Micro Ch 2

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Micro Ch 2
2016-05-20 12:46:51

Micro Ch 2
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  1. amino acid
    subunit of a protein
  2. atom
    • basic unit of matter
    • made up of 3 major components:
    • neutrons, protons, electrons
  3. Recall structure of an atom
    • Protons and neutrons in center of atom making up heaviest part of atom - the nucleus - , electrons for "electron cloud" around the nucleus
    • Number of protons normally equals the number of electrons, so atom has no charge
  4. atomic number
    • is the number of protons in it's nucleus
    • an atom is distinguished by it's atomic number
    • Is the bottom number next to element symbol
  5. mass number
    • the sum of the number of protons and neutrons
    • (electrons are too light to contribute to the mass)
    • Is the top number next to element symbol
  6. element
    • consists of only one kind of atom and cannot be separated into simpler parts 
    • smallest unit
    • are 92 naturally occurring elements
  7. 4 basic elements living material is made up of
    • C - carbon
    • H - hydrogen
    • O - oxygen
    • N - nitrogen
  8. What two other elements are also found in all livings
    • P ~ Phosphorus
    • S ~ Sulfur
  9. isotopes
    elements which have different numbers of neutrons
  10. octet rule
    • most atoms are most stable when their outer shell has 8 electrons (or a full outer shell)
    • *exception is hydrogen,
    • Recall first shell has limit of 2 electrons
  11. ion
    an atom that gains or loses an electron, making it no longer neutral
  12. cations
    • positively charged ions
    • "you ran over the 'cat'.. hahaha"
  13. anions
    • negatively charged ions
    • "your an 'a-hole"
  14. ionic bonds
    • weak bonds
    • formed btwn cations and anions because of strong attractions btwn positive and negative charges
    • resulting product is call a salt
    • Ex: NaCl = sodium chloride (table salt)
  15. covalent bond
    • formed when atoms share pairs of valence electrons
    • strong bonds
    • number of covalent bonds an atom can form is the number of electrons the atom must gain or lose to fill it's outer shell

    • indicated by a dash btwn two atoms sharing a pair of electrons: C-H; double bond C=H
    • "They entered into a covenant"...
  16. molecule
    • two or more atoms joined together by covalent bonds
    • may be of the same or different elements
  17. compound
    a molecule consisting of more than one element
  18. non-polar covalent bond
    forms when the electrons are shared equally

    "No one is bi-polar. It's a happy covenant"
  19. valence electrons
    • those electrons found in an atoms outer shell
    • particularly important in chemical bond formation
  20. What exactly is electronegativity?
    The ability of an atom to attract electrons to itself in a molecule
  21. polar covalent bond
    • when one atom in a covalent bond is significantly more electronegative than the other, the electrons are shared unequally
    • slight separation of the charge is called a dipole (the atom that is pulling harder has a more negative charge, and vise versa)
  22. Dipole
    • The slight separation of charge in polar covalent bond
    • indicated by greek symbol Delta ( δ )
    • The atom with slight positive charge is δ+

    The atom with slight neg charge is δ-
  23. hydrogen bonds
    weak bonds that result from the attraction of the hydrogen atom in a polar molecule to an electronegative atom in the same or another polar molecule
  24. electronegativity
    • the ability of an atom to attract electrons to itself in a molecule
    • an atom with a significantly higher electronegativity is better able to attract electrons
  25. mole
    • a mole of a compound is the same number of molecules as a mole of another compound
    • equal to 6.022 x 1023
    • Ex: One mole of sodium chloride weighs 58.4 grams, whereas one mole of potassium chloride weighs 74.55 grams
  26. molarity
    • the molarity (M) of a solution is the number of moles of a compound dissolved in 1 liter of solution
    • Ex: 1 M solution of NaCl has 58.4 grams of NaCl dissolved in 1 liter of aqueous solution
  27. most important molecule in the cell
    • water
    • making up over 70% of all living organisms by weight
    • Hydrogen bonding plays a very important role in the properties of water ~ depends on temp
    • the polar nature of water accounts for it's ability to dissolve a large number of compounds (If compounds are polar or have + or - charge)
  28. hydrophilic
    • water loving
    • includes salts and polar molecules
  29. hydrophobic
    • water fearing
    • do not dissolve in water because they cannot form hydrogen bonds
  30. pH
    • Important property of aqueous solutions
    • a measure of their acidity on scale of 0 -14, in which lower the number the more acidic

    Measures the concentration of Hin moles per liter
  31. buffers
    compounds which stabilize the pH of solutions
  32. adenosine triphosphate
    • ATP, energy currency of the cell
    • effective energy carrier cause the 3 negatively charged phosphate groups repel each other, so bonds joining them are unstable
    • Easily broken to release sufficient amt of energy to drive cellular process
  33. high energy phosphate bonds
    • refers to the phosphate bonds in ATP
    • relatively high amt of energy released when bonds are hydrolyzed makes them high energy
    • symbolized by ~ (see pg 24)
  34. What do organic molecules contain often contain that are important to the functioning of the molecule?
    • Important functional groups that modify the activity of the molecule:
    • Aldehyde
    • Amino
    • Carboxyl
    • Hydroxyl
    • Keto
    • Methyl
    • Phosphate
    • Sulfhydryl
    • *Always Aim Carefully, Help Keep My Pussy Safe
  35. What is significance of:
    Aldehyde group
    Amino Group
    • Aldehyde = carbohydrates
    • Amino = amino acids
  36. Whats significance of:
    Carboxyl group
    Hydroxyl group
    Keto group
    Carboxyl = Organic acids, including amino acids and fatty acids

    Hydroxyl = carbohydrates, fatty acids, alcohol, some amino acids

    Keto = carbohydrates, polypeptides
  37. What is significance of:
    Methyl group
    Phosphate group
    Sulfhydryl group
    Methyl = Some amino acids, attached to DNA

    Phosphate = nucleotides (subunit of nucleic acids), ATP, signaling molecules

    Sulfhydryl = Part of the amino acid cysteine
  38. Adenosine diphosphate
    • ADP 
    • formed when terminal phosphate bond of ATP breaks
  39. Macromolecules
    • Large molecules
    • 4 major classes: 
    • proteins
    • carbohydrates
    • nucleic acids
    • lipids
  40. Polymers
    • POLY means many
    • Most macromolecules are polymers, formed by joining subunits together
  41. dehydration synthesis
    a chemical reaction that removes H2O

    Used in forming macromolecules
  42. hydrolysis
    • the reverse of dehydration synthesis
    • involves breaking down macromolecule to it's subunits by adding H2)
  43. Some of the most important roles of proteins include:
    • Catalyzing reactions (enzymes)
    • Transporting molecules
    • Motility (proteins are essential components of flagella and cilia)
    • Cell framework (Protein make up cytoskeleton)
    • Sensing and responding to conditions outside of cell (P on cell surface recognize conditions in external environ & tell cell machinery)
    • Regulating gene expression (P bind to DNA & regulate gene expression)
    • *Proteins R Similar To Moms, Carry Cells Regularly
  44. amino acids
    • subunits that make up proteins
    • 20 major amino acids can be arranged to make infinite # of combos
    • Only source of nitrogen in diet. Also has sulfur
    • Held together by peptide bonds

    All amino acids have a central carbon atom bonded to a carboxyl group, an amino group, and a side chain (R). The side chain (which distinguishes different amino acids) gives it's characteristic properties
  45. peptide bond
    type of covalent bond formed when the carboxyl group of one amino acid reacts with the amino acid of another, releasing water (dehydration synthesis)

    Holds amino acids together
  46. Polypeptide
    • results from the joining of amino acid subunits by peptide bonds
    • One end of molecule has a free amino group (the N terminal or amino terminal end)
    • The other end has a free carboxyl group (the C terminal or carboxyl terminal end)

    *Recall in class, the backbone will be NCC NCC NCC NCC
  47. Protein
    one or more long polypeptides folded to create a functional molecule

    *Distinction btwn polypeptide and protein is not always clear, sometimes used interchangably
  48. Four levels of protein structure
    • Primary
    • Secondary
    • Tertiary
    • Quaternary
  49. Primary structure of a protein
    • Is determined by the number and sequence of amino acids in the polypeptide
    • In large part, determines the final shape of the protein and it's properties
    • average size polypeptide consists of about 250 amino acids
  50. Secondary structure of a protein
    • the three-dimensional shape of localized regions
    • results from folding of the various parts of the protein into two major patterns, either:
    • alpha (α)- helix (spherical)
    • beta (β) pleated sheet
  51. tertiary structure
    the distinctive 3D shape of the folded entire protein

    • determined primarily by sequence of amino acids and whether or not they interact with water
    • The combo of strong and weak bonds btwn various amino acids results in the tertiary structure
  52. What 2 major shapes exist for tertiary:
    Globular : tend to be spherical and water soluble

    Fibrous : are elongated and insoluble
  53. Quaternary structure
    The specific shape that results when proteins consist of more than one polypeptide, whether identical or different
  54. protein chaperones
    proteins that help other proteins fold properly
  55. protein domain
    • a region or substructure (of a protein) consisting of sheets and helices that fold into a stable structure independently of other parts of the molecule
    • different domains are associated with specific functions
  56. substituted proteins
    • proteins that have other molecules covalently bonded to side chains of some of their amino acids
    • Proteins are named after the molecules covalently joined. Ex: is sugar, is a glycoprotein; if lipid, is a lipoprotein
  57. denaturation
    • High temp, extreme pH, and certain solvents can break bonds within protein, causing it's shape to change
    • Becomes denatured and no longer functions
    • May be reversible, may be permanent
  58. Carbohydrates
    • Diverse group of compounds that include sugars and starches. 
    • Play critical roles in biology:
    • Energy source
    • Energy storage: organisms can store excess energy n nutrients for later by making certain carbs that function as reserve material
    • Source of carbon for biosynthetic products: many microbes can make all cell parts from single carb - glucose
    • Component of DNA & RNA: subunits contain sugar
    • Structural components of cells: some types of cell walls are composed of sugar-containing material
  59. What do carbs contain?
    all contain carbon, hydrogen and oxygen atoms in an approx ratio of 1:2:1
  60. Monosaccharides
    • simple sugars, only have single unit
    • Classified by # of carbon atoms they have, most common have 5-6
  61. 5 carbon Monosaccharides
    • Ribose - Component of RNA
    • Deoxyribose - component of DNA
  62. 6 carbon Monosaccharides
    • Glucose - common subunit of disaccharides
    • Galactose - component of milk sugar
    • Fructose - fruit sugar
    • Mannose - found on surface of some microbes
  63. Disaccharides
    • two monosaccharides joined together by covalent bonds
    • joined together by dehydration reaction btwn pair of their hydroxyl group, w loss of water
  64. Common disaccharides
    Lactose = Glucose + Galactose (Milk sugar)

    Maltose = Glucose + glucose  (breakdown product of starch)

    Sucrose = Glucose + fructose (table sugar)
  65. Polysaccharides
    • large molecules composed of long chains of monosaccharide subunits
    • Includes:
    • Cellulose: principle component of plant cell walls & most abundant organic molecule on earth
    • Starch: energy storage in plants
    • Glycogen: energy storage product in animals and some bacteria
    • Dextran: storage product in some bacterial cells
    • Chitin: major organic component in exoskeleton of insects, also in cell wall of fungi
    • Agar: found in cell walls of some algae, gelling agent for bacterial media
  66. DNA
    • deoxyribonucleic acid
    • the master molecule of the cell
    • is a double stranded helical molecule
    • encodes all of the cell's properties
    • Info in DNA is converted to form RNA, which is then translated to make proteins
  67. nucleic acids
    • carry genetic info
    • cells decode, convert info into sequence of nucleotides
  68. nucleotide of DNA
    • Is one subunit of DNA
    • has 3 parts: 
    • nucleobase
    • deoxyribose
    • a phosphate group
  69. What are the four bases for DNA
    • can be characterized by their ring structures:
    • Purines - Adenine and Guanine (Amy and Gertrude)  
    • Each consisting of 2 fused rings 

    • Pyrimidines - Cytosine and Thymine (Chris - in both DNA & RNA; Tim - ONLY IN DNA)
    • Each consists of single ring
  70. How specific is the hydrogen bonding between nucleobases in DNA.
    What is complementary & base pairing rules
    • Amy (Adenine) will only marry Tim (Thymine)
    • Gertrude (Guanine) will only marry Chris (Cytosine)

    The pair of nucleobases that bond are said to be complementary and are referred to as base-pairing rules.
  71. RNA
    Ribonucleic acid - involved in process that decodes info from DNA to crease sequence of amino acids in proteins
  72. Differences in RNA vs DNA
    • In RNA, contains Uracil instead of Tim
    • *Uracil is Russian guy, don't trust him with DNA
    • In RNA, sugar is ribose
    • RNA is shorter and exists as single chain of nucleotides
  73. Lipids
    • Critically important in structure of membranes, function as gatekeepers, prevent cell leakage and keep molecules from entering cells
    • Are non-polar & hydrophobic
  74. Simple lipids
    • contain only carbon, hydrogen and oxygen
    • most common are fats = fatty acids linked to glycerol
    • May be liquid or solid at room temp
  75. Explain fatty acids
    • are long chains of C atoms bonded to H atoms
    • Most have even # of carbon atoms
    • Can be divided into 2 groups based on the presence of double bonds btwn C atoms: 
    • Saturated fatty acids have NO double bonds. Saturated means they have max # of hydrogen atoms
    • Unsaturated fatty acids contain one or more double bonds.  Can be cis or trans
    • *Those w one double bond are monounsaturated
    • **Those with more than one double bond are polyunsaturated
  76. What is cis or trans
    • refers to unsaturated fatty acids
    • CIS means the hydrogen atoms attached to the double-bonded carbon molecules are on the same side of the bond
    • TRANS fatty acids have hydrogen atoms on opposite sides of the double bond
  77. Melting points of fats
    • Fats that contain only saturated fatty acids are typically solid at room temp, cause the straight long tails of fatty acids packed tightly together
    • Fats with one or more unsaturated fatty acids tend to be liquid at room temp cause fatty acids have kinks in long tails that prevent tight packing
  78. compound lipids
    • contain fatty acids and glycerol as well as other carbon, hydrogen and oxygen
    • Most important are phospholipids
  79. Phospholipids
    • most important compound lipids
    • contain phosphate group linked to one variety of other polar molecules
    • The phosphate-containing portion is the polar head and is soluble in water (hydrophilic)
    • The fatty acid portion is insoluble in water (hydrophobic)
    • Essential component of cytoplasmic membranes, forms bilayer
  80. Steroids
    • simple lipids that have a characteristic structure consisting of four connected rings
    • Structure is quite different from fats, but classified as lipid cause insoluble in water