Chapter 1: Amino Acids in Proteins

Question 1

Amino Acids:

Answer 1

These are molecules that contains the following functional groups: • An amino group (-NH2), • Carboxyl group (-COOH), • Hydrogen Atom, • Side Chain (R group)

Question 2

Side Chains (R groups):

Answer 2

One of the functional groups in amino acids. This determines the properties of amino acids, and their functions. Each amino acid has its own Side Chains.

Question 3

Proteinogenic Amino Acids:

Answer 3

These are the 20 α amino acids encoded by the human genetic code.

Question 4

Stereochemistry of Amino Acids:

Answer 4

α carbon is a chiral center, as it have four different groups attached to it. • Chiral molecules usually contain at least one carbon atom with four nonidentical substituents.

Question 5

All Chiral Amino acids and sugar are in what shaped?

Answer 5

They are in n L-Amino Acids and all other amino acids like protein are D-Amino Acids. L-amino acids are found in eukaryotes. ○ L and D shaped.

Question 6

Amino Acid Structures:

Answer 6

The amino acid structures can be classified by being: • Non-polar, nonaromatic side chains, • Aromatic side chains, • Polar Side Chains, • Negatively Charged (Acidic) Side Chains, • Positively Charged (Basic) Side Chains.

Question 7

Non-polar, Nonaromatic side chains:

Answer 7

Includes Glycine, Alanine, valine, leucine, isoleucine, methionine, and proline.

Question 8

Aromatic Side Chains:

Answer 8

3 side chains includes Tryptophan, phenylalanine, tyrosine.

Question 9

Polar Side Chains:

Answer 9

There are 5 amino acids have polar side chains and are not aromatic, this includes Serine, Threonine, Asparagine, Glutamine, and Cysteine.

Question 10

Negatively Charged (Acidic) Side Chains:

Answer 10

There is only 2 amino acids that have negative charges because of their side chains. These include Aspartic Acid, and Glutamic acid.

Question 11

Positively Charged (Basic) Side Chains:

Answer 11

There are 3 amino acids that are positively charge and they are Lysine, Arginine, and Histidine.

Question 12

Hydrophobic Amino Acids:

Answer 12

This includes amino acids that have long alkyl side chains. Alanine, isoleucine, valine, and phenylalanine.

Question 13

Hydrophilic Amino Acids:

Answer 13

Amino acids with charged side chains like (Positively - Histidine, arginine, & lysine), (Negatively - glutamate, & aspartate), (Amides - asparagine, & glutamine)

Question 14

Why are all amino acids are amphoteric?

Answer 14

They are amphoteric because it can accept or donate protons. • Amphoteric: The ability to act as an acid or a base.

Question 15

Why do amino acids have atleast two pKa values?

Answer 15

Amino acids have atleast two groups that can be deprotonated, so that is why they have atleast two pKa values.

Question 16

pKa:

Answer 16

pKa ~ is the pH at which half of the molecules of a given acid is deprotonated. [HA] =[A-] • The first pKa is for the carboxyl group and is usually around 2. • The second pKa is for the amino group and is usually around 9 and 10.

Question 17

Amino Acid pH levels:

Answer 17

Amino acids exists in different Ph values. • At low (acidic) pH, the amino acid is fully protonated. • At pH near the pI of the amino acid, the amino acid is a neutral zwitterion. • At high (basic) pH, the amino acid is fully deprotonated.

Question 18

Zwitterion:

Answer 18

This is a molecule that contains charges, but is neutral overall.

Question 19

Isoelectric Point (pI):

Answer 19

The pH at which an amino acid is predominantly in zwitterionic form. • This can be calculated by averaging the two pKa values. ○ Amino Acids without charged side chains have a pI around 6. ○ Amino Acids that are acidic have a pI below 6. ○ Amino Acids that are basic have a pI above 6.

Question 20

Residues: When there are 2 residues: 3 residues: Less than 20 residues: More than 20 residues:

Answer 20

These are amino acid subunits that make peptides. • Dipeptides have two amino acid residues. • Tripeptides have three amino acid residues. • Oligopeptides have a few amino acid residues (about or less than 20). • Polypeptides have many amino acid residues (more than 20)

Question 21

Condensation or dehydration reactions.

Answer 21

Peptide bond formation is done by these reactions. • A reaction in which the removal of a water molecule accompanies the formation of a bond. ○ H20 is released.

Question 22

Hydrolysis Reactions:

Answer 22

Hydrolysis reaction is the breaking of a covalent bond with the help of a water molecule. This breaks peptide bonds.

Question 23

Proteins:

Answer 23

These are polypeptides that range from just a few amino acids in length up to thousands. • Function as enzymes, hormones, membrane pores & receptors, and elements of cell structures. • They are the main actors in cells, and the genetic code. • Have four level of structures: primary (1°), secondary (2°), tertiary (3°), and quaternary (4°)

Question 24

Primary Structure of the proteins:

Answer 24

The linear arrangement of amino acids coded in an organisms DNA. It’s the sequence of amino acids listed from the N-terminus (amino end) to the C-terminus (carboxyl end). • It is determined by sequencing.

Question 25

How are primary structures of protein stabilized?

Answer 25

They are stabilized by the formation of covalent peptide bonds between adjacent amino acids.

Question 26

What do primary structures of protein do?

Answer 26

It encodes all the info needed for folding at all of the higher structural levels.

Question 27

Sequencing:

Answer 27

Sequencing: is a laboratory technique in determining the order of amino acids in polypeptides, or of nucleotides in a nucleic acid.

Question 28

Secondary Structure:

Answer 28

The local structure of neighboring amino acids, that results from hydrogen bonding between nearing amino acids. It has two types a-helices and B-pleated sheets. Both structures depend on the formation of the intramolecular hydrogen bonds between different residues.

Question 29

α-helices:

Answer 29

Part of the secondary structure. A rod-like structure where the peptide chain coils up around a central axis. ○ It is stabilized by intramolecular hydrogen bonds between carbonyl oxygen atom and an amide hydrogen atom four residues down the chain. ○ Important for keratin structure.

Question 30

Keratin:

Answer 30

Is a fibrous structural protein that is found in human skin, hair, and fingernails.

Question 31

β-pleated sheets:

Answer 31

Part of the secondary structure. It can be parallel or antiparallel, the peptide chains form rows or strands. ○ These are held together by intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain.

Question 32

Tertiary Structure:

Answer 32

This is the three-dimensional shape of a single polypeptide chain. • This is stabilized by hydrophobic interactions, acid-base interactions (salt bridges), hydrogen bonding, and disulfide bonds.

Question 33

Hydrophobic Interactions:

Answer 33

These push hydrophobic R groups to the interior of a protein, which increases entropy of the surrounding water molecules and creates a negative Gibbs Free Energy.

Question 34

Disulfide Bonds:

Answer 34

This occurs when two cysteine molecules are oxidized and creates a covalent bonds to form cystine.

Question 35

Quaternary Structure:

Answer 35

This structure is the interaction between peptides in proteins that contain multiple subunits.

Question 36

Conjugated Proteins:

Answer 36

These are proteins that are covalently attached with molecules. • Attached molecules are prosthetic group, and can be metal ion, vitamin, lipids, carbohydrates, or nucleic acids.

Question 37

Denaturation:

Answer 37

This is the loss of the three-dimensional protein structure that is caused by both heat and increasing the solute concentration. • Heat denatures a protein by increasing the kinetic energy and disrupting the hydrophobic interactions. • Solutes denature proteins by disrupting elements of the secondary, tertiary, and quaternary structures.