Concept 1: Biomolecules

Question 1

Isoelectric point

Answer 1

the average pKa’s of the groups in the amino acid

Question 2

The pKa of COOH and NH3+

Answer 2

2 and 9-10

Question 3

Primary structure of a protein consists of:

Answer 3

Peptide bonds

Question 4

Secondary structure of a protein consists of:

Answer 4

backbone interactions, H-bonds, a-helices, and B-sheets

Question 5

Tertiary structure of proteins consists of:

Answer 5

H-bonds, salt bridges, van der waals, hydrophobic interactions, S-S (heavy metal is a reducing agent).

Question 6

If you add alcohol to a protein, what happens?

Answer 6

disrupts secondary, tertiary bonds and H-bonds

Question 7

Temperature to a protein does what?

Answer 7

denatures to the primary structure

Question 8

pH does what to protein?

Answer 8

breaks down until the secondary structure and salt bridges

Question 9

What are the four types of enzymatic functions?

Answer 9

1. acids/base (protons) 2. covalent catalysis (electrons) 3. Electrostatic 4. Proximity and orientation

Question 10

delta G with double dagger means:

Answer 10

free energy of activation (Ea)

Question 11

delta G with degree means:

Answer 11

standard free energy of change (Erxn)

Question 12

What are the 6 types of enzymes (not functions)

Answer 12

1. Transferase-move functional groups 2. Ligase-break bonds with ATP 3. Oxidoreductase 4. Isomerase 5. Hydrolase (Protease) 6. Lyase-make double bond or ring to cleave

Question 13

Cofactors are:

Answer 13

nonorganic, directly involved in reaction (e.g. Mg2+)

Question 14

Coenzymes are:

Answer 14

organic carriers (e.g. NADH)

Question 15

Ester functional group

Answer 15

C-CO-O-

Question 16

Anhydride functional group

Answer 16

-CO-CO-

Question 17

Michaelis-Menton Constant

Answer 17

In terms of Molarity and think of it as affinity. Dissociation over association. K_M=[S] to achieve 1/2 V_max.

Question 18

Michaelis-Menton Equation

Answer 18

V₀, or V.

Question 19

What is Kcat?

Answer 19

Catalytic Turnover (s^-1): K_cat=V_max/[E]_T

Question 20

What is catalytic efficiency?

Answer 20

K_A=K_cat/K_M Bigger the number, the better.

Question 21

Lineweaver Burke Plot

Answer 21

Inverse of Michaelis-Menton Equation.

Question 22

Lineweaver Burke Equation

Answer 22

Question 23

Competitive Inhibitor

Answer 23

Binds to free enzyme. This changes the slope (K_M/V_max) but not the Y-int (V_max). You can add [S] to overcome Inhibitor.

Question 24

Uncompetitive Inhibitor

Answer 24

Binds to bound enzyme. Can enhance E+S binding. No change in slope (K_M/V_max) and a change in Y-int (1/V_max). K_M and V_max change proportionally.

Question 25

Noncompetitive Inhibitor

Answer 25

Also known as mixed inhibitor. Binds to free and bound enzymes. Increase slope (K_M/V_max) and Y-int (1/V_max).

Question 26

Homotropic regulator

Answer 26

A molecule that is a substrate and a regulator in a feedback loop

Question 27

Heterotropic feedback loop

Answer 27

The substrate and the regulator molecule are different

Question 28

What are the covalent modifications?

Answer 28

1. Post-translational modifications (ER/golgi: glycosylation, lipidation, ubiquination (destruction) and phosphorylation)
2. Co-translational modification (acetylation)
3. Zymogen (inactive form)
4. “Suicide” (permenant inactivation)

Question 29

Base + Deoxyribose =

Answer 29

Nucleoside

Question 30

What nucleotides are purines?

Answer 30

Pure As Gold: Adenine and Guanine

Question 31

What nucleotides are pyrimidines?

Answer 31

Thymine and Cytosine

Question 32

Phosphate + nucleoside =

Answer 32

Nucleotide

Question 33

What polarity (way) does DNA replication run?

Answer 33

5’–>3’

Question 34

What way do nucleotides link?

Answer 34

3’–>5’

Question 35

The phases of transcription and where it happens

Answer 35

Happens in the nucleus. Initiation, elongation, and termination. The coding strand is identical to the sequence, however, the template strand, which is complementary, is read.

Question 36

Translation

Answer 36

Occurs in the cytoplasm in ribosomes. APE sites.

Question 37

Mismatch repair system

Answer 37

remove by enxonuclease usually during DNA synthesis.

Question 38

Nucleotide Excision Repair

Answer 38

Removal of bumps (helical distortion) by removing the whole incorrect strand and adding new ones. Good for UV damage–pyrimidine dimers.

Question 39

Base excision repair

Answer 39

Removal of bases that usually do not cause distortion in helical shape.

Question 40

DNA Hybridization

Answer 40

The annealing of DNA pairs by A-T and C-G of complementary strands.

Question 41

DNA Annealing

Answer 41

When base complements bind by hydrogen bonding. Usually to describe a primer binding to a DNA sequence during PCR reaction.