Biochemistry

Organisms

Made up of matter

Matter

anything that takes up space and has mass

types- liquid, solid, gasses

-can’t be created or destroyed, can be rearranged and recycled

• made up of elements

Elements

• pure substance that can’t be broken down into simple substances.

• there are 90+ that naturally occur on Earth

• each elements has its own characteristics/emergent properties

• when you combine elements they produce new characteristics

Important Elements to Know

Oxygen, Carbon, Hydrogen, Nitrogen, Phosphorus

Subatomic Particles

Protons, Neutrons, Electrons

• each element is made up of a different # of protons, neutrons, and electrons

Identifying What the Numbers and Symbols of a Element of the Periodic Table Mean

Atomic Number

number of protons and electrons in a neutrally charged atom, #p = #e

Atomic mass

weight of protons and neutrons(they weight about the same)- electrons are every light so no point in adding the

(you can find the # of neutrons by atomic # subtracted from atomic mass)

Protons

• Positively charged

• make up the nucleus

• #stays stable

• - same # among all atoms of the same element

• weighs 1 amu

• determines an atoms characteristics

Neutrons

• Neutrally charged

• make up the nucleus

• - The number stays stable

• - not the same # among all atoms of the same element(isotopes)

• weighs 1 amu

• determines an atoms stability

Electrons

• negatively charged

• make up the cloud

• # can change

• - can be gained or lost by an atom

• causes an atom to become an ion(cat/anion)

• Weighs 0 amu

• determines an atoms reactivity

Valence Electrons

• Atoms 1-20 prefer to have a full outer shell (called the octet rule)

• we can predict how atoms will charge based on the electronegativity of an atom

• The outer shell holds a Mac of 8 e-

• if atoms tend to have a full outer shell, they tend to be nonreactive

• it they don’t they they are reactive

• when atoms bond with each other their electrons are interacting

Electronegativity

We can predict how atoms will share electrons based on how electronegative the atom is (how attracted the atom’s nucleus is to electrons)

Highly electronegative elements (top half more towards right side of the periodic table):

• Fluoride

• Oxygen

• Sulfur

• Nitrogen

• Chlorine

Bonds

Covalent, Ionic, and Hydrogen

Covalent Bonds

• 2 atoms can be shared

• How many electrons are shard

• - single (sharing 2 electrons)

• -double (sharing 4 electrons)

• -triple (sharing 6 electrons)

• How equally electrons are shared

• - nonpoplar= shared

• -polar = not shared

• Charges: It creates a dipole with a partial negative charge (\(\delta-\)) on the stronger atom and a partial positive charge (\(\delta+\)) on the weaker atom.

• shared

Ionic Bonds

• electrons can be transferred from one atom to another

• forming Ionic bons and ions(atoms that are not neutral/have a charge due to gained (-) or transferred electrons(+)

• one positive and one negative

• transferred

Hydrogen Bonds

Between the hydrogen of 1 molecule and the fluorine, oxygen, or Nitrogen of another (FON)

• when hydrogen bond is a covalent bonded to FON ; a polar covalent bond is formed

• meaning the e- spends more time around the FON causing H to become slightly more positive. This males H more attracted to other because they are slightly negative

• INTERMOLECULAR

Chemical Reactions

They occur when a bond makes or breaks with each other

• when atoms bond with each other their electrons are interacting

Water Molecule

Oxygen would like to have 8 valence electrons while hydrogen would like to have 2.

• even though oxygen and hydrogen are sharing electrons in a covalent bond, oxygen has a higher electronegativity (pull for electrons) than hydrogen.

• - this causes the oxygen atom in water to have a partial negative charge while the hydrogen atoms in water have a partial positive charge.

• THIS IS POLARITY

Polarity

• even though water is an electrically neutral molecule (rather than charged ion), each end of the molecule has a slight charge

• when a partially positive hydrogen of one water molecules is close to a partially negative oxygen of another water molecules, hydrogen bonds are formed

Hydrogen Bonds

weak, but still enable water to have unique properties. Because of these bonds, water is attracted to itself and other polar molecules.

Capillary action

the spontaneous flow of a liquid through narrow spaces, pores, or thin tubes without the help of external forces like gravity.

Key forces of Capillary Action

Cohesion- water molecules are attached to themselves

Adhesion- water molecules are attracted to other polar substances

Surface Tension- cohesion- results in surface tension, water has high surface tension.

Cohesion

- water molecules are attracted to themselves

Adhesion

water molecules are attracted to other polar substances

Surface Tension

Cohesion- results in surface tension, water has high surface tension.

Specific Heat

Heat Capacity and Vaporization

Heat Capacity

Polarity and hydrogen bonding result in waters high heat capacity (high specific heat)

• where water can absorb large amounts of heat energy before it rises in temperature.

Vaporization

High heat capacity results in a high heat Vaporization

• where water absorbs a large amount of heat before it becomes a gas.

How Hydrogen Bonds Work- Heat Capacity

• Absorbing Heat: When heat energy enters water, much of that energy is used to break hydrogen bonds rather than immediately increasing the speed (kinetic energy) of the molecules. Because energy goes into disrupting these bonds, the actual temperature rises very slowly. [1, 2, 3]

• Releasing Heat: When water cools down, the hydrogen bonds re-form, releasing a large amount of stored energy back into the environment. This keeps water temperatures remarkably steady

Evaporative cooling

the process where a liquid (like water or sweat) absorbs thermal energy from an organism's surface and transitions into a gas, lowering the remaining surface or body temperature

Evaporitive Cooling

• Attraction (Hydrogen Bonds): Water molecules are naturally magnetic-like; the positive (hydrogen) side of one water molecule is weakly attracted to the negative (oxygen) side of a neighboring water molecule. These sticky forces keep liquid water pooled together.

• Kinetic Energy (Motion): When you add heat or energy, the water molecules vibrate, spin, and zoom around faster. Their kinetic energy (energy of motion) increases. [1, 2]

• Breaking Free ("Overcoming"): Once the molecules move fast enough, that forward momentum is greater than the pull of the hydrogen bonds. Instead of sticking to each other, they snap the bonds, fly apart, and escape into the air as invisible water vapor or steam. [1, 2, 3]

Density

Polarity + hydrogen bonding also in water being less dense as a solid than a liquid

• usually solids are more dense

• liquid state, water molecules are closely held together by weak hydrogen bonds

• reaching solid state, hydrogen bonds become stable, arranging molecules far apart from each other.

Solution

When one substance is dissolved in another

Has 2 parts

• Solute- substance being dissolved in liquid

• solvent- substance doing the dissolving (usually a liquid)

• water is the universal solvent because of its abikoty to dissolve most substances

• - attracted to anything with a partial or full charge - neutral pH