4 biomolecules - amino acids and proteins

reagents

NaBH₄

give 3 aspects of a cell’s life cycle that proteins play a role in

signalling, proliferation and repair

what are peptides

chains of multiple amino acids

when do peptides become proteins

a molecular weight of > 10000

10,000 Da = 10 kDa

describe this peptide with 3-letter and 1-letter abbreviations

include the ends of the peptide

based on the charges on the peptide, what is the pH of the solution?

• Glu will be deprotonated - pKa = 4.5

• Amines are protonated - pKa 9-10

• If Glu fully deprotonated, pH must be at least one log unit higher = > 5.5

• so pH 6-8

which direction is it common to write peptide sequences in

N-terminus to C-terminus

steps to draw the full structure of a peptide

1. draw backbone first with correct number of amines

2. include correct stereochemistry for the branches, with wedges pointing up and dashed pointing down

3. add side chains

4. add charges

draw the full structure of this

what is the primary structure of a protein

the sequence of amino acids

what is the secondary structure of a protein

the 3D shape made by a chain of amino acids

what is the key criteria for the secondary structure

what does this lead to

every carbonyl group and amide proton in the peptide chain should have a hydrogen-bonding partner

leads to 2 main types of secondary structure - α-helix and β-sheet

what is an α-helix

a coil of amino acids with hydrogen bonds between every third or fourth residue

where do the side chains of an α-helix point

point outwards into space

carbonyl dipoles in an α-helix?

what is a β-sheet

a sequential, linear sheet of amino acid chains forming a generally flat surface

where does hydrogen bonding occur in a β-sheet

in between the individual β-strands

2 alternative names for the turning point of a β-sheet

β-turn or β-hairpin

what does the turning region of a β-sheet usually include#

example?

amino acids with unique conformational properties, e.g Gly or Pro

what is ϕ on a peptide linkage?

what is ψ on a peptide linkage?

what is ω on a peptide linkage?

what are/can be the values of ϕ,ψ,ω?

what does plotting these angles give

a Ramachandran plot

what is demonstrated by a Ramachandran plot

bonds in peptides and proteins do not rotate freely and adopt very specific conformations

what does the Ramachandran plot lead to for β-sheets?

what is the consequence for the properties of the molecule?

the amino acid side chains are positioned on opposite faces of the sheet, ie every other amino acid side chain is pointing up

this gives two faces of the molecule with different properties

what is the sequence of amino acids on the same face for an α-helix?

what does this allow?

i, i+4, i+7

means you can code for a chain with very specific properties on one side

what is the tertiary structure of a protein and how is it formed

the full 3D shape of the protein, formed from the properties of the secondary structure combining

how do proteins tend to fold

such that the hydrophobic residues are all buried into the core of the structure and hydrophilic residues point out into the solvent

what is this protein fold called?

TIM barrel

what is the quaternary structure of a protein?

many proteins assemble into higher order structures

each colour = individual protein - all pack together

give 4 examples of higher-order quaternary structures that can be formed

dimers

trimers

tetramers

pentamers