Part 4

Question 4

Polar Amino Acids

Answer 4

Methionine, Serine, Threonine, Cysteine, Tyrosine, Asparagine, and Glutamine.

Have polar, uncharged R-groups that are HYDROPHILIC, increasing the solubility of the amino acid in water.

Usually found on protein surfaces.

Question 5

Acidic Amino Acids

Answer 5

Aspartic Acid, Glutamic Acid

R-group contains carboxyl groups. They have net negative charge at physiological pH and exist in salt form in the body. Play important role in substrate-binding sites of enzymes.

Have three distinct pKa’s

Question 6

Basic Amino Acids

Answer 6

Arginine, Lysine, Histidine

Amino acids whose R-group contains an amino group and carry a net positive charge at physiological pH.

Question 7

pH vs pI

Answer 7

If pH < pI, think positive charge.

If pH > pI think negative charge.

Question 8

Peptide bonds

Answer 8

Link amino acid subunits between the carboxyl group of one amino acid and the amino group of another.

Formed via condensation reaction (water is lost).

Question 9

Primary Structure

Answer 9

Refers to sequence of amino acids listed from N- to C- terminus, linked by COVALENT bonds btw neighboring chains.

Question 10

Secondary Structure

Answer 10

Local structure of neighboring amino acids, governed mostly by HYDROGEN bond interactions.

Most common types are alpha-helix and beta-pleated sheet.

Question 11

Alpha-Helix

Answer 11

Rod-like structure in which the peptide chain coils clockwise about a central axis.

e.g. keratin

Question 12

Tertiary Structure

Answer 12

Three-dimensional shape of the protein

Question 13

Quaternary Structure

Answer 13

Arrangement of polypeptide units

Question 14

Conjugated proteins

Answer 14

Have prosthetic groups.

Question 15

Denaturation

Answer 15

Loss of three-dimensional structure.

Question 16

Carbohydrates

Answer 16

Aldehydes and ketons with many hydroxyl groups

Question 17

Monosaccharides

Answer 17

Simplest units and are classified by the number of carbons.

Question 18

D and L designations

Answer 18

Based on stereochemistry of glyceraldehude.

If Lowest -OH is on the LEFT, the molecule is L.

If the -OH is on the RIGHT, its D.

Question 19

Epimers

Answer 19

Differ in configuration at only one carbon.

Question 20

Ketose

Answer 20

Fructose

Question 21

Aldose

Answer 21

Glucose, Galactose, and Mannose

Question 22

Pyranose

Answer 22

Six-membered rings

Question 23

Furanose

Answer 23

five-membered rings

Question 27

Glycosidic Reactions

Answer 27

hemiacetal + alcohol –> acetal

Question 28

Spectroscopy

Answer 28

Process of measuring the energy differences between the possible states of a molecular system by determining the frequencies of electromagnetic radiation absorbed by the molecules.

Question 29

Infrared Spectroscopy

Answer 29

Measures molecular vibrations, which include bond stretching, bending, and rotation.

Best used for identification of functional groups.

Alcohols are BROAD peaks
Acids are BROADEST peaks
Ketones and Amines are SHARP peaks.

Question 30

Nuclear Magnetic Resonance (NMR)

Answer 30

One of the most widely used spectroscopic tools in organic chemistry. NMR is based on the fact that certain nuclei have magnetic moments that are normally oriented at random.

Most commonly used to study H nuclei (protons) and 13C nuclei, but any atom possessing a nuclear spin can be studied.

Question 31

1H NMR

Answer 31

1H nuclei come into resonance between 0 and 10 delta downfield from TMS.

Each peak represents a single proton or a group of equivalent protons. (the number of peaks represent the number of groups of nonequivalent protons).

The relative area of each peak reflects the ratio of the protons producing each peak.

The position of the peak (upfield or downfield) due to shielding or deshielding effects reflects the chemical environment of the protons.

Proton NMR is good for:
1. Determining the relative number of protons and their relative chemical environments.

2. Showing how many adjacent protons there are by splittting patterns.
3. Showing certain functional groups.