Intro to Biochem and Water Structure and Function

Atom

 smallest piece of an element => too small for eyes, cannot see at all 

Nucleus

 atoms center and contains neutrons & protons

Outer most region/orbital

region or space around the nucleus where an electron is likely to be found

Electrons:

• Negative charge (each electron has negative change equal to + charge

• have less mass than protons (not very significant to overall mass)

Protons

positively charged 

Neutron

uncharged and only contribute to mass not the atom’s charge 

Neutral Atoms:

• Electron orbiting nucleus = # of protons in nucleus

• positive and negative charges cancel each other out and have a 0 net charge

Atomic #

total number of protons in atom’s nucleus 

Mass number

 total sum of protons and neutrons combined (count of particles in nucleus) 

Atomic mass

Total mass of an atom (measured in amu or Daltons)

• Ignore mass of electrons

• Calculate based on # of protons and neutrons 

• Protons, neutrons both have similar mass => their mass is the atomic mass unit (amu) or Dalton 

Atomic number

# of protons determine element’s atomic #

• Used to distinguish elements

# of neutrons vary

• Isotopes

• different forms of same atom that have different # of neutrons

•  different forms of an element that have the same # of protons but different number of neutrons

 mass #

Together, # of protons & neutrons determine an element’s mass #

valance shell

• Full valence shell is the most stable electron configuration

  • Partially fillers shells need to gain or lose electrons to get a stable configuration

• If not all elements have enough electrons, the atoms form chemical bonds

  • When 2 or more atoms bond, a molecule forms 

Ionic bond(no sharing)

•  Transferring electrons between metal and non-metal

  • One atom transfers 1 or more electrons to another atom, creating 2 oppositely charged ions that attract each other

Covalent bond

• sharing electrons between non-metals

• Sharing electrons between atoms to form covalent bonds => more common

Polar covalent bond (unequal sharing)

• atoms unequal sharing the electrons as the electrons are attracted more to one nucleus than the other

• Uneven distribution of power leads to a slightly positive of negative charge

• Electrons are shared unequally because one atom is more negative 

• Water is a polar molecule because there is a negative and positive side and the electrons are not shared evenly

Nonpolar covalent bonds(equal sharing)

 bonds from between two atoms of the same element or between different elements that share electrons equally

• The electrons are shared equally because the charges are the same or cancel out

• Molecules that have balanced charges and there are no charged poles that make the electrons go a certain way

• If an element has a higher electronegativity than another, the electrons will more more attracted to it

Ion:

•  atom or molecule that has a Net charge

• Since number of electrons are not equal to number of protons, each Ion has a Net charge 

  • Ions with positive charge => Cations

  • Ions with negative charge => Anions

hydrogen bond

A hydrogen bond is a strong type of intermolecular (between atoms) or intramolecular (within atoms) attraction. It happens when a hydrogen atom is covalently bonded to a highly electronegative atom (electron loving) like nitrogen, oxygen, or fluorine. Because hydrogen only has one electron to begin with, when the electronegative atoms pull that one electron away, the hydrogen is left with a slightly positive charge. Then the other element becomes more negatively charged when they share the electrons. 

electronegative

• Elements are electronegative because they have more protons in the nucleus and can thus pull shared bonding electrons more strongly. 

Hydrophilic

 water loving, polar substance that interacts with water quickly or dissolved in water 

Hydrophobic

 nonpolar molecules, compounds, that do not interact with water well (water fearing). 

water freezing

When water freezes the molecules form a crystalline structure bc of hydrogen bonding (not enough energy to break bonds) => ice is less dense than water because the water molecules push further apart compared to liquid H2O

High Heat Capacity

• hydrogen bonds between hydrogen atoms absorb large amount of thermal energy because it’s temperature of atom changes

• water takes a long time to heat and cool

Heat of vaporization

• liquid water molecules are strongly bounded by hydrogen bonds

“Universal” Solvent

• distinct changes make it good solvent for ionic compounds + polar molecules

• water is solvent because it’s poles react with other ions

• salt dissolves in water

Cohesion and Adhesion

Cohesion: Water molecules are attracted to each other (hydrogen bonding)

Adhesion: attraction between water molecules and other molecules

Hydrogen bonding causes water to be attracted to each other

Capillary Action

• movement of liquid in a narrow space against an opposing force like gravity

• Polar H2O molecules attract to a solid surface because the glass contains polar molecules that move the water upwards

• ex: roots of plants get water to the leaves because of capillary action

Identify and be able to label the polar structure of water