Bio Chapter 2: The Chemical Basis of Life

Element

• chemical substance that cannot be broken down into a different substance

Atom

• smallest unit that retains the properties of an element

Atomic structure

• atoms are comprised of protons, electrons, and neutrons

Protons

• positively charged particles in the nucleus

neutrons

• uncharged (neutral) particles in the nucleus

electrons

• negatively charged particles orbiting around the nucleus

atomic number

• # of protons (6 for carbon)

atomic mass

• # of protons + # of neutrons in the nucleus (12 for carbon)

isotopes

• elemental variations

• number of neutrons differs

radioactivity

• The atomic nucleus becomes unstable as the difference between # of protons and neutrons grows

• can be dangerous

• When radioactive atoms decay (break down) they can release several types of radiation

• Unstable nuclei of isotopes can be radioactive and release neutrons at high velocity that can damage other atoms

• This is called neutron radiation (there are other types)

• This can lead to mutations in our DNA, resulting in illnesses such as cancer

carbon dating

• can age remains of organic matter (e.g. bones)

• Limit of ~ 60,000 years

chemical bonds

• attractive forces between atoms

chemical reactions

• “reactant” molecules transformed into “products” by forming / breaking bonds

molecule

• group of 2 or more atoms held together by chemical bonds

• size ranges from 2 atoms to 200 million

covalent bonds

• strong

• atoms share electrons (one or more pairs)

• The majority of organic molecules (those that make up living things) are built with covalent bonds

• Example: oxygen has 2 electrons in valence shell that aren’t partnered

  • Therefore, can form 2 covalent bonds (in this case, with hydrogens to form water, H2O)

Ionic bonds

• strong

• an electron is taken from one atom and given to another, the resulting atoms are attracted to each other

• The negative and positive ions attract each other – strong bond!

hydrogen bonds

• weak

• interactions between positive/negative regions (our focus will be between water molecules)

• critical for water, DNA, and protein

Electrons’ Role in Chemical Bonding

• Electrons exist in shells around the nucleus, and they prefer to be in pairs

• High energy electrons orbit farther away from the nucleus than low energy electrons

• The outermost “valence” shell is involved in forming chemical bonds

• The atom “wants” its valence shell full of electron pairs

water

• is composed of 2 hydrogen and 1 oxygen atom

• Its electrons are not shared equally

• Electrons are more attracted to oxygen than the hydrogen atoms

• The result is partial negative charge near the oxygen and partial positive charge near the hydrogens

Properties of water

• Temperature Moderation

• Frozen water (ice) floats

• Universal solvent

Water Moderates Temperature Fluctuations

• Water can absorb or give off large amounts of heat with little change in temperature

• Evaporation is a cooling process

Ice insulates water

• Solid water (ice) is unique in that it is less dense than liquid water: ice floats

  • Why? Hydrogen bonds less tightly packed in ice than liquid water

  • In cold winters, ice acts as an insulator

solute

• dissolved substance

solvent

• dissolving agent

• The solvent property of water breaks down nutrients so that our cells can move them and absorb them

solution

• combo of solute and solvent

pH (potential of Hydrogen)

• measure of the relative amount of hydrogen ions (H+) and hydroxide ions (OH-) in a solution

more H+ (hydrogen) ions

• more acidic

  • lower numbers on scale

more OH- (hydroxide) ions

• more alkaline (basic)

  • higher numbers on scale

Stable pH is Important for the Body

• Optimum pH of our bodies ~ 7.4 (close to the neutral pH of water: 7)

  • Has to be kept at a fairly narrow range o If they get to acidic or basic, the proteins will denature

• Acidity or alkalinity can denature proteins, which need proper shape to function

Buffer (bicarbonate)

• one way we maintain neutral pH

• Our kidneys maintain blood pH by producing this

• serves as a sponge and can absorb extra hydrogen ions or can squeeze the sponge to release them to keep those ions there

• are special molecules that can release or absorb H+ to keep pH steady

Metabolic Acidosis

• Slight blood pH deviation is enough to cause issues: <7.35 compared to 7.4 (normal)

• Some causes of buffering capacity being exceeded:

  • Kidneys can’t eliminate enough hydrogen, or lose too much bicarbonate buffer

  • Lactic acid buildup

  • Untreated diabetes