substance with a pH of 4 is?

    · 10^-10
  18. Carbon
    • 1. Variations in bonding allows variety of organic compounds
    • 2. Able to be form nonpolar and polar bonds

    3. Stable in wide range of temp. 
  19. Hydrocarbon
    molecules with majority/entirely H-C bonds

    Cause: C and H similar electronegativity

    Effect: poorly soluble in water
  20. functional groups
    groups of atoms w/ characteristic chemical features and properties
  21. isomers
    • 2 structures w/ identical
    • molecular formula but DIFFERENT STRUCTURES and CHARACTERISTICS 
    • 2 types: structural and stereoisomers
  22. structural isomers
    1. contain same atoms just different bonding relationships

    • Ex/ urea and
    • ammonium cyanate
  23. stereoisomers
    identical bonding but spatial positioning of atoms differ in 2 isomers

    3 types: cis, trans, and enantiomers
  24. Cis-Trans
    • a. Cis: when the 2
    • H’s in between the C- -C are adjacent

    • b. Trans: 2 Hs in
    • betw. Are opposite of each other 
  25. Enantiomers
    ·mirror images but not identical

    · share identical chem. Properties

    · different noncovalent bindings

    ·ex/ enzymes recognize one enantiomer but not the other one

    · ex. Think of a pair of gloves
  26. Carbohydrates
    • · bonded to hydroxylgroups
    • ·  composed of C, H,and O (all or close to Cn(H2O)n; n = whole #
    • 4 parts/types w/carbs:
    • 1. Monosaccharides
    • 2. disaccharides
    • 3. polysaccharides
    • 4. glycosidic bond
  27. monosaccharides
    A.single , simple sugars

    a. very water-soluble, can be transported across plasma membranes

    • b. most common, 5-6 C’s
    •                                                    
    • i.     Pentose- ribose
    •                                                   
    • ii.     Hexose
  28. disaccharides
    A. monosacc. Joined together by dehydration to form larger carbs.

    · Ex/ sucrose (table sugar) composed of fructose and glucose
  29. glycosidic bond
    A. bond formed betw. 2 sugar molecules

    · Allow molecule to branch off

    · Dehydration reaction (liberate DE WATEHHH!)
  30. polysaccharides
    • A. many monosacc.
    • Linked together to form long polymers

    • · Ex/ starch and glycogen (higher branching in glycogen, more soluble bc of open OH- sides that
    • H bond with water

    • ·Ex/ plant cellulose: for structure; chitin (in celery, external skeleton for insects) ;
    • glycosaminoglycan (for animals)

    • ·Cellulose , lacks
    • strands (why it can be stored very compactly)
  31. Lipids:
    hydrophobic molecules composed mainly of H and C atoms

    · Non-P (insoluble in water)

    · 4 types: Fats, phospholipids, steroids, and waxes
  32. How triglycerides/triacylglycerols are formed:
    · Initially:  glycerol + fatty acid –(ester bond)-> triglyceride + 3H2O

    · Dehydration reaction

    hydroxyl of glycerol and carboxyl group of fatty acids disassociate to form water 
  33. Fatty Acids
    • long chains
    • 3 types:
    • A. Unsaturated
    • B. Saturated
    • C. Trans
  34. saturated fatty acid:
    all C’s in fatty acid are linked by single covalent bonds
  35. unsaturated fats
    dif. between mono and polysaturated fatty acids:
    A. f.a. that contain one or more C- - C (double bonded CC)

    · Introduces kink into linear shape, so unsat. Fats can NOT pack as tightly as saturated fats

    • · Low melting point,
    • present as oils

    · Mostly exist in cis form

    a. Mono saturated fatty acid: one C- -C bond

    b. Polysaturated fatty acid: 2 or more C - - C bonds
  36. Trans fat
    • A. formed by synthetic process when cis is
    • altered to trans configuration

    · Cause :Gives fats more linear structure

    · Effect: higher melting point

    · Linked w/ human diseases
  37. Phospholipid
    1. similar to triglycerides, EXCEPT 3rd hydroxyl of glycerol is linked to phosphate NOT a fatty acid

    · Amphipathic: (charged, polar nitrogen head and nonpolar fatty acid end)

    ·In water, organized in bilayers : hydrophilic end towards water molecules, hydrophobic ends inward

    · Critical for cellular membrane structure
  38. Steroid
    1.4 fused rings of C atoms form skeleton of all steroids

    · Usually insoluble

    · 1 or few OH attached

    · Tiny differences in chem. Structure that lead to very different and potent hormones EX/ estrogen, testosterone 
  39. sterol
    • steroids w/ a hydroxyl group
    • ex/ cholesterol
  40. Cholesterol
    : important membrane lipid produced in liver or taken in by diet

    · Too much fat in our diets produces LDL cholesterol

    • · High levels of LDL cholesterol (bad cholesterol) lead to
    • formation of plaques in arteries

    · Cholesterol esters are produced by oxidation

    · Clots can lead to arthrosclerosis, heart attack, and stroke
  41. Waxes
    • · Contain 1 or more hydrocarbons and long structures that resemble a fatty acid attached to carboxyl group  to another long
    • hydrocarbon chain

    · Most NON – Polar, so usually act as barrier to water loss

    · Or structural suchas for bee hives
  42. Protein
    · "proteios” meaning of the 1st rank

    · Roughly 50% of organic material in animal’s body

    · C,H,O,N, and small amount of etc. like S

    When pH is lowered, increase in acidity, H attaches to carboxyl side
  43. Amino acid
    -  building blocks of proteins

    Monomers

    - 20 different amino acids

    - When C atom attached to amino group (NH2) and carboxyl group (COOH) that acts like an acid

    - When dissolved in water, central C atom gains H+ ion ( in pic) and loses H from COOH (not shown in pic)

    - All in L and D enantiomeric form except glycine bc of of 2 H attached to C
  44. side chain
    ·  determine amino acid

    · Hydro-phobic
  45. Peptide Bond
    covalent bond between carboxyl and amino group (between C and N)
  46. polypeptide
    ·  when many amino acids are joined by peptide bonds

    Linear chain

    Free amino side of chain = N terminus

    Free carboxyl side of chain= C-terminus
  47. Dehydration Reaction
    · COOH sacrifices one O2- while NH3 sacrifices 2 H+
  48. primary structure (of proteins)
    • 1. total amino acid
    • sequence from beginning to end

    Determined by: genes
  49. secondary structure of proteins
    1. folding of polypeptides

    Determined by: flexibility of amino acids that can rotate around bonds w/in peptide

    A. Helix bond: polypeptide backbone forms repeating helical structure

    • B. Determined by amino acids rotating around bonds and creating H bonds between polypeptide backbone
    • and atoms of side chains

    · Stabilized by H bonds along backbone

    C.Pleated sheet: regions of polypeptide backbone lie parallel to each other

    D. H bonds

    E. Key determinants of protein’s characteristics

    F. some shapes fall in neither category, “called random coiled regions”
  50. Tertiary Structure
    2ndary structures and “random coiled regions” fold to produce 3-D shapes

    · 3D shape of single polypeptide

    · For some proteins this is final structure

    · Determined by: amino acid side chain interaction and van der waal forces

    o Ionic bonds may form between oppositely charged side chains,

    o  Non-P amino acids: may twist into center of shape

    o  Link between 2 cystines
  51. Quarternary Structure of proteins:
    assembly of 2 or more polypeptides w/ a tertiary structure

    · Protein subunits: individual polypeptide

    EX/ hemoglobin

    · Interaction of 2 or more tertiary structures
  52. cysteine
    responsible for formation of disulfide bonds

    stabilizes tertiary structure
  53. 5 critical factors for protein stability and folding:
    1. H bonds:  vast amounts w/in polypeptide and amongst polypeptides add up to collective strong force

    2. Ionic Bonds and other polar interactions:  

    · if +,- charge on side chains, then may link by ionic bond

    · uncharged polar side chains and ionic amino acids may link

    3. Hydrophobic effect:

    • · side chains that are nonpolar anchor the amino acid that they are a part of in hydrophobic portion of
    • membrane

    4. van der waals forces: important for tertiary structure

    • 5. disulfide bridges: amino acid side chain
    • sulfhydryl(-SH) with another to create (-S-S-)

    · important for tertiary structure
  54. protein-protein interaction
    • surface of 1 protein precisely fits
    • into surface of another

    USE:

    1. H bonds

    2. ionic/other polar interactions

    3. hydrophobic effects

    4. van der waals forces

    important :

    · so that cellular processes can occur in a series of steps

    · provides shape and organization to structure
  55. domains
    (modules) portions of the protein have distinct structures and f(x)s
  56. Nucleic Acids
    · account for only 2% of animal body weight

    · responsible for storage, expression, and transmission of genetic info.

    Polymers made of nucleotides (their word for monomer) linked in phosphate backbone 
  57. Nucleotides
    a. Phosphate group

    b. Pentose (5-C) sugar

    c. Base: single or double ring of C and N atoms

    d. Phosphodiester linkages( 2 pentoses and 1 phosphate) connect nucleotides
  58. Deoxyribonucleic acid
    ·  Store genetic info. Coded in sequenced monomer building blocks

    · Double helix of 2 nucleotides

    · 4 different nucleotides based off of 4 dif. purine Bases:

    Purine Bases:

    1. Adenine(A) double rings of C and N

    2. Guanine (G) double rings of C and N

    Pyrimidine bases:

    3. Cytosine© (single ring)

    4.Thymine (T) (single ring)

    · G-C bond stronger than C-T 
  59. Deoxyribose
    • sugar associated with DNA
    • · 5-C  sugar

    ·Transmission of genetic info. To daughter cells
  60. Ribonucleic acid (RNA)
    a. Messenger RNA (mRNA)

    b. Ribosomal RNA (rRNA)

    • c. Transfer RNA (tRNA)
    •      
    • · Sugar is ribose

    · Transfer of genetic info. Into protein

    ·Contains base uracil instead of DNA’s thymine

    · Involved in decoding this information into instructions for linking together a specific sequence of amino acids to form a polypeptide chain
  61. Resolution
    ability to observe 2 adjacent objects as distinct from one another

    measure of clarity of image
  62. Contrast
    how different 1 structure looks from another- enhanced by dyes

     to visualize using by comparing  the difference in cellular structure/appearance
  63. Magnification
    • : ratio of size produced by
    • microscope to actual size
  64. light microscope
    utilizes light for illumination

    · Resolution .2 micrometers
  65. electron microscope
    • uses an electron beam for
    • illumination

    · 2 general types: TEM & SEM
  66. Transmission electron microscope:
    • beam of e’s emitted through biological  sample
    • (the b & w pics)

    · Allow to see organelles

    · Thin slices stained with heavy metals

    · Some electrons are scattered while others pass through to form an image.3
  67. Scanning electron microscope
    view surface of sample

    · Sample coated with heavy metal

    · Scan beam SURFACE to make 3D image
  68. Genome
    · defined as species’ entire complement of its genetic material 
  69. genes
    information to create cells
  70. Prokaryotes
    · Lack a membrane-enclosed nucleus

    • · 2 categories:
    • bacteria and archaea
  71. Bacteria and Archaea
    • B:
    • · Very common

    • · Most are harmless to humans, some are pathogenic
    • A:
    • ·Less common than bacteria

    · Occupy extreme environments like hot springs and deep sea vents

  72. plasma membrane
    1. double layer of phospholipids and embedded proteins

    · Important barrier between cell and external environment
  73. Cytoplasm
    1.region of cell contained w/in plasma membrane

    · Site of metabolism

    includes organelles
  74. cell wall
    1.supports and protects plasma membrane and cytoplasm

    · Made of peptides and carbohydrates

    ·Relatively porous, allows nutrients in environment to reach plasma membrane
  75. Glycocalyx
    1.an outer viscous covering surrounding the bacterium

    · Traps water and protects bacteria from drying out
  76. Capsule
    • A.(type of glycocalyx)
    • a defense system some pathogenic bacterium have

    · Thick gelatinous glycocalyx that prevents it being destroyed by animal’s immune system

    · Gelatinous also aids in attachment to cell surfaces
  77. Pili
    allow to attach to surfaces and to each other (appendage)
  78. Flagella
    1.      provide motility to prokaryote
  79. cilia
    shorter than flagella
  80. Nucleioid
    where genetic material is stored
  81. Ribosomes
    apart of protein synthesis
  82. eukaryotic cells
    Include protists, fungi, plants, and animals

    · True nucleus where DNA is housed

    ·Possess compartmentalization
  83. Organelle
    membrane-bound compartment with its own unique structure and function
  84. compartmentalization
    have membrane-bound organelles that separate cell into different regions
  85. Proteome
    all of the types and relative amounts of proteins that are made in a particular cell at a particular time and under specific conditions

    · Healthy proteomes are different than cancerous proteomes

    · Determines cell structure and f(x)

    · Gene regulation, amount of protein, amino acid sequence of a particular protein, and protein modification can influence a cell’s proteome
  86. cytosol
    region of cell not enclosed by membrane-bound organelles but inside plasma membrane

    · site of many chemical reactions (metabolism) that produces necessary materials for life

    · cytoplasm-organelles= cytosol
  87. Metabolism
    Sum of all chemical reactions by cells

    · Cytosol is hotspot for metabolism

    ·  Metabolic pathway:

    A. Catalyzed by enzyme (protein that accelerates rate of a chemical change)

    B. Some involve breakdown of a molecule into smaller components (catabolism)

    C. Others require anabolism
  88. catabolism
    breakdown of a molecule into smaller components
  89. anabolism
    synthesis of cellular molecules and macromolecules
  90. Translation
    process of polypeptide synthesis

    • Information within a gene is ultimately translated into the sequence of amino acids in a polypeptide 
  91. Ribosomes
    site of synthesis 
  92. Transfer RNA (tRNA)
    (tRNA)- brings amino acids 
  93. messenger RNA
    (mRNA)- information to make a polypeptide
  94. cytoskeleton
    3 dif. Protein filaments that aid in movement and provide structure

    · Ex of protein-protein interactions

    · Found in primarily in cytosol (but also along inner nuclear membrane)
  95. Microtubules
    · Long hollow cylindrical structures

    o Dynamic instability: when microtubules oscillate between growing and shortening phases

    o  Made by tubulin ,grow from positive end

    o  Formed at many sites in plant cells, particularly found in nuclear membrane

    o  importance: cell shape, organization and movement of chromosomes in mitosis, and orientation of cells during cell division
  96. dynamic instability
    when microtubules oscillate between growing and shortening phases
  97. centrosome/ microtubule organizing center
    site where microtubules form
  98. centrioles
    · perpendicular pair of structures

    · plants lack centrioles and centrosomes
  99. intermediate filaments
    o Found in most animal species

    o Bind in staggered array to create twisted, rope-like structure

    o  tension bearing fibers that maintain cell shape and rigidity

    o  Found inside nucleus
  100. actin filaments (microfilaments)
    o Thinnest cytoskeletal filaments

    o  Have + and – ends

    o  Key role in strength and cell shape

    • o  Anchor on proteins
    • near plasma membrane 
  101. motor proteins
    · Move on cytoskeleton

    • · category of cellular
    • proteins that use ATP as source of
    • energy to promote movement

    · 3 domains called head, hinge, and tail

    · Walking analogy:

    o Ground is a cytoskeletal filament, your leg is the head of the motor  protein, and hip=hinge

    · 3 kinds of movements:

    1. Move cargo from a to b

    2. Can remain in place and cause filament to move EX/ myacin stay in place and move actin

    3.Attempting to walk, generate force 

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