what are covalent bonds
- Shared electron pairs
- strongest bond
- Backbones of polymers, proteins, DNA, RNA, polysaccharides, etc
- Molecules formed by stable covalent bonds (80Kcal/mol)
what are the three main types of non covalent bonds
Ionic
Hydrogen
Van der Waals
what are ionic bonds
- Ionic bonds (Electrostatic Bonds)
- Charge-Charge interactions
- 4x weaker than covalent (~20kcal/mol)
- depends on type of charge, strength of charge, dielectric constant of the environment (is it water, air, fat, etc), and the distance apart
what are hydrogen bonds
- Hydrogen bonds
- Make Watson-Crick pairings in DNA, Secondary Structure in proteins
- Strong electronegative atom (such as O or N) attached to H pulls electrons to it. Makes H partially positive. It then attracts partially negative N or O atoms towards it
- Up to strength of ionic bonds 20kcal/mol
- Water loves hydrogen bonds
what are van Der Waals interactions
- Van der waals interactions
- Weakest ~1kcal/mol
- caused by electron distribution around atoms
Van de waals are between uncharged and non polar molecules
Transient asymmetries in electric charge mediates the weak interactions
Weak (~1kcal/mol) but add up
how is water unique
water has a number of interesting and unique properties
Looking at hydrogen:
Water-hydrogen bonding forms flickering clusters (very dynamic formation and reformation of H bonds)
Effects:
- High specific heat capacity, so needs a lot of energy to raise its temperature
- Can have up to 4 H bonds at a time, averages 3.6 at any point
- High heat of vaporization
- Responsible for ice crystallization
what is the hydrophobic effect of
Water has electrostatic interactions with ionic solutes
Molecules will arrange in such a way to minimize hydrophobic interactions with water
Water will form a highly ordered case around the hydrophobic alkyl chains of a lipid.
In a cell water is highly concentrated ~55.5 M
The cage that water forms around a hydrophobic lipid tail is low entropy, by clustering lipid molecules together the number of H2O molecules per lipid decreases, increasing entropu
= Hydrophobic effect
what do proteins do
Proteins are the most versatile macromolecules, they carry out most of the catalytic activities of a cell:
- Catalytic rxn of enzymes
- structural supprot
- movement
- regulatory proteins
- transport
- cell signeling
- storage of amino acids
- hormonal
what are some common protein terms
a.a. = amino acids = residue (1 unit)
Protein = polypeptide
R groups = Amino acid side chains
Dalton = MW (molecular weight) = unit of mass (g/mol), MW of aas ~190g/mol
Conformation = spatial arrangement of atoms in a protein
Native = lowest energy state of a protein (lowest Gibbs free energy)
what determines the properties of an amino acid
Properties are determined by the R group
what are the isomers of a protein
The alpha carbon is a potential stereocentre
Can have an L and D isomer
The L isomer is the only one produced by ribosomes
isomers not assigned R and S, since the R group would dictate which is which, too complicated.
what is the L isomer of a protein
Levorotatory = L isomer = Absolute configuration L
When H is in the back, can spell CORN going left (anticlockwise)
what are D isomers in proteins
Dextrorotatory = D isomer = absolute configuration D
When H is in the back, can spell CORN going right
D isomer amino acids are not made by ribosomes, but they are used in nature. notably they make up the shell found around bacteria. Enzymes don’t recognize them so they make good defense.
how many amino acids do we use
All life uses 20 amino acids, these 20 are grouped into Non Polar, Uncharged Polar, Acidic, and Basic based on their side chains
what are 3 more misuses of science
Alber Neisser (1855-1916) detected Neisseria gonorrhoeae in methyl violet, he injected it into prostitutes without consent before a cure was invented. Used it for study
Tuberculosis was common in residential schools. The government knew, but did nothing, and used the students for experiments
In 1932-1972 the US public heath service gave black patients with syphilis a placebo instead of real treatment in order to study the long term effects of syphilis. Some of them spent 40 years with syphilis being study while they thought they were getting treatment.
what’s up with bacterial cell walls
The cell wall of bacteria is made of various amino acids including, D-Glutamic acid, and D-alanine
These two proteins are not made by ribosomes, but through other enzymatic pathways.
what is a peptide bond
Amino acids covalently link via peptide bonds
Very stable, with a half life of 7 years
Amino acid + Amino acid → Peptide + water = Condensation reaction
R-COO- + H3N-R’ → R-CO-NH-R’ + H2O
Peptide bonds don’t twist or turn. They have partial double bond characteristics
Links amino acids together in chains
N terminus = end with H3N+
C terminus = end with COO-
Equilibrium favours broken bonds so they spontaneously break. But it takes a lot of time, so the half life is 7 years.
what are the four types of bonds within peptides
- Disulphide bond -CH2-S-S-CH2
- Hydrogen bonds -C=O - - - HO-
- Ionic bonds -NH3+ - - - -OOC-
- Van der waals and hydrophobic interactions
what are the levels of protein structure
Primary structure: Includes the sequence of amino acids linked together by peptide bonds in a chain
Secondary structure: Local regions of the polypeptide can be coiled into an alpha helix or beta pleated sheat
Tertiary structure: regions of secondary structure associate with each other in specific ways to form the tertiary structure. Blob
Quaterny structure: made up of several polypeptide chains
what is protein primary structure
- Linear sequence of amino acids in a protein
- has a distinct amino (N) terminus and a Carboxyl (C) terminus and is built from N → C during translation of mRNA
what is protein secondary structure
- Regular repeating structure adapted by polypeptide
- alpha helix, Beta sheet, turns and loops
- Formed by regular pattern of H bonds between peptide N-H and C=O groups of residues that are near one another in linear sequence
- Cannot form within an amino acid since they can’t twist
what is an Alpha Helix
- Alpha Helix
- Hydrogen bonds between residues that are 3 apart (C=O bonds to forth N-H after it) coils a peptide into a helix
- can be right or left handed.
- Right coils clockwise down and is more stable
- Left coils counter clockwise down
- R groups can project outwards from the helix, they can stabilize of destabilize the helix. (based on attraction and repulsion)
- Sometimes the R groups are too large to form a helix
- Parts of the helix can be hydrophobic or hydrophilic. This can allow the protein to side on a membrane if one side is hydrophobic and the other is hydrophilic.
- Amphipahtic = hates both
- Amphiphilic = likes both
what is a Beta sheet
- Beta Sheet
- Polypeptide gets turned on its side and the two sides interact side to side via H-bonds
- R groups poke up and below sheet. Can make amphiphilic if one side if hydrophilic and the other is hydrophobic
- Sheets can be parallel or antiparallel resulting in slightly different structure
what is Tertiary Structure
The overall bonding and folding of a polypeptide chain into 3D
Can be predominantly alpha helixes, predominantly beta sheets, or a mix of the two
Stabilized by weak bonds
Alterable by environmental changes
