Biochemistry Chapter 2

at what distance does our life happen at

at a distance of 4 angstroms, which is the typical distance between two non-bonding reacting atoms

Robert Brown (1827)

observed that granules of pollen that were suspended in water darted randomly about. He also observed this with dye particles in water

Brownian motion

the movement of large particles due to random collions of small particles and atoms in thermal motion

Thermal Motion

water and gas molecules randomly bouncing at a rate determined by temperature

what percent water are humans

65%

what percent water are cells

70%

Water

a polar molecule due to the difference in electronegativity that can dissolve polar or charged molecules (hydrophilic)

redwood trees with water

it shows how cohesive water can be as the water rises to the top and evaporates through the leaves, the transpiration column is maintained with hydrogen bonds. when a hydrogen bond breaks it creates a bubble, which stops the growth of the tree

Hydrophobic effect

when molecules that dissolve poorly in water seperate completely from the water (like water and oil)

Fundamental Non-covalent interactions

1. ionic interactions

2. dipole-dipole interactions (hydrogen bonds)

3. van der Waal interactions

these vary in geometry, strength and are greatly affected by water

Ionic Interactions

The interactions between distant electrical charges on atoms are usually a negative and postive charge. The interaction changes based on the medium they are in and the distance they are from each other.

Hydrogen Bonds

Partially negative and partially positive charges interact. Hydrogen bonds are the strongest non-covalent bond. It is an H that is covalently bonded to a N,O, or F, non-covalently interacting with the lone pairs of a N, O or F.

Hydrogen-bond donor

the covalently bonded N,O, or F

Hydrogen-bond acceptor

the lone pairs on the non-covently bonded O, F, or N

van der Waal Interactions

molecules that are not polar or charged but create temporary dipoles which interact with each other

van der Waal contact distance

the distance where the attraction is still the dominating force but as class as it can get before the repulsive forces become dominant

Weak non-covalent Interactions

These can be easily broken. This is important in DNA so that the strands can open. The interactions are strong enough to stabilize it, but still weak enough to break when needed

second law of thermodynamics

The total entropy of a system and it’s surroundings is always increasing in a spontaneous process

Entropy

The measure of chaos in a system, the higher the entropy, the more chaotic is higher entropy, less chaotic it is low entropy

entropy in hydrophobic effect

A hydrophobic atom in water makes more hydrogen bonds form around the hydrophobic molecule than water naturally has, making it more ordered and having lower entropy. Two hydrophobic molecules will be forced together, allowing more hydrogen bonds to break, and increase the entropy

Membrane formation

A phospholipid with a hydrophilic head and hydrophobic tail bends to form a membrane. where the head interacts with the extracellular fluid. The tails only interact with the tails of another phosopholipid molecule

amphipathic molecules

molecules with hydrophobic and hydrophilic properties

what do membranes define

the inside and outside of the cell, as well as separate the Eukaryotic compartments (organelles).

The hydrophobic effect in protein folding

proteins fold spontaneously in appropiate conditions, which decreases entropy. entropy increases on the inside of the protein with non-polar groups interact

Functional Groups

These are the only groups of atoms with distinctive chemical properties, which are necessary for biomolecules to function. All biomoleucles have one or more of these groups

pH

the reversible reaction of binding or releasing of a proton

GERD

a digestive disease where stomach acid refluxes into the esophagus, irritating the lining.

steady-state system

the maintance of blood pH through physical activity and breathing rate

Marie Curie

her work allowed people to track atoms and molecules individually