Module 1 - Lecture 1: Amino Acids and Chemical Interactions

Proteins

Is a string of amino acids, a polypeptide chain or polymer of other small molecules

Glutamine syntheses

Forms a large donut-shape structure with an active domain in the middle

Y shape

Typical shape of the immunoglobulin protein that is necessary for recognizing antigens, viruses and bacteria in the cell and removing them

Adenylate Kinase - Smaller enzyme

Containing a structure that is essential for defining the substrate binding domain and the activity domain for this enzyme

Peptide Bond

Connects each amino acid together to form a chain of amino acid residues. Formed by a condensation reaction (water is released during the formation of the bond). Ex. if two amino acids have a carboxyl group on the side, a condensation will release one molecule and a bond will form

Amino Acid

Has a hydrogen side chain, amino group, carboxyl group and variable R group. All connected to a alpha carbon, in four side chains.

Solubility

Is a physical property of a molecule that refers to its ability to transiently interact with water through hydrogen bonding

Soluble

If hydrogen bonds can form with water, the molecule is soluble

Insoluble

If a molecule cannon form with these hydrogen bonds, it is insoluble

Hydrophobic molecules

Not polarized and cannot form these hydrogen bonds, so water repels these molecules in favour of bonding with itself

Hydrocarbons

Saturated hydrophobic long carbon chains

Hydrophobic Aromatic Amino Acids

Includes aromatic rings that are hydrophobic. Amino acids include —> Phenylalanine, tyrosine and tryptophan.

Hydrophobic Aliphatic amino acids

The R-groups for these amino acids have long hydrocarbon chains. Amino acids include —> Alanine, valine, isoleucine, leucine and methionine

Hydrophilic molecules

Are charge polarized and capable of forming hydrogen bonds - Water soluble, pH of 7

Positively Charged Amino acid

Lysine and Arginine

Negatively Charged Side Chain

Aspartic Acid and Glutamic Acid

Threonine and Serine

Uncharged at neutral pH but have polar hydroxy groups that can participate in hydrogen bonds

Asparagine and glutamine

Uncharged but have these polar amide groups

Cysteine

Special amino acid because it is able to form covalent bonds, through sulpher atom, with other cysteine amino acids (disulphide/cysteine bridges)

Glycine

Special amino acid because it is small and has a single hydrogen

Proline

Special amino acid because it’s R group forms a covalent bond with amino group of the amino acid —> lead to kink/bend in chain

Histidine

Has an amino diethyl side chain, shifts between positive and neutral charge depending on the pH

N-termnius

Amino end —> left

C-terminus

Carboxyl end —> right

Polypeptide String

Is a linear array of amino acids that is not functional yet in the cell

Three-dimensional Protein

Has a series of loops, bends and sheets that define structural and functional domains

Primary Structure

Linear array or sequence of amino acids and is determined by the sequence of nucleotides in the coding DNA

Random-coil Structure

A periodically ordered structure of the protein

Statistical coil

Protein spends most of its time in a particular structure but not 100% of its time

Functional Protein Structure

Structure that the polypeptide assumes most of the time, or native structure

Hydrophobic effect

Local interactions that maintain protein shape are mostly non-covalent interactions

Ionic Bond

Attraction between a positively charged cation and a negatively charged anion

Hydrogen Bond

Interaction between a partially charged hydrogen atom in a molecular dipole, and an unpaired electron from another atom —> contributes to protein shape

Hydrophobic Effects

Aggregation of non-polar molecules in aqueous medium, simply to reduce the number of interactions with water —> minimize the surface area that is exposed to the hydrophilic aqueous environment

Van Der Waals Interactions

A weak non-specific attractive force. Results from a transient dipole that is induced when two atoms are very close together, they perturb the distribution of electron in each other

Folding

It is a random process; bonds are forming and bonds are also breaking as different bonds form. Is a result of interactions between amino acid residue that hold a polypeptide into shape.