Chapter 2: Chemistry of Life (Chemistry Comes Alive)

Chapter 2:Chemistry of Life(Chemistry Comes Alive)

Niels Bohr – originator of the model of the atom we utilize in BIOL 232 & BIOL

233..

Selman Waksman He investigated how soil microbes defended themselves against invaders which

lead to the He and coworkers isolation of twenty-two different defensive compounds produced by soil microbes. These discoveries lead to the discovery

streptomycin, the first antibiotic effective against tuberculosis. Waksman received the 1952 Nobel Prize in physiology or medicine.

Chemistry still plays a significant role in the cutting-edge research into physiology today. Researchers with deep understanding of chemistry are needed in medicine, physiology, and related fields.

Figure 2.1 Two models of the structure of an atom.

(a) Planetary model (b) Orbital model

Helium atom

2 protons (p+)2 neutrons (n0)2 electrons (e–)

Helium atom

2 protons (p+)2 neutrons (n0)2 electrons (e–)

Nucleus Nucleus

Proton Neutron Electroncloud

Electron

Figure 2.2 Atomic structure of the three smallest atoms.

Proton

Neutron

Electron

Helium (He)(2p+; 2n0; 2e–)

Lithium (Li)(3p+; 4n0; 3e–)

Hydrogen (H)(1p+; 0n0; 1e–)

Figure 2.3 Isotopes of hydrogen.

Proton

Neutron

Electron

Deuterium (2H)(1p+; 1n0; 1e–)

Tritium (3H)(1p+; 2n0; 1e–)

Hydrogen (1H)(1p+; 0n0; 1e–)

Figure 2.5 Chemically inert and reactive elements.

Helium (He)(2p+; 2n0; 2e–)

Neon (Ne)(10p+; 10n0; 10e–)

2e 2e8e

2e4e

2e8e

1e

(b) Chemically reactive elements

Outermost energy level (valence shell) incomplete

Hydrogen (H)(1p+; 0n0; 1e–)

Carbon (C)(6p+; 6n0; 6e–)

1e

Oxygen (O)(8p+; 8n0; 8e–) Sodium (Na)

(11p+; 12n0; 11e–)

2e6e

(a) Chemically inert elements

Outermost energy level (valence shell) complete

Figure 2.6 Formation of an ionic bond.

Sodium atom (Na)(11p+; 12n0; 11e–)

Chlorine atom (Cl)(17p+; 18n0; 17e–)

Sodium ion (Na+) Chloride ion (Cl–)

Sodium chloride (NaCl)

CI–

Na+

+ –

(a) Sodium gains stability by losing one electron, and chlorine becomes stable by gaining one electron.

(b) After electron transfer, the oppositely charged ions formed attract each other.

(c) Large numbers of Na+ and Cl– ionsassociate to form salt (NaCl) crystals.

Figure 2.7 Formation of covalent bonds.

or

Oxygen atom Oxygen atom Molecule of oxygen gas (O2)

+ or

Nitrogen atom Nitrogen atom Molecule of nitrogen gas (N2)

+

Hydrogen atoms Carbon atom Molecule of methane gas (CH4)

Structural formulashows single bonds.

Structural formulashows double bond.

Structural formulashows triple bond.

(b) Formation of a double covalent bond: Twooxygen atoms share two electron pairs.

(c) Formation of a triple covalent bond: Twonitrogen atoms share three electron pairs.

(a) Formation of four single covalent bonds:Carbon shares four electron pairs with fourhydrogen atoms.

or

Resulting moleculesReacting atoms

+

Figure 2.8 Carbon dioxide and water molecules have different shapes, as illustrated by molecular models.

Figure 2.9 Ionic, polar covalent, and nonpolar covalent bonds compared along a continuum.

Figure 2.10 Hydrogen bonding between polar water molecules.

(a) The slightly positive ends (+) of the water molecules becomealigned with the slightly negative ends (–) of other watermolecules.

(b) A water strider can walk on a pond because of the highsurface tension of water, a result of the combinedstrength of its hydrogen bonds.

+

–

–

–– –

+

+

+

+

+

Hydrogen bond(indicated bydotted line)

Figure 2.13 The pH scale and pH values of representative substances.

Concentration(moles/liter)

[OH–]

100 10–14

10–1 10–13

10–2 10–12

10–3 10–11

10–4 10–10

10–5 10–9

10–6 10–8

10–7 10–7

10–8 10–6

10–9 10–5

10–10 10–4

10–11 10–3

10–12 10–2

10–13 10–1

[H+] pHExamples

1M Sodiumhydroxide (pH=14)

Oven cleaner, lye(pH=13.5)

Household ammonia(pH=10.5–11.5)

Neutral

Household bleach(pH=9.5)

Egg white (pH=8)

Blood (pH=7.4)

Milk (pH=6.3–6.6)

Black coffee (pH=5)

Wine (pH=2.5–3.5)

Lemon juice; gastricjuice (pH=2)

1M Hydrochloricacid (pH=0)10–14 100

14

13

12

11

10

9

8

7

6

5

4

3

2

1

0

Figure 2.12 Dissociation of salt in water.

Water molecule

Ions in solutionSalt crystal

–

+

+

Figure 2.16c Lipids.

ExampleCholesterol (cholesterol is thebasis for all steroids formed in the body)

(c) Simplified structure of a steroid

Four interlocking hydrocarbon rings form a steroid.

Figure 2.19 Levels of protein structure.

Secondary structure:The primary chain formsspirals (-helices) andsheets (-sheets).

Tertiary structure:Superimposed on secondary structure.

-Helices and/or -sheets are folded upto form a compact globular moleculeheld together by intramolecular bonds.

Quaternary structure:Two or more polypeptide chains, eachwith its own tertiary structure, combineto form a functional protein.

Tertiary structure of prealbumin(transthyretin), a protein thattransports the thyroid hormonethyroxine in serum and cerebro-spinal fluid.

Quaternary structure of afunctional prealbumin molecule.Two identical prealbumin subunitsjoin head to tail to form the dimer.

Amino acid Amino acid Amino acid Amino acid Amino acid

-Helix: The primary chain is coiledto form a spiral structure, which isstabilized by hydrogen bonds.

-Sheet: The primary chain “zig-zags” backand forth forming a “pleated” sheet. Adjacentstrands are held together by hydrogen bonds.

(a) Primary structure: The sequence of amino acids forms the polypeptide chain.

(b)

(c)

(d)

Figure 2.19a Levels of protein structure.

(a) Primary structure: The sequence of amino acids forms the polypeptide chain.

Amino acid Amino acid Amino acid Amino acid Amino acid

Figure 2.19b Levels of protein structure.

-Helix: The primary chain is coiledto form a spiral structure, which isstabilized by hydrogen bonds.

-Sheet: The primary chain “zig-zags” backand forth forming a “pleated” sheet. Adjacentstrands are held together by hydrogen bonds.

(b) Secondary structure:The primary chain forms spirals (-helices) and sheets (-sheets).

Figure 2.19c Levels of protein structure.

Tertiary structure of prealbumin(transthyretin), a protein thattransports the thyroid hormonethyroxine in serum and cerebro-spinal fluid.

(c) Tertiary structure: Superimposed on secondary structure. -Helices and/or -sheets are folded up to form a compact globular molecule held together by intramolecular bonds.

Figure 2.19d Levels of protein structure.

Quaternary structure ofa functional prealbuminmolecule. Two identicalprealbumin subunitsjoin head to tail to formthe dimer.

(d) Quaternary structure: Two or more polypeptide chains, each with its own tertiary structure, combine to form a functional protein.

An example of the progression in complexity of structure in proteins with the final quaternary structure being that of hemoglobin.

Figure 2.20 Enzymes lower the activation energy required for a reaction to proceed rapidly.

Activationenergy required

Less activationenergy required

WITHOUT ENZYME WITH ENZYME

Reactants

Product Product

Reactants

Figure 2.21 Mechanism of enzyme action.

Substrates (S)e.g., amino acids

Enzyme (E)

Enzyme-substratecomplex (E-S)

Enzyme (E)

Product (P)e.g., dipeptide

Energy isabsorbed;bond isformed.

Water isreleased.

Peptidebond

1 Substrates bind at active site. Enzyme changes shape to hold substrates in proper position.

2 Internalrearrangements leading to catalysis occur.

3 Product isreleased. Enzyme returns to original shape and is available to catalyze another reaction.

Active site

+

Substrate “fits” with active site

Active site

Functionalenzyme

Substrate unable to bind

Denatured enzyme

(a) (b)

Active siteAmino acids

Enzyme (E)Enzyme-substratecomplex (E-S)

Internal rearrangementsleading to catalysis

Dipeptide product (P)

Free enzyme (E)

Substrates (S)

Peptide bond

H2O

+

Figure 2.22 Structure of DNA.

Deoxyribosesugar

Phosphate

Sugar-phosphatebackbone

Adenine nucleotideHydrogenbond

Thymine nucleotide

PhosphateSugar:

Deoxyribose PhosphateSugarThymine (T)Base:

Adenine (A)

Adenine (A)

Thymine (T)

Cytosine (C)

Guanine (G)

(b)

(a)

(c) Computer-generated image of a DNA molecule

Figure 2.23 Structure of ATP (adenosine triphosphate).

Adenosine triphosphate (ATP)

Adenosine diphosphate (ADP)

Adenosine monophosphate (AMP)

Adenosine

Adenine

Ribose

Phosphate groups

High-energy phosphatebonds can be hydrolyzedto release energy.

Figure 2.24 Three examples of cellular work driven by energy from ATP.

Solute

Membraneprotein

Relaxed smoothmuscle cell

Contracted smoothmuscle cell

+

+

+

Transport work: ATP phosphorylates transportproteins, activating them to transport solutes(ions, for example) across cell membranes.

Mechanical work: ATP phosphorylates contractile proteins in muscle cells so the cells can shorten.

Chemical work: ATP phosphorylates key reactants, providing energy to drive energy-absorbing chemical reactions.

(a)

(b)

(c)

Table 2.1 Common Elements Composing the Human Body (1 of 2)

Notice how there are three broad categories of these elements, major, lessor, and trace.

Table 2.1 Common Elements Composing the Human Body (2 of 2)