L5: Amino acids and their polymerization

polypeptides

• long chain of aa

• fold into proteins

functions of proteins

• enzymes

• signaling

• motor proteins

• gene regulation

what determines how a polypeptide folds

• aa sequence

• polarity of each aa residue

what are aa attached to

aa backbone

generic aa structure

• central alpha carbon

• amino group

• carboxyl group

• hydrogen

• R group

what does an aa look like at a physiological level

its ionized

draw an generic aa

x

what determines the properties of aa

• R group

what does R group vary in

• size

• shape

• polarity

• hydrophobicity

• charge

• chemical reactivity

draw all 20 aa. include polarity, charge, acidity/basicity, abbr.

x

how many aa are np

10

how many aa are polar

• 10

• 5 are uncharged

• 2 are negatively charged

• 3 are positively charged

polar, uncharged R groups

usually an amide or a hydroxyl

what makes uncharged aa polar 

• have electrons unevenly distributed within their structure

• makes one part of the structure more positive and others more negative = polar

polar, negatively charged R groups

• acidic at physiological pH

• donates an H and becomes negatively charged

• has a carboxyl group

polar, positively charged R groups

• basic at physiological pH

• accepts an H and becomes positively charged

• amino, guanidium or an imidazole group

electron distribution in polar side chains

uneven

electron distribution in np side chains

even

why do dipoles exist in water

• o2 atom draws electrons away from H atoms

• o2 atom becomes more negative and Hs more positive

why is threonine more hydrophobic than serine

threonine has an extra methyl group

aa that can be both polar or np

cysteine

aa that impact protein folding strongly

• glycine

• proline

• cysteine

how does glycine impact protein folding

• smallest aa

• makes polypeptide backbone very flexible

how does proline impact protein folding

• has a sidechain that connects to its N

• makes polypeptide backbone very inflexible

how does cysteine impact protein folding

can form disulfide bonds with other cysteine residues to covently link 2 polypeptide backbones

properties of aa with aromatic rings

• larger and bulkier

• takes up more space when proteins fold

UV absorbance of aromatic aa

• tyrosine, phenylalanine, tryptophan

• 270-280nm

• histidine does not absorb UV

histidine

• pKa of about 6.0

• only some are positively charged at physiological pH

• others are uncharged

• small changes in pH can dramatically affect its behaviour

how is the flexibility of histidine used

used by enzymes to handle protons on/off of of other molecules

kinase

any enzyme that adds phosphate group to target

phosphatase

• any enzyme that removes phosphate group from target

• dephosphorylation

phosphorylation and ex.

• used to regulate protein function after it has been made

• cells phosphorylate/dephosphorylate to turn proteins on/off

• example of post-translational modification

aa with hydroxyl groups

exposed hydroxyl groups are great targets for phosphorylation

C-terminus

the end of the peptide with a free carboxyl group

how do 2 aa attach

• incoming aa attaches to the hydroxyl on the C terminus

• condensation reaction joins carboxyl C to nitrogen of incoming aa

• creates water

bond between aa

peptide

aa residue backbone

• nitrogen

• alpha carbon

• carboxyl carbon

peptide backbone

long chain of repeating ‘NCC’

N-terminus

• amino terminus

• front of the peptide backbone with a free amino group

polypeptide vs protein

• polypeptide is a chain of aa polymerized via peptide bonds

• proteins are defined more vaguely

proteins

• longer polypeptide that folds into a unique 3D shape

• obtains biological function

• over 100s aa residues long