#import "template.typ": *
#show: template.with(
  title: "Lecture 2",
  subtitle: "7.016"
)

= Introduction

Most of chemistry happens in an aqueous environment since 75% of cells are water.

#define(
  title: "Biomolecular Interactions"
)[
  / Specificity: One on one interactions
  / Diversity: Many possible interactions that can combine in many ways
]

For the most part, Sulfur copies Oxygen. However, it is not the case that Phosphorus behaves the same as Nitrogen, in fact it can form five bonds which makes it unique.

#define(
  title: "Ester"
)[
  An ester bond is when you have an element that is double bonded to one Oxygen and single bonded to another. If we have two of these, for example an element double bonded to one Oxygen, then single bonded to two different Oxygens, then it is called a phosphodiester.
]

= Bonds

Bond polarity refers to the difference in electronegativity between the two bonding elements. In order from weakest to strongest we have $"H ", "P ", "C ", "S ", "N ", "O "$

#define(
  title: "Hydrogen Bonds"
)[
  Hydrogen bonds happen between an exposed Hydrogen molecule and a lone pair on an element such as Oxygen.
]

#define(
  title: "Hydrophobic Bonds"
)[
  Happens when molecules that are detracted from water group together in order to stay away. 
]

Ionic bonds are also classified under electrostatic interactions.

Within water, the bond strength go $"Covalent" -> "Ionic" -> "Hydrogen" -> "Hydrophobic" -> "Van Der Waals"$

= Line Angle Drawing

This is a shorthand way of drawing organic molecules. Every bend or end is a carbon, and each carbon should have four connections, so we need to fill the missing ones with hydrogen bonds.

= Functional Groups

/ Hydroxyl: $"OH"$, can lose the $"H "$ to become negatively charged.
/ Carboxyl: Carbon double bonded to an Oxygen with a $"OH"$, same as above, it can lose the hydrogen to be negatively charged.
/ Amino: $"NH"_2$, can *gain* a Hydrogen to become positively charged.
/ Sulfhydrl: Sulfur bound to a Hydrogen, it can lose the Hydrogen to become negatively charged.
/ Amide: Results from condensation between a Carboxyl and Amino group. The $"OH"$ from the Carboxyl bonds with one of the $"H "$ from the Amino to form a water. The Carbon then bonds to the Nitrogen.
/ Ester: Any element that has a double bond to one Oxygen and a single bond to another.

= Phospholipids

In a phospholipids, the tail is hydrophobic and non-polar, while the head is hydrophilic and polar. This is because the tail contains mostly Carbons and is non-polar, while the head contains Nitrogen, Oxygen, and other electronegative elements meaning that it is polar.

#define(
  title: "Amphipathic"
)[
  A molecule that is two sided, having a hydrophobic and hydrophilic side.
]

Thus the way that the phospholipid bilayer works is by having the heads face outward while the tails are inside, allowing for cells to compartmentalize.

Prokaryotic cells have a single phospholipid bilayer, while eukaryotic cells have more internal structures which also have a phospholipid bilayer around them.
