HTHS Mod 3

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jskunz
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HTHS Mod 3
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2013-10-07 18:45:41
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Molecular Level of Organization
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  1. Organic vs. inorganic compounds
    • Inorganic are relatively simple, their molecules have only a few atoms & can't be used by cells to perform complicated biological functions
    • Organic, by contrast, are relatively large, have unique characteristics which allow them to carry out complex functions
  2. Important categories of organic compounds
    • Carbohydrates
    • Lipids
    • Proteins
    • Nucleic acids (DNA, RNA)
  3. Carbons properties that make it useful to living organisms
    • Can form bonds w one to thousands of other carbon atoms to produce large molecules that can have different shapes. Due to this, the body can build many different organic compounds
    • The large size & fact it does not dissolve easily in water makes it useful materials for building body structures
  4. Organic Compound bonds
    • Carbon always makes four bonds, usually covalent bonds. (carbon has 4 electrons in outer shell, so can either give 4 electrons or take 4 electrons to complete outer shell)
    • The 4 bonds can be single, double, or triple covalent. 
    • Single and double ar commonly found in organic molecules from living things; triple bonds are uncommon in nature
  5. carbon skeleton
    the chain of carbon atoms in an organic molecule
  6. hydrocarbon
    when carbons are bonded to hydrogen, in the carbon skeleton
  7. functional atoms
    • other atoms or molecules bound to a hydrocarbon skeleton
    • each type has specific arrangement of atoms that confers characteristic chemical properties on the organic molecule
  8. Other atoms that often bond with carbon are
    hydrogen, oxygen, and nitrogen. Sulfur and phosphorus are also present in organic compounds
  9. Isotopes
    • atoms which vary in the number of neutrons
    • Elements can occur in different forms... different # of neutrons are the isotopes of an element
    • *A neutral atom of a particular element has equal number of protons and electrons, but number of neutrons can vary. This variation changes the atom's mass but not it's chemical properties
  10. Review: Ions
    When atoms readily lose or gain electrons, which form charged atoms

    • Ions that have given away electrons become cations ("give that cat away!!")
    • Ion that take an electron become anions ("your an ass for taking that electron")
  11. cation
    • an ion that has given away electrons
    • has more protons than electrons
    • ("Give that 'cat' away") *makes me happy cause the cat has been given away
    • **Elements on the left side of periodic table are cations cause they like to give away electrons
  12. anion
    • Ion that takes an electron from another atom to fill it's outer shell, so now it has an excess # of electrons.
    • Therefore, it has more electrons than protons, giving it an negative charge
    • (* I hate unions)
  13. How many electrons does each electron shell hold?
    • 1st holds 2
    • 2nd holds 8
    • 3rd holds 8
    • 4th holds 18
  14. *review: acid
    • a substance which dissolves in water to form one or more hydrogen ions (H+) as a cation (positive ion) and one or more anions (negative ion)
    • HCl → H+ + Cl-

    Because H+ is a single proton w 1 positive charge, an acid is also referred to as a proton donor

    When mixed w an acid, forms salt
  15. *review: base
    • a substance that dissolves in water to form one or more OH- ions (negative ions) and one or more cations (positive ions)
    • KOH → K+ + OH-

    • Because it removes H+ from a solution, also called a proton acceptor
    • When mixed with an acid, forms salt
  16. when writing an element w it's atomic # or mass outside the periodic table
    • scientists put atomic number as subscript and mass number as superscript before the symbol. So inverted from periodic table
    • 816O
  17. atomic #
    number of all protons
  18. Mass #
    sum of protons and neutrons
  19. In "amino acids"..."Amino" refers to; "acids" refers to..."
    • "amino" ~ refers to the amino, a nitrogen-containing group which acts as a base, attracting hydrogen ions
    • "acid" refers to the carboxylic acid (-COOH) group, which has a wandering hydrogen. Because this group releases hydrogen, it's an acid.

    • Thus, an amino acid is basic at one end and acidic at the other.
    • make good buffers for this reason.
  20. Isomers
    • When molecules have the same # of atoms of each element, but different arrangements
    • So they have the same chemical formula
    • Ex: both glucose and fructose have the same formula but different structure
  21. organic functional group
    • just different ways of arranging the common atoms which we see in organic molecules that are seen repeatedly in alot of different places
    • Each group has different chemistry which gives the different molecules different properties
  22. Major functional groups
    • Hydroxyl
    • Sulfhydryl
    • Carbonyl
    • Carboxyl
    • Ester
    • Phosphate
    • Amino
  23. * - O - H


    Or   -OH
    • Hydroxyl; a major functional group. found in alcohol and sugars
    • Makes organic molecules water-soluble since having many -OH groups dissolve easily in water
    • *Remember that with acids and bases, bases donate a hydroxyl group. This is the same except within organic molecules, the carbon and oxygen are bound so tightly that they don't donate -OH, they just lose H, and therefore are not bases
  24. Occurrence and significance of -OH
    • hydroxyl
    • Alcohols contain an -OH group, which is polar and hydrophilic due to it's electronegative O atom.
  25. R - S - H  OR  -SH
    • Sulfhydryl ~ a major functional group
    • Has Sulfur and hydrogen; Sulfur is central member of this group
    • Sulfur is looking for 2 electrons to complete it's shell. Takes one from hydrogen atom...
    • Occurs in Thiols
  26. Thiols
    • have an -SH group, which is polar and hydrophilic due to it's electronegative S atom.
    • Certain amino acids, building blocks of proteins, contain -SH groups, which help stabilize the shape of proteins.
  27.   Or same structure, except on of the variables (R) is a hydrogen
    • Carbonyl ~ major functional group
    • "Carbon eel" ... carbon is double-bonded to an oxygen
    • found in ketones,
    • is polar and hydrophilic due to it's electronegative O atom (O will have -2 charge)
  28. Ketones
    • contain a carbonyl group within the carbon skeleton
    • *pts with diabetes, often metabolize fats in such a way it forms ketones. When they do that, they also form an acid... so we say the pt is in diabetic ketoacidosis
    • has a kind of fruity aroma, which is why diabetics breath in ketoacidosis smell fruity
    • Example is acetone, used for fingernail polish remover
    • Love water!
  29. Aldehydes
    • have a carbonyl group at the end of carbon skeleton
    • One of the carbons 4 bonds is to another carbon; two are to oxygen, and the fourth is to hydrogen. This hydrogen gets lonely and goes wantering. Aldehydes are very reactive for this reason
  30.   OR 
     O
      ⇊
    - C - O - C -
    • Ester ~ a major functional group
    • A carbon is double bonded with an oxygen, single bonded with another oxygen, and single bonded to another atom
    • Carbon - oxygen - carbon is characteristic of ester  *R on right side of formula should be C
  31. How is ester formed and where is it found
    • formed from reaction of alcohol and acid
    • found in fats, oils, also nerve chemical acetylcholine and in our body triglycerides
    • Aspirin is an ester of salicylic acid, a pain-relieving molecule found in the bark of the willow tree
  32.   or  
    • Carboxyl ~ a major organic functional group
    • (-COOH)
    • Important part of amino acids
    • Has a Carbon double bonded to an oxygen, single bonded to a hydroxyl group, and single bonded to another atom
    • Organic acid ~ (Heasily donated, so it's a donor)
  33. Carboxylic acids
    • contain a carboxyl group at tend of carbon skeleton
    • All amino acids have a -COOH group at one end
    • The negatively charged form predominated at the pH of body cells and is hydrophilic
    • Once it's donated it's hydrogen, its written -COO-
    • *Carbon can be bound to something on the left hand side.  Because of the type of bonding btwn C and O, the electrons tend to hang out between the C and O; the H gets lonely so the H leaves.
  34. Hydrogen ion =
    • H= proton
    • proton and hydrogen ion are used interchangeably
  35.    
    • Amino ~ a major functional group ~
    • Can be written as NHor NH3+
    • nitrogen-containing
    • A nitrogen is bound to something (on left hand side, doesn't matter what), then 2 single covalent bonds to 2 hydrogen 
    • acts as base, attracting hydrogen ions
    • In a cellular pH (7.30) binds with another H+ to form -NH3+
    • Phosphate ~ major function group 
    • found in energy-storing molecules and in nucleic acids (DNA, RNA)
    • Has phosphorus as central element (valence of +5) makes a double covalent bond to 1 oxygen, then a single covalent bond with 2 hydroxyl groups (-OH)
    • Again, bonding between the O and P can keep the electrons btwn those two elements, and so the H leave, making them an acid and therefore a donor
  36. In regards to naming organic acids, and the difference between "acid" and "-ate"
    ex: aspartic acid =aspartate
    • Only difference is (using the example of aspartic acid) the aspartic acid HAS IT'S HYDROGEN and ready to donate it. (has COOH group on it)
    • IF IT HAS DONATED THE HYDROGEN ALREADY, then it is referred to as "-ate"... "aspartate", has a COO- group on it, so negatively charged
  37. Four main kinds of organic molecules
    • Carbohydrates (sugars)
    • lipids (fats)
    • proteins
    • nucleic acids
    • Carbs, lipids and proteins are important components of food, Carbs being the most important
  38. Carbohydrates
    • one of four major classes of organic molecules
    • "watered carbon" = Carbo (carbon) and hydrate (water) ~ always has ratio of one carbon to one water in the formula: CxH2xOx
    • Example: glucose & fructose (x=6) C6H12O6
  39. Lipids
    • one of four major classes of organic molecules
    • More carbon than oxygen; repel water (hydrophobic)
    • so made up of mostly carbon and hydrogens
    • fats, oils, waxes
    • very important in body to build cell membranes
  40. Proteins
    • one of four major classes of organic molecules
    • made up of amino acids, which always contain carbon, hydrogen, oxygen and nitrogen
    • Some amino acids include sulfur
  41. Nucleic acids
    • sugar (carbohydrate) "backbone" plus nitrogenous base (base which has lots of nitrogen in them); so still have carbon, but lots of nitrogen mixed in
    • Form ring structures, where atoms come back around and bind to themselves forming a ring arrangement  
    • Deoxyribose backbone: DNA
    • Ribose backbone: RNA
  42. Pyrimidines and purines
    • type of nucleic acid structure, where it forms a ring. The atoms come back around and bind to themselves forming a ring arrangement
    • pyrimidines are one-ring structures (as in the bases for DNA & RNA) (includes uracil, thymine, cytosine)
    • purines are two ring structures (includes adenine, guanine)
  43. Monomer or polymer
    • Monomers are the basic building blocks: the carbohydrate or lipid or protein = one unit
    • When these units of monomers string together (or in a branched structure) they form a polymer, so many units, and can become very long
    • *Organic molecules can be really big; they do this by combining monomers into polymers.
  44. monosaccharide
    • monomer of sugar (carbohydrate)
    • simple sugars which have 3 to 7 carbons.
    • ex: glucose, fructose, galactose all have 6 carbons; deoxyribose and ribose have 5 carbons
  45. what is glucose
    • sugar monomer, making it a monosaccharide
    • the main blood sugar
    • MOST IMPORTANT OF HEXOSES
  46. What is fructose
    • a sugar monomer, making it a monosaccharide
    • found in fruits
  47. what is galactose
    • a monomer of sugar, making it a monosaccharide
    • in milk sugar
  48. what is deoxyribose and ribose?
    • monomers of sugar, making them a monosaccharide
    • Deoxyribose in DNA; Ribose in RNA
    • **deoxyribose violates carb rule of CxH2xOx. The "de" refers to the lack of an oxygen compared to ribose
  49. amino acid
    • a protein monomer
    • Polymers of amino acids ar Polypeptides and proteins
  50. nucleotide
    • a nucleic acid monomer; includes a nucleoside plus a sugar plus a phosphate group
    • When these monomers are strung together, they form DNA (if the sugar is deoxyribose) or RNA (if the sugar is ribose)
  51. In humans, carbohydrates have the structure of:
    • Either C5H10O5  Or  C6H12O6  
    • Remember, the ratio of carbon:hydrogen:oxygen in carbohydrates is always 1:2:1
    • So carbs always have the same # of carbon atoms as water molecules

    Carbohydrates can change from a linear structure to a ring structure; form ring structure by linking carbons 1 through 5 with an O
  52. Shorthand for writing organic chemical structures
    • one way of writing organic structures (shorthand is to drop the C atoms altogether. This is because carbons always form 4 bonds, so anytime we see four lines converging on a point, we assume that point contains a C atom
    • *also, we drop the hydrogens since they're the only places we find a single bond. So, anytime you see a single line ending in nothingness, you should put a hydrogen there. 
  53. Pentoses
    • five carbon carbohydrates; NOT FOOD SOURCE
    • *Ribose, Deoxyribose
    • Usually has formula C5H10O5; Deoxyribose is exception w formula C5H10O4
    • **Remember "pentoses" refers to the # of carbons, NOT the number of sides to the molecule
    • Think of the pentagon
  54. hexoses
    • six carbon carbohydrates
    • IS A FOOD SOURCE; essential structure of nucleic acids, RNA and DNA
    • because some of the carbons stick out to one side, many, but not all, hexoses form six-sided rings
    • *glucose, fructose, and galactose
    • All have formula C6H12O6
    • **Remember Hexoses refers to the # of carbons, NOT the # of sides to the molecule
  55. Disaccharides
    • two monosaccharides joined together by dehydration synthesis, and are the simplest kind of sugar polymers
    • Ex: sucrose (table sugar) and lactose (milk sugar) and maltose
  56. polysaccharides
    • Tens to hundreds of larger polymers of monosaccharides joined by dehydration synthesis
    • Ex: Glycogen (the stored form of carbs in animals); Starch (stored form of carbs in plants & main carb in food); Cellulose (part of cell walls in plants that cannot be digested by humans but aids movement of food through intestines)
  57. 3 major hexoses
    • Glucose ~ MOST IMPORTANT of hexoses; major sugar found in blood; human prefer as energy source. Blood sugar = blood glucose
    • Fructose ~ major sugar found in fruit and honey. In the body, converted to glucose for use by cells
    • Galactose ~ found as a component of lactose, "milk sugar"
  58. sucrose
    • table sugar = glucose + fructose
    • made by dehydration synthesis
  59. lactose
    • milk sugar = glucose + galactose
    • made by dehydration synthesis
  60. maltose
    • glucose + glucose
    • found in malt (fermented grain)
    • made by dehydration synthesis
  61. dehydration synthesis
    • Combination of two monosaccharides w formation of a water molecule (separate, meaning water is a byproduct, dehydrates)
    • the bond btwn two hexoses occurs at a place where the -OH for one sugar finds the -H from another. 
    • As these two hexoses are combined, a water molecule (HOH) is formed.
  62. hydrolysis
    • the opposite of dehydration: a water molecule is added to sucrose as it is broken into glucose and fructose
    • This happens inside our cells as table sugar in the diet is metabolized
  63. invertase
    • also called sucrase
    • Hydrolysis of sucrose is catalyzed by this enzyme
  64. Polysaccharides in plants
    • Long strings of monomers; may be branched or unbranched
    • Most important are starch, which is digestible & major source of carbs in diet, and cellulose (fiber - makes up cell walls), which is non-digestible polysaccharide
    • Ex: Starch = potatoes
  65. Polysaccharides in Humans
    • Most important is glycogen, which is a storage form of glucose. 
    • When glucose is plentiful, is converted by liver to glycogen and stored in liver and muscles.
    • When glucose is needed rapidly, such as in aerobic exercise, glycogen is broken by hydrolysis into individual glucose molecules which are then used to fuel cellular processes
  66. If a chemical name ends in "-ose"...
    its a carbohydrate
  67. Where and how much glycogen can be stored in humans
    • Liver: 70 - 100 g = 280 - 400 Cal
    • Muscle: 200 - 400 g = 800 - 1600 Cal
  68. ABO blood groups arise from...
    glycolipids
  69. glycolipids
    • combinations of lipids and sugar groups
    • these sugar groups mark specific cell types
  70. polysaccharides that are basis for ABO blood grouping
    • in this case, a polysaccharide is attached to a lipid molecule
    • One monosaccharide involved is galactose
    • The composition of polysaccharides and the branching pattern make each of these three molecules unique
  71. Blood typing:
    • ALL blood types have blood type O marker on blood cell surface
    • People w blood type A have both A and O polymer of surface of RBC
    • People w blood type B have both B & O polymer
    • People w blood type AB have all A, B and O markers
    • People w blood type O have neither A or B markers
  72. Why are carbohydrates so important?
    • Give us energy yielding nutrients (starch from plants)
    • building materials (cellulose - because it's not broken down - used in wood construction, paper, cotton based clothing and cell walls in higher plants)
    • Water-Soluable molecules (mono- and disaccharides are used as sweetners
  73. Examples of dehydration synthesis
    • In lipids, dehydration synthesis is used to add fatty acids to a glycerol backbone
    • In proteins, the bonds that hold amino acid monomers together are formed from dehydration reactions that each create a peptide bond
  74. In the forming of a peptide bond...
    • A water molecule is taken out
    • The -OH group of the carboxyl acid end of the amino acid plus the -H from the amino end of the amino acid leaves us with a bond btwn the C and N, which is quite strong
    • So the bond btwn the C = O and N - H, with the C and N bonding
  75. Polar vs. non-polar molecules
    • Polar are charged ions & like being around water (hydrophilic)
    • Non-polar molecules are not charged (no ions), and hate being around water
  76. 4 categories of lipids
    • Simple lipids: fats, oils, waxes
    • Compound lipids: phospholipids, sphingolipids
    • Steroids
    • Miscellaneous: Lipoproteins, fat-soluble vitamins
  77. fatty acids
    • the basic building blocks of lipids
    • has a carboxyl acid at one end, rest of molecules is long chain made of carbon and hydrogen (making them very hydrophobic... since lack of oxygen)
  78. triglyceride
    • formed when 3 chains of fatty acids are combined with a glycerol backbone (which has 3 carbons), by dehydration synthesis, so it has three fatty acid tails
    • each fatty acid chain ends in a -COOH
    • The fatty acid's terminal -OH and -H on glycerol combine to release water and the leftover O bridges the glycerol backbone to the fatty acid "tails"
  79. phospholipid
    • when one of the three long fatty acid chains in a triglyceride is replaced with a phosphorus-containing group on the polar end. still have 2 non polar tails
    • inside the cells the main lipids are phospholipid,
    • has a polar head on one end so can interact w  water with inside or outside of cell, 
    • non-polar group on other end (tails) which only interact with each other;helps make cell membrane w/o any help
    • Is amphipathic
  80. steriods
    are lipid compounds which include many of the hormones, as well as cholesterol
  81. Lipoproteins
    • specialized protein carriers in the blood which carry lipids (since lipids are insoluble in water
    • fairly large structures,
  82. unsaturated fatty acid
    • when a double bonds form btwn two of the carbon atoms in the chain of carbon & hydrogen
    • "missing a hydrogen" cause the double bond excludes hydrogen
    • This double bond puts a "kink" in the regular zigzag pattern of the carbon backbone
    • Monounsaturated = one double bond = one kink
    • Polyunsaturated = many double bonds = many kinks
  83. saturated fatty acid
    • fatty acids where all the carbons are filled, or saturated, with hydrogen bonds
    • Saturated = no double bonds = no kinks
  84. moiety
    • just a fancy name... a named part of a molecule
    • So if you have a long, complicated molecule, we tend to break it down into groups. Each group is a moiety
  85. kincky tails in polyunsaturated fatty acids =
    more fluid membrane, more space btwn molecules
  86. Amphipathic molecule
    • molecules that have one part which loves water, and another part which hates water
    • Ex: phospholipids, soaps
  87. hydrophilic
    • same thing a polar
    • loves water
  88. hydrophobic
    • same thing as non-polar
    • hates water
  89. Steroids
    • a major category of lipids; four ring structures
    • cholesterol is major basis for this class of molecule
  90. cholesterol
    • an important lipid, used a precursor for synthesis of many other lipids
    • not all cholesterol is harmful
    • Can't live w/o it, essential component of cell membrane
    • has role regulating the fluidity of cell membranes
    • not soluble by itself in blood; in order to reach cells, has to be carried by protein/lipid complex
  91. examples of steroid hormones based on cholesterol molecule
    • Vitamin D: a steroid vitamin essential for bone growth and repair
    • Estradiol : type of estrogen, high levels in females
    • Testosterone: sex hormone, high levels in males
    • Cortisol: released from the adrenal glands in times of stress
  92. Eicosanoids
    • lipids derived from arachidonic acid which are key chemicals in immune defense and inflammation
    • Ex: prostaglandins and leukotrienes
  93. two different kinds of vitamins
    fat-soluble and water soluble
  94. Fat-soluble vitamins
    • Vitamin A, D, E and K
    • In misc. category for lipids
  95. Vitamin A
    • (retinol)fat-soluble vitamin, needed for vision
    • synthesized from carotenes: which the name tells us carrots are high in carotenes; also foods which are yellow or orange in color, such as squash and tomatoes
    • Deficiency: poor teeth & gums; night blindness
  96. Vitamin D
    • fat soluble, based on cholesterol
    • essential for bone growth and repair
    • Deficiency Signs: Rickets (low blood calcium, soft bones, distorted skeleton)
  97. Vitamin E
    • fat-soluble vitamin
    • not well-understood, but is thought to protect cells from free radical damage
  98. Vitamin C
    • Ascorbic Acid... water-soluble
    • Deficiency: scurvy (bleeding gums, loose teeth, swollen joints; slow wound healing; weight loss)
  99. Vitamin K
    • fat soluble, needed for blood clotting
    • Deficiency: slow blood clotting
  100. lipoprotein
    • the lipid carriers in blood
    • 3 different types differing by density & have different effects on health
    • (VLDL) -very low density lipoprotein
    • (LDL) = low density lipoprotein
    • (HDL) = high density lipoprotein
    • On health effects, high density is good, low is bad
    • *lipids are less dense than water, which is why oil floats.
  101. VLDL (in lipoprotein)
    • Very low density lipoprotein ~ meaning the lipid content is high
    • believed to be most damaging on health, deposited into adipose (fat) tissue
    • believed that people with high VLDL are more prone to heart disease,
  102. LDL (in lipoprotein)
    • low density lipoprotein
    • has intermediate lipid content
  103. HDL (in lipoprotein)
    • has highest protein content & lowest lipid content
    • believed to have good health benefits
    • believed to exert a protective effect, people with high HDL tend to be less prone to heart disease
    • increased by exercise
  104. amino acid
    • the monomer which makes up proteins
    • have simple structure: 2 carbons & nitrogen form backbone
    • has 3 parts, eached attached to a carbon and hydrogen atom (-CH)
    • 1) amino group  2) carboxyl group  3) R group (the variable group, which is sandwiched btwn the other 2 groups)
  105. polypeptides
    • small strings of amino acids 
    • there really is no sharp dividing line btwn a polypeptide and the larger, longer protein
  106. proteins
    polymers of amino acids joined by dehydration synthesis
  107. Amino group in an amino acid
    • -NH2 when uncharged
    • -NH3+ when charged (ionized)
  108. Carboxyl group in amino acids
    • -COOH when uncharged
    • -COO- when charged (ionized)
  109. R group in amino acids
    • the variable group, sandwiched btwn the amino and carboxyl group 
    • gives the protein it's properties
  110. dipeptide
    • the resulting combination of two amino acids (bonded through dehydration synthesis)
    • Two amino acids, one peptide bond
  111. tripeptide
    three amino acids, two peptide bonds
  112. polypeptide
    • when more than two amino acids are bonded by dehydration synthesis
    • no clear dividing line when polypeptide is large enough to be termed protein
  113. ribosome
    a specialized cell machine which synthesizes proteins
  114. peptidases or proteases
    • enzymes which break peptide bonds by hydrolysis
    • (recall that hydrolysis is the opposite of dehydration synthesis)
  115. The only way that the 20 amino acids found in the human body differ ....
    • In the "R" group
    • Can be very simple or very complex
  116. Disulfide bond
    when two sulfhydryl (-SH) bond
  117. acidic polar charged amino acids
    • Ex: aspartic acid and glutamic acid
    • act as hydrogen donors, leaving a residual negative charge on the -R groups carboxyl (-COO-)
    • hydrophilic = LOVE WATER
  118. basic polar charged amino acids
    • Ex: lysine, arginine, and histidine
    • carry a positive charge on their -R groups amino (-NH3+)
  119. If amino acid become backbone of protein
    • *all amino acids have carboxyl and amino parts
    • if they become the backbone of proteins, they are not available to participate in chemical reactions.
    • Watch for the -R group...
  120. polar uncharged amino acids
    • Ex: serine, threonine, glutamine, asparagine, and tyrosine
    • The hydrophilic -R groups tend to have a partial positive or negative charge
    • This allows them to participate in chemical reactions, form hydrogen bonds, and associate with water
  121. non polar amino acids
    • hydrophobic
    • The -R groups consist almost entirely of D and H atoms (If S or N are present, they're completely tied up and not free to participate in reactions)
    • They want to associate with other hydrophobic R-groups or lipids. 
    • play important role in membranes by associating w the membrane lipid bilayer
  122. Any time you have a lot of oxygen or nitrogen or sulfur atoms,
    • makes functional groups hydrophilic
    • -OH, -SH, -NH
  123. w amino acids, the CH2 or CH3
    have no electronegative atoms on them, tend not to like being around water
  124. four levels of protein structure
    primary ,secondary, tertiary, and quaternary
  125. primary structure of proteins
    • where the protein structure starts
    • the order in which amino acids are strung together w peptide bonds
  126. secondary structure of a protein
    • how the sequence is folded, held together by hydrogen bonds
    • 2 types of folding:
    • helix : "spiral staircase",(alpha-helix) due to formation of hydrogen bonds btwn nitrogen of one amino acid to the oxygen of another located in another part of polypeptide chain
    • Sheet like: (beta-pleated sheet) occurs due to hydrogen bonding btwn polypeptide chains laying side by side
  127. tertiary structure of protein
    The 3-dimensional arrangement of how these helix spirals and sheets are put together, forming a larger folded structure
  128. Types of atomic interactions leading to tertiary structure
    • Ionic bonds: formed when + & - charges attract each other
    • Hydrophobic: occur where non-polar groups snuggle up to each other, excluding water
    • Van der Waals - NOT WELL UNDERSTOOD, occur when "shapes" of molecules fit together like puzzle, 
    • Disulfide bridges: formed btwn cysteine (only amino acid with -SH group)
    • Hydrogen bonds: formed btwn H and O, N, S and adjacent O, N, or S atoms
  129. quaternary structure
    • the final 3 dim structure formed by all polypeptide chains making up the protein
    • in some proteins, two or more subunits (each w own 1st, 2nd, and 3rd structure) combine
  130. What makes up hair
    • an alfa-helical structure formed from the protein keratin
    • made up of three a-helices twisted together in a cable
  131. In many figures (examples) how are α-helical regions and β-pleated sheets usually shown
    • α-helical regions are shown as spirals or by a straight tube
    • β-pleated sheets are usually shown as arrows or as flat ribbons
  132. amino acids which don't have a secondary structure
    are threads
  133. A change in the primary structure of a protein molecule leads to
    • changes in the 2nd, 3rd, and 4th structure
    • Ex: sickle cell anemia
  134. heme group
    an iron-containing group with holds onto the oxygen molecule.
  135. denaturation
    • when the interactions of a protein is disrupted while in it's secondary, tertiary, or quaternary structure, and the protean is unfolded, leaving the primary structure intact
    • So NOT EFFECTING THE PEPTIDE BONDS but are effecting the weaker interactions: ex :hydrogen bonds
    • some proteins can reconfigure; so were temporarily denatured (warming milk)
  136. albumin
    • the clear, liquid protein of the chicken egg
    • Can be denatured in a few ways: 
    • heat denaturation, or mechanical denaturation (by mixing to for meringue)
    • Wont go back to previous form
  137. collagen
    main structural protein in body
  138. How are proteins able to carry out so many different functions
    • their diverse shapes
    • Proteins are what allows all the different functions of the human body to be carried out
  139. Functions of proteins
    • Structural
    • Regulatory
    • Contractile
    • Immunology
    • Transport
    • catalytic
  140. enzymes
    • type of proteins that speed up (catalyze) chemical reactions
    • They lower the amount of energy needed to start the reaction
    • They CANNOT - and do not - change the amount of energy lost or gained
    • are specific on what molecules it helpe
  141. *review: endergonic reaction
    reaction which required energy
  142. *review: exergonic reaction
    Reaction which releases energy
  143. anabolism
    energy stored in chemical bonds
  144. catabolism
    • energy released form chemical bonds
    • this energy can be turned into work
  145. activation energy
    energy required to begin a chemical reaction
  146. substrates
    • the reactants, bind to enzyme's active site
    • The active site changes shape, resulting in better fit w the substrates
  147. naming enzymes
    almost always the substance which is acted on - the substrate - plus the suffix "-ase"
  148. nucleotide
    the monomer for both DNA and RNA, which is comprised of a base (nucleoside), a sugar, and a phosphate (-PO4) group
  149. Bases used in DNA and RNA
    • Both use: Adenine (A), cytosine (C) and guanine (G)
    • The fourth base differs: DNA uses thymine (T); RNA uses Uracil (U) (a molecule closely related to T)
  150. Nucleic acids
    • DNA and RNA
    • called this cause their found in high concentrations in nucleus of cell
    • huge molecules
  151. DNA
    • used to transmit genetic info
    • structure is double helix
    • backbone is sugar (deoxyribose) and phosphate
    • bases hold strands together: Adenine, Cytosine, Guanine, and Thymine
    • Hydrogen bonds btwn bases hold strands together
  152. The gaping sequence in DNA
    • The wide gaps are called major groove
    • The narrower gaps are called minor groove
  153. Pyrimidines and purines in DNA
    • The pyrimidines are one ring structures
    • The purines are 2 ring stuctures
  154. Pairing with bases in DNA
    • Adenine forms two hydrogen bonds with Thymine (only thymine) 
    • Cytosine forms three hydrogen bonds with guanine (and only guanine)
    • A-T and G-C
    • ** A and T cannot bind with C or G; A cannot bind with A; and A can only bind with T
  155. Differences btwn DNA and RNA
    • 1- In the sugar-phosphate backbone, DNA has deoxyribose as the sugar; RNA has ribose as sugar
    • 2- difference in 4th base: DNA uses Thymine, RNA uses Uracil. Both have identical hydrogen bonding properties & pairs only with adenine
    • 3- RNA DOESN'T FORM DOUBLE HELICES, generally found in a single-stranded form, so no base pairs to keep track of
    • 4- DNA incredibly stable, RNA incredibly difficult to isolate and work w/. 
    • DNA is permanent set of instructions, RNA is a "scratchpad" used for temp. storage and manipulation of genetic info.
  156. mitochondrion
    the subcellular compartment
  157. ATP
    • adenosine triphosphate
    • Is a nucleic acid
    • Potential energy
    • how the cells store energy
    • it's also used as an energy currency; so regardless of the energy needed to carry out a process, it uses ATP
  158. what is ATP made up of
    • Adenine nitrogenous base - two ring structure
    • Ribose pentose sugar - in the middle
    • other end is composed of three phosphate groups
    • If energy is needed, the last phosphate group is released, and ATP becomes ADP (Adenosine diphosphate)
    • When energy is to be stored again, a phosphate group reattaches becoming ATP again
  159. How is energy released from ATP?
    • The high-energy phosphate bond is broken by hydrolysis
    • Since this bond is like a coiled spring, the phosphate group separates rapidly and energy is released when the bond is broken
  160. how is ATP made:
    • Almost all energy sources are converted by the digestive system to glucose
    • Glucose may be stored in glycogen in the liver and muscles, and used later when needed... or may circulate in blood to meet immediate needs
    • Glucose is converted to ATP inside of cells
  161. vitamins
    • chemical cofactors which work in a similar fashion as enzymes to help speed up essential chemical reactions in cells
    • As cofactors, vitamin helps enzymes to form a pocket for substrate
  162. essential minerals
    trace elements, most work with enzymes and vitamins to help speed up chemical reactions in cells.
  163. fluorine
    • an essential mineral
    • Function: structure of teeth and bones. Effect on cells which build or break down bone; inhibits microorganisms which degrade teeth
    • Deficiency: increased incidence of dental caries (cavities); osteoporosis
  164. chromium
    • an essential mineral
    • Function: Efficient use of insulin
    • Deficiency: Relative insulin resistance; impaired glucose tolerance; elevated serum lipids
  165. iron
    • an essential mineral
    • Function: oxygen & electron transport; heme group of hemoglobin
    • Deficiency: anemia
  166. iodine
    • an essential mineral
    • Function: constituent of thyroid hormones
    • Deficiency: goiter (enlarged thyroid); depression of thyroid function; (if congential ~before or at the time of birth) cretinism which is mental retardation and characteristic physical signs & lower metabolism

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