BIOL UNIT 1

excusion of nonpolar molecules from an aqueous solution
- entropy driven: freeing move water moleucles to interact with each other

histidine and phosphate contribute to the intracellular buffering

-carbonic acid-bicarbonate buffer system
-dihydrogen phosphate-hydrogen phosphate system
- proteins

CORN clockwise
D form: CORN counterclockwise

-selenocystein
-pyrrolysine

suitable for making a turn in polypeptide chain

TIM LV HK FW

pathway to make phenylalanine

after incorporated into the proteins, the side chain of certain amino acids can be further chemically modified

- exist as cations at very acific pH
- exist as anions at very basic pH

phi: hetero (N-C bond)
psi: the C-C bond (same)

a map that displays the polypeptide backbone confirmation
- pro limits its range of phi to be around -60 degree, making it restricted
- gly: less streically hindered

native ribonuclease to unfolded protein by adding 8M urea and B-meraptoethanol

back to native ribonuclease by removing utre and the B meraptoethanol

primary structure: sequence in the structure of a protein
- secondary structure: hydrogen-bonding
- tertiary structure: interaction between polypeptide chain (disulfide bond etc)
-quaternary structure: multiple polypeptide chains

alpha helix: residue i and i+4 having hydrogen bond
B-sheet: backbonds interaction with adjacent backbones

right handed (common), left-handed (very rare)
- not all amino acids are compatible: pro, lle, thr, val, ser, asp, asn, gly

ex) ASLTAQFN
one side is polar, the other side is non polar
(non polar amino acids: FAMIL VW PG)

FAMIL VW PG

stable and hydrogen bond is not uniformly distributed, linear,

Parallel B-sheet: hydrogen bond uniformly distributed, not linear (weak)

- large proteins can be constructed incrementally
- minimizes impact of errors in transcription and translation
- affords an opportunity for subunits to influence and regulate each other (cooperative behavior)

permantly unfolded proteins: nonglobular state is preferred

transient: unfolded, but become ordered when bound to their target protein

proteins fold by progressive stabilization of intermediates

secondary structure of native protein but poor defined teriary structure

1. formation of incorrect disulfide bonds
2. isomerization of proline residues (wrong confirmation)
3. aggregation of the intermediates through exposed hydrophobic groups

1. protein disulfide isomerase (PDI)
2. peptidyl prolyl isomerases (PPI)
3. Molecular chaperones

- catalyzes disulfide interchange reactions
- facilitates the formation of correct disulfide bond

incorrect disulfide bonds are the preferred substrate, as they tend to be exposed on the protein structure
- correct conformation is inaccessible to PDI because it will be buried in hydrophobic core

-catalyzes conversion of X-pro peptide bonds from trans to cis conformation (cis-proline are found in tight bends and are essential for their activity)
- accelerating the folding of proline-containing proteins

- HSP 70 and HSP 60
- stabilization of unfolded proteins

1. proteasmes
- highly selective
- ubiquitin tags
- ubiquitin binds to lysine

2. lysosomes
- non selective

dissociation constant
less Kd: higher binding

turnover number (molecules catalyzed per second in optimal conditions)

estimate affinity
kcat/km = catalytic efficiency

- tightly bound either covalently or non covalently
- dissociates from its target enzyme very slowly

- enzyme-inhibitor rapidly dissociates
- competitive, nonceompetitive, uncompeptitive

binds free enzyme, structure mimic or sub strate

either free zymes or Es complex

binds to ES complex

uncompetitive inhibitor: parallel to the normal graph but higher on y-axis

-allosteric control
- reversible covalent modification
- multiple forms of enzymes
- proteolytic activation
- controlling the amount of enzyme present

- adopt two or more different conformations
- two or more binding sites

fractionation based on charge
- anion exchangers: binds anion
- cation exchangers: binds cation
whichever binds elute out the last

fractionation based on size
- packed with porous beads
- big one moves out rapidly
- samll ones later
- can be used to estimate the weight

based on binding

based on hydrophobicity

allows cloning and easy manipulation of genes that encode proteins of interest
- allows the addition of affinity tags to proteins of interest
- His tag

migration of the chraged molecules in the electric field
- gel composed of cross-linked polyacrylamide
- used for protein separation

- separating based on their isoelectric points
- when the pH of the gel region equals PI of a protein, stop migrating
- requires the usage of a gel with a stable pH gradient

1st separation: isoelectric focusing
2nd separation: SDS page

network of protein filaments int he cels that play important roles

1. actin filaments: the thinnest
2. microtubules: strong, rigid hollow tubes, the thickest
3. intermediate filaments: rope like and easy to bend

G actin (monomeric form), F-actin (filamentous form)
- subunits usually add more rapidly to the + end
- provides support for plasma membrane and plays an important role in determining the shape of the cell

- polymers of tubulin, tublin dimers add to protofilament (alph and beta tubulin forms dimers)

structural role in extracellular matric, in connective tissue
- triple helic structure
- glycine on every third residue

- muscle contractions: myosin acts on actin filaments
- intracellular transport: kinesin acts on microtubule tracks

1. Oxidoreductases
2. Transferases
3. Hydrolases
4. Lyases
5. Isomerases
6. Ligases

coenzyme: organic molecule, prosthetic group: coenzyme taht is tightly

holoenzyme: apoenzyme + required cofactor/ bound to the enzyme protein
- enzyme with coenzyme and or metal ion

-tetramer, two alpha subunits and tow beta subunits
- allosteric, displays cooperativity in oxygen binding and release

- single bound hem
- not cooperatie
- single polypeptide chain

facilitate the release of oxygen

have higher affinity for oxygen

alpha-thalassemia: alpha chain is not produced enough, binds to oxygen with high affinity

beta-thalassemia: beta chain is not produced enough, without b chain, alpha chain form is insoluble and it aggregate

secondary structure

purifying the protein, growing protein crystal, obtaining diffraction pattern, solving the structure

responsible for specifying the substrate protein for ubiquitination

a cycle of ATP binding, hydrolysis and ADP release in myosin

A drug is more likely to be absorbed if it is small, uncharged and lipophilic

No more than 5 hydrogen bond donors (nitrogen or oxygen atoms with one or more hydrogen atoms e.g. OH or NH2)

No more than 10 hydrogen bond acceptors (nitrogen or oxygen atoms)

Molecular weight < 500g/mol

A partition coefficient logP<5