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The Chemical Foundations of LifeChapter 2
(pages 22-44)
Major Topics
• Atomic structure
• Chemical bonds– Valence electrons– Ionic, covalent, hydrogen
• Molecules in cells– Sugars, fatty acids, amino acids, nucleotides
• Macromolecules in cells– Sugars, lipids, proteins, nucleic acids
Atomic Structure
• Protons
• Neutron
• Electrons
Helium atom
• Atomic number– Number of protons (= number of electrons)
• Atomic weight– Number of protons + neutrons
• Isotopes– Neutron number varies
Figure 2-2 Essential Cell Biology (© Garland Science 2010)
• Atomic weight is determined by:– Number of protons and neutrons– Relative percentages of each kind of isotope
Atomic weight = 0.9889 (12) +0.0111 (13) = 12.01
The proton shrinks in size!• 2010 paper in Nature
• Proton 0.00000000000003 mm smaller than thought!– 4% smaller!
• Fired “muons” at hydrogen atoms and measured energy
Figure 2-4 Essential Cell Biology (© Garland Science 2010)
Elements in Biology
• Organic vs. Inorganic– Organic chem =
hydrocarbons• Biological origins• Covalent bonds
– Inorganic = minerals
• Covalent and ionic bonding
Chemical bonding
• Chemical bonding involves ONLY the valence electrons– Stability of an atom is
determined by the number of valence electrons is has
– Octet rule
Figure 2-1 Essential Cell Biology (© Garland Science 2010)
• Valence electron number determines if chemical bonding occurs– Octet rule: Atoms are happiest with a complete
octet in their valence ring
• Options to get that octet:– Share electrons– Give away electrons– Accept electrons
Ionic bonding
Covalent bonding
Chemical bonding in biology
Figure 2-6 Essential Cell Biology (© Garland Science 2010)
Covalent bonding
• Predominant type of bonding in organic chemistry– Carbon can form four covalent bonds
• Two types:– Polar– Nonpolar
Figure 2-12 Essential Cell Biology (© Garland Science 2010)
• Polar– Charge– Non-symmetrical
• Nonpolar– No charge– Symmetrical
• “Like dissolves like”– Key concept in cell
biology
Figure 2-11 Essential Cell Biology (© Garland Science 2010)
Shape and Polarity
Figure 2-13 Essential Cell Biology (© Garland Science 2010)
Protein associations
are determined by
charge
Vps25
Wernimont and Weissenhorn. BMC Structural Biology 2004, 4(1):10
http://www.biochemj.org/bj/412/0399/bj4120399add.htm
Ions and ionic bonding• Ions are critical in setting up membrane
potential in cells– Na+, K+, Cl-
• Electrolytes– Gatorade, Vit H20
• Salts– NaCl
• Halogen-containing
– Electricity
Figure 2-8 Essential Cell Biology (© Garland Science 2010)
Hydrogen bonding• Weakest type of
chemical bond, but incredibly important in bonding between and among molecules– Collective force
• Water, DNA
• Secondary structure of proteins
Figure 2-9 Essential Cell Biology (© Garland Science 2010)
Figure 2-15 Essential Cell Biology (© Garland Science 2010)
Molecules in Cells
Carbon-rich molecules
Carbohydrates
• Building block = Monosaccharide
• Sugars and starches
• Provide a quick source of energy– Simple ring structure
• Also important in the structural integrity of the cells of certain organisms
Figure 2-16 Essential Cell Biology (© Garland Science 2010)
Figure 2-17 Essential Cell Biology (© Garland Science 2010)
Using bacteria to fight cancer
• Clostridium sporogenes
• Harmless bacteria found in soil
• Anaerobic– Tumor cells = no O2
• Enzyme + cancer drug = activated drug
Fatty acids
• Carboxylic tail with hydrocarbon chain
• Form fats, lipids, membranes
• Two major functions:– Make up cell
membranes– Store chemical energy
• Cell signaling events
Figure 2-18 Essential Cell Biology (© Garland Science 2010)
Types of fatty acids• Saturated vs. Unsaturated
– Difference in structure– Single C-C bond = 83 ΔH°– Double C=C bond = 146 ΔH°
Saturated vs. Unsaturated
• Saturated fats– Animal products– Processed foods– Solid at room temperature
• Unsaturated fats– Nuts– Olive oil– Avocados– Liquid at room temperature
Fats in neural development
• Axons covered by myelin sheath
• Fat cells
• Fatty acids are delivered to infants through breast milk
Figure 2-19 Essential Cell Biology (© Garland Science 2010)
Figure 2-20 Essential Cell Biology (© Garland Science 2010)http://www.3dchem.com/moremolecules.asp?ID=382&othername=LA
Membrane fluidity varies among species
• Bigger mammals=less unsaturated fatty acids than smaller mammals– Less membrane fluidity– Lower Na+-K+-ATPase activity
• Smaller animals= more unsaturated fatty acids than bigger mammals– More membrane fluidity– Higher Na+-K+-ATPase activity– Increased permeability of the membrane?
Amino acids• Link together to form proteins
• Defining property: all possess a carboxylic acid group and an amino group– COOH
– NH2
• Proteins are polymers of amino acids
Figure 2-21 Essential Cell Biology (© Garland Science 2010)
• 20 amino acids
• Each amino acid corresponds to one codon
• One codon is three nucleotides
• Sequence of amino acids dictates a protein’s properties
Figure 2-22 Essential Cell Biology (© Garland Science 2010)
Nucleotides
• Adenine, Guanine, Cytosine, Thymine, Uracil
• Form DNA and RNA
• Provide all the information a cell needs to carry out important processes
Figure 2-23 Essential Cell Biology (© Garland Science 2010)
Figure 2-24 Essential Cell Biology (© Garland Science 2010)
3’ carbon that will form bond with the phosphate group Attached to the 5’ carbon of the next nucleotide
• Nucleotides provide the coding for amino acids– 3 nucleotides = codon=
1 amino acid
• Chains of amino acids make up proteins
Proteins• Sequence of nucleotides
• Levels of protein organization– Primary: sequence– Secondary: alpha helix and beta sheets– Tertiary: final specific geometry that a protein
assumes– Quaternary: clustering of several protein chains
into a final specific structure
Figure 2-32 Essential Cell Biology (© Garland Science 2010)
Diseases attributable to defects in protein function
• Sickle Cell Anemia
• Huntington’s disease
• Achondroplasia
Sickle Cell Anemia
• Hemoglobin• Single amino acid change
drastically changes the shape of the red blood cell
• Problems with blood clotting
Huntington’s Disease
• CAG repeat on chromosome 4o Normal: 10-35 repeatso Huntington’s: 36-120
• Symptoms show up earlier as it is passed down in a family
• Causes degeneration of nervous tissueo Basal ganglia responsible for movement
Achondroplasia
• FGFR3 (Fibroblast growth factor gene)o Receptor that regulates bone growth by
limiting the formation of bone from cartilage in the long bones
o Hyperactive • Chromosome 4
Mad Cow Disease• How is Mad Cow Disease transmitted?
• How is Alzheimer’s “transmitted?”
• How could these two possibly be related?– Protein vs. Prion
Molecular Biology of prion diseases. Prusiner, SB, Science 1991; 252; 1515-1522
Acids and Bases• pH = concentration of
hydrogen (hydronium ion-H3O+)
– 0-14– 7 = neutral
• Acid = donates a hydrogen
• Base = accepts a hydrogen or donates a hydroxyl group
Figure 2-14 Essential Cell Biology (© Garland Science 2010)