Scott Chapter 12.1 to 12.5: Amino Acids, Peptides, & Proteins

Question 1

Physical properties of some small carboxylic acids

Compared to other organic compounds with similar molecular weight, carboxylic acids have a relatively ____ boiling point due to their ability to form ________ bonds with one another.

Answer 1

High boiling point

Hydrogen Bonds

_{<em>i.e. Hexan 65°, Hexanoic Acid 205°</em>}

Question 2

Physical properties of some small carboxylic acids

What gives small carboxylic acids a significant water solubility?

Answer 2

The ability to form hydrogen bonds, in addition to the presence of polar C=O, C-O, and O-H bonds, gives small carboxylic acids a significant water solubility.

_{<em>i.e. once the tail gets too long it deflects water and becomes less soluble as a result. </em>}

Question 3

Carboxylic Acids are Weak Organic Acids

K_a = ………………. = 1.8 x 10^-5

Small # = __________

Answer 3

Small # = weak organic acid

Question 4

Carboxylic Acids are Weak Organic Acids

pH 7 =

Answer 4

Physiological pH

Question 5

Carboxylic Acids are Weak Organic Acids

Physiological pH =

Answer 5

Carboxylic Acids are Weak Organic Acids

pH 7

Question 6

Amines

Amines are classified based on what?

Answer 6

Number of Carbon atoms directly attached to the nitrogen atom

1°, 2°, 3°, 4°

Question 7

Amines

Amines are ______ of one another.

What type of bonding takes place in 1°, 2°, and 3° amines?

Answer 7

Isomers

1° = H-Bonding _{(strong IMF)}

2° = H-Bonding _{(strong IMF)}

3° = No H-Bonding _{(Bp drops due to no IMF holding together. <u>More soluble</u>)}

Question 8

Amines

___° and ___° amines form hydrogen bonds with like amines.

___° amines do not form hydrogen bonds with each other.

Answer 8

1° and 2°

3°

Question 9

Amines as Weak Organic Bases

Amines _____ H⁺ from water.

Amines _____ H⁺ from acid.

Answer 9

accept

accept

Question 10

Amino Acids

Describe the structure of amino acids and the system used to classify amino acids.

Answer 10

Amino acids are molecules that contain at least one caboxyl (CO₂H) group and one amino group (NH₂).

Amino acids are classified into four different types based on the nature of their side chain. _{(side chain determines solubility)}

Question 11

Amino Acids

Distinguish between oligopeptides, polypeptides, and proteins.

Answer 11

Length: A polypeptide is a single linear chain of many amino acids, held together by amide bonds. A protein consists of one or more polypeptides (more than about 50 amino acids long). An oligopeptide consists of only a few amino acids(between two and twenty).

Question 12

Amino Acids

In a protein, amino acid residues are connected to one another through a _________.

Answer 12

Peptide Bond

_{also called amide bond}

Question 13

Amino Acids

The end of the peptide chain with the unreacted amino group is called the _______.

The end of the peptide chain with the amino group that’s modified to an amide is called the _______.

Answer 13

N-terminus (left)

C-terminus (right)

Question 14

Amino Acids

What is chymotrypsin?

Answer 14

A Digestive Enzyme

Question 15

Amino Acids

Peptides and proteins are named by listing the amino acid residue, in order, from the __________ to the ___________.

Answer 15

N-terminus to the C-terminus

Question 16

Amino Acids

In terms of peptides and proteins, define primary structures.

Name the covalent and noncovalent forces.

Answer 16

The order of amino acid residues in a peptide or protein is referred to as its primary structure.

_{same letters diff meanings: edit, diet, tide, tied}

H-Bonding

Question 17

Amino Acids

In terms of peptides and proteins, define secondary structures.

Name the covalent and noncovalent forces.

Answer 17

The properties of proteins depend not only on their sequence of amino acid residues but also on how they are folded and twisted.

H-Bonding

Question 18

Amino Acids

In terms of peptides and proteins, define tertiary structures.

Name the covalent an noncovalent forces.

Answer 18

The overall three-dimensional shape of a protein is referred to as its tertiary structure.

H-Bonding, Salt Bridges, Disulfide Bonds, Londons Forces

Question 19

Amino Acids

The conformation in the tertiary structure that leads to a biologically active protein is called ________.

Tertiary structures sometimes include nonpeptide components called ________.

Answer 19

a native conformation

Prosthetic groups

Question 20

Amino Acids

Proteins that require a prosthetic group for biological activity are called ____ and those without are called _____.

_{(not made of amino acids)}

Answer 20

Complex

Simple

_{(not made of amino acids)}

Question 21

Amino Acids

In terms of peptides and proteins, define quaternary structures.

Name the covalent and noncovalent forces.

Cooperation between subunits is a factor in regulation of _______.

Answer 21

Require more than one polypeptide chain to be biologically active. Quaternary structure refers to the arrangement of these chains.

H-Bonding, Londons, Salt Bridges

Protein activity. _{(hands working together to peal orange)}

Question 22

Amino Acids

Any change of protein conformation caused by disruption on noncovalent forces and disulfide bridges responsible for maintaining native conformation is called _________

Answer 22

Denaturation

Question 23

Amino Acids

List some ways to denature a protein.

Answer 23

Heat

Changes in pH

Agitation

Denaturing agents (soap/detergent)

Question 24

Amino Acids

What is the solubility rule for proteins that maximizes its interaction with water

Answer 24

nonpolar in, polar out

Question 25

Amino Acids

The arrangement of multiple polypeptide chains in a functioning protein is called the ________ structure of the protein.

Answer 25

Quaternary

Question 26

Amino Acids

A major structural protein found in tendons, cartilage and bones is called

Answer 26

Collagen

Question 27

Amino Acids

Prosthetic groups are nonpeptide components tightly bound to a polypeptide chain. What is the name of the prosthetic group in hemoglobin?

Answer 27

Heme

Question 28

Amino Acids

The form of the amino acid that has one positive and one negative charge is called a (an)

Answer 28

Zwitterion

Question 29

Amino Acids

Polar Basic vs Polar Acidic vs Polar Neutral

Answer 29

Polar Basic contains an amid (O=C–NH₂)

Polar Acidic contains carboxylate ion (O=C–O^-)

Polar Neutral contains zwitterions (+)(-)

Question 30

Describe the quaternary structure of hemoglobin. The binding of oxygen to hemoglobin is cooperative. Explain this term.

Answer 30

A single hemoglobin molecule is a tetramer consisting of four separate polypeptide chains, two identical alpha chains two identical beta chains. Each alpha and beta chain carries a heme prosthetic group.

In molecules with multiple binding sites binding is said to be cooperative if binding at one site impacts the binding at other sites. Hemoglobin has four oxygen binding sites. The binding of oxygen to any one subunit leads to change in shape at three other sites or subunits which increases its ability to bind to oxygen.