Chapter 2 Protein Structure

Question 1

Alpha Helix

Answer 1

1. most commonly found in nature
2. rigid
3. right handed spiral structure
4. coiled polypeptide backbonde (tightly packed)
5. side chains of “L” extend outward (avoid interferance)

Question 2

Name the four organizational levels ?

Answer 2

1. Primary
2. Secondary
3. Tertiary
4. Quatinary

Question 3

define B-bends

Answer 3

• reverse the direction of polypeptide chains
• form a compact globular shape
• found on the surface of proteins
• have charged residues
• composed of anti-parallel B-sheets
• composed of 4 A.A.stabilized by Hydrogen bonds between first and last residue in the bend

Question 4

Proline causes ?

Answer 4

a kink

Question 5

Formation

1. how are B-sheets formed ?
2. how are they stabilized ?

Answer 5

1. formed by two or more peptide chains ( B-strands) aligned laterally
2. stabilized by hydrogen bonds

Question 6

contains information needed to generate a protein molecule with a 3 dimensional shape that determines function

Answer 6

Linear proteins

Question 7

Qutenary Structure

1. how many polypeptide chains are involved ?
2. how are the structures held in together ?
3. Examples of non-covalent bonds ?
4. proteins that perform the same function but different primary structures?

Answer 7

1. two or more polypeptide chains
2. held together by primary “non-covalent” interactions
3. H-bonds, ionic and hydrophobic interactions
4. ISOforms if they function as enzymes then theu are called ISOzymes

Question 8

1. when amino acids combine together, what recation generally is involved ?

Answer 8

1. condensation reaction ( loss of water)
2. forms a peptide bond

Question 9

Peptide Bond Polarity

Answer 9

• Amino group and carboxyl group are unbranched
• do not accept or release protons over pH range 2-12
• are POLAR and involve HYDROGEN bonds

Question 10

what usually is the primary force for protein folding ?

Answer 10

hydrophobic interactions

Question 11

Secondary structure contains ?

Answer 11

• alpha helix
• beta sheets

Question 12

Compare alpha helices and B-sheets

Answer 12

• B sheets**, the B-strands are almost fully **extended** and their hydrogen bonds between strands are **perpendicular to the polypeptide backbone
• Alpha helices:** polypeptide is **COILED**; hydrogen bonds are **PARALLEL to the backbone

Question 13

what structures can be arranged parallel or antiparralel ?

Answer 13

B-strands

Question 14

alpha helix are stabilized by ?

Answer 14

hydrogen bonds

Question 15

Amino Acid that disrupt the Alpha-Helix

Answer 15

• proline disrupts the alpha helix because of it’s secondary rigid A.A.
• Glycine is a HELIX BREAKER because of (R=Hydrogen)

Question 16

Primary Structure

Answer 16

• is the “sequence” linear
• genetic diseases result in abnormal A.A. sequences

Question 17

name all the interactions in Tertiary structure

Answer 17

• Disulfide bonds
• Hydrogen bonds
• Vanderwalls
• Hydrophobic
• Ionic

Question 18

1. Amino Acids are what ?
2. name two examples of protein structural elements
3. repeating unit ?
4. individual unit ?

Answer 18

1. building blocks of proteins (monomers of proteins)
2. repeated structural elements (B-sheet and alpha helix)
3. polymer: polypeptide
4. monomer: amino acid

Question 19

B-SHEET

1. where can you find B-sheets in level of orgbanization ?
2. how do B-sheets appear on the surface ?
3. Pleating results from ?
4. what do B-sheets look like ?

Answer 19

1. secondary structure
2. pleated
3. successive alpha carbons being slightly above or below the plane
4. not flat ! right handed curl (twist)

Question 20

1. define what it means with “interactions between side chains”** in linear polypeptides that fold into intricate **3 dimensional shape?
2. biologically active proteins with lack of a stable tertiary structure?

Answer 20

1. folding
2. intrinsically disordered proteins

Question 21

what A.A. has the smalles R group

Answer 21

Glycine

Question 22

• what is the difference between a polypeptide and a protein ?
• peptide bond ?

Answer 22

1. polypeptide is composed of 3 or more A.A. linked through a peptide bond between the carboxyl group and amino group.

• proteins: can be single polypeptide folded or multiple folded polypeptides
• a covalent bond- links together with a loss of water

Question 23

Myoglobin

Answer 23

type of globular protein

highly alpha-helical

in contrast to keratins

Question 24

1. another term for unfold ?
2. what is a motif ? sort of folding
3. In tertiary structure define what a domain is ?
4. how many domains do chains of “less” than 200 amino acids give?

Answer 24

1. denaturation
2. suprasecondary structures (formed geometric patterns)
3. three dimensional units of polypeptides
4. two

Question 25

Keratins

Answer 25

type of fibrous proteins Alpha-helical

Question 26

How do we read and name peptides ?

Answer 26

1. N Terminal (left free end) 2. C Terminal (right free end) 3. All A.A. sequences are read from N to C end

Question 27

Name some transporter proteins ?

Answer 27

* hemoglobin * myoglobin * serum albumins * transferin * ceruloplasmin

Question 28

Conjugated Proteins proteins that bind to other things via covalent bonds

Answer 28

glyco- proteins metallo- proteins nucleo- proteins phospho- proteins lipo- proteins