Biologically Important Molecules

Question 1

Amino acid structure:

Answer 1

Tetrahedral a-carbon with side chain (variable R-group); a-carboxylic acid (COOH), and a-amino group (NH2)

Question 2

___ different kinds of AA exist.

Answer 2

20

Question 3

4 different broad categories of AA by property are ___.

Answer 3

1. Non-polar, hydrophobic AA; R=hydrocarbon

Question 4

Non-polar hydrophobic AA have R-groups that are___. The hydrophobic character is due to ___; this characteristic is amplified when ___. These AA are found ___.

Answer 4

hydrocarbon chains; affinity of hydrocarbon residues for each other; hydrocarbon chain is larger; dry interior of folded globular proteins.

Question 5

Polar and neutral AA have R-groups that are ___ compared to non-polar hydrophobic AA and ___ compared to polar acidic or polar basic AA. In general, these R-groups tend to contain ___ atoms like ___.

Answer 5

more polar; less polar. Electrophillic; O, N, S.

Question 6

___ groups of serine, threonine, and tyrosine are modified by addition of ___ by ___. The effect of the modification is ___. This modification is significant because ___.

Answer 6

hydroxyl (-OH); phosphate group (-PO4) by kinase; AA becoming highly hydrophillic; this will cause a change in protein conformation.

Question 7

Polar and acidic AA have R-groups that are ___. There are ___ acidic proteins in these AA, which are ___. At physiological pH, these AA are ___.

Answer 7

carboxylic acid (-COOH); 2; glutamic acid, and aspartic acid; anions (deprotonated with - charge).

Question 8

Polar and basic AA have R-groups that ___. At physiological pH, these AA are ___.

Answer 8

contain :N(s); cations (protonated with + charge), except Histidine.

Question 9

AA with N: are neither acidic nor basic when ___.

Answer 9

it is connected to an electrophillic O that “weaken” the effect of the :

Question 10

AA that is amphopheric at physiological pH is ___; this is because ___. As a result of its flexible nature, it is often found in ___.

Answer 10

histidine; its R-group pKa is ~7; protein active sites. “His goes both ways.”

Question 11

AA that has sulfur: Two sulfur-containing organic groups are ___. Cysteine has ___ and is (a/b/n). Methionine has ___ and is (a/b/n).

Answer 11

thiol and thioether; thiol (-SH); acidic; thioether (R-S-R); neutral.

Question 12

AA with a secondary a-amino group is ___. Its structure is important for ___.

Answer 12

Proline; protein folding.

Question 13

Describe the formation of polypeptide bond; what is the leftover product?

Answer 13

:NH2 alpha to central C of one AA attacks nucleophilic center of COOH of another AA; H20 leaves

Question 14

The backbone of PP is ___; which functional groups do each atoms come from?

Answer 14

N-C-C-N-C-C (Amine, central Carbon, Carboxylic acid)

Question 15

A PP made of just glycine has ___ acidic or basic sites

Answer 15

2; N- and C-terminus are basic and acidic

Question 16

Given it is of 2 AA vs. dipeptide, how is the bond formed and maintained? Use the terms kinetically and thermodynamically favored

Answer 16

Formed by using stored energy to overcome the activation energy;

maintained because the high activation energy makes the hydrolysis reaction thermodynamically favored but kinetically unfavored.

Question 17

Proteolysis/Proteolytic cleavage is an enzyme reaction by proteolytic enzyme/protease; therefore, the reaction is (non/specific) to ___

Answer 17

specific to the relative position of the AA the protease recognize

Question 18

Disulfide bond is formed by AA ___, specifically due to the interaction of functional groups ___, which is (oxidized/reduced). The result of disulfide bonding is ____.

Answer 18

Cysteine;

Thiol (-SH); reduced to S-S

Cystine

Question 19

Define denaturation and 4 examples of denaturing forces. Mention which structures are being disrupted.

Answer 19

Disruption of protien’s shape (and therefore its function) without breaking peptide bonds;

1. Urea (disrupt H-bonding in 2’ structure)
2. pH
3. T
4. [Salt]

Question 20

1’ Structure: What is it, and what bond determines 1’ structure?

Answer 20

AA sequence; peptide bond

Question 21

2’ Structure: What is it, and what bonds determine it?

Answer 21

Initial folding of chain stabilized by bonds between bacbone NH and CO groups;

H-bonding in alpha-helix or beta-sheets

Question 22

2’ Structure: What AA is never found in one of the 2’ structures (and what is that structure)? Why?

Answer 22

Proline residue never appears in alpha-helix because its ring structure (with NH embedded in it) kinks the chain

Question 23

2’ Structure: Why would alpha-helix be a good structure found in ion channels and hormone receptors? 2 structural reasons.

Answer 23

Integrated within the hydrophobic membrane;

all polar groups (NH and CO of the backbone) interact with each other via H-bonding in the center of the helix & side chains are hydrophobic and interact with the hydrophobic membrane

Question 24

2’ Structure: The differences between alpha helix and beta sheets, and similarities?

Answer 24

Similarities: both H-bonding between NH and CO of backbone

Difference: that same H-bonding occurs in distant residues in beta sheets; otherwise in alpha helix

Question 25

3’ Structure: What is it, and what interaction/bonds determine it? Give example of two.

Answer 25

Interaction between R-groups of distant AA residue;

Covalent disulfide bridge of cystienes & Van Der Waals hydrophillic/phobic interaction of appropriate R-groups in (aq)

Question 26

4’ Structure: What is it, and what bonds determine it?

Answer 26

Interaction between the subunits (different chains of AA) that make up a larger protein;

both H-bonding (~ 2’) and VDW/covalent (~3’)

Question 27

During the formation of a dissaccharide: What is the bond called? What is the byproduct? Is it spontaneous?

Answer 27

Glycosidic linkage; water; no, needs an enzyme

Question 28

Hydrolysis of glycosidic linkages is (thermodynamically/kinetically) favored. Why is this good for energy storage?

Answer 28

Thermodynamically; (like with peptide bonds), usually the gloycosidic linkage is maintained because the high activation energy makes the hydrolysis reaction thermodynamically favored but kinetically unfavored; however the fact that it is thermodynamically favored = energy is released from bonds.

Question 29

Mammals can’t hydrolyze beta-glycosidic linkages except ___

Answer 29

lactose

Question 30

Lipids have 3 different functions according to 3 different subtypes. List:

Answer 30

1. Triglycerides store E
2. Phospholipids form a cellular barrier
3. Cholesterol makes up steroids

Question 31

Fatty Acid is made up of two parts: ___ and ___.

Answer 31

hydrocarbon chain containing even number of C and often cis-double bonds; COOH

Question 32

Fatty Acids form micelle in water because of hydrophobic interaction. Explain how it happens, thermodynamically.

Answer 32

H2O must form solvation shell around each FA, resulting in unfavorable - ∆S; therefore, rather than forming solvation shells, micelle is formed instead.

Question 33

Triglycrol (TG) is made up of 2 substitudent compounds, which are ___ and ___. The process that connects them two is called ____. The resulting TG looks something like: ___

Answer 33

Glycerol (3-C triol) and 3 FA (COOH-R);

Esterifiation ( H2C-O-CO-R…)

Question 34

TG is broken down into glycerol and 3 Na+ salt of FA in the process known as ___ (2 names).

Answer 34

base-catalyzed hydrolysis, or saponification.

Question 35

TG packs (better/worse) than carbohydrates because ___;

TG stores (more/less) E than carbohydrates

Answer 35

saturated; carbohydrates carry more water-of-solvation (bonded to OH group); TG doesn’t have that problem;

More

Question 36

Phospholipids (PL) are derived from diacylglycerol phosphate (DG-P), which are detergents. Detergents are water soluble yet can solubilize oils. How?

Answer 36

phospho group highly (-) carge, while diacylglycerol has 2 R-groups that can solubilize oils

Question 37

Fluidity means (stronger/weaker) VDW interaction between the Phospholipid FA in the membrane. 3 Factors that effect it are:

Answer 37

weaker;

1. unsaturation &
2. decreasing length increase fluidity.
3. Cholesterol stabilize fluidity

Question 38

Terpenes are built from isoprene units that look like: ___; it is (cyclic/linear/both)

Answer 38

2-methyl but-2-ene;

Both

Question 39

Steroids have the basic ____ ring system, and are derivative of cholesterol. Cholesterol is a polycyclic amphimorph, which means that it has ___.

Steroid hormones have their receptors at ___ (why?).

Answer 39

tetracyclic ring system;

both hydrophillic and hydrophobic characteristics;

inside the cell because tetracyclic ring system = ++ hydrophobic; will go straight through the PL bilayer

Question 40

Phosphoric acid (orthophosphate) look like : ___.

____ can form from anhydride linkage of 2 phosphoric acid; its hydrolysis is (thermodynamically/kinetically) favorable. 3 reasons are:

Answer 40

O=P-(OH)3;

pyrophosphate; thermodynamically

1. reactant has many - charges repelling each other
2. product resonance stabilized
3. product solvated better in (aq)

Question 41

ATP (stands for _____) has three parts, which are: ___

Answer 41

Adenine Tri-Phosphate

1. Nitrogenous base at 1’C
2. 5-C ring
3. 3 phosphates at 5’C

Question 42

FA and PL are (linear/cyclic); Steroid and Cholesterol is (linear/cyclic)

Answer 42

linear

cyclic