Ch.3 - Protein Structure & Regulation

What is the basic structure of amino acids?

• amino group

• carboxyl group

• alpha carbon

• side chain (R)

Peptide bond

• covalent bond that connects two amino acids

• carboxyl group of one amino acid reacts with amino group of another amino acid

  • c-terminus to n-terminus

Primary structure

amino acid sequence of polypeptide

Secondary structure

• segments of polypeptide

• alpha helix

• beta sheet

Tertiary structure

completely folded conformation of polypeptide

Where do nonpolar side chains cluster in folded polypeptide? Polar side chains?

nonpolar: core of protein; away from aqueous surroundings

polar: surface; exposed to aqueous surroundings

What do nonpolar amino acids form?

transmembrane domains of membrane proteins

3 Phosphorylatable amino acids

• Serine (Ser) S

• Threonine (Thr) T

• Tyrosine (Tyr) Y

Maturation of proteins involve: (5 factors)

• correct folding

• proteolytic cleavage

• chemical modifications

• formation of quaternary structures

• association of co-factors

Quaternary structure

multiple polypeptides into single protein

Example of quaternary strucutre

hemoglobin

What does hemoglobin contain?

• 2 alpha globin polypeptides

• 2 beta globin polypeptides

• each globin has oxygen-carrying heme cofactor

Cofactor

ligand; associates in active sites & participates in activities of protein

What causes sickle cell anemia

• single amino acid substitution in B-chains

• glutamic acid (acidic) replaced by valine (non-polar)

Fibrillar collagens

major structural proteins of connective tissue

What are fibrillar collagens made of?

triple helices of procollagen polypeptides

What causes osteogenesis imperfecta (brittle-bone disease)

substitution in C-terminal part of triple helix

Prions

misfolded proteins that cause TSEs (family of fatal brain diseases)

Normal prion protein name vs. Mutant name

normal: PrP^c

mutant: PrP^sc

Denaturants

unfold polypeptide by breaking all non-covalent interactions btwn amino acids

Reducing agents

break disulfide bonds

Reducing agent example

2-mercaptoethanol (2-ME)

Disulfide bonds

covalent bond that forms between adjacent cysteine side chains of proteins by oxidation reaction

Elastin fibers

• found in extracellular matrix of tissues

• allow tissues to stretch and recoil without tearing

What bonds are the cross links btwn single elastin molecules?

disulfide bonds

Phosphorylation

covalent modification for activation/inactivation of proteins

Protein kinases

enzyme that transfers phosphate groups from ATP to proteins

Protein phosphateses

enzymes that remove phosphate groups from phosphorylated proteins

Ligand

molecule that binds to specific protein

Is cAMP a ligand? A cofactor?

yes; no

What does cAMP activate? How?

activates PKA by binding to regulatory subunits

Enzymes

biological catalysts

Competitive inhibitors

• recognize enzymes

• enzymes bind to this instead of active site

• reduces enzymatic activity

• negative regulation

Allosteric regulation

regulatory molecules binds to protein and changes its conformation (shape)

Negative allosteric regulation

when the binding of regulatory molecule dec enzymatic activity

Feedback inhibition

end product of biosynthetic pathway inhibits enzyme that catalyzes first step & causes pathway to shut down

Positive allosteric inhibition

binding of regulatory molecule to protein inc enzymatic activity

Example of positive allosteric regulation

1. cell uses ATP for energy

2. ATP turns into ADP

3. ADP accumulates: means that body has used up too much energy (ATP) and needs more

4. ADP accumulation activates enzyme that catalyzes oxidation of sugars to make ATP

Ubiquitin

small protein that covalently attaches to target protein to label for regulation (destruction)

Ubiquitylation / Proteasomal degradation

1. enzyme ubiquitin ligase attaches ubiquitins to target protein

2. proteasome recognizes polyubiquitylated target protein

3. ubiquitins removes/recycled

4. proteasome degrades target protein by ATP dependent steps

What part of the proteasome contains active protease domain?

central cylinder