Lecture 1-5 Flashcards
W5
5 water molecule structure
W1
Free water molecules. Only exist in equilibrium with steam at boiling point.
Average liquid H-bonds
3.4
H-bonds in ice
4 (max that 1 molecule can form)
Water boiling point
High compared to molecular weight. Low compared to Earth’s temperature
Glucose phosphorylation
Enzymatically catalyzed by hexokinase. Catalyzed rxn reaches eq in 1 sec compared to uncatalyzed rxn in 1 billion sec (30 yrs). Hexokinase phosphorylates oxygen on C6. Hexokinase regulated by glucose-6-P
Hydrolysis
Breaking apart of molecules by H2O
Ionic hydrolysis
Ionic substances being hydrated by H2O. Uncatalyzed.
Covalent hydrolysis
Enzyme-catalyzed hydrolysis rxns
Autoprotolysis
Proton transferred between 2 identical molecules. One H2O acts as Bronsted acid (donor) and the other as base (acceptor)
Henderson-Hasselbalch equation
pH = pKa + log(A-/HA)
Bicarbonate buffer system
CO2 + H2O <> H2CO3 <> H+ + HCO3-
Buffer system becomes powerful acid/base regulator when combined with respiratory compensation. Catalyzed by carbonic anhydrase
Proteogenic amino acids
Amino acids used to create proteins
Isoelectric point
pH where AA has average charge of 0
Noncovalent interaction types
H-bonds, ionic bonds, hydrophobic interactions, van der Waals interactions
Salt bridge
H-bonding + electrostatic (ionic) interaction
Pi stacking
Stacking of aromatic rings that delocalizes pi electrons
Hydrophobic interactions
Drive protein folding. Release of water drives large positive entropy.
Pi-cation interactions
Delocalized pi-electron orbitals can interact with positive ions/charges (commonly quaternary amino groups). Can tune pKa of nitrogenous side-chains and increase abundance of protonated form.
Trypsin cleavage
Cleaves on carboxyl side of Arg and Lys
Chymotrypsin cleavage
Cleaves on carboxyl side of aromatic AAs (Phe, Trp, Tyr)
Cyanogen bromide cleavage
Cleaves on carboxyl side of Met (forms homoserine lactone at C-terminus)
Edman Sequencing
Repetitive removal of AA from N-terminus. Phenyl-isothionate (PTH) bonds to N-terminal AA and drives its elimination. PTH-AA can then identified.
Primary structure
Sequence of amino acids
Secondary structure
Special inter-amide interactions that form helices, sheets, and turns
Tertiary structure
3D folding of a single polypeptide chain into specific configuration
Quaternary structure
Arrangement of subunits (subunit = polypeptide chain)
C-N peptide bond
1.32Å length. Consistently shorter than common amide C-N bond - explained by resonance. Geometry and dimensions studied by Pauling and Corey. C=O and N-H atoms of peptide bonds are approximately coplanar
Planarity of peptide bonds
Ensures side-chains direct folding and stability of final protein conformation
Phi angle
Torsion angle between alpha carbon and nitrogen
Psi angle
Torsion angle between carboxyl group and alpha carbon
Omega angle
Torsion angle between carboxyl group and nitrogen (peptide bond)
Trans-planarity
Omega bond = 180º. Most common torsion angle found in all main-chain peptide bonds
Cis-planarity
Omega bond = 0º. Found only in rare cases - usually involving Pro (cyclic side-chain reduces energetic barrier). Pro with cis-planarity acts as helix terminator
Turn
Short sequences that connect helices and/or sheets. Allow proteins to be compact and stable
Alpha-helix
First observed in alpha-keratin. Combination of rotation and translation. 3.6 residues per turn and 100º rotation per residue. Every NH forms H-bond with every fourth carboxyl O. Helix curls slightly (can form coiled-coil structure with second helix). Phi angle = -57º and psi angle = -47º
Beta-sheet
First observed in beta-keratin. Polypeptide chain zig-zags to form extended conformation. Side-chains point in and out of sheet plane. Can be parallel or antiparallel with other sheets. Phi angle = -140º and psi angle = 130º
Ramachandran plot
Helps to define the allowable protein conformations related to phi and psi angles. Represents allowable torsion angles for each residue.
Native structure
Biologically active conformation of a protein
Angstrom-scale forces
Short-range, noncovalent forces or interactions between residues. Ex: hydrophobic interactions, electrostatic interactions, and van der Waals interactions. Strongest when water is excluded
Tropocollagen
Structural building block of collagen. Triple-repeat made of three polypeptide chains that twist around each other. Strength arises from X-linking between aligned molecules. Tripeptide pattern begins with Gly, Pro usually follows Gly, use of Hydroxyproline (Hyp)
Collagen
Plays central role in mechanical strength of tissues. Rod-shaped molecule 3000Å in length and 15Å in diameter
