the chemical foundations of life chapter 2 (pages 22-44)

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)