life’s chemical basis -...

Life’s Chemical Basis

Life’s Chemical Basis

Ø Atoms and Elements

Ø Why Electrons Matter

Ø Atomic Bonds

Ø Water molecule properties

Ø Hydrogen Power (pH)

Matter & Elements

Ø Matter is anything that occupies space and has mass

Ø Matter is composed of chemical elements

Ø An element is a substance that cannot be broken down into other substances

Elements and Atoms

Ø The three subatomic particles are: •  Protons are positively charged •  Neutrons are electrically neutral •  Electrons are negatively charged

Ø Each element consists of one kind of atoms

Ø An atom is the smallest unit of matter that still retains the properties of an element

Terminology/ Elements Ø Atomic Number: The number of protons in an atom

atomic number

mass number

element symbol

Ø Mass Number: The sum of the numbers of protons and neutrons in the nucleus

atomic number

element symbol

mass number

elemental substance element name

carbon

Periodic Table of Elements

Elements Required for Life Ø O, C, H, N make up

about 96% of the human body weight

Ø Ca, P, K, S, Na, Cl, Mg make up most of the rest

Ø Trace elements make less than 0.01% of human body weight

Required in minute amounts but they are crucial!

Isotopes Isotopes of an element have the same number of protons but different numbers of neutrons (different mass numbers)

Stable isotope: enough binding energy to hold the nucleus together permanently 12C and 13C

Isotopes

the nucleus decays spontaneously, giving off particles and energy

Unstable isotope, Radioactive isotopes, Radioisotopes Isotope with an unstable nucleus/ 14C

nucleus of 14C, with

6 protons, 8 neutrons

nucleus of 14N, with

7 protons, 7 neutrons

Ø Under natural conditions, elements occur as a mixture of isotopes

Ø Different isotopes of an element behave identically in chemical reactions Ø Living cells cannot distinguish between isotopes of the same element

Ø Isotopes have fixed half-life/ radioisotopes decay at a predictable rate into predictable products

14C 14N

Biological Applications of Radioactive Isotopes

Basic Research/ radioactive tracers/ detectable component/can be tracked after delivery into the body or system Archaeological Dating/ based on decay rate of radioisotopes (half life) Medical Treatments and Diagnosis

β-amyloid/ PiB

Why do Atoms Interact?

Ø Of the three subatomic particles, only electrons are directly involved in chemical activity

Ø Electrons occupy different orbitals (volumes of space around an atom’s nucleus)

Ø Orbitals are filled from lower to higher energy Ø The farther an electron is from the nucleus, the

greater its energy

Arrangement of electrons around the nucleus

shell model

first shell hydrogen (H) helium (He)

second shell carbon (C) oxygen (O)

third shell sodium (Na) chlorine (Cl)

neon (Ne)

argon (Ar)

one proton

one electron

Vacancies/ Can the outer shell hold more electrons?

Ø No vacancies: an atom’s outermost shell is filled with electrons Ø  Most stable state

Ø Vacancy: an atom’s outermost shell has room for other electrons Ø  Chemically active; atoms

interact with one another Ø  Example: oxygen atom has

six electrons in its outer (second) shell, which can hold eight

Oxygen (O) Neon (Ne)

Chemical Bonds An atom can get rid of vacancies by participating in chemical bonds with other atoms Atoms with incomplete outer shells share, donate or receive electrons

Chemical bond is the attractive force that keeps atoms together in a molecule

electron loss

Sodium atom Sodium ion 11p+

11e-

charge: 0

11p+

10e-

charge: +1

Ø Atoms with an unequal number of protons and electrons are called ions Ø Carry a net (overall) charge

Compounds

Ø A compound is a substance consisting of two or more different elements in a fixed ratio

Ø Compounds are more common than pure elements

Ø Sodium chloride, table salt, is a common compound of equal parts of sodium (Na) and chlorine (Cl)

Sodium Chlorine

Sodium Chloride

+

Types of chemical bonds

Ø Covalent Bonds

Ø Ionic Bonds

Ø Hydrogen Bonds

Ionic Bonds

Ø An ion is an atom or group of atoms with an electrical charge resulting from gain or loss of electrons

Ø Two ions with opposite charges attract each other

Ø When the attraction holds the ions together ionic bond

Example of ionic bond: Sodium Chloride

Transfer of electron

Sodium atom Chlorine atom Na+

Sodium ion Cl-

Chloride ion

Sodium chloride (NaCl)

Ions retain their respective charges when participating in an ionic bond

Electronegativity measure of the ability of an atom to pull electrons away from other atoms

Polarity separation of charge into positive and negative regions

Covalent Bonds

Ø Two atoms with incomplete outer shells share one or more electrons

Types of Covalent Bonds Non-polar:

Ø Bond between atoms with the same electronegativity

Polar: Ø Bond between atoms of

different electronegativity

Methane Water

Hydrogen Bonds Ø  Hydrogen, as part of a polar

covalent bond, has a partial positive charge

Ø Hydrogen atoms that are covalently bonded in a molecule can be attracted to atoms with slight negative charges in other molecules such as oxygen and nitrogen

Ø Because the positively charged region is always a hydrogen atom, the bond is called a hydrogen bond

Ø H-bonds help define the properties of water, create the shape of proteins, hold DNA strands together, etc

Water’s Life-supporting Properties

Ø 70% of Earth is covered with water

Ø All living organisms require water more than any other substance

Ø Most cells are surrounded by water, and cells themselves are about 70-95% water

Polar Molecule Hydrogen Bonds

Universal Solvent

Solution/ homogeneous mixture Solvent + Solute Aqueous solution

hydrophilic (“water-loving”) molecules/ polar hydrophobic (“water-hating”) molecules/ non-polar

Universal Solvent

Ø Water is an effective solvent because of its polarity

Ø When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules, a hydration shell

Universal Solvent

Non ionic compounds such as sugar dissolve as water molecules surround them and form hydrogen bonds with their polar regions

Cohesion Ø The tendency of molecules of the same kind to stick together

•  Hydrogen bonds make liquid water cohesive

•  Surface tension

Ø Cohesion in water is much stronger than other liquids

https://youtu.be/iAT_iBgn1QI

Ø Because of hydrogen bonds between water molecules, it takes more heat to raise the temperature of water compared with other liquids (Temperature: measure of molecular motion)

Ø Below 0°C (32°F), water molecules become locked in the bonding pattern of ice (lattice pattern) Ø Sheets of ice that form on the surface of ponds,

lakes, and streams insulate the water Ø Protects aquatic organisms during cold winters

Water stabilizes temperature

Ice is less dense than liquid water

Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense

Ø pH: measure of the number of hydrogen ions in a fluid

Ø Base: substance that accepts hydrogen ions in water Ø pH above 7

Ø Acid: substance that releases hydrogen ions in water Ø pH below 7

Ø Most biological systems can function properly only within a narrow range of pH

Ø The fluids inside cells stay within a consistent range of pH because they are buffered

Ø Buffer: set of chemicals that can keep the pH

of a solution stable by alternately donating and accepting ions that contribute to pH

household ammonia

gastric fluid

acid rain lemon juice

cola vinegar

tomatoes, wine bananas

urine, tea, typical rain

corn

milk pure water

blood, tears

baking soda Tums

oven cleaner

bleach

13

11

10

9

8

7

6

5

4

3

2

1

0

14

HCl is a strong acid (the gastric fluid) Carbonic acid is a weak acid: CO2 + H2O = H2CO3 H2CO3 H+ + HCO3

- H2CO3 Carbonic Acid Bicarbonate

Ø Acid rain (pH < 5.2)

Changes in Acidity can Have Environmental Consequences

Ø Ocean acidification

CO2 + H2O H2CO3