Chapter 2.1: Biomolecules & water

Iron

element which is responsible in transporting oxygen and electrons in various human systems

monomer

a molecule which can be covalently bonded to a similar or identical molecule to create a polymer

• AA

• carbohydrates

• nucleotides

• Lipids are not considered monomers since they do not join to make polymers

Carbohydrates

(C H2 O)n formula

Each carbon is technically “hydrated“ with a water

• n-1 hydroxyl groups

1 carbonyl group

red, black, blue, white, yellow, orange

List the colors in order separated by a comma for spacefilling/ball and stick diagrams

• oxygen

• carbon

• nitrogen

• hydrogen

• sulfur

• phosphorous

organic compounds

• thiol

• ketones

• aldehydes

• carboxylic acids

• alcohol

• amines

thiol - organic compound

organic compound

alcohol - organic compound

aldehyde - organic compound

organic compound

Ketone - organic compound

organic compound

carboxylic acid - organic compound

amine - organic compound

organic compound

Hydroxyl - Functional group

functional group

Acyl - functional group

carbonyl - functional group

functional group

carboxylate - functional group

ester - functional group, linkage

ether - functional group, linkage

amide - functional group, linkage

sulfhydryl - functional group

functional group

amino - functional group

functional group

phosphate - functional group

• can exist without H

• 4 oxygens

phosphoryl - functional group

• 3 oxygens

phosphate ester - functional group, linkage

phosphoanhydride - functional group, linkage

residue

A monomer in a polymer

• is referred to as a ____ since it loses a part of itself when bonding

polymer

__ are created from monomers being linking together in one direction. All covalent bonds are in one direction.

• has a reducing end and a non reducing end

directionality

refers to when all covalent bonds are in the same direction

peptide bond

a bond for amino acids into proteins

• C - N bonded

Phosphodiester bond

a bond between nucleotides to create nucleic acid

• 5’ to 3’

glycosidic bond

a bond between monosaccharides to polysaccharides

donor, acceptor

A hydrogen bond requires a donor and an acceptor.

a hydrogen ___ is one where a hydrogen is bonded to a electronegative atom, while a hydrogen ___ is one where a lone pair on a electronegative atom accepts a hydrogen

• donors can be N/S/O H

• Acceptors can be N/S/O electron pair

3, 2, 2

water has __ HB

ice has __ - donors, and __ - acceptors

electrostatic forces

ionic interactions

• weaker than covalent

• intramolecular, rather than intermolecular

Hydrogen bonds

• dipole dipole interaction

van der waals

• Dipole dipole interaction

• london dispersion forces

dipole - dipole interaction

• between polar non-charged groups

• weaker than HB

London dispersion forces

• between nonpolar

• weaker than DD

Hydrophobic effect

when a nonpolar substance is placed ina polar substance, the surrounding water molecules forces the nonpolar substance to clump and stick together

• tendency of water to minimize contact with nonpolar substances

• involves london dispersion forces

• is not the nonpolar coming together, it is water moleculars pushing them together

driven by entropy

when nonpolar substance comes into contact with water, water cannot form hydrogen bonds. This disrupts the hydrogen bond system of water, thereby causing water to create this shell which is more ordered and prevents disorder. This in turn lowers entropy.

• if multiple clumps of nonpolar substances appear, water will push it all into one clump. This is again driven by entropy since it minimizes contact with nonpolar substance, less water moleculars are in a cage like structure, therefore increasing entropy and making it more thermodynamically favourable.

amphipathic/amphiphilic

experiences both hydrophobic and hydrophilic effect

• depends on how much of the molecule is hydrophobic/hydrophilic

micelle

example of an amphipathic molecule, where hydrophobic fatty acid tails point inside away from water, and hydrophilic heads point outside