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Chapter 4B: Structure - Coggle Diagram
Chapter 4B: Structure
How do side chains contribute to protein shape and function
Side chains have DISTINCT POLARITIES - partial or full charges
Ionic, polar = hydrophilic
partially charged amino acids can form hydrogen bonds
fully charges side chains can form ionic bonds
oxygens and nitrogens tend to generate polarity
nonpolar = hydrophobic
can form "greasy blobs"
Non-covalent bonds drive PROTEIN FOLDING and STRUCTURE in water
nonpolar side chains CLUMP AWAY from water because protein is surrounded by polar water, pulls proteins together
polar side chains form HYDROGEN BONDS with each other and water
van der Waals forces contribute to HOLDING SHAPE TOGETHER
ionic side chains ionic bond with OPPOSITE CHARGE ionic sidechains
Side chains have DIFFERENT SIZES
very small ones allow for more structural FLEXIBILITY
allows chains to make very tight turn
makes chain "wiggly," flexible
Some amino acids have "special properties"
glycine: small, for flexibility and chain rotation
cysteine: can form disulfide bonds (a covalent bond OUTSIDE cells)
ex. keratin: cys-cys bonds holds a perm in place
proline sidechain: covalently linked to backbone in 2 places - FORCES BENDS, BREAKS alpha helices (RESTRICTS backbone flexibility)
SECONDARY STRUCTURE
interactions of nearby amino acids
peptide backbone interactions (hydrogen-bonding between carbonyl in one peptide group and amide in another peptide group)
amide - partial POSITIVE charge
carbonyl - partial NEGATIVE charge
hydrogen bond with each other so they can BEND and COME TOGETHER
Secondary structure 1: alpha helix: STABILITY from MANY non-covalent bonds
stabilized from h-bonding between carbonyl and amide group
3.6 amino acids per turn
side chains FACE OUT (determine WHERE alpha helix is positioned in the folded protein and HOW it interacts with other molecules)
proline and glycine DON'T LIKE alpha helices
example: alpha keratin
Secondary structure 2: Beta-pleated sheet
can be ANTI-PARALLEL or PARALLEL (flat arrows)
example: spider webs, silk (fibroin)
backbone to backbone hydrogen bonds across CHAINS
polypeptide folds back and forth on itself, forming a pleated sheet stabilized by hydrogen bonds between carbonyl in one chain and amid in the other chain
Primary structure: SEQUENCE of amino acids
DNA sequencing projects: allow PREDICTION of protein sequences
Results 1: protein alignments (30% identity over protein -indicates common ancestry)
gene families: paralogs (within organism) and orthologs (between organisms)
conservation: how we are related to other living organisms
Sequence motifs
short regions of alignment: often have a specific SHARED FUNCTION