Molecular Biology and Metabolism Explain living processes in
terms of the chemical substances involved Many processes are
controlled by protein catalysts called enzmyes. The sum of all
enzyme- catalyzed reactions is called metabolism. Metabolism
includes Catabolism (breaking large molecules into smaller
molecules) Anabolism (building small molecules into larger
molecules)
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Basic chemistry review Bohr Model of an atom Protons and
Neutrons in nucleus Electrons orbit the nucleus
Particle:Charge:Mass:Determines: ProtonNeutronElectron +1 0 -1 -1
~1 amu ~0 (~1/1800 amu) elementisotope ion / charge Note that the
electrons are actually much farther from the nucleus than
shown.
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Bonding Gain / loss of electrons results in an ionic bond.
Sharing electrons results in a covalent bond.
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Polar Covalent Bonds Sometimes atoms in a covalent bond do not
share electrons equally. The result is a bond with a slightly
positive end and a slightly negative end as seen in water
molecules.
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Hydrogen Bonding Since water is polar, the positive ends
attract the negative ends. This attraction creates hydrogen bonds.
Hydrogen bonds are weak individually, but together they can be very
important! Hydrogen Bonding in Water and DNA
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Carbon Biochemistry Life is based on atoms of the element
CARBON Carbon can form a variety of stable compounds because it can
form 4 covalent bonds Compounds are called organic if they contain
carbon atoms bonded to hydrogen atoms (C-H) + a few others
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Organic molecules can be made by living things OR artificially
Urea is made by living things (as a waste product) and also by
artificial synthesis: Wohler Synthesis Helped show that there is no
fundamental difference between organic molecules and other
molecules same rules apply. (Disproved vitalism)
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Type of Carbon Macromolecule Monomer Elements Used
FeaturesMajor functions Carbohydrate (sugars) Monosac- charide
CHORing(s), CH 2 OStructure, energy storage Lipid (fats and oils)
Fatty acid, steroid, glycerol CHO Long chain, O at one end, (4
rings in steroid) Energy storage, hormones, buoyancy, insulation
Protein Amino acid CHON N-C-C backbone, R-group SO MANY THINGS!
Enzymes, structure, movement, defense, etc. Nucleic
AcidNucleotideCHOPS sugar +N-base +phosphate Information storage
(genetics), production of proteins ElementSymbol Number of Covalent
Bonds HydrogenH1 OxygenO2 NitrogenN3 CarbonC4 PhosphorusP5
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Carbohydrates Carbo = carbon, Hydrate = water Carbo = carbon,
Hydrate = water Formula is (CH 2 O) n Formula is (CH 2 O) n Often
have a ring structure Often have a ring structure Carbohydrate:3
examples:Use in animals:Use in plants: Monosaccharides (single
sugars) Glucose Fructose Galactose Carried in blood to supply
energy to the body Sweetens fruits to help seed dispersal (attracts
animals) Disaccharides (two sugars) Lactose Sucrose Maltose In milk
to provide energy to dependent young Carried by (some) phloem (sap)
to supply energy Polysaccharides (many sugars) Glycogen Cellulose
Starch In liver and muscles for short- term energy storage Forms
strong fibers in cell wall for structure / support Energy
storage
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Draw a Monosaccharide! How many carbons in your sugar? Draw a
figure with that number of sides BUT one C will stick out and one O
will go in ring Each carbon will have an O-H and H attached EXCEPT
around the 2 carbons on the arm Count number of atoms and number of
bonds! C C C CC O -O-H -H H|H| H- C 5 H 10 O 5
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Examples of monosaccharides Be able to DRAW and D-glucose Be
able to DRAW D-ribose Fructose Other monosaccharides Galactose RNA
found in DNA
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Disaccharides Two monosaccharides covalently bonded: + = + =
Examples include: sucrose (table sugar) lactose (in milk) maltose
(malt flavoring) Monosaccharides and disaccharides are called
sugars and taste sweet!
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Condensation Reactions in Sugars Joins monosaccharides together
(creates a covalent bond) Creates a water molecule (hydroxyl (OH)
from one monomer and hydrogen (H) from the other)
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Hydrolysis Reactions in Carbs Condensation reactions in reverse
Water is used up Produces monosaccharides from disaccharides
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Anabolism: Repeated Condensation Reactions Produces polymers
from monomers Each covalent bond formed releases a water molecule
Ex. Monosaccharides Polysaccharides + Water PolysaccharideFound
inBuilt fromType of linksFunction Cellulose Plants-glucose1C-4C
onlyStructure (cell wall) Starch (types of) Plants-glucoseEnergy
storage Amylose 1C-4C only Amylopectin 1C-4C and 1C- 6C (some)
Glycogen Humans (and some other animals) -glucose1C-4C and 1C- 6C
(many) Energy storage (liver and muscles)
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Catabolism: Repeated Hydrolysis Reactions Produces monomers
from polymers Each covalent bond broken uses a water molecule Ex.
Polysaccharides + Water Monosaccharides H2OH2O
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Molecular Visualization Software See AWESOME jsmol interactives
of most molecules here. here Visit interactives and build your own
with Molecular Workbench Molecular Workbench Molecular Workbench
Two rotations of ribose at biotopics. You may need to use a
particular browser and/or update Java.
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Lesson 2: Lipids
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Lipids Lipids are mostly non-polar molecules. Used in energy
storage, membrane structure, insulation, cell-to-cell
communication, buoyancy, and more. Two building blocks of
glycerides: / OH Glycerol:C 3 H 8 O 3 Fatty acid:CH 3 -(CH 2 ) x
-C=O
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Condensation in Glycerides Glycerol bonded to a fatty acid
makes a glyeride Monoglyceride + 1 water = glycerol + 1 fatty acid
Diglyceride + 2 waters = glycerol + 2 fatty acids Triglyceride + 3
waters = glycerol + 3 fatty acids
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Lipids to know: Types of Fatty Acids Saturated Unsaturated Cis
Trans Polyunsaturate d Be able to draw a saturated fatty acid.
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Lipids to know: Glycerides: Phospholipids: Steroids:
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Lipids v. Carbohydrates ~9 Calories / gram Long-term storage
Non-polar (water insoluble) ~4 Calories / gram Short-term storage
Polar, water soluble Why are lipids preferable to carbohydrates for
long term energy storage in animals? Why are lipids used less
frequently for energy storage in plants? Some seeds have high lipid
content. Why?
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Body Mass Index BMI used as an indicator of health risks due to
weight Does not take into account fat / muscle Calculate by formula
or nomogram What would be the BMI for a person who is: a)80 kilos
& 160 cm b)80 kilos & 145 cm
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Is BMI an effective predictor? What % of people had a BMI
indicating they were overweight, but body fat did NOT confirm
it?
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Lipids and Heath: Links for Methods and Evidence METHODS Animal
models Randomized, controlled studies Before and after cohort
studies MEASURE Levels of lipids in blood, lipid metabolism
enzymes... Genetics (Alleles related to lipid metabolism) Health
(CVD, cardiac events) Google scholar, JSTOR, etc. 2009 AU Review
(on Haiku) LipidWorld (example of free journal) LipidWorld
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Health Risks of Trans Fats From WHO Scientific Update on Trans
Fatty Acids (2009, Eur J Clin Nutr) on Haiku Meta-analysis esp. of
research in humans Findings: Increased LDL-C bad cholesterol
Decreased HDL-C good cholesterol Increased CHD (coronary heart
disease) Increased coronary events (e.g. heart attack) Inflammatory
effects Type of trans fat matters - 18:1 and 18:2 especially
harmful Possible findings: Increased insulin resistance (Type II
Diabetes) Increase membrane dysfunction Source may be important
(natural source in some meats) Also a nice summary with some
citations on WikipediaWikipedia
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Health Risks of Saturated Fats Currently evidence is
contradictory Recent meta-analyses show (2010) and no significant
evidence for concluding that dietary saturated fat is associated
with an increased risk of CHD or CVD. (2010) and2010 Current
evidence does not clearly support cardiovascular guidelines that
encourage high consumption of polyunsaturated fatty acids and low
consumption of total saturated fats (2014)2014 (showed saturated
about the same as cis-monounsaturated, better than trans, and worse
than polyunsaturated omega-3 and omega-6) Other recent
meta-analyses show consuming PUFA in place of SFA reduces CHD
events (2010) and2010 reducing saturated fat by reducing and/or
modifying dietary fat reduced the risk of cardiovascular events by
14%. (2012)2012 See Wikipedia for further links to relevant
studies.Wikipedia
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Lesson 3: Water
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Water molecules are polar Hydrogen bonds form between water
molecules
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Properties of Water Cohesive Adhesive Solvent Thermal Heat
capacity Boiling / freezing points Evaporative cooling
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Cohesion Water molecules stick to each other due to hydrogen
bonds between them Surface tension Organisms benefit from cohesion.
In plants, cohesion helps transport water up to the leaves. Surface
tension and capillary action also involve cohesion.
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Cohesion from a bugs eye More cohesion: Basilisk Running On
Water
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Adhesion Attraction between water molecules and other molecules
(polar or charged) Living things benefit from adhesion when water
sticks to cell walls allowing water to move to leaves.
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Versatile Solvent Because water has partial positive and
negative charge, it can dissolve many substances that are polar,
positively charged, or negatively charged Water does NOT dissolve
non- polar, uncharged substances well (lipids / fats / oils) Living
things benefit because they dissolve the molecules of life and
metabolism in water, where they can interact and react.
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Substances Interact with Water HYDROPHILIC Water loving Polar
or charged Gets wet or dissolves HYDROPHOBIC Water fearing
Non-polar, uncharged Repels water, not soluble
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Transport in Blood by Solubility
SubstanceChargeSolubilityMethod of Transport GlucosePolarHigh
Dissolved in blood plasma Amino AcidsPolarHigh Dissolved in blood
plasma CholesterolNon-polarLow In Lipoproteins (HDL, LDL)
FatsNon-polarLow In lipoproteins such as chylomicrons
OxygenNon-polarLow Attached to hemoglobin protein Sodium Chloride
Ionic (charged) High Dissolved in blood plasma
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Thermal Properties High heat capacity: large amounts of energy
are needed to raise the temperature of water High (latent) heat of
vaporization: large amounts of energy are necessary to vaporize
water Low density as a solid: because of packing of water molecules
by hydrogen bonds ice is less dense than liquid water (at most
temperatures)
Slide 45
Water and Cooling Evaporative cooling: Terrestrial organisms
may sweat, pant, or transpire. As water evaporates and breaks
hydrogen bonds, it takes energy from the remaining water which
becomes cooler High heat capacity: Water organisms may transfer
heat to the environment without raising the water temperature by
much; have a stable environment to live in
Slide 46
Low Density as a Solid A frozen layer of ice can insulate a
pond and prevent it from freezing solid during the winter. This
allows organisms to survive in the pond year round.
Slide 47
Thermal Properties of Water v. Methane Specific Heat Capacity
(J/gK) Heat of Vaporization (kJ/mol) Freezing Point (C) Boiling
Point (C) Water4.18440100 Methane2.268.2-182.6-161.7 What causes
these differences? Why are they significant?