Biochem Lecture 2

Question 1

List the bond strength from strongest to weakest

Answer 1

1. Covalent 2. Disulfide 3. Salt Bridge 4. Hydrogen bond 5. Van der Waals

Question 2

Polypeptide chain that is planar with repeating backbone - Determines the tertiary structure

Answer 2

Primary Structure

Question 3

What is the secondary structure composed of

Answer 3

Alpha helices + Beta sheets with hydrogen bonds

Question 4

Composed of Amino Acid Right-hand spiral w/ R groups facing outward

Answer 4

Alpha Helix

Question 5

Side chains alternate between being above and below the plane

Answer 5

Beta Sheets

Question 6

What is Reverse Turn

Answer 6

a hydrogen bond between every 3rd AA

Question 7

List the characteristics of a Primary Structure

Answer 7

• AA sequence contains all the info required for protein folding
• Peptide bonds are planar
• Proteins are also known as polypeptides
• Repeating backbone

Question 8

What type of bonding is in Primary Structure

Answer 8

• sequence of covalent bonds in proteins
• Very stable
• Covalently joined by amide bonds another name for peptide bonds

Question 9

Secondary Structure CHaracteristics

Answer 9

• Contains alpha and beta helices
• Twisted B sheet and Beta barrel
• Beta Strands make up Beta Sheets

Question 10

Same Direction

H bonding connects 2 AA to 1 AA on an adjacent strand

Answer 10

Parallel Beta Sheet

Question 11

Tertiary Structure Characteristics

Answer 11

• All other types of non-covalent bonds form 3D structures
• Have similar sec structures but different tertiary structures

native = Functional

• Hydrophobic AA = INSIDE
• Hydrophilic/charged AA = OUTSIDE

Porin - inside out model of AA distribution

Water filled channel

• Hydrophobic exterior

Question 12

Example of Tertiary Structure

Answer 12

Myoglobin

Question 13

Quaternary Structure

Answer 13

• More than one polypeptide chain associating with each other
• Can also establish fxn in certain proteins

Question 14

Quaternary Structure Bonding

Answer 14

Uses noncovalent bonds

Question 15

Example of Quaternary Structure

Answer 15

Hemoglobin

Question 16

Types of Quaternary Structures

Answer 16

Homodimer

Heterodimer

Heterotetamer

heteropentomer

homopentamer

Question 17

A covalent bond formed when the reduced –S-H groups of 2 Cys residues react with one another to make an oxidized –S-S linkage

Answer 17

Disulfide bridge

Question 18

Noncovalent interaction between atoms or groups of atoms due to the attraction of opposite charges

Answer 18

Electrostatic interaction

Question 19

a noncovalent interaction between the donor atom, which is bound to a positively polarized H atom, and the acceptor atom, which is negatively polarized

Answer 19

Hydrogen bond

Question 20

Protein Denaturation:

To denature a protein from 3/4 –> 1

Answer 20

Add 8 M Urea and Beta-Mercaptoethanol

Question 21

Protein Denaturation:

To break disulfide bonds

Answer 21

Add Beta-mercaptoethanol

Question 22

Protein Denaturation:

To detect an aromatic

Answer 22

Trp and Tyr = 280 nm

Phe = 260 nm

Question 23

Strong acid breaks peptide bonds

Edmans degradation releases N terminal Amino Acid

Uses proteases: Cleave @ C terminal

Answer 23

To sequence a peptide

Question 24

To sequence a peptide

Answer 24

Trypsin: Arg, Lys

Chymotrypsin: Phe, Tyr, Trp

Bromelain: Lys, Ala, Tyr, Gly

CNBr: Met

Question 25

How do you determine Primary Structure?

Answer 25

**Mass Spectroscopy**

Question 26

How do you determine a Secondary Structure?

Answer 26

CD Spectroscopy

Question 27

How do you determine Quaternary Structure?

Answer 27

X-ray Crystallography

Question 28

predominantly located on the surface of proteins

Answer 28

**Hydrophilic amino acids**

Question 29

located inside of folded proteins

Answer 29

**hydrophobic amino acids**

Question 30

causes loss of secondary, tertiary, and quaternary structures due to the unfolding of the polypeptide chain

Answer 30

**Denaturation**

Question 31

True or Falso: A denatured protein is incapable of carrying out its biochemical and biological functions

Answer 31

**True**

Question 32

What determines tertiary structure?

Answer 32

**Primary Structure and Polypeptide**

Question 33

A sequence of covalent bonds in proteins is known as

Answer 33

**Primary Structure**

Question 34

The ultimate 3-dimensional structure of a protein is determined by its:

Answer 34

**Primary Structure**

Question 35

The two most common forms of protein secondary structure are:

Answer 35

**Alpha and Beta**

Question 36

Denaturation leads to loss of what structures

Answer 36

**Primary, Secondary and Tertiary Structures**

Question 37

In order to determine a protein’s secondary structure, what can be used?

Answer 37

**CD Spectroscopy**