EXAM 1 BIOCHEM

Need to finish TBD

3 Distinct Domains of Life

1. Bacteria

2. Archaea

3. Eukarya

Bacteria

inhabit soils, surface waters, and the tissues of other living or decaying

organisms; prokaryotes

Archaea

inhabit extreme environments—salt lakes, hot springs, highly acidic

bogs, and the ocean depths; prokaryotes

Eukarya

more closely related to archaea than to bacteria

Characteristics of Bacteria

• Small (0.001 – 0.01 mm; diameter 0.2-2 μm)

• Unicellular (single-celled organism)

• Single membrane

• No nucleus or organelles

• Prokaryotes

Characteristics of Eukarya

• 10³-10⁴ times larger

• Single or multi-celled

• Multi-membrane

• Nuclei and many organelles

Biomolecules

are carbon compounds

-Tetrahedral nature of 4 covalent bonds, C-C bond is most versatile (Cyclic, branched, planar, and linear),

What is the structural organization of complex biomolecules?

The Hierarchy of Life

• Inorganic Precursors

• Metabolites

• Building Blocks

• Macromolecules (aka biomolecules)

• Supramolecular complexes

• Organelles

• Cell

Inorganic Precursors

(18-64 daltons); CO2, H2O, Ammonia, Nitrogen (N2), Nitrate (NO3-)

Metabolites

(50-250 daltons); pyruvate, citrate, succinate, glyceraldehyde-3-phosphate, fructose-1,6-biphosphate, 3-phosphoglyceric acid

Building Blocks

(100-350 daltons; amino acids, nucleotides, monosaccharides, fatty acids, glycerol

Macromolecules

(10³-10⁹ daltons), proteins, nucleic acids, polysaccharides, and lipids

Supramolecular complexes

(10⁶-10⁹ daltons), ribosomes, cytoskeleton, multienzyme complexes

Organelles

Nucleus, mitochondria, chloroplasts, ER, golgi apparatus, vacuole

Properties of biomolecules

• Macromolecules are informational

• Biomolecules have characteristic three-dimensional architecture

• Weak forces maintain biological structure and determine biomolecular interactions

• Macromolecules are polymers

Biological macromolecules and their building blocks

• proteins and amino acids

• polysaccharides, sugars, and lipids

• polynucleotides (DNA and RNA) and nucleotides

Weak forces include:

• Van der Waals interactions

• Ionic interactions

• Hydrogen bonds

• Hydrophobic interactions

Van der Waals Interactions (London Forces)

• Induced electrical interactions between the positively charged nuclei and the electrons of nearby atoms (interactions caused by charged electron clouds fluctuations in time)

• Strength=0.4-4.0 kJ/mol

• Distance=0.3-0.6 nm

• Compare to a C-C bond at 0.154 nm and 343 kJ/mol

• Need several to occur simultaneously

• Facilitated by structural or shape complementarity

Strength depends on the distance apart (r ) and radii of the atoms involved

Ionic Interactions

• Attractive forces between oppositely charged structures

• Strength = 20 kJ/mol

• Distance = 0.25 nm

• Charge may depend on pH

• Strength depends on charge and distance

Hydrophobic Interactions

Result from the strong tendency of water to exclude non-polar groups or molecules.

Van der Waals Interactions

0.4-4.0 kJ/mol

Hydrogen Bonds

12-30 kJ/mol

Ionic Interactions

20 kJ/mol

Hydrophobic Interactions

<40 kJ/mol

2 important points about weak forces

1. Biomolecular recognition is mediated by weak forces.

2. Weak forces restrict organisms to a narrow range of environmental conditions (temperature, ionic strength and pH)

Weak Forces

These interactions influence profoundly the nature of

biological structures.

Properties of Weak Forces

Maintain biological structure and determine biomolecular interactions

• Influence the structures and behaviors of all biological molecules

• Create interactions that are constantly forming and breaking under physiological conditions

• Are collective

Hydrogen Bonding in Water

Between 2 water molecules

The potential to form 4 H-bonds per water molecules (2 as donor and 2 as acceptor)

H-bond lifetime - about 10 psec (aka 1 × 10^-11 sec )

Unusual Properties of Water

• High boiling point, melting point, heat of vaporization, and surface tension

• Bent structure that makes it polar – separation of positive and negative centers

• Non-tetrahedral bond angles (104.3°; not 109°like CH4)

• H-bond donor and H-bond acceptor

• Potential to form 4 H-bonds per molecule

• Low density in the solid state

• Cooperative H-bonding

• High Dielectric constant

Dielectric constant

An indicator of a solution’s ability to separate charge

Water’s dielectric constant

78.5 D

K_a

Is the acid dissociation constant

K_a = [H⁺][A^-]/[HA]

pK_a

the pH at which the acid and conjugate base are equal

pK_a =pH

-log K_a=pK_a

Henderson-Hasselbalch equation

pH=pK_a+log₁₀[A^-]/[HA]

Formic Acid HCOOH

-Weak Acid

-pKa=3.75

Acetic Acid (CH3COOH)

-Weak Acid

-pKa = 4.76

Propionic Acid (CH3CH2COOH)

-Weak acid

-pKa = 4.87

Lactic Acid (CH3CHOHCOOH)

-Weak acid

-pKa = 3.86

Succinic Acid (HOOCCH2CH2COOH)

-Weak acid

-pK1= 4.21

Phosphoric Acid (H3PO4)

-weak acid

-pK1=2.15

Phosphoric Acid (H2PO4-)

-weak acid

pk2 = 7.20

Phosphoric acid (HPO₄^2-)

-weak acid

pK3 = 12.40

Imidazole (C3N2H5+)

Weak Acid

pKa = 6.99

Histidine-imidazole group (C6O2N3H11+)

-weak acid

pKR=6.04

Carbonic Acid (H2CO3)

-weak acid

pK1 = 3.77

Bicarbonate (HCO3-)

-weak acid

pK2 = 10.24

tris-hydroxymethyl aminomethane (HOCH2)3 CNH3+

Weak acid

pKa=8.07

Ammonium (NH4+)

Weak acid

pKa=9.25

Methylammonium (CH3NH3+)

-weak acid

pKa=10.62