Week 2

Amino acid

The building blocks of proteins, 20 types, composed of Amine group, central carbon bonded to H and R-group, carboxyl group

Peptide bonds

bonds amino acids via condensation reaction between carboxyl and amino group, C-N single bond that behaves like double

Anfinsen experiment

proved that primary sequence determines protein shape/structure

• Purified protein isolated from cells exposed to high concentration of urea

• Caused denaturing of protein down to its primary structure

• Removed denaturing agents and protein folded back into shape

• Basically the amino acids sequencing for structure was denatured, causing it to break its secondary/tertiary structure

Primary structure

The unique sequence of amino acids in a protein, Order of R-groups matter because R-groups affect size, shape, reactivity, solubility

Secondary structure

H-bonds between amino group and carboxyl group on amino acid backbone causing folding into a-helix or b-pleated

Tertiary structure

3D shape of protein, bonds and other interactions between R-groups or R-groups and peptide-bonded backbone

Quaternary structure

interactions between multiple protein subunits, specifically between R-groups or between peptide-bonded backbone of diff polypeptides

Hydrophobic effect

In tertiary structures: hydrophobic clustering to avoid water in the interior, water connected by H-bonds which is very dynamic/many possibilities, disruption is highly costly (Think nonpolar R-groups cluster together in hydrophobic core while polar R-groups are on outside H-bond with water)

Noncovalent interactions

• Used to fold up single polypeptide

• Allow multiple polypeptide subunits to stably interact and form a complex protein (quaternary structure)

• Allow interactions between a protein and other molecules (different protein x different type of molecule sugar steroid ATP DNA mineral etc.)

Conformational change

some proteins adopt two different shapes

• Transport protein conformation change allows solute passage (sodium-potassium pump)

• EGF Receptor conformation change allows dimerization

  • 1. Ligand binds 2. EGFR protein changes from A to B conformation 3. In B conformation, two molecules “bind” to each other 4. Causes a further conformational change in the internal domain which activates enzymatic activity

• Can modify protein binding (sodium-potassium pump)

• Can shut enzymes off (active to inactive)

• Can enhance enzyme-substrate interactions

  • Molecular recognition (specificity for substrates) 

  • Facilitates a chemical reaction

Oligopeptide

A chain of fewer than 50 amino acids.

Polypeptides

Chains of 50 or more amino acids.

Dimers

Proteins composed of two polypeptide subunits.

Molecular chaperones

special proteins facilitate protein folding, Prevents clumping of non-polar (hydrophobic) R-groups by attaching to them beforehand

Prions

proteinaceous infectious particles (induces protein folding, Occurs when infection prions bind to normal ones, causing conformational change)

Protein functions

• Catalysis: proteins specialized to catalyze via enzymes

• Structure: structural proteins make up body components + form internal skeleton of individuals + keeps red blood cells flexible in their normal disc-like shape

• Movement: motor/contractile proteins

• Signaling: proteins carry/receive signals 

• Transport: proteins allow particular molecules to enter/exit cells

• Defense: antibody proteins attack/destroy viruses 

proteins shapes are flexible

when inactive often flexible, Protein folding regulated since protein function depends on shape (protein folding only begins after binding to molecules during signaling event)

myoglobin / hemoglobin

1 / 4 subunits

protein

chain of amino acids, complete, + functional form of molecule

peptide-bonded backbone

• R-group orientation: side chains extend out for interactions

• Directionality: N-terminus to C-terminus (anime group to carboxyl group)

• Flexibility: peptide bonds do not rotate but single bonds can

H-bonds

determines secondary structure, between R-group and carbonyl

covalent bonds

disulfide bonds between R-groups

Ionic bonding

between R-groups with opposite charges

EGFR protein

membrane spanning protein causing cell growth

enzymes

highly specific, binds via noncovalent interactions

potassium channel

selective, K+ hydrated by in aq solution, channel has affinity for it and pulls K+ by breaking hydrated bonds and providing needed bonds in channel, specific (e.g: Na+ too small to pass)