Atoms and Moleculesin Biology

The hierarchy of biological order

BIO 202

Sizes of molecules, cells and organisms

Chemical elements in living cells

Elements• Element = a substance that cannot be broken

down by chemical reactions• There are 92 naturally occurring elements

(+artificial=>103)• Each element has a 1- or 2-letter symbol (e.g., O,

N, Na, Ca)• Life requires ~25 elements• Trace elements = elements required in minute

amounts, but their lack can cause severedisorders

• Elements are made of atoms• Atom is the smallest unit of matter that retains the

properties of an element

Structure of atomsAtoms are made of subatomic particles:

•Protons and neutronsmake up the atomic nucleus

•Neutron mass = Proton mass= 1.7 x 10-24 g = 1 Dalton

•Neutron = 0 charge

•Proton = +1 charge

•Thus, atomic nucleus ispositively charged,and its mass =mass of protons+mass of neutrons

Structure of atoms• The nucleus is orbited by electrons• Electron charge = -1• The attraction between the nucleus and the

electrons keeps the electrons in the vicinity ofthe nucleus, and thus preserves the atomicstructure

• Atoms overall are neutral:– # protons = # electrons

• Electron mass = 1/2000 (=0.05%) mass of aproton (negligible in biological calculations)

• Atomic mass ≈ mass of the nucleus = mass ofprotons + mass of neutrons

Uniqueness of elements

• Various elements differ in number ofsubatomic particles in their atoms

• Each element has a unique number ofprotons in the nucleus of its atoms =atomic number = # protons

• Each element is also characterized by itsmass number– Mass number = # protons + # neutrons

Na2311

Atomic number = # of protons = # of electrons

Mass number = # of protons + # of neutrons

Therefore:

Sodium has 11 protons and 12 neutrons

Because mass # ≈ atomic weight, atomic weight ≈ 23

All atoms of an element have the same number ofprotons

What about neutrons?

Uniqueness of elements

Number of neutrons can vary

• Atomic forms of the same element (same numberof protons and electrons) with different numberof neutrons are called isotopes.

• Isotopes differ in mass

Example: isotopes of carbon

C126

Stable isotopes Radioactive isotope

(neutron releaseselectron andbecomes proton)Decays to N14

7C136 C

1466 neutrons 7 neutrons

8 neutrons

Radioactive isotopes in biology• Radioactive isotopes are very valuable tools in biology1. Determining the age of samples

• Radioactive elements have specific and constantperiods of decay called “half-life”• e.g., half-life of 14C=5,715 years, 8C=2 x 10-21

seconds, 32P=2 weeks2. Cytotoxic agents

• Kill proliferating cells (treatment of cancer)3. Induce mutations in DNA (usually large deletions)4. Biological tracers

• Radioactive labeling of biological molecules (DNA,proteins, etc.), and following their fate in a cell ororganism

Chemical bonds

•Atoms combine into chemical compounds•Combinations of atoms in a fixed ratio =molecules example: Na + Cl = NaCl (1:1 ratio)

Chemical characteristics of a compound canbe different from those of its combinedelements (atoms)

Chemical bonds• Atoms interact with each other through

their electrons. Atomic nuclei do notdirectly participate in chemical reactions

• Electrons are characterized by theirenergy levels– Energy is the ability to do work– Potential energy = energy stored in matter

due to its location– In atoms, the potential energy of the electron

is determined by its distance relative to thenucleus—the further it is, the more potentialenergy it has

Bonding

• When electrons receiveenergy, they jump to a higherenergy level

• When electrons lose energy,they drop to a lower level

• These changes in energyoccur in discrete steps– e.g., the energy of the sun

excites electrons in plantcompounds; when theylose this energy, it is usedfor work (biosynthesis)

• Different states in electron potential energy are calledenergy levels or energy shells

OrbitalsOrbital - volume of space in whichelectron spends most of its time

- one orbital can contain a maximum of 2 electrons- orbitals have characteristic shapes: spherical (s),dumbbell-shaped (p), and more complex shapes

Energy

Chemical behavior• The chemical behavior of atoms depends

on its electron configuration– Mainly on the number of electrons (=valence

electrons) in the outermost shell (=valenceshell)

– An atom with a full valence shell is non-reactive (e.g., inert elements He, Ne, Ar)

– In atoms, electrons first fill all the orbitals inthe valence shell, and then start filling them tocapacity

Chemical behavior• Atoms with unfilled valence

shells strive to fill them. To doso, they must grab electronsfrom other atoms (=chemicalreaction)

• Different atoms with the samenumber of valence electrons(=chemical valency) exhibitsimilar chemical behavior;e.g., Cl (chlorine), F (fluorine)

• Two atoms that interact witheach other to fill their valencyshells share electrons andform a chemical bond