Lecture 1-5

Question 1

W5

Answer 1

5 water molecule structure

Question 2

W1

Answer 2

Free water molecules. Only exist in equilibrium with steam at boiling point.

Question 3

Average liquid H-bonds

Answer 3

3.4

Question 4

H-bonds in ice

Answer 4

4 (max that 1 molecule can form)

Question 5

Water boiling point

Answer 5

High compared to molecular weight. Low compared to Earth’s temperature

Question 6

Glucose phosphorylation

Answer 6

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

Question 7

Hydrolysis

Answer 7

Breaking apart of molecules by H2O

Question 8

Ionic hydrolysis

Answer 8

Ionic substances being hydrated by H2O. Uncatalyzed.

Question 9

Covalent hydrolysis

Answer 9

Enzyme-catalyzed hydrolysis rxns

Question 10

Autoprotolysis

Answer 10

Proton transferred between 2 identical molecules. One H2O acts as Bronsted acid (donor) and the other as base (acceptor)

Question 11

Henderson-Hasselbalch equation

Answer 11

pH = pKa + log(A-/HA)

Question 12

Bicarbonate buffer system

Answer 12

CO2 + H2O <> H2CO3 <> H+ + HCO3-
Buffer system becomes powerful acid/base regulator when combined with respiratory compensation. Catalyzed by carbonic anhydrase

Question 13

Proteogenic amino acids

Answer 13

Amino acids used to create proteins

Question 14

Isoelectric point

Answer 14

pH where AA has average charge of 0

Question 15

Noncovalent interaction types

Answer 15

H-bonds, ionic bonds, hydrophobic interactions, van der Waals interactions

Question 16

Salt bridge

Answer 16

H-bonding + electrostatic (ionic) interaction

Question 17

Pi stacking

Answer 17

Stacking of aromatic rings that delocalizes pi electrons

Question 18

Hydrophobic interactions

Answer 18

Drive protein folding. Release of water drives large positive entropy.

Question 19

Pi-cation interactions

Answer 19

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.

Question 20

Trypsin cleavage

Answer 20

Cleaves on carboxyl side of Arg and Lys

Question 21

Chymotrypsin cleavage

Answer 21

Cleaves on carboxyl side of aromatic AAs (Phe, Trp, Tyr)

Question 22

Cyanogen bromide cleavage

Answer 22

Cleaves on carboxyl side of Met (forms homoserine lactone at C-terminus)

Question 23

Edman Sequencing

Answer 23

Repetitive removal of AA from N-terminus. Phenyl-isothionate (PTH) bonds to N-terminal AA and drives its elimination. PTH-AA can then identified.

Question 24

Primary structure

Answer 24

Sequence of amino acids

Question 25

Secondary structure

Answer 25

Special inter-amide interactions that form helices, sheets, and turns

Question 26

Tertiary structure

Answer 26

3D folding of a single polypeptide chain into specific configuration

Question 27

Quaternary structure

Answer 27

Arrangement of subunits (subunit = polypeptide chain)

Question 28

C-N peptide bond

Answer 28

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

Question 29

Planarity of peptide bonds

Answer 29

Ensures side-chains direct folding and stability of final protein conformation

Question 30

Phi angle

Answer 30

Torsion angle between alpha carbon and nitrogen

Question 31

Psi angle

Answer 31

Torsion angle between carboxyl group and alpha carbon

Question 32

Omega angle

Answer 32

Torsion angle between carboxyl group and nitrogen (peptide bond)

Question 33

Trans-planarity

Answer 33

Omega bond = 180º. Most common torsion angle found in all main-chain peptide bonds

Question 34

Cis-planarity

Answer 34

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

Question 35

Turn

Answer 35

Short sequences that connect helices and/or sheets. Allow proteins to be compact and stable

Question 36

Alpha-helix

Answer 36

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

Question 37

Beta-sheet

Answer 37

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

Question 38

Ramachandran plot

Answer 38

Helps to define the allowable protein conformations related to phi and psi angles. Represents allowable torsion angles for each residue.

Question 39

Native structure

Answer 39

Biologically active conformation of a protein

Question 40

Angstrom-scale forces

Answer 40

Short-range, noncovalent forces or interactions between residues. Ex: hydrophobic interactions, electrostatic interactions, and van der Waals interactions. Strongest when water is excluded

Question 41

Tropocollagen

Answer 41

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)

Question 42

Collagen

Answer 42

Plays central role in mechanical strength of tissues. Rod-shaped molecule 3000Å in length and 15Å in diameter