Study Guide for Midterm 3 – Chem 109 C
Ch. 23
1. Primary structure of a protein => sequence of amino acids - held together by peptide bonds
2. Secondary structure of a protein => Repetitive conformations of the backbone of a protein maximizing H-Bonds between the carbonyl oxygen and the H on the N in the backbone
A. Alpha helix - coiling of the backbone - proline can't be in the alpha helix due to its shape
causing distortion - valine, isoleucine and threonine can't be adjacent to each other due
to steric repulsion - adjacent amino acids can't have the same charge ( for example two
lys) due to electrostatic repulsion
B. Beta pleated sheet - extended zigzag structure - parallel beta sheets have the adjacent
chains both running N end to C end - anti parallel beta sheets run in opposite directions
which enables a higher degree of H Bonding between the sheets
3. Tertiary structure of a protein => three dimensional arrangement => interactions of the side
chains with each other as well as with the environment (such as a solvent) influence the
overall 3D shape - such interactions include...
A. Disulfide bridges are the result of two cysteine residues oxidizing together - this is the only
covalent bond holding a protein together other than the peptide bonds in the primary
structure
B. Hydrogen bonding
C. Electrostatic interactions
D. Hydrophobic interactions
4. Quaternary structure of a protein => arrangement of the subunits (aka peptides) in an oligomer
( aka a protein with more than subunit) - subunits are held together by the same
interactions as the tertiary structure ( see above)
5. Denaturation => anything that can break apart the forces that hold the secondary, tertiary or
quaternary structure together - such as...
A. Changing pH
B. Certain reagents
C. Detergent
D. Organic solvents
E. Heat or agitation
Ch. 24
1. A catalyst is anything that can stabilize the transition state of the slowest step in a mechanism
thereby lowering the activation energy and increasing the rate constant (k) - know
problem 1 p. 1023
2. Four types of catalysts
A. Acid - adds protons to make stronger electrophiles and/or better leaving groups
i. Specific - adds a proton before the slow step - the stronger the acid the more likely it will
be specific
ii. General - adds a proton during the slow step - weaker acids tend to be general - know
problem 4 (p. 1027) and the two general acid mechanisms on page 1027
iii. Intramolecular - this is the most ideal
B. Base - removes a proton to promote the collapsing of a tetrahedral or removing a proton
from a nucleophile to make it stronger
i. Specific - remove a proton before the slow step
ii. General - remove a proton during the slow step - know general base mechanism on p.
1029 and problem 6 on p. 1029
iii. Intramolecular
C. Nucleophilic - aka covalent - provides a stronger nucleophile and better leaving group temporarily covalent lay bonded to substrate - can be inter or intramolecular (intra is
better) - I order to be intra the group must be in the proper configuration - know 2
mechanisms on p. 1030 and last mech on the bottom of p. 1035 - know problem 11 on p.
1035
D. . Metal ion - be able to draw - A, B, and C on top of p. 1031 - know mech on top of page
1032 and problem 8 on p. 1032
i. Coordinates with carbonyl oxygen making carbonyl a stronger electrophile
ii. Coordinates with leaving groups making them better by becoming weaker bases
iii. Coordinates with water thereby lowering its pKa causing a higher degree of ionization
and results in a higher concentration of hydroxide which is a stronger nucleophile than
water
3. Enzymes - proteins that act as catalysts
A. 4 ways proteins catalyze reactions
i. Stabilize transition states
ii. Align reactive sites of molecules toward each other
iii. Side chains can act as acid, base or nucleophilic catalysts
iv. May contain a metal ion
B. Be able to add all the mechanism arrows in figures 24.5, 24.7, and 24.9 - in addition be able
to say what type of catalyst the side chains are doing in each step (see answers 14-17
http://clas.sa.ucsb.edu/staff/terri/Ch%2024%20slide%20answers.pdf )
4. Relative rates of intra vs. intermolecular – know Table 24.2 on p. 1033 – know problems 29,
30, and 31 on p. 1053
Ch. 25
1. Know the following terms
A. Cofactor – assists enzymes
B. Coenzyme – organic cofactor made from vitamins
C. Vitamin – required substance that the body can not synthesize
D. Holoenzyme – enzyme with its cofactor
E. Apoenzyme – enzyme missing its cofactor
2. Vitamin B3 aka niacin => coenzymes used to make the coenzymes NAD+, NADP+, NADH, and
NADPH
A. NAD+ => used for oxidation of oxygen containing functional groups in catabolic pathways
B. NADP+ => used for oxidation of oxygen containing functional groups in anabolic pathways
C. NADH => used for reduction of oxygen containing functional groups in catabolic pathways
D. NADPH => used for reduction of oxygen containing functional groups in anabolic pathways
E. Be able to recognize/draw the active site for NAD+, NADP+, NADH, and NADPH
F. Know the reactions and mechanisms for NAD+, NADP+, NADH, and NADPH
3. Vitamin B2 aka riboflavin => used to make the coenzymes FAD, FMN, FADH 2 and FMNH2
A. FAD and FMN => used for oxidation of non oxygen containing functional groups
B. FADH2 and FMNH2 => used for the reduction of non oxygen containing functional groups
C. Be able to recognize/draw the active site for FAD, FMN, FADH2 and FMNH2
C. Know all the reactions on p. 1065 and mechanisms on p. 1066 and p. 1067
4. Vitamin B1 aka thiamine => used to make TPP
A. TPP is used for 2 types of reactions both on alpha keto acids such as pyruvate
i. decarboxylation
ii. two carbon transfers
B. Be able to recognize/draw the active site of TPP
C. Know the reactions on p.1068 and p. 1070
D. Know the mechanism on p. 1069
E. Know the pyruvate dehydrogenase system on p. 1070
5. Vitamin H aka biotin
A. Used for carboxylation reactions of alpha carbons
B. Biotin is always accompanied with ATP, and Mg2+
C. The source of CO2 is bicarbonate ion (HCO3-)
D. Be able to recognize/draw the active site of biotin
E. Know the reactions on p. 1073 and mechanism on p. 1074